Psyllid ID: psy11867

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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-------40
Protein Sequence
MTSLSDWIAATKNTSALKPDDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS
Secondary Structure (PSIPRED)
cccccHHHHHHccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccccEEEEcccccHHHHHHHHHHHHcccccccccEEEEEcccHHHHHHHHHHHHHHHccccccEEEEEEccccccccccccccEEEcccccccccccccccccccccEEEEEEcHHHHHHccccHHHHHHHHHHccccccEEEEEEcccHHHHHHHHHHcccccEEEEEccccccccccEEEEEccccccHHHHHHHHHccccccEEEEEEcccccHHHHHHHHHHcccEEEEccccccHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccEEEEccccccccccccHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcccccccEEEEEEccccHHHHHccccEEEEEcccHHHHHHHHcccccHHHEEEEEEcHHHHHHHHccccHHHHHHHHHccHcccEEEEEccccHHHHHHHHHHccccEEEEEEEcccccccEEEEEEEEccHHHHHHHHHHHHHcccccEEEEEEEccHcHHHHHHHHHHccccEHHHcccccHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
MTSLSDWIAAtkntsalkpddlidvlsnvnlkqadtpsptedakpapsspdssapgnkdeedkplSVAEKSLLQKIVRRGLIEskqeleiqrkdphsplysvktfealhLKPELLKGVYEmgfyapskiqetalptlladpphnmiaqsqsgtgktAAFTLTMLsrvnpsiqepqvlclaptyELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIigtpgkvldwglkyrffdlskikvfvLDEADVMIATQGHQDFSIRIqkrlpsdcqIMLFSATYDKEVMEFAqdmvpnpliIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFregefkiys
Flexible Loop (DISEMBL)
MTSLSDWIAAtkntsalkpddlIDVLSNVNLKQadtpsptedakpapsspdssapgnkdeedkplSVAEKSLLQKIVRRGLieskqeleiqrkdphsplySVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRyavrgenlernkkiteqiiigtpgkvldWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGllsgeltveqrlsildrfregefkiys
Low Complexity Region (SEG)
MTSLSDWIAATKNTSALKPDDLIDVLSNVNLKQADTPSPTEdakpapsspdssapGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS
Disordered region (IsUnstruct)
**********************IDV**************************************************IV*********************LYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLL******************AAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREG******
Disordered Region (DISOPRED)
*********************************************************************************************D**SPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS
Disordered Region (DISEMBL)
MTSLSDWIAATKNTSALKPDDLIDVLSNVNLKQ*******************************LSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS
Disordered Region (DISPRO)
*************************************************************DKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTSLSDWIAATKNTSALKPDDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS
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	399	2.2.26 [Sep-21-2011]
O61305	460	DEAD-box helicase Dbp80 O	yes	N/A	0.827	0.717	0.660	1e-132
Q9NUU7	478	ATP-dependent RNA helicas	yes	N/A	0.827	0.690	0.645	1e-129
Q61655	478	ATP-dependent RNA helicas	yes	N/A	0.827	0.690	0.642	1e-129
Q3ZBV2	478	ATP-dependent RNA helicas	yes	N/A	0.827	0.690	0.645	1e-129
Q9UMR2	479	ATP-dependent RNA helicas	yes	N/A	0.827	0.688	0.639	1e-128
Q9UHL0	483	ATP-dependent RNA helicas	no	N/A	0.854	0.706	0.598	1e-115
Q9QY15	484	ATP-dependent RNA helicas	no	N/A	0.829	0.683	0.613	1e-114
Q9QY16	483	ATP-dependent RNA helicas	no	N/A	0.829	0.685	0.604	1e-114
Q2TBP1	483	ATP-dependent RNA helicas	no	N/A	0.829	0.685	0.604	1e-114
Q9DGP9	483	ATP-dependent RNA helicas	N/A	N/A	0.849	0.701	0.545	1e-109

>sp|O61305|DDX19_DROME DEAD-box helicase Dbp80 OS=Drosophila melanogaster GN=Dbp80 PE=1 SV=1

 Score =  471 bits (1212), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 218/330 (66%), Positives = 271/330 (82%)

Query: 68  AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
           AE SLL KI+ +GL+ +K  L++Q+K+P+SPL+SVKTFEALHLK  LLKG+Y MGF  PS
Sbjct: 38  AETSLLIKILGKGLVNTKLSLDLQQKNPNSPLHSVKTFEALHLKASLLKGIYAMGFNTPS 97

Query: 128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
           KIQETALPTLLADPP NMIAQSQSGTGKTAAF L MLSRVN  +  PQVLCL+PTYELAI
Sbjct: 98  KIQETALPTLLADPPQNMIAQSQSGTGKTAAFVLAMLSRVNVCLNHPQVLCLSPTYELAI 157

Query: 188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           Q GEV A+MG+   ++ +R+AVRGE ++R+KKI E I+IGTPGK+LDWG+K+R FD+ KI
Sbjct: 158 QTGEVAARMGQFCREIKLRFAVRGEEVDRSKKIEEHILIGTPGKLLDWGIKFRLFDMKKI 217

Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
            VFVLDEADVMIATQGH D  IRI K L   CQ++ FSATY KEVM+FA+ +V +P II+
Sbjct: 218 SVFVLDEADVMIATQGHHDQCIRIHKMLNPHCQMLFFSATYGKEVMDFARLIVADPTIIR 277

Query: 308 LKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE 367
           L REEESL+NIKQ+YV CKN + K+ A+ NIYG +++GQA+IFCHT++TAAWLA KM+ +
Sbjct: 278 LMREEESLENIKQYYVKCKNEEGKYNAIQNIYGCISVGQAIIFCHTKRTAAWLAAKMTSD 337

Query: 368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           G +V +L+G+LTV QRL +LDRFR G  K+
Sbjct: 338 GHSVAVLTGDLTVVQRLDVLDRFRSGLEKV 367

ATP-dependent RNA helicase involved in mRNA export from the nucleus.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q9NUU7|DD19A_HUMAN ATP-dependent RNA helicase DDX19A OS=Homo sapiens GN=DDX19A PE=1 SV=1

 Score =  463 bits (1191), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 213/330 (64%), Positives = 271/330 (82%)

Query: 68  AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
           A +SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PS
Sbjct: 56  AAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPS 115

Query: 128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
           KIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLSRV PS + PQ LCL+PTYELA+
Sbjct: 116 KIQENALPMMLAEPPQNLIAQSQSGTGKTAAFVLAMLSRVEPSDRYPQCLCLSPTYELAL 175

Query: 188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           Q G+V+ +MGK   +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KI
Sbjct: 176 QTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKI 235

Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           KVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IK
Sbjct: 236 KVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIK 295

Query: 308 LKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE 367
           LKREEE+LD IKQ+YV+C + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKE
Sbjct: 296 LKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKE 355

Query: 368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           G  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct: 356 GHQVALLSGEMMVEQRAAVIERFREGKEKV 385

ATP-dependent RNA helicase involved in mRNA export from the nucleus.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q61655|DD19A_MOUSE ATP-dependent RNA helicase DDX19A OS=Mus musculus GN=Ddx19a PE=2 SV=2

 Score =  461 bits (1185), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 212/330 (64%), Positives = 270/330 (81%)

Query: 68  AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
           A +SLL K++R  L+++  ++E+ ++DP SPLYSVK+FE L LKP+LL+GVY MGF  PS
Sbjct: 56  AAQSLLNKLIRSNLVDNTNQVEVLQRDPSSPLYSVKSFEELRLKPQLLQGVYAMGFNRPS 115

Query: 128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
           KIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLSRV P+ + PQ LCL+PTYELA+
Sbjct: 116 KIQENALPMMLAEPPQNLIAQSQSGTGKTAAFVLAMLSRVEPADRYPQCLCLSPTYELAL 175

Query: 188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           Q G+V+ +MGK   +L + YAVRG  LER +K++EQI+IGTPG VLDW  K +F D  KI
Sbjct: 176 QTGKVIEQMGKFHPELKLAYAVRGNKLERGQKVSEQIVIGTPGTVLDWCSKLKFIDPKKI 235

Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           KVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P IIK
Sbjct: 236 KVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNIIK 295

Query: 308 LKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE 367
           LKREEE+LD IKQ+YV+C N +EKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKE
Sbjct: 296 LKREEETLDTIKQYYVLCNNREEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKE 355

Query: 368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           G  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct: 356 GHQVALLSGEMMVEQRAAVIERFREGKEKV 385

ATP-dependent RNA helicase involved in mRNA export from the nucleus.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q3ZBV2|DD19A_BOVIN ATP-dependent RNA helicase DDX19A OS=Bos taurus GN=DDX19A PE=2 SV=1

 Score =  460 bits (1184), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 213/330 (64%), Positives = 270/330 (81%)

Query: 68  AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
           A +SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PS
Sbjct: 56  AAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPS 115

Query: 128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
           KIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLSRV P+ + PQ LCL+PTYELA+
Sbjct: 116 KIQENALPMMLAEPPQNLIAQSQSGTGKTAAFVLAMLSRVEPAERYPQCLCLSPTYELAL 175

Query: 188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           Q G+V+ +MGK   +L + YAVRG  LER +KI+E I+IGTPG VLDW  K +F D  KI
Sbjct: 176 QTGKVIEQMGKFHPELKLAYAVRGNKLERGQKISEHIVIGTPGTVLDWCSKLKFIDPKKI 235

Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           KVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P IIK
Sbjct: 236 KVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNIIK 295

Query: 308 LKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE 367
           LKREEE+LD IKQ+YV+C + DEKF+A+ NIYG +TI QAMIFCHTRKTA+WLA ++SKE
Sbjct: 296 LKREEETLDTIKQYYVLCNSRDEKFQALCNIYGAITIAQAMIFCHTRKTASWLAAELSKE 355

Query: 368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           G  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct: 356 GHQVALLSGEMVVEQRAAVIERFREGKEKV 385

ATP-dependent RNA helicase involved in mRNA export from the nucleus.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9UMR2|DD19B_HUMAN ATP-dependent RNA helicase DDX19B OS=Homo sapiens GN=DDX19B PE=1 SV=1

 Score =  459 bits (1182), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 211/330 (63%), Positives = 271/330 (82%)

Query: 68  AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
           A +SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PS
Sbjct: 57  AAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPS 116

Query: 128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
           KIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+
Sbjct: 117 KIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELAL 176

Query: 188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           Q G+V+ +MGK   +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KI
Sbjct: 177 QTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKI 236

Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           KVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IK
Sbjct: 237 KVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIK 296

Query: 308 LKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE 367
           LKREEE+LD IKQ+YV+C + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKE
Sbjct: 297 LKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKE 356

Query: 368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           G  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct: 357 GHQVALLSGEMMVEQRAAVIERFREGKEKV 386

ATP-dependent RNA helicase involved in mRNA export from the nucleus.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9UHL0|DDX25_HUMAN ATP-dependent RNA helicase DDX25 OS=Homo sapiens GN=DDX25 PE=1 SV=2

 Score =  416 bits (1070), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 204/341 (59%), Positives = 262/341 (76%)

Query: 57  NKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLK 116
           N+D+E+  + +A  SLL K++ + L+ES   +E+ +KDP SPLYSVKTFE L LK ELLK
Sbjct: 51  NEDDEEDVVDLAANSLLNKLIHQSLVESSHRVEVLQKDPSSPLYSVKTFEELRLKEELLK 110

Query: 117 GVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQV 176
           G+Y MGF  PSKIQE ALP +LA PP N+IAQSQSGTGKTAAF L MLSRVN     PQ 
Sbjct: 111 GIYAMGFNRPSKIQEMALPMMLAHPPQNLIAQSQSGTGKTAAFVLAMLSRVNALELFPQC 170

Query: 177 LCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWG 236
           LCLAPTYELA+Q G VV +MGK   D+ V YA+RG  + R   IT+QIIIGTPG VLDW 
Sbjct: 171 LCLAPTYELALQTGRVVEQMGKFCVDVQVMYAIRGNRIPRGTDITKQIIIGTPGTVLDWC 230

Query: 237 LKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFA 296
            K +  DL+KI+VFVLDEADVMI TQG  D SIRIQ+ LPS+CQ++LFSAT++  V  FA
Sbjct: 231 FKLKLIDLTKIRVFVLDEADVMIDTQGFSDHSIRIQRALPSECQMLLFSATFEDSVWHFA 290

Query: 297 QDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKT 356
           + ++P+P +IKL++EE +L+NI+Q+YV+C++  +K++A+ NIYG +TIGQA+IFC TR+ 
Sbjct: 291 ERIIPDPNVIKLRKEELTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRN 350

Query: 357 AAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           A WL  +M ++G  V LLSGELTVEQR SI+ RFR+G+ K+
Sbjct: 351 AKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKV 391

ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9QY15|DDX25_MOUSE ATP-dependent RNA helicase DDX25 OS=Mus musculus GN=Ddx25 PE=1 SV=2

 Score =  412 bits (1060), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 203/331 (61%), Positives = 257/331 (77%)

Query: 67  VAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAP 126
           +A  SLL K++R+ LIES   +E+ +KDP SPLYSVKTFE L LK ELLKG+Y MGF  P
Sbjct: 62  LAANSLLNKLIRQSLIESSHRVEVLQKDPSSPLYSVKTFEELRLKEELLKGIYAMGFNRP 121

Query: 127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA 186
           SKIQE ALP +LA PP N+IAQSQSGTGKTAAF L MLSRVN     PQ LCLAPTYELA
Sbjct: 122 SKIQEMALPMMLAHPPQNLIAQSQSGTGKTAAFVLAMLSRVNALELFPQCLCLAPTYELA 181

Query: 187 IQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSK 246
           +Q G VV +MGK   D+ V YA+RG  + R  ++T+QIIIGTPG VLDW  K +  DL+K
Sbjct: 182 LQTGRVVERMGKFCVDVEVMYAIRGNRIPRGTEVTKQIIIGTPGTVLDWCFKRKLIDLTK 241

Query: 247 IKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII 306
           I+VFVLDEADVMI TQG  D SIRIQ+ LPS+CQ++LFSAT++  V +FA+ ++P+P +I
Sbjct: 242 IRVFVLDEADVMIDTQGFSDQSIRIQRALPSECQMLLFSATFEDSVWQFAERIIPDPNVI 301

Query: 307 KLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSK 366
           KL++EE +L+NI+Q+YV+C+N   K++A+ NIYG +TIGQA+IFC TR+ A WL  +M +
Sbjct: 302 KLRKEELTLNNIRQYYVLCENRKGKYQALCNIYGGITIGQAIIFCQTRRNAKWLTVEMMQ 361

Query: 367 EGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           +G  V LLSGELTVEQR SI+ RFR+G+ K+
Sbjct: 362 DGHQVSLLSGELTVEQRASIIQRFRDGKEKV 392

ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9QY16|DDX25_RAT ATP-dependent RNA helicase DDX25 OS=Rattus norvegicus GN=Ddx25 PE=1 SV=2

 Score =  410 bits (1055), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 200/331 (60%), Positives = 257/331 (77%)

Query: 67  VAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAP 126
           +A  SLL K++R+ L+ES   +E+ +KDP SPLYSVKTFE L LK ELLKG+Y MGF  P
Sbjct: 61  LAANSLLNKLIRQSLVESSHRVEVLQKDPSSPLYSVKTFEELRLKEELLKGIYAMGFNRP 120

Query: 127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA 186
           SKIQE ALP +LA PP N+IAQSQSGTGKTAAF L ML+RVN     PQ LCLAPTYELA
Sbjct: 121 SKIQEMALPMMLAHPPQNLIAQSQSGTGKTAAFVLAMLNRVNALELFPQCLCLAPTYELA 180

Query: 187 IQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSK 246
           +Q G VV +MGK   D+ V YA+RG  + R   +T+QI+IGTPG VLDW  K +  DL+K
Sbjct: 181 LQTGRVVERMGKFCVDVEVMYAIRGNRIPRGTDVTKQIVIGTPGTVLDWCFKRKLIDLTK 240

Query: 247 IKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII 306
           I+VFVLDEADVMI TQG  D SIRIQ+ LPS+CQ++LFSAT++  V +FA+ ++P+P +I
Sbjct: 241 IRVFVLDEADVMIDTQGFSDQSIRIQRALPSECQMLLFSATFEDSVWQFAERIIPDPNVI 300

Query: 307 KLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSK 366
           KL++EE +L+NI+Q+YV+C+N  +K++A+ NIYG +TIGQA+IFC TR+ A WL  +M +
Sbjct: 301 KLRKEELTLNNIRQYYVLCENRKDKYQALCNIYGGITIGQAIIFCQTRRNAKWLTVEMMQ 360

Query: 367 EGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           +G  V LLSGELTVEQR SI+ RFR+G+ K+
Sbjct: 361 DGHQVSLLSGELTVEQRASIIQRFRDGKEKV 391

ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2TBP1|DDX25_BOVIN ATP-dependent RNA helicase DDX25 OS=Bos taurus GN=DDX25 PE=2 SV=1

 Score =  410 bits (1055), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 200/331 (60%), Positives = 257/331 (77%)

Query: 67  VAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAP 126
           +A  SLL K++R+ L+ES   +E+ +KDP SPLYSVKTFE L LK ELLKG+Y MGF  P
Sbjct: 61  LAANSLLNKLIRQSLVESSHRVEVLQKDPSSPLYSVKTFEELRLKEELLKGIYAMGFNRP 120

Query: 127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA 186
           SKIQE ALP +LA PP N+IAQSQSGTGKTAAF L MLSRVN     PQ LCLAPTYELA
Sbjct: 121 SKIQEMALPMMLAHPPQNLIAQSQSGTGKTAAFVLAMLSRVNALKLFPQCLCLAPTYELA 180

Query: 187 IQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSK 246
           +Q G VV +MGK   D+ V YA+RG  + R   +T+QI+IGTPG VLDW  K +  DL+K
Sbjct: 181 LQTGRVVERMGKFCVDVQVMYAIRGNRIPRGTDVTKQIVIGTPGTVLDWCFKRKLIDLTK 240

Query: 247 IKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII 306
           I+VFVLDEADVMI TQG +D SIRIQ+ LPS+CQ++LFSAT++  V +FA+ ++P+P +I
Sbjct: 241 IRVFVLDEADVMIDTQGFEDQSIRIQRALPSECQMLLFSATFEDSVWQFAERIIPDPNVI 300

Query: 307 KLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSK 366
           KL++EE +L+NI+Q+YV+C N  +K++A+ NIYG +TIGQA+IFC TR+ A WL  +M +
Sbjct: 301 KLRKEELTLNNIRQYYVLCGNRKDKYQALCNIYGGITIGQAIIFCQTRRNAKWLTVEMMQ 360

Query: 367 EGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           +G  V LLSGELTV+QR SI+ RFR+G+ K+
Sbjct: 361 DGHQVSLLSGELTVDQRASIIQRFRDGKEKV 391

ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9DGP9|DDX25_XENLA ATP-dependent RNA helicase DDX25 OS=Xenopus laevis GN=deadsouth PE=2 SV=1

 Score =  397 bits (1019), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 187/343 (54%), Positives = 250/343 (72%), Gaps = 4/343 (1%)

Query: 59  DEEDKPLS----VAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPEL 114
           DEED        +A  SLL K++RR L++S   +E+ ++DP SPL+SVK+FE LHLK EL
Sbjct: 49  DEEDVRRGHIEDLANHSLLNKLLRRTLVDSPHNVEVLQRDPTSPLFSVKSFEELHLKNEL 108

Query: 115 LKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEP 174
           L+G+Y MGF  PSKIQE ALP +LADPP N+IAQSQSGTGKTAAF L MLSRV+ + + P
Sbjct: 109 LRGIYAMGFNRPSKIQENALPMMLADPPQNLIAQSQSGTGKTAAFVLAMLSRVDANKKYP 168

Query: 175 QVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLD 234
           Q +CL+PT+ELA+Q G+VV +MGK    + V YA+RG    +  ++  QI+IGTPG VLD
Sbjct: 169 QCICLSPTFELALQTGKVVEEMGKFCAGIEVIYALRGNRPGKGSRLEAQIVIGTPGTVLD 228

Query: 235 WGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVME 294
           W  K R   +  I VFVLDEADVMI  QGH D S+R+++ +P  CQ++LFSAT++  V  
Sbjct: 229 WCFKLRLITVENISVFVLDEADVMINVQGHSDHSVRVKRSMPKSCQMLLFSATFEDSVWA 288

Query: 295 FAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTR 354
           FA+ +VP+P IIKLK+EE +L NI+Q Y  C+N ++K+ A+ N+YGV+TI QA++FC TR
Sbjct: 289 FAERIVPDPNIIKLKKEELTLKNIQQFYDQCENKEQKYSALCNLYGVITIAQAIVFCQTR 348

Query: 355 KTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           K A+WL++K+S +G  V LLSGEL V  R  ++ RFREG  K+
Sbjct: 349 KIASWLSQKLSDDGHQVALLSGELPVYDRADMIQRFREGREKV 391

ATP-dependent RNA helicase.

Xenopus laevis (taxid: 8355)

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	399
350418469	475	PREDICTED: DEAD-box helicase Dbp80-like	0.919	0.772	0.664	1e-146
157124559	524	DEAD box ATP-dependent RNA helicase [Aed	0.902	0.687	0.672	1e-146
307199044	473	DEAD-box helicase Dbp80 [Harpegnathos sa	0.879	0.742	0.692	1e-146
307173630	482	DEAD-box helicase Dbp80 [Camponotus flor	0.937	0.775	0.661	1e-146
170034912	530	DEAD-box helicase Dbp80 [Culex quinquefa	0.902	0.679	0.670	1e-146
383849834	475	PREDICTED: DEAD-box helicase Dbp80-like	0.879	0.738	0.700	1e-145
66547453	475	PREDICTED: DEAD-box helicase Dbp80 [Apis	0.854	0.717	0.712	1e-145
332019714	481	DEAD-box helicase Dbp80 [Acromyrmex echi	0.957	0.794	0.647	1e-144
157131180	510	DEAD box ATP-dependent RNA helicase [Aed	0.977	0.764	0.631	1e-144
347969816	510	AGAP003397-PA [Anopheles gambiae str. PE	0.874	0.684	0.698	1e-144

>gi|350418469|ref|XP_003491867.1| PREDICTED: DEAD-box helicase Dbp80-like [Bombus impatiens]

 Score =  525 bits (1351), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 251/378 (66%), Positives = 303/378 (80%), Gaps = 11/378 (2%)

Query: 20  DDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRR 79
           D L   +SN+N+          D +P  ++ ++ +  N D  D+ +S AEKSL QKI+R+
Sbjct: 16  DKLSAKVSNLNI----------DKEPKENTANTDSK-NDDGSDEQISAAEKSLFQKIIRK 64

Query: 80  GLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLA 139
           GL+E+ Q++E+QRKDP SPLYSVK+FEALHLKP LLKGVY MGF APSKIQETALPTLLA
Sbjct: 65  GLVETTQDIEVQRKDPSSPLYSVKSFEALHLKPALLKGVYAMGFNAPSKIQETALPTLLA 124

Query: 140 DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH 199
           DPP NMIAQSQSGTGKTAAF L MLSRVN +   PQVLCL+PTYELAIQ GEV AKM   
Sbjct: 125 DPPQNMIAQSQSGTGKTAAFVLAMLSRVNTTKNYPQVLCLSPTYELAIQTGEVAAKMSAF 184

Query: 200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI 259
             ++ ++YAVRGE + R  KITE IIIGTPGKVLDW +K++FF LSKI VFVLDEADVMI
Sbjct: 185 CNEIKIKYAVRGEEMSRGSKITEHIIIGTPGKVLDWAVKFKFFSLSKISVFVLDEADVMI 244

Query: 260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIK 319
           ATQGHQD  IRI K+LP  CQ+M FSATY+ EVM+FA+ +V NPLII+L ++EESLDNIK
Sbjct: 245 ATQGHQDQCIRIHKQLPRTCQMMFFSATYEPEVMKFAEIIVNNPLIIRLLKKEESLDNIK 304

Query: 320 QHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT 379
           Q+YV CK++D K+ A++NIYGV+TIGQA+IFCHTRKTA WLAEKM+K+G  V +LSGELT
Sbjct: 305 QYYVKCKDLDGKYAAITNIYGVITIGQAIIFCHTRKTAGWLAEKMTKDGHAVAVLSGELT 364

Query: 380 VEQRLSILDRFREGEFKI 397
           VEQR+S+LDRFR G  K+
Sbjct: 365 VEQRISVLDRFRAGLEKV 382

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157124559|ref|XP_001654105.1| DEAD box ATP-dependent RNA helicase [Aedes aegypti] gi|108873951|gb|EAT38176.1| AAEL009913-PA [Aedes aegypti]

 Score =  525 bits (1351), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 248/369 (67%), Positives = 299/369 (81%), Gaps = 9/369 (2%)

Query: 38  SPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAE---------KSLLQKIVRRGLIESKQEL 88
           S  E A  APS P +   G   E  + +S AE          SLL KI+R+GL+ESK +L
Sbjct: 63  STAEPATAAPSEPAAKEEGANSENGETVSSAEDAEAFNPADASLLMKIIRKGLVESKLDL 122

Query: 89  EIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQ 148
           E+QRKDP SPLYSVKTFEALHLKPELL+GVY MGF APSKIQETALPTLLADPP NMIAQ
Sbjct: 123 EVQRKDPSSPLYSVKTFEALHLKPELLQGVYAMGFNAPSKIQETALPTLLADPPQNMIAQ 182

Query: 149 SQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYA 208
           SQSGTGKTAAF L MLSRV+P    PQV+CL+PTYELAIQ GEV AKM K   ++ +RYA
Sbjct: 183 SQSGTGKTAAFVLAMLSRVDPRKNYPQVICLSPTYELAIQTGEVAAKMAKFCPEIKLRYA 242

Query: 209 VRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFS 268
           VRGE + +  K+T+ IIIGTPGK++DWG+K+R FDL KI VFVLDEADVMIATQGHQD  
Sbjct: 243 VRGEEIAKGAKLTDHIIIGTPGKLMDWGIKFRAFDLKKITVFVLDEADVMIATQGHQDQC 302

Query: 269 IRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI 328
           IRI K+L S CQ+M FSATY++EVMEFA+ +VPNP++I+L RE+ESLDNIKQ+YV C+N 
Sbjct: 303 IRIHKQLSSRCQMMFFSATYEREVMEFAEYIVPNPIVIRLAREQESLDNIKQYYVKCRNQ 362

Query: 329 DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILD 388
           D+K++A+SNIYGV+T+GQA+IFCHTRKTA+WL+ KMS++G +V +LSGELTVEQRL++LD
Sbjct: 363 DDKYQAISNIYGVITVGQAIIFCHTRKTASWLSGKMSQDGHSVAVLSGELTVEQRLAVLD 422

Query: 389 RFREGEFKI 397
           RFR G  K+
Sbjct: 423 RFRAGLEKV 431

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307199044|gb|EFN79768.1| DEAD-box helicase Dbp80 [Harpegnathos saltator]

 Score =  524 bits (1350), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 243/351 (69%), Positives = 297/351 (84%)

Query: 47  PSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFE 106
           P+S       + D  D+ +S+AEKSLLQKI+R+GL+E+ +++EIQRKDP+SPLYSVK+F+
Sbjct: 30  PNSVKDGDTKSDDGSDEQISLAEKSLLQKIIRKGLVETTKDVEIQRKDPNSPLYSVKSFD 89

Query: 107 ALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSR 166
           ALHLKP LLKGVY MGF APS+IQETALPTLLADPP NMIAQSQSGTGKTAAF L MLSR
Sbjct: 90  ALHLKPALLKGVYAMGFNAPSRIQETALPTLLADPPQNMIAQSQSGTGKTAAFVLAMLSR 149

Query: 167 VNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIII 226
           V+ + + PQVLCL+PTYELAIQ GEV AKM ++  ++ ++YAVRGE + R  K+TE III
Sbjct: 150 VDTTKEYPQVLCLSPTYELAIQTGEVAAKMSRYCPEIKIKYAVRGEEISRGSKVTEHIII 209

Query: 227 GTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSA 286
           GTPGKVLDWG K++FFDL+KI VFVLDEADVMIATQGHQD  IRI K LP  CQ+M FSA
Sbjct: 210 GTPGKVLDWGQKFKFFDLNKISVFVLDEADVMIATQGHQDQCIRIHKMLPRTCQMMFFSA 269

Query: 287 TYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQ 346
           TY+ EVM FA+ +V NPLII+L REEESLDNIKQ+Y+ CKN+D+K+ A++NIYGV+TIGQ
Sbjct: 270 TYEPEVMNFAEIIVSNPLIIRLLREEESLDNIKQYYIKCKNVDDKYTAITNIYGVITIGQ 329

Query: 347 AMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           A+IFCHT+KTA+WLAEKM+K+G  V +LSG+LTVEQR+S+LDRFR G  K+
Sbjct: 330 AIIFCHTKKTASWLAEKMTKDGHAVAILSGDLTVEQRISVLDRFRAGLEKV 380

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307173630|gb|EFN64481.1| DEAD-box helicase Dbp80 [Camponotus floridanus]

 Score =  523 bits (1348), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 250/378 (66%), Positives = 302/378 (79%), Gaps = 4/378 (1%)

Query: 20  DDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRR 79
           D L   ++N+NL Q +  +P        S  D  A    D  +  +S AEKSLLQKI+R+
Sbjct: 16  DKLASKVTNLNLDQTNASAPIS----IVSINDGDARSEDDTSEDQISPAEKSLLQKIIRK 71

Query: 80  GLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLA 139
           GL+E+ ++ EIQRKDP SPLYSVK+FEALHLKP LL+GVY MGF APS+IQETALPTLLA
Sbjct: 72  GLVETTKDPEIQRKDPQSPLYSVKSFEALHLKPALLQGVYGMGFNAPSRIQETALPTLLA 131

Query: 140 DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH 199
           DPP NMIAQSQSGTGKTAAF L MLSRV+ +   PQVLCL+PTYELAIQ GEV AKM + 
Sbjct: 132 DPPQNMIAQSQSGTGKTAAFVLAMLSRVDTTKDYPQVLCLSPTYELAIQTGEVAAKMSRF 191

Query: 200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI 259
             ++ ++YAVRGE + R  KITE IIIGTPGKVLDWG K++FFDLSKI VFVLDEADVMI
Sbjct: 192 CPEIKIKYAVRGEEISRGSKITEHIIIGTPGKVLDWGQKFKFFDLSKISVFVLDEADVMI 251

Query: 260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIK 319
           ATQGHQD  IRI K LP  CQ+M FSATY+ EVM FA+ +V NP+IIKL R++ESLDNIK
Sbjct: 252 ATQGHQDQCIRIHKLLPRTCQMMFFSATYEPEVMNFAEIIVSNPIIIKLLRQQESLDNIK 311

Query: 320 QHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT 379
           Q+Y+ CKN+DEK+ A++NIYGV+TIGQA+IFCHT+KTA+WLAEKM+++G  V +LSG+LT
Sbjct: 312 QYYIKCKNVDEKYTAITNIYGVITIGQAIIFCHTKKTASWLAEKMTRDGHAVAILSGDLT 371

Query: 380 VEQRLSILDRFREGEFKI 397
           VEQR+S+LDRFR G  K+
Sbjct: 372 VEQRISVLDRFRAGLEKV 389

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170034912|ref|XP_001845316.1| DEAD-box helicase Dbp80 [Culex quinquefasciatus] gi|167876609|gb|EDS39992.1| DEAD-box helicase Dbp80 [Culex quinquefasciatus]

 Score =  523 bits (1348), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 246/367 (67%), Positives = 301/367 (82%), Gaps = 7/367 (1%)

Query: 31  LKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEI 90
           +  A TPS     +PA S    +A   +D E    + A+ SLL KI+R+GL+ES+Q++E+
Sbjct: 78  VSSAGTPS-----EPAASENGETASSTEDAE--AFNPADASLLMKIIRKGLVESRQDIEV 130

Query: 91  QRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQ 150
           QRK+P SPLYSVKTFEALHLKPELL+GVY MGF APSKIQETALPTLLA+PP NMIAQSQ
Sbjct: 131 QRKNPMSPLYSVKTFEALHLKPELLQGVYAMGFNAPSKIQETALPTLLAEPPQNMIAQSQ 190

Query: 151 SGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVR 210
           SGTGKTAAF L MLSRVNP+   PQV+CL+PTYELAIQ GEV AKM K   ++ +RYAVR
Sbjct: 191 SGTGKTAAFVLAMLSRVNPAKNYPQVICLSPTYELAIQTGEVAAKMAKFCPEIKLRYAVR 250

Query: 211 GENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIR 270
           GE + +  K+T+ IIIGTPGK+LDWG+K+R FDL KI VFVLDEADVMIATQGHQD  IR
Sbjct: 251 GEEISKGSKLTDHIIIGTPGKLLDWGIKFRAFDLKKISVFVLDEADVMIATQGHQDQCIR 310

Query: 271 IQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDE 330
           I K+L S CQ+M FSATY++EVMEFA+ +VPNP++I+L RE+ESLDNIKQ+YV C+N DE
Sbjct: 311 IHKQLSSSCQMMFFSATYEREVMEFAEYIVPNPIVIRLAREQESLDNIKQYYVKCRNQDE 370

Query: 331 KFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRF 390
           K++A+SNIYGV+T+GQA+IFCHTRKTA WL+ KMS++G +V +LSG+LTVEQRL +LDRF
Sbjct: 371 KYQAISNIYGVITVGQAIIFCHTRKTAGWLSGKMSQDGHSVAVLSGDLTVEQRLMVLDRF 430

Query: 391 REGEFKI 397
           R G  K+
Sbjct: 431 RAGMEKV 437

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849834|ref|XP_003700540.1| PREDICTED: DEAD-box helicase Dbp80-like [Megachile rotundata]

 Score =  521 bits (1341), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 248/354 (70%), Positives = 294/354 (83%), Gaps = 3/354 (0%)

Query: 44  KPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVK 103
           K + +S DS +    +E+  P   AE SLLQKI+R+GL+E+ ++LEIQRKDP SPLYSVK
Sbjct: 32  KESNASADSKSDDGTEEQISP---AENSLLQKIIRKGLVETTKDLEIQRKDPSSPLYSVK 88

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           +FEALHLKP LLKGVY MGF APSKIQETALPTLLADPP NMIAQSQSGTGKTAAF L M
Sbjct: 89  SFEALHLKPALLKGVYAMGFNAPSKIQETALPTLLADPPQNMIAQSQSGTGKTAAFVLAM 148

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQ 223
           LSRV+ +   PQVLCL+PTYELAIQ GEV AKM +   ++ ++YAVRGE + R  KITE 
Sbjct: 149 LSRVDTAKNYPQVLCLSPTYELAIQTGEVAAKMSRFCNEIKIKYAVRGEEISRGSKITEH 208

Query: 224 IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIML 283
           IIIGTPGKVLDW +K++FF LSKI VFVLDEADVMIATQGHQD  IRI K+LP  CQ+M 
Sbjct: 209 IIIGTPGKVLDWAVKFKFFSLSKISVFVLDEADVMIATQGHQDQCIRIHKQLPRTCQMMF 268

Query: 284 FSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVT 343
           FSATY+ EVM+FA+ +V NPLII+L +EEESLDNIKQ+YV CK++DEK+ A++NIYGV+T
Sbjct: 269 FSATYEPEVMKFAEIIVNNPLIIRLLKEEESLDNIKQYYVKCKDLDEKYAAITNIYGVIT 328

Query: 344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           IGQA+IFCHTRKTA WLAEKM+K+G  V +LSGELTVEQR+S+LDRFR G  K+
Sbjct: 329 IGQAIIFCHTRKTANWLAEKMTKDGHAVAVLSGELTVEQRISVLDRFRAGLEKV 382

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66547453|ref|XP_624946.1| PREDICTED: DEAD-box helicase Dbp80 [Apis mellifera] gi|380014255|ref|XP_003691155.1| PREDICTED: DEAD-box helicase Dbp80-like [Apis florea]

 Score =  520 bits (1338), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 243/341 (71%), Positives = 288/341 (84%)

Query: 57  NKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLK 116
           + D  D+ +S AEKSLLQKI+RRGL+E+ +++EIQRKDP SPLYSVK+F+ALHLKP LLK
Sbjct: 42  DDDVADEQISPAEKSLLQKIIRRGLVETTKDIEIQRKDPSSPLYSVKSFDALHLKPALLK 101

Query: 117 GVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQV 176
           GVY MGF APSKIQETALPTLLADPP NMIAQSQSGTGKTAAF L MLSRV+ +   PQV
Sbjct: 102 GVYAMGFNAPSKIQETALPTLLADPPQNMIAQSQSGTGKTAAFVLAMLSRVDTTKNYPQV 161

Query: 177 LCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWG 236
           LCL+PTYELAIQ GEV AKM     ++ ++YAVRGE + R  K+TE IIIGTPGKVLDW 
Sbjct: 162 LCLSPTYELAIQTGEVAAKMSAFCNEIKIKYAVRGEEISRGTKVTEHIIIGTPGKVLDWA 221

Query: 237 LKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFA 296
            K++FF LSKI VFVLDEADVMIATQGHQD  IRI K+LP  CQ+M FSATY+ EVM+FA
Sbjct: 222 FKFKFFSLSKISVFVLDEADVMIATQGHQDQCIRIHKQLPRTCQMMFFSATYEPEVMKFA 281

Query: 297 QDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKT 356
           + +V NPLII+L +EEE+LDNIKQ+YV CK++DEK+ A++NIYGV+TIGQA+IFCHTRKT
Sbjct: 282 EIIVNNPLIIRLLKEEETLDNIKQYYVKCKDLDEKYAAITNIYGVITIGQAIIFCHTRKT 341

Query: 357 AAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           A WLAEKM+K+G  V +LSGELTVEQR+S+LDRFR G  K+
Sbjct: 342 ANWLAEKMTKDGHAVAVLSGELTVEQRISVLDRFRAGLEKV 382

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332019714|gb|EGI60184.1| DEAD-box helicase Dbp80 [Acromyrmex echinatior]

 Score =  519 bits (1336), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 254/392 (64%), Positives = 314/392 (80%), Gaps = 10/392 (2%)

Query: 6   DWIAATKNTSALKPDDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPL 65
           DW        A + D L   ++++NL   D P+ T  + PAP+  D  +  + D  ++ +
Sbjct: 7   DW-----GQCADEQDKLASKVTSLNL---DKPNST--SIPAPTVKDGDSKSDDDTSEEQI 56

Query: 66  SVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYA 125
           S AEKSLLQKI+R+GL+E+ +++EIQR+DP+SPLYSVKTF+ALHLKP LLKGVY +GF A
Sbjct: 57  SPAEKSLLQKIIRKGLVETTKDIEIQRQDPNSPLYSVKTFDALHLKPALLKGVYALGFNA 116

Query: 126 PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL 185
           PS+IQETALPTLLADPP NMIAQSQSGTGKTAAF L MLSRV+ + + PQVLCL+PTYEL
Sbjct: 117 PSRIQETALPTLLADPPQNMIAQSQSGTGKTAAFVLAMLSRVDVTKEYPQVLCLSPTYEL 176

Query: 186 AIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLS 245
           AIQ GEV AKM +   ++ ++YAVRGE + R  KI+E IIIGTPGKVLDWG K++FFDLS
Sbjct: 177 AIQTGEVAAKMSRFCPEIKIKYAVRGEEISRGSKISEHIIIGTPGKVLDWGQKFKFFDLS 236

Query: 246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLI 305
           KI VFVLDEADVMIATQGHQD  IRI K LP  CQ+M FSATY+ EVM FA+ +V NPLI
Sbjct: 237 KISVFVLDEADVMIATQGHQDQCIRIHKLLPRACQMMFFSATYEPEVMNFAEIIVSNPLI 296

Query: 306 IKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMS 365
           I+L REEESLDNIKQ+Y+ CKN+DEK+ A++NIYGV+TIGQA+IFCHT+KTA+WLA KM+
Sbjct: 297 IRLLREEESLDNIKQYYIRCKNVDEKYTAITNIYGVITIGQAIIFCHTKKTASWLAGKMT 356

Query: 366 KEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           K+G  V +LSG+LTVEQR+S+LDRFR G  K+
Sbjct: 357 KDGHAVAILSGDLTVEQRISVLDRFRAGLEKV 388

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157131180|ref|XP_001662155.1| DEAD box ATP-dependent RNA helicase [Aedes aegypti] gi|108871623|gb|EAT35848.1| AAEL012015-PA [Aedes aegypti]

 Score =  518 bits (1334), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 255/404 (63%), Positives = 311/404 (76%), Gaps = 14/404 (3%)

Query: 5   SDWIAATKNTSALKPDDLIDVLSNV----NLKQADTP-------SPTEDAKPAPSSPDSS 53
           SDWI   K     +  DL++ LS V      K   +P       S T ++  A     S 
Sbjct: 17  SDWI---KKAEEQEISDLVNELSFVKDERTTKNEKSPEWGKVLNSGTTESATAGKESASG 73

Query: 54  APGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPE 113
             G   E+ +  + A+ SLL+KI+R+GL+ESK + E+QR DP SPLYSVKTFEALHLKPE
Sbjct: 74  ENGEIAEDAEEFNPADASLLRKIIRKGLVESKLDPEVQRNDPLSPLYSVKTFEALHLKPE 133

Query: 114 LLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQE 173
           LL+GVY MGF APSKIQETALPTLLADPP NMIAQSQSGTGKTAAF L MLSRV+P    
Sbjct: 134 LLQGVYAMGFNAPSKIQETALPTLLADPPQNMIAQSQSGTGKTAAFVLAMLSRVDPKKNY 193

Query: 174 PQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVL 233
           PQV+CL+PTYELAIQ GEV AKM K   ++ +RYAVRGE L +  K+T+ IIIGTPGK++
Sbjct: 194 PQVICLSPTYELAIQTGEVAAKMAKFCPEIKLRYAVRGEELAKGDKLTDHIIIGTPGKLM 253

Query: 234 DWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVM 293
           DWG+KYR FDL KI VFVLDEADVMIATQGHQD  IRI K+L S CQ+M FSATY++EVM
Sbjct: 254 DWGIKYRSFDLKKITVFVLDEADVMIATQGHQDQCIRIHKQLSSRCQMMFFSATYEREVM 313

Query: 294 EFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHT 353
           EFA+ +VPNP++I+L RE+ESLDNIKQ+YV C+  DEK++A+SNIYGV+T+GQA+IFCHT
Sbjct: 314 EFAEYIVPNPIVIRLAREQESLDNIKQYYVKCRTQDEKYQAISNIYGVITVGQAIIFCHT 373

Query: 354 RKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           RKTA+WL+ KMS++G +V +LSGELTVEQRL++LDRFR G  K+
Sbjct: 374 RKTASWLSVKMSQDGHSVAVLSGELTVEQRLAVLDRFRAGLEKV 417

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347969816|ref|XP_311683.4| AGAP003397-PA [Anopheles gambiae str. PEST] gi|333467603|gb|EAA07398.4| AGAP003397-PA [Anopheles gambiae str. PEST]

 Score =  518 bits (1333), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 246/352 (69%), Positives = 296/352 (84%), Gaps = 3/352 (0%)

Query: 46  APSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTF 105
           +  SP S A     EE + ++ A+ SLL KI+R+GL+ESK +LE+QRKDP SPL+SVK+F
Sbjct: 69  SAGSPPSVA---GSEEIETVNPADASLLMKIIRKGLVESKLDLEVQRKDPSSPLHSVKSF 125

Query: 106 EALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLS 165
           EALHLKPELL+GVY MGF APSKIQETALPTLLADPP NMIAQSQSGTGKTAAF L MLS
Sbjct: 126 EALHLKPELLQGVYAMGFNAPSKIQETALPTLLADPPQNMIAQSQSGTGKTAAFVLAMLS 185

Query: 166 RVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQII 225
           RV+P    PQV+CL+PTYELAIQ GEV AKM K   ++ +R+AVRGE L + KKIT+ II
Sbjct: 186 RVDPRKPYPQVICLSPTYELAIQTGEVAAKMAKFCKEIKLRFAVRGEELPKGKKITDHII 245

Query: 226 IGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS 285
           IGTPGK++DWG+K+R FDL KI VFVLDEADVMIATQGHQD  IRI K+L S CQ+M FS
Sbjct: 246 IGTPGKLMDWGIKFRAFDLRKISVFVLDEADVMIATQGHQDQCIRIHKQLSSSCQMMFFS 305

Query: 286 ATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIG 345
           ATY+KEVMEFA+ +VPNP+II+L RE+ESLDNIKQ+YV CKN DEK++A+SNIYGV+T+G
Sbjct: 306 ATYEKEVMEFAEYIVPNPIIIRLAREQESLDNIKQYYVKCKNQDEKYQAISNIYGVITVG 365

Query: 346 QAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           QA+IFCHTRKTA WL+ KM+++G +V +LSGELTVEQRL++LDRFR G  K+
Sbjct: 366 QAIIFCHTRKTAGWLSGKMTQDGHSVAVLSGELTVEQRLAVLDRFRAGLEKV 417

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	399
FB|FBgn0024804	460	Dbp80 "Dead box protein 80" [D	0.827	0.717	0.660	1e-116
UNIPROTKB|Q5ZMC1	479	DDX19B "Uncharacterized protei	0.919	0.766	0.596	1.6e-116
UNIPROTKB|E9PTL9	482	Ddx19b "Protein Ddx19b" [Rattu	0.927	0.767	0.596	2.1e-116
UNIPROTKB|Q9NUU7	478	DDX19A "ATP-dependent RNA heli	0.847	0.707	0.640	3.4e-116
UNIPROTKB|F1S432	481	DDX19B "Uncharacterized protei	0.922	0.765	0.589	4.4e-116
UNIPROTKB|F1MUT6	484	DDX19B "Uncharacterized protei	0.919	0.758	0.591	7.1e-116
UNIPROTKB|I3LC00	478	DDX19A "Uncharacterized protei	0.847	0.707	0.640	7.1e-116
UNIPROTKB|E2RR50	478	DDX19A "Uncharacterized protei	0.852	0.711	0.635	9.1e-116
UNIPROTKB|H3BQK0	484	DDX19B "HCG1998531, isoform CR	0.919	0.758	0.594	9.1e-116
UNIPROTKB|Q9UMR2	479	DDX19B "ATP-dependent RNA heli	0.919	0.766	0.594	9.1e-116

FB|FBgn0024804 Dbp80 "Dead box protein 80" [Drosophila melanogaster (taxid:7227)]

 Score = 1150 (409.9 bits), Expect = 1.0e-116, P = 1.0e-116
 Identities = 218/330 (66%), Positives = 271/330 (82%)

Query:    68 AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
             AE SLL KI+ +GL+ +K  L++Q+K+P+SPL+SVKTFEALHLK  LLKG+Y MGF  PS
Sbjct:    38 AETSLLIKILGKGLVNTKLSLDLQQKNPNSPLHSVKTFEALHLKASLLKGIYAMGFNTPS 97

Query:   128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
             KIQETALPTLLADPP NMIAQSQSGTGKTAAF L MLSRVN  +  PQVLCL+PTYELAI
Sbjct:    98 KIQETALPTLLADPPQNMIAQSQSGTGKTAAFVLAMLSRVNVCLNHPQVLCLSPTYELAI 157

Query:   188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
             Q GEV A+MG+   ++ +R+AVRGE ++R+KKI E I+IGTPGK+LDWG+K+R FD+ KI
Sbjct:   158 QTGEVAARMGQFCREIKLRFAVRGEEVDRSKKIEEHILIGTPGKLLDWGIKFRLFDMKKI 217

Query:   248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
              VFVLDEADVMIATQGH D  IRI K L   CQ++ FSATY KEVM+FA+ +V +P II+
Sbjct:   218 SVFVLDEADVMIATQGHHDQCIRIHKMLNPHCQMLFFSATYGKEVMDFARLIVADPTIIR 277

Query:   308 LKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE 367
             L REEESL+NIKQ+YV CKN + K+ A+ NIYG +++GQA+IFCHT++TAAWLA KM+ +
Sbjct:   278 LMREEESLENIKQYYVKCKNEEGKYNAIQNIYGCISVGQAIIFCHTKRTAAWLAAKMTSD 337

Query:   368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
             G +V +L+G+LTV QRL +LDRFR G  K+
Sbjct:   338 GHSVAVLTGDLTVVQRLDVLDRFRSGLEKV 367

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

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0044614 "nuclear pore cytoplasmic filaments" evidence=ISS

UNIPROTKB|Q5ZMC1 DDX19B "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 1148 (409.2 bits), Expect = 1.6e-116, P = 1.6e-116
 Identities = 222/372 (59%), Positives = 284/372 (76%)

Query:    26 LSNVNLKQADTPSPTEXXXXXXXXXXXXXXGNKDEEDKPLSVAEKSLLQKIVRRGLIESK 85
             LS + LK+ +   P                 ++++ED+    A +SLL K++R  L+++ 
Sbjct:    20 LSTLQLKE-EKAKPDANGAVPKADDNVERTEDEEKEDR----AAQSLLNKLIRSNLVDTT 74

Query:    86 QELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNM 145
              ++E+ ++DP+SPLYSVK+FE LHLKP+LL+GVY MGF  PSKIQE ALP +LA+PP N+
Sbjct:    75 NQVEVLQRDPNSPLYSVKSFEELHLKPQLLQGVYAMGFNRPSKIQENALPMMLAEPPQNL 134

Query:   146 IAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV 205
             IAQSQSGTGKTAAF L MLSRV P  + PQ LCL+PTYELA+Q G+V+ +MGK   +L +
Sbjct:   135 IAQSQSGTGKTAAFVLAMLSRVEPGNKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 194

Query:   206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ 265
              YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KIKVFVLDEADVMIATQGHQ
Sbjct:   195 AYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQ 254

Query:   266 DFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMC 325
             D SIRIQ+ LP DCQ++LFSAT++  V +FAQ +VP+P IIKLKREEE+LD IKQ+YV+C
Sbjct:   255 DQSIRIQRMLPRDCQMLLFSATFEDSVWKFAQKVVPDPNIIKLKREEETLDTIKQYYVLC 314

Query:   326 KNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLS 385
              + DEKF A+ NIYG +TI QAM+FCHTRKTA WLA ++SKEG  V LLSGE+ VEQR +
Sbjct:   315 NSRDEKFRALCNIYGAITIAQAMVFCHTRKTAGWLAAELSKEGHQVALLSGEMMVEQRAA 374

Query:   386 ILDRFREGEFKI 397
             +++RFREG+ K+
Sbjct:   375 VIERFREGKEKV 386

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|E9PTL9 Ddx19b "Protein Ddx19b" [Rattus norvegicus (taxid:10116)]

 Score = 1147 (408.8 bits), Expect = 2.1e-116, P = 2.1e-116
 Identities = 222/372 (59%), Positives = 285/372 (76%)

Query:    26 LSNVNLKQADTPSPTEXXXXXXXXXXXXXXGNKDEEDKPLSVAEKSLLQKIVRRGLIESK 85
             LSN++LK+ +   P +                K EED+    A +SLL K++R  L+++ 
Sbjct:    20 LSNLHLKE-EKIKP-DANGDQGAVVKTSANTEKTEEDEKEDRAAQSLLNKLIRSNLVDNT 77

Query:    86 QELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNM 145
              ++E+ ++DP SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +LA+PP N+
Sbjct:    78 NQVEVLQRDPSSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 137

Query:   146 IAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV 205
             IAQSQSGTGKTAAF L MLSRV P+ + PQ LCL+PTYELA+Q G+V+ +MGK   +L +
Sbjct:   138 IAQSQSGTGKTAAFVLAMLSRVEPADRHPQCLCLSPTYELALQTGKVIEQMGKFHPELKL 197

Query:   206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ 265
              YAVRG  LER +K+ EQI+IGTPG VLDW  K +F D  KIKVFVLDEADVMIATQGHQ
Sbjct:   198 AYAVRGNKLERGQKVGEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQ 257

Query:   266 DFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMC 325
             D SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P IIKLKREEE+LD IKQ+YV+C
Sbjct:   258 DQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNIIKLKREEETLDTIKQYYVLC 317

Query:   326 KNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLS 385
              N +EKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKEG  V LLSGE+ VEQR +
Sbjct:   318 NNREEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAA 377

Query:   386 ILDRFREGEFKI 397
             +++RFREG+ K+
Sbjct:   378 VIERFREGKEKV 389

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|Q9NUU7 DDX19A "ATP-dependent RNA helicase DDX19A" [Homo sapiens (taxid:9606)]

 Score = 1145 (408.1 bits), Expect = 3.4e-116, P = 3.4e-116
 Identities = 217/339 (64%), Positives = 276/339 (81%)

Query:    59 DEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGV 118
             DEE+K    A+ SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GV
Sbjct:    48 DEEEKEDRAAQ-SLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGV 106

Query:   119 YEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLC 178
             Y MGF  PSKIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLSRV PS + PQ LC
Sbjct:   107 YAMGFNRPSKIQENALPMMLAEPPQNLIAQSQSGTGKTAAFVLAMLSRVEPSDRYPQCLC 166

Query:   179 LAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLK 238
             L+PTYELA+Q G+V+ +MGK   +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K
Sbjct:   167 LSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSK 226

Query:   239 YRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQD 298
              +F D  KIKVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ 
Sbjct:   227 LKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQK 286

Query:   299 MVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAA 358
             +VP+P +IKLKREEE+LD IKQ+YV+C + DEKF+A+ N+YG +TI QAMIFCHTRKTA+
Sbjct:   287 VVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTAS 346

Query:   359 WLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
             WLA ++SKEG  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct:   347 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKV 385

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0006917 "induction of apoptosis" evidence=IEA

GO:0010043 "response to zinc ion" evidence=IEA

GO:0005643 "nuclear pore" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0031965 "nuclear membrane" evidence=IEA

UNIPROTKB|F1S432 DDX19B "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1144 (407.8 bits), Expect = 4.4e-116, P = 4.4e-116
 Identities = 220/373 (58%), Positives = 285/373 (76%)

Query:    26 LSNVNLKQADT-PSPTEXXXXXXXXXXXXXXGNKDEEDKPLSVAEKSLLQKIVRRGLIES 84
             LSN++LK     P   +                +++ED+    A +SLL K++R  L+++
Sbjct:    20 LSNLHLKDEKVKPDANDKGAVVKTNANAEKTDEEEKEDR----AAQSLLNKLIRSNLVDN 75

Query:    85 KQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHN 144
               ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +LA+PP N
Sbjct:    76 TNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQN 135

Query:   145 MIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS 204
             +IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+Q G+V+ +MGK   +L 
Sbjct:   136 LIAQSQSGTGKTAAFVLAMLSQVEPANRYPQCLCLSPTYELALQTGKVIEQMGKFYPELK 195

Query:   205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGH 264
             + YAVRG  LER +KI+E I+IGTPG VLDW  K +F D  KIKVFVLDEADVMIATQGH
Sbjct:   196 LAYAVRGNKLERGQKISEHIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGH 255

Query:   265 QDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVM 324
             QD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P IIKLKREEE+LD IKQ+YV+
Sbjct:   256 QDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNIIKLKREEETLDTIKQYYVL 315

Query:   325 CKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRL 384
             C N DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKEG  V LLSGE+ VEQR 
Sbjct:   316 CNNRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMVVEQRA 375

Query:   385 SILDRFREGEFKI 397
             ++++RFREG+ K+
Sbjct:   376 AVIERFREGKEKV 388

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1MUT6 DDX19B "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 1142 (407.1 bits), Expect = 7.1e-116, P = 7.1e-116
 Identities = 220/372 (59%), Positives = 286/372 (76%)

Query:    26 LSNVNLKQADTPSPTEXXXXXXXXXXXXXXGNKDEEDKPLSVAEKSLLQKIVRRGLIESK 85
             LSN++LK+ +   P                  +++ED+    A +SLL K++R  L+++ 
Sbjct:    25 LSNLHLKE-EKIKPDANGAVVKTNANAEKADEEEKEDR----AAQSLLNKLIRSNLVDNT 79

Query:    86 QELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNM 145
              ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +LA+PP N+
Sbjct:    80 NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 139

Query:   146 IAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV 205
             IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+Q G+V+ +MGK   +L +
Sbjct:   140 IAQSQSGTGKTAAFVLAMLSQVEPANRHPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 199

Query:   206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ 265
              YAVRG  LER +KI+E I+IGTPG VLDW  K +F D  KIKVFVLDEADVMIATQGHQ
Sbjct:   200 AYAVRGNKLERGQKISEHIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQ 259

Query:   266 DFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMC 325
             D SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P IIKLKREEE+LD IKQ+YV+C
Sbjct:   260 DQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNIIKLKREEETLDTIKQYYVLC 319

Query:   326 KNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLS 385
              + DEKF+A+ NIYG +TI QAMIFCHTRKTA+WLA ++SKEG  V LLSGE+ VEQR +
Sbjct:   320 NSRDEKFQALCNIYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMVVEQRAA 379

Query:   386 ILDRFREGEFKI 397
             +++RFREG+ K+
Sbjct:   380 VIERFREGKEKV 391

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|I3LC00 DDX19A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1142 (407.1 bits), Expect = 7.1e-116, P = 7.1e-116
 Identities = 217/339 (64%), Positives = 275/339 (81%)

Query:    59 DEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGV 118
             DEE+K    A+ SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GV
Sbjct:    48 DEEEKEDRAAQ-SLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGV 106

Query:   119 YEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLC 178
             Y MGF  PSKIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLSRV P+ + PQ LC
Sbjct:   107 YAMGFNRPSKIQENALPMMLAEPPQNLIAQSQSGTGKTAAFVLAMLSRVEPAERYPQCLC 166

Query:   179 LAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLK 238
             L+PTYELA+Q G+V+ +MGK   +L + YAVRG  LER +KI+E I+IGTPG VLDW  K
Sbjct:   167 LSPTYELALQTGKVIEQMGKFHPELKLAYAVRGNKLERGQKISEHIVIGTPGTVLDWCSK 226

Query:   239 YRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQD 298
              +F D  KIKVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ 
Sbjct:   227 LKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQK 286

Query:   299 MVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAA 358
             +VP+P IIKLKREEE+LD IKQ+YV+C N DEKF+A+ N+YG +TI QAMIFCHTRKTA+
Sbjct:   287 VVPDPNIIKLKREEETLDTIKQYYVLCNNRDEKFQALCNLYGAITIAQAMIFCHTRKTAS 346

Query:   359 WLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
             WLA ++SKEG  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct:   347 WLAAELSKEGHQVALLSGEMVVEQRAAVIERFREGKEKV 385

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E2RR50 DDX19A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1141 (406.7 bits), Expect = 9.1e-116, P = 9.1e-116
 Identities = 216/340 (63%), Positives = 275/340 (80%)

Query:    58 KDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKG 117
             K EE++    A +SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+G
Sbjct:    46 KAEEEEKEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQG 105

Query:   118 VYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVL 177
             VY MGF  PSKIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLSRV P+ + PQ L
Sbjct:   106 VYAMGFNRPSKIQENALPMMLAEPPQNLIAQSQSGTGKTAAFVLAMLSRVEPAERYPQCL 165

Query:   178 CLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGL 237
             CL+PTYELA+Q G+V+ +MGK   +L + YAVRG  LER +KI+E I+IGTPG VLDW  
Sbjct:   166 CLSPTYELALQTGKVIEQMGKFHPELKLAYAVRGNKLERGQKISEHIVIGTPGTVLDWCS 225

Query:   238 KYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ 297
             K +F D  KIKVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ
Sbjct:   226 KLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPKNCQMLLFSATFEDSVWKFAQ 285

Query:   298 DMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTA 357
              +VP+P IIKLKREEE+LD IKQ+YV+C N DEKF+A+ N+YG +TI QAMIFCHTRKTA
Sbjct:   286 KVVPDPNIIKLKREEETLDTIKQYYVLCNNRDEKFQALCNLYGAITIAQAMIFCHTRKTA 345

Query:   358 AWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
             +WLA ++SKEG  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct:   346 SWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKV 385

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|H3BQK0 DDX19B "HCG1998531, isoform CRA_g" [Homo sapiens (taxid:9606)]

 Score = 1141 (406.7 bits), Expect = 9.1e-116, P = 9.1e-116
 Identities = 221/372 (59%), Positives = 285/372 (76%)

Query:    26 LSNVNLKQADTPSPTEXXXXXXXXXXXXXXGNKDEEDKPLSVAEKSLLQKIVRRGLIESK 85
             LSN++LK+      T                  DEE+K    A+ SLL K++R  L+++ 
Sbjct:    25 LSNLHLKEEKIKPDTNGAVVKTNANAEKT----DEEEKEDRAAQ-SLLNKLIRSNLVDNT 79

Query:    86 QELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNM 145
              ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +LA+PP N+
Sbjct:    80 NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 139

Query:   146 IAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV 205
             IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+Q G+V+ +MGK   +L +
Sbjct:   140 IAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 199

Query:   206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ 265
              YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KIKVFVLDEADVMIATQGHQ
Sbjct:   200 AYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQ 259

Query:   266 DFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMC 325
             D SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IKLKREEE+LD IKQ+YV+C
Sbjct:   260 DQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLC 319

Query:   326 KNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLS 385
              + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKEG  V LLSGE+ VEQR +
Sbjct:   320 SSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAA 379

Query:   386 ILDRFREGEFKI 397
             +++RFREG+ K+
Sbjct:   380 VIERFREGKEKV 391

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q9UMR2 DDX19B "ATP-dependent RNA helicase DDX19B" [Homo sapiens (taxid:9606)]

 Score = 1141 (406.7 bits), Expect = 9.1e-116, P = 9.1e-116
 Identities = 221/372 (59%), Positives = 285/372 (76%)

Query:    26 LSNVNLKQADTPSPTEXXXXXXXXXXXXXXGNKDEEDKPLSVAEKSLLQKIVRRGLIESK 85
             LSN++LK+      T                  DEE+K    A+ SLL K++R  L+++ 
Sbjct:    20 LSNLHLKEEKIKPDTNGAVVKTNANAEKT----DEEEKEDRAAQ-SLLNKLIRSNLVDNT 74

Query:    86 QELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNM 145
              ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +LA+PP N+
Sbjct:    75 NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 134

Query:   146 IAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV 205
             IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+Q G+V+ +MGK   +L +
Sbjct:   135 IAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 194

Query:   206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ 265
              YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KIKVFVLDEADVMIATQGHQ
Sbjct:   195 AYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQ 254

Query:   266 DFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMC 325
             D SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IKLKREEE+LD IKQ+YV+C
Sbjct:   255 DQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLC 314

Query:   326 KNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLS 385
              + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKEG  V LLSGE+ VEQR +
Sbjct:   315 SSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAA 374

Query:   386 ILDRFREGEFKI 397
             +++RFREG+ K+
Sbjct:   375 VIERFREGKEKV 386

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0005643 "nuclear pore" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0031965 "nuclear membrane" evidence=IEA

GO:0004386 "helicase activity" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0005635 "nuclear envelope" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q61655	DD19A_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6424	0.8270	0.6903	yes	N/A
A2QUY7	DBP5_ASPNC	3, ., 6, ., 4, ., 1, 3	0.4383	0.7593	0.6286	yes	N/A
P20449	DBP5_YEAST	3, ., 6, ., 4, ., 1, 3	0.4621	0.9323	0.7717	yes	N/A
Q75C39	DBP5_ASHGO	3, ., 6, ., 4, ., 1, 3	0.4531	0.9122	0.7811	yes	N/A
Q2U8K6	DBP5_ASPOR	3, ., 6, ., 4, ., 1, 3	0.4354	0.7644	0.6262	yes	N/A
Q3ZBV2	DD19A_BOVIN	3, ., 6, ., 4, ., 1, 3	0.6454	0.8270	0.6903	yes	N/A
Q6CJU1	DBP5_KLULA	3, ., 6, ., 4, ., 1, 3	0.4444	0.8947	0.7611	yes	N/A
A3GH91	DBP5_PICST	3, ., 6, ., 4, ., 1, 3	0.4691	0.7944	0.634	yes	N/A
Q09747	DBP5_SCHPO	3, ., 6, ., 4, ., 1, 3	0.5015	0.7869	0.6242	yes	N/A
Q4HY71	DBP5_GIBZE	3, ., 6, ., 4, ., 1, 3	0.3719	0.8671	0.7090	yes	N/A
Q6FKN8	DBP5_CANGA	3, ., 6, ., 4, ., 1, 3	0.4689	0.7894	0.625	yes	N/A
Q54TF8	DDX19_DICDI	3, ., 6, ., 4, ., 1, 3	0.4625	0.7844	0.6731	yes	N/A
Q4WIN6	DBP5_ASPFU	3, ., 6, ., 4, ., 1, 3	0.4642	0.7593	0.6196	yes	N/A
Q9NUU7	DD19A_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6454	0.8270	0.6903	yes	N/A
Q6C3X7	DBP5_YARLI	3, ., 6, ., 4, ., 1, 3	0.4635	0.8320	0.6803	yes	N/A
O61305	DDX19_DROME	3, ., 6, ., 4, ., 1, 3	0.6606	0.8270	0.7173	yes	N/A
Q9UMR2	DD19B_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6393	0.8270	0.6889	yes	N/A
Q5AVM1	DBP5_EMENI	3, ., 6, ., 4, ., 1, 3	0.4350	0.7593	0.6352	yes	N/A
Q6BRE4	DBP5_DEBHA	3, ., 6, ., 4, ., 1, 3	0.4395	0.9323	0.7545	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.914
3rd Layer	3.6.4	0.921

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	399
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	8e-80
cd00268	203	cd00268, DEADc, DEAD-box helicases	4e-75
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-63
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	3e-42
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	4e-41
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	9e-41
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	3e-40
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	9e-40
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-36
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-36
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	4e-36
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	8e-36
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	1e-31
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-27
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-26
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	6e-13
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	3e-06
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	1e-05
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	3e-04
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	6e-04

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

 Score =  254 bits (650), Expect = 8e-80
 Identities = 107/305 (35%), Positives = 173/305 (56%), Gaps = 13/305 (4%)

Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
           +   F +L L PELL+ + ++GF  P+ IQ  A+P +LA    +++ Q+Q+GTGKTAAF 
Sbjct: 27  TPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAG--RDVLGQAQTGTGKTAAFL 84

Query: 161 LTMLSRVN--PSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE-RN 217
           L +L ++      +    L LAPT ELA+QI E + K+GK++  L V     G ++  + 
Sbjct: 85  LPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQI 144

Query: 218 KKITE--QIIIGTPGKVLDWGLKYR-FFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR 274
           + +     I++ TPG++LD  L  R   DLS ++  VLDEAD  +   G  D   +I K 
Sbjct: 145 EALKRGVDIVVATPGRLLD--LIKRGKLDLSGVETLVLDEAD-RMLDMGFIDDIEKILKA 201

Query: 275 LPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE--EESLDNIKQHYVMCKNIDEKF 332
           LP D Q +LFSAT   ++ E A+  + +P+ I++  E  E +L  IKQ Y+  ++ +EK 
Sbjct: 202 LPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKL 261

Query: 333 EAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFRE 392
           E +  +      G+ ++F  T++    LAE + K G  V  L G+L  E+R   L++F++
Sbjct: 262 ELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKD 321

Query: 393 GEFKI 397
           GE ++
Sbjct: 322 GELRV 326

Length = 513

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

 Score =  231 bits (592), Expect = 4e-75
 Identities = 93/208 (44%), Positives = 131/208 (62%), Gaps = 10/208 (4%)

Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML 164
           FE L L PELL+G+Y +GF  P+ IQ  A+P LL+    ++I Q+Q+G+GKTAAF + +L
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLS--GRDVIGQAQTGSGKTAAFLIPIL 58

Query: 165 SRVN--PSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL-ERNKKIT 221
            +++  P    PQ L LAPT ELA+QI EV  K+GKH T+L V     G ++ ++ +K+ 
Sbjct: 59  EKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKH-TNLKVVVIYGGTSIDKQIRKLK 117

Query: 222 E--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
               I++ TPG++LD  L+    DLSK+K  VLDEAD M+   G +D    I K LP D 
Sbjct: 118 RGPHIVVATPGRLLDL-LERGKLDLSKVKYLVLDEADRML-DMGFEDQIREILKLLPKDR 175

Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           Q +LFSAT  KEV + A+  + NP+ I 
Sbjct: 176 QTLLFSATMPKEVRDLARKFLRNPVRIL 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|185609 PTZ00424, PTZ00424, helicase 45; Provisional

 Score =  209 bits (533), Expect = 1e-63
 Identities = 107/301 (35%), Positives = 175/301 (58%), Gaps = 12/301 (3%)

Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           V +F+AL L  +LL+G+Y  GF  PS IQ+  +  +L    ++ I Q+QSGTGKTA F +
Sbjct: 27  VDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDG--YDTIGQAQSGTGKTATFVI 84

Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVR-YAVRGENLERNK-- 218
             L  ++  +   Q L LAPT ELA QI +VV  +G +   L VR +A  G  + R+   
Sbjct: 85  AALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDY---LKVRCHACVGGTVVRDDIN 141

Query: 219 --KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
             K    +++GTPG+V D  +  R   +  +K+F+LDEAD M+ ++G +     + K+LP
Sbjct: 142 KLKAGVHMVVGTPGRVYDM-IDKRHLRVDDLKLFILDEADEML-SRGFKGQIYDVFKKLP 199

Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
            D Q+ LFSAT   E++E     + +P  I +K++E +L+ I+Q YV  +  + KF+ + 
Sbjct: 200 PDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLC 259

Query: 337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK 396
           ++Y  +TI QA+I+C+TR+   +L +KM +    V  + G++  + R  I+  FR G  +
Sbjct: 260 DLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTR 319

Query: 397 I 397
           +
Sbjct: 320 V 320

Length = 401

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

 Score =  153 bits (389), Expect = 3e-42
 Identities = 95/302 (31%), Positives = 149/302 (49%), Gaps = 43/302 (14%)

Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
           S+  F  L L P LL  + E+G+   + IQ  +LP +LA    ++IAQ+++G+GKTAAF 
Sbjct: 2   SMTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAG--KDVIAQAKTGSGKTAAFG 59

Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI 220
           L +L +++      Q L L PT ELA Q    VAK         +R   R      N K+
Sbjct: 60  LGLLQKLDVKRFRVQALVLCPTRELADQ----VAK--------EIRRLARFI---PNIKV 104

Query: 221 TE------------------QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ 262
                                II+GTPG++LD  L+    DL  +   VLDEAD M+   
Sbjct: 105 LTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDH-LRKGTLDLDALNTLVLDEADRML-DM 162

Query: 263 GHQDFSIR-IQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQH 321
           G QD +I  I ++ P+  Q +LFSATY + +   +Q    +P+ +K++     L  I+Q 
Sbjct: 163 GFQD-AIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVE-STHDLPAIEQR 220

Query: 322 YVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVE 381
           +      DE+  A+  +         ++FC+T+K    +A+ ++ +G +   L G+L  E
Sbjct: 221 FYEVSP-DERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDL--E 277

Query: 382 QR 383
           QR
Sbjct: 278 QR 279

Length = 460

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

 Score =  151 bits (382), Expect = 4e-41
 Identities = 102/379 (26%), Positives = 191/379 (50%), Gaps = 27/379 (7%)

Query: 32  KQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQ 91
             A    P      AP++  ++        +KP    +K   ++  +   +   ++  ++
Sbjct: 24  PAAAPAPPPPAKTAAPATKAAAPAAAAPRAEKP--KKDKPRRERKPKPASLWKLEDFVVE 81

Query: 92  RKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQS 151
                 P      F   +L PEL+  ++++GF   + IQ   L   LA   H+ I ++Q+
Sbjct: 82  ------PQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAG--HDAIGRAQT 133

Query: 152 GTGKTAAFTLTMLSRV--NPS-----IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS 204
           GTGKTAAF +++++++   P      + EP+ L +APT EL +QI +  A + K+ T L+
Sbjct: 134 GTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKY-TGLN 192

Query: 205 VRYAVRGENLERNKKITEQ----IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA 260
           V   V G + ++  K  E     I++ TPG++LD+  +     L  ++V VLDEAD M+ 
Sbjct: 193 VMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVH-LDMVEVMVLDEADRML- 250

Query: 261 TQGHQDFSIRIQKRLP--SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNI 318
             G      +I ++ P   + Q +LFSAT+  +VM  A+    +P I++++ E  + D +
Sbjct: 251 DMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTV 310

Query: 319 KQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGEL 378
           +QH       D K++ + N+       + M+F + +     + E++ K+G+N   LSG++
Sbjct: 311 EQHVYAVAGSD-KYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDV 369

Query: 379 TVEQRLSILDRFREGEFKI 397
              +R+  L+ FREG+ ++
Sbjct: 370 PQHKRIKTLEGFREGKIRV 388

Length = 475

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

 Score =  152 bits (385), Expect = 9e-41
 Identities = 96/301 (31%), Positives = 156/301 (51%), Gaps = 16/301 (5%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TF  L LK  +L+ + ++G+  PS IQ   +P LL     +++  +Q+G+GKTAAF+L +
Sbjct: 7   TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNG--RDVLGMAQTGSGKTAAFSLPL 64

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV-------RYAVRGENLER 216
           L  ++P ++ PQ+L LAPT ELA+Q+ E +    KH+  ++V       RY V+   L +
Sbjct: 65  LHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQ 124

Query: 217 NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
                 QI++GTPG++LD  LK    DLSK+   VLDEAD M+     +D    I  ++P
Sbjct: 125 GP----QIVVGTPGRLLD-HLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVE-TIMAQIP 178

Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
              Q  LFSAT  + +    +  +  P  ++++    +  +I Q Y     +  K EA+ 
Sbjct: 179 EGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGM-RKNEALV 237

Query: 337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK 396
                     A+IF  T+     +AE + + G N   L+G++    R   L+R ++G   
Sbjct: 238 RFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLD 297

Query: 397 I 397
           I
Sbjct: 298 I 298

Length = 629

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

 Score =  148 bits (375), Expect = 3e-40
 Identities = 94/306 (30%), Positives = 164/306 (53%), Gaps = 21/306 (6%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           +F++L L P++L+ V E G+  P+ IQ+ A+P +L     +++A +Q+GTGKTA FTL +
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEG--RDLMASAQTGTGKTAGFTLPL 59

Query: 164 LSRVNPSIQEPQ------VLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN 217
           L  +       +       L L PT ELA QIGE V    K+   L++R  V    +  N
Sbjct: 60  LQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKY---LNIRSLVVFGGVSIN 116

Query: 218 KKITE-----QIIIGTPGKVLDWGLKY-RFFDLSKIKVFVLDEADVMIATQGHQDFSIRI 271
            ++ +      +++ TPG++LD  L++     L ++++ VLDEAD M+      D   R+
Sbjct: 117 PQMMKLRGGVDVLVATPGRLLD--LEHQNAVKLDQVEILVLDEADRMLDMGFIHDIR-RV 173

Query: 272 QKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEK 331
             +LP+  Q +LFSAT+  ++   A+ ++ NPL I++ R   + + + QH V   +   K
Sbjct: 174 LAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQH-VHFVDKKRK 232

Query: 332 FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFR 391
            E +S + G     Q ++F  T+  A  LAE+++K+G+    + G  +   R   L  F+
Sbjct: 233 RELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFK 292

Query: 392 EGEFKI 397
            G+ ++
Sbjct: 293 SGDIRV 298

Length = 456

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

 Score =  139 bits (352), Expect = 9e-40
 Identities = 61/173 (35%), Positives = 93/173 (53%), Gaps = 8/173 (4%)

Query: 127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA 186
           + IQ  A+P +L+    +++ Q+ +G+GKT AF L +L  + P    PQ L LAPT ELA
Sbjct: 1   TPIQAQAIPAILSG--KDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELA 58

Query: 187 IQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE----QIIIGTPGKVLDWGLKYRFF 242
            QI E + K+ K    L V     G +L+   +  +     I++GTPG++LD   + +  
Sbjct: 59  EQIYEELKKLFKI-LGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLK 117

Query: 243 DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEF 295
            L  +K+ VLDEA  ++   G  D    I  RLP D QI+L SAT  + + + 
Sbjct: 118 LLKNLKLLVLDEAHRLL-DMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 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|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional

 Score =  140 bits (353), Expect = 1e-36
 Identities = 97/315 (30%), Positives = 170/315 (53%), Gaps = 24/315 (7%)

Query: 98  PLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTA 157
           PL  + TF +  L P LL G+   GF   + IQ   LP  L  P  ++  Q+Q+GTGKT 
Sbjct: 5   PLTDL-TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVAL--PGGDVAGQAQTGTGKTL 61

Query: 158 AFTLTMLSR-------VNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAV- 209
           AF + +++R        +   ++P+ L LAPT ELAIQI +   K G    DL +R+A+ 
Sbjct: 62  AFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFG---ADLGLRFALV 118

Query: 210 -RGENLERNKKITEQ---IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ 265
             G + ++ +++ +Q   +II TPG+++D+  +++   L   ++ VLDEAD M      +
Sbjct: 119 YGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIK 178

Query: 266 DFSIR-IQKRLPSDC--QIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHY 322
           D  IR + +R+P     Q +LFSAT    V+E A + +  P  + ++ E  +   ++Q  
Sbjct: 179 D--IRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRI 236

Query: 323 VMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQ 382
               + +EK   +  +       + M+F +T+     +A  + + G  VG+LSG++  ++
Sbjct: 237 YFPAD-EEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKK 295

Query: 383 RLSILDRFREGEFKI 397
           R S+L+RF++G+ +I
Sbjct: 296 RESLLNRFQKGQLEI 310

Length = 572

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

 Score =  137 bits (347), Expect = 2e-36
 Identities = 90/323 (27%), Positives = 151/323 (46%), Gaps = 53/323 (16%)

Query: 103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALP------TLLADPPHNMIAQSQSGTGKT 156
            TF  L L   LL+ + + G+  P+ IQ  A+P       +L   P        +GTGKT
Sbjct: 1   TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAP--------TGTGKT 52

Query: 157 AAFTLTMLSRVNPSIQ-----------EPQVLCLAPTYELAIQIGEVVAKMGKHITDLS- 204
           AAF L       P++Q            P++L L PT ELA+Q+ +   ++ KH T L  
Sbjct: 53  AAFLL-------PALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKH-THLDI 104

Query: 205 ------VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM 258
                 V Y    E    N    + I++ TPG++L + +K   FD   ++  +LDEAD M
Sbjct: 105 ATITGGVAYMNHAEVFSEN----QDIVVATPGRLLQY-IKEENFDCRAVETLILDEADRM 159

Query: 259 IATQGHQDF-SIRIQKRLPSDCQIMLFSATYDKE-VMEFAQDMVPNPLIIKLK--REEES 314
           +     QD  +I  + R     Q +LFSAT + + V +FA+ ++ +P+ ++ +  R E  
Sbjct: 160 LDMGFAQDIETIAAETRWRK--QTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERK 217

Query: 315 LDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLL 374
              I Q Y    +++ K   + ++     + ++++F  TR+    LA  + K G+N   L
Sbjct: 218 --KIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYL 275

Query: 375 SGELTVEQRLSILDRFREGEFKI 397
            GE+   +R   + R  +G   +
Sbjct: 276 EGEMVQAKRNEAIKRLTDGRVNV 298

Length = 434

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

 Score =  130 bits (329), Expect = 4e-36
 Identities = 57/207 (27%), Positives = 98/207 (47%), Gaps = 9/207 (4%)

Query: 118 VYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVL 177
           + + GF      Q+ A+  LL+    ++I  + +G+GKT A  L  L  +    +  +VL
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGL-RDVILAAPTGSGKTLAALLPALEALKRG-KGGRVL 58

Query: 178 CLAPTYELAIQIGEVVAKMGKHITDLSVRY---AVRGENLERNKKITEQIIIGTPGKVLD 234
            L PT ELA Q  E + K+G  +    V       + E L + +     I++ TPG++LD
Sbjct: 59  VLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLD 118

Query: 235 WGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVME 294
                    LS + + +LDEA  ++   G  D   ++ K LP + Q++L SAT  +E+  
Sbjct: 119 LLEN-DKLSLSNVDLVILDEAHRLLD-GGFGDQLEKLLKLLPKNVQLLLLSATPPEEIEN 176

Query: 295 FAQDMVPNPLIIKLKREEESLDNIKQH 321
             +  + +P+ I        L+ I+Q 
Sbjct: 177 LLELFLNDPVFI--DVGFTPLEPIEQF 201

Length = 201

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

 Score =  135 bits (342), Expect = 8e-36
 Identities = 101/313 (32%), Positives = 164/313 (52%), Gaps = 30/313 (9%)

Query: 103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLT 162
           + F    L P++++ + + GF+  + IQ  ALP  LA    ++  Q+Q+GTGKT AF LT
Sbjct: 8   QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAG--RDVAGQAQTGTGKTMAF-LT 64

Query: 163 -----MLSRVNP---SIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL 214
                +LS   P    + +P+ L +APT ELA+QI      + +  T L +  A  G+  
Sbjct: 65  ATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQA-TGLKLGLAYGGDGY 123

Query: 215 ERNKKITEQ---IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIR- 270
           ++  K+ E    I+IGT G+++D+  K    +L  I+V VLDEAD M      +D  IR 
Sbjct: 124 DKQLKVLESGVDILIGTTGRLIDY-AKQNHINLGAIQVVVLDEADRMFDLGFIKD--IRW 180

Query: 271 IQKRLPSDCQ--IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI 328
           + +R+P   Q   MLFSAT    V E A + + NP  ++++ E+++   IK+      N 
Sbjct: 181 LFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSN- 239

Query: 329 DEKFEAVSNIYGVVTIGQAMIFCHTR----KTAAWLAEKMSKEGLNVGLLSGELTVEQRL 384
           +EK   +  +       +A+IF +T+    +    LA     +G  VGLL+G++  ++RL
Sbjct: 240 EEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLA----ADGHRVGLLTGDVAQKKRL 295

Query: 385 SILDRFREGEFKI 397
            IL+ F  G+  I
Sbjct: 296 RILEEFTRGDLDI 308

Length = 423

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

 Score =  117 bits (294), Expect = 1e-31
 Identities = 48/148 (32%), Positives = 81/148 (54%), Gaps = 8/148 (5%)

Query: 143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD 202
            +++  + +G+GKT A  L +L  ++   +  QVL LAPT ELA Q+ E + ++      
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFGE--G 57

Query: 203 LSVRYAVRGEN---LERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI 259
           + V Y + G +    E+       I++GTPG++LD  L+     L K+ + +LDEA  ++
Sbjct: 58  IKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLD-ELERLKLSLKKLDLLILDEAHRLL 116

Query: 260 ATQGHQDFSIRIQKRLPSDCQIMLFSAT 287
             QG     ++I  +LP D Q++L SAT
Sbjct: 117 N-QGFGLLGLKILLKLPKDRQVLLLSAT 143

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

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

 Score =  114 bits (286), Expect = 1e-27
 Identities = 99/356 (27%), Positives = 175/356 (49%), Gaps = 43/356 (12%)

Query: 58  KDEEDK-PLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLK 116
           +D      LS ++  LL    RR L     E+ ++ +    P+ S   F +  L P+LL 
Sbjct: 87  RDPGSTSGLSSSQAELL----RRKL-----EIHVKGEAVPPPILS---FSSCGLPPKLLL 134

Query: 117 GVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRV------NPS 170
            +   G+  P+ IQ  A+P  L+    +++  + +G+GKTA+F + ++SR       +PS
Sbjct: 135 NLETAGYEFPTPIQMQAIPAALSG--RSLLVSADTGSGKTASFLVPIISRCCTIRSGHPS 192

Query: 171 IQE-PQVLCLAPTYELAIQIGEVVAKMGKHI---TDLSVRYAVRGENLERNKKITEQIII 226
            Q  P  + L PT EL +Q+ +    +GK +   T L V      + L R ++  E +I+
Sbjct: 193 EQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVE-LIV 251

Query: 227 GTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSA 286
           GTPG+++D   K+   +L  + V VLDE D M+  +G +D  ++I + L    Q++LFSA
Sbjct: 252 GTPGRLIDLLSKHDI-ELDNVSVLVLDEVDCML-ERGFRDQVMQIFQALSQP-QVLLFSA 308

Query: 287 TYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQH--YVMCKNIDEKFEAVSNIYGVVTI 344
           T   EV +FA  +  + ++I +         +KQ   +V  K   +K      ++ ++  
Sbjct: 309 TVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQK------LFDILKS 362

Query: 345 GQ-----AMIFCHTRKTAAWLAEKMSK-EGLNVGLLSGELTVEQRLSILDRFREGE 394
            Q     A++F  +R  A  LA  ++   GL    + GE ++++R  ++  F  GE
Sbjct: 363 KQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGE 418

Length = 518

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

 Score =  109 bits (274), Expect = 5e-26
 Identities = 95/322 (29%), Positives = 152/322 (47%), Gaps = 46/322 (14%)

Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           V +FE       +LK +   GF  P+ IQ    P  L+    +MI  +++G+GKT AF L
Sbjct: 129 VVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSG--RDMIGIAETGSGKTLAFLL 186

Query: 162 TMLSRVN--PSIQE---PQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER 216
             +  +N  P ++    P VL LAPT ELA QI E   K G       +R  V    + +
Sbjct: 187 PAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFG---ASSKIRNTVAYGGVPK 243

Query: 217 NKKITE-----QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRI 271
             +I       +I+I  PG+++D+ L+    +L ++   VLDEAD M+       F  +I
Sbjct: 244 RGQIYALRRGVEILIACPGRLIDF-LESNVTNLRRVTYLVLDEADRML----DMGFEPQI 298

Query: 272 QK---RLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE------SLD-----N 317
           +K   ++  D Q +++SAT+ KEV   A+D         L +EE       SLD     N
Sbjct: 299 RKIVSQIRPDRQTLMWSATWPKEVQSLARD---------LCKEEPVHVNVGSLDLTACHN 349

Query: 318 IKQHYVMCKNIDEKFEAVSNIYGVVTI--GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLS 375
           IKQ  V      EK   +  +   +     + +IF  T+K A +L +++  +G     + 
Sbjct: 350 IKQ-EVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIH 408

Query: 376 GELTVEQRLSILDRFREGEFKI 397
           G+   E+R  +L+ F+ G+  I
Sbjct: 409 GDKKQEERTWVLNEFKTGKSPI 430

Length = 545

>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 = 65.0 bits (159), Expect = 6e-13
 Identities = 29/83 (34%), Positives = 46/83 (55%), Gaps = 4/83 (4%)

Query: 317 NIKQHYVMCKNIDEKFEAVSNIY--GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLL 374
            IKQ+ +  +  DEK EA+  +    +   G+ +IFC ++K    LAE + K G+ V  L
Sbjct: 1   PIKQYVLPVE--DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAAL 58

Query: 375 SGELTVEQRLSILDRFREGEFKI 397
            G+ + E+R  +L  FREGE  +
Sbjct: 59  HGDGSQEEREEVLKDFREGEIVV 81

Length = 131

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

 Score = 48.8 bits (117), Expect = 3e-06
 Identities = 38/174 (21%), Positives = 71/174 (40%), Gaps = 28/174 (16%)

Query: 240 RFFD-LSKIKV--FVLDEADVMIATQGHQDFS------IRIQKRLPSDCQIMLFSATYDK 290
           RF + L ++ +    +DEA   I+  GH DF        R++  LP +  ++  +AT   
Sbjct: 122 RFLELLKRLPISLVAIDEAHC-ISQWGH-DFRPDYRRLGRLRAGLP-NPPVLALTATATP 178

Query: 291 EVMEFAQDMV-------PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVT 343
            V     D+         N       R   +L  +++         ++   ++ +   ++
Sbjct: 179 RV---RDDIREQLGLQDANIFRGSFDRPNLALKVVEKGEPS-----DQLAFLATVLPQLS 230

Query: 344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
               +I+C TRK    LAE + K G++ G     L+ E+R  +   F   E K+
Sbjct: 231 -KSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKV 283

Length = 590

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 16/39 (41%), Positives = 24/39 (61%)

Query: 359 WLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            LAE + + G+ V  L G L+ E+R  ILD+F  G+ K+
Sbjct: 2   ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKV 40

Length = 82

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

 Score = 39.0 bits (92), Expect = 3e-04
 Identities = 14/36 (38%), Positives = 22/36 (61%)

Query: 362 EKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           + + K G+ V  L G L+ E+R  IL+ FR G+ K+
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKV 36

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

 Score = 41.6 bits (98), Expect = 6e-04
 Identities = 56/262 (21%), Positives = 91/262 (34%), Gaps = 66/262 (25%)

Query: 144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL 203
           N++  + +G+GKT    L +LS +       +V+ + P   LA    E   +  + + +L
Sbjct: 49  NVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALA---EEKYEEFSR-LEEL 102

Query: 204 SVRYAV-------RGENLERNKKITEQIIIGTPGKVLDWGLKYRFFD--LSKIKVFVLDE 254
            +R  +         E L R       +I+ TP K LD     R     + ++ + V+DE
Sbjct: 103 GIRVGISTGDYDLDDERLARY-----DVIVTTPEK-LDSLT--RKRPSWIEEVDLVVIDE 154

Query: 255 ADVMIATQGHQ-DFSIR------IQKRLP---SDCQIMLFSATYDKEVMEFAQDMVPNPL 304
                    H      R      I  R+       +I+  SAT      E A D +   L
Sbjct: 155 I--------HLLGDRTRGPVLESIVARMRRLNELIRIVGLSATL-PNAEEVA-DWLNAKL 204

Query: 305 IIKLKREEESLDNIKQHYVMCK----NIDEKFEAVSNIYGVVTI----------GQAMIF 350
           +    R            V         D K +    +   + +          GQ ++F
Sbjct: 205 VESDWRPVPLR-----RGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVF 259

Query: 351 CHTRK----TAAWLAEKMSKEG 368
            H+RK    TA  L  KMS   
Sbjct: 260 VHSRKEAEKTAKKLRIKMSATL 281

Length = 766

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	399
KOG0332|consensus	477		100.0
KOG0330|consensus	476		100.0
KOG0328|consensus	400		100.0
KOG0331|consensus	519		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0338|consensus	691		100.0
KOG0326|consensus	459		100.0
KOG0343|consensus	758		100.0
KOG0333|consensus	673		100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0340|consensus	442		100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0342|consensus	543		100.0
KOG0345|consensus	567		100.0
KOG0339|consensus	731		100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0346|consensus	569		100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0341|consensus	610		100.0
KOG0335|consensus	482		100.0
KOG0336|consensus	629		100.0
KOG0327|consensus	397		100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0348|consensus	708		100.0
KOG0334|consensus	997		100.0
KOG4284|consensus	980		100.0
KOG0347|consensus	731		100.0
KOG0337|consensus	529		100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG0344|consensus	593		100.0
KOG0350|consensus	620		100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
PRK00254	720	ski2-like helicase; Provisional	100.0
KOG0329|consensus	387		100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
PRK01172	674	ski2-like helicase; Provisional	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
PRK10689	1147	transcription-repair coupling factor; Provisional	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	100.0
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	100.0
COG1202	830	Superfamily II helicase, archaea-specific [General	100.0
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.98
COG1204	766	Superfamily II helicase [General function predicti	99.97
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.97
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.97
COG1205	851	Distinct helicase family with a unique C-terminal	99.97
PHA02653	675	RNA helicase NPH-II; Provisional	99.97
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.97
KOG0349|consensus	725		99.97
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.97
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.96
KOG0952|consensus	1230		99.96
PHA02558	501	uvsW UvsW helicase; Provisional	99.96
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.96
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.95
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.94
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.93
KOG0951|consensus	1674		99.93
PRK13766	773	Hef nuclease; Provisional	99.93
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.92
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.92
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.92
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.91
KOG0351|consensus	941		99.91
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.91
PRK05580	679	primosome assembly protein PriA; Validated	99.91
PRK09694	878	helicase Cas3; Provisional	99.9
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.9
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.89
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.89
KOG0352|consensus	641		99.89
KOG0354|consensus	746		99.89
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.88
KOG0353|consensus	695		99.88
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.88
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.86
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.85
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.84
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.83
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.83
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.83
PRK04914	956	ATP-dependent helicase HepA; Validated	99.82
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.81
KOG0948|consensus	1041		99.81
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.8
KOG0947|consensus	1248		99.78
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.78
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.77
KOG0950|consensus	1008		99.75
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.73
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.68
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.68
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.67
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.65
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.65
KOG0951|consensus	1674		99.62
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.6
COG4096	875	HsdR Type I site-specific restriction-modification	99.6
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.58
KOG0920|consensus	924		99.45
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.42
KOG0949|consensus	1330		99.42
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.42
KOG0922|consensus	674		99.41
KOG1123|consensus	776		99.4
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.33
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.3
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.28
KOG0385|consensus	971		99.28
KOG4150|consensus	1034		99.27
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.27
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.24
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.22
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.21
KOG0387|consensus	923		99.21
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.17
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.16
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.12
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.09
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.09
KOG0924|consensus	1042		99.08
KOG0923|consensus	902		99.08
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.08
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.08
KOG1000|consensus	689		99.06
KOG0925|consensus	699		99.05
KOG0389|consensus	941		99.03
KOG0926|consensus	1172		99.02
KOG0390|consensus	776		99.02
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	99.02
KOG0953|consensus	700		99.02
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.99
COG4889	1518	Predicted helicase [General function prediction on	98.99
KOG0392|consensus	1549		98.96
KOG0952|consensus	1230		98.93
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.84
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	98.81
KOG0384|consensus	1373		98.76
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.72
PRK14873	665	primosome assembly protein PriA; Provisional	98.59
KOG1002|consensus	791		98.56
PRK05298	652	excinuclease ABC subunit B; Provisional	98.53
COG0610	962	Type I site-specific restriction-modification syst	98.53
PRK15483	986	type III restriction-modification system StyLTI en	98.45
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	98.41
KOG4439|consensus	901		98.37
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.37
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.36
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.31
KOG2340|consensus	698		98.31
KOG0391|consensus	1958		98.15
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.1
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.1
KOG0386|consensus	1157		98.04
PRK10536	262	hypothetical protein; Provisional	98.02
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.01
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.0
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.94
PF13245	76	AAA_19: Part of AAA domain	97.9
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.89
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.83
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.8
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.79
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.74
KOG1802|consensus	935		97.69
COG3587	985	Restriction endonuclease [Defense mechanisms]	97.68
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.52
KOG0989|consensus	346		97.49
KOG1803|consensus	649		97.48
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.4
KOG0388|consensus	1185		97.27
KOG0921|consensus	1282		97.26
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.21
PRK06526	254	transposase; Provisional	97.17
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.15
PRK04296	190	thymidine kinase; Provisional	97.14
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	97.11
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.09
PRK08181	269	transposase; Validated	97.09
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.07
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	97.03
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.01
PRK13889	988	conjugal transfer relaxase TraA; Provisional	96.98
KOG1132|consensus	945		96.92
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	96.91
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.88
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.86
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	96.86
PRK13826	1102	Dtr system oriT relaxase; Provisional	96.83
PRK05642	234	DNA replication initiation factor; Validated	96.82
PRK14974	336	cell division protein FtsY; Provisional	96.8
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.78
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.77
PHA02533	534	17 large terminase protein; Provisional	96.77
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.76
smart00382	148	AAA ATPases associated with a variety of cellular	96.73
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	96.71
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.67
smart00490	82	HELICc helicase superfamily c-terminal domain.	96.67
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.66
KOG1805|consensus	1100		96.54
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.53
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.52
PRK08084	235	DNA replication initiation factor; Provisional	96.51
PRK08727	233	hypothetical protein; Validated	96.46
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	96.46
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.45
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.43
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	96.43
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.43
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.4
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.38
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.36
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.35
PRK06893	229	DNA replication initiation factor; Validated	96.34
PHA03368	738	DNA packaging terminase subunit 1; Provisional	96.33
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.33
KOG1015|consensus	1567		96.31
PRK06835	329	DNA replication protein DnaC; Validated	96.31
PRK07952	244	DNA replication protein DnaC; Validated	96.28
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.27
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.23
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.19
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.18
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.11
CHL00181	287	cbbX CbbX; Provisional	96.1
PRK11054	684	helD DNA helicase IV; Provisional	96.07
PRK05298	652	excinuclease ABC subunit B; Provisional	96.07
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.06
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.05
KOG1001|consensus	674		95.96
PLN03025	319	replication factor C subunit; Provisional	95.95
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	95.95
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.94
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	95.94
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.93
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.92
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	95.91
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	95.86
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.84
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	95.84
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.81
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.8
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	95.74
KOG0991|consensus	333		95.73
PRK14088	440	dnaA chromosomal replication initiation protein; P	95.7
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	95.68
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.57
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.55
PHA03333	752	putative ATPase subunit of terminase; Provisional	95.55
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.55
PRK12422	445	chromosomal replication initiation protein; Provis	95.48
PRK08116	268	hypothetical protein; Validated	95.48
PRK12377	248	putative replication protein; Provisional	95.48
PHA03372	668	DNA packaging terminase subunit 1; Provisional	95.45
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.42
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.41
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	95.41
PRK04328	249	hypothetical protein; Provisional	95.38
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.35
KOG0298|consensus	1394		95.35
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.31
PF13173	128	AAA_14: AAA domain	95.29
PF00004	132	AAA: ATPase family associated with various cellula	95.27
KOG2004|consensus	906		95.25
PRK14086	617	dnaA chromosomal replication initiation protein; P	95.21
PTZ00112	1164	origin recognition complex 1 protein; Provisional	95.12
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.11
KOG0739|consensus	439		95.11
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.01
PRK12402	337	replication factor C small subunit 2; Reviewed	94.98
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	94.96
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.96
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	94.85
PRK13897	606	type IV secretion system component VirD4; Provisio	94.84
PRK06921	266	hypothetical protein; Provisional	94.81
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	94.77
PRK08769	319	DNA polymerase III subunit delta'; Validated	94.74
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.65
PRK08533	230	flagellar accessory protein FlaH; Reviewed	94.56
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	94.51
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	94.51
PRK09183	259	transposase/IS protein; Provisional	94.51
COG2256	436	MGS1 ATPase related to the helicase subunit of the	94.48
PRK13850	670	type IV secretion system protein VirD4; Provisiona	94.43
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	94.39
PRK00411	394	cdc6 cell division control protein 6; Reviewed	94.38
PF05729	166	NACHT: NACHT domain	94.38
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	94.36
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	94.34
PRK13342	413	recombination factor protein RarA; Reviewed	94.24
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.17
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	94.16
PRK14873	665	primosome assembly protein PriA; Provisional	94.13
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	94.12
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	94.1
PHA02544	316	44 clamp loader, small subunit; Provisional	94.08
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	94.04
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	94.01
PRK11823	446	DNA repair protein RadA; Provisional	93.96
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	93.86
PRK05973	237	replicative DNA helicase; Provisional	93.85
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	93.78
PRK07940	394	DNA polymerase III subunit delta'; Validated	93.72
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	93.69
PRK07471	365	DNA polymerase III subunit delta'; Validated	93.68
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	93.65
PRK13851	344	type IV secretion system protein VirB11; Provision	93.61
KOG0738|consensus	491		93.6
PRK00440	319	rfc replication factor C small subunit; Reviewed	93.59
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	93.59
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	93.56
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	93.55
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	93.52
PRK13876	663	conjugal transfer coupling protein TraG; Provision	93.5
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	93.49
TIGR00064	272	ftsY signal recognition particle-docking protein F	93.49
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	93.49
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	93.48
PHA00012	361	I assembly protein	93.46
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	93.45
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	93.44
COG0593	408	DnaA ATPase involved in DNA replication initiation	93.44
PRK10867	433	signal recognition particle protein; Provisional	93.39
TIGR00959	428	ffh signal recognition particle protein. This mode	93.36
TIGR00595	505	priA primosomal protein N'. All proteins in this f	93.33
PRK09112	351	DNA polymerase III subunit delta'; Validated	93.29
KOG1016|consensus	1387		93.25
PRK05580	679	primosome assembly protein PriA; Validated	93.24
PRK08939	306	primosomal protein DnaI; Reviewed	93.23
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	93.23
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	93.2
KOG1133|consensus	821		93.2
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	93.19
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	93.19
PRK13341	725	recombination factor protein RarA/unknown domain f	93.18
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	93.17
COG1198	730	PriA Primosomal protein N' (replication factor Y)	93.12
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	93.12
cd03115	173	SRP The signal recognition particle (SRP) mediates	93.11
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	93.1
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	93.08
KOG0733|consensus	802		93.04
PRK13822	641	conjugal transfer coupling protein TraG; Provision	93.03
PRK08699	325	DNA polymerase III subunit delta'; Validated	93.01
PRK04195	482	replication factor C large subunit; Provisional	92.86
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	92.85
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	92.78
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	92.77
PHA00729	226	NTP-binding motif containing protein	92.62
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	92.61
PRK13880	636	conjugal transfer coupling protein TraG; Provision	92.59
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	92.58
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	92.58
COG4626	546	Phage terminase-like protein, large subunit [Gener	92.53
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	92.37
PRK06871	325	DNA polymerase III subunit delta'; Validated	92.36
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	92.33
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	92.3
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	92.27
PRK06964	342	DNA polymerase III subunit delta'; Validated	92.2
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.17
PRK10865	857	protein disaggregation chaperone; Provisional	92.16
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	92.14
PTZ00293	211	thymidine kinase; Provisional	92.1
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	92.1
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	92.09
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	92.07
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	92.06
PRK10436	462	hypothetical protein; Provisional	92.05
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	92.01
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	92.01
TIGR02533	486	type_II_gspE general secretory pathway protein E.	91.91
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	91.91
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	91.82
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	91.78
TIGR02237	209	recomb_radB DNA repair and recombination protein R	91.72
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	91.62
KOG0383|consensus	696		91.52
PRK07993	334	DNA polymerase III subunit delta'; Validated	91.47
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	91.46
KOG2170|consensus	344		91.45
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	91.42
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	91.42
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	91.37
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	91.27
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	91.23
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	91.2
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	91.19
PRK10416	318	signal recognition particle-docking protein FtsY;	91.16
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	91.15
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	91.07
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	91.06
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	91.0
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	90.98
PRK06090	319	DNA polymerase III subunit delta'; Validated	90.98
KOG2028|consensus	554		90.97
TIGR00767	415	rho transcription termination factor Rho. Members	90.88
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	90.82
CHL00095	821	clpC Clp protease ATP binding subunit	90.77
PHA00350	399	putative assembly protein	90.71
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	90.64
PRK06067	234	flagellar accessory protein FlaH; Validated	90.63
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	90.54
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	90.52
PRK09354	349	recA recombinase A; Provisional	90.4
KOG0732|consensus	1080		90.29
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	90.28
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	90.21
cd01394	218	radB RadB. The archaeal protein radB shares simila	90.2
KOG1513|consensus	1300		90.17
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	90.17
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	90.13
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	90.07
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	90.04
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	89.98
PRK13764	602	ATPase; Provisional	89.96
KOG1806|consensus	1320		89.87
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	89.85
COG1221	403	PspF Transcriptional regulators containing an AAA-	89.76
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	89.75
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	89.7
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	89.56
cd00983	325	recA RecA is a bacterial enzyme which has roles in	89.51
PRK09087	226	hypothetical protein; Validated	89.48
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	89.41
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	89.4
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	89.36
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	89.27
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	89.05
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	88.78
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	88.67
PRK14701	1638	reverse gyrase; Provisional	88.52
COG4185	187	Uncharacterized protein conserved in bacteria [Fun	88.52
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	88.46
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	88.45
PF12846	304	AAA_10: AAA-like domain	88.42
COG0606	490	Predicted ATPase with chaperone activity [Posttran	88.41
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	88.32
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	88.19
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	87.99
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	87.91
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	87.87
PRK09376	416	rho transcription termination factor Rho; Provisio	87.85
PRK07399	314	DNA polymerase III subunit delta'; Validated	87.82
KOG0740|consensus	428		87.81
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	87.77
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	87.67
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	87.63
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	87.56
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	87.39
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	87.39
cd01128	249	rho_factor Transcription termination factor rho is	87.26
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	87.21
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	87.07
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	87.01
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	86.92
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	86.91
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	86.76
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	86.68
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	86.63
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	86.57
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	86.5
KOG2228|consensus	408		86.48
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	86.48
KOG0344|consensus	593		86.26
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	86.01
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	85.96
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	85.96
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	85.79
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	85.42
PRK04841	903	transcriptional regulator MalT; Provisional	85.36
KOG2036|consensus	1011		85.3
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	85.26
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	85.22
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	85.19
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	85.18
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	85.13
PHA02542	473	41 41 helicase; Provisional	85.06
KOG0741|consensus	744		84.96
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	84.91
KOG0331|consensus	519		84.81
PF13555	62	AAA_29: P-loop containing region of AAA domain	84.43
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	83.86
KOG1131|consensus	755		83.7
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	83.69
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	83.68

>KOG0332|consensus

Probab=100.00  E-value=3.2e-65  Score=459.20  Aligned_cols=329  Identities=61%  Similarity=0.942  Sum_probs=310.2

Q ss_pred             CCCCCChHhHHHHHHHHHhhhccccccceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC
Q psy11867         61 EDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLAD  140 (399)
Q Consensus        61 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~  140 (399)
                      .++....++.+++++.++..         +.-.+|++|++|+++|++|+|.|+++++++.|+|.+|+.||+.|+|.++..
T Consensus        57 ~~~~~e~~~~~ll~~~~~~~---------vk~~dpnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~  127 (477)
T KOG0332|consen   57 HEKKEEPADSSLLNKFIESN---------VKLADPNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAE  127 (477)
T ss_pred             hhccCCcchhhhhcchhhhc---------eeecCCCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcC
Confidence            33444555667777766543         333469999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhcc
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI  220 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (399)
                      |++|+|++++.|+|||.||.+.+|.++......|++++|+||||||.|+.+++.++|++. ++...++..+....+....
T Consensus       128 Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~-~ita~yair~sk~~rG~~i  206 (477)
T KOG0332|consen  128 PPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFT-ELTASYAIRGSKAKRGNKL  206 (477)
T ss_pred             CchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCchHHHHHHHHHHHHHhcCce-eeeEEEEecCcccccCCcc
Confidence            999999999999999999999999999998899999999999999999999999999998 8999999999877777777


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhC
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~  300 (399)
                      ..+|+|+|||.+.+|+.+.+.+++..++.+|+||||.|++.+||.+...+|...+|+++|+++||||+...++.|+..+.
T Consensus       207 ~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kiv  286 (477)
T KOG0332|consen  207 TEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIV  286 (477)
T ss_pred             hhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhc
Confidence            78999999999999998888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCH
Q psy11867        301 PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTV  380 (399)
Q Consensus       301 ~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~  380 (399)
                      +++..+.+.+++..+.+|+|+|+.|...++|++.|.+++.....++.||||.++++|.||+..|+..|+.|.++||+|+.
T Consensus       287 pn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~  366 (477)
T KOG0332|consen  287 PNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTV  366 (477)
T ss_pred             CCCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCcccC
Q psy11867        381 EQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       381 ~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+|.+++++||.|+.+|||
T Consensus       367 ~~R~~ii~~Fr~g~~kVLi  385 (477)
T KOG0332|consen  367 EQRAAIIDRFREGKEKVLI  385 (477)
T ss_pred             HHHHHHHHHHhcCcceEEE
Confidence            9999999999999999986

>KOG0330|consensus

Probab=100.00  E-value=5e-58  Score=414.97  Aligned_cols=295  Identities=31%  Similarity=0.483  Sum_probs=280.3

Q ss_pred             ccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEE
Q psy11867        100 YSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCL  179 (399)
Q Consensus       100 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil  179 (399)
                      .+..+|.++++.+.+.+++...|+..||+||+++||.++.  |+|||+.|+||||||.+|++|+++++......++++||
T Consensus        58 e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~--g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVL  135 (476)
T KOG0330|consen   58 ESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALG--GRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVL  135 (476)
T ss_pred             hhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhC--CCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEe
Confidence            3467899999999999999999999999999999999998  79999999999999999999999999888888999999


Q ss_pred             eCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechh
Q psy11867        180 APTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD  256 (399)
Q Consensus       180 ~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah  256 (399)
                      +||||||.|+.+.++.++..+ ++.+...+||.++..+.   ...+||+|+|||+|++++.+.+.|.++.++++|+||||
T Consensus       136 tPtRELA~QI~e~fe~Lg~~i-glr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEAD  214 (476)
T KOG0330|consen  136 TPTRELAQQIAEQFEALGSGI-GLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEAD  214 (476)
T ss_pred             cCcHHHHHHHHHHHHHhcccc-CeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHH
Confidence            999999999999999999987 89999999998775543   67899999999999999998999999999999999999


Q ss_pred             hHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHH
Q psy11867        257 VMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS  336 (399)
Q Consensus       257 ~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  336 (399)
                      +++++ .|...+..|++.+|..+|+++||||++..+.++.+..+.+|..+.......+.+.++|.|.+++. ..|...|.
T Consensus       215 rlLd~-dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~-k~K~~yLV  292 (476)
T KOG0330|consen  215 RLLDM-DFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPG-KDKDTYLV  292 (476)
T ss_pred             hhhhh-hhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccc-cccchhHH
Confidence            99986 89999999999999999999999999999999999999999999999999999999999999976 56888999


Q ss_pred             HHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       337 ~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+++......+||||++..++.+++-.|+..|+.+..+||.|++..|.-+++.|++|...|||
T Consensus       293 ~ll~e~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv  355 (476)
T KOG0330|consen  293 YLLNELAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILV  355 (476)
T ss_pred             HHHHhhcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEE
Confidence            999988889999999999999999999999999999999999999999999999999999986

>KOG0328|consensus

Probab=100.00  E-value=4e-56  Score=386.94  Aligned_cols=297  Identities=36%  Similarity=0.662  Sum_probs=279.2

Q ss_pred             CCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEE
Q psy11867         98 PLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVL  177 (399)
Q Consensus        98 ~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~l  177 (399)
                      .+..+.+|++++|.+.+++++++.||..|+.||..|+|.+++  |+||+++|++|+|||.+|-+.+++.+.-..+..++|
T Consensus        22 ~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~Ilk--GrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~l   99 (400)
T KOG0328|consen   22 KVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILK--GRDVIAQAQSGTGKTATFSISVLQSLDISVRETQAL   99 (400)
T ss_pred             CcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhc--ccceEEEecCCCCceEEEEeeeeeecccccceeeEE
Confidence            344578999999999999999999999999999999999999  799999999999999999999999988877778999


Q ss_pred             EEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEec
Q psy11867        178 CLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDE  254 (399)
Q Consensus       178 il~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDE  254 (399)
                      ||+||||||.|+.+.+..++.++ ++.+..+.||.++....   ..+.|++.+|||++++++ +.+.+.-+.++++|+||
T Consensus       100 ilsPTRELa~Qi~~vi~alg~~m-nvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmi-kr~~L~tr~vkmlVLDE  177 (400)
T KOG0328|consen  100 ILSPTRELAVQIQKVILALGDYM-NVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMI-KRRSLRTRAVKMLVLDE  177 (400)
T ss_pred             EecChHHHHHHHHHHHHHhcccc-cceEEEEecCCccchhhhhhcccceEeeCCCchHHHHH-HhccccccceeEEEecc
Confidence            99999999999999999999987 78888999998865443   457799999999999996 44678889999999999


Q ss_pred             hhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHH
Q psy11867        255 ADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEA  334 (399)
Q Consensus       255 ah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~  334 (399)
                      ||.|++. +|.+++..+.+.+|+.+|++++|||+|.++.++...++.||+.+-+.+.+.++++++|+|+.++.++-|++.
T Consensus       178 aDemL~k-gfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdt  256 (400)
T KOG0328|consen  178 ADEMLNK-GFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDT  256 (400)
T ss_pred             HHHHHHh-hHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhHhH
Confidence            9999986 999999999999999999999999999999999999999999999999999999999999999988889999


Q ss_pred             HHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        335 VSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       335 l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      |..++......+++||||+++.+.||.+.|+...+.|..+||+|++++|+.++++||+|+.+||+
T Consensus       257 LcdLYd~LtItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLi  321 (400)
T KOG0328|consen  257 LCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLI  321 (400)
T ss_pred             HHHHhhhhehheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999984

>KOG0331|consensus

Probab=100.00  E-value=2.2e-55  Score=421.93  Aligned_cols=290  Identities=30%  Similarity=0.506  Sum_probs=264.7

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC------CCCCCeEE
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP------SIQEPQVL  177 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~------~~~~~~~l  177 (399)
                      .|.+++|++.+.+.++..||..|||||.++||.++.  |+|+++.|.||||||++|++|++.++..      ...+|++|
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~--GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vL  169 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALS--GRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVL  169 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceecc--CCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEE
Confidence            799999999999999999999999999999999999  7999999999999999999999999875      34689999


Q ss_pred             EEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEec
Q psy11867        178 CLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDE  254 (399)
Q Consensus       178 il~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDE  254 (399)
                      ||+||||||.|+.+.+.+++..+ .++..+.+||.....+.   ..+.+|+|+|||||.+++ +.+..+++++.|+|+||
T Consensus       170 VL~PTRELA~QV~~~~~~~~~~~-~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~l-e~g~~~l~~v~ylVLDE  247 (519)
T KOG0331|consen  170 VLAPTRELAVQVQAEAREFGKSL-RLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLL-EEGSLNLSRVTYLVLDE  247 (519)
T ss_pred             EEcCcHHHHHHHHHHHHHHcCCC-CccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHH-HcCCccccceeEEEecc
Confidence            99999999999999999999887 58889999998775554   567889999999999996 55788999999999999


Q ss_pred             hhhHhhcCCchHHHHHHHHhC-CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccccc--ccccceeEEEEEeCChhhH
Q psy11867        255 ADVMIATQGHQDFSIRIQKRL-PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREE--ESLDNIKQHYVMCKNIDEK  331 (399)
Q Consensus       255 ah~l~~~~~~~~~~~~i~~~l-~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~--~~~~~i~~~~~~~~~~~~k  331 (399)
                      ||+|+++ ||..++..|+..+ ++..|++++|||||.++..++..++.+|..+.+....  .+..++.|....|+ ...|
T Consensus       248 ADrMldm-GFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~-~~~K  325 (519)
T KOG0331|consen  248 ADRMLDM-GFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCD-ETAK  325 (519)
T ss_pred             HHhhhcc-ccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcC-HHHH
Confidence            9999987 8999999999999 5566899999999999999999999999999988553  56788999999998 4667


Q ss_pred             HHHHHHHhccC---CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        332 FEAVSNIYGVV---TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       332 ~~~l~~ll~~~---~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...|..++...   ..+|+||||++++.|+.|+..|+..++++..+||+.+|.||+.+++.|++|+..|||
T Consensus       326 ~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLV  396 (519)
T KOG0331|consen  326 LRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLV  396 (519)
T ss_pred             HHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEE
Confidence            77777777665   457999999999999999999999999999999999999999999999999999997

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

Probab=100.00  E-value=1.3e-54  Score=432.31  Aligned_cols=293  Identities=36%  Similarity=0.578  Sum_probs=270.4

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC--CCCCCeEEEEe
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP--SIQEPQVLCLA  180 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~--~~~~~~~lil~  180 (399)
                      ..|++++|++.+++++.++||..|||||.++||.++.  |+|++++|+||||||+||++|+++.+..  ......+||++
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~--g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~  106 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILA--GRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILA  106 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEEC
Confidence            5799999999999999999999999999999999999  7999999999999999999999999874  22222299999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      ||||||.|+++.++.++.+..++.+..++||.+...+.   ..+++|||+|||||++++.+ +.++++++.++|+||||+
T Consensus       107 PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~-~~l~l~~v~~lVlDEADr  185 (513)
T COG0513         107 PTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKR-GKLDLSGVETLVLDEADR  185 (513)
T ss_pred             CCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHc-CCcchhhcCEEEeccHhh
Confidence            99999999999999999887568889999998765544   33589999999999999755 488999999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccc--cccceeEEEEEeCChhhHHHHH
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE--SLDNIKQHYVMCKNIDEKFEAV  335 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~--~~~~i~~~~~~~~~~~~k~~~l  335 (399)
                      |+++ ||.+.+..|+..++.+.|+++||||++..+..+++.++.+|..+.+.....  +...+.|+|+.+...+.|...|
T Consensus       186 mLd~-Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L  264 (513)
T COG0513         186 MLDM-GFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELL  264 (513)
T ss_pred             hhcC-CCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHH
Confidence            9987 999999999999999999999999999999999999999999988885555  8899999999998866799999


Q ss_pred             HHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        336 SNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       336 ~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..++......++||||++++.|+.|+..|...|+++..+||+|++++|..+++.|++|+++|||
T Consensus       265 ~~ll~~~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLV  328 (513)
T COG0513         265 LKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLV  328 (513)
T ss_pred             HHHHhcCCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEE
Confidence            9999999989999999999999999999999999999999999999999999999999999997

>KOG0338|consensus

Probab=100.00  E-value=1e-54  Score=404.86  Aligned_cols=294  Identities=31%  Similarity=0.491  Sum_probs=271.5

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC---CCCeEEE
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI---QEPQVLC  178 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~---~~~~~li  178 (399)
                      ..+|.+++|+..+++++..+||..|||||..+||..+.  |+|++.||.||||||.||++|+|+++.-.+   ...|+||
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvall--gkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLV  257 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALL--GKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLV  257 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhh--cchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEE
Confidence            45899999999999999999999999999999999998  799999999999999999999999986443   2358999


Q ss_pred             EeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEech
Q psy11867        179 LAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEA  255 (399)
Q Consensus       179 l~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEa  255 (399)
                      |+|||||+.|++.+.+++..++ .+.+.+++||-++..+.   +..++|||+|||||.+|+.+...|++.++.++|+|||
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            9999999999999999999987 69999999998875543   7889999999999999999999999999999999999


Q ss_pred             hhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCCh--hhHHH
Q psy11867        256 DVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI--DEKFE  333 (399)
Q Consensus       256 h~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~--~~k~~  333 (399)
                      |+|++. +|.+.+..|++.+|+++|+++||||++..+.+++...+..|+.+.++........+.|.|+.....  ..+..
T Consensus       337 DRMLee-gFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea  415 (691)
T KOG0338|consen  337 DRMLEE-GFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREA  415 (691)
T ss_pred             HHHHHH-HHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHH
Confidence            999986 999999999999999999999999999999999999999999999999988899999998866532  34667


Q ss_pred             HHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        334 AVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       334 ~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+..++......++|||+.+++.|+.+.-.|.-.|.+++-+||.++|.||.+.++.|+++++.|||
T Consensus       416 ~l~~l~~rtf~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLi  481 (691)
T KOG0338|consen  416 MLASLITRTFQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLI  481 (691)
T ss_pred             HHHHHHHHhcccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEE
Confidence            777888877788999999999999999999988899999999999999999999999999999986

>KOG0326|consensus

Probab=100.00  E-value=8.5e-53  Score=371.91  Aligned_cols=291  Identities=31%  Similarity=0.563  Sum_probs=273.5

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      -..|+++.|...++.+++++||..|+|+|+++||..+.  |+|+++.|..|+|||.||.+|+++.+.......+++|++|
T Consensus        84 G~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLt--GrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVP  161 (459)
T KOG0326|consen   84 GNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALT--GRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVP  161 (459)
T ss_pred             CccHHHhhhhHHHHHHHHHhccCCCCCccccccceeec--chhhhhhccCCCCCccceechhhhhcCccccceeEEEEee
Confidence            35799999999999999999999999999999999998  7999999999999999999999999999888999999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      |||||.|+....+.+++++ ++.+....||.++....   ....|++|+||||++++. +.+..+++++.++|+||||.|
T Consensus       162 trelALQtSqvc~~lskh~-~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~-~KgVa~ls~c~~lV~DEADKl  239 (459)
T KOG0326|consen  162 TRELALQTSQVCKELSKHL-GIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLA-KKGVADLSDCVILVMDEADKL  239 (459)
T ss_pred             cchhhHHHHHHHHHHhccc-CeEEEEecCCcccccceeeecCceEEEEcCChhHHHHH-hcccccchhceEEEechhhhh
Confidence            9999999999999999998 69999999999886654   456799999999999995 446778999999999999999


Q ss_pred             hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHH
Q psy11867        259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI  338 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  338 (399)
                      ++. .|...+..++..+|+++|++++|||+|..|..|..+++.+|..|.+-. +.++.++.|+|.++.. .+|...|..+
T Consensus       240 Ls~-~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~-eLtl~GvtQyYafV~e-~qKvhCLntL  316 (459)
T KOG0326|consen  240 LSV-DFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLME-ELTLKGVTQYYAFVEE-RQKVHCLNTL  316 (459)
T ss_pred             hch-hhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhh-hhhhcchhhheeeech-hhhhhhHHHH
Confidence            974 899999999999999999999999999999999999999999998874 4678899999999976 6899999999


Q ss_pred             hccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        339 YGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       339 l~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +......+.||||||...++.||..+.+.|+.|..+|+.|-++.|..+++.||+|.++.||
T Consensus       317 fskLqINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLV  377 (459)
T KOG0326|consen  317 FSKLQINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLV  377 (459)
T ss_pred             HHHhcccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceee
Confidence            9999999999999999999999999999999999999999999999999999999999987

>KOG0343|consensus

Probab=100.00  E-value=7e-51  Score=382.42  Aligned_cols=292  Identities=27%  Similarity=0.443  Sum_probs=268.4

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC----CCCCeEE
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS----IQEPQVL  177 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~----~~~~~~l  177 (399)
                      +..|++++|+...+++|+..+|..+|.+|+.+||..|.  |+||+..|.||||||+||++|+++.+...    ..|--||
T Consensus        68 ~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~--G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGal  145 (758)
T KOG0343|consen   68 IKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQ--GHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGAL  145 (758)
T ss_pred             hhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhcc--CcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeE
Confidence            56799999999999999999999999999999999999  79999999999999999999999988442    2455699


Q ss_pred             EEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh--hccCCcEEEeCchhHHHhhhccccccCCceeEEEEech
Q psy11867        178 CLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN--KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEA  255 (399)
Q Consensus       178 il~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEa  255 (399)
                      ||+||||||.|+++++.+.+++. .+...++.||....-.  .....+|+|||||||++|+.....++..+++++|+|||
T Consensus       146 IISPTRELA~QtFevL~kvgk~h-~fSaGLiiGG~~~k~E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEA  224 (758)
T KOG0343|consen  146 IISPTRELALQTFEVLNKVGKHH-DFSAGLIIGGKDVKFELERISQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEA  224 (758)
T ss_pred             EecchHHHHHHHHHHHHHHhhcc-ccccceeecCchhHHHHHhhhcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccH
Confidence            99999999999999999999986 7899999999876443  35678999999999999999999999999999999999


Q ss_pred             hhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccc--ccccccceeEEEEEeCChhhHHH
Q psy11867        256 DVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR--EEESLDNIKQHYVMCKNIDEKFE  333 (399)
Q Consensus       256 h~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~--~~~~~~~i~~~~~~~~~~~~k~~  333 (399)
                      |+|+++ ||...+..|+..+|+.+|+++||||-+..+.++++..+.||..|.+..  ...+++++.|+|+.++. .+|+.
T Consensus       225 DR~LDM-GFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l-~~Ki~  302 (758)
T KOG0343|consen  225 DRMLDM-GFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPL-EDKID  302 (758)
T ss_pred             HHHHHH-hHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEeh-hhHHH
Confidence            999997 999999999999999999999999999999999999999999988763  34678999999999976 78999


Q ss_pred             HHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        334 AVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       334 ~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                      .|..+++.+...+.|||+.|.+++..+++.+++.  |+++..+||+|+|..|..++..|-..+--||
T Consensus       303 ~L~sFI~shlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vL  369 (758)
T KOG0343|consen  303 MLWSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVL  369 (758)
T ss_pred             HHHHHHHhccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEE
Confidence            9999999999999999999999999999999887  8999999999999999999999987665554

>KOG0333|consensus

Probab=100.00  E-value=3.1e-50  Score=376.25  Aligned_cols=293  Identities=31%  Similarity=0.455  Sum_probs=271.4

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC---------CC
Q psy11867        101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP---------SI  171 (399)
Q Consensus       101 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~---------~~  171 (399)
                      ++.+|++.+++..+++.+...||..|+|||.+|+|..+.  .+|+|..|.||||||++|++|++..+..         ..
T Consensus       243 plrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ--~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~  320 (673)
T KOG0333|consen  243 PLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQ--NRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNI  320 (673)
T ss_pred             cccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhc--cCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcc
Confidence            378899999999999999999999999999999999998  6999999999999999999999877632         23


Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCcee
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIK  248 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~  248 (399)
                      .+|+++|++|||+||+|+.++-.+|++.+ ++.+..++||.+.+.+   ...+|+|+|+|||+|++.+ .+..+-++++.
T Consensus       321 ~gpyaiilaptReLaqqIeeEt~kf~~~l-g~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~L-enr~lvl~qct  398 (673)
T KOG0333|consen  321 EGPYAIILAPTRELAQQIEEETNKFGKPL-GIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSL-ENRYLVLNQCT  398 (673)
T ss_pred             cCceeeeechHHHHHHHHHHHHHHhcccc-cceEEEEecccchhhhhhhhhccceeeecCchHHHHHH-HHHHHHhccCc
Confidence            58999999999999999999999999988 6899999999988766   3678999999999999985 55788899999


Q ss_pred             EEEEechhhHhhcCCchHHHHHHHHhCCCC-------------------------CcEEEEEeeCChhHHHHHHhhCCCC
Q psy11867        249 VFVLDEADVMIATQGHQDFSIRIQKRLPSD-------------------------CQIMLFSATYDKEVMEFAQDMVPNP  303 (399)
Q Consensus       249 ~lViDEah~l~~~~~~~~~~~~i~~~l~~~-------------------------~q~l~~SAT~~~~v~~~~~~~~~~p  303 (399)
                      +||+||||+|+++ ||.+.+..++..+|..                         +|+++||||+|+.+..+++.|+++|
T Consensus       399 yvvldeadrmiDm-gfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~p  477 (673)
T KOG0333|consen  399 YVVLDEADRMIDM-GFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRP  477 (673)
T ss_pred             eEeccchhhhhcc-cccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCC
Confidence            9999999999987 9999999999988631                         6999999999999999999999999


Q ss_pred             eEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHH
Q psy11867        304 LIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQR  383 (399)
Q Consensus       304 ~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R  383 (399)
                      +.+.++......+.++|.++.+.. ++|...|..++......++|||+|+++.|++||+.|.+.|++|..|||+-+++||
T Consensus       478 v~vtig~~gk~~~rveQ~v~m~~e-d~k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQR  556 (673)
T KOG0333|consen  478 VVVTIGSAGKPTPRVEQKVEMVSE-DEKRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQR  556 (673)
T ss_pred             eEEEeccCCCCccchheEEEEecc-hHHHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHH
Confidence            999999999999999999998876 6679999999999888899999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCcccC
Q psy11867        384 LSILDRFREGEFKIYS  399 (399)
Q Consensus       384 ~~v~~~F~~G~~~ILV  399 (399)
                      +.+++.||+|...|||
T Consensus       557 e~aL~~fr~~t~dIlV  572 (673)
T KOG0333|consen  557 ENALADFREGTGDILV  572 (673)
T ss_pred             HHHHHHHHhcCCCEEE
Confidence            9999999999999987

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=1.7e-49  Score=394.46  Aligned_cols=292  Identities=31%  Similarity=0.504  Sum_probs=263.4

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|++++|++.++++|.++||..|||+|.+|+|.++.  |+|++++||||||||++|++|+++.+......+++|||+|
T Consensus         3 ~~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~--g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~P   80 (460)
T PRK11776          3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILA--GKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCP   80 (460)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhc--CCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeC
Confidence            35799999999999999999999999999999999998  7999999999999999999999999976656678999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      |++||.|+.+.++.++....++.+...+||.....+.   ...++|+|+||++|.+++.+ +.+.++++++||+||||+|
T Consensus        81 treLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~-~~~~l~~l~~lViDEad~~  159 (460)
T PRK11776         81 TRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRK-GTLDLDALNTLVLDEADRM  159 (460)
T ss_pred             CHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHc-CCccHHHCCEEEEECHHHH
Confidence            9999999999999998776678888888887664432   45779999999999998654 5677899999999999999


Q ss_pred             hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHH
Q psy11867        259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI  338 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  338 (399)
                      ++. +|...+..++..++...|+++||||+++.+..++..++.+|..+.+.... ....+.+.++.+.. ..|...+..+
T Consensus       160 l~~-g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~~-~~k~~~l~~l  236 (460)
T PRK11776        160 LDM-GFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVSP-DERLPALQRL  236 (460)
T ss_pred             hCc-CcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeCc-HHHHHHHHHH
Confidence            975 78888999999999999999999999999999999999999988876544 34568888888876 4588999999


Q ss_pred             hccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        339 YGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       339 l~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +......++||||++++.|+.+++.|...|+.+..+||+|++.+|..+++.|++|+++|||
T Consensus       237 l~~~~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLV  297 (460)
T PRK11776        237 LLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLV  297 (460)
T ss_pred             HHhcCCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEE
Confidence            9888888999999999999999999999999999999999999999999999999999986

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=1.6e-49  Score=399.24  Aligned_cols=294  Identities=29%  Similarity=0.438  Sum_probs=255.8

Q ss_pred             ccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-----CCCC
Q psy11867        100 YSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-----IQEP  174 (399)
Q Consensus       100 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-----~~~~  174 (399)
                      .++.+|+++++++.++++|.++||..||++|.++||.+++  |+|+|++||||||||++|++|++.++...     ..++
T Consensus       127 ~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~--G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp  204 (545)
T PTZ00110        127 KPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALS--GRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGP  204 (545)
T ss_pred             cccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhc--CCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCc
Confidence            3477899999999999999999999999999999999999  79999999999999999999999876432     2468


Q ss_pred             eEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeEEE
Q psy11867        175 QVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFV  251 (399)
Q Consensus       175 ~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lV  251 (399)
                      ++|||+||+|||.|+.+.+++++... .+.+...++|.....+   ....++|+|+||++|++++.. ....++++++||
T Consensus       205 ~~LIL~PTreLa~Qi~~~~~~~~~~~-~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~-~~~~l~~v~~lV  282 (545)
T PTZ00110        205 IVLVLAPTRELAEQIREQCNKFGASS-KIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLES-NVTNLRRVTYLV  282 (545)
T ss_pred             EEEEECChHHHHHHHHHHHHHHhccc-CccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHc-CCCChhhCcEEE
Confidence            89999999999999999999998765 6777788888655433   245689999999999998654 566789999999


Q ss_pred             EechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCC-CCeEEeccccc-ccccceeEEEEEeCChh
Q psy11867        252 LDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVP-NPLIIKLKREE-ESLDNIKQHYVMCKNID  329 (399)
Q Consensus       252 iDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~-~p~~i~~~~~~-~~~~~i~~~~~~~~~~~  329 (399)
                      |||||+|++. +|...+..++..+++.+|+++||||++..+..+++.++. +|+.+.+.... ....++.+.+..+.. .
T Consensus       283 iDEAd~mld~-gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~-~  360 (545)
T PTZ00110        283 LDEADRMLDM-GFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEE-H  360 (545)
T ss_pred             eehHHhhhhc-chHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEec-h
Confidence            9999999985 899999999999999999999999999999999998875 58877766544 345678888777754 5


Q ss_pred             hHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        330 EKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       330 ~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .|...|..++...  ..+++||||++++.|+.|++.|...|+.+..+||++++.+|..+++.|++|+.+|||
T Consensus       361 ~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILV  432 (545)
T PTZ00110        361 EKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMI  432 (545)
T ss_pred             hHHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEE
Confidence            6777777777665  357999999999999999999999999999999999999999999999999999986

>KOG0340|consensus

Probab=100.00  E-value=4.5e-50  Score=359.38  Aligned_cols=293  Identities=27%  Similarity=0.420  Sum_probs=263.0

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ...|..|||++|+.+.|.++|++.|||+|..|||.||+  |+|+|.+|.||||||++|.+|+++++..+..+..++|++|
T Consensus         6 ~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILe--Grdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTP   83 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILE--GRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTP   83 (442)
T ss_pred             cCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhc--ccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecc
Confidence            56799999999999999999999999999999999999  7999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhcc---ccccCCceeEEEEech
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKY---RFFDLSKIKVFVLDEA  255 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~---~~~~~~~~~~lViDEa  255 (399)
                      |||||.|+.+.|..+++.+ ++++..++||.++-.+.   ...+|++|+||||+.+++..+   -.+.+++++++|+|||
T Consensus        84 TrELA~QiaEQF~alGk~l-~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEA  162 (442)
T KOG0340|consen   84 TRELALQIAEQFIALGKLL-NLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEA  162 (442)
T ss_pred             hHHHHHHHHHHHHHhcccc-cceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecch
Confidence            9999999999999999987 89999999998774443   567899999999999997665   2345889999999999


Q ss_pred             hhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCC--CeEEecccccccccceeEEEEEeCChhhHHH
Q psy11867        256 DVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPN--PLIIKLKREEESLDNIKQHYVMCKNIDEKFE  333 (399)
Q Consensus       256 h~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~--p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~  333 (399)
                      |++++. .|.+.+..+...+|..+|+++||||+++.+..+.......  +..........+++.+.|.|+.|+. +.|..
T Consensus       163 DrvL~~-~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~-~vkda  240 (442)
T KOG0340|consen  163 DRVLAG-CFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSI-DVKDA  240 (442)
T ss_pred             hhhhcc-chhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecch-hhhHH
Confidence            999974 8999999999999999999999999999888776655554  4444555666788899999999975 67778


Q ss_pred             HHHHHhccCCC---CcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        334 AVSNIYGVVTI---GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       334 ~l~~ll~~~~~---~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .++.+++....   +.++||+|+..+|+.|+..|...++++..+||.|+|.+|...+.+||++.++||+
T Consensus       241 YLv~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~ili  309 (442)
T KOG0340|consen  241 YLVHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILI  309 (442)
T ss_pred             HHHHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEE
Confidence            88888876644   6799999999999999999999999999999999999999999999999999985

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=4.9e-49  Score=399.35  Aligned_cols=293  Identities=31%  Similarity=0.525  Sum_probs=266.3

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|.+++|++.++++|.++||..|||+|.++||.++.  |+|+|++||||||||++|++|+++.+......+++|||+|
T Consensus         5 ~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~--g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~P   82 (629)
T PRK11634          5 ETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLN--GRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAP   82 (629)
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHc--CCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeC
Confidence            34699999999999999999999999999999999998  7999999999999999999999999877666789999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      |++||.|+++.++.+...+.++.+...+||.....+.   ...++|+|+||++|++++.+ ..+.++++++|||||||.|
T Consensus        83 TreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r-~~l~l~~l~~lVlDEAd~m  161 (629)
T PRK11634         83 TRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKR-GTLDLSKLSGLVLDEADEM  161 (629)
T ss_pred             cHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcchhhceEEEeccHHHH
Confidence            9999999999999998877788888888988765443   45689999999999998654 5678999999999999999


Q ss_pred             hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHH
Q psy11867        259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI  338 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  338 (399)
                      +.. +|...+..++..++..+|+++||||+|..+..+++.++.+|..+.+.........+.+.|+.+.. ..|...+..+
T Consensus       162 l~~-gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~-~~k~~~L~~~  239 (629)
T PRK11634        162 LRM-GFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWG-MRKNEALVRF  239 (629)
T ss_pred             hhc-ccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEech-hhHHHHHHHH
Confidence            875 88888999999999999999999999999999999999999998888777777788888877754 5688889999


Q ss_pred             hccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        339 YGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       339 l~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +......++||||++++.|..|+..|...|+.+..+||+|++.+|..++++|++|+++|||
T Consensus       240 L~~~~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILV  300 (629)
T PRK11634        240 LEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILI  300 (629)
T ss_pred             HHhcCCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEE
Confidence            8887778999999999999999999999999999999999999999999999999999997

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=9.5e-49  Score=385.07  Aligned_cols=292  Identities=29%  Similarity=0.470  Sum_probs=257.4

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-------CCCC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-------IQEP  174 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-------~~~~  174 (399)
                      -.+|++++|++.++++|.++||..|||+|.+|||.++.  |+|++++||||||||++|++|+++.+...       ..++
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~--g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~   84 (423)
T PRK04837          7 EQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLA--GRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQP   84 (423)
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCc
Confidence            36899999999999999999999999999999999998  79999999999999999999999887532       2357


Q ss_pred             eEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEE
Q psy11867        175 QVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFV  251 (399)
Q Consensus       175 ~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lV  251 (399)
                      ++|||+||++||.|+++.+..+.... ++.+....||.......   ...++|+|+||++|++++. ...+.+++++++|
T Consensus        85 ~~lil~PtreLa~Qi~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~-~~~~~l~~v~~lV  162 (423)
T PRK04837         85 RALIMAPTRELAVQIHADAEPLAQAT-GLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAK-QNHINLGAIQVVV  162 (423)
T ss_pred             eEEEECCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHH-cCCcccccccEEE
Confidence            89999999999999999999998876 68888888887654432   4567999999999999864 4567899999999


Q ss_pred             EechhhHhhcCCchHHHHHHHHhCCC--CCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChh
Q psy11867        252 LDEADVMIATQGHQDFSIRIQKRLPS--DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNID  329 (399)
Q Consensus       252 iDEah~l~~~~~~~~~~~~i~~~l~~--~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~  329 (399)
                      +||||+|++. ++...+..++..++.  ..+.++||||++..+..++...+.+|..+.+.........+.+.+..+ ...
T Consensus       163 iDEad~l~~~-~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~-~~~  240 (423)
T PRK04837        163 LDEADRMFDL-GFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYP-SNE  240 (423)
T ss_pred             EecHHHHhhc-ccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeC-CHH
Confidence            9999999975 788888888888874  567899999999999999999999999888877666667777776655 446


Q ss_pred             hHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        330 EKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       330 ~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .|...+..++......++||||++++.|+.+++.|...|+++..+||+|++.+|..+++.|++|+++|||
T Consensus       241 ~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLV  310 (423)
T PRK04837        241 EKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILV  310 (423)
T ss_pred             HHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEE
Confidence            7888899998877778999999999999999999999999999999999999999999999999999986

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.1e-48  Score=394.48  Aligned_cols=292  Identities=30%  Similarity=0.500  Sum_probs=258.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-------CCCCe
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-------IQEPQ  175 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-------~~~~~  175 (399)
                      .+|++++|++.++++|.++||..|||+|.++||.+++  |+|++++||||||||++|++|+++++...       ...++
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~--G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~r   86 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALP--GGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPR   86 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCce
Confidence            4699999999999999999999999999999999998  79999999999999999999999987432       12478


Q ss_pred             EEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEE
Q psy11867        176 VLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVL  252 (399)
Q Consensus       176 ~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lVi  252 (399)
                      +|||+||++||.|+++.+++++... ++.+...+|+.....+.   ...++|+|+||++|++++.....+.+..+++|||
T Consensus        87 aLIl~PTreLa~Qi~~~~~~l~~~~-~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lVi  165 (572)
T PRK04537         87 ALILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVL  165 (572)
T ss_pred             EEEEeCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEe
Confidence            9999999999999999999998876 78888889987765432   4567999999999999977666678899999999


Q ss_pred             echhhHhhcCCchHHHHHHHHhCCC--CCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhh
Q psy11867        253 DEADVMIATQGHQDFSIRIQKRLPS--DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDE  330 (399)
Q Consensus       253 DEah~l~~~~~~~~~~~~i~~~l~~--~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~  330 (399)
                      ||||+|++. +|...+..+++.++.  .+|+++||||++..+..++..++.+|..+.+.........+.+.++.+.. ..
T Consensus       166 DEAh~lld~-gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~~-~~  243 (572)
T PRK04537        166 DEADRMFDL-GFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPAD-EE  243 (572)
T ss_pred             cCHHHHhhc-chHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecCH-HH
Confidence            999999875 788888889988886  68999999999999999999999988877766655566777888776654 67


Q ss_pred             HHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        331 KFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       331 k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      |...+..++......++||||++++.|+.|++.|...|+.+..+||+|++.+|..+++.|++|+++|||
T Consensus       244 k~~~L~~ll~~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLV  312 (572)
T PRK04537        244 KQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILV  312 (572)
T ss_pred             HHHHHHHHHhcccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEE
Confidence            888888888877778999999999999999999999999999999999999999999999999999997

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

Probab=100.00  E-value=2.3e-48  Score=389.77  Aligned_cols=304  Identities=26%  Similarity=0.463  Sum_probs=260.6

Q ss_pred             ccceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHH
Q psy11867         86 QELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLS  165 (399)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~  165 (399)
                      .++.+.+.+.+.   ++.+|++++|++.++++|.++||..|||+|.+|||.+++  |+|++++||||||||++|++|++.
T Consensus       107 ~~i~~~g~~~p~---pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~--g~dviv~ApTGSGKTlayllPil~  181 (518)
T PLN00206        107 LEIHVKGEAVPP---PILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALS--GRSLLVSADTGSGKTASFLVPIIS  181 (518)
T ss_pred             CCCEecCCCCCc---hhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhc--CCCEEEEecCCCCccHHHHHHHHH
Confidence            345555554444   467899999999999999999999999999999999998  799999999999999999999998


Q ss_pred             hhCC-------CCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHh
Q psy11867        166 RVNP-------SIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDW  235 (399)
Q Consensus       166 ~l~~-------~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~  235 (399)
                      ++..       ...++++|||+||+|||.|+++.++.+.... ++.+....||.....+.   ..+++|+|+||++|.++
T Consensus       182 ~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~-~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~  260 (518)
T PLN00206        182 RCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGL-PFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDL  260 (518)
T ss_pred             HHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHH
Confidence            7632       2256899999999999999999999998776 57777788887654432   45679999999999998


Q ss_pred             hhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccc
Q psy11867        236 GLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESL  315 (399)
Q Consensus       236 ~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~  315 (399)
                      +.+ ..+.++++++|||||||+|++. +|...+..++..++ +.|+++||||+++.+..++..++.++..+.+.......
T Consensus       261 l~~-~~~~l~~v~~lViDEad~ml~~-gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~  337 (518)
T PLN00206        261 LSK-HDIELDNVSVLVLDEVDCMLER-GFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPN  337 (518)
T ss_pred             HHc-CCccchheeEEEeecHHHHhhc-chHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCC
Confidence            755 4678999999999999999975 78888888888875 68999999999999999999999999999888776666


Q ss_pred             cceeEEEEEeCChhhHHHHHHHHhccCC--CCcEEEEecchHhHHHHHHHHHH-CCCeEEEEcCCCCHHHHHHHHHHHhc
Q psy11867        316 DNIKQHYVMCKNIDEKFEAVSNIYGVVT--IGQAMIFCHTRKTAAWLAEKMSK-EGLNVGLLSGELTVEQRLSILDRFRE  392 (399)
Q Consensus       316 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~--~~k~IIF~~s~~~a~~l~~~L~~-~g~~v~~lhg~~~~~~R~~v~~~F~~  392 (399)
                      ..+.+.+.++.. ..|...+.+++....  .+++||||+++..|+.+++.|.. .|+++..+||+|++.+|..+++.|++
T Consensus       338 ~~v~q~~~~~~~-~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~  416 (518)
T PLN00206        338 KAVKQLAIWVET-KQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLV  416 (518)
T ss_pred             cceeEEEEeccc-hhHHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHC
Confidence            778888888765 456667777776543  36899999999999999999975 58999999999999999999999999


Q ss_pred             CCCcccC
Q psy11867        393 GEFKIYS  399 (399)
Q Consensus       393 G~~~ILV  399 (399)
                      |+++|||
T Consensus       417 G~~~ILV  423 (518)
T PLN00206        417 GEVPVIV  423 (518)
T ss_pred             CCCCEEE
Confidence            9999986

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=2.7e-48  Score=384.52  Aligned_cols=290  Identities=31%  Similarity=0.541  Sum_probs=257.1

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC------CCCeEE
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI------QEPQVL  177 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~------~~~~~l  177 (399)
                      +|++++|++.++++|.++||..||++|.++||.+++  |+|++++||||||||++|++|+++.+....      ...++|
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~--g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aL   79 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLE--GRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRAL   79 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEE
Confidence            589999999999999999999999999999999998  799999999999999999999999885432      235899


Q ss_pred             EEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEec
Q psy11867        178 CLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDE  254 (399)
Q Consensus       178 il~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDE  254 (399)
                      ||+||++||.|+++.++.+.... ++.+...+||.....+.   ...++|+|+||++|++++.. ..+.++++++|||||
T Consensus        80 il~PtreLa~Qi~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~-~~~~l~~v~~lViDE  157 (456)
T PRK10590         80 ILTPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQ-NAVKLDQVEILVLDE  157 (456)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccC-CCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHc-CCcccccceEEEeec
Confidence            99999999999999999998775 67777888887665432   45679999999999998643 566799999999999


Q ss_pred             hhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHH
Q psy11867        255 ADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEA  334 (399)
Q Consensus       255 ah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~  334 (399)
                      ||+|++. ++...+..++..++...|+++||||+++.+..++..++.+|..+.+.........+.+.+..+.. ..+...
T Consensus       158 ah~ll~~-~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~  235 (456)
T PRK10590        158 ADRMLDM-GFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDK-KRKREL  235 (456)
T ss_pred             HHHHhcc-ccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCH-HHHHHH
Confidence            9999975 78888888999999999999999999999999999999999988877666667778888877654 567778


Q ss_pred             HHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        335 VSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       335 l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +..++......++||||++++.|+.+++.|...|+.+..+||+|++.+|..+++.|++|+++|||
T Consensus       236 l~~l~~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLV  300 (456)
T PRK10590        236 LSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLV  300 (456)
T ss_pred             HHHHHHcCCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEE
Confidence            88888877778999999999999999999999999999999999999999999999999999997

>KOG0342|consensus

Probab=100.00  E-value=3.4e-49  Score=367.54  Aligned_cols=296  Identities=28%  Similarity=0.392  Sum_probs=267.8

Q ss_pred             ccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC----CCCe
Q psy11867        100 YSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI----QEPQ  175 (399)
Q Consensus       100 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~----~~~~  175 (399)
                      .....|++..|++..++++.++||...|++|..++|.++.  |+|+++.|.||||||+||++|+++.+....    .+..
T Consensus        79 ~~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~--gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~  156 (543)
T KOG0342|consen   79 TTTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLE--GKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTG  156 (543)
T ss_pred             hhhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCC--CccceeeeccCCCceeeehhHHHHHHHhcccCCCCCee
Confidence            3456789999999999999999999999999999999999  699999999999999999999999885433    3456


Q ss_pred             EEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEE
Q psy11867        176 VLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVL  252 (399)
Q Consensus       176 ~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lVi  252 (399)
                      +||+|||||||.|++.+++++..+.+.+.+..+.||.+.....   ...++|+|+|||||++|+.+...+-.++++++|+
T Consensus       157 vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvl  236 (543)
T KOG0342|consen  157 VLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVL  236 (543)
T ss_pred             EEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEe
Confidence            9999999999999999999999988788999999998764332   4488999999999999999999999999999999


Q ss_pred             echhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhC-CCCeEEecccc--cccccceeEEEEEeCChh
Q psy11867        253 DEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMV-PNPLIIKLKRE--EESLDNIKQHYVMCKNID  329 (399)
Q Consensus       253 DEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~-~~p~~i~~~~~--~~~~~~i~~~~~~~~~~~  329 (399)
                      ||||++++. ||.+.+..|++.+|..+|+++||||.+..|.++++..+ ++|+.+.....  ..+.+.+.|.|+.++. +
T Consensus       237 DEADrlLd~-GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~-~  314 (543)
T KOG0342|consen  237 DEADRLLDI-GFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPS-D  314 (543)
T ss_pred             ecchhhhhc-ccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccc-c
Confidence            999999986 99999999999999999999999999999999999776 46888877654  4578899999999987 4


Q ss_pred             hHHHHHHHHhccCCC-CcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        330 EKFEAVSNIYGVVTI-GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       330 ~k~~~l~~ll~~~~~-~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .++..+..+++.+.. .++||||.|...+..+++.|.....+|..+||+++|..|..+..+|++.+.-|||
T Consensus       315 ~~f~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~  385 (543)
T KOG0342|consen  315 SRFSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILV  385 (543)
T ss_pred             chHHHHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEE
Confidence            558889999988877 8999999999999999999999999999999999999999999999999988885

>KOG0345|consensus

Probab=100.00  E-value=1.6e-48  Score=360.90  Aligned_cols=291  Identities=27%  Similarity=0.446  Sum_probs=260.8

Q ss_pred             ccccCC--CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC--C-CC--CeE
Q psy11867        104 TFEALH--LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS--I-QE--PQV  176 (399)
Q Consensus       104 ~f~~~~--l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~--~-~~--~~~  176 (399)
                      .|++++  |++++++++..+||...||+|..+||.+++  ++||++.|+||||||+||++|+++.+...  . ..  .-+
T Consensus         5 ~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~--~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vga   82 (567)
T KOG0345|consen    5 SFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLK--NKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGA   82 (567)
T ss_pred             chhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhc--CCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeE
Confidence            466664  669999999999999999999999999999  69999999999999999999999998221  1 11  258


Q ss_pred             EEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh----ccCCcEEEeCchhHHHhhhc-cccccCCceeEEE
Q psy11867        177 LCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK----KITEQIIIGTPGKVLDWGLK-YRFFDLSKIKVFV  251 (399)
Q Consensus       177 lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~Tp~~l~~~~~~-~~~~~~~~~~~lV  251 (399)
                      |||+||||||.|+.+++..|..+++.++..+.+||...+...    ..+++|+|||||||.+++.+ ...++++++.++|
T Consensus        83 lIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LV  162 (567)
T KOG0345|consen   83 LIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILV  162 (567)
T ss_pred             EEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEE
Confidence            999999999999999999999998899999999997765543    56789999999999999866 4556788999999


Q ss_pred             EechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccc--cccceeEEEEEeCChh
Q psy11867        252 LDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE--SLDNIKQHYVMCKNID  329 (399)
Q Consensus       252 iDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~--~~~~i~~~~~~~~~~~  329 (399)
                      +||||+++++ ||...+..|+..+|+.+++=+||||....+.++.+..+++|+.+.+.....  +++.+..+|..|.. +
T Consensus       163 LDEADrLldm-gFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a-~  240 (567)
T KOG0345|consen  163 LDEADRLLDM-GFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEA-D  240 (567)
T ss_pred             ecchHhHhcc-cHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecH-H
Confidence            9999999987 999999999999999999999999999999999999999999999987775  78889999999976 7


Q ss_pred             hHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        330 EKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       330 ~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                      .|...+.+++.....+++|||++|...++..+..|...  ...+..+||.|.+.+|..+++.|++-.-.||
T Consensus       241 eK~~~lv~~L~~~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl  311 (567)
T KOG0345|consen  241 EKLSQLVHLLNNNKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVL  311 (567)
T ss_pred             HHHHHHHHHHhccccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceE
Confidence            89999999999999999999999999999999988776  6789999999999999999999998544443

>KOG0339|consensus

Probab=100.00  E-value=9.8e-49  Score=364.61  Aligned_cols=298  Identities=29%  Similarity=0.462  Sum_probs=272.7

Q ss_pred             CCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-----C
Q psy11867         97 SPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-----I  171 (399)
Q Consensus        97 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-----~  171 (399)
                      +|..++.+|+.++++..|+.++.+.-|.+|||+|.+++|..+.  |+||+..|.||||||.||+.|++.+++..     .
T Consensus       217 s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptals--grdvigIAktgSgktaAfi~pm~~himdq~eL~~g  294 (731)
T KOG0339|consen  217 SPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALS--GRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPG  294 (731)
T ss_pred             CCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccc--cccchheeeccCcchhHHHHHHHHHhcchhhhcCC
Confidence            3344578899999999999999999999999999999999999  79999999999999999999999988543     3


Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCcee
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIK  248 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~  248 (399)
                      .+|..||++|||+||.|++.++++|++.+ ++++.+++||.+...+.   ..++.|||||||||+++ .+.+..++.++.
T Consensus       295 ~gPi~vilvPTrela~Qi~~eaKkf~K~y-gl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~-VkmKatn~~rvS  372 (731)
T KOG0339|consen  295 EGPIGVILVPTRELASQIFSEAKKFGKAY-GLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDM-VKMKATNLSRVS  372 (731)
T ss_pred             CCCeEEEEeccHHHHHHHHHHHHHhhhhc-cceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHH-HHhhcccceeee
Confidence            68999999999999999999999999987 88988888887664443   56789999999999999 466888999999


Q ss_pred             EEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCCh
Q psy11867        249 VFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI  328 (399)
Q Consensus       249 ~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~  328 (399)
                      ||||||||+|++. ||..++..|...+++++|+|+||||++..++.+++.++.+|+.+....-......|.|.+.+|.+.
T Consensus       373 ~LV~DEadrmfdm-Gfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~  451 (731)
T KOG0339|consen  373 YLVLDEADRMFDM-GFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSE  451 (731)
T ss_pred             EEEEechhhhhcc-ccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCc
Confidence            9999999999986 999999999999999999999999999999999999999999998888788889999999999999


Q ss_pred             hhHHHHHHH-HhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSN-IYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~-ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..|...|.. |......+++|||+.-+..++.++..|...|+.|..+||+|.|.+|.+++..|+.+...|||
T Consensus       452 ~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~Vlv  523 (731)
T KOG0339|consen  452 EKKLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLV  523 (731)
T ss_pred             HHHHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEE
Confidence            999887655 44555669999999999999999999999999999999999999999999999999999986

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=2.2e-47  Score=377.01  Aligned_cols=291  Identities=27%  Similarity=0.467  Sum_probs=261.2

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC----CCCCeEEEE
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS----IQEPQVLCL  179 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~----~~~~~~lil  179 (399)
                      +|++++|++.+++.|.++||..|+++|.+++|.+++  |+|++++||||+|||++|++|+++.+...    ...+++||+
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~--g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil   79 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALD--GRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILIL   79 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEE
Confidence            699999999999999999999999999999999998  79999999999999999999999987532    234689999


Q ss_pred             eCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechh
Q psy11867        180 APTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD  256 (399)
Q Consensus       180 ~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah  256 (399)
                      +||++||.|+++.+..+.... ++.+....||.......   ...++|+|+||++|++++.. +.++++++++|||||||
T Consensus        80 ~Pt~eLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~-~~~~~~~v~~lViDEah  157 (434)
T PRK11192         80 TPTRELAMQVADQARELAKHT-HLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKE-ENFDCRAVETLILDEAD  157 (434)
T ss_pred             CCcHHHHHHHHHHHHHHHccC-CcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHc-CCcCcccCCEEEEECHH
Confidence            999999999999999998876 68888888887664433   45678999999999998644 67788999999999999


Q ss_pred             hHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCCh-hHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHH
Q psy11867        257 VMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDK-EVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAV  335 (399)
Q Consensus       257 ~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~-~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l  335 (399)
                      +|++. ++...+..+...++...|+++||||++. .+..+...++.+|..+..........++.+.+..+.....|...+
T Consensus       158 ~~l~~-~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l  236 (434)
T PRK11192        158 RMLDM-GFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALL  236 (434)
T ss_pred             HHhCC-CcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHH
Confidence            99975 7888888999988889999999999985 588888899999999888777777778889888888778899999


Q ss_pred             HHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        336 SNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       336 ~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..++.....+++||||++++.|+.++..|...|+.+..+||+|++.+|..+++.|++|+++|||
T Consensus       237 ~~l~~~~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLV  300 (434)
T PRK11192        237 CHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLV  300 (434)
T ss_pred             HHHHhcCCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEE
Confidence            9999877778999999999999999999999999999999999999999999999999999997

>KOG0346|consensus

Probab=100.00  E-value=8.2e-49  Score=359.81  Aligned_cols=293  Identities=28%  Similarity=0.436  Sum_probs=257.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC------CCCCCeE
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP------SIQEPQV  176 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~------~~~~~~~  176 (399)
                      .+|++++|++.+++++.+.||.+||-||+.|||.+|.  |+|+++.|.||||||+||++|+++.+..      ...++.+
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLE--gKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa   96 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALE--GKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSA   96 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhc--CcceeeeeccCCCchHHHHHHHHHHHHHhhhccccccccee
Confidence            6899999999999999999999999999999999999  7999999999999999999999998732      3457889


Q ss_pred             EEEeCcHHHHHHHHHHHHHHhccCC-CcE---EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEE
Q psy11867        177 LCLAPTYELAIQIGEVVAKMGKHIT-DLS---VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVL  252 (399)
Q Consensus       177 lil~Pt~~La~Q~~~~~~~~~~~~~-~~~---~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lVi  252 (399)
                      +||+||+|||+|+|.++.++...++ .++   +................++|+|+||++++.++.......+..+.++|+
T Consensus        97 ~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVv  176 (569)
T KOG0346|consen   97 VILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVV  176 (569)
T ss_pred             EEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEe
Confidence            9999999999999999999987764 222   222222333333346778999999999999976544467899999999


Q ss_pred             echhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccc-cccceeEEEEEeCChhhH
Q psy11867        253 DEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE-SLDNIKQHYVMCKNIDEK  331 (399)
Q Consensus       253 DEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~-~~~~i~~~~~~~~~~~~k  331 (399)
                      ||||.++. .||.+.+..+.+.+|+.+|.++||||+++++..+-+.++.+|+++.+...+. ....+.|+++.|. ..+|
T Consensus       177 DEADLlls-fGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cs-e~DK  254 (569)
T KOG0346|consen  177 DEADLLLS-FGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCS-EEDK  254 (569)
T ss_pred             chhhhhhh-cccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEec-cchh
Confidence            99999997 4999999999999999999999999999999999999999999998876553 4578899999998 5789


Q ss_pred             HHHHHHHhccCC-CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        332 FEAVSNIYGVVT-IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       332 ~~~l~~ll~~~~-~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +..++.+++..- .|+.|||+|+.+.|..|.-.|.+.|++..++.|+|+..-|.-++++|..|-++|++
T Consensus       255 flllyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivI  323 (569)
T KOG0346|consen  255 FLLLYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVI  323 (569)
T ss_pred             HHHHHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEE
Confidence            999888887654 48999999999999999999999999999999999999999999999999999874

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.8e-46  Score=372.49  Aligned_cols=292  Identities=30%  Similarity=0.533  Sum_probs=255.5

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC-------CCC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI-------QEP  174 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~-------~~~  174 (399)
                      ...|.+++|++.++++|.++||..|+++|.++|+.+++  |+|+++++|||||||++|++|+++.+....       ..+
T Consensus        86 ~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~--G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~  163 (475)
T PRK01297         86 KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLA--GHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEP  163 (475)
T ss_pred             CCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCc
Confidence            45789999999999999999999999999999999998  799999999999999999999999886532       257


Q ss_pred             eEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh----ccCCcEEEeCchhHHHhhhccccccCCceeEE
Q psy11867        175 QVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK----KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVF  250 (399)
Q Consensus       175 ~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~l  250 (399)
                      ++|||+||++||.|+++.++.+.... ++.+....||.......    ...++|+|+||++|+++... ....++++++|
T Consensus       164 ~aLil~PtreLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~-~~~~l~~l~~l  241 (475)
T PRK01297        164 RALIIAPTRELVVQIAKDAAALTKYT-GLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQR-GEVHLDMVEVM  241 (475)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHhhccC-CCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHc-CCcccccCceE
Confidence            89999999999999999999998776 67888888886554322    34679999999999987543 45678999999


Q ss_pred             EEechhhHhhcCCchHHHHHHHHhCCC--CCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCCh
Q psy11867        251 VLDEADVMIATQGHQDFSIRIQKRLPS--DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI  328 (399)
Q Consensus       251 ViDEah~l~~~~~~~~~~~~i~~~l~~--~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~  328 (399)
                      ||||||++++. ++...+..+...++.  +.|+++||||++..+..++..++.+|..+.+........++.+.+..+.. 
T Consensus       242 ViDEah~l~~~-~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~-  319 (475)
T PRK01297        242 VLDEADRMLDM-GFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAG-  319 (475)
T ss_pred             EechHHHHHhc-ccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecc-
Confidence            99999999875 787888888888764  57999999999999999999999999998877766666677777776654 


Q ss_pred             hhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..|...+..++......++||||++++.|+.+++.|...|+.+..+||++++++|..+++.|++|+++|||
T Consensus       320 ~~k~~~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLv  390 (475)
T PRK01297        320 SDKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLV  390 (475)
T ss_pred             hhHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEE
Confidence            56788888888887778999999999999999999999999999999999999999999999999999986

>KOG0341|consensus

Probab=100.00  E-value=1.2e-48  Score=353.61  Aligned_cols=310  Identities=24%  Similarity=0.379  Sum_probs=270.4

Q ss_pred             hccccccceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867         81 LIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      +++....+.+.+.+++.|   +++|.++.++..+++.|++.|+.+|||||.+.+|.+++  |+|+|..|-||||||++|+
T Consensus       151 ~vRk~~~I~veGd~ipPP---IksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLs--GRDmIGIAfTGSGKTlvFv  225 (610)
T KOG0341|consen  151 LVRKQLHILVEGDDIPPP---IKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLS--GRDMIGIAFTGSGKTLVFV  225 (610)
T ss_pred             HHHHhheEEeeCCCCCCc---hhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEee--cCceeeEEeecCCceEEEe
Confidence            344445566667777766   67899999999999999999999999999999999999  7999999999999999999


Q ss_pred             HHHHHhhC--------CCCCCCeEEEEeCcHHHHHHHHHHHHHHhc-----cCCCcEEEEEEcCchhhhhh---ccCCcE
Q psy11867        161 LTMLSRVN--------PSIQEPQVLCLAPTYELAIQIGEVVAKMGK-----HITDLSVRYAVRGENLERNK---KITEQI  224 (399)
Q Consensus       161 l~il~~l~--------~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~---~~~~~I  224 (399)
                      +|++....        ....+|..||+||+||||.|+++.+..+..     .++.++.....||..+..+.   +.+.||
T Consensus       226 LP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHi  305 (610)
T KOG0341|consen  226 LPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHI  305 (610)
T ss_pred             HHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeE
Confidence            99987542        234689999999999999999999998864     34567778889998876654   678899


Q ss_pred             EEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCe
Q psy11867        225 IIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPL  304 (399)
Q Consensus       225 lV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~  304 (399)
                      +|+|||||.+++.+ +...+.-++++++||||+|+++ ||.+.+..++..+...+|+++||||+|..++.|++.-+..|+
T Consensus       306 vVATPGRL~DmL~K-K~~sLd~CRyL~lDEADRmiDm-GFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPv  383 (610)
T KOG0341|consen  306 VVATPGRLMDMLAK-KIMSLDACRYLTLDEADRMIDM-GFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPV  383 (610)
T ss_pred             EEcCcchHHHHHHH-hhccHHHHHHhhhhhHHHHhhc-cchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccce
Confidence            99999999999654 6778899999999999999997 999999999999999999999999999999999999999999


Q ss_pred             EEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHH
Q psy11867        305 IIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRL  384 (399)
Q Consensus       305 ~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~  384 (399)
                      .+.+++...+.-++.|.+.+++. +.|.-.+.+.+... ..+++|||..+..+..+.++|--.|..+..+|||-.+++|.
T Consensus       384 tvNVGRAGAAsldViQevEyVkq-EaKiVylLeCLQKT-~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~  461 (610)
T KOG0341|consen  384 TVNVGRAGAASLDVIQEVEYVKQ-EAKIVYLLECLQKT-SPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRH  461 (610)
T ss_pred             EEecccccccchhHHHHHHHHHh-hhhhhhHHHHhccC-CCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHH
Confidence            99999988877777777666654 44555555555433 36899999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCcccC
Q psy11867        385 SILDRFREGEFKIYS  399 (399)
Q Consensus       385 ~v~~~F~~G~~~ILV  399 (399)
                      ..++.||.|+-+|||
T Consensus       462 ~ai~afr~gkKDVLV  476 (610)
T KOG0341|consen  462 YAIEAFRAGKKDVLV  476 (610)
T ss_pred             HHHHHHhcCCCceEE
Confidence            999999999999997

>KOG0335|consensus

Probab=100.00  E-value=5.1e-47  Score=358.41  Aligned_cols=313  Identities=26%  Similarity=0.380  Sum_probs=269.6

Q ss_pred             hccccccceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867         81 LIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+..+..+.+.......|. .+.+|.+..+.+.+..++...||..|||+|+.+||.+..  |+++++||+||||||.||+
T Consensus        53 nfd~~~~i~v~~~G~~~p~-~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~--Grdl~acAqTGsGKT~aFL  129 (482)
T KOG0335|consen   53 NFDKYNDIPVKVSGRDVPP-HIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISG--GRDLMACAQTGSGKTAAFL  129 (482)
T ss_pred             ccCCccceeeeccCCccCC-CcccccccchhHHHhhccccccccCCCcceeeccceeec--CCceEEEccCCCcchHHHH
Confidence            3455555555444333332 245889889999999999999999999999999999998  7999999999999999999


Q ss_pred             HHHHHhhCCCC----------CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEe
Q psy11867        161 LTMLSRVNPSI----------QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIG  227 (399)
Q Consensus       161 l~il~~l~~~~----------~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~  227 (399)
                      +|++..+....          .+|++||++||||||.|++++.+++.-.. .+.....+||.+...+.   ...++|+||
T Consensus       130 iPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s-~~~~~~~ygg~~~~~q~~~~~~gcdIlva  208 (482)
T KOG0335|consen  130 IPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLS-GMKSVVVYGGTDLGAQLRFIKRGCDILVA  208 (482)
T ss_pred             HHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccc-cceeeeeeCCcchhhhhhhhccCccEEEe
Confidence            99999885432          25899999999999999999999986543 67888888986654433   678999999


Q ss_pred             CchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCC----CCcEEEEEeeCChhHHHHHHhhCCC-
Q psy11867        228 TPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPS----DCQIMLFSATYDKEVMEFAQDMVPN-  302 (399)
Q Consensus       228 Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~----~~q~l~~SAT~~~~v~~~~~~~~~~-  302 (399)
                      |||+|.+++ +.+.+.+.++++||+||||+|++..+|..++..|+.....    ..|+++||||+|..+..++..++.+ 
T Consensus       209 TpGrL~d~~-e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~  287 (482)
T KOG0335|consen  209 TPGRLKDLI-ERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDN  287 (482)
T ss_pred             cCchhhhhh-hcceeehhhCcEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhcc
Confidence            999999985 6688999999999999999999966999999999887743    7899999999999999999999987 


Q ss_pred             CeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCC----CC-----cEEEEecchHhHHHHHHHHHHCCCeEEE
Q psy11867        303 PLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVT----IG-----QAMIFCHTRKTAAWLAEKMSKEGLNVGL  373 (399)
Q Consensus       303 p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~----~~-----k~IIF~~s~~~a~~l~~~L~~~g~~v~~  373 (399)
                      .+.+.+.....+..++.|.+.++.. .+|...|.+++....    .+     +++|||.+++.|..|+..|...++++..
T Consensus       288 yi~laV~rvg~~~~ni~q~i~~V~~-~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~s  366 (482)
T KOG0335|consen  288 YIFLAVGRVGSTSENITQKILFVNE-MEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKS  366 (482)
T ss_pred             ceEEEEeeeccccccceeEeeeecc-hhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCcee
Confidence            8888888888999999999999977 456667777776433    23     7999999999999999999999999999


Q ss_pred             EcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        374 LSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       374 lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +||+.++.+|.+.++.|+.|++.|||
T Consensus       367 Ihg~~tq~er~~al~~Fr~g~~pvlV  392 (482)
T KOG0335|consen  367 IHGDRTQIEREQALNDFRNGKAPVLV  392 (482)
T ss_pred             ecchhhhhHHHHHHHHhhcCCcceEE
Confidence            99999999999999999999999987

>KOG0336|consensus

Probab=100.00  E-value=7.5e-47  Score=344.03  Aligned_cols=292  Identities=30%  Similarity=0.439  Sum_probs=256.2

Q ss_pred             ccccccc-CCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC------CCCC
Q psy11867        101 SVKTFEA-LHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP------SIQE  173 (399)
Q Consensus       101 ~~~~f~~-~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~------~~~~  173 (399)
                      ++.+|++ ++..+++++++.+.||.+|||||++|||.+|+  |.|++..|+||+|||++||+|.+-++..      ...+
T Consensus       217 P~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQ--G~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~  294 (629)
T KOG0336|consen  217 PVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQ--GIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNG  294 (629)
T ss_pred             CcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeec--CcceEEEEecCCCcCHHHhccceeeeeccchhhhccCC
Confidence            3567775 58899999999999999999999999999999  7999999999999999999999887743      2357


Q ss_pred             CeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeEE
Q psy11867        174 PQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVF  250 (399)
Q Consensus       174 ~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~l  250 (399)
                      +.+|+++||++||.|+.-..+++.-  .+++..+++||.+-..+   .+.+.+|+|+||++|.++. ....+++..+.|+
T Consensus       295 p~~lvl~ptreLalqie~e~~kysy--ng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~-~~n~i~l~siTYl  371 (629)
T KOG0336|consen  295 PGVLVLTPTRELALQIEGEVKKYSY--NGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQ-MDNVINLASITYL  371 (629)
T ss_pred             CceEEEeccHHHHHHHHhHHhHhhh--cCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhh-hcCeeeeeeeEEE
Confidence            8899999999999999888877643  36677777777544332   3667899999999999984 4467899999999


Q ss_pred             EEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccc-cccceeEEEEEeCChh
Q psy11867        251 VLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE-SLDNIKQHYVMCKNID  329 (399)
Q Consensus       251 ViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~-~~~~i~~~~~~~~~~~  329 (399)
                      |+||||+|+++ +|..++.+|+--.++++|+++.|||||+.|..++..|+++|+.+.++..+. +...++|.+ .+....
T Consensus       372 VlDEADrMLDM-gFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i-~v~~d~  449 (629)
T KOG0336|consen  372 VLDEADRMLDM-GFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNI-IVTTDS  449 (629)
T ss_pred             Eecchhhhhcc-cccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeE-EecccH
Confidence            99999999997 999999999999999999999999999999999999999999999887664 456778887 555667


Q ss_pred             hHHHHHHHHhccCCC-CcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        330 EKFEAVSNIYGVVTI-GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       330 ~k~~~l~~ll~~~~~-~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +|...+..++..... .++||||.++..|..|...|.-.|+.+..+||+..|.+|+.+++.|++|+++|||
T Consensus       450 ~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILv  520 (629)
T KOG0336|consen  450 EKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILV  520 (629)
T ss_pred             HHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEE
Confidence            898888888877654 7999999999999999999988999999999999999999999999999999996

>KOG0327|consensus

Probab=100.00  E-value=4.3e-47  Score=344.71  Aligned_cols=290  Identities=39%  Similarity=0.672  Sum_probs=267.4

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      +.+|++++|+++|+++++..||.+|+.||+.||..+..  |.|+++++++|+|||.+|.+++++.+.......++|+++|
T Consensus        25 vdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~--G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaP  102 (397)
T KOG0327|consen   25 VDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIK--GHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAP  102 (397)
T ss_pred             hhhhhhcCCCHHHHhHHHhhccCCchHHHhcccccccc--CCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcc
Confidence            45899999999999999999999999999999999998  7999999999999999999999999987777788999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh----hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      |++||+|+.++.+.++... +.++....||....+.    ....++|+|+|||++.+.+.. ..+..+.++++|+||||.
T Consensus       103 treLa~qi~~v~~~lg~~~-~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~-~~l~~~~iKmfvlDEaDE  180 (397)
T KOG0327|consen  103 TRELAQQIQKVVRALGDHM-DVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNR-GSLSTDGIKMFVLDEADE  180 (397)
T ss_pred             hHHHHHHHHHHHHhhhccc-ceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhcc-ccccccceeEEeecchHh
Confidence            9999999999999998876 6777777777665432    245679999999999999655 477888999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHH
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSN  337 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~  337 (399)
                      |+.. +|.+++..++..+|++.|++++|||+|.++....+.++.+|+.+.++..+.+++.++|+|+..... .|+..++.
T Consensus       181 mLs~-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  181 MLSR-GFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKE-EKLDTLCD  258 (397)
T ss_pred             hhcc-chHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeecccc-ccccHHHH
Confidence            9975 999999999999999999999999999999999999999999999999999999999999988774 49999999


Q ss_pred             HhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        338 IYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       338 ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++.  ...+.+||||+++.+.++...|...|+.+..+||+|.+.+|..++++|+.|..+||+
T Consensus       259 l~~--~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlI  318 (397)
T KOG0327|consen  259 LYR--RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLI  318 (397)
T ss_pred             HHH--hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEe
Confidence            999  667999999999999999999999999999999999999999999999999999985

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=3e-45  Score=358.76  Aligned_cols=293  Identities=35%  Similarity=0.622  Sum_probs=258.1

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|+++++++.+.++|.++||..|+|+|.+|++.+++  |+|++++||||||||++|++|++..+.....+.++|||+|
T Consensus        27 ~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~--~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~P  104 (401)
T PTZ00424         27 VDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILD--GYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAP  104 (401)
T ss_pred             cCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECC
Confidence            46799999999999999999999999999999999998  7999999999999999999999999876656788999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      |++|+.|+.+.++.++... .+......|+.......   ....+|+|+||+++.+++.+ +.+.+++++++|+||||++
T Consensus       105 t~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~-~~~~l~~i~lvViDEah~~  182 (401)
T PTZ00424        105 TRELAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDK-RHLRVDDLKLFILDEADEM  182 (401)
T ss_pred             CHHHHHHHHHHHHHHhhhc-CceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHh-CCcccccccEEEEecHHHH
Confidence            9999999999999988764 55666666765443322   34578999999999988654 4567899999999999999


Q ss_pred             hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHH
Q psy11867        259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI  338 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  338 (399)
                      .+. ++...+..+++.+++..|++++|||+++.+..+...++.+|..+.+........++.+.++.+.....+...+..+
T Consensus       183 ~~~-~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  261 (401)
T PTZ00424        183 LSR-GFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDL  261 (401)
T ss_pred             Hhc-chHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHH
Confidence            874 7777888889999999999999999999999999999999988777766667778888888887666677888888


Q ss_pred             hccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        339 YGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       339 l~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +......++||||++++.|+.+++.|...++.+..+||+|++.+|..+++.|++|+++|||
T Consensus       262 ~~~~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLv  322 (401)
T PTZ00424        262 YETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLI  322 (401)
T ss_pred             HHhcCCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEE
Confidence            8877778999999999999999999999999999999999999999999999999999986

>KOG0348|consensus

Probab=100.00  E-value=7.3e-46  Score=347.61  Aligned_cols=295  Identities=26%  Similarity=0.406  Sum_probs=247.9

Q ss_pred             ccccccccCCCCHHHHHHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC------CCC
Q psy11867        100 YSVKTFEALHLKPELLKGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP------SIQ  172 (399)
Q Consensus       100 ~~~~~f~~~~l~~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~------~~~  172 (399)
                      +....|.++||++.+...|.. |++..||.+|.++||.++.  |+|++|.|+||||||+||++|+++.+..      ...
T Consensus       133 fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~--grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~  210 (708)
T KOG0348|consen  133 FTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLE--GRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSD  210 (708)
T ss_pred             cccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhc--CcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccC
Confidence            445779999999999999986 8999999999999999999  7999999999999999999999998843      246


Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeE
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKV  249 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~  249 (399)
                      |+.+|||+||||||.|+|+.+.++.+.+.-+.-...+||+.-...   .+.+.+|+|+|||||++|+.+...+.+++++|
T Consensus       211 G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRw  290 (708)
T KOG0348|consen  211 GPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRW  290 (708)
T ss_pred             CceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeE
Confidence            789999999999999999999999988755566677788755433   37889999999999999999999999999999


Q ss_pred             EEEechhhHhhcCCchHHHHHHHHhC-------------CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccc-----
Q psy11867        250 FVLDEADVMIATQGHQDFSIRIQKRL-------------PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE-----  311 (399)
Q Consensus       250 lViDEah~l~~~~~~~~~~~~i~~~l-------------~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~-----  311 (399)
                      +|+||||++++. ||...+..|++.+             |+..|.+++|||+++.|.+++...+.||+.|.++..     
T Consensus       291 lVlDEaDrlleL-Gfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~  369 (708)
T KOG0348|consen  291 LVLDEADRLLEL-GFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLN  369 (708)
T ss_pred             EEecchhHHHhc-cchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcC
Confidence            999999999987 8888888888766             224688999999999999999999999999984321     


Q ss_pred             --------------------cccccceeEEEEEeCChhhHHHHHHHHh----ccCCCCcEEEEecchHhHHHHHHHHHHC
Q psy11867        312 --------------------EESLDNIKQHYVMCKNIDEKFEAVSNIY----GVVTIGQAMIFCHTRKTAAWLAEKMSKE  367 (399)
Q Consensus       312 --------------------~~~~~~i~~~~~~~~~~~~k~~~l~~ll----~~~~~~k~IIF~~s~~~a~~l~~~L~~~  367 (399)
                                          ...++.+.|+|+.++..- .+-.|..++    +.....++|||+.+.+.++.-+..|...
T Consensus       370 p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKL-RLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~  448 (708)
T KOG0348|consen  370 PKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKL-RLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEA  448 (708)
T ss_pred             cchhhhhhcCCcccccccccccCcHHhhhceEecCCch-hHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhh
Confidence                                123456788888887632 333344433    3344468999999999999999888651


Q ss_pred             ----------------------CCeEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        368 ----------------------GLNVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       368 ----------------------g~~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                                            +.++.-+||+|+|++|..+++.|...+-.||
T Consensus       449 l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VL  501 (708)
T KOG0348|consen  449 LLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVL  501 (708)
T ss_pred             hhcccccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEE
Confidence                                  4568899999999999999999998776665

>KOG0334|consensus

Probab=100.00  E-value=7e-46  Score=373.42  Aligned_cols=305  Identities=28%  Similarity=0.463  Sum_probs=275.3

Q ss_pred             ceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhh
Q psy11867         88 LEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRV  167 (399)
Q Consensus        88 ~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l  167 (399)
                      +.+.+.+.+.|   +.+|.+.+++..++..++++||..|+|||.+|||+++.  |+|||.+|.||||||++|++|++.++
T Consensus       353 i~v~g~~~pkp---v~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~Ims--GrdvIgvakTgSGKT~af~LPmirhi  427 (997)
T KOG0334|consen  353 IKVKGKECPKP---VTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMS--GRDVIGVAKTGSGKTLAFLLPMIRHI  427 (997)
T ss_pred             eeeccCCCCcc---cchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhcc--CcceEEeeccCCccchhhhcchhhhh
Confidence            55566666665   67899999999999999999999999999999999999  79999999999999999999999887


Q ss_pred             CCC-----CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhcc
Q psy11867        168 NPS-----IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKY  239 (399)
Q Consensus       168 ~~~-----~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~  239 (399)
                      ...     ..+|.+||++||++||.|+++++++|.+.+ ++.+.+++||.....+.   +.+..|+|||||++++.+..+
T Consensus       428 ~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l-~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n  506 (997)
T KOG0334|consen  428 KDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLL-GIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCAN  506 (997)
T ss_pred             hcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhc-CceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhc
Confidence            432     358999999999999999999999999985 89999999998776554   445889999999999886433


Q ss_pred             --ccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccc
Q psy11867        240 --RFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDN  317 (399)
Q Consensus       240 --~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~  317 (399)
                        +..+++++.++|+||||+|+++ +|..+...|+..+++.+|+++||||+|..++.+++..+..|+.+.+........+
T Consensus       507 ~grvtnlrR~t~lv~deaDrmfdm-gfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~  585 (997)
T KOG0334|consen  507 SGRVTNLRRVTYLVLDEADRMFDM-GFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKE  585 (997)
T ss_pred             CCccccccccceeeechhhhhhee-ccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEecc
Confidence              3346778889999999999965 8999999999999999999999999999999999999999999999988888899


Q ss_pred             eeEEEEEeCChhhHHHHHHHHhccCC-CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc
Q psy11867        318 IKQHYVMCKNIDEKFEAVSNIYGVVT-IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK  396 (399)
Q Consensus       318 i~~~~~~~~~~~~k~~~l~~ll~~~~-~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~  396 (399)
                      +.|.+..|...+.|+..|..++.... .+++||||.....|..+.+.|.+.|+.|..+||+.++.+|..++++|++|.+.
T Consensus       586 V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~  665 (997)
T KOG0334|consen  586 VTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVN  665 (997)
T ss_pred             ceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCce
Confidence            99999999988999999999997764 48999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q psy11867        397 IYS  399 (399)
Q Consensus       397 ILV  399 (399)
                      +||
T Consensus       666 LLv  668 (997)
T KOG0334|consen  666 LLV  668 (997)
T ss_pred             EEE
Confidence            885

>KOG4284|consensus

Probab=100.00  E-value=6.5e-46  Score=354.18  Aligned_cols=295  Identities=28%  Similarity=0.466  Sum_probs=277.3

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ...|+++.|...++.+|...+|..||+||..|||.++.  +.|+|++|..|+|||++|.+.+++.+......++.+||+|
T Consensus        24 ~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~--kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~P  101 (980)
T KOG4284|consen   24 TPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFS--KMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTP  101 (980)
T ss_pred             CCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhc--ccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEec
Confidence            56899999999999999999999999999999999999  6999999999999999999999999998888999999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh--ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK--KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      |||+|.|+.+.+.+++..+.++.+..++||.......  ...++|+||||||+.++ .+.+.++..++++||+||||.|+
T Consensus       102 TREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~~rIvIGtPGRi~qL-~el~~~n~s~vrlfVLDEADkL~  180 (980)
T KOG4284|consen  102 TREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQTRIVIGTPGRIAQL-VELGAMNMSHVRLFVLDEADKLM  180 (980)
T ss_pred             chhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhhceEEecCchHHHHH-HHhcCCCccceeEEEeccHHhhh
Confidence            9999999999999999998899999999998765443  56788999999999988 57789999999999999999999


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCCh-------hhHH
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI-------DEKF  332 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~-------~~k~  332 (399)
                      +...|.+.+..|...||..+|++.||||+|..+.+.+..+|++|..+++......+-+|+|+|+.....       ..|.
T Consensus       181 ~t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlkl  260 (980)
T KOG4284|consen  181 DTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKL  260 (980)
T ss_pred             chhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHH
Confidence            988899999999999999999999999999999999999999999999999999999999999876554       3488


Q ss_pred             HHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        333 EAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       333 ~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.|-.+++..+..++||||+....|+-++..|...|+.|.++.|.|++.+|..+++.+|.-.++|||
T Consensus       261 q~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILV  327 (980)
T KOG4284|consen  261 QKLTHVFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILV  327 (980)
T ss_pred             HHHHHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEE
Confidence            8999999999999999999999999999999999999999999999999999999999999999997

>KOG0347|consensus

Probab=100.00  E-value=8.4e-46  Score=348.16  Aligned_cols=297  Identities=23%  Similarity=0.396  Sum_probs=252.7

Q ss_pred             CCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-------
Q psy11867         98 PLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-------  170 (399)
Q Consensus        98 ~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-------  170 (399)
                      ...++..|..|.++..++++|..+||..||+||..++|.+..+ ..|++..|.||||||+||.+||++.+...       
T Consensus       176 ~~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~g-k~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~  254 (731)
T KOG0347|consen  176 SKVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRG-KVDILGAAETGSGKTLAFGIPIVERLLESSDDSQEL  254 (731)
T ss_pred             cccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhcc-chhcccccccCCCceeeecchhhhhhhhccchHhhh
Confidence            3456788999999999999999999999999999999999984 48999999999999999999999965322       


Q ss_pred             ----CCCCe--EEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhcccc
Q psy11867        171 ----IQEPQ--VLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRF  241 (399)
Q Consensus       171 ----~~~~~--~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~  241 (399)
                          ..+++  +||++||||||.|+...+..+.... ++.+..++||....++.   ...++|||+||||||.++.+...
T Consensus       255 ~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t-~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~  333 (731)
T KOG0347|consen  255 SNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKT-QIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNT  333 (731)
T ss_pred             hhHHhccCcceeEEecChHHHHHHHHHHHHHhcccc-CeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhh
Confidence                12444  9999999999999999999998764 89999999998876655   56889999999999999876544


Q ss_pred             c--cCCceeEEEEechhhHhhcCCchHHHHHHHHhCC-----CCCcEEEEEeeCCh---------------------hHH
Q psy11867        242 F--DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP-----SDCQIMLFSATYDK---------------------EVM  293 (399)
Q Consensus       242 ~--~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~-----~~~q~l~~SAT~~~---------------------~v~  293 (399)
                      +  ++++++++|+||||||.+. |+.+.+..+++.+.     ..+|++.||||++-                     .++
T Consensus       334 ~l~~~k~vkcLVlDEaDRmvek-ghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq  412 (731)
T KOG0347|consen  334 HLGNFKKVKCLVLDEADRMVEK-GHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQ  412 (731)
T ss_pred             hhhhhhhceEEEEccHHHHhhh-ccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHH
Confidence            2  6889999999999999986 77777778887775     46899999999632                     344


Q ss_pred             HHHHh--hCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeE
Q psy11867        294 EFAQD--MVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNV  371 (399)
Q Consensus       294 ~~~~~--~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v  371 (399)
                      .+++.  +...|.+|.+.+...+...+....+.|+. .+|-..++.++...+ |++|||||++..+.+|+-.|...++..
T Consensus       413 ~Lmk~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~-~eKD~ylyYfl~ryP-GrTlVF~NsId~vKRLt~~L~~L~i~p  490 (731)
T KOG0347|consen  413 HLMKKIGFRGKPKIIDLTPQSATASTLTESLIECPP-LEKDLYLYYFLTRYP-GRTLVFCNSIDCVKRLTVLLNNLDIPP  490 (731)
T ss_pred             HHHHHhCccCCCeeEecCcchhHHHHHHHHhhcCCc-cccceeEEEEEeecC-CceEEEechHHHHHHHHHHHhhcCCCC
Confidence            44443  23567899998888888889889999955 567666777766655 899999999999999999999999999


Q ss_pred             EEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        372 GLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       372 ~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+|+.|.|.+|...+++|++....||+
T Consensus       491 ~~LHA~M~QKqRLknLEkF~~~~~~VLi  518 (731)
T KOG0347|consen  491 LPLHASMIQKQRLKNLEKFKQSPSGVLI  518 (731)
T ss_pred             chhhHHHHHHHHHHhHHHHhcCCCeEEE
Confidence            9999999999999999999998888774

>KOG0337|consensus

Probab=100.00  E-value=8.8e-44  Score=325.25  Aligned_cols=292  Identities=28%  Similarity=0.449  Sum_probs=267.6

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-CCCCeEEEEe
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-IQEPQVLCLA  180 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-~~~~~~lil~  180 (399)
                      ...|+.+||+..+++++.+.||+.|||||+..+|.+|.  ++|++..|-||||||.||++|+++++... ..+.|+++++
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe--~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralils   97 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILE--GRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILS   97 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceee--ccccceeeecCCcchhhHHHHHHHHHhhccccccceeecc
Confidence            35799999999999999999999999999999999999  79999999999999999999999998654 3567999999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      ||++|+.|+.+.++.+++.. ++...+.+||..++.+.   ..+++||++|||+++++..+. .+.++.+.||||||||+
T Consensus        98 ptreLa~qtlkvvkdlgrgt-~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem-~l~l~sveyVVfdEadr  175 (529)
T KOG0337|consen   98 PTRELALQTLKVVKDLGRGT-KLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEM-TLTLSSVEYVVFDEADR  175 (529)
T ss_pred             CcHHHHHHHHHHHHHhcccc-chhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehhe-eccccceeeeeehhhhH
Confidence            99999999999999999987 78888899998887765   446899999999999876554 37899999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHH
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSN  337 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~  337 (399)
                      ++++ ||.+++..++..+|...|+++||||+|..+..+++.-+.+|..++++.+....+..+..+..+.. ++|...|..
T Consensus       176 lfem-gfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~-a~K~aaLl~  253 (529)
T KOG0337|consen  176 LFEM-GFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRK-AEKEAALLS  253 (529)
T ss_pred             HHhh-hhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeecc-HHHHHHHHH
Confidence            9986 99999999999999999999999999999999999999999999999888888888888888876 678888888


Q ss_pred             HhccCCC-CcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        338 IYGVVTI-GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       338 ll~~~~~-~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++..... .+++|||.++.+++.+...|...|+.+..+.|.|.+..|..-+++|+.|+..+||
T Consensus       254 il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lv  316 (529)
T KOG0337|consen  254 ILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILV  316 (529)
T ss_pred             HHhccccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEE
Confidence            8876654 6899999999999999999999999999999999999999999999999999886

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

Probab=100.00  E-value=8.8e-41  Score=345.38  Aligned_cols=279  Identities=16%  Similarity=0.193  Sum_probs=215.5

Q ss_pred             CCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHH
Q psy11867        109 HLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQ  188 (399)
Q Consensus       109 ~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q  188 (399)
                      .+++.+.++|.++||.+||++|.+++|.+++  |+|+++++|||||||+||++|+++.+... .+.++|||+||+|||.|
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~--G~nvvv~apTGSGKTla~~LPiL~~l~~~-~~~~aL~l~PtraLa~q   96 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHA--GRHVVVATGTASGKSLAYQLPVLSALADD-PRATALYLAPTKALAAD   96 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHC--CCCEEEECCCCCcHHHHHHHHHHHHHhhC-CCcEEEEEcChHHHHHH
Confidence            3889999999999999999999999999998  79999999999999999999999998653 56799999999999999


Q ss_pred             HHHHHHHHhccCCCcEEEEEEcCchhhhh--hccCCcEEEeCchhHHHhhhcccc---ccCCceeEEEEechhhHhhcCC
Q psy11867        189 IGEVVAKMGKHITDLSVRYAVRGENLERN--KKITEQIIIGTPGKVLDWGLKYRF---FDLSKIKVFVLDEADVMIATQG  263 (399)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~IlV~Tp~~l~~~~~~~~~---~~~~~~~~lViDEah~l~~~~~  263 (399)
                      +.+.++.++  ..++++....|+......  ....++|+|+||++|...+.....   ..++++++|||||||+|.+  .
T Consensus        97 ~~~~l~~l~--~~~i~v~~~~Gdt~~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g--~  172 (742)
T TIGR03817        97 QLRAVRELT--LRGVRPATYDGDTPTEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG--V  172 (742)
T ss_pred             HHHHHHHhc--cCCeEEEEEeCCCCHHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC--c
Confidence            999999987  236777666666554332  245689999999998754332111   1278999999999999864  3


Q ss_pred             chHHHHHHHH-------hCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCC---------
Q psy11867        264 HQDFSIRIQK-------RLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKN---------  327 (399)
Q Consensus       264 ~~~~~~~i~~-------~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~---------  327 (399)
                      |...+..+++       ..+.++|+++||||+++... ++..++..|..+ +.... ......+.+.+...         
T Consensus       173 fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~-i~~~~-~~~~~~~~~~~~p~~~~~~~~~~  249 (742)
T TIGR03817       173 FGSHVALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVA-VTEDG-SPRGARTVALWEPPLTELTGENG  249 (742)
T ss_pred             cHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEE-ECCCC-CCcCceEEEEecCCccccccccc
Confidence            4444433333       34567899999999998855 567777777554 22222 22222333332221         


Q ss_pred             -------hhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC--------CCeEEEEcCCCCHHHHHHHHHHHhc
Q psy11867        328 -------IDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE--------GLNVGLLSGELTVEQRLSILDRFRE  392 (399)
Q Consensus       328 -------~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~--------g~~v~~lhg~~~~~~R~~v~~~F~~  392 (399)
                             ...+...+..++..  ..++||||+|++.|+.++..|+..        +.++..+||++++++|..++++|++
T Consensus       250 ~~~r~~~~~~~~~~l~~l~~~--~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~  327 (742)
T TIGR03817       250 APVRRSASAEAADLLADLVAE--GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRD  327 (742)
T ss_pred             cccccchHHHHHHHHHHHHHC--CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHc
Confidence                   12455666666654  469999999999999999988763        5689999999999999999999999


Q ss_pred             CCCcccC
Q psy11867        393 GEFKIYS  399 (399)
Q Consensus       393 G~~~ILV  399 (399)
                      |+++|||
T Consensus       328 G~i~vLV  334 (742)
T TIGR03817       328 GELLGVA  334 (742)
T ss_pred             CCceEEE
Confidence            9999986

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.

>KOG0344|consensus

Probab=100.00  E-value=3.8e-41  Score=320.67  Aligned_cols=312  Identities=25%  Similarity=0.355  Sum_probs=261.2

Q ss_pred             ccccccceeeccCCCCCCcccccccc----CCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCcee
Q psy11867         82 IESKQELEIQRKDPHSPLYSVKTFEA----LHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTA  157 (399)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~f~~----~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~  157 (399)
                      .+..+.+.+.+.+.+.|+.   +|.+    ...++.+++++...||..|+|+|.+|+|.++.  ++|+++|||||||||+
T Consensus       114 ~Rk~~k~~v~G~~~~~~l~---~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~--~r~~lAcapTGsgKtl  188 (593)
T KOG0344|consen  114 IRKSNKINVDGFHLPPPLL---SFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLE--KRDVLACAPTGSGKTL  188 (593)
T ss_pred             chhcceeeccCCCCCCccc---cccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhc--ccceEEeccCCCcchh
Confidence            4445567777777776654   4554    56899999999999999999999999999999  6999999999999999


Q ss_pred             hhHHHHHHhhCCC-----CCCCeEEEEeCcHHHHHHHHHHHHHHh--ccCCCcEEEEEEcC-chhhhh---hccCCcEEE
Q psy11867        158 AFTLTMLSRVNPS-----IQEPQVLCLAPTYELAIQIGEVVAKMG--KHITDLSVRYAVRG-ENLERN---KKITEQIII  226 (399)
Q Consensus       158 ~~~l~il~~l~~~-----~~~~~~lil~Pt~~La~Q~~~~~~~~~--~~~~~~~~~~~~~~-~~~~~~---~~~~~~IlV  226 (399)
                      +|.+|++.++...     ..+.+++|+.||++||.|+++++.++.  ... .+........ ....+.   ....++|+|
T Consensus       189 af~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t-~~~a~~~~~~~~~~qk~a~~~~~k~dili  267 (593)
T KOG0344|consen  189 AFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGT-SLRAAQFSKPAYPSQKPAFLSDEKYDILI  267 (593)
T ss_pred             hhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCC-chhhhhcccccchhhccchhHHHHHHHHh
Confidence            9999999998543     356799999999999999999999987  322 1221111111 001111   123457999


Q ss_pred             eCchhHHHhhhcc-ccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC-CCCcEEEEEeeCChhHHHHHHhhCCCCe
Q psy11867        227 GTPGKVLDWGLKY-RFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP-SDCQIMLFSATYDKEVMEFAQDMVPNPL  304 (399)
Q Consensus       227 ~Tp~~l~~~~~~~-~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~l~~SAT~~~~v~~~~~~~~~~p~  304 (399)
                      +||.++..++... ..+++..+.++|+||||++++..+|..+...|...+. +...+-+||||++.+++++++..+.+++
T Consensus       268 ~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~  347 (593)
T KOG0344|consen  268 STPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLK  347 (593)
T ss_pred             cCHHHHHHHhcCCCccchhheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccce
Confidence            9999998885432 2368999999999999999975478888888877664 5667779999999999999999999999


Q ss_pred             EEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHH-HHCCCeEEEEcCCCCHHHH
Q psy11867        305 IIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKM-SKEGLNVGLLSGELTVEQR  383 (399)
Q Consensus       305 ~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L-~~~g~~v~~lhg~~~~~~R  383 (399)
                      .+.++..+.....+.|..++|.+...|+.++++++......+++||+.+.+.|..|+..| .-.++++.++||+.++.+|
T Consensus       348 ~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qr  427 (593)
T KOG0344|consen  348 RVIVGLRNSANETVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQR  427 (593)
T ss_pred             eEEEecchhHhhhhhhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHH
Confidence            999999888899999999999999999999999999999999999999999999999999 6678999999999999999


Q ss_pred             HHHHHHHhcCCCcccC
Q psy11867        384 LSILDRFREGEFKIYS  399 (399)
Q Consensus       384 ~~v~~~F~~G~~~ILV  399 (399)
                      +.++++||.|+++||+
T Consensus       428 de~~~~FR~g~IwvLi  443 (593)
T KOG0344|consen  428 DETMERFRIGKIWVLI  443 (593)
T ss_pred             HHHHHHHhccCeeEEE
Confidence            9999999999999985

>KOG0350|consensus

Probab=100.00  E-value=7.2e-40  Score=305.31  Aligned_cols=295  Identities=20%  Similarity=0.339  Sum_probs=240.3

Q ss_pred             ccccccCCCCHHH----------HHHHHHcCCCCChHHHHHHhhhhhcC-------CCCcEEEEccCCCCceehhHHHHH
Q psy11867        102 VKTFEALHLKPEL----------LKGVYEMGFYAPSKIQETALPTLLAD-------PPHNMIAQSQSGTGKTAAFTLTML  164 (399)
Q Consensus       102 ~~~f~~~~l~~~l----------~~~l~~~g~~~p~~iQ~~ai~~ll~~-------~g~~vi~~a~TGsGKT~~~~l~il  164 (399)
                      ...|+.++++..+          .+++.++++....|+|..++|.++..       .++|+++.||||||||++|.+||+
T Consensus       126 lq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIV  205 (620)
T KOG0350|consen  126 LQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIV  205 (620)
T ss_pred             eeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHH
Confidence            3445666655444          44589999999999999999999653       279999999999999999999999


Q ss_pred             HhhCCC-CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh----cc----CCcEEEeCchhHHHh
Q psy11867        165 SRVNPS-IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK----KI----TEQIIIGTPGKVLDW  235 (399)
Q Consensus       165 ~~l~~~-~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~----~~~IlV~Tp~~l~~~  235 (399)
                      +.+... .+.-|||||+||++|+.|+++.|+++.... ++.+....|..+++...    ..    ..+|+|+|||||.+|
T Consensus       206 Q~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~t-gL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDH  284 (620)
T KOG0350|consen  206 QLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGT-GLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDH  284 (620)
T ss_pred             HHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCC-ceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHh
Confidence            998665 345789999999999999999999999886 78888888887775543    12    238999999999999


Q ss_pred             hhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC----------------------------------CCCCcE
Q psy11867        236 GLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL----------------------------------PSDCQI  281 (399)
Q Consensus       236 ~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l----------------------------------~~~~q~  281 (399)
                      +.+.+.|++++++|+||||||||++. .|.+|+..++..+                                  .+..+.
T Consensus       285 l~~~k~f~Lk~LrfLVIDEADRll~q-sfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~k  363 (620)
T KOG0350|consen  285 LNNTKSFDLKHLRFLVIDEADRLLDQ-SFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWK  363 (620)
T ss_pred             ccCCCCcchhhceEEEechHHHHHHH-HHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHh
Confidence            99899999999999999999999974 6777766554332                                  123358


Q ss_pred             EEEEeeCChhHHHHHHhhCCCCeEEecc----cccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhH
Q psy11867        282 MLFSATYDKEVMEFAQDMVPNPLIIKLK----REEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTA  357 (399)
Q Consensus       282 l~~SAT~~~~v~~~~~~~~~~p~~i~~~----~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a  357 (399)
                      +.||||+..+-..+...-+..|-.+.+.    .....+..+.+.++.++. .-|...++.++......++|||+++...+
T Consensus       364 L~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~-~~kpl~~~~lI~~~k~~r~lcf~~S~~sa  442 (620)
T KOG0350|consen  364 LVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEP-KFKPLAVYALITSNKLNRTLCFVNSVSSA  442 (620)
T ss_pred             hhcchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeeccc-ccchHhHHHHHHHhhcceEEEEecchHHH
Confidence            8999999888777777777777444333    334556677888887765 45777888888888889999999999999


Q ss_pred             HHHHHHHH----HCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        358 AWLAEKMS----KEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       358 ~~l~~~L~----~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+++..|.    ....++..+.|++....|...++.|+.|+++|||
T Consensus       443 ~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLI  488 (620)
T KOG0350|consen  443 NRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLI  488 (620)
T ss_pred             HHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEE
Confidence            99998886    3366788899999999999999999999999986

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=3.8e-38  Score=328.62  Aligned_cols=285  Identities=21%  Similarity=0.197  Sum_probs=208.7

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      .|++++|++.+++.+.+.||.+|+|+|.+|++..+.. |+|++++||||||||++|.+|++..+..   +.++|||+|++
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~-g~nvlv~APTGSGKTlia~lail~~l~~---~~kal~i~P~r   77 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLD-GKNLLAAIPTASGKTLIAELAMLKAIAR---GGKALYIVPLR   77 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhC-CCcEEEECCCcchHHHHHHHHHHHHHhc---CCcEEEEeChH
Confidence            4788999999999999999999999999999984433 7999999999999999999999998853   56799999999


Q ss_pred             HHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCC
Q psy11867        184 ELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQG  263 (399)
Q Consensus       184 ~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~  263 (399)
                      +||.|+++.++++...  ++++....|+...........+|+|+||+++..++.+ ...++++++++|+||+|++.+. +
T Consensus        78 aLa~q~~~~~~~~~~~--g~~v~~~tGd~~~~~~~l~~~~IiV~Tpek~~~llr~-~~~~l~~v~lvViDE~H~l~d~-~  153 (737)
T PRK02362         78 ALASEKFEEFERFEEL--GVRVGISTGDYDSRDEWLGDNDIIVATSEKVDSLLRN-GAPWLDDITCVVVDEVHLIDSA-N  153 (737)
T ss_pred             HHHHHHHHHHHHhhcC--CCEEEEEeCCcCccccccCCCCEEEECHHHHHHHHhc-ChhhhhhcCEEEEECccccCCC-c
Confidence            9999999999987542  6777777777654443345678999999999887654 3456889999999999999763 4


Q ss_pred             chHHHHHHH---HhCCCCCcEEEEEeeCChhHHHHHHhhCC-------CCeEEe--cccccccccceeEEEEEeCChhhH
Q psy11867        264 HQDFSIRIQ---KRLPSDCQIMLFSATYDKEVMEFAQDMVP-------NPLIIK--LKREEESLDNIKQHYVMCKNIDEK  331 (399)
Q Consensus       264 ~~~~~~~i~---~~l~~~~q~l~~SAT~~~~v~~~~~~~~~-------~p~~i~--~~~~~~~~~~i~~~~~~~~~~~~k  331 (399)
                      +...+..++   +.+++..|++++|||+++. .+++...-.       .|+.+.  +...........+...........
T Consensus       154 rg~~le~il~rl~~~~~~~qii~lSATl~n~-~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~  232 (737)
T PRK02362        154 RGPTLEVTLAKLRRLNPDLQVVALSATIGNA-DELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDT  232 (737)
T ss_pred             chHHHHHHHHHHHhcCCCCcEEEEcccCCCH-HHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccchHH
Confidence            555554443   3345789999999999863 233322211       121111  110000000001111111121233


Q ss_pred             HHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC------------------------------------CCeEEEEc
Q psy11867        332 FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE------------------------------------GLNVGLLS  375 (399)
Q Consensus       332 ~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~------------------------------------g~~v~~lh  375 (399)
                      ...+.+.+.  ..+++||||++++.|+.++..|...                                    ...++.+|
T Consensus       233 ~~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hH  310 (737)
T PRK02362        233 LNLVLDTLE--EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHH  310 (737)
T ss_pred             HHHHHHHHH--cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeec
Confidence            444444443  4579999999999999999888643                                    13689999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        376 GELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       376 g~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      |+|++.+|..+++.|++|.++|||
T Consensus       311 agl~~~eR~~ve~~Fr~G~i~VLv  334 (737)
T PRK02362        311 AGLSREHRELVEDAFRDRLIKVIS  334 (737)
T ss_pred             CCCCHHHHHHHHHHHHcCCCeEEE
Confidence            999999999999999999999986

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=3.6e-37  Score=320.52  Aligned_cols=283  Identities=20%  Similarity=0.191  Sum_probs=212.1

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhh-hhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPT-LLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~-ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      +|+++++++.+.+.+.++||..|+|+|.+|++. ++.  |+|++++||||||||++|.+|++..+..  .+.++|||+|+
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~--g~nvlv~apTGsGKT~~~~l~il~~l~~--~~~~~l~l~P~   77 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLE--GKNLVLAIPTASGKTLVAEIVMVNKLLR--EGGKAVYLVPL   77 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhC--CCcEEEECCCCcHHHHHHHHHHHHHHHh--cCCeEEEEeCh
Confidence            478899999999999999999999999999997 455  7999999999999999999999998764  35689999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ  262 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~  262 (399)
                      ++|+.|+++.++.+.. + ++.+....|+..........++|+|+||+++..++. .+..++++++++|+||+|.+.+. 
T Consensus        78 ~aLa~q~~~~~~~~~~-~-g~~v~~~~Gd~~~~~~~~~~~~IiV~Tpe~~~~ll~-~~~~~l~~l~lvViDE~H~l~~~-  153 (720)
T PRK00254         78 KALAEEKYREFKDWEK-L-GLRVAMTTGDYDSTDEWLGKYDIIIATAEKFDSLLR-HGSSWIKDVKLVVADEIHLIGSY-  153 (720)
T ss_pred             HHHHHHHHHHHHHHhh-c-CCEEEEEeCCCCCchhhhccCCEEEEcHHHHHHHHh-CCchhhhcCCEEEEcCcCccCCc-
Confidence            9999999999988643 2 677777777765444444567999999999988754 34456899999999999999753 


Q ss_pred             CchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccc-cc-eeEEEEEeCCh------hhHHHH
Q psy11867        263 GHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESL-DN-IKQHYVMCKNI------DEKFEA  334 (399)
Q Consensus       263 ~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~-~~-i~~~~~~~~~~------~~k~~~  334 (399)
                      ++...+..++..+..+.|++++|||+++. .+++.. +....... ....... .. ..+.+......      ......
T Consensus       154 ~rg~~le~il~~l~~~~qiI~lSATl~n~-~~la~w-l~~~~~~~-~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (720)
T PRK00254        154 DRGATLEMILTHMLGRAQILGLSATVGNA-EELAEW-LNAELVVS-DWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESL  230 (720)
T ss_pred             cchHHHHHHHHhcCcCCcEEEEEccCCCH-HHHHHH-hCCccccC-CCCCCcceeeEecCCeeeccCcchhcchHHHHHH
Confidence            56677788888888899999999999863 455543 32221111 0000000 00 11111111111      111223


Q ss_pred             HHHHhccCCCCcEEEEecchHhHHHHHHHHHHC---------------------------------CCeEEEEcCCCCHH
Q psy11867        335 VSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE---------------------------------GLNVGLLSGELTVE  381 (399)
Q Consensus       335 l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~---------------------------------g~~v~~lhg~~~~~  381 (399)
                      +.+.+.  ..+++||||++++.|+.++..|...                                 ...|+.+||+|+++
T Consensus       231 ~~~~i~--~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~  308 (720)
T PRK00254        231 VYDAVK--KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRT  308 (720)
T ss_pred             HHHHHH--hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHH
Confidence            344443  3468999999999999888666421                                 23599999999999


Q ss_pred             HHHHHHHHHhcCCCcccC
Q psy11867        382 QRLSILDRFREGEFKIYS  399 (399)
Q Consensus       382 ~R~~v~~~F~~G~~~ILV  399 (399)
                      +|..+++.|++|.++|||
T Consensus       309 eR~~ve~~F~~G~i~VLv  326 (720)
T PRK00254        309 ERVLIEDAFREGLIKVIT  326 (720)
T ss_pred             HHHHHHHHHHCCCCeEEE
Confidence            999999999999999986

>KOG0329|consensus

Probab=100.00  E-value=8e-38  Score=269.13  Aligned_cols=252  Identities=30%  Similarity=0.514  Sum_probs=227.7

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      .-|.++-|.|++++++...||.+|+.+|.+|||...-  |.|++++|.+|-|||.+|+++-++++.+......+|++|.|
T Consensus        42 sgfrdfllkpellraivdcgfehpsevqhecipqail--gmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmcht  119 (387)
T KOG0329|consen   42 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAIL--GMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHT  119 (387)
T ss_pred             cchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhh--cchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEecc
Confidence            4588888999999999999999999999999999988  79999999999999999999999999988777789999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      ||||.|+.++..++.++++.+++...+||..+.+..   +..+||+|+||||++.+. +.+.+++++++++|+||||.|+
T Consensus       120 relafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALv-r~k~l~lk~vkhFvlDEcdkml  198 (387)
T KOG0329|consen  120 RELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALV-RNRSLNLKNVKHFVLDECDKML  198 (387)
T ss_pred             HHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHH-HhccCchhhcceeehhhHHHHH
Confidence            999999999999999999999999999998775543   557899999999999884 5688999999999999999998


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccc-cccceeEEEEEeCChhhHHHHHHHH
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE-SLDNIKQHYVMCKNIDEKFEAVSNI  338 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~-~~~~i~~~~~~~~~~~~k~~~l~~l  338 (399)
                      +.-.....+..|.+..|...|+++||||+++++...++.++.||..+.++.+.. ++.++.|+|+..+. .+|...+.++
T Consensus       199 e~lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke-~eKNrkl~dL  277 (387)
T KOG0329|consen  199 EQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKE-NEKNRKLNDL  277 (387)
T ss_pred             HHHHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhh-hhhhhhhhhh
Confidence            765667778889999999999999999999999999999999999999887654 57788899988765 6788899999


Q ss_pred             hccCCCCcEEEEecchHhHH
Q psy11867        339 YGVVTIGQAMIFCHTRKTAA  358 (399)
Q Consensus       339 l~~~~~~k~IIF~~s~~~a~  358 (399)
                      +......+++||+.+.....
T Consensus       278 Ld~LeFNQVvIFvKsv~Rl~  297 (387)
T KOG0329|consen  278 LDVLEFNQVVIFVKSVQRLS  297 (387)
T ss_pred             hhhhhhcceeEeeehhhhhh
Confidence            99998999999999977643

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=1.2e-35  Score=295.12  Aligned_cols=261  Identities=16%  Similarity=0.234  Sum_probs=193.0

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      .+||..|+|+|.++++.+++  |+|+++++|||||||++|++|++..      +..+|||+||++|+.|+.+.++.+   
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~--g~dvlv~apTGsGKTl~y~lp~l~~------~~~~lVi~P~~~L~~dq~~~l~~~---   74 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLL--GRDCFVVMPTGGGKSLCYQLPALCS------DGITLVISPLISLMEDQVLQLKAS---   74 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHc--CCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHHHHHHHc---
Confidence            37999999999999999999  6999999999999999999999852      346999999999999999988865   


Q ss_pred             CCCcEEEEEEcCchhhh-------hhccCCcEEEeCchhHHHhhhccccc-cCCceeEEEEechhhHhhcC-CchHHHHH
Q psy11867        200 ITDLSVRYAVRGENLER-------NKKITEQIIIGTPGKVLDWGLKYRFF-DLSKIKVFVLDEADVMIATQ-GHQDFSIR  270 (399)
Q Consensus       200 ~~~~~~~~~~~~~~~~~-------~~~~~~~IlV~Tp~~l~~~~~~~~~~-~~~~~~~lViDEah~l~~~~-~~~~~~~~  270 (399)
                        ++......++.....       ......+|+++||+++.........+ ...+++++||||||++.+.+ .|......
T Consensus        75 --gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~  152 (470)
T TIGR00614        75 --GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKA  152 (470)
T ss_pred             --CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHH
Confidence              344455555443221       12345789999999985432111222 56789999999999997531 24444333


Q ss_pred             ---HHHhCCCCCcEEEEEeeCChhHHHHHHhhC--CCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhc-cCCC
Q psy11867        271 ---IQKRLPSDCQIMLFSATYDKEVMEFAQDMV--PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG-VVTI  344 (399)
Q Consensus       271 ---i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~--~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~-~~~~  344 (399)
                         +...+ ++.+++++|||.++.+...+...+  .+|..+.....   ..++.  +.......+....+..++. ....
T Consensus       153 l~~l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~~---r~nl~--~~v~~~~~~~~~~l~~~l~~~~~~  226 (470)
T TIGR00614       153 LGSLKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFCTSFD---RPNLY--YEVRRKTPKILEDLLRFIRKEFKG  226 (470)
T ss_pred             HHHHHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCCCC---CCCcE--EEEEeCCccHHHHHHHHHHHhcCC
Confidence               33333 578999999999988776555543  45555433221   22332  2222222245555666665 3444


Q ss_pred             CcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        345 GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       345 ~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+||||++++.|+.++..|...|+.+..+||+|++.+|..+++.|++|+++|||
T Consensus       227 ~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLV  281 (470)
T TIGR00614       227 KSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVV  281 (470)
T ss_pred             CceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEE
Confidence            5679999999999999999999999999999999999999999999999999986

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

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

Probab=100.00  E-value=7.2e-35  Score=296.76  Aligned_cols=261  Identities=19%  Similarity=0.213  Sum_probs=196.5

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCC-cEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEE-EeCcHHHHHHHHHHHHHHhc
Q psy11867        121 MGFYAPSKIQETALPTLLADPPH-NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLC-LAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~-~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~li-l~Pt~~La~Q~~~~~~~~~~  198 (399)
                      .||. |||||.+++|.++.  |+ ++++++|||||||.+|.++++.. ......++.|| ++|||+||.|+++.++++++
T Consensus        12 ~G~~-PtpiQ~~~i~~il~--G~~~v~~~apTGSGKTaa~aafll~~-~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k   87 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVA--GQPPESCSTPTGLGKTSIIAAWLLAV-EIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGE   87 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHc--CCCcceEecCCCCcccHHHHHhhccc-cccccccceEEEeCchHHHHHHHHHHHHHHHH
Confidence            5887 99999999999998  56 68888999999999776555532 23334566665 66999999999999999988


Q ss_pred             cCC----------------------CcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhc--------cccc---
Q psy11867        199 HIT----------------------DLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLK--------YRFF---  242 (399)
Q Consensus       199 ~~~----------------------~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~--------~~~~---  242 (399)
                      .++                      .+++..++||.....+.   ..+++|||+|++.+.+-...        ...+   
T Consensus        88 ~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~sr~L~~gYg~~~~~~pi~ag  167 (844)
T TIGR02621        88 RLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIGSRLLFSGYGCGFKSRPLHAG  167 (844)
T ss_pred             HhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHcCCccccccccccccccchhh
Confidence            653                      37788889998776554   45679999996544332110        0001   


Q ss_pred             cCCceeEEEEechhhHhhcCCchHHHHHHHHhC--CCC---CcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccc
Q psy11867        243 DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL--PSD---CQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDN  317 (399)
Q Consensus       243 ~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l--~~~---~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~  317 (399)
                      .+++++++|+||||  ++ .+|.+.+..|++.+  ++.   +|+++||||++.++..+...++.++..+.+........+
T Consensus       168 ~L~~v~~LVLDEAD--Ld-~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~~l~a~k  244 (844)
T TIGR02621       168 FLGQDALIVHDEAH--LE-PAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKKRLAAKK  244 (844)
T ss_pred             hhccceEEEEehhh--hc-cccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccccccccc
Confidence            26889999999999  33 48999999999864  432   699999999999888888888878877766655555566


Q ss_pred             eeEEEEEeCChhhHHHHHHHHh---ccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHH-----HHHHH
Q psy11867        318 IKQHYVMCKNIDEKFEAVSNIY---GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRL-----SILDR  389 (399)
Q Consensus       318 i~~~~~~~~~~~~k~~~l~~ll---~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~-----~v~~~  389 (399)
                      +.+++ .+.. +.|...+...+   .....+++||||||++.|+.+++.|.+.++  ..+||+|++.+|.     .++++
T Consensus       245 i~q~v-~v~~-e~Kl~~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~  320 (844)
T TIGR02621       245 IVKLV-PPSD-EKFLSTMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNR  320 (844)
T ss_pred             eEEEE-ecCh-HHHHHHHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHH
Confidence            66643 3332 33433322221   123457899999999999999999998886  8999999999999     88999


Q ss_pred             Hhc
Q psy11867        390 FRE  392 (399)
Q Consensus       390 F~~  392 (399)
                      |++
T Consensus       321 Fk~  323 (844)
T TIGR02621       321 FLP  323 (844)
T ss_pred             Hhc
Confidence            997

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.

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

Probab=100.00  E-value=5.8e-35  Score=301.68  Aligned_cols=274  Identities=16%  Similarity=0.177  Sum_probs=201.1

Q ss_pred             CCCCHHHHHHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH
Q psy11867        108 LHLKPELLKGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA  186 (399)
Q Consensus       108 ~~l~~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La  186 (399)
                      ++....+...++. +||..|+|+|.++|+.++.  |+|+++++|||+|||+||++|++..      .+.+|||+|+++|+
T Consensus       442 fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~--GrDVLVimPTGSGKSLcYQLPAL~~------~GiTLVISPLiSLm  513 (1195)
T PLN03137        442 FPWTKKLEVNNKKVFGNHSFRPNQREIINATMS--GYDVFVLMPTGGGKSLTYQLPALIC------PGITLVISPLVSLI  513 (1195)
T ss_pred             CCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHc--CCCEEEEcCCCccHHHHHHHHHHHc------CCcEEEEeCHHHHH
Confidence            4455666666665 7999999999999999998  7999999999999999999999853      34699999999999


Q ss_pred             HHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---------ccCCcEEEeCchhHHHh--hhc-cccc-cCCceeEEEEe
Q psy11867        187 IQIGEVVAKMGKHITDLSVRYAVRGENLERNK---------KITEQIIIGTPGKVLDW--GLK-YRFF-DLSKIKVFVLD  253 (399)
Q Consensus       187 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~IlV~Tp~~l~~~--~~~-~~~~-~~~~~~~lViD  253 (399)
                      .++...+...     ++......++.......         ....+|+|+||++|...  +.. ...+ ....+.+||||
T Consensus       514 qDQV~~L~~~-----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVID  588 (1195)
T PLN03137        514 QDQIMNLLQA-----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVID  588 (1195)
T ss_pred             HHHHHHHHhC-----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccC
Confidence            8666655543     56667777765543221         14678999999998631  111 1111 23458999999


Q ss_pred             chhhHhhcC-CchHHHHH--HHHhCCCCCcEEEEEeeCChhHHHHHHhhC--CCCeEEecccccccccceeEEEEEeCCh
Q psy11867        254 EADVMIATQ-GHQDFSIR--IQKRLPSDCQIMLFSATYDKEVMEFAQDMV--PNPLIIKLKREEESLDNIKQHYVMCKNI  328 (399)
Q Consensus       254 Eah~l~~~~-~~~~~~~~--i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~--~~p~~i~~~~~~~~~~~i~~~~~~~~~~  328 (399)
                      |||++.+.+ .|...+..  ++....+..++++||||.+..+...+...+  .++..+...   ....++  +|.+....
T Consensus       589 EAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~S---f~RpNL--~y~Vv~k~  663 (1195)
T PLN03137        589 EAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQS---FNRPNL--WYSVVPKT  663 (1195)
T ss_pred             cchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeecc---cCccce--EEEEeccc
Confidence            999998642 25554443  233344578999999999998887665544  344433221   122333  34334333


Q ss_pred             hhHHHHHHHHhccC-CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSNIYGVV-TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~ll~~~-~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ......+..++... ...++||||++++.|+.++..|...|+.+..|||+|++.+|..++++|+.|+++|||
T Consensus       664 kk~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLV  735 (1195)
T PLN03137        664 KKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIIC  735 (1195)
T ss_pred             hhHHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEE
Confidence            33345566666543 346799999999999999999999999999999999999999999999999999987

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=7.6e-35  Score=310.97  Aligned_cols=262  Identities=21%  Similarity=0.225  Sum_probs=204.1

Q ss_pred             HHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHH
Q psy11867        116 KGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVA  194 (399)
Q Consensus       116 ~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~  194 (399)
                      +.+.+ .|+ .|+++|..++|.++.  |+|++++||||||||+ |.++++..+..  .+.+++||+||++||.|+++.++
T Consensus        71 ~~f~~~~G~-~pt~iQ~~~i~~il~--g~dv~i~ApTGsGKT~-f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~  144 (1176)
T PRK09401         71 KFFKKKTGS-KPWSLQRTWAKRLLL--GESFAIIAPTGVGKTT-FGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLE  144 (1176)
T ss_pred             HHHHHhcCC-CCcHHHHHHHHHHHC--CCcEEEEcCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHH
Confidence            33434 466 899999999999998  7999999999999995 55666555533  46789999999999999999999


Q ss_pred             HHhccCCCcEEEEEEcCchh-----hhh----hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc----
Q psy11867        195 KMGKHITDLSVRYAVRGENL-----ERN----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT----  261 (399)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~-----~~~----~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~----  261 (399)
                      .++... ++.+....++...     ...    ....++|+|+||++|.+++.   .+...+++++|+||||+|++.    
T Consensus       145 ~l~~~~-~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~---~l~~~~~~~lVvDEaD~~L~~~k~i  220 (1176)
T PRK09401        145 KFGEKV-GCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD---ELPKKKFDFVFVDDVDAVLKSSKNI  220 (1176)
T ss_pred             HHhhhc-CceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH---hccccccCEEEEEChHHhhhcccch
Confidence            998875 5666666655432     111    13468999999999998753   455667999999999999852    


Q ss_pred             ------CCch-HHHHHHHHhCCC------------------------CCcEEEEEeeCChh-HHHHHHhhCCCCeEEecc
Q psy11867        262 ------QGHQ-DFSIRIQKRLPS------------------------DCQIMLFSATYDKE-VMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       262 ------~~~~-~~~~~i~~~l~~------------------------~~q~l~~SAT~~~~-v~~~~~~~~~~p~~i~~~  309 (399)
                            .||. +.+..++..++.                        ..|+++||||+++. +..   .++.++..+.+.
T Consensus       221 d~~l~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~  297 (1176)
T PRK09401        221 DKLLYLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVG  297 (1176)
T ss_pred             hhHHHhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEec
Confidence                  2564 566666666654                        68999999999864 332   234566667777


Q ss_pred             cccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHh---HHHHHHHHHHCCCeEEEEcCCCCHHHHHHH
Q psy11867        310 REEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKT---AAWLAEKMSKEGLNVGLLSGELTVEQRLSI  386 (399)
Q Consensus       310 ~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~---a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v  386 (399)
                      .......++.+.|+.+.   ++...+..+++... .++||||++++.   |+++++.|...|+++..+||+|   +  ..
T Consensus       298 ~~~~~~rnI~~~yi~~~---~k~~~L~~ll~~l~-~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l---~--~~  368 (1176)
T PRK09401        298 SPVFYLRNIVDSYIVDE---DSVEKLVELVKRLG-DGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF---E--RK  368 (1176)
T ss_pred             CcccccCCceEEEEEcc---cHHHHHHHHHHhcC-CCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH---H--HH
Confidence            76667789999998775   46667777776554 589999999888   9999999999999999999999   2  34


Q ss_pred             HHHHhcCCCcccC
Q psy11867        387 LDRFREGEFKIYS  399 (399)
Q Consensus       387 ~~~F~~G~~~ILV  399 (399)
                      +++|++|+++|||
T Consensus       369 l~~F~~G~~~VLV  381 (1176)
T PRK09401        369 FEKFEEGEVDVLV  381 (1176)
T ss_pred             HHHHHCCCCCEEE
Confidence            5999999999997

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=7.2e-35  Score=301.94  Aligned_cols=283  Identities=19%  Similarity=0.187  Sum_probs=203.0

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      .|++++|++.+++.+...||. ++++|.++++.+..  ++|++++||||||||++|.++++..+..   +.++||++|++
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~--~~nvlv~apTGSGKTl~a~lail~~l~~---~~k~v~i~P~r   75 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRK--GENVIVSVPTAAGKTLIAYSAIYETFLA---GLKSIYIVPLR   75 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhc--CCcEEEECCCCchHHHHHHHHHHHHHHh---CCcEEEEechH
Confidence            477889999999999999886 99999999999877  7999999999999999999999988764   35799999999


Q ss_pred             HHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCC
Q psy11867        184 ELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQG  263 (399)
Q Consensus       184 ~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~  263 (399)
                      +||.|+++.++++.. . +..+....|+...........+|+|+||+++..++.+. ...+++++++|+||||++.+. +
T Consensus        76 aLa~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~~~~~~~dIiv~Tpek~~~l~~~~-~~~l~~v~lvViDEaH~l~d~-~  151 (674)
T PRK01172         76 SLAMEKYEELSRLRS-L-GMRVKISIGDYDDPPDFIKRYDVVILTSEKADSLIHHD-PYIINDVGLIVADEIHIIGDE-D  151 (674)
T ss_pred             HHHHHHHHHHHHHhh-c-CCeEEEEeCCCCCChhhhccCCEEEECHHHHHHHHhCC-hhHHhhcCEEEEecchhccCC-C
Confidence            999999999998643 2 56777777765543333456799999999998876543 345889999999999998753 4


Q ss_pred             chHHHHHH---HHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccccccccc-ceeE-EEEEeCChhhHHHHHHHH
Q psy11867        264 HQDFSIRI---QKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLD-NIKQ-HYVMCKNIDEKFEAVSNI  338 (399)
Q Consensus       264 ~~~~~~~i---~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~-~i~~-~~~~~~~~~~k~~~l~~l  338 (399)
                      +...+..+   .+.++++.|++++|||+++. .++...+- .+. +.......... ++.. ....+.........+..+
T Consensus       152 rg~~le~ll~~~~~~~~~~riI~lSATl~n~-~~la~wl~-~~~-~~~~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~~  228 (674)
T PRK01172        152 RGPTLETVLSSARYVNPDARILALSATVSNA-NELAQWLN-ASL-IKSNFRPVPLKLGILYRKRLILDGYERSQVDINSL  228 (674)
T ss_pred             ccHHHHHHHHHHHhcCcCCcEEEEeCccCCH-HHHHHHhC-CCc-cCCCCCCCCeEEEEEecCeeeecccccccccHHHH
Confidence            44444444   34456789999999999763 44544322 111 11000000000 0000 000111111111112222


Q ss_pred             hcc--CCCCcEEEEecchHhHHHHHHHHHHC-------------------------CCeEEEEcCCCCHHHHHHHHHHHh
Q psy11867        339 YGV--VTIGQAMIFCHTRKTAAWLAEKMSKE-------------------------GLNVGLLSGELTVEQRLSILDRFR  391 (399)
Q Consensus       339 l~~--~~~~k~IIF~~s~~~a~~l~~~L~~~-------------------------g~~v~~lhg~~~~~~R~~v~~~F~  391 (399)
                      +..  ...+++||||++++.|+.++..|...                         ...++.+||+|++++|..+++.|+
T Consensus       229 i~~~~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~  308 (674)
T PRK01172        229 IKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFR  308 (674)
T ss_pred             HHHHHhCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHH
Confidence            222  23579999999999999999888653                         135889999999999999999999


Q ss_pred             cCCCcccC
Q psy11867        392 EGEFKIYS  399 (399)
Q Consensus       392 ~G~~~ILV  399 (399)
                      +|.++|||
T Consensus       309 ~g~i~VLv  316 (674)
T PRK01172        309 NRYIKVIV  316 (674)
T ss_pred             cCCCeEEE
Confidence            99999986

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=9.2e-35  Score=306.27  Aligned_cols=281  Identities=20%  Similarity=0.232  Sum_probs=196.4

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC------CCCCeEEEEeCcH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS------IQEPQVLCLAPTY  183 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~------~~~~~~lil~Pt~  183 (399)
                      +++.+.+.+. .+|..|||+|.+|+|.+++  |+|++++||||||||++|++|+++.+...      ..+.++|||+||+
T Consensus        18 l~~~v~~~~~-~~~~~~tpiQ~~Ai~~il~--g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtr   94 (876)
T PRK13767         18 LRPYVREWFK-EKFGTFTPPQRYAIPLIHE--GKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLR   94 (876)
T ss_pred             cCHHHHHHHH-HccCCCCHHHHHHHHHHHc--CCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHH
Confidence            5566666554 4899999999999999998  79999999999999999999999887531      2457899999999


Q ss_pred             HHHHHHHHHHHHH-----------hccCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccc-cCCcee
Q psy11867        184 ELAIQIGEVVAKM-----------GKHITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFF-DLSKIK  248 (399)
Q Consensus       184 ~La~Q~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~-~~~~~~  248 (399)
                      +|+.|+++.+...           +..++++.+....|+......   ....++|+|+||++|..++...+.. .+++++
T Consensus        95 aLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~  174 (876)
T PRK13767         95 ALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVK  174 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCC
Confidence            9999998765532           233345677777777654332   2457899999999998775433221 478999


Q ss_pred             EEEEechhhHhhcCCchH----HHHHHHHhCCCCCcEEEEEeeCChh--HHHHHHhhC----CCCeEEecccccccccce
Q psy11867        249 VFVLDEADVMIATQGHQD----FSIRIQKRLPSDCQIMLFSATYDKE--VMEFAQDMV----PNPLIIKLKREEESLDNI  318 (399)
Q Consensus       249 ~lViDEah~l~~~~~~~~----~~~~i~~~l~~~~q~l~~SAT~~~~--v~~~~~~~~----~~p~~i~~~~~~~~~~~i  318 (399)
                      +||+||+|.+.+. ....    .+.++....+...|++++|||+++.  +..+.....    ..+..+.-...   ....
T Consensus       175 ~VVIDE~H~l~~~-~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~~~~va~~L~~~~~~~~~r~~~iv~~~~---~k~~  250 (876)
T PRK13767        175 WVIVDEIHSLAEN-KRGVHLSLSLERLEELAGGEFVRIGLSATIEPLEEVAKFLVGYEDDGEPRDCEIVDARF---VKPF  250 (876)
T ss_pred             EEEEechhhhccC-ccHHHHHHHHHHHHHhcCCCCeEEEEecccCCHHHHHHHhcCccccCCCCceEEEccCC---Cccc
Confidence            9999999999854 2222    2334444445688999999999862  333322211    11222211100   0111


Q ss_pred             eEEEE-------EeCC---hhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC------CCeEEEEcCCCCHHH
Q psy11867        319 KQHYV-------MCKN---IDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE------GLNVGLLSGELTVEQ  382 (399)
Q Consensus       319 ~~~~~-------~~~~---~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~------g~~v~~lhg~~~~~~  382 (399)
                      .....       ....   .......+..++..  .+++||||||++.|+.++..|.+.      +..+..+||+|++++
T Consensus       251 ~i~v~~p~~~l~~~~~~~~~~~l~~~L~~~i~~--~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~  328 (876)
T PRK13767        251 DIKVISPVDDLIHTPAEEISEALYETLHELIKE--HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREV  328 (876)
T ss_pred             eEEEeccCccccccccchhHHHHHHHHHHHHhc--CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHH
Confidence            00000       0111   01223344444433  468999999999999999999873      468999999999999


Q ss_pred             HHHHHHHHhcCCCcccC
Q psy11867        383 RLSILDRFREGEFKIYS  399 (399)
Q Consensus       383 R~~v~~~F~~G~~~ILV  399 (399)
                      |..+++.|++|+++|||
T Consensus       329 R~~ve~~fk~G~i~vLV  345 (876)
T PRK13767        329 RLEVEEKLKRGELKVVV  345 (876)
T ss_pred             HHHHHHHHHcCCCeEEE
Confidence            99999999999999986

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

Probab=100.00  E-value=9.6e-34  Score=287.08  Aligned_cols=279  Identities=21%  Similarity=0.234  Sum_probs=213.4

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-----CCCCeEEEEeCcHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-----IQEPQVLCLAPTYE  184 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-----~~~~~~lil~Pt~~  184 (399)
                      |++.+++.++.. |..||+.|.+|||.+.+  |+|+++.||||||||+|+++|++..+...     ..+..||||+|.++
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~--G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkA   84 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHS--GENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKA   84 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhC--CCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHH
Confidence            678999999888 99999999999999998  79999999999999999999999988655     23468999999999


Q ss_pred             HHHHHHHHHHHHhccCCCcEEEEEEcCchhhh---hhccCCcEEEeCchhHHHhhhccccc-cCCceeEEEEechhhHhh
Q psy11867        185 LAIQIGEVVAKMGKHITDLSVRYAVRGENLER---NKKITEQIIIGTPGKVLDWGLKYRFF-DLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       185 La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~IlV~Tp~~l~~~~~~~~~~-~~~~~~~lViDEah~l~~  260 (399)
                      |..++.+.++.++..+ ++.+..-.|......   ..+..+||+|+||+.|.-++...+.. .+++++++|+||.|.+.+
T Consensus        85 Ln~Di~~rL~~~~~~~-G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~  163 (814)
T COG1201          85 LNNDIRRRLEEPLREL-GIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAE  163 (814)
T ss_pred             HHHHHHHHHHHHHHHc-CCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhc
Confidence            9999999999999876 777766666654432   22667899999999998776543322 489999999999999986


Q ss_pred             cCCchHH---HHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCC--CeEEecccccccccceeEEEEEeCCh-------
Q psy11867        261 TQGHQDF---SIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPN--PLIIKLKREEESLDNIKQHYVMCKNI-------  328 (399)
Q Consensus       261 ~~~~~~~---~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~--p~~i~~~~~~~~~~~i~~~~~~~~~~-------  328 (399)
                      .......   +.++....+ +.|.+++|||..+. ...++.....  +..|......   .............       
T Consensus       164 sKRG~~Lsl~LeRL~~l~~-~~qRIGLSATV~~~-~~varfL~g~~~~~~Iv~~~~~---k~~~i~v~~p~~~~~~~~~~  238 (814)
T COG1201         164 SKRGVQLALSLERLRELAG-DFQRIGLSATVGPP-EEVAKFLVGFGDPCEIVDVSAA---KKLEIKVISPVEDLIYDEEL  238 (814)
T ss_pred             cccchhhhhhHHHHHhhCc-ccEEEeehhccCCH-HHHHHHhcCCCCceEEEEcccC---CcceEEEEecCCccccccch
Confidence            5322222   234444444 89999999999843 4444444433  3333222211   1122222222111       


Q ss_pred             -hhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCC-CeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 -DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEG-LNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 -~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g-~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                       ..-+..+.++++.+.  .+|||+|||..|+.++..|.+.+ ..+..+||.++.++|..+.++|++|+++++|
T Consensus       239 ~~~~~~~i~~~v~~~~--ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV  309 (814)
T COG1201         239 WAALYERIAELVKKHR--TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVV  309 (814)
T ss_pred             hHHHHHHHHHHHhhcC--cEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEE
Confidence             335566667776654  89999999999999999999986 8999999999999999999999999999876

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=1.7e-33  Score=287.08  Aligned_cols=268  Identities=14%  Similarity=0.217  Sum_probs=196.8

Q ss_pred             CHHHHHHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        111 KPELLKGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       111 ~~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      .+...+.|++ +||..|+|+|.++++.+++  |+|+++++|||+|||++|++|++..      ...+|||+|+++|+.|+
T Consensus        10 ~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~--g~dvlv~apTGsGKTl~y~lpal~~------~g~tlVisPl~sL~~dq   81 (607)
T PRK11057         10 ESLAKQVLQETFGYQQFRPGQQEIIDAVLS--GRDCLVVMPTGGGKSLCYQIPALVL------DGLTLVVSPLISLMKDQ   81 (607)
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHc--CCCEEEEcCCCchHHHHHHHHHHHc------CCCEEEEecHHHHHHHH
Confidence            3344444544 6999999999999999998  7999999999999999999999853      34699999999999999


Q ss_pred             HHHHHHHhccCCCcEEEEEEcCchhhh-------hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC
Q psy11867        190 GEVVAKMGKHITDLSVRYAVRGENLER-------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ  262 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~  262 (399)
                      .+.++.++     +......++.....       ......+++++||+++...... ..+...+++++||||||++.+.+
T Consensus        82 v~~l~~~g-----i~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~-~~l~~~~l~~iVIDEaH~i~~~G  155 (607)
T PRK11057         82 VDQLLANG-----VAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFL-EHLAHWNPALLAVDEAHCISQWG  155 (607)
T ss_pred             HHHHHHcC-----CcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHH-HHHhhCCCCEEEEeCcccccccc
Confidence            99888763     44444444432221       1134568999999998742111 22334578999999999987531


Q ss_pred             -CchHHHH---HHHHhCCCCCcEEEEEeeCChhHHHHHHhh--CCCCeEEecccccccccceeEEEEEeCChhhHHHHHH
Q psy11867        263 -GHQDFSI---RIQKRLPSDCQIMLFSATYDKEVMEFAQDM--VPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS  336 (399)
Q Consensus       263 -~~~~~~~---~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~--~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  336 (399)
                       .|...+.   .+...+ ++.+++++|||.+..+...+...  +.+|.......   ...++.  |..+.. ..+...+.
T Consensus       156 ~~fr~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~~~~---~r~nl~--~~v~~~-~~~~~~l~  228 (607)
T PRK11057        156 HDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSF---DRPNIR--YTLVEK-FKPLDQLM  228 (607)
T ss_pred             CcccHHHHHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEEECCC---CCCcce--eeeeec-cchHHHHH
Confidence             2443333   333333 57899999999998876544433  34555433221   123332  222222 33456677


Q ss_pred             HHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       337 ~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .++......++||||+++++|+.++..|...|+.+..+||+|++++|..+++.|+.|+++|||
T Consensus       229 ~~l~~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLV  291 (607)
T PRK11057        229 RYVQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVV  291 (607)
T ss_pred             HHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEE
Confidence            777777778999999999999999999999999999999999999999999999999999986

>PRK10689 transcription-repair coupling factor; Provisional

Probab=100.00  E-value=5.3e-33  Score=296.29  Aligned_cols=265  Identities=16%  Similarity=0.155  Sum_probs=205.8

Q ss_pred             HHHHHHHHcCCCCChHHHHHHhhhhhcC----CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHH
Q psy11867        113 ELLKGVYEMGFYAPSKIQETALPTLLAD----PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQ  188 (399)
Q Consensus       113 ~l~~~l~~~g~~~p~~iQ~~ai~~ll~~----~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q  188 (399)
                      ...+...+++| .||++|.+||+.++++    .++|++++|+||+|||.+|+.+++..+.   .+.+++||+||++||.|
T Consensus       589 ~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~---~g~qvlvLvPT~eLA~Q  664 (1147)
T PRK10689        589 QYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE---NHKQVAVLVPTTLLAQQ  664 (1147)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH---cCCeEEEEeCcHHHHHH
Confidence            33444556777 7999999999999884    2489999999999999999988877664   45789999999999999


Q ss_pred             HHHHHHHHhccCCCcEEEEEEcCchhhhhh-------ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc
Q psy11867        189 IGEVVAKMGKHITDLSVRYAVRGENLERNK-------KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT  261 (399)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~  261 (399)
                      +++.+++.+..+ .+++....++.......       .+.++|+|+||+.+.      ..+.+++++++||||+|++.  
T Consensus       665 ~~~~f~~~~~~~-~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~------~~v~~~~L~lLVIDEahrfG--  735 (1147)
T PRK10689        665 HYDNFRDRFANW-PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQ------SDVKWKDLGLLIVDEEHRFG--  735 (1147)
T ss_pred             HHHHHHHhhccC-CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHh------CCCCHhhCCEEEEechhhcc--
Confidence            999999876655 56666666665432221       246899999997431      34567899999999999973  


Q ss_pred             CCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhcc
Q psy11867        262 QGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGV  341 (399)
Q Consensus       262 ~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~  341 (399)
                        +..  ...++.++.++|+++||||..+....++...+.++..+.......  ..+++.+..+.....+...+.++.+ 
T Consensus       736 --~~~--~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~r--~~v~~~~~~~~~~~~k~~il~el~r-  808 (1147)
T PRK10689        736 --VRH--KERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARR--LAVKTFVREYDSLVVREAILREILR-  808 (1147)
T ss_pred             --hhH--HHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCCC--CCceEEEEecCcHHHHHHHHHHHhc-
Confidence              221  234566788999999999988888888888888998887654332  2355555444333334444445543 


Q ss_pred             CCCCcEEEEecchHhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        342 VTIGQAMIFCHTRKTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       342 ~~~~k~IIF~~s~~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                        .++++||||+++.++.+++.|.+.  +.++..+||+|++.+|.+++++|++|+++|||
T Consensus       809 --~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLV  866 (1147)
T PRK10689        809 --GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLV  866 (1147)
T ss_pred             --CCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEE
Confidence              479999999999999999999987  78999999999999999999999999999997

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=4.4e-33  Score=284.51  Aligned_cols=262  Identities=14%  Similarity=0.189  Sum_probs=197.2

Q ss_pred             HHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        117 GVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       117 ~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      .|++ +||..|+|+|.++++.+++  |+|+++++|||+|||++|++|++..      ...++||+|+++|+.|+.+.++.
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~--g~dvlv~~PTG~GKTl~y~lpal~~------~g~~lVisPl~sL~~dq~~~l~~   75 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLD--GRDVLVVMPTGGGKSLCYQVPALLL------KGLTVVISPLISLMKDQVDQLRA   75 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHc--CCCEEEEcCCCccHhHHHHHHHHHc------CCcEEEEcCCHHHHHHHHHHHHH
Confidence            3444 7999999999999999998  6999999999999999999999842      34589999999999999999988


Q ss_pred             HhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC-CchHH
Q psy11867        196 MGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ-GHQDF  267 (399)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~-~~~~~  267 (399)
                      +     ++.+....++......       ..+..+|+++||+++...... ..+...++++|||||||++.+.+ .|...
T Consensus        76 ~-----gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~-~~l~~~~l~~iViDEaH~i~~~g~~frp~  149 (591)
T TIGR01389        76 A-----GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFL-NMLQRIPIALVAVDEAHCVSQWGHDFRPE  149 (591)
T ss_pred             c-----CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHH-HHHhcCCCCEEEEeCCcccccccCccHHH
Confidence            6     3445555555433221       135678999999998643221 23456789999999999987531 24444


Q ss_pred             HHH---HHHhCCCCCcEEEEEeeCChhHHHHHHhhCC--CCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccC
Q psy11867        268 SIR---IQKRLPSDCQIMLFSATYDKEVMEFAQDMVP--NPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVV  342 (399)
Q Consensus       268 ~~~---i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~--~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~  342 (399)
                      +..   +...++ ..+++++|||.+..+...+...+.  ++..+...   ....++.  |..... ..+...+..++...
T Consensus       150 y~~l~~l~~~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~~---~~r~nl~--~~v~~~-~~~~~~l~~~l~~~  222 (591)
T TIGR01389       150 YQRLGSLAERFP-QVPRIALTATADAETRQDIRELLRLADANEFITS---FDRPNLR--FSVVKK-NNKQKFLLDYLKKH  222 (591)
T ss_pred             HHHHHHHHHhCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEecC---CCCCCcE--EEEEeC-CCHHHHHHHHHHhc
Confidence            333   334444 455999999999988776666553  44433211   1122332  222222 34666777777776


Q ss_pred             CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...++||||++++.|+.+++.|...|+.+..+||+|+.++|..+++.|++|+++|||
T Consensus       223 ~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlV  279 (591)
T TIGR01389       223 RGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMV  279 (591)
T ss_pred             CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEE
Confidence            678999999999999999999999999999999999999999999999999999986

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.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=100.00  E-value=1.6e-32  Score=286.80  Aligned_cols=268  Identities=18%  Similarity=0.191  Sum_probs=202.0

Q ss_pred             CCHHHHHHHHH-cCCCCChHHHHHHhhhhhcC----CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        110 LKPELLKGVYE-MGFYAPSKIQETALPTLLAD----PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       110 l~~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~----~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      ....+.+.+.+ ++| .||++|.+||+.++++    .++|++++|+||||||.+|++|++..+..   +.+++||+||++
T Consensus       436 ~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~---g~qvlvLvPT~~  511 (926)
T TIGR00580       436 PDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD---GKQVAVLVPTTL  511 (926)
T ss_pred             CCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh---CCeEEEEeCcHH
Confidence            34555666655 577 5999999999999874    24799999999999999999999988764   468999999999


Q ss_pred             HHHHHHHHHHHHhccCCCcEEEEEEcCchhhh-------hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        185 LAIQIGEVVAKMGKHITDLSVRYAVRGENLER-------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       185 La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      ||.|+++.++++...+ ++++....++.....       ...+.++||||||. ++.     +.+.+++++++||||+|+
T Consensus       512 LA~Q~~~~f~~~~~~~-~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~-ll~-----~~v~f~~L~llVIDEahr  584 (926)
T TIGR00580       512 LAQQHFETFKERFANF-PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHK-LLQ-----KDVKFKDLGLLIIDEEQR  584 (926)
T ss_pred             HHHHHHHHHHHHhccC-CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHH-Hhh-----CCCCcccCCEEEeecccc
Confidence            9999999999987765 566666666543211       11346899999994 322     345688999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHH
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSN  337 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~  337 (399)
                      +..      .....++.++.++|+++||||..+....+......++..+.......  ..+..++..... ......+..
T Consensus       585 fgv------~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~R--~~V~t~v~~~~~-~~i~~~i~~  655 (926)
T TIGR00580       585 FGV------KQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDR--LPVRTFVMEYDP-ELVREAIRR  655 (926)
T ss_pred             cch------hHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCCc--cceEEEEEecCH-HHHHHHHHH
Confidence            632      12234556677899999999987776666666667877776554332  234444443322 111222222


Q ss_pred             HhccCCCCcEEEEecchHhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        338 IYGVVTIGQAMIFCHTRKTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       338 ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      -+.  ..++++|||++++.++.+++.|.+.  +.++..+||+|++.+|..++++|++|+++|||
T Consensus       656 el~--~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILV  717 (926)
T TIGR00580       656 ELL--RGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLV  717 (926)
T ss_pred             HHH--cCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEE
Confidence            222  3479999999999999999999885  78999999999999999999999999999997

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.

>TIGR01054 rgy reverse gyrase

Probab=100.00  E-value=1.3e-32  Score=294.25  Aligned_cols=266  Identities=17%  Similarity=0.181  Sum_probs=199.8

Q ss_pred             HHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHH
Q psy11867        113 ELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEV  192 (399)
Q Consensus       113 ~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~  192 (399)
                      .+.+.+.+.....|+++|..++|.++.  |+|++++||||||||+ |.+|++..+..  .++++|||+||++||.|+++.
T Consensus        66 ~f~~~f~~~~g~~p~~iQ~~~i~~il~--G~d~vi~ApTGsGKT~-f~l~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~  140 (1171)
T TIGR01054        66 EFEEFFKKAVGSEPWSIQKMWAKRVLR--GDSFAIIAPTGVGKTT-FGLAMSLFLAK--KGKRCYIILPTTLLVIQVAEK  140 (1171)
T ss_pred             HHHHHHHHhcCCCCcHHHHHHHHHHhC--CCeEEEECCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeCHHHHHHHHHHH
Confidence            344555554555899999999999998  7999999999999996 66777665543  367899999999999999999


Q ss_pred             HHHHhccCCCcEE---EEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc-
Q psy11867        193 VAKMGKHITDLSV---RYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT-  261 (399)
Q Consensus       193 ~~~~~~~~~~~~~---~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~-  261 (399)
                      ++.++... ++..   ....|+......       ..+.++|+|+||++|.+++...   .. +++++|+||||+|++. 
T Consensus       141 l~~l~~~~-~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l---~~-~~~~iVvDEaD~~L~~~  215 (1171)
T TIGR01054       141 ISSLAEKA-GVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDEL---GP-KFDFIFVDDVDALLKAS  215 (1171)
T ss_pred             HHHHHHhc-CCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHh---cC-CCCEEEEeChHhhhhcc
Confidence            99998764 3332   234566544321       1345899999999998875432   12 8999999999999872 


Q ss_pred             ---------CCchHH-HHHHH----------------------HhCCCCCc--EEEEEee-CChhHHHHHHhhCCCCeEE
Q psy11867        262 ---------QGHQDF-SIRIQ----------------------KRLPSDCQ--IMLFSAT-YDKEVMEFAQDMVPNPLII  306 (399)
Q Consensus       262 ---------~~~~~~-~~~i~----------------------~~l~~~~q--~l~~SAT-~~~~v~~~~~~~~~~p~~i  306 (399)
                               .||.+. +..++                      +.++..+|  +++|||| .|..+..   .+++++..+
T Consensus       216 k~vd~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~r~ll~~  292 (1171)
T TIGR01054       216 KNVDKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLFRELLGF  292 (1171)
T ss_pred             ccHHHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHcccccce
Confidence                     256543 33332                      23445555  5679999 5655432   345566677


Q ss_pred             ecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecch---HhHHHHHHHHHHCCCeEEEEcCCCCHHHH
Q psy11867        307 KLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTR---KTAAWLAEKMSKEGLNVGLLSGELTVEQR  383 (399)
Q Consensus       307 ~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~---~~a~~l~~~L~~~g~~v~~lhg~~~~~~R  383 (399)
                      .++.......++.+.|+.+..   +...+..+++.. ..++||||+++   +.|+.|++.|.+.|+++..+||+|++   
T Consensus       293 ~v~~~~~~~r~I~~~~~~~~~---~~~~L~~ll~~l-~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~---  365 (1171)
T TIGR01054       293 EVGGGSDTLRNVVDVYVEDED---LKETLLEIVKKL-GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK---  365 (1171)
T ss_pred             EecCccccccceEEEEEeccc---HHHHHHHHHHHc-CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH---
Confidence            777777778899999886643   234566666554 36899999999   99999999999999999999999973   


Q ss_pred             HHHHHHHhcCCCcccC
Q psy11867        384 LSILDRFREGEFKIYS  399 (399)
Q Consensus       384 ~~v~~~F~~G~~~ILV  399 (399)
                       .+++.|++|+++|||
T Consensus       366 -~~l~~Fr~G~~~vLV  380 (1171)
T TIGR01054       366 -EDYEKFAEGEIDVLI  380 (1171)
T ss_pred             -HHHHHHHcCCCCEEE
Confidence             689999999999997

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.

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=1.3e-32  Score=299.78  Aligned_cols=269  Identities=18%  Similarity=0.172  Sum_probs=205.9

Q ss_pred             HHHHHHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH
Q psy11867        112 PELLKGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG  190 (399)
Q Consensus       112 ~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~  190 (399)
                      ..+.+.+++ .|| .|+++|..++|.+++  |+|++++||||||||++++++++....   .+.++|||+||++|+.|++
T Consensus        66 ~~~~~~f~~~~G~-~pt~iQ~~~i~~il~--G~d~li~APTGsGKTl~~~~~al~~~~---~g~~aLVl~PTreLa~Qi~  139 (1638)
T PRK14701         66 EEFEEFFEKITGF-EFWSIQKTWAKRILR--GKSFSIVAPTGMGKSTFGAFIALFLAL---KGKKCYIILPTTLLVKQTV  139 (1638)
T ss_pred             HHHHHHHHHhhCC-CCCHHHHHHHHHHHc--CCCEEEEEcCCCCHHHHHHHHHHHHHh---cCCeEEEEECHHHHHHHHH
Confidence            445556665 799 699999999999999  799999999999999976666654432   4568999999999999999


Q ss_pred             HHHHHHhccCC-CcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc-
Q psy11867        191 EVVAKMGKHIT-DLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT-  261 (399)
Q Consensus       191 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~-  261 (399)
                      +.++.++..+. ++.+....|+......       ..+.++|+|+||++|.+++...   ...+++++|+||||+|+.. 
T Consensus       140 ~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l---~~~~i~~iVVDEAD~ml~~~  216 (1638)
T PRK14701        140 EKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM---KHLKFDFIFVDDVDAFLKAS  216 (1638)
T ss_pred             HHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH---hhCCCCEEEEECceeccccc
Confidence            99999987652 3556666777654332       1345899999999998865431   1267999999999999751 


Q ss_pred             ---------CCchHHHHH----HHH----------------------hCCCCCc-EEEEEeeCChhHHHHHHhhCCCCeE
Q psy11867        262 ---------QGHQDFSIR----IQK----------------------RLPSDCQ-IMLFSATYDKEVMEFAQDMVPNPLI  305 (399)
Q Consensus       262 ---------~~~~~~~~~----i~~----------------------~l~~~~q-~l~~SAT~~~~v~~~~~~~~~~p~~  305 (399)
                               .||...+..    +++                      .+++..| ++++|||++...  .....++++..
T Consensus       217 knid~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~--~~~~l~~~~l~  294 (1638)
T PRK14701        217 KNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKG--DRVKLYRELLG  294 (1638)
T ss_pred             cccchhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchh--HHHHHhhcCeE
Confidence                     266665543    321                      2344556 678999998631  11233467788


Q ss_pred             EecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHh---HHHHHHHHHHCCCeEEEEcCCCCHHH
Q psy11867        306 IKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKT---AAWLAEKMSKEGLNVGLLSGELTVEQ  382 (399)
Q Consensus       306 i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~---a~~l~~~L~~~g~~v~~lhg~~~~~~  382 (399)
                      +.++.......++.+.|+.+.. ..+ ..+..+++.. ..++||||++++.   |+.+++.|...|+++..+||+     
T Consensus       295 f~v~~~~~~lr~i~~~yi~~~~-~~k-~~L~~ll~~~-g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----  366 (1638)
T PRK14701        295 FEVGSGRSALRNIVDVYLNPEK-IIK-EHVRELLKKL-GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----  366 (1638)
T ss_pred             EEecCCCCCCCCcEEEEEECCH-HHH-HHHHHHHHhC-CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----
Confidence            8888777788899999987653 334 5677777665 4689999999875   589999999999999999995     


Q ss_pred             HHHHHHHHhcCCCcccC
Q psy11867        383 RLSILDRFREGEFKIYS  399 (399)
Q Consensus       383 R~~v~~~F~~G~~~ILV  399 (399)
                      |..++++|++|+++|||
T Consensus       367 R~~~l~~F~~G~~~VLV  383 (1638)
T PRK14701        367 NKKGFDLFEEGEIDYLI  383 (1638)
T ss_pred             HHHHHHHHHcCCCCEEE
Confidence            89999999999999997

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=100.00  E-value=4e-31  Score=272.44  Aligned_cols=267  Identities=21%  Similarity=0.259  Sum_probs=192.8

Q ss_pred             HHHHHHHHH-cCCCCChHHHHHHhhhhhcCC----CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH
Q psy11867        112 PELLKGVYE-MGFYAPSKIQETALPTLLADP----PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA  186 (399)
Q Consensus       112 ~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~~----g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La  186 (399)
                      ..+.+.+.+ ++| .||++|.+|++.+.++.    ..|++++|+||||||++|++|++..+..   +.+++|++||++||
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~---g~q~lilaPT~~LA  323 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA---GYQAALMAPTEILA  323 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEeccHHHH
Confidence            445555544 566 79999999999998751    3589999999999999999999988753   56899999999999


Q ss_pred             HHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        187 IQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       187 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      .|+++.+++++..+ ++++....|+......       ..+.++|+||||+.+.+      ...+++++++|+||+|++.
T Consensus       324 ~Q~~~~l~~l~~~~-~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~------~v~~~~l~lvVIDE~Hrfg  396 (681)
T PRK10917        324 EQHYENLKKLLEPL-GIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD------DVEFHNLGLVIIDEQHRFG  396 (681)
T ss_pred             HHHHHHHHHHHhhc-CcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc------cchhcccceEEEechhhhh
Confidence            99999999998776 6888888888764221       13468999999987643      3457899999999999974


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHh
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIY  339 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll  339 (399)
                      ..     .. ..+.......++++||||..+....+......+...+....  .....+...+......+..+..+...+
T Consensus       397 ~~-----qr-~~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~~p--~~r~~i~~~~~~~~~~~~~~~~i~~~~  468 (681)
T PRK10917        397 VE-----QR-LALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELP--PGRKPITTVVIPDSRRDEVYERIREEI  468 (681)
T ss_pred             HH-----HH-HHHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCceEEEecCC--CCCCCcEEEEeCcccHHHHHHHHHHHH
Confidence            32     11 22233355789999999976654444332222333332211  112335555544333233334444333


Q ss_pred             ccCCCCcEEEEecch--------HhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        340 GVVTIGQAMIFCHTR--------KTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       340 ~~~~~~k~IIF~~s~--------~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                        ....+++|||+..        ..++.+++.|.+.  ++++..+||+|++.+|..++++|++|+++|||
T Consensus       469 --~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILV  536 (681)
T PRK10917        469 --AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILV  536 (681)
T ss_pred             --HcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEE
Confidence              2346999999954        4567788888765  57899999999999999999999999999997

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

Probab=100.00  E-value=2.2e-31  Score=252.44  Aligned_cols=284  Identities=21%  Similarity=0.252  Sum_probs=230.9

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      ..+++.+++.+.+-|+..|+..+.|+|..|+..-|-. |.|.++.++|+||||+..-++-+..+..  .+.+.|+|+|..
T Consensus       195 ~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLe-G~nllVVSaTasGKTLIgElAGi~~~l~--~g~KmlfLvPLV  271 (830)
T COG1202         195 PVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLE-GENLLVVSATASGKTLIGELAGIPRLLS--GGKKMLFLVPLV  271 (830)
T ss_pred             cccccCCcHHHHHHHHhcCcceecchhhhhhhhcccc-CCceEEEeccCCCcchHHHhhCcHHHHh--CCCeEEEEehhH
Confidence            4578899999999999999999999999999987766 9999999999999999999988888765  355699999999


Q ss_pred             HHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechh
Q psy11867        184 ELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD  256 (399)
Q Consensus       184 ~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah  256 (399)
                      +||+|-|+.|+.-...+ ++.+..-+|-..+...       .....+|||+|.+-+-.++ +.+ -++.++..+||||+|
T Consensus       272 ALANQKy~dF~~rYs~L-glkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lL-Rtg-~~lgdiGtVVIDEiH  348 (830)
T COG1202         272 ALANQKYEDFKERYSKL-GLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLL-RTG-KDLGDIGTVVIDEIH  348 (830)
T ss_pred             HhhcchHHHHHHHhhcc-cceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHH-HcC-CcccccceEEeeeee
Confidence            99999999999877766 6777666665444222       1345689999999876554 433 578999999999999


Q ss_pred             hHhhc-CC-chHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHH
Q psy11867        257 VMIAT-QG-HQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEA  334 (399)
Q Consensus       257 ~l~~~-~~-~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~  334 (399)
                      .+-+. .| ..+-++.-++.+-+..|++.+|||..+. ..+++.+-..++...     .-+-.+..+.++|.+..+|.+.
T Consensus       349 tL~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp-~elA~~l~a~lV~y~-----~RPVplErHlvf~~~e~eK~~i  422 (830)
T COG1202         349 TLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNP-EELAKKLGAKLVLYD-----ERPVPLERHLVFARNESEKWDI  422 (830)
T ss_pred             eccchhcccchhhHHHHHHHhCCCCeEEEEEeecCCh-HHHHHHhCCeeEeec-----CCCCChhHeeeeecCchHHHHH
Confidence            98753 22 2333444455666799999999999876 567777655554432     2334567788899988899888


Q ss_pred             HHHHhccC--------CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        335 VSNIYGVV--------TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       335 l~~ll~~~--------~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +..+.+..        ..|+||||.+|++.|+.||..|...|+++..||+||+..+|..+...|.+|++.++|
T Consensus       423 i~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VV  495 (830)
T COG1202         423 IARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVV  495 (830)
T ss_pred             HHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEe
Confidence            88876542        347999999999999999999999999999999999999999999999999998876

>cd00268 DEADc DEAD-box helicases

Probab=99.98  E-value=4e-31  Score=234.57  Aligned_cols=197  Identities=47%  Similarity=0.728  Sum_probs=172.6

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC--CCCCeEEEEeCc
Q psy11867        105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS--IQEPQVLCLAPT  182 (399)
Q Consensus       105 f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~--~~~~~~lil~Pt  182 (399)
                      |+++++++.+.+.+.++|+..|+++|.++++.+++  |+|+++++|||+|||++|++|++..+...  ..+++++|++||
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~--~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~   78 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLS--GRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPT   78 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhc--CCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCC
Confidence            67889999999999999999999999999999998  79999999999999999999999998776  467899999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      ++|+.|+.+.++.+.... ++.+....|+.......   ...++|+|+||+++.+++.+. .+.+++++++|+||+|.+.
T Consensus        79 ~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~-~~~~~~l~~lIvDE~h~~~  156 (203)
T cd00268          79 RELALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERG-KLDLSKVKYLVLDEADRML  156 (203)
T ss_pred             HHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcC-CCChhhCCEEEEeChHHhh
Confidence            999999999999987664 67777777776543322   346789999999998886544 4778899999999999998


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEE
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII  306 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i  306 (399)
                      + .++...+..+...++..+|++++|||+++.+..++..++.+|+.+
T Consensus       157 ~-~~~~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         157 D-MGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             c-cChHHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            5 367888888888998899999999999999999999999998876

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.

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.97  E-value=6e-31  Score=269.87  Aligned_cols=282  Identities=20%  Similarity=0.222  Sum_probs=206.7

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      +.+.+.+-+...|+.++.+-|+.++...+-+ ++|+++++|||||||+.+++.+++.+...  +.+++||||+++||.+.
T Consensus        16 ~~~~v~~i~~~~~~~el~~~qq~av~~~~~~-~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~Ek   92 (766)
T COG1204          16 LDDRVLEILKGDGIDELFNPQQEAVEKGLLS-DENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAEEK   92 (766)
T ss_pred             ccHHHHHHhccCChHHhhHHHHHHhhccccC-CCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHHHH
Confidence            6677777777788888888888888777766 89999999999999999999999999874  56799999999999999


Q ss_pred             HHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc-CC-chHH
Q psy11867        190 GEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT-QG-HQDF  267 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~-~~-~~~~  267 (399)
                      ++.++++-..  ++++...+|+..........++|+|+||+++-....+. ..++..+++||+||+|.+.+. +| ....
T Consensus        93 ~~~~~~~~~~--GirV~~~TgD~~~~~~~l~~~~ViVtT~EK~Dsl~R~~-~~~~~~V~lvViDEiH~l~d~~RG~~lE~  169 (766)
T COG1204          93 YEEFSRLEEL--GIRVGISTGDYDLDDERLARYDVIVTTPEKLDSLTRKR-PSWIEEVDLVVIDEIHLLGDRTRGPVLES  169 (766)
T ss_pred             HHHhhhHHhc--CCEEEEecCCcccchhhhccCCEEEEchHHhhHhhhcC-cchhhcccEEEEeeeeecCCcccCceehh
Confidence            9999955433  89999999998877777788899999999998876554 347889999999999999765 33 2233


Q ss_pred             HHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc--cccccccceeEEEEEeCChh------hHHHHHHHHh
Q psy11867        268 SIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK--REEESLDNIKQHYVMCKNID------EKFEAVSNIY  339 (399)
Q Consensus       268 ~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~--~~~~~~~~i~~~~~~~~~~~------~k~~~l~~ll  339 (399)
                      +..-...+...+|++++|||+|+. .+++...-.++..-...  ....... ..+.+.......      .....+...+
T Consensus       170 iv~r~~~~~~~~rivgLSATlpN~-~evA~wL~a~~~~~~~rp~~l~~~v~-~~~~~~~~~~~~k~~~~~~~~~~~~~v~  247 (766)
T COG1204         170 IVARMRRLNELIRIVGLSATLPNA-EEVADWLNAKLVESDWRPVPLRRGVP-YVGAFLGADGKKKTWPLLIDNLALELVL  247 (766)
T ss_pred             HHHHHHhhCcceEEEEEeeecCCH-HHHHHHhCCcccccCCCCcccccCCc-cceEEEEecCccccccccchHHHHHHHH
Confidence            333334444558999999999964 45555444343311111  1111111 122222222111      1122333333


Q ss_pred             ccC-CCCcEEEEecchHhHHHHHHHHHHC-------------------------------------CCeEEEEcCCCCHH
Q psy11867        340 GVV-TIGQAMIFCHTRKTAAWLAEKMSKE-------------------------------------GLNVGLLSGELTVE  381 (399)
Q Consensus       340 ~~~-~~~k~IIF~~s~~~a~~l~~~L~~~-------------------------------------g~~v~~lhg~~~~~  381 (399)
                      ... ..+++||||+|++.+...|+.++..                                     -..++.+|+||+.+
T Consensus       248 ~~~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~  327 (766)
T COG1204         248 ESLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPRE  327 (766)
T ss_pred             HHHhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHH
Confidence            333 3479999999999999999998830                                     12478999999999


Q ss_pred             HHHHHHHHHhcCCCcccC
Q psy11867        382 QRLSILDRFREGEFKIYS  399 (399)
Q Consensus       382 ~R~~v~~~F~~G~~~ILV  399 (399)
                      +|..+.+.|+.|+++|||
T Consensus       328 ~R~~vE~~Fr~g~ikVlv  345 (766)
T COG1204         328 DRQLVEDAFRKGKIKVLV  345 (766)
T ss_pred             HHHHHHHHHhcCCceEEE
Confidence            999999999999999996

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.97  E-value=4.5e-30  Score=262.98  Aligned_cols=265  Identities=22%  Similarity=0.255  Sum_probs=186.8

Q ss_pred             HHHHHHHcCCCCChHHHHHHhhhhhcC----CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        114 LLKGVYEMGFYAPSKIQETALPTLLAD----PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       114 l~~~l~~~g~~~p~~iQ~~ai~~ll~~----~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      +.+.+...+| .||++|.+|++.++++    .+.+.+++|+||||||++|++|++..+..   +.+++|++||++||.|+
T Consensus       225 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~---g~qvlilaPT~~LA~Q~  300 (630)
T TIGR00643       225 LTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA---GYQVALMAPTEILAEQH  300 (630)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc---CCcEEEECCHHHHHHHH
Confidence            3445566788 7999999999999874    13578999999999999999999988764   56799999999999999


Q ss_pred             HHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC
Q psy11867        190 GEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ  262 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~  262 (399)
                      ++.+++++..+ ++++....|+......       ..+..+|+|+||+.+.+      .+.+++++++|+||+|++... 
T Consensus       301 ~~~~~~l~~~~-gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~------~~~~~~l~lvVIDEaH~fg~~-  372 (630)
T TIGR00643       301 YNSLRNLLAPL-GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE------KVEFKRLALVIIDEQHRFGVE-  372 (630)
T ss_pred             HHHHHHHhccc-CcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc------cccccccceEEEechhhccHH-
Confidence            99999998765 6888888888654321       13467999999997753      345789999999999997421 


Q ss_pred             CchHHHHHHHHhCC--CCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhc
Q psy11867        263 GHQDFSIRIQKRLP--SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG  340 (399)
Q Consensus       263 ~~~~~~~~i~~~l~--~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~  340 (399)
                          ....+.....  ..+++++||||..+....+......+...+....  .....+...+....   .+...+..+..
T Consensus       373 ----qr~~l~~~~~~~~~~~~l~~SATp~prtl~l~~~~~l~~~~i~~~p--~~r~~i~~~~~~~~---~~~~~~~~i~~  443 (630)
T TIGR00643       373 ----QRKKLREKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELP--PGRKPITTVLIKHD---EKDIVYEFIEE  443 (630)
T ss_pred             ----HHHHHHHhcccCCCCCEEEEeCCCCcHHHHHHhcCCcceeeeccCC--CCCCceEEEEeCcc---hHHHHHHHHHH
Confidence                2222333332  2689999999975543333221111222221111  11123444333222   22222222222


Q ss_pred             c-CCCCcEEEEecch--------HhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        341 V-VTIGQAMIFCHTR--------KTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       341 ~-~~~~k~IIF~~s~--------~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      . ....+++|||+..        +.++.+++.|...  +++|..+||+|++.+|..++++|++|+.+|||
T Consensus       444 ~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILV  513 (630)
T TIGR00643       444 EIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILV  513 (630)
T ss_pred             HHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEE
Confidence            2 2346899999876        4577788888764  78899999999999999999999999999997

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.97  E-value=1.5e-30  Score=279.33  Aligned_cols=250  Identities=18%  Similarity=0.180  Sum_probs=174.8

Q ss_pred             EEccCCCCceehhHHHHHHhhCCC----------CCCCeEEEEeCcHHHHHHHHHHHHHHh-----------ccCCCcEE
Q psy11867        147 AQSQSGTGKTAAFTLTMLSRVNPS----------IQEPQVLCLAPTYELAIQIGEVVAKMG-----------KHITDLSV  205 (399)
Q Consensus       147 ~~a~TGsGKT~~~~l~il~~l~~~----------~~~~~~lil~Pt~~La~Q~~~~~~~~~-----------~~~~~~~~  205 (399)
                      ++||||||||++|++|++..+...          ..+.++|||+|+++|+.|+++.++...           ....++++
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            479999999999999999988532          235789999999999999999887522           12236778


Q ss_pred             EEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC-C--chHHHHHHHHhCCCCC
Q psy11867        206 RYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ-G--HQDFSIRIQKRLPSDC  279 (399)
Q Consensus       206 ~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~-~--~~~~~~~i~~~l~~~~  279 (399)
                      ....|+.......   +..++|+|+||++|..++.+.....++++++|||||+|.|.+.. |  +...+.++...++.+.
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            8888887664432   45789999999999887654333468999999999999998642 2  2345566777777889


Q ss_pred             cEEEEEeeCChhHHHHHHhhCC-CCeEEecccccccccceeEEEEEeCChh-------------------h-HHHHHHHH
Q psy11867        280 QIMLFSATYDKEVMEFAQDMVP-NPLIIKLKREEESLDNIKQHYVMCKNID-------------------E-KFEAVSNI  338 (399)
Q Consensus       280 q~l~~SAT~~~~v~~~~~~~~~-~p~~i~~~~~~~~~~~i~~~~~~~~~~~-------------------~-k~~~l~~l  338 (399)
                      |+|++|||+++. .++++.+.. .|+.+....... ...+. .++......                   . .......+
T Consensus       161 QrIgLSATI~n~-eevA~~L~g~~pv~Iv~~~~~r-~~~l~-v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~i  237 (1490)
T PRK09751        161 QRIGLSATVRSA-SDVAAFLGGDRPVTVVNPPAMR-HPQIR-IVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETGI  237 (1490)
T ss_pred             eEEEEEeeCCCH-HHHHHHhcCCCCEEEECCCCCc-ccceE-EEEecCchhhccccccccccccchhhhhhhhHHHHHHH
Confidence            999999999873 555544332 355543221111 11222 122111100                   0 00011122


Q ss_pred             hcc-CCCCcEEEEecchHhHHHHHHHHHHCC---------------------------------CeEEEEcCCCCHHHHH
Q psy11867        339 YGV-VTIGQAMIFCHTRKTAAWLAEKMSKEG---------------------------------LNVGLLSGELTVEQRL  384 (399)
Q Consensus       339 l~~-~~~~k~IIF~~s~~~a~~l~~~L~~~g---------------------------------~~v~~lhg~~~~~~R~  384 (399)
                      +.. ....++||||||++.|+.++..|.+..                                 +.+..+||+|++++|.
T Consensus       238 l~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~  317 (1490)
T PRK09751        238 LDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRA  317 (1490)
T ss_pred             HHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHH
Confidence            222 234789999999999999999987641                                 1267899999999999


Q ss_pred             HHHHHHhcCCCcccC
Q psy11867        385 SILDRFREGEFKIYS  399 (399)
Q Consensus       385 ~v~~~F~~G~~~ILV  399 (399)
                      .+++.|++|++++||
T Consensus       318 ~IE~~fK~G~LrvLV  332 (1490)
T PRK09751        318 ITEQALKSGELRCVV  332 (1490)
T ss_pred             HHHHHHHhCCceEEE
Confidence            999999999999986

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

Probab=99.97  E-value=1.7e-29  Score=262.51  Aligned_cols=283  Identities=20%  Similarity=0.221  Sum_probs=212.5

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      ....+..++.+.|+..|+++|.+|+..+.+  |+|++++++||||||.+|++||++.+..... .++|+|.||++||+.+
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~--G~~vvVtTgTgSGKTe~FllPIld~~l~~~~-a~AL~lYPtnALa~DQ  131 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIRE--GRNVVVTTGTGSGKTESFLLPILDHLLRDPS-ARALLLYPTNALANDQ  131 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHC--CCCEEEECCCCCchhHHHHHHHHHHHhhCcC-ccEEEEechhhhHhhH
Confidence            345568888899999999999999999999  7999999999999999999999999987643 4899999999999999


Q ss_pred             HHHHHHHhccCC-CcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccc---cCCceeEEEEechhhHhhcC
Q psy11867        190 GEVVAKMGKHIT-DLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFF---DLSKIKVFVLDEADVMIATQ  262 (399)
Q Consensus       190 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~---~~~~~~~lViDEah~l~~~~  262 (399)
                      .+.++++...++ .+......|...-.+.   ....++|+++||.+|..++......   .++++++||+||+|.+-.  
T Consensus       132 ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrG--  209 (851)
T COG1205         132 AERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRG--  209 (851)
T ss_pred             HHHHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccc--
Confidence            999999998876 4555566666554444   3778999999999998865554433   367899999999999854  


Q ss_pred             CchHHHHHHHHh-------CCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCC--------
Q psy11867        263 GHQDFSIRIQKR-------LPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKN--------  327 (399)
Q Consensus       263 ~~~~~~~~i~~~-------l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~--------  327 (399)
                      .+...+..++++       .+.+.|+|+.|||+.+. ..++..+........ ..........+..+...+.        
T Consensus       210 v~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~-v~~~g~~~~~~~~~~~~p~~~~~~~~~  287 (851)
T COG1205         210 VQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVP-VDEDGSPRGLRYFVRREPPIRELAESI  287 (851)
T ss_pred             cchhHHHHHHHHHHHHHhccCCCceEEEEeccccCh-HHHHHHhcCCcceee-ccCCCCCCCceEEEEeCCcchhhhhhc
Confidence            344444433333       35688999999999876 445555555444433 2333344444444444430        


Q ss_pred             hhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHH----HHHHHCC----CeEEEEcCCCCHHHHHHHHHHHhcCCCcc
Q psy11867        328 IDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLA----EKMSKEG----LNVGLLSGELTVEQRLSILDRFREGEFKI  397 (399)
Q Consensus       328 ~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~----~~L~~~g----~~v~~lhg~~~~~~R~~v~~~F~~G~~~I  397 (399)
                      ...+...+..+....  ..-++|+||.+++.++.++    ..+...+    ..+..++|+|...+|..++..|++|++.+
T Consensus       288 r~s~~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~  367 (851)
T COG1205         288 RRSALAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLG  367 (851)
T ss_pred             ccchHHHHHHHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccE
Confidence            123344444444332  3458999999999999997    4454555    67999999999999999999999999987


Q ss_pred             cC
Q psy11867        398 YS  399 (399)
Q Consensus       398 LV  399 (399)
                      ++
T Consensus       368 ~~  369 (851)
T COG1205         368 VI  369 (851)
T ss_pred             Ee
Confidence            63

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.97  E-value=4.6e-29  Score=252.82  Aligned_cols=255  Identities=15%  Similarity=0.196  Sum_probs=187.6

Q ss_pred             hHHHHHHhhhhhcCCCCcEEEEccCCCCceeh---------hHHHHHHhhC---CCCCCCeEEEEeCcHHHHHHHHHHHH
Q psy11867        127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAA---------FTLTMLSRVN---PSIQEPQVLCLAPTYELAIQIGEVVA  194 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~---------~~l~il~~l~---~~~~~~~~lil~Pt~~La~Q~~~~~~  194 (399)
                      ..+|.++++.+++  |++++++|+||||||.+         |++|.+..+.   ......+++|++||++||.|+...+.
T Consensus       166 ~~iQ~qil~~i~~--gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~  243 (675)
T PHA02653        166 PDVQLKIFEAWIS--RKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLL  243 (675)
T ss_pred             HHHHHHHHHHHHh--CCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHH
Confidence            3689999999998  79999999999999997         5555665543   23345689999999999999999988


Q ss_pred             HHhcc--CCCcEEEEEEcCchhh--hhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHH
Q psy11867        195 KMGKH--ITDLSVRYAVRGENLE--RNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIR  270 (399)
Q Consensus       195 ~~~~~--~~~~~~~~~~~~~~~~--~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~  270 (399)
                      +....  +.+..+...+||....  .......+|+|+|++..        ...++++++|||||||.+...   .+.+..
T Consensus       244 ~~vg~~~~~g~~v~v~~Gg~~~~~~~t~~k~~~Ilv~T~~L~--------l~~L~~v~~VVIDEaHEr~~~---~DllL~  312 (675)
T PHA02653        244 KSLGFDEIDGSPISLKYGSIPDELINTNPKPYGLVFSTHKLT--------LNKLFDYGTVIIDEVHEHDQI---GDIIIA  312 (675)
T ss_pred             HHhCccccCCceEEEEECCcchHHhhcccCCCCEEEEeCccc--------ccccccCCEEEccccccCccc---hhHHHH
Confidence            76643  3355667778876532  12233668999998621        124778999999999998643   355555


Q ss_pred             HHHhC-CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCC---------hhhHHHHHHHHhc
Q psy11867        271 IQKRL-PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKN---------IDEKFEAVSNIYG  340 (399)
Q Consensus       271 i~~~l-~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~---------~~~k~~~l~~ll~  340 (399)
                      +++.+ +..+|+++||||++.++..+ ..++.+|..+.+.  ..+...+++.|.....         ...+...+..+..
T Consensus       313 llk~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~--grt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~  389 (675)
T PHA02653        313 VARKHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIP--GGTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKK  389 (675)
T ss_pred             HHHHhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeC--CCcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHH
Confidence            55544 34469999999999888776 5788888888765  2344667777764321         1223223333332


Q ss_pred             c--CCCCcEEEEecchHhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHH-hcCCCcccC
Q psy11867        341 V--VTIGQAMIFCHTRKTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRF-REGEFKIYS  399 (399)
Q Consensus       341 ~--~~~~k~IIF~~s~~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F-~~G~~~ILV  399 (399)
                      .  ...+++||||+++++|+.+++.|.+.  ++.+..+||+|++.  ++++++| ++|+.+|||
T Consensus       390 ~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILV  451 (675)
T PHA02653        390 YTPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIII  451 (675)
T ss_pred             hhcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEe
Confidence            2  23468999999999999999999887  78999999999974  5777887 689999986

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.97  E-value=1.7e-28  Score=254.27  Aligned_cols=243  Identities=18%  Similarity=0.246  Sum_probs=182.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      +++++++|+||||||++|.+++++...   .+.+++|+.|||++|.|+++.+.+......+..+.+.+++...   ....
T Consensus        17 ~~~vIi~a~TGSGKTT~vpl~lL~~~~---~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~~~~---~s~~   90 (819)
T TIGR01970        17 HPQVVLEAPPGAGKSTAVPLALLDAPG---IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRGENK---VSRR   90 (819)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhhc---cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEccccc---cCCC
Confidence            689999999999999999999998763   3458999999999999999988644332225566666665432   2234


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechh-hHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhC
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD-VMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah-~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~  300 (399)
                      .+|+|+|||+|++++..  ...++++++|||||+| ++++..........+...++++.|+++||||++...   ...++
T Consensus        91 t~I~v~T~G~Llr~l~~--d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSATl~~~~---l~~~l  165 (819)
T TIGR01970        91 TRLEVVTEGILTRMIQD--DPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSATLDGER---LSSLL  165 (819)
T ss_pred             CcEEEECCcHHHHHHhh--CcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCCCCHHH---HHHHc
Confidence            68999999999998754  3578999999999999 566542223344556667788999999999999764   34566


Q ss_pred             CCCeEEecccccccccceeEEEEEeCChhhH----HHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHH---CCCeEEE
Q psy11867        301 PNPLIIKLKREEESLDNIKQHYVMCKNIDEK----FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSK---EGLNVGL  373 (399)
Q Consensus       301 ~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k----~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~---~g~~v~~  373 (399)
                      .++..+.+...   ...++++|..+...+..    ...+..++.. ..+++||||+++++++.+++.|.+   .++.+..
T Consensus       166 ~~~~vI~~~gr---~~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~p  241 (819)
T TIGR01970       166 PDAPVVESEGR---SFPVEIRYLPLRGDQRLEDAVSRAVEHALAS-ETGSILVFLPGQAEIRRVQEQLAERLDSDVLICP  241 (819)
T ss_pred             CCCcEEEecCc---ceeeeeEEeecchhhhHHHHHHHHHHHHHHh-cCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEE
Confidence            65555544322   22366677655432221    1234444433 357899999999999999999987   4789999


Q ss_pred             EcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        374 LSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       374 lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +||+|++++|.++++.|++|+.+|||
T Consensus       242 LHg~L~~~eq~~~~~~~~~G~rkVlV  267 (819)
T TIGR01970       242 LYGELSLAAQDRAIKPDPQGRRKVVL  267 (819)
T ss_pred             ecCCCCHHHHHHHHhhcccCCeEEEE
Confidence            99999999999999999999999985

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

>KOG0349|consensus

Probab=99.97  E-value=9.4e-30  Score=234.01  Aligned_cols=226  Identities=23%  Similarity=0.365  Sum_probs=174.7

Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc--EEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCc
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDL--SVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSK  246 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~  246 (399)
                      +.|.++|+-|.+||+.|++..+++|..++.+-  +.-+..||.....+   ...+.||+|+||+|+.+.+ ..+...+..
T Consensus       285 Nap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~i-s~g~~~lt~  363 (725)
T KOG0349|consen  285 NAPEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPI-SKGLVTLTH  363 (725)
T ss_pred             CCcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhh-hccceeeee
Confidence            34679999999999999999998887766443  33366676554333   3667899999999999985 446778999


Q ss_pred             eeEEEEechhhHhhcCCchHHHHHHHHhCCC------CCcEEEEEeeCCh-hHHHHHHhhCCCCeEEeccccccccccee
Q psy11867        247 IKVFVLDEADVMIATQGHQDFSIRIQKRLPS------DCQIMLFSATYDK-EVMEFAQDMVPNPLIIKLKREEESLDNIK  319 (399)
Q Consensus       247 ~~~lViDEah~l~~~~~~~~~~~~i~~~l~~------~~q~l~~SAT~~~-~v~~~~~~~~~~p~~i~~~~~~~~~~~i~  319 (399)
                      ++|+|+||||.++. +++.+.+.++...+|.      +.|.+++|||+.. ++..+..+.|.=|..+.++.++..++.+.
T Consensus       364 crFlvlDead~lL~-qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvH  442 (725)
T KOG0349|consen  364 CRFLVLDEADLLLG-QGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVH  442 (725)
T ss_pred             eEEEEecchhhhhh-cccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhc
Confidence            99999999999986 5899999999888863      5799999999874 57777788888899999888776666665


Q ss_pred             EEEEEeC-ChhhHHHHH----------------------------HH---------HhccCCCCcEEEEecchHhHHHHH
Q psy11867        320 QHYVMCK-NIDEKFEAV----------------------------SN---------IYGVVTIGQAMIFCHTRKTAAWLA  361 (399)
Q Consensus       320 ~~~~~~~-~~~~k~~~l----------------------------~~---------ll~~~~~~k~IIF~~s~~~a~~l~  361 (399)
                      +....+. ..+.....+                            ..         .++.+...++||||.++..|..|.
T Consensus       443 hvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLe  522 (725)
T KOG0349|consen  443 HVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLE  522 (725)
T ss_pred             cceeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHH
Confidence            5443321 111111111                            11         122334468999999999999999


Q ss_pred             HHHHHCC---CeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        362 EKMSKEG---LNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       362 ~~L~~~g---~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++|.+.|   +.|.++||+..+.+|.+.++.|+.+.++.|+
T Consensus       523 r~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkfli  563 (725)
T KOG0349|consen  523 RMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLI  563 (725)
T ss_pred             HHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEE
Confidence            9998874   5899999999999999999999999998774

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.97  E-value=2e-29  Score=243.21  Aligned_cols=248  Identities=17%  Similarity=0.213  Sum_probs=168.5

Q ss_pred             cEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCch----------
Q psy11867        144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGEN----------  213 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~----------  213 (399)
                      +++++||||||||++|++|++..+.. ....+++|++|+++|+.|+++.++.+...    .+....++..          
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~-~~~~~ii~v~P~~~L~~q~~~~l~~~f~~----~~~~~~~~~~~~~~~~~~~~   75 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKS-QKADRVIIALPTRATINAMYRRAKELFGS----NLGLLHSSSSFKRIKEMGDS   75 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhh-CCCCeEEEEeehHHHHHHHHHHHHHHhCc----ccEEeeccHHHHHHhccCCc
Confidence            58999999999999999999988754 35678999999999999999999997432    1111122111          


Q ss_pred             --hhhh---------hccCCcEEEeCchhHHHhhhc-ccc--ccCC--ceeEEEEechhhHhhcCCchHHHHHHHHhCC-
Q psy11867        214 --LERN---------KKITEQIIIGTPGKVLDWGLK-YRF--FDLS--KIKVFVLDEADVMIATQGHQDFSIRIQKRLP-  276 (399)
Q Consensus       214 --~~~~---------~~~~~~IlV~Tp~~l~~~~~~-~~~--~~~~--~~~~lViDEah~l~~~~~~~~~~~~i~~~l~-  276 (399)
                        ....         .....+|+|+||++++..+.. .+.  +.+.  ..+++||||||.+.+. + ...+..+++.+. 
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~-~-~~~l~~~l~~l~~  153 (358)
T TIGR01587        76 EEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEY-T-LALILAVLEVLKD  153 (358)
T ss_pred             hhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHH-H-HHHHHHHHHHHHH
Confidence              0000         012357999999999877554 111  1122  2378999999999753 2 222445554443 


Q ss_pred             CCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeC-ChhhHHHHHHHHhccC-CCCcEEEEecch
Q psy11867        277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCK-NIDEKFEAVSNIYGVV-TIGQAMIFCHTR  354 (399)
Q Consensus       277 ~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~-~~~~k~~~l~~ll~~~-~~~k~IIF~~s~  354 (399)
                      .+.|+++||||+|+.+.+++..+...+......... ......+.+..+. ....+...+..++... ..+++||||+++
T Consensus       154 ~~~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~  232 (358)
T TIGR01587       154 NDVPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKE-ERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTV  232 (358)
T ss_pred             cCCCEEEEecCchHHHHHHHhcCCCcccccCCCCcc-ccccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCH
Confidence            578999999999988888777654432221111110 0001123332222 2233455555555443 357999999999


Q ss_pred             HhHHHHHHHHHHCCC--eEEEEcCCCCHHHHHHH----HHHHhcCCCcccC
Q psy11867        355 KTAAWLAEKMSKEGL--NVGLLSGELTVEQRLSI----LDRFREGEFKIYS  399 (399)
Q Consensus       355 ~~a~~l~~~L~~~g~--~v~~lhg~~~~~~R~~v----~~~F~~G~~~ILV  399 (399)
                      ++|+.++..|.+.+.  .+..+||++++.+|.++    ++.|++|+.+|||
T Consensus       233 ~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilv  283 (358)
T TIGR01587       233 DRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIV  283 (358)
T ss_pred             HHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEE
Confidence            999999999988765  59999999999999764    8999999999986

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.96  E-value=2.1e-28  Score=254.06  Aligned_cols=248  Identities=17%  Similarity=0.252  Sum_probs=184.9

Q ss_pred             hhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCch
Q psy11867        134 LPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGEN  213 (399)
Q Consensus       134 i~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~  213 (399)
                      +..+.+  +++++++|+||||||++|.+++++....   ..+++|+.|||++|.|+++.+........+..+.+.+++..
T Consensus        14 ~~~l~~--~~~vvv~A~TGSGKTt~~pl~lL~~~~~---~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~~~   88 (812)
T PRK11664         14 LTALKT--APQVLLKAPTGAGKSTWLPLQLLQHGGI---NGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRAES   88 (812)
T ss_pred             HHHHHh--CCCEEEEcCCCCCHHHHHHHHHHHcCCc---CCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecCcc
Confidence            344444  6899999999999999999999976432   34899999999999999998865433323567777777664


Q ss_pred             hhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh-HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhH
Q psy11867        214 LERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV-MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEV  292 (399)
Q Consensus       214 ~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~-l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v  292 (399)
                      ...   ...+|+|+|||+|++++..  ...++++++|||||+|. .++..........+.+.++++.|+++||||++...
T Consensus        89 ~~~---~~t~I~v~T~G~Llr~l~~--d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmSATl~~~~  163 (812)
T PRK11664         89 KVG---PNTRLEVVTEGILTRMIQR--DPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSATLDNDR  163 (812)
T ss_pred             ccC---CCCcEEEEChhHHHHHHhh--CCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEecCCCHHH
Confidence            322   2347999999999998754  45789999999999996 33332233444566677888999999999998652


Q ss_pred             HHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHH-----HHHHHhccCCCCcEEEEecchHhHHHHHHHHHH-
Q psy11867        293 MEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFE-----AVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSK-  366 (399)
Q Consensus       293 ~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~-----~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~-  366 (399)
                         ...++.++..+.....   ...++++|..+... .+..     .+..++.. ..+.+||||+++++++.+++.|.+ 
T Consensus       164 ---l~~~~~~~~~I~~~gr---~~pV~~~y~~~~~~-~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~ei~~l~~~L~~~  235 (812)
T PRK11664        164 ---LQQLLPDAPVIVSEGR---SFPVERRYQPLPAH-QRFDEAVARATAELLRQ-ESGSLLLFLPGVGEIQRVQEQLASR  235 (812)
T ss_pred             ---HHHhcCCCCEEEecCc---cccceEEeccCchh-hhHHHHHHHHHHHHHHh-CCCCEEEEcCCHHHHHHHHHHHHHh
Confidence               2456666555543322   22467777655432 2322     34444443 358999999999999999999987 


Q ss_pred             --CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        367 --EGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       367 --~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                        .++.+..+||+|++++|..+++.|++|+.+|||
T Consensus       236 ~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlv  270 (812)
T PRK11664        236 VASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVL  270 (812)
T ss_pred             ccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEE
Confidence              578899999999999999999999999999985

>KOG0952|consensus

Probab=99.96  E-value=7e-29  Score=249.23  Aligned_cols=273  Identities=20%  Similarity=0.285  Sum_probs=201.2

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-------CCCCCeEEEEeCcHHHHHHHHHH
Q psy11867        120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-------SIQEPQVLCLAPTYELAIQIGEV  192 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-------~~~~~~~lil~Pt~~La~Q~~~~  192 (399)
                      -++|..++.+|+.++|.+.+. ..|++||||||||||..|+|.||+.+.+       .....+++||+|+++||..+++.
T Consensus       105 ~f~f~~fN~iQS~vFp~aY~S-neNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~  183 (1230)
T KOG0952|consen  105 FFSFEEFNRIQSEVFPVAYKS-NENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDK  183 (1230)
T ss_pred             cccHHHHHHHHHHhhhhhhcC-CCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHH
Confidence            367889999999999999987 8999999999999999999999999864       23456899999999999999888


Q ss_pred             HHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcccc---ccCCceeEEEEechhhHhhcCCch--HH
Q psy11867        193 VAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRF---FDLSKIKVFVLDEADVMIATQGHQ--DF  267 (399)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~---~~~~~~~~lViDEah~l~~~~~~~--~~  267 (399)
                      +.+-...+ ++.+.-.+|.....+.....++|+|+||+.+--. .+...   --++.+++|||||+|.+-+..|..  ..
T Consensus       184 ~~kkl~~~-gi~v~ELTGD~ql~~tei~~tqiiVTTPEKwDvv-TRk~~~d~~l~~~V~LviIDEVHlLhd~RGpvlEti  261 (1230)
T KOG0952|consen  184 FSKKLAPL-GISVRELTGDTQLTKTEIADTQIIVTTPEKWDVV-TRKSVGDSALFSLVRLVIIDEVHLLHDDRGPVLETI  261 (1230)
T ss_pred             Hhhhcccc-cceEEEecCcchhhHHHHHhcCEEEecccceeee-eeeeccchhhhhheeeEEeeeehhhcCcccchHHHH
Confidence            87766655 8899999999988777777889999999986433 22222   136789999999999998765432  22


Q ss_pred             HHHHHH---hCCCCCcEEEEEeeCChhHHHHHHhhCCCC--eEEecccccccccceeEEEEEeCCh----------hhHH
Q psy11867        268 SIRIQK---RLPSDCQIMLFSATYDKEVMEFAQDMVPNP--LIIKLKREEESLDNIKQHYVMCKNI----------DEKF  332 (399)
Q Consensus       268 ~~~i~~---~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p--~~i~~~~~~~~~~~i~~~~~~~~~~----------~~k~  332 (399)
                      +.+.++   ......+++++|||+|+. .+++.....+|  ..+..+.... +-.+.+.++-++..          +..+
T Consensus       262 VaRtlr~vessqs~IRivgLSATlPN~-eDvA~fL~vn~~~glfsFd~~yR-PvpL~~~~iG~k~~~~~~~~~~~d~~~~  339 (1230)
T KOG0952|consen  262 VARTLRLVESSQSMIRIVGLSATLPNY-EDVARFLRVNPYAGLFSFDQRYR-PVPLTQGFIGIKGKKNRQQKKNIDEVCY  339 (1230)
T ss_pred             HHHHHHHHHhhhhheEEEEeeccCCCH-HHHHHHhcCCCccceeeeccccc-ccceeeeEEeeecccchhhhhhHHHHHH
Confidence            223332   234577899999999975 34444333332  1222222222 22355555554432          1123


Q ss_pred             HHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC-----------------------CCeEEEEcCCCCHHHHHHHHHH
Q psy11867        333 EAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE-----------------------GLNVGLLSGELTVEQRLSILDR  389 (399)
Q Consensus       333 ~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~-----------------------g~~v~~lhg~~~~~~R~~v~~~  389 (399)
                      +.+.+++.  .+.+++|||++++.+...|+.|.+.                       ....+++|+||...+|..+.+.
T Consensus       340 ~kv~e~~~--~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~  417 (1230)
T KOG0952|consen  340 DKVVEFLQ--EGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKE  417 (1230)
T ss_pred             HHHHHHHH--cCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHH
Confidence            33444433  3469999999999999999888762                       1347889999999999999999


Q ss_pred             HhcCCCcccC
Q psy11867        390 FREGEFKIYS  399 (399)
Q Consensus       390 F~~G~~~ILV  399 (399)
                      |..|-++|||
T Consensus       418 F~~G~i~vL~  427 (1230)
T KOG0952|consen  418 FKEGHIKVLC  427 (1230)
T ss_pred             HhcCCceEEE
Confidence            9999999986

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.96  E-value=3.8e-28  Score=242.80  Aligned_cols=259  Identities=14%  Similarity=0.075  Sum_probs=176.0

Q ss_pred             CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        123 FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      ...|+++|.+|++.++.  +++.++++|||+|||+++...+...+..  ...++|||+||++|+.|+.+.+++++... .
T Consensus       112 ~~~~r~~Q~~av~~~l~--~~~~il~apTGsGKT~i~~~l~~~~~~~--~~~~vLilvpt~eL~~Q~~~~l~~~~~~~-~  186 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLK--NNRRLLNLPTSAGKSLIQYLLSRYYLEN--YEGKVLIIVPTTSLVTQMIDDFVDYRLFP-R  186 (501)
T ss_pred             cCCCCHHHHHHHHHHHh--cCceEEEeCCCCCHHHHHHHHHHHHHhc--CCCeEEEEECcHHHHHHHHHHHHHhcccc-c
Confidence            45899999999999998  5889999999999999765432222222  33489999999999999999999987432 3


Q ss_pred             cEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEE
Q psy11867        203 LSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM  282 (399)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l  282 (399)
                      ..+....+|....    ...+|+|+||+++.+..    ...+++++++|+||||++.+.     ....++..+++..+++
T Consensus       187 ~~~~~i~~g~~~~----~~~~I~VaT~qsl~~~~----~~~~~~~~~iIvDEaH~~~~~-----~~~~il~~~~~~~~~l  253 (501)
T PHA02558        187 EAMHKIYSGTAKD----TDAPIVVSTWQSAVKQP----KEWFDQFGMVIVDECHLFTGK-----SLTSIITKLDNCKFKF  253 (501)
T ss_pred             cceeEEecCcccC----CCCCEEEeeHHHHhhch----hhhccccCEEEEEchhcccch-----hHHHHHHhhhccceEE
Confidence            3333444554321    34689999999987642    224678999999999998642     2446666777778999


Q ss_pred             EEEeeCChhHHHHHH-hhCCCCeEEecccccc----cccceeEEEEE----------------------eCChhhHHHHH
Q psy11867        283 LFSATYDKEVMEFAQ-DMVPNPLIIKLKREEE----SLDNIKQHYVM----------------------CKNIDEKFEAV  335 (399)
Q Consensus       283 ~~SAT~~~~v~~~~~-~~~~~p~~i~~~~~~~----~~~~i~~~~~~----------------------~~~~~~k~~~l  335 (399)
                      +||||+......... ..+.+|+...+...+.    .+...+...+.                      ......+...+
T Consensus       254 GLTATp~~~~~~~~~~~~~fG~i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~~~Rn~~I  333 (501)
T PHA02558        254 GLTGSLRDGKANILQYVGLFGDIFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSHTKRNKWI  333 (501)
T ss_pred             EEeccCCCccccHHHHHHhhCCceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhccHHHHHHH
Confidence            999998653221111 1112232222211100    00000000000                      01112233344


Q ss_pred             HHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        336 SNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       336 ~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .++....  ...+++|||++.++|+.|++.|.+.|.++..+||+|+.++|..+++.|++|+..|||
T Consensus       334 ~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLv  399 (501)
T PHA02558        334 ANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIV  399 (501)
T ss_pred             HHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEE
Confidence            4443322  346899999999999999999999999999999999999999999999999988875

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

Probab=99.96  E-value=6.1e-28  Score=236.90  Aligned_cols=265  Identities=18%  Similarity=0.241  Sum_probs=196.5

Q ss_pred             HHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHH
Q psy11867        116 KGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVA  194 (399)
Q Consensus       116 ~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~  194 (399)
                      ..|+. +||..+++-|.++|..+++  |+|+++..|||+||++||.+|++-.      .+-+|||+|..+|++.+.+.++
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~--g~d~lvvmPTGgGKSlCyQiPAll~------~G~TLVVSPLiSLM~DQV~~l~   78 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLS--GKDTLVVMPTGGGKSLCYQIPALLL------EGLTLVVSPLISLMKDQVDQLE   78 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHc--CCcEEEEccCCCCcchHhhhHHHhc------CCCEEEECchHHHHHHHHHHHH
Confidence            34554 7999999999999999999  7999999999999999999999854      2359999999999999999998


Q ss_pred             HHhccCCCcEEEEEEcCchhhh-------hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC-CchH
Q psy11867        195 KMGKHITDLSVRYAVRGENLER-------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ-GHQD  266 (399)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~-~~~~  266 (399)
                      ..+     +...+..+..+.+.       ...+..+++.-+|++|..-.. .+.+.-..+.++||||||++...+ .|..
T Consensus        79 ~~G-----i~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f-~~~L~~~~i~l~vIDEAHCiSqWGhdFRP  152 (590)
T COG0514          79 AAG-----IRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRF-LELLKRLPISLVAIDEAHCISQWGHDFRP  152 (590)
T ss_pred             HcC-----ceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHH-HHHHHhCCCceEEechHHHHhhcCCccCH
Confidence            874     44444444322211       113456899999999865311 123335678899999999997531 2666


Q ss_pred             HHHHH---HHhCCCCCcEEEEEeeCChhHHHHHHhhC--CCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhcc
Q psy11867        267 FSIRI---QKRLPSDCQIMLFSATYDKEVMEFAQDMV--PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGV  341 (399)
Q Consensus       267 ~~~~i---~~~l~~~~q~l~~SAT~~~~v~~~~~~~~--~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~  341 (399)
                      ...++   ...++ +..++++|||-++.+...+...+  .++..+...   ...+|+....+...+...+...+.+ ...
T Consensus       153 ~Y~~lg~l~~~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~s---fdRpNi~~~v~~~~~~~~q~~fi~~-~~~  227 (590)
T COG0514         153 DYRRLGRLRAGLP-NPPVLALTATATPRVRDDIREQLGLQDANIFRGS---FDRPNLALKVVEKGEPSDQLAFLAT-VLP  227 (590)
T ss_pred             hHHHHHHHHhhCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcceEEec---CCCchhhhhhhhcccHHHHHHHHHh-hcc
Confidence            55544   44455 88999999999999888777655  344333322   2234554444333323334443333 224


Q ss_pred             CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        342 VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       342 ~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...+..||||.|++.++.+++.|...|+++..|||||+.++|+.+.++|..|+++|+|
T Consensus       228 ~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiV  285 (590)
T COG0514         228 QLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMV  285 (590)
T ss_pred             ccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEE
Confidence            4456799999999999999999999999999999999999999999999999999987

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.95  E-value=1.8e-26  Score=221.15  Aligned_cols=257  Identities=17%  Similarity=0.178  Sum_probs=168.7

Q ss_pred             HHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC---CcEE
Q psy11867        129 IQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT---DLSV  205 (399)
Q Consensus       129 iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~---~~~~  205 (399)
                      +|.++++.+.++...+++++||||||||.+|++|++..      ..++++++|+++|+.|+++.++.+...+.   +..+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v   74 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG------ENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNL   74 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceE
Confidence            59999999998522358999999999999999999842      23589999999999999999998874331   2333


Q ss_pred             EEEEcCch-----hh----------------hh--hccCCcEEEeCchhHHHhhhcc---cc-c---cCCceeEEEEech
Q psy11867        206 RYAVRGEN-----LE----------------RN--KKITEQIIIGTPGKVLDWGLKY---RF-F---DLSKIKVFVLDEA  255 (399)
Q Consensus       206 ~~~~~~~~-----~~----------------~~--~~~~~~IlV~Tp~~l~~~~~~~---~~-~---~~~~~~~lViDEa  255 (399)
                      ....|...     ..                +.  ....++|+++||+.|..++...   +. .   .+.+++++||||+
T Consensus        75 ~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~  154 (357)
T TIGR03158        75 LHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEF  154 (357)
T ss_pred             EEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecc
Confidence            33333211     00                00  0235789999999887654321   11 1   2578999999999


Q ss_pred             hhHhhcCC-chH---HHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhh--CCCCeEEeccc-----c-------------
Q psy11867        256 DVMIATQG-HQD---FSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDM--VPNPLIIKLKR-----E-------------  311 (399)
Q Consensus       256 h~l~~~~~-~~~---~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~--~~~p~~i~~~~-----~-------------  311 (399)
                      |.+...+. ...   ....+.+......+++++|||+++.+...+...  +..|....-+.     .             
T Consensus       155 H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~  234 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSF  234 (357)
T ss_pred             cccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeecCcccccCCChhhhcccccccc
Confidence            99753211 111   222333333445799999999999888877765  44554332222     0             


Q ss_pred             cccccceeEEEEEeCChhhHHHHHHH-------HhccCCCCcEEEEecchHhHHHHHHHHHHCC--CeEEEEcCCCCHHH
Q psy11867        312 EESLDNIKQHYVMCKNIDEKFEAVSN-------IYGVVTIGQAMIFCHTRKTAAWLAEKMSKEG--LNVGLLSGELTVEQ  382 (399)
Q Consensus       312 ~~~~~~i~~~~~~~~~~~~k~~~l~~-------ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g--~~v~~lhg~~~~~~  382 (399)
                      ......+.+.+.. .. ..|...+..       .++....+++||||++++.|+.++..|++.|  +.+..+||.+++.+
T Consensus       235 ~~~~~~i~~~~~~-~~-~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~  312 (357)
T TIGR03158       235 RPVLPPVELELIP-AP-DFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKD  312 (357)
T ss_pred             ceeccceEEEEEe-CC-chhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHH
Confidence            0011345555554 21 222222222       2223355799999999999999999998864  57889999999999


Q ss_pred             HHHHHHHHhcCCCcccC
Q psy11867        383 RLSILDRFREGEFKIYS  399 (399)
Q Consensus       383 R~~v~~~F~~G~~~ILV  399 (399)
                      |.++      ++.+|||
T Consensus       313 R~~~------~~~~iLV  323 (357)
T TIGR03158       313 RERA------MQFDILL  323 (357)
T ss_pred             HHHh------ccCCEEE
Confidence            9754      3566654

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.

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

Probab=99.94  E-value=5e-26  Score=195.68  Aligned_cols=162  Identities=27%  Similarity=0.419  Sum_probs=134.6

Q ss_pred             hHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEE
Q psy11867        127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVR  206 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~  206 (399)
                      ||+|.++++.+.+  |+++++.||||+|||++|++|++..+... ...+++|++|+++|+.|+++.+..++.. ..+.+.
T Consensus         1 t~~Q~~~~~~i~~--~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~-~~~~~~   76 (169)
T PF00270_consen    1 TPLQQEAIEAIIS--GKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSN-TNVRVV   76 (169)
T ss_dssp             -HHHHHHHHHHHT--TSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTT-TTSSEE
T ss_pred             CHHHHHHHHHHHc--CCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeecccccccccccccccccc-cccccc
Confidence            7899999999996  79999999999999999999999988776 5568999999999999999999999876 367777


Q ss_pred             EEEcCchhhhh----hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC--CCCc
Q psy11867        207 YAVRGENLERN----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP--SDCQ  280 (399)
Q Consensus       207 ~~~~~~~~~~~----~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~--~~~q  280 (399)
                      ...++......    ....++|+|+||++|.+++...+. ++.+++++|+||+|.+... .+...+..+...+.  .+.|
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~~~~~~~iViDE~h~l~~~-~~~~~~~~i~~~~~~~~~~~  154 (169)
T PF00270_consen   77 LLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKI-NISRLSLIVIDEAHHLSDE-TFRAMLKSILRRLKRFKNIQ  154 (169)
T ss_dssp             EESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSS-TGTTESEEEEETHHHHHHT-THHHHHHHHHHHSHTTTTSE
T ss_pred             cccccccccccccccccccccccccCcchhhcccccccc-ccccceeeccCcccccccc-cHHHHHHHHHHHhcCCCCCc
Confidence            77777654311    135689999999999998766333 6777999999999999875 66777777777763  3689


Q ss_pred             EEEEEeeCChhHHH
Q psy11867        281 IMLFSATYDKEVME  294 (399)
Q Consensus       281 ~l~~SAT~~~~v~~  294 (399)
                      ++++|||+++.+++
T Consensus       155 ~i~~SAT~~~~~~~  168 (169)
T PF00270_consen  155 IILLSATLPSNVEK  168 (169)
T ss_dssp             EEEEESSSTHHHHH
T ss_pred             EEEEeeCCChhHhh
Confidence            99999999966654

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 ....

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.93  E-value=1.1e-24  Score=217.82  Aligned_cols=263  Identities=16%  Similarity=0.124  Sum_probs=191.6

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..|+++|..++|.++.  |+  |+++.||+|||++|++|++.....   ++.++|++||++||.|.++++..+...+ ++
T Consensus       102 ~~p~~VQ~~~~~~ll~--G~--Iae~~TGeGKTla~~lp~~~~al~---G~~v~VvTptreLA~qdae~~~~l~~~l-Gl  173 (656)
T PRK12898        102 QRHFDVQLMGGLALLS--GR--LAEMQTGEGKTLTATLPAGTAALA---GLPVHVITVNDYLAERDAELMRPLYEAL-GL  173 (656)
T ss_pred             CCCChHHHHHHHHHhC--CC--eeeeeCCCCcHHHHHHHHHHHhhc---CCeEEEEcCcHHHHHHHHHHHHHHHhhc-CC
Confidence            3799999999999998  56  999999999999999999987653   5679999999999999999999999887 89


Q ss_pred             EEEEEEcCchhhh-hhccCCcEEEeCchhH-HHhhhccc------------------------cccCCceeEEEEechhh
Q psy11867        204 SVRYAVRGENLER-NKKITEQIIIGTPGKV-LDWGLKYR------------------------FFDLSKIKVFVLDEADV  257 (399)
Q Consensus       204 ~~~~~~~~~~~~~-~~~~~~~IlV~Tp~~l-~~~~~~~~------------------------~~~~~~~~~lViDEah~  257 (399)
                      ++.+..|+..... .....++|+|+|...| .+++..+-                        ..-.+.+.+.||||+|.
T Consensus       174 sv~~i~gg~~~~~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEvDS  253 (656)
T PRK12898        174 TVGCVVEDQSPDERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIVDEADS  253 (656)
T ss_pred             EEEEEeCCCCHHHHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEeecccc
Confidence            9999999865432 3356789999999988 55543221                        11246689999999995


Q ss_pred             Hhhc----------C-Cch---H---HHHHHHHhC---------------------------------------------
Q psy11867        258 MIAT----------Q-GHQ---D---FSIRIQKRL---------------------------------------------  275 (399)
Q Consensus       258 l~~~----------~-~~~---~---~~~~i~~~l---------------------------------------------  275 (399)
                      ++=.          . ...   .   ....+.+.+                                             
T Consensus       254 iLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~~~v~lt~~g~~~~e~~~~~l~~~~~~~~~~~~~  333 (656)
T PRK12898        254 VLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAGRARIAELAESLPPAWRGAVRREEL  333 (656)
T ss_pred             eeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCCCeEEEcHHHHHHHHHHhCcchhhcccchHHHHH
Confidence            5300          0 000   0   000000000                                             


Q ss_pred             -----------------------------------C---------------------C----------------CCcEEE
Q psy11867        276 -----------------------------------P---------------------S----------------DCQIML  283 (399)
Q Consensus       276 -----------------------------------~---------------------~----------------~~q~l~  283 (399)
                                                         +                     +                -.++.+
T Consensus       334 i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQaieaKE~v~i~~e~~t~a~It~q~~Fr~Y~kl~G  413 (656)
T PRK12898        334 VRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQMIEAKEGCELTDPRETLARITYQRFFRRYLRLAG  413 (656)
T ss_pred             HHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHHHHHhcCCCCCcCceeeeeehHHHHHHhhHHHhc
Confidence                                               0                     0                016778


Q ss_pred             EEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCC--CCcEEEEecchHhHHHHH
Q psy11867        284 FSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVT--IGQAMIFCHTRKTAAWLA  361 (399)
Q Consensus       284 ~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~--~~k~IIF~~s~~~a~~l~  361 (399)
                      ||||.+....++...|..+++.|......  .....+.++.+. ...|...|.+++....  ..++||||+|++.++.++
T Consensus       414 mTGTa~~~~~El~~~y~l~vv~IPt~kp~--~r~~~~~~v~~t-~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~L~  490 (656)
T PRK12898        414 MTGTAREVAGELWSVYGLPVVRIPTNRPS--QRRHLPDEVFLT-AAAKWAAVAARVRELHAQGRPVLVGTRSVAASERLS  490 (656)
T ss_pred             ccCcChHHHHHHHHHHCCCeEEeCCCCCc--cceecCCEEEeC-HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHH
Confidence            99999988888888888887776554332  223344455554 4678888998887643  468999999999999999


Q ss_pred             HHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        362 EKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       362 ~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..|.+.|+++..+||++.+.+  +.+..|+.+...|||
T Consensus       491 ~~L~~~gi~~~~Lhg~~~~rE--~~ii~~ag~~g~VlV  526 (656)
T PRK12898        491 ALLREAGLPHQVLNAKQDAEE--AAIVARAGQRGRITV  526 (656)
T ss_pred             HHHHHCCCCEEEeeCCcHHHH--HHHHHHcCCCCcEEE
Confidence            999999999999999966544  455555555555664

>KOG0951|consensus

Probab=99.93  E-value=4.3e-25  Score=224.84  Aligned_cols=284  Identities=19%  Similarity=0.217  Sum_probs=208.2

Q ss_pred             CCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCC--------CCeEEEEe
Q psy11867        109 HLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQ--------EPQVLCLA  180 (399)
Q Consensus       109 ~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~--------~~~~lil~  180 (399)
                      .++.+-..++  .|...++++|....++.+.+ ..|+++|||||+|||..+++.|++.+..+.+        ..+++|++
T Consensus       295 elP~Wnq~aF--~g~~sLNrIQS~v~daAl~~-~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIA  371 (1674)
T KOG0951|consen  295 ELPKWNQPAF--FGKQSLNRIQSKVYDAALRG-DENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIA  371 (1674)
T ss_pred             CCcchhhhhc--ccchhhhHHHHHHHHHHhcC-cCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEe
Confidence            4555555554  46677999999999999987 7899999999999999999999998865432        34799999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccc-cCCceeEEEEechhhHh
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFF-DLSKIKVFVLDEADVMI  259 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~-~~~~~~~lViDEah~l~  259 (399)
                      |+++|++.+...+.+....+ +++|.-..|............+|+||||+..--.-.+.... ..+-++++|+||.|.+.
T Consensus       372 PmKaLvqE~VgsfSkRla~~-GI~V~ElTgD~~l~~~qieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLh  450 (1674)
T KOG0951|consen  372 PMKALVQEMVGSFSKRLAPL-GITVLELTGDSQLGKEQIEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLH  450 (1674)
T ss_pred             eHHHHHHHHHHHHHhhcccc-CcEEEEecccccchhhhhhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcc
Confidence            99999999999998888777 88888888888877777777899999999864332222222 24467899999999997


Q ss_pred             hcCCchH--HHHHHHHhC---CCCCcEEEEEeeCChh--HHHHHHhhCCCCeEEecccccccccceeEEEEEeCCh--hh
Q psy11867        260 ATQGHQD--FSIRIQKRL---PSDCQIMLFSATYDKE--VMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI--DE  330 (399)
Q Consensus       260 ~~~~~~~--~~~~i~~~l---~~~~q~l~~SAT~~~~--v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~--~~  330 (399)
                      +..|-.-  .+.+..+..   ...++.+++|||+|+.  |..|++-..  +-.+..++... +-.++|.|+-+...  ..
T Consensus       451 DdRGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy~DV~~Fl~v~~--~glf~fd~syR-pvPL~qq~Igi~ek~~~~  527 (1674)
T KOG0951|consen  451 DDRGPVLESIVARTFRRSESTEEGSRLVGLSATLPNYEDVASFLRVDP--EGLFYFDSSYR-PVPLKQQYIGITEKKPLK  527 (1674)
T ss_pred             cccchHHHHHHHHHHHHhhhcccCceeeeecccCCchhhhHHHhccCc--ccccccCcccC-cCCccceEeccccCCchH
Confidence            7655332  222333332   3478999999999975  334333222  22333333333 33466666654322  23


Q ss_pred             HHHH-----HHHHhccCCCCcEEEEecchHhHHHHHHHHHH-------------------------------------CC
Q psy11867        331 KFEA-----VSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSK-------------------------------------EG  368 (399)
Q Consensus       331 k~~~-----l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~-------------------------------------~g  368 (399)
                      ++++     ..+++.....+++|||+++|+++...|+.++.                                     ..
T Consensus       528 ~~qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLp  607 (1674)
T KOG0951|consen  528 RFQAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLP  607 (1674)
T ss_pred             HHHHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhh
Confidence            3333     33345555668999999999998888888773                                     14


Q ss_pred             CeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        369 LNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       369 ~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.++++|+||+..+|..+.+.|++|.++|||
T Consensus       608 ygfaIHhAGl~R~dR~~~EdLf~~g~iqvlv  638 (1674)
T KOG0951|consen  608 YGFAIHHAGLNRKDRELVEDLFADGHIQVLV  638 (1674)
T ss_pred             ccceeeccCCCcchHHHHHHHHhcCceeEEE
Confidence            5689999999999999999999999999986

>PRK13766 Hef nuclease; Provisional

Probab=99.93  E-value=4.2e-24  Score=225.50  Aligned_cols=270  Identities=19%  Similarity=0.253  Sum_probs=186.2

Q ss_pred             CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        122 GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       122 g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      +...|+++|.+++..++.   +|+++++|||+|||++|++++...+.  ..+.++|||+||++|+.|+.+.++.+.... 
T Consensus        12 ~~~~~r~yQ~~~~~~~l~---~n~lv~~ptG~GKT~~a~~~i~~~l~--~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~-   85 (773)
T PRK13766         12 NTIEARLYQQLLAATALK---KNTLVVLPTGLGKTAIALLVIAERLH--KKGGKVLILAPTKPLVEQHAEFFRKFLNIP-   85 (773)
T ss_pred             CcCCccHHHHHHHHHHhc---CCeEEEcCCCccHHHHHHHHHHHHHH--hCCCeEEEEeCcHHHHHHHHHHHHHHhCCC-
Confidence            455899999999999887   59999999999999999999988874  345789999999999999999999876432 


Q ss_pred             CcEEEEEEcCchhhh--hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCC
Q psy11867        202 DLSVRYAVRGENLER--NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC  279 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~--~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~  279 (399)
                      ...+....|+.....  ......+|+|+||+.+...+.. +.+.+.+++++||||||++.... ....+...........
T Consensus        86 ~~~v~~~~g~~~~~~r~~~~~~~~iiv~T~~~l~~~l~~-~~~~~~~~~liVvDEaH~~~~~~-~~~~i~~~~~~~~~~~  163 (773)
T PRK13766         86 EEKIVVFTGEVSPEKRAELWEKAKVIVATPQVIENDLIA-GRISLEDVSLLIFDEAHRAVGNY-AYVYIAERYHEDAKNP  163 (773)
T ss_pred             CceEEEEeCCCCHHHHHHHHhCCCEEEECHHHHHHHHHc-CCCChhhCcEEEEECCccccccc-cHHHHHHHHHhcCCCC
Confidence            345555555544322  1244678999999999776543 45678899999999999986542 2333334444445567


Q ss_pred             cEEEEEeeCCh---hHHHHHHhhCCCCeEEe--------------------cc--cc----------------------c
Q psy11867        280 QIMLFSATYDK---EVMEFAQDMVPNPLIIK--------------------LK--RE----------------------E  312 (399)
Q Consensus       280 q~l~~SAT~~~---~v~~~~~~~~~~p~~i~--------------------~~--~~----------------------~  312 (399)
                      ++++||||...   .+...+.......+.+.                    +.  ..                      .
T Consensus       164 ~il~lTaTP~~~~~~i~~~~~~L~i~~v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~~~i~~~l~~~~~~~l~~l~~~~  243 (773)
T PRK13766        164 LVLGLTASPGSDEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKELG  243 (773)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHhCCceEEEEcCCCChhHHhhhccceeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence            89999999532   22222222211111100                    00  00                      0


Q ss_pred             cc--cc-------------ceeEE--------------------------------------------------------
Q psy11867        313 ES--LD-------------NIKQH--------------------------------------------------------  321 (399)
Q Consensus       313 ~~--~~-------------~i~~~--------------------------------------------------------  321 (399)
                      ..  ..             .+.+.                                                        
T Consensus       244 ~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~~~~~~~~~~  323 (773)
T PRK13766        244 VIVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGSKAS  323 (773)
T ss_pred             CcccCCCCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHhhccccCCcHHH
Confidence            00  00             00000                                                        


Q ss_pred             ---------------EEEeCChhhHHHHHHHHhcc----CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCC-----
Q psy11867        322 ---------------YVMCKNIDEKFEAVSNIYGV----VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGE-----  377 (399)
Q Consensus       322 ---------------~~~~~~~~~k~~~l~~ll~~----~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~-----  377 (399)
                                     ...+.....|...|.+++..    ...+++||||+++++|+.|++.|...|+++..+||.     
T Consensus       324 ~~l~~~~~~~~~~~~~~~~~~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~  403 (773)
T PRK13766        324 KRLVEDPRFRKAVRKAKELDIEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDG  403 (773)
T ss_pred             HHHHhCHHHHHHHHHHHhcccCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccc
Confidence                           00001112355555555544    456799999999999999999999999999999986     


Q ss_pred             ---CCHHHHHHHHHHHhcCCCcccC
Q psy11867        378 ---LTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       378 ---~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                         |++.+|..++++|++|+.+|||
T Consensus       404 ~~~~~~~~r~~~~~~F~~g~~~vLv  428 (773)
T PRK13766        404 DKGMSQKEQIEILDKFRAGEFNVLV  428 (773)
T ss_pred             cCCCCHHHHHHHHHHHHcCCCCEEE
Confidence               9999999999999999999985

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.92  E-value=8.8e-24  Score=215.77  Aligned_cols=262  Identities=17%  Similarity=0.191  Sum_probs=179.8

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      .|. .|+++|..+.+.++.  |+  |+++.||+|||++|++|++.....   +..++|++||++||.|.++++..+...+
T Consensus        75 ~g~-~p~~vQl~~~~~l~~--G~--Iaem~TGeGKTL~a~lp~~l~al~---G~~v~VvTpt~~LA~qd~e~~~~l~~~l  146 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHE--GN--IAEMQTGEGKTLTATMPLYLNALE---GKGVHLITVNDYLAKRDAEEMGQVYEFL  146 (790)
T ss_pred             hCC-CCchHHHHhHHHHcC--Cc--eeeecCCCcchHHHHHHHHHHHHc---CCCeEEEeCCHHHHHHHHHHHHHHHhhc
Confidence            465 899999999998876  45  999999999999999999865543   5569999999999999999999999987


Q ss_pred             CCcEEEEEEcCch-h-hhhhccCCcEEEeCchhH-HHhhhcc-----ccccCCceeEEEEechhhHhhcC----------
Q psy11867        201 TDLSVRYAVRGEN-L-ERNKKITEQIIIGTPGKV-LDWGLKY-----RFFDLSKIKVFVLDEADVMIATQ----------  262 (399)
Q Consensus       201 ~~~~~~~~~~~~~-~-~~~~~~~~~IlV~Tp~~l-~~~~~~~-----~~~~~~~~~~lViDEah~l~~~~----------  262 (399)
                       ++++.+..|+.. . .+.....++|++|||++| .+++...     ....++.++++|+||||.|+=..          
T Consensus       147 -Gl~v~~i~g~~~~~~~r~~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDea~tpliisg~  225 (790)
T PRK09200        147 -GLTVGLNFSDIDDASEKKAIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDEAQTPLIISGK  225 (790)
T ss_pred             -CCeEEEEeCCCCcHHHHHHhcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceeccCCCceeeeCC
Confidence             899999998876 2 333356789999999999 5544332     12346889999999999774110          


Q ss_pred             -----CchHHHHHHHHhCCC--------CC--------------------------------------------------
Q psy11867        263 -----GHQDFSIRIQKRLPS--------DC--------------------------------------------------  279 (399)
Q Consensus       263 -----~~~~~~~~i~~~l~~--------~~--------------------------------------------------  279 (399)
                           ........+...+..        ..                                                  
T Consensus       226 ~~~~~~~y~~~~~~~~~l~~~~dy~~d~~~~~~~lt~~g~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~~~~~~d~dY  305 (790)
T PRK09200        226 PRVQSNLYHIAAKFVKTLEEDVDYEFDEEKKEVWLTDQGIEKAESYFGIDNLYSLEHQVLYRHIILALRAHVLFKRDVDY  305 (790)
T ss_pred             CccccHHHHHHHHHHHhcccCCCeEEecCCCeEEecHhHHHHHHHhcCCccccChhhhHHHHHHHHHHHHHHHhhcCCcE
Confidence                 011111122222211        11                                                  


Q ss_pred             -----------------------------------------------------------cEEEEEeeCChhHHHHHHhhC
Q psy11867        280 -----------------------------------------------------------QIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       280 -----------------------------------------------------------q~l~~SAT~~~~v~~~~~~~~  300 (399)
                                                                                 ++.+||.|....-.++...|-
T Consensus       306 iV~~~~v~ivD~~TGr~~~gr~~s~GlhQaieaKe~v~i~~e~~t~a~It~q~~fr~Y~kl~GmTGTa~t~~~e~~~~Y~  385 (790)
T PRK09200        306 IVYDGEIVLVDRFTGRVLPGRKLQDGLHQAIEAKEGVEITEENRTMASITIQNLFRMFPKLSGMTGTAKTEEKEFFEVYN  385 (790)
T ss_pred             EEECCEEEEEECCCCcCCCCCccChHHHHHHHHhcCCCcCCCceehhhhhHHHHHHHhHHHhccCCCChHHHHHHHHHhC
Confidence                                                                       223333333222222222221


Q ss_pred             CCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCC
Q psy11867        301 PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGEL  378 (399)
Q Consensus       301 ~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~  378 (399)
                      -+  .+.+... .........-........|...+...+...  ...++||||+|++.++.++..|.+.|+++..+||++
T Consensus       386 l~--v~~IPt~-kp~~r~d~~~~i~~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~  462 (790)
T PRK09200        386 ME--VVQIPTN-RPIIRIDYPDKVFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKN  462 (790)
T ss_pred             Cc--EEECCCC-CCcccccCCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCc
Confidence            11  1111111 111111111112224467888888887653  457899999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHhcCC
Q psy11867        379 TVEQRLSILDRFREGE  394 (399)
Q Consensus       379 ~~~~R~~v~~~F~~G~  394 (399)
                      .+.+|..+...++.|.
T Consensus       463 ~~~e~~~i~~ag~~g~  478 (790)
T PRK09200        463 AAKEAQIIAEAGQKGA  478 (790)
T ss_pred             cHHHHHHHHHcCCCCe
Confidence            9999999999988884

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.92  E-value=1.7e-23  Score=210.61  Aligned_cols=265  Identities=17%  Similarity=0.171  Sum_probs=181.0

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      .|. .|+++|..+.+.++.  |+  |++++||+|||++|.+|++-....   +..+.|++||++||.|.++++.++...+
T Consensus        53 lg~-~p~~vQlig~~~l~~--G~--Iaem~TGeGKTLva~lpa~l~aL~---G~~V~VvTpt~~LA~qdae~~~~l~~~L  124 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIALHK--GK--IAEMKTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAEWMGQVYRFL  124 (745)
T ss_pred             hCC-CccchHHhhhhhhcC--Cc--eeeecCCCccHHHHHHHHHHHHHh---CCCEEEEcCCHHHHHHHHHHHHHHhccC
Confidence            344 799999999998876  44  999999999999999999543333   3359999999999999999999999987


Q ss_pred             CCcEEEEEEcCchhhhh-hccCCcEEEeCchhH-HHhhhccc-----cccCCceeEEEEechhhHhhcC--------C--
Q psy11867        201 TDLSVRYAVRGENLERN-KKITEQIIIGTPGKV-LDWGLKYR-----FFDLSKIKVFVLDEADVMIATQ--------G--  263 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~~~-~~~~~~IlV~Tp~~l-~~~~~~~~-----~~~~~~~~~lViDEah~l~~~~--------~--  263 (399)
                       ++++.+..++...... ....++|+||||++| .+++...-     .+.++.+.++|+||+|+|+-..        |  
T Consensus       125 -GLsv~~i~g~~~~~~r~~~y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDeaRtpLiisg~~  203 (745)
T TIGR00963       125 -GLSVGLILSGMSPEERREAYACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEARTPLIISGPA  203 (745)
T ss_pred             -CCeEEEEeCCCCHHHHHHhcCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhhhhHHhhcCCC
Confidence             7999999988665433 345689999999999 88865442     3467899999999999886311        0  


Q ss_pred             --chH---HHHHHHHhCCC--------CC---------------------------------------------------
Q psy11867        264 --HQD---FSIRIQKRLPS--------DC---------------------------------------------------  279 (399)
Q Consensus       264 --~~~---~~~~i~~~l~~--------~~---------------------------------------------------  279 (399)
                        ...   ....+.+.+..        ..                                                   
T Consensus       204 ~~~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~Al~A~~l~~~d~dYi  283 (745)
T TIGR00963       204 EKSTELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGVDNLYDLENSPLIHYINNALKAKELFEKDVDYI  283 (745)
T ss_pred             CCchHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCCccccChhhhHHHHHHHHHHHHHHHHhcCCcEE
Confidence              000   01112222211        01                                                   


Q ss_pred             ----------------------------------------------------------cEEEEEeeCChhHHHHHHhhCC
Q psy11867        280 ----------------------------------------------------------QIMLFSATYDKEVMEFAQDMVP  301 (399)
Q Consensus       280 ----------------------------------------------------------q~l~~SAT~~~~v~~~~~~~~~  301 (399)
                                                                                ++.+||.|.......+...|--
T Consensus       284 V~d~~V~ivD~~TGR~~~gr~ws~GLhQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~E~~~iY~l  363 (745)
T TIGR00963       284 VRDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNFFRLYEKLSGMTGTAKTEEEEFEKIYNL  363 (745)
T ss_pred             EECCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeeeeHHHHHhhCchhhccCCCcHHHHHHHHHHhCC
Confidence                                                                      2223333332222222222211


Q ss_pred             CCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhcc--CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCC
Q psy11867        302 NPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGV--VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT  379 (399)
Q Consensus       302 ~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~--~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~  379 (399)
                      +-+.  +.. +.........-..+.....|..++.+.+..  ....|+||||++++.++.++..|.+.|+++..+||+  
T Consensus       364 ~vv~--IPt-nkp~~R~d~~d~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--  438 (745)
T TIGR00963       364 EVVV--VPT-NRPVIRKDLSDLVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--  438 (745)
T ss_pred             CEEE--eCC-CCCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--
Confidence            1111  111 111111111112334456788777765532  245689999999999999999999999999999999  


Q ss_pred             HHHHHHHHHHHhcCCCcccC
Q psy11867        380 VEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       380 ~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.+|++.+..|+.|...|+|
T Consensus       439 q~~rEa~ii~~ag~~g~VtI  458 (745)
T TIGR00963       439 NHEREAEIIAQAGRKGAVTI  458 (745)
T ss_pred             hHHHHHHHHHhcCCCceEEE
Confidence            88999999999999988875

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.92  E-value=2.8e-23  Score=210.34  Aligned_cols=263  Identities=17%  Similarity=0.194  Sum_probs=173.3

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      .|. .|+++|......+..  |  .+++++||+|||++|++|++.....   +..++|++|+++||.|.++++..+...+
T Consensus        67 lgl-rpydVQlig~l~l~~--G--~Iaem~TGeGKTLta~Lpa~l~aL~---g~~V~VVTpn~yLA~Rdae~m~~l~~~L  138 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVLHQ--G--NIAEMKTGEGKTLTATMPLYLNALT---GKGAMLVTTNDYLAKRDAEEMGPVYEWL  138 (762)
T ss_pred             cCC-CccHHHHHHHHHhcC--C--ceeEecCCcchHHHHHHHHHHHhhc---CCceEEeCCCHHHHHHHHHHHHHHHhhc
Confidence            454 667777666665543  3  6999999999999999998776654   3459999999999999999999998887


Q ss_pred             CCcEEEEEEcCc---hh---hhhhccCCcEEEeCchhH-HHhhhcc-----ccccCCceeEEEEechhhHhhcCC-----
Q psy11867        201 TDLSVRYAVRGE---NL---ERNKKITEQIIIGTPGKV-LDWGLKY-----RFFDLSKIKVFVLDEADVMIATQG-----  263 (399)
Q Consensus       201 ~~~~~~~~~~~~---~~---~~~~~~~~~IlV~Tp~~l-~~~~~~~-----~~~~~~~~~~lViDEah~l~~~~~-----  263 (399)
                       ++++....++.   .+   .+.....++|++|||++| .+++...     ....++.+.++|+||||.|+-...     
T Consensus       139 -GLsv~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiDeartpli  217 (762)
T TIGR03714       139 -GLTVSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLDSAQTPLV  217 (762)
T ss_pred             -CCcEEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhccCcCCee
Confidence             78877766652   12   122345789999999999 4544321     234477899999999998852110     


Q ss_pred             ----------chHHHHHHHHhCCCC--------C----------------------------------------------
Q psy11867        264 ----------HQDFSIRIQKRLPSD--------C----------------------------------------------  279 (399)
Q Consensus       264 ----------~~~~~~~i~~~l~~~--------~----------------------------------------------  279 (399)
                                .......+.+.+.+.        .                                              
T Consensus       218 isg~~~~~~~~y~~~~~~v~~l~~~~dy~~d~~~~~v~lt~~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~  297 (762)
T TIGR03714       218 ISGAPRVQSNLYHIADTFVRTLKEDVDYIFKKDKKEVWLTDKGIEKAEQYFKIDNLYSEEYFELVRHINLALRAHYLFKR  297 (762)
T ss_pred             eeCCCccchHHHHHHHHHHHhcCCCCCeEEEcCCCeeeecHhHHHHHHHHcCCCccCChhhHHHHHHHHHHHHHHHHHhc
Confidence                      011111222222111        1                                              


Q ss_pred             ---------------------------------------------------------------cEEEEEeeCChhHHHHH
Q psy11867        280 ---------------------------------------------------------------QIMLFSATYDKEVMEFA  296 (399)
Q Consensus       280 ---------------------------------------------------------------q~l~~SAT~~~~v~~~~  296 (399)
                                                                                     ++.+||.|......+|.
T Consensus       298 d~dYiV~~~~v~ivD~~TGr~~~gr~~~~GLhQaieaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~~~~~Ef~  377 (762)
T TIGR03714       298 NKDYVVTNGEVVLLDRITGRLLEGTKLQSGIHQAIEAKEHVELSKETRAMASITYQNLFKMFNKLSGMTGTGKVAEKEFI  377 (762)
T ss_pred             CCceEEECCEEEEEECCCCcCCCCCCcchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCChhHHHHHH
Confidence                                                                           23333444332233333


Q ss_pred             HhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhcc--CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEE
Q psy11867        297 QDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGV--VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLL  374 (399)
Q Consensus       297 ~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~--~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~l  374 (399)
                      ..|-.+  .+.+... .........-..+.....|..++...+..  ....++||||++++.++.++..|.+.|+++.++
T Consensus       378 ~iY~l~--v~~IPt~-kp~~r~d~~d~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L  454 (762)
T TIGR03714       378 ETYSLS--VVKIPTN-KPIIRIDYPDKIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLL  454 (762)
T ss_pred             HHhCCC--EEEcCCC-CCeeeeeCCCeEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEe
Confidence            222111  1111111 11111111112233456788888887765  345789999999999999999999999999999


Q ss_pred             cCCCCHHHHHHHHHHHhcCCC
Q psy11867        375 SGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       375 hg~~~~~~R~~v~~~F~~G~~  395 (399)
                      ||++.+.+|..+.+.|+.|.+
T Consensus       455 ~a~~~~~E~~ii~~ag~~g~V  475 (762)
T TIGR03714       455 NAQNAAKEAQIIAEAGQKGAV  475 (762)
T ss_pred             cCCChHHHHHHHHHcCCCCeE
Confidence            999999999999888888843

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.

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

Probab=99.91  E-value=9.2e-23  Score=192.59  Aligned_cols=159  Identities=20%  Similarity=0.162  Sum_probs=121.6

Q ss_pred             CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        122 GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       122 g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      +..+++.+|.......+.   +|.+++.|||-|||..+++-+...+.... + ++|+++||+-|+.|..+.++++..- +
T Consensus        12 ~~ie~R~YQ~~i~a~al~---~NtLvvlPTGLGKT~IA~~V~~~~l~~~~-~-kvlfLAPTKPLV~Qh~~~~~~v~~i-p   85 (542)
T COG1111          12 NTIEPRLYQLNIAAKALF---KNTLVVLPTGLGKTFIAAMVIANRLRWFG-G-KVLFLAPTKPLVLQHAEFCRKVTGI-P   85 (542)
T ss_pred             ccccHHHHHHHHHHHHhh---cCeEEEecCCccHHHHHHHHHHHHHHhcC-C-eEEEecCCchHHHHHHHHHHHHhCC-C
Confidence            345789999999998886   79999999999999999998888887643 3 8999999999999999999998643 2


Q ss_pred             CcEEEEEEcCchhhhh--hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCC
Q psy11867        202 DLSVRYAVRGENLERN--KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC  279 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~~--~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~  279 (399)
                      .-.+....|...-++.  .....+|+|+||+.+.+-+ ..+.+++.++.++|||||||-.....+.. +....-....++
T Consensus        86 ~~~i~~ltGev~p~~R~~~w~~~kVfvaTPQvveNDl-~~Grid~~dv~~lifDEAHRAvGnyAYv~-Va~~y~~~~k~~  163 (542)
T COG1111          86 EDEIAALTGEVRPEEREELWAKKKVFVATPQVVENDL-KAGRIDLDDVSLLIFDEAHRAVGNYAYVF-VAKEYLRSAKNP  163 (542)
T ss_pred             hhheeeecCCCChHHHHHHHhhCCEEEeccHHHHhHH-hcCccChHHceEEEechhhhccCcchHHH-HHHHHHHhccCc
Confidence            3445555555444322  2566789999999998775 45788999999999999999754322222 333233335678


Q ss_pred             cEEEEEeeC
Q psy11867        280 QIMLFSATY  288 (399)
Q Consensus       280 q~l~~SAT~  288 (399)
                      .++++|||.
T Consensus       164 ~ilgLTASP  172 (542)
T COG1111         164 LILGLTASP  172 (542)
T ss_pred             eEEEEecCC
Confidence            899999993

>KOG0351|consensus

Probab=99.91  E-value=1.7e-23  Score=216.78  Aligned_cols=266  Identities=16%  Similarity=0.153  Sum_probs=193.1

Q ss_pred             HHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        118 VYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       118 l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ...+|...+++-|.+||..++.  |+|+++..|||.||++||.+|++-      .++..|||+|..+|++.+...+... 
T Consensus       257 ~~~Fg~~~FR~~Q~eaI~~~l~--Gkd~fvlmpTG~GKSLCYQlPA~l------~~gitvVISPL~SLm~DQv~~L~~~-  327 (941)
T KOG0351|consen  257 KEVFGHKGFRPNQLEAINATLS--GKDCFVLMPTGGGKSLCYQLPALL------LGGVTVVISPLISLMQDQVTHLSKK-  327 (941)
T ss_pred             HHHhccccCChhHHHHHHHHHc--CCceEEEeecCCceeeEeeccccc------cCCceEEeccHHHHHHHHHHhhhhc-
Confidence            3457999999999999999998  799999999999999999999872      3347999999999998877766443 


Q ss_pred             ccCCCcEEEEEEcCchhhh-------hhcc--CCcEEEeCchhHHHhhhcc-ccccCCc---eeEEEEechhhHhhcC-C
Q psy11867        198 KHITDLSVRYAVRGENLER-------NKKI--TEQIIIGTPGKVLDWGLKY-RFFDLSK---IKVFVLDEADVMIATQ-G  263 (399)
Q Consensus       198 ~~~~~~~~~~~~~~~~~~~-------~~~~--~~~IlV~Tp~~l~~~~~~~-~~~~~~~---~~~lViDEah~l~~~~-~  263 (399)
                          ++......++.....       ...+  ..+|+.-||+++...-.-. ....+..   +.++||||||+....+ .
T Consensus       328 ----~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHd  403 (941)
T KOG0351|consen  328 ----GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHD  403 (941)
T ss_pred             ----CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhccc
Confidence                444455544443321       1123  4589999999987542111 1223445   8999999999986431 2


Q ss_pred             chHHHHHHHH--hCCCCCcEEEEEeeCChhHHHHHHhhC--CCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHh
Q psy11867        264 HQDFSIRIQK--RLPSDCQIMLFSATYDKEVMEFAQDMV--PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIY  339 (399)
Q Consensus       264 ~~~~~~~i~~--~l~~~~q~l~~SAT~~~~v~~~~~~~~--~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll  339 (399)
                      |+....++..  .-.+...+|++|||.+..+...+-..+  ++|..+.-.   ....|+...+..-...+.-+..+...-
T Consensus       404 FRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~s---fnR~NL~yeV~~k~~~~~~~~~~~~~~  480 (941)
T KOG0351|consen  404 FRPSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKSS---FNRPNLKYEVSPKTDKDALLDILEESK  480 (941)
T ss_pred             ccHHHHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceeccc---CCCCCceEEEEeccCccchHHHHHHhh
Confidence            4444443322  222348899999999988877666554  556544322   234555444443332233344444455


Q ss_pred             ccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        340 GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       340 ~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..++....||||.+++.|+.++..|+..|+.+..||+||+..+|..|.+.|..|+++|+|
T Consensus       481 ~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~Viv  540 (941)
T KOG0351|consen  481 LRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIV  540 (941)
T ss_pred             hcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEE
Confidence            556667899999999999999999999999999999999999999999999999999986

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

Probab=99.91  E-value=1e-22  Score=199.93  Aligned_cols=270  Identities=20%  Similarity=0.248  Sum_probs=191.6

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcC----CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLAD----PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~----~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      ....+.+.+.+.--+++|..|++++..|..+    .+.+-+++|..|||||++++++++..+..   |.++..++||.-|
T Consensus       247 ~~~~l~~~~~~~LPF~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~---G~Q~ALMAPTEIL  323 (677)
T COG1200         247 ANGELLAKFLAALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA---GYQAALMAPTEIL  323 (677)
T ss_pred             ccHHHHHHHHHhCCCCccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc---CCeeEEeccHHHH
Confidence            4455666655443448999999999999865    35788999999999999999999988865   5679999999999


Q ss_pred             HHHHHHHHHHHhccCCCcEEEEEEcCchh-------hhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        186 AIQIGEVVAKMGKHITDLSVRYAVRGENL-------ERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       186 a~Q~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      |.|.++.+.++...+ ++.+.+..|...-       .....+..+|+|||..-+.      ....++++.++|+||-||+
T Consensus       324 A~QH~~~~~~~l~~~-~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQ------d~V~F~~LgLVIiDEQHRF  396 (677)
T COG1200         324 AEQHYESLRKWLEPL-GIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQ------DKVEFHNLGLVIIDEQHRF  396 (677)
T ss_pred             HHHHHHHHHHHhhhc-CCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhh------cceeecceeEEEEeccccc
Confidence            999999999999887 6888888876432       1222556799999987443      3556889999999999997


Q ss_pred             hhcCCchHHHHHHHHhCCC-CCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHH
Q psy11867        259 IATQGHQDFSIRIQKRLPS-DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSN  337 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~-~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~  337 (399)
                      .-     .+...+.. ... .+.++.||||.=+..  ++-..+.|--.=.++.-..-...|....+......+-++.+.+
T Consensus       397 GV-----~QR~~L~~-KG~~~Ph~LvMTATPIPRT--LAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~  468 (677)
T COG1200         397 GV-----HQRLALRE-KGEQNPHVLVMTATPIPRT--LALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIRE  468 (677)
T ss_pred             cH-----HHHHHHHH-hCCCCCcEEEEeCCCchHH--HHHHHhccccchhhccCCCCCCceEEEEeccccHHHHHHHHHH
Confidence            43     22333333 333 688999999943332  2222222221111111112223455555554444444444444


Q ss_pred             HhccCCCCcEEEEecchH--------hHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        338 IYGVVTIGQAMIFCHTRK--------TAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       338 ll~~~~~~k~IIF~~s~~--------~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      -+.  .+.++.+.|+-++        .|..+++.|+..  +.++..+||.|+.+++++++++|++|+++|||
T Consensus       469 ei~--~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILV  538 (677)
T COG1200         469 EIA--KGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILV  538 (677)
T ss_pred             HHH--cCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEE
Confidence            333  3468999998765        456777777754  66799999999999999999999999999997

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.91  E-value=3.1e-22  Score=205.93  Aligned_cols=258  Identities=16%  Similarity=0.160  Sum_probs=168.6

Q ss_pred             CChHHHHHHhhhhhcC-CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        125 APSKIQETALPTLLAD-PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~-~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      .+++.|.++++.+.++ .++++++.|+||||||.+|+.++...+..   +.++|||+||++|+.|+++.+++..    +.
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~---g~~vLvLvPt~~L~~Q~~~~l~~~f----g~  216 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ---GKQALVLVPEIALTPQMLARFRARF----GA  216 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHHh----CC
Confidence            6899999999999873 35889999999999999999888777654   4579999999999999999998753    34


Q ss_pred             EEEEEEcCchhhh-------hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC----CchHHHHHHH
Q psy11867        204 SVRYAVRGENLER-------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ----GHQDFSIRIQ  272 (399)
Q Consensus       204 ~~~~~~~~~~~~~-------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~----~~~~~~~~i~  272 (399)
                      .+....++.....       ...+..+|+|+|++.+.        ..+++++++|+||+|...-.+    .+......+.
T Consensus       217 ~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~--------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~~  288 (679)
T PRK05580        217 PVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF--------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVV  288 (679)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc--------ccccCCCEEEEECCCccccccCcCCCCcHHHHHHH
Confidence            5666666643321       12356789999998763        246789999999999864221    1111111233


Q ss_pred             HhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhh------HHHHHHHHh-ccC-CC
Q psy11867        273 KRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDE------KFEAVSNIY-GVV-TI  344 (399)
Q Consensus       273 ~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~------k~~~l~~ll-~~~-~~  344 (399)
                      +....+.+++++|||.+.+....+..-  ....+.+...........-.++.......      ....+.+.+ +.. ..
T Consensus       289 ra~~~~~~~il~SATps~~s~~~~~~g--~~~~~~l~~r~~~~~~p~v~~id~~~~~~~~~~~~ls~~l~~~i~~~l~~g  366 (679)
T PRK05580        289 RAKLENIPVVLGSATPSLESLANAQQG--RYRLLRLTKRAGGARLPEVEIIDMRELLRGENGSFLSPPLLEAIKQRLERG  366 (679)
T ss_pred             HhhccCCCEEEEcCCCCHHHHHHHhcc--ceeEEEeccccccCCCCeEEEEechhhhhhcccCCCCHHHHHHHHHHHHcC
Confidence            344568999999999775554444321  11222222111000001111111111000      001122222 222 22


Q ss_pred             CcEEEEecch------------------------------------------------------------HhHHHHHHHH
Q psy11867        345 GQAMIFCHTR------------------------------------------------------------KTAAWLAEKM  364 (399)
Q Consensus       345 ~k~IIF~~s~------------------------------------------------------------~~a~~l~~~L  364 (399)
                      .++|||+|++                                                            ..++++++.|
T Consensus       367 ~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~~e~l  446 (679)
T PRK05580        367 EQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEEEL  446 (679)
T ss_pred             CeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHHHH
Confidence            4788887752                                                            2567888888


Q ss_pred             HHC--CCeEEEEcCCCC--HHHHHHHHHHHhcCCCcccC
Q psy11867        365 SKE--GLNVGLLSGELT--VEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       365 ~~~--g~~v~~lhg~~~--~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+.  +.++..+|++++  ..+|+.++++|++|+.+|||
T Consensus       447 ~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILV  485 (679)
T PRK05580        447 AELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILI  485 (679)
T ss_pred             HHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEE
Confidence            876  789999999987  46799999999999999986

>PRK09694 helicase Cas3; Provisional

Probab=99.90  E-value=2.1e-22  Score=209.18  Aligned_cols=272  Identities=17%  Similarity=0.186  Sum_probs=171.2

Q ss_pred             CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC-C
Q psy11867        123 FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI-T  201 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~-~  201 (399)
                      ...|+|+|..+......  +..+++.||||+|||.+++..+...+.. ....+++|..||+++++|+++.++++.... .
T Consensus       284 ~~~p~p~Q~~~~~~~~~--pgl~ileApTGsGKTEAAL~~A~~l~~~-~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~  360 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQ--PGLTIIEAPTGSGKTEAALAYAWRLIDQ-GLADSIIFALPTQATANAMLSRLEALASKLFP  360 (878)
T ss_pred             CCCChHHHHHHHhhccC--CCeEEEEeCCCCCHHHHHHHHHHHHHHh-CCCCeEEEECcHHHHHHHHHHHHHHHHHHhcC
Confidence            45899999988554332  6789999999999999998876654443 345679999999999999999998754322 1


Q ss_pred             CcEEEEEEcCchhhh------------------------------hhccCCcEEEeCchhHHHhhhccccccCCcee---
Q psy11867        202 DLSVRYAVRGENLER------------------------------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIK---  248 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~------------------------------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~---  248 (399)
                      ...+....|...+..                              .......|+|||+.+++......+...++.+.   
T Consensus       361 ~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~La~  440 (878)
T PRK09694        361 SPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFGLGR  440 (878)
T ss_pred             CCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHhhcc
Confidence            234444444322110                              00112579999999998766555544444444   


Q ss_pred             -EEEEechhhHhhcCCchHHHHHHHHhC-CCCCcEEEEEeeCChhHHHHHHhhCCC----------CeEEecccc---cc
Q psy11867        249 -VFVLDEADVMIATQGHQDFSIRIQKRL-PSDCQIMLFSATYDKEVMEFAQDMVPN----------PLIIKLKRE---EE  313 (399)
Q Consensus       249 -~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~l~~SAT~~~~v~~~~~~~~~~----------p~~i~~~~~---~~  313 (399)
                       +|||||+|.+-.  .....+..+++.+ .....+|+||||+|....+.+...+..          |........   ..
T Consensus       441 svvIiDEVHAyD~--ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~~YPlvt~~~~~~~~~~  518 (878)
T PRK09694        441 SVLIVDEVHAYDA--YMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDTYGGHDPVELSSAYPLITWRGVNGAQRF  518 (878)
T ss_pred             CeEEEechhhCCH--HHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhccccccccccccccccccccccceee
Confidence             899999999732  3344455555544 246789999999998766543332111          111000000   00


Q ss_pred             ccc------ceeEEEE--Ee--CChhhHHHHHHHHhcc-CCCCcEEEEecchHhHHHHHHHHHHCC---CeEEEEcCCCC
Q psy11867        314 SLD------NIKQHYV--MC--KNIDEKFEAVSNIYGV-VTIGQAMIFCHTRKTAAWLAEKMSKEG---LNVGLLSGELT  379 (399)
Q Consensus       314 ~~~------~i~~~~~--~~--~~~~~k~~~l~~ll~~-~~~~k~IIF~~s~~~a~~l~~~L~~~g---~~v~~lhg~~~  379 (399)
                      ...      .....+.  ..  .........+..+++. ...++++|||||++.|+.+++.|++.+   .++..+||+++
T Consensus       519 ~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~  598 (878)
T PRK09694        519 DLSAHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFT  598 (878)
T ss_pred             eccccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCC
Confidence            000      0111111  11  1111112233333332 234689999999999999999998764   68999999999


Q ss_pred             HHHH----HHHHHHH-hcCC---CcccC
Q psy11867        380 VEQR----LSILDRF-REGE---FKIYS  399 (399)
Q Consensus       380 ~~~R----~~v~~~F-~~G~---~~ILV  399 (399)
                      ..+|    .++++.| ++|+   .+|||
T Consensus       599 ~~dR~~~E~~vl~~fgk~g~r~~~~ILV  626 (878)
T PRK09694        599 LNDRREKEQRVIENFGKNGKRNQGRILV  626 (878)
T ss_pred             HHHHHHHHHHHHHHHHhcCCcCCCeEEE
Confidence            9999    4678888 6776   35765

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.90  E-value=2.5e-22  Score=204.90  Aligned_cols=127  Identities=19%  Similarity=0.195  Sum_probs=104.9

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|+++|...--.+..    .-|+.++||+|||++|.+|++.....+   ..++||+||++||.|.++++..+..++ +++
T Consensus        82 ~~ydvQliGg~~Lh~----G~Iaem~TGeGKTL~a~Lpa~~~al~G---~~V~VvTpn~yLA~qd~e~m~~l~~~l-GLt  153 (896)
T PRK13104         82 RHFDVQLIGGMVLHE----GNIAEMRTGEGKTLVATLPAYLNAISG---RGVHIVTVNDYLAKRDSQWMKPIYEFL-GLT  153 (896)
T ss_pred             CcchHHHhhhhhhcc----CccccccCCCCchHHHHHHHHHHHhcC---CCEEEEcCCHHHHHHHHHHHHHHhccc-Cce
Confidence            688888877666544    458999999999999999999776543   359999999999999999999999887 799


Q ss_pred             EEEEEcCchhhhh-hccCCcEEEeCchhH-HHhhhccccccC-----CceeEEEEechhhHh
Q psy11867        205 VRYAVRGENLERN-KKITEQIIIGTPGKV-LDWGLKYRFFDL-----SKIKVFVLDEADVMI  259 (399)
Q Consensus       205 ~~~~~~~~~~~~~-~~~~~~IlV~Tp~~l-~~~~~~~~~~~~-----~~~~~lViDEah~l~  259 (399)
                      +.+..+|...... ....++|+||||++| .+++...-.+++     +.+.++|+||||.|+
T Consensus       154 v~~i~gg~~~~~r~~~y~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiL  215 (896)
T PRK13104        154 VGVIYPDMSHKEKQEAYKADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSIL  215 (896)
T ss_pred             EEEEeCCCCHHHHHHHhCCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhh
Confidence            9999998765433 345789999999999 888765534444     689999999999885

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.89  E-value=4.4e-22  Score=201.53  Aligned_cols=254  Identities=16%  Similarity=0.160  Sum_probs=165.7

Q ss_pred             CCChHHHHHHhhhhhcCCC--CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        124 YAPSKIQETALPTLLADPP--HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g--~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      ..++|+|.+|+..++.. |  +..++++|||+|||++.+..+. .+.     .++|||||+.+|+.|+.+.+.++... .
T Consensus       254 ~~LRpYQ~eAl~~~~~~-gr~r~GIIvLPtGaGKTlvai~aa~-~l~-----k~tLILvps~~Lv~QW~~ef~~~~~l-~  325 (732)
T TIGR00603       254 TQIRPYQEKSLSKMFGN-GRARSGIIVLPCGAGKSLVGVTAAC-TVK-----KSCLVLCTSAVSVEQWKQQFKMWSTI-D  325 (732)
T ss_pred             CCcCHHHHHHHHHHHhc-CCCCCcEEEeCCCCChHHHHHHHHH-HhC-----CCEEEEeCcHHHHHHHHHHHHHhcCC-C
Confidence            46899999999999864 3  5789999999999999876554 332     34999999999999999999988532 2


Q ss_pred             CcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcc-------ccccCCceeEEEEechhhHhhcCCchHHHHHHHHh
Q psy11867        202 DLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKY-------RFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR  274 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~-------~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~  274 (399)
                      ...+....|+....  ......|+|+|+..+.....+.       ..+.-..++++|+||||++.+.     ....++..
T Consensus       326 ~~~I~~~tg~~k~~--~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~-----~fr~il~~  398 (732)
T TIGR00603       326 DSQICRFTSDAKER--FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAA-----MFRRVLTI  398 (732)
T ss_pred             CceEEEEecCcccc--cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHH-----HHHHHHHh
Confidence            33344444432111  1123579999999875431111       1222356889999999998542     23334554


Q ss_pred             CCCCCcEEEEEeeCChh--HHHHHHhhCCCCeEEeccccc----ccccceeEEEEEeCC---------------------
Q psy11867        275 LPSDCQIMLFSATYDKE--VMEFAQDMVPNPLIIKLKREE----ESLDNIKQHYVMCKN---------------------  327 (399)
Q Consensus       275 l~~~~q~l~~SAT~~~~--v~~~~~~~~~~p~~i~~~~~~----~~~~~i~~~~~~~~~---------------------  327 (399)
                      +. ....+++|||....  ....+ .++.+|..+...-.+    .-+......-++|+-                     
T Consensus       399 l~-a~~RLGLTATP~ReD~~~~~L-~~LiGP~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k~~l~~  476 (732)
T TIGR00603       399 VQ-AHCKLGLTATLVREDDKITDL-NFLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYV  476 (732)
T ss_pred             cC-cCcEEEEeecCcccCCchhhh-hhhcCCeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhhhHHhh
Confidence            43 44579999997521  11112 122344443332111    111122222222221                     


Q ss_pred             -hhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC-CCcccC
Q psy11867        328 -IDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREG-EFKIYS  399 (399)
Q Consensus       328 -~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G-~~~ILV  399 (399)
                       ...|+..+..+++.+  ...++||||++...++.++..|   +  +..+||++++.+|..++++|+.| .+++||
T Consensus       477 ~np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L---~--~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv  547 (732)
T TIGR00603       477 MNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKL---G--KPFIYGPTSQQERMQILQNFQHNPKVNTIF  547 (732)
T ss_pred             hChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHc---C--CceEECCCCHHHHHHHHHHHHhCCCccEEE
Confidence             124666666676654  5579999999999999998887   2  56799999999999999999975 778775

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).

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.89  E-value=7.6e-22  Score=209.25  Aligned_cols=236  Identities=18%  Similarity=0.216  Sum_probs=154.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC----cHHHHHHHHHHHHH-HhccCCCcEEEEEEcCchhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP----TYELAIQIGEVVAK-MGKHITDLSVRYAVRGENLER  216 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P----t~~La~Q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  216 (399)
                      ++.++++|+||||||.  .+|.+..-........+++.-|    +++||.|+.+++.. ++..     +.+.+...   .
T Consensus        89 ~~VviI~GeTGSGKTT--qlPq~lle~g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~-----VGY~vrf~---~  158 (1294)
T PRK11131         89 HQVVIVAGETGSGKTT--QLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGC-----VGYKVRFN---D  158 (1294)
T ss_pred             CCeEEEECCCCCCHHH--HHHHHHHHcCCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcce-----eceeecCc---c
Confidence            5788899999999998  5674332211111123333446    56888888887764 3322     22322222   2


Q ss_pred             hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechh-hHhhcCCch-HHHHHHHHhCCCCCcEEEEEeeCChhHHH
Q psy11867        217 NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD-VMIATQGHQ-DFSIRIQKRLPSDCQIMLFSATYDKEVME  294 (399)
Q Consensus       217 ~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah-~l~~~~~~~-~~~~~i~~~l~~~~q~l~~SAT~~~~v~~  294 (399)
                      ......+|+|+|||+|++.+...  ..++++++||||||| ++++. ++. ..+..++.. .++.|+|+||||++.  ..
T Consensus       159 ~~s~~t~I~v~TpG~LL~~l~~d--~~Ls~~~~IIIDEAHERsLn~-DfLLg~Lk~lL~~-rpdlKvILmSATid~--e~  232 (1294)
T PRK11131        159 QVSDNTMVKLMTDGILLAEIQQD--RLLMQYDTIIIDEAHERSLNI-DFILGYLKELLPR-RPDLKVIITSATIDP--ER  232 (1294)
T ss_pred             ccCCCCCEEEEChHHHHHHHhcC--CccccCcEEEecCcccccccc-chHHHHHHHhhhc-CCCceEEEeeCCCCH--HH
Confidence            22345789999999999987643  348999999999999 56654 333 223333222 246899999999974  46


Q ss_pred             HHHhhCCCCeEEecccccccccceeEEEEEeCCh-----hhHHHHHHHHh---ccCCCCcEEEEecchHhHHHHHHHHHH
Q psy11867        295 FAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI-----DEKFEAVSNIY---GVVTIGQAMIFCHTRKTAAWLAEKMSK  366 (399)
Q Consensus       295 ~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~-----~~k~~~l~~ll---~~~~~~k~IIF~~s~~~a~~l~~~L~~  366 (399)
                      +.+.+...|+ +.+....   ..+.++|..+...     .+....+...+   .....+.+||||+++++++.+++.|.+
T Consensus       233 fs~~F~~apv-I~V~Gr~---~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg~~EIe~lae~L~~  308 (1294)
T PRK11131        233 FSRHFNNAPI-IEVSGRT---YPVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSGEREIRDTADALNK  308 (1294)
T ss_pred             HHHHcCCCCE-EEEcCcc---ccceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCCHHHHHHHHHHHHh
Confidence            6666655564 4443221   2355666654321     12223332222   223458899999999999999999998


Q ss_pred             CCCe---EEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        367 EGLN---VGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       367 ~g~~---v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+++   +..+||+|++++|..+++.  .|..+|||
T Consensus       309 ~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIV  342 (1294)
T PRK11131        309 LNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVL  342 (1294)
T ss_pred             cCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEE
Confidence            7654   7889999999999999986  47777775

>KOG0352|consensus

Probab=99.89  E-value=3e-23  Score=191.08  Aligned_cols=278  Identities=15%  Similarity=0.210  Sum_probs=186.0

Q ss_pred             HHHHHHHH-cCCCC-ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH
Q psy11867        113 ELLKGVYE-MGFYA-PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG  190 (399)
Q Consensus       113 ~l~~~l~~-~g~~~-p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~  190 (399)
                      .+.++|++ +|+.. -++.|++|+..+..+ .+||.++.|||+||++||.+|.|..      +...||++|..+|.+++.
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~-k~DVyVsMPTGaGKSLCyQLPaL~~------~gITIV~SPLiALIkDQi   78 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKR-KCDVYVSMPTGAGKSLCYQLPALVH------GGITIVISPLIALIKDQI   78 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhc-cCcEEEeccCCCchhhhhhchHHHh------CCeEEEehHHHHHHHHHH
Confidence            34556665 57654 478999999999987 7999999999999999999999843      236899999999999999


Q ss_pred             HHHHHHhccCCCcEEEEEEcCc--hhhhhh--ccCCcEEEeCchhHHHhhhc---cccccCCceeEEEEechhhHhhcC-
Q psy11867        191 EVVAKMGKHITDLSVRYAVRGE--NLERNK--KITEQIIIGTPGKVLDWGLK---YRFFDLSKIKVFVLDEADVMIATQ-  262 (399)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~--~~~~~IlV~Tp~~l~~~~~~---~~~~~~~~~~~lViDEah~l~~~~-  262 (399)
                      +.+.++--.+..++........  -+-...  +....++.-||+.-..-...   +....-..+.++|+||||+....+ 
T Consensus        79 DHL~~LKVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGH  158 (641)
T KOG0352|consen   79 DHLKRLKVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGH  158 (641)
T ss_pred             HHHHhcCCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhhcc
Confidence            9999886554444433322111  111111  23346999999875332111   011223468999999999986421 


Q ss_pred             CchHHHHHHHH--hCCCCCcEEEEEeeCChhHHHHHH--hhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHH
Q psy11867        263 GHQDFSIRIQK--RLPSDCQIMLFSATYDKEVMEFAQ--DMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI  338 (399)
Q Consensus       263 ~~~~~~~~i~~--~l~~~~q~l~~SAT~~~~v~~~~~--~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  338 (399)
                      .|......+-.  ..-+...-+.++||-+..|++.+-  ..+++|+-+.-.+..  ..|+-....+-....+-+..|.++
T Consensus       159 DFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~F--R~NLFYD~~~K~~I~D~~~~LaDF  236 (641)
T KOG0352|consen  159 DFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTF--RDNLFYDNHMKSFITDCLTVLADF  236 (641)
T ss_pred             ccCcchhhhhhHHhhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcch--hhhhhHHHHHHHHhhhHhHhHHHH
Confidence            24444433322  122467789999999988876543  345677665322111  111111011111112233334443


Q ss_pred             hccC----------C---CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        339 YGVV----------T---IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       339 l~~~----------~---~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ....          +   .|-.||||.|++.|+++|-.|...|+++..||+|+...+|..+.+.|.+|++.|+|
T Consensus       237 ~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~  310 (641)
T KOG0352|consen  237 SSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIA  310 (641)
T ss_pred             HHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEE
Confidence            3211          1   13479999999999999999999999999999999999999999999999999975

>KOG0354|consensus

Probab=99.89  E-value=2.1e-21  Score=193.26  Aligned_cols=173  Identities=17%  Similarity=0.068  Sum_probs=126.8

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      +.+.......--+...++.+|.+..-..|   |+|+|+++|||+|||.++...++.++.... ..++|+++||+-|+.|+
T Consensus        47 ~~~s~~~~~~~p~~~~lR~YQ~eivq~AL---gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p-~~KiVF~aP~~pLv~QQ  122 (746)
T KOG0354|consen   47 LDESAAQRWIYPTNLELRNYQEELVQPAL---GKNTIIALPTGSGKTFIAAVIMKNHFEWRP-KGKVVFLAPTRPLVNQQ  122 (746)
T ss_pred             CChhhhccccccCcccccHHHHHHhHHhh---cCCeEEEeecCCCccchHHHHHHHHHhcCC-cceEEEeeCCchHHHHH
Confidence            33444444333445689999999998888   499999999999999999999999988764 47899999999999999


Q ss_pred             HHHHHHHhccCCCcEEEEEEcCchhhh---hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchH
Q psy11867        190 GEVVAKMGKHITDLSVRYAVRGENLER---NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQD  266 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~  266 (399)
                      ...+..++.+   -.+....+|.....   ......+|+|+||+.|.+.+.....-.++.+.++||||||+-.....+..
T Consensus       123 ~a~~~~~~~~---~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~  199 (746)
T KOG0354|consen  123 IACFSIYLIP---YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNN  199 (746)
T ss_pred             HHHHhhccCc---ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHH
Confidence            8888887755   23333333322111   22446789999999998886654444579999999999999765434444


Q ss_pred             HHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        267 FSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       267 ~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      .+..++..-....|+|++|||..
T Consensus       200 Vmr~~l~~k~~~~qILgLTASpG  222 (746)
T KOG0354|consen  200 IMREYLDLKNQGNQILGLTASPG  222 (746)
T ss_pred             HHHHHHHhhhccccEEEEecCCC
Confidence            44445544444559999999954

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

Probab=99.88  E-value=6.2e-22  Score=194.52  Aligned_cols=257  Identities=21%  Similarity=0.221  Sum_probs=166.5

Q ss_pred             CCCChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        123 FYAPSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      ...|+++|.+|+..+.+.  .++..++++|||+|||..++..+-....      .+||||||++|+.|+.+.+.+.....
T Consensus        34 ~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~------~~Lvlv~~~~L~~Qw~~~~~~~~~~~  107 (442)
T COG1061          34 EFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKR------STLVLVPTKELLDQWAEALKKFLLLN  107 (442)
T ss_pred             CCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcC------CEEEEECcHHHHHHHHHHHHHhcCCc
Confidence            347999999999999872  1488999999999999988766553322      29999999999999987777765331


Q ss_pred             CCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCc
Q psy11867        201 TDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ  280 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q  280 (399)
                         ......++.......   ..|.|+|.+.+.... ....+....++++|+||||++.+. .+..    +...+.....
T Consensus       108 ---~~~g~~~~~~~~~~~---~~i~vat~qtl~~~~-~l~~~~~~~~~liI~DE~Hh~~a~-~~~~----~~~~~~~~~~  175 (442)
T COG1061         108 ---DEIGIYGGGEKELEP---AKVTVATVQTLARRQ-LLDEFLGNEFGLIIFDEVHHLPAP-SYRR----ILELLSAAYP  175 (442)
T ss_pred             ---cccceecCceeccCC---CcEEEEEhHHHhhhh-hhhhhcccccCEEEEEccccCCcH-HHHH----HHHhhhcccc
Confidence               112223332221111   369999999987641 113344557999999999998653 3333    3333332222


Q ss_pred             EEEEEeeCChhH---HHHHHhhCCCCeEEeccccc----ccccceeEEEEEe----------------------------
Q psy11867        281 IMLFSATYDKEV---MEFAQDMVPNPLIIKLKREE----ESLDNIKQHYVMC----------------------------  325 (399)
Q Consensus       281 ~l~~SAT~~~~v---~~~~~~~~~~p~~i~~~~~~----~~~~~i~~~~~~~----------------------------  325 (399)
                      ++++|||.+..-   ...... ..+|+.......+    .-+.......+.+                            
T Consensus       176 ~LGLTATp~R~D~~~~~~l~~-~~g~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~  254 (442)
T COG1061         176 RLGLTATPEREDGGRIGDLFD-LIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLR  254 (442)
T ss_pred             eeeeccCceeecCCchhHHHH-hcCCeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhhhhhhhhh
Confidence            899999965221   011111 1223333322111    0111111111111                            


Q ss_pred             ---------CChhhHHHHHHHHhccC-CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        326 ---------KNIDEKFEAVSNIYGVV-TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       326 ---------~~~~~k~~~l~~ll~~~-~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                               .....+...+..++..+ ...+++|||.+..++..++..|...|. +..+.|+.+..+|..+++.|+.|.+
T Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~  333 (442)
T COG1061         255 AENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGI  333 (442)
T ss_pred             HHHHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCC
Confidence                     01122344444455544 356999999999999999999988887 9999999999999999999999999


Q ss_pred             cccC
Q psy11867        396 KIYS  399 (399)
Q Consensus       396 ~ILV  399 (399)
                      ++||
T Consensus       334 ~~lv  337 (442)
T COG1061         334 KVLV  337 (442)
T ss_pred             CEEE
Confidence            9886

>KOG0353|consensus

Probab=99.88  E-value=4.8e-22  Score=180.75  Aligned_cols=285  Identities=18%  Similarity=0.212  Sum_probs=203.9

Q ss_pred             ccCCCCHHHHHHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        106 EALHLKPELLKGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       106 ~~~~l~~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      ++++.+.....-|+. +....++|.|..+|+..++  |.++++..|||.||++||.+|++.      ....+|++||...
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma--~ed~~lil~tgggkslcyqlpal~------adg~alvi~plis  145 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMA--GEDAFLILPTGGGKSLCYQLPALC------ADGFALVICPLIS  145 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhc--cCceEEEEeCCCccchhhhhhHHh------cCCceEeechhHH
Confidence            355666666666664 4567899999999999999  799999999999999999999983      3456999999999


Q ss_pred             HHHHHHHHHHHHhccCCCcEEEEEEcC-chhhhh---hccCCcEEEeCchhHHHh---hhc-cccccCCceeEEEEechh
Q psy11867        185 LAIQIGEVVAKMGKHITDLSVRYAVRG-ENLERN---KKITEQIIIGTPGKVLDW---GLK-YRFFDLSKIKVFVLDEAD  256 (399)
Q Consensus       185 La~Q~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~---~~~~~~IlV~Tp~~l~~~---~~~-~~~~~~~~~~~lViDEah  256 (399)
                      |+..+.-++++++....-++....-.. ...+..   ......++..||+.+...   +.+ .+.+....+.++.+||+|
T Consensus       146 lmedqil~lkqlgi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevh  225 (695)
T KOG0353|consen  146 LMEDQILQLKQLGIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVH  225 (695)
T ss_pred             HHHHHHHHHHHhCcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeeccee
Confidence            999999899998754322221110000 001111   123446999999998543   111 134457789999999999


Q ss_pred             hHhhcC-CchHHH--HHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeC-ChhhHH
Q psy11867        257 VMIATQ-GHQDFS--IRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCK-NIDEKF  332 (399)
Q Consensus       257 ~l~~~~-~~~~~~--~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~-~~~~k~  332 (399)
                      +-...+ .|+...  ..++++.-+...+++++||-++.+...++.++--...+.+.. .-..+++...++.-+ +.++-.
T Consensus       226 ccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~a-~fnr~nl~yev~qkp~n~dd~~  304 (695)
T KOG0353|consen  226 CCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFRA-GFNRPNLKYEVRQKPGNEDDCI  304 (695)
T ss_pred             ehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheeec-ccCCCCceeEeeeCCCChHHHH
Confidence            975421 133222  245566567889999999999888887777663322222221 123455555554433 335555


Q ss_pred             HHHHHHhccCCCC-cEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        333 EAVSNIYGVVTIG-QAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       333 ~~l~~ll~~~~~~-k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.+..+++....+ ..||||-+++.|+.++..|+.+|+.+..||+.|.+.+|.-+-+.|-.|+++|+|
T Consensus       305 edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqviv  372 (695)
T KOG0353|consen  305 EDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIV  372 (695)
T ss_pred             HHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEE
Confidence            6666666655444 579999999999999999999999999999999999999999999999999986

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=4.7e-21  Score=195.42  Aligned_cols=264  Identities=17%  Similarity=0.165  Sum_probs=182.6

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHH-HhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML-SRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il-~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      .|. .|+++|.-..-.+..  |  -|+.++||+|||++|.+|++ ..+ .+   ..+-|++||..||.|.++++..+...
T Consensus        78 lg~-~~~dvQlig~l~L~~--G--~Iaem~TGeGKTLva~lpa~l~aL-~G---~~V~IvTpn~yLA~rd~e~~~~l~~~  148 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVLHE--G--KIAEMKTGEGKTLVATLPAYLNAL-TG---KGVHVVTVNDYLAKRDAEWMGPLYEF  148 (830)
T ss_pred             hCC-CCCccHHHhhHHhcC--C--chhhhhcCCCcHHHHHHHHHHHHH-cC---CCEEEEecCHHHHHHHHHHHHHHHhh
Confidence            344 789999988876654  3  49999999999999999996 444 32   23779999999999999999999988


Q ss_pred             CCCcEEEEEEcCchhhhhh-ccCCcEEEeCchhH-HHhhhcccc-----ccCCceeEEEEechhhHhhcC----------
Q psy11867        200 ITDLSVRYAVRGENLERNK-KITEQIIIGTPGKV-LDWGLKYRF-----FDLSKIKVFVLDEADVMIATQ----------  262 (399)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~~-~~~~~IlV~Tp~~l-~~~~~~~~~-----~~~~~~~~lViDEah~l~~~~----------  262 (399)
                      + ++++.+..++....... ...++|+++||++| .+++.....     ..++.+.++||||||.|+=..          
T Consensus       149 L-Glsv~~i~~~~~~~er~~~y~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDeArtpLiiSg~  227 (830)
T PRK12904        149 L-GLSVGVILSGMSPEERREAYAADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDEARTPLIISGP  227 (830)
T ss_pred             c-CCeEEEEcCCCCHHHHHHhcCCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheeccCCCceeeECC
Confidence            7 89999999886654333 45689999999999 888754432     246789999999999875110          


Q ss_pred             -----CchHHHHHHHHhCCC--------CC--------------------------------------------------
Q psy11867        263 -----GHQDFSIRIQKRLPS--------DC--------------------------------------------------  279 (399)
Q Consensus       263 -----~~~~~~~~i~~~l~~--------~~--------------------------------------------------  279 (399)
                           ........+...+..        ..                                                  
T Consensus       228 ~~~~~~~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~~~ly~~~~~~~~~~i~~AL~A~~l~~~d~dY  307 (830)
T PRK12904        228 AEDSSELYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHLNQALRAHELFKRDVDY  307 (830)
T ss_pred             CCcccHHHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCCccccChhhhHHHHHHHHHHHHHHHHhcCCcE
Confidence                 011112222232211        11                                                  


Q ss_pred             -----------------------------------------------------------cEEEEEeeCChhHHHHHHhhC
Q psy11867        280 -----------------------------------------------------------QIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       280 -----------------------------------------------------------q~l~~SAT~~~~v~~~~~~~~  300 (399)
                                                                                 ++.+||.|......++...|-
T Consensus       308 iV~dg~V~ivDe~TGR~~~gr~ws~GLHQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~E~~~iY~  387 (830)
T PRK12904        308 IVKDGEVVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMTGTADTEAEEFREIYN  387 (830)
T ss_pred             EEECCEEEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeeeeHHHHHHhcchhcccCCCcHHHHHHHHHHhC
Confidence                                                                       223333333333333332222


Q ss_pred             CCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhcc--CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCC
Q psy11867        301 PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGV--VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGEL  378 (399)
Q Consensus       301 ~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~--~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~  378 (399)
                      .+-+  .+.. +.........-........|..++.+.+..  ....|+||||+|++.++.|+..|.+.|+++..+||. 
T Consensus       388 l~vv--~IPt-nkp~~r~d~~d~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak-  463 (830)
T PRK12904        388 LDVV--VIPT-NRPMIRIDHPDLIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK-  463 (830)
T ss_pred             CCEE--EcCC-CCCeeeeeCCCeEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc-
Confidence            2211  1111 111111111222334557789999988865  455799999999999999999999999999999996 


Q ss_pred             CHHHHHHHHHHHhcCCCcccC
Q psy11867        379 TVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       379 ~~~~R~~v~~~F~~G~~~ILV  399 (399)
                       +.+|++.+..|+.|...|+|
T Consensus       464 -q~eREa~Iia~Ag~~g~VtI  483 (830)
T PRK12904        464 -NHEREAEIIAQAGRPGAVTI  483 (830)
T ss_pred             -hHHHHHHHHHhcCCCceEEE
Confidence             88999999999999999886

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=2.7e-21  Score=197.16  Aligned_cols=147  Identities=18%  Similarity=0.224  Sum_probs=126.5

Q ss_pred             ccCCCCHHHHHHHH-----HcCCCCC---hHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEE
Q psy11867        106 EALHLKPELLKGVY-----EMGFYAP---SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVL  177 (399)
Q Consensus       106 ~~~~l~~~l~~~l~-----~~g~~~p---~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~l  177 (399)
                      +.+.+...+.+++.     .+||..|   +|+|.+++|.++.  +++++++++||+|||++|++|++..+....   .++
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l--~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~---~v~  139 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAM--HKGFITEMQTGEGKTLTAVMPLYLNALTGK---PVH  139 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhc--CCCeEEEeCCCCChHHHHHHHHHHHHhhcC---CeE
Confidence            56778899998887     6899999   9999999999998  699999999999999999999998775432   389


Q ss_pred             EEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh-ccCCcEEEeCchhH-HHhhhccccccCC-------cee
Q psy11867        178 CLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK-KITEQIIIGTPGKV-LDWGLKYRFFDLS-------KIK  248 (399)
Q Consensus       178 il~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~IlV~Tp~~l-~~~~~~~~~~~~~-------~~~  248 (399)
                      ||+||++||.|+.+++..++.++ ++++.+..||.....+. ...++|+||||++| .+++.. +.+.++       .+.
T Consensus       140 IVTpTrELA~Qdae~m~~L~k~l-GLsV~~i~GG~~~~eq~~~y~~DIVygTPgRLgfDyLrd-~~~~~~~~~~vqr~~~  217 (970)
T PRK12899        140 LVTVNDYLAQRDCEWVGSVLRWL-GLTTGVLVSGSPLEKRKEIYQCDVVYGTASEFGFDYLRD-NSIATRKEEQVGRGFY  217 (970)
T ss_pred             EEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHHcCCCEEEECCChhHHHHhhC-CCCCcCHHHhhccccc
Confidence            99999999999999999999887 78999999998876554 44689999999999 998654 334433       568


Q ss_pred             EEEEechhhHh
Q psy11867        249 VFVLDEADVMI  259 (399)
Q Consensus       249 ~lViDEah~l~  259 (399)
                      ++||||||.|+
T Consensus       218 ~~IIDEADsmL  228 (970)
T PRK12899        218 FAIIDEVDSIL  228 (970)
T ss_pred             EEEEechhhhh
Confidence            99999999986

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

Probab=99.85  E-value=2.3e-19  Score=185.65  Aligned_cols=269  Identities=17%  Similarity=0.178  Sum_probs=204.9

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcC----CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLAD----PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~----~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      .+......+.+.--+.-|+-|..||..+.++    .+.|-++||..|.|||-+++-++...+..   +.++.+||||.-|
T Consensus       579 ~d~~~q~~F~~~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~---GKQVAvLVPTTlL  655 (1139)
T COG1197         579 PDTEWQEEFEASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMD---GKQVAVLVPTTLL  655 (1139)
T ss_pred             CChHHHHHHHhcCCCcCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcC---CCeEEEEcccHHh
Confidence            4455555565543347899999999999765    47899999999999999999888877765   4679999999999


Q ss_pred             HHHHHHHHHHHhccCCCcEEEEEEcCchh-------hhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        186 AIQIGEVVAKMGKHITDLSVRYAVRGENL-------ERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       186 a~Q~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      |+|.++.|+.-..++ .+++....+-...       .....+..+|||||.. |++     +.+.+++++++||||=|++
T Consensus       656 A~QHy~tFkeRF~~f-PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHr-LL~-----kdv~FkdLGLlIIDEEqRF  728 (1139)
T COG1197         656 AQQHYETFKERFAGF-PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHR-LLS-----KDVKFKDLGLLIIDEEQRF  728 (1139)
T ss_pred             HHHHHHHHHHHhcCC-CeeEEEecccCCHHHHHHHHHHHhcCCccEEEechH-hhC-----CCcEEecCCeEEEechhhc
Confidence            999999999988877 5676665544332       2223567899999985 332     4677899999999999997


Q ss_pred             hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHH
Q psy11867        259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI  338 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  338 (399)
                      .-  .+.+    -++.+..+.-++-+|||.=+...++.-.-++|-..|...+.+.  -.++.++....+.--+...++++
T Consensus       729 GV--k~KE----kLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R--~pV~T~V~~~d~~~ireAI~REl  800 (1139)
T COG1197         729 GV--KHKE----KLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDR--LPVKTFVSEYDDLLIREAILREL  800 (1139)
T ss_pred             Cc--cHHH----HHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCC--cceEEEEecCChHHHHHHHHHHH
Confidence            53  2343    3455557888999999966666777777778877776665443  22444444333333333444444


Q ss_pred             hccCCCCcEEEEecchHhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        339 YGVVTIGQAMIFCHTRKTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       339 l~~~~~~k~IIF~~s~~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+   +|++-..+|..+..+.+++.|+..  ..++++.||.|+..+-+.++..|.+|+++|||
T Consensus       801 ~R---gGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv  860 (1139)
T COG1197         801 LR---GGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLV  860 (1139)
T ss_pred             hc---CCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEE
Confidence            33   489999999999999999999987  56899999999999999999999999999997

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.84  E-value=2.8e-19  Score=190.48  Aligned_cols=242  Identities=18%  Similarity=0.168  Sum_probs=154.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      ++.++++|+||||||.  .+|.+..-.......++++.-|.|--|..+.+.+.+....-.+-.+.+.+...+.   ....
T Consensus        82 ~~vvii~g~TGSGKTT--qlPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~vR~~~~---~s~~  156 (1283)
T TIGR01967        82 NQVVIIAGETGSGKTT--QLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFHDQ---VSSN  156 (1283)
T ss_pred             CceEEEeCCCCCCcHH--HHHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeEEcCCcc---cCCC
Confidence            5788999999999998  4565433222122335566668887777766555544322113344443333322   2345


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechh-hHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhC
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD-VMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah-~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~  300 (399)
                      .+|.++|+|+|+..+...  ..+.++++||||||| ++++.......+..++.. .++.|+|+||||++.  ..+.+.+.
T Consensus       157 T~I~~~TdGiLLr~l~~d--~~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~-rpdLKlIlmSATld~--~~fa~~F~  231 (1283)
T TIGR01967       157 TLVKLMTDGILLAETQQD--RFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPR-RPDLKIIITSATIDP--ERFSRHFN  231 (1283)
T ss_pred             ceeeeccccHHHHHhhhC--cccccCcEEEEcCcchhhccchhHHHHHHHHHhh-CCCCeEEEEeCCcCH--HHHHHHhc
Confidence            679999999999987553  348899999999999 577653333334455433 357899999999974  46666655


Q ss_pred             CCCeEEecccccccccceeEEEEEeCCh-----hhHHHHHHHHhc---cCCCCcEEEEecchHhHHHHHHHHHHCC---C
Q psy11867        301 PNPLIIKLKREEESLDNIKQHYVMCKNI-----DEKFEAVSNIYG---VVTIGQAMIFCHTRKTAAWLAEKMSKEG---L  369 (399)
Q Consensus       301 ~~p~~i~~~~~~~~~~~i~~~~~~~~~~-----~~k~~~l~~ll~---~~~~~k~IIF~~s~~~a~~l~~~L~~~g---~  369 (399)
                      ..|+ +.+....   ..+..+|..+...     ..+...+...+.   ....+.+||||++.++++.+++.|.+.+   .
T Consensus       232 ~apv-I~V~Gr~---~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~EI~~l~~~L~~~~~~~~  307 (1283)
T TIGR01967       232 NAPI-IEVSGRT---YPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGEREIRDAAEILRKRNLRHT  307 (1283)
T ss_pred             CCCE-EEECCCc---ccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHHHHHHHHHHHhcCCCCc
Confidence            5554 3333211   2244455433211     123333333222   1245899999999999999999998764   4


Q ss_pred             eEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        370 NVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       370 ~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+..+||+|++++|..+++.+  +..+|||
T Consensus       308 ~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVL  335 (1283)
T TIGR01967       308 EILPLYARLSNKEQQRVFQPH--SGRRIVL  335 (1283)
T ss_pred             EEEeccCCCCHHHHHHHhCCC--CCceEEE
Confidence            688999999999999996654  2345553

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.

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=99.83  E-value=2.2e-19  Score=185.60  Aligned_cols=263  Identities=15%  Similarity=0.145  Sum_probs=182.8

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      ..|| .|-++|++|+-.+-+  |.+|+++||||+|||++...++...+..+   .+++|.+|.++|..|.++.+......
T Consensus       115 ~~~F-~LD~fQ~~a~~~Ler--~esVlV~ApTssGKTvVaeyAi~~al~~~---qrviYTsPIKALsNQKyrdl~~~fgd  188 (1041)
T COG4581         115 EYPF-ELDPFQQEAIAILER--GESVLVCAPTSSGKTVVAEYAIALALRDG---QRVIYTSPIKALSNQKYRDLLAKFGD  188 (1041)
T ss_pred             hCCC-CcCHHHHHHHHHHhC--CCcEEEEccCCCCcchHHHHHHHHHHHcC---CceEeccchhhhhhhHHHHHHHHhhh
Confidence            3555 688999999999988  79999999999999999988887776543   34999999999999999888775443


Q ss_pred             CCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCC
Q psy11867        200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC  279 (399)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~  279 (399)
                      . .-.+....|...+.    ....++|.|.+-|-+++.. +...+..+.+||+||+|.|.+. .....+..++..+|...
T Consensus       189 v-~~~vGL~TGDv~IN----~~A~clvMTTEILRnMlyr-g~~~~~~i~~ViFDEvHyi~D~-eRG~VWEE~Ii~lP~~v  261 (1041)
T COG4581         189 V-ADMVGLMTGDVSIN----PDAPCLVMTTEILRNMLYR-GSESLRDIEWVVFDEVHYIGDR-ERGVVWEEVIILLPDHV  261 (1041)
T ss_pred             h-hhhccceecceeeC----CCCceEEeeHHHHHHHhcc-CcccccccceEEEEeeeecccc-ccchhHHHHHHhcCCCC
Confidence            2 11223445555443    3356999999988888655 4667999999999999999874 44445567778889999


Q ss_pred             cEEEEEeeCChhH--HHHHHhhCCCCeEEecccccccccceeEEEEEeC-------Chhh--------------------
Q psy11867        280 QIMLFSATYDKEV--MEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCK-------NIDE--------------------  330 (399)
Q Consensus       280 q~l~~SAT~~~~v--~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~-------~~~~--------------------  330 (399)
                      +++++|||+++..  ...+...-..|..+.......  ..+.+++. +.       +...                    
T Consensus       262 ~~v~LSATv~N~~EF~~Wi~~~~~~~~~vv~t~~Rp--vPL~~~~~-~~~~l~~lvde~~~~~~~~~~~a~~~l~~~~~~  338 (1041)
T COG4581         262 RFVFLSATVPNAEEFAEWIQRVHSQPIHVVSTEHRP--VPLEHFVY-VGKGLFDLVDEKKKFNAENFPSANRSLSCFSEK  338 (1041)
T ss_pred             cEEEEeCCCCCHHHHHHHHHhccCCCeEEEeecCCC--CCeEEEEe-cCCceeeeecccccchhhcchhhhhhhhccchh
Confidence            9999999999763  223332223444332221111  11111111 10       0000                    


Q ss_pred             ---------------------------HHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC----------------
Q psy11867        331 ---------------------------KFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE----------------  367 (399)
Q Consensus       331 ---------------------------k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~----------------  367 (399)
                                                 +...+.+.+.....-++|+||-+++.|+..+..+...                
T Consensus       339 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii  418 (1041)
T COG4581         339 VRETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREII  418 (1041)
T ss_pred             ccccCccccccccccccccCCcccccccchHHHhhhhhhcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHH
Confidence                                       0011222222233358999999999999998887631                


Q ss_pred             ------------CC-------------eEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        368 ------------GL-------------NVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       368 ------------g~-------------~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                                  +.             .++++|+||-+..|..+.+.|..|-++||
T Consensus       419 ~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvv  474 (1041)
T COG4581         419 DHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVKVV  474 (1041)
T ss_pred             HHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHhccceeEE
Confidence                        11             25689999999999999999999999987

>TIGR00595 priA primosomal protein N'

Probab=99.83  E-value=3.2e-19  Score=177.55  Aligned_cols=235  Identities=17%  Similarity=0.212  Sum_probs=147.2

Q ss_pred             EEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhh-------hh
Q psy11867        146 IAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER-------NK  218 (399)
Q Consensus       146 i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~  218 (399)
                      ++.|+||||||.+|+..+...+..   +.++||++|+++|+.|+++.+++.+    +..+....++.....       ..
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~---g~~vLvlvP~i~L~~Q~~~~l~~~f----~~~v~vlhs~~~~~er~~~~~~~~   73 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLAL---GKSVLVLVPEIALTPQMIQRFKYRF----GSQVAVLHSGLSDSEKLQAWRKVK   73 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHHh----CCcEEEEECCCCHHHHHHHHHHHH
Confidence            467999999999998776655543   4579999999999999999998754    234445555433211       12


Q ss_pred             ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC----CchHHHHHHHHhCCCCCcEEEEEeeCChhHHH
Q psy11867        219 KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ----GHQDFSIRIQKRLPSDCQIMLFSATYDKEVME  294 (399)
Q Consensus       219 ~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~----~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~  294 (399)
                      .+..+|+|||+..+.        ..+++++++||||+|...-.+    .+...-..+......+.+++++|||.+.+...
T Consensus        74 ~g~~~IVVGTrsalf--------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~~~~~vil~SATPsles~~  145 (505)
T TIGR00595        74 NGEILVVIGTRSALF--------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYH  145 (505)
T ss_pred             cCCCCEEECChHHHc--------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHhcCCCEEEEeCCCCHHHHH
Confidence            346789999998663        236789999999999864221    11111112223333588999999996544433


Q ss_pred             HHHhhCCCCeEEecccccccccceeEEEEEeCCh-------hhHHHHHHHHhccCCCCcEEEEecchHh-----------
Q psy11867        295 FAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI-------DEKFEAVSNIYGVVTIGQAMIFCHTRKT-----------  356 (399)
Q Consensus       295 ~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~-------~~k~~~l~~ll~~~~~~k~IIF~~s~~~-----------  356 (399)
                      .+..  .....+.+.............++.....       ..-.+.+.+.++  .++++|||+|++.-           
T Consensus       146 ~~~~--g~~~~~~l~~r~~~~~~p~v~vid~~~~~~~~~ls~~l~~~i~~~l~--~g~qvLvflnrrGya~~~~C~~Cg~  221 (505)
T TIGR00595       146 NAKQ--KAYRLLVLTRRVSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLA--AGEQSILFLNRRGYSKNLLCRSCGY  221 (505)
T ss_pred             HHhc--CCeEEeechhhhcCCCCCeEEEEecccccccCCccHHHHHHHHHHHH--cCCcEEEEEeCCcCCCeeEhhhCcC
Confidence            3321  1111222221111111111122222111       111222222222  23589999877643           


Q ss_pred             -------------------------------------------------HHHHHHHHHHC--CCeEEEEcCCCCHHHH--
Q psy11867        357 -------------------------------------------------AAWLAEKMSKE--GLNVGLLSGELTVEQR--  383 (399)
Q Consensus       357 -------------------------------------------------a~~l~~~L~~~--g~~v~~lhg~~~~~~R--  383 (399)
                                                                       ++++++.|.+.  +.++..+|++++...+  
T Consensus       222 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~  301 (505)
T TIGR00595       222 ILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAH  301 (505)
T ss_pred             ccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEecccccCccHH
Confidence                                                             58888888876  7899999999988776  


Q ss_pred             HHHHHHHhcCCCcccC
Q psy11867        384 LSILDRFREGEFKIYS  399 (399)
Q Consensus       384 ~~v~~~F~~G~~~ILV  399 (399)
                      +.+++.|++|+.+|||
T Consensus       302 ~~~l~~f~~g~~~ILV  317 (505)
T TIGR00595       302 EALLNQFANGKADILI  317 (505)
T ss_pred             HHHHHHHhcCCCCEEE
Confidence            9999999999999986

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).

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.83  E-value=4.6e-19  Score=155.49  Aligned_cols=185  Identities=30%  Similarity=0.448  Sum_probs=144.6

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCC-CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        120 EMGFYAPSKIQETALPTLLADPP-HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g-~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      ..++..|+++|.++++.++.  . +++++.++||+|||.++..+++..+.... ..+++|++|+..++.|+.+.+..++.
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~--~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~   79 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLS--GLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGP   79 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHc--CCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhc
Confidence            35688999999999999997  5 89999999999999999999998887642 45799999999999999999998876


Q ss_pred             cCCCcEEEEEEcCchh-h--hhhccCC-cEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHh
Q psy11867        199 HITDLSVRYAVRGENL-E--RNKKITE-QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR  274 (399)
Q Consensus       199 ~~~~~~~~~~~~~~~~-~--~~~~~~~-~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~  274 (399)
                      ... .......++... .  ....... +++++|++.+.+...... .....++++|+||+|.+... .+...+..+...
T Consensus        80 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~-~~~~~~~~iIiDE~h~~~~~-~~~~~~~~~~~~  156 (201)
T smart00487       80 SLG-LKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDL-LELSNVDLVILDEAHRLLDG-GFGDQLEKLLKL  156 (201)
T ss_pred             cCC-eEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCC-cCHhHCCEEEEECHHHHhcC-CcHHHHHHHHHh
Confidence            532 222333333321 1  1112333 899999999998865433 56778899999999999752 577777788888


Q ss_pred             CCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccc
Q psy11867        275 LPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR  310 (399)
Q Consensus       275 l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~  310 (399)
                      +++..+++++|||.++........+..+...+....
T Consensus       157 ~~~~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      157 LPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             CCccceEEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            888999999999999999999888888776665543

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.82  E-value=2.4e-18  Score=180.18  Aligned_cols=269  Identities=14%  Similarity=0.155  Sum_probs=166.6

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|.|+|..++..++......+++...+|.|||..+.+.+-..+..+ ...++|||||. .|..|+..++.+..    ++.
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g-~~~rvLIVvP~-sL~~QW~~El~~kF----~l~  225 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG-RAERVLILVPE-TLQHQWLVEMLRRF----NLR  225 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC-CCCcEEEEcCH-HHHHHHHHHHHHHh----CCC
Confidence            5999999999887765456899999999999998876665554443 44579999998 89999988886533    222


Q ss_pred             EEEEEcCchhh--h---hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC-CC
Q psy11867        205 VRYAVRGENLE--R---NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP-SD  278 (399)
Q Consensus       205 ~~~~~~~~~~~--~---~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~  278 (399)
                      .....++....  .   ......+++|+|.+.+...-.....+.-..++++|+||||++-............+..+. ..
T Consensus       226 ~~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~~  305 (956)
T PRK04914        226 FSLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVI  305 (956)
T ss_pred             eEEEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhcc
Confidence            22222221110  0   112245799999987764211112233347899999999998532111122233333333 34


Q ss_pred             CcEEEEEeeCCh-------------------hHHHH------------------------------HHhhCCC-------
Q psy11867        279 CQIMLFSATYDK-------------------EVMEF------------------------------AQDMVPN-------  302 (399)
Q Consensus       279 ~q~l~~SAT~~~-------------------~v~~~------------------------------~~~~~~~-------  302 (399)
                      ..++++|||.-.                   +...|                              +..++.+       
T Consensus       306 ~~~LLLTATP~q~~~~e~falL~lLdP~~f~~~~~F~~e~~~~~~~a~~v~~l~~~~~~~~~~~~~l~~ll~~~~~~~l~  385 (956)
T PRK04914        306 PGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLGEQDIEPLL  385 (956)
T ss_pred             CCEEEEEcCcccCCcHHHHHhhhhhCCCcCCCHHHHHHHHHhhHHHHHHHHHHhcCCcCCHHHHHHHHHHhcccchhHHH
Confidence            578999999210                   00000                              0001100       


Q ss_pred             ----------------------------CeEEeccccc--ccccceeEEE-EE---------------------------
Q psy11867        303 ----------------------------PLIIKLKREE--ESLDNIKQHY-VM---------------------------  324 (399)
Q Consensus       303 ----------------------------p~~i~~~~~~--~~~~~i~~~~-~~---------------------------  324 (399)
                                                  ++.++-.+..  ..+....+.+ ..                           
T Consensus       386 ~~~~~~~~~~~~~~~~~i~~L~d~hg~~rvm~RntR~~v~~fp~R~~~~~~l~~~~~y~~~~~~~~~~~~~~~l~pe~~~  465 (956)
T PRK04914        386 QAANSDSEEAQAARQELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPIPLPLPEQYQTAIKVSLEARARDMLYPEQIY  465 (956)
T ss_pred             hhhcccccccHHHHHHHHHHHHhhcCcceEEEeccHHhhcCCCcCceeEeecCCCHHHHHHHHHhHHHHHHhhcCHHHHH
Confidence                                        0000000000  0000000000 00                           


Q ss_pred             --------eCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHH-HCCCeEEEEcCCCCHHHHHHHHHHHhcC--
Q psy11867        325 --------CKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMS-KEGLNVGLLSGELTVEQRLSILDRFREG--  393 (399)
Q Consensus       325 --------~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~-~~g~~v~~lhg~~~~~~R~~v~~~F~~G--  393 (399)
                              ....+.|...|.++++.....|+||||+++.++..|++.|+ ..|+++..+||+|++.+|.++++.|+++  
T Consensus       466 ~~~~~~~~~~~~d~Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~  545 (956)
T PRK04914        466 QEFEDNATWWNFDPRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEED  545 (956)
T ss_pred             HHHhhhhhccccCHHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCC
Confidence                    00113467778888888778899999999999999999995 5699999999999999999999999984  


Q ss_pred             CCcccC
Q psy11867        394 EFKIYS  399 (399)
Q Consensus       394 ~~~ILV  399 (399)
                      ..+|||
T Consensus       546 ~~~VLI  551 (956)
T PRK04914        546 GAQVLL  551 (956)
T ss_pred             CccEEE
Confidence            588875

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.81  E-value=5.1e-19  Score=180.37  Aligned_cols=127  Identities=21%  Similarity=0.193  Sum_probs=103.1

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|+++|...--.+.    +.-|+.++||.|||++|.+|++.....+   ..+.||+|+..||.|..+++..+..++ +++
T Consensus        82 ~~ydVQliGgl~L~----~G~IaEm~TGEGKTL~a~lp~~l~al~g---~~VhIvT~ndyLA~RD~e~m~~l~~~l-Gls  153 (908)
T PRK13107         82 RHFDVQLLGGMVLD----SNRIAEMRTGEGKTLTATLPAYLNALTG---KGVHVITVNDYLARRDAENNRPLFEFL-GLT  153 (908)
T ss_pred             CcCchHHhcchHhc----CCccccccCCCCchHHHHHHHHHHHhcC---CCEEEEeCCHHHHHHHHHHHHHHHHhc-CCe
Confidence            68888887665554    4458999999999999999999777654   339999999999999999999999987 899


Q ss_pred             EEEEEcCchhhhh-hccCCcEEEeCchhH-HHhhhcccccc-----CCceeEEEEechhhHh
Q psy11867        205 VRYAVRGENLERN-KKITEQIIIGTPGKV-LDWGLKYRFFD-----LSKIKVFVLDEADVMI  259 (399)
Q Consensus       205 ~~~~~~~~~~~~~-~~~~~~IlV~Tp~~l-~~~~~~~~~~~-----~~~~~~lViDEah~l~  259 (399)
                      +.+..++...... ....++|+++||++| .+++..+-.+.     .+.+.++||||||.++
T Consensus       154 v~~i~~~~~~~~r~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiL  215 (908)
T PRK13107        154 VGINVAGLGQQEKKAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSIL  215 (908)
T ss_pred             EEEecCCCCHHHHHhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhc
Confidence            9988887655333 345789999999999 88866542333     3788999999999775

>KOG0948|consensus

Probab=99.81  E-value=5.6e-19  Score=172.81  Aligned_cols=255  Identities=16%  Similarity=0.183  Sum_probs=184.2

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..+-|.|..||.-+-+  +..|+++|-|.+|||.++-.+|.+.+..   +.|++|-+|.++|..|-|+.+..-.+..   
T Consensus       128 F~LDpFQ~~aI~Cidr--~eSVLVSAHTSAGKTVVAeYAIA~sLr~---kQRVIYTSPIKALSNQKYREl~~EF~DV---  199 (1041)
T KOG0948|consen  128 FTLDPFQSTAIKCIDR--GESVLVSAHTSAGKTVVAEYAIAMSLRE---KQRVIYTSPIKALSNQKYRELLEEFKDV---  199 (1041)
T ss_pred             cccCchHhhhhhhhcC--CceEEEEeecCCCcchHHHHHHHHHHHh---cCeEEeeChhhhhcchhHHHHHHHhccc---
Confidence            3677999999998877  7999999999999999999988888765   3469999999999999999888765543   


Q ss_pred             EEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEE
Q psy11867        204 SVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIML  283 (399)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~  283 (399)
                        .+.+|...+..    ....+|.|.+.|.+++.+... -++.+.|+|+||+|.|-+.....- +..-+-.+|.+.++++
T Consensus       200 --GLMTGDVTInP----~ASCLVMTTEILRsMLYRGSE-vmrEVaWVIFDEIHYMRDkERGVV-WEETIIllP~~vr~VF  271 (1041)
T KOG0948|consen  200 --GLMTGDVTINP----DASCLVMTTEILRSMLYRGSE-VMREVAWVIFDEIHYMRDKERGVV-WEETIILLPDNVRFVF  271 (1041)
T ss_pred             --ceeecceeeCC----CCceeeeHHHHHHHHHhccch-HhheeeeEEeeeehhcccccccee-eeeeEEeccccceEEE
Confidence              34445444432    245899999999888766433 478999999999999987533222 2333456789999999


Q ss_pred             EEeeCChhHHHHHHh---hCCCCeEEecccccccccceeEEEEE----------eCCh----hhHHH-------------
Q psy11867        284 FSATYDKEVMEFAQD---MVPNPLIIKLKREEESLDNIKQHYVM----------CKNI----DEKFE-------------  333 (399)
Q Consensus       284 ~SAT~~~~v~~~~~~---~~~~p~~i~~~~~~~~~~~i~~~~~~----------~~~~----~~k~~-------------  333 (399)
                      +|||+|+. .+|+.+   +-..|..+.......+   --|+|++          ++..    ++.+.             
T Consensus       272 LSATiPNA-~qFAeWI~~ihkQPcHVVYTdyRPT---PLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~  347 (1041)
T KOG0948|consen  272 LSATIPNA-RQFAEWICHIHKQPCHVVYTDYRPT---PLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESD  347 (1041)
T ss_pred             EeccCCCH-HHHHHHHHHHhcCCceEEeecCCCC---cceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCCc
Confidence            99999976 344444   4466766544332221   1222222          2110    11111             


Q ss_pred             -------------------------HHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC---------------------
Q psy11867        334 -------------------------AVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE---------------------  367 (399)
Q Consensus       334 -------------------------~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~---------------------  367 (399)
                                               .+..++-.....|+|||+-+++.|+.+|-.|.+.                     
T Consensus       348 ~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~  427 (1041)
T KOG0948|consen  348 GKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQ  427 (1041)
T ss_pred             cccccccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHh
Confidence                                     2222333334468999999999999999998762                     


Q ss_pred             ------------------CCeEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        368 ------------------GLNVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       368 ------------------g~~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                                        ...++++|||+-+--++-+.-.|.+|-++||
T Consensus       428 LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvL  476 (1041)
T KOG0948|consen  428 LSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVL  476 (1041)
T ss_pred             cChhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHH
Confidence                              1237899999999999999999999999887

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

Probab=99.80  E-value=1.2e-18  Score=186.20  Aligned_cols=270  Identities=15%  Similarity=0.144  Sum_probs=156.5

Q ss_pred             CCChHHHHHHhhhhhc---CCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        124 YAPSKIQETALPTLLA---DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~---~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      ..++++|.+|+..+..   ...++.+++++||||||.+++. ++.++.......++|||+|+.+|+.|..+.++.+....
T Consensus       412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~-li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~  490 (1123)
T PRK11448        412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIA-LMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEG  490 (1123)
T ss_pred             CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHH-HHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhccccc
Confidence            3589999999988763   2257899999999999987543 44444433455689999999999999999998874321


Q ss_pred             CCcEEEEEEcCchhhh-hhccCCcEEEeCchhHHHhhhcc----ccccCCceeEEEEechhhHhhcC--------C----
Q psy11867        201 TDLSVRYAVRGENLER-NKKITEQIIIGTPGKVLDWGLKY----RFFDLSKIKVFVLDEADVMIATQ--------G----  263 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~~-~~~~~~~IlV~Tp~~l~~~~~~~----~~~~~~~~~~lViDEah~l~~~~--------~----  263 (399)
                       ........+...+.. .......|+|+|...+...+...    ..+.+.++++||+||||+-....        .    
T Consensus       491 -~~~~~~i~~i~~L~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~~  569 (1123)
T PRK11448        491 -DQTFASIYDIKGLEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRDQ  569 (1123)
T ss_pred             -ccchhhhhchhhhhhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccchh
Confidence             111111111111111 11334679999999987654321    22457789999999999953100        0    


Q ss_pred             --chHHHHHHHHhCCCCCcEEEEEeeCChhHHH-------------HHH-hhCC---CCeEEecccc--------ccccc
Q psy11867        264 --HQDFSIRIQKRLPSDCQIMLFSATYDKEVME-------------FAQ-DMVP---NPLIIKLKRE--------EESLD  316 (399)
Q Consensus       264 --~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~-------------~~~-~~~~---~p~~i~~~~~--------~~~~~  316 (399)
                        +......++...  +...|+||||.......             .+. .++.   .|..+.....        .....
T Consensus       570 ~~~~~~yr~iL~yF--dA~~IGLTATP~r~t~~~FG~pv~~Ysl~eAI~DG~Lv~~~~p~~i~t~~~~~gi~~~~~e~~~  647 (1123)
T PRK11448        570 LDYVSKYRRVLDYF--DAVKIGLTATPALHTTEIFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQEGIHFEKGEEVE  647 (1123)
T ss_pred             hhHHHHHHHHHhhc--CccEEEEecCCccchhHHhCCeeEEeeHHHHHhcCCcccCcCCEEEEEEeccccccccccchhh
Confidence              122334455543  35789999995422111             111 1111   1222221000        00000


Q ss_pred             ceeE---EE--EEeCCh--------hh------HH----HHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC------
Q psy11867        317 NIKQ---HY--VMCKNI--------DE------KF----EAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE------  367 (399)
Q Consensus       317 ~i~~---~~--~~~~~~--------~~------k~----~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~------  367 (399)
                      ....   .+  ...+..        +.      ..    ..+.+.+.....+++||||.++++|+.+++.|.+.      
T Consensus       648 ~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l~~~~~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~  727 (1123)
T PRK11448        648 VINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYLDPTGEGKTLIFAATDAHADMVVRLLKEAFKKKYG  727 (1123)
T ss_pred             hcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHhccCCCcEEEEEcCHHHHHHHHHHHHHHHHhhcC
Confidence            0000   00  000000        00      00    11222232233479999999999999999887653      


Q ss_pred             C---CeEEEEcCCCCHHHHHHHHHHHhcCCC-cccC
Q psy11867        368 G---LNVGLLSGELTVEQRLSILDRFREGEF-KIYS  399 (399)
Q Consensus       368 g---~~v~~lhg~~~~~~R~~v~~~F~~G~~-~ILV  399 (399)
                      +   ..+..+||+.+  ++..++++|++|.. +|||
T Consensus       728 ~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlV  761 (1123)
T PRK11448        728 QVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVV  761 (1123)
T ss_pred             CcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEE
Confidence            2   24667999985  56789999999987 4654

>KOG0947|consensus

Probab=99.78  E-value=3.6e-18  Score=171.04  Aligned_cols=258  Identities=13%  Similarity=0.106  Sum_probs=181.0

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ++|-..|++||-.+..  |..|++.|+|.+|||+++-.++...-   ....|++|-+|.++|..|-++.|+.-....   
T Consensus       296 FelD~FQk~Ai~~ler--g~SVFVAAHTSAGKTvVAEYAialaq---~h~TR~iYTSPIKALSNQKfRDFk~tF~Dv---  367 (1248)
T KOG0947|consen  296 FELDTFQKEAIYHLER--GDSVFVAAHTSAGKTVVAEYAIALAQ---KHMTRTIYTSPIKALSNQKFRDFKETFGDV---  367 (1248)
T ss_pred             CCccHHHHHHHHHHHc--CCeEEEEecCCCCcchHHHHHHHHHH---hhccceEecchhhhhccchHHHHHHhcccc---
Confidence            3788999999999998  79999999999999999877665332   245679999999999999999998865543   


Q ss_pred             EEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEE
Q psy11867        204 SVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIML  283 (399)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~  283 (399)
                        ...+|...+..    ...++|.|.+.|-+++.+. .--++++.+|||||+|.+.+. .....+..++-.+|...++|+
T Consensus       368 --gLlTGDvqinP----eAsCLIMTTEILRsMLYrg-adliRDvE~VIFDEVHYiND~-eRGvVWEEViIMlP~HV~~Il  439 (1248)
T KOG0947|consen  368 --GLLTGDVQINP----EASCLIMTTEILRSMLYRG-ADLIRDVEFVIFDEVHYINDV-ERGVVWEEVIIMLPRHVNFIL  439 (1248)
T ss_pred             --ceeecceeeCC----CcceEeehHHHHHHHHhcc-cchhhccceEEEeeeeecccc-cccccceeeeeeccccceEEE
Confidence              25556554433    3569999999999887653 334788999999999999765 344445677788999999999


Q ss_pred             EEeeCChhHHHHHHhhCCC-CeEEecccc-ccccc---------------------------------------------
Q psy11867        284 FSATYDKEVMEFAQDMVPN-PLIIKLKRE-EESLD---------------------------------------------  316 (399)
Q Consensus       284 ~SAT~~~~v~~~~~~~~~~-p~~i~~~~~-~~~~~---------------------------------------------  316 (399)
                      +|||.|+.. +|+.+.-+. -..|.+... ...++                                             
T Consensus       440 LSATVPN~~-EFA~WIGRtK~K~IyViST~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~~~a~~~~~~~ak~~~~~~~  518 (1248)
T KOG0947|consen  440 LSATVPNTL-EFADWIGRTKQKTIYVISTSKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGIKDAKDSLKKEAKFVDVEKS  518 (1248)
T ss_pred             EeccCCChH-HHHHHhhhccCceEEEEecCCCccceEEEEEeccceehhhcccchhhhhcchhhhhhhcccccccccccc
Confidence            999999763 444443210 001111000 00000                                             


Q ss_pred             -----------ceeEEEE-------EeCChhh---HHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC--------
Q psy11867        317 -----------NIKQHYV-------MCKNIDE---KFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE--------  367 (399)
Q Consensus       317 -----------~i~~~~~-------~~~~~~~---k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~--------  367 (399)
                                 +.++.+-       .......   ....+.+.++...--|+||||-+++.|+..+..|...        
T Consensus       519 ~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L~k~~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EK  598 (1248)
T KOG0947|consen  519 DARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHLRKKNLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEK  598 (1248)
T ss_pred             cccccccccccCCcCCCCCCCcccccccccccccchHHHHHHHHhhcccCceEEEEEccccHHHHHHHHhccCcccchhH
Confidence                       0000000       0000001   1233444444444468999999999999999998651        


Q ss_pred             -------------------------------CCeEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        368 -------------------------------GLNVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       368 -------------------------------g~~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                                                     -..++++|||+-+--++-+.-.|..|-++||
T Consensus       599 seV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGlVKVL  660 (1248)
T KOG0947|consen  599 SEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGLVKVL  660 (1248)
T ss_pred             HHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHHHHHHHhcCceEEE
Confidence                                           1237899999999999999999999999997

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=99.78  E-value=2e-17  Score=167.48  Aligned_cols=262  Identities=23%  Similarity=0.265  Sum_probs=179.6

Q ss_pred             HHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        116 KGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       116 ~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      +.+.+.....|...|+-....++.  |++.-+.||||.|||.--++..+...   ..+.+++||+||+.|+.|+++.+++
T Consensus        73 ~fF~k~~G~~~ws~QR~WakR~~r--g~SFaiiAPTGvGKTTfg~~~sl~~a---~kgkr~yii~PT~~Lv~Q~~~kl~~  147 (1187)
T COG1110          73 EFFKKATGFRPWSAQRVWAKRLVR--GKSFAIIAPTGVGKTTFGLLMSLYLA---KKGKRVYIIVPTTTLVRQVYERLKK  147 (1187)
T ss_pred             HHHHHhhCCCchHHHHHHHHHHHc--CCceEEEcCCCCchhHHHHHHHHHHH---hcCCeEEEEecCHHHHHHHHHHHHH
Confidence            344444444999999999999999  79999999999999964443333222   2457899999999999999999999


Q ss_pred             HhccCCCcEEEEEEcCc--------hhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC-----
Q psy11867        196 MGKHITDLSVRYAVRGE--------NLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ-----  262 (399)
Q Consensus       196 ~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~-----  262 (399)
                      ++.......+...+.+.        ..++...++.+|+|+|.+-|....   ..+.-.+++++++|++|.++...     
T Consensus       148 ~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~---e~L~~~kFdfifVDDVDA~LkaskNvDr  224 (1187)
T COG1110         148 FAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRF---EELSKLKFDFIFVDDVDAILKASKNVDR  224 (1187)
T ss_pred             HHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhH---HHhcccCCCEEEEccHHHHHhccccHHH
Confidence            98776445544433332        122233567899999988665443   22222478999999999776322     


Q ss_pred             -----CchHHH-------HHHHHhC------------------------CCCCcEEEEEeeCChhH--HHHHHhhCCCCe
Q psy11867        263 -----GHQDFS-------IRIQKRL------------------------PSDCQIMLFSATYDKEV--MEFAQDMVPNPL  304 (399)
Q Consensus       263 -----~~~~~~-------~~i~~~l------------------------~~~~q~l~~SAT~~~~v--~~~~~~~~~~p~  304 (399)
                           ||.+..       ..+...+                        .+..+++..|||..+.-  ..+.+..    .
T Consensus       225 iL~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReL----l  300 (1187)
T COG1110         225 LLRLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFREL----L  300 (1187)
T ss_pred             HHHHcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHH----h
Confidence                 222211       1111111                        13468899999976532  1222222    2


Q ss_pred             EEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecc---hHhHHHHHHHHHHCCCeEEEEcCCCCHH
Q psy11867        305 IIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHT---RKTAAWLAEKMSKEGLNVGLLSGELTVE  381 (399)
Q Consensus       305 ~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s---~~~a~~l~~~L~~~g~~v~~lhg~~~~~  381 (399)
                      .+.++.....+.||...|+.... .++   +.++++... .-.|||++.   ++.|+.+++.|+..|+++..+|++    
T Consensus       301 gFevG~~~~~LRNIvD~y~~~~~-~e~---~~elvk~lG-~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~----  371 (1187)
T COG1110         301 GFEVGSGGEGLRNIVDIYVESES-LEK---VVELVKKLG-DGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE----  371 (1187)
T ss_pred             CCccCccchhhhheeeeeccCcc-HHH---HHHHHHHhC-CCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc----
Confidence            34555555667788888876622 333   333333332 247999999   999999999999999999999994    


Q ss_pred             HHHHHHHHHhcCCCcccC
Q psy11867        382 QRLSILDRFREGEFKIYS  399 (399)
Q Consensus       382 ~R~~v~~~F~~G~~~ILV  399 (399)
                       ++..++.|..|+++|||
T Consensus       372 -~~~~le~F~~GeidvLV  388 (1187)
T COG1110         372 -KEEALEDFEEGEVDVLV  388 (1187)
T ss_pred             -chhhhhhhccCceeEEE
Confidence             37789999999999996

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

Probab=99.77  E-value=4.3e-17  Score=147.16  Aligned_cols=252  Identities=15%  Similarity=0.201  Sum_probs=176.8

Q ss_pred             CChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        125 APSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      ++++.|+.+-..++..  ...+.++.|-||+|||-...-.+-..+.   .|.++.+.+|....+..++..+++-..   +
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~---~G~~vciASPRvDVclEl~~Rlk~aF~---~  170 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALN---QGGRVCIASPRVDVCLELYPRLKQAFS---N  170 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHh---cCCeEEEecCcccchHHHHHHHHHhhc---c
Confidence            6889999888777643  3689999999999999764433333333   466799999999999999999988654   3


Q ss_pred             cEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEE
Q psy11867        203 LSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM  282 (399)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l  282 (399)
                      ..+...+|+....    ...+++|+|.-+|+..-        +.++++||||+|.+.=. .-...-..+.+......-+|
T Consensus       171 ~~I~~Lyg~S~~~----fr~plvVaTtHQLlrFk--------~aFD~liIDEVDAFP~~-~d~~L~~Av~~ark~~g~~I  237 (441)
T COG4098         171 CDIDLLYGDSDSY----FRAPLVVATTHQLLRFK--------QAFDLLIIDEVDAFPFS-DDQSLQYAVKKARKKEGATI  237 (441)
T ss_pred             CCeeeEecCCchh----ccccEEEEehHHHHHHH--------hhccEEEEecccccccc-CCHHHHHHHHHhhcccCceE
Confidence            4555666554332    22579999998887652        35789999999997421 11222223444445677899


Q ss_pred             EEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHH------HHHHHhccCC--CCcEEEEecch
Q psy11867        283 LFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFE------AVSNIYGVVT--IGQAMIFCHTR  354 (399)
Q Consensus       283 ~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~------~l~~ll~~~~--~~k~IIF~~s~  354 (399)
                      ++|||-++.++.-+..-  +...+.+.......+-..-.++++.+-.+++.      .|..+++...  ..+++||+++.
T Consensus       238 ylTATp~k~l~r~~~~g--~~~~~klp~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p~I  315 (441)
T COG4098         238 YLTATPTKKLERKILKG--NLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPEI  315 (441)
T ss_pred             EEecCChHHHHHHhhhC--CeeEeecchhhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEecch
Confidence            99999887766544432  23334444443333344456777776655542      4666665543  36899999999


Q ss_pred             HhHHHHHHHHHHC-C-CeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        355 KTAAWLAEKMSKE-G-LNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       355 ~~a~~l~~~L~~~-g-~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +..+.++..|++. + ..++.+|+.  ...|.+.+++||+|++.+|+
T Consensus       316 ~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLi  360 (441)
T COG4098         316 ETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLI  360 (441)
T ss_pred             HHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEE
Confidence            9999999999544 3 356899988  56899999999999999985

>KOG0950|consensus

Probab=99.75  E-value=9.9e-18  Score=168.76  Aligned_cols=273  Identities=21%  Similarity=0.246  Sum_probs=180.6

Q ss_pred             CCHHHHHH-HHHcCCCCChHHHHHHh--hhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH
Q psy11867        110 LKPELLKG-VYEMGFYAPSKIQETAL--PTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA  186 (399)
Q Consensus       110 l~~~l~~~-l~~~g~~~p~~iQ~~ai--~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La  186 (399)
                      +++...+. .+..|....+.||.+|+  |.++.  ++|.|..+||+.|||+++-+-++..+...  ...++.+.|..+.+
T Consensus       207 ~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e--~~nliys~Pts~gktlvaeilml~~~l~~--rr~~llilp~vsiv  282 (1008)
T KOG0950|consen  207 LPTKVSHLYAKDKGILKLFEWQAECLSLPRLLE--RKNLIYSLPTSAGKTLVAEILMLREVLCR--RRNVLLILPYVSIV  282 (1008)
T ss_pred             CchHHHHHHHHhhhHHHHHHHHHHHhcchhhhc--ccceEEeCCCccchHHHHHHHHHHHHHHH--hhceeEecceeehh
Confidence            34444443 34578899999999998  66664  89999999999999999998888776543  33489999999999


Q ss_pred             HHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcc-ccccCCceeEEEEechhhHhhcCCch
Q psy11867        187 IQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKY-RFFDLSKIKVFVLDEADVMIATQGHQ  265 (399)
Q Consensus       187 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~-~~~~~~~~~~lViDEah~l~~~~~~~  265 (399)
                      +.-...+..+.... ++.+....|...-. ......++.|||-++-..++... +.-++..++++|+||.|.+++. +..
T Consensus       283 ~Ek~~~l~~~~~~~-G~~ve~y~g~~~p~-~~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~-~rg  359 (1008)
T KOG0950|consen  283 QEKISALSPFSIDL-GFPVEEYAGRFPPE-KRRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDK-GRG  359 (1008)
T ss_pred             HHHHhhhhhhcccc-CCcchhhcccCCCC-CcccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeecc-ccc
Confidence            88888888888776 66766655443332 23445679999999876553221 2225778999999999999875 444


Q ss_pred             HHHHHHHHh-----CCCCCcEEEEEeeCChh--HHHHHHhhC----CCCeEEecccccccccceeEEEEEeCChhhHHHH
Q psy11867        266 DFSIRIQKR-----LPSDCQIMLFSATYDKE--VMEFAQDMV----PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEA  334 (399)
Q Consensus       266 ~~~~~i~~~-----l~~~~q~l~~SAT~~~~--v~~~~~~~~----~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~  334 (399)
                      ..+..++..     .....|+|+||||+++-  +..+....+    ..|+...        +.++-....+.. + +...
T Consensus       360 ~~lE~~l~k~~y~~~~~~~~iIGMSATi~N~~lL~~~L~A~~y~t~fRPv~L~--------E~ik~G~~i~~~-~-r~~~  429 (1008)
T KOG0950|consen  360 AILELLLAKILYENLETSVQIIGMSATIPNNSLLQDWLDAFVYTTRFRPVPLK--------EYIKPGSLIYES-S-RNKV  429 (1008)
T ss_pred             hHHHHHHHHHHHhccccceeEeeeecccCChHHHHHHhhhhheecccCcccch--------hccCCCcccccc-h-hhHH
Confidence            444433322     23346799999999863  444433221    1121110        000000000000 0 1112


Q ss_pred             HHHHh--------------------ccCCC-CcEEEEecchHhHHHHHHHHHH---------------------------
Q psy11867        335 VSNIY--------------------GVVTI-GQAMIFCHTRKTAAWLAEKMSK---------------------------  366 (399)
Q Consensus       335 l~~ll--------------------~~~~~-~k~IIF~~s~~~a~~l~~~L~~---------------------------  366 (399)
                      +.++-                    ..... .++||||++++.|+.+|..+..                           
T Consensus       430 lr~ia~l~~~~~g~~dpD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~  509 (1008)
T KOG0950|consen  430 LREIANLYSSNLGDEDPDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRI  509 (1008)
T ss_pred             HHHhhhhhhhhcccCCCcceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcC
Confidence            22211                    11122 3599999999999999876654                           


Q ss_pred             -----------CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        367 -----------EGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       367 -----------~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                                 ..+.++++|+|++.++|+.+...||+|.+.|++
T Consensus       510 ~~~ld~Vl~~ti~~GvAyHhaGLT~eER~~iE~afr~g~i~vl~  553 (1008)
T KOG0950|consen  510 PGILDPVLAKTIPYGVAYHHAGLTSEEREIIEAAFREGNIFVLV  553 (1008)
T ss_pred             CcccchHHheeccccceecccccccchHHHHHHHHHhcCeEEEE
Confidence                       024589999999999999999999999999875

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.73  E-value=1.4e-16  Score=165.70  Aligned_cols=262  Identities=18%  Similarity=0.196  Sum_probs=167.9

Q ss_pred             CChHHHHHHhhhhhcC-CCC-cEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        125 APSKIQETALPTLLAD-PPH-NMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~-~g~-~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      .+++.|..++..++.. ... .+++.||||+|||.+.+.++...+.. .....+++++.|++.++.++++.++.+.....
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~  274 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFS  274 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcccc
Confidence            3489999999988765 234 89999999999999999999988876 45678999999999999999999998765431


Q ss_pred             CcEEEEEEcCchhhhh------------------hccCCcEEEeCchhHHHhhhcccccc-CC--ceeEEEEechhhHhh
Q psy11867        202 DLSVRYAVRGENLERN------------------KKITEQIIIGTPGKVLDWGLKYRFFD-LS--KIKVFVLDEADVMIA  260 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~~------------------~~~~~~IlV~Tp~~l~~~~~~~~~~~-~~--~~~~lViDEah~l~~  260 (399)
                      ... .. ..+......                  ......+.++||-...........+. +.  -...+|+||+|.+.+
T Consensus       275 ~~~-~~-~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~  352 (733)
T COG1203         275 VIG-KS-LHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYAD  352 (733)
T ss_pred             ccc-cc-ccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcc
Confidence            111 10 111111000                  01112355556555444211111111 11  236899999999865


Q ss_pred             cCCchHHHHHHHHhCC-CCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccccc---ccccceeEEEEEeCChhhHH--HH
Q psy11867        261 TQGHQDFSIRIQKRLP-SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREE---ESLDNIKQHYVMCKNIDEKF--EA  334 (399)
Q Consensus       261 ~~~~~~~~~~i~~~l~-~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~---~~~~~i~~~~~~~~~~~~k~--~~  334 (399)
                      .. ....+..++..+. ....+|++|||+|+.....+.........+......   ..-..+.+....+  .....  ..
T Consensus       353 ~~-~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~--~~~~~~~~~  429 (733)
T COG1203         353 ET-MLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVD--VEDGPQEEL  429 (733)
T ss_pred             cc-hHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchh--hhhhhhHhh
Confidence            32 3444444444442 478899999999999998888877654444332110   0001111111111  01110  11


Q ss_pred             HHHHh-ccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHh
Q psy11867        335 VSNIY-GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFR  391 (399)
Q Consensus       335 l~~ll-~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~  391 (399)
                      ..... .....++++|.|||++.|..+++.|+..+.++..+||.++..+|.+.+++++
T Consensus       430 ~~~~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~  487 (733)
T COG1203         430 IELISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELK  487 (733)
T ss_pred             hhcchhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHH
Confidence            11111 2223468999999999999999999998878999999999999999999655

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=99.68  E-value=6.7e-15  Score=156.21  Aligned_cols=83  Identities=22%  Similarity=0.217  Sum_probs=65.2

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhh---hcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTL---LADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA  186 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~l---l~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La  186 (399)
                      +++.+.+.+...||. +++.|.+.+..+   +.+ ++++++.||||+|||++|++|++....   .+.+++|.+||++|.
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~-~~~~~~eA~TG~GKT~ayLlp~~~~~~---~~~~vvi~t~t~~Lq  305 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTH-SEKSLIEAPTGTGKTLGYLLPALYYAI---TEKPVVISTNTKVLQ  305 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhcc-CCcEEEECCCCCchhHHHHHHHHHHhc---CCCeEEEEeCcHHHH
Confidence            445677778788886 889999866643   233 799999999999999999999988765   234799999999999


Q ss_pred             HHHHH-HHHHHh
Q psy11867        187 IQIGE-VVAKMG  197 (399)
Q Consensus       187 ~Q~~~-~~~~~~  197 (399)
                      .|+.. .+..+.
T Consensus       306 ~Ql~~~~~~~l~  317 (850)
T TIGR01407       306 SQLLEKDIPLLN  317 (850)
T ss_pred             HHHHHHHHHHHH
Confidence            99854 444443

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.68  E-value=1.6e-15  Score=125.29  Aligned_cols=141  Identities=31%  Similarity=0.519  Sum_probs=103.2

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh---hc
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KK  219 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~  219 (399)
                      +++++.++||+|||..++..+...... ....+++|++|++.++.|+.+.+......  ...+....+.......   ..
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~-~~~~~~lv~~p~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~   77 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS-LKGGQVLVLAPTRELANQVAERLKELFGE--GIKVGYLIGGTSIKQQEKLLS   77 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc-ccCCCEEEEcCcHHHHHHHHHHHHHHhhC--CcEEEEEecCcchhHHHHHhc
Confidence            478999999999999999888887765 24568999999999999999998887754  4555655555433322   24


Q ss_pred             cCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeC
Q psy11867        220 ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATY  288 (399)
Q Consensus       220 ~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~  288 (399)
                      ...+|+++|++.+........ ......+++|+||+|.+.... ................+++++|||.
T Consensus        78 ~~~~i~i~t~~~~~~~~~~~~-~~~~~~~~iiiDE~h~~~~~~-~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          78 GKTDIVVGTPGRLLDELERLK-LSLKKLDLLILDEAHRLLNQG-FGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCCCEEEECcHHHHHHHHcCC-cchhcCCEEEEeCHHHHhhcc-hHHHHHHHHhhCCccceEEEEeccC
Confidence            567899999999987654332 345678899999999997542 2222122334446788999999994

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

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.67  E-value=3.7e-15  Score=152.01  Aligned_cols=261  Identities=15%  Similarity=0.150  Sum_probs=176.6

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..|++.|..+.-.+..  |+  |+...||+|||+++.+|++.....+   ..+-+++||.-||.|-++.+..+...+ ++
T Consensus        79 ~~~~dvQlig~l~l~~--G~--iaEm~TGEGKTLvA~l~a~l~al~G---~~v~vvT~neyLA~Rd~e~~~~~~~~L-Gl  150 (796)
T PRK12906         79 LRPFDVQIIGGIVLHE--GN--IAEMKTGEGKTLTATLPVYLNALTG---KGVHVVTVNEYLSSRDATEMGELYRWL-GL  150 (796)
T ss_pred             CCCchhHHHHHHHHhc--CC--cccccCCCCCcHHHHHHHHHHHHcC---CCeEEEeccHHHHHhhHHHHHHHHHhc-CC
Confidence            3799999988776654  44  9999999999999999998777654   448999999999999999999999987 79


Q ss_pred             EEEEEEcCchh-hhhhccCCcEEEeCchhH-HHhhhcc-----ccccCCceeEEEEechhhHhhcC------------Cc
Q psy11867        204 SVRYAVRGENL-ERNKKITEQIIIGTPGKV-LDWGLKY-----RFFDLSKIKVFVLDEADVMIATQ------------GH  264 (399)
Q Consensus       204 ~~~~~~~~~~~-~~~~~~~~~IlV~Tp~~l-~~~~~~~-----~~~~~~~~~~lViDEah~l~~~~------------~~  264 (399)
                      ++.+..++... .+.....++|+.+|...| .+++..+     .....+.+.+.||||+|.++=..            ..
T Consensus       151 ~vg~i~~~~~~~~r~~~y~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiDeartPLiisg~~~~~  230 (796)
T PRK12906        151 TVGLNLNSMSPDEKRAAYNCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDEARTPLIISGQAEKA  230 (796)
T ss_pred             eEEEeCCCCCHHHHHHHhcCCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeeccCCCceecCCCCCcc
Confidence            99888776543 344456789999999887 3333322     11234678999999999553000            00


Q ss_pred             ---hHHHHHHHHhCCC----------------------------------------------------------------
Q psy11867        265 ---QDFSIRIQKRLPS----------------------------------------------------------------  277 (399)
Q Consensus       265 ---~~~~~~i~~~l~~----------------------------------------------------------------  277 (399)
                         ......+...+..                                                                
T Consensus       231 ~~~y~~~~~~v~~l~~~~~~~~~~~~~~~dy~id~~~k~v~lte~G~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~~l  310 (796)
T PRK12906        231 TDLYIRADRFVKTLIKDEAEDGDDDEDTGDYKIDEKTKTISLTEQGIRKAEKLFGLDNLYDSENTALAHHIDQALRANYI  310 (796)
T ss_pred             hHHHHHHHHHHHHHHhhhhccccccCCCCceEEEcccCceeecHHHHHHHHHHcCCccccCchhhhHHHHHHHHHHHHHH
Confidence               0000001000000                                                                


Q ss_pred             ----------------------------------------------------------------CCcEEEEEeeCChhHH
Q psy11867        278 ----------------------------------------------------------------DCQIMLFSATYDKEVM  293 (399)
Q Consensus       278 ----------------------------------------------------------------~~q~l~~SAT~~~~v~  293 (399)
                                                                                      -.++.+||.|......
T Consensus       311 ~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLHQaieaKe~v~i~~e~~t~a~It~qnfFr~Y~kl~GmTGTa~~e~~  390 (796)
T PRK12906        311 MLKDIDYVVQDGEVLIVDEFTGRVMEGRRYSDGLHQAIEAKEGVKIQEENQTLATITYQNFFRMYKKLSGMTGTAKTEEE  390 (796)
T ss_pred             HhcCCcEEEECCEEEEEeCCCCCcCCCCccChHHHHHHHHhcCCCcCCCceeeeeehHHHHHHhcchhhccCCCCHHHHH
Confidence                                                                            0134455555544434


Q ss_pred             HHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeE
Q psy11867        294 EFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNV  371 (399)
Q Consensus       294 ~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v  371 (399)
                      .+...|--+  .+.+.. +.........-..+.....|...+...+...  ...|+||||+|++.++.|+..|.+.|+++
T Consensus       391 Ef~~iY~l~--vv~IPt-nkp~~r~d~~d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~  467 (796)
T PRK12906        391 EFREIYNME--VITIPT-NRPVIRKDSPDLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGIPH  467 (796)
T ss_pred             HHHHHhCCC--EEEcCC-CCCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCe
Confidence            443333222  122222 1111111122223345577888888887543  55799999999999999999999999999


Q ss_pred             EEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        372 GLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       372 ~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                      .++|+++.+.++..+.+.++.|.+
T Consensus       468 ~~Lna~~~~~Ea~ii~~ag~~g~V  491 (796)
T PRK12906        468 AVLNAKNHAKEAEIIMNAGQRGAV  491 (796)
T ss_pred             eEecCCcHHHHHHHHHhcCCCceE
Confidence            999999999999999999999884

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=99.65  E-value=6.4e-15  Score=151.90  Aligned_cols=154  Identities=19%  Similarity=0.183  Sum_probs=100.7

Q ss_pred             CChHHHHHHhhhhhcC--------CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLAD--------PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~--------~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      .|+.+|..|+..+...        ..+..+++.+||||||+..+..+...+ .....+++|||+|+.+|..|+.+.++.+
T Consensus       238 ~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~~~~~vl~lvdR~~L~~Q~~~~f~~~  316 (667)
T TIGR00348       238 YQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELLKNPKVFFVVDRRELDYQLMKEFQSL  316 (667)
T ss_pred             ehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhcCCCeEEEEECcHHHHHHHHHHHHhh
Confidence            3788999999887532        146899999999999988776555444 3346688999999999999999999998


Q ss_pred             hccCCCcEEEEEEcCchhhhhh-ccCCcEEEeCchhHHHhhhcc-ccccCCce-eEEEEechhhHhhcCCchHHHHHHHH
Q psy11867        197 GKHITDLSVRYAVRGENLERNK-KITEQIIIGTPGKVLDWGLKY-RFFDLSKI-KVFVLDEADVMIATQGHQDFSIRIQK  273 (399)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~IlV~Tp~~l~~~~~~~-~~~~~~~~-~~lViDEah~l~~~~~~~~~~~~i~~  273 (399)
                      +....    ........+.... .....|+|+|.+.|...+... ..+....- -+||+||||+..    +......+.+
T Consensus       317 ~~~~~----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~----~~~~~~~l~~  388 (667)
T TIGR00348       317 QKDCA----ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQ----YGELAKNLKK  388 (667)
T ss_pred             CCCCC----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCcccc----chHHHHHHHh
Confidence            64211    0011111121111 234579999999997632221 11111111 289999999953    3333333434


Q ss_pred             hCCCCCcEEEEEeeC
Q psy11867        274 RLPSDCQIMLFSATY  288 (399)
Q Consensus       274 ~l~~~~q~l~~SAT~  288 (399)
                      .++ +..+++||||.
T Consensus       389 ~~p-~a~~lGfTaTP  402 (667)
T TIGR00348       389 ALK-NASFFGFTGTP  402 (667)
T ss_pred             hCC-CCcEEEEeCCC
Confidence            554 67899999995

Members of this family are assumed to differ from each other in DNA site specificity.

>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=99.65  E-value=6.9e-16  Score=134.10  Aligned_cols=153  Identities=16%  Similarity=0.148  Sum_probs=103.1

Q ss_pred             CChHHHHHHhhhhhcC-----CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        125 APSKIQETALPTLLAD-----PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~-----~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      +|+++|.+|+..+...     .++++++.+|||||||.+++..+.....      ++++++|+..|+.|+.+.+..+...
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------~~l~~~p~~~l~~Q~~~~~~~~~~~   76 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------KVLIVAPNISLLEQWYDEFDDFGSE   76 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------EEEEEESSHHHHHHHHHHHHHHSTT
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------ceeEecCHHHHHHHHHHHHHHhhhh
Confidence            5889999999999841     1599999999999999998866666555      6999999999999999999777654


Q ss_pred             CCCcEEEE---------EE-cCch--h-hhhhccCCcEEEeCchhHHHhhhccc----------cccCCceeEEEEechh
Q psy11867        200 ITDLSVRY---------AV-RGEN--L-ERNKKITEQIIIGTPGKVLDWGLKYR----------FFDLSKIKVFVLDEAD  256 (399)
Q Consensus       200 ~~~~~~~~---------~~-~~~~--~-~~~~~~~~~IlV~Tp~~l~~~~~~~~----------~~~~~~~~~lViDEah  256 (399)
                      ........         .. ....  . ........+++++|..++........          .......+++|+||||
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH  156 (184)
T PF04851_consen   77 KYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAH  156 (184)
T ss_dssp             SEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGG
T ss_pred             hhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhh
Confidence            21111110         00 0010  1 11124456799999999987643311          1234567899999999


Q ss_pred             hHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        257 VMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       257 ~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      ++.....    ...+..  .+...+|+||||..
T Consensus       157 ~~~~~~~----~~~i~~--~~~~~~l~lTATp~  183 (184)
T PF04851_consen  157 HYPSDSS----YREIIE--FKAAFILGLTATPF  183 (184)
T ss_dssp             CTHHHHH----HHHHHH--SSCCEEEEEESS-S
T ss_pred             hcCCHHH----HHHHHc--CCCCeEEEEEeCcc
Confidence            9865421    333434  46778999999964

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 ....

>KOG0951|consensus

Probab=99.62  E-value=2.7e-15  Score=154.19  Aligned_cols=308  Identities=17%  Similarity=0.224  Sum_probs=200.2

Q ss_pred             HHHHHHHhhhccccccceee--------ccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCC
Q psy11867         72 LLQKIVRRGLIESKQELEIQ--------RKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPH  143 (399)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~  143 (399)
                      ++-.++...|..+...+++.        ...|+.++.+.....-+.+.......|+    ....|+|.++++.+.+. ..
T Consensus      1086 ~fi~lvSd~wl~s~~~~Pvsfr~l~lpek~p~pt~lld~~~~~~~~l~N~~~~~lf----~~~n~iqtqVf~~~y~~-nd 1160 (1674)
T KOG0951|consen 1086 YFIRLVSDRWLHSETVLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNPSFETLF----QDFNPIQTQVFTSLYNT-ND 1160 (1674)
T ss_pred             eEEEEeeccccCCCcccccchhhccCcccCCCCchhhhccccchhccCCcchhhhc----cccCCceEEEEeeeecc-cc
Confidence            34445555555555544443        2344455554444444555555555553    34489999999999987 89


Q ss_pred             cEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCc
Q psy11867        144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQ  223 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (399)
                      +|++.+|+|||||.++-++++.    .....+++++.|..+.+..+++.+.+-.....++.+....|...+........+
T Consensus      1161 ~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~~~l~ge~s~~lkl~~~~~ 1236 (1674)
T KOG0951|consen 1161 NVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRIVKLTGETSLDLKLLQKGQ 1236 (1674)
T ss_pred             eEEEecCCCCchhHHHHHHhcC----CccceEEEEecchHHHHHHHHHHHHHhhccccCceEEecCCccccchHHhhhcc
Confidence            9999999999999999998886    235678999999999998888777665555567787777777777766677789


Q ss_pred             EEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCch----HHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhh
Q psy11867        224 IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ----DFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDM  299 (399)
Q Consensus       224 IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~----~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~  299 (399)
                      |+|+||+++-.+ +     ..+.++++|.||+|.+.+..|..    ..+..|...+-++.+++.+|..+.+. .+++  .
T Consensus      1237 vii~tpe~~d~l-q-----~iQ~v~l~i~d~lh~igg~~g~v~evi~S~r~ia~q~~k~ir~v~ls~~lana-~d~i--g 1307 (1674)
T KOG0951|consen 1237 VIISTPEQWDLL-Q-----SIQQVDLFIVDELHLIGGVYGAVYEVICSMRYIASQLEKKIRVVALSSSLANA-RDLI--G 1307 (1674)
T ss_pred             eEEechhHHHHH-h-----hhhhcceEeeehhhhhcccCCceEEEEeeHHHHHHHHHhheeEEEeehhhccc-hhhc--c
Confidence            999999987544 2     57789999999999987543211    11445666667788899999887643 2221  1


Q ss_pred             CCCCeEEeccccccccc-ceeEEEEEeCChhh--------HHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC---
Q psy11867        300 VPNPLIIKLKREEESLD-NIKQHYVMCKNIDE--------KFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE---  367 (399)
Q Consensus       300 ~~~p~~i~~~~~~~~~~-~i~~~~~~~~~~~~--------k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~---  367 (399)
                      ......+.+.......+ .+.-.-+.....+.        -+..+....  ...++++||++++++|..++.-|-..   
T Consensus      1308 ~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a--~~~k~~~vf~p~rk~~~~~a~~~~~~s~~ 1385 (1674)
T KOG0951|consen 1308 ASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHA--GNRKPAIVFLPTRKHARLVAVDLVTFSHA 1385 (1674)
T ss_pred             ccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHh--cCCCCeEEEeccchhhhhhhhccchhhcc
Confidence            11122222222222111 11111111111111        122222222  24468999999999998887554320   


Q ss_pred             -------------------CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        368 -------------------GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       368 -------------------g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                                         ..+..+=|.+++..+...+-..|..|.++|+|
T Consensus      1386 ~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v 1436 (1674)
T KOG0951|consen 1386 DEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCV 1436 (1674)
T ss_pred             CcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEE
Confidence                               11222229999999999999999999999875

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

Probab=99.60  E-value=9.4e-14  Score=143.18  Aligned_cols=243  Identities=22%  Similarity=0.228  Sum_probs=160.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      .+-++++|+||||||...-..+++...  ..+..+.+.-|.|--|..+.+.+.+-...-.+-.|.|.+...+..   ...
T Consensus        65 ~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~iRfe~~~---s~~  139 (845)
T COG1643          65 NQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYSIRFESKV---SPR  139 (845)
T ss_pred             CCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEEEEeeccC---CCC
Confidence            588999999999999876555554433  234456777799876666666555543332355566666555443   223


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhH-hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhC
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM-IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l-~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~  300 (399)
                      ..|-+.|.|.|+..+..  ...++.++++||||||.= ++.......+..++...+++.++|+||||+..+  .|. .++
T Consensus       140 Trik~mTdGiLlrei~~--D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSATld~~--rfs-~~f  214 (845)
T COG1643         140 TRIKVMTDGILLREIQN--DPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLDAE--RFS-AYF  214 (845)
T ss_pred             ceeEEeccHHHHHHHhh--CcccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEecccCHH--HHH-HHc
Confidence            46999999999998764  345899999999999963 222123334445566667789999999998853  343 344


Q ss_pred             CCCeEEecccccccccceeEEEEEeCChhh-H---HHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHH----CCCeEE
Q psy11867        301 PNPLIIKLKREEESLDNIKQHYVMCKNIDE-K---FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSK----EGLNVG  372 (399)
Q Consensus       301 ~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~-k---~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~----~g~~v~  372 (399)
                      .+.-.+.+....   ..+..+|......+. -   +............|-++||.+..++.+.+++.|.+    ....+.
T Consensus       215 ~~apvi~i~GR~---fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~  291 (845)
T COG1643         215 GNAPVIEIEGRT---YPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERTAEWLEKAELGDDLEIL  291 (845)
T ss_pred             CCCCEEEecCCc---cceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEe
Confidence            433333332211   223444433322222 2   23333333444568999999999999999999987    347899


Q ss_pred             EEcCCCCHHHHHHHHHHHhcCCCcc
Q psy11867        373 LLSGELTVEQRLSILDRFREGEFKI  397 (399)
Q Consensus       373 ~lhg~~~~~~R~~v~~~F~~G~~~I  397 (399)
                      .+||.|+.++..++++---.|+-+|
T Consensus       292 PLy~~L~~~eQ~rvF~p~~~~~RKV  316 (845)
T COG1643         292 PLYGALSAEEQVRVFEPAPGGKRKV  316 (845)
T ss_pred             eccccCCHHHHHhhcCCCCCCcceE
Confidence            9999999999999888777775444

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

Probab=99.60  E-value=2.3e-14  Score=143.45  Aligned_cols=253  Identities=17%  Similarity=0.176  Sum_probs=151.3

Q ss_pred             CCCChHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        123 FYAPSKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      -..|+.+|..||..+...   +.+.+++++.||+|||-.+. +++.+|.+.....|+|+|+-+++|+.|.+..+..+...
T Consensus       163 ~i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAi-aii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~  241 (875)
T COG4096         163 AIGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAI-AIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPF  241 (875)
T ss_pred             cccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHH-HHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCC
Confidence            357899999999877532   24569999999999998764 67777777777789999999999999999988887654


Q ss_pred             CCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcc----ccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC
Q psy11867        200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKY----RFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL  275 (399)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~----~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l  275 (399)
                      -   .......+....    ..++|.|+|..++.......    ..+....++++|+|||||-+-.     ....|+.++
T Consensus       242 ~---~~~n~i~~~~~~----~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi~~-----~~~~I~dYF  309 (875)
T COG4096         242 G---TKMNKIEDKKGD----TSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGIYS-----EWSSILDYF  309 (875)
T ss_pred             c---cceeeeecccCC----cceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhHHh-----hhHHHHHHH
Confidence            2   222222222111    14679999999997764332    3455677999999999995432     122454444


Q ss_pred             CCCCcEEEEEeeCChhHH------------------HHH-HhhCCCC--eEEecc--cccccccc-----------e---
Q psy11867        276 PSDCQIMLFSATYDKEVM------------------EFA-QDMVPNP--LIIKLK--REEESLDN-----------I---  318 (399)
Q Consensus       276 ~~~~q~l~~SAT~~~~v~------------------~~~-~~~~~~p--~~i~~~--~~~~~~~~-----------i---  318 (399)
                      ..-.  ++++||..+.+.                  +-+ ..++.++  +.+.+.  ...-.+..           +   
T Consensus       310 dA~~--~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i~~d  387 (875)
T COG4096         310 DAAT--QGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAIDED  387 (875)
T ss_pred             HHHH--HhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhccccCcc
Confidence            3222  233777543221                  111 1222222  222211  10000000           0   


Q ss_pred             eEEE--------EEeC-ChhhHHHHHHHHhcc--CC--CCcEEEEecchHhHHHHHHHHHHC-----CCeEEEEcCCCCH
Q psy11867        319 KQHY--------VMCK-NIDEKFEAVSNIYGV--VT--IGQAMIFCHTRKTAAWLAEKMSKE-----GLNVGLLSGELTV  380 (399)
Q Consensus       319 ~~~~--------~~~~-~~~~k~~~l~~ll~~--~~--~~k~IIF~~s~~~a~~l~~~L~~~-----g~~v~~lhg~~~~  380 (399)
                      .+.|        ..+. ..+--...+.+.+..  ..  .+|+||||.+..+|+.+.+.|...     |--+..+.|+-.+
T Consensus       388 d~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~~~  467 (875)
T COG4096         388 DQNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAEQ  467 (875)
T ss_pred             cccccccccchhccccchHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccchh
Confidence            0111        1111 111122334444544  22  479999999999999999999875     3346777777554


Q ss_pred             HHHHHHHHHHhc
Q psy11867        381 EQRLSILDRFRE  392 (399)
Q Consensus       381 ~~R~~v~~~F~~  392 (399)
                      .++  .+..|..
T Consensus       468 ~q~--~Id~f~~  477 (875)
T COG4096         468 AQA--LIDNFID  477 (875)
T ss_pred             hHH--HHHHHHh
Confidence            443  4555543

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.58  E-value=1.2e-13  Score=145.68  Aligned_cols=258  Identities=14%  Similarity=0.120  Sum_probs=159.2

Q ss_pred             CChHHHHHHhhhhhc--CCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        125 APSKIQETALPTLLA--DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~--~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      .+.++|.+++..++.  ..|.+.|++..+|.|||+..+..+............+|||||. .+..|+.+.++++.   +.
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~---p~  244 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFC---PV  244 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHC---CC
Confidence            678999999998863  2378899999999999987543332222222233458999997 56677888888775   35


Q ss_pred             cEEEEEEcCchhhhh------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC
Q psy11867        203 LSVRYAVRGENLERN------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP  276 (399)
Q Consensus       203 ~~~~~~~~~~~~~~~------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~  276 (399)
                      +.+....|.......      .....+|+|+|++.+....   ..+.--.+++||+||||++-   .........++.+.
T Consensus       245 l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~---~~L~k~~W~~VIvDEAHrIK---N~~Sklskalr~L~  318 (1033)
T PLN03142        245 LRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEK---TALKRFSWRYIIIDEAHRIK---NENSLLSKTMRLFS  318 (1033)
T ss_pred             CceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHH---HHhccCCCCEEEEcCccccC---CHHHHHHHHHHHhh
Confidence            555555555432111      1235689999999886542   22222356899999999984   33444555566664


Q ss_pred             CCCcEEEEEeeCC-h---hHHHHHHhhCCC--------------------------------CeEEe-cccc-cccccce
Q psy11867        277 SDCQIMLFSATYD-K---EVMEFAQDMVPN--------------------------------PLIIK-LKRE-EESLDNI  318 (399)
Q Consensus       277 ~~~q~l~~SAT~~-~---~v~~~~~~~~~~--------------------------------p~~i~-~~~~-~~~~~~i  318 (399)
                       ....+++|+|.- +   +++.++....++                                |..++ +... ...++..
T Consensus       319 -a~~RLLLTGTPlqNnl~ELwsLL~FL~P~~f~s~~~F~~~f~~~~~~~~~e~i~~L~~~L~pf~LRR~KsdV~~~LPpK  397 (1033)
T PLN03142        319 -TNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLPPK  397 (1033)
T ss_pred             -cCcEEEEecCCCCCCHHHHHHHHhcCCCCcCCCHHHHHHHHccccccchHHHHHHHHHHhhHHHhhhhHHHHhhhCCCc
Confidence             345688999931 1   122221111111                                00000 0000 0000111


Q ss_pred             eEEEEEeC--------------------------------------------------------------ChhhHHHHHH
Q psy11867        319 KQHYVMCK--------------------------------------------------------------NIDEKFEAVS  336 (399)
Q Consensus       319 ~~~~~~~~--------------------------------------------------------------~~~~k~~~l~  336 (399)
                      ....+.|.                                                              ....|...|.
T Consensus       398 ~e~iv~v~LS~~Qk~lY~~ll~k~~~~l~~g~~~~~LlnilmqLRk~cnHP~L~~~~ep~~~~~~~e~lie~SgKl~lLd  477 (1033)
T PLN03142        398 KETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGEHLVENSGKMVLLD  477 (1033)
T ss_pred             eeEEEeeCCCHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCHHhhhcccccCcccchhHHhhhhhHHHHHH
Confidence            11111111                                                              0123444444


Q ss_pred             HHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC
Q psy11867        337 NIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREG  393 (399)
Q Consensus       337 ~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G  393 (399)
                      .++...  ...++||||........|.+.|...|+....+||+++..+|..+++.|.+.
T Consensus       478 kLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~  536 (1033)
T PLN03142        478 KLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKP  536 (1033)
T ss_pred             HHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccc
Confidence            444332  336999999999999999999999999999999999999999999999864

>KOG0920|consensus

Probab=99.45  E-value=8.7e-12  Score=128.51  Aligned_cols=263  Identities=19%  Similarity=0.206  Sum_probs=171.0

Q ss_pred             ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEE
Q psy11867        126 PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV  205 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~  205 (399)
                      .+..+.+.+..+.+  .+.++++|.||+|||.-..--++..........+++|--|.|--|.-+++.+.+-.....+-.+
T Consensus       174 a~~~r~~Il~~i~~--~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~V  251 (924)
T KOG0920|consen  174 AYKMRDTILDAIEE--NQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEV  251 (924)
T ss_pred             cHHHHHHHHHHHHh--CceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCee
Confidence            34667777777777  5999999999999998877777776644445566777779998888888877665444335555


Q ss_pred             EEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      .+.++.......   ...+++||.|.|+..+..  .-.+..+.++|+||+|.=.-...|.-.+.+.+-..++..++++||
T Consensus       252 GYqvrl~~~~s~---~t~L~fcTtGvLLr~L~~--~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p~LkvILMS  326 (924)
T KOG0920|consen  252 GYQVRLESKRSR---ETRLLFCTTGVLLRRLQS--DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNPDLKVILMS  326 (924)
T ss_pred             eEEEeeecccCC---ceeEEEecHHHHHHHhcc--CcccccCceeeeeeEEEccCCcccHHHHHHHHhhhCCCceEEEee
Confidence            665555433222   246999999999998765  446889999999999974322223333333333445789999999


Q ss_pred             eeCChhHHHHHHhhCCCCeEEecc-cccc---------------cccceeEEE-----------EEeCChhhHHHHHHH-
Q psy11867        286 ATYDKEVMEFAQDMVPNPLIIKLK-REEE---------------SLDNIKQHY-----------VMCKNIDEKFEAVSN-  337 (399)
Q Consensus       286 AT~~~~v~~~~~~~~~~p~~i~~~-~~~~---------------~~~~i~~~~-----------~~~~~~~~k~~~l~~-  337 (399)
                      ||+..+   ....|+.+.-.+.+. ....               ......+..           ..+-..+..+..+.. 
T Consensus       327 AT~dae---~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~Li~~l  403 (924)
T KOG0920|consen  327 ATLDAE---LFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDLIEDL  403 (924)
T ss_pred             eecchH---HHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHHHHHH
Confidence            998833   233334333222221 1000               000001110           000011122233333 


Q ss_pred             ---HhccCCCCcEEEEecchHhHHHHHHHHHHC-------CCeEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        338 ---IYGVVTIGQAMIFCHTRKTAAWLAEKMSKE-------GLNVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       338 ---ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~-------g~~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                         +......|.+|||.+.......+++.|...       .+-+..+|+.|+..+...+...--.|.-+|+
T Consensus       404 i~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKII  474 (924)
T KOG0920|consen  404 IEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKII  474 (924)
T ss_pred             HHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhh
Confidence               333444588999999999999999999652       2568899999999999999998888877765

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=99.42  E-value=8.1e-12  Score=127.19  Aligned_cols=156  Identities=19%  Similarity=0.231  Sum_probs=109.3

Q ss_pred             CCChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        124 YAPSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      ..+++-|..|+..+...  .-...++.+.||||||-+|+-.+-..+..+   .++|+|+|-.+|..|+...++....   
T Consensus       197 ~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~G---kqvLvLVPEI~Ltpq~~~rf~~rFg---  270 (730)
T COG1198         197 LALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQG---KQVLVLVPEIALTPQLLARFKARFG---  270 (730)
T ss_pred             cccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcC---CEEEEEeccccchHHHHHHHHHHhC---
Confidence            35778999999999764  236789999999999999998877777654   5699999999999999999988653   


Q ss_pred             CcEEEEEEcCc-------hhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh----hcCCchHHHHH
Q psy11867        202 DLSVRYAVRGE-------NLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI----ATQGHQDFSIR  270 (399)
Q Consensus       202 ~~~~~~~~~~~-------~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~----~~~~~~~~~~~  270 (399)
                       .++....++-       .+.+...+...|+|||=..+        ..-+++++++|+||=|--.    +...+..--..
T Consensus       271 -~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl--------F~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA  341 (730)
T COG1198         271 -AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSAL--------FLPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVA  341 (730)
T ss_pred             -CChhhhcccCChHHHHHHHHHHhcCCceEEEEechhh--------cCchhhccEEEEeccccccccCCcCCCcCHHHHH
Confidence             3333333332       22233356778999995443        2347899999999999642    11123332334


Q ss_pred             HHHhCCCCCcEEEEEeeCChhHHH
Q psy11867        271 IQKRLPSDCQIMLFSATYDKEVME  294 (399)
Q Consensus       271 i~~~l~~~~q~l~~SAT~~~~v~~  294 (399)
                      +.+.-..++++|+-|||-.-+...
T Consensus       342 ~~Ra~~~~~pvvLgSATPSLES~~  365 (730)
T COG1198         342 VLRAKKENAPVVLGSATPSLESYA  365 (730)
T ss_pred             HHHHHHhCCCEEEecCCCCHHHHH
Confidence            444444689999999995544333

>KOG0949|consensus

Probab=99.42  E-value=8.5e-12  Score=126.21  Aligned_cols=161  Identities=17%  Similarity=0.137  Sum_probs=111.6

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..|-.||.+.+..+=.  +..++++|||.+|||.+-...+- ...+......+|+++||++|+.|+...+........-.
T Consensus       510 F~Pd~WQ~elLDsvDr--~eSavIVAPTSaGKTfisfY~iE-KVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~  586 (1330)
T KOG0949|consen  510 FCPDEWQRELLDSVDR--NESAVIVAPTSAGKTFISFYAIE-KVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFL  586 (1330)
T ss_pred             cCCcHHHHHHhhhhhc--ccceEEEeeccCCceeccHHHHH-HHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccc
Confidence            3678899999998876  69999999999999987655444 44444566789999999999999988777665322122


Q ss_pred             EEEEEEcCchhhhhh-ccCCcEEEeCchhHHHhhhcc--ccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCc
Q psy11867        204 SVRYAVRGENLERNK-KITEQIIIGTPGKVLDWGLKY--RFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ  280 (399)
Q Consensus       204 ~~~~~~~~~~~~~~~-~~~~~IlV~Tp~~l~~~~~~~--~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q  280 (399)
                      ......|....+-.. .-.|+|+|+-|+.+-.++...  ..-+..+++++|+||+|.+....... .+..++-  -..|.
T Consensus       587 rg~sl~g~ltqEYsinp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l-~~Eqll~--li~CP  663 (1330)
T KOG0949|consen  587 RGVSLLGDLTQEYSINPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGL-LWEQLLL--LIPCP  663 (1330)
T ss_pred             cchhhHhhhhHHhcCCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccch-HHHHHHH--hcCCC
Confidence            222223332222222 346899999999998876653  34468899999999999986532211 1222222  24788


Q ss_pred             EEEEEeeCCh
Q psy11867        281 IMLFSATYDK  290 (399)
Q Consensus       281 ~l~~SAT~~~  290 (399)
                      ++++|||+.+
T Consensus       664 ~L~LSATigN  673 (1330)
T KOG0949|consen  664 FLVLSATIGN  673 (1330)
T ss_pred             eeEEecccCC
Confidence            9999999764

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.42  E-value=2.8e-11  Score=121.62  Aligned_cols=127  Identities=19%  Similarity=0.172  Sum_probs=99.6

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|++.|....-.++.  |  -|+...||.|||+++.+|+......   +..+-|++||.-||.|-++++..+...+ +++
T Consensus        78 r~ydvQlig~l~Ll~--G--~VaEM~TGEGKTLvA~l~a~l~AL~---G~~VhvvT~NdyLA~RDae~m~~ly~~L-GLs  149 (764)
T PRK12326         78 RPFDVQLLGALRLLA--G--DVIEMATGEGKTLAGAIAAAGYALQ---GRRVHVITVNDYLARRDAEWMGPLYEAL-GLT  149 (764)
T ss_pred             CcchHHHHHHHHHhC--C--CcccccCCCCHHHHHHHHHHHHHHc---CCCeEEEcCCHHHHHHHHHHHHHHHHhc-CCE
Confidence            799999999988886  3  4779999999999999998877654   3459999999999999999999999887 889


Q ss_pred             EEEEEcCchhh-hhhccCCcEEEeCchhH-HHhhhcc-----ccccCCceeEEEEechhhHh
Q psy11867        205 VRYAVRGENLE-RNKKITEQIIIGTPGKV-LDWGLKY-----RFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       205 ~~~~~~~~~~~-~~~~~~~~IlV~Tp~~l-~~~~~~~-----~~~~~~~~~~lViDEah~l~  259 (399)
                      +.+..++.... +.....++|+.+|...| .+++..+     .....+.+.+.|+||+|.++
T Consensus       150 vg~i~~~~~~~err~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiL  211 (764)
T PRK12326        150 VGWITEESTPEERRAAYACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVL  211 (764)
T ss_pred             EEEECCCCCHHHHHHHHcCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhhe
Confidence            98887765443 33356789999999876 2332221     22235678899999999664

>KOG0922|consensus

Probab=99.41  E-value=4.3e-11  Score=117.61  Aligned_cols=239  Identities=23%  Similarity=0.283  Sum_probs=152.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHH-HhccCCCcEEEEEEcCchhhhhhcc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK-MGKHITDLSVRYAVRGENLERNKKI  220 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  220 (399)
                      .+-+|+.|+||||||.----.+.+.--.  ...++.|.-|.|--|.-+++.... ++..+ +-.+.+.+.-.+....   
T Consensus        66 nqvlIviGeTGsGKSTQipQyL~eaG~~--~~g~I~~TQPRRVAavslA~RVAeE~~~~l-G~~VGY~IRFed~ts~---  139 (674)
T KOG0922|consen   66 NQVLIVIGETGSGKSTQIPQYLAEAGFA--SSGKIACTQPRRVAAVSLAKRVAEEMGCQL-GEEVGYTIRFEDSTSK---  139 (674)
T ss_pred             CCEEEEEcCCCCCccccHhHHHHhcccc--cCCcEEeecCchHHHHHHHHHHHHHhCCCc-CceeeeEEEecccCCC---
Confidence            5899999999999997532222222111  223366777988777766654443 44333 5556665554433222   


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC---CCCCcEEEEEeeCChhHHHHHH
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL---PSDCQIMLFSATYDKEVMEFAQ  297 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l---~~~~q~l~~SAT~~~~v~~~~~  297 (399)
                      ...|.+.|-|.|+..+..  .-.+++.+++|+||||.=.   -+.|.+..+++.+   ++..+++++|||+..+  . ..
T Consensus       140 ~TrikymTDG~LLRE~l~--Dp~LskYsvIIlDEAHERs---l~TDiLlGlLKki~~~R~~LklIimSATlda~--k-fS  211 (674)
T KOG0922|consen  140 DTRIKYMTDGMLLREILK--DPLLSKYSVIILDEAHERS---LHTDILLGLLKKILKKRPDLKLIIMSATLDAE--K-FS  211 (674)
T ss_pred             ceeEEEecchHHHHHHhc--CCccccccEEEEechhhhh---hHHHHHHHHHHHHHhcCCCceEEEEeeeecHH--H-HH
Confidence            346999999999987654  3358899999999999631   2445555555544   3467899999999843  3 33


Q ss_pred             hhCCC-CeEEecccccccccceeEEEEEeCCh---hhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC----CC
Q psy11867        298 DMVPN-PLIIKLKREEESLDNIKQHYVMCKNI---DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE----GL  369 (399)
Q Consensus       298 ~~~~~-p~~i~~~~~~~~~~~i~~~~~~~~~~---~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~----g~  369 (399)
                      .|+.+ |+...-++.    -.++..|..-+..   +.-+..+.++-...+.|-++||....++.+.+++.|.+.    +.
T Consensus       212 ~yF~~a~i~~i~GR~----fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~  287 (674)
T KOG0922|consen  212 EYFNNAPILTIPGRT----FPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACELLRERAKSLPE  287 (674)
T ss_pred             HHhcCCceEeecCCC----CceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccc
Confidence            44444 443322221    1233444432222   223344445555566788999999999999999998775    11


Q ss_pred             ----eEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        370 ----NVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       370 ----~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                          -+..+||.|+.++..++++---.|.-+|+
T Consensus       288 ~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvI  320 (674)
T KOG0922|consen  288 DCPELILPLYGALPSEEQSRVFDPAPPGKRKVI  320 (674)
T ss_pred             cCcceeeeecccCCHHHhhccccCCCCCcceEE
Confidence                25789999999999998877666655554

>KOG1123|consensus

Probab=99.40  E-value=4e-12  Score=120.33  Aligned_cols=251  Identities=16%  Similarity=0.180  Sum_probs=151.1

Q ss_pred             CCCChHHHHHHhhhhhcC-CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        123 FYAPSKIQETALPTLLAD-PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~-~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      -..++|+|+.++..+.-+ ..+.-||..|.|+|||++-+-++. .     -..+|||||.+---+.|+...++.+..--+
T Consensus       300 st~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~-t-----ikK~clvLcts~VSVeQWkqQfk~wsti~d  373 (776)
T KOG1123|consen  300 STQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAAC-T-----IKKSCLVLCTSAVSVEQWKQQFKQWSTIQD  373 (776)
T ss_pred             ccccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeee-e-----ecccEEEEecCccCHHHHHHHHHhhcccCc
Confidence            357889999999998854 346889999999999998765443 2     234599999999999999999988753322


Q ss_pred             CcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcc-------ccccCCceeEEEEechhhHhhcCCchHHHHHHHHh
Q psy11867        202 DLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKY-------RFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR  274 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~-------~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~  274 (399)
                      . .+..+....  ......++.|+|+|..++..--.+.       ..+.-+..+++++||+|.+.+. -|...+..+.. 
T Consensus       374 ~-~i~rFTsd~--Ke~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~-MFRRVlsiv~a-  448 (776)
T KOG1123|consen  374 D-QICRFTSDA--KERFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAK-MFRRVLSIVQA-  448 (776)
T ss_pred             c-ceEEeeccc--cccCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHH-HHHHHHHHHHH-
Confidence            1 222222211  1112456779999998875431111       1123456889999999998764 34433333322 


Q ss_pred             CCCCCcEEEEEeeCChhHHHHHH-hhCCCCeEEeccc----ccccccceeEEEEEeCCh---------------------
Q psy11867        275 LPSDCQIMLFSATYDKEVMEFAQ-DMVPNPLIIKLKR----EEESLDNIKQHYVMCKNI---------------------  328 (399)
Q Consensus       275 l~~~~q~l~~SAT~~~~v~~~~~-~~~~~p~~i~~~~----~~~~~~~i~~~~~~~~~~---------------------  328 (399)
                         .| .++++||+-.+-..... .++-.|......=    ...-..++...-+||+-.                     
T Consensus       449 ---Hc-KLGLTATLvREDdKI~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eYL~~~t~kr~lLyvM  524 (776)
T KOG1123|consen  449 ---HC-KLGLTATLVREDDKITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREYLRENTRKRMLLYVM  524 (776)
T ss_pred             ---Hh-hccceeEEeeccccccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHHHhhhhhhhheeeec
Confidence               22 58999997433222111 1222332211100    001112233333344321                     


Q ss_pred             -hhHHHHHHHHhcc--CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC
Q psy11867        329 -DEKFEAVSNIYGV--VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREG  393 (399)
Q Consensus       329 -~~k~~~l~~ll~~--~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G  393 (399)
                       ..|+.+-.-+++-  ..+.++|||..+.-.....|-.|.+     -.+.|..++.+|..+++.|+-.
T Consensus       525 NP~KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~K-----pfIYG~Tsq~ERm~ILqnFq~n  587 (776)
T KOG1123|consen  525 NPNKFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLGK-----PFIYGPTSQNERMKILQNFQTN  587 (776)
T ss_pred             CcchhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHcCC-----ceEECCCchhHHHHHHHhcccC
Confidence             1233333333322  2457999999887776666666633     3688999999999999999854

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

Probab=99.33  E-value=1.3e-10  Score=111.38  Aligned_cols=56  Identities=25%  Similarity=0.415  Sum_probs=54.3

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+++|-+-|++.|+.|.++|...|+++..+|++..--+|.++++.+|.|.++|||
T Consensus       446 ~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLV  501 (663)
T COG0556         446 NERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLV  501 (663)
T ss_pred             CCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEE
Confidence            37999999999999999999999999999999999999999999999999999997

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.30  E-value=9.4e-11  Score=120.64  Aligned_cols=128  Identities=20%  Similarity=0.143  Sum_probs=98.4

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..|+++|...--.+.    +.-|+...||+|||+++.+|++-....   +..+-|++||.-||.|-++++..+...+ ++
T Consensus        81 m~~ydVQliGg~~Lh----~G~iaEM~TGEGKTLvA~l~a~l~al~---G~~VhvvT~ndyLA~RD~e~m~~l~~~l-Gl  152 (913)
T PRK13103         81 MRHFDVQLIGGMTLH----EGKIAEMRTGEGKTLVGTLAVYLNALS---GKGVHVVTVNDYLARRDANWMRPLYEFL-GL  152 (913)
T ss_pred             CCcchhHHHhhhHhc----cCccccccCCCCChHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHhccc-CC
Confidence            478899987765554    456889999999999999999866654   3459999999999999999999999887 88


Q ss_pred             EEEEEEcCchh-hhhhccCCcEEEeCchhH-HHhhhccc-----cccCCceeEEEEechhhHh
Q psy11867        204 SVRYAVRGENL-ERNKKITEQIIIGTPGKV-LDWGLKYR-----FFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       204 ~~~~~~~~~~~-~~~~~~~~~IlV~Tp~~l-~~~~~~~~-----~~~~~~~~~lViDEah~l~  259 (399)
                      ++.+..++... ++.....++|++||...| .+++...-     ..-.+.+.++||||+|.++
T Consensus       153 ~v~~i~~~~~~~err~~Y~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        153 SVGIVTPFQPPEEKRAAYAADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             EEEEECCCCCHHHHHHHhcCCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            98888776543 333355689999999886 33332221     1124789999999999764

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

Probab=99.28  E-value=2.2e-11  Score=128.05  Aligned_cols=74  Identities=26%  Similarity=0.364  Sum_probs=58.6

Q ss_pred             cCCCCChHHHHHHhhhh---hcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH-HHHHHHH
Q psy11867        121 MGFYAPSKIQETALPTL---LADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI-GEVVAKM  196 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~l---l~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~-~~~~~~~  196 (399)
                      .|| ++++-|.+....+   +.+ +.+++++|+||+|||++|++|++...    .+.+++|++||++|+.|+ .+.+..+
T Consensus       242 ~~~-e~R~~Q~~ma~~V~~~l~~-~~~~~~eA~tGtGKT~ayllp~l~~~----~~~~vvI~t~T~~Lq~Ql~~~~i~~l  315 (820)
T PRK07246        242 LGL-EERPKQESFAKLVGEDFHD-GPASFIEAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQIMAEEVKAI  315 (820)
T ss_pred             CCC-ccCHHHHHHHHHHHHHHhC-CCcEEEECCCCCcHHHHHHHHHHHhc----CCCcEEEEeCcHHHHHHHHHHHHHHH
Confidence            344 6899999955444   444 79999999999999999999998754    246799999999999999 4666666


Q ss_pred             hccC
Q psy11867        197 GKHI  200 (399)
Q Consensus       197 ~~~~  200 (399)
                      .+.+
T Consensus       316 ~~~~  319 (820)
T PRK07246        316 QEVF  319 (820)
T ss_pred             HHhc
Confidence            5543

>KOG0385|consensus

Probab=99.28  E-value=1.6e-10  Score=114.69  Aligned_cols=257  Identities=18%  Similarity=0.207  Sum_probs=161.6

Q ss_pred             CChHHHHHHhhhhhc--CCCCcEEEEccCCCCceehhHHHHHHhhC--CCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        125 APSKIQETALPTLLA--DPPHNMIAQSQSGTGKTAAFTLTMLSRVN--PSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~--~~g~~vi~~a~TGsGKT~~~~l~il~~l~--~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      .++++|.+.++.+.+  ..|-|.|.....|-|||+.-. +++..+.  .+..+| -||++|...|..    ++..+..++
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtI-s~l~yl~~~~~~~GP-fLVi~P~StL~N----W~~Ef~rf~  240 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTI-SLLGYLKGRKGIPGP-FLVIAPKSTLDN----WMNEFKRFT  240 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHH-HHHHHHHHhcCCCCC-eEEEeeHhhHHH----HHHHHHHhC
Confidence            678999999988854  248899999999999997532 2333222  222333 689999988753    344445556


Q ss_pred             CCcEEEEEEcCchhhhhh------ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHh
Q psy11867        201 TDLSVRYAVRGENLERNK------KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR  274 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~------~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~  274 (399)
                      |.+++...+|........      ....+|+|+|.+..+.-   ...+.--+.+++|||||||+-   .....+..+++.
T Consensus       241 P~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d---k~~lk~~~W~ylvIDEaHRiK---N~~s~L~~~lr~  314 (971)
T KOG0385|consen  241 PSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD---KSFLKKFNWRYLVIDEAHRIK---NEKSKLSKILRE  314 (971)
T ss_pred             CCcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh---HHHHhcCCceEEEechhhhhc---chhhHHHHHHHH
Confidence            788888888876432221      34668999999987653   223333467899999999984   455556677776


Q ss_pred             CCCCCcEEEEEeeC-Ch---hHHHHHHhhCCC------------------------------------------------
Q psy11867        275 LPSDCQIMLFSATY-DK---EVMEFAQDMVPN------------------------------------------------  302 (399)
Q Consensus       275 l~~~~q~l~~SAT~-~~---~v~~~~~~~~~~------------------------------------------------  302 (399)
                      +.... .+++|.|. -+   +++.++...+++                                                
T Consensus       315 f~~~n-rLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~sLp  393 (971)
T KOG0385|consen  315 FKTDN-RLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEKSLP  393 (971)
T ss_pred             hcccc-eeEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHhhhhHHHHHHHHHhHhhcCC
Confidence            65444 46677771 00   011111111100                                                


Q ss_pred             -C--eEEeccc---------------------cc----cc--------ccceeEEEEEeC--------------ChhhHH
Q psy11867        303 -P--LIIKLKR---------------------EE----ES--------LDNIKQHYVMCK--------------NIDEKF  332 (399)
Q Consensus       303 -p--~~i~~~~---------------------~~----~~--------~~~i~~~~~~~~--------------~~~~k~  332 (399)
                       .  +.+.++-                     ..    ..        ..+..+.|.+-.              ....|+
T Consensus       394 pKkE~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~~k~kL~NI~mQLRKccnHPYLF~g~ePg~pyttdehLv~nSGKm  473 (971)
T KOG0385|consen  394 PKKELIIYVGMSSMQKKWYKAILMKDLDALNGEGKGEKTKLQNIMMQLRKCCNHPYLFDGAEPGPPYTTDEHLVTNSGKM  473 (971)
T ss_pred             CcceeeEeccchHHHHHHHHHHHHhcchhhcccccchhhHHHHHHHHHHHhcCCccccCCCCCCCCCCcchHHHhcCcce
Confidence             0  1111100                     00    00        001122222111              113466


Q ss_pred             HHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC
Q psy11867        333 EAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGE  394 (399)
Q Consensus       333 ~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~  394 (399)
                      ..|-.++...  .+.++|||.+--.....|-.++.-.++...-+-|.++.++|...++.|..-.
T Consensus       474 ~vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~  537 (971)
T KOG0385|consen  474 LVLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPP  537 (971)
T ss_pred             ehHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCC
Confidence            6666666543  3469999999999999999998888999999999999999999999998755

>KOG4150|consensus

Probab=99.27  E-value=1e-11  Score=119.21  Aligned_cols=275  Identities=11%  Similarity=0.001  Sum_probs=181.7

Q ss_pred             HHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        118 VYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       118 l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      +..+--.....+|.+++..+..  |+++++...|.+||.++|.+.....+... .....+++.|+.++++...+.+.-..
T Consensus       279 ~~~~~~E~~~~~~~~~~~~~~~--G~~~~~~~~~~~GK~~~~~~~s~~~~~~~-~~s~~~~~~~~~~~~~~~~~~~~V~~  355 (1034)
T KOG4150|consen  279 LNKNTGESGIAISLELLKFASE--GRADGGNEARQAGKGTCPTSGSRKFQTLC-HATNSLLPSEMVEHLRNGSKGQVVHV  355 (1034)
T ss_pred             HhcccccchhhhhHHHHhhhhh--cccccccchhhcCCccCcccchhhhhhcC-cccceecchhHHHHhhccCCceEEEE
Confidence            3445556788999999999888  79999999999999999998877655433 33458999999999987655443333


Q ss_pred             ccCCCcEEEEE---EcCchhhhh--hccCCcEEEeCchhHHHhhhcccccc---CCceeEEEEechhhHhhcCC-ch-HH
Q psy11867        198 KHITDLSVRYA---VRGENLERN--KKITEQIIIGTPGKVLDWGLKYRFFD---LSKIKVFVLDEADVMIATQG-HQ-DF  267 (399)
Q Consensus       198 ~~~~~~~~~~~---~~~~~~~~~--~~~~~~IlV~Tp~~l~~~~~~~~~~~---~~~~~~lViDEah~l~~~~~-~~-~~  267 (399)
                      ..++..+..++   .+.......  .+.+.+++.+.|.............+   +-...+++.||+|.+....+ +. +.
T Consensus       356 ~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~  435 (1034)
T KOG4150|consen  356 EVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQ  435 (1034)
T ss_pred             EehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHH
Confidence            33333332222   222222221  25677899999998876554332221   23456899999998753211 11 22


Q ss_pred             HHHHHHhC-----CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCCh--------hhHHHH
Q psy11867        268 SIRIQKRL-----PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI--------DEKFEA  334 (399)
Q Consensus       268 ~~~i~~~l-----~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~--------~~k~~~  334 (399)
                      +.++.+..     +.+.|++-+|||+...++.....+  +-..+.+...+.++..-++.++|.++.        +.+..-
T Consensus       436 ~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~--~~~E~~Li~~DGSPs~~K~~V~WNP~~~P~~~~~~~~~i~E  513 (1034)
T KOG4150|consen  436 LRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELA--NLSELELVTIDGSPSSEKLFVLWNPSAPPTSKSEKSSKVVE  513 (1034)
T ss_pred             HHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhc--CCcceEEEEecCCCCccceEEEeCCCCCCcchhhhhhHHHH
Confidence            22332222     457899999999998887765544  334445555566777788888887532        122222


Q ss_pred             HHHHhccC--CCCcEEEEecchHhHHHHHHHHHHC----C----CeEEEEcCCCCHHHHHHHHHHHhcCCCcc
Q psy11867        335 VSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKE----G----LNVGLLSGELTVEQRLSILDRFREGEFKI  397 (399)
Q Consensus       335 l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~----g----~~v~~lhg~~~~~~R~~v~~~F~~G~~~I  397 (399)
                      ...++...  .+-++|.||.+|+-|+.+....+..    |    -.+..|.||...++|..+..++..|++.-
T Consensus       514 ~s~~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~g  586 (1034)
T KOG4150|consen  514 VSHLFAEMVQHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCG  586 (1034)
T ss_pred             HHHHHHHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeE
Confidence            22232221  2348999999999999887665442    2    24778999999999999999999998753

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

Probab=99.27  E-value=2.3e-11  Score=122.90  Aligned_cols=55  Identities=18%  Similarity=0.289  Sum_probs=48.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ++.+++.|+||+|||++|++|++..+... .+.++||++||++|+.|+.+.+..+.
T Consensus        16 ~~~lliEA~TGtGKTlAYLlpal~~~~~~-~~~rvlIstpT~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117        16 KRIGMLEASTGVGKTLAMIMAALTMLKER-PDQKIAIAVPTLALMGQLWSELERLT   70 (636)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHhc-cCceEEEECCcHHHHHHHHHHHHHHH
Confidence            78999999999999999999999876532 35689999999999999999888776

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.

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.24  E-value=4.9e-10  Score=114.90  Aligned_cols=130  Identities=21%  Similarity=0.183  Sum_probs=97.9

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      .|+ .|++.|..+.-.+.    +.-|+...||.|||+++.+|+.-....   +..+-|++++..||.+-++++..+...+
T Consensus        73 lG~-r~ydvQlig~l~L~----~G~IaEm~TGEGKTL~a~l~ayl~aL~---G~~VhVvT~NdyLA~RD~e~m~pvy~~L  144 (870)
T CHL00122         73 LGL-RHFDVQLIGGLVLN----DGKIAEMKTGEGKTLVATLPAYLNALT---GKGVHIVTVNDYLAKRDQEWMGQIYRFL  144 (870)
T ss_pred             hCC-CCCchHhhhhHhhc----CCccccccCCCCchHHHHHHHHHHHhc---CCceEEEeCCHHHHHHHHHHHHHHHHHc
Confidence            455 58899988765443    568999999999999999998644333   3448999999999999999999999888


Q ss_pred             CCcEEEEEEcCchh-hhhhccCCcEEEeCchhHH-Hhhhcc-----ccccCCceeEEEEechhhHh
Q psy11867        201 TDLSVRYAVRGENL-ERNKKITEQIIIGTPGKVL-DWGLKY-----RFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       201 ~~~~~~~~~~~~~~-~~~~~~~~~IlV~Tp~~l~-~~~~~~-----~~~~~~~~~~lViDEah~l~  259 (399)
                       ++++.+..++... ++.....++|+.+|...|- +++..+     .....+.+.+.|+||+|.++
T Consensus       145 -GLsvg~i~~~~~~~err~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        145 -GLTVGLIQEGMSSEERKKNYLKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             -CCceeeeCCCCChHHHHHhcCCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence             7888887776554 3344667899999997652 333221     11235678999999999663

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.22  E-value=5.6e-10  Score=115.54  Aligned_cols=127  Identities=20%  Similarity=0.151  Sum_probs=94.5

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|+++|...--.+.    +.-|+...||-|||+++.+|+.-....+..   +=||+.+--||..=.+++..+..++ +++
T Consensus       138 ~~ydVQLiGgivLh----~G~IAEM~TGEGKTLvatlp~yLnAL~G~g---VHvVTvNDYLA~RDaewm~p~y~fl-GLt  209 (1025)
T PRK12900        138 VPYDVQLIGGIVLH----SGKISEMATGEGKTLVSTLPTFLNALTGRG---VHVVTVNDYLAQRDKEWMNPVFEFH-GLS  209 (1025)
T ss_pred             cccchHHhhhHHhh----cCCccccCCCCCcchHhHHHHHHHHHcCCC---cEEEeechHhhhhhHHHHHHHHHHh-CCe
Confidence            57778876655554    446789999999999999998766555422   7778888899999999999998887 899


Q ss_pred             EEEEEcCch-hhhhhccCCcEEEeCchhH-HHhhhccc-----cccCCceeEEEEechhhHh
Q psy11867        205 VRYAVRGEN-LERNKKITEQIIIGTPGKV-LDWGLKYR-----FFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       205 ~~~~~~~~~-~~~~~~~~~~IlV~Tp~~l-~~~~~~~~-----~~~~~~~~~lViDEah~l~  259 (399)
                      +.+...+.. ..+.....++|++||...| .+++..+-     ..-.+.+.|.||||+|.++
T Consensus       210 Vg~i~~~~~~~~Rr~aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        210 VGVILNTMRPEERREQYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             eeeeCCCCCHHHHHHhCCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            988866543 3444567889999999876 34433221     1225678999999999664

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.21  E-value=1.1e-09  Score=112.32  Aligned_cols=127  Identities=21%  Similarity=0.158  Sum_probs=98.7

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|+++|...--.+.    +.-|+...||-|||+++.+|+.-....+   ..+-||+++.-||.+=.+++..+..++ +++
T Consensus        85 r~ydVQliGgl~Lh----~G~IAEM~TGEGKTL~atlpaylnAL~G---kgVhVVTvNdYLA~RDae~m~~vy~~L-GLt  156 (939)
T PRK12902         85 RHFDVQLIGGMVLH----EGQIAEMKTGEGKTLVATLPSYLNALTG---KGVHVVTVNDYLARRDAEWMGQVHRFL-GLS  156 (939)
T ss_pred             CcchhHHHhhhhhc----CCceeeecCCCChhHHHHHHHHHHhhcC---CCeEEEeCCHHHHHhHHHHHHHHHHHh-CCe
Confidence            78889988776664    4568999999999999999988655543   349999999999999999999999888 899


Q ss_pred             EEEEEcCchh-hhhhccCCcEEEeCchhH-----HHhhhc-cccccCCceeEEEEechhhHh
Q psy11867        205 VRYAVRGENL-ERNKKITEQIIIGTPGKV-----LDWGLK-YRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       205 ~~~~~~~~~~-~~~~~~~~~IlV~Tp~~l-----~~~~~~-~~~~~~~~~~~lViDEah~l~  259 (399)
                      +.+..++... ++.....++|+++|+..|     .+.+.. ......+.+.+.||||+|.++
T Consensus       157 vg~i~~~~~~~err~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        157 VGLIQQDMSPEERKKNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             EEEECCCCChHHHHHhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            8887766543 344467889999999988     333221 222346788999999999664

>KOG0387|consensus

Probab=99.21  E-value=4.6e-09  Score=104.95  Aligned_cols=272  Identities=15%  Similarity=0.123  Sum_probs=163.7

Q ss_pred             ccccc-CCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehh--HHHHHHhhCCCCCCCeEE
Q psy11867        103 KTFEA-LHLKPELLKGVYEMGFYAPSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAF--TLTMLSRVNPSIQEPQVL  177 (399)
Q Consensus       103 ~~f~~-~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~--~l~il~~l~~~~~~~~~l  177 (399)
                      ..++. +.++..+..        .+.++|.+++..+.+-  .+..-|+....|-|||..-  .|+.+++-.  .-...+|
T Consensus       190 ~~~~~~~~vPg~I~~--------~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~--k~~~paL  259 (923)
T KOG0387|consen  190 KKLEGGFKVPGFIWS--------KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSG--KLTKPAL  259 (923)
T ss_pred             ccccccccccHHHHH--------HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhcc--cccCceE
Confidence            33443 455655544        4568999999988642  3567788899999999542  223333321  2235699


Q ss_pred             EEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchh----------------hhhhccCCcEEEeCchhHHHhhhcccc
Q psy11867        178 CLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL----------------ERNKKITEQIIIGTPGKVLDWGLKYRF  241 (399)
Q Consensus       178 il~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~~IlV~Tp~~l~~~~~~~~~  241 (399)
                      ||||. .++.|+.+++..+..   .+++...++....                .+......+|+|+|...+.-.   ...
T Consensus       260 IVCP~-Tii~qW~~E~~~w~p---~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~---~d~  332 (923)
T KOG0387|consen  260 IVCPA-TIIHQWMKEFQTWWP---PFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ---GDD  332 (923)
T ss_pred             EEccH-HHHHHHHHHHHHhCc---ceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc---Ccc
Confidence            99998 466777777777654   5566655544331                111122446999999876432   123


Q ss_pred             ccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeC-Chh---HHHHHHhhCC--------------CC
Q psy11867        242 FDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATY-DKE---VMEFAQDMVP--------------NP  303 (399)
Q Consensus       242 ~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~-~~~---v~~~~~~~~~--------------~p  303 (399)
                      +.-...+++|+||.|++-.   -...+....+.++ ..+.+++|.|. -+.   ++.+.....+              .|
T Consensus       333 l~~~~W~y~ILDEGH~IrN---pns~islackki~-T~~RiILSGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~p  408 (923)
T KOG0387|consen  333 LLGILWDYVILDEGHRIRN---PNSKISLACKKIR-TVHRIILSGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHP  408 (923)
T ss_pred             cccccccEEEecCcccccC---CccHHHHHHHhcc-ccceEEeeCccccchHHHHHHHhhhccCCcccchHHHHhhhhhh
Confidence            3344678999999999843   3334444444444 55667778882 111   1111111111              11


Q ss_pred             eEEec-------------------------------cc--ccccccceeEEEEEeC------------------------
Q psy11867        304 LIIKL-------------------------------KR--EEESLDNIKQHYVMCK------------------------  326 (399)
Q Consensus       304 ~~i~~-------------------------------~~--~~~~~~~i~~~~~~~~------------------------  326 (399)
                      +.+--                               +.  ....++.-...+++|.                        
T Consensus       409 I~~GgyaNAs~~qv~~aykca~~Lr~lI~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng  488 (923)
T KOG0387|consen  409 INRGGYANASPRQVQTAYKCAVALRDLISPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNG  488 (923)
T ss_pred             eeccccCCCCHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhccCCCccceEEEEeccHHHHHHHHHHhhhHHHHHHHcC
Confidence            11100                               00  0001111223334441                        


Q ss_pred             --------------------------------------ChhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHH-
Q psy11867        327 --------------------------------------NIDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMS-  365 (399)
Q Consensus       327 --------------------------------------~~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~-  365 (399)
                                                            ....|...+..++...  .+.++|.|..++.....|...|. 
T Consensus       489 ~~~~l~Gi~iLrkICnHPdll~~~~~~~~~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~  568 (923)
T KOG0387|consen  489 KRNCLSGIDILRKICNHPDLLDRRDEDEKQGPDYEGDPKRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRR  568 (923)
T ss_pred             CccceechHHHHhhcCCcccccCcccccccCCCcCCChhhcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHh
Confidence                                                  1123555666655543  23589999999999999999998 


Q ss_pred             HCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        366 KEGLNVGLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       366 ~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                      ..|+...-+.|..+...|...+++|.++..
T Consensus       569 ~~~ysylRmDGtT~~~~R~~lVd~Fne~~s  598 (923)
T KOG0387|consen  569 AKGYSYLRMDGTTPAALRQKLVDRFNEDES  598 (923)
T ss_pred             cCCceEEEecCCCccchhhHHHHhhcCCCc
Confidence            479999999999999999999999998753

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

Probab=99.17  E-value=1.2e-10  Score=94.29  Aligned_cols=136  Identities=16%  Similarity=0.200  Sum_probs=78.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |.--++...+|+|||--.+.-++.....  .+.++|||.|||.++..+++.++..     .+.  +.....  ......+
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~--~~~rvLvL~PTRvva~em~~aL~~~-----~~~--~~t~~~--~~~~~g~   72 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIK--RRLRVLVLAPTRVVAEEMYEALKGL-----PVR--FHTNAR--MRTHFGS   72 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHH--TT--EEEEESSHHHHHHHHHHTTTS-----SEE--EESTTS--S----SS
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHH--ccCeEEEecccHHHHHHHHHHHhcC-----Ccc--cCceee--eccccCC
Confidence            5667888999999998877655553332  4567999999999999888877643     122  211111  1122344


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC-CchHHHHHHHHhCCCCCcEEEEEeeCChhH
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ-GHQDFSIRIQKRLPSDCQIMLFSATYDKEV  292 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~-~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v  292 (399)
                      .-|-|.|.+.+...+.+  .....+++++|+||||..-... .+...+.... . ...+.+|++|||-|...
T Consensus        73 ~~i~vMc~at~~~~~~~--p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~~-~-~g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   73 SIIDVMCHATYGHFLLN--PCRLKNYDVIIMDECHFTDPTSIAARGYLRELA-E-SGEAKVIFMTATPPGSE  140 (148)
T ss_dssp             SSEEEEEHHHHHHHHHT--SSCTTS-SEEEECTTT--SHHHHHHHHHHHHHH-H-TTS-EEEEEESS-TT--
T ss_pred             CcccccccHHHHHHhcC--cccccCccEEEEeccccCCHHHHhhheeHHHhh-h-ccCeeEEEEeCCCCCCC
Confidence            45889999988877654  3456899999999999862110 0111111221 1 13468999999977554

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 ....

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.16  E-value=3.9e-09  Score=108.31  Aligned_cols=71  Identities=21%  Similarity=0.339  Sum_probs=60.5

Q ss_pred             hhHHHHHHHHhcc--CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSNIYGV--VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~ll~~--~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..++..+...+..  ....++||||++++.|+.|++.|.+.|+++..+||++++.+|..+++.|+.|++.|||
T Consensus       425 ~~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV  497 (655)
T TIGR00631       425 DGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLV  497 (655)
T ss_pred             cchHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEE
Confidence            3445555554443  2346899999999999999999999999999999999999999999999999999984

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

>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=99.12  E-value=2.9e-10  Score=106.66  Aligned_cols=154  Identities=19%  Similarity=0.123  Sum_probs=90.3

Q ss_pred             HHHHHhhhhhc-----------CCCCcEEEEccCCCCceehhHHHHHHhhCCCC--CCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        129 IQETALPTLLA-----------DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI--QEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       129 iQ~~ai~~ll~-----------~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~--~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      +|.+++..++.           .+.+.++++..+|+|||+..+..+........  ....+|||+|. .+..|+..++.+
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~   79 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEK   79 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhcc
Confidence            46666665532           23688999999999999887765543332221  22259999999 788899999999


Q ss_pred             HhccCCCcEEEEEEcCchh---hhhhccCCcEEEeCchhHHHhh--hccccccCCceeEEEEechhhHhhcCCchHHHHH
Q psy11867        196 MGKHITDLSVRYAVRGENL---ERNKKITEQIIIGTPGKVLDWG--LKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIR  270 (399)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~IlV~Tp~~l~~~~--~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~  270 (399)
                      +.... .+++....+....   ........+++|+|.+.+....  .....+.--+++++|+||+|.+-   +.......
T Consensus        80 ~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k---~~~s~~~~  155 (299)
T PF00176_consen   80 WFDPD-SLRVIIYDGDSERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLK---NKDSKRYK  155 (299)
T ss_dssp             HSGT--TS-EEEESSSCHHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGT---TTTSHHHH
T ss_pred             ccccc-cccccccccccccccccccccccceeeeccccccccccccccccccccccceeEEEecccccc---cccccccc
Confidence            87542 3455555555411   1122445689999999988110  01112223458999999999983   23333334


Q ss_pred             HHHhCCCCCcEEEEEeeC
Q psy11867        271 IQKRLPSDCQIMLFSATY  288 (399)
Q Consensus       271 i~~~l~~~~q~l~~SAT~  288 (399)
                      .+..+. ....+++|||.
T Consensus       156 ~l~~l~-~~~~~lLSgTP  172 (299)
T PF00176_consen  156 ALRKLR-ARYRWLLSGTP  172 (299)
T ss_dssp             HHHCCC-ECEEEEE-SS-
T ss_pred             cccccc-cceEEeecccc
Confidence            444455 66778999993

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.

>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=99.09  E-value=4.9e-08  Score=94.39  Aligned_cols=230  Identities=20%  Similarity=0.230  Sum_probs=153.2

Q ss_pred             CCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc------EEEE-------------------------EEcCchh--
Q psy11867        168 NPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL------SVRY-------------------------AVRGENL--  214 (399)
Q Consensus       168 ~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~------~~~~-------------------------~~~~~~~--  214 (399)
                      .++-..|++|||+|+|..|.++.+.+-++......+      .-.+                         ..+|...  
T Consensus        32 DQGftRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~  111 (442)
T PF06862_consen   32 DQGFTRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDC  111 (442)
T ss_pred             ccCCCCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccce
Confidence            445567999999999999999888887765330000      0000                         0011000  


Q ss_pred             -------hh------hhccCCcEEEeCchhHHHhhhc----cccc-cCCceeEEEEechhhHhhcCCchHHHHHHHHhCC
Q psy11867        215 -------ER------NKKITEQIIIGTPGKVLDWGLK----YRFF-DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP  276 (399)
Q Consensus       215 -------~~------~~~~~~~IlV~Tp~~l~~~~~~----~~~~-~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~  276 (399)
                             .+      ..-...+||||+|=-|...+..    .+.. .++.+.++|+|.||.|.- |. .+.+..+++.++
T Consensus       112 FrlGik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~M-QN-W~Hv~~v~~~lN  189 (442)
T PF06862_consen  112 FRLGIKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLM-QN-WEHVLHVFEHLN  189 (442)
T ss_pred             EEEeEEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHH-hh-HHHHHHHHHHhc
Confidence                   00      0012357999999777655442    2222 388999999999999873 33 333444555442


Q ss_pred             ---C---------------------CCcEEEEEeeCChhHHHHHHhhCCCC---eEEecccc-----cccccceeEEEEE
Q psy11867        277 ---S---------------------DCQIMLFSATYDKEVMEFAQDMVPNP---LIIKLKRE-----EESLDNIKQHYVM  324 (399)
Q Consensus       277 ---~---------------------~~q~l~~SAT~~~~v~~~~~~~~~~p---~~i~~~~~-----~~~~~~i~~~~~~  324 (399)
                         .                     -+|+|++|+...+++..+......+.   +.+.....     ......+.|.+..
T Consensus       190 ~~P~~~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r  269 (442)
T PF06862_consen  190 LQPKKSHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQR  269 (442)
T ss_pred             cCCCCCCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEE
Confidence               1                     25999999999999999888865442   22222222     2345567787765


Q ss_pred             eC--Ch----hhHHHHHHH----Hhc-cCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC
Q psy11867        325 CK--NI----DEKFEAVSN----IYG-VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREG  393 (399)
Q Consensus       325 ~~--~~----~~k~~~l~~----ll~-~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G  393 (399)
                      .+  +.    +.+++...+    -+. ....+.+|||++|--.=-.|.+.|.+.++..+.+|.-.+..+-.++-..|..|
T Consensus       270 ~~~~s~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G  349 (442)
T PF06862_consen  270 FDCSSPADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHG  349 (442)
T ss_pred             ecCCCcchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcC
Confidence            33  22    333333222    222 34457899999999999999999999999999999999999999999999999


Q ss_pred             CCcccC
Q psy11867        394 EFKIYS  399 (399)
Q Consensus       394 ~~~ILV  399 (399)
                      +.+||.
T Consensus       350 ~~~iLL  355 (442)
T PF06862_consen  350 RKPILL  355 (442)
T ss_pred             CceEEE
Confidence            999874

; GO: 0005634 nucleus

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.09  E-value=6.2e-09  Score=106.53  Aligned_cols=129  Identities=17%  Similarity=0.124  Sum_probs=96.8

Q ss_pred             CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        122 GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       122 g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      |. .|+++|...--.+..  |  -|+...||-|||+++.+|+.-....+   ..+=|++.+--||..=.+++..+..++ 
T Consensus        76 G~-r~ydVQliGglvLh~--G--~IAEMkTGEGKTLvAtLpayLnAL~G---kgVhVVTvNdYLA~RDae~mg~vy~fL-  146 (925)
T PRK12903         76 GK-RPYDVQIIGGIILDL--G--SVAEMKTGEGKTITSIAPVYLNALTG---KGVIVSTVNEYLAERDAEEMGKVFNFL-  146 (925)
T ss_pred             CC-CcCchHHHHHHHHhc--C--CeeeecCCCCccHHHHHHHHHHHhcC---CceEEEecchhhhhhhHHHHHHHHHHh-
Confidence            44 789999988866554  3  47999999999999999886544433   338888999999999899999988887 


Q ss_pred             CcEEEEEEcCchh-hhhhccCCcEEEeCchhH-HHhhhccc-----cccCCceeEEEEechhhHh
Q psy11867        202 DLSVRYAVRGENL-ERNKKITEQIIIGTPGKV-LDWGLKYR-----FFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       202 ~~~~~~~~~~~~~-~~~~~~~~~IlV~Tp~~l-~~~~~~~~-----~~~~~~~~~lViDEah~l~  259 (399)
                      ++++.+...+... .+.....++|+++|...| .+++..+-     ..-.+.+.|.|+||+|.++
T Consensus       147 GLsvG~i~~~~~~~~rr~aY~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        147 GLSVGINKANMDPNLKREAYACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             CCceeeeCCCCChHHHHHhccCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            8888887766443 444466789999999887 44443221     1235678899999999664

>KOG0924|consensus

Probab=99.08  E-value=1.4e-08  Score=99.98  Aligned_cols=252  Identities=21%  Similarity=0.255  Sum_probs=151.0

Q ss_pred             HHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHH-HhccCCCcEEEE
Q psy11867        129 IQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK-MGKHITDLSVRY  207 (399)
Q Consensus       129 iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~-~~~~~~~~~~~~  207 (399)
                      ++.+.+..+-.  ++-|++.+.||||||....-.+++.-..  .+..+-|--|.|.-|..+++.+.. ++..+ +-.+.+
T Consensus       360 ~R~~ll~~ir~--n~vvvivgETGSGKTTQl~QyL~edGY~--~~GmIGcTQPRRvAAiSVAkrVa~EM~~~l-G~~VGY  434 (1042)
T KOG0924|consen  360 CRDQLLSVIRE--NQVVVIVGETGSGKTTQLAQYLYEDGYA--DNGMIGCTQPRRVAAISVAKRVAEEMGVTL-GDTVGY  434 (1042)
T ss_pred             HHHHHHHHHhh--CcEEEEEecCCCCchhhhHHHHHhcccc--cCCeeeecCchHHHHHHHHHHHHHHhCCcc-ccccce
Confidence            34444444444  5889999999999997533222211111  222344445999888887766554 43333 445555


Q ss_pred             EEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC---CCCCcEEEE
Q psy11867        208 AVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL---PSDCQIMLF  284 (399)
Q Consensus       208 ~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l---~~~~q~l~~  284 (399)
                      .+.-.+....   ...|=+.|-|.|+.-...  .-.+.+..++|+||||.-.   -..+.+..+++..   +.+.++|.+
T Consensus       435 sIRFEdvT~~---~T~IkymTDGiLLrEsL~--d~~L~kYSviImDEAHERs---lNtDilfGllk~~larRrdlKliVt  506 (1042)
T KOG0924|consen  435 SIRFEDVTSE---DTKIKYMTDGILLRESLK--DRDLDKYSVIIMDEAHERS---LNTDILFGLLKKVLARRRDLKLIVT  506 (1042)
T ss_pred             EEEeeecCCC---ceeEEEeccchHHHHHhh--hhhhhheeEEEechhhhcc---cchHHHHHHHHHHHHhhccceEEEe
Confidence            5554444322   234888999999875443  3457889999999999742   2233333444332   347889999


Q ss_pred             EeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccC---CCCcEEEEecchHhHHHHH
Q psy11867        285 SATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVV---TIGQAMIFCHTRKTAAWLA  361 (399)
Q Consensus       285 SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~---~~~k~IIF~~s~~~a~~l~  361 (399)
                      |||+..  +.|...+-.-|.+..-++.    ..+.-.|...+-.+-...++...+.-+   ..|-++||....+..+-.+
T Consensus       507 SATm~a--~kf~nfFgn~p~f~IpGRT----yPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~  580 (1042)
T KOG0924|consen  507 SATMDA--QKFSNFFGNCPQFTIPGRT----YPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTC  580 (1042)
T ss_pred             eccccH--HHHHHHhCCCceeeecCCc----cceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHH
Confidence            999874  4555444434543322221    123334444433333333444444332   3477999998877555544


Q ss_pred             HH----HHHC------CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        362 EK----MSKE------GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       362 ~~----L~~~------g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..    |.+.      +..|..+++.|+.+-...+++.--.|.-+++|
T Consensus       581 ~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~Iv  628 (1042)
T KOG0924|consen  581 DIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIV  628 (1042)
T ss_pred             HHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEE
Confidence            44    4332      56899999999999999998887777766654

>KOG0923|consensus

Probab=99.08  E-value=1.5e-08  Score=99.40  Aligned_cols=253  Identities=21%  Similarity=0.284  Sum_probs=154.8

Q ss_pred             hHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH-HHHHHHhccCCCcEE
Q psy11867        127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG-EVVAKMGKHITDLSV  205 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~-~~~~~~~~~~~~~~~  205 (399)
                      +++-.+.+.++-.  .+-+||.|.||||||...--.+.+. .-...+.++-|--|.|--|..+. ++.+.++..+ +..+
T Consensus       267 y~ykdell~av~e--~QVLiI~GeTGSGKTTQiPQyL~Ea-Gytk~gk~IgcTQPRRVAAmSVAaRVA~EMgvkL-G~eV  342 (902)
T KOG0923|consen  267 YPYKDELLKAVKE--HQVLIIVGETGSGKTTQIPQYLYEA-GYTKGGKKIGCTQPRRVAAMSVAARVAEEMGVKL-GHEV  342 (902)
T ss_pred             hhhHHHHHHHHHh--CcEEEEEcCCCCCccccccHHHHhc-ccccCCceEeecCcchHHHHHHHHHHHHHhCccc-cccc
Confidence            3444555566655  5899999999999997532111111 11123344666679998887775 4445555444 3334


Q ss_pred             EEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHH---hCCCCCcEE
Q psy11867        206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQK---RLPSDCQIM  282 (399)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~---~l~~~~q~l  282 (399)
                      .+.....+...   ...-|=+.|-|+|+.-++  ...++....++||||||.=-   -+.+.+..+++   ..+++.+++
T Consensus       343 GYsIRFEdcTS---ekTvlKYMTDGmLlREfL--~epdLasYSViiiDEAHERT---L~TDILfgLvKDIar~RpdLKll  414 (902)
T KOG0923|consen  343 GYSIRFEDCTS---EKTVLKYMTDGMLLREFL--SEPDLASYSVIIVDEAHERT---LHTDILFGLVKDIARFRPDLKLL  414 (902)
T ss_pred             ceEEEeccccC---cceeeeeecchhHHHHHh--ccccccceeEEEeehhhhhh---hhhhHHHHHHHHHHhhCCcceEE
Confidence            44443333222   122377899999988654  45679999999999999631   23344444433   335789999


Q ss_pred             EEEeeCChhHHHHHHhhCCC-CeEEecccccccccceeEEEEEeCChhhHHHHHHHHhc---cCCCCcEEEEecchHhHH
Q psy11867        283 LFSATYDKEVMEFAQDMVPN-PLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG---VVTIGQAMIFCHTRKTAA  358 (399)
Q Consensus       283 ~~SAT~~~~v~~~~~~~~~~-p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~---~~~~~k~IIF~~s~~~a~  358 (399)
                      +.|||+..+  .|- .|+.+ |++..-++.    ..+.-+|..++..+---.++..+++   ..+.|-+|||....+..+
T Consensus       415 IsSAT~DAe--kFS-~fFDdapIF~iPGRR----yPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIE  487 (902)
T KOG0923|consen  415 ISSATMDAE--KFS-AFFDDAPIFRIPGRR----YPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIE  487 (902)
T ss_pred             eeccccCHH--HHH-HhccCCcEEeccCcc----cceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHH
Confidence            999998743  333 34444 444332222    2344566666554444344444443   335578999998887766


Q ss_pred             HHHHHHHH----CC-----CeEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        359 WLAEKMSK----EG-----LNVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       359 ~l~~~L~~----~g-----~~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                      ...+.|..    +|     +-+..+|+.++.+.+..|++---.|.-+|+
T Consensus       488 t~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVV  536 (902)
T KOG0923|consen  488 TVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVV  536 (902)
T ss_pred             HHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEE
Confidence            66555543    33     347889999999999998876666655543

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.08  E-value=2.6e-10  Score=106.14  Aligned_cols=72  Identities=22%  Similarity=0.167  Sum_probs=56.3

Q ss_pred             CChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHHhhCCCCC---CCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQ---EPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~---~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      .|+|.|.+.+..+...  .|.++++.||||+|||++|++|++..+.....   +.+++|.++|..+..|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            4799999955554321  27999999999999999999999876543222   247999999999999887777665

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.08  E-value=2.6e-10  Score=106.14  Aligned_cols=72  Identities=22%  Similarity=0.167  Sum_probs=56.3

Q ss_pred             CChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHHhhCCCCC---CCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQ---EPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~---~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      .|+|.|.+.+..+...  .|.++++.||||+|||++|++|++..+.....   +.+++|.++|..+..|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            4799999955554321  27999999999999999999999876543222   247999999999999887777665

>KOG1000|consensus

Probab=99.06  E-value=3.9e-08  Score=93.65  Aligned_cols=257  Identities=12%  Similarity=0.131  Sum_probs=156.8

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..+.|+|.+.+...++. |..+++....|-|||+.++. |.........   .||+||. .+-..+.+.+.++...+.  
T Consensus       197 s~LlPFQreGv~faL~R-gGR~llADeMGLGKTiQAla-IA~yyraEwp---lliVcPA-svrftWa~al~r~lps~~--  268 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALER-GGRILLADEMGLGKTIQALA-IARYYRAEWP---LLIVCPA-SVRFTWAKALNRFLPSIH--  268 (689)
T ss_pred             HhhCchhhhhHHHHHhc-CCeEEEecccccchHHHHHH-HHHHHhhcCc---EEEEecH-HHhHHHHHHHHHhccccc--
Confidence            45679999999999886 88899999999999988753 3333333223   7999997 455566777777765442  


Q ss_pred             EEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEE
Q psy11867        204 SVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIML  283 (399)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~  283 (399)
                      .+....++.+.....-....|.|.+.+.+..+-   ..+.-...+++|+||.|.+-...  ......+...+..-.++|+
T Consensus       269 pi~vv~~~~D~~~~~~t~~~v~ivSye~ls~l~---~~l~~~~~~vvI~DEsH~Lk~sk--tkr~Ka~~dllk~akhvIL  343 (689)
T KOG1000|consen  269 PIFVVDKSSDPLPDVCTSNTVAIVSYEQLSLLH---DILKKEKYRVVIFDESHMLKDSK--TKRTKAATDLLKVAKHVIL  343 (689)
T ss_pred             ceEEEecccCCccccccCCeEEEEEHHHHHHHH---HHHhcccceEEEEechhhhhccc--hhhhhhhhhHHHHhhheEE
Confidence            244455554433222223458888998776542   22234458899999999986532  2223333333344567899


Q ss_pred             EEeeC-------------------ChhHHHHHHhhCCC---CeEEecccc------------------------cccccc
Q psy11867        284 FSATY-------------------DKEVMEFAQDMVPN---PLIIKLKRE------------------------EESLDN  317 (399)
Q Consensus       284 ~SAT~-------------------~~~v~~~~~~~~~~---p~~i~~~~~------------------------~~~~~~  317 (399)
                      +|.|.                   -+...+++..|...   +........                        ...++.
T Consensus       344 LSGTPavSRP~elytqi~avd~tlfp~f~efa~rYCd~k~vr~~~Dykg~tnl~EL~~lL~k~lMIRRlK~dvL~qLPpK  423 (689)
T KOG1000|consen  344 LSGTPAVSRPSELYTQIRAVDHTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADVLKQLPPK  423 (689)
T ss_pred             ecCCcccCCchhhhhhhhhhcccccccHHHHHHHhcCccccceeeecCCCCCHHHHHHHHHHHHHHHHHHHHHHhhCCcc
Confidence            99982                   11122233222211   111111000                        011111


Q ss_pred             eeEEEEEeCC---------------------hhh---------------HHHHHHHHhcc------CCCCcEEEEecchH
Q psy11867        318 IKQHYVMCKN---------------------IDE---------------KFEAVSNIYGV------VTIGQAMIFCHTRK  355 (399)
Q Consensus       318 i~~~~~~~~~---------------------~~~---------------k~~~l~~ll~~------~~~~k~IIF~~s~~  355 (399)
                      -++..+.+..                     .+.               |...+.+.+..      .+..+.+|||+-..
T Consensus       424 rr~Vv~~~~gr~da~~~~lv~~a~~~t~~~~~e~~~~~l~l~y~~tgiaK~~av~eyi~~~~~l~d~~~~KflVFaHH~~  503 (689)
T KOG1000|consen  424 RREVVYVSGGRIDARMDDLVKAAADYTKVNSMERKHESLLLFYSLTGIAKAAAVCEYILENYFLPDAPPRKFLVFAHHQI  503 (689)
T ss_pred             ceEEEEEcCCccchHHHHHHHHhhhcchhhhhhhhhHHHHHHHHHhcccccHHHHHHHHhCcccccCCCceEEEEehhHH
Confidence            1222222211                     111               22233333332      23468999999999


Q ss_pred             hHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC
Q psy11867        356 TAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREG  393 (399)
Q Consensus       356 ~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G  393 (399)
                      ..+.+..++.+.++...-+.|..+..+|....+.|...
T Consensus       504 vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~s  541 (689)
T KOG1000|consen  504 VLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTS  541 (689)
T ss_pred             HHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccc
Confidence            99999999999999999999999999999999999864

>KOG0925|consensus

Probab=99.05  E-value=7.5e-09  Score=98.22  Aligned_cols=257  Identities=20%  Similarity=0.192  Sum_probs=144.5

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      +..|...+.++.-.+-|++.---.-...+.+-+..+.+  ++-+++.|.||||||...--..+.......  ..+.+--|
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~--nQ~~v~vGetgsGKttQiPq~~~~~~~~~~--~~v~CTQp   99 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLN--NQIIVLVGETGSGKTTQIPQFVLEYELSHL--TGVACTQP   99 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhc--CceEEEEecCCCCccccCcHHHHHHHHhhc--cceeecCc
Confidence            45678888888887777664322223333444444444  699999999999999754333333322221  33677779


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH-hh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM-IA  260 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l-~~  260 (399)
                      .|--|.++......-.+-.-+-.+.+....++-....   .=+-.+|-|+|+.-...  .-.+...+++|+||||.- ++
T Consensus       100 rrvaamsva~RVadEMDv~lG~EVGysIrfEdC~~~~---T~Lky~tDgmLlrEams--~p~l~~y~viiLDeahERtlA  174 (699)
T KOG0925|consen  100 RRVAAMSVAQRVADEMDVTLGEEVGYSIRFEDCTSPN---TLLKYCTDGMLLREAMS--DPLLGRYGVIILDEAHERTLA  174 (699)
T ss_pred             hHHHHHHHHHHHHHHhccccchhccccccccccCChh---HHHHHhcchHHHHHHhh--CcccccccEEEechhhhhhHH
Confidence            9988888766554432211122222222221111000   01234566666553222  234788999999999953 22


Q ss_pred             cCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhH---HHHHHH
Q psy11867        261 TQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEK---FEAVSN  337 (399)
Q Consensus       261 ~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k---~~~l~~  337 (399)
                      .......+..+...- ++.+++.+|||+...   -.+.|+.++-.+.+...    ..+.-+|..-...+.-   +..+..
T Consensus       175 TDiLmGllk~v~~~r-pdLk~vvmSatl~a~---Kfq~yf~n~Pll~vpg~----~PvEi~Yt~e~erDylEaairtV~q  246 (699)
T KOG0925|consen  175 TDILMGLLKEVVRNR-PDLKLVVMSATLDAE---KFQRYFGNAPLLAVPGT----HPVEIFYTPEPERDYLEAAIRTVLQ  246 (699)
T ss_pred             HHHHHHHHHHHHhhC-CCceEEEeecccchH---HHHHHhCCCCeeecCCC----CceEEEecCCCChhHHHHHHHHHHH
Confidence            222233333444444 589999999997643   33455666555555431    1222233322222222   333444


Q ss_pred             HhccCCCCcEEEEecchHhHHHHHHHHHHC---------CCeEEEEc
Q psy11867        338 IYGVVTIGQAMIFCHTRKTAAWLAEKMSKE---------GLNVGLLS  375 (399)
Q Consensus       338 ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~---------g~~v~~lh  375 (399)
                      +-.....|-+++|....++.+..++.+...         ..+|..+|
T Consensus       247 ih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy  293 (699)
T KOG0925|consen  247 IHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY  293 (699)
T ss_pred             HHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC
Confidence            445556789999999999888888877643         24677777

>KOG0389|consensus

Probab=99.03  E-value=2e-09  Score=107.29  Aligned_cols=130  Identities=18%  Similarity=0.166  Sum_probs=91.0

Q ss_pred             CChHHHHHHhhhhh--cCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        125 APSKIQETALPTLL--ADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll--~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      .+-++|.-.++++.  ...+-+.|+....|-|||... ++.+..+.+......-|||||...|    ..|++.+.++||.
T Consensus       399 ~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQv-IaFlayLkq~g~~gpHLVVvPsSTl----eNWlrEf~kwCPs  473 (941)
T KOG0389|consen  399 QLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQV-IAFLAYLKQIGNPGPHLVVVPSSTL----ENWLREFAKWCPS  473 (941)
T ss_pred             cccchhhhhHHHHHHHHHccccceehhhccCcchhHH-HHHHHHHHHcCCCCCcEEEecchhH----HHHHHHHHHhCCc
Confidence            36689998888773  223678899999999999653 3444444333333446899998776    4566777778899


Q ss_pred             cEEEEEEcCchhhhhh-------ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        203 LSVRYAVRGENLERNK-------KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       203 ~~~~~~~~~~~~~~~~-------~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      +++...+|.....+..       ....+|+|+|......--.....+.-.++.++|+||+|.+-
T Consensus       474 l~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLK  537 (941)
T KOG0389|consen  474 LKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLK  537 (941)
T ss_pred             eEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhh
Confidence            9999988887544333       23668999999866543233344556788999999999774

>KOG0926|consensus

Probab=99.02  E-value=6.8e-09  Score=103.69  Aligned_cols=226  Identities=23%  Similarity=0.306  Sum_probs=130.5

Q ss_pred             CCChHHHHHHh------------hhhhcCCCCcEEEEccCCCCceehhHHHHHHhh---CCCCCCCeEEEEeCcHHHHHH
Q psy11867        124 YAPSKIQETAL------------PTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRV---NPSIQEPQVLCLAPTYELAIQ  188 (399)
Q Consensus       124 ~~p~~iQ~~ai------------~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l---~~~~~~~~~lil~Pt~~La~Q  188 (399)
                      .+|..||..-+            .+|..  +--|||||.||||||...---+.+.-   .+...+..+=|--|.|--|..
T Consensus       243 ~R~~EIQ~sR~~LPI~aeEq~IMEaIn~--n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaia  320 (1172)
T KOG0926|consen  243 SRPAEIQESRLDLPIVAEEQRIMEAINE--NPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIA  320 (1172)
T ss_pred             cCcHHHHHHHhcCchhHHHHHHHHHhhc--CCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHH
Confidence            46777776432            33333  56789999999999975322222211   111122244455588877766


Q ss_pred             HHHHHH-HHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHH
Q psy11867        189 IGEVVA-KMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF  267 (399)
Q Consensus       189 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~  267 (399)
                      +.+... .++. + +-.+.+.++...   .......|-+.|-|-|+.-+.  ..|-+.....+|+||||.-.   -+.+.
T Consensus       321 mAkRVa~EL~~-~-~~eVsYqIRfd~---ti~e~T~IkFMTDGVLLrEi~--~DflL~kYSvIIlDEAHERS---vnTDI  390 (1172)
T KOG0926|consen  321 MAKRVAFELGV-L-GSEVSYQIRFDG---TIGEDTSIKFMTDGVLLREIE--NDFLLTKYSVIILDEAHERS---VNTDI  390 (1172)
T ss_pred             HHHHHHHHhcc-C-ccceeEEEEecc---ccCCCceeEEecchHHHHHHH--HhHhhhhceeEEechhhhcc---chHHH
Confidence            655443 3433 2 334444333221   112234699999999987654  36778999999999999631   23333


Q ss_pred             HHHHHH-------hCCC------CCcEEEEEeeCChhHHHHH--HhhC--CCCeEEecccccccccceeEEEEEeCC---
Q psy11867        268 SIRIQK-------RLPS------DCQIMLFSATYDKEVMEFA--QDMV--PNPLIIKLKREEESLDNIKQHYVMCKN---  327 (399)
Q Consensus       268 ~~~i~~-------~l~~------~~q~l~~SAT~~~~v~~~~--~~~~--~~p~~i~~~~~~~~~~~i~~~~~~~~~---  327 (399)
                      +..++.       .+..      ..++|+||||+.-  .+|.  +..+  ..| .+.++...-.   +.-+|-.-..   
T Consensus       391 LiGmLSRiV~LR~k~~ke~~~~kpLKLIIMSATLRV--sDFtenk~LFpi~pP-likVdARQfP---VsIHF~krT~~DY  464 (1172)
T KOG0926|consen  391 LIGMLSRIVPLRQKYYKEQCQIKPLKLIIMSATLRV--SDFTENKRLFPIPPP-LIKVDARQFP---VSIHFNKRTPDDY  464 (1172)
T ss_pred             HHHHHHHHHHHHHHHhhhhcccCceeEEEEeeeEEe--cccccCceecCCCCc-eeeeecccCc---eEEEeccCCCchH
Confidence            333332       2222      5679999999752  2222  1222  223 4444432211   1112211111   


Q ss_pred             hhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC
Q psy11867        328 IDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE  367 (399)
Q Consensus       328 ~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~  367 (399)
                      ..+-+...+.+-+..+.|-+|||+.....+..|++.|++.
T Consensus       465 i~eAfrKtc~IH~kLP~G~ILVFvTGQqEV~qL~~kLRK~  504 (1172)
T KOG0926|consen  465 IAEAFRKTCKIHKKLPPGGILVFVTGQQEVDQLCEKLRKR  504 (1172)
T ss_pred             HHHHHHHHHHHhhcCCCCcEEEEEeChHHHHHHHHHHHhh
Confidence            1344555666667778899999999999999999999875

>KOG0390|consensus

Probab=99.02  E-value=3.3e-08  Score=100.77  Aligned_cols=153  Identities=16%  Similarity=0.157  Sum_probs=97.4

Q ss_pred             CChHHHHHHhhhhhcC--------CCCcEEEEccCCCCceehhHHHHHHhhCCCCCC-----CeEEEEeCcHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLAD--------PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQE-----PQVLCLAPTYELAIQIGE  191 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~--------~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~-----~~~lil~Pt~~La~Q~~~  191 (399)
                      .++|+|.+.+..+...        .....|+.-..|+|||+.... .+..+.+....     .++|||+|. .|+.-+++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~Is-flwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCIS-FIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHH-HHHHHHHhCcCccccccccEEEccH-HHHHHHHH
Confidence            6789999999888643        123566667799999987543 33333332344     679999997 68888888


Q ss_pred             HHHHHhccCCCcEEEEEEcCchh--hh--------hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc
Q psy11867        192 VVAKMGKHITDLSVRYAVRGENL--ER--------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT  261 (399)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~--~~--------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~  261 (399)
                      +|.++... ..+......++..-  ..        ......-|++-+.+.+.+++   +.+....++++|+||.|++-. 
T Consensus       316 EF~KWl~~-~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~---~~il~~~~glLVcDEGHrlkN-  390 (776)
T KOG0390|consen  316 EFGKWLGN-HRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYC---RKILLIRPGLLVCDEGHRLKN-  390 (776)
T ss_pred             HHHHhccc-cccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHH---HHHhcCCCCeEEECCCCCccc-
Confidence            88887653 13444444444431  00        01222347788888876654   344567899999999999743 


Q ss_pred             CCchHHHHHHHHhCCCCCcEEEEEee
Q psy11867        262 QGHQDFSIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       262 ~~~~~~~~~i~~~l~~~~q~l~~SAT  287 (399)
                        ........+..+. ..+.|++|.|
T Consensus       391 --~~s~~~kaL~~l~-t~rRVLLSGT  413 (776)
T KOG0390|consen  391 --SDSLTLKALSSLK-TPRRVLLTGT  413 (776)
T ss_pred             --hhhHHHHHHHhcC-CCceEEeeCC
Confidence              2333333444443 4567888999

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=99.02  E-value=2.3e-08  Score=101.74  Aligned_cols=229  Identities=14%  Similarity=0.125  Sum_probs=140.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      ..-.++.||.|||||.+..-++-..+..  ...++|+|+..++|+.++.+.++..+-.  ++.......+..+..   ..
T Consensus        49 ~~V~vVRSpMGTGKTtaLi~wLk~~l~~--~~~~VLvVShRrSL~~sL~~rf~~~~l~--gFv~Y~d~~~~~i~~---~~  121 (824)
T PF02399_consen   49 RGVLVVRSPMGTGKTTALIRWLKDALKN--PDKSVLVVSHRRSLTKSLAERFKKAGLS--GFVNYLDSDDYIIDG---RP  121 (824)
T ss_pred             CCeEEEECCCCCCcHHHHHHHHHHhccC--CCCeEEEEEhHHHHHHHHHHHHhhcCCC--cceeeeccccccccc---cc
Confidence            4556888999999998765554444332  4567999999999999999998865421  333222222222221   12


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHH------HH-HHHHhCCCCCcEEEEEeeCChhHHH
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF------SI-RIQKRLPSDCQIMLFSATYDKEVME  294 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~------~~-~i~~~l~~~~q~l~~SAT~~~~v~~  294 (399)
                      .+-+++..+.|...    ..-.+.+.++|||||+--.+.. -+...      +. .+...+.....+|++-|++.....+
T Consensus       122 ~~rLivqIdSL~R~----~~~~l~~yDvVIIDEv~svL~q-L~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvd  196 (824)
T PF02399_consen  122 YDRLIVQIDSLHRL----DGSLLDRYDVVIIDEVMSVLNQ-LFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVD  196 (824)
T ss_pred             cCeEEEEehhhhhc----ccccccccCEEEEehHHHHHHH-HhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHH
Confidence            34666666777554    1224667899999999877643 22222      22 2334455677899999999999999


Q ss_pred             HHHhhCCCCeEEecccccccccceeEEEEEeC-----------------------------------ChhhHHHHHHHHh
Q psy11867        295 FAQDMVPNPLIIKLKREEESLDNIKQHYVMCK-----------------------------------NIDEKFEAVSNIY  339 (399)
Q Consensus       295 ~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~-----------------------------------~~~~k~~~l~~ll  339 (399)
                      ++..+.++..+..+........-....-+.++                                   ...........++
T Consensus       197 Fl~~~Rp~~~i~vI~n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tF~~~L~  276 (824)
T PF02399_consen  197 FLASCRPDENIHVIVNTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDETTFFSELL  276 (824)
T ss_pred             HHHHhCCCCcEEEEEeeeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchhhHHHHHH
Confidence            99998765332222111110000000000000                                   0011223344444


Q ss_pred             ccCCC-CcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHH
Q psy11867        340 GVVTI-GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQ  382 (399)
Q Consensus       340 ~~~~~-~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~  382 (399)
                      ..... .++-|||.|...++.+++.....+.+|..++|+-+..+
T Consensus       277 ~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~d  320 (824)
T PF02399_consen  277 ARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLED  320 (824)
T ss_pred             HHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccc
Confidence            44444 45667999999999999999988999999999876663

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

>KOG0953|consensus

Probab=99.02  E-value=3e-09  Score=102.39  Aligned_cols=217  Identities=15%  Similarity=0.181  Sum_probs=144.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh-cc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK-KI  220 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~  220 (399)
                      .+-++-+|||.||||-    -+++++...+.   .++--|.|-||..+++.+.+.+-.+     ...+|.+...... ..
T Consensus       191 RkIi~H~GPTNSGKTy----~ALqrl~~aks---GvycGPLrLLA~EV~~r~na~gipC-----dL~TGeE~~~~~~~~~  258 (700)
T KOG0953|consen  191 RKIIMHVGPTNSGKTY----RALQRLKSAKS---GVYCGPLRLLAHEVYDRLNALGIPC-----DLLTGEERRFVLDNGN  258 (700)
T ss_pred             heEEEEeCCCCCchhH----HHHHHHhhhcc---ceecchHHHHHHHHHHHhhhcCCCc-----cccccceeeecCCCCC
Confidence            3456667899999995    45666665544   6888999999999999999886655     3333332211111 12


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhC
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~  300 (399)
                      ..+.+=||.+++--         -..+++.||||.++|-+......+...++.....+.++++     .+.+..+.+.++
T Consensus       259 ~a~hvScTVEM~sv---------~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~AdEiHLCG-----epsvldlV~~i~  324 (700)
T KOG0953|consen  259 PAQHVSCTVEMVSV---------NTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADEIHLCG-----EPSVLDLVRKIL  324 (700)
T ss_pred             cccceEEEEEEeec---------CCceEEEEehhHHhhcCcccchHHHHHHHhhhhhhhhccC-----CchHHHHHHHHH
Confidence            24566777765421         2356799999999998876677777778777666766665     455666666654


Q ss_pred             C---CCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCe-EEEEcC
Q psy11867        301 P---NPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLN-VGLLSG  376 (399)
Q Consensus       301 ~---~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~-v~~lhg  376 (399)
                      .   +-+.++             .|...... .-.+.+..-++....|-||| |-|++....+...+.+.|.. +++++|
T Consensus       325 k~TGd~vev~-------------~YeRl~pL-~v~~~~~~sl~nlk~GDCvV-~FSkk~I~~~k~kIE~~g~~k~aVIYG  389 (700)
T KOG0953|consen  325 KMTGDDVEVR-------------EYERLSPL-VVEETALGSLSNLKPGDCVV-AFSKKDIFTVKKKIEKAGNHKCAVIYG  389 (700)
T ss_pred             hhcCCeeEEE-------------eecccCcc-eehhhhhhhhccCCCCCeEE-EeehhhHHHHHHHHHHhcCcceEEEec
Confidence            2   322221             11111110 01112333344455566655 55788899999999888665 999999


Q ss_pred             CCCHHHHHHHHHHHhc--CCCcccC
Q psy11867        377 ELTVEQRLSILDRFRE--GEFKIYS  399 (399)
Q Consensus       377 ~~~~~~R~~v~~~F~~--G~~~ILV  399 (399)
                      +++++.|.+--..|.+  ++++|||
T Consensus       390 sLPPeTr~aQA~~FNd~~~e~dvlV  414 (700)
T KOG0953|consen  390 SLPPETRLAQAALFNDPSNECDVLV  414 (700)
T ss_pred             CCCCchhHHHHHHhCCCCCccceEE
Confidence            9999999999999998  9999987

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

Probab=98.99  E-value=3.5e-09  Score=113.49  Aligned_cols=65  Identities=23%  Similarity=0.303  Sum_probs=53.7

Q ss_pred             CCChHHHHHHhhhhh---cCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHH
Q psy11867        124 YAPSKIQETALPTLL---ADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGE  191 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll---~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~  191 (399)
                      .++++-|.+.+..+.   .+ ++++++.||||+|||++|++|++.....  .+.+++|-++|+.|..|+..
T Consensus       256 ~e~R~~Q~~m~~~v~~~l~~-~~~~~iEA~TGtGKTlaYLlpa~~~a~~--~~~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        256 YEKREGQQEMMKEVYTALRD-SEHALIEAGTGTGKSLAYLLPAAYFAKK--KEEPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             CcCCHHHHHHHHHHHHHHhc-CCCEEEECCCCCchhHHHHHHHHHHhhc--cCCeEEEEcCCHHHHHHHHH
Confidence            489999999665553   33 7899999999999999999999876543  34569999999999999865

>COG4889 Predicted helicase [General function prediction only]

Probab=98.99  E-value=4.9e-10  Score=112.58  Aligned_cols=146  Identities=16%  Similarity=0.155  Sum_probs=89.8

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA  180 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  180 (399)
                      +|+.+.. ..+..++.-..-.+|+|+|..|+...+++   +.|.-++ ...|+|||...+- +.+.+..    .++|+|+
T Consensus       141 DW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLI-MAcGTGKTfTsLk-isEala~----~~iL~Lv  213 (1518)
T COG4889         141 DWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLI-MACGTGKTFTSLK-ISEALAA----ARILFLV  213 (1518)
T ss_pred             ChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEE-EecCCCccchHHH-HHHHHhh----hheEeec
Confidence            4444432 34445555556679999999999999865   1222233 3469999988764 3333332    5799999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhh----------------------------hhhccCCcEEEeCchhH
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE----------------------------RNKKITEQIIIGTPGKV  232 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------~~~~~~~~IlV~Tp~~l  232 (399)
                      |+.+|..|+.+.+..-..-  .+....++......                            ++...+--||.+|.+.+
T Consensus       214 PSIsLLsQTlrew~~~~~l--~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl  291 (1518)
T COG4889         214 PSISLLSQTLREWTAQKEL--DFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSL  291 (1518)
T ss_pred             chHHHHHHHHHHHhhccCc--cceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccch
Confidence            9999999998887653221  22222222111110                            01112234889999887


Q ss_pred             HHhhhccccccCCceeEEEEechhhHh
Q psy11867        233 LDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       233 ~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      ...- .-....+..++++|+|||||-.
T Consensus       292 ~~i~-eAQe~G~~~fDliicDEAHRTt  317 (1518)
T COG4889         292 PRIK-EAQEAGLDEFDLIICDEAHRTT  317 (1518)
T ss_pred             HHHH-HHHHcCCCCccEEEecchhccc
Confidence            6542 2223347789999999999974

>KOG0392|consensus

Probab=98.96  E-value=8.5e-09  Score=107.10  Aligned_cols=152  Identities=20%  Similarity=0.104  Sum_probs=97.5

Q ss_pred             CChHHHHHHhhhh--hcCCCCcEEEEccCCCCceehhHHHHHHhh-CCC----CCCCe-EEEEeCcHHHHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTL--LADPPHNMIAQSQSGTGKTAAFTLTMLSRV-NPS----IQEPQ-VLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       125 ~p~~iQ~~ai~~l--l~~~g~~vi~~a~TGsGKT~~~~l~il~~l-~~~----~~~~~-~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      .++.||.+.++++  |+..+-|-|.|...|-|||+..+.-+..-. .+.    ..... .|||||. .|+--+..+++++
T Consensus       975 ~LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf 1053 (1549)
T KOG0392|consen  975 KLRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKF 1053 (1549)
T ss_pred             HHHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHh
Confidence            4567899988876  444467899999999999987654443322 221    01222 7999997 6887777777777


Q ss_pred             hccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHH
Q psy11867        197 GKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQK  273 (399)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~  273 (399)
                      ..   .+++...+|+.......   ..+.+|+|+..+.+.+-..   .+.-....|+|+||-|.+-   .....+....+
T Consensus      1054 ~p---fL~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d---~l~~~~wNYcVLDEGHVik---N~ktkl~kavk 1124 (1549)
T KOG0392|consen 1054 FP---FLKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVD---YLIKIDWNYCVLDEGHVIK---NSKTKLTKAVK 1124 (1549)
T ss_pred             cc---hhhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHH---HHHhcccceEEecCcceec---chHHHHHHHHH
Confidence            54   45665566655443332   3456899999998754322   2222356699999999974   23344445555


Q ss_pred             hCCCCCcEEEEEee
Q psy11867        274 RLPSDCQIMLFSAT  287 (399)
Q Consensus       274 ~l~~~~q~l~~SAT  287 (399)
                      .+..+. .+.+|.|
T Consensus      1125 qL~a~h-RLILSGT 1137 (1549)
T KOG0392|consen 1125 QLRANH-RLILSGT 1137 (1549)
T ss_pred             HHhhcc-eEEeeCC
Confidence            554343 4666777

>KOG0952|consensus

Probab=98.93  E-value=2.2e-10  Score=117.18  Aligned_cols=136  Identities=18%  Similarity=0.200  Sum_probs=103.2

Q ss_pred             CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        123 FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      +....|+|.+.+-.+..- ..++++-+|||+|||++|.+++...+... .+.+++|++|-.+|+..-...+.+.... ++
T Consensus       925 ~~~fn~~q~~if~~~y~t-d~~~~~g~ptgsgkt~~ae~a~~~~~~~~-p~~kvvyIap~kalvker~~Dw~~r~~~-~g 1001 (1230)
T KOG0952|consen  925 YKYFNPIQTQIFHCLYHT-DLNFLLGAPTGSGKTVVAELAIFRALSYY-PGSKVVYIAPDKALVKERSDDWSKRDEL-PG 1001 (1230)
T ss_pred             hcccCCccceEEEEEeec-chhhhhcCCccCcchhHHHHHHHHHhccC-CCccEEEEcCCchhhcccccchhhhccc-CC
Confidence            346678899888887765 68999999999999999999988877654 5578999999999998776666654433 36


Q ss_pred             cEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccc-cCCceeEEEEechhhHhhc
Q psy11867        203 LSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFF-DLSKIKVFVLDEADVMIAT  261 (399)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~-~~~~~~~lViDEah~l~~~  261 (399)
                      +++.-..|...-+.......+|+|+||++.......+... .++++..+|+||.|++.+.
T Consensus      1002 ~k~ie~tgd~~pd~~~v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~ 1061 (1230)
T KOG0952|consen 1002 IKVIELTGDVTPDVKAVREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED 1061 (1230)
T ss_pred             ceeEeccCccCCChhheecCceEEcccccccCccccccchhhhccccceeecccccccCC
Confidence            6666666555444333456789999999987765544433 3778999999999998753

>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=98.84  E-value=2.8e-08  Score=90.39  Aligned_cols=129  Identities=19%  Similarity=0.168  Sum_probs=94.8

Q ss_pred             CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        123 FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      -..|++.|..+.-.+..  |+  |++..||=|||++..+|+.-....+   ..+=|++.+.-||..=++++..+...+ +
T Consensus        75 g~~p~~vQll~~l~L~~--G~--laEm~TGEGKTli~~l~a~~~AL~G---~~V~vvT~NdyLA~RD~~~~~~~y~~L-G  146 (266)
T PF07517_consen   75 GLRPYDVQLLGALALHK--GR--LAEMKTGEGKTLIAALPAALNALQG---KGVHVVTSNDYLAKRDAEEMRPFYEFL-G  146 (266)
T ss_dssp             S----HHHHHHHHHHHT--TS--EEEESTTSHHHHHHHHHHHHHHTTS---S-EEEEESSHHHHHHHHHHHHHHHHHT-T
T ss_pred             CCcccHHHHhhhhhccc--ce--eEEecCCCCcHHHHHHHHHHHHHhc---CCcEEEeccHHHhhccHHHHHHHHHHh-h
Confidence            34799999999977755  34  9999999999999988877666543   448899999999999999999999887 8


Q ss_pred             cEEEEEEcCchhh-hhhccCCcEEEeCchhHH-Hhhhcc----ccc-cCCceeEEEEechhhHh
Q psy11867        203 LSVRYAVRGENLE-RNKKITEQIIIGTPGKVL-DWGLKY----RFF-DLSKIKVFVLDEADVMI  259 (399)
Q Consensus       203 ~~~~~~~~~~~~~-~~~~~~~~IlV~Tp~~l~-~~~~~~----~~~-~~~~~~~lViDEah~l~  259 (399)
                      +.+.....+.... +.....++|+.+|...+. +++...    ... ..+.++++||||+|.++
T Consensus       147 lsv~~~~~~~~~~~r~~~Y~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  147 LSVGIITSDMSSEERREAYAADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             --EEEEETTTEHHHHHHHHHSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             hccccCccccCHHHHHHHHhCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            9999988876543 334556789999999884 333221    111 25788999999999886

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 ....

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=98.81  E-value=1.4e-07  Score=98.56  Aligned_cols=167  Identities=14%  Similarity=0.122  Sum_probs=103.7

Q ss_pred             CChHHHHHHhhhhhc----C--CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        125 APSKIQETALPTLLA----D--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~----~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      .-+.+|-.|+..+.+    .  .|-=++-.|.||+|||++=.- |+..+.....+.|..|-.-.|.|..|+.+.+++-..
T Consensus       408 ~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNAR-ImyaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~  486 (1110)
T TIGR02562       408 PRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANAR-AMYALRDDKQGARFAIALGLRSLTLQTGHALKTRLN  486 (1110)
T ss_pred             CCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHH-HHHHhCCCCCCceEEEEccccceeccchHHHHHhcC
Confidence            345799999988864    1  356677789999999987653 444555556778888889999999999988877432


Q ss_pred             cCCCcEEEEEEcCchhh------------------------------------------h--------h----hccCCcE
Q psy11867        199 HITDLSVRYAVRGENLE------------------------------------------R--------N----KKITEQI  224 (399)
Q Consensus       199 ~~~~~~~~~~~~~~~~~------------------------------------------~--------~----~~~~~~I  224 (399)
                      - .+-...+.+|+....                                          .        .    ......+
T Consensus       487 L-~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~~rll~apv  565 (1110)
T TIGR02562       487 L-SDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKEKTLLAAPV  565 (1110)
T ss_pred             C-CccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhhhhhhcCCe
Confidence            1 111222222221000                                          0        0    0011249


Q ss_pred             EEeCchhHHHhhhccc--cccCC--c--eeEEEEechhhHhhcCCchHHHHHHHHhCC-CCCcEEEEEeeCChhHHHH
Q psy11867        225 IIGTPGKVLDWGLKYR--FFDLS--K--IKVFVLDEADVMIATQGHQDFSIRIQKRLP-SDCQIMLFSATYDKEVMEF  295 (399)
Q Consensus       225 lV~Tp~~l~~~~~~~~--~~~~~--~--~~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~l~~SAT~~~~v~~~  295 (399)
                      +|||++.++-.....+  ...+.  .  =+.|||||+|.+-.  .....+.+++..+. -...++++|||+|+.+...
T Consensus       566 ~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~--~~~~~L~rlL~w~~~lG~~VlLmSATLP~~l~~~  641 (1110)
T TIGR02562       566 LVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEP--EDLPALLRLVQLAGLLGSRVLLSSATLPPALVKT  641 (1110)
T ss_pred             EEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCH--HHHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHH
Confidence            9999999987753222  22111  1  25799999998732  23333444444322 3678999999999875443

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.

>KOG0384|consensus

Probab=98.76  E-value=1.9e-07  Score=97.50  Aligned_cols=256  Identities=20%  Similarity=0.207  Sum_probs=150.4

Q ss_pred             CCChHHHHHHhhhhhcC--CCCcEEEEccCCCCceeh---hHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        124 YAPSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAA---FTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~---~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      ..++.+|.+.++.++..  .+.|+|+.-..|-|||+-   |+-.+.+....  .|| .||++|...+.. +.+.+..+. 
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~--~gp-flvvvplst~~~-W~~ef~~w~-  443 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQI--HGP-FLVVVPLSTITA-WEREFETWT-  443 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhc--cCC-eEEEeehhhhHH-HHHHHHHHh-
Confidence            57889999999988643  479999999999999954   44444433322  233 688999876653 455555554 


Q ss_pred             cCCCcEEEEEEcCch---hhhh---------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchH
Q psy11867        199 HITDLSVRYAVRGEN---LERN---------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQD  266 (399)
Q Consensus       199 ~~~~~~~~~~~~~~~---~~~~---------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~  266 (399)
                         .+++.+.+|...   +-++         .....+++++|.+.++.-..   .+.--...++++||||+|-.   -..
T Consensus       444 ---~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~---~L~~i~w~~~~vDeahrLkN---~~~  514 (1373)
T KOG0384|consen  444 ---DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKA---ELSKIPWRYLLVDEAHRLKN---DES  514 (1373)
T ss_pred             ---hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHh---hhccCCcceeeecHHhhcCc---hHH
Confidence               455555555422   1111         11256899999998865322   22222457899999999842   333


Q ss_pred             HHHHHHHhCCCCCcEEEEEeeC-ChhHHHHHHhh-CCCCeEEec-------------------------------c-ccc
Q psy11867        267 FSIRIQKRLPSDCQIMLFSATY-DKEVMEFAQDM-VPNPLIIKL-------------------------------K-REE  312 (399)
Q Consensus       267 ~~~~i~~~l~~~~q~l~~SAT~-~~~v~~~~~~~-~~~p~~i~~-------------------------------~-~~~  312 (399)
                      .+...+..+.-+. .++.|.|. -+.+.++.... +..|..+..                               . ..+
T Consensus       515 ~l~~~l~~f~~~~-rllitgTPlQNsikEL~sLl~Fl~P~kf~~~~~f~~~~~~~~e~~~~~L~~~L~P~~lRr~kkdve  593 (1373)
T KOG0384|consen  515 KLYESLNQFKMNH-RLLITGTPLQNSLKELWSLLHFLMPGKFDSWDEFLEEFDEETEEQVRKLQQILKPFLLRRLKKDVE  593 (1373)
T ss_pred             HHHHHHHHhcccc-eeeecCCCccccHHHHHHHhcccCCCCCCcHHHHHHhhcchhHHHHHHHHHHhhHHHHHHHHhhhc
Confidence            3444455544333 46667772 22333322111 011110000                               0 000


Q ss_pred             ccc-cce-------------------------------------------------eEEEEEeCChhh---HH------H
Q psy11867        313 ESL-DNI-------------------------------------------------KQHYVMCKNIDE---KF------E  333 (399)
Q Consensus       313 ~~~-~~i-------------------------------------------------~~~~~~~~~~~~---k~------~  333 (399)
                      .++ ...                                                 .|-|..-...+.   .+      .
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            000 000                                                 111111111100   11      2


Q ss_pred             HHHHHhccC---------------CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC
Q psy11867        334 AVSNIYGVV---------------TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGE  394 (399)
Q Consensus       334 ~l~~ll~~~---------------~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~  394 (399)
                      .|..++...               .+++||||.+-.+....|+++|...+++..-+-|.+..+.|.++++.|..-.
T Consensus       674 ~L~~lI~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~  749 (1373)
T KOG0384|consen  674 ALQALIQSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPD  749 (1373)
T ss_pred             HHHHHHHhcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCC
Confidence            333333221               3479999999999999999999999999999999999999999999998643

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.72  E-value=5e-08  Score=101.51  Aligned_cols=65  Identities=17%  Similarity=0.281  Sum_probs=52.0

Q ss_pred             CCChHHHHHHhhhhh---cCC----CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH
Q psy11867        124 YAPSKIQETALPTLL---ADP----PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG  190 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll---~~~----g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~  190 (399)
                      .++++-|.+....+.   .+.    ++.+++.|+||+|||++|++|++.....  .+.+++|=+.|+.|-.|+.
T Consensus        24 ~e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~--~~k~vVIST~T~~LQeQL~   95 (697)
T PRK11747         24 FIPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARA--EKKKLVISTATVALQEQLV   95 (697)
T ss_pred             CCcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHH--cCCeEEEEcCCHHHHHHHH
Confidence            478999999776664   321    4789999999999999999999876543  3446899999999999874

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.59  E-value=4.7e-07  Score=92.98  Aligned_cols=135  Identities=9%  Similarity=0.114  Sum_probs=88.5

Q ss_pred             EccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCch-------hhhhhcc
Q psy11867        148 QSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGEN-------LERNKKI  220 (399)
Q Consensus       148 ~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~  220 (399)
                      .+.+|||||.+|+-.+-..+..   +.++|||+|...|+.|+.+.++..+.   ...+....++..       +.+...+
T Consensus       166 ~~~~GSGKTevyl~~i~~~l~~---Gk~vLvLvPEi~lt~q~~~rl~~~f~---~~~v~~lhS~l~~~~R~~~w~~~~~G  239 (665)
T PRK14873        166 QALPGEDWARRLAAAAAATLRA---GRGALVVVPDQRDVDRLEAALRALLG---AGDVAVLSAGLGPADRYRRWLAVLRG  239 (665)
T ss_pred             hcCCCCcHHHHHHHHHHHHHHc---CCeEEEEecchhhHHHHHHHHHHHcC---CCcEEEECCCCCHHHHHHHHHHHhCC
Confidence            3446999999999877766654   44599999999999999999987653   123444444322       2222355


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC----CchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHH
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ----GHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFA  296 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~----~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~  296 (399)
                      ...|+|||-..+        ..-+.+++++|+||=|.-.=.+    .+..--..+.+....++.+|+-|||-+-+....+
T Consensus       240 ~~~IViGtRSAv--------FaP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSles~~~~  311 (665)
T PRK14873        240 QARVVVGTRSAV--------FAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQALV  311 (665)
T ss_pred             CCcEEEEcceeE--------EeccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHHHHHHH
Confidence            678999996543        2357899999999988542111    1222222333333468899999999765544443

>KOG1002|consensus

Probab=98.56  E-value=2.3e-05  Score=75.20  Aligned_cols=128  Identities=21%  Similarity=0.214  Sum_probs=83.0

Q ss_pred             CCChHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        124 YAPSKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      ..+-|+|.+.+-.+...   .-..-|+....|.|||....--++..    ..+...||++|+.+|. |+.+++.+.... 
T Consensus       183 i~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae----~~ra~tLVvaP~VAlm-QW~nEI~~~T~g-  256 (791)
T KOG1002|consen  183 IPLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAE----VDRAPTLVVAPTVALM-QWKNEIERHTSG-  256 (791)
T ss_pred             ecchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhc----cccCCeeEEccHHHHH-HHHHHHHHhccC-
Confidence            35678999988777653   12334666889999997765444442    2334499999999985 677778877653 


Q ss_pred             CCcEEEEEEcCchhhh-hhccCCcEEEeCchhHHHhhhcccc-c-----------cCCce--eEEEEechhhH
Q psy11867        201 TDLSVRYAVRGENLER-NKKITEQIIIGTPGKVLDWGLKYRF-F-----------DLSKI--KVFVLDEADVM  258 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~~-~~~~~~~IlV~Tp~~l~~~~~~~~~-~-----------~~~~~--~~lViDEah~l  258 (399)
                       .+++....|...... ....+.+++.+|...+-+...+... +           -+.++  --+|+||||-+
T Consensus       257 -slkv~~YhG~~R~~nikel~~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~I  328 (791)
T KOG1002|consen  257 -SLKVYIYHGAKRDKNIKELMNYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNI  328 (791)
T ss_pred             -ceEEEEEecccccCCHHHhhcCcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhccc
Confidence             456555555543322 2245678999999887665443211 1           13333  45999999965

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=98.53  E-value=9.3e-07  Score=91.46  Aligned_cols=69  Identities=17%  Similarity=0.306  Sum_probs=58.9

Q ss_pred             HHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        331 KFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       331 k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +...+...+...  ...++||||++++.|+.|++.|...|+++..+||++++.+|..+++.|+.|++.|||
T Consensus       431 q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV  501 (652)
T PRK05298        431 QVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLV  501 (652)
T ss_pred             cHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEE
Confidence            344444444332  346899999999999999999999999999999999999999999999999999984

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

Probab=98.53  E-value=6.1e-07  Score=96.16  Aligned_cols=139  Identities=19%  Similarity=0.123  Sum_probs=92.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhc-c
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKK-I  220 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  220 (399)
                      ++..+|.--+|||||+..+..+-..+.. ...+.+++|+-.++|-.|+.+.++.+........  -...+..+.+... .
T Consensus       273 ~~~G~IWHtqGSGKTlTm~~~A~~l~~~-~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~--~~~s~~~Lk~~l~~~  349 (962)
T COG0610         273 GKGGYIWHTQGSGKTLTMFKLARLLLEL-PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP--KAESTSELKELLEDG  349 (962)
T ss_pred             CCceEEEeecCCchHHHHHHHHHHHHhc-cCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc--cccCHHHHHHHHhcC
Confidence            5678999999999998876655444443 6788999999999999999999999876542211  2222333333333 3


Q ss_pred             CCcEEEeCchhHHHhhhccccccC-CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeC
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDL-SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATY  288 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~-~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~  288 (399)
                      ...|+|+|-..|-........... ++=-+||+|||||-    .+...-..+...+ ++...++||.|.
T Consensus       350 ~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRS----Q~G~~~~~~~~~~-~~a~~~gFTGTP  413 (962)
T COG0610         350 KGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRS----QYGELAKLLKKAL-KKAIFIGFTGTP  413 (962)
T ss_pred             CCcEEEEEecccchhhhcccccccCCCcEEEEEechhhc----cccHHHHHHHHHh-ccceEEEeeCCc
Confidence            447999999998776544311111 22237899999994    2222223334444 358899999993

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

Probab=98.45  E-value=5.4e-07  Score=94.43  Aligned_cols=142  Identities=18%  Similarity=0.227  Sum_probs=84.3

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHH-----HHhc-cCCCcEEEE--EEcCc--
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVA-----KMGK-HITDLSVRY--AVRGE--  212 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~-----~~~~-~~~~~~~~~--~~~~~--  212 (399)
                      .++.+.++||||||.+|+-.|+..... .+..+.||+||+.++-..+...+.     .... .+.+..+.+  ..++.  
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~-~~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~  138 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQK-YGLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKK  138 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHH-cCCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCccc
Confidence            589999999999999999888776544 345679999999999888776654     1111 122222222  22221  


Q ss_pred             -----hhhhh----------hccCCcEEEeCchhHHHhhhcccc------------c-cCCce-eEEEEechhhHhhcCC
Q psy11867        213 -----NLERN----------KKITEQIIIGTPGKVLDWGLKYRF------------F-DLSKI-KVFVLDEADVMIATQG  263 (399)
Q Consensus       213 -----~~~~~----------~~~~~~IlV~Tp~~l~~~~~~~~~------------~-~~~~~-~~lViDEah~l~~~~~  263 (399)
                           .+...          .....+|+|.|-+.|..-......            + .++.. =+||+||+|++-..  
T Consensus       139 k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~~~--  216 (986)
T PRK15483        139 KSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFPRD--  216 (986)
T ss_pred             ccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCCcc--
Confidence                 11111          112458999999988542110000            0 11111 36999999998431  


Q ss_pred             chHHHHHHHHhCCCCCcEEEEEeeCCh
Q psy11867        264 HQDFSIRIQKRLPSDCQIMLFSATYDK  290 (399)
Q Consensus       264 ~~~~~~~i~~~l~~~~q~l~~SAT~~~  290 (399)
                       ......| ..+.+.+ ++.||||.+.
T Consensus       217 -~k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        217 -NKFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             -hHHHHHH-HhcCccc-EEEEeeecCC
Confidence             2223344 4444433 5679999986

>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=98.41  E-value=2.3e-06  Score=69.55  Aligned_cols=71  Identities=37%  Similarity=0.573  Sum_probs=63.9

Q ss_pred             hhHHHHHHHHhccCC--CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSNIYGVVT--IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~ll~~~~--~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.|...+.+++....  .+++||||++.+.++.+++.|.+.+..+..+||+++..+|..+++.|++|..+||+
T Consensus        11 ~~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili   83 (131)
T cd00079          11 DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLV   83 (131)
T ss_pred             HHHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEE
Confidence            368888888877664  67999999999999999999998889999999999999999999999999988874

>KOG4439|consensus

Probab=98.37  E-value=8.2e-06  Score=81.19  Aligned_cols=132  Identities=23%  Similarity=0.184  Sum_probs=82.3

Q ss_pred             CChHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhHHHHHHhh-----CCC--CCCCeEEEEeCcHHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSRV-----NPS--IQEPQVLCLAPTYELAIQIGEVVA  194 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~l-----~~~--~~~~~~lil~Pt~~La~Q~~~~~~  194 (399)
                      .+-|+|..++..++-.   ++...|+....|-|||+...--+++.-     ...  ......|||||- .|..|++.++.
T Consensus       325 ~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~Pa-Sli~qW~~Ev~  403 (901)
T KOG4439|consen  325 ELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPA-SLIHQWEAEVA  403 (901)
T ss_pred             ecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcH-HHHHHHHHHHH
Confidence            4568999999888632   467788889999999987655555432     111  111248999997 56677777666


Q ss_pred             HHhccCCCcEEEEEEcCch--hhhhhccCCcEEEeCchhHHHh----hhccccc-cCCc--eeEEEEechhhH
Q psy11867        195 KMGKHITDLSVRYAVRGEN--LERNKKITEQIIIGTPGKVLDW----GLKYRFF-DLSK--IKVFVLDEADVM  258 (399)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~IlV~Tp~~l~~~----~~~~~~~-~~~~--~~~lViDEah~l  258 (399)
                      .-...- .+++...+|...  .........+|||+|+.-+..-    ....+.- .+.+  ...||+||||.+
T Consensus       404 ~rl~~n-~LsV~~~HG~n~r~i~~~~L~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~I  475 (901)
T KOG4439|consen  404 RRLEQN-ALSVYLYHGPNKREISAKELRKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNI  475 (901)
T ss_pred             HHHhhc-ceEEEEecCCccccCCHHHHhhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhh
Confidence            554432 567776666653  2222245678999999765441    0000100 1222  356999999965

>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=98.37  E-value=1.9e-06  Score=75.45  Aligned_cols=141  Identities=21%  Similarity=0.225  Sum_probs=75.0

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH-------HHHHHH
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG-------EVVAKM  196 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~-------~~~~~~  196 (399)
                      ...+.-|..++.+++.  ..-+++.||.|||||+.++..+++.+.. ....+.+|.-|..+....+.       +.+..+
T Consensus         3 ~p~~~~Q~~~~~al~~--~~~v~~~G~AGTGKT~LA~a~Al~~v~~-g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~   79 (205)
T PF02562_consen    3 KPKNEEQKFALDALLN--NDLVIVNGPAGTGKTFLALAAALELVKE-GEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPY   79 (205)
T ss_dssp             ---SHHHHHHHHHHHH---SEEEEE--TTSSTTHHHHHHHHHHHHT-TS-SEEEEEE-S--TT----SS---------TT
T ss_pred             cCCCHHHHHHHHHHHh--CCeEEEECCCCCcHHHHHHHHHHHHHHh-CCCcEEEEEecCCCCccccccCCCCHHHHHHHH
Confidence            3457899999999997  5899999999999999999999988876 46677888889876422211       111111


Q ss_pred             h----ccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHH
Q psy11867        197 G----KHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQ  272 (399)
Q Consensus       197 ~----~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~  272 (399)
                      .    ..+..+.     +....+.. .....|-+..+..+     +.+.  +++ .++|+|||+.+.     ...+..++
T Consensus        80 ~~p~~d~l~~~~-----~~~~~~~~-~~~~~Ie~~~~~~i-----RGrt--~~~-~~iIvDEaQN~t-----~~~~k~il  140 (205)
T PF02562_consen   80 LRPIYDALEELF-----GKEKLEEL-IQNGKIEIEPLAFI-----RGRT--FDN-AFIIVDEAQNLT-----PEELKMIL  140 (205)
T ss_dssp             THHHHHHHTTTS------TTCHHHH-HHTTSEEEEEGGGG-----TT----B-S-EEEEE-SGGG-------HHHHHHHH
T ss_pred             HHHHHHHHHHHh-----ChHhHHHH-hhcCeEEEEehhhh-----cCcc--ccc-eEEEEecccCCC-----HHHHHHHH
Confidence            0    0000000     11111111 12334666555432     1122  222 799999999873     34566788


Q ss_pred             HhCCCCCcEEEEEe
Q psy11867        273 KRLPSDCQIMLFSA  286 (399)
Q Consensus       273 ~~l~~~~q~l~~SA  286 (399)
                      .++..+++++++.-
T Consensus       141 TR~g~~skii~~GD  154 (205)
T PF02562_consen  141 TRIGEGSKIIITGD  154 (205)
T ss_dssp             TTB-TT-EEEEEE-
T ss_pred             cccCCCcEEEEecC
Confidence            88888888877643

; GO: 0005524 ATP binding; PDB: 3B85_A.

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

Probab=98.36  E-value=2e-06  Score=77.38  Aligned_cols=67  Identities=21%  Similarity=0.367  Sum_probs=49.1

Q ss_pred             ChHHHHHHhhhhhcCCCCc-EEEEccCCCCceehhHHHHHHhh------CCCCCCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        126 PSKIQETALPTLLADPPHN-MIAQSQSGTGKTAAFTLTMLSRV------NPSIQEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~~g~~-vi~~a~TGsGKT~~~~l~il~~l------~~~~~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      +++-|.+|+..++.  ... .+++||+|||||.... .++..+      .....+.++|+++|+..-+.++.+.+.+
T Consensus         2 ln~~Q~~Ai~~~~~--~~~~~~i~GpPGTGKT~~l~-~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALS--SNGITLIQGPPGTGKTTTLA-SIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCT--SSE-EEEE-STTSSHHHHHH-HHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHc--CCCCEEEECCCCCChHHHHH-HHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            57889999999998  466 9999999999995433 333333      1134667899999999999999888877

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

Probab=98.31  E-value=2.7e-06  Score=74.71  Aligned_cols=125  Identities=21%  Similarity=0.232  Sum_probs=71.1

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      ++++-|.+++..++....+-.+++|+.|+|||.+. -.+...+..  .+.++++++||...+..+.+...        +.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~--~g~~v~~~apT~~Aa~~L~~~~~--------~~   69 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEA--AGKRVIGLAPTNKAAKELREKTG--------IE   69 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHH--TT--EEEEESSHHHHHHHHHHHT--------S-
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHh--CCCeEEEECCcHHHHHHHHHhhC--------cc
Confidence            36889999999998753456788899999999643 334444443  34679999999988876555421        11


Q ss_pred             EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccc---cccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCC-CCc
Q psy11867        205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYR---FFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPS-DCQ  280 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~---~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~-~~q  280 (399)
                                           ..|-.+++.......   ...+...+++|||||-.+.     ...+..++...+. ..+
T Consensus        70 ---------------------a~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~-----~~~~~~ll~~~~~~~~k  123 (196)
T PF13604_consen   70 ---------------------AQTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVD-----SRQLARLLRLAKKSGAK  123 (196)
T ss_dssp             ---------------------EEEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-B-----HHHHHHHHHHS-T-T-E
T ss_pred             ---------------------hhhHHHHHhcCCcccccccccCCcccEEEEecccccC-----HHHHHHHHHHHHhcCCE
Confidence                                 112222221100000   0014456799999998863     2345566666665 566


Q ss_pred             EEEEEe
Q psy11867        281 IMLFSA  286 (399)
Q Consensus       281 ~l~~SA  286 (399)
                      ++++-=
T Consensus       124 lilvGD  129 (196)
T PF13604_consen  124 LILVGD  129 (196)
T ss_dssp             EEEEE-
T ss_pred             EEEECC
Confidence            666543

>KOG2340|consensus

Probab=98.31  E-value=1.3e-05  Score=77.54  Aligned_cols=272  Identities=18%  Similarity=0.225  Sum_probs=163.6

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccC-CCCc--eehhHHHHHHhhC----------------------------CCCC
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQS-GTGK--TAAFTLTMLSRVN----------------------------PSIQ  172 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~T-GsGK--T~~~~l~il~~l~----------------------------~~~~  172 (399)
                      ..+|+.|.+.+..+.+  -+|++..-.| +.|+  +-.|.+-++.++.                            ++..
T Consensus       215 ~pltalQ~~L~~~m~~--YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~t  292 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFN--YRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFT  292 (698)
T ss_pred             CcchHHHHHHHHHHHh--hhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCC
Confidence            5789999999999888  5888764322 3344  4567777777651                            2234


Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEE--------EEEEcC---------------------c---------hh
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV--------RYAVRG---------------------E---------NL  214 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~--------~~~~~~---------------------~---------~~  214 (399)
                      .|++|||||+|+-|..+...+..+......-+.        ..-++|                     .         .+
T Consensus       293 RpkVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~f  372 (698)
T KOG2340|consen  293 RPKVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAF  372 (698)
T ss_pred             CceEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHH
Confidence            688999999999999999888877433211000        001111                     0         00


Q ss_pred             hhh------hccCCcEEEeCchhHHHhhh----cccccc-CCceeEEEEechhhHhhcCCchHHHHHHHHhC---CCC--
Q psy11867        215 ERN------KKITEQIIIGTPGKVLDWGL----KYRFFD-LSKIKVFVLDEADVMIATQGHQDFSIRIQKRL---PSD--  278 (399)
Q Consensus       215 ~~~------~~~~~~IlV~Tp~~l~~~~~----~~~~~~-~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l---~~~--  278 (399)
                      .+.      .-...+|+||+|=-|.-.+.    +.+.++ ++.+.++|||-||.|+.. .+. .+..++..|   |..  
T Consensus       373 tkKtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~Q-NwE-hl~~ifdHLn~~P~k~h  450 (698)
T KOG2340|consen  373 TKKTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQ-NWE-HLLHIFDHLNLQPSKQH  450 (698)
T ss_pred             HHHHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHh-hHH-HHHHHHHHhhcCccccc
Confidence            000      01234799999976644433    122332 788999999999999853 333 333444444   221  


Q ss_pred             -------------------CcEEEEEeeCChhHHHHHHhhCCC---CeEEecccccccc----cceeEEE--EEeCCh--
Q psy11867        279 -------------------CQIMLFSATYDKEVMEFAQDMVPN---PLIIKLKREEESL----DNIKQHY--VMCKNI--  328 (399)
Q Consensus       279 -------------------~q~l~~SAT~~~~v~~~~~~~~~~---p~~i~~~~~~~~~----~~i~~~~--~~~~~~--  328 (399)
                                         +|+++||+--.+....+...+..+   .+..+-.....+.    -.+.|.+  +.|.+.  
T Consensus       451 ~~DfSRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~Gkv~~~~~~~~gsi~~v~~~l~Qvf~ri~~~si~~  530 (698)
T KOG2340|consen  451 DVDFSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQSGGSISNVGIPLCQVFQRIEVKSIIE  530 (698)
T ss_pred             CCChhheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhhhcceeeeccccCCCchhhccchhhhhhhheeccCccc
Confidence                               488899887666555555444322   2221111111111    1222222  122221  


Q ss_pred             --hhHHHHHHHHhccCC----CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 --DEKFEAVSNIYGVVT----IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 --~~k~~~l~~ll~~~~----~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                        +..+.....-+.-.-    ..-++||.++--.--++.++|.+.++....+|.=.++..-.++-+.|..|..+||+
T Consensus       531 ~~D~RFkyFv~~ImPq~~k~t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlL  607 (698)
T KOG2340|consen  531 TPDARFKYFVDKIMPQLIKRTESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLL  607 (698)
T ss_pred             CchHHHHHHHHhhchhhcccccCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEE
Confidence              334443333222111    23479999999999999999999988888888877788888888999999998874

>KOG0391|consensus

Probab=98.15  E-value=7.8e-06  Score=85.22  Aligned_cols=158  Identities=18%  Similarity=0.152  Sum_probs=101.7

Q ss_pred             CChHHHHHHhhhhhc--CCCCcEEEEccCCCCceehhHHHHHHhh-CCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        125 APSKIQETALPTLLA--DPPHNMIAQSQSGTGKTAAFTLTMLSRV-NPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~--~~g~~vi~~a~TGsGKT~~~~l~il~~l-~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      .++.||...+.++..  ...-|-|+....|-|||.--. .++.++ ....+-+=-|||+||.-+. .+.-+|++   +++
T Consensus       615 qLReYQkiGLdWLatLYeknlNGILADEmGLGKTIQtI-SllAhLACeegnWGPHLIVVpTsviL-nWEMElKR---wcP  689 (1958)
T KOG0391|consen  615 QLREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQTI-SLLAHLACEEGNWGPHLIVVPTSVIL-NWEMELKR---WCP  689 (1958)
T ss_pred             HHHHHHHhhHHHHHHHHHhcccceehhhhcccchhHHH-HHHHHHHhcccCCCCceEEeechhhh-hhhHHHhh---hCC
Confidence            456789988887732  126788999999999997533 334333 2222222358999997654 34444554   567


Q ss_pred             CcEEEEEEcCchhhhhhc------cCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC
Q psy11867        202 DLSVRYAVRGENLERNKK------ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL  275 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~------~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l  275 (399)
                      ++++-..+|.....+.++      +..||.|+++..+..-+   ..|.-++.+|+|+||||.+-   +|.......+-.+
T Consensus       690 glKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~---~AFkrkrWqyLvLDEaqnIK---nfksqrWQAllnf  763 (1958)
T KOG0391|consen  690 GLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDL---TAFKRKRWQYLVLDEAQNIK---NFKSQRWQALLNF  763 (1958)
T ss_pred             cceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHH---HHHHhhccceeehhhhhhhc---chhHHHHHHHhcc
Confidence            889888888765444332      23489999988776543   45566788999999999983   5665555555455


Q ss_pred             CCCCcEEEEEee-CChhHHH
Q psy11867        276 PSDCQIMLFSAT-YDKEVME  294 (399)
Q Consensus       276 ~~~~q~l~~SAT-~~~~v~~  294 (399)
                      +..+ .++++.| +-+.+.+
T Consensus       764 nsqr-RLLLtgTPLqNslmE  782 (1958)
T KOG0391|consen  764 NSQR-RLLLTGTPLQNSLME  782 (1958)
T ss_pred             chhh-eeeecCCchhhHHHH
Confidence            4444 5566666 4444333

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

Probab=98.10  E-value=2.4e-05  Score=71.70  Aligned_cols=164  Identities=15%  Similarity=0.127  Sum_probs=103.0

Q ss_pred             ChHHHHHHhhhhhc-------C-CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        126 PSKIQETALPTLLA-------D-PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       126 p~~iQ~~ai~~ll~-------~-~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ++..|.+++-....       + .+...++--.||.||--...--|++.+.++  ..++|.++.+..|-....+-++.++
T Consensus        38 LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~G--r~r~vwvS~s~dL~~Da~RDl~DIG  115 (303)
T PF13872_consen   38 LSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRG--RKRAVWVSVSNDLKYDAERDLRDIG  115 (303)
T ss_pred             ccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcC--CCceEEEECChhhhhHHHHHHHHhC
Confidence            46777777754432       1 246778888899999866655667766653  3469999999999999999999987


Q ss_pred             ccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcc----ccc-----cC--CceeEEEEechhhHhhcCC---
Q psy11867        198 KHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKY----RFF-----DL--SKIKVFVLDEADVMIATQG---  263 (399)
Q Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~----~~~-----~~--~~~~~lViDEah~l~~~~~---  263 (399)
                      ..  .+.+.-...- ...........|+.+|...|.......    ..+     ++  ..=.++||||||.+-....   
T Consensus       116 ~~--~i~v~~l~~~-~~~~~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~~~~  192 (303)
T PF13872_consen  116 AD--NIPVHPLNKF-KYGDIIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSSGSK  192 (303)
T ss_pred             CC--cccceechhh-ccCcCCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCccCc
Confidence            65  2222211110 000111234469999999887653211    000     11  1235899999999854322   


Q ss_pred             ----chHHHHHHHHhCCCCCcEEEEEeeCChhHHHH
Q psy11867        264 ----HQDFSIRIQKRLPSDCQIMLFSATYDKEVMEF  295 (399)
Q Consensus       264 ----~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~  295 (399)
                          ....+..+...+| +.+++.+|||-..+..++
T Consensus       193 ~~sk~g~avl~LQ~~LP-~ARvvY~SATgasep~Nm  227 (303)
T PF13872_consen  193 KPSKTGIAVLELQNRLP-NARVVYASATGASEPRNM  227 (303)
T ss_pred             cccHHHHHHHHHHHhCC-CCcEEEecccccCCCcee
Confidence                1134455667775 666999999977665544

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

Probab=98.10  E-value=1.4e-05  Score=76.96  Aligned_cols=110  Identities=20%  Similarity=0.147  Sum_probs=67.9

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCC
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE  222 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (399)
                      +-++|.|..|||||+..+--+ ..+.....+..+++++++..|...+++.+......                    ...
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~-~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~--------------------~~~   60 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLA-KELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYNP--------------------KLK   60 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHH-HHhhccccCCceEEEEecchHHHHHHHHHhhhccc--------------------chh
Confidence            357899999999998766433 33322335667999999999998888777654300                    001


Q ss_pred             cEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC------CchHHHHHHHHh
Q psy11867        223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ------GHQDFSIRIQKR  274 (399)
Q Consensus       223 ~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~------~~~~~~~~i~~~  274 (399)
                      ...+..+..+..... .........+++||||||+|....      .....+..+++.
T Consensus        61 ~~~~~~~~~~i~~~~-~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   61 KSDFRKPTSFINNYS-ESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             hhhhhhhHHHHhhcc-cccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence            123334444443321 122345688999999999998621      123455555554

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>KOG0386|consensus

Probab=98.04  E-value=1.3e-05  Score=82.73  Aligned_cols=65  Identities=22%  Similarity=0.317  Sum_probs=53.8

Q ss_pred             hHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC
Q psy11867        330 EKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGE  394 (399)
Q Consensus       330 ~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~  394 (399)
                      .|+..|-.++-..  .+++++.||.-..-...+-.+|.-.+++...+-|....++|...++.|..-.
T Consensus       710 GKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pd  776 (1157)
T KOG0386|consen  710 GKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPD  776 (1157)
T ss_pred             cHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCC
Confidence            4666666655433  3479999999988888888999888999999999999999999999998643

>PRK10536 hypothetical protein; Provisional

Probab=98.02  E-value=4.1e-05  Score=69.04  Aligned_cols=143  Identities=13%  Similarity=0.124  Sum_probs=83.6

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHH-----------HH
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI-----------QI  189 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~-----------Q~  189 (399)
                      .++..-+..|...+..+.+  ...+++.|++|||||+......++.+... ...+++|.-|+.+...           -+
T Consensus        55 ~~i~p~n~~Q~~~l~al~~--~~lV~i~G~aGTGKT~La~a~a~~~l~~~-~~~kIiI~RP~v~~ge~LGfLPG~~~eK~  131 (262)
T PRK10536         55 SPILARNEAQAHYLKAIES--KQLIFATGEAGCGKTWISAAKAAEALIHK-DVDRIIVTRPVLQADEDLGFLPGDIAEKF  131 (262)
T ss_pred             ccccCCCHHHHHHHHHHhc--CCeEEEECCCCCCHHHHHHHHHHHHHhcC-CeeEEEEeCCCCCchhhhCcCCCCHHHHH
Confidence            4566678899999998887  57999999999999998887777666442 3445666667754322           12


Q ss_pred             HHHHHHHhccCCCcEEEEEEcCchhhhhhc-cCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHH
Q psy11867        190 GEVVAKMGKHITDLSVRYAVRGENLERNKK-ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFS  268 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~  268 (399)
                      .-++..+.+.+..     ..+......... ....|-|.....+     +.+.  + +-+++|+|||+.+-     ..++
T Consensus       132 ~p~~~pi~D~L~~-----~~~~~~~~~~~~~~~~~Iei~~l~ym-----RGrt--l-~~~~vIvDEaqn~~-----~~~~  193 (262)
T PRK10536        132 APYFRPVYDVLVR-----RLGASFMQYCLRPEIGKVEIAPFAYM-----RGRT--F-ENAVVILDEAQNVT-----AAQM  193 (262)
T ss_pred             HHHHHHHHHHHHH-----HhChHHHHHHHHhccCcEEEecHHHh-----cCCc--c-cCCEEEEechhcCC-----HHHH
Confidence            2222222222111     011122221111 1223545443321     2222  2 22699999999973     2566


Q ss_pred             HHHHHhCCCCCcEEEE
Q psy11867        269 IRIQKRLPSDCQIMLF  284 (399)
Q Consensus       269 ~~i~~~l~~~~q~l~~  284 (399)
                      ..++..+..+++++++
T Consensus       194 k~~ltR~g~~sk~v~~  209 (262)
T PRK10536        194 KMFLTRLGENVTVIVN  209 (262)
T ss_pred             HHHHhhcCCCCEEEEe
Confidence            7788888888887764

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

Probab=98.01  E-value=7.8e-06  Score=85.36  Aligned_cols=76  Identities=20%  Similarity=0.217  Sum_probs=61.0

Q ss_pred             HHcCCCCChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        119 YEMGFYAPSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       119 ~~~g~~~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      ..+....|++.|.+.+..+...  .++.+++.||||+|||++|++|++......  +..++|.++|+.|-.|+.+....+
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~--~~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREE--GKKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHc--CCcEEEECCCHHHHHHHHHhhcch
Confidence            3456678999999998666421  267799999999999999999999887553  256999999999999988766553

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.00  E-value=1.1e-05  Score=84.78  Aligned_cols=77  Identities=18%  Similarity=0.134  Sum_probs=64.1

Q ss_pred             cCCCCChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        121 MGFYAPSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      +-|..++|.|.+.+..+...  .+.++++.||||+|||++.+.|++.........++++|.+.|..-..|..++++++.
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhhh
Confidence            34666799999988777542  389999999999999999999999877654445789999999999999999999853

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).

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.94  E-value=2e-05  Score=82.61  Aligned_cols=127  Identities=21%  Similarity=0.162  Sum_probs=94.2

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|+++|...--.+.    +.-|+...||-|||+++.+|+.-....+..   +-||+.+--||..=.+++..+..++ +++
T Consensus       169 ~~yDVQliGgivLh----~G~IAEM~TGEGKTLvAtlp~yLnAL~Gkg---VHvVTVNDYLA~RDaewmgply~fL-GLs  240 (1112)
T PRK12901        169 VHYDVQLIGGVVLH----QGKIAEMATGEGKTLVATLPVYLNALTGNG---VHVVTVNDYLAKRDSEWMGPLYEFH-GLS  240 (1112)
T ss_pred             cccchHHhhhhhhc----CCceeeecCCCCchhHHHHHHHHHHHcCCC---cEEEEechhhhhccHHHHHHHHHHh-CCc
Confidence            57777766554443    556889999999999999998766655433   7788888899998889999988887 888


Q ss_pred             EEEEEc-C-chhhhhhccCCcEEEeCchhH-HHhhhccc-----cccCCceeEEEEechhhHh
Q psy11867        205 VRYAVR-G-ENLERNKKITEQIIIGTPGKV-LDWGLKYR-----FFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       205 ~~~~~~-~-~~~~~~~~~~~~IlV~Tp~~l-~~~~~~~~-----~~~~~~~~~lViDEah~l~  259 (399)
                      +.+... . ....+.....++|..+|...| .+++..+-     ....+.+.|.||||+|-++
T Consensus       241 vg~i~~~~~~~~~rr~aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        241 VDCIDKHQPNSEARRKAYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             eeecCCCCCCHHHHHHhCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            887765 3 344555577899999998876 34433221     2235678999999999764

>PF13245 AAA_19: Part of AAA domain

Probab=97.90  E-value=2.8e-05  Score=56.86  Aligned_cols=51  Identities=27%  Similarity=0.352  Sum_probs=38.8

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhC--CCCCCCeEEEEeCcHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVN--PSIQEPQVLCLAPTYELAIQIGEVV  193 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~--~~~~~~~~lil~Pt~~La~Q~~~~~  193 (399)
                      +.-+++.||.|||||...+-.+...+.  ... +.++++++||+..+..+.+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCC-CCeEEEECCCHHHHHHHHHHH
Confidence            355666999999999766655555552  223 668999999999999888877

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.89  E-value=0.0001  Score=75.18  Aligned_cols=142  Identities=22%  Similarity=0.256  Sum_probs=84.9

Q ss_pred             hHHHHHHhhhhhcCCCCcEEEEccCCCCceehh--HHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAF--TLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~--~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      ..+|+.|+...+.  ++-.++.|+.|||||...  ++..+..........++++.+||-.-|..+.+.+......+.   
T Consensus       147 ~~~Qk~A~~~al~--~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~---  221 (586)
T TIGR01447       147 QNWQKVAVALALK--SNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNLA---  221 (586)
T ss_pred             cHHHHHHHHHHhh--CCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhcccc---
Confidence            3799999999998  589999999999999653  333333222211235799999998888877776655432221   


Q ss_pred             EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcccc-----ccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCC
Q psy11867        205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRF-----FDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC  279 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~-----~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~  279 (399)
                      ..     ...    .....+-..|-.+|+........     -+.-.+++||||||-++-     ...+..+++.+++.+
T Consensus       222 ~~-----~~~----~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd-----~~l~~~ll~al~~~~  287 (586)
T TIGR01447       222 AA-----EAL----IAALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVD-----LPLMAKLLKALPPNT  287 (586)
T ss_pred             cc-----hhh----hhccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccCC-----HHHHHHHHHhcCCCC
Confidence            00     000    00001123343344332111011     123357899999997752     345667888888888


Q ss_pred             cEEEEEee
Q psy11867        280 QIMLFSAT  287 (399)
Q Consensus       280 q~l~~SAT  287 (399)
                      ++|++.=.
T Consensus       288 rlIlvGD~  295 (586)
T TIGR01447       288 KLILLGDK  295 (586)
T ss_pred             EEEEECCh
Confidence            88876433

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.

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

Probab=97.83  E-value=0.00044  Score=71.58  Aligned_cols=127  Identities=20%  Similarity=0.165  Sum_probs=92.7

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|..+|...--.+.    ..-++...||-|||+++.+|+.-....+   ..+.+++-..-||..-.+++.++..++ +++
T Consensus        80 ~~~dVQliG~i~lh----~g~iaEM~TGEGKTL~atlp~ylnaL~g---kgVhvVTvNdYLA~RDae~m~~l~~~L-Gls  151 (822)
T COG0653          80 RHFDVQLLGGIVLH----LGDIAEMRTGEGKTLVATLPAYLNALAG---KGVHVVTVNDYLARRDAEWMGPLYEFL-GLS  151 (822)
T ss_pred             ChhhHHHhhhhhhc----CCceeeeecCCchHHHHHHHHHHHhcCC---CCcEEeeehHHhhhhCHHHHHHHHHHc-CCc
Confidence            45566665544332    5578889999999999999887554443   338888999999999999999998887 888


Q ss_pred             EEEEEcCchhh-hhhccCCcEEEeCchhH-HHhhhcc-----ccccCCceeEEEEechhhHh
Q psy11867        205 VRYAVRGENLE-RNKKITEQIIIGTPGKV-LDWGLKY-----RFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       205 ~~~~~~~~~~~-~~~~~~~~IlV~Tp~~l-~~~~~~~-----~~~~~~~~~~lViDEah~l~  259 (399)
                      +.+...+.... +.....++|..+|...| .+++..+     .......+.+.|+||+|-++
T Consensus       152 vG~~~~~m~~~ek~~aY~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         152 VGVILAGMSPEEKRAAYACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             eeeccCCCChHHHHHHHhcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence            88887776554 44467889999998877 3332221     22235578999999999663

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.80  E-value=0.00013  Score=74.59  Aligned_cols=141  Identities=20%  Similarity=0.230  Sum_probs=85.3

Q ss_pred             hHHHHHHhhhhhcCCCCcEEEEccCCCCceehh--HHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAF--TLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~--~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .++|+.|+-..+.  .+-.++.|++|+|||...  ++..+..... ....++++.+||..-|..+.+.+......++ +.
T Consensus       154 ~d~Qk~Av~~a~~--~~~~vItGgpGTGKTt~v~~ll~~l~~~~~-~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~-~~  229 (615)
T PRK10875        154 VDWQKVAAAVALT--RRISVISGGPGTGKTTTVAKLLAALIQLAD-GERCRIRLAAPTGKAAARLTESLGKALRQLP-LT  229 (615)
T ss_pred             CHHHHHHHHHHhc--CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC-CCCcEEEEECCcHHHHHHHHHHHHhhhhccc-cc
Confidence            5899999999888  589999999999999654  2222322221 1235688889999888888776655433221 00


Q ss_pred             EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccc-----cccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCC
Q psy11867        205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYR-----FFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC  279 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~-----~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~  279 (399)
                            .     ........-..|--+|+.......     .-+.-.++++|||||-++     -...+..+++.+++.+
T Consensus       230 ------~-----~~~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMv-----d~~lm~~ll~al~~~~  293 (615)
T PRK10875        230 ------D-----EQKKRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMV-----DLPMMARLIDALPPHA  293 (615)
T ss_pred             ------h-----hhhhcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhcc-----cHHHHHHHHHhcccCC
Confidence                  0     000000011233333333211111     112335689999999775     2455667888899999


Q ss_pred             cEEEEEee
Q psy11867        280 QIMLFSAT  287 (399)
Q Consensus       280 q~l~~SAT  287 (399)
                      ++|++.=.
T Consensus       294 rlIlvGD~  301 (615)
T PRK10875        294 RVIFLGDR  301 (615)
T ss_pred             EEEEecch
Confidence            98887544

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=97.79  E-value=0.00014  Score=64.26  Aligned_cols=152  Identities=18%  Similarity=0.202  Sum_probs=92.5

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC-CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLAD-PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~-~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      .|+-..-+.+++=.+. .++ -.++.|.+....+.+. .|.|.+.+.-+|.|||.+- +|++..+..+. ..-+.+++|.
T Consensus         4 ~w~p~~~P~wLl~E~e-~~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI-~Pmla~~LAdg-~~LvrviVpk   79 (229)
T PF12340_consen    4 NWDPMEYPDWLLFEIE-SNI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVI-VPMLALALADG-SRLVRVIVPK   79 (229)
T ss_pred             CCCchhChHHHHHHHH-cCc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchH-HHHHHHHHcCC-CcEEEEEcCH
Confidence            4555555566664443 223 5789999999988863 3689999999999999874 57777766542 2346666774


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEE--EcCchhh-----------hhhccCCcEEEeCchhHHHhhhccc------c--
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYA--VRGENLE-----------RNKKITEQIIIGTPGKVLDWGLKYR------F--  241 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~--~~~~~~~-----------~~~~~~~~IlV~Tp~~l~~~~~~~~------~--  241 (399)
                       +|..|+...+..-...+-+-.+...  .......           ........|+++||+.+++.....-      .  
T Consensus        80 -~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~l~~~~~~  158 (229)
T PF12340_consen   80 -ALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLERLQDGKPE  158 (229)
T ss_pred             -HHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHHHHhcCHH
Confidence             7999998888765443322222221  1111110           0112344699999999877532210      0  


Q ss_pred             ---------ccCCceeEEEEechhhHhh
Q psy11867        242 ---------FDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       242 ---------~~~~~~~~lViDEah~l~~  260 (399)
                               -++.....=|+||+|..+.
T Consensus       159 ~~~~l~~~q~~l~~~~rdilDEsDe~L~  186 (229)
T PF12340_consen  159 EARELLKIQKWLDEHSRDILDESDEILS  186 (229)
T ss_pred             HHHHHHHHHHHHHhcCCeEeECchhccC
Confidence                     0123344568888887654

There are two conserved sequence motifs: LLE and NMG.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.74  E-value=0.00024  Score=74.47  Aligned_cols=127  Identities=24%  Similarity=0.296  Sum_probs=78.4

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..+++-|++|+..+..  ++-+++.|+.|||||...- .++..+........+++++||-.-|..+.+..        +.
T Consensus       322 ~~l~~~Q~~Ai~~~~~--~~~~iitGgpGTGKTt~l~-~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~--------g~  390 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQ--HKVVILTGGPGTGKTTITR-AIIELAEELGGLLPVGLAAPTGRAAKRLGEVT--------GL  390 (720)
T ss_pred             CCCCHHHHHHHHHHHh--CCeEEEECCCCCCHHHHHH-HHHHHHHHcCCCceEEEEeCchHHHHHHHHhc--------CC
Confidence            4789999999999987  5799999999999996432 33444433221245888899987776544321        10


Q ss_pred             EEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcc----ccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCC
Q psy11867        204 SVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKY----RFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC  279 (399)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~----~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~  279 (399)
                      .      .               .|-.+++.+....    ..-.....++||+|||+++-     ...+..+++.++..+
T Consensus       391 ~------a---------------~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd-----~~~~~~Ll~~~~~~~  444 (720)
T TIGR01448       391 T------A---------------STIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMD-----TWLALSLLAALPDHA  444 (720)
T ss_pred             c------c---------------ccHHHHhhccCCccchhhhhccccCCEEEEeccccCC-----HHHHHHHHHhCCCCC
Confidence            0      0               1222222210000    00012356899999999973     234567777888888


Q ss_pred             cEEEEEee
Q psy11867        280 QIMLFSAT  287 (399)
Q Consensus       280 q~l~~SAT  287 (399)
                      +++++.=+
T Consensus       445 rlilvGD~  452 (720)
T TIGR01448       445 RLLLVGDT  452 (720)
T ss_pred             EEEEECcc
Confidence            88887544

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.

>KOG1802|consensus

Probab=97.69  E-value=0.0002  Score=71.18  Aligned_cols=75  Identities=23%  Similarity=0.201  Sum_probs=61.4

Q ss_pred             HHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        119 YEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       119 ~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ...|+.+++.-|..|+..+|.  ..-.++++|+|+|||....--+.+.+..  ....+||.+|+.--++|+.+.+.+.+
T Consensus       404 s~~~lpkLN~SQ~~AV~~VL~--rplsLIQGPPGTGKTvtsa~IVyhl~~~--~~~~VLvcApSNiAVDqLaeKIh~tg  478 (935)
T KOG1802|consen  404 SVPNLPKLNASQSNAVKHVLQ--RPLSLIQGPPGTGKTVTSATIVYHLARQ--HAGPVLVCAPSNIAVDQLAEKIHKTG  478 (935)
T ss_pred             cCCCchhhchHHHHHHHHHHc--CCceeeecCCCCCceehhHHHHHHHHHh--cCCceEEEcccchhHHHHHHHHHhcC
Confidence            345667888999999999998  4778999999999999877655555554  45569999999999999999887764

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=97.68  E-value=0.00016  Score=73.82  Aligned_cols=146  Identities=16%  Similarity=0.188  Sum_probs=79.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc-----CCCcEEEEEEcCchhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH-----ITDLSVRYAVRGENLER  216 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~  216 (399)
                      .-|+=|.+.||+|||.+|+-.|...- +...-.+.+|+|||.+.-.-+....+....+     +.+.+.....-......
T Consensus        74 ~lNiDI~METGTGKTy~YlrtmfeLh-k~YG~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~~~~~~  152 (985)
T COG3587          74 KLNIDILMETGTGKTYTYLRTMFELH-KKYGLFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYDEDIEK  152 (985)
T ss_pred             cceeeEEEecCCCceeeHHHHHHHHH-HHhCceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeechHHHH
Confidence            56788889999999999987666532 2334456899999998766544333332222     22233333332222222


Q ss_pred             h---hccCCcEEEeCchhHHHh------hh-----ccccc--------cCCce-eEEEEechhhHhhcCCchHHHHHHHH
Q psy11867        217 N---KKITEQIIIGTPGKVLDW------GL-----KYRFF--------DLSKI-KVFVLDEADVMIATQGHQDFSIRIQK  273 (399)
Q Consensus       217 ~---~~~~~~IlV~Tp~~l~~~------~~-----~~~~~--------~~~~~-~~lViDEah~l~~~~~~~~~~~~i~~  273 (399)
                      .   ....+.+++.|...+..-      +.     ....+        .+..+ -.+|+||-|+|...   ......+. 
T Consensus       153 ~~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~---~k~~~~i~-  228 (985)
T COG3587         153 FKFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPHRFLGD---DKTYGAIK-  228 (985)
T ss_pred             HhhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChhhcccc---hHHHHHHH-
Confidence            1   134556777765544221      00     00000        01111 26999999999642   11222222 


Q ss_pred             hCCCCCcEEEEEeeCChhHH
Q psy11867        274 RLPSDCQIMLFSATYDKEVM  293 (399)
Q Consensus       274 ~l~~~~q~l~~SAT~~~~v~  293 (399)
                      .+ ...-++=|+||+++...
T Consensus       229 ~l-~pl~ilRfgATfkd~y~  247 (985)
T COG3587         229 QL-NPLLILRFGATFKDEYN  247 (985)
T ss_pred             hh-CceEEEEecccchhhhc
Confidence            22 13336679999987655

>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=97.52  E-value=0.00017  Score=67.90  Aligned_cols=123  Identities=17%  Similarity=0.181  Sum_probs=76.8

Q ss_pred             ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        126 PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      +++-|.+++.. .   .++++|.|..|||||.+.+.-++..+... ....++|++++|+..|..+.+.+...........
T Consensus         1 l~~eQ~~~i~~-~---~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~~~~~~   76 (315)
T PF00580_consen    1 LTDEQRRIIRS-T---EGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLEEEQQES   76 (315)
T ss_dssp             S-HHHHHHHHS-----SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHCC
T ss_pred             CCHHHHHHHhC-C---CCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcCcccccc
Confidence            47889999987 3   49999999999999998777666666544 4556799999999999999998888654320000


Q ss_pred             EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccC-CceeEEEEechh
Q psy11867        205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDL-SKIKVFVLDEAD  256 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~-~~~~~lViDEah  256 (399)
                          .....+.........+.|+|-..+...+.+...... -.-.+-++|+..
T Consensus        77 ----~~~~~~~~~~~~~~~~~i~T~hsf~~~ll~~~~~~~~~~~~~~i~~~~~  125 (315)
T PF00580_consen   77 ----SDNERLRRQLSNIDRIYISTFHSFCYRLLREYGYEIGIDPNFEILDEEE  125 (315)
T ss_dssp             ----TT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHH
T ss_pred             ----cccccccccccccchheeehhhhhhhhhhhhhhhhhhccccceeecchh
Confidence                000011112223345888888777654433211111 123456777776

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 ....

>KOG0989|consensus

Probab=97.49  E-value=0.0005  Score=62.78  Aligned_cols=59  Identities=17%  Similarity=0.213  Sum_probs=38.3

Q ss_pred             cCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeC---ChhHHHHHHhhCCCC
Q psy11867        243 DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATY---DKEVMEFAQDMVPNP  303 (399)
Q Consensus       243 ~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~---~~~v~~~~~~~~~~p  303 (399)
                      ....++.+|+||||.|..  .....+.+.+...+...++++.+.-+   +..+..-+.+|...+
T Consensus       126 ~~~~fKiiIlDEcdsmts--daq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~  187 (346)
T KOG0989|consen  126 PCPPFKIIILDECDSMTS--DAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKK  187 (346)
T ss_pred             CCCcceEEEEechhhhhH--HHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCCC
Confidence            356678999999999964  34445556666666777777776653   344444455554443

>KOG1803|consensus

Probab=97.48  E-value=0.00061  Score=67.43  Aligned_cols=65  Identities=23%  Similarity=0.259  Sum_probs=52.7

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVV  193 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~  193 (399)
                      .+.+-|..|+....+. ..-.+++||+|+|||..-..-+.+.+.+   +.++||.+||.+-+..+.+.+
T Consensus       185 ~ln~SQk~Av~~~~~~-k~l~~I~GPPGTGKT~TlvEiI~qlvk~---~k~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINN-KDLLIIHGPPGTGKTRTLVEIISQLVKQ---KKRVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             cccHHHHHHHHHHhcc-CCceEeeCCCCCCceeeHHHHHHHHHHc---CCeEEEEcCchHHHHHHHHHh
Confidence            5678899999998875 3667899999999999877766666654   357999999999888888754

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

Probab=97.40  E-value=0.00026  Score=66.10  Aligned_cols=70  Identities=24%  Similarity=0.219  Sum_probs=57.0

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      ..|+..-+..|.-|+..++...=.=|.+.++.|||||+.++.+.+.+....+...+.++-=|+..+.+.+
T Consensus       223 vwGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dI  292 (436)
T COG1875         223 VWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDI  292 (436)
T ss_pred             hhccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCccccc
Confidence            3678778889999999999854456778899999999999999999988777777788887887766443

>KOG0388|consensus

Probab=97.27  E-value=0.00039  Score=69.67  Aligned_cols=152  Identities=15%  Similarity=0.121  Sum_probs=91.5

Q ss_pred             ChHHHHHHhhhhhc--CCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        126 PSKIQETALPTLLA--DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       126 p~~iQ~~ai~~ll~--~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      +-.+|...+..+.+  +.|-|.|+....|-|||+..+--+.+......--+-.|||+|...|-    .+...+..++|.+
T Consensus       568 LKEYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQsisvlAhLaE~~nIwGPFLVVtpaStL~----NWaqEisrFlP~~  643 (1185)
T KOG0388|consen  568 LKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQSISVLAHLAETHNIWGPFLVVTPASTLH----NWAQEISRFLPSF  643 (1185)
T ss_pred             hHHHhhccHHHHHHHHHccccceehhhhccchhHHHHHHHHHHHHhccCCCceEEeehHHHHh----HHHHHHHHhCccc
Confidence            34678888777643  24899999999999999876543333333332223368899987663    4444455556677


Q ss_pred             EEEEEEcCchhhhh------------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHH
Q psy11867        204 SVRYAVRGENLERN------------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRI  271 (399)
Q Consensus       204 ~~~~~~~~~~~~~~------------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i  271 (399)
                      ++.-.-|+......            .....||+|++.+.+..-   .+.+.--+.++.|+|||+.+-..  ...-+..+
T Consensus       644 k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtD---eky~qkvKWQYMILDEAQAIKSS--sS~RWKtL  718 (1185)
T KOG0388|consen  644 KVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTD---EKYLQKVKWQYMILDEAQAIKSS--SSSRWKTL  718 (1185)
T ss_pred             eeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeech---HHHHHhhhhhheehhHHHHhhhh--hhhHHHHH
Confidence            76655555432221            123568999999876432   12222224578999999998543  22222333


Q ss_pred             HHhCCCCCcEEEEEeeC
Q psy11867        272 QKRLPSDCQIMLFSATY  288 (399)
Q Consensus       272 ~~~l~~~~q~l~~SAT~  288 (399)
                      +..  +.+-.++++.|.
T Consensus       719 LsF--~cRNRLLLTGTP  733 (1185)
T KOG0388|consen  719 LSF--KCRNRLLLTGTP  733 (1185)
T ss_pred             hhh--hccceeeecCCc
Confidence            332  234468888883

>KOG0921|consensus

Probab=97.26  E-value=0.0016  Score=67.15  Aligned_cols=249  Identities=19%  Similarity=0.215  Sum_probs=134.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCC-Ce-EEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQE-PQ-VLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKK  219 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~-~~-~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (399)
                      .+-+++-+.||.|||.-+.--+|+.+..+..+ .+ +.+--|++-.+.-+.+.+.+--..-.+-.+.+...-.+...  +
T Consensus       393 n~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~vRf~Sa~p--r  470 (1282)
T KOG0921|consen  393 NRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYNVRFDSATP--R  470 (1282)
T ss_pred             CceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhccccccccccccccc--c
Confidence            57778889999999999988888877654332 22 44444888877777665544321111112222222211111  1


Q ss_pred             cCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC---CCCCcEEEEEeeCChh-----
Q psy11867        220 ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL---PSDCQIMLFSATYDKE-----  291 (399)
Q Consensus       220 ~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l---~~~~q~l~~SAT~~~~-----  291 (399)
                      .-.-|+.||-+-++..+..    -+..+.++++||.|..--   -.+++..+++-+   .....++++|||+..+     
T Consensus       471 pyg~i~fctvgvllr~~e~----glrg~sh~i~deiherdv---~~dfll~~lr~m~~ty~dl~v~lmsatIdTd~f~~~  543 (1282)
T KOG0921|consen  471 PYGSIMFCTVGVLLRMMEN----GLRGISHVIIDEIHERDV---DTDFVLIVLREMISTYRDLRVVLMSATIDTDLFTNF  543 (1282)
T ss_pred             cccceeeeccchhhhhhhh----cccccccccchhhhhhcc---chHHHHHHHHhhhccchhhhhhhhhcccchhhhhhh
Confidence            1224999999999887533    256778999999997532   223333332222   2233444445543221     


Q ss_pred             ---------------HHHHHHhhCCCCeEEe-----------cccccccccc--eeEEEEEeCC---------------h
Q psy11867        292 ---------------VMEFAQDMVPNPLIIK-----------LKREEESLDN--IKQHYVMCKN---------------I  328 (399)
Q Consensus       292 ---------------v~~~~~~~~~~p~~i~-----------~~~~~~~~~~--i~~~~~~~~~---------------~  328 (399)
                                     +..|....+..+....           .........+  -+..-..|++               .
T Consensus       544 f~~~p~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~~~~~~~~~~ddK~~n~n~~~dd~~~~~~~~am~~~se~  623 (1282)
T KOG0921|consen  544 FSSIPDVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKKDDDEEDEEVDDKGRNMNILCDPSYNESTRTAMSRLSEK  623 (1282)
T ss_pred             hccccceeeccccccHHHHHHHHhhhhhhccCCCcCccchhhcccccCchhhhcccccccccChhhcchhhhhhhcchhh
Confidence                           2222222211111100           0000000000  0000011110               0


Q ss_pred             ---hhHHHHHHHHhccC-CCCcEEEEecchHhHHHHHHHHHHC-------CCeEEEEcCCCCHHHHHHHHHHHhcCCCcc
Q psy11867        329 ---DEKFEAVSNIYGVV-TIGQAMIFCHTRKTAAWLAEKMSKE-------GLNVGLLSGELTVEQRLSILDRFREGEFKI  397 (399)
Q Consensus       329 ---~~k~~~l~~ll~~~-~~~k~IIF~~s~~~a~~l~~~L~~~-------g~~v~~lhg~~~~~~R~~v~~~F~~G~~~I  397 (399)
                         ..-.+++...+... -.+-+++|-+-......|...|...       .+++..+|+..+..+...+.+.-..|..+|
T Consensus       624 d~~f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~ki  703 (1282)
T KOG0921|consen  624 DIPFGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKI  703 (1282)
T ss_pred             cchhHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCccccccccc
Confidence               11122222222222 2367899999998888888887654       467899999999999999998888888877


Q ss_pred             cC
Q psy11867        398 YS  399 (399)
Q Consensus       398 LV  399 (399)
                      ++
T Consensus       704 i~  705 (1282)
T KOG0921|consen  704 IL  705 (1282)
T ss_pred             cc
Confidence            63

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.21  E-value=0.0007  Score=54.93  Aligned_cols=20  Identities=20%  Similarity=0.371  Sum_probs=13.5

Q ss_pred             CCcEEEEccCCCCceehhHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l  161 (399)
                      ++.+++.|++|+|||.+...
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~   23 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKR   23 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHH
Confidence            57899999999999976543

>PRK06526 transposase; Provisional

Probab=97.17  E-value=0.00071  Score=61.77  Aligned_cols=20  Identities=30%  Similarity=0.287  Sum_probs=17.3

Q ss_pred             CCcEEEEccCCCCceehhHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l  161 (399)
                      +.++++.||+|+|||....-
T Consensus        98 ~~nlll~Gp~GtGKThLa~a  117 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIG  117 (254)
T ss_pred             CceEEEEeCCCCchHHHHHH
Confidence            78999999999999976553

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.15  E-value=0.0038  Score=65.83  Aligned_cols=63  Identities=17%  Similarity=0.144  Sum_probs=45.9

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG  190 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~  190 (399)
                      ..+++-|..|+..++.+ ++-++++|+.|+|||...- .+...+..  .+.++++++||---|..+.
T Consensus       351 ~~Ls~~Q~~Av~~i~~s-~~~~il~G~aGTGKTtll~-~i~~~~~~--~g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       351 YRLSEEQYEAVRHVTGS-GDIAVVVGRAGTGKSTMLK-AAREAWEA--AGYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             CCCCHHHHHHHHHHhcC-CCEEEEEecCCCCHHHHHH-HHHHHHHh--CCCeEEEEeCcHHHHHHHH
Confidence            35899999999999875 4678999999999995532 33433433  3567999999976655443

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=97.14  E-value=0.00049  Score=60.10  Aligned_cols=110  Identities=15%  Similarity=0.152  Sum_probs=57.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc---HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT---YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK  218 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt---~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (399)
                      |.=.++.+|+|+|||...+--+.....   .+.+++++-|.   +....       .+...+ ++.         ..   
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~---~g~~v~i~k~~~d~~~~~~-------~i~~~l-g~~---------~~---   58 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEE---RGMKVLVFKPAIDDRYGEG-------KVVSRI-GLS---------RE---   58 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHH---cCCeEEEEeccccccccCC-------cEecCC-CCc---------cc---
Confidence            456788999999999765544433333   24568877663   21111       011111 000         00   


Q ss_pred             ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEee
Q psy11867        219 KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       219 ~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT  287 (399)
                          .+.+..+..+++.+..    .-.+.++|||||+|.+.     .+++..+.+.+.+....+++++-
T Consensus        59 ----~~~~~~~~~~~~~~~~----~~~~~dvviIDEaq~l~-----~~~v~~l~~~l~~~g~~vi~tgl  114 (190)
T PRK04296         59 ----AIPVSSDTDIFELIEE----EGEKIDCVLIDEAQFLD-----KEQVVQLAEVLDDLGIPVICYGL  114 (190)
T ss_pred             ----ceEeCChHHHHHHHHh----hCCCCCEEEEEccccCC-----HHHHHHHHHHHHHcCCeEEEEec
Confidence                0223444555554432    23567899999998752     23344455554444445555554

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

Probab=97.11  E-value=0.0016  Score=70.34  Aligned_cols=135  Identities=16%  Similarity=0.045  Sum_probs=86.4

Q ss_pred             CCCChHHHHHHhhhhh---cCCCCcEEEEccCCCCceehhHHHHHHhhCCCCC-CCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        123 FYAPSKIQETALPTLL---ADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQ-EPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll---~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~-~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      +..+.++|...++.+.   ...+.+.++....|.|||+..+..+......... .+.++|++|+ +++.++.+.+.++..
T Consensus       336 ~~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~-s~~~nw~~e~~k~~~  414 (866)
T COG0553         336 SAELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPA-SLLSNWKREFEKFAP  414 (866)
T ss_pred             hhhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecH-HHHHHHHHHHhhhCc
Confidence            3467788999887754   3346788888999999997766555442322222 3579999998 455667777766654


Q ss_pred             cCCCcEEEEEEcCch-----hhhhh-ccC------CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhh
Q psy11867        199 HITDLSVRYAVRGEN-----LERNK-KIT------EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       199 ~~~~~~~~~~~~~~~-----~~~~~-~~~------~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~  260 (399)
                      ....  +....|...     ..... ...      .+++++|.+.+.........+.-...+++|+||+|++-.
T Consensus       415 ~~~~--~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn  486 (866)
T COG0553         415 DLRL--VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKN  486 (866)
T ss_pred             cccc--eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhh
Confidence            4321  444444432     11111 111      689999999887632222344455778999999999754

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.09  E-value=0.0038  Score=60.39  Aligned_cols=131  Identities=12%  Similarity=0.048  Sum_probs=67.1

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhh-CCCCCCCeEEEEe--CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRV-NPSIQEPQVLCLA--PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK  218 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l-~~~~~~~~~lil~--Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (399)
                      ++.+++.||||+|||....--+.... .....+.++.+++  +.|.-+..+   ++.++..+ ++.+.            
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQ---L~~~a~~l-gvpv~------------  237 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQ---IQTYGDIM-GIPVK------------  237 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHH---HHHHhhcC-CcceE------------
Confidence            56899999999999977643222222 1111233444444  333333322   44444322 22221            


Q ss_pred             ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCC-CcEEEEEeeCCh-hHHHHH
Q psy11867        219 KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSD-CQIMLFSATYDK-EVMEFA  296 (399)
Q Consensus       219 ~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~-~q~l~~SAT~~~-~v~~~~  296 (399)
                            ++-++..+...+..     +.+.++++||++.++.........+..++....+. -..+.+|||... .+.+.+
T Consensus       238 ------~~~~~~~l~~~L~~-----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~  306 (388)
T PRK12723        238 ------AIESFKDLKEEITQ-----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIF  306 (388)
T ss_pred             ------eeCcHHHHHHHHHH-----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHH
Confidence                  11234444433222     35788999999998742111112333444433333 356889999874 455555


Q ss_pred             Hhh
Q psy11867        297 QDM  299 (399)
Q Consensus       297 ~~~  299 (399)
                      ..+
T Consensus       307 ~~~  309 (388)
T PRK12723        307 HQF  309 (388)
T ss_pred             HHh
Confidence            555

>PRK08181 transposase; Validated

Probab=97.09  E-value=0.0048  Score=56.76  Aligned_cols=45  Identities=20%  Similarity=0.212  Sum_probs=27.1

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG  190 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~  190 (399)
                      ++++++.||+|+|||..........+..   +..+++ .+..+|..++.
T Consensus       106 ~~nlll~Gp~GtGKTHLa~Aia~~a~~~---g~~v~f-~~~~~L~~~l~  150 (269)
T PRK08181        106 GANLLLFGPPGGGKSHLAAAIGLALIEN---GWRVLF-TRTTDLVQKLQ  150 (269)
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHc---CCceee-eeHHHHHHHHH
Confidence            7999999999999995544222222222   233444 44556665553

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.07  E-value=0.043  Score=63.78  Aligned_cols=237  Identities=14%  Similarity=0.170  Sum_probs=127.1

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .+++-|.+|+..++....+-.+++++.|+|||.+.- .++..+..  .+.+++.++||-.-+.++.+.......      
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l~-~l~~~~~~--~G~~V~~lAPTgrAA~~L~e~~g~~A~------  499 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIAQ-LLLHLASE--QGYEIQIITAGSLSAQELRQKIPRLAS------  499 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHHH-HHHHHHHh--cCCeEEEEeCCHHHHHHHHHHhcchhh------
Confidence            578999999999998656888999999999996532 34444433  356799999998766655543211100      


Q ss_pred             EEEEEcCchhhhhhc-cCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC-CCCCcEE
Q psy11867        205 VRYAVRGENLERNKK-ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL-PSDCQIM  282 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~-~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~l  282 (399)
                              .+.+... .....-..|...+++     +...+..-++||||||-++..     ..+..+++.. +.+.++|
T Consensus       500 --------Ti~~~l~~l~~~~~~~tv~~fl~-----~~~~l~~~~vlIVDEAsMl~~-----~~~~~Ll~~a~~~garvV  561 (1960)
T TIGR02760       500 --------TFITWVKNLFNDDQDHTVQGLLD-----KSSPFSNKDIFVVDEANKLSN-----NELLKLIDKAEQHNSKLI  561 (1960)
T ss_pred             --------hHHHHHHhhcccccchhHHHhhc-----ccCCCCCCCEEEEECCCCCCH-----HHHHHHHHHHhhcCCEEE
Confidence                    0000000 000011112222321     122345678999999987632     3344555544 4678888


Q ss_pred             EEEee--CC----hhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhcc-CCC-CcEEEEecch
Q psy11867        283 LFSAT--YD----KEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGV-VTI-GQAMIFCHTR  354 (399)
Q Consensus       283 ~~SAT--~~----~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~-~~~-~k~IIF~~s~  354 (399)
                      ++.=+  ++    ..+...+...-  --.+.+.........+  .+ .-.....++..+..-+.. ... .+++|+..+.
T Consensus       562 lvGD~~QL~sV~aG~~f~~L~~~g--v~t~~l~~i~rq~~~v--~i-~~~~~~~r~~~ia~~y~~L~~~r~~tliv~~t~  636 (1960)
T TIGR02760       562 LLNDSAQRQGMSAGSAIDLLKEGG--VTTYAWVDTKQQKASV--EI-SEAVDKLRVDYIASAWLDLTPDRQNSQVLATTH  636 (1960)
T ss_pred             EEcChhhcCccccchHHHHHHHCC--CcEEEeecccccCcce--ee-eccCchHHHHHHHHHHHhcccccCceEEEcCCc
Confidence            87654  22    13333333321  1111221111111111  11 112223334444443333 322 3589999998


Q ss_pred             HhHHHHHHHHHH----C------CCeEEEEc-CCCCHHHHHHHHHHHhcCC
Q psy11867        355 KTAAWLAEKMSK----E------GLNVGLLS-GELTVEQRLSILDRFREGE  394 (399)
Q Consensus       355 ~~a~~l~~~L~~----~------g~~v~~lh-g~~~~~~R~~v~~~F~~G~  394 (399)
                      +....|...++.    .      ++.+..+. ..|+..++... ..|+.|.
T Consensus       637 ~dr~~Ln~~iR~~L~~~G~L~~~~~~~~~L~p~~lt~~e~r~~-~~Yr~Gd  686 (1960)
T TIGR02760       637 REQQDLTQIIRNALKQEGQLSRQEVTVPTLKPVNLTGIQRRNA-AHYKQGM  686 (1960)
T ss_pred             HHHHHHHHHHHHHHHHcCCcCCCceEEEEeccCCCCHHHHhhH-hhcCCCC
Confidence            887777766644    2      23344444 46888888854 7777775

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.

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=97.03  E-value=0.007  Score=62.50  Aligned_cols=157  Identities=20%  Similarity=0.248  Sum_probs=94.1

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      ..+..-..++....+.+..-|.+.+..++..+++-+++.|.-|=|||.+.-+.+....... ...+++|.+|+.+-++.+
T Consensus       199 ~~~~~~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~-~~~~iiVTAP~~~nv~~L  277 (758)
T COG1444         199 LDPVFPRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLA-GSVRIIVTAPTPANVQTL  277 (758)
T ss_pred             CCCCCCHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhc-CCceEEEeCCCHHHHHHH
Confidence            3333345577777777777888888888887666899999999999999887664333332 256799999999988777


Q ss_pred             HHHHHHHhccCCCcEEEEE--EcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHH
Q psy11867        190 GEVVAKMGKHITDLSVRYA--VRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF  267 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~  267 (399)
                      .+.+.+-...+ +.+-...  ..|... ........|=+-.|....           ..-+++|||||=.+.     ...
T Consensus       278 f~fa~~~l~~l-g~~~~v~~d~~g~~~-~~~~~~~~i~y~~P~~a~-----------~~~DllvVDEAAaIp-----lpl  339 (758)
T COG1444         278 FEFAGKGLEFL-GYKRKVAPDALGEIR-EVSGDGFRIEYVPPDDAQ-----------EEADLLVVDEAAAIP-----LPL  339 (758)
T ss_pred             HHHHHHhHHHh-CCcccccccccccee-eecCCceeEEeeCcchhc-----------ccCCEEEEehhhcCC-----hHH
Confidence            66665544333 1111111  111100 000111124444554322           116799999996653     333


Q ss_pred             HHHHHHhCCCCCcEEEEEeeCC
Q psy11867        268 SIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       268 ~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      +..+..    ..+.++||.|+.
T Consensus       340 L~~l~~----~~~rv~~sTTIh  357 (758)
T COG1444         340 LHKLLR----RFPRVLFSTTIH  357 (758)
T ss_pred             HHHHHh----hcCceEEEeeec
Confidence            334433    445788999964

>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=97.01  E-value=0.0068  Score=49.51  Aligned_cols=19  Identities=42%  Similarity=0.726  Sum_probs=16.1

Q ss_pred             CCCcEEEEccCCCCceehh
Q psy11867        141 PPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~  159 (399)
                      .++.+++.|++|+|||...
T Consensus        18 ~~~~v~i~G~~G~GKT~l~   36 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLA   36 (151)
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3689999999999999543

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.

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=96.98  E-value=0.0031  Score=67.73  Aligned_cols=124  Identities=17%  Similarity=0.037  Sum_probs=74.5

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .+++-|.+|+..++.+ +.-++++|..|+|||.+ +-++...+..  .+.+++.++||---|..+.+       .. ++.
T Consensus       346 ~Ls~eQr~Av~~il~s-~~v~vv~G~AGTGKTT~-l~~~~~~~e~--~G~~V~~~ApTGkAA~~L~e-------~t-Gi~  413 (988)
T PRK13889        346 VLSGEQADALAHVTDG-RDLGVVVGYAGTGKSAM-LGVAREAWEA--AGYEVRGAALSGIAAENLEG-------GS-GIA  413 (988)
T ss_pred             CCCHHHHHHHHHHhcC-CCeEEEEeCCCCCHHHH-HHHHHHHHHH--cCCeEEEecCcHHHHHHHhh-------cc-Ccc
Confidence            6899999999999974 34578999999999975 3344444433  35679999999765544332       10 111


Q ss_pred             EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC-CCCCcEEE
Q psy11867        205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL-PSDCQIML  283 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~l~  283 (399)
                      .                     .|-.+|+.-. ......+...++||||||-++..     ..+..+++.. ...+++|+
T Consensus       414 a---------------------~TI~sll~~~-~~~~~~l~~~~vlIVDEASMv~~-----~~m~~LL~~a~~~garvVL  466 (988)
T PRK13889        414 S---------------------RTIASLEHGW-GQGRDLLTSRDVLVIDEAGMVGT-----RQLERVLSHAADAGAKVVL  466 (988)
T ss_pred             h---------------------hhHHHHHhhh-cccccccccCcEEEEECcccCCH-----HHHHHHHHhhhhCCCEEEE
Confidence            0                     1222222110 11122355678999999987632     2344555433 45677777


Q ss_pred             EEee
Q psy11867        284 FSAT  287 (399)
Q Consensus       284 ~SAT  287 (399)
                      +.=+
T Consensus       467 VGD~  470 (988)
T PRK13889        467 VGDP  470 (988)
T ss_pred             ECCH
Confidence            6544

>KOG1132|consensus

Probab=96.92  E-value=0.0019  Score=66.55  Aligned_cols=74  Identities=20%  Similarity=0.297  Sum_probs=52.3

Q ss_pred             CCChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHH---hhC-----------C--------C---------
Q psy11867        124 YAPSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLS---RVN-----------P--------S---------  170 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~---~l~-----------~--------~---------  170 (399)
                      ++|++.|...+..++..  ...|.++.+|||+|||++-+-..|.   ++.           .        .         
T Consensus        20 ~qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e   99 (945)
T KOG1132|consen   20 FQPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEE   99 (945)
T ss_pred             CCcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhh
Confidence            47899999888877653  3688999999999999887654443   221           0        0         


Q ss_pred             --------CCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        171 --------IQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       171 --------~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                              ...|++.|-+-|..-..|+.+++++.+
T Consensus       100 ~~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~  134 (945)
T KOG1132|consen  100 AGEPIACYTGIPKIYYASRTHSQLTQVVRELRRTG  134 (945)
T ss_pred             hcCccccccCCceEEEecchHHHHHHHHHHHhhcC
Confidence                    013566777778877788888887754

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.91  E-value=0.0011  Score=65.58  Aligned_cols=142  Identities=20%  Similarity=0.177  Sum_probs=73.9

Q ss_pred             EccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhh-------hhcc
Q psy11867        148 QSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER-------NKKI  220 (399)
Q Consensus       148 ~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~  220 (399)
                      .+.||||||++..--||+....+.+  ..|+.|........+..-+..-...---++-....++...+-       .-..
T Consensus         3 ~matgsgkt~~ma~lil~~y~kgyr--~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~fsehnd   80 (812)
T COG3421           3 EMATGSGKTLVMAGLILECYKKGYR--NFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNNFSEHND   80 (812)
T ss_pred             ccccCCChhhHHHHHHHHHHHhchh--hEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecccCccCC
Confidence            4679999999988888888776433  477888766655544332211000000000011111111110       0123


Q ss_pred             CCcEEEeCchhHHHhhhcccc--c---cCCcee-EEEEechhhHhhcC--CchH-------HHHHHH--HhCCCCCcEEE
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRF--F---DLSKIK-VFVLDEADVMIATQ--GHQD-------FSIRIQ--KRLPSDCQIML  283 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~--~---~~~~~~-~lViDEah~l~~~~--~~~~-------~~~~i~--~~l~~~~q~l~  283 (399)
                      ...|..+|.+.|...+.+.+.  +   ++.+.. +++-||||++-...  ...+       +-..+.  ..-.++.-++.
T Consensus        81 ~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nkd~~~le  160 (812)
T COG3421          81 AIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNKDNLLLE  160 (812)
T ss_pred             ceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCCCceeeh
Confidence            346999999998766543322  2   344444 45679999985311  0111       111111  22234556779


Q ss_pred             EEeeCChh
Q psy11867        284 FSATYDKE  291 (399)
Q Consensus       284 ~SAT~~~~  291 (399)
                      ||||.+.+
T Consensus       161 f~at~~k~  168 (812)
T COG3421         161 FSATIPKE  168 (812)
T ss_pred             hhhcCCcc
Confidence            99999843

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.88  E-value=0.0066  Score=58.30  Aligned_cols=171  Identities=16%  Similarity=0.139  Sum_probs=80.5

Q ss_pred             cccccCCCCHHHHHHHHHc---C--CCCChH---HHHHHhhh----hhc-----CCCCcEEEEccCCCCceehhHHHHHH
Q psy11867        103 KTFEALHLKPELLKGVYEM---G--FYAPSK---IQETALPT----LLA-----DPPHNMIAQSQSGTGKTAAFTLTMLS  165 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~---g--~~~p~~---iQ~~ai~~----ll~-----~~g~~vi~~a~TGsGKT~~~~l~il~  165 (399)
                      ..+...++++.+.+.|.+.   +  ...+..   +....+..    +-.     ..|..+++.||||+|||.....-+..
T Consensus        81 ~~L~~~g~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~g~ii~lvGptGvGKTTtiakLA~~  160 (374)
T PRK14722         81 KYLFAAGFSAQLVRMIVDNLPEGEGYDTLDAAADWAQSVLAANLPVLDSEDALMERGGVFALMGPTGVGKTTTTAKLAAR  160 (374)
T ss_pred             HHHHHCCCCHHHHHHHHHhhhhhcccCCHHHHHHHHHHHHHhcchhhcCCCccccCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4566778888888887542   1  112222   22222211    100     12789999999999999776543333


Q ss_pred             hhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCC
Q psy11867        166 RVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLS  245 (399)
Q Consensus       166 ~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~  245 (399)
                      ..... ...++.+++ +...-.--.+.++.++..+ ++.+                  ..+-+++.+...+.     .+.
T Consensus       161 ~~~~~-G~~~V~lit-~D~~R~ga~EqL~~~a~~~-gv~~------------------~~~~~~~~l~~~l~-----~l~  214 (374)
T PRK14722        161 CVMRF-GASKVALLT-TDSYRIGGHEQLRIFGKIL-GVPV------------------HAVKDGGDLQLALA-----ELR  214 (374)
T ss_pred             HHHhc-CCCeEEEEe-cccccccHHHHHHHHHHHc-CCce------------------EecCCcccHHHHHH-----Hhc
Confidence            22221 112343333 2221001123333333322 2222                  22334444433322     234


Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhH-HHHHHhh
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEV-MEFAQDM  299 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v-~~~~~~~  299 (399)
                      +.++++||.+-+..-.....+.+..+.....+...++.+|||..... .+.++.|
T Consensus       215 ~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~evi~~f  269 (374)
T PRK14722        215 NKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNEVVQAY  269 (374)
T ss_pred             CCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChHHHHHHHHHH
Confidence            66889999986642111122222222222222344778899986543 3444444

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.86  E-value=0.0078  Score=57.82  Aligned_cols=131  Identities=13%  Similarity=0.186  Sum_probs=66.9

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe--CcH-HHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA--PTY-ELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK  218 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~--Pt~-~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (399)
                      ++.+.+.||||+|||.....-+.....   .+.++.++.  |.| .-+.|+....+.+     ++.+             
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~~L~~---~GkkVglI~aDt~RiaAvEQLk~yae~l-----gipv-------------  299 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAWQFHG---KKKTVGFITTDHSRIGTVQQLQDYVKTI-----GFEV-------------  299 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHH---cCCcEEEEecCCcchHHHHHHHHHhhhc-----CCcE-------------
Confidence            578899999999999766544433322   233344444  333 2333333322221     1111             


Q ss_pred             ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC-hhHHHHHH
Q psy11867        219 KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD-KEVMEFAQ  297 (399)
Q Consensus       219 ~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~-~~v~~~~~  297 (399)
                           +++.+|..+.+.+....  ...++++++||-+=+..........+..++....+..-++.+|||.. .++.+.++
T Consensus       300 -----~v~~d~~~L~~aL~~lk--~~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~  372 (436)
T PRK11889        300 -----IAVRDEAAMTRALTYFK--EEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIIT  372 (436)
T ss_pred             -----EecCCHHHHHHHHHHHH--hccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHH
Confidence                 22345666655432211  11257889999887753221122223344433334444567898865 45566666


Q ss_pred             hhC
Q psy11867        298 DMV  300 (399)
Q Consensus       298 ~~~  300 (399)
                      .|-
T Consensus       373 ~F~  375 (436)
T PRK11889        373 NFK  375 (436)
T ss_pred             Hhc
Confidence            653

>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=96.86  E-value=0.0014  Score=48.02  Aligned_cols=38  Identities=26%  Similarity=0.676  Sum_probs=35.1

Q ss_pred             HHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        362 EKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       362 ~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.|+..|+++..+||+++..+|..+++.|++|+.+||+
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli   38 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLI   38 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEE
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEE
Confidence            35788899999999999999999999999999998885

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 ....

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=96.83  E-value=0.012  Score=63.91  Aligned_cols=137  Identities=18%  Similarity=0.188  Sum_probs=80.8

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      .++..+......+ ..+++-|.+|+..+... ++-++++|+.|+|||.+.- ++...+..  .+.+++.++||-.-|..+
T Consensus       367 v~~~~l~a~~~~~-~~Ls~eQ~~Av~~i~~~-~r~~~v~G~AGTGKTt~l~-~~~~~~e~--~G~~V~g~ApTgkAA~~L  441 (1102)
T PRK13826        367 VREAVLAATFARH-ARLSDEQKTAIEHVAGP-ARIAAVVGRAGAGKTTMMK-AAREAWEA--AGYRVVGGALAGKAAEGL  441 (1102)
T ss_pred             CCHHHHHHHHhcC-CCCCHHHHHHHHHHhcc-CCeEEEEeCCCCCHHHHHH-HHHHHHHH--cCCeEEEEcCcHHHHHHH
Confidence            3344444433333 46899999999988654 6788999999999996533 34444433  356789999997655444


Q ss_pred             HHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhH-HHhhhccccccCCceeEEEEechhhHhhcCCchHHH
Q psy11867        190 GEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKV-LDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFS  268 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l-~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~  268 (399)
                      .+..        ++..                     .|-.++ +.+  ......+..-++||||||-++..     ..+
T Consensus       442 ~e~~--------Gi~a---------------------~TIas~ll~~--~~~~~~l~~~~vlVIDEAsMv~~-----~~m  485 (1102)
T PRK13826        442 EKEA--------GIQS---------------------RTLSSWELRW--NQGRDQLDNKTVFVLDEAGMVAS-----RQM  485 (1102)
T ss_pred             HHhh--------CCCe---------------------eeHHHHHhhh--ccCccCCCCCcEEEEECcccCCH-----HHH
Confidence            3211        1111                     122222 111  11122355667999999987632     334


Q ss_pred             HHHHHhCC-CCCcEEEEEee
Q psy11867        269 IRIQKRLP-SDCQIMLFSAT  287 (399)
Q Consensus       269 ~~i~~~l~-~~~q~l~~SAT  287 (399)
                      ..+++..+ ..++++++.=+
T Consensus       486 ~~Ll~~~~~~garvVLVGD~  505 (1102)
T PRK13826        486 ALFVEAVTRAGAKLVLVGDP  505 (1102)
T ss_pred             HHHHHHHHhcCCEEEEECCH
Confidence            45555554 56777777544

>PRK05642 DNA replication initiation factor; Validated

Probab=96.82  E-value=0.0029  Score=57.17  Aligned_cols=47  Identities=17%  Similarity=0.316  Sum_probs=29.1

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChh
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE  291 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~  291 (399)
                      .+++++|+|++|.+.........+..++..+......++++++.++.
T Consensus        96 ~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~  142 (234)
T PRK05642         96 EQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPR  142 (234)
T ss_pred             hhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHH
Confidence            35678999999987533233444555555544444557777776543

>PRK14974 cell division protein FtsY; Provisional

Probab=96.80  E-value=0.0088  Score=56.79  Aligned_cols=132  Identities=21%  Similarity=0.194  Sum_probs=71.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc---HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT---YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK  218 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt---~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (399)
                      +.-+++.|++|+|||....-.+. .+..  .+.+++++...   ..-..|+......++     +.+.....+.      
T Consensus       140 ~~vi~~~G~~GvGKTTtiakLA~-~l~~--~g~~V~li~~Dt~R~~a~eqL~~~a~~lg-----v~v~~~~~g~------  205 (336)
T PRK14974        140 PVVIVFVGVNGTGKTTTIAKLAY-YLKK--NGFSVVIAAGDTFRAGAIEQLEEHAERLG-----VKVIKHKYGA------  205 (336)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHH-HHHH--cCCeEEEecCCcCcHHHHHHHHHHHHHcC-----CceecccCCC------
Confidence            46788999999999975433222 2222  23345555432   233455544444442     2221111111      


Q ss_pred             ccCCcEEEeCchhH-HHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHH
Q psy11867        219 KITEQIIIGTPGKV-LDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ  297 (399)
Q Consensus       219 ~~~~~IlV~Tp~~l-~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~  297 (399)
                               .|..+ .+.+.   .....+.+++++|.+.++.........+..+.+...+...++.++||...+....++
T Consensus       206 ---------dp~~v~~~ai~---~~~~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~  273 (336)
T PRK14974        206 ---------DPAAVAYDAIE---HAKARGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQAR  273 (336)
T ss_pred             ---------CHHHHHHHHHH---HHHhCCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHH
Confidence                     11111 11111   111235679999999997432234445556666666777788999998877666565


Q ss_pred             hh
Q psy11867        298 DM  299 (399)
Q Consensus       298 ~~  299 (399)
                      .+
T Consensus       274 ~f  275 (336)
T PRK14974        274 EF  275 (336)
T ss_pred             HH
Confidence            54

>TIGR00376 DNA helicase, putative

Probab=96.78  E-value=0.0029  Score=65.47  Aligned_cols=68  Identities=22%  Similarity=0.189  Sum_probs=53.3

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      ..+++.|..|+..++.. ...++++||+|||||....-.+.+.+..   +.++|+++||..-+.++.+.+..
T Consensus       156 ~~ln~~Q~~Av~~~l~~-~~~~lI~GpPGTGKT~t~~~ii~~~~~~---g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       156 PNLNESQKEAVSFALSS-KDLFLIHGPPGTGKTRTLVELIRQLVKR---GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCCHHHHHHHHHHhcC-CCeEEEEcCCCCCHHHHHHHHHHHHHHc---CCCEEEEcCcHHHHHHHHHHHHh
Confidence            35789999999998874 4788999999999996654444444433   44799999999999998888876

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.

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

Probab=96.77  E-value=0.0045  Score=63.08  Aligned_cols=127  Identities=13%  Similarity=0.102  Sum_probs=81.0

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH-HHHHHHhccCCCc
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG-EVVAKMGKHITDL  203 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~-~~~~~~~~~~~~~  203 (399)
                      ..+|+|.+.+..+....-+.|+++.++-+|||.+.+..+...+....  .-+|++.||.++|.... ..+..+....+.+
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P--~~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~l   93 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDP--GPMLYVQPTDDAAKDFSKERLDPMIRASPVL   93 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCC--CCEEEEEEcHHHHHHHHHHHHHHHHHhCHHH
Confidence            56899999999887654578999999999999966665555555433  34899999999998875 6777777666554


Q ss_pred             EEEEEE-----cCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhh
Q psy11867        204 SVRYAV-----RGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       204 ~~~~~~-----~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~  260 (399)
                      .-.+.-     ++.........+..+.++..+.       -..+.-..++++++||+|.+..
T Consensus        94 ~~~~~~~~~~~~~~t~~~k~f~gg~l~~~ga~S-------~~~l~s~~~r~~~~DEvD~~p~  148 (557)
T PF05876_consen   94 RRKLSPSKSRDSGNTILYKRFPGGFLYLVGANS-------PSNLRSRPARYLLLDEVDRYPD  148 (557)
T ss_pred             HHHhCchhhcccCCchhheecCCCEEEEEeCCC-------CcccccCCcCEEEEechhhccc
Confidence            422221     1111111111122344332221       1222334678999999999853

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 [].

>PHA02533 17 large terminase protein; Provisional

Probab=96.77  E-value=0.014  Score=59.09  Aligned_cols=150  Identities=15%  Similarity=0.082  Sum_probs=85.1

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .+.|+|...+..+..  ++-.++..+=..|||.+....++..... ..+..+++++|++.-|..+.+.++.+....+.+.
T Consensus        59 ~L~p~Q~~i~~~~~~--~R~~ii~~aRq~GKStl~a~~al~~a~~-~~~~~v~i~A~~~~QA~~vF~~ik~~ie~~P~l~  135 (534)
T PHA02533         59 QMRDYQKDMLKIMHK--NRFNACNLSRQLGKTTVVAIFLLHYVCF-NKDKNVGILAHKASMAAEVLDRTKQAIELLPDFL  135 (534)
T ss_pred             CCcHHHHHHHHHHhc--CeEEEEEEcCcCChHHHHHHHHHHHHHh-CCCCEEEEEeCCHHHHHHHHHHHHHHHHhCHHHh
Confidence            578999999887754  4556788889999998776544433322 2356899999999999999988887766554321


Q ss_pred             EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCC--CCcEE
Q psy11867        205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPS--DCQIM  282 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~--~~q~l  282 (399)
                      -..........-....+..|.+.|-+        .+...=.+.+++++||+|.+.+   +......+...+..  ..+++
T Consensus       136 ~~~i~~~~~~~I~l~NGS~I~~lss~--------~~t~rG~~~~~liiDE~a~~~~---~~e~~~ai~p~lasg~~~r~i  204 (534)
T PHA02533        136 QPGIVEWNKGSIELENGSKIGAYASS--------PDAVRGNSFAMIYIDECAFIPN---FIDFWLAIQPVISSGRSSKII  204 (534)
T ss_pred             hcceeecCccEEEeCCCCEEEEEeCC--------CCccCCCCCceEEEeccccCCC---HHHHHHHHHHHHHcCCCceEE
Confidence            10000000000000223334333321        1111223567899999998632   22333333333322  24566


Q ss_pred             EEEeeC
Q psy11867        283 LFSATY  288 (399)
Q Consensus       283 ~~SAT~  288 (399)
                      ++|.+.
T Consensus       205 iiSTp~  210 (534)
T PHA02533        205 ITSTPN  210 (534)
T ss_pred             EEECCC
Confidence            666664

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

Probab=96.76  E-value=0.0039  Score=60.29  Aligned_cols=60  Identities=22%  Similarity=0.314  Sum_probs=40.7

Q ss_pred             ChHHHHHHhhhhh----cCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHH
Q psy11867        126 PSKIQETALPTLL----ADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQ  188 (399)
Q Consensus       126 p~~iQ~~ai~~ll----~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q  188 (399)
                      +++-|+.++..++    ...+.++++.|+-|+|||..+- .+...+..  .+..+++++||-.-|..
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~-~i~~~~~~--~~~~~~~~a~tg~AA~~   65 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIK-AIIDYLRS--RGKKVLVTAPTGIAAFN   65 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHH-HHHHHhcc--ccceEEEecchHHHHHh
Confidence            5677888877772    2238999999999999996442 23333333  34568889998655443

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.73  E-value=0.0026  Score=51.49  Aligned_cols=41  Identities=17%  Similarity=0.215  Sum_probs=25.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      +..+++.||+|+|||..... ++..+....  ..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~-l~~~~~~~~--~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARA-LARELGPPG--GGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHH-HHhccCCCC--CCEEEECCEEcc
Confidence            68899999999999976543 222222211  246777766543

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.

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=96.71  E-value=0.003  Score=57.12  Aligned_cols=84  Identities=25%  Similarity=0.289  Sum_probs=58.2

Q ss_pred             CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEc-Cchhhhh----hccCCcEEEeCchhHHHhhhccccccCC
Q psy11867        171 IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVR-GENLERN----KKITEQIIIGTPGKVLDWGLKYRFFDLS  245 (399)
Q Consensus       171 ~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~----~~~~~~IlV~Tp~~l~~~~~~~~~~~~~  245 (399)
                      ...|.+|||+..---|..+.+.++.+...  +..+.-.+. ...++.+    .....+|.||||+|+..++ ..+.+.++
T Consensus       124 ~gsP~~lvvs~SalRa~dl~R~l~~~~~k--~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLl-e~~~L~l~  200 (252)
T PF14617_consen  124 KGSPHVLVVSSSALRAADLIRALRSFKGK--DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLL-ENGALSLS  200 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhccC--CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHH-HcCCCCcc
Confidence            45788999999988888888888877311  112111111 1122222    2456789999999999996 66788999


Q ss_pred             ceeEEEEechhh
Q psy11867        246 KIKVFVLDEADV  257 (399)
Q Consensus       246 ~~~~lViDEah~  257 (399)
                      ++.++|||--|+
T Consensus       201 ~l~~ivlD~s~~  212 (252)
T PF14617_consen  201 NLKRIVLDWSYL  212 (252)
T ss_pred             cCeEEEEcCCcc
Confidence            999999998653

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.67  E-value=0.021  Score=54.75  Aligned_cols=134  Identities=13%  Similarity=0.112  Sum_probs=71.8

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      ++.+.+.||||.|||..-.=-+............+||-+-|.-.+.  .++++.+++-+ ++.+                
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA--~EQLk~Ya~im-~vp~----------------  263 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGA--VEQLKTYADIM-GVPL----------------  263 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhH--HHHHHHHHHHh-CCce----------------
Confidence            7889999999999996543222222222234445677666655442  34455554433 3333                


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCCh-hHHHHHHhhC
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDK-EVMEFAQDMV  300 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~-~v~~~~~~~~  300 (399)
                        .+|-+|.-|...+.     .+++++++.+|=+-+-.-.......+..+.....+---.+.+|||... ++...+..|.
T Consensus       264 --~vv~~~~el~~ai~-----~l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~~f~  336 (407)
T COG1419         264 --EVVYSPKELAEAIE-----ALRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIKQFS  336 (407)
T ss_pred             --EEecCHHHHHHHHH-----HhhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHHHhc
Confidence              34445555554432     245667888887755211111122223333333334456788999764 4666666664


Q ss_pred             C
Q psy11867        301 P  301 (399)
Q Consensus       301 ~  301 (399)
                      .
T Consensus       337 ~  337 (407)
T COG1419         337 L  337 (407)
T ss_pred             c
Confidence            3

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=96.67  E-value=0.003  Score=46.18  Aligned_cols=41  Identities=37%  Similarity=0.598  Sum_probs=37.2

Q ss_pred             HHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        359 WLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       359 ~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .++..|...++.+..+||+++..+|..+++.|++|...||+
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli   42 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLV   42 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEE
Confidence            46778888899999999999999999999999999988874

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.66  E-value=0.0044  Score=64.83  Aligned_cols=69  Identities=19%  Similarity=0.161  Sum_probs=55.2

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      .+++-|.+|+...    ..+++|.|..|||||.+-..-+...+.. +....++|+|+.|+.-|..+.+.+.++.
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 RLNPGQQQAVEFV----TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhCC----CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            4788999998642    4788899999999998877766666653 3344579999999999999999888764

>KOG1805|consensus

Probab=96.54  E-value=0.0056  Score=63.86  Aligned_cols=137  Identities=20%  Similarity=0.128  Sum_probs=82.3

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      +.|.+.+-    -+..++.-|++|+-..++. ....+|.|=+|||||......+-..+.   .+.++|..+=|..-+..+
T Consensus       658 ~~p~~~~~----~~~~LN~dQr~A~~k~L~a-edy~LI~GMPGTGKTTtI~~LIkiL~~---~gkkVLLtsyThsAVDNI  729 (1100)
T KOG1805|consen  658 LIPKIKKI----ILLRLNNDQRQALLKALAA-EDYALILGMPGTGKTTTISLLIKILVA---LGKKVLLTSYTHSAVDNI  729 (1100)
T ss_pred             cCchhhHH----HHhhcCHHHHHHHHHHHhc-cchheeecCCCCCchhhHHHHHHHHHH---cCCeEEEEehhhHHHHHH
Confidence            44554443    2346788999999988875 567788899999999765433322222   344588888888777777


Q ss_pred             HHHHHHHhccCCCcEEE----------EEEcCchh---hh--hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEec
Q psy11867        190 GEVVAKMGKHITDLSVR----------YAVRGENL---ER--NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDE  254 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~----------~~~~~~~~---~~--~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDE  254 (399)
                      .-.++.++..+-.+...          +...+.+.   ..  .......||.+|.=-+.+     ..|..+.++++|+||
T Consensus       730 LiKL~~~~i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~-----plf~~R~FD~cIiDE  804 (1100)
T KOG1805|consen  730 LIKLKGFGIYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINH-----PLFVNRQFDYCIIDE  804 (1100)
T ss_pred             HHHHhccCcceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCc-----hhhhccccCEEEEcc
Confidence            77676654332111000          00111111   11  113445688888644433     344556789999999


Q ss_pred             hhhHh
Q psy11867        255 ADVMI  259 (399)
Q Consensus       255 ah~l~  259 (399)
                      |-.+.
T Consensus       805 ASQI~  809 (1100)
T KOG1805|consen  805 ASQIL  809 (1100)
T ss_pred             ccccc
Confidence            98653

>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=96.53  E-value=0.0046  Score=55.27  Aligned_cols=107  Identities=20%  Similarity=0.269  Sum_probs=57.0

Q ss_pred             cEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCc
Q psy11867        144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQ  223 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (399)
                      -+++.|++|+|||-. +-++...+.....+.+++++... +....+...++.                            
T Consensus        36 ~l~l~G~~G~GKTHL-L~Ai~~~~~~~~~~~~v~y~~~~-~f~~~~~~~~~~----------------------------   85 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHL-LQAIANEAQKQHPGKRVVYLSAE-EFIREFADALRD----------------------------   85 (219)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHHCTTS-EEEEEHH-HHHHHHHHHHHT----------------------------
T ss_pred             ceEEECCCCCCHHHH-HHHHHHHHHhccccccceeecHH-HHHHHHHHHHHc----------------------------
Confidence            589999999999963 33444444332334456666543 333333332221                            


Q ss_pred             EEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC-CCCcEEEEEeeCChh
Q psy11867        224 IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP-SDCQIMLFSATYDKE  291 (399)
Q Consensus       224 IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~l~~SAT~~~~  291 (399)
                         .....+.+.        +...++++||++|.+...+.....+..++..+. .+.++|+.|...|..
T Consensus        86 ---~~~~~~~~~--------~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~  143 (219)
T PF00308_consen   86 ---GEIEEFKDR--------LRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSE  143 (219)
T ss_dssp             ---TSHHHHHHH--------HCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTT
T ss_pred             ---ccchhhhhh--------hhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCcc
Confidence               011122221        347889999999998643333444444444432 355666666565544

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.52  E-value=0.021  Score=56.26  Aligned_cols=129  Identities=13%  Similarity=0.073  Sum_probs=63.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhh-CCCCCCCeEEEEe--CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRV-NPSIQEPQVLCLA--PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK  218 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l-~~~~~~~~~lil~--Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (399)
                      ++.+++.+|||+|||....--+.... ..  .+.++.++.  |.+.-+.   +.++.++... ++.+             
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~--~g~~V~li~~D~~r~~a~---eqL~~~a~~~-~vp~-------------  281 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLY--GKKKVALITLDTYRIGAV---EQLKTYAKIM-GIPV-------------  281 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhc--CCCeEEEEECCccHHHHH---HHHHHHHHHh-CCce-------------
Confidence            57889999999999976543222222 12  223444444  3332222   2232222211 2211             


Q ss_pred             ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC-CCCCcEEEEEeeCCh-hHHHHH
Q psy11867        219 KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL-PSDCQIMLFSATYDK-EVMEFA  296 (399)
Q Consensus       219 ~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~l~~SAT~~~-~v~~~~  296 (399)
                           ..+.++..+...+..     +.+.++|+||.+-+..........+..++... .+....+++|||... .+.+.+
T Consensus       282 -----~~~~~~~~l~~~l~~-----~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~~  351 (424)
T PRK05703        282 -----EVVYDPKELAKALEQ-----LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDIY  351 (424)
T ss_pred             -----EccCCHHhHHHHHHH-----hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHHH
Confidence                 122344444444322     33678999998865422111222333444421 223447789999874 455555


Q ss_pred             Hhh
Q psy11867        297 QDM  299 (399)
Q Consensus       297 ~~~  299 (399)
                      ..+
T Consensus       352 ~~f  354 (424)
T PRK05703        352 KHF  354 (424)
T ss_pred             HHh
Confidence            554

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.51  E-value=0.0054  Score=55.44  Aligned_cols=18  Identities=17%  Similarity=0.324  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      +..+++.||+|+|||...
T Consensus        45 ~~~l~l~Gp~G~GKThLl   62 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLL   62 (235)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            478999999999999543

>PRK08727 hypothetical protein; Validated

Probab=96.46  E-value=0.012  Score=53.13  Aligned_cols=17  Identities=29%  Similarity=0.321  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCCceehh
Q psy11867        143 HNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~  159 (399)
                      ..+++.|++|+|||...
T Consensus        42 ~~l~l~G~~G~GKThL~   58 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLA   58 (233)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            55999999999999543

>TIGR01075 uvrD DNA helicase II

Probab=96.46  E-value=0.0076  Score=63.68  Aligned_cols=70  Identities=16%  Similarity=0.214  Sum_probs=55.9

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ..+++-|.+|+..-    ..+++|.|..|||||.+-..-+...+.. .....++|+|+.|+.-|..+.+.+.++.
T Consensus         3 ~~Ln~~Q~~av~~~----~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~   73 (715)
T TIGR01075         3 DGLNDKQREAVAAP----PGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALL   73 (715)
T ss_pred             cccCHHHHHHHcCC----CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHh
Confidence            35889999998642    4789999999999998876666666643 3345679999999999999999998875

Designed to identify uvrD members of the uvrD/rep subfamily.

>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=96.45  E-value=0.01  Score=51.99  Aligned_cols=53  Identities=19%  Similarity=0.154  Sum_probs=30.6

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHH
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ  297 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~  297 (399)
                      ++.++++||-+-+..........+..+...+.+..-.+.+|||........+.
T Consensus        82 ~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~  134 (196)
T PF00448_consen   82 KGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQAL  134 (196)
T ss_dssp             TTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHH
T ss_pred             cCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHH
Confidence            45678888887654321122334445555655566678899998765443333

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 ....

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.43  E-value=0.0072  Score=60.23  Aligned_cols=45  Identities=11%  Similarity=0.171  Sum_probs=26.6

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      ..+++.||+|+|||.... ++...+.....+.+++++ +..++..+.
T Consensus       149 ~~l~l~G~~G~GKThL~~-ai~~~~~~~~~~~~v~yi-~~~~~~~~~  193 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLH-AIGNYILEKNPNAKVVYV-TSEKFTNDF  193 (450)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEE-EHHHHHHHH
Confidence            569999999999996543 333444332234456655 444554443

>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=96.43  E-value=0.00087  Score=57.27  Aligned_cols=124  Identities=19%  Similarity=0.217  Sum_probs=52.7

Q ss_pred             EEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEE
Q psy11867        146 IAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQII  225 (399)
Q Consensus       146 i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Il  225 (399)
                      ++.|+-|-|||.+..+.+...+...  ..+++|-+|+.+-++.+.+.+..-...+ +.+...................|-
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~--~~~I~vtAP~~~~~~~lf~~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~i~   77 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKG--KIRILVTAPSPENVQTLFEFAEKGLKAL-GYKEEKKKRIGQIIKLRFNKQRIE   77 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC---------------------------CCC--
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhc--CceEEEecCCHHHHHHHHHHHHhhcccc-ccccccccccccccccccccceEE
Confidence            5789999999987766555544443  2569999999988877776555433222 111100000000000001123455


Q ss_pred             EeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        226 IGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       226 V~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      ...|+.+...        ....+++|||||=.+.-     ..+..++    .....++||.|..
T Consensus        78 f~~Pd~l~~~--------~~~~DlliVDEAAaIp~-----p~L~~ll----~~~~~vv~stTi~  124 (177)
T PF05127_consen   78 FVAPDELLAE--------KPQADLLIVDEAAAIPL-----PLLKQLL----RRFPRVVFSTTIH  124 (177)
T ss_dssp             B--HHHHCCT------------SCEEECTGGGS-H-----HHHHHHH----CCSSEEEEEEEBS
T ss_pred             EECCHHHHhC--------cCCCCEEEEechhcCCH-----HHHHHHH----hhCCEEEEEeecc
Confidence            5566554332        12357999999976532     2333333    3444678888864

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.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.43  E-value=0.0062  Score=57.51  Aligned_cols=67  Identities=19%  Similarity=0.274  Sum_probs=46.2

Q ss_pred             HHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        115 LKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       115 ~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      +..+...|+  +++.|...+..+... +.+++++|+|||||| .++-+++..+.......+++++-.+.||
T Consensus       124 l~~l~~~g~--~~~~~~~~L~~~v~~-~~~ilI~G~tGSGKT-Tll~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        124 LDQYVERGI--MTAAQREAIIAAVRA-HRNILVIGGTGSGKT-TLVNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHc-CCeEEEECCCCCCHH-HHHHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            445555665  456788888777665 799999999999999 4445555544222234567777788776

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.40  E-value=0.013  Score=52.37  Aligned_cols=19  Identities=21%  Similarity=0.330  Sum_probs=16.4

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.++++.|++|+|||....
T Consensus        38 ~~~lll~G~~G~GKT~la~   56 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLLQ   56 (226)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            6899999999999996554

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.38  E-value=0.013  Score=58.26  Aligned_cols=49  Identities=16%  Similarity=0.262  Sum_probs=30.3

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVV  193 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~  193 (399)
                      ..+++.|++|+|||... .++...+.....+.+++++.. .++..++...+
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l  190 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVDIL  190 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHH
Confidence            45899999999999443 344454443334556766655 45655554443

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

Probab=96.36  E-value=0.0074  Score=60.60  Aligned_cols=150  Identities=14%  Similarity=0.122  Sum_probs=81.5

Q ss_pred             HHHHHHhhhhhc---CC----CCcEEEEccCCCCceehhHHHHHHhh-CCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        128 KIQETALPTLLA---DP----PHNMIAQSQSGTGKTAAFTLTMLSRV-NPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       128 ~iQ~~ai~~ll~---~~----g~~vi~~a~TGsGKT~~~~l~il~~l-~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      |+|.-.+-.++-   +.    -+.+++.-+=|.|||.....-++..+ .....+..+++.+++++-|..+++.++++...
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~i~~   80 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKMIEA   80 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            456666555541   11    25678888999999976544444333 34446778999999999999999999998876


Q ss_pred             CCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhh-hccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC--C
Q psy11867        200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWG-LKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL--P  276 (399)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~-~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l--~  276 (399)
                      .+.+........  ...   ....|.....+.+...+ ...+..+=.+..++|+||+|.+-+    .+.+..+..-+  .
T Consensus        81 ~~~l~~~~~~~~--~~~---~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~----~~~~~~l~~g~~~r  151 (477)
T PF03354_consen   81 SPELRKRKKPKI--IKS---NKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKD----DELYDALESGMGAR  151 (477)
T ss_pred             Chhhccchhhhh--hhh---hceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCC----HHHHHHHHhhhccC
Confidence            544432111100  000   00112221111111110 111222333678999999999743    12333333333  2


Q ss_pred             CCCcEEEEEe
Q psy11867        277 SDCQIMLFSA  286 (399)
Q Consensus       277 ~~~q~l~~SA  286 (399)
                      ++.+++.+|.
T Consensus       152 ~~pl~~~IST  161 (477)
T PF03354_consen  152 PNPLIIIIST  161 (477)
T ss_pred             CCceEEEEeC
Confidence            4556665543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.35  E-value=0.0091  Score=58.66  Aligned_cols=38  Identities=13%  Similarity=0.225  Sum_probs=24.1

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+++.|++|+|||.... ++...+.....+.+++++..
T Consensus       137 n~l~l~G~~G~GKThL~~-ai~~~l~~~~~~~~v~yi~~  174 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLH-AIGNEILENNPNAKVVYVSS  174 (405)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHHhCCCCcEEEEEH
Confidence            468999999999996543 34444433323445666643

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).

>PRK06893 DNA replication initiation factor; Validated

Probab=96.34  E-value=0.0089  Score=53.82  Aligned_cols=48  Identities=15%  Similarity=0.244  Sum_probs=28.8

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCC-CCCcEEEEEeeCChhH
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLP-SDCQIMLFSATYDKEV  292 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~l~~SAT~~~~v  292 (399)
                      .+.+++|+||+|.+.....+...+..++.... ...+++++|++.++..
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~  138 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHA  138 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHH
Confidence            46779999999998532222333334443333 3456778888876543

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=96.33  E-value=0.032  Score=56.78  Aligned_cols=133  Identities=13%  Similarity=0.130  Sum_probs=80.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC-CCcEEEEEEcCchhhhhhcc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI-TDLSVRYAVRGENLERNKKI  220 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  220 (399)
                      .+-.++..|--.|||.... +++..+.....+.++++.+|.+.-++.+++.++...... +...+... .|..+.-....
T Consensus       254 qk~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~v-kGe~I~i~f~n  331 (738)
T PHA03368        254 QRATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHV-KGETISFSFPD  331 (738)
T ss_pred             ccceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeee-cCcEEEEEecC
Confidence            4778888999999998655 666655444457789999999999999999998876532 11112121 22211000011


Q ss_pred             C--CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEee
Q psy11867        221 T--EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       221 ~--~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT  287 (399)
                      +  ..|..++-       .+...+.=..++++|+|||+.+-.. .+...+ -.+  ...+++++++|.|
T Consensus       332 G~kstI~FaSa-------rntNsiRGqtfDLLIVDEAqFIk~~-al~~il-p~l--~~~n~k~I~ISS~  389 (738)
T PHA03368        332 GSRSTIVFASS-------HNTNGIRGQDFNLLFVDEANFIRPD-AVQTIM-GFL--NQTNCKIIFVSST  389 (738)
T ss_pred             CCccEEEEEec-------cCCCCccCCcccEEEEechhhCCHH-HHHHHH-HHH--hccCccEEEEecC
Confidence            1  13433321       1222333457899999999998542 222222 221  2248899999988

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.33  E-value=0.0081  Score=63.48  Aligned_cols=71  Identities=14%  Similarity=0.153  Sum_probs=56.1

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      ..+++-|.+|+...    ..+++|.|..|||||.+-.--+...+.. +....++|+|+-|+..|..+.+.+.++..
T Consensus         8 ~~Ln~~Q~~av~~~----~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          8 DSLNDKQREAVAAP----LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             HhcCHHHHHHHhCC----CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            35899999998642    4789999999999998876666666643 33456799999999999999999988753

>KOG1015|consensus

Probab=96.31  E-value=0.033  Score=58.19  Aligned_cols=149  Identities=15%  Similarity=0.105  Sum_probs=77.0

Q ss_pred             HHhhhhhcCCCCcEEEEccCCCCceeh---hHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC---CcEE
Q psy11867        132 TALPTLLADPPHNMIAQSQSGTGKTAA---FTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT---DLSV  205 (399)
Q Consensus       132 ~ai~~ll~~~g~~vi~~a~TGsGKT~~---~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~---~~~~  205 (399)
                      +.+......+|...|+.--.|-|||+.   |+..+|....  ..-.++|||||...+ ..+...|.++...+.   .+.+
T Consensus       686 eSlkr~~~~~GsGcILAHcMGLGKTlQVvtflhTvL~c~k--lg~ktaLvV~PlNt~-~NW~~EFekWm~~~e~~~~leV  762 (1567)
T KOG1015|consen  686 ESLKRTKKSPGSGCILAHCMGLGKTLQVVTFLHTVLLCDK--LGFKTALVVCPLNTA-LNWMNEFEKWMEGLEDDEKLEV  762 (1567)
T ss_pred             HHHHhhcCCCCcchHHHHhhcccceehhhHHHHHHHHhhc--cCCceEEEEcchHHH-HHHHHHHHHhccccccccccee
Confidence            333333334678888888899999975   4444443333  244679999998654 445666666654321   1222


Q ss_pred             EEEEcCchhhh------hhccCCcEEEeCchhHHHhhhcccc--------c----cCCceeEEEEechhhHhhcCCchHH
Q psy11867        206 RYAVRGENLER------NKKITEQIIIGTPGKVLDWGLKYRF--------F----DLSKIKVFVLDEADVMIATQGHQDF  267 (399)
Q Consensus       206 ~~~~~~~~~~~------~~~~~~~IlV~Tp~~l~~~~~~~~~--------~----~~~~~~~lViDEah~l~~~~~~~~~  267 (399)
                      .-...-...+.      .......|.|.-+..+-.+......        |    --...++||+||+|.+-.   -...
T Consensus       763 ~eL~~vkr~e~R~~~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKN---eksa  839 (1567)
T KOG1015|consen  763 SELATVKRPEERSYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKN---EKSA  839 (1567)
T ss_pred             ehhhhccChHHHHHHHHHHHhcCCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhcc---chHH
Confidence            22111111111      1122234655555555444322110        0    112358999999999843   2233


Q ss_pred             HHHHHHhCCCCCcEEEEEee
Q psy11867        268 SIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       268 ~~~i~~~l~~~~q~l~~SAT  287 (399)
                      +...+..+...+ .|++|.|
T Consensus       840 ~Skam~~irtkR-RI~LTGT  858 (1567)
T KOG1015|consen  840 VSKAMNSIRTKR-RIILTGT  858 (1567)
T ss_pred             HHHHHHHHHhhe-eEEeecC
Confidence            333333333334 4566666

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.31  E-value=0.028  Score=53.29  Aligned_cols=45  Identities=20%  Similarity=0.222  Sum_probs=27.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG  190 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~  190 (399)
                      +.++++.|+||+|||.... ++...+..  .+..+++ .+..+|..++.
T Consensus       183 ~~~Lll~G~~GtGKThLa~-aIa~~l~~--~g~~V~y-~t~~~l~~~l~  227 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSN-CIAKELLD--RGKSVIY-RTADELIEILR  227 (329)
T ss_pred             CCcEEEECCCCCcHHHHHH-HHHHHHHH--CCCeEEE-EEHHHHHHHHH
Confidence            6899999999999996544 33333322  2334544 44455654443

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.28  E-value=0.021  Score=51.70  Aligned_cols=104  Identities=16%  Similarity=0.244  Sum_probs=54.2

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCC
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE  222 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (399)
                      ..+++.+++|+|||.... ++...+..  .+..++++ +..+|...+...+.    .          ..           
T Consensus       100 ~~~~l~G~~GtGKThLa~-aia~~l~~--~g~~v~~i-t~~~l~~~l~~~~~----~----------~~-----------  150 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAA-AICNELLL--RGKSVLII-TVADIMSAMKDTFS----N----------SE-----------  150 (244)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHh--cCCeEEEE-EHHHHHHHHHHHHh----h----------cc-----------
Confidence            579999999999996554 33333333  23345555 44444433332211    0          00           


Q ss_pred             cEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHh-CCCCCcEEEEEee
Q psy11867        223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR-LPSDCQIMLFSAT  287 (399)
Q Consensus       223 ~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~-l~~~~q~l~~SAT  287 (399)
                          .+...+++.        +.++++|||||++......+....+..|+.. ......+++.|--
T Consensus       151 ----~~~~~~l~~--------l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl  204 (244)
T PRK07952        151 ----TSEEQLLND--------LSNVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNS  204 (244)
T ss_pred             ----ccHHHHHHH--------hccCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCC
Confidence                022233332        4578899999999865332222333344432 3335566665554

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.27  E-value=0.0099  Score=56.08  Aligned_cols=67  Identities=16%  Similarity=0.279  Sum_probs=45.9

Q ss_pred             HHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH
Q psy11867        116 KGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA  186 (399)
Q Consensus       116 ~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La  186 (399)
                      ..+...|.  .++.|...+..+... +.+++++|+||||||.. +-+++..+.......+++.+=.+.||.
T Consensus       121 ~~lv~~g~--~~~~~~~~L~~~v~~-~~nilI~G~tGSGKTTl-l~aL~~~i~~~~~~~rivtiEd~~El~  187 (323)
T PRK13833        121 DDYVTSKI--MTEAQASVIRSAIDS-RLNIVISGGTGSGKTTL-ANAVIAEIVASAPEDRLVILEDTAEIQ  187 (323)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHHc-CCeEEEECCCCCCHHHH-HHHHHHHHhcCCCCceEEEecCCcccc
Confidence            34455555  457788888877776 78999999999999964 345555553322345677777777763

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.23  E-value=0.074  Score=44.33  Aligned_cols=38  Identities=18%  Similarity=0.247  Sum_probs=23.8

Q ss_pred             EEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        145 MIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       145 vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      +++.|++|+|||.....-+.....   .+..++++.....+
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~---~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIAT---KGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHh---cCCEEEEEECCcch
Confidence            678999999999765433332222   34557777655443

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.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.19  E-value=0.014  Score=61.34  Aligned_cols=68  Identities=19%  Similarity=0.169  Sum_probs=54.3

Q ss_pred             ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        126 PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      +++-|.+++..  .  ..+++|.|..|||||.+-+--+...+.. .....++|+|+.|+.-|.++.+.+.+..
T Consensus         2 Ln~~Q~~av~~--~--~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074         2 LNPQQQEAVEY--V--TGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCHHHHHHHhC--C--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            67889998864  2  4789999999999998877777766643 3345679999999999999998887654

Designed to identify rep members of the uvrD/rep subfamily.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.18  E-value=0.027  Score=51.00  Aligned_cols=54  Identities=17%  Similarity=0.185  Sum_probs=39.3

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      +|..+++.|++|+|||...+-.+...+..   +..++|++ +.+-..|+.+.++.++-
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~---ge~~lyvs-~ee~~~~i~~~~~~~g~   73 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGIYVA-LEEHPVQVRRNMAQFGW   73 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc---CCcEEEEE-eeCCHHHHHHHHHHhCC
Confidence            37899999999999998665555555433   44588888 55677778887777654

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.11  E-value=0.044  Score=51.00  Aligned_cols=19  Identities=32%  Similarity=0.345  Sum_probs=16.5

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.++++.||+|+|||.++.
T Consensus        58 ~~~vll~G~pGTGKT~lA~   76 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVAL   76 (284)
T ss_pred             CceEEEEcCCCCCHHHHHH
Confidence            5799999999999997663

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.

>CHL00181 cbbX CbbX; Provisional

Probab=96.10  E-value=0.042  Score=51.19  Aligned_cols=20  Identities=30%  Similarity=0.257  Sum_probs=17.1

Q ss_pred             CCcEEEEccCCCCceehhHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l  161 (399)
                      |.++++.||+|+|||..+-.
T Consensus        59 ~~~ill~G~pGtGKT~lAr~   78 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALK   78 (287)
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            67899999999999977654

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.07  E-value=0.036  Score=57.88  Aligned_cols=70  Identities=19%  Similarity=0.153  Sum_probs=53.8

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-CCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-IQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ..+++-|.+|+-.  .  ..+++|.|..|||||.+.+--+...+... ....++|+|+.|+..|..+.+.+....
T Consensus       195 ~~L~~~Q~~av~~--~--~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        195 SPLNPSQARAVVN--G--EDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             CCCCHHHHHHHhC--C--CCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            4689999999853  2  36789999999999987766555555432 234579999999999999998887654

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.07  E-value=0.025  Score=58.91  Aligned_cols=69  Identities=23%  Similarity=0.311  Sum_probs=53.1

Q ss_pred             CCChHHHHHHhhhhhcC--CC-CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        124 YAPSKIQETALPTLLAD--PP-HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~--~g-~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      ..|++.|..++..+.+.  .+ ++.++.+.+|||||+... .++...     +..+|||+|+...|.|+++.++.+..
T Consensus        11 ~~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~~-----~r~vLIVt~~~~~A~~l~~dL~~~~~   82 (652)
T PRK05298         11 YKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIARL-----QRPTLVLAHNKTLAAQLYSEFKEFFP   82 (652)
T ss_pred             CCCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHHh-----CCCEEEEECCHHHHHHHHHHHHHhcC
Confidence            37999999999998654  12 356799999999997643 233322     23499999999999999999988853

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.06  E-value=0.029  Score=63.08  Aligned_cols=64  Identities=22%  Similarity=0.325  Sum_probs=46.9

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh--HHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF--TLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~--~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      .+++-|.+|+..++..+.+-++++|..|+|||.+.  ++.++..+.. ..+..++.++||-.-+..+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e-~~g~~V~glAPTgkAa~~L  900 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE-SERPRVVGLGPTHRAVGEM  900 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh-ccCceEEEEechHHHHHHH
Confidence            68999999999999755689999999999999763  2233332222 2346688899997666554

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.05  E-value=0.028  Score=50.39  Aligned_cols=43  Identities=12%  Similarity=0.221  Sum_probs=25.2

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCc-EEEEEeeCCh
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ-IMLFSATYDK  290 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q-~l~~SAT~~~  290 (399)
                      ..+++||||+|.+..  .....+..++........ +++++++.++
T Consensus        90 ~~~~liiDdi~~l~~--~~~~~L~~~~~~~~~~~~~~vl~~~~~~~  133 (227)
T PRK08903         90 EAELYAVDDVERLDD--AQQIALFNLFNRVRAHGQGALLVAGPAAP  133 (227)
T ss_pred             cCCEEEEeChhhcCc--hHHHHHHHHHHHHHHcCCcEEEEeCCCCH
Confidence            456899999998742  233334444444333333 5777777553

>KOG1001|consensus

Probab=95.96  E-value=0.041  Score=56.95  Aligned_cols=110  Identities=20%  Similarity=0.173  Sum_probs=68.4

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCC------CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSI------QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE  215 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~------~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  215 (399)
                      -+-.|+.-..|-|||..-+.-++.+-....      .....||+||+ ++..|+..++.+.... ..+.+.+..| ....
T Consensus       152 ~~ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~-s~~~qW~~elek~~~~-~~l~v~v~~g-r~kd  228 (674)
T KOG1001|consen  152 LRGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPT-SLLTQWKTELEKVTEE-DKLSIYVYHG-RTKD  228 (674)
T ss_pred             cccceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecch-HHHHHHHHHHhccCCc-cceEEEEecc-cccc
Confidence            355677788999999876654444322222      34457999998 4556777777544433 3566666665 2222


Q ss_pred             hhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        216 RNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       216 ~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      .......+||++|++.+...    ..+. -..-.+|+||||.+.
T Consensus       229 ~~el~~~dVVltTy~il~~~----~l~~-i~w~Riildea~~ik  267 (674)
T KOG1001|consen  229 KSELNSYDVVLTTYDILKNS----PLVK-IKWLRIVLDEAHTIK  267 (674)
T ss_pred             cchhcCCceEEeeHHHhhcc----cccc-eeEEEEEeccccccC
Confidence            33345567999999987631    1111 123469999999974

>PLN03025 replication factor C subunit; Provisional

Probab=95.95  E-value=0.1  Score=49.52  Aligned_cols=39  Identities=26%  Similarity=0.299  Sum_probs=24.6

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ...+++|+||+|.|...  ....+.+++...+..+.+++.+
T Consensus        98 ~~~kviiiDE~d~lt~~--aq~aL~~~lE~~~~~t~~il~~  136 (319)
T PLN03025         98 GRHKIVILDEADSMTSG--AQQALRRTMEIYSNTTRFALAC  136 (319)
T ss_pred             CCeEEEEEechhhcCHH--HHHHHHHHHhcccCCceEEEEe
Confidence            35789999999998542  3344445555555556555543

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=95.95  E-value=0.048  Score=55.67  Aligned_cols=96  Identities=25%  Similarity=0.249  Sum_probs=65.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |.-+++.||+|.|||                           +|+..+++.+.       .--+....||...+...++.
T Consensus       350 GpILcLVGPPGVGKT---------------------------SLgkSIA~al~-------RkfvR~sLGGvrDEAEIRGH  395 (782)
T COG0466         350 GPILCLVGPPGVGKT---------------------------SLGKSIAKALG-------RKFVRISLGGVRDEAEIRGH  395 (782)
T ss_pred             CcEEEEECCCCCCch---------------------------hHHHHHHHHhC-------CCEEEEecCccccHHHhccc
Confidence            677888999999999                           34444444332       22346677887777666665


Q ss_pred             CcEEE-eCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC
Q psy11867        222 EQIII-GTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP  276 (399)
Q Consensus       222 ~~IlV-~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~  276 (399)
                      -.-.| +-||++.+-+.+-+..+.    ++++||.|.|... ...+-...++.-|.
T Consensus       396 RRTYIGamPGrIiQ~mkka~~~NP----v~LLDEIDKm~ss-~rGDPaSALLEVLD  446 (782)
T COG0466         396 RRTYIGAMPGKIIQGMKKAGVKNP----VFLLDEIDKMGSS-FRGDPASALLEVLD  446 (782)
T ss_pred             cccccccCChHHHHHHHHhCCcCC----eEEeechhhccCC-CCCChHHHHHhhcC
Confidence            54444 479999998766554333    7999999999764 45555666666664

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.94  E-value=0.022  Score=53.40  Aligned_cols=68  Identities=22%  Similarity=0.305  Sum_probs=45.4

Q ss_pred             HHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH
Q psy11867        115 LKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA  186 (399)
Q Consensus       115 ~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La  186 (399)
                      +..+.+.|.  +++-|...+..++.. +.+++++|+||||||... -.++..+.......+++++=.+.|+.
T Consensus       108 l~~l~~~g~--~~~~~~~~L~~~v~~-~~~ilI~G~tGSGKTTll-~al~~~i~~~~~~~ri~tiEd~~El~  175 (299)
T TIGR02782       108 LDDYVEAGI--MTAAQRDVLREAVLA-RKNILVVGGTGSGKTTLA-NALLAEIAKNDPTDRVVIIEDTRELQ  175 (299)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHc-CCeEEEECCCCCCHHHHH-HHHHHHhhccCCCceEEEECCchhhc
Confidence            444555554  445666777666665 789999999999999643 44555554322345688887887764

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.

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=95.94  E-value=0.018  Score=64.34  Aligned_cols=124  Identities=16%  Similarity=0.195  Sum_probs=82.0

Q ss_pred             ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEE
Q psy11867        126 PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV  205 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~  205 (399)
                      .|+-|.+||..  .  ++++++.|..|||||.+-+--++..+..+....++|+|+=|+.-|..+.+.+.+-....  +.-
T Consensus         2 ~t~~Q~~ai~~--~--~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~~~--~~~   75 (1232)
T TIGR02785         2 WTDEQWQAIYT--R--GQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQKA--LQQ   75 (1232)
T ss_pred             CCHHHHHHHhC--C--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHHHH--Hhc
Confidence            58899999973  2  79999999999999988777777766554334569999999999999888777654321  000


Q ss_pred             EEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCC-ceeEEEEechhh
Q psy11867        206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLS-KIKVFVLDEADV  257 (399)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~-~~~~lViDEah~  257 (399)
                        ......+.++...-...-|+|-..+...+.+.....+. +-.|=|.||...
T Consensus        76 --~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        76 --EPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             --CchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence              00112233333444567899988887665543222211 124556898875

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.

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.93  E-value=0.033  Score=55.63  Aligned_cols=91  Identities=18%  Similarity=0.188  Sum_probs=58.8

Q ss_pred             CCCHHH-HHHHHHcCCCCCh----HHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhC---CCCCCCeEEEEe
Q psy11867        109 HLKPEL-LKGVYEMGFYAPS----KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVN---PSIQEPQVLCLA  180 (399)
Q Consensus       109 ~l~~~l-~~~l~~~g~~~p~----~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~---~~~~~~~~lil~  180 (399)
                      +..+++ ..+|.+.--.++.    -||.+==..|....+.-++++|..|||||.+++--+...+.   .......+||+.
T Consensus       188 ~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~  267 (747)
T COG3973         188 GGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLG  267 (747)
T ss_pred             chHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEc
Confidence            344444 4445544333332    24444444444445788999999999999988765544442   222334499999


Q ss_pred             CcHHHHHHHHHHHHHHhcc
Q psy11867        181 PTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~  199 (399)
                      |++-++.-+.+++-.+|..
T Consensus       268 PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         268 PNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             CcHHHHHHHHHhchhhccC
Confidence            9999999888888888754

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

Probab=95.92  E-value=0.034  Score=51.06  Aligned_cols=48  Identities=25%  Similarity=0.459  Sum_probs=33.6

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS  170 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~  170 (399)
                      +.+|+++++++-+.+ +..                   .+..=+++.+|||||||.. +.+|+..+++.
T Consensus       105 i~~~e~LglP~i~~~-~~~-------------------~~~GLILVTGpTGSGKSTT-lAamId~iN~~  152 (353)
T COG2805         105 IPTLEELGLPPIVRE-LAE-------------------SPRGLILVTGPTGSGKSTT-LAAMIDYINKH  152 (353)
T ss_pred             CCCHHHcCCCHHHHH-HHh-------------------CCCceEEEeCCCCCcHHHH-HHHHHHHHhcc
Confidence            567788887776655 321                   2246789999999999865 34677777664

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=95.91  E-value=0.059  Score=57.36  Aligned_cols=42  Identities=21%  Similarity=0.394  Sum_probs=27.9

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      .+.+++||||+|+|..  .....+.++++..+..+.+|+.+ |-.
T Consensus       119 ~~~KV~IIDEad~lt~--~a~NaLLK~LEEpP~~~~fIl~t-t~~  160 (824)
T PRK07764        119 SRYKIFIIDEAHMVTP--QGFNALLKIVEEPPEHLKFIFAT-TEP  160 (824)
T ss_pred             CCceEEEEechhhcCH--HHHHHHHHHHhCCCCCeEEEEEe-CCh
Confidence            4678999999999964  23334555666666666666654 433

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=95.86  E-value=0.016  Score=61.41  Aligned_cols=70  Identities=20%  Similarity=0.206  Sum_probs=55.5

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ..+++-|.+|+...    ..+++|.|..|||||.+..--+...+.. .....++|+++-|+.-|..+.+.+.++.
T Consensus         3 ~~Ln~~Q~~av~~~----~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~   73 (726)
T TIGR01073         3 AHLNPEQREAVKTT----EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLL   73 (726)
T ss_pred             cccCHHHHHHHhCC----CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHh
Confidence            35889999999742    4789999999999998877666666643 2334579999999999999998888764

Designed to identify pcrA members of the uvrD/rep subfamily.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=95.84  E-value=0.014  Score=53.29  Aligned_cols=49  Identities=12%  Similarity=0.087  Sum_probs=33.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVA  194 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~  194 (399)
                      +.++++.|++|+|||..+..-....+ .  . +..++++++.+|+.++...+.
T Consensus       105 ~~nl~l~G~~G~GKThLa~Ai~~~l~-~--~-g~sv~f~~~~el~~~Lk~~~~  153 (254)
T COG1484         105 GENLVLLGPPGVGKTHLAIAIGNELL-K--A-GISVLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHH-H--c-CCeEEEEEHHHHHHHHHHHHh
Confidence            78999999999999976543333333 2  2 335667778888877665443

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.84  E-value=0.067  Score=49.25  Aligned_cols=132  Identities=12%  Similarity=0.149  Sum_probs=67.2

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe-CcH--HHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA-PTY--ELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN  217 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~-Pt~--~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  217 (399)
                      ++..+.+.+++|+|||..+..-+.....   .+.++.++. .+.  ..+.|+......+     ++.+.           
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~~---~~~~v~~i~~D~~ri~~~~ql~~~~~~~-----~~~~~-----------  134 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHG---KKKTVGFITTDHSRIGTVQQLQDYVKTI-----GFEVI-----------  134 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHHH---cCCeEEEEecCCCCHHHHHHHHHHhhhc-----CceEE-----------
Confidence            3689999999999999876644333222   223344443 222  3444444333222     11111           


Q ss_pred             hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC-hhHHHHH
Q psy11867        218 KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD-KEVMEFA  296 (399)
Q Consensus       218 ~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~-~~v~~~~  296 (399)
                             ...+|..+.+.+...  -...++++++||-+=+..........+..+.....+..-.+.+|||.. .+..+.+
T Consensus       135 -------~~~~~~~l~~~l~~l--~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~~  205 (270)
T PRK06731        135 -------AVRDEAAMTRALTYF--KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEII  205 (270)
T ss_pred             -------ecCCHHHHHHHHHHH--HhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHHH
Confidence                   112444444432211  112367899999986652111112222233333333444667999865 4677777


Q ss_pred             HhhC
Q psy11867        297 QDMV  300 (399)
Q Consensus       297 ~~~~  300 (399)
                      +.|-
T Consensus       206 ~~f~  209 (270)
T PRK06731        206 TNFK  209 (270)
T ss_pred             HHhC
Confidence            7653

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.81  E-value=0.044  Score=52.03  Aligned_cols=36  Identities=22%  Similarity=0.263  Sum_probs=27.9

Q ss_pred             ChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHH
Q psy11867        126 PSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l  161 (399)
                      .+|||...+..+++.  -++-.++.||.|.|||..+..
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~   41 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAER   41 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHH
Confidence            478888888888765  134688999999999976554

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.80  E-value=0.064  Score=49.27  Aligned_cols=20  Identities=35%  Similarity=0.483  Sum_probs=16.7

Q ss_pred             CCcEEEEccCCCCceehhHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l  161 (399)
                      ..++++.||+|+|||..+-.
T Consensus        42 ~~~vll~GppGtGKTtlA~~   61 (261)
T TIGR02881        42 VLHMIFKGNPGTGKTTVARI   61 (261)
T ss_pred             cceEEEEcCCCCCHHHHHHH
Confidence            57899999999999976543

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.

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=95.74  E-value=0.073  Score=60.65  Aligned_cols=65  Identities=28%  Similarity=0.396  Sum_probs=46.7

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhC--CCCCCCeEEEEeCcHHHHHHH
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVN--PSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~--~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      ..+++.|.+|+..++..+.+-+++++..|+|||...- .++..+.  ....+..++.++||-.-|..+
T Consensus       966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l~-~v~~~~~~l~~~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQFR-AVMSAVNTLPESERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHH-HHHHHHHHhhcccCceEEEECCcHHHHHHH
Confidence            3689999999999998656789999999999996532 2333322  112345688899997666544

>KOG0991|consensus

Probab=95.73  E-value=0.02  Score=50.56  Aligned_cols=43  Identities=28%  Similarity=0.313  Sum_probs=32.5

Q ss_pred             CCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeC
Q psy11867        244 LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATY  288 (399)
Q Consensus       244 ~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~  288 (399)
                      ..+.+.+|+||||.|-+  |....+.+.+....+.+++.+-..+.
T Consensus       111 ~grhKIiILDEADSMT~--gAQQAlRRtMEiyS~ttRFalaCN~s  153 (333)
T KOG0991|consen  111 PGRHKIIILDEADSMTA--GAQQALRRTMEIYSNTTRFALACNQS  153 (333)
T ss_pred             CCceeEEEeeccchhhh--HHHHHHHHHHHHHcccchhhhhhcch
Confidence            35678999999999964  67777777777777777777655553

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=95.70  E-value=0.052  Score=53.85  Aligned_cols=38  Identities=16%  Similarity=0.236  Sum_probs=24.5

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+++.||+|+|||.... ++...+.....+.+++++..
T Consensus       131 n~l~lyG~~G~GKTHLl~-ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQ-SIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHHH-HHHHHHHHhCCCCeEEEEEH
Confidence            469999999999996543 34444433323446776654

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=95.68  E-value=0.055  Score=52.96  Aligned_cols=135  Identities=13%  Similarity=0.166  Sum_probs=72.1

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH-HHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhcc-
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE-LAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI-  220 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~-La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  220 (399)
                      +-.++.|..|||||.+..+-++..+.....+.+++|+-|+.. |..-++..++.....+ ++..........+.-.... 
T Consensus         2 ~~~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~-g~~~~~~~~~~~~~i~~~~~   80 (396)
T TIGR01547         2 EEIIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLLSIE-GINYEFKKSKSSMEIKILNT   80 (396)
T ss_pred             ceEEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHHHHc-CChhheeecCCccEEEecCC
Confidence            346788999999999888777776655434577899999887 5555666666554433 2221111111110000111 


Q ss_pred             CCcEEEeCc-hhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC--CCCcEEEEEeeCC
Q psy11867        221 TEQIIIGTP-GKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP--SDCQIMLFSATYD  289 (399)
Q Consensus       221 ~~~IlV~Tp-~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~--~~~q~l~~SAT~~  289 (399)
                      +..|++..- +.-..      ......+.++.+|||..+...     ....+...++  .....+++|.+.+
T Consensus        81 g~~i~f~g~~d~~~~------ik~~~~~~~~~idEa~~~~~~-----~~~~l~~rlr~~~~~~~i~~t~NP~  141 (396)
T TIGR01547        81 GKKFIFKGLNDKPNK------LKSGAGIAIIWFEEASQLTFE-----DIKELIPRLRETGGKKFIIFSSNPE  141 (396)
T ss_pred             CeEEEeecccCChhH------hhCcceeeeehhhhhhhcCHH-----HHHHHHHHhhccCCccEEEEEcCcC
Confidence            223444332 21111      112334689999999987431     2222333333  2222467777744

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.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.57  E-value=0.053  Score=56.70  Aligned_cols=131  Identities=11%  Similarity=0.097  Sum_probs=62.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe-CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhcc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA-PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI  220 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~-Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (399)
                      |+-+.+.||||+|||.....-+....... .+.++.++. -|.-.+  ..+.++.++... ++.+               
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~-G~kkV~lit~Dt~Rig--A~eQL~~~a~~~-gvpv---------------  245 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVARE-GADQLALLTTDSFRIG--ALEQLRIYGRIL-GVPV---------------  245 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHc-CCCeEEEecCcccchH--HHHHHHHHHHhC-CCCc---------------
Confidence            45678999999999876654332221111 112343333 232211  123344433322 2211               


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChh-HHHHHHhh
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE-VMEFAQDM  299 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~-v~~~~~~~  299 (399)
                         .++.+|..+.+.+..     +.+.++|+||=+=+..........+..+.....+...++.+|||.... +.+.++.|
T Consensus       246 ---~~~~~~~~l~~al~~-----~~~~D~VLIDTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~l~~i~~~f  317 (767)
T PRK14723        246 ---HAVKDAADLRFALAA-----LGDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDTLNEVVHAY  317 (767)
T ss_pred             ---cccCCHHHHHHHHHH-----hcCCCEEEEeCCCCCccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHHHHHHHHHH
Confidence               223355555544332     335567888877664321112222223333333445577888887543 44455554

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.55  E-value=0.05  Score=52.15  Aligned_cols=23  Identities=22%  Similarity=0.196  Sum_probs=18.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTML  164 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il  164 (399)
                      ++.+++.+|+|+|||....--+.
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~  228 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGW  228 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            77889999999999976544333

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=95.55  E-value=0.23  Score=50.96  Aligned_cols=72  Identities=14%  Similarity=0.168  Sum_probs=51.0

Q ss_pred             CChHHHHHHhhhhhcC-CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        125 APSKIQETALPTLLAD-PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~-~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      -|+|.=.+-|..++.. ..+-.++.+|=|.|||.+..+.+...+..  .+.+++|.+|...-+.++.+.++....
T Consensus       169 ~~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~~La~f--~Gi~IlvTAH~~~ts~evF~rv~~~le  241 (752)
T PHA03333        169 APSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILAAMISF--LEIDIVVQAQRKTMCLTLYNRVETVVH  241 (752)
T ss_pred             CCChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHHHHHHh--cCCeEEEECCChhhHHHHHHHHHHHHH
Confidence            3455555555555432 14667788999999998876655544432  346799999999999998888877765

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

Probab=95.55  E-value=0.048  Score=47.03  Aligned_cols=50  Identities=18%  Similarity=0.148  Sum_probs=33.8

Q ss_pred             EEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        145 MIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       145 vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      +++.|++|+|||...+--+...+.   .+..++|++. .+-..++.+.++.++-
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~---~g~~v~~~s~-e~~~~~~~~~~~~~g~   51 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLA---RGEPGLYVTL-EESPEELIENAESLGW   51 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHH---CCCcEEEEEC-CCCHHHHHHHHHHcCC
Confidence            688999999999766544444443   3445777764 4566777777776643

A related protein is found in archaea.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.48  E-value=0.054  Score=53.71  Aligned_cols=41  Identities=12%  Similarity=0.190  Sum_probs=25.0

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI  187 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~  187 (399)
                      ..+++.||+|+|||.... ++...+..  .+.+++++.. ..+..
T Consensus       142 npl~L~G~~G~GKTHLl~-Ai~~~l~~--~~~~v~yi~~-~~f~~  182 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQ-AAVHALRE--SGGKILYVRS-ELFTE  182 (445)
T ss_pred             ceEEEEcCCCCCHHHHHH-HHHHHHHH--cCCCEEEeeH-HHHHH
Confidence            568999999999996543 33443332  2345666653 34443

>PRK08116 hypothetical protein; Validated

Probab=95.48  E-value=0.039  Score=50.86  Aligned_cols=45  Identities=18%  Similarity=0.138  Sum_probs=27.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG  190 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~  190 (399)
                      +..+++.|++|+|||..+. ++...+...  +..+++ .+..++...+.
T Consensus       114 ~~gl~l~G~~GtGKThLa~-aia~~l~~~--~~~v~~-~~~~~ll~~i~  158 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLAA-CIANELIEK--GVPVIF-VNFPQLLNRIK  158 (268)
T ss_pred             CceEEEECCCCCCHHHHHH-HHHHHHHHc--CCeEEE-EEHHHHHHHHH
Confidence            3459999999999997654 344444432  233444 44455554443

>PRK12377 putative replication protein; Provisional

Probab=95.48  E-value=0.064  Score=48.74  Aligned_cols=46  Identities=17%  Similarity=0.249  Sum_probs=27.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGE  191 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~  191 (399)
                      ..++++.|++|+|||.... ++...+..  .+..+ +.++..+|..++..
T Consensus       101 ~~~l~l~G~~GtGKThLa~-AIa~~l~~--~g~~v-~~i~~~~l~~~l~~  146 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAA-AIGNRLLA--KGRSV-IVVTVPDVMSRLHE  146 (248)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHH--cCCCe-EEEEHHHHHHHHHH
Confidence            4789999999999996543 33333332  22234 44455566665544

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=95.45  E-value=0.19  Score=50.71  Aligned_cols=128  Identities=16%  Similarity=0.097  Sum_probs=80.7

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh-ccCCCcEEEEEEcCchhhhhhccC
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG-KHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      +-.+.--|--.|||+ |+.|++..+...-.+.++.|+++-+.-++-+.+++..-. .+++.-.+...           .+
T Consensus       203 kaTVFLVPRRHGKTW-f~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~-----------k~  270 (668)
T PHA03372        203 KATVFLVPRRHGKTW-FIIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIEN-----------KD  270 (668)
T ss_pred             cceEEEecccCCcee-hHHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeee-----------cC
Confidence            666777899999996 678899888887788999999999988877666665432 22222111111           11


Q ss_pred             CcEEEeCchhH----HHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC-CCCCcEEEEEee
Q psy11867        222 EQIIIGTPGKV----LDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL-PSDCQIMLFSAT  287 (399)
Q Consensus       222 ~~IlV~Tp~~l----~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~l~~SAT  287 (399)
                      ..|.+.-||.=    .-...+...+.=++++++++||||.+-.     +.+..|+-.+ ..++++|..|.|
T Consensus       271 ~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~~-----~a~~tilgfm~q~~~KiIfISS~  336 (668)
T PHA03372        271 NVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIKK-----DAFNTILGFLAQNTTKIIFISST  336 (668)
T ss_pred             cEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccCH-----HHHHHhhhhhcccCceEEEEeCC
Confidence            12444444321    0111233445567889999999998732     2333444444 357888888887

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.42  E-value=0.071  Score=62.06  Aligned_cols=64  Identities=23%  Similarity=0.289  Sum_probs=47.0

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH---HHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT---LTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~---l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      ..+++.|..|+..++.++++-+++++..|+|||....   -++...+..  .+..++.++||-.-+.++
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~--~g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES--EQLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh--cCCeEEEEeChHHHHHHH
Confidence            3689999999999987656778899999999996541   233333332  356788899997666544

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.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.41  E-value=0.11  Score=51.19  Aligned_cols=22  Identities=23%  Similarity=0.401  Sum_probs=17.5

Q ss_pred             CCcEEEEccCCCCceehhHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      +..+++++++|+|||....--+
T Consensus        95 p~vI~lvG~~GsGKTTtaakLA  116 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAKLA  116 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHHHH
Confidence            6788999999999997665433

>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=95.41  E-value=0.12  Score=43.70  Aligned_cols=41  Identities=24%  Similarity=0.422  Sum_probs=27.0

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEee
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT  287 (399)
                      ...+++||||||.|..  .....+.+.+..-+.++.++++|..
T Consensus       101 ~~~KviiI~~ad~l~~--~a~NaLLK~LEepp~~~~fiL~t~~  141 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTE--EAQNALLKTLEEPPENTYFILITNN  141 (162)
T ss_dssp             SSSEEEEEETGGGS-H--HHHHHHHHHHHSTTTTEEEEEEES-
T ss_pred             CCceEEEeehHhhhhH--HHHHHHHHHhcCCCCCEEEEEEECC
Confidence            5689999999999864  2444455566665666666666554

...

>PRK04328 hypothetical protein; Provisional

Probab=95.38  E-value=0.082  Score=48.19  Aligned_cols=53  Identities=15%  Similarity=0.166  Sum_probs=37.1

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      |..+++.+++|+|||...+--+...+..   +..++|++ +.+-..++.+.++.++-
T Consensus        23 gs~ili~G~pGsGKT~l~~~fl~~~~~~---ge~~lyis-~ee~~~~i~~~~~~~g~   75 (249)
T PRK04328         23 RNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGVYVA-LEEHPVQVRRNMRQFGW   75 (249)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhc---CCcEEEEE-eeCCHHHHHHHHHHcCC
Confidence            7899999999999997655445554443   33477777 55566677777777654

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

Probab=95.35  E-value=0.021  Score=51.17  Aligned_cols=136  Identities=13%  Similarity=0.070  Sum_probs=68.5

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc----EEEEEEcCchhhh
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL----SVRYAVRGENLER  216 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~----~~~~~~~~~~~~~  216 (399)
                      .|..+++.|++|+|||.-.+--+...+...  +..+++++- .+-..++.+.++.++-.+...    .............
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~--ge~vlyvs~-ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~~   94 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNF--GEKVLYVSF-EEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERIG   94 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH--T--EEEEES-SS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGST
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc--CCcEEEEEe-cCCHHHHHHHHHHcCCcHHHHhhcCCEEEEeccccccc
Confidence            378999999999999976554444444430  234888873 455567777777664322110    0111111110000


Q ss_pred             hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC---CchHHHHHHHHhCCCCCcEEEEEeeC
Q psy11867        217 NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ---GHQDFSIRIQKRLPSDCQIMLFSATY  288 (399)
Q Consensus       217 ~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~---~~~~~~~~i~~~l~~~~q~l~~SAT~  288 (399)
                      ..       -..++.+...+..  .+.-.+.+.+|||-...+....   .....+..+...+.....+.++++..
T Consensus        95 ~~-------~~~~~~l~~~i~~--~i~~~~~~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~~  160 (226)
T PF06745_consen   95 WS-------PNDLEELLSKIRE--AIEELKPDRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSEM  160 (226)
T ss_dssp             -T-------SCCHHHHHHHHHH--HHHHHTSSEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEEE
T ss_pred             cc-------ccCHHHHHHHHHH--HHHhcCCCEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEcc
Confidence            00       1122233332211  1111233799999999883221   23344455555555566677777774

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 ....

>KOG0298|consensus

Probab=95.35  E-value=0.047  Score=58.80  Aligned_cols=139  Identities=16%  Similarity=0.107  Sum_probs=84.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCC-----------C----CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEE
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNP-----------S----IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVR  206 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~-----------~----~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~  206 (399)
                      |.+++..-..|.|||.+-+...+.....           .    ...+..|||+|. ++..|+.+++.+-...  .+++.
T Consensus       374 g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~--~lKv~  450 (1394)
T KOG0298|consen  374 GKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISS--LLKVL  450 (1394)
T ss_pred             CcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhccc--cceEE
Confidence            7888998999999998877655544211           0    112458999998 5567777777665433  24555


Q ss_pred             EEEcCchh---hhhhccCCcEEEeCchhHHHhhhccccc-cCC----------------cee--EEEEechhhHhhcCCc
Q psy11867        207 YAVRGENL---ERNKKITEQIIIGTPGKVLDWGLKYRFF-DLS----------------KIK--VFVLDEADVMIATQGH  264 (399)
Q Consensus       207 ~~~~~~~~---~~~~~~~~~IlV~Tp~~l~~~~~~~~~~-~~~----------------~~~--~lViDEah~l~~~~~~  264 (399)
                      ...|-...   .......++||++|...|..-+...+.. ..+                .+.  -+++|||+++..   -
T Consensus       451 ~Y~Girk~~~~~~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMves---s  527 (1394)
T KOG0298|consen  451 LYFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVES---S  527 (1394)
T ss_pred             EEechhhhcccCchhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcc---h
Confidence            55544322   2233456799999999886543322111 011                111  289999999854   3


Q ss_pred             hHHHHHHHHhCCCCCcEEEEEee
Q psy11867        265 QDFSIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       265 ~~~~~~i~~~l~~~~q~l~~SAT  287 (399)
                      .....++...++ ....=++|.|
T Consensus       528 sS~~a~M~~rL~-~in~W~VTGT  549 (1394)
T KOG0298|consen  528 SSAAAEMVRRLH-AINRWCVTGT  549 (1394)
T ss_pred             HHHHHHHHHHhh-hhceeeecCC
Confidence            344445555554 4445678888

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.31  E-value=0.19  Score=50.35  Aligned_cols=58  Identities=16%  Similarity=0.121  Sum_probs=34.4

Q ss_pred             cccccCCCCHHHHHHHHHc-CC-CCChHHHHHHhhhh-----------hcCCCCcEEEEccCCCCceehhHH
Q psy11867        103 KTFEALHLKPELLKGVYEM-GF-YAPSKIQETALPTL-----------LADPPHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~-g~-~~p~~iQ~~ai~~l-----------l~~~g~~vi~~a~TGsGKT~~~~l  161 (399)
                      ..+...|+++.+.+.|... .- .....-.......+           +. .|+.+.+.||+|+|||.....
T Consensus       299 ~~L~~~Gvs~~la~~L~~~l~~~~~~~~~~~~l~~~L~~~l~v~~~~~l~-~G~vIaLVGPtGvGKTTtaak  369 (559)
T PRK12727        299 ELMDDYGFDAGLTRDVAMQIPADTELHRGRGLMLGLLSKRLPVAPVDPLE-RGGVIALVGPTGAGKTTTIAK  369 (559)
T ss_pred             HHHHHCCCCHHHHHHHHHhhhcccchhhHHHHHHHHHHHhcCcCcccccc-CCCEEEEECCCCCCHHHHHHH
Confidence            5567778888888888652 11 11111111111111           22 278899999999999976543

>PF13173 AAA_14: AAA domain

Probab=95.29  E-value=0.15  Score=41.18  Aligned_cols=38  Identities=16%  Similarity=0.163  Sum_probs=25.4

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEee
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT  287 (399)
                      .-.+++|||+|.+.   .+...+..+.... ++.++++.+..
T Consensus        61 ~~~~i~iDEiq~~~---~~~~~lk~l~d~~-~~~~ii~tgS~   98 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP---DWEDALKFLVDNG-PNIKIILTGSS   98 (128)
T ss_pred             CCcEEEEehhhhhc---cHHHHHHHHHHhc-cCceEEEEccc
Confidence            45689999999983   4666666666644 45666655443

>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=95.27  E-value=0.11  Score=41.76  Aligned_cols=15  Identities=27%  Similarity=0.392  Sum_probs=12.9

Q ss_pred             eeEEEEechhhHhhc
Q psy11867        247 IKVFVLDEADVMIAT  261 (399)
Q Consensus       247 ~~~lViDEah~l~~~  261 (399)
                      -.+++|||+|.+...
T Consensus        59 ~~vl~iDe~d~l~~~   73 (132)
T PF00004_consen   59 PCVLFIDEIDKLFPK   73 (132)
T ss_dssp             SEEEEEETGGGTSHH
T ss_pred             ceeeeeccchhcccc
Confidence            579999999999765

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 ....

>KOG2004|consensus

Probab=95.25  E-value=0.12  Score=52.85  Aligned_cols=113  Identities=19%  Similarity=0.200  Sum_probs=70.0

Q ss_pred             CChHHHHHHhhhhh----cC--CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        125 APSKIQETALPTLL----AD--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll----~~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      -+..+-.+.+..+.    ++  .|+-+++.+|+|-|||-.                           +..+++.+   +.
T Consensus       415 gm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI---------------------------~kSIA~AL---nR  464 (906)
T KOG2004|consen  415 GMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSI---------------------------AKSIARAL---NR  464 (906)
T ss_pred             chHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccH---------------------------HHHHHHHh---CC
Confidence            34455555555542    22  478899999999999943                           22233322   21


Q ss_pred             cCCCcEEEEEEcCchhhhhhccCCcEE-EeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC
Q psy11867        199 HITDLSVRYAVRGENLERNKKITEQII-IGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP  276 (399)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~Il-V~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~  276 (399)
                          --..+.+||.......++...-. =+-||++.+.+.+-+.-+.    ++.|||+|.+.. +...+-...++..|.
T Consensus       465 ----kFfRfSvGG~tDvAeIkGHRRTYVGAMPGkiIq~LK~v~t~NP----liLiDEvDKlG~-g~qGDPasALLElLD  534 (906)
T KOG2004|consen  465 ----KFFRFSVGGMTDVAEIKGHRRTYVGAMPGKIIQCLKKVKTENP----LILIDEVDKLGS-GHQGDPASALLELLD  534 (906)
T ss_pred             ----ceEEEeccccccHHhhcccceeeeccCChHHHHHHHhhCCCCc----eEEeehhhhhCC-CCCCChHHHHHHhcC
Confidence                12355677776666666655444 4579999998755433222    799999999973 345555666766664

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=95.21  E-value=0.046  Score=55.69  Aligned_cols=108  Identities=14%  Similarity=0.169  Sum_probs=55.8

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCC
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE  222 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (399)
                      ..+++.|++|+|||.... ++.+.+.....+.+++|+. ..+++.++...+..   .                       
T Consensus       315 NpL~LyG~sGsGKTHLL~-AIa~~a~~~~~g~~V~Yit-aeef~~el~~al~~---~-----------------------  366 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLH-AIGHYARRLYPGTRVRYVS-SEEFTNEFINSIRD---G-----------------------  366 (617)
T ss_pred             CcEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEee-HHHHHHHHHHHHHh---c-----------------------
Confidence            348999999999995432 3344433322344455554 34555443332211   0                       


Q ss_pred             cEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC-CCCcEEEEEeeCChh
Q psy11867        223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP-SDCQIMLFSATYDKE  291 (399)
Q Consensus       223 ~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~l~~SAT~~~~  291 (399)
                           ..+.+..        .+.++++|||||+|.+.........+..++..+. .+.++|+.|-..+..
T Consensus       367 -----~~~~f~~--------~y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~e  423 (617)
T PRK14086        367 -----KGDSFRR--------RYREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQ  423 (617)
T ss_pred             -----cHHHHHH--------HhhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHh
Confidence                 0011111        1346789999999998543333333444444443 356666544443333

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=95.12  E-value=0.17  Score=53.40  Aligned_cols=40  Identities=15%  Similarity=0.365  Sum_probs=22.9

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCC-CCCcEEEEEe
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLP-SDCQIMLFSA  286 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~l~~SA  286 (399)
                      ..+.+|||||+|.|...  ..+.+..+++... ...+++++..
T Consensus       868 r~v~IIILDEID~L~kK--~QDVLYnLFR~~~~s~SKLiLIGI  908 (1164)
T PTZ00112        868 RNVSILIIDEIDYLITK--TQKVLFTLFDWPTKINSKLVLIAI  908 (1164)
T ss_pred             ccceEEEeehHhhhCcc--HHHHHHHHHHHhhccCCeEEEEEe
Confidence            45678999999999642  3344444544322 2344444333

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.11  E-value=0.16  Score=49.67  Aligned_cols=43  Identities=16%  Similarity=0.088  Sum_probs=25.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      |.-+.+.||||+|||.....-+-..+.........++.+.+.-
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~r  233 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYR  233 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcc
Confidence            6778999999999997664322222222112223556666543

>KOG0739|consensus

Probab=95.11  E-value=2.1  Score=39.62  Aligned_cols=154  Identities=15%  Similarity=0.210  Sum_probs=77.7

Q ss_pred             cccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       105 f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      |++.-=-+.-.++|++.=+-   |   -=+|.+..+   +-+.+++-+|+|+||+  |+.-++.. ..  .  -..+=+.
T Consensus       132 WsDVAGLE~AKeALKEAVIL---P---IKFPqlFtGkR~PwrgiLLyGPPGTGKS--YLAKAVAT-EA--n--STFFSvS  198 (439)
T KOG0739|consen  132 WSDVAGLEGAKEALKEAVIL---P---IKFPQLFTGKRKPWRGILLYGPPGTGKS--YLAKAVAT-EA--N--STFFSVS  198 (439)
T ss_pred             hhhhccchhHHHHHHhheee---c---ccchhhhcCCCCcceeEEEeCCCCCcHH--HHHHHHHh-hc--C--CceEEee
Confidence            55442224555666553111   1   113566654   3568999999999999  33322211 11  1  2445555


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT  261 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~  261 (399)
                      +..|+..+..+-+++.+.                                |..+..      -+.-..+.|||+|.+...
T Consensus       199 SSDLvSKWmGESEkLVkn--------------------------------LFemAR------e~kPSIIFiDEiDslcg~  240 (439)
T KOG0739|consen  199 SSDLVSKWMGESEKLVKN--------------------------------LFEMAR------ENKPSIIFIDEIDSLCGS  240 (439)
T ss_pred             hHHHHHHHhccHHHHHHH--------------------------------HHHHHH------hcCCcEEEeehhhhhccC
Confidence            556665443333333211                                222222      234568999999988754


Q ss_pred             CCc--hHHHHHHHHh----C----CCCCcEEEEEeeCChhH-HHHHHhhCCCCeEEecc
Q psy11867        262 QGH--QDFSIRIQKR----L----PSDCQIMLFSATYDKEV-MEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       262 ~~~--~~~~~~i~~~----l----~~~~q~l~~SAT~~~~v-~~~~~~~~~~p~~i~~~  309 (399)
                      .+.  .+...+|...    +    ..+--++.+.||--+++ ...+++-+...+.|.+.
T Consensus       241 r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRRRFekRIYIPLP  299 (439)
T KOG0739|consen  241 RSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYIPLP  299 (439)
T ss_pred             CCCCchHHHHHHHHHHHHhhhccccCCCceEEEecCCCchhHHHHHHHHhhcceeccCC
Confidence            322  2222333221    1    23456888999965554 34444444444444443

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=95.01  E-value=0.054  Score=50.79  Aligned_cols=82  Identities=20%  Similarity=0.299  Sum_probs=53.5

Q ss_pred             CCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeE
Q psy11867         97 SPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQV  176 (399)
Q Consensus        97 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~  176 (399)
                      .|..++..|..-.+.   +..|-  .|...++-|...+..+... ..|+++++.||||||.. +-+++..+..   .-|+
T Consensus       134 Gp~lsIRKf~k~~lt---l~dli--~~gt~~~~~a~~L~~av~~-r~NILisGGTGSGKTTl-LNal~~~i~~---~eRv  203 (355)
T COG4962         134 GPTLSIRKFPKIKLT---LLDLI--IFGTMIRRAAKFLRRAVGI-RCNILISGGTGSGKTTL-LNALSGFIDS---DERV  203 (355)
T ss_pred             CCccccccccccccc---HHHHH--HcCCcCHHHHHHHHHHHhh-ceeEEEeCCCCCCHHHH-HHHHHhcCCC---cccE
Confidence            344555666544332   22332  4667889999999999885 56999999999999953 1122222222   2378


Q ss_pred             EEEeCcHHHHHH
Q psy11867        177 LCLAPTYELAIQ  188 (399)
Q Consensus       177 lil~Pt~~La~Q  188 (399)
                      +++=-|.||-.+
T Consensus       204 ItiEDtaELql~  215 (355)
T COG4962         204 ITIEDTAELQLA  215 (355)
T ss_pred             EEEeehhhhccC
Confidence            999888887544

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=94.98  E-value=0.19  Score=47.82  Aligned_cols=39  Identities=21%  Similarity=0.405  Sum_probs=24.4

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ...+++|+||+|.+..  .....+..++...+..+++++.+
T Consensus       124 ~~~~vlilDe~~~l~~--~~~~~L~~~le~~~~~~~~Il~~  162 (337)
T PRK12402        124 ADYKTILLDNAEALRE--DAQQALRRIMEQYSRTCRFIIAT  162 (337)
T ss_pred             CCCcEEEEeCcccCCH--HHHHHHHHHHHhccCCCeEEEEe
Confidence            4457999999998843  23334455555555566655543

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

Probab=94.96  E-value=0.41  Score=46.17  Aligned_cols=35  Identities=31%  Similarity=0.582  Sum_probs=24.1

Q ss_pred             HhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhC
Q psy11867        133 ALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVN  168 (399)
Q Consensus       133 ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~  168 (399)
                      ..|.+..+.+.|+++-|+||+|||++... ++..+.
T Consensus        33 l~~~~~~~~p~n~~iyG~~GTGKT~~~~~-v~~~l~   67 (366)
T COG1474          33 LAPALRGERPSNIIIYGPTGTGKTATVKF-VMEELE   67 (366)
T ss_pred             HHHHhcCCCCccEEEECCCCCCHhHHHHH-HHHHHH
Confidence            34555555577899999999999977554 344443

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.96  E-value=0.023  Score=55.33  Aligned_cols=49  Identities=20%  Similarity=0.237  Sum_probs=39.5

Q ss_pred             cEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      |+++.|+||||||.++++|-+...     ...++|+=|.-|+...+....++.+
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-----~~s~vv~D~Kge~~~~t~~~r~~~G   49 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-----PGSVVVLDPKGENFELTSEHRRALG   49 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-----CCCEEEEccchhHHHHHHHHHHHcC
Confidence            689999999999999998877543     2348888899999988887776654

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.85  E-value=0.074  Score=52.70  Aligned_cols=21  Identities=29%  Similarity=0.344  Sum_probs=16.8

Q ss_pred             CcEEEEccCCCCceehhHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      +.+++.||.|+|||.++.+-+
T Consensus        41 ha~Lf~GP~GtGKTTlAriLA   61 (484)
T PRK14956         41 HAYIFFGPRGVGKTTIARILA   61 (484)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            447999999999998776533

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=94.84  E-value=0.042  Score=56.31  Aligned_cols=52  Identities=17%  Similarity=0.132  Sum_probs=43.9

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      ..++++.||||||||..+++|-+.....     -++|+=|--|+...+....++++.
T Consensus       158 ~~hvLviapTgSGKg~g~VIPnLL~~~~-----S~VV~DpKGEl~~~Ta~~R~~~G~  209 (606)
T PRK13897        158 FQHALLFAPTGSGKGVGFVIPNLLFWED-----SVVVHDIKLENYELTSGWREKQGQ  209 (606)
T ss_pred             CceEEEEcCCCCCcceEEehhhHHhCCC-----CEEEEeCcHHHHHHHHHHHHHCCC
Confidence            5799999999999999999999876532     388888999999999888887653

>PRK06921 hypothetical protein; Provisional

Probab=94.81  E-value=0.077  Score=48.85  Aligned_cols=45  Identities=20%  Similarity=0.197  Sum_probs=27.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      +.++++.|++|+|||.... ++...+... .+..++++. ..++..++
T Consensus       117 ~~~l~l~G~~G~GKThLa~-aia~~l~~~-~g~~v~y~~-~~~l~~~l  161 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLT-AAANELMRK-KGVPVLYFP-FVEGFGDL  161 (266)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHhhh-cCceEEEEE-HHHHHHHH
Confidence            6889999999999996543 344444331 134455554 44444443

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=94.77  E-value=0.15  Score=48.24  Aligned_cols=41  Identities=20%  Similarity=0.362  Sum_probs=24.7

Q ss_pred             CCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEe
Q psy11867        244 LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSA  286 (399)
Q Consensus       244 ~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SA  286 (399)
                      ....++++|||||.|..  .......+.+..-+.+..+++.+-
T Consensus       107 ~~~~kviiidead~mt~--~A~nallk~lEep~~~~~~il~~n  147 (325)
T COG0470         107 EGGYKVVIIDEADKLTE--DAANALLKTLEEPPKNTRFILITN  147 (325)
T ss_pred             CCCceEEEeCcHHHHhH--HHHHHHHHHhccCCCCeEEEEEcC
Confidence            36788999999999964  233333344444444555555443

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=94.74  E-value=0.13  Score=48.50  Aligned_cols=39  Identities=26%  Similarity=0.191  Sum_probs=29.3

Q ss_pred             CCCChHHHHHHhhhhhcC----C-CCcEEEEccCCCCceehhHH
Q psy11867        123 FYAPSKIQETALPTLLAD----P-PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~----~-g~~vi~~a~TGsGKT~~~~l  161 (399)
                      +..++|+|..++..+...    . ++-+++.||.|.||+..+..
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~   45 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALA   45 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHH
Confidence            356789999999887642    1 33589999999999976544

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

Probab=94.65  E-value=0.039  Score=55.33  Aligned_cols=50  Identities=22%  Similarity=0.323  Sum_probs=40.7

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      .|+++.||||||||..+++|.+-....     -++|.-|--||...+...+++.+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~~~~-----s~iV~D~KgEl~~~t~~~r~~~G   94 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLNYPG-----SMIVTDPKGELYEKTAGYRKKRG   94 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHhccC-----CEEEEECCCcHHHHHHHHHHHCC
Confidence            489999999999999999998743221     47888899999988888777765

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

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=94.56  E-value=0.35  Score=43.50  Aligned_cols=53  Identities=11%  Similarity=0.074  Sum_probs=35.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      |.-+++.+++|+|||...+-.+...+.   .+.++++++ +.+-..+..+.+..++.
T Consensus        24 g~~~~i~G~~G~GKTtl~~~~~~~~~~---~g~~~~yi~-~e~~~~~~~~~~~~~g~   76 (230)
T PRK08533         24 GSLILIEGDESTGKSILSQRLAYGFLQ---NGYSVSYVS-TQLTTTEFIKQMMSLGY   76 (230)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHh---CCCcEEEEe-CCCCHHHHHHHHHHhCC
Confidence            689999999999999765433343333   235588888 44444666666666543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.51  E-value=0.17  Score=51.07  Aligned_cols=39  Identities=18%  Similarity=0.438  Sum_probs=24.9

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      .+.+++||||+|+|... .+ ..+.+.+...|+.+.+|+.+
T Consensus       118 ~~~kV~iIDE~~~ls~~-a~-naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGH-SF-NALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHH-HH-HHHHHHHhccCCCeEEEEEE
Confidence            46789999999998542 22 33344555555666666644

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=94.51  E-value=0.068  Score=51.55  Aligned_cols=42  Identities=10%  Similarity=0.233  Sum_probs=25.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      +..+++++|||||||.. +-.++..+.......+++.+=-..|
T Consensus       149 ~GlilI~G~TGSGKTT~-l~al~~~i~~~~~~~~IvtiEdp~E  190 (372)
T TIGR02525       149 AGLGLICGETGSGKSTL-AASIYQHCGETYPDRKIVTYEDPIE  190 (372)
T ss_pred             CCEEEEECCCCCCHHHH-HHHHHHHHHhcCCCceEEEEecCch
Confidence            46899999999999964 3455555543222334554433333

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).

>PRK09183 transposase/IS protein; Provisional

Probab=94.51  E-value=0.22  Score=45.69  Aligned_cols=44  Identities=23%  Similarity=0.222  Sum_probs=26.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      +.++++.||+|+|||.....-......   .+..++++ +..+|..++
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a~~---~G~~v~~~-~~~~l~~~l  145 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEAVR---AGIKVRFT-TAADLLLQL  145 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHH---cCCeEEEE-eHHHHHHHH
Confidence            799999999999999655432222222   23345554 334554433

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

Probab=94.48  E-value=0.1  Score=49.84  Aligned_cols=48  Identities=23%  Similarity=0.248  Sum_probs=29.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      -.++|+.+|+|+|||..+-+-.-      ..+....-+..+..=+.++.+.+++
T Consensus        48 l~SmIl~GPPG~GKTTlA~liA~------~~~~~f~~~sAv~~gvkdlr~i~e~   95 (436)
T COG2256          48 LHSMILWGPPGTGKTTLARLIAG------TTNAAFEALSAVTSGVKDLREIIEE   95 (436)
T ss_pred             CceeEEECCCCCCHHHHHHHHHH------hhCCceEEeccccccHHHHHHHHHH
Confidence            36899999999999976644221      1222355556665555555554443

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=94.43  E-value=0.062  Score=55.78  Aligned_cols=52  Identities=15%  Similarity=0.154  Sum_probs=42.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      ..|+++.||||||||..+++|-+....     ..++|+=|--|+...+....++.+.
T Consensus       139 ~~hvlviApTgSGKgvg~VIPnLL~~~-----gS~VV~DpKGE~~~~Ta~~R~~~G~  190 (670)
T PRK13850        139 QPHSLVVAPTRAGKGVGVVIPTLLTFK-----GSVIALDVKGELFELTSRARKASGD  190 (670)
T ss_pred             CceEEEEecCCCCceeeehHhHHhcCC-----CCEEEEeCCchHHHHHHHHHHhCCC
Confidence            569999999999999999999876543     2488888999998888777776543

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.39  E-value=0.18  Score=53.61  Aligned_cols=44  Identities=16%  Similarity=0.355  Sum_probs=26.1

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChh
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE  291 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~  291 (399)
                      .+.+++||||||+|..  .....+.+++..-+..+.+|+. .|-+..
T Consensus       118 gk~KViIIDEAh~LT~--eAqNALLKtLEEPP~~vrFILa-TTe~~k  161 (944)
T PRK14949        118 GRFKVYLIDEVHMLSR--SSFNALLKTLEEPPEHVKFLLA-TTDPQK  161 (944)
T ss_pred             CCcEEEEEechHhcCH--HHHHHHHHHHhccCCCeEEEEE-CCCchh
Confidence            4678999999999943  2333334444444455655554 454433

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=94.38  E-value=0.26  Score=48.14  Aligned_cols=37  Identities=19%  Similarity=0.345  Sum_probs=22.9

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEE
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCL  179 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil  179 (399)
                      +.++++.||+|+|||...- .++..+........++++
T Consensus        55 ~~~~lI~G~~GtGKT~l~~-~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         55 PLNVLIYGPPGTGKTTTVK-KVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHhcCCcEEEEE
Confidence            5789999999999997643 334433322222334444

>PF05729 NACHT: NACHT domain

Probab=94.38  E-value=0.48  Score=39.55  Aligned_cols=40  Identities=18%  Similarity=0.324  Sum_probs=24.3

Q ss_pred             EEEEechhhHhhcCC------chHHHHHHHHh-CCCCCcEEEEEeeC
Q psy11867        249 VFVLDEADVMIATQG------HQDFSIRIQKR-LPSDCQIMLFSATY  288 (399)
Q Consensus       249 ~lViDEah~l~~~~~------~~~~~~~i~~~-l~~~~q~l~~SAT~  288 (399)
                      ++|||-+|.+.....      ..+.+..++.. ++++.++++.|.+.
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~  130 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPR  130 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCC
Confidence            599999999865322      22334344444 45677777766653

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.36  E-value=0.16  Score=52.14  Aligned_cols=39  Identities=13%  Similarity=0.381  Sum_probs=23.9

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      .+.+++||||+|+|...  ....+..+++..+....+|+.+
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            45689999999998532  2333444555545555555543

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.34  E-value=0.18  Score=51.56  Aligned_cols=44  Identities=18%  Similarity=0.351  Sum_probs=26.5

Q ss_pred             CCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCCh
Q psy11867        244 LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDK  290 (399)
Q Consensus       244 ~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~  290 (399)
                      ....+++||||+|+|...  ....+...+...+..+.+|+.+ |-+.
T Consensus       116 ~~~~KVvIIDEah~Lt~~--A~NALLK~LEEpp~~~~fIL~t-te~~  159 (584)
T PRK14952        116 QSRYRIFIVDEAHMVTTA--GFNALLKIVEEPPEHLIFIFAT-TEPE  159 (584)
T ss_pred             cCCceEEEEECCCcCCHH--HHHHHHHHHhcCCCCeEEEEEe-CChH
Confidence            356789999999998542  2333344555545555555544 5333

>PRK13342 recombination factor protein RarA; Reviewed

Probab=94.24  E-value=0.54  Score=46.29  Aligned_cols=19  Identities=37%  Similarity=0.382  Sum_probs=15.9

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      ..++++.||+|+|||..+.
T Consensus        36 ~~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         36 LSSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4589999999999996554

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.17  E-value=0.42  Score=42.79  Aligned_cols=52  Identities=19%  Similarity=0.151  Sum_probs=33.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      |..+++.+++|+|||...+.-+...+..   +..+++++- .+...++.+.++.++
T Consensus        20 G~~~~i~G~~G~GKT~l~~~~~~~~~~~---g~~~~~is~-e~~~~~i~~~~~~~g   71 (229)
T TIGR03881        20 GFFVAVTGEPGTGKTIFCLHFAYKGLRD---GDPVIYVTT-EESRESIIRQAAQFG   71 (229)
T ss_pred             CeEEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEEc-cCCHHHHHHHHHHhC
Confidence            7899999999999997654434444432   335777764 444556666666554

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.

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=94.16  E-value=0.24  Score=45.96  Aligned_cols=114  Identities=17%  Similarity=0.154  Sum_probs=57.9

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCC-C---CCCCeEEEEeCcHHHHHHHHHHH-HHHhccCCCcEEEEEEcCchhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNP-S---IQEPQVLCLAPTYELAIQIGEVV-AKMGKHITDLSVRYAVRGENLER  216 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~-~---~~~~~~lil~Pt~~La~Q~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  216 (399)
                      -.++++.|+||-|||...---.-.+-.. .   ..-|.+++-+|...-....|..+ ..++..+..        ..    
T Consensus        61 mp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~--------~~----  128 (302)
T PF05621_consen   61 MPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRP--------RD----  128 (302)
T ss_pred             CCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcccCC--------CC----
Confidence            3689999999999996432111111100 0   11245566667666555555433 333322210        00    


Q ss_pred             hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCch--HHHHHHHHhCCCCCcE
Q psy11867        217 NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ--DFSIRIQKRLPSDCQI  281 (399)
Q Consensus       217 ~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~--~~~~~i~~~l~~~~q~  281 (399)
                                 +...+.....  ..+.--+++++||||.|.++.. ...  ......++.+.+..++
T Consensus       129 -----------~~~~~~~~~~--~llr~~~vrmLIIDE~H~lLaG-s~~~qr~~Ln~LK~L~NeL~i  181 (302)
T PF05621_consen  129 -----------RVAKLEQQVL--RLLRRLGVRMLIIDEFHNLLAG-SYRKQREFLNALKFLGNELQI  181 (302)
T ss_pred             -----------CHHHHHHHHH--HHHHHcCCcEEEeechHHHhcc-cHHHHHHHHHHHHHHhhccCC
Confidence                       1111111100  1222347889999999998752 333  2344566777666553

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK14873 primosome assembly protein PriA; Provisional

Probab=94.13  E-value=0.14  Score=53.22  Aligned_cols=71  Identities=13%  Similarity=0.139  Sum_probs=59.4

Q ss_pred             hhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHC-C-CeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKE-G-LNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~-g-~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.|.+.+..++...  .++++||.++....+.++.+.|+.. | ..++.+|++++..+|.+...+.++|+.+|+|
T Consensus       171 SGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IVi  245 (665)
T PRK14873        171 EDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVV  245 (665)
T ss_pred             CcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEE
Confidence            35666666665443  2458999999999999999999875 4 6799999999999999999999999999875

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=94.12  E-value=0.43  Score=46.84  Aligned_cols=19  Identities=26%  Similarity=0.392  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.-++++|++|+|||....
T Consensus       100 ~~vi~lvG~~GvGKTTtaa  118 (429)
T TIGR01425       100 QNVIMFVGLQGSGKTTTCT  118 (429)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4567899999999986544

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.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.10  E-value=0.34  Score=47.28  Aligned_cols=55  Identities=9%  Similarity=0.069  Sum_probs=29.1

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCC---CCCcEEEEEeeCCh-hHHHHHHhh
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLP---SDCQIMLFSATYDK-EVMEFAQDM  299 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~---~~~q~l~~SAT~~~-~v~~~~~~~  299 (399)
                      .+.++++||=+-+..........+..+.....   +.-.++.+|||... .+...++.+
T Consensus       298 ~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f  356 (432)
T PRK12724        298 DGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAY  356 (432)
T ss_pred             CCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHh
Confidence            45678888876554211112222233333321   22356788999887 455555544

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=94.08  E-value=0.37  Score=45.46  Aligned_cols=39  Identities=18%  Similarity=0.270  Sum_probs=24.8

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ..+++||||+|.+... .....+..++...+..+++++.|
T Consensus       100 ~~~vliiDe~d~l~~~-~~~~~L~~~le~~~~~~~~Ilt~  138 (316)
T PHA02544        100 GGKVIIIDEFDRLGLA-DAQRHLRSFMEAYSKNCSFIITA  138 (316)
T ss_pred             CCeEEEEECcccccCH-HHHHHHHHHHHhcCCCceEEEEc
Confidence            4579999999998322 23344555666666667666544

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=94.04  E-value=0.15  Score=54.12  Aligned_cols=67  Identities=18%  Similarity=0.135  Sum_probs=53.6

Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      ...|+++||..|..-+.. +.+++..+..+||||||+..+. ....++.++.+.-++..-+.+|||...
T Consensus         7 ~ggi~~~T~rIl~~DlL~-~ri~~~~itgiiv~~Ahr~~~~-~~eaFI~rlyr~~n~~gfIkafSdsP~   73 (814)
T TIGR00596         7 EGGIFSITSRILVVDLLT-GIIPPELITGILVLRADRIIES-SQEAFILRLYRQKNKTGFIKAFSDNPE   73 (814)
T ss_pred             cCCEEEEechhhHhHHhc-CCCCHHHccEEEEeeccccccc-ccHHHHHHHHHHhCCCcceEEecCCCc
Confidence            446999999998766544 5688999999999999999764 566667777777777778999999854

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

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

Probab=94.01  E-value=0.065  Score=52.81  Aligned_cols=43  Identities=30%  Similarity=0.423  Sum_probs=34.2

Q ss_pred             hHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC
Q psy11867        127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS  170 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~  170 (399)
                      ++.|...+-.+++.+..=+++.||||||||.. +..++..+...
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            57888888888888777889999999999965 55667766554

>PRK11823 DNA repair protein RadA; Provisional

Probab=93.96  E-value=0.24  Score=49.26  Aligned_cols=88  Identities=17%  Similarity=0.174  Sum_probs=53.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |.-+++.+++|+|||...+--+.....   .+.+++|++- .+-..|+...+++++.....                   
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~---~g~~vlYvs~-Ees~~qi~~ra~rlg~~~~~-------------------  136 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAA---AGGKVLYVSG-EESASQIKLRAERLGLPSDN-------------------  136 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHh---cCCeEEEEEc-cccHHHHHHHHHHcCCChhc-------------------
Confidence            688899999999999755443333322   2456888874 45566777777666533211                   


Q ss_pred             CcEEEeCc---hhHHHhhhccccccCCceeEEEEechhhHhh
Q psy11867        222 EQIIIGTP---GKVLDWGLKYRFFDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       222 ~~IlV~Tp---~~l~~~~~~~~~~~~~~~~~lViDEah~l~~  260 (399)
                        +.+...   ..+...+      .-.+.+++|||+++.+..
T Consensus       137 --l~~~~e~~l~~i~~~i------~~~~~~lVVIDSIq~l~~  170 (446)
T PRK11823        137 --LYLLAETNLEAILATI------EEEKPDLVVIDSIQTMYS  170 (446)
T ss_pred             --EEEeCCCCHHHHHHHH------HhhCCCEEEEechhhhcc
Confidence              222222   2233332      123678999999998753

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=93.86  E-value=0.19  Score=46.65  Aligned_cols=58  Identities=16%  Similarity=0.126  Sum_probs=32.9

Q ss_pred             ccccCCCCHHHHHHHHHc--CCCCChHHHHHHhhhhhc------------CCCCcEEEEccCCCCceehhHH
Q psy11867        104 TFEALHLKPELLKGVYEM--GFYAPSKIQETALPTLLA------------DPPHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~--g~~~p~~iQ~~ai~~ll~------------~~g~~vi~~a~TGsGKT~~~~l  161 (399)
                      .+...++++.+.+.+.+.  .+..+...+......+..            ..++.++++||||+|||....-
T Consensus       142 ~L~~~gv~~~la~~L~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~vi~~vGptGvGKTTt~~k  213 (282)
T TIGR03499       142 RLLRAGVSPELARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLAK  213 (282)
T ss_pred             HHHHCCCCHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHhccCCccccccCCCeEEEEECCCCCCHHHHHHH
Confidence            345567777777776652  222223333322222211            1256888999999999976543

>PRK05973 replicative DNA helicase; Provisional

Probab=93.85  E-value=0.61  Score=42.04  Aligned_cols=52  Identities=10%  Similarity=0.094  Sum_probs=35.9

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      |.-+++.|++|+|||...+--+.+....   +..++|++-- +-..|+.+.+..++
T Consensus        64 Gsl~LIaG~PG~GKT~lalqfa~~~a~~---Ge~vlyfSlE-es~~~i~~R~~s~g  115 (237)
T PRK05973         64 GDLVLLGARPGHGKTLLGLELAVEAMKS---GRTGVFFTLE-YTEQDVRDRLRALG  115 (237)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEEEEe-CCHHHHHHHHHHcC
Confidence            7889999999999997666555544432   4457777633 33567777777764

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.78  E-value=0.18  Score=51.81  Aligned_cols=21  Identities=24%  Similarity=0.355  Sum_probs=16.5

Q ss_pred             CcEEEEccCCCCceehhHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      +-+|++|+.|+|||....+-+
T Consensus        39 HA~LFtGP~GvGKTTLAriLA   59 (700)
T PRK12323         39 HAYLFTGTRGVGKTTLSRILA   59 (700)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            456999999999998766533

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=93.72  E-value=0.41  Score=46.65  Aligned_cols=20  Identities=20%  Similarity=0.395  Sum_probs=16.4

Q ss_pred             CCcEEEEccCCCCceehhHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l  161 (399)
                      ++.+++.||.|+|||..+..
T Consensus        36 ~ha~Lf~Gp~G~GKt~lA~~   55 (394)
T PRK07940         36 THAWLFTGPPGSGRSVAARA   55 (394)
T ss_pred             CeEEEEECCCCCcHHHHHHH
Confidence            46799999999999976554

>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=93.69  E-value=0.087  Score=46.71  Aligned_cols=18  Identities=28%  Similarity=0.368  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCCceehhH
Q psy11867        143 HNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~  160 (399)
                      .++++.||+|.|||..+.
T Consensus        51 ~h~lf~GPPG~GKTTLA~   68 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLAR   68 (233)
T ss_dssp             -EEEEESSTTSSHHHHHH
T ss_pred             ceEEEECCCccchhHHHH
Confidence            589999999999996543

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.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=93.68  E-value=0.24  Score=47.86  Aligned_cols=42  Identities=21%  Similarity=0.317  Sum_probs=25.2

Q ss_pred             CCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEee
Q psy11867        244 LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       244 ~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT  287 (399)
                      ....+++||||+|.|-.  .....+.+.++..+..+.+|++|..
T Consensus       139 ~~~~kVviIDead~m~~--~aanaLLK~LEepp~~~~~IL~t~~  180 (365)
T PRK07471        139 EGGWRVVIVDTADEMNA--NAANALLKVLEEPPARSLFLLVSHA  180 (365)
T ss_pred             cCCCEEEEEechHhcCH--HHHHHHHHHHhcCCCCeEEEEEECC
Confidence            35678999999999843  2333344444544445555555443

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=93.65  E-value=0.42  Score=50.60  Aligned_cols=29  Identities=31%  Similarity=0.346  Sum_probs=20.3

Q ss_pred             HHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867        132 TALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       132 ~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.+..+......|+++.||+|+|||...-
T Consensus       197 ~~i~iL~r~~~~n~LLvGppGvGKT~lae  225 (758)
T PRK11034        197 RAIQVLCRRRKNNPLLVGESGVGKTAIAE  225 (758)
T ss_pred             HHHHHHhccCCCCeEEECCCCCCHHHHHH
Confidence            33344444336799999999999997643

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=93.61  E-value=0.09  Score=50.19  Aligned_cols=50  Identities=24%  Similarity=0.424  Sum_probs=32.6

Q ss_pred             HHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH
Q psy11867        132 TALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA  186 (399)
Q Consensus       132 ~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La  186 (399)
                      ..+..+... +.+++++|+||||||.. +-+++..+..   ..+++.+=.+.||.
T Consensus       153 ~~l~~~v~~-~~nilI~G~tGSGKTTl-l~aLl~~i~~---~~rivtiEd~~El~  202 (344)
T PRK13851        153 AFLHACVVG-RLTMLLCGPTGSGKTTM-SKTLISAIPP---QERLITIEDTLELV  202 (344)
T ss_pred             HHHHHHHHc-CCeEEEECCCCccHHHH-HHHHHcccCC---CCCEEEECCCcccc
Confidence            334444443 79999999999999953 3344544433   34577777887764

>KOG0738|consensus

Probab=93.60  E-value=1.3  Score=42.36  Aligned_cols=65  Identities=18%  Similarity=0.298  Sum_probs=35.2

Q ss_pred             ceeEEEEechhhHhhcCCch---HHHHHH----HHhC-------CCCCcEEEEEee-CChhHHHHHHhhCCCCeEEeccc
Q psy11867        246 KIKVFVLDEADVMIATQGHQ---DFSIRI----QKRL-------PSDCQIMLFSAT-YDKEVMEFAQDMVPNPLIIKLKR  310 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~---~~~~~i----~~~l-------~~~~q~l~~SAT-~~~~v~~~~~~~~~~p~~i~~~~  310 (399)
                      --..+.|||+|-+....|..   +...++    +-.+       .....++.+-|| +|=++.+-.++-+...+.|.+..
T Consensus       304 APStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrRRlEKRIyIPLP~  383 (491)
T KOG0738|consen  304 APSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEALRRRLEKRIYIPLPD  383 (491)
T ss_pred             CCceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHHHHHHhhheeeeCCC
Confidence            45689999999998654322   222222    2111       122335566777 55556665555555555555543

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=93.59  E-value=0.65  Score=43.71  Aligned_cols=38  Identities=24%  Similarity=0.313  Sum_probs=23.9

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ..+++++||+|.+...  ....+..++...+..+.+++.+
T Consensus       102 ~~~vviiDe~~~l~~~--~~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        102 PFKIIFLDEADNLTSD--AQQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             CceEEEEeCcccCCHH--HHHHHHHHHhcCCCCCeEEEEe
Confidence            4679999999998532  2334445555555566666544

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=93.59  E-value=0.28  Score=42.47  Aligned_cols=144  Identities=15%  Similarity=0.086  Sum_probs=77.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH-HHHHHHHHHHhccCCCcEEEEEEcCchhhhhhcc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA-IQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI  220 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La-~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (399)
                      ..++++..++|.|||.+++--++..+..+   .+++++-=.+--. .--...++++    +++.....-.+..+....  
T Consensus        22 ~g~v~v~~g~GkGKtt~a~g~a~ra~g~G---~~V~ivQFlKg~~~~GE~~~l~~l----~~v~~~~~g~~~~~~~~~--   92 (191)
T PRK05986         22 KGLLIVHTGNGKGKSTAAFGMALRAVGHG---KKVGVVQFIKGAWSTGERNLLEFG----GGVEFHVMGTGFTWETQD--   92 (191)
T ss_pred             CCeEEEECCCCCChHHHHHHHHHHHHHCC---CeEEEEEEecCCCccCHHHHHhcC----CCcEEEECCCCCcccCCC--
Confidence            57999999999999999887777666543   3466554222110 0001222221    222222111111111100  


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCc--hHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHh
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGH--QDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQD  298 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~--~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~  298 (399)
                       ..--+......++...  ..+.-..+++||+||+-..+.. ++  .+.+..+++..|...-+|+.--..|+.+.+.+..
T Consensus        93 -~~e~~~~~~~~~~~a~--~~l~~~~ydlvVLDEi~~Al~~-gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie~ADl  168 (191)
T PRK05986         93 -RERDIAAAREGWEEAK--RMLADESYDLVVLDELTYALKY-GYLDVEEVLEALNARPGMQHVVITGRGAPRELIEAADL  168 (191)
T ss_pred             -cHHHHHHHHHHHHHHH--HHHhCCCCCEEEEehhhHHHHC-CCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCch
Confidence             0000011112232211  2333467899999999888764 43  4556677777777777777777777777776644

>TIGR00763 lon ATP-dependent protease La

Probab=93.56  E-value=0.36  Score=51.61  Aligned_cols=18  Identities=22%  Similarity=0.145  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      +..+++.+|+|+|||..+
T Consensus       347 ~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            567999999999999654

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.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.55  E-value=0.47  Score=47.49  Aligned_cols=46  Identities=20%  Similarity=0.308  Sum_probs=29.1

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC-CCCcEEEEccCCCCceehhHHHH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLAD-PPHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~-~g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      ++|+++--.+.+.+.|...               +..+ -++..+++||.|+|||.++.+-+
T Consensus        10 ~~f~dliGQe~vv~~L~~a---------------~~~~ri~ha~Lf~Gp~G~GKTT~ArilA   56 (491)
T PRK14964         10 SSFKDLVGQDVLVRILRNA---------------FTLNKIPQSILLVGASGVGKTTCARIIS   56 (491)
T ss_pred             CCHHHhcCcHHHHHHHHHH---------------HHcCCCCceEEEECCCCccHHHHHHHHH
Confidence            4567665556666655421               1111 14679999999999998765533

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=93.52  E-value=0.13  Score=44.98  Aligned_cols=52  Identities=19%  Similarity=0.296  Sum_probs=25.0

Q ss_pred             ceeEEEEechhhHhhcCCch----HHHHHHHHhCCCC-CcEEEEEeeCChhHHHHHHh
Q psy11867        246 KIKVFVLDEADVMIATQGHQ----DFSIRIQKRLPSD-CQIMLFSATYDKEVMEFAQD  298 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~----~~~~~i~~~l~~~-~q~l~~SAT~~~~v~~~~~~  298 (399)
                      .=.++||||||.+.......    ......+...+.. .-++++|-. +..+...++.
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~-~~~id~~ir~  135 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQS-PSQIDKFIRD  135 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES--GGGB-HHHHC
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCC-HHHHhHHHHH
Confidence            44699999999987654442    1222333333433 445555554 4455555554

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=93.50  E-value=0.11  Score=53.88  Aligned_cols=51  Identities=14%  Similarity=0.146  Sum_probs=41.8

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ..++++.||||||||..+++|-|-....     -+||+=|--|+...+....++.+
T Consensus       144 ~~hvLviApTrSGKgvg~VIPnLL~~~~-----S~VV~D~KGEl~~~Ta~~R~~~G  194 (663)
T PRK13876        144 PEHVLCFAPTRSGKGVGLVVPTLLTWPG-----SAIVHDIKGENWQLTAGFRARFG  194 (663)
T ss_pred             CceEEEEecCCCCcceeEehhhHHhCCC-----CEEEEeCcchHHHHHHHHHHhCC
Confidence            6899999999999999999998865432     37888899999888777766654

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.49  E-value=0.35  Score=48.39  Aligned_cols=19  Identities=37%  Similarity=0.517  Sum_probs=15.8

Q ss_pred             CcEEEEccCCCCceehhHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l  161 (399)
                      +.+++.||+|+|||..+.+
T Consensus        37 ~~~Lf~GPpGtGKTTlA~~   55 (472)
T PRK14962         37 HAYIFAGPRGTGKTTVARI   55 (472)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4579999999999977654

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=93.49  E-value=0.56  Score=43.31  Aligned_cols=36  Identities=25%  Similarity=0.262  Sum_probs=22.9

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA  180 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  180 (399)
                      ++-+++.+++|+|||....--+.....   .+.+++++.
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA~~l~~---~g~~V~li~  107 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLANKLKK---QGKSVLLAA  107 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHh---cCCEEEEEe
Confidence            567788899999999765443333322   234566555

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.49  E-value=0.27  Score=49.62  Aligned_cols=19  Identities=32%  Similarity=0.489  Sum_probs=15.6

Q ss_pred             CcEEEEccCCCCceehhHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l  161 (399)
                      +-+++.||.|+|||.++..
T Consensus        37 ha~Lf~GppGtGKTTlA~~   55 (504)
T PRK14963         37 HAYLFSGPRGVGKTTTARL   55 (504)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4459999999999987654

>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=93.48  E-value=0.89  Score=43.81  Aligned_cols=110  Identities=15%  Similarity=0.208  Sum_probs=62.3

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhcc
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI  220 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (399)
                      .++.+.+.|+.|.|||+..  -++....+...+.|    ++-.+-+.++++.+.++...           ...+      
T Consensus        61 ~~~GlYl~G~vG~GKT~Lm--d~f~~~lp~~~k~R----~HFh~Fm~~vh~~l~~~~~~-----------~~~l------  117 (362)
T PF03969_consen   61 PPKGLYLWGPVGRGKTMLM--DLFYDSLPIKRKRR----VHFHEFMLDVHSRLHQLRGQ-----------DDPL------  117 (362)
T ss_pred             CCceEEEECCCCCchhHHH--HHHHHhCCcccccc----ccccHHHHHHHHHHHHHhCC-----------CccH------
Confidence            3799999999999999643  33333222222223    25567888888877776410           0000      


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC-CCCCcEEEEEeeCChh
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL-PSDCQIMLFSATYDKE  291 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~l~~SAT~~~~  291 (399)
                               ..+.+.+       .+...++.|||.|.- + -+-.-.+.+++..+ ....-++..|-+.|.+
T Consensus       118 ---------~~va~~l-------~~~~~lLcfDEF~V~-D-iaDAmil~rLf~~l~~~gvvlVaTSN~~P~~  171 (362)
T PF03969_consen  118 ---------PQVADEL-------AKESRLLCFDEFQVT-D-IADAMILKRLFEALFKRGVVLVATSNRPPED  171 (362)
T ss_pred             ---------HHHHHHH-------HhcCCEEEEeeeecc-c-hhHHHHHHHHHHHHHHCCCEEEecCCCChHH
Confidence                     0112211       335668999999874 1 12333344555544 3456677777776643

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

>PHA00012 I assembly protein

Probab=93.46  E-value=0.66  Score=43.49  Aligned_cols=26  Identities=15%  Similarity=0.259  Sum_probs=20.4

Q ss_pred             EEEEccCCCCceehhHHHHHHhhCCC
Q psy11867        145 MIAQSQSGTGKTAAFTLTMLSRVNPS  170 (399)
Q Consensus       145 vi~~a~TGsGKT~~~~l~il~~l~~~  170 (399)
                      -++.|..|||||+..+--++..+.++
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~~G   29 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVKG   29 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHcC
Confidence            47889999999998877666666554

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=93.45  E-value=0.12  Score=53.87  Aligned_cols=44  Identities=20%  Similarity=0.302  Sum_probs=27.7

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCC-CCcEEEEccCCCCceehhHH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADP-PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~-g~~vi~~a~TGsGKT~~~~l  161 (399)
                      ++|+++--.+.+++.|...               +-.+. .+-+|++|+.|+|||....+
T Consensus        13 qtFdEVIGQe~Vv~~L~~a---------------L~~gRL~HAyLFtGPpGvGKTTlAri   57 (830)
T PRK07003         13 KDFASLVGQEHVVRALTHA---------------LDGGRLHHAYLFTGTRGVGKTTLSRI   57 (830)
T ss_pred             CcHHHHcCcHHHHHHHHHH---------------HhcCCCCeEEEEECCCCCCHHHHHHH
Confidence            4567665566666666542               11111 24468999999999976654

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=93.44  E-value=0.34  Score=41.94  Aligned_cols=20  Identities=20%  Similarity=0.262  Sum_probs=16.0

Q ss_pred             CCcEEEEccCCCCceehhHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l  161 (399)
                      ++.+++.||.|+|||.....
T Consensus        14 ~~~~L~~G~~G~gkt~~a~~   33 (188)
T TIGR00678        14 AHAYLFAGPEGVGKELLALA   33 (188)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            36689999999999976543

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.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=93.44  E-value=0.25  Score=47.96  Aligned_cols=48  Identities=19%  Similarity=0.233  Sum_probs=30.7

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCC-CCcEEEEEeeCChhHH
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPS-DCQIMLFSATYDKEVM  293 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~-~~q~l~~SAT~~~~v~  293 (399)
                      ++++++||+++.+............++..+.. ..|+++.|...|..+.
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~  223 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELN  223 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhc
Confidence            78899999999986543344444455555543 4466666666665443

>PRK10867 signal recognition particle protein; Provisional

Probab=93.39  E-value=0.7  Score=45.55  Aligned_cols=43  Identities=21%  Similarity=0.167  Sum_probs=25.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe--CcHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA--PTYELA  186 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~--Pt~~La  186 (399)
                      +.-+++++++|+|||....--+......  .+.+++++.  +.|.-+
T Consensus       100 p~vI~~vG~~GsGKTTtaakLA~~l~~~--~G~kV~lV~~D~~R~aa  144 (433)
T PRK10867        100 PTVIMMVGLQGAGKTTTAGKLAKYLKKK--KKKKVLLVAADVYRPAA  144 (433)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHh--cCCcEEEEEccccchHH
Confidence            4668899999999997655433332222  133455554  444443

>TIGR00959 ffh signal recognition particle protein

Probab=93.36  E-value=0.61  Score=45.91  Aligned_cols=23  Identities=22%  Similarity=0.332  Sum_probs=17.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTML  164 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il  164 (399)
                      +.-+++++++|+|||....--+.
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~  121 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAY  121 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHH
Confidence            45788999999999977554333

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.

>TIGR00595 priA primosomal protein N'

Probab=93.33  E-value=0.33  Score=49.10  Aligned_cols=56  Identities=13%  Similarity=0.249  Sum_probs=50.9

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKE-GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~-g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+++||.++++.-+.++++.|++. |..+.++||+++..+|.++..+.++|+.+|+|
T Consensus        25 g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVV   81 (505)
T TIGR00595        25 GKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVI   81 (505)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEE
Confidence            468999999999999999999764 77899999999999999999999999998875

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).

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=93.29  E-value=0.25  Score=47.35  Aligned_cols=39  Identities=18%  Similarity=0.331  Sum_probs=25.3

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ...+++||||||.|..  .....+...++..+.+..++++|
T Consensus       140 g~~rVviIDeAd~l~~--~aanaLLk~LEEpp~~~~fiLit  178 (351)
T PRK09112        140 GNWRIVIIDPADDMNR--NAANAILKTLEEPPARALFILIS  178 (351)
T ss_pred             CCceEEEEEchhhcCH--HHHHHHHHHHhcCCCCceEEEEE
Confidence            4678999999999853  23333445555555556666665

>KOG1016|consensus

Probab=93.25  E-value=0.35  Score=49.85  Aligned_cols=181  Identities=14%  Similarity=0.070  Sum_probs=99.1

Q ss_pred             ccCCCCHHHHHHHHHc---CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        106 EALHLKPELLKGVYEM---GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       106 ~~~~l~~~l~~~l~~~---g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      +++-|-+.|.+.++-.   |+..++.--.+.+...-...|..+|+.-..|-|||+... ....-+.+......+|+|+|.
T Consensus       243 e~iflapqla~v~kPHQiGGiRFlYDN~iESl~rykkSsGFGCILAHSMGLGKTlQVi-sF~diflRhT~AKtVL~ivPi  321 (1387)
T KOG1016|consen  243 EDIFLAPQLAHVLKPHQIGGIRFLYDNTIESLGRYKKSSGFGCILAHSMGLGKTLQVI-SFSDIFLRHTKAKTVLVIVPI  321 (1387)
T ss_pred             cceeehhhhHhhcCccccCcEEEehhhHHHHHhhccccCCcceeeeeccccCceeEEe-ehhHHHhhcCccceEEEEEeh
Confidence            3445778888877632   455555555555555554468899999999999997643 233333344455679999998


Q ss_pred             HHHHHHHHHHHHHHhccC--------CCcEEEEEEcCc-hhhhhh------ccCCcEEEeCchhHHHhhhcc--------
Q psy11867        183 YELAIQIGEVVAKMGKHI--------TDLSVRYAVRGE-NLERNK------KITEQIIIGTPGKVLDWGLKY--------  239 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~--------~~~~~~~~~~~~-~~~~~~------~~~~~IlV~Tp~~l~~~~~~~--------  239 (399)
                      ..|-. ++.++..+...+        ..+.+...-.+. .+....      .....++..-.+++.-+..+.        
T Consensus       322 NTlQN-WlsEfnmWiP~y~sD~~vrpR~F~vf~LnD~~KT~~~Rakvi~~Wv~~GGVlLvGYemfRLL~lk~~~~~grpk  400 (1387)
T KOG1016|consen  322 NTLQN-WLSEFNMWIPKYFSDTGVRPRSFEVFLLNDGVKTFDQRAKVIEQWVQTGGVLLVGYEMFRLLILKTLPKKGRPK  400 (1387)
T ss_pred             HHHHH-HHHHhhhhcCCCcccCCCccceeEEEEecCchhhHHHHHHHHHHHhccCCEEEehHHHHHHHHHhcccccCCcc
Confidence            87743 333344333221        012222222221 111111      112235554455443222210        


Q ss_pred             --------cccc-------------------CCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChh
Q psy11867        240 --------RFFD-------------------LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE  291 (399)
Q Consensus       240 --------~~~~-------------------~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~  291 (399)
                              ..++                   --.-++||+||-|++-   .....+...++.++..+++++....+-+.
T Consensus       401 kt~kr~~~~~i~~d~eD~~qe~~~li~~AL~~PGPDlVICDEGHrIK---N~~A~iS~aLk~IrtrRRiVLTGYPLQNN  476 (1387)
T KOG1016|consen  401 KTLKRISSGFIKDDSEDQRQEAYSLIRSALLEPGPDLVICDEGHRIK---NITAEISMALKAIRTRRRIVLTGYPLQNN  476 (1387)
T ss_pred             ccccccCCcccCCchhhhHHHHHHHHHHHhcCCCCCeEEecCCceec---cchHHHHHHHHHhhhceeEEEeccccccc
Confidence                    0000                   1124799999999984   34444555666777778888877665544

>PRK05580 primosome assembly protein PriA; Validated

Probab=93.24  E-value=0.3  Score=51.29  Aligned_cols=56  Identities=20%  Similarity=0.260  Sum_probs=51.2

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKE-GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~-g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.++||.++++.-+.++++.|++. |..+..+||+++..+|.+.......|+.+|+|
T Consensus       190 g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVV  246 (679)
T PRK05580        190 GKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVI  246 (679)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEE
Confidence            468999999999999999999774 78899999999999999999999999998875

>PRK08939 primosomal protein DnaI; Reviewed

Probab=93.23  E-value=0.31  Score=45.84  Aligned_cols=19  Identities=16%  Similarity=0.247  Sum_probs=16.2

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++++++.|++|+|||....
T Consensus       156 ~~gl~L~G~~G~GKThLa~  174 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLA  174 (306)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5789999999999996544

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

Probab=93.23  E-value=0.078  Score=45.67  Aligned_cols=44  Identities=23%  Similarity=0.215  Sum_probs=26.1

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      ++++++.|++|+|||..+...+-..+..   +..+++ ++..+|...+
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~---g~~v~f-~~~~~L~~~l   90 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRK---GYSVLF-ITASDLLDEL   90 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEE-EEHHHHHHHH
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccC---CcceeE-eecCceeccc
Confidence            7999999999999997765433333332   233444 4555666544

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.

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=93.20  E-value=0.13  Score=52.89  Aligned_cols=51  Identities=25%  Similarity=0.333  Sum_probs=41.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ..|+++.||||||||..+++|-+-...     .-++|+=|.-|+...+...-++.+
T Consensus       211 ~~H~lv~ApTgsGKgvg~VIPnLL~~~-----gS~VV~DpKgE~~~~Ta~~R~~~G  261 (623)
T TIGR02767       211 STHMIFFAGSGGFKTTSVVVPTALKYG-----GPLVCLDPSTEVAPMVCEHRRQAG  261 (623)
T ss_pred             CceEEEEeCCCCCccceeehhhhhcCC-----CCEEEEEChHHHHHHHHHHHHHcC
Confidence            579999999999999999999764332     238888899999888877766665

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>KOG1133|consensus

Probab=93.20  E-value=0.077  Score=53.77  Aligned_cols=44  Identities=30%  Similarity=0.387  Sum_probs=35.4

Q ss_pred             CCChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHHhh
Q psy11867        124 YAPSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLSRV  167 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~~l  167 (399)
                      .+|+.||.+.+..+.+-  .|+--|..+|||+|||+.-+-..+..+
T Consensus        14 y~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL   59 (821)
T KOG1133|consen   14 YTPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWL   59 (821)
T ss_pred             CCchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHH
Confidence            47999999988777431  388899999999999998877776654

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=93.19  E-value=0.4  Score=49.35  Aligned_cols=40  Identities=13%  Similarity=0.358  Sum_probs=25.1

Q ss_pred             CCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        244 LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       244 ~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ....+++||||+|.|...  ....+...++..+..+.+|+.+
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            456789999999998532  2233334445555566666654

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=93.19  E-value=0.24  Score=52.58  Aligned_cols=68  Identities=21%  Similarity=0.309  Sum_probs=54.9

Q ss_pred             HHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCC-----CeEEE-EcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        332 FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEG-----LNVGL-LSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       332 ~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g-----~~v~~-lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +-.+..++-...++++.+.++|.--+.+.++.|.+.+     ..+.+ |||.|+.++++.++++|.+|..+|||
T Consensus       113 fg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIli  186 (1187)
T COG1110         113 FGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILI  186 (1187)
T ss_pred             HHHHHHHHHHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEE
Confidence            3445555555556889999999999999998887752     44433 99999999999999999999999986

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=93.18  E-value=0.38  Score=50.64  Aligned_cols=43  Identities=23%  Similarity=0.333  Sum_probs=26.0

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHH
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVME  294 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~  294 (399)
                      +..++||||+|++...  ..+   .++..+ .+.++++++||-++....
T Consensus       109 ~~~IL~IDEIh~Ln~~--qQd---aLL~~l-E~g~IiLI~aTTenp~~~  151 (725)
T PRK13341        109 KRTILFIDEVHRFNKA--QQD---ALLPWV-ENGTITLIGATTENPYFE  151 (725)
T ss_pred             CceEEEEeChhhCCHH--HHH---HHHHHh-cCceEEEEEecCCChHhh
Confidence            4568999999998532  222   233333 346678888885554333

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=93.17  E-value=0.67  Score=49.20  Aligned_cols=22  Identities=27%  Similarity=0.323  Sum_probs=17.6

Q ss_pred             cCCCCcEEEEccCCCCceehhH
Q psy11867        139 ADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       139 ~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .....|+++.||+|+|||...-
T Consensus       200 ~~~~~n~lL~G~pG~GKT~l~~  221 (731)
T TIGR02639       200 RRKKNNPLLVGEPGVGKTAIAE  221 (731)
T ss_pred             cCCCCceEEECCCCCCHHHHHH
Confidence            3346799999999999997653

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=93.12  E-value=0.13  Score=53.62  Aligned_cols=71  Identities=20%  Similarity=0.250  Sum_probs=59.7

Q ss_pred             hhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKE-GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~-g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.|.+.+.+++...  .++++||.++.+....++...|+.. |.+++++|+++++.+|.....+.+.|+.+|++
T Consensus       228 SGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVI  301 (730)
T COG1198         228 SGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVI  301 (730)
T ss_pred             CcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEE
Confidence            55666666665443  2358999999999999888888776 89999999999999999999999999999874

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=93.12  E-value=0.14  Score=49.21  Aligned_cols=27  Identities=11%  Similarity=0.316  Sum_probs=20.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNP  169 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~  169 (399)
                      +..++++||||||||... -.++..+..
T Consensus       134 ~glilI~GpTGSGKTTtL-~aLl~~i~~  160 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLL-AAIIRELAE  160 (358)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHhh
Confidence            689999999999999653 345555543

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.

>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=93.11  E-value=0.57  Score=39.86  Aligned_cols=55  Identities=13%  Similarity=0.232  Sum_probs=27.9

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhh
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDM  299 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~  299 (399)
                      ...+++|+|....+.........+..+........-++.++|....+..+.+..+
T Consensus        81 ~~~d~viiDt~g~~~~~~~~l~~l~~l~~~~~~~~~~lVv~~~~~~~~~~~~~~~  135 (173)
T cd03115          81 ENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTGQDAVNQAKAF  135 (173)
T ss_pred             CCCCEEEEECcccchhhHHHHHHHHHHHhhcCCCeEEEEEECCCChHHHHHHHHH
Confidence            4667889999877521111122222222222344456677776555555555444

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.

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=93.10  E-value=0.3  Score=50.56  Aligned_cols=39  Identities=18%  Similarity=0.404  Sum_probs=24.0

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      .+.+++||||+|.|...  ....+.+.+...+..+.+|+.+
T Consensus       118 gk~KVIIIDEad~Ls~~--A~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKS--AFNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             CCcEEEEEECccccCHH--HHHHHHHHHHhCCCCcEEEEEe
Confidence            46789999999987532  2223344444445566666554

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

Probab=93.08  E-value=0.18  Score=46.43  Aligned_cols=55  Identities=22%  Similarity=0.378  Sum_probs=32.4

Q ss_pred             hHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      .+-|.+.+..++..++..++++++||||||... ..++..+..  ...+++.+=-..|
T Consensus        65 ~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~~--~~~~iitiEdp~E  119 (264)
T cd01129          65 KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELNT--PEKNIITVEDPVE  119 (264)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhCC--CCCeEEEECCCce
Confidence            344555665555543567999999999999653 345555533  2223444443333

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.

>KOG0733|consensus

Probab=93.04  E-value=0.77  Score=46.38  Aligned_cols=176  Identities=16%  Similarity=0.206  Sum_probs=91.0

Q ss_pred             ccccccCCCCHHHHHHHHHc---CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEE
Q psy11867        102 VKTFEALHLKPELLKGVYEM---GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLC  178 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~---g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~li  178 (399)
                      --+|++.|--..+...|.-.   -+++|--++.-.+.     .+..+++++|+|+|||+.+-..+    ++  .      
T Consensus       507 dVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~-----~PsGvLL~GPPGCGKTLlAKAVA----NE--a------  569 (802)
T KOG0733|consen  507 DVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGID-----APSGVLLCGPPGCGKTLLAKAVA----NE--A------  569 (802)
T ss_pred             CCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCC-----CCCceEEeCCCCccHHHHHHHHh----hh--c------
Confidence            45788888777777766532   23344333333332     26889999999999997542111    00  0      


Q ss_pred             EeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        179 LAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       179 l~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                                             +.+...+-|...+.        -.|+--++-...+...  -.-+.-.++.|||.|.|
T Consensus       570 -----------------------g~NFisVKGPELlN--------kYVGESErAVR~vFqR--AR~saPCVIFFDEiDaL  616 (802)
T KOG0733|consen  570 -----------------------GANFISVKGPELLN--------KYVGESERAVRQVFQR--ARASAPCVIFFDEIDAL  616 (802)
T ss_pred             -----------------------cCceEeecCHHHHH--------HHhhhHHHHHHHHHHH--hhcCCCeEEEecchhhc
Confidence                                   11111111211111        1122222322221110  11335578999999998


Q ss_pred             hhcCCc--h----HHHHHHHHhC---CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChh
Q psy11867        259 IATQGH--Q----DFSIRIQKRL---PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNID  329 (399)
Q Consensus       259 ~~~~~~--~----~~~~~i~~~l---~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~  329 (399)
                      ....+.  .    ..+..++..|   .....+.++-||-.+++.        ||-..+-++-+      +..|+-.++.+
T Consensus       617 ~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiI--------DpAiLRPGRlD------k~LyV~lPn~~  682 (802)
T KOG0733|consen  617 VPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDII--------DPAILRPGRLD------KLLYVGLPNAE  682 (802)
T ss_pred             CcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCccc--------chhhcCCCccC------ceeeecCCCHH
Confidence            643221  1    2233333333   345678888999766533        33333333222      23566777778


Q ss_pred             hHHHHHHHHhcc
Q psy11867        330 EKFEAVSNIYGV  341 (399)
Q Consensus       330 ~k~~~l~~ll~~  341 (399)
                      ++...|..+.+.
T Consensus       683 eR~~ILK~~tkn  694 (802)
T KOG0733|consen  683 ERVAILKTITKN  694 (802)
T ss_pred             HHHHHHHHHhcc
Confidence            888888777764

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=93.03  E-value=0.14  Score=53.03  Aligned_cols=51  Identities=20%  Similarity=0.214  Sum_probs=40.8

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ..|+++.||||+|||..+++|-+-...     .-++|+=|..|+...+....++.+
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL~~~-----gS~VV~DpKgEl~~~Ta~~R~~~G  274 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTALKWG-----GPLVVLDPSTEVAPMVSEHRRDAG  274 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhhcCC-----CCEEEEeCcHHHHHHHHHHHHHCC
Confidence            579999999999999999999864322     237777799999888887776664

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=93.01  E-value=0.54  Score=44.64  Aligned_cols=37  Identities=16%  Similarity=0.231  Sum_probs=26.5

Q ss_pred             hHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhHHHH
Q psy11867        127 SKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      +|+|...+..+...   -++-+++.||.|.|||..+..-+
T Consensus         3 yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~~a   42 (325)
T PRK08699          3 YPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARFAA   42 (325)
T ss_pred             CCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHHHH
Confidence            57777777776632   13568899999999997765433

>PRK04195 replication factor C large subunit; Provisional

Probab=92.86  E-value=0.34  Score=48.78  Aligned_cols=46  Identities=20%  Similarity=0.274  Sum_probs=28.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC-CCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLAD-PPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~-~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+|+++-.++...+.|...            +.....+ +.+.+++.||+|+|||....
T Consensus        11 ~~l~dlvg~~~~~~~l~~~------------l~~~~~g~~~~~lLL~GppG~GKTtla~   57 (482)
T PRK04195         11 KTLSDVVGNEKAKEQLREW------------IESWLKGKPKKALLLYGPPGVGKTSLAH   57 (482)
T ss_pred             CCHHHhcCCHHHHHHHHHH------------HHHHhcCCCCCeEEEECCCCCCHHHHHH
Confidence            4567776666666666542            0011111 25789999999999996543

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.85  E-value=0.52  Score=47.00  Aligned_cols=20  Identities=20%  Similarity=0.194  Sum_probs=16.6

Q ss_pred             CCcEEEEccCCCCceehhHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l  161 (399)
                      |+-+.+.||||+|||.....
T Consensus       256 g~Vi~LvGpnGvGKTTTiaK  275 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAK  275 (484)
T ss_pred             CcEEEEECCCCccHHHHHHH
Confidence            56788999999999987654

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=92.78  E-value=0.31  Score=49.26  Aligned_cols=40  Identities=18%  Similarity=0.421  Sum_probs=26.0

Q ss_pred             CCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        244 LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       244 ~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ....+++||||||+|..  .....+.+.+...|+.+.+++++
T Consensus       115 ~~~~KVvIIDEad~Lt~--~A~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        115 MARFKIFIIDEVHMLTK--EAFNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             cCCeEEEEEECcccCCH--HHHHHHHHHHhhcCCceEEEEEE
Confidence            35678999999999854  23333445555556666666655

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.77  E-value=0.5  Score=48.00  Aligned_cols=39  Identities=15%  Similarity=0.339  Sum_probs=25.0

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ...+++||||+|+|..  .....+...+...+....+|+.+
T Consensus       118 g~~kViIIDEa~~ls~--~a~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        118 GRYKVYLIDEVHMLSK--QSFNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             CCcEEEEEechhhccH--HHHHHHHHHHhcCCCCceEEEEE
Confidence            4668999999999854  23334445555555566666544

>PHA00729 NTP-binding motif containing protein

Probab=92.62  E-value=0.87  Score=40.61  Aligned_cols=74  Identities=8%  Similarity=0.079  Sum_probs=36.2

Q ss_pred             EEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCch----HHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHh
Q psy11867        224 IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ----DFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQD  298 (399)
Q Consensus       224 IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~----~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~  298 (399)
                      .++.+...++..+.... -.....+++||||+=.-.....+.    .....+...+.+.++++.+...-+..+...++.
T Consensus        61 ~~fid~~~Ll~~L~~a~-~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr~  138 (226)
T PHA00729         61 SYFFELPDALEKIQDAI-DNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALIRTRVSAVIFTTPSPEDLAFYLRE  138 (226)
T ss_pred             EEEEEHHHHHHHHHHHH-hcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHHHhhCcEEEEecCCHHHHHHHHHh
Confidence            44444455555432211 112345789999943222111111    111123333445677788877766666666655

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.61  E-value=0.31  Score=50.23  Aligned_cols=21  Identities=24%  Similarity=0.376  Sum_probs=16.6

Q ss_pred             CcEEEEccCCCCceehhHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      +-++++||.|+|||.++.+-+
T Consensus        39 ha~Lf~Gp~GvGKTtlAr~lA   59 (618)
T PRK14951         39 HAYLFTGTRGVGKTTVSRILA   59 (618)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            445999999999998776543

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=92.59  E-value=0.16  Score=52.76  Aligned_cols=49  Identities=14%  Similarity=0.114  Sum_probs=39.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      ..|+++.||||||||..+++|-+...     +..++|+=|--|+..-+....++
T Consensus       175 ~~HvlviapTgSGKgvg~ViPnLL~~-----~~S~VV~D~KGE~~~~Tag~R~~  223 (636)
T PRK13880        175 PEHVLTYAPTRSGKGVGLVVPTLLSW-----GHSSVITDLKGELWALTAGWRQK  223 (636)
T ss_pred             CceEEEEecCCCCCceEEEccchhhC-----CCCEEEEeCcHHHHHHHHHHHHH
Confidence            58999999999999999999988643     23488888999998766665543

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=92.58  E-value=0.16  Score=48.33  Aligned_cols=50  Identities=20%  Similarity=0.269  Sum_probs=31.7

Q ss_pred             HHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH
Q psy11867        132 TALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA  186 (399)
Q Consensus       132 ~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La  186 (399)
                      ..+..+... +.+++++|+||||||.. +-+++..+..   ..+++.+=-+.||.
T Consensus       151 ~~L~~~v~~-~~nili~G~tgSGKTTl-l~aL~~~ip~---~~ri~tiEd~~El~  200 (332)
T PRK13900        151 EFLEHAVIS-KKNIIISGGTSTGKTTF-TNAALREIPA---IERLITVEDAREIV  200 (332)
T ss_pred             HHHHHHHHc-CCcEEEECCCCCCHHHH-HHHHHhhCCC---CCeEEEecCCCccc
Confidence            334444444 79999999999999953 3455555533   34566655555554

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.58  E-value=0.59  Score=45.16  Aligned_cols=19  Identities=32%  Similarity=0.473  Sum_probs=15.5

Q ss_pred             CcEEEEccCCCCceehhHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l  161 (399)
                      +.+++.||.|+|||..+..
T Consensus        39 h~~L~~Gp~G~GKTtla~~   57 (363)
T PRK14961         39 HAWLLSGTRGVGKTTIARL   57 (363)
T ss_pred             eEEEEecCCCCCHHHHHHH
Confidence            4468999999999977654

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

Probab=92.53  E-value=0.97  Score=45.23  Aligned_cols=148  Identities=14%  Similarity=0.054  Sum_probs=85.4

Q ss_pred             CChHHHHHHhhhhhc----CCC----CcEEEEccCCCCceehhH-HHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLA----DPP----HNMIAQSQSGTGKTAAFT-LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~----~~g----~~vi~~a~TGsGKT~~~~-l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      .+-|+|.-.+-.++-    +.|    .-.+|..|-|-|||.... +.....+.....+....|++|+.+-+.+....++.
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F~~ar~  140 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSFNPARD  140 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhhHHHHH
Confidence            567889988888861    112    356888899999995443 33333333335667799999999999988888887


Q ss_pred             HhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHh----hhccccccCCceeEEEEechhhHhhcCCchHHHHHH
Q psy11867        196 MGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDW----GLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRI  271 (399)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~----~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i  271 (399)
                      +......+...           .....+....+.+.....    .......+-.+..+.|+||.|.....   .+.+..+
T Consensus       141 mv~~~~~l~~~-----------~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~---~~~~~~~  206 (546)
T COG4626         141 MVKRDDDLRDL-----------CNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQ---EDMYSEA  206 (546)
T ss_pred             HHHhCcchhhh-----------hccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCH---HHHHHHH
Confidence            76554321111           111111111121111111    01223344557789999999997532   1445555


Q ss_pred             HHhC--CCCCcEEEEEe
Q psy11867        272 QKRL--PSDCQIMLFSA  286 (399)
Q Consensus       272 ~~~l--~~~~q~l~~SA  286 (399)
                      ..-+  .++.+++..|.
T Consensus       207 ~~g~~ar~~~l~~~ITT  223 (546)
T COG4626         207 KGGLGARPEGLVVYITT  223 (546)
T ss_pred             HhhhccCcCceEEEEec
Confidence            4444  34566666655

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=92.37  E-value=0.49  Score=48.47  Aligned_cols=46  Identities=24%  Similarity=0.304  Sum_probs=28.5

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC-CCCcEEEEccCCCCceehhHHHH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLAD-PPHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~-~g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      .+|+++--.+.+.+.|...               +..+ .++-.+++||.|+|||.++-+-+
T Consensus        13 ~~f~~viGq~~v~~~L~~~---------------i~~~~~~hayLf~Gp~GtGKTt~Ak~lA   59 (559)
T PRK05563         13 QTFEDVVGQEHITKTLKNA---------------IKQGKISHAYLFSGPRGTGKTSAAKIFA   59 (559)
T ss_pred             CcHHhccCcHHHHHHHHHH---------------HHcCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            4566665556666555432               1111 14567889999999998776543

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=92.36  E-value=0.82  Score=43.30  Aligned_cols=37  Identities=11%  Similarity=0.159  Sum_probs=25.2

Q ss_pred             hHHHHHHhhhhhcC-----CCCcEEEEccCCCCceehhHHHH
Q psy11867        127 SKIQETALPTLLAD-----PPHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~-----~g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      +|+|...+..+.+.     -++-.++.||.|.||+..+..-+
T Consensus         4 yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A   45 (325)
T PRK06871          4 YPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALA   45 (325)
T ss_pred             CcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHH
Confidence            56777777666432     13567799999999997665433

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=92.33  E-value=0.28  Score=46.83  Aligned_cols=64  Identities=20%  Similarity=0.308  Sum_probs=42.7

Q ss_pred             HHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        115 LKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       115 ~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      +..+.+.|+  .++.+...+..+... +.+++++++||||||... -.++..+..   ..+.+++--+.||
T Consensus       154 l~~l~~~g~--~~~~~~~~L~~~v~~-~~~ili~G~tGsGKTTll-~al~~~i~~---~~riv~iEd~~El  217 (340)
T TIGR03819       154 LDELVASGT--FPPGVARLLRAIVAA-RLAFLISGGTGSGKTTLL-SALLALVAP---DERIVLVEDAAEL  217 (340)
T ss_pred             HHHHHHcCC--CCHHHHHHHHHHHhC-CCeEEEECCCCCCHHHHH-HHHHccCCC---CCcEEEECCccee
Confidence            455556666  346677777777765 789999999999998643 234444332   3356777777676

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.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=92.30  E-value=0.28  Score=48.23  Aligned_cols=33  Identities=36%  Similarity=0.429  Sum_probs=24.9

Q ss_pred             ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867        126 PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      |-......+..+..  ++++++.+++|+|||..+.
T Consensus       180 ~e~~le~l~~~L~~--~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        180 PETTIETILKRLTI--KKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CHHHHHHHHHHHhc--CCCEEEECCCCCCHHHHHH
Confidence            44455556666666  7999999999999997654

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=92.27  E-value=1  Score=45.41  Aligned_cols=22  Identities=18%  Similarity=0.283  Sum_probs=17.8

Q ss_pred             CCcEEEEccCCCCceehhHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      ++.++++||.|+|||.++.+-+
T Consensus        43 ~~a~Lf~Gp~G~GKTT~ArilA   64 (507)
T PRK06645         43 AGGYLLTGIRGVGKTTSARIIA   64 (507)
T ss_pred             CceEEEECCCCCCHHHHHHHHH
Confidence            3689999999999998776533

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=92.20  E-value=0.76  Score=43.87  Aligned_cols=37  Identities=24%  Similarity=0.214  Sum_probs=26.3

Q ss_pred             hHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhHHHH
Q psy11867        127 SKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      +|+|...+..+.+.   -++-+++.||.|.||+..+..-+
T Consensus         3 yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA~~~A   42 (342)
T PRK06964          3 YPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFAQHLA   42 (342)
T ss_pred             CcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHHHHHH
Confidence            57777777666542   24678899999999997665433

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.17  E-value=0.55  Score=47.25  Aligned_cols=62  Identities=18%  Similarity=0.168  Sum_probs=44.0

Q ss_pred             HhhhhhcC---CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        133 ALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       133 ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      .+..++.+   +|.-+++.+|+|+|||...+--+...+.   .+.+++|++ ..|-..|+.+.++.++-
T Consensus       251 ~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~---~ge~~~y~s-~eEs~~~i~~~~~~lg~  315 (484)
T TIGR02655       251 RLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACA---NKERAILFA-YEESRAQLLRNAYSWGI  315 (484)
T ss_pred             hHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEE-eeCCHHHHHHHHHHcCC
Confidence            34555544   4789999999999999866554444443   344688877 66777888888888753

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=92.16  E-value=1  Score=48.64  Aligned_cols=22  Identities=27%  Similarity=0.368  Sum_probs=17.5

Q ss_pred             cCCCCcEEEEccCCCCceehhH
Q psy11867        139 ADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       139 ~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .....|+++.||+|+|||...-
T Consensus       196 r~~~~n~lL~G~pGvGKT~l~~  217 (857)
T PRK10865        196 RRTKNNPVLIGEPGVGKTAIVE  217 (857)
T ss_pred             cCCcCceEEECCCCCCHHHHHH
Confidence            3345799999999999997653

>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=92.14  E-value=0.15  Score=47.07  Aligned_cols=54  Identities=19%  Similarity=0.351  Sum_probs=34.3

Q ss_pred             HHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH
Q psy11867        129 IQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA  186 (399)
Q Consensus       129 iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La  186 (399)
                      ...+.+....+. +.+++++|+||||||... -.++..+...  ..+++++-.+.|+-
T Consensus       115 ~~~~~l~~~v~~-~~~ili~G~tGSGKTT~l-~all~~i~~~--~~~iv~iEd~~E~~  168 (270)
T PF00437_consen  115 EIAEFLRSAVRG-RGNILISGPTGSGKTTLL-NALLEEIPPE--DERIVTIEDPPELR  168 (270)
T ss_dssp             HHHHHHHHCHHT-TEEEEEEESTTSSHHHHH-HHHHHHCHTT--TSEEEEEESSS-S-
T ss_pred             HHHHHHhhcccc-ceEEEEECCCccccchHH-HHHhhhcccc--ccceEEecccccee
Confidence            333444444444 799999999999999654 4555555443  35677777776653

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 ....

>PTZ00293 thymidine kinase; Provisional

Probab=92.10  E-value=0.44  Score=42.00  Aligned_cols=39  Identities=13%  Similarity=0.118  Sum_probs=25.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      |+=.++.||++||||.-.+- .+.+...  .+.+++++-|..
T Consensus         4 G~i~vi~GpMfSGKTteLLr-~i~~y~~--ag~kv~~~kp~~   42 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMR-LVKRFTY--SEKKCVVIKYSK   42 (211)
T ss_pred             eEEEEEECCCCChHHHHHHH-HHHHHHH--cCCceEEEEecc
Confidence            56678899999999954333 3333322  234578887754

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=92.10  E-value=0.33  Score=46.49  Aligned_cols=42  Identities=14%  Similarity=0.379  Sum_probs=27.1

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      +..++++||||||||... -.++..+... ...+++.+--..|+
T Consensus       122 ~g~ili~G~tGSGKTT~l-~al~~~i~~~-~~~~i~tiEdp~E~  163 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTL-ASMIDYINKN-AAGHIITIEDPIEY  163 (343)
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHhhCcC-CCCEEEEEcCChhh
Confidence            688999999999999654 3455555432 23456665554444

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.09  E-value=0.71  Score=47.82  Aligned_cols=22  Identities=23%  Similarity=0.321  Sum_probs=17.6

Q ss_pred             CCcEEEEccCCCCceehhHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      +..+++.||.|+|||.++..-+
T Consensus        38 ~~a~Lf~Gp~G~GKttlA~~lA   59 (620)
T PRK14948         38 APAYLFTGPRGTGKTSSARILA   59 (620)
T ss_pred             CceEEEECCCCCChHHHHHHHH
Confidence            3678999999999998765533

>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=92.07  E-value=0.2  Score=44.47  Aligned_cols=26  Identities=19%  Similarity=0.477  Sum_probs=18.2

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhh
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRV  167 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l  167 (399)
                      +++.+++.||.|+|||.. +--++..+
T Consensus        19 ~~~~~~l~G~rg~GKTsL-l~~~~~~~   44 (234)
T PF01637_consen   19 PSQHILLYGPRGSGKTSL-LKEFINEL   44 (234)
T ss_dssp             -SSEEEEEESTTSSHHHH-HHHHHHHC
T ss_pred             cCcEEEEEcCCcCCHHHH-HHHHHHHh
Confidence            358899999999999963 33344444

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=92.06  E-value=0.63  Score=39.13  Aligned_cols=142  Identities=15%  Similarity=0.132  Sum_probs=73.9

Q ss_pred             cEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHH-HHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCC
Q psy11867        144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA-IQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE  222 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La-~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (399)
                      -+.+-.++|.|||.+++--++..+..   +.+++++-=.+.-. .--...++++    +++.....-.+..+...... .
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~~---g~~v~~vQFlKg~~~~gE~~~l~~l----~~v~~~~~g~~~~~~~~~~~-~   75 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALGH---GYRVGVVQFLKGGWKYGELKALERL----PNIEIHRMGRGFFWTTENDE-E   75 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEEEeCCCCccCHHHHHHhC----CCcEEEECCCCCccCCCChH-H
Confidence            35566778999999887777766654   34566632111100 0001223333    23332221111111000000 0


Q ss_pred             cEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCC-chHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHH
Q psy11867        223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQG-HQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ  297 (399)
Q Consensus       223 ~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~-~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~  297 (399)
                      +.  ......+....  +.+....++++|+||+-..+..+. -.+.+..+++..|...-+|+.+-..|+.+.+.+.
T Consensus        76 ~~--~~a~~~~~~a~--~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD  147 (159)
T cd00561          76 DI--AAAAEGWAFAK--EAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAAD  147 (159)
T ss_pred             HH--HHHHHHHHHHH--HHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCc
Confidence            00  00011222211  233356789999999988765321 3456677888888888888888888888777654

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.

>PRK10436 hypothetical protein; Provisional

Probab=92.05  E-value=0.16  Score=50.44  Aligned_cols=42  Identities=21%  Similarity=0.388  Sum_probs=29.0

Q ss_pred             hHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC
Q psy11867        127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP  169 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~  169 (399)
                      .+-|.+.+..++..++.-++++||||||||... ..++..+..
T Consensus       203 ~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~~  244 (462)
T PRK10436        203 TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLNT  244 (462)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhCC
Confidence            355666666666554678999999999999753 345665543

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=92.01  E-value=0.48  Score=49.00  Aligned_cols=38  Identities=16%  Similarity=0.385  Sum_probs=22.8

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLF  284 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~  284 (399)
                      ...+++||||+|+|...  ....+.+.+..-+..+.+|+.
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            46789999999998542  223333444444444555554

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=92.01  E-value=0.4  Score=50.45  Aligned_cols=57  Identities=32%  Similarity=0.350  Sum_probs=51.1

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSKE----GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~~----g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...+++|.++++.-|.+.++.+++.    |+++..+||+++..+|..+++.+.+|+.+|+|
T Consensus       309 ~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvV  369 (681)
T PRK10917        309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVI  369 (681)
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEE
Confidence            3468999999999999998887654    78999999999999999999999999999876

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=91.91  E-value=0.27  Score=49.39  Aligned_cols=47  Identities=26%  Similarity=0.441  Sum_probs=31.3

Q ss_pred             HHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhC
Q psy11867        118 VYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVN  168 (399)
Q Consensus       118 l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~  168 (399)
                      |..+||   .+-|.+.+..++..+..-++++||||||||... ..++..+.
T Consensus       221 l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       221 LETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             HHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            444554   466677777666653456889999999999653 34555554

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.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=91.91  E-value=0.12  Score=44.83  Aligned_cols=33  Identities=24%  Similarity=0.311  Sum_probs=26.9

Q ss_pred             ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        126 PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      .++-|...+...+.. |..+++.+|||||||...
T Consensus        10 ~~~~~~~~l~~~v~~-g~~i~I~G~tGSGKTTll   42 (186)
T cd01130          10 FSPLQAAYLWLAVEA-RKNILISGGTGSGKTTLL   42 (186)
T ss_pred             CCHHHHHHHHHHHhC-CCEEEEECCCCCCHHHHH
Confidence            456677777777776 899999999999999654

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.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=91.82  E-value=0.87  Score=44.08  Aligned_cols=90  Identities=14%  Similarity=0.141  Sum_probs=51.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |.-+++.+++|+|||...+..+.....   .+.+++|++-. +-..|+...+.+++.....+.   ....          
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~---~g~~VlYvs~E-Es~~qi~~Ra~rlg~~~~~l~---l~~e----------  144 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAK---RGGKVLYVSGE-ESPEQIKLRADRLGISTENLY---LLAE----------  144 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHh---cCCeEEEEECC-cCHHHHHHHHHHcCCCcccEE---EEcc----------
Confidence            688899999999999755433332222   23468888754 445677666666543221110   0000          


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                           ...+.+.+.+.      -.+.+++|||+++.+.
T Consensus       145 -----~~le~I~~~i~------~~~~~lVVIDSIq~l~  171 (372)
T cd01121         145 -----TNLEDILASIE------ELKPDLVIIDSIQTVY  171 (372)
T ss_pred             -----CcHHHHHHHHH------hcCCcEEEEcchHHhh
Confidence                 11233333321      2367899999999885

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.

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=91.78  E-value=0.7  Score=47.28  Aligned_cols=22  Identities=27%  Similarity=0.362  Sum_probs=17.3

Q ss_pred             CCcEEEEccCCCCceehhHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      ++.+++.||.|+|||..+..-+
T Consensus        38 ~hA~Lf~GP~GvGKTTlA~~lA   59 (605)
T PRK05896         38 THAYIFSGPRGIGKTSIAKIFA   59 (605)
T ss_pred             CceEEEECCCCCCHHHHHHHHH
Confidence            3568899999999998766533

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=91.72  E-value=0.8  Score=40.28  Aligned_cols=38  Identities=13%  Similarity=0.170  Sum_probs=27.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      |.-+.+.+++|+|||...+..+.+....   +.+++++.-.
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~---g~~v~yi~~e   49 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQ---GKKVVYIDTE   49 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC
Confidence            6788999999999998766555444332   3457777764

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.62  E-value=0.96  Score=46.54  Aligned_cols=43  Identities=16%  Similarity=0.345  Sum_probs=25.0

Q ss_pred             CCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        244 LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       244 ~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      ....+++||||+|+|..  .....+...+..-+..+.+|+.+ |-+
T Consensus       117 ~~~~KVvIIdev~~Lt~--~a~naLLk~LEepp~~~~fIl~t-~~~  159 (576)
T PRK14965        117 RSRYKIFIIDEVHMLST--NAFNALLKTLEEPPPHVKFIFAT-TEP  159 (576)
T ss_pred             cCCceEEEEEChhhCCH--HHHHHHHHHHHcCCCCeEEEEEe-CCh
Confidence            35678999999999853  22233334444444455555444 533

>KOG0383|consensus

Probab=91.52  E-value=0.023  Score=58.38  Aligned_cols=61  Identities=20%  Similarity=0.341  Sum_probs=50.0

Q ss_pred             HHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhc
Q psy11867        331 KFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFRE  392 (399)
Q Consensus       331 k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~  392 (399)
                      |+..|..+++..  ..++++||..-.+..+.|-..+...+ ....+.|..+..+|.+++.+|..
T Consensus       616 k~~~l~~~~~~l~~~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~~~~rq~ai~~~n~  678 (696)
T KOG0383|consen  616 KLTLLLKMLKKLKSSGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPITGPERQAAIDRFNA  678 (696)
T ss_pred             HHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCccchhhhhhccccCC
Confidence            444555555443  33699999999999999999998888 88899999999999999999984

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=91.47  E-value=0.85  Score=43.46  Aligned_cols=36  Identities=17%  Similarity=0.170  Sum_probs=25.9

Q ss_pred             ChHHHHHHhhhhhcC-----CCCcEEEEccCCCCceehhHH
Q psy11867        126 PSKIQETALPTLLAD-----PPHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~-----~g~~vi~~a~TGsGKT~~~~l  161 (399)
                      .+|||...+..+.+.     -++-.++.||.|.||+..+..
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~   43 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYA   43 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHH
Confidence            467777777766432     245778999999999976654

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=91.46  E-value=0.19  Score=52.51  Aligned_cols=43  Identities=14%  Similarity=0.155  Sum_probs=35.8

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      ..-++|+|+.|++.+. .....+.+++++.|++...++.|-+-|
T Consensus       129 ~pl~LVlDDyHli~~~-~l~~~l~fLl~~~P~~l~lvv~SR~rP  171 (894)
T COG2909         129 GPLYLVLDDYHLISDP-ALHEALRFLLKHAPENLTLVVTSRSRP  171 (894)
T ss_pred             CceEEEeccccccCcc-cHHHHHHHHHHhCCCCeEEEEEeccCC
Confidence            3459999999998764 666778899999999999999988854

>KOG2170|consensus

Probab=91.45  E-value=0.4  Score=44.19  Aligned_cols=51  Identities=20%  Similarity=0.317  Sum_probs=35.0

Q ss_pred             eEEEEechhhHhhcCCchHHHHHHHHhCC-------CCCcEEEEEeeCChhHHHHHHhhC
Q psy11867        248 KVFVLDEADVMIATQGHQDFSIRIQKRLP-------SDCQIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       248 ~~lViDEah~l~~~~~~~~~~~~i~~~l~-------~~~q~l~~SAT~~~~v~~~~~~~~  300 (399)
                      .++|+||+|.|..  +..+.+.-++...+       .+.-+|++|.+-...+.+++....
T Consensus       180 slFIFDE~DKmp~--gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~eI~~~aL~~~  237 (344)
T KOG2170|consen  180 SLFIFDEVDKLPP--GLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGSEIARIALENA  237 (344)
T ss_pred             ceEEechhhhcCH--hHHHHHhhhhccccccccccccceEEEEEcCCcchHHHHHHHHHH
Confidence            4899999999953  56666655555433       234578999888877776665544

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=91.42  E-value=0.47  Score=46.23  Aligned_cols=19  Identities=32%  Similarity=0.513  Sum_probs=16.7

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.|++..||+|+|||-.|.
T Consensus       209 ~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       209 NYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             CCcEEEECCCCCCHHHHHH
Confidence            7999999999999996554

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=91.42  E-value=1.7  Score=46.97  Aligned_cols=20  Identities=30%  Similarity=0.419  Sum_probs=16.9

Q ss_pred             CCCcEEEEccCCCCceehhH
Q psy11867        141 PPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~  160 (399)
                      ...|.++.||+|+|||...-
T Consensus       193 ~~~n~lL~G~pGvGKT~l~~  212 (852)
T TIGR03346       193 TKNNPVLIGEPGVGKTAIVE  212 (852)
T ss_pred             CCCceEEEcCCCCCHHHHHH
Confidence            46799999999999996654

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.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=91.37  E-value=0.79  Score=39.08  Aligned_cols=56  Identities=11%  Similarity=0.188  Sum_probs=40.8

Q ss_pred             cCCceeEEEEechhhHhhcCC-chHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHh
Q psy11867        243 DLSKIKVFVLDEADVMIATQG-HQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQD  298 (399)
Q Consensus       243 ~~~~~~~lViDEah~l~~~~~-~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~  298 (399)
                      .-..+++||+||+-..+..+. -.+.+..+++..|+...+|+..-..|+.+.+.+..
T Consensus        94 ~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD~  150 (173)
T TIGR00708        94 ADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELADL  150 (173)
T ss_pred             hcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCce
Confidence            346789999999988775421 33456677787788888888777788877776643

Alternate name: corrinoid adenosyltransferase.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=91.27  E-value=0.21  Score=51.19  Aligned_cols=47  Identities=23%  Similarity=0.437  Sum_probs=32.7

Q ss_pred             HHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhC
Q psy11867        118 VYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVN  168 (399)
Q Consensus       118 l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~  168 (399)
                      |.++||   .+-|.+.+..++..+...++++||||||||... ..++..+.
T Consensus       295 l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       295 IDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            445555   456666776666654678899999999999763 45666654

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.23  E-value=0.93  Score=44.40  Aligned_cols=20  Identities=35%  Similarity=0.429  Sum_probs=16.5

Q ss_pred             CcEEEEccCCCCceehhHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLT  162 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~  162 (399)
                      +.++++||.|+|||.++.+-
T Consensus        39 ha~lf~Gp~G~GKtt~A~~~   58 (397)
T PRK14955         39 HGYIFSGLRGVGKTTAARVF   58 (397)
T ss_pred             eeEEEECCCCCCHHHHHHHH
Confidence            45889999999999877653

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=91.20  E-value=1.1  Score=42.39  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=15.9

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      ++++++.+++|+|||...
T Consensus        64 ~~~ilL~G~pGtGKTtla   81 (327)
T TIGR01650        64 DRRVMVQGYHGTGKSTHI   81 (327)
T ss_pred             CCcEEEEeCCCChHHHHH
Confidence            689999999999999643

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

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

Probab=91.19  E-value=1.1  Score=48.99  Aligned_cols=56  Identities=14%  Similarity=0.168  Sum_probs=42.1

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHHCCC--eEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSKEGL--NVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~~g~--~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                      ..++++||++|.+..+.++..|.....  ...++.-+++...|..++++|+.++-.||
T Consensus       751 ~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iL  808 (928)
T PRK08074        751 TKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAIL  808 (928)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEE
Confidence            457999999999999999999976422  13333335555678999999998877776

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=91.16  E-value=2.4  Score=40.10  Aligned_cols=19  Identities=26%  Similarity=0.510  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.-+.+.||+|+|||....
T Consensus       114 ~~vi~lvGpnGsGKTTt~~  132 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIG  132 (318)
T ss_pred             CeEEEEECCCCCcHHHHHH
Confidence            6778899999999996654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=91.15  E-value=0.7  Score=49.13  Aligned_cols=52  Identities=19%  Similarity=0.300  Sum_probs=29.9

Q ss_pred             cccccCCCCHHHHHHHHHc---CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        103 KTFEALHLKPELLKGVYEM---GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~---g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      .+|++++-.+.+.+.|...   .+..|.-++..-    + .+++.+++.||+|+|||+.+
T Consensus       450 ~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g----~-~~~~giLL~GppGtGKT~la  504 (733)
T TIGR01243       450 VRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMG----I-RPPKGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             cchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcC----C-CCCceEEEECCCCCCHHHHH
Confidence            3566666666666666542   222222222111    1 12578999999999999654

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.

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.07  E-value=0.72  Score=47.44  Aligned_cols=21  Identities=19%  Similarity=0.246  Sum_probs=17.3

Q ss_pred             CcEEEEccCCCCceehhHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      ..+|+.+|.|+|||.++.+-+
T Consensus        39 ha~Lf~GPpG~GKTtiArilA   59 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARIFA   59 (624)
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            578899999999998876544

>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=91.06  E-value=0.56  Score=44.26  Aligned_cols=74  Identities=22%  Similarity=0.328  Sum_probs=46.7

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      +..+..-.+++.   .|.+  +..+++.|..-+..+... +++++++++||||||. ++.+++..+...   .+.+.+=-
T Consensus       109 IRk~~~~~~t~~---~l~~--~gt~~~~~~ayL~~~ie~-~~siii~G~t~sGKTt-~lnall~~Ip~~---~rivtIEd  178 (312)
T COG0630         109 IRKFSDEPITPE---DLIE--YGTISPEQAAYLWLAIEA-RKSIIICGGTASGKTT-LLNALLDFIPPE---ERIVTIED  178 (312)
T ss_pred             EEcCCCCCCCHH---HHhh--cCCCCHHHHHHHHHHHHc-CCcEEEECCCCCCHHH-HHHHHHHhCCch---hcEEEEec
Confidence            444554444443   3333  335667777777777766 8999999999999995 355666555433   33666656


Q ss_pred             cHHH
Q psy11867        182 TYEL  185 (399)
Q Consensus       182 t~~L  185 (399)
                      |.|+
T Consensus       179 t~E~  182 (312)
T COG0630         179 TPEL  182 (312)
T ss_pred             cccc
Confidence            6554

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.00  E-value=0.81  Score=46.51  Aligned_cols=39  Identities=15%  Similarity=0.414  Sum_probs=23.8

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      .+.+++||||+|+|...  ....+.+.+...+....+|+.+
T Consensus       118 ~~~kVvIIDEad~ls~~--a~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKS--AFNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             CCceEEEEcCcccCCHH--HHHHHHHHHhCCCCCEEEEEEe
Confidence            46789999999998542  2223334444445556666554

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=90.98  E-value=0.17  Score=45.27  Aligned_cols=14  Identities=21%  Similarity=0.596  Sum_probs=12.0

Q ss_pred             EEEEccCCCCceeh
Q psy11867        145 MIAQSQSGTGKTAA  158 (399)
Q Consensus       145 vi~~a~TGsGKT~~  158 (399)
                      +++.|+.|||||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999964

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

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=90.98  E-value=1.4  Score=41.72  Aligned_cols=37  Identities=19%  Similarity=0.168  Sum_probs=25.9

Q ss_pred             CChHHHHHHhhhhhc----C-CCCcEEEEccCCCCceehhHH
Q psy11867        125 APSKIQETALPTLLA----D-PPHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~----~-~g~~vi~~a~TGsGKT~~~~l  161 (399)
                      .++|+|...+..+.+    + -++-.++.||.|.||+..+..
T Consensus         3 ~~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~   44 (319)
T PRK06090          3 NDYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVEL   44 (319)
T ss_pred             cCcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHH
Confidence            356777777766643    1 145789999999999966543

>KOG2028|consensus

Probab=90.97  E-value=0.73  Score=43.69  Aligned_cols=50  Identities=20%  Similarity=0.230  Sum_probs=32.2

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      -.+|+.+|.|+|||..+-+-+-..   .....+.+=++-|.+-.+.+.+.+++
T Consensus       163 pSmIlWGppG~GKTtlArlia~ts---k~~SyrfvelSAt~a~t~dvR~ife~  212 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIASTS---KKHSYRFVELSATNAKTNDVRDIFEQ  212 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhhc---CCCceEEEEEeccccchHHHHHHHHH
Confidence            478999999999997654432211   11234567777777776666665554

>TIGR00767 rho transcription termination factor Rho

Probab=90.88  E-value=0.72  Score=44.74  Aligned_cols=28  Identities=11%  Similarity=0.143  Sum_probs=20.4

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCC
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNP  169 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~  169 (399)
                      .|+.+++.||+|+|||..... +...+..
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~~-i~~~I~~  194 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQK-IAQAITR  194 (415)
T ss_pred             CCCEEEEECCCCCChhHHHHH-HHHhhcc
Confidence            489999999999999975433 4444443

Members of this family differ in the specificity of RNA binding.

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

Probab=90.82  E-value=2.1  Score=40.85  Aligned_cols=42  Identities=21%  Similarity=0.253  Sum_probs=24.2

Q ss_pred             EEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHH
Q psy11867        146 IAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQ  188 (399)
Q Consensus       146 i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q  188 (399)
                      ++.++.|+|||.+....++..+.......++++. ||..-+.+
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~-~~~~~~~~   42 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIA-STYRQARD   42 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEE-ESSHHHHH
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEe-cCHHHHHH
Confidence            4678999999998877677666543333445555 66554444

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=90.77  E-value=1.3  Score=47.74  Aligned_cols=20  Identities=35%  Similarity=0.395  Sum_probs=17.1

Q ss_pred             CCCcEEEEccCCCCceehhH
Q psy11867        141 PPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~  160 (399)
                      ...|+++.||+|+|||...-
T Consensus       199 ~~~n~lL~G~pGvGKTal~~  218 (821)
T CHL00095        199 TKNNPILIGEPGVGKTAIAE  218 (821)
T ss_pred             ccCCeEEECCCCCCHHHHHH
Confidence            46799999999999997654

>PHA00350 putative assembly protein

Probab=90.71  E-value=1.5  Score=42.58  Aligned_cols=25  Identities=8%  Similarity=0.159  Sum_probs=17.7

Q ss_pred             EEEEccCCCCceehhHH-HHHHhhCC
Q psy11867        145 MIAQSQSGTGKTAAFTL-TMLSRVNP  169 (399)
Q Consensus       145 vi~~a~TGsGKT~~~~l-~il~~l~~  169 (399)
                      .++.|..|||||+..+- -++..+..
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk~   29 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALKD   29 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHHC
Confidence            46789999999987764 34444443

>TIGR03689 pup_AAA proteasome ATPase

Probab=90.64  E-value=0.92  Score=45.65  Aligned_cols=18  Identities=28%  Similarity=0.460  Sum_probs=15.9

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      ++.+++.||+|+|||+..
T Consensus       216 p~GILLyGPPGTGKT~LA  233 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLIA  233 (512)
T ss_pred             CcceEEECCCCCcHHHHH
Confidence            688999999999999754

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=90.63  E-value=1.1  Score=40.40  Aligned_cols=52  Identities=13%  Similarity=0.217  Sum_probs=34.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      |.-+++.+++|+|||.....-+...+.   .+.+++++.=- +-..++.+.+..++
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~---~g~~~~y~~~e-~~~~~~~~~~~~~g   76 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALK---QGKKVYVITTE-NTSKSYLKQMESVK   76 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHh---CCCEEEEEEcC-CCHHHHHHHHHHCC
Confidence            788999999999999765544444443   24457777653 33456666666664

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=90.54  E-value=0.42  Score=41.26  Aligned_cols=92  Identities=14%  Similarity=0.112  Sum_probs=49.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |.=.++.+|..||||..-+--+-....   .+.++++..|-..-             .+ +........|..       .
T Consensus         4 g~l~~i~gpM~SGKT~eLl~r~~~~~~---~g~~v~vfkp~iD~-------------R~-~~~~V~Sr~G~~-------~   59 (201)
T COG1435           4 GWLEFIYGPMFSGKTEELLRRARRYKE---AGMKVLVFKPAIDT-------------RY-GVGKVSSRIGLS-------S   59 (201)
T ss_pred             EEEEEEEccCcCcchHHHHHHHHHHHH---cCCeEEEEeccccc-------------cc-ccceeeeccCCc-------c
Confidence            456789999999999743322222212   33457777664310             00 111111111211       2


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      ..++|-.+..+.+.+.....  ...+++|.||||+.+-
T Consensus        60 ~A~~i~~~~~i~~~i~~~~~--~~~~~~v~IDEaQF~~   95 (201)
T COG1435          60 EAVVIPSDTDIFDEIAALHE--KPPVDCVLIDEAQFFD   95 (201)
T ss_pred             cceecCChHHHHHHHHhccc--CCCcCEEEEehhHhCC
Confidence            23667777777776543221  1128899999998864

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=90.52  E-value=1.3  Score=39.45  Aligned_cols=53  Identities=17%  Similarity=0.144  Sum_probs=35.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      |.-+++.+++|+|||...+--+...+..   +..++|++- .+-..++.+.+..++.
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~---g~~~~y~s~-e~~~~~l~~~~~~~~~   68 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKN---GEKAMYISL-EEREERILGYAKSKGW   68 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEEC-CCCHHHHHHHHHHcCC
Confidence            6889999999999986544334443432   345777765 3456777777776643

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PRK09354 recA recombinase A; Provisional

Probab=90.40  E-value=0.67  Score=44.19  Aligned_cols=91  Identities=11%  Similarity=0.112  Sum_probs=53.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |+-+.+.+|+|||||...+..+.+...   .+..|+|+..-..+-.   +.++.++-.+.                    
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~---~G~~~~yId~E~s~~~---~~a~~lGvdld--------------------  113 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQK---AGGTAAFIDAEHALDP---VYAKKLGVDID--------------------  113 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEECCccchHH---HHHHHcCCCHH--------------------
Confidence            688889999999999877665555443   3456888876655543   33444432211                    


Q ss_pred             CcEEEeCchhHHHhhhcc-ccccCCceeEEEEechhhHh
Q psy11867        222 EQIIIGTPGKVLDWGLKY-RFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~-~~~~~~~~~~lViDEah~l~  259 (399)
                       ++++..|...-+.+... ..+.-..+++||||=+-.+.
T Consensus       114 -~lli~qp~~~Eq~l~i~~~li~s~~~~lIVIDSvaaL~  151 (349)
T PRK09354        114 -NLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALV  151 (349)
T ss_pred             -HeEEecCCCHHHHHHHHHHHhhcCCCCEEEEeChhhhc
Confidence             24445443322211100 11223468899999987664

>KOG0732|consensus

Probab=90.29  E-value=0.52  Score=50.72  Aligned_cols=53  Identities=21%  Similarity=0.334  Sum_probs=36.6

Q ss_pred             ccccccCCCCHHHHHHHHHcCCC---CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFY---APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~---~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      ...|++.|........|+++-+.   +|.-+|.-.|     .+++.++.++|.|+|||+.+
T Consensus       261 ~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~i-----tpPrgvL~~GppGTGkTl~a  316 (1080)
T KOG0732|consen  261 SVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNI-----TPPRGVLFHGPPGTGKTLMA  316 (1080)
T ss_pred             ccCccccccHHHHHHHHHHHHHhHhhhhhHhhhccc-----CCCcceeecCCCCCchhHHH
Confidence            46788888888888888876432   2222222222     24789999999999999754

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=90.28  E-value=0.66  Score=48.37  Aligned_cols=56  Identities=21%  Similarity=0.308  Sum_probs=50.6

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKE----GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~----g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+++|.++++.-|.+.++.+++.    |.++..+||+++..+|..+++...+|+.+|+|
T Consensus       284 g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiV  343 (630)
T TIGR00643       284 GYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVV  343 (630)
T ss_pred             CCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEE
Confidence            458999999999999998887764    78999999999999999999999999998875

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=90.21  E-value=2.6  Score=36.22  Aligned_cols=142  Identities=17%  Similarity=0.163  Sum_probs=74.4

Q ss_pred             cEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH-HHHHHHHHHHHhccCCCcEEEEEEcC--chhhhhhcc
Q psy11867        144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL-AIQIGEVVAKMGKHITDLSVRYAVRG--ENLERNKKI  220 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L-a~Q~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~  220 (399)
                      -+++-...|-|||.+++=-++..+-.   +.++.|+-=.+-= -.--+..+.++     +..+.+..-+  ...+.+.+.
T Consensus        30 li~V~TG~GKGKTTAAlG~alRa~Gh---G~rv~vvQFiKg~~~~GE~~~~~~~-----~~~v~~~~~~~g~tw~~~~~~  101 (198)
T COG2109          30 LIIVFTGNGKGKTTAALGLALRALGH---GLRVGVVQFIKGGWKYGEEAALEKF-----GLGVEFHGMGEGFTWETQDRE  101 (198)
T ss_pred             eEEEEecCCCChhHHHHHHHHHHhcC---CCEEEEEEEeecCcchhHHHHHHhh-----ccceeEEecCCceeCCCcCcH
Confidence            36677778889999988777776654   3456555421111 01112223333     1122221111  111111000


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCch--HHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHh
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ--DFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQD  298 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~--~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~  298 (399)
                       .++  ..+...+....  ..+.-...++||+||.-..+.. ++.  +.+..++..-|....+|+..-..|+.+.+.+..
T Consensus       102 -~d~--~aa~~~w~~a~--~~l~~~~ydlviLDEl~~al~~-g~l~~eeV~~~l~~kP~~~~vIiTGr~ap~~lie~ADl  175 (198)
T COG2109         102 -ADI--AAAKAGWEHAK--EALADGKYDLVILDELNYALRY-GLLPLEEVVALLKARPEHTHVIITGRGAPPELIELADL  175 (198)
T ss_pred             -HHH--HHHHHHHHHHH--HHHhCCCCCEEEEehhhHHHHc-CCCCHHHHHHHHhcCCCCcEEEEECCCCCHHHHHHHHH
Confidence             022  33344444322  2333447899999999988764 433  455666666666666776666677777776654


Q ss_pred             h
Q psy11867        299 M  299 (399)
Q Consensus       299 ~  299 (399)
                      .
T Consensus       176 V  176 (198)
T COG2109         176 V  176 (198)
T ss_pred             H
Confidence            3

>cd01394 radB RadB

Probab=90.20  E-value=1.3  Score=39.19  Aligned_cols=36  Identities=19%  Similarity=0.146  Sum_probs=25.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA  180 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  180 (399)
                      |.-+++.+++|+|||...+.-+.....   .+..++++.
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~---~g~~v~yi~   54 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAG---QGKKVAYID   54 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh---cCCeEEEEE
Confidence            677899999999999766554444332   245688874

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>KOG1513|consensus

Probab=90.17  E-value=0.56  Score=48.58  Aligned_cols=156  Identities=16%  Similarity=0.156  Sum_probs=89.7

Q ss_pred             CChHHHHHHhhhhhcC--------CCCcEEEEc--cCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLAD--------PPHNMIAQS--QSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVA  194 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~--------~g~~vi~~a--~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~  194 (399)
                      .++..|.+|+-.....        ..-..++-.  ..|-|.|.|-.+  ++...+  ...++|.++-+..|-.+-.+-++
T Consensus       264 ~lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAgiI--feNyLk--GRKrAlW~SVSsDLKfDAERDL~  339 (1300)
T KOG1513|consen  264 HLSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAGII--FENYLK--GRKRALWFSVSSDLKFDAERDLR  339 (1300)
T ss_pred             chhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEEEE--ehhhhc--ccceeEEEEeccccccchhhchh
Confidence            5667788777555432        112334433  355566766543  333333  34579999999999888888888


Q ss_pred             HHhccCCCcEEEEEEcC----chhhhhhccCCcEEEeCchhHHHhhhc-cccc---------c--CCceeEEEEechhhH
Q psy11867        195 KMGKHITDLSVRYAVRG----ENLERNKKITEQIIIGTPGKVLDWGLK-YRFF---------D--LSKIKVFVLDEADVM  258 (399)
Q Consensus       195 ~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~IlV~Tp~~l~~~~~~-~~~~---------~--~~~~~~lViDEah~l  258 (399)
                      .++..  ++.+.....-    -+-+.....+..++++|...|+--... .+..         |  -..=.++||||||+-
T Consensus       340 DigA~--~I~V~alnK~KYakIss~en~n~krGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIvfDECHkA  417 (1300)
T KOG1513|consen  340 DIGAT--GIAVHALNKFKYAKISSKENTNTKRGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIVFDECHKA  417 (1300)
T ss_pred             hcCCC--CccceehhhcccccccccccCCccceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEEehhhhhh
Confidence            87654  4444322111    111111122335999999877643221 1110         0  122368999999975


Q ss_pred             hh--------cCCchHHHHHHHHhCCCCCcEEEEEee
Q psy11867        259 IA--------TQGHQDFSIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       259 ~~--------~~~~~~~~~~i~~~l~~~~q~l~~SAT  287 (399)
                      -.        .-.....+..+.+.|| +.+++.-|||
T Consensus       418 KNL~p~~~~k~TKtG~tVLdLQk~LP-~ARVVYASAT  453 (1300)
T KOG1513|consen  418 KNLVPTAGAKSTKTGKTVLDLQKKLP-NARVVYASAT  453 (1300)
T ss_pred             cccccccCCCcCcccHhHHHHHHhCC-CceEEEeecc
Confidence            32        0123455667888886 7789999999

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=90.17  E-value=0.13  Score=47.62  Aligned_cols=19  Identities=26%  Similarity=0.398  Sum_probs=16.8

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      ..|+++.+|||||||+.+.
T Consensus        97 KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             eccEEEECCCCCcHHHHHH
Confidence            5899999999999997664

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.13  E-value=1.4  Score=45.50  Aligned_cols=21  Identities=24%  Similarity=0.412  Sum_probs=16.7

Q ss_pred             CCcEEEEccCCCCceehhHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLT  162 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~  162 (399)
                      ++.+|+.||.|+|||.+..+-
T Consensus        38 ~~a~Lf~Gp~G~GKTtlA~~l   58 (585)
T PRK14950         38 AHAYLFTGPRGVGKTSTARIL   58 (585)
T ss_pred             ceEEEEECCCCCCHHHHHHHH
Confidence            355799999999999876543

>TIGR02012 tigrfam_recA protein RecA

Probab=90.07  E-value=0.61  Score=44.00  Aligned_cols=91  Identities=11%  Similarity=0.123  Sum_probs=51.8

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |+-+.+.+|+|||||...+..+......   +..++++..-..+-.+   .++.++-...                    
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~~---g~~v~yId~E~~~~~~---~a~~lGvd~~--------------------  108 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDPV---YARKLGVDID--------------------  108 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEcccchhHHH---HHHHcCCCHH--------------------
Confidence            6888999999999998766555544432   4557777655444432   3444432110                    


Q ss_pred             CcEEEeCchhHHHhhhcc-ccccCCceeEEEEechhhHh
Q psy11867        222 EQIIIGTPGKVLDWGLKY-RFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~-~~~~~~~~~~lViDEah~l~  259 (399)
                       ++++..|...-+.+... ..+.-..++++|||-+-.+.
T Consensus       109 -~l~v~~p~~~eq~l~~~~~li~~~~~~lIVIDSv~al~  146 (321)
T TIGR02012       109 -NLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALV  146 (321)
T ss_pred             -HeEEecCCCHHHHHHHHHHHhhccCCcEEEEcchhhhc
Confidence             24455444332221110 11123468899999988764

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.

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

Probab=90.04  E-value=0.48  Score=52.76  Aligned_cols=55  Identities=18%  Similarity=0.275  Sum_probs=45.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCC--CCCCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPS--IQEPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~--~~~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      +.++++.|..|||||.+-..-++..+...  ..-.+.|||+-|+.=+..+.+.+..-
T Consensus        16 ~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~   72 (1139)
T COG1074          16 GQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDR   72 (1139)
T ss_pred             CCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHH
Confidence            78999999999999988777777777663  45668999999999888877666553

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=89.98  E-value=1.3  Score=39.43  Aligned_cols=41  Identities=17%  Similarity=0.097  Sum_probs=26.8

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCC---CCCCeEEEEeCc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPS---IQEPQVLCLAPT  182 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~---~~~~~~lil~Pt  182 (399)
                      |.-+.+.+++|+|||...+.-+.......   .....++++..-
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e   62 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTE   62 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecC
Confidence            68889999999999976655444433221   012457777754

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PRK13764 ATPase; Provisional

Probab=89.96  E-value=0.5  Score=48.41  Aligned_cols=26  Identities=12%  Similarity=0.253  Sum_probs=19.9

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVN  168 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~  168 (399)
                      +++++++|+||||||.. +-+++..+.
T Consensus       257 ~~~ILIsG~TGSGKTTl-l~AL~~~i~  282 (602)
T PRK13764        257 AEGILIAGAPGAGKSTF-AQALAEFYA  282 (602)
T ss_pred             CCEEEEECCCCCCHHHH-HHHHHHHHh
Confidence            68899999999999964 345555554

>KOG1806|consensus

Probab=89.87  E-value=0.61  Score=49.57  Aligned_cols=72  Identities=18%  Similarity=0.160  Sum_probs=56.2

Q ss_pred             CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        122 GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       122 g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      ++-..++-|-+++-.-..  +....+.+|+|+|||-... -++.-+......++++|++....-..|..+.+.+.
T Consensus       735 n~v~ft~~qveai~sg~q--pgltmvvgppgtgktd~av-qil~~lyhn~p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  735 NQVKFTPTQVEAILSGMQ--PGLTMVVGPPGTGKTDVAV-QILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             chhccCHHHHHHHHhcCC--CCceeeecCCCCCCcchhh-hhhhhhhhcCCCcceEEEEecccchhHHHHHHHhc
Confidence            345678899999988777  7999999999999997765 34444444557788999999888778877776654

>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=89.85  E-value=0.45  Score=42.88  Aligned_cols=38  Identities=24%  Similarity=0.472  Sum_probs=25.4

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      .-++++.|++|||||. +++-++..+...  ...+++++|.
T Consensus        13 ~fr~viIG~sGSGKT~-li~~lL~~~~~~--f~~I~l~t~~   50 (241)
T PF04665_consen   13 PFRMVIIGKSGSGKTT-LIKSLLYYLRHK--FDHIFLITPE   50 (241)
T ss_pred             CceEEEECCCCCCHHH-HHHHHHHhhccc--CCEEEEEecC
Confidence            5689999999999995 444555554432  2446666673

This is thought to be an ATPase involved in viral DNA packaging [].

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=89.76  E-value=1.4  Score=42.72  Aligned_cols=19  Identities=21%  Similarity=0.242  Sum_probs=17.2

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      |.+|++.++||+||++.+.
T Consensus       101 ~~~vLi~GetGtGKel~A~  119 (403)
T COG1221         101 GLPVLIIGETGTGKELFAR  119 (403)
T ss_pred             CCcEEEecCCCccHHHHHH
Confidence            7999999999999997664

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=89.75  E-value=2.4  Score=45.18  Aligned_cols=19  Identities=37%  Similarity=0.614  Sum_probs=16.2

Q ss_pred             CCCcEEEEccCCCCceehh
Q psy11867        141 PPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~  159 (399)
                      +++.+++.||+|+|||...
T Consensus       211 ~~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       211 PPKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CCceEEEECCCCCChHHHH
Confidence            3689999999999999643

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.

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=89.70  E-value=1.3  Score=47.14  Aligned_cols=18  Identities=22%  Similarity=0.145  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      |..+++.+|+|+|||...
T Consensus       349 g~~i~l~GppG~GKTtl~  366 (784)
T PRK10787        349 GPILCLVGPPGVGKTSLG  366 (784)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            678999999999999543

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=89.56  E-value=0.69  Score=51.77  Aligned_cols=57  Identities=21%  Similarity=0.316  Sum_probs=45.6

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      +.+++++.|+.|||||.+-.--++..+..+.....+++|+-|+.=|..+.+.+....
T Consensus         9 p~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L   65 (1141)
T TIGR02784         9 PKTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRL   65 (1141)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHH
Confidence            468999999999999988776677666555455679999999999988877666554

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 alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

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

Probab=89.51  E-value=0.7  Score=43.69  Aligned_cols=89  Identities=13%  Similarity=0.218  Sum_probs=52.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |+-+.+.+|+|||||...+..+.....   .+..++++..-..+-.+   .++.++-..              +      
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~---~g~~~vyId~E~~~~~~---~a~~lGvd~--------------~------  108 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQK---LGGTVAFIDAEHALDPV---YAKKLGVDL--------------D------  108 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---cCCCEEEECccccHHHH---HHHHcCCCH--------------H------
Confidence            688899999999999766655544433   34568888875555432   334433211              1      


Q ss_pred             CcEEEeCchh---HHHhhhccccccCCceeEEEEechhhHh
Q psy11867        222 EQIIIGTPGK---VLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       222 ~~IlV~Tp~~---l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                       ++++..|..   ++..+..  .+.-..++++|||-+-.+.
T Consensus       109 -~l~v~~p~~~eq~l~i~~~--li~s~~~~lIVIDSvaal~  146 (325)
T cd00983         109 -NLLISQPDTGEQALEIADS--LVRSGAVDLIVVDSVAALV  146 (325)
T ss_pred             -HheecCCCCHHHHHHHHHH--HHhccCCCEEEEcchHhhc
Confidence             244444433   3332211  1223468899999987664

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK09087 hypothetical protein; Validated

Probab=89.48  E-value=1.1  Score=40.10  Aligned_cols=41  Identities=5%  Similarity=-0.013  Sum_probs=23.9

Q ss_pred             eEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChh
Q psy11867        248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE  291 (399)
Q Consensus       248 ~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~  291 (399)
                      +++++|++|.+.   .....+..++..+......++++++.++.
T Consensus        89 ~~l~iDDi~~~~---~~~~~lf~l~n~~~~~g~~ilits~~~p~  129 (226)
T PRK09087         89 GPVLIEDIDAGG---FDETGLFHLINSVRQAGTSLLMTSRLWPS  129 (226)
T ss_pred             CeEEEECCCCCC---CCHHHHHHHHHHHHhCCCeEEEECCCChH
Confidence            379999999863   22344445554444434456666665544

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=89.41  E-value=2.7  Score=45.38  Aligned_cols=31  Identities=23%  Similarity=0.428  Sum_probs=22.0

Q ss_pred             HHHHhhhhh----cCCCCcEEEEccCCCCceehhH
Q psy11867        130 QETALPTLL----ADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       130 Q~~ai~~ll----~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      |...+..++    .....|+++.||.|+|||...-
T Consensus       192 r~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~  226 (852)
T TIGR03345       192 RDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVE  226 (852)
T ss_pred             CHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHH
Confidence            555555443    4345799999999999996543

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.

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=89.40  E-value=3.6  Score=44.22  Aligned_cols=114  Identities=11%  Similarity=0.047  Sum_probs=70.5

Q ss_pred             CcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhcc-C-CCCcEEEEecchHh
Q psy11867        279 CQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGV-V-TIGQAMIFCHTRKT  356 (399)
Q Consensus       279 ~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~-~-~~~k~IIF~~s~~~  356 (399)
                      .++.+||.|......++..-|-.+-  +.+.... ........-..+.....|..++.+-+.. + ...|+||-|.|.+.
T Consensus       504 ~kl~GmTGTa~~e~~Ef~~iY~l~v--~~iPt~k-p~~r~d~~d~iy~t~~~k~~ai~~ei~~~~~~grPvLigt~si~~  580 (970)
T PRK12899        504 EKLAGMTGTAITESREFKEIYNLYV--LQVPTFK-PCLRIDHNDEFYMTEREKYHAIVAEIASIHRKGNPILIGTESVEV  580 (970)
T ss_pred             chhcccCCCCHHHHHHHHHHhCCCE--EECCCCC-CceeeeCCCcEecCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHH
Confidence            3678999998766666655554332  2222221 1111111112334556777776664433 3 33589999999999


Q ss_pred             HHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        357 AAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       357 a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                      .+.|+..|.+.|++..+++..-...|-..+-+.=+.|.+
T Consensus       581 se~ls~~L~~~gi~h~vLNak~~~~Ea~iia~AG~~g~V  619 (970)
T PRK12899        581 SEKLSRILRQNRIEHTVLNAKNHAQEAEIIAGAGKLGAV  619 (970)
T ss_pred             HHHHHHHHHHcCCcceecccchhhhHHHHHHhcCCCCcE
Confidence            999999999999999999998554444444443344443

>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=89.36  E-value=0.27  Score=42.07  Aligned_cols=44  Identities=18%  Similarity=0.198  Sum_probs=28.0

Q ss_pred             hhccCCcEEEeCchhHHHhhhccccc-cCCceeEEEEechhhHhh
Q psy11867        217 NKKITEQIIIGTPGKVLDWGLKYRFF-DLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       217 ~~~~~~~IlV~Tp~~l~~~~~~~~~~-~~~~~~~lViDEah~l~~  260 (399)
                      ......+|||++..-|++-....... ...+-.+|||||||.+.+
T Consensus       115 ~~~~~adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  115 ELAKNADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLED  159 (174)
T ss_dssp             HCGGG-SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGG
T ss_pred             HhcccCCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHH
Confidence            33456789999999887653322221 122346999999999865

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.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=89.27  E-value=0.82  Score=41.91  Aligned_cols=52  Identities=17%  Similarity=0.149  Sum_probs=33.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe---CcHHHHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA---PTYELAIQIGEVVAKM  196 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~---Pt~~La~Q~~~~~~~~  196 (399)
                      |.-+++.|++|+|||...+--+.+.+..   +.+++|++   |...+..++.+....+
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~---Ge~vlyis~Ee~~~~~~~~l~~~a~~~   90 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASR---GNPVLFVTVESPANFVYTSLKERAKAM   90 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhC---CCcEEEEEecCCchHHHHHHHHHHHHc
Confidence            7889999999999997665544444432   44588888   3333444444444444

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=89.05  E-value=1.4  Score=42.32  Aligned_cols=19  Identities=32%  Similarity=0.452  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++.+++.||.|+|||....
T Consensus        36 ~~~~Ll~G~~G~GKt~~a~   54 (355)
T TIGR02397        36 AHAYLFSGPRGTGKTSIAR   54 (355)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3568999999999996654

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.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=88.78  E-value=0.24  Score=43.44  Aligned_cols=28  Identities=32%  Similarity=0.386  Sum_probs=18.9

Q ss_pred             HHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        131 ETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       131 ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      +.|+.....+ ++++++.+|.|+|||+.+
T Consensus        12 KrAL~iAAaG-~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   12 KRALEIAAAG-GHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             HHHHHHHHHC-C--EEEES-CCCTHHHHH
T ss_pred             HHHHHHHHcC-CCCeEEECCCCCCHHHHH
Confidence            3455555566 899999999999999765

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=88.67  E-value=0.53  Score=44.35  Aligned_cols=23  Identities=30%  Similarity=0.455  Sum_probs=18.1

Q ss_pred             hhhhcCCCCcEEEEccCCCCceeh
Q psy11867        135 PTLLADPPHNMIAQSQSGTGKTAA  158 (399)
Q Consensus       135 ~~ll~~~g~~vi~~a~TGsGKT~~  158 (399)
                      ...... +.+++++++||||||..
T Consensus       138 ~~~v~~-~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       138 RLAIAS-RKNIIISGGTGSGKTTF  160 (308)
T ss_pred             HHHhhC-CCEEEEECCCCCCHHHH
Confidence            333443 79999999999999964

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.

>PRK14701 reverse gyrase; Provisional

Probab=88.52  E-value=2.1  Score=49.33  Aligned_cols=57  Identities=18%  Similarity=0.239  Sum_probs=50.4

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHHC------CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSKE------GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~~------g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...+++|.++++.-+.+++..|...      +..+..+||+++..++..+++.+++|+.+|||
T Consensus       121 ~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV  183 (1638)
T PRK14701        121 KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILV  183 (1638)
T ss_pred             cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEE
Confidence            3458999999999999999998773      46788999999999999999999999999885

>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.52  E-value=0.32  Score=40.52  Aligned_cols=40  Identities=23%  Similarity=0.338  Sum_probs=26.9

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      +-.|+.+|.|||||..|........    .   +++++.+-++|.|+
T Consensus         3 ~l~IvaG~NGsGKstv~~~~~~~~~----~---~~~~VN~D~iA~~i   42 (187)
T COG4185           3 RLDIVAGPNGSGKSTVYASTLAPLL----P---GIVFVNADEIAAQI   42 (187)
T ss_pred             eEEEEecCCCCCceeeeeccchhhc----C---CeEEECHHHHhhhc
Confidence            3457889999999998865433221    1   56777777777664

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=88.46  E-value=1.8  Score=39.09  Aligned_cols=51  Identities=22%  Similarity=0.332  Sum_probs=29.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe--CcHHHHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA--PTYELAIQIGEVVAKM  196 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~--Pt~~La~Q~~~~~~~~  196 (399)
                      ..-+.++++.|||||..-- +++..+..+   ..++++.  ||...+.=....+..+
T Consensus        51 qg~~~vtGevGsGKTv~~R-al~~s~~~d---~~~~v~i~~~~~s~~~~~~ai~~~l  103 (269)
T COG3267          51 QGILAVTGEVGSGKTVLRR-ALLASLNED---QVAVVVIDKPTLSDATLLEAIVADL  103 (269)
T ss_pred             CceEEEEecCCCchhHHHH-HHHHhcCCC---ceEEEEecCcchhHHHHHHHHHHHh
Confidence            3488899999999998766 455444432   2344444  4544443333333333

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

Probab=88.45  E-value=3.2  Score=44.68  Aligned_cols=54  Identities=15%  Similarity=0.204  Sum_probs=40.9

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..++++|+++|.+..+.++..|......+ ...|.-.  .|..++++|++++-.||+
T Consensus       646 ~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLl  699 (820)
T PRK07246        646 LQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILL  699 (820)
T ss_pred             cCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEE
Confidence            45899999999999999999997665555 4444222  356789999998777763

>PF12846 AAA_10: AAA-like domain

Probab=88.42  E-value=0.51  Score=43.83  Aligned_cols=42  Identities=17%  Similarity=0.322  Sum_probs=29.1

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI  187 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~  187 (399)
                      .|+++.|+||||||.....-+.+.+..   +..++++=|..+...
T Consensus         2 ~h~~i~G~tGsGKT~~~~~l~~~~~~~---g~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLKNLLEQLIRR---GPRVVIFDPKGDYSP   43 (304)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHc---CCCEEEEcCCchHHH
Confidence            789999999999997776444344433   355777767655544

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=88.41  E-value=0.28  Score=48.07  Aligned_cols=28  Identities=36%  Similarity=0.421  Sum_probs=21.4

Q ss_pred             HHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        131 ETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       131 ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      ++|+....++ |+|+++.+|.|||||+.+
T Consensus       188 KrAleiAAAG-gHnLl~~GpPGtGKTmla  215 (490)
T COG0606         188 KRALEIAAAG-GHNLLLVGPPGTGKTMLA  215 (490)
T ss_pred             HHHHHHHHhc-CCcEEEecCCCCchHHhh
Confidence            3444555566 999999999999999643

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.32  E-value=1.8  Score=44.80  Aligned_cols=20  Identities=35%  Similarity=0.429  Sum_probs=16.6

Q ss_pred             CcEEEEccCCCCceehhHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLT  162 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~  162 (399)
                      +..|++||.|+|||.++.+-
T Consensus        39 ha~Lf~Gp~GvGKttlA~~l   58 (620)
T PRK14954         39 HGYIFSGLRGVGKTTAARVF   58 (620)
T ss_pred             eeEEEECCCCCCHHHHHHHH
Confidence            55899999999999877553

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

Probab=88.19  E-value=0.97  Score=41.46  Aligned_cols=20  Identities=20%  Similarity=0.297  Sum_probs=16.4

Q ss_pred             CCcEEEEccCCCCceehhHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l  161 (399)
                      -.|+++.+|+|.|||..+.+
T Consensus        52 lDHvLl~GPPGlGKTTLA~I   71 (332)
T COG2255          52 LDHVLLFGPPGLGKTTLAHI   71 (332)
T ss_pred             cCeEEeeCCCCCcHHHHHHH
Confidence            47899999999999965543

>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=87.99  E-value=0.44  Score=46.46  Aligned_cols=47  Identities=15%  Similarity=0.297  Sum_probs=30.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGE  191 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~  191 (399)
                      .+|+++.|.||||||. ++..++..+..  .+.+++|.=|.-+.....++
T Consensus        15 ~~~~li~G~~GsGKT~-~i~~ll~~~~~--~g~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen   15 NRHILIIGATGSGKTQ-AIRHLLDQIRA--RGDRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             GG-EEEEE-TTSSHHH-HHHHHHHHHHH--TT-EEEEEEETTHHHHHH--
T ss_pred             hCcEEEECCCCCCHHH-HHHHHHHHHHH--cCCEEEEEECCchHHHHhcC
Confidence            5999999999999996 44566766644  24567777787766554444

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.

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=87.91  E-value=0.93  Score=41.14  Aligned_cols=24  Identities=21%  Similarity=0.401  Sum_probs=17.4

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSR  166 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~  166 (399)
                      ..-+|+.++|||||+.... +++.+
T Consensus       127 RGLviiVGaTGSGKSTtmA-aMi~y  150 (375)
T COG5008         127 RGLVIIVGATGSGKSTTMA-AMIGY  150 (375)
T ss_pred             CceEEEECCCCCCchhhHH-HHhcc
Confidence            4678899999999997543 44443

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=87.87  E-value=0.26  Score=45.49  Aligned_cols=26  Identities=35%  Similarity=0.470  Sum_probs=20.2

Q ss_pred             HhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        133 ALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       133 ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      .+..++.. +++++++||+|+|||...
T Consensus        25 ll~~l~~~-~~pvLl~G~~GtGKT~li   50 (272)
T PF12775_consen   25 LLDLLLSN-GRPVLLVGPSGTGKTSLI   50 (272)
T ss_dssp             HHHHHHHC-TEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHHc-CCcEEEECCCCCchhHHH
Confidence            34444555 899999999999999754

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=87.85  E-value=1.6  Score=42.27  Aligned_cols=27  Identities=11%  Similarity=0.204  Sum_probs=19.5

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhC
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVN  168 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~  168 (399)
                      .|+..++.||.|+|||.... .+...+.
T Consensus       168 kGQR~lIvgppGvGKTTLaK-~Ian~I~  194 (416)
T PRK09376        168 KGQRGLIVAPPKAGKTVLLQ-NIANSIT  194 (416)
T ss_pred             cCceEEEeCCCCCChhHHHH-HHHHHHH
Confidence            48999999999999995432 2444443

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=87.82  E-value=1.9  Score=40.66  Aligned_cols=39  Identities=15%  Similarity=0.285  Sum_probs=24.2

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEe
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSA  286 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SA  286 (399)
                      ...+++|||+||.|..  .....+.+++..-| +..++++|.
T Consensus       123 ~~~kVvII~~ae~m~~--~aaNaLLK~LEEPp-~~~fILi~~  161 (314)
T PRK07399        123 APRKVVVIEDAETMNE--AAANALLKTLEEPG-NGTLILIAP  161 (314)
T ss_pred             CCceEEEEEchhhcCH--HHHHHHHHHHhCCC-CCeEEEEEC
Confidence            5678999999999854  23333444444444 565555544

>KOG0740|consensus

Probab=87.81  E-value=2.1  Score=41.78  Aligned_cols=58  Identities=19%  Similarity=0.227  Sum_probs=32.4

Q ss_pred             CceeEEEEechhhHhhcCCch--H-----HHHHHH----HhCCCCCcEEEEEee-CChhHHHHHHhhCCC
Q psy11867        245 SKIKVFVLDEADVMIATQGHQ--D-----FSIRIQ----KRLPSDCQIMLFSAT-YDKEVMEFAQDMVPN  302 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~--~-----~~~~i~----~~l~~~~q~l~~SAT-~~~~v~~~~~~~~~~  302 (399)
                      ....+++|||+|.++....-.  +     ....++    .....+-++++++|| .|..+.+-++..+..
T Consensus       244 ~qPsvifidEidslls~Rs~~e~e~srr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~Rrf~k  313 (428)
T KOG0740|consen  244 LQPSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARRRFVK  313 (428)
T ss_pred             cCCeEEEechhHHHHhhcCCcccccchhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHHHhhc
Confidence            356688899999998543111  1     111111    122345689999999 444555555444333

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=87.77  E-value=2.1  Score=44.90  Aligned_cols=20  Identities=30%  Similarity=0.454  Sum_probs=16.2

Q ss_pred             CcEEEEccCCCCceehhHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLT  162 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~  162 (399)
                      +-++++||.|+|||.++.+-
T Consensus        41 HAYLF~GP~GtGKTt~AriL   60 (725)
T PRK07133         41 HAYLFSGPRGTGKTSVAKIF   60 (725)
T ss_pred             eEEEEECCCCCcHHHHHHHH
Confidence            45689999999999877543

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=87.67  E-value=2.5  Score=42.08  Aligned_cols=22  Identities=27%  Similarity=0.350  Sum_probs=17.3

Q ss_pred             CCcEEEEccCCCCceehhHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      ++.+++.||.|+|||.++..-+
T Consensus        39 ~ha~Lf~Gp~G~GKtt~A~~lA   60 (451)
T PRK06305         39 AHAYLFSGIRGTGKTTLARIFA   60 (451)
T ss_pred             ceEEEEEcCCCCCHHHHHHHHH
Confidence            3568899999999998765533

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=87.63  E-value=3.6  Score=37.05  Aligned_cols=54  Identities=15%  Similarity=0.142  Sum_probs=30.3

Q ss_pred             cEEEEccCCCCceehhHHHHHHhhC---------CCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        144 NMIAQSQSGTGKTAAFTLTMLSRVN---------PSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l~il~~l~---------~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      -.++.||.|+|||...+--++....         ....+.+++|++- ..=..++.+.+..++.
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~-Ed~~~~i~~Rl~~i~~   65 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSA-EDPREEIHRRLEAILQ   65 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEEC-CCCHHHHHHHHHHHHh
Confidence            3578899999999766554443221         1123456888882 1122344445555544

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=87.56  E-value=0.8  Score=47.56  Aligned_cols=54  Identities=17%  Similarity=0.292  Sum_probs=38.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH--HHHHHHHHHHHHhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE--LAIQIGEVVAKMGK  198 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~--La~Q~~~~~~~~~~  198 (399)
                      .+|+++.|+||+|||..+.+-+.+.+..   +..++++=|-..  |...++..++..+.
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i~~---g~~viv~DpKgD~~l~~~~~~~~~~~G~  231 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDIRR---GDVVIVIDPKGDADLKRRMRAEAKRAGR  231 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCchHHHHHHHHHHHHhCC
Confidence            6899999999999998875555555543   334666667654  77777777777654

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>TIGR00416 sms DNA repair protein RadA

Probab=87.39  E-value=2.1  Score=42.70  Aligned_cols=52  Identities=17%  Similarity=0.219  Sum_probs=35.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      |.-+++.+++|+|||...+.-+.....   .+.+++|++.- +-..|+...+.+++
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~---~g~kvlYvs~E-Es~~qi~~ra~rlg  145 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAK---NQMKVLYVSGE-ESLQQIKMRAIRLG  145 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHh---cCCcEEEEECc-CCHHHHHHHHHHcC
Confidence            788999999999999765543333322   23458888754 45567776666654

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)).

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=87.39  E-value=0.75  Score=46.32  Aligned_cols=56  Identities=16%  Similarity=0.074  Sum_probs=39.9

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      +|+-+++.+++|+|||.-.+--+.+.+.+  .+-.++|++- .|-..++.+.++.++-.
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~--~ge~~lyvs~-eE~~~~l~~~~~~~G~~   75 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIH--FDEPGVFVTF-EESPQDIIKNARSFGWD   75 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHh--CCCCEEEEEE-ecCHHHHHHHHHHcCCC
Confidence            37999999999999997766555554443  1234888884 46667778888877644

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.

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=87.26  E-value=2  Score=39.03  Aligned_cols=18  Identities=17%  Similarity=0.165  Sum_probs=15.9

Q ss_pred             CCCcEEEEccCCCCceeh
Q psy11867        141 PPHNMIAQSQSGTGKTAA  158 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~  158 (399)
                      .|+.+++.++.|+|||..
T Consensus        15 ~Gqr~~I~G~~G~GKTTL   32 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTL   32 (249)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            389999999999999953

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.

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=87.21  E-value=2  Score=36.55  Aligned_cols=36  Identities=25%  Similarity=0.321  Sum_probs=19.2

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM  282 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l  282 (399)
                      ...+++|+||+=.|-.  ....+...+...+.++..++
T Consensus        94 ~~~~liviDEIG~mEl--~~~~F~~~v~~~l~s~~~vi  129 (168)
T PF03266_consen   94 SSSDLIVIDEIGKMEL--KSPGFREAVEKLLDSNKPVI  129 (168)
T ss_dssp             HCCHEEEE---STTCC--C-CHHHHHHHHHHCTTSEEE
T ss_pred             CCCCEEEEeccchhhh--cCHHHHHHHHHHHcCCCcEE
Confidence            5678999999998843  23334444555555555544

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=87.07  E-value=0.72  Score=40.48  Aligned_cols=27  Identities=19%  Similarity=0.340  Sum_probs=17.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVN  168 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~  168 (399)
                      ..|+++.|.||||||.+....+.+.+.
T Consensus        38 ~~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             S-SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             CceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            359999999999999776554444444

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.01  E-value=2.8  Score=42.19  Aligned_cols=20  Identities=35%  Similarity=0.454  Sum_probs=15.5

Q ss_pred             CcEEEEccCCCCceehhHHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTLT  162 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~  162 (399)
                      +-.++.||.|+|||.++.+-
T Consensus        39 hayLf~Gp~G~GKTtlAr~l   58 (486)
T PRK14953         39 HAYIFAGPRGTGKTTIARIL   58 (486)
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            34578999999999776553

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=86.92  E-value=0.45  Score=46.80  Aligned_cols=45  Identities=16%  Similarity=0.301  Sum_probs=30.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      .+|+++.|+||||||.. +..++..+..  .+.+++|+=|..++....
T Consensus        42 ~~h~~i~g~tGsGKt~~-i~~l~~~~~~--~~~~~vi~D~kg~~~~~~   86 (410)
T cd01127          42 EAHTMIIGTTGTGKTTQ-IRELLASIRA--RGDRAIIYDPNGGFVSKF   86 (410)
T ss_pred             hccEEEEcCCCCCHHHH-HHHHHHHHHh--cCCCEEEEeCCcchhHhh
Confidence            58999999999999975 3344444332  234577777777765443

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=86.91  E-value=2.4  Score=43.46  Aligned_cols=19  Identities=26%  Similarity=0.352  Sum_probs=16.1

Q ss_pred             CcEEEEccCCCCceehhHH
Q psy11867        143 HNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l  161 (399)
                      +-+++.||.|+|||.++.+
T Consensus        39 hayLf~Gp~G~GKTt~Ar~   57 (563)
T PRK06647         39 NAYIFSGPRGVGKTSSARA   57 (563)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            5589999999999987655

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=86.76  E-value=1.2  Score=33.29  Aligned_cols=37  Identities=16%  Similarity=0.325  Sum_probs=32.0

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCH
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTV  380 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~  380 (399)
                      ..++++||.+-..+...+..|+..|+++..+.||+..
T Consensus        51 ~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~~   87 (90)
T cd01524          51 DKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYKT   87 (90)
T ss_pred             CCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHHH
Confidence            3689999998778888999999999999999999753

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=86.68  E-value=0.4  Score=44.05  Aligned_cols=19  Identities=26%  Similarity=0.251  Sum_probs=17.1

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      |+++++.||+|+|||..+.
T Consensus        21 g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        21 GYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             CCeEEEEcCCCCCHHHHHH
Confidence            7999999999999997664

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).

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

Probab=86.63  E-value=5.6  Score=33.90  Aligned_cols=141  Identities=15%  Similarity=0.166  Sum_probs=64.4

Q ss_pred             EEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcE
Q psy11867        145 MIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQI  224 (399)
Q Consensus       145 vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I  224 (399)
                      +.+-...|-|||.|++=-++..+-.   +.+++++-=.+.  ...+.+...+. .++.+.....-.+......... .+ 
T Consensus         6 i~vytG~GKGKTTAAlGlalRA~G~---G~rV~ivQFlKg--~~~~GE~~~l~-~l~~~~~~~~g~~f~~~~~~~~-~~-   77 (172)
T PF02572_consen    6 IQVYTGDGKGKTTAALGLALRAAGH---GMRVLIVQFLKG--GRYSGELKALK-KLPNVEIERFGKGFVWRMNEEE-ED-   77 (172)
T ss_dssp             EEEEESSSS-HHHHHHHHHHHHHCT---T--EEEEESS----SS--HHHHHHG-GGT--EEEE--TT----GGGHH-HH-
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHhC---CCEEEEEEEecC--CCCcCHHHHHH-hCCeEEEEEcCCcccccCCCcH-HH-
Confidence            4555668999999988777776654   345777764443  01112222222 2223222211111111100000 00 


Q ss_pred             EEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCc--hHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHH
Q psy11867        225 IIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGH--QDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ  297 (399)
Q Consensus       225 lV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~--~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~  297 (399)
                       .......++...  +.+.-..+++||+||+-..+.. ++  .+.+..+++..|...-+|+.--..|+.+.+.+.
T Consensus        78 -~~~~~~~~~~a~--~~i~~~~~dlvILDEi~~a~~~-gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~AD  148 (172)
T PF02572_consen   78 -RAAAREGLEEAK--EAISSGEYDLVILDEINYAVDY-GLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEAAD  148 (172)
T ss_dssp             -HHHHHHHHHHHH--HHTT-TT-SEEEEETHHHHHHT-TSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH-S
T ss_pred             -HHHHHHHHHHHH--HHHhCCCCCEEEEcchHHHhHC-CCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHhCC
Confidence             011112222211  2333567899999999888764 43  345667777777788888877777877777664

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.

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=86.57  E-value=1.7  Score=45.65  Aligned_cols=70  Identities=19%  Similarity=0.207  Sum_probs=55.5

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-CCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-IQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      .+++-|.+|+...    ...++|.|..|||||.+-.--+.+.+... ....+++.++=|+.-|.++.+.+.++..
T Consensus         2 ~Ln~~Q~~av~~~----~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP----DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC----CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHhC
Confidence            5788999999765    47788889999999988776666666553 2344689999999999999999988875

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=86.50  E-value=2.6  Score=39.78  Aligned_cols=55  Identities=11%  Similarity=0.021  Sum_probs=32.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCC---CCCCCeEEEEeCcHHH-HHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNP---SIQEPQVLCLAPTYEL-AIQIGEVVAKM  196 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~---~~~~~~~lil~Pt~~L-a~Q~~~~~~~~  196 (399)
                      |.-+.+.+++|+|||...+-.++....+   ...+.+++||.--..+ ..++.+.++.+
T Consensus        96 G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~~  154 (313)
T TIGR02238        96 MSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAERF  154 (313)
T ss_pred             CeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHHc
Confidence            6778899999999996654433322211   1234578888743321 34455544444

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>KOG2228|consensus

Probab=86.48  E-value=13  Score=35.29  Aligned_cols=19  Identities=26%  Similarity=0.412  Sum_probs=16.4

Q ss_pred             CCCCcEEEEccCCCCceeh
Q psy11867        140 DPPHNMIAQSQSGTGKTAA  158 (399)
Q Consensus       140 ~~g~~vi~~a~TGsGKT~~  158 (399)
                      +.+..+++.+|-|||||..
T Consensus        47 gEsnsviiigprgsgkT~l   65 (408)
T KOG2228|consen   47 GESNSVIIIGPRGSGKTIL   65 (408)
T ss_pred             cCCCceEEEccCCCCceEe
Confidence            3478999999999999964

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=86.48  E-value=6.7  Score=41.45  Aligned_cols=59  Identities=15%  Similarity=0.364  Sum_probs=40.1

Q ss_pred             HHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhc----CCCccc
Q psy11867        334 AVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE-GLNVGLLSGELTVEQRLSILDRFRE----GEFKIY  398 (399)
Q Consensus       334 ~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~-g~~v~~lhg~~~~~~R~~v~~~F~~----G~~~IL  398 (399)
                      .+..++.  ..+.++||++|.+..+.++..|... +.. ...+|.   ..|..+++.|++    |+-.||
T Consensus       526 ~i~~l~~--~~gg~LVlFtSy~~l~~v~~~l~~~~~~~-ll~Q~~---~~~~~ll~~f~~~~~~~~~~VL  589 (697)
T PRK11747        526 FLPELLE--KHKGSLVLFASRRQMQKVADLLPRDLRLM-LLVQGD---QPRQRLLEKHKKRVDEGEGSVL  589 (697)
T ss_pred             HHHHHHh--cCCCEEEEeCcHHHHHHHHHHHHHhcCCc-EEEeCC---chHHHHHHHHHHHhccCCCeEE
Confidence            3444545  3456999999999999999998743 333 344554   357788877774    555565

>KOG0344|consensus

Probab=86.26  E-value=7.9  Score=38.98  Aligned_cols=96  Identities=18%  Similarity=0.134  Sum_probs=71.9

Q ss_pred             ccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhh-------hhhccC
Q psy11867        149 SQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE-------RNKKIT  221 (399)
Q Consensus       149 a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~  221 (399)
                      .-.+.||+..-++++.+.+..+ -.|-+||.+-+.+-|.|++..+.    .+.++++..++|.....       +-..+.
T Consensus       364 elvF~gse~~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~L~~~L~----~~~~i~v~vIh~e~~~~qrde~~~~FR~g~  438 (593)
T KOG0344|consen  364 ELVFCGSEKGKLLALRQLVASG-FKPPVLIFVQSKERAKQLFEELE----IYDNINVDVIHGERSQKQRDETMERFRIGK  438 (593)
T ss_pred             hheeeecchhHHHHHHHHHhcc-CCCCeEEEEecHHHHHHHHHHhh----hccCcceeeEecccchhHHHHHHHHHhccC
Confidence            3468899988888888877765 56779999999999999999887    23578888888874432       222455


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechh
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD  256 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah  256 (399)
                      ..++|||-  ++.     +.+++.++.+||.++.-
T Consensus       439 IwvLicTd--ll~-----RGiDf~gvn~VInyD~p  466 (593)
T KOG0344|consen  439 IWVLICTD--LLA-----RGIDFKGVNLVINYDFP  466 (593)
T ss_pred             eeEEEehh--hhh-----ccccccCcceEEecCCC
Confidence            67999995  222     45899999999997753

>smart00450 RHOD Rhodanese Homology Domain

Probab=86.01  E-value=1.9  Score=32.16  Aligned_cols=41  Identities=22%  Similarity=0.332  Sum_probs=34.3

Q ss_pred             ccCCCCcEEEEecchHhHHHHHHHHHHCCCe-EEEEcCCCCH
Q psy11867        340 GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLN-VGLLSGELTV  380 (399)
Q Consensus       340 ~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~-v~~lhg~~~~  380 (399)
                      ......++|+||.+-..+..++..|...|+. +..|.||+..
T Consensus        52 ~~~~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~~   93 (100)
T smart00450       52 GLDKDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYKE   93 (100)
T ss_pred             CCCCCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHHH
Confidence            3344568999999988999999999999987 9999999754

An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=85.96  E-value=1.8  Score=47.03  Aligned_cols=56  Identities=20%  Similarity=0.198  Sum_probs=50.4

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKE----GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~----g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+++|.++|+.-|.+.++.+.+.    ++++..++|..+..++..+++.+++|+.+|+|
T Consensus       500 g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVI  559 (926)
T TIGR00580       500 GKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILI  559 (926)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEE
Confidence            468999999999999999888764    67889999999999999999999999999875

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.

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

Probab=85.96  E-value=3.6  Score=43.12  Aligned_cols=60  Identities=18%  Similarity=0.268  Sum_probs=41.1

Q ss_pred             HHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCe-EEEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        332 FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLN-VGLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       332 ~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~-v~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                      ...+..++...+ ++++||++|.+..+.+++.+...... ....+|..   .+...++.|+.+.-
T Consensus       468 ~~~i~~~~~~~~-~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~---~~~~~l~~f~~~~~  528 (654)
T COG1199         468 AAYLREILKASP-GGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGED---EREELLEKFKASGE  528 (654)
T ss_pred             HHHHHHHHhhcC-CCEEEEeccHHHHHHHHHHHhhcCccceeeecCCC---cHHHHHHHHHHhcC
Confidence            334444555444 59999999999999999999876542 34444544   44478888887543

>cd01131 PilT Pilus retraction ATPase PilT

Probab=85.79  E-value=0.78  Score=40.15  Aligned_cols=39  Identities=18%  Similarity=0.440  Sum_probs=23.6

Q ss_pred             cEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      -+++++|||||||... ..++..+... .+.+++.+--..|
T Consensus         3 lilI~GptGSGKTTll-~~ll~~~~~~-~~~~i~t~e~~~E   41 (198)
T cd01131           3 LVLVTGPTGSGKSTTL-AAMIDYINKN-KTHHILTIEDPIE   41 (198)
T ss_pred             EEEEECCCCCCHHHHH-HHHHHHhhhc-CCcEEEEEcCCcc
Confidence            4789999999999764 3345554432 2334555554434

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.

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=85.42  E-value=6.1  Score=34.86  Aligned_cols=139  Identities=15%  Similarity=0.193  Sum_probs=70.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe---CcHHHHHHHHHH----HHHHhccCCCcEEEE-EEcCch
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA---PTYELAIQIGEV----VAKMGKHITDLSVRY-AVRGEN  213 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~---Pt~~La~Q~~~~----~~~~~~~~~~~~~~~-~~~~~~  213 (399)
                      |.=+++.++.|+|||+.-+--+.-.+..   +.++.+++   ++++...|+...    ...+...  .+.+.. ...+..
T Consensus        28 GsL~lIEGd~~tGKSvLsqr~~YG~L~~---g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G--~l~~~~~~~~~~~  102 (235)
T COG2874          28 GSLILIEGDNGTGKSVLSQRFAYGFLMN---GYRVTYVSTELTVREFIKQMESLSYDVSDFLLSG--RLLFFPVNLEPVN  102 (235)
T ss_pred             CeEEEEECCCCccHHHHHHHHHHHHHhC---CceEEEEEechhHHHHHHHHHhcCCCchHHHhcc--eeEEEEecccccc
Confidence            6788999999999996554433333333   34466665   566666665321    1111111  111111 112222


Q ss_pred             hhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHH---HHhCCCCCcEEEEEee---
Q psy11867        214 LERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRI---QKRLPSDCQIMLFSAT---  287 (399)
Q Consensus       214 ~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i---~~~l~~~~q~l~~SAT---  287 (399)
                      +.+..          -..+++.+.+  .....+-+++|+|-...+... .-...+..+   ++.+....+++++|+-   
T Consensus       103 ~~~~~----------~~~~L~~l~~--~~k~~~~dViIIDSls~~~~~-~~~~~vl~fm~~~r~l~d~gKvIilTvhp~~  169 (235)
T COG2874         103 WGRRS----------ARKLLDLLLE--FIKRWEKDVIIIDSLSAFATY-DSEDAVLNFMTFLRKLSDLGKVIILTVHPSA  169 (235)
T ss_pred             cChHH----------HHHHHHHHHh--hHHhhcCCEEEEecccHHhhc-ccHHHHHHHHHHHHHHHhCCCEEEEEeChhh
Confidence            22211          1123443322  222556779999999887643 222223222   3445567789999986   


Q ss_pred             CChhHHHHHHh
Q psy11867        288 YDKEVMEFAQD  298 (399)
Q Consensus       288 ~~~~v~~~~~~  298 (399)
                      +++++.-.++.
T Consensus       170 l~e~~~~rirs  180 (235)
T COG2874         170 LDEDVLTRIRS  180 (235)
T ss_pred             cCHHHHHHHHH
Confidence            34444433333

>PRK04841 transcriptional regulator MalT; Provisional

Probab=85.36  E-value=3.2  Score=45.19  Aligned_cols=43  Identities=9%  Similarity=0.184  Sum_probs=33.3

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      .--++|||++|.+-+ ....+.+..+++.++.+..+++.|-+.+
T Consensus       121 ~~~~lvlDD~h~~~~-~~~~~~l~~l~~~~~~~~~lv~~sR~~~  163 (903)
T PRK04841        121 QPLYLVIDDYHLITN-PEIHEAMRFFLRHQPENLTLVVLSRNLP  163 (903)
T ss_pred             CCEEEEEeCcCcCCC-hHHHHHHHHHHHhCCCCeEEEEEeCCCC
Confidence            345899999999743 3455677888888998999988887754

>KOG2036|consensus

Probab=85.30  E-value=3.6  Score=42.31  Aligned_cols=63  Identities=21%  Similarity=0.220  Sum_probs=41.8

Q ss_pred             hHHHHHHhhhhhc----C-CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHH
Q psy11867        127 SKIQETALPTLLA----D-PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGE  191 (399)
Q Consensus       127 ~~iQ~~ai~~ll~----~-~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~  191 (399)
                      |--|..|+-.+..    . -..-+-+.|.-|-||+.|..+.+...+.-+.  ..+.|-+|.-+=..-..+
T Consensus       255 T~dQakav~~f~dai~eK~lr~~vsLtA~RGRGKSAALGlsiA~AVa~Gy--snIyvtSPspeNlkTlFe  322 (1011)
T KOG2036|consen  255 TLDQAKAVLTFFDAIVEKTLRSTVSLTASRGRGKSAALGLSIAGAVAFGY--SNIYVTSPSPENLKTLFE  322 (1011)
T ss_pred             hHHHHHHHHHHHHHHHHhhhcceEEEEecCCCCchhhhhHHHHHHHhcCc--ceEEEcCCChHHHHHHHH
Confidence            5567777755432    1 1345667789999999999998887776543  336667788765444333

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=85.26  E-value=2.4  Score=40.95  Aligned_cols=19  Identities=21%  Similarity=0.345  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+.+++.||.|+|||....
T Consensus        39 ~~~~L~~G~~G~GKt~~a~   57 (367)
T PRK14970         39 AQALLFCGPRGVGKTTCAR   57 (367)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3679999999999996554

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=85.22  E-value=2.5  Score=42.43  Aligned_cols=56  Identities=14%  Similarity=0.260  Sum_probs=51.4

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+.+||.+++++-+...+..|...|+.+..++|+.+..++..++...+.|+.+||+
T Consensus        51 ~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~  106 (470)
T TIGR00614        51 DGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLY  106 (470)
T ss_pred             CCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEE
Confidence            46799999999999999999999999999999999999999999999999988874

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

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=85.19  E-value=16  Score=34.55  Aligned_cols=132  Identities=20%  Similarity=0.178  Sum_probs=66.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe-C-cHHHH-HHHHHHHHHHhccCCCcEEEEEEcCchhhhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA-P-TYELA-IQIGEVVAKMGKHITDLSVRYAVRGENLERNK  218 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~-P-t~~La-~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (399)
                      +.-+++.+..|+|||..-.=-+-....   .+.++++.+ - -|+=| .|...+.++.     ++.+.....|.      
T Consensus       139 p~Vil~vGVNG~GKTTTIaKLA~~l~~---~g~~VllaA~DTFRAaAiEQL~~w~er~-----gv~vI~~~~G~------  204 (340)
T COG0552         139 PFVILFVGVNGVGKTTTIAKLAKYLKQ---QGKSVLLAAGDTFRAAAIEQLEVWGERL-----GVPVISGKEGA------  204 (340)
T ss_pred             cEEEEEEecCCCchHhHHHHHHHHHHH---CCCeEEEEecchHHHHHHHHHHHHHHHh-----CCeEEccCCCC------
Confidence            456788999999999765432222222   333455554 2 34433 4444444443     22222211111      


Q ss_pred             ccCCcEEEeCchhH-HHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCC------cEEEEEeeCChh
Q psy11867        219 KITEQIIIGTPGKV-LDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC------QIMLFSATYDKE  291 (399)
Q Consensus       219 ~~~~~IlV~Tp~~l-~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~------q~l~~SAT~~~~  291 (399)
                               -|..+ .+.+.   .-.-+++++|++|=|-||-......+.+..|.+.+.+..      -++.+-||...+
T Consensus       205 ---------DpAaVafDAi~---~Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqn  272 (340)
T COG0552         205 ---------DPAAVAFDAIQ---AAKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQN  272 (340)
T ss_pred             ---------CcHHHHHHHHH---HHHHcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChh
Confidence                     11111 11111   112346677777777777544344555556665554433      234448998877


Q ss_pred             HHHHHHhh
Q psy11867        292 VMEFAQDM  299 (399)
Q Consensus       292 v~~~~~~~  299 (399)
                      ...-++.|
T Consensus       273 al~QAk~F  280 (340)
T COG0552         273 ALSQAKIF  280 (340)
T ss_pred             HHHHHHHH
Confidence            65555554

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=85.18  E-value=2  Score=37.01  Aligned_cols=57  Identities=14%  Similarity=0.094  Sum_probs=34.1

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCC-------CCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPS-------IQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~-------~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      |.-+++.|++|+|||...+--+...+...       ....+++++..-.. ..++.+.+..+...
T Consensus        32 g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~~   95 (193)
T PF13481_consen   32 GELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQD   95 (193)
T ss_dssp             TSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHTT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhcc
Confidence            67899999999999976554444444211       13456777765443 55777777776643

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=85.13  E-value=0.87  Score=40.72  Aligned_cols=41  Identities=17%  Similarity=0.347  Sum_probs=27.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      ++|+.|.|.||||||..... +++.+.. ..+..++|+=|.-|
T Consensus        23 ~~H~~I~G~TGsGKS~~~~~-ll~~l~~-~~~~~~ii~D~~GE   63 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVKV-LLEELLK-KKGAKVIIFDPHGE   63 (229)
T ss_pred             cceEEEECCCCCCHHHHHHH-HHHHHHh-cCCCCEEEEcCCCc
Confidence            48999999999999976554 3333332 23445777767654

It contains several conserved aspartates and histidines that could be metal ligands.

>PHA02542 41 41 helicase; Provisional

Probab=85.06  E-value=2.5  Score=42.35  Aligned_cols=43  Identities=14%  Similarity=0.085  Sum_probs=27.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe---CcHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA---PTYELAI  187 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~---Pt~~La~  187 (399)
                      |.-+++.|.+|.|||...+--+.....   .+..+++++   |...|+.
T Consensus       190 G~LiiIaarPgmGKTtfalniA~~~a~---~g~~Vl~fSLEM~~~ql~~  235 (473)
T PHA02542        190 KTLNVLLAGVNVGKSLGLCSLAADYLQ---QGYNVLYISMEMAEEVIAK  235 (473)
T ss_pred             CcEEEEEcCCCccHHHHHHHHHHHHHh---cCCcEEEEeccCCHHHHHH
Confidence            567788999999999766654444442   234467666   4444443

>KOG0741|consensus

Probab=84.96  E-value=6.7  Score=39.32  Aligned_cols=71  Identities=23%  Similarity=0.199  Sum_probs=43.0

Q ss_pred             cCCCCHHHHHHHHHcCCCCChHHHHHHhhhh-------hc---CCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeE
Q psy11867        107 ALHLKPELLKGVYEMGFYAPSKIQETALPTL-------LA---DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQV  176 (399)
Q Consensus       107 ~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~l-------l~---~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~  176 (399)
                      .+|.+++-++.....|...-.+.-.+.+..-       ..   .+-..+++.+|.|||||..+.-.++     ....|.+
T Consensus       493 AFG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLAA~iA~-----~S~FPFv  567 (744)
T KOG0741|consen  493 AFGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAAKIAL-----SSDFPFV  567 (744)
T ss_pred             ccCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHHHHHHHh-----hcCCCeE
Confidence            4678888888888777654443333333211       00   1236899999999999954433222     2345667


Q ss_pred             EEEeCc
Q psy11867        177 LCLAPT  182 (399)
Q Consensus       177 lil~Pt  182 (399)
                      =|++|.
T Consensus       568 KiiSpe  573 (744)
T KOG0741|consen  568 KIISPE  573 (744)
T ss_pred             EEeChH
Confidence            777774

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=84.91  E-value=1.6  Score=45.17  Aligned_cols=54  Identities=15%  Similarity=0.218  Sum_probs=40.8

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH--HHHHHHHHHHHHHhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY--ELAIQIGEVVAKMGK  198 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~--~La~Q~~~~~~~~~~  198 (399)
                      ..|.++.|+||+|||..+.+-+.+.+..   +..++++=|-.  ++...++..++..+.
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i~~---g~~vi~fDpkgD~el~~~~~~~~~~~GR  235 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDIRR---GDVVIVFDPKGDADLLKRMYAEAKRAGR  235 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCCHHHHHHHHHHHHHhCC
Confidence            5899999999999999887766666643   34577777765  577777777777765

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>KOG0331|consensus

Probab=84.81  E-value=4.4  Score=40.67  Aligned_cols=70  Identities=10%  Similarity=0.150  Sum_probs=51.1

Q ss_pred             CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh-------ccCCcEEEeCchhHHHhhhcccccc
Q psy11867        171 IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK-------KITEQIIIGTPGKVLDWGLKYRFFD  243 (399)
Q Consensus       171 ~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~IlV~Tp~~l~~~~~~~~~~~  243 (399)
                      ....++||.|-|+.-|.++.+.++..+     .+...++|........       .+.+.|+|||-       .-.+.++
T Consensus       339 ~~~~KvIIFc~tkr~~~~l~~~l~~~~-----~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATd-------VAaRGLD  406 (519)
T KOG0331|consen  339 DSEGKVIIFCETKRTCDELARNLRRKG-----WPAVAIHGDKSQSERDWVLKGFREGKSPVLVATD-------VAARGLD  406 (519)
T ss_pred             cCCCcEEEEecchhhHHHHHHHHHhcC-----cceeeecccccHHHHHHHHHhcccCCcceEEEcc-------cccccCC
Confidence            356789999999999999988887753     4556666765543322       45678999996       2336788


Q ss_pred             CCceeEEEE
Q psy11867        244 LSKIKVFVL  252 (399)
Q Consensus       244 ~~~~~~lVi  252 (399)
                      +.++++||-
T Consensus       407 i~dV~lVIn  415 (519)
T KOG0331|consen  407 VPDVDLVIN  415 (519)
T ss_pred             CccccEEEe
Confidence            899999985

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=84.43  E-value=0.49  Score=32.84  Aligned_cols=18  Identities=17%  Similarity=0.370  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      |...++.+++|||||..+
T Consensus        23 g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            457999999999999643

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=83.86  E-value=1.4  Score=47.62  Aligned_cols=17  Identities=29%  Similarity=0.350  Sum_probs=14.3

Q ss_pred             cEEEEccCCCCceehhH
Q psy11867        144 NMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~  160 (399)
                      .+++.||||+|||..+-
T Consensus       598 ~~lf~Gp~GvGKT~lA~  614 (852)
T TIGR03345       598 VFLLVGPSGVGKTETAL  614 (852)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47999999999996653

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.

>KOG1131|consensus

Probab=83.70  E-value=4.2  Score=40.47  Aligned_cols=73  Identities=15%  Similarity=0.097  Sum_probs=40.1

Q ss_pred             CCCChHHHHHHhhhh---hcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC-CCCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        123 FYAPSKIQETALPTL---LADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI-QEPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~l---l~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~-~~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      |..-+|-|-+=.-.+   +.. +.+.++..|+|+|||.+.+--++..-..-+ ...+.++-+-|..=......+++.+
T Consensus        14 Y~~iYPEQ~~YM~elKrsLDa-kGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~l   90 (755)
T KOG1131|consen   14 YDYIYPEQYEYMRELKRSLDA-KGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKRL   90 (755)
T ss_pred             CcccCHHHHHHHHHHHHhhcc-CCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHHH
Confidence            444556665444333   322 789999999999999876544443322222 2334555555544334444444443

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=83.69  E-value=1.5  Score=46.53  Aligned_cols=17  Identities=24%  Similarity=0.397  Sum_probs=14.1

Q ss_pred             cEEEEccCCCCceehhH
Q psy11867        144 NMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~  160 (399)
                      .+++.||||+|||..+-
T Consensus       486 ~~lf~Gp~GvGKT~lA~  502 (731)
T TIGR02639       486 SFLFTGPTGVGKTELAK  502 (731)
T ss_pred             eEEEECCCCccHHHHHH
Confidence            57999999999995543

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=83.68  E-value=4.8  Score=41.00  Aligned_cols=18  Identities=28%  Similarity=0.488  Sum_probs=16.1

Q ss_pred             CCCcEEEEccCCCCceeh
Q psy11867        141 PPHNMIAQSQSGTGKTAA  158 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~  158 (399)
                      +|+-+.+.||+|||||..
T Consensus       360 ~G~~vaIvG~SGsGKSTL  377 (529)
T TIGR02868       360 PGERVAILGPSGSGKSTL  377 (529)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            489999999999999964

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	399
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-130
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-129
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-129
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-126
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-92
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		2e-89
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		6e-80
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-79
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		9e-69
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-62
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		3e-50
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-49
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-49
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-49
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		4e-49
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		5e-49
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		6e-49
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-48
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		4e-48
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		5e-48
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-41
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		1e-34
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		4e-33
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		1e-30
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		4e-30
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		4e-30
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		6e-30
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		4e-29
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		3e-28
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		1e-24
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		1e-24
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		2e-24
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		3e-24
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		1e-23
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		1e-20
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		7e-20
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		9e-20
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		1e-19
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-18
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		4e-18
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		4e-17
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		4e-17
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		5e-17
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		1e-15
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		6e-15
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		7e-15
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		1e-14
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		2e-14
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		8e-14
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		1e-13
3ly5_A	262	Ddx18 Dead-Domain Length = 262		6e-13
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		3e-12
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		9e-09
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		3e-08
3kx2_B	767	Crystal Structure Of Prp43p In Complex With Adp Len		3e-06
2xau_A	773	Crystal Structure Of The Prp43p Deah-Box Rna Helica		3e-06
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		4e-04

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score =  460 bits (1184), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 211/330 (63%), Positives = 271/330 (82%)
Query: 68  AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
           A +SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PS
Sbjct: 57  AAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPS 116
Query: 128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
           KIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+
Sbjct: 117 KIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELAL 176
Query: 188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           Q G+V+ +MGK   +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KI
Sbjct: 177 QTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKI 236
Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           KVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IK
Sbjct: 237 KVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIK 296
Query: 308 LKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE 367
           LKREEE+LD IKQ+YV+C + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKE
Sbjct: 297 LKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKE 356
Query: 368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           G  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct: 357 GHQVALLSGEMMVEQRAAVIERFREGKEKV 386

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score =  459 bits (1180), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 211/330 (63%), Positives = 271/330 (82%)
Query: 68  AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
           A +SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PS
Sbjct: 6   AAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPS 65
Query: 128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
           KIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+
Sbjct: 66  KIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELAL 125
Query: 188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           Q G+V+ +MGK   +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KI
Sbjct: 126 QTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKI 185
Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           KVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IK
Sbjct: 186 KVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIK 245
Query: 308 LKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE 367
           LKREEE+LD IKQ+YV+C + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKE
Sbjct: 246 LKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKE 305
Query: 368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           G  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct: 306 GHQVALLSGEMMVEQRAAVIERFREGKEKV 335

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score =  458 bits (1179), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 211/330 (63%), Positives = 271/330 (82%)
Query: 68  AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
           A +SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PS
Sbjct: 27  AAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPS 86
Query: 128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
           KIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+
Sbjct: 87  KIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELAL 146
Query: 188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           Q G+V+ +MGK   +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KI
Sbjct: 147 QTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKI 206
Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           KVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IK
Sbjct: 207 KVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIK 266
Query: 308 LKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE 367
           LKREEE+LD IKQ+YV+C + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKE
Sbjct: 267 LKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKE 326
Query: 368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           G  V LLSGE+ VEQR ++++RFREG+ K+
Sbjct: 327 GHQVALLSGEMMVEQRAAVIERFREGKEKV 356

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  446 bits (1148), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 205/318 (64%), Positives = 262/318 (82%)
Query: 80  GLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLA 139
            L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +LA
Sbjct: 2   NLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLA 61
Query: 140 DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH 199
           +PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+Q G+V+ +MGK 
Sbjct: 62  EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKF 121
Query: 200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI 259
             +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KIKVFVLDEADVMI
Sbjct: 122 YPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 181
Query: 260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIK 319
           ATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IKLKREEE+LD IK
Sbjct: 182 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIK 241
Query: 320 QHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT 379
           Q+YV+C + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKEG  V LLSGE+ 
Sbjct: 242 QYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMM 301
Query: 380 VEQRLSILDRFREGEFKI 397
           VEQR ++++RFREG+ K+
Sbjct: 302 VEQRAAVIERFREGKEKV 319

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score =  335 bits (860), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 156/244 (63%), Positives = 198/244 (81%)
Query: 68  AEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPS 127
           A +SLL K++R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PS
Sbjct: 57  AAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPS 116
Query: 128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI 187
           KIQE ALP +LA+PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+
Sbjct: 117 KIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELAL 176
Query: 188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           Q G+V+ +MGK   +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KI
Sbjct: 177 QTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKI 236
Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           KVFVLDEADVMIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IK
Sbjct: 237 KVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIK 296
Query: 308 LKRE 311
           LKRE
Sbjct: 297 LKRE 300

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score =  325 bits (834), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 152/234 (64%), Positives = 191/234 (81%)
Query: 80  GLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLA 139
            L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +LA
Sbjct: 2   NLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLA 61
Query: 140 DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH 199
           +PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+Q G+V+ +MGK 
Sbjct: 62  EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKF 121
Query: 200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI 259
             +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KIKVFVLDEADVMI
Sbjct: 122 YPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 181
Query: 260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE 313
           ATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IKLKREEE
Sbjct: 182 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE 235

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  294 bits (752), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 151/295 (51%), Positives = 207/295 (70%), Gaps = 3/295 (1%)
Query: 103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLT 162
           K+F+ L L PELLKG+Y M F  PSKIQE ALP LL +PP NMIAQSQSGTGKTAAF+LT
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 163 MLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE 222
           ML+RVNP    PQ +CLAP+ ELA Q  EVV +MGK  T ++ +  V  ++ E+NK+I  
Sbjct: 65  MLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGK-FTKITSQLIV-PDSFEKNKQINA 122
Query: 223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM 282
           Q+I+GTPG VLD  ++ +   L KIK+FVLDEAD M+  QG  D  IR+++ LP D Q++
Sbjct: 123 QVIVGTPGTVLDL-MRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLV 181
Query: 283 LFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVV 342
           LFSAT+   V ++A+ +VPN   ++L+  E ++D IKQ Y+ CKN  +KF+ ++ +YGV+
Sbjct: 182 LFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGVM 241
Query: 343 TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           TIG ++IF  T+KTA  L  K+  EG  V +L G+L  ++R  ++D FREG  K+
Sbjct: 242 TIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKV 296

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  293 bits (749), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 150/295 (50%), Positives = 207/295 (70%), Gaps = 3/295 (1%)
Query: 103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLT 162
           K+F+ L L PELLKG+Y M F  PSKIQE ALP LL +PP NMIAQSQSGTGKTAAF+LT
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 163 MLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE 222
           ML+RVNP    PQ +CLAP+ ELA Q  EVV +MGK  T ++ +  V  ++ E+NK+I  
Sbjct: 65  MLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGK-FTKITSQLIV-PDSFEKNKQINA 122
Query: 223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM 282
           Q+I+GTPG VLD  ++ +   L KIK+FVLDEAD M+  QG  D  IR+++ LP D Q++
Sbjct: 123 QVIVGTPGTVLDL-MRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLV 181
Query: 283 LFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVV 342
           LFSAT+   V ++A+ +VPN   ++L+  E ++D IKQ Y+ CKN  +KF+ ++ +YG++
Sbjct: 182 LFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLM 241
Query: 343 TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           TIG ++IF  T+KTA  L  K+  EG  V +L G+L  ++R  ++D FREG  K+
Sbjct: 242 TIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKV 296

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score =  236 bits (601), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 123/227 (54%), Positives = 162/227 (71%), Gaps = 3/227 (1%)
Query: 83  ESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPP 142
           E K +L   + DP+SPLYS K+F+ L L PELLKG+Y M F  PSKIQE ALP LL +PP
Sbjct: 2   EVKVKLADIQADPNSPLYSAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPP 61
Query: 143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD 202
            NMIAQSQSGTGKTAAF+LTML+RVNP    PQ +CLAP+ ELA Q  EVV +MGK  T 
Sbjct: 62  RNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGK-FTK 120
Query: 203 LSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ 262
           ++ +  V  ++ E+NK+I  Q+I+GTPG VLD  ++ +   L KIK+FVLDEAD M+  Q
Sbjct: 121 ITSQLIV-PDSFEKNKQINAQVIVGTPGTVLDL-MRRKLMQLQKIKIFVLDEADNMLDQQ 178
Query: 263 GHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK 309
           G  D  IR+++ LP D Q++LFSAT+   V ++A+ +VPN   ++L+
Sbjct: 179 GLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQ 225

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  195 bits (496), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 108/298 (36%), Positives = 181/298 (60%), Gaps = 7/298 (2%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           V  F+ + L   LL+GV+  GF  PS IQ+ A+  ++    H+++AQ+QSGTGKT  F++
Sbjct: 21  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPII--EGHDVLAQAQSGTGKTGTFSI 78
Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT 221
             L R++ S++ PQ L LAPT ELA+QI +VV  +  H+ D+ V   + G +   + +  
Sbjct: 79  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGL 137
Query: 222 E--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
              QI++GTPG+V D  ++ R F   KIK+F+LDEAD M+++ G ++   +I   LP   
Sbjct: 138 RDAQIVVGTPGRVFD-NIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTT 195
Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIY 339
           Q++L SAT   +V+E     + NP+ I +K++E +L+ IKQ YV  +  + K+E ++++Y
Sbjct: 196 QVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLY 255
Query: 340 GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
             +++ QA+IFC+TR+    L  K+  +   V  +  +L  ++R +I+  FR G  +I
Sbjct: 256 DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI 313

>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 =  192 bits (489), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 104/297 (35%), Positives = 179/297 (60%), Gaps = 8/297 (2%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TF+ + L+ +LL+G+Y  GF  PS IQ+ A+  ++     ++IAQSQSGTGKTA F++++
Sbjct: 39  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQII--KGRDVIAQSQSGTGKTATFSISV 96
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE---RNKKI 220
           L  ++  ++E Q L LAPT ELA+QI + +  +G ++ ++     + G N+    R    
Sbjct: 97  LQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDY 155
Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
            + ++ GTPG+V D  ++ R      IK+ VLDEAD M+  +G ++    + + LP   Q
Sbjct: 156 GQHVVAGTPGRVFDM-IRRRSLRTRAIKMLVLDEADEML-NKGFKEQIYDVYRYLPPATQ 213
Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG 340
           ++L SAT   E++E     + +P+ I +KR+E +L+ IKQ +V  +  + KF+ + ++Y 
Sbjct: 214 VVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 273
Query: 341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            +TI QA+IFC+T++   WL EKM +    V  + G++  ++R SI+  FR G  ++
Sbjct: 274 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRV 330

>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 =  192 bits (489), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 104/297 (35%), Positives = 179/297 (60%), Gaps = 8/297 (2%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TF+ + L+ +LL+G+Y  GF  PS IQ+ A+  ++     ++IAQSQSGTGKTA F++++
Sbjct: 39  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQII--KGRDVIAQSQSGTGKTATFSISV 96
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE---RNKKI 220
           L  ++  ++E Q L LAPT ELA+QI + +  +G ++ ++     + G N+    R    
Sbjct: 97  LQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDY 155
Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
            + ++ GTPG+V D  ++ R      IK+ VLDEAD M+  +G ++    + + LP   Q
Sbjct: 156 GQHVVAGTPGRVFDM-IRRRSLRTRAIKMLVLDEADEML-NKGFKEQIYDVYRYLPPATQ 213
Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG 340
           ++L SAT   E++E     + +P+ I +KR+E +L+ IKQ +V  +  + KF+ + ++Y 
Sbjct: 214 VVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 273
Query: 341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            +TI QA+IFC+T++   WL EKM +    V  + G++  ++R SI+  FR G  ++
Sbjct: 274 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRV 330

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  192 bits (489), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 104/297 (35%), Positives = 179/297 (60%), Gaps = 8/297 (2%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TF+ + L+ +LL+G+Y  GF  PS IQ+ A+  ++     ++IAQSQSGTGKTA F++++
Sbjct: 38  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQII--KGRDVIAQSQSGTGKTATFSISV 95
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE---RNKKI 220
           L  ++  ++E Q L LAPT ELA+QI + +  +G ++ ++     + G N+    R    
Sbjct: 96  LQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDY 154
Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
            + ++ GTPG+V D  ++ R      IK+ VLDEAD M+  +G ++    + + LP   Q
Sbjct: 155 GQHVVAGTPGRVFDM-IRRRSLRTRAIKMLVLDEADEML-NKGFKEQIYDVYRYLPPATQ 212
Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG 340
           ++L SAT   E++E     + +P+ I +KR+E +L+ IKQ +V  +  + KF+ + ++Y 
Sbjct: 213 VVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 272
Query: 341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            +TI QA+IFC+T++   WL EKM +    V  + G++  ++R SI+  FR G  ++
Sbjct: 273 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRV 329

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  192 bits (487), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 104/297 (35%), Positives = 179/297 (60%), Gaps = 8/297 (2%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TF+ + L+ +LL+G+Y  GF  PS IQ+ A+  ++     ++IAQSQSGTGKTA F++++
Sbjct: 17  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFSISV 74
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE---RNKKI 220
           L  ++  ++E Q L LAPT ELA+QI + +  +G ++ ++     + G N+    R    
Sbjct: 75  LQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDY 133
Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
            + ++ GTPG+V D  ++ R      IK+ VLDEAD M+  +G ++    + + LP   Q
Sbjct: 134 GQHVVAGTPGRVFDM-IRRRSLRTRAIKMLVLDEADEML-NKGFKEQIYDVYRYLPPATQ 191
Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG 340
           ++L SAT   E++E     + +P+ I +KR+E +L+ IKQ +V  +  + KF+ + ++Y 
Sbjct: 192 VVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 251
Query: 341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            +TI QA+IFC+T++   WL EKM +    V  + G++  ++R SI+  FR G  ++
Sbjct: 252 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRV 308

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  191 bits (486), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 104/297 (35%), Positives = 179/297 (60%), Gaps = 8/297 (2%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TF+ + L+ +LL+G+Y  GF  PS IQ+ A+  ++     ++IAQSQSGTGKTA F++++
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFSVSV 59
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE---RNKKI 220
           L  ++  ++E Q L LAPT ELA+Q+ + +  +G ++ ++     + G N+    R    
Sbjct: 60  LQCLDIQVRETQALILAPTRELAVQVQKGLLALGDYM-NVQSHACIGGTNVGEDIRKLDY 118
Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
            + ++ GTPG+V D  ++ R      IK+ VLDEAD M+  +G ++    + + LP   Q
Sbjct: 119 GQHVVAGTPGRVFDM-IRRRSLRTRAIKMLVLDEADEML-NKGFKEQIYDVYRYLPPATQ 176
Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG 340
           ++L SAT   EV+E     + +P+ I +KR+E +L+ IKQ +V  +  + KF+ + ++Y 
Sbjct: 177 VVLISATLPHEVLEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 236
Query: 341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            +TI QA+IFC+T++   WL EKM +    V  + G++  ++R SI+  FR G  ++
Sbjct: 237 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRV 293

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  191 bits (485), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 103/297 (34%), Positives = 179/297 (60%), Gaps = 8/297 (2%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TF+ + L+ +LL+G+Y  GF  PS IQ+ A+  ++     ++IAQSQSGTGKTA F++++
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFSVSV 59
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE---RNKKI 220
           L  ++  ++E Q L LAPT ELA+Q+ + +  +G ++ ++     + G N+    R    
Sbjct: 60  LQCLDIQVRETQALILAPTRELAVQVQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDY 118
Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
            + ++ GTPG+V D  ++ R      IK+ VLDEAD M+  +G ++    + + LP   Q
Sbjct: 119 GQHVVAGTPGRVFDM-IRRRSLRTRAIKMLVLDEADEML-NKGFKEQIYDVYRYLPPATQ 176
Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG 340
           ++L SAT   E++E     + +P+ I +KR+E +L+ IKQ +V  +  + KF+ + ++Y 
Sbjct: 177 VVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYD 236
Query: 341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            +TI QA+IFC+T++   WL EKM +    V  + G++  ++R SI+  FR G  ++
Sbjct: 237 TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRV 293

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  190 bits (482), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 107/298 (35%), Positives = 175/298 (58%), Gaps = 7/298 (2%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           V  F+   L   LL+GV+  GF  PS IQ+ A+  ++    H+++AQ+QSGTGKT  F++
Sbjct: 20  VYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEG--HDVLAQAQSGTGKTGTFSI 77
Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT 221
             L R++ S++ PQ L LAPT ELA+QI +VV  +  H  D+ V   + G +   + +  
Sbjct: 78  AALQRIDTSVKAPQALXLAPTRELALQIQKVVXALAFH-XDIKVHACIGGTSFVEDAEGL 136
Query: 222 E--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
              QI++GTPG+V D  ++ R F   KIK F+LDEAD  +++ G ++   +I   LP   
Sbjct: 137 RDAQIVVGTPGRVFD-NIQRRRFRTDKIKXFILDEADEXLSS-GFKEQIYQIFTLLPPTT 194
Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIY 339
           Q++L SAT   +V+E       NP+ I +K++E +L+ IKQ YV  +  + K+E ++++Y
Sbjct: 195 QVVLLSATXPNDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLY 254
Query: 340 GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
             +++ QA+IFC+TR+    L  K+  +   V  +  +L  ++R +I   FR G  +I
Sbjct: 255 DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRI 312

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  188 bits (478), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 109/301 (36%), Positives = 180/301 (59%), Gaps = 11/301 (3%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETA-LPTLLADPPHNMIAQSQSGTGKTAAFT 160
           V +F+ ++L   LL+G+Y  GF  PS IQ+ A LP +     +++IAQ+QSGTGKTA F 
Sbjct: 39  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKG---YDVIAQAQSGTGKTATFA 95
Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL----ER 216
           +++L ++   ++  Q L LAPT ELA QI +VV  +G ++   S    + G N+    ++
Sbjct: 96  ISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMG-ASCHACIGGTNVRAEVQK 154
Query: 217 NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
            +     II+GTPG+V D  L  R+     IK+FVLDEAD M+ ++G +D    I ++L 
Sbjct: 155 LQMEAPHIIVGTPGRVFDM-LNRRYLSPKYIKMFVLDEADEML-SRGFKDQIYDIFQKLN 212
Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
           S+ Q++L SAT   +V+E  +  + +P+ I +K+EE +L+ I+Q Y+  +  + K + + 
Sbjct: 213 SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLC 272
Query: 337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK 396
           ++Y  +TI QA+IF +TR+   WL EKM      V  + G++  ++R  I+  FR G  +
Sbjct: 273 DLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSR 332
Query: 397 I 397
           +
Sbjct: 333 V 333

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  188 bits (477), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 112/301 (37%), Positives = 180/301 (59%), Gaps = 11/301 (3%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETA-LPTLLADPPHNMIAQSQSGTGKTAAFT 160
           V +F+ ++L   LL+G+Y  GF  PS IQ+ A LP +     +++IAQ+QSGTGKTA F 
Sbjct: 13  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCI---KGYDVIAQAQSGTGKTATFA 69
Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL--ERNK 218
           +++L ++   ++  Q L LAPT ELA QI +VV  +G ++   S    + G N+  E  K
Sbjct: 70  ISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQK 128
Query: 219 KITE--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
              E   II+GTPG+V D  L  R+     IK+FVLDEAD M++ +G +D    I ++L 
Sbjct: 129 LQMEAPHIIVGTPGRVFDM-LNRRYLSPKYIKMFVLDEADEMLS-RGFKDQIYDIFQKLN 186
Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
           S+ Q++L SAT   +V+E  +  + +P+ I +K+EE +L+ I+Q Y+  +  + K + + 
Sbjct: 187 SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLC 246
Query: 337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK 396
           ++Y  +TI QA+IF +TR+   WL EKM      V  + G++  ++R  I+  FR G  +
Sbjct: 247 DLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSR 306
Query: 397 I 397
           +
Sbjct: 307 V 307

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  165 bits (418), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 105/299 (35%), Positives = 166/299 (55%), Gaps = 16/299 (5%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TFE  +LK ELL G++E GF  PS IQE A+P  +A    +++A++++GTGKTAAF +  
Sbjct: 22  TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIP--VAITGRDILARAKNGTGKTAAFVIPT 79
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KKI 220
           L +V P + + Q L + PT ELA+Q  +VV  +GKH   +S      G NL  +      
Sbjct: 80  LEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKH-CGISCMVTTGGTNLRDDILRLNE 138
Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQK---RLPS 277
           T  I++GTPG+VLD   + +  DLS   +F++DEAD M++    +DF   I++    LP 
Sbjct: 139 TVHILVGTPGRVLDLASR-KVADLSDCSLFIMDEADKMLS----RDFKTIIEQILSFLPP 193
Query: 278 DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSN 337
             Q +LFSAT+   V EF    +  P  I L  EE +L  I Q+Y   +   +K   ++ 
Sbjct: 194 THQSLLFSATFPLTVKEFMVKHLHKPYEINLM-EELTLKGITQYYAFVEE-RQKLHCLNT 251
Query: 338 IYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK 396
           ++  + I QA+IFC++      LA+K++  G +       +  ++R  +   FR+G+ +
Sbjct: 252 LFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVR 310

>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 =  144 bits (362), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 83/217 (38%), Positives = 134/217 (61%), Gaps = 7/217 (3%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           V  F+ + L   LL+GV+  GF  PS IQ+ A+  ++    H+++AQ+QSGTGKT  F++
Sbjct: 13  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEG--HDVLAQAQSGTGKTGTFSI 70
Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT 221
             L R++ S++ PQ L LAPT ELA+QI +VV  +  H+ D+ V   + G +   + +  
Sbjct: 71  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGL 129
Query: 222 E--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
              QI++GTPG+V D  ++ R F   KIK+F+LDEAD M+++ G ++   +I   LP   
Sbjct: 130 RDAQIVVGTPGRVFD-NIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTT 187
Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLD 316
           Q++L SAT   +V+E     + NP+ I +K++E +L+
Sbjct: 188 QVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 224

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  139 bits (349), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 80/207 (38%), Positives = 127/207 (61%), Gaps = 7/207 (3%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           V  F+ + L  +LL+GV+  GF  PS IQ+ A+  ++    H+++AQ+QSGTGKT  F++
Sbjct: 20  VYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEG--HDVLAQAQSGTGKTGTFSI 77
Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT 221
             L R++ S++ PQ L LAPT ELA+QI +VV  +  H+ D+ V   + G +   + +  
Sbjct: 78  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGL 136
Query: 222 E--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
              QI++GTPG+V D  ++ R F   KIK+F+LDEAD M+++ G ++   +I   LP   
Sbjct: 137 RDAQIVVGTPGRVFD-NIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTT 194
Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLII 306
           Q++L SAT   +V+E     + NP+ I
Sbjct: 195 QVVLLSATMPNDVLEVTTKFMRNPVRI 221

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  130 bits (327), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 78/214 (36%), Positives = 129/214 (60%), Gaps = 9/214 (4%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           V  F+ ++LK  LL+G+Y  GF  PS IQ+ A+   +    +++IAQ+QSGTGKTA F +
Sbjct: 29  VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKG--YDVIAQAQSGTGKTATFAI 86
Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGEN----LERN 217
           ++L ++    +E Q L LAPT ELA QI +V+  +G ++   +    + G N    +++ 
Sbjct: 87  SILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKL 145
Query: 218 KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPS 277
           +     I++GTPG+V D  L  R+     IK+FVLDEAD M+ ++G +D    I ++L +
Sbjct: 146 QAEAPHIVVGTPGRVFDM-LNRRYLSPKWIKMFVLDEADEML-SRGFKDQIYEIFQKLNT 203
Query: 278 DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE 311
             Q++L SAT   +V+E  +  + +P+ I +K+E
Sbjct: 204 SIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  129 bits (323), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 86/306 (28%), Positives = 160/306 (52%), Gaps = 9/306 (2%)
Query: 97  SPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKT 156
           SP +    F    LKPELL+ + + GF  PS++Q   +P  +     +++ Q++SG GKT
Sbjct: 2   SPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGKT 59
Query: 157 AAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER 216
           A F L  L ++ P   +  VL +  T ELA QI +   +  K++ ++ V     G ++++
Sbjct: 60  AVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKK 119
Query: 217 N----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQ 272
           +    KK    I++GTPG++L    + +  +L  IK F+LDE D M+     +     I 
Sbjct: 120 DEEVLKKNCPHIVVGTPGRILALA-RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIF 178
Query: 273 KRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE-SLDNIKQHYVMCKNIDEK 331
           +  P + Q+M+FSAT  KE+    +  + +P+ I +  E + +L  ++Q+YV  K+ +EK
Sbjct: 179 RMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKD-NEK 237
Query: 332 FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFR 391
              + ++  V+   Q +IF  + +    LA+ + ++      +   +  E+RLS   +F+
Sbjct: 238 NRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFK 297
Query: 392 EGEFKI 397
           + + +I
Sbjct: 298 DFQRRI 303

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  129 bits (323), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 86/306 (28%), Positives = 160/306 (52%), Gaps = 9/306 (2%)
Query: 97  SPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKT 156
           SP +    F    LKPELL+ + + GF  PS++Q   +P  +     +++ Q++SG GKT
Sbjct: 2   SPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGKT 59
Query: 157 AAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER 216
           A F L  L ++ P   +  VL +  T ELA QI +   +  K++ ++ V     G ++++
Sbjct: 60  AVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKK 119
Query: 217 N----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQ 272
           +    KK    I++GTPG++L    + +  +L  IK F+LDE D M+     +     I 
Sbjct: 120 DEEVLKKNCPHIVVGTPGRILALA-RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIF 178
Query: 273 KRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE-SLDNIKQHYVMCKNIDEK 331
           +  P + Q+M+FSAT  KE+    +  + +P+ I +  E + +L  ++Q+YV  K+ +EK
Sbjct: 179 RMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKD-NEK 237
Query: 332 FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFR 391
              + ++  V+   Q +IF  + +    LA+ + ++      +   +  E+RLS   +F+
Sbjct: 238 NRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFK 297
Query: 392 EGEFKI 397
           + + +I
Sbjct: 298 DFQRRI 303

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  128 bits (321), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 85/298 (28%), Positives = 158/298 (53%), Gaps = 9/298 (3%)
Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML 164
           F    LKPELL+ + + GF  PS++Q   +P  +     +++ Q++SG GKTA F L  L
Sbjct: 9   FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGKTAVFVLATL 66
Query: 165 SRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN----KKI 220
            ++ P   +  VL +  T ELA QI +   +  K++ ++ V     G +++++    KK 
Sbjct: 67  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 126
Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
              I++GTPG++L    + +  +L  IK F+LDEAD M+     +     I +  P + Q
Sbjct: 127 CPHIVVGTPGRILALA-RNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRMTPHEKQ 185
Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE-SLDNIKQHYVMCKNIDEKFEAVSNIY 339
           +M+FSAT  KE+    +  + +P+ I +  E + +L  ++Q+YV  K+ +EK   + ++ 
Sbjct: 186 VMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKD-NEKNRKLFDLL 244
Query: 340 GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            V+   Q +IF  + +    LA+ + ++      +   +  E+RLS   +F++ + +I
Sbjct: 245 DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 302

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

Iteration: 1
 Score =  125 bits (315), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 89/302 (29%), Positives = 153/302 (50%), Gaps = 25/302 (8%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
            F  L+L   +L  +   GF  P+ IQ   +P  L D  +N++AQ+++G+GKTA+F + +
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDE-YNIVAQARTGSGKTASFAIPL 65
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI--T 221
           +  VN +    + + L PT ELAIQ+ + +  + K   +L +     G+ +    K    
Sbjct: 66  IELVNEN-NGIEAIILTPTRELAIQVADEIESL-KGNKNLKIAKIYGGKAIYPQIKALKN 123
Query: 222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQI 281
             I++GTPG++LD  +     +L  +K F+LDEAD  +     +D   +I      D +I
Sbjct: 124 ANIVVGTPGRILDH-INRGTLNLKNVKYFILDEADEXLNXGFIKDVE-KILNACNKDKRI 181
Query: 282 MLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI--- 338
           +LFSAT  +E++  A+    +   IK K       NI+Q YV   N +E+FEA+  +   
Sbjct: 182 LLFSATXPREILNLAKKYXGDYSFIKAKINA----NIEQSYVEV-NENERFEALCRLLKN 236
Query: 339 ---YGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEF 395
              YG       ++FC T++    LA  +   G   G + G+L+  QR  ++  F++ + 
Sbjct: 237 KEFYG-------LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI 289
Query: 396 KI 397
           +I
Sbjct: 290 RI 291

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  122 bits (307), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 78/210 (37%), Positives = 119/210 (56%), Gaps = 11/210 (5%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETA-LPTLLADPPHNMIAQSQSGTGKTAAFT 160
           V +F+ ++L   LL+G+Y  GF  PS IQ+ A LP +     +++IAQ+QSGTG TA F 
Sbjct: 14  VDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXG---YDVIAQAQSGTGXTATFA 70
Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI 220
           +++L ++   +   Q L LAPT ELA QI  VV  +G ++   S    + G N+    + 
Sbjct: 71  ISILQQIELDLXATQALVLAPTRELAQQIQXVVMALGDYM-GASCHACIGGTNVRAEVQX 129
Query: 221 TE----QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
            +     II+GTPG+V D  L  R+     I +FVLDEAD M+ ++G  D    I + L 
Sbjct: 130 LQMEAPHIIVGTPGRVFDM-LNRRYLSPXYIXMFVLDEADEML-SRGFXDQIYDIFQXLN 187
Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLII 306
           S+ Q++L SAT   +V+E     + +P+ I
Sbjct: 188 SNTQVVLLSATMPSDVLEVTXXFMRDPIRI 217

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  110 bits (275), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 72/211 (34%), Positives = 115/211 (54%), Gaps = 15/211 (7%)
Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML 164
           F+   LKPE+L+ ++  G   P+ IQ  ALP  LA    ++I Q+++GTGKT AF L + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALP--LALEGKDLIGQARTGTGKTLAFALPIA 60
Query: 165 SRVNPSIQ---EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVR----YAVRGENLERN 217
            R+ PS +   +P+ L L PT ELA+Q+   +  +  H+  ++V     Y  + E L R 
Sbjct: 61  ERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRG 120
Query: 218 KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPS 277
                  ++ TPG+ LD+ L+    DLS+++V VLDEAD M+ + G ++    +    P 
Sbjct: 121 A----DAVVATPGRALDY-LRQGVLDLSRVEVAVLDEADEML-SMGFEEEVEALLSATPP 174
Query: 278 DCQIMLFSATYDKEVMEFAQDMVPNPLIIKL 308
             Q +LFSAT        A+  + NP++I +
Sbjct: 175 SRQTLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  110 bits (275), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 118/206 (57%), Gaps = 15/206 (7%)
Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML 164
           FE   LK ELL G++EMG+  PS IQE ++P  L+    +++A++++GTGK+ A+ + +L
Sbjct: 5   FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSG--RDILARAKNGTGKSGAYLIPLL 62
Query: 165 SRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KKIT 221
            R++      Q + + PT ELA+Q+ ++  ++ KH+    V     G NL  +      T
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122
Query: 222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQK----RLPS 277
             ++I TPG++LD  +K     +  +++ VLDEAD +++    QDF ++I +     LP 
Sbjct: 123 VHVVIATPGRILDL-IKKGVAKVDHVQMIVLDEADKLLS----QDF-VQIMEDIILTLPK 176
Query: 278 DCQIMLFSATYDKEVMEFAQDMVPNP 303
           + QI+L+SAT+   V +F    +  P
Sbjct: 177 NRQILLYSATFPLSVQKFMNSHLEKP 202

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score =  109 bits (273), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 47/84 (55%), Positives = 68/84 (80%)
Query: 314 SLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGL 373
           +L+NI+Q+YV+C++  +K++A+ NIYG +TIGQA+IFC TR+ A WL  +M ++G  V L
Sbjct: 4   TLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSL 63
Query: 374 LSGELTVEQRLSILDRFREGEFKI 397
           LSGELTVEQR SI+ RFR+G+ K+
Sbjct: 64  LSGELTVEQRASIIQRFRDGKEKV 87

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  109 bits (272), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 71/211 (33%), Positives = 115/211 (54%), Gaps = 15/211 (7%)
Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML 164
           F+   LKPE+L+ ++  G   P+ I+  ALP  LA    ++I Q+++GTGKT AF L + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALP--LALEGKDLIGQARTGTGKTLAFALPIA 60
Query: 165 SRVNPSIQ---EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVR----YAVRGENLERN 217
            R+ PS +   +P+ L L PT ELA+Q+   +  +  H+  ++V     Y  + E L R 
Sbjct: 61  ERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRG 120
Query: 218 KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPS 277
                  ++ TPG+ LD+ L+    DLS+++V VLDEAD M++    ++    +    PS
Sbjct: 121 A----DAVVATPGRALDY-LRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPS 175
Query: 278 DCQIMLFSATYDKEVMEFAQDMVPNPLIIKL 308
             Q +LFSAT        A+  + NP++I +
Sbjct: 176 R-QTLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  107 bits (268), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 64/206 (31%), Positives = 110/206 (53%), Gaps = 7/206 (3%)
Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML 164
           F    LKPELL+ + + GF  PS++Q   +P  +     +++ Q++SG GKTA F L  L
Sbjct: 16  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGKTAVFVLATL 73
Query: 165 SRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN----KKI 220
            ++ P   +  VL +  T ELA QI +   +  K++ ++ V     G +++++    KK 
Sbjct: 74  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 133
Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
              I++GTPG++L    + +  +L  IK F+LDE D M+     +     I +  P + Q
Sbjct: 134 CPHIVVGTPGRILALA-RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQ 192
Query: 281 IMLFSATYDKEVMEFAQDMVPNPLII 306
           +M+FSAT  KE+    +  + +P+ I
Sbjct: 193 VMMFSATLSKEIRPVCRKFMQDPMEI 218

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 97.4 bits (241), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 79/307 (25%), Positives = 153/307 (49%), Gaps = 19/307 (6%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           ++ F +  L+  ++  V + G+  P+ IQ+ ++P + +    +++A +Q+G+GKTAAF L
Sbjct: 55  IQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSG--RDLMACAQTGSGKTAAFLL 112
Query: 162 TMLSRV--NP---SIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL-E 215
            +LS++  +P    +  PQV+ ++PT ELAIQI     K     + L +     G +   
Sbjct: 113 PILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFE-SYLKIGIVYGGTSFRH 171
Query: 216 RNKKITE--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF-SIRIQ 272
           +N+ IT    ++I TPG++LD+ +   F      +  VLDEAD M+     +D   I   
Sbjct: 172 QNECITRGCHVVIATPGRLLDF-VDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTH 230
Query: 273 KRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKF 332
             +  + Q ++FSAT+ +E+   A + + N + + +     +  ++KQ          K+
Sbjct: 231 VTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVN----KY 286
Query: 333 EAVSNIYGVVT--IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRF 390
              S +  +++      ++F  T++ A +LA  +S++      + G+    QR   L  F
Sbjct: 287 AKRSKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDF 346
Query: 391 REGEFKI 397
           + G  K+
Sbjct: 347 KNGSMKV 353

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 94.7 bits (234), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 72/212 (33%), Positives = 112/212 (52%), Gaps = 21/212 (9%)
Query: 103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLT 162
           KTF+ L +   L +   ++G+  P+KIQ  A+P  LA    ++I  +++G+GKT AF L 
Sbjct: 43  KTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIP--LALQGRDIIGLAETGSGKTGAFALP 100
Query: 163 MLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAV-------RGENLE 215
           +L+ +  + Q    L L PT ELA QI E    +G  I    V+ AV         ++L 
Sbjct: 101 ILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSI---GVQSAVIVGGIDSMSQSLA 157
Query: 216 RNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSI---RIQ 272
             KK    III TPG+++D     + F+L  +K  V+DEAD ++    + DF     +I 
Sbjct: 158 LAKK--PHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRIL----NMDFETEVDKIL 211
Query: 273 KRLPSDCQIMLFSATYDKEVMEFAQDMVPNPL 304
           K +P D +  LFSAT  K+V +  +  + NP+
Sbjct: 212 KVIPRDRKTFLFSATMTKKVQKLQRAALKNPV 243

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 94.4 bits (233), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 106/210 (50%), Gaps = 10/210 (4%)
Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML 164
           F     +P +++ +  + FY P++IQE  +P  L     + + QSQ+GTGKT A+ L + 
Sbjct: 6   FTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRG--ESXVGQSQTGTGKTHAYLLPIX 63
Query: 165 SRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD---LSVRYAVRGENLER---NK 218
            ++ P   E Q +  APT ELA QI     K+ K       +  R  + G + ++     
Sbjct: 64  EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKL 123
Query: 219 KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSD 278
            +   I+IGTPG++ D+ ++ +  D+    + V+DEAD+ +      D   +I  R P D
Sbjct: 124 NVQPHIVIGTPGRINDF-IREQALDVHTAHILVVDEADLXLDXGFITDVD-QIAARXPKD 181
Query: 279 CQIMLFSATYDKEVMEFAQDMVPNPLIIKL 308
            Q ++FSAT  +++  F +    NP  + +
Sbjct: 182 LQXLVFSATIPEKLKPFLKKYXENPTFVHV 211

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 94.0 bits (232), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 62/206 (30%), Positives = 108/206 (52%), Gaps = 5/206 (2%)
Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML 164
           FE+L L   +L+G+   GF  PS +Q  A+P  L     ++I Q++SGTGKT  F+   L
Sbjct: 26  FESLLLSRPVLEGLRAAGFERPSPVQLKAIP--LGRCGLDLIVQAKSGTGKTCVFSTIAL 83
Query: 165 SRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQ- 223
             +       Q+L LAPT E+A+QI  V+  +G  +  L     + G  L ++K   ++ 
Sbjct: 84  DSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKC 143
Query: 224 -IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM 282
            I +G+PG++    ++  + +   I++F+LDEAD ++     Q+    I   LP+  Q++
Sbjct: 144 HIAVGSPGRIKQL-IELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQML 202
Query: 283 LFSATYDKEVMEFAQDMVPNPLIIKL 308
             SATY + +       + +P  ++L
Sbjct: 203 AVSATYPEFLANALTKYMRDPTFVRL 228

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 87/320 (27%), Positives = 142/320 (44%), Gaps = 49/320 (15%)
Query: 113 ELLKGVYEMGFYA-PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLS------ 165
           E++ G  E+  Y  P+ +Q+ A+P +      +++A +Q+G+GKTAAF L +LS      
Sbjct: 24  EIIMGNIELTRYTRPTPVQKHAIPII--KEKRDLMACAQTGSGKTAAFLLPILSQIYSDG 81
Query: 166 ------------RVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGEN 213
                       R     Q P  L LAPT ELA+QI E   K        S R  VR   
Sbjct: 82  PGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARK-------FSYRSRVRPCV 134
Query: 214 LERNKKITEQI---------IIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGH 264
           +     I +QI         ++ TPG+++D  ++     L   K  VLDEAD M+     
Sbjct: 135 VYGGADIGQQIRDLERGCHLLVATPGRLVDM-MERGKIGLDFCKYLVLDEADRML----D 189
Query: 265 QDFSIRIQKRLPSDC-------QIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDN 317
             F  +I++ +  D          M+FSAT+ KE+   A+D +   + + + R   + +N
Sbjct: 190 MGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSEN 249
Query: 318 IKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGE 377
           I Q  V  +  D++   +  +         ++F  T+K A  L + +  EG     + G+
Sbjct: 250 ITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGD 309
Query: 378 LTVEQRLSILDRFREGEFKI 397
            +   R   L +FR G+  I
Sbjct: 310 RSQRDREEALHQFRSGKSPI 329

>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 = 89.0 bits (219), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 124/240 (51%), Gaps = 31/240 (12%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           ++ F+ L L P +   +    +  P+ IQ+ A+P +L     +++A +Q+G+GKTAAF +
Sbjct: 22  IENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEH--RDIMACAQTGSGKTAAFLI 79
Query: 162 TMLSRV---------NPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGE 212
            +++ +               P+ L LAPT ELAIQI   +++  K   +  +R  V   
Sbjct: 80  PIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQI---LSESQKFSLNTPLRSCVVYG 136
Query: 213 NLERNKKITE-----QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF 267
             + + +I E      +++ TPG+++D+  K +   L   K  VLDEAD M+       F
Sbjct: 137 GADTHSQIREVQMGCHLLVATPGRLVDFIEKNKI-SLEFCKYIVLDEADRML----DMGF 191
Query: 268 SIRIQK-----RLPS--DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQ 320
             +I+K      +PS  + Q ++FSAT+ KE+ + A D + N + + + R   + D+IKQ
Sbjct: 192 EPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQ 251

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 85.9 bits (211), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 156/317 (49%), Gaps = 35/317 (11%)
Query: 110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP 169
           L  E+ K +  M F   + +Q+  +  +L+   H++IA++++GTGKT AF + +   +  
Sbjct: 79  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 138
Query: 170 SIQEPQVLC----LAPTYELAIQIGEVVAKMGKHITDLSVRYA----VRGEN----LERN 217
           +  + Q +     +APT +LA+QI   V K+      L  +YA    V G +    + + 
Sbjct: 139 TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLK-KYACVSLVGGTDFRAAMNKM 197
Query: 218 KKITEQIIIGTPGKVLDWGLKY--RFFDLSKIKVFVLDEADVMIATQGHQDF----SIRI 271
            K+   I+I TPG+++D   KY  +FF     K  VLDEAD ++      D      I  
Sbjct: 198 NKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYK--VLDEADRLLEIGFRDDLETISGILN 255
Query: 272 QKRLPS--DCQIMLFSATYDKEVMEFAQDMVPNPLIIKL----KREEESLDNIKQHYVMC 325
           +K   S  + + +LFSAT D +V + A +++     + L    K E E+ + I Q  V+ 
Sbjct: 256 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS 315
Query: 326 -KNIDEKFEAVSNIYGVV----TIGQAMIFCHTRKTAAWLAEKMS---KEGLNVGLLSGE 377
            K  +  F AV +I   +    +  +A+IF  T K  ++L   +    K+ L +    G+
Sbjct: 316 EKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGK 375
Query: 378 LTVEQRLSILDRFREGE 394
           +T  +R S++ RF++ E
Sbjct: 376 ITQNKRTSLVKRFKKDE 392

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 85.9 bits (211), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 156/317 (49%), Gaps = 35/317 (11%)
Query: 110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP 169
           L  E+ K +  M F   + +Q+  +  +L+   H++IA++++GTGKT AF + +   +  
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 170 SIQEPQVLC----LAPTYELAIQIGEVVAKMGKHITDLSVRYA----VRGEN----LERN 217
           +  + Q +     +APT +LA+QI   V K+      L  +YA    V G +    + + 
Sbjct: 88  TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLK-KYACVSLVGGTDFRAAMNKM 146
Query: 218 KKITEQIIIGTPGKVLDWGLKY--RFFDLSKIKVFVLDEADVMIATQGHQDF----SIRI 271
            K+   I+I TPG+++D   KY  +FF     K  VLDEAD ++      D      I  
Sbjct: 147 NKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYK--VLDEADRLLEIGFRDDLETISGILN 204
Query: 272 QKRLPS--DCQIMLFSATYDKEVMEFAQDMVPNPLIIKL----KREEESLDNIKQHYVMC 325
           +K   S  + + +LFSAT D +V + A +++     + L    K E E+ + I Q  V+ 
Sbjct: 205 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS 264
Query: 326 -KNIDEKFEAVSNIYGVV----TIGQAMIFCHTRKTAAWLAEKMS---KEGLNVGLLSGE 377
            K  +  F AV +I   +    +  +A+IF  T K  ++L   +    K+ L +    G+
Sbjct: 265 EKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGK 324
Query: 378 LTVEQRLSILDRFREGE 394
           +T  +R S++ RF++ E
Sbjct: 325 ITQNKRTSLVKRFKKDE 341

>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 = 85.5 bits (210), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 156/317 (49%), Gaps = 35/317 (11%)
Query: 110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP 169
           L  E+ K +  M F   + +Q+  +  +L+   H++IA++++GTGKT AF + +   +  
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 170 SIQEPQVLC----LAPTYELAIQIGEVVAKMGKHITDLSVRYA----VRGEN----LERN 217
           +  + Q +     +APT +LA+QI   V K+      L  +YA    V G +    + + 
Sbjct: 88  TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLK-KYACVSLVGGTDFRAAMNKM 146
Query: 218 KKITEQIIIGTPGKVLDWGLKY--RFFDLSKIKVFVLDEADVMIATQGHQDF----SIRI 271
            K+   I+I TPG+++D   KY  +FF     K  VLDEAD ++      D      I  
Sbjct: 147 NKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYK--VLDEADRLLEIGFRDDLETISGILN 204
Query: 272 QKRLPS--DCQIMLFSATYDKEVMEFAQDMVPNPLIIKL----KREEESLDNIKQHYVMC 325
           +K   S  + + +LFSAT D +V + A +++     + L    K E E+ + I Q  V+ 
Sbjct: 205 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVIS 264
Query: 326 -KNIDEKFEAVSNIYGVV----TIGQAMIFCHTRKTAAWLAEKMS---KEGLNVGLLSGE 377
            K  +  F AV +I   +    +  +A+IF  T K  ++L   +    K+ L +    G+
Sbjct: 265 EKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGK 324
Query: 378 LTVEQRLSILDRFREGE 394
           +T  +R S++ RF++ E
Sbjct: 325 ITQNKRTSLVKRFKKDE 341

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 80.9 bits (198), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 79/288 (27%), Positives = 138/288 (47%), Gaps = 35/288 (12%)
Query: 116 KGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQ 175
           + + EMGF   +++Q   +P +L     N++ ++++G+GKTAA+ + +L     S     
Sbjct: 7   QAIREMGFKNFTEVQSKTIPLML--QGKNVVVRAKTGSGKTAAYAIPILELGMKS----- 59
Query: 176 VLCLAPTYELAIQIGEVVAKMGKHI-TDLSVRYAVRGENLERNKKITEQIIIGTPGKVLD 234
            L + PT EL  Q+   +  +G+++ T ++  Y       + N+     I++ TPG++LD
Sbjct: 60  -LVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLD 118
Query: 235 WGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM-LFSATYDKEVM 293
              K    DLS  ++ ++DEAD+M       D  I + +   S+ +I  LFSAT  +E+ 
Sbjct: 119 LWSKG-VIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQ--TSNRKITGLFSATIPEEIR 175
Query: 294 EFAQDMVPNPLIIKLKREEES---LDNIKQHYVMCK-NIDEKFEAV--SNIYGVVTIGQA 347
           +  +D + N        E E+   L N++  +V  K +   K +A+  +   GV+     
Sbjct: 176 KVVKDFITN------YEEIEACIGLANVEHKFVHVKDDWRSKVQALRENKDKGVI----- 224
Query: 348 MIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEF 395
            +F  TR   A L         N   L G+L    R   +D FREGE+
Sbjct: 225 -VFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEY 267

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 78.6 bits (192), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 38/86 (44%), Positives = 56/86 (65%)
Query: 312 EESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNV 371
           E ++D IKQ Y  CKN  +KF+ ++ +YGV TIG ++IF  T+KTA  L  K+  EG  V
Sbjct: 4   EVNVDAIKQLYXDCKNEADKFDVLTELYGVXTIGSSIIFVATKKTANVLYGKLKSEGHEV 63
Query: 372 GLLSGELTVEQRLSILDRFREGEFKI 397
            +L G+L  ++R  ++D FREG  K+
Sbjct: 64  SILHGDLQTQERDRLIDDFREGRSKV 89

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 78.2 bits (191), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 37/86 (43%), Positives = 58/86 (67%)
Query: 312 EESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNV 371
           E ++D IKQ Y+ CKN  +KF+ ++ +YG++TIG ++IF  T+KTA  L  K+  EG  V
Sbjct: 3   EVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEV 62
Query: 372 GLLSGELTVEQRLSILDRFREGEFKI 397
            +L G+L  ++R  ++D FREG  K+
Sbjct: 63  SILHGDLQTQERDRLIDDFREGRSKV 88

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/210 (32%), Positives = 107/210 (50%), Gaps = 14/210 (6%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF-- 159
           +  F    L  + LKG+ E  +   ++IQ+  +   LA    +++  +++G+GKT AF  
Sbjct: 24  ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIG--LALQGKDVLGAAKTGSGKTLAFLV 81
Query: 160 -TLTMLSRVN-PSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL--- 214
             L  L R+   S     VL ++PT ELA Q  EV+ K+GK+  D S    + G++L   
Sbjct: 82  PVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKN-HDFSAGLIIGGKDLKHE 140
Query: 215 -ERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQK 273
            ER   I   I++ TPG++L    +   F  + +++ VLDEAD  I   G  D    + +
Sbjct: 141 AERINNIN--ILVCTPGRLLQHMDETVSFHATDLQMLVLDEAD-RILDMGFADTMNAVIE 197
Query: 274 RLPSDCQIMLFSATYDKEVMEFAQDMVPNP 303
            LP   Q +LFSAT  K V + A+  + NP
Sbjct: 198 NLPKKRQTLLFSATQTKSVKDLARLSLKNP 227

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 77.0 bits (188), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/86 (43%), Positives = 56/86 (65%)
Query: 312 EESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNV 371
           E ++D IKQ Y  CKN  +KF+ ++ +YG+ TIG ++IF  T+KTA  L  K+  EG  V
Sbjct: 5   EVNVDAIKQLYXDCKNEADKFDVLTELYGLXTIGSSIIFVATKKTANVLYGKLKSEGHEV 64
Query: 372 GLLSGELTVEQRLSILDRFREGEFKI 397
            +L G+L  ++R  ++D FREG  K+
Sbjct: 65  SILHGDLQTQERDRLIDDFREGRSKV 90

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 74.7 bits (182), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 19/233 (8%)
Query: 82  IESKQELEIQRKDP------HSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALP 135
           + + QE+E  R+        H+    V  F   +    ++  +    F  P+ IQ    P
Sbjct: 2   MRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWP 61
Query: 136 TLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVN--PSIQE---PQVLCLAPTYELAIQIG 190
             L+    +M+  +Q+G+GKT ++ L  +  +N  P ++    P  L LAPT ELA Q+ 
Sbjct: 62  VALSG--LDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQ 119
Query: 191 EVVAKMGKHITDLSVRY---AVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKI 247
           +V A+  +     S      A +G  + R+ +   +I I TPG+++D+ L+    +L + 
Sbjct: 120 QVAAEYCRACRLKSTCIYGGAPKGPQI-RDLERGVEICIATPGRLIDF-LECGKTNLRRT 177
Query: 248 KVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMV 300
              VLDEAD M+   G +    +I  ++  D Q +++SAT+ KEV + A+D +
Sbjct: 178 TYLVLDEADRML-DMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFL 229

>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 = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/257 (27%), Positives = 126/257 (49%), Gaps = 26/257 (10%)
Query: 69  EKSLLQK---IVRRGLIESKQELEIQRKDP------HSPLYSVKTFEALHLKPELLKGVY 119
           EK+  Q+   + RR    + QE+E  R+        H+    V  F   +    ++  + 
Sbjct: 4   EKNFYQEHPDLARR----TAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIA 59
Query: 120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVN--PSIQE---P 174
              F  P+ IQ    P  L+    +M+  +Q+G+GKT ++ L  +  +N  P ++    P
Sbjct: 60  RQNFTEPTAIQAQGWPVALSG--LDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGP 117
Query: 175 QVLCLAPTYELAIQIGEVVAKMGKHITDLSVRY---AVRGENLERNKKITEQIIIGTPGK 231
             L LAPT ELA Q+ +V A+  +     S      A +G  + R+ +   +I I TPG+
Sbjct: 118 ICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQI-RDLERGVEICIATPGR 176
Query: 232 VLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE 291
           ++D+ L+    +L +    VLDEAD M+   G +    +I  ++  D Q +++SAT+ KE
Sbjct: 177 LIDF-LECGKTNLRRTTYLVLDEADRML-DMGFEPQIRKIVDQIRPDRQTLMWSATWPKE 234
Query: 292 VMEFAQDMVPNPLIIKL 308
           V + A+D + + + I +
Sbjct: 235 VRQLAEDFLKDYIHINI 251

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 71.6 bits (174), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 103/203 (50%), Gaps = 17/203 (8%)
Query: 115 LKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEP 174
           LK + EMGF   ++IQ  ++  LL     +++A +++G+GKT AF +  +  +      P
Sbjct: 66  LKAIKEMGFTNMTEIQHKSIRPLLEG--RDLLAAAKTGSGKTLAFLIPAVELIVKLRFMP 123
Query: 175 Q----VLCLAPTYELAIQIGEVVAK-MGKHITDLSVRYAVRGENLERNKKITE-QIIIGT 228
           +    VL L+PT ELA+Q   V+ + M  H+    +       + E  K      II+ T
Sbjct: 124 RNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVAT 183
Query: 229 PGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATY 288
           PG++LD       F    ++  V+DEAD ++   G ++   +I K LP+  Q MLFSAT 
Sbjct: 184 PGRLLDHMQNTPGFMYKNLQCLVIDEADRILDV-GFEEELKQIIKLLPTRRQTMLFSATQ 242
Query: 289 DKEVMEFAQDMVPNPLIIKLKRE 311
            ++V + A+        I LK+E
Sbjct: 243 TRKVEDLAR--------ISLKKE 257

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 106/216 (49%), Gaps = 27/216 (12%)
Query: 106 EALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLS 165
           +A    P+LLK +  +G   P+ IQ  A P +L     ++I  +Q+GTGKT ++ +    
Sbjct: 23  DAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQG--IDLIVVAQTGTGKTLSYLMPGFI 80
Query: 166 RVN--PSIQE----PQVLCLAPTYELAIQIGEVVAKMG-KHITDLSVRYAVRGENLERNK 218
            ++  P  +E    P +L L PT ELA+ +    +K   K +  + + Y  R     RN 
Sbjct: 81  HLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICI-YGGR----NRNG 135
Query: 219 KITE-----QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQK 273
           +I +      III TPG++ D  +     +L  I   V+DEAD M+      +F  +I+K
Sbjct: 136 QIEDISKGVDIIIATPGRLNDLQMN-NSVNLRSITYLVIDEADKML----DMEFEPQIRK 190
Query: 274 RL---PSDCQIMLFSATYDKEVMEFAQDMVPNPLII 306
            L     D Q ++ SAT+   V + A   + +P+I+
Sbjct: 191 ILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIV 226

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 58.2 bits (139), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 49/83 (59%)
Query: 315 LDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLL 374
           L+ IKQ YV  +  + K+E ++++Y  +++ QA+IFC+TR+    L  K+  +   V  +
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60
Query: 375 SGELTVEQRLSILDRFREGEFKI 397
             +L  ++R +I+  FR G  +I
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRI 83

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 112/230 (48%), Gaps = 19/230 (8%)
Query: 81  LIESKQELEIQRKDPHSPLYSVKTFEAL----HLKPELLKGVYEMGFYAPSKIQETALPT 136
            + +K ++ +Q  D   P   + TF+ L     +   LL+ + + GF  P+ IQ  A+P 
Sbjct: 6   FLRNKHKIHVQGTDLPDP---IATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPV 62
Query: 137 LLADPPHNMIAQSQSGTGKTAAFTLTMLSRV-NPSIQEPQVLCLAPTYELAIQIGEVVAK 195
           +L      ++A + +G+GKT AF++ +L ++  P+ +  + L ++PT ELA QI   + K
Sbjct: 63  MLHG--RELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIK 120
Query: 196 MGKHI---TDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYR--FFDLSKIKVF 250
           + +       +  + AV  +           I++ TP +++ + LK      DL+ ++  
Sbjct: 121 ISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLI-YLLKQDPPGIDLASVEWL 179
Query: 251 VLDEADVMI--ATQGHQDFSIRIQKRLPSD-CQIMLFSATYDKEVMEFAQ 297
           V+DE+D +      G +D    I     S   +  +FSAT+  +V ++ +
Sbjct: 180 VVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCK 229

>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp Length = 767

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 46/153 (30%), Positives = 74/153 (48%), Gaps = 17/153 (11%)
Query: 145 MIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVA-----KMGKH 199
           M+   ++G+GKT      +L    P ++  QV C  P    A+ + + VA     K+G+ 
Sbjct: 112 MVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEMDVKLGE- 170
Query: 200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEA-DVM 258
                V Y++R EN   NK I + +   T G +L   ++    DLS+    +LDEA +  
Sbjct: 171 ----EVGYSIRFENKTSNKTILKYM---TDGMLLREAMEDH--DLSRYSCIILDEAHERT 221
Query: 259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE 291
           +AT        ++ KR P D +I++ SAT D E
Sbjct: 222 LATDILMGLLKQVVKRRP-DLKIIIMSATLDAE 253

>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In Complex With Adp Length = 773

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 46/153 (30%), Positives = 74/153 (48%), Gaps = 17/153 (11%)
Query: 145 MIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVA-----KMGKH 199
           M+   ++G+GKT      +L    P ++  QV C  P    A+ + + VA     K+G+ 
Sbjct: 112 MVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEMDVKLGE- 170
Query: 200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEA-DVM 258
                V Y++R EN   NK I + +   T G +L   ++    DLS+    +LDEA +  
Sbjct: 171 ----EVGYSIRFENKTSNKTILKYM---TDGMLLREAMEDH--DLSRYSCIILDEAHERT 221
Query: 259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE 291
           +AT        ++ KR P D +I++ SAT D E
Sbjct: 222 LATDILMGLLKQVVKRRP-DLKIIIMSATLDAE 253

>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 = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 311 EEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLN 370
           EE +L  + Q+Y       +K   ++ ++  + I Q++IFC++ +    LA+K+S+ G +
Sbjct: 12  EELTLKGVTQYYAYVTE-RQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYS 70
Query: 371 VGLLSGELTVEQRLSILDRFREG 393
              +  ++  E R  +   FR G
Sbjct: 71  CFYIHAKMRQEHRNRVFHDFRNG 93

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	399
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	0.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-174
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-154
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-152
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-134
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-107
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-104
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	4e-97
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-94
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-92
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-72
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	9e-68
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	9e-67
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	2e-66
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	2e-65
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	2e-65
3bor_A	237	Human initiation factor 4A-II; translation initiat	3e-65
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	3e-63
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	5e-63
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	2e-57
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-54
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	1e-52
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	7e-51
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	3e-48
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	2e-45
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	2e-45
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	2e-40
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	5e-40
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-39
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-38
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	6e-37
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	5e-32
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	3e-28
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	2e-26
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	1e-21
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	2e-14
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	3e-13
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	4e-13
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	3e-11
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	8e-09
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-07
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-05
1yks_A	440	Genome polyprotein [contains: flavivirin protease	3e-07
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	3e-06
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	3e-05
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	3e-05
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	4e-05
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	5e-05
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	7e-05
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	8e-05
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	9e-05
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	1e-04
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	2e-04
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	3e-04
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	4e-04

>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 =  516 bits (1330), Expect = 0.0
 Identities = 221/380 (58%), Positives = 292/380 (76%), Gaps = 5/380 (1%)

Query: 18  KPDDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIV 77
           + +   + LSN++LK+      T  A        ++A   K +E++    A +SLL K++
Sbjct: 12  EQEAAAESLSNLHLKEEKIKPDTNGA-----VVKTNANAEKTDEEEKEDRAAQSLLNKLI 66

Query: 78  RRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTL 137
           R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +
Sbjct: 67  RSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLM 126

Query: 138 LADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG 197
           LA+PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+Q G+V+ +MG
Sbjct: 127 LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMG 186

Query: 198 KHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV 257
           K   +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KIKVFVLDEADV
Sbjct: 187 KFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV 246

Query: 258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDN 317
           MIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IKLKREEE+LD 
Sbjct: 247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDT 306

Query: 318 IKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGE 377
           IKQ+YV+C + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKEG  V LLSGE
Sbjct: 307 IKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGE 366

Query: 378 LTVEQRLSILDRFREGEFKI 397
           + VEQR ++++RFREG+ K+
Sbjct: 367 MMVEQRAAVIERFREGKEKV 386

>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 =  491 bits (1267), Expect = e-174
 Identities = 205/318 (64%), Positives = 262/318 (82%)

Query: 80  GLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLA 139
            L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +LA
Sbjct: 2   NLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLA 61

Query: 140 DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH 199
           +PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+Q G+V+ +MGK 
Sbjct: 62  EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKF 121

Query: 200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI 259
             +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KIKVFVLDEADVMI
Sbjct: 122 YPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 181

Query: 260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIK 319
           ATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IKLKREEE+LD IK
Sbjct: 182 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIK 241

Query: 320 QHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT 379
           Q+YV+C + DEKF+A+ N+YG +TI QAMIFCHTRKTA+WLA ++SKEG  V LLSGE+ 
Sbjct: 242 QYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMM 301

Query: 380 VEQRLSILDRFREGEFKI 397
           VEQR ++++RFREG+ K+
Sbjct: 302 VEQRAAVIERFREGKEKV 319

>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 =  440 bits (1135), Expect = e-154
 Identities = 150/298 (50%), Positives = 205/298 (68%), Gaps = 3/298 (1%)

Query: 100 YSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF 159
              K+F+ L L PELLKG+Y M F  PSKIQE ALP LL +PP NMIAQSQSGTGKTAAF
Sbjct: 2   AMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAF 61

Query: 160 TLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKK 219
           +LTML+RVNP    PQ +CLAP+ ELA Q  EVV +MGK  T ++ +  V     E+NK+
Sbjct: 62  SLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKF-TKITSQLIVPDSF-EKNKQ 119

Query: 220 ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
           I  Q+I+GTPG VLD  ++ +   L KIK+FVLDEAD M+  QG  D  IR+++ LP D 
Sbjct: 120 INAQVIVGTPGTVLDL-MRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDT 178

Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIY 339
           Q++LFSAT+   V ++A+ +VPN   ++L+  E ++D IKQ Y+ CKN  +KF+ ++ +Y
Sbjct: 179 QLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELY 238

Query: 340 GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           G++TIG ++IF  T+KTA  L  K+  EG  V +L G+L  ++R  ++D FREG  K+
Sbjct: 239 GLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKV 296

>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 =  385 bits (992), Expect = e-134
 Identities = 166/294 (56%), Positives = 219/294 (74%), Gaps = 5/294 (1%)

Query: 18  KPDDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIV 77
           + +   + LSN++LK+      T  A        ++A   K +E++    A +SLL K++
Sbjct: 12  EQEAAAESLSNLHLKEEKIKPDTNGA-----VVKTNANAEKTDEEEKEDRAAQSLLNKLI 66

Query: 78  RRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTL 137
           R  L+++  ++E+ ++DP+SPLYSVK+FE L LKP+LL+GVY MGF  PSKIQE ALP +
Sbjct: 67  RSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLM 126

Query: 138 LADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG 197
           LA+PP N+IAQSQSGTGKTAAF L MLS+V P+ + PQ LCL+PTYELA+Q G+V+ +MG
Sbjct: 127 LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMG 186

Query: 198 KHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV 257
           K   +L + YAVRG  LER +KI+EQI+IGTPG VLDW  K +F D  KIKVFVLDEADV
Sbjct: 187 KFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV 246

Query: 258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE 311
           MIATQGHQD SIRIQ+ LP +CQ++LFSAT++  V +FAQ +VP+P +IKLKRE
Sbjct: 247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

>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 =  321 bits (824), Expect = e-107
 Identities = 110/317 (34%), Positives = 185/317 (58%), Gaps = 8/317 (2%)

Query: 84  SKQELEIQRKDPHS-PLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPP 142
           S+   +I+     +     V  F+ + L   LL+GV+  GF  PS IQ+ A+  ++    
Sbjct: 1   SEGITDIEESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEG-- 58

Query: 143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD 202
           H+++AQ+QSGTGKT  F++  L R++ S++ PQ L LAPT ELA+QI +VV  +  H  D
Sbjct: 59  HDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFH-MD 117

Query: 203 LSVRYAVRGENLERNKKITE--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA 260
           + V   + G +   + +     QI++GTPG+V D  ++ R F   KIK+F+LDEAD M+ 
Sbjct: 118 IKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDN-IQRRRFRTDKIKMFILDEADEML- 175

Query: 261 TQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQ 320
           + G ++   +I   LP   Q++L SAT   +V+E     + NP+ I +K++E +L+ IKQ
Sbjct: 176 SSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQ 235

Query: 321 HYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTV 380
            YV  +  + K+E ++++Y  +++ QA+IFC+TR+    L  K+  +   V  +  +L  
Sbjct: 236 FYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQ 295

Query: 381 EQRLSILDRFREGEFKI 397
           ++R +I+  FR G  +I
Sbjct: 296 QERDTIMKEFRSGSSRI 312

>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 =  312 bits (802), Expect = e-104
 Identities = 107/301 (35%), Positives = 176/301 (58%), Gaps = 9/301 (2%)

Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
            V +F+ ++L   LL+G+Y  GF  PS IQ+ A+   +    +++IAQ+QSGTGKTA F 
Sbjct: 38  IVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKG--YDVIAQAQSGTGKTATFA 95

Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN--- 217
           +++L ++   ++  Q L LAPT ELA QI +VV  +G +    S    + G N+      
Sbjct: 96  ISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDY-MGASCHACIGGTNVRAEVQK 154

Query: 218 -KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
            +     II+GTPG+V D  L  R+     IK+FVLDEAD M+ ++G +D    I ++L 
Sbjct: 155 LQMEAPHIIVGTPGRVFDM-LNRRYLSPKYIKMFVLDEADEML-SRGFKDQIYDIFQKLN 212

Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
           S+ Q++L SAT   +V+E  +  + +P+ I +K+EE +L+ I+Q Y+  +  + K + + 
Sbjct: 213 SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLC 272

Query: 337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK 396
           ++Y  +TI QA+IF +TR+   WL EKM      V  + G++  ++R  I+  FR G  +
Sbjct: 273 DLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSR 332

Query: 397 I 397
           +
Sbjct: 333 V 333

>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 =  294 bits (756), Expect = 4e-97
 Identities = 103/300 (34%), Positives = 179/300 (59%), Gaps = 8/300 (2%)

Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
              TF+ + L+ +LL+G+Y  GF  PS IQ+ A+  ++     ++IAQSQSGTGKTA F+
Sbjct: 35  VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFS 92

Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI 220
           +++L  ++  ++E Q L LAPT ELA+QI + +  +G +  ++     + G N+  + + 
Sbjct: 93  ISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDY-MNVQCHACIGGTNVGEDIRK 151

Query: 221 TE---QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPS 277
            +    ++ GTPG+V D  ++ R      IK+ VLDEAD M+  +G ++    + + LP 
Sbjct: 152 LDYGQHVVAGTPGRVFDM-IRRRSLRTRAIKMLVLDEADEML-NKGFKEQIYDVYRYLPP 209

Query: 278 DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSN 337
             Q++L SAT   E++E     + +P+ I +KR+E +L+ IKQ +V  +  + KF+ + +
Sbjct: 210 ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCD 269

Query: 338 IYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           +Y  +TI QA+IFC+T++   WL EKM +    V  + G++  ++R SI+  FR G  ++
Sbjct: 270 LYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRV 329

>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 =  287 bits (736), Expect = 2e-94
 Identities = 84/299 (28%), Positives = 157/299 (52%), Gaps = 9/299 (3%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
            F    LKPELL+ + + GF  PS++Q   +P  +     +++ Q++SG GKTA F L  
Sbjct: 9   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGKTAVFVLAT 66

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN----KK 219
           L ++ P   +  VL +  T ELA QI +   +  K++ ++ V     G +++++    KK
Sbjct: 67  LQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK 126

Query: 220 ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
               I++GTPG++L    + +  +L  IK F+LDE D M+     +     I +  P + 
Sbjct: 127 NCPHIVVGTPGRILAL-ARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEK 185

Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE-SLDNIKQHYVMCKNIDEKFEAVSNI 338
           Q+M+FSAT  KE+    +  + +P+ I +  E + +L  ++Q+YV  K+ +EK   + ++
Sbjct: 186 QVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKD-NEKNRKLFDL 244

Query: 339 YGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
             V+   Q +IF  + +    LA+ + ++      +   +  E+RLS   +F++ + +I
Sbjct: 245 LDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 303

>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 =  283 bits (726), Expect = 1e-92
 Identities = 100/297 (33%), Positives = 160/297 (53%), Gaps = 10/297 (3%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TFE  +LK ELL G++E GF  PS IQE A+P  +     +++A++++GTGKTAAF +  
Sbjct: 22  TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITG--RDILARAKNGTGKTAAFVIPT 79

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE- 222
           L +V P + + Q L + PT ELA+Q  +VV  +GKH   +S      G NL  +      
Sbjct: 80  LEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNE 138

Query: 223 --QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
              I++GTPG+VLD     +  DLS   +F++DEAD M+ ++  +    +I   LP   Q
Sbjct: 139 TVHILVGTPGRVLD-LASRKVADLSDCSLFIMDEADKML-SRDFKTIIEQILSFLPPTHQ 196

Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG 340
            +LFSAT+   V EF    +  P  I L   E +L  I Q+Y   +   +K   ++ ++ 
Sbjct: 197 SLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLKGITQYYAFVEE-RQKLHCLNTLFS 254

Query: 341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            + I QA+IFC++      LA+K++  G +       +  ++R  +   FR+G+ + 
Sbjct: 255 KLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRT 311

>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 =  230 bits (588), Expect = 1e-72
 Identities = 85/301 (28%), Positives = 151/301 (50%), Gaps = 17/301 (5%)

Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
               F  L+L   +L  +   GF  P+ IQ   +P  L D  +N++AQ+++G+GKTA+F 
Sbjct: 4   EYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDE-YNIVAQARTGSGKTASFA 62

Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH--ITDLSVRYAVRGENLERNK 218
           + ++  VN +    + + L PT ELAIQ+ + +  +  +  +    + Y   G+ +    
Sbjct: 63  IPLIELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKI-YG--GKAIYPQI 118

Query: 219 KITE--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
           K  +   I++GTPG++LD  +     +L  +K F+LDEAD M+   G      +I     
Sbjct: 119 KALKNANIVVGTPGRILDH-INRGTLNLKNVKYFILDEADEML-NMGFIKDVEKILNACN 176

Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
            D +I+LFSAT  +E++  A+  + +   IK K       NI+Q YV     + +FEA+ 
Sbjct: 177 KDKRILLFSATMPREILNLAKKYMGDYSFIKAKINA----NIEQSYVEVNENE-RFEALC 231

Query: 337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK 396
            +         ++FC T++    LA  +   G   G + G+L+  QR  ++  F++ + +
Sbjct: 232 RLLKNKEF-YGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIR 290

Query: 397 I 397
           I
Sbjct: 291 I 291

>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 =  213 bits (544), Expect = 9e-68
 Identities = 83/218 (38%), Positives = 133/218 (61%), Gaps = 7/218 (3%)

Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
            V  F+ + L   LL+GV+  GF  PS IQ+ A+  ++    H+++AQ+QSGTGKT  F+
Sbjct: 12  VVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEG--HDVLAQAQSGTGKTGTFS 69

Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI 220
           +  L R++ S++ PQ L LAPT ELA+QI +VV  +  H+ D+ V   + G +   + + 
Sbjct: 70  IAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEG 128

Query: 221 TE--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSD 278
               QI++GTPG+V D  ++ R F   KIK+F+LDEAD M+ + G ++   +I   LP  
Sbjct: 129 LRDAQIVVGTPGRVFDN-IQRRRFRTDKIKMFILDEADEML-SSGFKEQIYQIFTLLPPT 186

Query: 279 CQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLD 316
            Q++L SAT   +V+E     + NP+ I +K++E +L+
Sbjct: 187 TQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 224

>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 =  221 bits (564), Expect = 9e-67
 Identities = 82/344 (23%), Positives = 152/344 (44%), Gaps = 31/344 (9%)

Query: 84  SKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPH 143
           S + + + ++D    +      E   L  E+ K +  M F   + +Q+  +  +L+   H
Sbjct: 2   SSKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDH 61

Query: 144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEP----QVLCLAPTYELAIQIGEVVAKMGKH 199
           ++IA++++GTGKT AF + +   +  +  +     + + +APT +LA+QI   V K+   
Sbjct: 62  DVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDM 121

Query: 200 ---ITDLSVRYAVRGENLERN----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVL 252
              +   +    V G +         K+   I+I TPG+++D   KY       +   VL
Sbjct: 122 NYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVL 181

Query: 253 DEADVMIATQGHQDFSIRIQKRLP-------SDCQIMLFSATYDKEVMEFAQDMVPNPLI 305
           DEAD ++   G +D    I   L         + + +LFSAT D +V + A +++     
Sbjct: 182 DEADRLL-EIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKEC 240

Query: 306 IKL----KREEESLDNIKQHYVMCKNIDEKF-----EAVSNIYGVVTIGQAMIFCHTRKT 356
           + L    K E E+ + I Q  V+ +                I    +  +A+IF  T K 
Sbjct: 241 LFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKF 300

Query: 357 AAWLAEKMSKE---GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
            ++L   +  E    L +    G++T  +R S++ RF++ E  I
Sbjct: 301 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 344

>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 =  209 bits (535), Expect = 2e-66
 Identities = 61/208 (29%), Positives = 106/208 (50%), Gaps = 5/208 (2%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
            FE+L L   +L+G+   GF  PS +Q  A+P        ++I Q++SGTGKT  F+   
Sbjct: 25  DFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCG--LDLIVQAKSGTGKTCVFSTIA 82

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE- 222
           L  +       Q+L LAPT E+A+QI  V+  +G  +  L     + G  L ++K   + 
Sbjct: 83  LDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK 142

Query: 223 -QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQI 281
             I +G+PG++    ++  + +   I++F+LDEAD ++     Q+    I   LP+  Q+
Sbjct: 143 CHIAVGSPGRIKQL-IELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQM 201

Query: 282 MLFSATYDKEVMEFAQDMVPNPLIIKLK 309
           +  SATY + +       + +P  ++L 
Sbjct: 202 LAVSATYPEFLANALTKYMRDPTFVRLN 229

>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 =  217 bits (554), Expect = 2e-65
 Identities = 84/399 (21%), Positives = 164/399 (41%), Gaps = 39/399 (9%)

Query: 32  KQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQ 91
              D      +      + +S+   N     +P + + +   +    +      + + + 
Sbjct: 3   LYNDGNRDQRNFGRNQRNNNSNRYRNSRFNSRPRTRSREDDDEVHFDKT--TFSKLIHVP 60

Query: 92  RKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQS 151
           ++D    +      E   L  E+ K +  M F   + +Q+  +  +L+   H++IA++++
Sbjct: 61  KEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKT 120

Query: 152 GTGKTAAFTLTMLSRVNPSIQEP----QVLCLAPTYELAIQIGEVVAKMGKH---ITDLS 204
           GTGKT AF + +   +  +  +     + + +APT +LA+QI   V K+      +   +
Sbjct: 121 GTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYA 180

Query: 205 VRYAVRGENLERN----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA 260
               V G +         K+   I+I TPG+++D   KY       +   VLDEAD ++ 
Sbjct: 181 CVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLL- 239

Query: 261 TQGHQDF--SIR-IQKRLP-------SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKL-- 308
                 F   +  I   L         + + +LFSAT D +V + A +++     + L  
Sbjct: 240 ---EIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDT 296

Query: 309 --KREEESLDNIKQHYVMCKNIDEKF-----EAVSNIYGVVTIGQAMIFCHTRKTAAWLA 361
             K E E+ + I Q  V+ +                I    +  +A+IF  T K  ++L 
Sbjct: 297 VDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLC 356

Query: 362 EKMSKE---GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
             +  E    L +    G++T  +R S++ RF++ E  I
Sbjct: 357 SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGI 395

>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 =  210 bits (538), Expect = 2e-65
 Identities = 68/293 (23%), Positives = 128/293 (43%), Gaps = 29/293 (9%)

Query: 110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP 169
           +  ++ + + EMGF   +++Q   +P +L     N++ ++++G+GKTAA+ + +L     
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQG--KNVVVRAKTGSGKTAAYAIPILEL--- 55

Query: 170 SIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVR--GENLERNKKITE--QII 225
                + L + PT EL  Q+   +  +G++   +  + A    G   +          I+
Sbjct: 56  ---GMKSLVVTPTRELTRQVASHIRDIGRY---MDTKVAEVYGGMPYKAQINRVRNADIV 109

Query: 226 IGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS 285
           + TPG++LD        DLS  ++ ++DEAD+M    G  D    I  +  +     LFS
Sbjct: 110 VATPGRLLDL-WSKGVIDLSSFEIVIIDEADLMF-EMGFIDDIKIILAQTSNRKITGLFS 167

Query: 286 ATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIG 345
           AT  +E+ +  +D + N   I+       L N++  +V    + + + +           
Sbjct: 168 ATIPEEIRKVVKDFITNYEEIEACI---GLANVEHKFVH---VKDDWRSKVQALRENKDK 221

Query: 346 QAMIFCHTRKTAAWLAEKMSK-EGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
             ++F  TR   A L         L      G+L    R   +D FREGE+ +
Sbjct: 222 GVIVFVRTRNRVAKLVRLFDNAIELR-----GDLPQSVRNRNIDAFREGEYDM 269

>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 =  207 bits (528), Expect = 3e-65
 Identities = 78/215 (36%), Positives = 127/215 (59%), Gaps = 9/215 (4%)

Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
            V  F+ ++LK  LL+G+Y  GF  PS IQ+ A+   +    +++IAQ+QSGTGKTA F 
Sbjct: 28  IVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKG--YDVIAQAQSGTGKTATFA 85

Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN--- 217
           +++L ++    +E Q L LAPT ELA QI +V+  +G ++   +    + G N+      
Sbjct: 86  ISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQK 144

Query: 218 -KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
            +     I++GTPG+V D  L  R+     IK+FVLDEAD M+ ++G +D    I ++L 
Sbjct: 145 LQAEAPHIVVGTPGRVFDM-LNRRYLSPKWIKMFVLDEADEML-SRGFKDQIYEIFQKLN 202

Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE 311
           +  Q++L SAT   +V+E  +  + +P+ I +K+E
Sbjct: 203 TSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>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 =  200 bits (512), Expect = 3e-63
 Identities = 67/206 (32%), Positives = 113/206 (54%), Gaps = 7/206 (3%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
            FE   LK ELL G++EMG+  PS IQE ++P  L+    +++A++++GTGK+ A+ + +
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSG--RDILARAKNGTGKSGAYLIPL 61

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE---RNKKI 220
           L R++      Q + + PT ELA+Q+ ++  ++ KH+    V     G NL         
Sbjct: 62  LERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDD 121

Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
           T  ++I TPG++LD  +K     +  +++ VLDEAD ++ +Q        I   LP + Q
Sbjct: 122 TVHVVIATPGRILDL-IKKGVAKVDHVQMIVLDEADKLL-SQDFVQIMEDIILTLPKNRQ 179

Query: 281 IMLFSATYDKEVMEFAQDMVPNPLII 306
           I+L+SAT+   V +F    +  P  I
Sbjct: 180 ILLYSATFPLSVQKFMNSHLEKPYEI 205

>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 =  200 bits (512), Expect = 5e-63
 Identities = 64/208 (30%), Positives = 110/208 (52%), Gaps = 7/208 (3%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
            F    LKPELL+ + + GF  PS++Q   +P  +     +++ Q++SG GKTA F L  
Sbjct: 15  GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGKTAVFVLAT 72

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN----KK 219
           L ++ P   +  VL +  T ELA QI +   +  K++ ++ V     G +++++    KK
Sbjct: 73  LQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK 132

Query: 220 ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
               I++GTPG++L    + +  +L  IK F+LDE D M+     +     I +  P + 
Sbjct: 133 NCPHIVVGTPGRILAL-ARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEK 191

Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLIIK 307
           Q+M+FSAT  KE+    +  + +P+ I 
Sbjct: 192 QVMMFSATLSKEIRPVCRKFMQDPMEIF 219

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  186 bits (474), Expect = 2e-57
 Identities = 63/217 (29%), Positives = 113/217 (52%), Gaps = 10/217 (4%)

Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
           +   F     +P +++ +  + FY P++IQE  +P  L     +M+ QSQ+GTGKT A+ 
Sbjct: 2   AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRG--ESMVGQSQTGTGKTHAYL 59

Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD---LSVRYAVRGENLERN 217
           L ++ ++ P   E Q +  APT ELA QI     K+ K       +  R  + G + ++ 
Sbjct: 60  LPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKA 119

Query: 218 KKITE---QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR 274
            +       I+IGTPG++ D+ ++ +  D+    + V+DEAD+M+   G      +I  R
Sbjct: 120 LEKLNVQPHIVIGTPGRINDF-IREQALDVHTAHILVVDEADLML-DMGFITDVDQIAAR 177

Query: 275 LPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE 311
           +P D Q+++FSAT  +++  F +  + NP  + +   
Sbjct: 178 MPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLEH 214

>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 =  178 bits (453), Expect = 2e-54
 Identities = 71/214 (33%), Positives = 114/214 (53%), Gaps = 15/214 (7%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
            F+   LKPE+L+ ++  G   P+ IQ  ALP  L     ++I Q+++GTGKT AF L +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEG--KDLIGQARTGTGKTLAFALPI 59

Query: 164 LSRVNPSIQE---PQVLCLAPTYELAIQIGEVVAKMGKHITDLSV----RYAVRGENLER 216
             R+ PS +    P+ L L PT ELA+Q+   +  +  H+  ++V     Y  + E L R
Sbjct: 60  AERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLR 119

Query: 217 NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
                   ++ TPG+ LD+ L+    DLS+++V VLDEAD M+ + G ++    +    P
Sbjct: 120 GA----DAVVATPGRALDY-LRQGVLDLSRVEVAVLDEADEML-SMGFEEEVEALLSATP 173

Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR 310
              Q +LFSAT        A+  + NP++I + +
Sbjct: 174 PSRQTLLFSATLPSWAKRLAERYMKNPVLINVIK 207

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  179 bits (457), Expect = 1e-52
 Identities = 43/318 (13%), Positives = 96/318 (30%), Gaps = 45/318 (14%)

Query: 106 EALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLS 165
           E  +   +      +      +  Q      ++     +    + +G GKT    +T L 
Sbjct: 2   EFWNEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQG--KSFTMVAPTGVGKTTFGMMTALW 59

Query: 166 RVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRY-----AVRGENLERNKKI 220
                 +  +   + PT  L  Q  E + K+      +   Y       + +  +  ++ 
Sbjct: 60  LAR---KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEED 116

Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
              I++ +   V             +     +D+ D ++        ++ +   +P +  
Sbjct: 117 DYHILVFSTQFVSK---NREKLSQKRFDFVFVDDVDAVLKA-SRNIDTLLMMVGIPEEII 172

Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKL---------------------KREEESLDNIK 319
              FS     ++ E  +++ P  L++                        R      NI 
Sbjct: 173 RKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNIT 232

Query: 320 QHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT 379
              +  ++  EK   +  I+        +IF  T +    L E + +   NVG    E  
Sbjct: 233 HVRISSRS-KEKLVELLEIFR----DGILIFAQTEEEGKELYEYLKRFKFNVGETWSE-- 285

Query: 380 VEQRLSILDRFREGEFKI 397
                   + F+ G+  I
Sbjct: 286 ---FEKNFEDFKVGKINI 300

>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 =  170 bits (432), Expect = 7e-51
 Identities = 68/231 (29%), Positives = 111/231 (48%), Gaps = 13/231 (5%)

Query: 83  ESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPP 142
             + +   +   P       KTF+ L +   L +   ++G+  P+KIQ  A+P  L    
Sbjct: 23  MEEHDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQG-- 80

Query: 143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD 202
            ++I  +++G+GKT AF L +L+ +  + Q    L L PT ELA QI E    +G  I  
Sbjct: 81  RDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSI-G 139

Query: 203 LSVRYAVRGENLERNKKITEQ---IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI 259
           +     V G +         +   III TPG+++D     + F+L  +K  V+DEAD ++
Sbjct: 140 VQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRIL 199

Query: 260 ATQGHQDFSI---RIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
               + DF     +I K +P D +  LFSAT  K+V +  +  + NP+   
Sbjct: 200 ----NMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCA 246

>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 =  168 bits (428), Expect = 3e-48
 Identities = 76/327 (23%), Positives = 149/327 (45%), Gaps = 32/327 (9%)

Query: 87  ELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMI 146
            +++   D   P   ++ F +  L+  ++  V + G+  P+ IQ+ ++P + +    +++
Sbjct: 43  PVKVTGSDVPQP---IQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSG--RDLM 97

Query: 147 AQSQSGTGKTAAFTLTMLSRVN-----PSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT 201
           A +Q+G+GKTAAF L +LS++        +  PQV+ ++PT ELAIQI     K      
Sbjct: 98  ACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFE-- 155

Query: 202 DLSVRYAV------RGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEA 255
              ++  +           E   +    ++I TPG++LD+ +   F      +  VLDEA
Sbjct: 156 -SYLKIGIVYGGTSFRHQNECITRGCH-VVIATPGRLLDF-VDRTFITFEDTRFVVLDEA 212

Query: 256 DVMIATQGHQDFSIRIQK-----RLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR 310
           D M+       FS  +++      +  + Q ++FSAT+ +E+   A + + N + + +  
Sbjct: 213 DRML----DMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGI 268

Query: 311 EEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLN 370
              +  ++KQ          K   +  I         ++F  T++ A +LA  +S++   
Sbjct: 269 VGGACSDVKQTIYEVNK-YAKRSKLIEILS-EQADGTIVFVETKRGADFLASFLSEKEFP 326

Query: 371 VGLLSGELTVEQRLSILDRFREGEFKI 397
              + G+    QR   L  F+ G  K+
Sbjct: 327 TTSIHGDRLQSQREQALRDFKNGSMKV 353

>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 =  155 bits (394), Expect = 2e-45
 Identities = 60/238 (25%), Positives = 113/238 (47%), Gaps = 16/238 (6%)

Query: 83  ESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPP 142
           E +    + +      +  +  F    L  + LKG+ E  +   ++IQ+  +   L    
Sbjct: 5   ERESISRLMQNYEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQG-- 62

Query: 143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQ----VLCLAPTYELAIQIGEVVAKMGK 198
            +++  +++G+GKT AF + +L  +            VL ++PT ELA Q  EV+ K+GK
Sbjct: 63  KDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGK 122

Query: 199 HITDLSVRYAVRGENLERNKKITE--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD 256
           +  D S    + G++L+   +      I++ TPG++L    +   F  + +++ VLDEAD
Sbjct: 123 N-HDFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEAD 181

Query: 257 VMIATQGHQDFSI---RIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE 311
            ++       F+     + + LP   Q +LFSAT  K V + A+  + NP  + +  +
Sbjct: 182 RIL----DMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK 235

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  160 bits (407), Expect = 2e-45
 Identities = 81/343 (23%), Positives = 149/343 (43%), Gaps = 47/343 (13%)

Query: 87  ELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMI 146
            +E    +       +++F  + +   ++  +    +  P+ +Q+ A+P +      +++
Sbjct: 2   MVEATGNNCPPH---IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEK--RDLM 56

Query: 147 AQSQSGTGKTAAFTLTMLSRVN------------------PSIQEPQVLCLAPTYELAIQ 188
           A +Q+G+GKTAAF L +LS++                      Q P  L LAPT ELA+Q
Sbjct: 57  ACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQ 116

Query: 189 IGEVVAKMGKHITDLSVRYAV------RGENLERNKKITEQIIIGTPGKVLDWGLKYRFF 242
           I E   K         VR  V       G+ +   ++    +++ TPG+++D  ++    
Sbjct: 117 IYEEARKFSYR---SRVRPCVVYGGADIGQQIRDLERGCH-LLVATPGRLVDM-MERGKI 171

Query: 243 DLSKIKVFVLDEADVMIATQGHQDFSIRIQK-----RLPSDC--QIMLFSATYDKEVMEF 295
            L   K  VLDEAD M+       F  +I++      +P       M+FSAT+ KE+   
Sbjct: 172 GLDFCKYLVLDEADRML----DMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQML 227

Query: 296 AQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI-YGVVTIGQAMIFCHTR 354
           A+D +   + + + R   + +NI Q  V  +   +K   + ++          ++F  T+
Sbjct: 228 ARDFLDEYIFLAVGRVGSTSENITQKVVWVEE-SDKRSFLLDLLNATGKDSLTLVFVETK 286

Query: 355 KTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
           K A  L + +  EG     + G+ +   R   L +FR G+  I
Sbjct: 287 KGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPI 329

>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 =  143 bits (362), Expect = 2e-40
 Identities = 63/262 (24%), Positives = 115/262 (43%), Gaps = 14/262 (5%)

Query: 55  PGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEAL--HLKP 112
             +        +          V +   +  +          +  +   +F +L   +  
Sbjct: 4   HHHHSSGVDLGTENLYFQSMNNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNE 63

Query: 113 ELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQ 172
             LK + EMGF   ++IQ  ++  LL     +++A +++G+GKT AF +  +  +     
Sbjct: 64  NTLKAIKEMGFTNMTEIQHKSIRPLLEG--RDLLAAAKTGSGKTLAFLIPAVELIVKLRF 121

Query: 173 EPQ----VLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQ---II 225
            P+    VL L+PT ELA+Q   V+ ++  H    +    + G N     +       II
Sbjct: 122 MPRNGTGVLILSPTRELAMQTFGVLKELMTH-HVHTYGLIMGGSNRSAEAQKLGNGINII 180

Query: 226 IGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS 285
           + TPG++LD       F    ++  V+DEAD ++   G ++   +I K LP+  Q MLFS
Sbjct: 181 VATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILD-VGFEEELKQIIKLLPTRRQTMLFS 239

Query: 286 ATYDKEVMEFAQD-MVPNPLII 306
           AT  ++V + A+  +   PL +
Sbjct: 240 ATQTRKVEDLARISLKKEPLYV 261

>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 =  141 bits (359), Expect = 5e-40
 Identities = 68/257 (26%), Positives = 122/257 (47%), Gaps = 34/257 (13%)

Query: 87  ELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMI 146
            + +   D  +    ++ F+ L L P +   +    +  P+ IQ+ A+P +L     +++
Sbjct: 8   PVSVTGPDYSAT-NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEH--RDIM 64

Query: 147 AQSQSGTGKTAAFTLTMLSRVNP---------SIQEPQVLCLAPTYELAIQIGEVVAKMG 197
           A +Q+G+GKTAAF + +++ +               P+ L LAPT ELAIQI     K  
Sbjct: 65  ACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFS 124

Query: 198 KHITDLSVRYAV------RGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFV 251
            +     +R  V          +   +     +++ TPG+++D+ ++     L   K  V
Sbjct: 125 LN---TPLRSCVVYGGADTHSQIREVQMGCH-LLVATPGRLVDF-IEKNKISLEFCKYIV 179

Query: 252 LDEADVMIATQGHQDFSIRIQK-----RLPS--DCQIMLFSATYDKEVMEFAQDMVPNPL 304
           LDEAD M+       F  +I+K      +PS  + Q ++FSAT+ KE+ + A D + N +
Sbjct: 180 LDEADRML----DMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYI 235

Query: 305 IIKLKREEESLDNIKQH 321
            + + R   + D+IKQ 
Sbjct: 236 FMTVGRVGSTSDSIKQE 252

>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 =  140 bits (356), Expect = 1e-39
 Identities = 54/238 (22%), Positives = 107/238 (44%), Gaps = 25/238 (10%)

Query: 85  KQELEIQRKDPHSPLYSVKTFEALH----LKPELLKGVYEMGFYAPSKIQETALPTLLAD 140
           K ++ +Q  D   P   + TF+ L     +   LL+ + + GF  P+ IQ  A+P +L  
Sbjct: 10  KHKIHVQGTDLPDP---IATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHG 66

Query: 141 PPHNMIAQSQSGTGKTAAFTLTMLSRVN-PSIQEPQVLCLAPTYELAIQIGEVVAKMGKH 199
               ++A + +G+GKT AF++ +L ++  P+ +  + L ++PT ELA QI   + K+ + 
Sbjct: 67  --RELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEG 124

Query: 200 ITDLSVRYAV------RGENLERNKKITEQIIIGTPGKVLD-WGLKYRFFDLSKIKVFVL 252
                 R  +        +           I++ TP +++          DL+ ++  V+
Sbjct: 125 ---TGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVV 181

Query: 253 DEADVMIATQG----HQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII 306
           DE+D +          Q  SI          +  +FSAT+  +V ++ +  + N + +
Sbjct: 182 DESDKLFEDGKTGFRDQLASI-FLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISV 238

>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 =  137 bits (348), Expect = 1e-38
 Identities = 62/223 (27%), Positives = 102/223 (45%), Gaps = 32/223 (14%)

Query: 102 VKTF-EALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
              F +A    P+LLK +  +G   P+ IQ  A P +L     ++I  +Q+GTGKT ++ 
Sbjct: 18  TCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQG--IDLIVVAQTGTGKTLSYL 75

Query: 161 LTMLSRVN--PSIQE----PQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAV----- 209
           +     ++  P  +E    P +L L PT ELA+ +    +K         ++        
Sbjct: 76  MPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSY----KGLKSICIYGGR 131

Query: 210 -RGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQD-- 266
            R   +E   K  + III TPG++ D        +L  I   V+DEAD M+      D  
Sbjct: 132 NRNGQIEDISKGVD-IIIATPGRLNDL-QMNNSVNLRSITYLVIDEADKML------DME 183

Query: 267 FSIRIQK---RLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII 306
           F  +I+K    +  D Q ++ SAT+   V + A   + +P+I+
Sbjct: 184 FEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIV 226

>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 =  133 bits (337), Expect = 6e-37
 Identities = 64/236 (27%), Positives = 114/236 (48%), Gaps = 32/236 (13%)

Query: 87  ELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMI 146
           E+ ++  +   P   V  F   +    ++  +    F  P+ IQ    P  L+    +M+
Sbjct: 16  EITVRGHNCPKP---VLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSG--LDMV 70

Query: 147 AQSQSGTGKTAAFTLTMLSRVN--PSIQE---PQVLCLAPTYELAIQIGEVVAKMGKHIT 201
             +Q+G+GKT ++ L  +  +N  P ++    P  L LAPT ELA Q+ +V A+  +   
Sbjct: 71  GVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRA-- 128

Query: 202 DLSVRYAV------RGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEA 255
              ++         +G  +   ++  E I I TPG+++D+ L+    +L +    VLDEA
Sbjct: 129 -CRLKSTCIYGGAPKGPQIRDLERGVE-ICIATPGRLIDF-LECGKTNLRRTTYLVLDEA 185

Query: 256 DVMIATQGHQD--F--SIR-IQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII 306
           D M+      D  F   IR I  ++  D Q +++SAT+ KEV + A+D + + + I
Sbjct: 186 DRML------DMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHI 235

>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 =  118 bits (298), Expect = 5e-32
 Identities = 47/86 (54%), Positives = 68/86 (79%)

Query: 312 EESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNV 371
             +L+NI+Q+YV+C++  +K++A+ NIYG +TIGQA+IFC TR+ A WL  +M ++G  V
Sbjct: 2   MLTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQV 61

Query: 372 GLLSGELTVEQRLSILDRFREGEFKI 397
            LLSGELTVEQR SI+ RFR+G+ K+
Sbjct: 62  SLLSGELTVEQRASIIQRFRDGKEKV 87

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  107 bits (270), Expect = 3e-28
 Identities = 26/83 (31%), Positives = 49/83 (59%)

Query: 315 LDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLL 374
           L+ IKQ YV  +  + K+E ++++Y  +++ QA+IFC+TR+    L  K+  +   V  +
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60

Query: 375 SGELTVEQRLSILDRFREGEFKI 397
             +L  ++R +I+  FR G  +I
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRI 83

>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 =  103 bits (258), Expect = 2e-26
 Identities = 20/84 (23%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 314 SLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGL 373
           SL  ++Q+YV  K+ +EK   + ++  V+   Q +IF  + +    LA+ + ++      
Sbjct: 2   SLHGLQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIA 60

Query: 374 LSGELTVEQRLSILDRFREGEFKI 397
           +   +  E+RLS   +F++ + +I
Sbjct: 61  IHRGMPQEERLSRYQQFKDFQRRI 84

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 89.9 bits (224), Expect = 1e-21
 Identities = 16/87 (18%), Positives = 38/87 (43%), Gaps = 1/87 (1%)

Query: 311 EEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLN 370
              +  NI+   +  +  + KF  + ++         +IFC T++    L +++   G  
Sbjct: 3   AGLTTRNIEHAVIQVRE-ENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYP 61

Query: 371 VGLLSGELTVEQRLSILDRFREGEFKI 397
              + G +  E R  +++ F+ GE++ 
Sbjct: 62  CDKIHGGMIQEDRFDVMNEFKRGEYRY 88

>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 = 69.9 bits (172), Expect = 2e-14
 Identities = 17/81 (20%), Positives = 35/81 (43%)

Query: 317 NIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSG 376
            I Q Y    +++ K   + ++       ++++F   R+    LA  + + G+N   L G
Sbjct: 3   KIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEG 62

Query: 377 ELTVEQRLSILDRFREGEFKI 397
           E+   +R   + R  EG   +
Sbjct: 63  EMVQGKRNEAIKRLTEGRVNV 83

>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 = 67.7 bits (166), Expect = 3e-13
 Identities = 19/85 (22%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 313 ESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVG 372
           +     ++  V       + E +S++  V +  +AM+F  T+     +A+ + + G    
Sbjct: 1   DEPVTYEEEAVPAPVRG-RLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQ 59

Query: 373 LLSGELTVEQRLSILDRFREGEFKI 397
            L G+L+  +R  +L  FR+GE ++
Sbjct: 60  ALHGDLSQGERERVLGAFRQGEVRV 84

>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 = 68.2 bits (167), Expect = 4e-13
 Identities = 17/81 (20%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 317 NIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSG 376
             ++  V       + E +S++  V +  +AM+F  T+     +A+ + + G     L G
Sbjct: 2   TYEEEAVPAPV-RGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHG 60

Query: 377 ELTVEQRLSILDRFREGEFKI 397
           +++  +R  ++  FR+GE ++
Sbjct: 61  DMSQGERERVMGAFRQGEVRV 81

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 63.9 bits (155), Expect = 3e-11
 Identities = 54/282 (19%), Positives = 92/282 (32%), Gaps = 54/282 (19%)

Query: 114 LLKGVYEMGFYAPSKIQETALPTLLADPP----------HNMIAQSQSGTGKTAAFTLTM 163
             +GV +   + P +  ET + + +                    + +G+GK+       
Sbjct: 194 CTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAY 253

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK-MGKHITDLSVRYAVRGENLERNKKITE 222
            ++        +VL L P+    +  G  ++K  G       +R  VR            
Sbjct: 254 AAQ------GYKVLVLNPSVAATLGFGAYMSKAHGIDPN---IRTGVR------TITTGA 298

Query: 223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM 282
            +   T GK L  G            + + DE     +T      ++  Q        ++
Sbjct: 299 PVTYSTYGKFLADGGC----SGGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVV 354

Query: 283 LFSATYDKEVMEFAQDMVPNPLIIKLKREEESLD--NIKQHYVMCKNIDEKFEAVSNIYG 340
           L +AT    V       VP+P I     EE +L        Y     I+           
Sbjct: 355 LATATPPGSVT------VPHPNI-----EEVALSNTGEIPFYGKAIPIE----------- 392

Query: 341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQ 382
            +  G+ +IFCH++K    LA K+S  G+N       L V  
Sbjct: 393 AIRGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV 434

>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 = 56.4 bits (136), Expect = 8e-09
 Identities = 56/339 (16%), Positives = 103/339 (30%), Gaps = 74/339 (21%)

Query: 110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP 169
           +    +  + E G       Q  A+  + +    N++    +  GKT    + M+     
Sbjct: 10  ISSYAVGILKEEGIEELFPPQAEAVEKVFSG--KNLLLAMPTAAGKTLLAEMAMVREA-- 65

Query: 170 SIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTP 229
            I+  + L + P   LA +  E   K  K    L +  +               II+ T 
Sbjct: 66  -IKGGKSLYVVPLRALAGEKYESFKKWEKI--GLRIGISTGDYESRDEHLGDCDIIVTTS 122

Query: 230 GKVLDWGLKYRFFDLSKIKVFVLDE----AD--------VMIATQGHQDFSIRIQKRLPS 277
            K  D  ++ R   +  +   V+DE              +++          ++ +R+  
Sbjct: 123 EK-ADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVT---------KM-RRMNK 171

Query: 278 DCQIMLFSAT---YDK-----EVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNID 329
             +++  SAT     +     +   +  D  P PL+  +  E                  
Sbjct: 172 ALRVIGLSATAPNVTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSR---R 228

Query: 330 EKFEAVSNIYGVVTIG-QAMIFCHTRK----TAAWLAEKMSKEGLN-------------- 370
            KFE +  +   V      ++F  TR+    TA  L+   +K   N              
Sbjct: 229 VKFEEL--VEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGE 286

Query: 371 ------------VGLLSGELTVEQRLSILDRFREGEFKI 397
                              L   QR  + D FR G  K+
Sbjct: 287 MSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKV 325

>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 = 55.6 bits (134), Expect = 1e-08
 Identities = 48/278 (17%), Positives = 91/278 (32%), Gaps = 27/278 (9%)

Query: 106 EALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLS 165
           + L +   +   + E G  +    Q  AL + + +   N +    + +GKT    + M+ 
Sbjct: 4   DELRVDERIKSTLKERGIESFYPPQAEALKSGILEG-KNALISIPTASGKTLIAEIAMVH 62

Query: 166 RVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQII 225
           R+       + + + P   LA +  +      K    L V  A    + +        II
Sbjct: 63  RILTQGG--KAVYIVPLKALAEEKFQEFQDWEK--IGLRVAMATGDYDSKDEWLGKYDII 118

Query: 226 IGTPGKVLDWGLKYRFFD-LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLF 284
           I T  K  D  L       +  +K+ V DE   +I ++        I   +    QI+  
Sbjct: 119 IATAEK-FD-SLLRHGSSWIKDVKILVADEIH-LIGSRDRGATLEVILAHMLGKAQIIGL 175

Query: 285 SAT---YDK-----EVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
           SAT    ++            D  P  L   +  +                 +  ++A+ 
Sbjct: 176 SATIGNPEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIR 235

Query: 337 NIYGVVTIGQAMIFCHTRK----TAAWLAEKMSKEGLN 370
                     A+IF + R+     A  L++K+      
Sbjct: 236 KK------KGALIFVNMRRKAERVALELSKKVKSLLTK 267

>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 = 53.3 bits (127), Expect = 9e-08
 Identities = 62/428 (14%), Positives = 121/428 (28%), Gaps = 124/428 (28%)

Query: 7   WIAATKNTSALKPDDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLS 66
           W+      S   P+ ++++L  + L Q D          + S   S+           L 
Sbjct: 186 WLNLKNCNS---PETVLEMLQKL-LYQIDPNWT------SRSDHSSNIKLRIHSIQAELR 235

Query: 67  VAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAP 126
              + L  K     L+       +   +    + + K + A +L                
Sbjct: 236 ---RLLKSKPYENCLL-------VLL-N----VQNAKAWNAFNLS--------------- 265

Query: 127 SKI----QETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSR-VNPSIQE--PQVLCL 179
            KI    +   +   L+      I+        T     ++L + ++   Q+   +VL  
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT 325

Query: 180 APTYELAI-QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWG-L 237
            P     +  I E +             +  +  N ++   I E  +      VL+    
Sbjct: 326 NP---RRLSIIAESIRDGLATWD----NW--KHVNCDKLTTIIESSL-----NVLEPAEY 371

Query: 238 KYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ 297
           +  F  LS   VF        I                P+    +++      +VM    
Sbjct: 372 RKMFDRLS---VF---PPSAHI----------------PTILLSLIWFDVIKSDVMVVVN 409

Query: 298 DMVPNPLI-----------------IKLKREEE-SL-DNIKQHYVMCKNIDEKFEAVSNI 338
            +    L+                 +K+K E E +L  +I  HY + K  D        +
Sbjct: 410 KLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL 469

Query: 339 ---------YGVVTIGQA-------MIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQ 382
                    + +  I          M+F   R    +L +K+  +          L   Q
Sbjct: 470 DQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR----FLEQKIRHDSTAWNASGSILNTLQ 525

Query: 383 RLSILDRF 390
           +L     +
Sbjct: 526 QLKFYKPY 533

>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 = 49.1 bits (116), Expect = 2e-06
 Identities = 51/353 (14%), Positives = 106/353 (30%), Gaps = 98/353 (27%)

Query: 58  KDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKG 117
           KD +D P S+  K  +  I+               KD  S    +  F  L  K E  + 
Sbjct: 36  KDVQDMPKSILSKEEIDHII-------------MSKDAVSGTLRL--FWTLLSKQE--EM 78

Query: 118 VYEMGFYAPSKIQETALPTLLADPPHNMIAQS-QSGTGKTAAFTLTMLSRVNPSIQEPQV 176
           V +  F       E  L        +  +    ++   + +  T   + + +    + QV
Sbjct: 79  VQK--FV------EEVL-----RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125

Query: 177 LCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGK-VL-- 233
                 Y ++           +    L  R A+    L   K +    ++G+ GK  +  
Sbjct: 126 F---AKYNVSRL---------QPYLKL--RQALL--ELRPAKNVLIDGVLGS-GKTWVAL 168

Query: 234 ----DWGLKYRFFDLSKIKVFVL-----DEADVMIATQGHQDFSIRIQKRLPSDCQIML- 283
                + ++ +       K+F L     +  + ++     Q    +I     S       
Sbjct: 169 DVCLSYKVQCKMDF----KIFWLNLKNCNSPETVLEML--QKLLYQIDPNWTSRSDHSSN 222

Query: 284 ----FSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIY 339
                 +   +           N L++        L N++            F     I 
Sbjct: 223 IKLRIHSIQAELRRLLKSKPYENCLLV--------LLNVQN-----AKAWNAFNLSCKI- 268

Query: 340 GVVTIGQAMIFCHTRKT--AAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRF 390
            ++T         TR      +L+   +   +++   S  LT ++  S+L ++
Sbjct: 269 -LLT---------TRFKQVTDFLSAATTTH-ISLDHHSMTLTPDEVKSLLLKY 310

>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 = 52.5 bits (125), Expect = 1e-07
 Identities = 37/192 (19%), Positives = 73/192 (38%), Gaps = 6/192 (3%)

Query: 143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD 202
            N +    +G GKT    +    R+       +VL LAPT  L +Q  E   ++     +
Sbjct: 24  TNCLIVLPTGLGKTLIAMMIAEYRLTK--YGGKVLMLAPTKPLVLQHAESFRRLFNLPPE 81

Query: 203 LSVRYAVRGENLERNKKITE-QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT 261
             V         ER+K     ++I+ TP  + +  L      L  + + V DEA   +  
Sbjct: 82  KIVALTGEKSPEERSKAWARAKVIVATPQTIEND-LLAGRISLEDVSLIVFDEAHRAVG- 139

Query: 262 QGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQH 321
                F  R  KR   +  ++  +A+      E   +++ N  I  ++   E+  +++ +
Sbjct: 140 NYAYVFIAREYKRQAKNPLVIGLTASPGST-PEKIMEVINNLGIEHIEYRSENSPDVRPY 198

Query: 322 YVMCKNIDEKFE 333
               +    + +
Sbjct: 199 VKGIRFEWVRVD 210

>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 = 45.2 bits (106), Expect = 2e-05
 Identities = 37/227 (16%), Positives = 77/227 (33%), Gaps = 25/227 (11%)

Query: 183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLK---- 238
            +L     EV   + + + D     A  G     +  I ++ ++     + +   K    
Sbjct: 209 VDLPEIYKEVRKLLREMLRDALKPLAETGLLESSSPDIPKKEVLRAGQIINEEMAKGNHD 268

Query: 239 YRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQD 298
            R   L       L  A  ++ TQG         K+L  + +     A+         ++
Sbjct: 269 LRGLLLYHAMALKLHHAIELLETQGLSAL-RAYIKKLYEEAKAGSTKAS---------KE 318

Query: 299 MVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAA 358
           +  +  + K          I   +     +D+  E +          + ++F + R+TA 
Sbjct: 319 IFSDKRMKKAISLLVQAKEIGLDHPK---MDKLKEIIREQLQRKQNSKIIVFTNYRETAK 375

Query: 359 WLAEKMSKEGLNVGLLSG--------ELTVEQRLSILDRFREGEFKI 397
            +  ++ K+G+      G         L+  ++  ILD F  GEF +
Sbjct: 376 KIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNV 422

>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 = 51.0 bits (122), Expect = 3e-07
 Identities = 37/264 (14%), Positives = 84/264 (31%), Gaps = 50/264 (18%)

Query: 144 NMIAQSQS-------GTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKM 196
           +M+ +  +       G GKT  F   +L+    + +  + L LAPT  +  ++ E    +
Sbjct: 3   HMLKKGMTTVLDFHPGAGKTRRFLPQILA--ECARRRLRTLVLAPTRVVLSEMKEAFHGL 60

Query: 197 GKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFD---LSKIKVFVLD 253
                   V++  +  +   + +    I            L YR  +   +   +V ++D
Sbjct: 61  -------DVKFHTQAFSAHGSGREV--IDAMCHAT-----LTYRMLEPTRVVNWEVIIMD 106

Query: 254 EADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE 313
           EA  +              +   ++   +L +AT      EF      N  I  +     
Sbjct: 107 EAHFLDPASI-AARGWAAHRARANESATILMTATPPGTSDEF---PHSNGEIEDV----- 157

Query: 314 SLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGL 373
                 Q  +  +  +   + +              F  + + A  +A  + K G +V +
Sbjct: 158 ------QTDIPSEPWNTGHDWILA-----DKRPTAWFLPSIRAANVMAASLRKAGKSVVV 206

Query: 374 LSGELTVEQRLSILDRFREGEFKI 397
           L+ +             ++ +   
Sbjct: 207 LNRKT----FEREYPTIKQKKPDF 226

>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 = 48.4 bits (115), Expect = 3e-06
 Identities = 39/267 (14%), Positives = 83/267 (31%), Gaps = 46/267 (17%)

Query: 122 GFYAPSKIQETALPTLLADPPHNMIAQSQ-------SGTGKTAAFTLTMLSRVNPSIQEP 174
           G Y  +  Q   +     +   ++  + +        G GKT     +++       +  
Sbjct: 159 GDYVSAITQAERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVRE--ALKRRL 216

Query: 175 QVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLD 234
           + L LAPT  +A       A+M + +  L +RY      ++ +    E + +        
Sbjct: 217 RTLILAPTRVVA-------AEMEEALRGLPIRYQTPA--VKSDHTGREIVDLMCHA---- 263

Query: 235 WGLKYRFF---DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE 291
                R      +    + V+DEA                 +    +   +  +AT    
Sbjct: 264 -TFTTRLLSSTRVPNYNLIVMDEAHFTDPCSV-AARGYISTRVEMGEAAAIFMTATPPGS 321

Query: 292 VMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFC 351
              F Q   P      ++  E  +   ++ +    +    ++           G+ + F 
Sbjct: 322 TDPFPQSNSP------IEDIEREIP--ERSWNTGFDWITDYQ-----------GKTVWFV 362

Query: 352 HTRKTAAWLAEKMSKEGLNVGLLSGEL 378
            + K    +A  + K G  V  LS + 
Sbjct: 363 PSIKAGNDIANCLRKSGKRVIQLSRKT 389

>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 = 45.3 bits (106), Expect = 3e-05
 Identities = 31/201 (15%), Positives = 67/201 (33%), Gaps = 14/201 (6%)

Query: 143 HNMIAQSQSGTGKT--AAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK-MGKH 199
            N +  + +G+GKT  +        +  P+ ++ +V+ LA    +  Q   V      + 
Sbjct: 23  KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ 82

Query: 200 ITDLSVRYAVRGENLERNKKITE-QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM 258
              +         N+   K I +  II+ TP  +++         LS   + + DE    
Sbjct: 83  GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNT 142

Query: 259 IA----TQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEES 314
                       +  +         QI+  +A+      +  ++       I+      S
Sbjct: 143 TGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEET------IEHICSLCS 196

Query: 315 LDNIKQHYVMCKNIDEKFEAV 335
             +I+    + +NI E    +
Sbjct: 197 YLDIQAISTVRENIQELQRFM 217

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 45.4 bits (106), Expect = 3e-05
 Identities = 34/197 (17%), Positives = 64/197 (32%), Gaps = 5/197 (2%)

Query: 143 HNMIAQSQSGTGKTAAFTLTMLS--RVNPSIQEPQVLCLAPTYELAIQIGEVVAK-MGKH 199
            N I  + +G GKT    L      +  P  Q+ +V+  A    +  Q   V +K   +H
Sbjct: 29  KNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSKYFERH 88

Query: 200 ITDLSVRYAVRGENLERNKKITE-QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM 258
              ++       EN+   + +    III TP  +++   K     LS   + + DE    
Sbjct: 89  GYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNT 148

Query: 259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNI 318
                +         +        L         +        +  +  + +   SLD  
Sbjct: 149 SKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLD-A 207

Query: 319 KQHYVMCKNIDEKFEAV 335
                +  N++E  + V
Sbjct: 208 SVIATVKHNLEELEQVV 224

>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 = 44.5 bits (105), Expect = 4e-05
 Identities = 39/230 (16%), Positives = 77/230 (33%), Gaps = 39/230 (16%)

Query: 152 GTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRG 211
           G GKT     +++      ++  + L LAPT  +A       A+M + +  L +RY    
Sbjct: 29  GAGKTKRILPSIVRE--ALLRRLRTLILAPTRVVA-------AEMEEALRGLPIRYQTPA 79

Query: 212 ENLERNKKITEQIIIGTPGKVLDWGLKYRFFD---LSKIKVFVLDEADVMIATQGHQDFS 268
             ++ +    E + +             R      +    + V+DEA             
Sbjct: 80  --VKSDHTGREIVDLMCHA-----TFTTRLLSSTRVPNYNLIVMDEAHFTDPCSV-AARG 131

Query: 269 IRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI 328
               +    +   +  +AT       F Q   P   I  ++RE              ++ 
Sbjct: 132 YISTRVEMGEAAAIFMTATPPGSTDPFPQSNSP---IEDIEREIPE-----------RSW 177

Query: 329 DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGEL 378
           +  F+ +++       G+ + F  + K    +A  + K G  V  LS + 
Sbjct: 178 NTGFDWITD-----YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKT 222

>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 = 44.6 bits (104), Expect = 5e-05
 Identities = 33/229 (14%), Positives = 73/229 (31%), Gaps = 17/229 (7%)

Query: 143 HNMIAQSQSGTGKT--AAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK-MGKH 199
            N +  + +G+GKT  +        +  P+ ++ +V+ LA    +  Q   V      + 
Sbjct: 264 KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ 323

Query: 200 ITDLSVRYAVRGENLERNKKITE-QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM 258
              +         N+   K I +  II+ TP  +++         LS   + + DE    
Sbjct: 324 GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNT 383

Query: 259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNI 318
                +                  L         +     +  +  +   K  EE++++I
Sbjct: 384 TGNHPYNVL-----------MTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHI 432

Query: 319 KQ--HYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMS 365
                Y+  + I    E +  +   +   +  +    R+     A  +S
Sbjct: 433 CSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIIS 481

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 44.1 bits (103), Expect = 7e-05
 Identities = 34/205 (16%), Positives = 72/205 (35%), Gaps = 21/205 (10%)

Query: 143 HNMIAQSQSGTGKTAAFTLTMLSRVN--PSIQEPQVLCLAPTYELAIQIGEVVAKM---- 196
            N I  + +G GKT    L     +   P  Q+ +V+  A    +  Q   V ++     
Sbjct: 20  KNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERL 79

Query: 197 GKHITDLSVRYAVRGENLERNKKITE-QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEA 255
           G +I  +S       +++     I +  III TP  +++         LS   + + DE 
Sbjct: 80  GYNIASISGAT---SDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDEC 136

Query: 256 DVMIATQGHQD-----FSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR 310
                   +          ++ +      Q++  +A+      + A++      +  + +
Sbjct: 137 HNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGVGDAKTAEEA-----MQHICK 191

Query: 311 EEESLDNIKQHYVMCKNIDEKFEAV 335
              +LD       +  N+ E  + V
Sbjct: 192 LCAALD-ASVIATVRDNVAELEQVV 215

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 43.3 bits (102), Expect = 8e-05
 Identities = 37/233 (15%), Positives = 72/233 (30%), Gaps = 45/233 (19%)

Query: 152 GTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK-MGKHITDLSVRYAVR 210
           G GKT      ++       +  + + LAPT         VVA  M + +    +RY   
Sbjct: 12  GAGKTRRVLPQLVRE--AVKKRLRTVILAPT--------RVVASEMYEALRGEPIRYMTP 61

Query: 211 GENLERNKKITEQIIIGTPGKVLDWGLKYRFF---DLSKIKVFVLDEADVMIATQGHQDF 267
              ++  +   E +               +      +    ++++DEA  +         
Sbjct: 62  A--VQSERTGNEIVDFMCHS-----TFTMKLLQGVRVPNYNLYIMDEAHFLDPASV-AAR 113

Query: 268 SIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKN 327
                +    D   +  +AT       F     P      +  EE  +            
Sbjct: 114 GYIETRVSMGDAGAIFMTATPPGTTEAFPPSNSP------IIDEETRIP----------- 156

Query: 328 IDEKFEAVSNIYGVVT--IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGEL 378
                +A ++ Y  +T   G+ + F H+ K  A +   + K G  V  L+ + 
Sbjct: 157 ----DKAWNSGYEWITEFDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRKT 205

>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 = 43.3 bits (102), Expect = 9e-05
 Identities = 17/117 (14%), Positives = 42/117 (35%), Gaps = 8/117 (6%)

Query: 284 FSATYDKEVMEFAQDMVPNPLIIKLKREE---ESLDNIKQHYVMCKNIDEKFEAVSNIYG 340
           +        +   +    N +++    +E   E+L   ++   +  N   K   +  I  
Sbjct: 286 YKQFLRARGITLRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILE 345

Query: 341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
                + +IF    +    +++        +  ++   + E+R  IL+ FR G F+ 
Sbjct: 346 RHRKDKIIIFTRHNELVYRISKV-----FLIPAITHRTSREEREEILEGFRTGRFRA 397

>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 = 42.9 bits (101), Expect = 1e-04
 Identities = 42/253 (16%), Positives = 77/253 (30%), Gaps = 50/253 (19%)

Query: 138 LADPPHNMIAQSQS-------GTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIG 190
           +     NM+ + Q        G+GKT      ++       Q  +   LAPT        
Sbjct: 10  MGRGSPNMLRKRQMTVLDLHPGSGKTRKILPQIIKD--AIQQRLRTAVLAPT-------- 59

Query: 191 EVVAK-MGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFF----DLS 245
            VVA  M + +  L VRY       +R  +  E + +     +               + 
Sbjct: 60  RVVAAEMAEALRGLPVRYQTSAV--QREHQGNEIVDVMCHATLT------HRLMSPNRVP 111

Query: 246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLI 305
              +FV+DEA             I  +  L  +   +  +AT       F     P    
Sbjct: 112 NYNLFVMDEAHFTDPASIAARGYIATKVELG-EAAAIFMTATPPGTTDPFPDSNAP---- 166

Query: 306 IKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMS 365
                ++E              I ++  +    +     G+ + F  + K    +A  + 
Sbjct: 167 -IHDLQDE--------------IPDRAWSSGYEWITEYAGKTVWFVASVKMGNEIAMCLQ 211

Query: 366 KEGLNVGLLSGEL 378
           + G  V  L+ + 
Sbjct: 212 RAGKKVIQLNRKS 224

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 14/107 (13%), Positives = 33/107 (30%), Gaps = 5/107 (4%)

Query: 294 EFAQDMVP---NPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIF 350
                          +  +    +  ++ Q     K  + K   +            +IF
Sbjct: 3   HHHHHSSGVDLGTENLYFQSMGAASLDVIQEVEYVKE-EAKMVYLLECLQKTP-PPVLIF 60

Query: 351 CHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
              +     + E +  +G+    + G    E+R   ++ FREG+  +
Sbjct: 61  AEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDV 107

>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 = 40.3 bits (95), Expect = 3e-04
 Identities = 19/82 (23%), Positives = 35/82 (42%)

Query: 316 DNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLS 375
           +NI Q  V  +  D++   +  +         ++F  T+K A  L + +  EG     + 
Sbjct: 18  ENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIH 77

Query: 376 GELTVEQRLSILDRFREGEFKI 397
           G+ +   R   L +FR G+  I
Sbjct: 78  GDRSQRDREEALHQFRSGKSPI 99

>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 = 41.6 bits (97), Expect = 4e-04
 Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 329 DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKM-SKEGLNVGLLSGELTVEQRLSIL 387
           D + E +          + ++ C    TA  L + +  +EG+   +    +++ +R    
Sbjct: 488 DPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAA 547

Query: 388 DRFREGE 394
             F E +
Sbjct: 548 AWFAEED 554

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	399
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	100.0
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	100.0
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	100.0
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	100.0
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.98
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.98
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.97
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.97
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.97
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.97
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.97
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.97
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.96
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.96
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.96
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.95
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.95
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.95
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.94
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.94
3h1t_A	590	Type I site-specific restriction-modification syst	99.94
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.93
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.91
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.91
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.91
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.9
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.9
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.9
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.89
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.88
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.84
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.83
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.81
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.79
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.7
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.67
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.64
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.57
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.36
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.35
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.33
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.29
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.29
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.28
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.2
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	98.62
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.01
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.0
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.98
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.22
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	98.12
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.12
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	98.11
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.99
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.99
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.92
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.9
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.42
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.26
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.07
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.59
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.44
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.42
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.31
3bos_A	242	Putative DNA replication factor; P-loop containing	96.26
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.21
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.13
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.13
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.13
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	96.1
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.09
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.03
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	95.96
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	95.9
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	95.83
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	95.76
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	95.61
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	95.57
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.57
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	95.42
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	95.39
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	95.36
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.13
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	95.11
3co5_A	143	Putative two-component system transcriptional RES	94.96
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	94.9
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	94.9
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	94.79
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.7
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	94.66
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	94.63
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	94.62
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	94.53
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	94.39
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	94.32
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	94.12
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.0
2qgz_A	308	Helicase loader, putative primosome component; str	93.93
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	93.71
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	93.62
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	93.45
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	93.41
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	93.34
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	93.27
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	93.09
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	92.95
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	92.89
2chq_A	319	Replication factor C small subunit; DNA-binding pr	92.83
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	92.15
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	92.13
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	92.04
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	91.58
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	91.52
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	91.46
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	90.79
3pvs_A	447	Replication-associated recombination protein A; ma	90.67
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	90.46
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	90.44
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	90.28
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	90.27
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	89.99
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	89.0
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	88.97
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	88.77
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	88.63
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	88.38
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	88.15
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	87.6
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	87.59
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	87.52
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	87.1
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	87.06
3io5_A	333	Recombination and repair protein; storage dimer, i	86.89
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	86.6
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	86.59
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	86.33
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	85.99
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	85.79
1p9r_A	418	General secretion pathway protein E; bacterial typ	85.63
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	84.76
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	84.55
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	84.51
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	84.4
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	84.2
1xp8_A	366	RECA protein, recombinase A; recombination, radior	84.08
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	83.99
2fna_A	357	Conserved hypothetical protein; structural genomic	83.92
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	83.74
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	83.71
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	83.55
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	82.93
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	82.9
2l82_A	162	Designed protein OR32; structural genomics, northe	82.71
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	82.64
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	82.53
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	81.66
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	81.38
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	81.17
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	80.7
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	80.25

>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=1.3e-55  Score=440.45  Aligned_cols=387  Identities=58%  Similarity=0.949  Sum_probs=212.7

Q ss_pred             CcchHHHhhhccccCCCCchhhhhhcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChHhHHHHHHHHHhhhc
Q psy11867          3 SLSDWIAATKNTSALKPDDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLI   82 (399)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (399)
                      +.|+|+..++++|.     .....++...+....++...+     ...+.....++.++.........+...++++.++.
T Consensus         2 ~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   71 (479)
T 3fmp_B            2 ATDSWALAVDEQEA-----AAESLSNLHLKEEKIKPDTNG-----AVVKTNANAEKTDEEEKEDRAAQSLLNKLIRSNLV   71 (479)
T ss_dssp             ------------------------------------------------------------------------------CC
T ss_pred             Ccchhhhhcchhhh-----hhcccccccccccccCccccc-----ccccCCCcchhhccccccchhhhHHHHHHhhhhhc
Confidence            36899999999986     344444444443322210000     01111112222223333445667788889999999


Q ss_pred             cccccceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHH
Q psy11867         83 ESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLT  162 (399)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~  162 (399)
                      .....+++...+++.|+.+..+|++++|++.++++|+++||..|+++|.+++|.++++++++++++||||||||++|++|
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~  151 (479)
T 3fmp_B           72 DNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLA  151 (479)
T ss_dssp             CCCSCEEEECSSTTSCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHH
T ss_pred             cCCccceecCCCCCCCccCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999855599999999999999999999


Q ss_pred             HHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccc
Q psy11867        163 MLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFF  242 (399)
Q Consensus       163 il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~  242 (399)
                      ++..+.....++++|||+||++|+.|+++.+++++...+.+.+.+..++...........+|+|+||++|++++.+.+.+
T Consensus       152 il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~  231 (479)
T 3fmp_B          152 MLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFI  231 (479)
T ss_dssp             HHTTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCCC
T ss_pred             HHHHHhhcCCCCcEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccccCCCCEEEECchHHHHHHHhcCCc
Confidence            99999887777899999999999999999999999887788888888888776666667899999999999998777778


Q ss_pred             cCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEE
Q psy11867        243 DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHY  322 (399)
Q Consensus       243 ~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~  322 (399)
                      .+.++++|||||||++.+..++......+.+.++..+|+++||||++..+..++..++.+|..+.+.........+.+.+
T Consensus       232 ~~~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~  311 (479)
T 3fmp_B          232 DPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYY  311 (479)
T ss_dssp             CGGGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC-------------
T ss_pred             CcccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEE
Confidence            88999999999999998766888888899999999999999999999999999999999999999988888888999999


Q ss_pred             EEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        323 VMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       323 ~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.+.....+...+..++.....+++||||++++.|+.++..|...|+.+..+||+|++.+|..+++.|++|+.+|||
T Consensus       312 ~~~~~~~~~~~~l~~~~~~~~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv  388 (479)
T 3fmp_B          312 VLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLV  388 (479)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             EEeCCHHHHHHHHHHHHhhccCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEE
Confidence            99988788999999998888888999999999999999999999999999999999999999999999999999986

>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=1.1e-49  Score=389.35  Aligned_cols=319  Identities=64%  Similarity=1.063  Sum_probs=291.9

Q ss_pred             hccccccceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867         81 LIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.++.+.+.+...+++.|+.+..+|+++++++.++++|.++||..|+++|.++++.++++.++++++++|||+|||++|+
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~   82 (412)
T 3fht_A            3 LVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFV   82 (412)
T ss_dssp             -----CHHHHHTTCTTSTTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHH
T ss_pred             hhcccccceeecccCCCCccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHH
Confidence            45667778888899999999999999999999999999999999999999999999998545999999999999999999


Q ss_pred             HHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccc
Q psy11867        161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYR  240 (399)
Q Consensus       161 l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~  240 (399)
                      +|++..+.....++++||++||++|+.|+++.+++++...+++.+....++...........+|+|+||++|.+++.+.+
T Consensus        83 ~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~  162 (412)
T 3fht_A           83 LAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLK  162 (412)
T ss_dssp             HHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTCCCCCSEEEECHHHHHHHHTTSC
T ss_pred             HHHHHHhhhcCCCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhhcCCCCEEEECchHHHHHHHhcC
Confidence            99999998777778999999999999999999999998877888888888887766666778999999999999987767


Q ss_pred             cccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeE
Q psy11867        241 FFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQ  320 (399)
Q Consensus       241 ~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~  320 (399)
                      .+.+.+++++|+||||++.+..++......+...++..+|+++||||+++.+..++..++.++..+.+.........+.+
T Consensus       163 ~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (412)
T 3fht_A          163 FIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQ  242 (412)
T ss_dssp             SSCGGGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEE
T ss_pred             CcChhhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceE
Confidence            77889999999999999987668888888999999999999999999999999999999999999998888888899999


Q ss_pred             EEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        321 HYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       321 ~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+..+.....+...+..++.....+++||||++++.|+.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||
T Consensus       243 ~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv  321 (412)
T 3fht_A          243 YYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLV  321 (412)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHSSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEE
T ss_pred             EEEEcCChHHHHHHHHHHHhhcCCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEE
Confidence            9999988889999999999988889999999999999999999999999999999999999999999999999999986

>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=2.8e-49  Score=389.55  Aligned_cols=302  Identities=25%  Similarity=0.428  Sum_probs=264.3

Q ss_pred             ceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhh
Q psy11867         88 LEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRV  167 (399)
Q Consensus        88 ~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l  167 (399)
                      +++.+.+.+.   ++.+|++++|++.++++|.++||..|||+|.+++|.+++  |+|++++||||||||++|++|++..+
T Consensus        44 ~~~~~~~~p~---~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~--g~d~i~~a~TGsGKT~a~~lpil~~l  118 (434)
T 2db3_A           44 VKVTGSDVPQ---PIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISS--GRDLMACAQTGSGKTAAFLLPILSKL  118 (434)
T ss_dssp             EEEESSSCCC---CCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             eEecCCCCCC---CcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhc--CCCEEEECCCCCCchHHHHHHHHHHH
Confidence            4455555544   467899999999999999999999999999999999998  79999999999999999999999887


Q ss_pred             CCC-----CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhcc
Q psy11867        168 NPS-----IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKY  239 (399)
Q Consensus       168 ~~~-----~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~  239 (399)
                      ...     ..++++|||+||++||.|+++.+++++... ++.+...+||.......   ..+++|+|+||++|++++.+ 
T Consensus       119 ~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~-  196 (434)
T 2db3_A          119 LEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDR-  196 (434)
T ss_dssp             HHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTS-SCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHT-
T ss_pred             HhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccC-CcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHh-
Confidence            432     246789999999999999999999998764 57777788887654332   45789999999999998654 


Q ss_pred             ccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC--CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccc
Q psy11867        240 RFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL--PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDN  317 (399)
Q Consensus       240 ~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l--~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~  317 (399)
                      ..+.+++++++|+||||+|++. +|...+..++..+  ++.+|+++||||+++.+..++..++.++..+.+........+
T Consensus       197 ~~~~l~~~~~lVlDEah~~~~~-gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~  275 (434)
T 2db3_A          197 TFITFEDTRFVVLDEADRMLDM-GFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSD  275 (434)
T ss_dssp             TSCCCTTCCEEEEETHHHHTST-TTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTT
T ss_pred             CCcccccCCeEEEccHhhhhcc-CcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccc
Confidence            4567899999999999999975 7888888888875  678999999999999999999999999999988877777888


Q ss_pred             eeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcc
Q psy11867        318 IKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI  397 (399)
Q Consensus       318 i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~I  397 (399)
                      +.+.+..+.. ..|...+.+++..... ++||||++++.|+.+++.|...|+.+..+||++++.+|..+++.|++|+.+|
T Consensus       276 i~~~~~~~~~-~~k~~~l~~~l~~~~~-~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~v  353 (434)
T 2db3_A          276 VKQTIYEVNK-YAKRSKLIEILSEQAD-GTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKV  353 (434)
T ss_dssp             EEEEEEECCG-GGHHHHHHHHHHHCCT-TEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSE
T ss_pred             cceEEEEeCc-HHHHHHHHHHHHhCCC-CEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcE
Confidence            9999888765 5678888888877654 4999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q psy11867        398 YS  399 (399)
Q Consensus       398 LV  399 (399)
                      ||
T Consensus       354 Lv  355 (434)
T 2db3_A          354 LI  355 (434)
T ss_dssp             EE
T ss_pred             EE
Confidence            86

>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=6.2e-50  Score=374.73  Aligned_cols=298  Identities=56%  Similarity=0.916  Sum_probs=215.6

Q ss_pred             CcchHHHhhhccccCCCCchhhhhhcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChHhHHHHHHHHHhhhc
Q psy11867          3 SLSDWIAATKNTSALKPDDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLI   82 (399)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (399)
                      ++|+|+.++++||.     ....+++...+........     ..+..+.....+..++++..+..+.++.+++++..+.
T Consensus         2 ~~~~~~~~~~~~e~-----~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   71 (300)
T 3fmo_B            2 ATDSWALAVDEQEA-----AAESLSNLHLKEEKIKPDT-----NGAVVKTNANAEKTDEEEKEDRAAQSLLNKLIRSNLV   71 (300)
T ss_dssp             -----------------------------------------------------------------------------CCC
T ss_pred             CcchHHHHHhhHHH-----Hhhhhhhhhhhcccccccc-----cccccccCCCccccccccchhhhHHHHHHhhhhcccc
Confidence            36899999999986     4455555544433221100     1111222223333334455567788999999999999


Q ss_pred             cccccceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHH
Q psy11867         83 ESKQELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLT  162 (399)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~  162 (399)
                      +..+++++.+.+++.|+.+..+|++++|++.++++|.++||..||++|.+++|.+++++++|++++||||||||++|++|
T Consensus        72 ~~~~~v~v~~~~~~~p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp  151 (300)
T 3fmo_B           72 DNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLA  151 (300)
T ss_dssp             CCCSCEEEECSSTTCCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHH
T ss_pred             cccccceeccCCCCCCcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999855599999999999999999999


Q ss_pred             HHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccc
Q psy11867        163 MLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFF  242 (399)
Q Consensus       163 il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~  242 (399)
                      +++.+.....++++|||+||++||.|+++.++.++..++++.+....++....+.....++|+|+||++|++++.+.+.+
T Consensus       152 ~l~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  231 (300)
T 3fmo_B          152 MLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFI  231 (300)
T ss_dssp             HHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTTCCC
T ss_pred             HHHhhhccCCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhhcCCCCEEEECHHHHHHHHHhcCCC
Confidence            99999887778899999999999999999999999887788888999888777666778899999999999998776778


Q ss_pred             cCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccc
Q psy11867        243 DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR  310 (399)
Q Consensus       243 ~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~  310 (399)
                      +++++++|||||||+|++..++...+..+.+.+++++|+++||||+++.+..+++.++.+|..|.+..
T Consensus       232 ~l~~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~  299 (300)
T 3fmo_B          232 DPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR  299 (300)
T ss_dssp             CGGGCSEEEETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEECC
T ss_pred             ChhhceEEEEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEecC
Confidence            89999999999999999866899999999999999999999999999999999999999999988764

>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=1.9e-46  Score=366.60  Aligned_cols=294  Identities=35%  Similarity=0.639  Sum_probs=265.2

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe
Q psy11867        101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA  180 (399)
Q Consensus       101 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  180 (399)
                      ...+|++++|++.+.++|.++||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+.....+.++||++
T Consensus        35 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~--~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~  112 (410)
T 2j0s_A           35 VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIK--GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILA  112 (410)
T ss_dssp             CCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEEC
T ss_pred             CCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEc
Confidence            456899999999999999999999999999999999998  699999999999999999999999987666778999999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      ||++|+.|+++.+++++... ++.+....|+.......   ...++|+|+||++|.+++.. ..+.+.+++++|+||||+
T Consensus       113 Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~-~~~~~~~~~~vViDEah~  190 (410)
T 2j0s_A          113 PTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRR-RSLRTRAIKMLVLDEADE  190 (410)
T ss_dssp             SSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEETHHH
T ss_pred             CcHHHHHHHHHHHHHHhccC-CeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHh-CCccHhheeEEEEccHHH
Confidence            99999999999999998765 67777778887654332   35679999999999998654 466788999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHH
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSN  337 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~  337 (399)
                      +.+. ++...+..+...+++..|+++||||++..+..+...++.+|..+.+........++.+.+..+.....|...+..
T Consensus       191 ~~~~-~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~  269 (410)
T 2j0s_A          191 MLNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCD  269 (410)
T ss_dssp             HTST-TTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHH
T ss_pred             HHhh-hhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHH
Confidence            9864 788888899999999999999999999999999999999999988887777888999999998887779999999


Q ss_pred             HhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        338 IYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       338 ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++.....+++||||++++.++.+++.|...|+.+..+||++++.+|..+++.|++|+.+|||
T Consensus       270 ~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv  331 (410)
T 2j0s_A          270 LYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLI  331 (410)
T ss_dssp             HHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEE
T ss_pred             HHHhcCCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEE
Confidence            99888888999999999999999999999999999999999999999999999999999986

>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=2.6e-45  Score=359.14  Aligned_cols=292  Identities=27%  Similarity=0.417  Sum_probs=251.0

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-----------
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-----------  170 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-----------  170 (399)
                      +.+|++++|++.+.++|..+||..|+|+|.+++|.++.  |+|++++||||||||++|++|++..+...           
T Consensus        14 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~--~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~   91 (417)
T 2i4i_A           14 IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKE--KRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKE   91 (417)
T ss_dssp             CSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_pred             cCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHcc--CCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhcccc
Confidence            56799999999999999999999999999999999998  79999999999999999999999876432           


Q ss_pred             -------CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccc
Q psy11867        171 -------IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYR  240 (399)
Q Consensus       171 -------~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~  240 (399)
                             ..++++||++||++|+.|+++.+++++... ++.+....|+.......   ...++|+|+||++|.+++.. .
T Consensus        92 ~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~-~  169 (417)
T 2i4i_A           92 NGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS-RVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMER-G  169 (417)
T ss_dssp             CBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHT-T
T ss_pred             ccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcC-CceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHc-C
Confidence                   124789999999999999999999998764 67777788876554332   45679999999999998654 4


Q ss_pred             cccCCceeEEEEechhhHhhcCCchHHHHHHHHh--CCC--CCcEEEEEeeCChhHHHHHHhhCCCCeEEeccccccccc
Q psy11867        241 FFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR--LPS--DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLD  316 (399)
Q Consensus       241 ~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~--l~~--~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~  316 (399)
                      .+.+.+++++|+||||++.+. ++...+..+...  ++.  ..|+++||||++..+..++..++.++..+.+........
T Consensus       170 ~~~~~~~~~iViDEah~~~~~-~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  248 (417)
T 2i4i_A          170 KIGLDFCKYLVLDEADRMLDM-GFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSE  248 (417)
T ss_dssp             SBCCTTCCEEEESSHHHHHHT-TCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC----CCS
T ss_pred             CcChhhCcEEEEEChhHhhcc-CcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCCCCcc
Confidence            567889999999999999875 688888888774  333  689999999999999999999999999888877777778


Q ss_pred             ceeEEEEEeCChhhHHHHHHHHhccC-CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        317 NIKQHYVMCKNIDEKFEAVSNIYGVV-TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       317 ~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                      ++.+.+..+.. ..|...+..++... ..+++||||++++.++.+++.|.+.|+.+..+||++++.+|..+++.|++|+.
T Consensus       249 ~i~~~~~~~~~-~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~  327 (417)
T 2i4i_A          249 NITQKVVWVEE-SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS  327 (417)
T ss_dssp             SEEEEEEECCG-GGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSS
T ss_pred             CceEEEEEecc-HhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCC
Confidence            88888887765 66888888888876 45789999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy11867        396 KIYS  399 (399)
Q Consensus       396 ~ILV  399 (399)
                      +|||
T Consensus       328 ~vlv  331 (417)
T 2i4i_A          328 PILV  331 (417)
T ss_dssp             CEEE
T ss_pred             CEEE
Confidence            9986

>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=8.7e-45  Score=352.31  Aligned_cols=295  Identities=50%  Similarity=0.802  Sum_probs=264.3

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|++++|++.++++|.++||..|+|+|.++++.++++.++++++++|||+|||++|++|++..+.....++++||++|
T Consensus         4 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   83 (395)
T 3pey_A            4 AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAP   83 (395)
T ss_dssp             CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             ccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECC
Confidence            46899999999999999999999999999999999998544999999999999999999999999887667789999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT  261 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~  261 (399)
                      |++|+.|+++.+++++... .+.+....++... ......++|+|+||++|.+++.. ..+.+.+++++|+||||++.+.
T Consensus        84 ~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~iIiDEah~~~~~  160 (395)
T 3pey_A           84 SRELARQTLEVVQEMGKFT-KITSQLIVPDSFE-KNKQINAQVIVGTPGTVLDLMRR-KLMQLQKIKIFVLDEADNMLDQ  160 (395)
T ss_dssp             SHHHHHHHHHHHHHHTTTS-CCCEEEESTTSSC-TTSCBCCSEEEECHHHHHHHHHT-TCBCCTTCCEEEEETHHHHHHS
T ss_pred             CHHHHHHHHHHHHHHhccc-CeeEEEEecCchh-hhccCCCCEEEEcHHHHHHHHHc-CCcccccCCEEEEEChhhhcCc
Confidence            9999999999999998765 5555555555432 22344678999999999988643 5667889999999999999876


Q ss_pred             CCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhcc
Q psy11867        262 QGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGV  341 (399)
Q Consensus       262 ~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~  341 (399)
                      .++...+..+...+++..|++++|||+++.+..+...++.++..+.+.........+.+.+..+.....+...+..++..
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  240 (395)
T 3pey_A          161 QGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGL  240 (395)
T ss_dssp             TTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHHTT
T ss_pred             cccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHHHh
Confidence            67888888999999999999999999999999999999999999888877777888999999998888899999999998


Q ss_pred             CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        342 VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       342 ~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...+++||||++++.|+.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||
T Consensus       241 ~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv  298 (395)
T 3pey_A          241 MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLI  298 (395)
T ss_dssp             TTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEE
T ss_pred             ccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEE
Confidence            8889999999999999999999999999999999999999999999999999999986

>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=1.6e-44  Score=353.09  Aligned_cols=293  Identities=36%  Similarity=0.621  Sum_probs=260.0

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|+++++++.+++.|.++||..|+++|.++++.+++  |+|+++++|||||||++|++|+++.+.....+.++||++|
T Consensus        39 ~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~--~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  116 (414)
T 3eiq_A           39 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIK--GYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAP  116 (414)
T ss_dssp             CCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHT--TCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             hcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhC--CCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeC
Confidence            46799999999999999999999999999999999998  6999999999999999999999999887667788999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh----ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK----KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      |++|+.|+++.+++++... +..+....++.......    ...++|+|+||++|++++.. +.+.+.+++++|+||||+
T Consensus       117 ~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~-~~~~~~~~~~vViDEah~  194 (414)
T 3eiq_A          117 TRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLDEADE  194 (414)
T ss_dssp             SHHHHHHHHHHHHHHGGGS-CCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHH-TSSCSTTCCEEEECSHHH
T ss_pred             hHHHHHHHHHHHHHHhccc-CceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcccccCcEEEEECHHH
Confidence            9999999999999998765 56777777776554332    25679999999999998654 556788899999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHH
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSN  337 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~  337 (399)
                      +.+. ++...+..++..+++++|+++||||++..+..+...++.+|..+...........+.+.+..+...+.+...+..
T Consensus       195 ~~~~-~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  273 (414)
T 3eiq_A          195 MLSR-GFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCD  273 (414)
T ss_dssp             HHHT-TTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHH
T ss_pred             hhcc-CcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHH
Confidence            9864 788888899999999999999999999999999999999999998888888888899999988887889999999


Q ss_pred             HhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        338 IYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       338 ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++.....+++||||++++.++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||
T Consensus       274 ~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv  335 (414)
T 3eiq_A          274 LYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLI  335 (414)
T ss_dssp             HHHSSCCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEE
T ss_pred             HHHhCCCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEE
Confidence            99999889999999999999999999999999999999999999999999999999999986

>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=9.7e-44  Score=344.94  Aligned_cols=293  Identities=28%  Similarity=0.480  Sum_probs=256.2

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      .+|+++++++.+.++|.++||..|+|+|.++++.++.  |+++++++|||+|||++|++|++..+.....+.++||++||
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~   85 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAIL--GMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHT   85 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTT--TCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSC
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhc--CCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCC
Confidence            5799999999999999999999999999999999998  69999999999999999999999998776667789999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh----ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK----KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      ++|+.|+++.++++....+++.+....|+.......    ...++|+|+||++|.+++.. ..+.+.+++++|+||||++
T Consensus        86 ~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~vViDEaH~~  164 (391)
T 1xti_A           86 RELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFILDECDKM  164 (391)
T ss_dssp             HHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCSEEEECSHHHH
T ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCccccccCEEEEeCHHHH
Confidence            999999999999998877778888888886654332    34578999999999987544 4567889999999999999


Q ss_pred             hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccccc-ccccceeEEEEEeCChhhHHHHHHH
Q psy11867        259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREE-ESLDNIKQHYVMCKNIDEKFEAVSN  337 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~-~~~~~i~~~~~~~~~~~~k~~~l~~  337 (399)
                      .+..++...+..+....+...|++++|||+++.+..++..++.+|..+.+.... .....+.+.+..+.. ..|...+..
T Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~  243 (391)
T 1xti_A          165 LEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKD-NEKNRKLFD  243 (391)
T ss_dssp             TSSHHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCG-GGHHHHHHH
T ss_pred             hhccchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCc-hhHHHHHHH
Confidence            753356667778888888899999999999999999999999999888776543 344567777776654 678888889


Q ss_pred             HhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        338 IYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       338 ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++.....+++||||++++.|+.+++.|...|+.+..+||++++.+|..+++.|++|+.+|||
T Consensus       244 ~l~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  305 (391)
T 1xti_A          244 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILV  305 (391)
T ss_dssp             HHHHSCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEE
T ss_pred             HHHhcCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEE
Confidence            99888889999999999999999999999999999999999999999999999999999986

>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=3e-43  Score=342.76  Aligned_cols=291  Identities=35%  Similarity=0.591  Sum_probs=253.5

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|++++|++.+.++|.++||..|+++|.++++.+++  ++++++++|||+|||++|++|++..+.....+.++||++|
T Consensus        20 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~--~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   97 (400)
T 1s2m_A           20 GNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAIT--GRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVP   97 (400)
T ss_dssp             -CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHH--TCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhc--CCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcC
Confidence            45799999999999999999999999999999999998  6999999999999999999999999877656778999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      |++|+.|+++.+++++... ++.+....|+.......   ...++|+|+||++|.+++.. ....+.+++++|+||||++
T Consensus        98 ~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~-~~~~~~~~~~vIiDEaH~~  175 (400)
T 1s2m_A           98 TRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASR-KVADLSDCSLFIMDEADKM  175 (400)
T ss_dssp             SHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEEESHHHH
T ss_pred             CHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHh-CCcccccCCEEEEeCchHh
Confidence            9999999999999998765 66777777776554322   35678999999999887543 4566889999999999998


Q ss_pred             hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHH
Q psy11867        259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI  338 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  338 (399)
                      .+. .+...+..+...+++..|+++||||++..+..++...+..|..+.+... ....++.+++..+.. ..|...+..+
T Consensus       176 ~~~-~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-~~k~~~l~~~  252 (400)
T 1s2m_A          176 LSR-DFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEE-LTLKGITQYYAFVEE-RQKLHCLNTL  252 (400)
T ss_dssp             SSH-HHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCSS-CBCTTEEEEEEECCG-GGHHHHHHHH
T ss_pred             hhh-chHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEeccc-cccCCceeEEEEech-hhHHHHHHHH
Confidence            764 5777788888888889999999999999999999999988887765533 445667777776654 6788888888


Q ss_pred             hccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        339 YGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       339 l~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.....+++||||++++.++.+++.|...|+.+..+||+|+..+|..+++.|++|+.+|||
T Consensus       253 ~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv  313 (400)
T 1s2m_A          253 FSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLV  313 (400)
T ss_dssp             HHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEE
T ss_pred             HhhcCCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEE
Confidence            8888888999999999999999999999999999999999999999999999999999986

>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=3.5e-44  Score=348.22  Aligned_cols=293  Identities=37%  Similarity=0.648  Sum_probs=180.1

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|+++++++.+.++|.++||..|+++|.++++.+++  |+++++++|||+|||++|++|++..+.....++++||++|
T Consensus        20 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~--~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P   97 (394)
T 1fuu_A           20 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIE--GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAP   97 (394)
T ss_dssp             CCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHH--TCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             cCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcC
Confidence            45699999999999999999999999999999999998  6999999999999999999999999887667789999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh--ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK--KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      |++|+.|+++.++++.... ++.+....|+.......  ....+|+|+||++|.+.+.. ..+.+.+++++|+||||++.
T Consensus        98 ~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~vIiDEah~~~  175 (394)
T 1fuu_A           98 TRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEML  175 (394)
T ss_dssp             SHHHHHHHHHHHHHHTTTS-CCCEEEECSSCCHHHHHHHHHHCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEETHHHHH
T ss_pred             CHHHHHHHHHHHHHHhccC-CeeEEEEeCCCchHHHHhhcCCCCEEEECHHHHHHHHHh-CCcchhhCcEEEEEChHHhh
Confidence            9999999999999988765 67777777776553322  23578999999999988644 45668899999999999998


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHh
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIY  339 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll  339 (399)
                      +. ++...+..+...+++..|++++|||+++.+..+...++.+|..+..........++.+.+..+...+.+...+..++
T Consensus       176 ~~-~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  254 (394)
T 1fuu_A          176 SS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLY  254 (394)
T ss_dssp             HT-TCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC-----------------------------
T ss_pred             CC-CcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHH
Confidence            75 78888889999999999999999999999999999999999998887776677788888887776666888888888


Q ss_pred             ccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        340 GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       340 ~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .....+++||||++++.++.+++.|...|+.+..+||+|+..+|..+++.|++|+.+|||
T Consensus       255 ~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  314 (394)
T 1fuu_A          255 DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILI  314 (394)
T ss_dssp             ------------------------------------------------------------
T ss_pred             hcCCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEE
Confidence            887778999999999999999999999999999999999999999999999999999986

>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=1.9e-42  Score=352.97  Aligned_cols=289  Identities=27%  Similarity=0.396  Sum_probs=236.0

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC----CCCCeEEEEeCcHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS----IQEPQVLCLAPTYEL  185 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~----~~~~~~lil~Pt~~L  185 (399)
                      |++.++++|..+||..|+|+|.++++.++.+.++|++++||||||||++|++|+++.+...    ..++++|||+||++|
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~L  107 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  107 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHH
Confidence            9999999999999999999999999999953379999999999999999999999887543    235689999999999


Q ss_pred             HHHHHHHHHHHhc---cCCCcEEEEEEcCchhhhhh----ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        186 AIQIGEVVAKMGK---HITDLSVRYAVRGENLERNK----KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       186 a~Q~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      +.|+++.++++..   ....+.+....++.......    ...++|+|+||++|++++.+.....++++++|||||||+|
T Consensus       108 a~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l  187 (579)
T 3sqw_A          108 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRL  187 (579)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHH
T ss_pred             HHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHHh
Confidence            9999999999864   23345667777776654332    3468999999999999876654556889999999999999


Q ss_pred             hhcCCchHHHHHHHHhCC-------CCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccc----ccccccceeEEEEEeCC
Q psy11867        259 IATQGHQDFSIRIQKRLP-------SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR----EEESLDNIKQHYVMCKN  327 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~-------~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~----~~~~~~~i~~~~~~~~~  327 (399)
                      .+. +|...+..+...++       ..+|+++||||+++.+..++..++.+|..+.+..    .......+.+.+..+..
T Consensus       188 ~~~-gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  266 (579)
T 3sqw_A          188 LEI-GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK  266 (579)
T ss_dssp             TST-TTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESS
T ss_pred             hcC-CCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecc
Confidence            875 68887777766553       3789999999999999999999998887765543    22345567777777765


Q ss_pred             hhhHH----HHHHHHhcc-CCCCcEEEEecchHhHHHHHHHHHHC---CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        328 IDEKF----EAVSNIYGV-VTIGQAMIFCHTRKTAAWLAEKMSKE---GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       328 ~~~k~----~~l~~ll~~-~~~~k~IIF~~s~~~a~~l~~~L~~~---g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...+.    ..+...+.. ...+++||||++++.|+.++..|...   ++.+..+||+|++.+|..+++.|++|+.+|||
T Consensus       267 ~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLV  346 (579)
T 3sqw_A          267 FANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV  346 (579)
T ss_dssp             TTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEE
T ss_pred             hhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEE
Confidence            43332    223333333 45579999999999999999999886   89999999999999999999999999999986

>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=4.1e-42  Score=349.56  Aligned_cols=297  Identities=26%  Similarity=0.376  Sum_probs=238.1

Q ss_pred             ccccccCC-CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC----CCCeE
Q psy11867        102 VKTFEALH-LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI----QEPQV  176 (399)
Q Consensus       102 ~~~f~~~~-l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~----~~~~~  176 (399)
                      ...|.+.+ |++.+++++.++||..|+|+|.++++.++.+.++|++++||||||||++|++|+++.+....    .++++
T Consensus        70 ~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~  149 (563)
T 3i5x_A           70 LDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKA  149 (563)
T ss_dssp             HHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCE
T ss_pred             HHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeE
Confidence            33443333 99999999999999999999999999999533799999999999999999999999875432    34689


Q ss_pred             EEEeCcHHHHHHHHHHHHHHhcc---CCCcEEEEEEcCchhhhhh----ccCCcEEEeCchhHHHhhhccccccCCceeE
Q psy11867        177 LCLAPTYELAIQIGEVVAKMGKH---ITDLSVRYAVRGENLERNK----KITEQIIIGTPGKVLDWGLKYRFFDLSKIKV  249 (399)
Q Consensus       177 lil~Pt~~La~Q~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~----~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~  249 (399)
                      |||+||++||.|+++.++++...   .....+....++.......    ...++|+|+||++|++++.+.....++++++
T Consensus       150 lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~  229 (563)
T 3i5x_A          150 VIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDY  229 (563)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCE
T ss_pred             EEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceE
Confidence            99999999999999999997542   2345567777776554332    4478999999999999876654556889999


Q ss_pred             EEEechhhHhhcCCchHHHHHHHHhC-------CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccc----ccccccce
Q psy11867        250 FVLDEADVMIATQGHQDFSIRIQKRL-------PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR----EEESLDNI  318 (399)
Q Consensus       250 lViDEah~l~~~~~~~~~~~~i~~~l-------~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~----~~~~~~~i  318 (399)
                      +||||||+|.+. +|...+..+...+       +..+|+++||||+++.+..++..++.++..+.+..    .......+
T Consensus       230 lViDEah~l~~~-~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  308 (563)
T 3i5x_A          230 KVLDEADRLLEI-GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERI  308 (563)
T ss_dssp             EEEETHHHHTST-TTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTE
T ss_pred             EEEeCHHHHhcc-chHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccC
Confidence            999999999875 6888777776554       34789999999999999999999998887765532    22345567


Q ss_pred             eEEEEEeCChhhHHH----HHHHHhcc-CCCCcEEEEecchHhHHHHHHHHHHC---CCeEEEEcCCCCHHHHHHHHHHH
Q psy11867        319 KQHYVMCKNIDEKFE----AVSNIYGV-VTIGQAMIFCHTRKTAAWLAEKMSKE---GLNVGLLSGELTVEQRLSILDRF  390 (399)
Q Consensus       319 ~~~~~~~~~~~~k~~----~l~~ll~~-~~~~k~IIF~~s~~~a~~l~~~L~~~---g~~v~~lhg~~~~~~R~~v~~~F  390 (399)
                      .+.+..+.....+..    .+...+.. ...+++||||++++.|+.++..|...   ++.+..+||+|++.+|..+++.|
T Consensus       309 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f  388 (563)
T 3i5x_A          309 DQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRF  388 (563)
T ss_dssp             EEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHH
T ss_pred             ceEEEECchhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHH
Confidence            777777765444332    22233332 45579999999999999999999886   89999999999999999999999


Q ss_pred             hcCCCcccC
Q psy11867        391 REGEFKIYS  399 (399)
Q Consensus       391 ~~G~~~ILV  399 (399)
                      ++|+.+|||
T Consensus       389 ~~g~~~vLv  397 (563)
T 3i5x_A          389 KKDESGILV  397 (563)
T ss_dssp             HHCSSEEEE
T ss_pred             hcCCCCEEE
Confidence            999999986

>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=5.3e-41  Score=322.48  Aligned_cols=286  Identities=30%  Similarity=0.511  Sum_probs=245.7

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      .+|++++|++.+.++|.++||..|+++|.++++.++++ ++++++++|||||||++|++|++..+... .+.++||++|+
T Consensus         6 ~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-~~~~~lil~P~   83 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLND-EYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPT   83 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHT-CSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSC
T ss_pred             CchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCC-CCCEEEECCCCChHHHHHHHHHHHHhccc-CCCcEEEEcCC
Confidence            46999999999999999999999999999999999984 47999999999999999999999887653 56789999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh--ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhh
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK--KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~  260 (399)
                      ++|+.|+++.++++.... ++.+....|+.......  ....+|+|+||++|.+++.. ..+.+.+++++|+||||++.+
T Consensus        84 ~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~iIiDEah~~~~  161 (367)
T 1hv8_A           84 RELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINR-GTLNLKNVKYFILDEADEMLN  161 (367)
T ss_dssp             HHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHT-TCSCTTSCCEEEEETHHHHHT
T ss_pred             HHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHhhcCCCCEEEecHHHHHHHHHc-CCcccccCCEEEEeCchHhhh
Confidence            999999999999987654 56777777776553322  23678999999999988643 456688999999999999986


Q ss_pred             cCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhc
Q psy11867        261 TQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG  340 (399)
Q Consensus       261 ~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~  340 (399)
                      . ++...+..+...+++..+++++|||++.........++.++..+....    ..++.+.+..+.. ..+...+..++.
T Consensus       162 ~-~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~-~~~~~~l~~~l~  235 (367)
T 1hv8_A          162 M-GFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKI----NANIEQSYVEVNE-NERFEALCRLLK  235 (367)
T ss_dssp             T-TTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCS----SSSSEEEEEECCG-GGHHHHHHHHHC
T ss_pred             h-chHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecC----CCCceEEEEEeCh-HHHHHHHHHHHh
Confidence            4 677888888888889999999999999999999998888877665432    2356667766644 678888888887


Q ss_pred             cCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       341 ~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                       ...+++||||++++.++.+++.|...|+.+..+||+++..+|..+++.|++|+.+|||
T Consensus       236 -~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  293 (367)
T 1hv8_A          236 -NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILI  293 (367)
T ss_dssp             -STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEE
T ss_pred             -cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEE
Confidence             4557899999999999999999999999999999999999999999999999999986

>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=2.8e-38  Score=300.08  Aligned_cols=269  Identities=27%  Similarity=0.398  Sum_probs=225.8

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      |++.+.++|.++||..|+|+|.++++.+++  ++++++++|||+|||++|++|++..      +.++||++|+++|+.|+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~--~~~~lv~~~TGsGKT~~~~~~~~~~------~~~~liv~P~~~L~~q~   72 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQ--GKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRELTRQV   72 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHH------TCCEEEECSSHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhc--CCCEEEEcCCCCcHHHHHHHHHHhh------cCCEEEEeCCHHHHHHH
Confidence            578999999999999999999999999998  6999999999999999999999874      45699999999999999


Q ss_pred             HHHHHHHhccCCCcEEEEEEcCchhhhhh--ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHH
Q psy11867        190 GEVVAKMGKHITDLSVRYAVRGENLERNK--KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF  267 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~  267 (399)
                      ++.+++++... +..+....++.......  ...++|+|+||++|.+++.. ..+.+.+++++|+||||++.+. ++...
T Consensus        73 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~iViDEah~~~~~-~~~~~  149 (337)
T 2z0m_A           73 ASHIRDIGRYM-DTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWSK-GVIDLSSFEIVIIDEADLMFEM-GFIDD  149 (337)
T ss_dssp             HHHHHHHTTTS-CCCEEEECTTSCHHHHHHHHTTCSEEEECHHHHHHHHHT-TSCCGGGCSEEEEESHHHHHHT-TCHHH
T ss_pred             HHHHHHHhhhc-CCcEEEEECCcchHHHHhhcCCCCEEEECHHHHHHHHHc-CCcchhhCcEEEEEChHHhhcc-ccHHH
Confidence            99999998765 56777777776543322  34578999999999987543 4566889999999999999874 78888


Q ss_pred             HHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcE
Q psy11867        268 SIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQA  347 (399)
Q Consensus       268 ~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~  347 (399)
                      +..++..++...+++++|||++..+......++.++..+...   ....++.+.+..+.....   .....+.....+++
T Consensus       150 ~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~  223 (337)
T 2z0m_A          150 IKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKDDWR---SKVQALRENKDKGV  223 (337)
T ss_dssp             HHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS---GGGGGEEEEEEECSSSSH---HHHHHHHTCCCSSE
T ss_pred             HHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc---cccCCceEEEEEeChHHH---HHHHHHHhCCCCcE
Confidence            888889999899999999999999999999998888766433   344566777776654322   22245556677899


Q ss_pred             EEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        348 MIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       348 IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ||||++++.++.+++.|.    ++..+||+++..+|.+++++|++|+.+|||
T Consensus       224 lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  271 (337)
T 2z0m_A          224 IVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLI  271 (337)
T ss_dssp             EEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEE
T ss_pred             EEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEE
Confidence            999999999999998885    688999999999999999999999999986

>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=1.4e-38  Score=289.04  Aligned_cols=218  Identities=27%  Similarity=0.406  Sum_probs=188.8

Q ss_pred             ccceeeccCCCCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHH
Q psy11867         86 QELEIQRKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLS  165 (399)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~  165 (399)
                      ..+.+.+.+.+.|   +.+|+++++++.+++++.++||..|+++|.++++.+++  |+|++++||||||||++|++|++.
T Consensus        15 ~~i~~~~~~~p~~---~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--g~~~l~~apTGsGKT~~~~l~~l~   89 (242)
T 3fe2_A           15 KEITVRGHNCPKP---VLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALS--GLDMVGVAQTGSGKTLSYLLPAIV   89 (242)
T ss_dssp             HTEEEESSCCCCC---CSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHH--TCCEEEEECTTSCHHHHHHHHHHH
T ss_pred             CceEEeCCCCCCc---cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCcCHHHHHHHHHHHH
Confidence            3555555555444   67899999999999999999999999999999999998  699999999999999999999999


Q ss_pred             hhCCC-----CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhh
Q psy11867        166 RVNPS-----IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGL  237 (399)
Q Consensus       166 ~l~~~-----~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~  237 (399)
                      .+...     ..++++|||+||++|+.|+++.++++.... ++.+....||.......   ..+++|+|+||++|.+++.
T Consensus        90 ~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~  168 (242)
T 3fe2_A           90 HINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLE  168 (242)
T ss_dssp             HHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHH
T ss_pred             HHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhc-CceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHH
Confidence            87532     357789999999999999999999998776 67788888887654332   4568999999999999865


Q ss_pred             ccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccc
Q psy11867        238 KYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE  311 (399)
Q Consensus       238 ~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~  311 (399)
                      . ....+++++++|+||||++.+. ++...+..+++.+++++|+++||||+++.+.++++.++.+|+.|.++..
T Consensus       169 ~-~~~~~~~~~~lViDEah~l~~~-~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          169 C-GKTNLRRTTYLVLDEADRMLDM-GFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             H-TSCCCTTCCEEEETTHHHHHHT-TCHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC-
T ss_pred             c-CCCCcccccEEEEeCHHHHhhh-CcHHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            4 4567899999999999999975 7999999999999999999999999999999999999999999988754

>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=1.4e-37  Score=315.62  Aligned_cols=279  Identities=15%  Similarity=0.197  Sum_probs=214.7

Q ss_pred             ccCCCCHHHHHHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        106 EALHLKPELLKGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       106 ~~~~l~~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      .++++++.+.+.|++ +||..|+|+|.++++.+++  |+|+++++|||+|||++|++|++..      .+++|||+|+++
T Consensus        24 ~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~--g~d~lv~~pTGsGKTl~~~lpal~~------~g~~lVisP~~~   95 (591)
T 2v1x_A           24 EDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMA--GKEVFLVMPTGGGKSLCYQLPALCS------DGFTLVICPLIS   95 (591)
T ss_dssp             SCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHT--TCCEEEECCTTSCTTHHHHHHHHTS------SSEEEEECSCHH
T ss_pred             ccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHc--CCCEEEEECCCChHHHHHHHHHHHc------CCcEEEEeCHHH
Confidence            457899999999998 6999999999999999999  7999999999999999999999852      458999999999


Q ss_pred             HHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh---------hccCCcEEEeCchhHHH---hhhc-cccccCCceeEEE
Q psy11867        185 LAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---------KKITEQIIIGTPGKVLD---WGLK-YRFFDLSKIKVFV  251 (399)
Q Consensus       185 La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~IlV~Tp~~l~~---~~~~-~~~~~~~~~~~lV  251 (399)
                      |+.|+.+.++++     ++.+....++......         .....+|+|+||++|..   ++.. .....+.++++||
T Consensus        96 L~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iV  170 (591)
T 2v1x_A           96 LMEDQLMVLKQL-----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIA  170 (591)
T ss_dssp             HHHHHHHHHHHH-----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEE
T ss_pred             HHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEE
Confidence            999999999987     4555666666543322         13467899999998742   1110 1234577999999


Q ss_pred             EechhhHhhcCC--chHHHHH--HHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeC-
Q psy11867        252 LDEADVMIATQG--HQDFSIR--IQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCK-  326 (399)
Q Consensus       252 iDEah~l~~~~~--~~~~~~~--i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~-  326 (399)
                      |||||++.+. +  |...+..  ++....+..++++||||+++.+...+..++..+..+.+.. .....++...+.... 
T Consensus       171 iDEAH~is~~-g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~-~~~r~nl~~~v~~~~~  248 (591)
T 2v1x_A          171 VDEVHCCSQW-GHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTA-SFNRPNLYYEVRQKPS  248 (591)
T ss_dssp             EETGGGGSTT-CTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEEC-CCCCTTEEEEEEECCS
T ss_pred             EECccccccc-ccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEec-CCCCcccEEEEEeCCC
Confidence            9999999753 3  4443322  3333345799999999999998888777765432222221 122344444433332 


Q ss_pred             ChhhHHHHHHHHhccC-CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        327 NIDEKFEAVSNIYGVV-TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       327 ~~~~k~~~l~~ll~~~-~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ....+...+..++... ..+++||||++++.|+.++..|...|+.+..|||+|++.+|..+++.|++|+++|||
T Consensus       249 ~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlV  322 (591)
T 2v1x_A          249 NTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVV  322 (591)
T ss_dssp             SHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEE
T ss_pred             cHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEE
Confidence            2345667777777644 567999999999999999999999999999999999999999999999999999986

>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=1.9e-37  Score=282.62  Aligned_cols=205  Identities=32%  Similarity=0.466  Sum_probs=182.8

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe
Q psy11867        101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA  180 (399)
Q Consensus       101 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  180 (399)
                      ...+|+++++++.+.++|.++||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+.....++++||++
T Consensus        41 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~--~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~  118 (249)
T 3ber_A           41 ETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQ--GRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLT  118 (249)
T ss_dssp             HHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEEC
T ss_pred             ccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEe
Confidence            356899999999999999999999999999999999998  699999999999999999999999887666678899999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      ||++|+.|+++.+++++... ++.+....|+......   ....++|+|+||++|.+++...+.+.+.+++++|+||||+
T Consensus       119 Ptr~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~  197 (249)
T 3ber_A          119 PTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADR  197 (249)
T ss_dssp             SSHHHHHHHHHHHHHHHGGG-TCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHH
T ss_pred             CCHHHHHHHHHHHHHHhccC-CeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhh
Confidence            99999999999999998765 6777777887654332   2457899999999999987766667789999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~  309 (399)
                      +.+. ++...+..++..+++.+|+++||||++..+.++++.++.+|..+.+.
T Consensus       198 l~~~-~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v~  248 (249)
T 3ber_A          198 ILNM-DFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVS  248 (249)
T ss_dssp             HHHT-TCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             hhcc-ChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEec
Confidence            9875 88888999999999999999999999999999999999999988654

>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=4.1e-37  Score=277.16  Aligned_cols=205  Identities=30%  Similarity=0.467  Sum_probs=180.6

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|+++++++.+.+.|.++||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+.....++++||++|
T Consensus        23 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~P  100 (230)
T 2oxc_A           23 PADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRC--GLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAP  100 (230)
T ss_dssp             -CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             CCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeC
Confidence            56799999999999999999999999999999999998  6999999999999999999999999876666789999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh--ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK--KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      |++|+.|+++.+++++....++.+....|+.......  ...++|+|+||++|.+++. .+.+.+.+++++|+||||++.
T Consensus       101 t~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~-~~~~~~~~~~~lViDEah~~~  179 (230)
T 2oxc_A          101 TREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIE-LDYLNPGSIRLFILDEADKLL  179 (230)
T ss_dssp             SHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTTSCSEEEECHHHHHHHHH-TTSSCGGGCCEEEESSHHHHH
T ss_pred             CHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhccCCCEEEECHHHHHHHHh-cCCcccccCCEEEeCCchHhh
Confidence            9999999999999998776678888888886654332  3467999999999998864 355678899999999999998


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~  309 (399)
                      +.+.+...+..+.+.++..+|+++||||+++.+.+++..++.+|..+.+.
T Consensus       180 ~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~~~  229 (230)
T 2oxc_A          180 EEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRLN  229 (230)
T ss_dssp             STTSSHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSCEEECC-
T ss_pred             cCcchHHHHHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCCeEEEcC
Confidence            75338889999999999999999999999999999999999999887653

>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=9.6e-37  Score=269.79  Aligned_cols=200  Identities=33%  Similarity=0.566  Sum_probs=178.7

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      .+|++++|++.++++|.++||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+.....++++||++||
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt   80 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALS--GRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPT   80 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHT--TCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSC
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHcc--CCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCc
Confidence            4699999999999999999999999999999999998  69999999999999999999999998776677899999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      ++|+.|+++.++++....+++.+....|+.......   ...++|+|+||+++.+.+.+ +...+.+++++|+||||++.
T Consensus        81 ~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~lViDEah~~~  159 (206)
T 1vec_A           81 RELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKK-GVAKVDHVQMIVLDEADKLL  159 (206)
T ss_dssp             HHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEEETHHHHT
T ss_pred             HHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHc-CCcCcccCCEEEEEChHHhH
Confidence            999999999999998877677888888887654332   45678999999999888643 45678899999999999998


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEE
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII  306 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i  306 (399)
                      +. ++...+..+...+++++|+++||||+++.+.++++.++.+|..+
T Consensus       160 ~~-~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          160 SQ-DFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             ST-TTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             hh-CcHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            64 78888899999999899999999999999999999999999875

>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=1.9e-37  Score=283.35  Aligned_cols=217  Identities=31%  Similarity=0.493  Sum_probs=176.9

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC---------C
Q psy11867        101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS---------I  171 (399)
Q Consensus       101 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~---------~  171 (399)
                      ++.+|+++++++.++++|..+||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+...         .
T Consensus        21 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~--~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~   98 (253)
T 1wrb_A           21 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILE--HRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKT   98 (253)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CC
T ss_pred             ccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCChHHHHHHHHHHHHHHhhcccccccccc
Confidence            467899999999999999999999999999999999998  69999999999999999999999887532         2


Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCcee
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIK  248 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~  248 (399)
                      .++++|||+||++|+.|+++.+++++... ++.+....||.......   ...++|+|+||++|.+++.. ..+.+++++
T Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~-~~~~~~~~~  176 (253)
T 1wrb_A           99 AYPKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEK-NKISLEFCK  176 (253)
T ss_dssp             BCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHT-TSBCCTTCC
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHc-CCCChhhCC
Confidence            34689999999999999999999998765 56777777776543322   45679999999999998654 456788999


Q ss_pred             EEEEechhhHhhcCCchHHHHHHHHh--CCC--CCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEE
Q psy11867        249 VFVLDEADVMIATQGHQDFSIRIQKR--LPS--DCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHY  322 (399)
Q Consensus       249 ~lViDEah~l~~~~~~~~~~~~i~~~--l~~--~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~  322 (399)
                      ++|+||||++.+. ++...+..++..  ++.  .+|+++||||+++.+..+++.++.+|..+.++.......+++|.+
T Consensus       177 ~lViDEah~~~~~-~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~q~~  253 (253)
T 1wrb_A          177 YIVLDEADRMLDM-GFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQEI  253 (253)
T ss_dssp             EEEEETHHHHHHT-TCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC-------------
T ss_pred             EEEEeCHHHHHhC-chHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCCCCcCCceecC
Confidence            9999999999875 788888888884  344  689999999999999999999999999999888777777777653

>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=7.2e-37  Score=275.12  Aligned_cols=203  Identities=28%  Similarity=0.428  Sum_probs=172.5

Q ss_pred             cccccccc-CCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC------CC
Q psy11867        100 YSVKTFEA-LHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS------IQ  172 (399)
Q Consensus       100 ~~~~~f~~-~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~------~~  172 (399)
                      .+..+|++ +++++.++++|.++||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+...      ..
T Consensus        16 ~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~   93 (228)
T 3iuy_A           16 KPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQ--GIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRN   93 (228)
T ss_dssp             CCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHHC---------C
T ss_pred             CChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccC
Confidence            34677888 79999999999999999999999999999998  79999999999999999999999887532      25


Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeE
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKV  249 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~  249 (399)
                      ++++||++||++|+.|+++.++++..  .++.+....|+......   ...+++|+|+||++|.+++.. ..+.++++++
T Consensus        94 ~~~~lil~Pt~~L~~q~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~-~~~~~~~~~~  170 (228)
T 3iuy_A           94 GPGMLVLTPTRELALHVEAECSKYSY--KGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMN-NSVNLRSITY  170 (228)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHCC--TTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHT-TCCCCTTCCE
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHhcc--cCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcCcccceE
Confidence            67899999999999999999999863  26677777777654332   245679999999999987543 5667899999


Q ss_pred             EEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEec
Q psy11867        250 FVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKL  308 (399)
Q Consensus       250 lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~  308 (399)
                      +|+||||++.+. ++...+..++..+++++|+++||||+++.+.++++.++.+|+.+.+
T Consensus       171 lViDEah~~~~~-~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~v  228 (228)
T 3iuy_A          171 LVIDEADKMLDM-EFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV  228 (228)
T ss_dssp             EEECCHHHHHHT-TCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEC
T ss_pred             EEEECHHHHhcc-chHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            999999999875 7899999999999999999999999999999999999999988753

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=8.3e-37  Score=273.03  Aligned_cols=205  Identities=31%  Similarity=0.536  Sum_probs=179.7

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|+++++++.+++++.++||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+.....++++||++|
T Consensus         3 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   80 (219)
T 1q0u_A            3 ETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALR--GESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAP   80 (219)
T ss_dssp             -CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHH--TCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcC
Confidence            35799999999999999999999999999999999998  6999999999999999999999999887666789999999


Q ss_pred             cHHHHHHHHHHHHHHhccCC---CcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEech
Q psy11867        182 TYELAIQIGEVVAKMGKHIT---DLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEA  255 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEa  255 (399)
                      |++|+.|+++.++++.....   ++.+....|+.......   ...++|+|+||+++.+++.. +.+.+.+++++|+|||
T Consensus        81 t~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~-~~~~~~~~~~lViDEa  159 (219)
T 1q0u_A           81 TRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIRE-QALDVHTAHILVVDEA  159 (219)
T ss_dssp             SHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHT-TCCCGGGCCEEEECSH
T ss_pred             cHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHc-CCCCcCcceEEEEcCc
Confidence            99999999999999987653   46677777777654433   34678999999999988644 5567889999999999


Q ss_pred             hhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccc
Q psy11867        256 DVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR  310 (399)
Q Consensus       256 h~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~  310 (399)
                      |++.+. ++...+..+...+++++|+++||||+++++.++++.++.+|..+.+..
T Consensus       160 h~~~~~-~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          160 DLMLDM-GFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             HHHHHT-TCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             hHHhhh-ChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence            999875 788888999999999999999999999999999999999999887653

>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=1e-36  Score=275.88  Aligned_cols=203  Identities=37%  Similarity=0.621  Sum_probs=173.8

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|+++++++.++++|.++||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+.....++++||++|
T Consensus        29 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~--~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P  106 (237)
T 3bor_A           29 VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIK--GYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAP  106 (237)
T ss_dssp             CCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHT--TCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEEC
Confidence            56799999999999999999999999999999999998  6999999999999999999999999876666789999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh----ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK----KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      |++|+.|+++.+++++... ++.+....|+.......    ...++|+|+||++|.+++.. +.+.+.+++++|+||||+
T Consensus       107 t~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~~~~lViDEah~  184 (237)
T 3bor_A          107 TRELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNR-RYLSPKWIKMFVLDEADE  184 (237)
T ss_dssp             SHHHHHHHHHHHHHHTTTT-TCCEEEECC-------------CCCSEEEECHHHHHHHHHT-TSSCSTTCCEEEEESHHH
T ss_pred             cHHHHHHHHHHHHHHhhhc-CceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHh-CCcCcccCcEEEECCchH
Confidence            9999999999999998765 56666777776543322    23479999999999998644 556788999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~  309 (399)
                      +.+. ++...+..+++.++..+|+++||||+++.+.++++.++.+|..+.++
T Consensus       185 ~~~~-~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~  235 (237)
T 3bor_A          185 MLSR-GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVK  235 (237)
T ss_dssp             HHHT-TCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC--
T ss_pred             hhcc-CcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEec
Confidence            9874 78888889999999999999999999999999999999999988765

>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=9.3e-37  Score=306.33  Aligned_cols=276  Identities=14%  Similarity=0.205  Sum_probs=214.5

Q ss_pred             cccccCCCCHHHHHHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        103 KTFEALHLKPELLKGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      .+|++++|++.+.+.|.+ +||..|+|+|.++++.+++  |+|+++++|||+|||++|++|++..      ..++|||+|
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~--g~d~lv~apTGsGKTl~~~lp~l~~------~g~~lvi~P   73 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLS--GRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSP   73 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHT--TCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECS
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHc--CCCEEEECCCCcHHHHHHHHHHHHh------CCCEEEECC
Confidence            579999999999999998 8999999999999999998  6999999999999999999999853      357999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhh-------hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEec
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER-------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDE  254 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDE  254 (399)
                      +++|+.|+.+.++.+     ++.+....++.....       ...+..+|+|+||++|..... ...+...++++|||||
T Consensus        74 ~~aL~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~-~~~l~~~~~~~vViDE  147 (523)
T 1oyw_A           74 LISLMKDQVDQLQAN-----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNF-LEHLAHWNPVLLAVDE  147 (523)
T ss_dssp             CHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTH-HHHHTTSCEEEEEESS
T ss_pred             hHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHH-HHHHhhCCCCEEEEeC
Confidence            999999999999886     345555555543321       124567999999999964311 1233457899999999


Q ss_pred             hhhHhhcC-CchHHHH---HHHHhCCCCCcEEEEEeeCChhHHHHHHh-h-CCCCeEEecccccccccceeEEEEEeCCh
Q psy11867        255 ADVMIATQ-GHQDFSI---RIQKRLPSDCQIMLFSATYDKEVMEFAQD-M-VPNPLIIKLKREEESLDNIKQHYVMCKNI  328 (399)
Q Consensus       255 ah~l~~~~-~~~~~~~---~i~~~l~~~~q~l~~SAT~~~~v~~~~~~-~-~~~p~~i~~~~~~~~~~~i~~~~~~~~~~  328 (399)
                      ||++.+.+ .|...+.   .+...+ ++.+++++|||.++.+...+.. + +.+|..+....   ...++...+.  .. 
T Consensus       148 aH~i~~~g~~fr~~~~~l~~l~~~~-~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~~~---~r~~l~~~v~--~~-  220 (523)
T 1oyw_A          148 AHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSF---DRPNIRYMLM--EK-  220 (523)
T ss_dssp             GGGGCTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEECCC---CCTTEEEEEE--EC-
T ss_pred             ccccCcCCCccHHHHHHHHHHHHhC-CCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeCCC---CCCceEEEEE--eC-
Confidence            99997531 1444333   334444 4689999999999887654433 3 34555443221   2234433332  22 


Q ss_pred             hhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+...+..++.....+++||||++++.++.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||
T Consensus       221 ~~~~~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlV  291 (523)
T 1oyw_A          221 FKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVV  291 (523)
T ss_dssp             SSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEE
T ss_pred             CCHHHHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEE
Confidence            45677788888877778999999999999999999999999999999999999999999999999999986

>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=1.4e-36  Score=271.61  Aligned_cols=203  Identities=31%  Similarity=0.537  Sum_probs=177.9

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      ..+|++++|++.++++|.++||..|+++|.++++.+++  ++|+++++|||+|||++|++|++..+.....++++||++|
T Consensus        13 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   90 (220)
T 1t6n_A           13 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAIL--GMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCH   90 (220)
T ss_dssp             -CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECS
T ss_pred             CCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeC
Confidence            35699999999999999999999999999999999998  6999999999999999999999999877656678999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh----ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK----KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      |++|+.|+++.++++....+++.+....|+.......    ...++|+|+||+++.+++.. ..+.+.+++++|+||||+
T Consensus        91 t~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~lViDEah~  169 (220)
T 1t6n_A           91 TRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFILDECDK  169 (220)
T ss_dssp             CHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEESHHH
T ss_pred             CHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHh-CCCCcccCCEEEEcCHHH
Confidence            9999999999999998877678888888876543322    34569999999999988644 556788999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEe
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK  307 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~  307 (399)
                      +.+..++...+..+.+.+++.+|+++||||+++.+.++++.++.+|..+.
T Consensus       170 ~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  219 (220)
T 1t6n_A          170 MLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  219 (220)
T ss_dssp             HHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             HhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEe
Confidence            98633677778888888888999999999999999999999999998775

>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=3.1e-37  Score=301.98  Aligned_cols=261  Identities=16%  Similarity=0.159  Sum_probs=202.8

Q ss_pred             HHHHHHHH-cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHH
Q psy11867        113 ELLKGVYE-MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGE  191 (399)
Q Consensus       113 ~l~~~l~~-~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~  191 (399)
                      .+.+.+++ .|| .|+|+|.++++.+++  |+|++++||||||||++|++|++..+.   .++++|||+||++|+.|+++
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~--~~~~lv~apTGsGKT~~~l~~~~~~~~---~~~~~lil~Pt~~L~~q~~~   82 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQ--GKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLE   82 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTT--TCCEECCSCSSSSHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHH
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhc--CCCEEEEeCCCCCHHHHHHHHHHHHhc---CCCEEEEEECCHHHHHHHHH
Confidence            44455555 455 899999999999998  699999999999999999999988773   45789999999999999999


Q ss_pred             HHHHHhccCCCcEEEEEEcCchhhh---h----hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc---
Q psy11867        192 VVAKMGKHITDLSVRYAVRGENLER---N----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT---  261 (399)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~~---~----~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~---  261 (399)
                      .+++++.  .++.+....|+.....   .    ....++|+|+||++|.+++..   +.+.+++++|+||||++...   
T Consensus        83 ~~~~~~~--~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~---~~~~~~~~iViDEaH~~~~~~~~  157 (414)
T 3oiy_A           83 RLQKLAD--EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRFDFVFVDDVDAVLKASRN  157 (414)
T ss_dssp             HHHHHCC--SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH---HTTCCCSEEEESCHHHHHHCHHH
T ss_pred             HHHHHcc--CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH---hccccccEEEEeChHhhhhccch
Confidence            9999877  4788888888876521   1    133489999999999887642   66779999999999876531   


Q ss_pred             -------CCchHH-HHHHHHhCC-----------CCCcEEEEEee-CChhHH-HHHHhhCCCCeEEecccccccccceeE
Q psy11867        262 -------QGHQDF-SIRIQKRLP-----------SDCQIMLFSAT-YDKEVM-EFAQDMVPNPLIIKLKREEESLDNIKQ  320 (399)
Q Consensus       262 -------~~~~~~-~~~i~~~l~-----------~~~q~l~~SAT-~~~~v~-~~~~~~~~~p~~i~~~~~~~~~~~i~~  320 (399)
                             .+|... +..++..++           ...|+++|||| .+..+. .+...++.    +.+........++.+
T Consensus       158 ~d~~l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~~~~~~~i~~  233 (414)
T 3oiy_A          158 IDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITH  233 (414)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCCCCCCCSEEE
T ss_pred             hhhHHhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCccccccccchh
Confidence                   356655 667777665           78999999999 565543 23333222    233344455677888


Q ss_pred             EEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEE-EEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        321 HYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVG-LLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       321 ~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~-~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+..+.    +...+..++.. ..+++||||++++.|+.++..|...|+.+. .+||+    +|.  ++.|++|+++|||
T Consensus       234 ~~~~~~----~~~~l~~~l~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLv  302 (414)
T 3oiy_A          234 VRISSR----SKEKLVELLEI-FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILI  302 (414)
T ss_dssp             EEESSC----CHHHHHHHHHH-HCSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEE
T ss_pred             eeeccC----HHHHHHHHHHH-cCCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEE
Confidence            887663    34455566655 338999999999999999999999999998 99995    444  9999999999986

>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=1.9e-36  Score=273.73  Aligned_cols=207  Identities=29%  Similarity=0.435  Sum_probs=179.5

Q ss_pred             ccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC----CCCCe
Q psy11867        100 YSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS----IQEPQ  175 (399)
Q Consensus       100 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~----~~~~~  175 (399)
                      .+..+|+++++++.++++|.++||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+...    ..+++
T Consensus        22 ~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~--~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~   99 (236)
T 2pl3_A           22 NEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQ--GKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLG   99 (236)
T ss_dssp             GGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCC
T ss_pred             cccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCce
Confidence            3467899999999999999999999999999999999998  69999999999999999999999876421    24678


Q ss_pred             EEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh--hccCCcEEEeCchhHHHhhhccccccCCceeEEEEe
Q psy11867        176 VLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN--KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLD  253 (399)
Q Consensus       176 ~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViD  253 (399)
                      +||++||++|+.|+++.+++++... ++.+....|+......  ....++|+|+||++|.+++.....+.+.+++++|+|
T Consensus       100 ~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViD  178 (236)
T 2pl3_A          100 VLIISPTRELAYQTFEVLRKVGKNH-DFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLD  178 (236)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS-SCCEEEECCC--CHHHHHHHTTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEET
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhCCC-CeeEEEEECCCCHHHHHHhCCCCCEEEECHHHHHHHHHhcCCcccccccEEEEe
Confidence            9999999999999999999998765 5777777777654332  235679999999999998766556778899999999


Q ss_pred             chhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccc
Q psy11867        254 EADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR  310 (399)
Q Consensus       254 Eah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~  310 (399)
                      |||++.+. ++...+..++..+++.+|+++||||+++.+.++++.++.+|..+.+..
T Consensus       179 Eah~~~~~-~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~~  234 (236)
T 2pl3_A          179 EADRILDM-GFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHE  234 (236)
T ss_dssp             THHHHHHT-TTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECCC
T ss_pred             ChHHHhcC-CcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeCC
Confidence            99999874 788889999999999999999999999999999999999999887653

>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=1.4e-36  Score=276.15  Aligned_cols=221  Identities=24%  Similarity=0.407  Sum_probs=181.7

Q ss_pred             cccceeeccCCCCCCccccccccC----CCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867         85 KQELEIQRKDPHSPLYSVKTFEAL----HLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~f~~~----~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+.+.+.+.+.+.|.   .+|+++    ++++.+++++.++||..|+++|.++++.+++  |+|++++||||||||++|+
T Consensus        10 ~~~i~~~~~~~p~~~---~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--~~~~l~~a~TGsGKT~~~~   84 (245)
T 3dkp_A           10 KHKIHVQGTDLPDPI---ATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLH--GRELLASAPTGSGKTLAFS   84 (245)
T ss_dssp             HTTEEEESSSCCCCC---SSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHH
T ss_pred             hCceEecCCCCCCcc---cCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCCEEEECCCCCcHHHHHH
Confidence            456667667766664   456665    8999999999999999999999999999998  6999999999999999999


Q ss_pred             HHHHHhhCCC-CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh----hccCCcEEEeCchhHHHh
Q psy11867        161 LTMLSRVNPS-IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN----KKITEQIIIGTPGKVLDW  235 (399)
Q Consensus       161 l~il~~l~~~-~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~IlV~Tp~~l~~~  235 (399)
                      +|++..+... ..++++||++||++|+.|+++.+++++... ++.+....++......    ....++|+|+||++|.++
T Consensus        85 l~~l~~l~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~  163 (245)
T 3dkp_A           85 IPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGT-GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYL  163 (245)
T ss_dssp             HHHHHHHCSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHH
T ss_pred             HHHHHHHhhcccCCceEEEEeCCHHHHHHHHHHHHHHhccc-CceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHH
Confidence            9999988643 356789999999999999999999998765 5565555555433222    245678999999999998


Q ss_pred             hhccc-cccCCceeEEEEechhhHhhc--CCchHHHHHHHHhC-CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccc
Q psy11867        236 GLKYR-FFDLSKIKVFVLDEADVMIAT--QGHQDFSIRIQKRL-PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE  311 (399)
Q Consensus       236 ~~~~~-~~~~~~~~~lViDEah~l~~~--~~~~~~~~~i~~~l-~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~  311 (399)
                      +.... .+.+.+++++|+||||++.+.  .++...+..++..+ +.+.|+++||||+++++.++++.++.+|+.+.++..
T Consensus       164 l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          164 LKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             HHSSSCSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             HHhCCCCcccccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            76543 467899999999999999874  36777777777665 457899999999999999999999999999987754

>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=5.2e-36  Score=268.65  Aligned_cols=206  Identities=40%  Similarity=0.674  Sum_probs=175.1

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      +.+|+++++++.+++.+.++||..|+++|.++++.+++  |+|+++++|||+|||++|++|++..+.....++++||++|
T Consensus        13 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (224)
T 1qde_A           13 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIE--GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAP   90 (224)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhc--CCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEEC
Confidence            56799999999999999999999999999999999998  6999999999999999999999999877767789999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh--ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK--KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      |++|+.|+++.++++.... ++.+....|+.......  ...++|+|+||++|.+++.. ..+.+.+++++|+||||++.
T Consensus        91 t~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~-~~~~~~~~~~iViDEah~~~  168 (224)
T 1qde_A           91 TRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEML  168 (224)
T ss_dssp             SHHHHHHHHHHHHHHTTTS-CCCEEEECC----------CTTCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEETHHHHH
T ss_pred             CHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHhcCCCCCEEEECHHHHHHHHHh-CCcchhhCcEEEEcChhHHh
Confidence            9999999999999998765 67777777776543332  23479999999999988654 46678899999999999998


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEeccccc
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREE  312 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~  312 (399)
                      +. ++...+..+...+++.+|+++||||+++.+.++++.++.+|..+.+...+
T Consensus       169 ~~-~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~~  220 (224)
T 1qde_A          169 SS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDE  220 (224)
T ss_dssp             HT-TCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC-----
T ss_pred             hh-hhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCCc
Confidence            74 78888889999999999999999999999999999999999998776543

>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=1.9e-36  Score=316.00  Aligned_cols=280  Identities=21%  Similarity=0.189  Sum_probs=213.7

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhh-hhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPT-LLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~-ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      +|++++|++.+.+.+.+.||..|+++|.++++. +..  ++|++++||||||||++|.+|++..+..  .+.+++|++|+
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~--~~~~lv~apTGsGKT~~~~l~il~~~~~--~~~~~l~i~P~   77 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILE--GKNALISIPTASGKTLIAEIAMVHRILT--QGGKAVYIVPL   77 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGG--TCEEEEECCGGGCHHHHHHHHHHHHHHH--HCSEEEEECSS
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcC--CCcEEEEcCCccHHHHHHHHHHHHHHHh--CCCEEEEEcCc
Confidence            589999999999999999999999999999998 666  7999999999999999999999987753  25689999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ  262 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~  262 (399)
                      ++|+.|+++.++++...  ++.+....|+...........+|+|+||+++..++.. ....+++++++|+||||++.+. 
T Consensus        78 raLa~q~~~~~~~l~~~--g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vIiDE~H~l~~~-  153 (720)
T 2zj8_A           78 KALAEEKFQEFQDWEKI--GLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRH-GSSWIKDVKILVADEIHLIGSR-  153 (720)
T ss_dssp             GGGHHHHHHHTGGGGGG--TCCEEEECSCSSCCCGGGGGCSEEEECHHHHHHHHHH-TCTTGGGEEEEEEETGGGGGCT-
T ss_pred             HHHHHHHHHHHHHHHhc--CCEEEEecCCCCccccccCCCCEEEECHHHHHHHHHc-ChhhhhcCCEEEEECCcccCCC-
Confidence            99999999999766543  6777777776655444445789999999999887654 3445789999999999999753 


Q ss_pred             CchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEE-----EEeCC-----hhhHH
Q psy11867        263 GHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHY-----VMCKN-----IDEKF  332 (399)
Q Consensus       263 ~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~-----~~~~~-----~~~k~  332 (399)
                      .+...+..++..++.+.|++++|||+++ ...+...+ ..+. +.....   +..+...+     +.+..     ...+.
T Consensus       154 ~r~~~~~~ll~~l~~~~~ii~lSATl~n-~~~~~~~l-~~~~-~~~~~r---p~~l~~~~~~~~~~~~~~~~~~~~~~~~  227 (720)
T 2zj8_A          154 DRGATLEVILAHMLGKAQIIGLSATIGN-PEELAEWL-NAEL-IVSDWR---PVKLRRGVFYQGFVTWEDGSIDRFSSWE  227 (720)
T ss_dssp             TTHHHHHHHHHHHBTTBEEEEEECCCSC-HHHHHHHT-TEEE-EECCCC---SSEEEEEEEETTEEEETTSCEEECSSTT
T ss_pred             cccHHHHHHHHHhhcCCeEEEEcCCcCC-HHHHHHHh-CCcc-cCCCCC---CCcceEEEEeCCeeeccccchhhhhHHH
Confidence            5666677777777668999999999986 34444433 2211 111100   00111111     01111     13344


Q ss_pred             HHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC---------------------------------CCeEEEEcCCCC
Q psy11867        333 EAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE---------------------------------GLNVGLLSGELT  379 (399)
Q Consensus       333 ~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~---------------------------------g~~v~~lhg~~~  379 (399)
                      ..+.+.+.  ..+++||||++++.|+.++..|.+.                                 ...+..+||+|+
T Consensus       228 ~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~  305 (720)
T 2zj8_A          228 ELVYDAIR--KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLG  305 (720)
T ss_dssp             HHHHHHHH--TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSC
T ss_pred             HHHHHHHh--CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCC
Confidence            55555554  3479999999999999999998753                                 124999999999


Q ss_pred             HHHHHHHHHHHhcCCCcccC
Q psy11867        380 VEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       380 ~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.+|..+++.|++|+++|||
T Consensus       306 ~~~R~~v~~~f~~g~~~vlv  325 (720)
T 2zj8_A          306 RDERVLVEENFRKGIIKAVV  325 (720)
T ss_dssp             HHHHHHHHHHHHTTSSCEEE
T ss_pred             HHHHHHHHHHHHCCCCeEEE
Confidence            99999999999999999986

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=100.00  E-value=1.6e-35  Score=308.98  Aligned_cols=281  Identities=17%  Similarity=0.152  Sum_probs=213.2

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      .+|++++|++.+.+.+.++||..|+++|.++++.++.. +++++++||||||||++|.++++..+..  .+.+++|++|+
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~-~~~~lv~apTGsGKT~~~~l~il~~~~~--~~~~il~i~P~   84 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLE-GNRLLLTSPTGSGKTLIAEMGIISFLLK--NGGKAIYVTPL   84 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTT-TCCEEEECCTTSCHHHHHHHHHHHHHHH--SCSEEEEECSC
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcC-CCcEEEEcCCCCcHHHHHHHHHHHHHHH--CCCeEEEEeCc
Confidence            46999999999999999999999999999999994433 7999999999999999999999987753  24689999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ  262 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~  262 (399)
                      ++||.|+++.++.+...  ++.+...+|+...........+|+|+||++|..++.. ....++++++||+||||.+.+. 
T Consensus        85 r~La~q~~~~~~~~~~~--g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vIiDE~H~l~~~-  160 (715)
T 2va8_A           85 RALTNEKYLTFKDWELI--GFKVAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRH-RPEWLNEVNYFVLDELHYLNDP-  160 (715)
T ss_dssp             HHHHHHHHHHHGGGGGG--TCCEEECCSCSSSCCGGGGGCSEEEECHHHHHHHHHH-CCGGGGGEEEEEECSGGGGGCT-
T ss_pred             HHHHHHHHHHHHHhhcC--CCEEEEEeCCCCCchhhcCCCCEEEEcHHHHHHHHhC-ChhHhhccCEEEEechhhcCCc-
Confidence            99999999999655432  5677777776554433334689999999999988655 3445889999999999998653 


Q ss_pred             CchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeE------------EEEEeC----
Q psy11867        263 GHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQ------------HYVMCK----  326 (399)
Q Consensus       263 ~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~------------~~~~~~----  326 (399)
                      .+...+..++..++ +.|++++|||+++ ...+...+. .+. +......  . .+..            .+....    
T Consensus       161 ~~~~~l~~i~~~~~-~~~ii~lSATl~n-~~~~~~~l~-~~~-~~~~~r~--~-~l~~~~~~~~~~~~~~~~~~~~~~~~  233 (715)
T 2va8_A          161 ERGPVVESVTIRAK-RRNLLALSATISN-YKQIAKWLG-AEP-VATNWRP--V-PLIEGVIYPERKKKEYNVIFKDNTTK  233 (715)
T ss_dssp             TTHHHHHHHHHHHH-TSEEEEEESCCTT-HHHHHHHHT-CEE-EECCCCS--S-CEEEEEEEECSSTTEEEEEETTSCEE
T ss_pred             ccchHHHHHHHhcc-cCcEEEEcCCCCC-HHHHHHHhC-CCc-cCCCCCC--C-CceEEEEecCCcccceeeecCcchhh
Confidence            56666666666665 8999999999985 345554432 211 1111000  0 0111            111111    


Q ss_pred             ---ChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCC-----------------------------------
Q psy11867        327 ---NIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEG-----------------------------------  368 (399)
Q Consensus       327 ---~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g-----------------------------------  368 (399)
                         ..+.+...+.+.+.  ..+++||||++++.|+.++..|.+..                                   
T Consensus       234 ~~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~  311 (715)
T 2va8_A          234 KVHGDDAIIAYTLDSLS--KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLI  311 (715)
T ss_dssp             EEESSSHHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHH
T ss_pred             hcccchHHHHHHHHHHh--cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHH
Confidence               12445666666654  45899999999999999999998642                                   


Q ss_pred             -CeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        369 -LNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       369 -~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                       ..+..+||+|+..+|..+++.|++|+++|||
T Consensus       312 ~~~v~~~h~~l~~~~r~~v~~~f~~g~~~vlv  343 (715)
T 2va8_A          312 SKGVAYHHAGLSKALRDLIEEGFRQRKIKVIV  343 (715)
T ss_dssp             TTTEEEECTTSCHHHHHHHHHHHHTTCSCEEE
T ss_pred             hcCEEEECCCCCHHHHHHHHHHHHcCCCeEEE
Confidence             2489999999999999999999999999986

>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=4.2e-36  Score=275.81  Aligned_cols=198  Identities=30%  Similarity=0.412  Sum_probs=170.0

Q ss_pred             cccccCC--CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC----CCCCeE
Q psy11867        103 KTFEALH--LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS----IQEPQV  176 (399)
Q Consensus       103 ~~f~~~~--l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~----~~~~~~  176 (399)
                      .+|++++  +++.++++|.++||..|+++|.++++.++.  |+|++++||||||||++|++|++..+...    ..+.++
T Consensus        52 ~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~--~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~  129 (262)
T 3ly5_A           52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLE--GRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGV  129 (262)
T ss_dssp             GCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHH--TCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCE
T ss_pred             CChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhC--CCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceE
Confidence            4566666  999999999999999999999999999999  69999999999999999999999877532    246789


Q ss_pred             EEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEe
Q psy11867        177 LCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLD  253 (399)
Q Consensus       177 lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViD  253 (399)
                      ||++||++||.|+++.+++++... +..+....|+.......   ..+++|+|+||+++.+++.....+.+++++++|+|
T Consensus       130 lil~Pt~~La~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViD  208 (262)
T 3ly5_A          130 LILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVID  208 (262)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTC-CSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEEC
T ss_pred             EEEeCCHHHHHHHHHHHHHHHhhc-CceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEc
Confidence            999999999999999999998775 56777777776554332   34689999999999998877666788999999999


Q ss_pred             chhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCe
Q psy11867        254 EADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPL  304 (399)
Q Consensus       254 Eah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~  304 (399)
                      |||++.+. ++...+..+++.++..+|+++||||+++.+.++++.++.++.
T Consensus       209 Eah~l~~~-~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          209 EADRILDV-GFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             SHHHHHHT-TCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             ChHHHhhh-hHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            99999975 799999999999999999999999999999999999887543

>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=3.5e-36  Score=323.71  Aligned_cols=278  Identities=14%  Similarity=0.125  Sum_probs=216.5

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      .|..+++++.+...+...++..|+++|.++++.+++  |++++++||||||||++|++|++..+..   +.++||++||+
T Consensus       163 ~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~--g~dvLV~ApTGSGKTlva~l~i~~~l~~---g~rvlvl~Ptr  237 (1108)
T 3l9o_A          163 NYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDR--GESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIK  237 (1108)
T ss_dssp             CCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTT--TCCEEEECCSSSHHHHHHHHHHHHHHHT---TCEEEEEESSH
T ss_pred             CcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHc--CCCEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEcCcH
Confidence            566777777777777777888999999999999988  7999999999999999999999998843   56899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCC
Q psy11867        184 ELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQG  263 (399)
Q Consensus       184 ~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~  263 (399)
                      +|+.|+++.+++++.     .+.+..|+...    ....+|+|+||++|.+++.. ....++++++|||||||+|.+. +
T Consensus       238 aLa~Q~~~~l~~~~~-----~VglltGd~~~----~~~~~IlV~Tpe~L~~~L~~-~~~~l~~l~lVVIDEaH~l~d~-~  306 (1108)
T 3l9o_A          238 ALSNQKYRELLAEFG-----DVGLMTGDITI----NPDAGCLVMTTEILRSMLYR-GSEVMREVAWVIFDEVHYMRDK-E  306 (1108)
T ss_dssp             HHHHHHHHHHHHHTS-----SEEEECSSCBC----CCSCSEEEEEHHHHHHHHHH-CSSHHHHEEEEEEETGGGTTSH-H
T ss_pred             HHHHHHHHHHHHHhC-----CccEEeCcccc----CCCCCEEEeChHHHHHHHHc-CccccccCCEEEEhhhhhcccc-c
Confidence            999999999999864     34556666543    23578999999999998765 3445789999999999999864 6


Q ss_pred             chHHHHHHHHhCCCCCcEEEEEeeCChh--HHHHHHhhCCCCeEEecccccccccceeEEEEEeCC---------h----
Q psy11867        264 HQDFSIRIQKRLPSDCQIMLFSATYDKE--VMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKN---------I----  328 (399)
Q Consensus       264 ~~~~~~~i~~~l~~~~q~l~~SAT~~~~--v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~---------~----  328 (399)
                      +...+..++..+++..|+++||||+++.  +..++.....+|..+.......  ..+.++++....         .    
T Consensus       307 rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~rp--~pl~~~~~~~~~~~~~~~vd~~~~~~  384 (1108)
T 3l9o_A          307 RGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRP--TPLQHYLFPAHGDGIYLVVDEKSTFR  384 (1108)
T ss_dssp             HHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCCS--SCEEEEEEETTSSCCEEEEETTTEEC
T ss_pred             hHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCc--ccceEEEeecCCcceeeeeccccchh
Confidence            7777888899999999999999999874  4466666666666554332221  112222211100         0    


Q ss_pred             -----------------------------------------hhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC
Q psy11867        329 -----------------------------------------DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE  367 (399)
Q Consensus       329 -----------------------------------------~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~  367 (399)
                                                               ..+...+...+.....+++||||++++.|+.++..|...
T Consensus       385 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~  464 (1108)
T 3l9o_A          385 EENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKL  464 (1108)
T ss_dssp             HHHHHHHHTTC-----------------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSH
T ss_pred             hhhHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhc
Confidence                                                     223334445555556679999999999999999998653


Q ss_pred             CCe---------------------------------------EEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        368 GLN---------------------------------------VGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       368 g~~---------------------------------------v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++.                                       ++.+||+|++.+|..+++.|++|.++|||
T Consensus       465 ~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLV  535 (1108)
T 3l9o_A          465 DFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLF  535 (1108)
T ss_dssp             HHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEE
T ss_pred             cCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEE
Confidence            222                                       89999999999999999999999999986

>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=3.9e-35  Score=259.59  Aligned_cols=199  Identities=34%  Similarity=0.550  Sum_probs=173.5

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC---CCCCeEEEEe
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS---IQEPQVLCLA  180 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~---~~~~~~lil~  180 (399)
                      +|+++++++.+++++.++||..|+++|.++++.+++  |+|+++++|||||||++|++|++..+...   ..++++||++
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~--~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~   79 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALE--GKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLT   79 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEEC
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcC--CCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEE
Confidence            589999999999999999999999999999999998  69999999999999999999999988642   3567899999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      ||++|+.|+++.++++...   +.+....|+......   ....++|+|+||+++.+++.. +.+.+.+++++|+||||+
T Consensus        80 P~~~L~~q~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~iViDEah~  155 (207)
T 2gxq_A           80 PTRELALQVASELTAVAPH---LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQ-GVLDLSRVEVAVLDEADE  155 (207)
T ss_dssp             SSHHHHHHHHHHHHHHCTT---SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHH-TSSCCTTCSEEEEESHHH
T ss_pred             CCHHHHHHHHHHHHHHhhc---ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHc-CCcchhhceEEEEEChhH
Confidence            9999999999999998754   456666676543222   235689999999999988654 566788999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~  309 (399)
                      +.+. ++...+..++..+++.+|+++||||+++.+.++++.++.+|..+.+.
T Consensus       156 ~~~~-~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~~  206 (207)
T 2gxq_A          156 MLSM-GFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVI  206 (207)
T ss_dssp             HHHT-TCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             hhcc-chHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEcC
Confidence            9874 78888899999999999999999999999999999999999988654

>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=2.3e-36  Score=314.56  Aligned_cols=279  Identities=18%  Similarity=0.137  Sum_probs=207.1

Q ss_pred             ccccCC--CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        104 TFEALH--LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       104 ~f~~~~--l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      +|++++  |++.+.+.+.++||..|+++|.++++.++.  ++|++++||||||||++|.+|++..+..   +.+++|++|
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~--~~~~lv~apTGsGKT~~~~l~il~~~~~---~~~~l~i~P   76 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFS--GKNLLLAMPTAAGKTLLAEMAMVREAIK---GGKSLYVVP   76 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTT--CSCEEEECSSHHHHHHHHHHHHHHHHHT---TCCEEEEES
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhC--CCcEEEEcCCccHHHHHHHHHHHHHHHh---CCcEEEEeC
Confidence            477888  999999999999999999999999999887  7999999999999999999999988754   467999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhc
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIAT  261 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~  261 (399)
                      +++||.|+++.++.+...  ++.+....|+...........+|+|+||+++..++.+ ....++++++||+||||++.+.
T Consensus        77 ~r~La~q~~~~~~~~~~~--g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~l~~-~~~~l~~~~~vIiDE~H~l~~~  153 (702)
T 2p6r_A           77 LRALAGEKYESFKKWEKI--GLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRN-RASWIKAVSCLVVDEIHLLDSE  153 (702)
T ss_dssp             SHHHHHHHHHHHTTTTTT--TCCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHT-TCSGGGGCCEEEETTGGGGGCT
T ss_pred             cHHHHHHHHHHHHHHHhc--CCEEEEEeCCCCcchhhccCCCEEEECHHHHHHHHHc-ChhHHhhcCEEEEeeeeecCCC
Confidence            999999999999655432  6777777777654443345789999999999988655 3445889999999999998753


Q ss_pred             CCchHHHHHHHHh---CCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEE------EEeCCh----
Q psy11867        262 QGHQDFSIRIQKR---LPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHY------VMCKNI----  328 (399)
Q Consensus       262 ~~~~~~~~~i~~~---l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~------~~~~~~----  328 (399)
                       ++...+..++..   +.++.|++++|||+++ ...+...+ ..+. +......   ..+...+      ......    
T Consensus       154 -~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~~l-~~~~-~~~~~r~---~~l~~~~~~~~~~~~~~~~~~~~  226 (702)
T 2p6r_A          154 -KRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEWL-DADY-YVSDWRP---VPLVEGVLCEGTLELFDGAFSTS  226 (702)
T ss_dssp             -TTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHHHT-TCEE-EECCCCS---SCEEEEEECSSEEEEEETTEEEE
T ss_pred             -CcccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHHHh-CCCc-ccCCCCC---ccceEEEeeCCeeeccCcchhhh
Confidence             455545444443   3678999999999986 45555543 3222 1111110   0111111      011110    


Q ss_pred             --hhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC------------------------------CCeEEEEcC
Q psy11867        329 --DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE------------------------------GLNVGLLSG  376 (399)
Q Consensus       329 --~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~------------------------------g~~v~~lhg  376 (399)
                        ..+...+.+.+.  ..+++||||++++.|+.++..|...                              +..+..+||
T Consensus       227 ~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~  304 (702)
T 2p6r_A          227 RRVKFEELVEECVA--ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHA  304 (702)
T ss_dssp             EECCHHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECT
T ss_pred             hhhhHHHHHHHHHh--cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecC
Confidence              014555555554  4579999999999999999988752                              235889999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcccC
Q psy11867        377 ELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       377 ~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +|++++|..+++.|++|+++|||
T Consensus       305 ~l~~~~R~~v~~~f~~g~~~vlv  327 (702)
T 2p6r_A          305 GLLNGQRRVVEDAFRRGNIKVVV  327 (702)
T ss_dssp             TSCHHHHHHHHHHHHTTSCCEEE
T ss_pred             CCCHHHHHHHHHHHHCCCCeEEE
Confidence            99999999999999999999986

>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=1.1e-34  Score=322.26  Aligned_cols=298  Identities=16%  Similarity=0.174  Sum_probs=215.7

Q ss_pred             CCCCccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCe
Q psy11867         96 HSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQ  175 (399)
Q Consensus        96 ~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~  175 (399)
                      +.++.+...+.-..|.+...++++..+|..++|+|.++++.++.+ +.|++++||||||||++|.+|+++.+... .+.+
T Consensus       897 ~t~lldl~plp~s~L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~-~~nvlv~APTGSGKTliaelail~~l~~~-~~~k  974 (1724)
T 4f92_B          897 PTELLDLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNS-DDNVFVGAPTGSGKTICAEFAILRMLLQS-SEGR  974 (1724)
T ss_dssp             CCCCCCCCCCBGGGSCCHHHHTTTTTTCSBCCHHHHHHHHHHHSC-CSCEEEECCTTSCCHHHHHHHHHHHHHHC-TTCC
T ss_pred             CCccccCCCCCcccccCHHHHHHHHhcCCCCCHHHHHHHHHHhcC-CCcEEEEeCCCCCchHHHHHHHHHHHHhC-CCCE
Confidence            344444444444457788899999999999999999999999976 78999999999999999999999988654 4567


Q ss_pred             EEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccc-cCCceeEEEEec
Q psy11867        176 VLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFF-DLSKIKVFVLDE  254 (399)
Q Consensus       176 ~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~-~~~~~~~lViDE  254 (399)
                      +||++|+++||.|+++.+++......++++....|+...........+|+|+||+++..++.++... .++++++||+||
T Consensus       975 avyi~P~raLa~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~~~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE 1054 (1724)
T 4f92_B          975 CVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDE 1054 (1724)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHTTTSCCCEEECCSCHHHHHHHHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECC
T ss_pred             EEEEcChHHHHHHHHHHHHHHhchhcCCEEEEEECCCCcchhhcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeec
Confidence            9999999999999999987654333377888888887665555566799999999997776554332 478999999999


Q ss_pred             hhhHhhcCCchHHHHH-------HHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCC-eEEecccccccccceeEEEEEeC
Q psy11867        255 ADVMIATQGHQDFSIR-------IQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNP-LIIKLKREEESLDNIKQHYVMCK  326 (399)
Q Consensus       255 ah~l~~~~~~~~~~~~-------i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p-~~i~~~~~~~~~~~i~~~~~~~~  326 (399)
                      +|++.+.  ....+..       +...+++++|+++||||+++ ..+++..+-.++ ..+.+..... +..+..++....
T Consensus      1055 ~H~l~d~--rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N-~~dla~WL~~~~~~~~~~~~~~R-PvpL~~~i~~~~ 1130 (1724)
T 4f92_B         1055 VHLIGGE--NGPVLEVICSRMRYISSQIERPIRIVALSSSLSN-AKDVAHWLGCSATSTFNFHPNVR-PVPLELHIQGFN 1130 (1724)
T ss_dssp             GGGGGST--THHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTT-HHHHHHHHTCCSTTEEECCGGGC-SSCEEEEEEEEC
T ss_pred             hhhcCCC--CCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCC-HHHHHHHhCCCCCCeEEeCCCCC-CCCeEEEEEecc
Confidence            9998753  2222222       22345778999999999986 356666554332 2222222222 222333333322


Q ss_pred             Chh--hHH----HHHHHHh-ccCCCCcEEEEecchHhHHHHHHHHHHC--------------------------------
Q psy11867        327 NID--EKF----EAVSNIY-GVVTIGQAMIFCHTRKTAAWLAEKMSKE--------------------------------  367 (399)
Q Consensus       327 ~~~--~k~----~~l~~ll-~~~~~~k~IIF~~s~~~a~~l~~~L~~~--------------------------------  367 (399)
                      ...  .+.    ..+...+ .....+++||||++++.|+.+|..|...                                
T Consensus      1131 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~ 1210 (1724)
T 4f92_B         1131 ISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKE 1210 (1724)
T ss_dssp             CCSHHHHHHTTHHHHHHHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHH
T ss_pred             CCCchhhhhhhcchHHHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHH
Confidence            211  111    1122222 3345579999999999999988776431                                


Q ss_pred             --CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        368 --GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       368 --g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                        ...++.+||||++.+|..+++.|++|.++|||
T Consensus      1211 ~l~~GIa~hHagL~~~~R~~VE~lF~~G~i~VLv 1244 (1724)
T 4f92_B         1211 TLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVV 1244 (1724)
T ss_dssp             HHHTTEEEECTTSCHHHHHHHHHHHHHTSBCEEE
T ss_pred             HHhCCEEEECCCCCHHHHHHHHHHHHCCCCeEEE
Confidence              23589999999999999999999999999986

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=100.00  E-value=8.7e-35  Score=302.78  Aligned_cols=172  Identities=16%  Similarity=0.067  Sum_probs=130.6

Q ss_pred             HHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC--CCCeEEEEeCcHHHHHHHHHH
Q psy11867        115 LKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI--QEPQVLCLAPTYELAIQIGEV  192 (399)
Q Consensus       115 ~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~--~~~~~lil~Pt~~La~Q~~~~  192 (399)
                      ...+..+||..|+++|.++++.+++  |+|+++++|||+|||++|++|+++.+....  .+.++|||+||++|+.|+.+.
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~--g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~   80 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMK--GKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSV   80 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHc--CCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHH
Confidence            3556789999999999999999998  699999999999999999999998875432  236899999999999999999


Q ss_pred             HHHHhccCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHH
Q psy11867        193 VAKMGKHITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSI  269 (399)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~  269 (399)
                      +++++... ++.+....|+......   .....+|+|+||++|.+++.......+.+++++||||||++.....+...+.
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 6777778887643221   1346799999999999987553333688999999999999864322333222


Q ss_pred             HHHHh-----CCCCCcEEEEEeeCC
Q psy11867        270 RIQKR-----LPSDCQIMLFSATYD  289 (399)
Q Consensus       270 ~i~~~-----l~~~~q~l~~SAT~~  289 (399)
                      .++..     .++..+++++|||..
T Consensus       160 ~~l~~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          160 NYLDQKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             HHHHHHHTTCCSCCCEEEEEESCCC
T ss_pred             HHHHHhhcccCCCCCeEEEEeCccc
Confidence            22221     246789999999986

>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=5.6e-34  Score=306.48  Aligned_cols=253  Identities=16%  Similarity=0.166  Sum_probs=202.1

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      +|| .|+++|.+++|.+++  |+|++++||||||||++|+++++..+.   .++++|||+||++||.|+++.+++++ . 
T Consensus        75 ~gf-~pt~iQ~~ai~~il~--g~dvlv~ApTGSGKTl~~l~~il~~~~---~~~~~Lil~PtreLa~Q~~~~l~~l~-~-  146 (1104)
T 4ddu_A           75 FGK-DLTGYQRLWAKRIVQ--GKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLERLQKLA-D-  146 (1104)
T ss_dssp             SSS-CCCHHHHHHHHHHTT--TCCEEECCSTTCCHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHHHHHTTS-C-
T ss_pred             cCC-CCCHHHHHHHHHHHc--CCCEEEEeCCCCcHHHHHHHHHHHHHh---cCCeEEEEechHHHHHHHHHHHHHhh-C-
Confidence            677 699999999999998  699999999999999999999888773   46789999999999999999999977 3 


Q ss_pred             CCcEEEEEEcCchh---hhh----hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh----------hcCC
Q psy11867        201 TDLSVRYAVRGENL---ERN----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI----------ATQG  263 (399)
Q Consensus       201 ~~~~~~~~~~~~~~---~~~----~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~----------~~~~  263 (399)
                      .++.+....|+...   ...    ....++|+|+||++|++++..   +.++++++|||||||++.          +..+
T Consensus       147 ~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~---l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~g  223 (1104)
T 4ddu_A          147 EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVG  223 (1104)
T ss_dssp             TTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH---HHTSCCSEEEESCHHHHTTSSHHHHHHHHTSS
T ss_pred             CCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh---hcccCcCEEEEeCCCccccccccchhhhHhcC
Confidence            37888888888765   111    133489999999999888642   667899999999997654          3136


Q ss_pred             chHH-HHHHHHhCC-----------CCCcEEEEEee-CChhHH-HHHHhhCCCCeEEecccccccccceeEEEEEeCChh
Q psy11867        264 HQDF-SIRIQKRLP-----------SDCQIMLFSAT-YDKEVM-EFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNID  329 (399)
Q Consensus       264 ~~~~-~~~i~~~l~-----------~~~q~l~~SAT-~~~~v~-~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~  329 (399)
                      |... +..+++.++           ...|+++|||| .+..+. .+....+.    +.+........++.+.++.+.   
T Consensus       224 f~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~~~~~i~~~~~~~~---  296 (1104)
T 4ddu_A          224 IPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISSR---  296 (1104)
T ss_dssp             CCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCCCCCCEEEEEESCC---
T ss_pred             CCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCCCcCCceeEEEecC---
Confidence            6666 778888776           78999999999 565544 23333332    444455566778888888773   


Q ss_pred             hHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEE-EEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        330 EKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVG-LLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       330 ~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~-~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                       +...+..++.. ..+++||||++++.|+.++..|...|+.+. .+||.     |.+ ++.|++|+++|||
T Consensus       297 -k~~~L~~ll~~-~~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~~VLV  359 (1104)
T 4ddu_A          297 -SKEKLVELLEI-FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKINILI  359 (1104)
T ss_dssp             -CHHHHHHHHHH-HCSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSCSEEE
T ss_pred             -HHHHHHHHHHh-cCCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCCCEEE
Confidence             44455666655 338999999999999999999999999998 99992     555 9999999999986

>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=2.3e-33  Score=311.68  Aligned_cols=273  Identities=18%  Similarity=0.217  Sum_probs=200.3

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC--------CCCCeEEEEeCcHHHHHHHHHH
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS--------IQEPQVLCLAPTYELAIQIGEV  192 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~--------~~~~~~lil~Pt~~La~Q~~~~  192 (399)
                      .||.+++++|++++|.++.. ++|++++||||||||++|.+|++..+...        ..+.++||++|+++||.|+++.
T Consensus        75 ~g~~~ln~iQs~~~~~al~~-~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~  153 (1724)
T 4f92_B           75 EGFKTLNRIQSKLYRAALET-DENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGS  153 (1724)
T ss_dssp             TTCSBCCHHHHHTHHHHHTC-CCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHcC-CCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHH
Confidence            38999999999999999976 89999999999999999999999988532        2466899999999999999999


Q ss_pred             HHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcccc-ccCCceeEEEEechhhHhhcCCchHHHH--
Q psy11867        193 VAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRF-FDLSKIKVFVLDEADVMIATQGHQDFSI--  269 (399)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~-~~~~~~~~lViDEah~l~~~~~~~~~~~--  269 (399)
                      +++....+ ++++...+|+..........++|+|+||+++..++.+... ..++++++|||||+|.+.+.  ....+.  
T Consensus       154 l~~~~~~~-gi~V~~~tGd~~~~~~~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d~--RG~~lE~~  230 (1724)
T 4f92_B          154 FGKRLATY-GITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDD--RGPVLEAL  230 (1724)
T ss_dssp             HHHHHTTT-TCCEEECCSSCSSCCTTGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGST--THHHHHHH
T ss_pred             HHHHHhhC-CCEEEEEECCCCCCccccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCCc--cHHHHHHH
Confidence            99887765 7888888888776655566789999999998665443322 24789999999999988653  222222  


Q ss_pred             --HH---HHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCe--EEecccccccccceeEEEEEeCCh--hhHHHH----HH
Q psy11867        270 --RI---QKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPL--IIKLKREEESLDNIKQHYVMCKNI--DEKFEA----VS  336 (399)
Q Consensus       270 --~i---~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~--~i~~~~~~~~~~~i~~~~~~~~~~--~~k~~~----l~  336 (399)
                        ++   ...+++..|+|++|||+++ ..++++..-.++.  .+.+..... +-.+.+.++.....  ......    +.
T Consensus       231 l~rl~~~~~~~~~~~riI~LSATl~N-~~dvA~wL~~~~~~~~~~~~~~~R-PvpL~~~~~~~~~~~~~~~~~~~~~~~~  308 (1724)
T 4f92_B          231 VARAIRNIEMTQEDVRLIGLSATLPN-YEDVATFLRVDPAKGLFYFDNSFR-PVPLEQTYVGITEKKAIKRFQIMNEIVY  308 (1724)
T ss_dssp             HHHHHHHHHHHTCCCEEEEEECSCTT-HHHHHHHTTCCHHHHEEECCGGGC-SSCEEEECCEECCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCcEEEEecccCC-HHHHHHHhCCCCCCCeEEECCCCc-cCccEEEEeccCCcchhhhhHHHHHHHH
Confidence              22   2345778999999999986 3555554433321  122222222 22345555444322  122222    22


Q ss_pred             HHh-ccCCCCcEEEEecchHhHHHHHHHHHHC-------------------------------------CCeEEEEcCCC
Q psy11867        337 NIY-GVVTIGQAMIFCHTRKTAAWLAEKMSKE-------------------------------------GLNVGLLSGEL  378 (399)
Q Consensus       337 ~ll-~~~~~~k~IIF~~s~~~a~~l~~~L~~~-------------------------------------g~~v~~lhg~~  378 (399)
                      ..+ .....+++||||+||+.|+.+|+.|.+.                                     ...++++||||
T Consensus       309 ~~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL  388 (1724)
T 4f92_B          309 EKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGM  388 (1724)
T ss_dssp             HHHTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSS
T ss_pred             HHHHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCC
Confidence            223 2334578999999999999998887541                                     23489999999


Q ss_pred             CHHHHHHHHHHHhcCCCcccC
Q psy11867        379 TVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       379 ~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++.+|..+++.|++|.++|||
T Consensus       389 ~~~~R~~vE~~F~~G~i~vlv  409 (1724)
T 4f92_B          389 TRVDRTLVEDLFADKHIQVLV  409 (1724)
T ss_dssp             CTHHHHHHHHHHHTTCCCEEE
T ss_pred             CHHHHHHHHHHHHCCCCeEEE
Confidence            999999999999999999986

>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=1.9e-33  Score=284.93  Aligned_cols=166  Identities=16%  Similarity=0.080  Sum_probs=123.8

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCC--CCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQ--EPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~--~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      ++...|+|+|.++++.++.  |+|+++++|||+|||++|++|++..+.....  ++++|||+||++|+.|+++.++++..
T Consensus         3 ~~~~~~~~~Q~~~i~~~~~--~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~   80 (556)
T 4a2p_A            3 METKKARSYQIELAQPAIN--GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFE   80 (556)
T ss_dssp             -----CCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             CCCCCCCHHHHHHHHHHHc--CCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            4567899999999999998  6999999999999999999999998865432  67899999999999999999999987


Q ss_pred             cCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHh-
Q psy11867        199 HITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR-  274 (399)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~-  274 (399)
                      .. ++.+....|+......   ....++|+|+||++|.+++.......+.+++++|+||||++.+...+...+..+... 
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 6777777777644322   234578999999999998655333378999999999999997643222222222222 


Q ss_pred             ---CCCCCcEEEEEeeCC
Q psy11867        275 ---LPSDCQIMLFSATYD  289 (399)
Q Consensus       275 ---l~~~~q~l~~SAT~~  289 (399)
                         ..+..|+++||||++
T Consensus       160 ~~~~~~~~~~l~lSAT~~  177 (556)
T 4a2p_A          160 FNSASQLPQILGLTASVG  177 (556)
T ss_dssp             HCC---CCEEEEEESCCC
T ss_pred             hcccCCCCeEEEEeCCcc
Confidence               135689999999984

>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=9.1e-33  Score=294.78  Aligned_cols=261  Identities=15%  Similarity=0.141  Sum_probs=197.4

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      ..+|. |+++|.++++.+++  |++++++||||||||++|.++++..+..   +.++||++||++|+.|+++.+++++. 
T Consensus        82 ~~~f~-L~~~Q~eai~~l~~--g~~vLV~apTGSGKTlva~lai~~~l~~---g~rvL~l~PtkaLa~Q~~~~l~~~~~-  154 (1010)
T 2xgj_A           82 TYPFT-LDPFQDTAISCIDR--GESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKALSNQKYRELLAEFG-  154 (1010)
T ss_dssp             CCSSC-CCHHHHHHHHHHHH--TCEEEEECCTTSCHHHHHHHHHHHHHHT---TCEEEEEESSHHHHHHHHHHHHHHHS-
T ss_pred             hCCCC-CCHHHHHHHHHHHc--CCCEEEECCCCCChHHHHHHHHHHHhcc---CCeEEEECChHHHHHHHHHHHHHHhC-
Confidence            35664 99999999999998  6999999999999999999999988753   46899999999999999999998764 


Q ss_pred             CCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCC
Q psy11867        200 ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC  279 (399)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~  279 (399)
                          .+....|+....    ...+|+|+||++|.+++.+ ....++++++|||||||++.+. ++...+..++..++...
T Consensus       155 ----~vglltGd~~~~----~~~~IvV~Tpe~L~~~L~~-~~~~l~~l~lVViDEaH~l~d~-~rg~~~e~il~~l~~~~  224 (1010)
T 2xgj_A          155 ----DVGLMTGDITIN----PDAGCLVMTTEILRSMLYR-GSEVMREVAWVIFDEVHYMRDK-ERGVVWEETIILLPDKV  224 (1010)
T ss_dssp             ----CEEEECSSCEEC----TTCSEEEEEHHHHHHHHHH-TCTTGGGEEEEEEETGGGGGCT-TTHHHHHHHHHHSCTTC
T ss_pred             ----CEEEEeCCCccC----CCCCEEEEcHHHHHHHHHc-CcchhhcCCEEEEechhhhccc-chhHHHHHHHHhcCCCC
Confidence                345566665443    2468999999999988654 4456889999999999999864 56666778888899999


Q ss_pred             cEEEEEeeCChhH--HHHHHhhCCCCeEEecccccccccceeEEEEEeC---------Ch--------------------
Q psy11867        280 QIMLFSATYDKEV--MEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCK---------NI--------------------  328 (399)
Q Consensus       280 q~l~~SAT~~~~v--~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~---------~~--------------------  328 (399)
                      |+++||||+++..  ..++......+..+......  +..+.+++....         ..                    
T Consensus       225 ~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~r--p~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  302 (1010)
T 2xgj_A          225 RYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR--PTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIG  302 (1010)
T ss_dssp             EEEEEECCCTTHHHHHHHHHHHHTSCEEEEEECCC--SSCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC----
T ss_pred             eEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCC--cccceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhhhc
Confidence            9999999998753  23333334455544333221  122333332211         00                    


Q ss_pred             -------------------------hhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCC--------------
Q psy11867        329 -------------------------DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGL--------------  369 (399)
Q Consensus       329 -------------------------~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~--------------  369 (399)
                                               ......+...+......++||||++++.|+.++..|...++              
T Consensus       303 ~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~  382 (1010)
T 2xgj_A          303 DDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFN  382 (1010)
T ss_dssp             --------------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHH
Confidence                                     11122344444444556999999999999999999977543              


Q ss_pred             -------------------------eEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        370 -------------------------NVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       370 -------------------------~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                                               .++.+||+|++.+|..+++.|++|.++|||
T Consensus       383 ~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLV  437 (1010)
T 2xgj_A          383 NAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLF  437 (1010)
T ss_dssp             HHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEE
T ss_pred             HHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEE
Confidence                                     288999999999999999999999999986

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=100.00  E-value=6.5e-33  Score=280.67  Aligned_cols=164  Identities=16%  Similarity=0.086  Sum_probs=130.3

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC--CCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI--QEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~--~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      ..|+++|.++++.++.  |+|+++++|||+|||++|++|++..+....  .++++|||+||++|+.|+++.++++.... 
T Consensus         3 ~~~~~~Q~~~i~~~~~--~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-   79 (555)
T 3tbk_A            3 LKPRNYQLELALPAKK--GKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERL-   79 (555)
T ss_dssp             CCCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTT-
T ss_pred             CCCcHHHHHHHHHHhC--CCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccC-
Confidence            4799999999999998  699999999999999999999999886543  26789999999999999999999998765 


Q ss_pred             CcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC---
Q psy11867        202 DLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL---  275 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l---  275 (399)
                      ++.+....|+......   ....++|+|+||++|.+++.......+.+++++|+||||++.+...+...+..++...   
T Consensus        80 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~  159 (555)
T 3tbk_A           80 GYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGE  159 (555)
T ss_dssp             TCCEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTSS
T ss_pred             CcEEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhcc
Confidence            6778888888754332   2345789999999999986554333788999999999999976433333333333321   


Q ss_pred             --CCCCcEEEEEeeCCh
Q psy11867        276 --PSDCQIMLFSATYDK  290 (399)
Q Consensus       276 --~~~~q~l~~SAT~~~  290 (399)
                        .+..|++++|||++.
T Consensus       160 ~~~~~~~~l~lSAT~~~  176 (555)
T 3tbk_A          160 SRDPLPQVVGLTASVGV  176 (555)
T ss_dssp             CCSCCCEEEEEESCCCC
T ss_pred             ccCCCCeEEEEecCccc
Confidence              256799999999853

>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=2.5e-34  Score=309.14  Aligned_cols=252  Identities=18%  Similarity=0.224  Sum_probs=201.8

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      .+||. | ++|.+++|.+++  |+|++++||||||||+ |++|++..+..  .++++|||+||++||.|+++.+++++..
T Consensus        53 ~~g~~-p-~iQ~~ai~~il~--g~dvlv~apTGSGKTl-~~lp~l~~~~~--~~~~~lil~PtreLa~Q~~~~l~~l~~~  125 (1054)
T 1gku_B           53 CVGEP-R-AIQKMWAKRILR--KESFAATAPTGVGKTS-FGLAMSLFLAL--KGKRCYVIFPTSLLVIQAAETIRKYAEK  125 (1054)
T ss_dssp             TTCSC-C-HHHHHHHHHHHT--TCCEECCCCBTSCSHH-HHHHHHHHHHT--TSCCEEEEESCHHHHHHHHHHHHHHHTT
T ss_pred             hcCCC-H-HHHHHHHHHHHh--CCCEEEEcCCCCCHHH-HHHHHHHHHhh--cCCeEEEEeccHHHHHHHHHHHHHHHhh
Confidence            47999 9 999999999998  7999999999999998 88899887754  4678999999999999999999999877


Q ss_pred             CCCc----EEEEEEcCchhhhh-----hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHH
Q psy11867        200 ITDL----SVRYAVRGENLERN-----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIR  270 (399)
Q Consensus       200 ~~~~----~~~~~~~~~~~~~~-----~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~  270 (399)
                      . ++    .+....|+......     ....++|+|+||++|++++.+     ++++++|||||||+|++   +...+..
T Consensus       126 ~-~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~~~IlV~TP~~L~~~l~~-----L~~l~~lViDEah~~l~---~~~~~~~  196 (1054)
T 1gku_B          126 A-GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRE-----LGHFDFIFVDDVDAILK---ASKNVDK  196 (1054)
T ss_dssp             T-CCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCSTT-----SCCCSEEEESCHHHHHT---STHHHHH
T ss_pred             c-CCCccceEEEEeCCCChhhHHHHHhhccCCCEEEEcHHHHHHHHHH-----hccCCEEEEeChhhhhh---ccccHHH
Confidence            5 55    77788887655331     112289999999999997643     66899999999999986   4455666


Q ss_pred             HHHhC-----------CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHh
Q psy11867        271 IQKRL-----------PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIY  339 (399)
Q Consensus       271 i~~~l-----------~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll  339 (399)
                      +...+           +...|+++||||++.. ..+...++.++..+.+........++.+.++.    ..+...+..++
T Consensus       197 i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~~----~~k~~~L~~ll  271 (1054)
T 1gku_B          197 LLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSSRITVRNVEDVAVN----DESISTLSSIL  271 (1054)
T ss_dssp             HHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCCEECCCCEEEEEES----CCCTTTTHHHH
T ss_pred             HHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCcccCcCCceEEEec----hhHHHHHHHHH
Confidence            66655           3578999999999877 54444444444445555555566778777762    34556677777


Q ss_pred             ccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        340 GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       340 ~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ... .+++||||++++.|+.+++.|... +++..+||+|     ..+++.|++|+++|||
T Consensus       272 ~~~-~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~-----~~~l~~F~~G~~~VLV  324 (1054)
T 1gku_B          272 EKL-GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATK-----KGDYEKFVEGEIDHLI  324 (1054)
T ss_dssp             TTS-CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSS-----SHHHHHHHHTSCSEEE
T ss_pred             hhc-CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccH-----HHHHHHHHcCCCcEEE
Confidence            665 478999999999999999999888 9999999998     4789999999999986

>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=1.3e-33  Score=288.14  Aligned_cols=266  Identities=16%  Similarity=0.190  Sum_probs=198.9

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      .+|| .||++|..++|.++.  |+  |++++||+|||++|.+|++.....   +..++||+||++||.|.++++..++.+
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~--G~--Iaea~TGeGKTlaf~LP~~l~aL~---g~~vlVltptreLA~qd~e~~~~l~~~  150 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHD--GN--IAEMKTGEGKTLTSTLPVYLNALT---GKGVHVVTVNEYLASRDAEQMGKIFEF  150 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHT--TS--EEECCTTSCHHHHHHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             HcCC-CCcHHHHHhhHHHhC--CC--EEEccCCcHHHHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHHhh
Confidence            4799 999999999999998  56  999999999999999999854432   457999999999999999999999988


Q ss_pred             CCCcEEEEEEcCchhhhhh-ccCCcEEEeCchhH-HHhhhcc-----ccccCCceeEEEEechhhHh-hcC---------
Q psy11867        200 ITDLSVRYAVRGENLERNK-KITEQIIIGTPGKV-LDWGLKY-----RFFDLSKIKVFVLDEADVMI-ATQ---------  262 (399)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~~-~~~~~IlV~Tp~~l-~~~~~~~-----~~~~~~~~~~lViDEah~l~-~~~---------  262 (399)
                      + ++++.+.+||.+..... ...++|+||||++| .+++...     +.+.++.+.++|+||||+|+ +..         
T Consensus       151 l-gl~v~~i~gg~~~~~r~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~  229 (844)
T 1tf5_A          151 L-GLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQ  229 (844)
T ss_dssp             T-TCCEEECCTTSCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEE
T ss_pred             c-CCeEEEEeCCCCHHHHHHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCC
Confidence            7 89999999987654332 45689999999999 5554332     34568899999999999998 431         


Q ss_pred             -----CchHHHHHHHHhCC---------CCCcEE-----------------EEEeeCCh---hHHHHH--HhhCC-C--C
Q psy11867        263 -----GHQDFSIRIQKRLP---------SDCQIM-----------------LFSATYDK---EVMEFA--QDMVP-N--P  303 (399)
Q Consensus       263 -----~~~~~~~~i~~~l~---------~~~q~l-----------------~~SAT~~~---~v~~~~--~~~~~-~--p  303 (399)
                           ++...+..+...++         +.+|++                 +||||++.   .+...+  ..++. +  +
T Consensus       230 ~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~~al~A~~l~~~d~dY  309 (844)
T 1tf5_A          230 AAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDY  309 (844)
T ss_dssp             EECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHHHHHHHHHTCCBTTTE
T ss_pred             cccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHHHHHHHHHHhhcCCce
Confidence                 25567788888887         367887                 99999874   343332  22221 1  1


Q ss_pred             eE----------------------------------Eeccccccccccee------------------------------
Q psy11867        304 LI----------------------------------IKLKREEESLDNIK------------------------------  319 (399)
Q Consensus       304 ~~----------------------------------i~~~~~~~~~~~i~------------------------------  319 (399)
                      +.                                  +.+.....+...+.                              
T Consensus       310 iv~dg~v~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmTGTa~te~~e~~~iY~  389 (844)
T 1tf5_A          310 VVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYN  389 (844)
T ss_dssp             EEETTEEEEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEESCCGGGHHHHHHHHC
T ss_pred             EEecCeeEEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCCcccchhHHHHHHHhC
Confidence            10                                  00111111111111                              


Q ss_pred             ----------------EEEEEeCChhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHH
Q psy11867        320 ----------------QHYVMCKNIDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVE  381 (399)
Q Consensus       320 ----------------~~~~~~~~~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~  381 (399)
                                      +....+.....|+..+...+...  ...++||||+|++.++.|+..|...|+++.++||++.+.
T Consensus       390 l~vv~IPtn~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~r  469 (844)
T 1tf5_A          390 MQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHER  469 (844)
T ss_dssp             CCEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHH
T ss_pred             CceEEecCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHH
Confidence                            11122235577888888877542  346899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCC
Q psy11867        382 QRLSILDRFREGE  394 (399)
Q Consensus       382 ~R~~v~~~F~~G~  394 (399)
                      +|..+.+.|+.|.
T Consensus       470 Er~ii~~ag~~g~  482 (844)
T 1tf5_A          470 EAQIIEEAGQKGA  482 (844)
T ss_dssp             HHHHHTTTTSTTC
T ss_pred             HHHHHHHcCCCCe
Confidence            9987877887774

>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=7e-33  Score=292.02  Aligned_cols=167  Identities=16%  Similarity=0.070  Sum_probs=127.3

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC--CCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI--QEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~--~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      .+|+..|+++|.++++.++.  |+|+++++|||+|||++|++|++..+....  .++++|||+||++|+.|+++.+++++
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~--~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~  320 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAIN--GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHF  320 (797)
T ss_dssp             -----CCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             hcCCCCCCHHHHHHHHHHHh--CCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhc
Confidence            36889999999999999998  699999999999999999999999886542  26789999999999999999999998


Q ss_pred             ccCCCcEEEEEEcCchhhh---hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHh
Q psy11867        198 KHITDLSVRYAVRGENLER---NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR  274 (399)
Q Consensus       198 ~~~~~~~~~~~~~~~~~~~---~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~  274 (399)
                      ... ++.+....|+.....   .....++|+|+||++|.+++.......+.++++|||||||++.....+...+..+...
T Consensus       321 ~~~-~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~~~  399 (797)
T 4a2q_A          321 ERQ-GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQ  399 (797)
T ss_dssp             GGG-TCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHHHH
T ss_pred             ccC-CceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHHHHHHH
Confidence            765 678888888774432   2245689999999999998754333378899999999999987643333333233322


Q ss_pred             ----CCCCCcEEEEEeeCC
Q psy11867        275 ----LPSDCQIMLFSATYD  289 (399)
Q Consensus       275 ----l~~~~q~l~~SAT~~  289 (399)
                          ..+..|++++|||..
T Consensus       400 ~~~~~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          400 KFNSASQLPQILGLTASVG  418 (797)
T ss_dssp             HHTTCCCCCEEEEEESCCC
T ss_pred             hhccCCCCCeEEEEcCCcc
Confidence                145689999999984

>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=1e-32  Score=280.86  Aligned_cols=265  Identities=15%  Similarity=0.130  Sum_probs=178.0

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      +|. .|+++|..++|.++.  |+  |++++||||||++|++|++.....   +.+++||+||++||.|+++++..++.++
T Consensus        71 lg~-~p~~VQ~~~i~~ll~--G~--Iaem~TGsGKTlaf~LP~l~~~l~---g~~vlVltPTreLA~Q~~e~~~~l~~~l  142 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNE--RC--IAEMRTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAENNRPLFEFL  142 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHS--SE--EEECCTTSCHHHHHHHHHHHHHTT---SSCCEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             cCC-CCChHHHhhcccccC--Ce--eeeecCCchHHHHHHHHHHHHHHc---CCcEEEEcCCHHHHHHHHHHHHHHHHhc
Confidence            564 899999999999998  45  999999999999999999865443   4579999999999999999999999887


Q ss_pred             CCcEEEEEEcCchhhhh-hccCCcEEEeCchhH-HHhhhccc-----cccCCceeEEEEechhhHhhcCC----------
Q psy11867        201 TDLSVRYAVRGENLERN-KKITEQIIIGTPGKV-LDWGLKYR-----FFDLSKIKVFVLDEADVMIATQG----------  263 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~~~-~~~~~~IlV~Tp~~l-~~~~~~~~-----~~~~~~~~~lViDEah~l~~~~~----------  263 (399)
                       ++++.+.+||...... ....++|+||||++| .+++...-     ...+++++++|+||||+|+...+          
T Consensus       143 -gl~v~~i~GG~~~~~r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~  221 (853)
T 2fsf_A          143 -GLTVGINLPGMPAPAKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIISGPA  221 (853)
T ss_dssp             -TCCEEECCTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEEEC-
T ss_pred             -CCeEEEEeCCCCHHHHHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccccccCCC
Confidence             7899999998765432 244689999999999 67765432     35678999999999999983222          


Q ss_pred             -----chHHHHHHHHhCCC--------------------CCcEE------------------------EEEeeCCh---h
Q psy11867        264 -----HQDFSIRIQKRLPS--------------------DCQIM------------------------LFSATYDK---E  291 (399)
Q Consensus       264 -----~~~~~~~i~~~l~~--------------------~~q~l------------------------~~SAT~~~---~  291 (399)
                           +...+..+...++.                    .+|++                        +||||.+.   .
T Consensus       222 ~~~~~~y~~i~~iv~~L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~~~~~Lfsat~~~~~~~  301 (853)
T 2fsf_A          222 EDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMDEGESLYSPANIMLMHH  301 (853)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccchhHHHHHHHHHHhchhhhccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCcccccccccCcccchHHHH
Confidence                 44556677777764                    45654                        89999764   2


Q ss_pred             HHHHH--------------------------HhhCC---------C----CeEEecccccccccceeE------------
Q psy11867        292 VMEFA--------------------------QDMVP---------N----PLIIKLKREEESLDNIKQ------------  320 (399)
Q Consensus       292 v~~~~--------------------------~~~~~---------~----p~~i~~~~~~~~~~~i~~------------  320 (399)
                      +...+                          ..++.         .    +..+.+..+..+...|.+            
T Consensus       302 i~~al~A~~l~~~d~dYiV~d~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e~~tla~It~qnyfr~Y~kl~G  381 (853)
T 2fsf_A          302 VTAALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLYEKLAG  381 (853)
T ss_dssp             -------------------------------------------------------CCCCCEEEEEEEHHHHHTTSSEEEE
T ss_pred             HHHHHHHHHHhhcCccceeecCcEEEEecccCcccCCCccchhhhHHHHhcccceecccccccceeehHHHHhhhhhhhc
Confidence            22111                          11111         0    122333333333333432            


Q ss_pred             ----------------------------------EEEEeCChhhHHHHHHHHhcc--CCCCcEEEEecchHhHHHHHHHH
Q psy11867        321 ----------------------------------HYVMCKNIDEKFEAVSNIYGV--VTIGQAMIFCHTRKTAAWLAEKM  364 (399)
Q Consensus       321 ----------------------------------~~~~~~~~~~k~~~l~~ll~~--~~~~k~IIF~~s~~~a~~l~~~L  364 (399)
                                                        ..+.+.....|+.++...+..  ....++||||+|++.++.|+..|
T Consensus       382 mTGTa~te~~ef~~iY~l~vv~IPtn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L  461 (853)
T 2fsf_A          382 MTGTADTEAFEFSSIYKLDTVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNEL  461 (853)
T ss_dssp             EECTTCCCHHHHHHHHCCEEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHH
T ss_pred             CCCCchhHHHHHHHHhCCcEEEcCCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHH
Confidence                                              112234567899999888754  24468999999999999999999


Q ss_pred             HHCCCeEEEEcCCCCHHHHHHHHHHHhcCC
Q psy11867        365 SKEGLNVGLLSGELTVEQRLSILDRFREGE  394 (399)
Q Consensus       365 ~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~  394 (399)
                      .+.|+++.++||++.+.+|..+.+.|+.|.
T Consensus       462 ~~~gi~~~vLnak~~~rEa~iia~agr~G~  491 (853)
T 2fsf_A          462 TKAGIKHNVLNAKFHANEAAIVAQAGYPAA  491 (853)
T ss_dssp             HHTTCCCEECCTTCHHHHHHHHHTTTSTTC
T ss_pred             HHCCCCEEEecCChhHHHHHHHHhcCCCCe
Confidence            999999999999999999999999999995

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.98  E-value=6.9e-32  Score=287.81  Aligned_cols=166  Identities=16%  Similarity=0.071  Sum_probs=126.7

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCC--CCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQ--EPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~--~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      .|+..|+++|.++++.++.  |+|+++++|||+|||++|++|++..+.....  +.++|||+||++|+.|+++.++++..
T Consensus       244 ~~~~~~r~~Q~~ai~~il~--g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~  321 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAIN--GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFE  321 (936)
T ss_dssp             ----CCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHc--CCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            5788999999999999998  6999999999999999999999998876432  67899999999999999999999987


Q ss_pred             cCCCcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHh-
Q psy11867        199 HITDLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR-  274 (399)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~-  274 (399)
                      .. ++.+....|+......   .....+|+|+||++|.+++.......+.+++++||||||++.....+...+..+... 
T Consensus       322 ~~-~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~~~~  400 (936)
T 4a2w_A          322 RQ-GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQK  400 (936)
T ss_dssp             TT-TCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHH
T ss_pred             cc-CceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHHHHHHHh
Confidence            65 6778888887644322   234678999999999998765433378899999999999987543233333233322 


Q ss_pred             ---CCCCCcEEEEEeeCC
Q psy11867        275 ---LPSDCQIMLFSATYD  289 (399)
Q Consensus       275 ---l~~~~q~l~~SAT~~  289 (399)
                         ..+..|+++||||..
T Consensus       401 ~~~~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          401 FNSASQLPQILGLTASVG  418 (936)
T ss_dssp             HTTCSCCCEEEEEESCCC
T ss_pred             hccCCCcCeEEEecCCcc
Confidence               145689999999984

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.98  E-value=1.5e-31  Score=285.33  Aligned_cols=263  Identities=15%  Similarity=0.155  Sum_probs=197.3

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      ++| .|+++|.++++.+++  |+|+++++|||||||++|++++...+.   .+.++||++|+++|+.|+++.+++++.  
T Consensus        36 ~~f-~l~~~Q~~aI~~il~--g~~vlv~apTGsGKTlv~~~~i~~~~~---~g~~vlvl~PtraLa~Q~~~~l~~~~~--  107 (997)
T 4a4z_A           36 WPF-ELDTFQKEAVYHLEQ--GDSVFVAAHTSAGKTVVAEYAIAMAHR---NMTKTIYTSPIKALSNQKFRDFKETFD--  107 (997)
T ss_dssp             CSS-CCCHHHHHHHHHHHT--TCEEEEECCTTSCSHHHHHHHHHHHHH---TTCEEEEEESCGGGHHHHHHHHHTTC---
T ss_pred             CCC-CCCHHHHHHHHHHHc--CCCEEEEECCCCcHHHHHHHHHHHHHh---cCCeEEEEeCCHHHHHHHHHHHHHHcC--
Confidence            455 589999999999998  699999999999999999999987764   356899999999999999999988643  


Q ss_pred             CCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCc
Q psy11867        201 TDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ  280 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q  280 (399)
                       ++.+....|+....    ...+|+|+||++|.+++.. ....+.++++|||||||++.+. ++...+..++..+++..|
T Consensus       108 -~~~v~~l~G~~~~~----~~~~IlV~Tpe~L~~~l~~-~~~~l~~l~lvViDEaH~l~d~-~~g~~~e~ii~~l~~~v~  180 (997)
T 4a4z_A          108 -DVNIGLITGDVQIN----PDANCLIMTTEILRSMLYR-GADLIRDVEFVIFDEVHYVNDQ-DRGVVWEEVIIMLPQHVK  180 (997)
T ss_dssp             --CCEEEECSSCEEC----TTSSEEEEEHHHHHHHHHH-TCSGGGGEEEEEECCTTCCCTT-CTTCCHHHHHHHSCTTCE
T ss_pred             -CCeEEEEeCCCccC----CCCCEEEECHHHHHHHHHh-CchhhcCCCEEEEECccccccc-chHHHHHHHHHhcccCCC
Confidence             45667777766433    3468999999999988654 3446789999999999998764 566667788889999999


Q ss_pred             EEEEEeeCChhHHHHHHhhC---CC------------CeEEecccccccc------------------------------
Q psy11867        281 IMLFSATYDKEVMEFAQDMV---PN------------PLIIKLKREEESL------------------------------  315 (399)
Q Consensus       281 ~l~~SAT~~~~v~~~~~~~~---~~------------p~~i~~~~~~~~~------------------------------  315 (399)
                      ++++|||+++.. .+...+.   ..            |....+.......                              
T Consensus       181 iIlLSAT~~n~~-ef~~~l~~~~~~~~~vi~~~~r~~pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  259 (997)
T 4a4z_A          181 FILLSATVPNTY-EFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGAP  259 (997)
T ss_dssp             EEEEECCCTTHH-HHHHHHHHHHTCCEEEEECSSCSSCEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHHC--------
T ss_pred             EEEEcCCCCChH-HHHHHHhcccCCceEEEecCCCCccceEEEecCCcchhcccchhhhhHHHHHHHHHHhhcccccccc
Confidence            999999998653 3333221   11            2221111000000                              


Q ss_pred             ------------------------------------------------cceeEEEEEeCChhhHHHHHHHHhccCCCCcE
Q psy11867        316 ------------------------------------------------DNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQA  347 (399)
Q Consensus       316 ------------------------------------------------~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~  347 (399)
                                                                      .+..+++........+...+...+......++
T Consensus       260 ~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~l~~~~~~~~  339 (997)
T 4a4z_A          260 SKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKRELLPM  339 (997)
T ss_dssp             ---------------------------------------------------------CCCCTTHHHHHHHHHHHTTCCSE
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhHHHHHHHHHHhCCCCCE
Confidence                                                            00000111111223456677777877777899


Q ss_pred             EEEecchHhHHHHHHHHHHCCC---------------------------------------eEEEEcCCCCHHHHHHHHH
Q psy11867        348 MIFCHTRKTAAWLAEKMSKEGL---------------------------------------NVGLLSGELTVEQRLSILD  388 (399)
Q Consensus       348 IIF~~s~~~a~~l~~~L~~~g~---------------------------------------~v~~lhg~~~~~~R~~v~~  388 (399)
                      ||||++++.|+.++..|...|+                                       .+..+||+|++.+|..+++
T Consensus       340 IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl~~~~R~~v~~  419 (997)
T 4a4z_A          340 VVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEI  419 (997)
T ss_dssp             EEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHH
T ss_pred             EEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeecCCCCHHHHHHHHH
Confidence            9999999999999999977655                                       5899999999999999999


Q ss_pred             HHhcCCCcccC
Q psy11867        389 RFREGEFKIYS  399 (399)
Q Consensus       389 ~F~~G~~~ILV  399 (399)
                      .|++|.++|||
T Consensus       420 ~F~~G~~kVLv  430 (997)
T 4a4z_A          420 LFSKGFIKVLF  430 (997)
T ss_dssp             HHHTTCCSEEE
T ss_pred             HHHCCCCcEEE
Confidence            99999999986

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.97  E-value=7.6e-32  Score=274.90  Aligned_cols=266  Identities=15%  Similarity=0.161  Sum_probs=201.6

Q ss_pred             HcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        120 EMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      .+|+ +|+++|..++|.++.  |+  |++++||+|||++|.+|++.....   +..++||+||++||.|.++++..++.+
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~--G~--Iaem~TGeGKTLa~~LP~~l~aL~---g~~v~VvTpTreLA~Qdae~m~~l~~~  178 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHL--GN--VAEMKTGEGKTLTCVLPAYLNALA---GNGVHIVTVNDYLAKRDSEWMGRVHRF  178 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHT--TE--EEECCTTSCHHHHTHHHHHHHHTT---TSCEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             HcCC-CCCHHHHHHHHhHhc--CC--EEEecCCCccHHHHHHHHHHHHHh---CCCeEEEeCCHHHHHHHHHHHHHHHhh
Confidence            3788 999999999999998  45  999999999999999999754433   346999999999999999999999988


Q ss_pred             CCCcEEEEEEcCchhhhh-hccCCcEEEeCchhH-HHhhhcc-----ccccCCceeEEEEechhhHhhcC----------
Q psy11867        200 ITDLSVRYAVRGENLERN-KKITEQIIIGTPGKV-LDWGLKY-----RFFDLSKIKVFVLDEADVMIATQ----------  262 (399)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~-~~~~~~IlV~Tp~~l-~~~~~~~-----~~~~~~~~~~lViDEah~l~~~~----------  262 (399)
                      + ++++.+.+||...... ....++|+||||++| .+++...     +.+.++.+.++||||||+|+...          
T Consensus       179 l-GLsv~~i~gg~~~~~r~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~  257 (922)
T 1nkt_A          179 L-GLQVGVILATMTPDERRVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGP  257 (922)
T ss_dssp             T-TCCEEECCTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEE
T ss_pred             c-CCeEEEEeCCCCHHHHHHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCC
Confidence            7 8999999998765332 245689999999999 6776543     24568899999999999998321          


Q ss_pred             -----CchHHHHHHHHhCC---------CCCcEE-----------------EEEeeCCh---hHHHHHH--hhCC-----
Q psy11867        263 -----GHQDFSIRIQKRLP---------SDCQIM-----------------LFSATYDK---EVMEFAQ--DMVP-----  301 (399)
Q Consensus       263 -----~~~~~~~~i~~~l~---------~~~q~l-----------------~~SAT~~~---~v~~~~~--~~~~-----  301 (399)
                           ++...+..+...++         +.+|++                 +||||.+.   .+...++  .++.     
T Consensus       258 ~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l~~~d~dY  337 (922)
T 1nkt_A          258 ADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSRDKDY  337 (922)
T ss_dssp             CCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHHCCBTTTE
T ss_pred             CCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHHhhcccce
Confidence                 35677888999997         678888                 99999875   3333221  1221     


Q ss_pred             ---CCeEEecc-----------------------------cccccccceeE-----------------------------
Q psy11867        302 ---NPLIIKLK-----------------------------REEESLDNIKQ-----------------------------  320 (399)
Q Consensus       302 ---~p~~i~~~-----------------------------~~~~~~~~i~~-----------------------------  320 (399)
                         ++..+.++                             .+..+...|.+                             
T Consensus       338 iV~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~Ef~~iY~  417 (922)
T 1nkt_A          338 IVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELHEIYK  417 (922)
T ss_dssp             EECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHHHHHHHHC
T ss_pred             eeecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHHHHHHHhC
Confidence               11111111                             11112222221                             


Q ss_pred             -----------------EEEEeCChhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHH
Q psy11867        321 -----------------HYVMCKNIDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVE  381 (399)
Q Consensus       321 -----------------~~~~~~~~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~  381 (399)
                                       ....+.....|+..+...+...  ...++||||+|++.++.|+..|.+.|+++.++||++.+.
T Consensus       418 l~vv~IPtn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~r  497 (922)
T 1nkt_A          418 LGVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQ  497 (922)
T ss_dssp             CEEEECCCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHH
T ss_pred             CCeEEeCCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHH
Confidence                             1122335577898888877543  345899999999999999999999999999999999988


Q ss_pred             HHHHHHHHHhcCC
Q psy11867        382 QRLSILDRFREGE  394 (399)
Q Consensus       382 ~R~~v~~~F~~G~  394 (399)
                      +|..+.+.|+.|.
T Consensus       498 Ea~iia~agr~G~  510 (922)
T 1nkt_A          498 EATIIAVAGRRGG  510 (922)
T ss_dssp             HHHHHHTTTSTTC
T ss_pred             HHHHHHhcCCCCe
Confidence            8888889999885

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.97  E-value=1.5e-30  Score=258.17  Aligned_cols=267  Identities=20%  Similarity=0.256  Sum_probs=193.4

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|+|+|.++++.++.  + ++++++|||+|||++++++++..+.  ..+.++|||+|+++|+.|+.+.++++... +...
T Consensus         9 ~l~~~Q~~~i~~~~~--~-~~ll~~~tG~GKT~~~~~~~~~~~~--~~~~~~liv~P~~~L~~q~~~~~~~~~~~-~~~~   82 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKE--T-NCLIVLPTGLGKTLIAMMIAEYRLT--KYGGKVLMLAPTKPLVLQHAESFRRLFNL-PPEK   82 (494)
T ss_dssp             CCCHHHHHHHHHGGG--S-CEEEECCTTSCHHHHHHHHHHHHHH--HSCSCEEEECSSHHHHHHHHHHHHHHBCS-CGGG
T ss_pred             CccHHHHHHHHHHhh--C-CEEEEcCCCCCHHHHHHHHHHHHHh--cCCCeEEEEECCHHHHHHHHHHHHHHhCc-chhh
Confidence            799999999999998  5 9999999999999999999988775  24567999999999999999999998632 2456


Q ss_pred             EEEEEcCchhhhhh--ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEE
Q psy11867        205 VRYAVRGENLERNK--KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM  282 (399)
Q Consensus       205 ~~~~~~~~~~~~~~--~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l  282 (399)
                      +....|+.......  ....+|+|+||++|...+.. +.+.+.+++++|+||||++... .....+........+..+++
T Consensus        83 v~~~~g~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~-~~~~~~~~~~vIiDEaH~~~~~-~~~~~~~~~~~~~~~~~~~l  160 (494)
T 1wp9_A           83 IVALTGEKSPEERSKAWARAKVIVATPQTIENDLLA-GRISLEDVSLIVFDEAHRAVGN-YAYVFIAREYKRQAKNPLVI  160 (494)
T ss_dssp             EEEECSCSCHHHHHHHHHHCSEEEECHHHHHHHHHT-TSCCTTSCSEEEEETGGGCSTT-CHHHHHHHHHHHHCSSCCEE
T ss_pred             eEEeeCCcchhhhhhhccCCCEEEecHHHHHHHHhc-CCcchhhceEEEEECCcccCCC-CcHHHHHHHHHhcCCCCeEE
Confidence            67777766543322  33578999999999987543 4567889999999999998753 23333444444456788999


Q ss_pred             EEEeeCChh---HHHHHHhhCCCCeEEeccccccc---ccceeEEEEE--------------------------------
Q psy11867        283 LFSATYDKE---VMEFAQDMVPNPLIIKLKREEES---LDNIKQHYVM--------------------------------  324 (399)
Q Consensus       283 ~~SAT~~~~---v~~~~~~~~~~p~~i~~~~~~~~---~~~i~~~~~~--------------------------------  324 (399)
                      ++|||....   +..+...+...+..+........   .......+..                                
T Consensus       161 ~lTaTp~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (494)
T 1wp9_A          161 GLTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAETGLLE  240 (494)
T ss_dssp             EEESCSCSSHHHHHHHHHHTTCCEEEECCTTSTTTGGGCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHTSSS
T ss_pred             EEecCCCCCcHHHHHHHHhcChheeeccCCCcHHHHHhcCCCceeEEecCCcHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            999998743   44444443322222211100000   0000000000                                


Q ss_pred             --------------------------------------------------------------------------------
Q psy11867        325 --------------------------------------------------------------------------------  324 (399)
Q Consensus       325 --------------------------------------------------------------------------------  324 (399)
                                                                                                      
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  320 (494)
T 1wp9_A          241 SSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIF  320 (494)
T ss_dssp             CCCTTSCHHHHHHHHHHHHHHHTTTCCSTTTHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             ccCCCcchhHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHHhhccccchhhhhhh
Confidence                                                                                            


Q ss_pred             -----------------eCChhhHHHHHHHHhcc----CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcC-------
Q psy11867        325 -----------------CKNIDEKFEAVSNIYGV----VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSG-------  376 (399)
Q Consensus       325 -----------------~~~~~~k~~~l~~ll~~----~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg-------  376 (399)
                                       +.....|...+.+++..    ...+++||||++++.++.+++.|...|+.+..+||       
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~  400 (494)
T 1wp9_A          321 SDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKEND  400 (494)
T ss_dssp             TSHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC---
T ss_pred             hhHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEecccccccc
Confidence                             00223466667777766    46789999999999999999999999999999999       


Q ss_pred             -CCCHHHHHHHHHHHhcCCCcccC
Q psy11867        377 -ELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       377 -~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                       +|+..+|.+++++|++|+.+|||
T Consensus       401 ~~~~~~~r~~~~~~F~~~~~~vLv  424 (494)
T 1wp9_A          401 RGLSQREQKLILDEFARGEFNVLV  424 (494)
T ss_dssp             ----CCHHHHHHHHHHHTSCSEEE
T ss_pred             ccCCHHHHHHHHHHHhcCCceEEE
Confidence             99999999999999999999986

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.97  E-value=6.2e-30  Score=276.67  Aligned_cols=269  Identities=16%  Similarity=0.139  Sum_probs=199.5

Q ss_pred             CCCHHHHHHHHH-cCCCCChHHHHHHhhhhhc----CCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        109 HLKPELLKGVYE-MGFYAPSKIQETALPTLLA----DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       109 ~l~~~l~~~l~~-~g~~~p~~iQ~~ai~~ll~----~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      +.++...+.+.+ ++| .|||+|.+|++.+++    +.++|++++++||+|||++|+++++..+..   +.+++|++||+
T Consensus       587 ~~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~---g~~vlvlvPt~  662 (1151)
T 2eyq_A          587 KHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVPTT  662 (1151)
T ss_dssp             CCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECSSH
T ss_pred             CCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh---CCeEEEEechH
Confidence            455666666654 566 479999999999987    323599999999999999999998877653   45899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCcEEEEEEcCchhhh-------hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechh
Q psy11867        184 ELAIQIGEVVAKMGKHITDLSVRYAVRGENLER-------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD  256 (399)
Q Consensus       184 ~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah  256 (399)
                      +||.|+++.+++....+ ++.+....+......       ...+..+|+|+||+.+.      +.+.+++++++||||||
T Consensus       663 ~La~Q~~~~~~~~~~~~-~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~------~~~~~~~l~lvIiDEaH  735 (1151)
T 2eyq_A          663 LLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ------SDVKFKDLGLLIVDEEH  735 (1151)
T ss_dssp             HHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH------SCCCCSSEEEEEEESGG
T ss_pred             HHHHHHHHHHHHHhhcC-CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh------CCccccccceEEEechH
Confidence            99999999999877654 466666655433221       11346899999998653      24567899999999999


Q ss_pred             hHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHH
Q psy11867        257 VMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS  336 (399)
Q Consensus       257 ~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~  336 (399)
                      ++..      ....+++.++.++++++||||..+....+....+.++..+.....  ....+..++..... ......+.
T Consensus       736 ~~g~------~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~~~--~r~~i~~~~~~~~~-~~i~~~il  806 (1151)
T 2eyq_A          736 RFGV------RHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPA--RRLAVKTFVREYDS-MVVREAIL  806 (1151)
T ss_dssp             GSCH------HHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCCCC--BCBCEEEEEEECCH-HHHHHHHH
T ss_pred             hcCh------HHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecCCC--CccccEEEEecCCH-HHHHHHHH
Confidence            9632      223445555678999999999887777777776666555433322  12234444443322 22222222


Q ss_pred             HHhccCCCCcEEEEecchHhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       337 ~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+  ...++++|||+++++++.+++.|++.  +.++..+||+|++.+|++++++|++|+++|||
T Consensus       807 ~~l--~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLV  869 (1151)
T 2eyq_A          807 REI--LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLV  869 (1151)
T ss_dssp             HHH--TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEE
T ss_pred             HHH--hcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEE
Confidence            222  23579999999999999999999887  88999999999999999999999999999986

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.97  E-value=7.1e-32  Score=280.95  Aligned_cols=163  Identities=17%  Similarity=0.063  Sum_probs=122.6

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC---CCCCeEEEEeCcHHHHHHH-HHHHHHHhcc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS---IQEPQVLCLAPTYELAIQI-GEVVAKMGKH  199 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~---~~~~~~lil~Pt~~La~Q~-~~~~~~~~~~  199 (399)
                      ..|+++|.++++.+++  |+|+++++|||+|||++|++|++..+...   ..+.++|||+|+++|+.|+ .+.+++++..
T Consensus         6 ~~l~~~Q~~~i~~il~--g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~   83 (699)
T 4gl2_A            6 LQLRPYQMEVAQPALE--GKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK   83 (699)
T ss_dssp             -CCCHHHHHHHHHHHS--SCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT
T ss_pred             CCccHHHHHHHHHHHh--CCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc
Confidence            4799999999999998  69999999999999999999999877542   1236799999999999999 9999998865


Q ss_pred             CCCcEEEEEEcCchhhh---hhccCCcEEEeCchhHHHhhh-----ccccccCCceeEEEEechhhHhhcCCchHHHHHH
Q psy11867        200 ITDLSVRYAVRGENLER---NKKITEQIIIGTPGKVLDWGL-----KYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRI  271 (399)
Q Consensus       200 ~~~~~~~~~~~~~~~~~---~~~~~~~IlV~Tp~~l~~~~~-----~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i  271 (399)
                        .+.+....|+.....   ......+|+|+||++|.+.+.     ....+.+.++++|||||||++.....+......+
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              367777777654432   224568999999999998764     2334578899999999999986543444444333


Q ss_pred             HHhC-------------CCCCcEEEEEeeCCh
Q psy11867        272 QKRL-------------PSDCQIMLFSATYDK  290 (399)
Q Consensus       272 ~~~l-------------~~~~q~l~~SAT~~~  290 (399)
                      +...             .+..+++++|||...
T Consensus       162 l~~~~~~~~~~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          162 LMQKLKNNRLKKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             HHHHHHHHHHHC----CCCCCEEEEECSCCCC
T ss_pred             HHhhhcccccccccccCCCCCEEEEecccccc
Confidence            3221             156799999999875

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.97  E-value=1.7e-31  Score=268.25  Aligned_cols=262  Identities=14%  Similarity=0.090  Sum_probs=189.0

Q ss_pred             CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        123 FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      ...|+++|.+|++.+++  +++++++++||+|||++|++++...+..  .+.++|||+||++|+.|+++.+++++.. +.
T Consensus       111 ~~~l~~~Q~~ai~~~~~--~~~~ll~~~tGsGKT~~~~~~~~~~~~~--~~~~vlvl~P~~~L~~Q~~~~~~~~~~~-~~  185 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLV--NRRRILNLPTSAGRSLIQALLARYYLEN--YEGKILIIVPTTALTTQMADDFVDYRLF-SH  185 (510)
T ss_dssp             EECCCHHHHHHHHHHHH--HSEEEEECCSTTTHHHHHHHHHHHHHHH--CSSEEEEEESSHHHHHHHHHHHHHTTSS-CG
T ss_pred             CCCCCHHHHHHHHHHHh--cCCcEEEeCCCCCHHHHHHHHHHHHHhC--CCCeEEEEECcHHHHHHHHHHHHHhhcC-Cc
Confidence            44899999999999998  5999999999999999999999887753  3348999999999999999999988554 35


Q ss_pred             cEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEE
Q psy11867        203 LSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM  282 (399)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l  282 (399)
                      ..+....++...........+|+|+||+.|...    ....+++++++|+||||++..     .....+++.+++..+++
T Consensus       186 ~~v~~~~~~~~~~~~~~~~~~I~i~T~~~l~~~----~~~~~~~~~liIiDE~H~~~~-----~~~~~il~~~~~~~~~l  256 (510)
T 2oca_A          186 AMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMMNDECHLATG-----KSISSIISGLNNCMFKF  256 (510)
T ss_dssp             GGEEECGGGCCTTGGGCTTCSEEEEEHHHHTTS----CGGGGGGEEEEEEETGGGCCH-----HHHHHHGGGCTTCCEEE
T ss_pred             cceEEEecCCccccccccCCcEEEEeHHHHhhc----hhhhhhcCCEEEEECCcCCCc-----ccHHHHHHhcccCcEEE
Confidence            566777777655444456789999999977543    334577899999999999854     34567778888889999


Q ss_pred             EEEeeCChhHHHHH-HhhCCCCeEEecccccc------cccceeEEEEEeC----------Ch----------hhHHHHH
Q psy11867        283 LFSATYDKEVMEFA-QDMVPNPLIIKLKREEE------SLDNIKQHYVMCK----------NI----------DEKFEAV  335 (399)
Q Consensus       283 ~~SAT~~~~v~~~~-~~~~~~p~~i~~~~~~~------~~~~i~~~~~~~~----------~~----------~~k~~~l  335 (399)
                      +||||.+....... ...+.++..+.+.....      ....+....+...          ..          ..+...+
T Consensus       257 ~lSATp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  336 (510)
T 2oca_A          257 GLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWI  336 (510)
T ss_dssp             EEESCGGGCSSCHHHHHHHHCSEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHHHHHHH
T ss_pred             EEEeCCCCCcccHHHhHHhhCCeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHHHHHHH
Confidence            99999876532211 11122344333322110      0111111111111          10          1233344


Q ss_pred             HHHhccC---CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        336 SNIYGVV---TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       336 ~~ll~~~---~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..++...   ...++||||+ .++++.+++.|...+.++..+||+|+..+|..+++.|++|+.+|||
T Consensus       337 ~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv  402 (510)
T 2oca_A          337 AKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIV  402 (510)
T ss_dssp             HHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEE
T ss_pred             HHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEE
Confidence            5544433   3345666666 8889999999999888999999999999999999999999999986

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.97  E-value=9.2e-31  Score=271.45  Aligned_cols=265  Identities=20%  Similarity=0.220  Sum_probs=186.3

Q ss_pred             HHHHHHHHHcCCCCChHHHHHHhhhhhcC----CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHH
Q psy11867        112 PELLKGVYEMGFYAPSKIQETALPTLLAD----PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI  187 (399)
Q Consensus       112 ~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~----~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~  187 (399)
                      +.+.+.+..++| .||++|.++++.++++    .++|++++|+||||||++|++|++..+..   +.+++|++||++||.
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~---g~qvlvlaPtr~La~  431 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILAI  431 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHH
Confidence            344455567899 9999999999999873    13699999999999999999999988753   467999999999999


Q ss_pred             HHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhh
Q psy11867        188 QIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       188 Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~  260 (399)
                      |+++.++++.... ++.+....|+......       ..+..+|+|+||+.+.+      ...+.+++++|+||+|++..
T Consensus       432 Q~~~~l~~~~~~~-gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~------~~~~~~l~lVVIDEaHr~g~  504 (780)
T 1gm5_A          432 QHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE------DVHFKNLGLVIIDEQHRFGV  504 (780)
T ss_dssp             HHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH------CCCCSCCCEEEEESCCCC--
T ss_pred             HHHHHHHHHhhhc-CceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh------hhhccCCceEEecccchhhH
Confidence            9999999998765 6788888888654321       13458999999998754      34578999999999999743


Q ss_pred             cCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhc
Q psy11867        261 TQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYG  340 (399)
Q Consensus       261 ~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~  340 (399)
                      .+      ...+......+++++||||..+....+......+...+...  ......+...+....    +...+...+.
T Consensus       505 ~q------r~~l~~~~~~~~vL~mSATp~p~tl~~~~~g~~~~s~i~~~--p~~r~~i~~~~~~~~----~~~~l~~~i~  572 (780)
T 1gm5_A          505 KQ------REALMNKGKMVDTLVMSATPIPRSMALAFYGDLDVTVIDEM--PPGRKEVQTMLVPMD----RVNEVYEFVR  572 (780)
T ss_dssp             ---------CCCCSSSSCCCEEEEESSCCCHHHHHHHTCCSSCEEECCC--CSSCCCCEECCCCSS----THHHHHHHHH
T ss_pred             HH------HHHHHHhCCCCCEEEEeCCCCHHHHHHHHhCCcceeeeecc--CCCCcceEEEEeccc----hHHHHHHHHH
Confidence            21      11122233578999999997766544433211222222111  111122332222111    1222223322


Q ss_pred             -c-CCCCcEEEEecch--------HhHHHHHHHHHH---CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        341 -V-VTIGQAMIFCHTR--------KTAAWLAEKMSK---EGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       341 -~-~~~~k~IIF~~s~--------~~a~~l~~~L~~---~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                       . ...++++|||++.        +.++.+++.|..   .++.+..+||+|++.+|..+++.|++|+++|||
T Consensus       573 ~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILV  644 (780)
T 1gm5_A          573 QEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILV  644 (780)
T ss_dssp             HHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCC
T ss_pred             HHHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEE
Confidence             2 2346899999965        457889999988   478999999999999999999999999999997

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=99.96  E-value=2.8e-29  Score=261.64  Aligned_cols=282  Identities=21%  Similarity=0.247  Sum_probs=202.8

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhh--CCCCCCCeEEEE
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRV--NPSIQEPQVLCL  179 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l--~~~~~~~~~lil  179 (399)
                      +.+|+++++++.+.+.+...+ ..|+++|.++++.++.+ +++++++||||||||+  ++|++...  .....+.+++|+
T Consensus        71 ~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~-~~~vii~gpTGSGKTt--llp~ll~~~~~~~~~g~~ilvl  146 (773)
T 2xau_A           71 INPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQN-NQIMVFVGETGSGKTT--QIPQFVLFDEMPHLENTQVACT  146 (773)
T ss_dssp             BCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHH-CSEEEEECCTTSSHHH--HHHHHHHHHHCGGGGTCEEEEE
T ss_pred             CCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhC-CCeEEEECCCCCCHHH--HHHHHHHHhccccCCCceEEec
Confidence            467999999999999999988 78999999999999986 7889999999999998  45555222  111125679999


Q ss_pred             eCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh-H
Q psy11867        180 APTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV-M  258 (399)
Q Consensus       180 ~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~-l  258 (399)
                      +|+++|+.|+++.+........+..+.+.....   .......+|+|+|||++...+..  ...+.++++|||||+|. +
T Consensus       147 ~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~---~~~~~~~~I~v~T~G~l~r~l~~--~~~l~~~~~lIlDEah~R~  221 (773)
T 2xau_A          147 QPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFE---NKTSNKTILKYMTDGMLLREAME--DHDLSRYSCIILDEAHERT  221 (773)
T ss_dssp             ESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTE---EECCTTCSEEEEEHHHHHHHHHH--STTCTTEEEEEECSGGGCC
T ss_pred             CchHHHHHHHHHHHHHHhCCchhheecceeccc---cccCCCCCEEEECHHHHHHHHhh--CccccCCCEEEecCccccc
Confidence            999999999988776543221122223222221   12234568999999999987654  24588999999999995 5


Q ss_pred             hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhh---HHHHH
Q psy11867        259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDE---KFEAV  335 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~---k~~~l  335 (399)
                      ++.......+..+.... ++.|+++||||++.  ..+. .++.++..+.+....   ..+.++|......+.   ....+
T Consensus       222 ld~d~~~~~l~~l~~~~-~~~~iIl~SAT~~~--~~l~-~~~~~~~vi~v~gr~---~pv~~~~~~~~~~~~~~~~l~~l  294 (773)
T 2xau_A          222 LATDILMGLLKQVVKRR-PDLKIIIMSATLDA--EKFQ-RYFNDAPLLAVPGRT---YPVELYYTPEFQRDYLDSAIRTV  294 (773)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCEEEEEESCSCC--HHHH-HHTTSCCEEECCCCC---CCEEEECCSSCCSCHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHhC-CCceEEEEeccccH--HHHH-HHhcCCCcccccCcc---cceEEEEecCCchhHHHHHHHHH
Confidence            54322334444454443 57899999999964  3343 344444444443222   345666655443322   23344


Q ss_pred             HHHhccCCCCcEEEEecchHhHHHHHHHHHH-----------CCCeEEEEcCCCCHHHHHHHHHHHh-----cCCCcccC
Q psy11867        336 SNIYGVVTIGQAMIFCHTRKTAAWLAEKMSK-----------EGLNVGLLSGELTVEQRLSILDRFR-----EGEFKIYS  399 (399)
Q Consensus       336 ~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~-----------~g~~v~~lhg~~~~~~R~~v~~~F~-----~G~~~ILV  399 (399)
                      ..+......+++||||++++.++.++..|.+           .++.+..+||+|++++|..+++.|+     +|+.+|||
T Consensus       295 ~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlV  374 (773)
T 2xau_A          295 LQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVI  374 (773)
T ss_dssp             HHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEE
T ss_pred             HHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEE
Confidence            4455555678999999999999999999985           5788999999999999999999999     99999986

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.96  E-value=1.9e-31  Score=271.55  Aligned_cols=251  Identities=16%  Similarity=0.156  Sum_probs=174.0

Q ss_pred             CCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHH
Q psy11867        108 LHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI  187 (399)
Q Consensus       108 ~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~  187 (399)
                      +++++.+.+.+... ...|+|+|+.++|.+++  |+|++++||||||||++|++|++..+..  .++++|||+||++||.
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~--g~dvlv~a~TGSGKT~~~~lpil~~l~~--~~~~vLvl~PtreLa~  229 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRK--KRLTIMDLHPGAGKTKRILPSIVREALK--RRLRTLILAPTRVVAA  229 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGST--TCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhc--CCeEEEEcCCCCCHHHHHHHHHHHHHHh--CCCeEEEEcChHHHHH
Confidence            45566555555433 58899999999999888  7999999999999999999999988754  4578999999999999


Q ss_pred             HHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHH
Q psy11867        188 QIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF  267 (399)
Q Consensus       188 Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~  267 (399)
                      |+++.++.       ..+.+  .+............+.+.|.+.+...+...  ..+++++++||||||++ + .++...
T Consensus       230 Qi~~~l~~-------~~v~~--~~~~l~~~~tp~~~i~~~t~~~l~~~l~~~--~~l~~~~~iViDEah~~-~-~~~~~~  296 (618)
T 2whx_A          230 EMEEALRG-------LPIRY--QTPAVKSDHTGREIVDLMCHATFTTRLLSS--TRVPNYNLIVMDEAHFT-D-PCSVAA  296 (618)
T ss_dssp             HHHHHTTT-------SCEEE--CCTTSSCCCCSSSCEEEEEHHHHHHHHHHC--SSCCCCSEEEEESTTCC-S-HHHHHH
T ss_pred             HHHHHhcC-------CceeE--ecccceeccCCCceEEEEChHHHHHHHhcc--ccccCCeEEEEECCCCC-C-ccHHHH
Confidence            99987762       22222  111111111122346677777776654432  35789999999999998 3 256666


Q ss_pred             HHHHHHhCC-CCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCc
Q psy11867        268 SIRIQKRLP-SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQ  346 (399)
Q Consensus       268 ~~~i~~~l~-~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k  346 (399)
                      +..+...++ +++|+++||||++..+..++.   .++..+.+.....             .  .+...+...+.. ..++
T Consensus       297 ~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~~~~~-------------~--~~~~~ll~~l~~-~~~~  357 (618)
T 2whx_A          297 RGYISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIEREIP-------------E--RSWNTGFDWITD-YQGK  357 (618)
T ss_dssp             HHHHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEEECCCC-------------S--SCCSSSCHHHHH-CCSC
T ss_pred             HHHHHHHhcccCccEEEEECCCchhhhhhhc---cCCceeeecccCC-------------H--HHHHHHHHHHHh-CCCC
Confidence            666666664 689999999999876543322   2333333322110             0  000111112222 2579


Q ss_pred             EEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        347 AMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       347 ~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +||||++++.|+.+++.|.+.|+++..+||+    +|.++++.|++|+.+|||
T Consensus       358 ~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLV  406 (618)
T 2whx_A          358 TVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVV  406 (618)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEE
T ss_pred             EEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEE
Confidence            9999999999999999999999999999995    788999999999999986

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.96  E-value=3.5e-30  Score=254.28  Aligned_cols=237  Identities=17%  Similarity=0.178  Sum_probs=165.7

Q ss_pred             CCCCChHHHHHHhhhhhcCCCCcE-EEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        122 GFYAPSKIQETALPTLLADPPHNM-IAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       122 g~~~p~~iQ~~ai~~ll~~~g~~v-i~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      |+.+|+|+|+ ++|.++++  +++ +++||||||||++|++|++..+..  .++++||++||++||.|+++.++      
T Consensus         1 G~~q~~~iq~-~i~~~l~~--~~~~lv~a~TGsGKT~~~~~~~l~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~------   69 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRK--KRLTIMDLHPGAGKTKRILPSIVREALL--RRLRTLILAPTRVVAAEMEEALR------   69 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGST--TCEEEECCCTTSSCCTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT------
T ss_pred             CCCCCCCcHH-HHHHHHhc--CCeEEEECCCCCCHhhHHHHHHHHHHHh--cCCcEEEECCCHHHHHHHHHHhc------
Confidence            7889999985 79999984  555 999999999999999999876644  45789999999999999999874      


Q ss_pred             CCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHH-HhCCCCC
Q psy11867        201 TDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQ-KRLPSDC  279 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~-~~l~~~~  279 (399)
                       +..+.+....  ..........|.++|++.+.+.+...  ..+.+++++||||||++ +. .+......+. ...++++
T Consensus        70 -g~~v~~~~~~--~~~~~~~~~~i~~~t~~~l~~~l~~~--~~l~~~~~iViDEah~~-~~-~~~~~~~~~~~~~~~~~~  142 (451)
T 2jlq_A           70 -GLPIRYQTPA--VKSDHTGREIVDLMCHATFTTRLLSS--TRVPNYNLIVMDEAHFT-DP-CSVAARGYISTRVEMGEA  142 (451)
T ss_dssp             -TSCEEECCTT--CSCCCCSSCCEEEEEHHHHHHHHHHC--SCCCCCSEEEEETTTCC-SH-HHHHHHHHHHHHHHTTSC
T ss_pred             -Cceeeeeecc--ccccCCCCceEEEEChHHHHHHhhCc--ccccCCCEEEEeCCccC-Cc-chHHHHHHHHHhhcCCCc
Confidence             2222222211  11112234469999999998876543  45789999999999987 21 1222222222 2235689


Q ss_pred             cEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHH
Q psy11867        280 QIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAW  359 (399)
Q Consensus       280 q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~  359 (399)
                      |+++||||++..+..+   +..++..+......   +.  ..|      ..+...    +.. ..+++||||++++.|+.
T Consensus       143 ~~i~~SAT~~~~~~~~---~~~~~~~~~~~~~~---p~--~~~------~~~~~~----l~~-~~~~~lVF~~s~~~a~~  203 (451)
T 2jlq_A          143 AAIFMTATPPGSTDPF---PQSNSPIEDIEREI---PE--RSW------NTGFDW----ITD-YQGKTVWFVPSIKAGND  203 (451)
T ss_dssp             EEEEECSSCTTCCCSS---CCCSSCEEEEECCC---CS--SCC------SSSCHH----HHH-CCSCEEEECSSHHHHHH
T ss_pred             eEEEEccCCCccchhh---hcCCCceEecCccC---Cc--hhh------HHHHHH----HHh-CCCCEEEEcCCHHHHHH
Confidence            9999999998754332   22344433332110   00  001      011111    222 24699999999999999


Q ss_pred             HHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        360 LAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       360 l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +++.|.+.|+.+..+||++.    ..+++.|++|+.+|||
T Consensus       204 l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLV  239 (451)
T 2jlq_A          204 IANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVV  239 (451)
T ss_dssp             HHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEE
T ss_pred             HHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEE
Confidence            99999999999999999864    5799999999999986

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.95  E-value=9.8e-31  Score=268.03  Aligned_cols=236  Identities=16%  Similarity=0.216  Sum_probs=158.4

Q ss_pred             HHHHcCCC-----CChHHHH-----HHhhhhh------cCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe
Q psy11867        117 GVYEMGFY-----APSKIQE-----TALPTLL------ADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA  180 (399)
Q Consensus       117 ~l~~~g~~-----~p~~iQ~-----~ai~~ll------~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  180 (399)
                      +++.+||.     +||++|.     ++||.++      +  |+|++++||||||||++|++|++..+..  .+.++||++
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~--g~dvlv~apTGSGKTl~~ll~il~~l~~--~~~~~lila  277 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKK--RQLTVLDLHPGAGKTRRILPQIIKDAIQ--KRLRTAVLA  277 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGST--TCEEEECCCTTTTTTTTHHHHHHHHHHH--TTCCEEEEE
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhc--CCeEEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEc
Confidence            44556776     8999999     9999988      5  7999999999999999999999987654  457899999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhcc-------ccccCCceeEEEEe
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKY-------RFFDLSKIKVFVLD  253 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~-------~~~~~~~~~~lViD  253 (399)
                      ||++||.|+++.++.+.     +.  +.  ...+.         .++||+++++++...       ....++++++||||
T Consensus       278 PTr~La~Q~~~~l~~~~-----i~--~~--~~~l~---------~v~tp~~ll~~l~~~~l~~~l~~~~~l~~l~lvViD  339 (673)
T 2wv9_A          278 PTRVVAAEMAEALRGLP-----VR--YL--TPAVQ---------REHSGNEIVDVMCHATLTHRLMSPLRVPNYNLFVMD  339 (673)
T ss_dssp             SSHHHHHHHHHHTTTSC-----CE--EC--CC------------CCCCSCCCEEEEEHHHHHHHHHSSSCCCCCSEEEEE
T ss_pred             cHHHHHHHHHHHHhcCC-----ee--ee--ccccc---------ccCCHHHHHHHHHhhhhHHHHhcccccccceEEEEe
Confidence            99999999999887542     11  11  11010         155555554332111       11357899999999


Q ss_pred             chhhHhhcCCchHHHHHHHHhC-CCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHH
Q psy11867        254 EADVMIATQGHQDFSIRIQKRL-PSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKF  332 (399)
Q Consensus       254 Eah~l~~~~~~~~~~~~i~~~l-~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~  332 (399)
                      |||++..  .+......+...+ +..+|+++||||++..+..+...  ..|+. .+..             .+.. ..+.
T Consensus       340 EaH~~~~--~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~--~~~i~-~v~~-------------~~~~-~~~~  400 (673)
T 2wv9_A          340 EAHFTDP--ASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT--NSPVH-DVSS-------------EIPD-RAWS  400 (673)
T ss_dssp             STTCCCH--HHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--SSCEE-EEEC-------------CCCS-SCCS
T ss_pred             CCcccCc--cHHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc--CCceE-EEee-------------ecCH-HHHH
Confidence            9999811  1122222333333 26799999999998664332211  11211 1100             0000 0011


Q ss_pred             HHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        333 EAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       333 ~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+..+..  ..+++||||++++.|+.+++.|+..|+++..+||+    +|..+++.|++|+++|||
T Consensus       401 ~~l~~l~~--~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLV  461 (673)
T 2wv9_A          401 SGFEWITD--YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVI  461 (673)
T ss_dssp             SCCHHHHS--CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEE
T ss_pred             HHHHHHHh--CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEE
Confidence            11112222  35799999999999999999999999999999994    899999999999999986

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.95  E-value=1.7e-28  Score=243.89  Aligned_cols=242  Identities=17%  Similarity=0.172  Sum_probs=175.1

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..|+++|.++++.+++  ++++++++|||+|||++|+.++...      +.++|||+|+++|+.|+.+.++++     ++
T Consensus        92 ~~l~~~Q~~ai~~i~~--~~~~ll~~~TGsGKT~~~l~~i~~~------~~~~Lvl~P~~~L~~Q~~~~~~~~-----~~  158 (472)
T 2fwr_A           92 ISLRDYQEKALERWLV--DKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF-----GE  158 (472)
T ss_dssp             CCBCHHHHHHHHHHTT--TTEEEEECCTTSCHHHHHHHHHHHH------CSCEEEEESSHHHHHHHHHHGGGG-----CG
T ss_pred             CCcCHHHHHHHHHHHh--cCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEECCHHHHHHHHHHHHhC-----CC
Confidence            3799999999999998  5789999999999999999998865      456999999999999999999884     34


Q ss_pred             E-EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEE
Q psy11867        204 S-VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM  282 (399)
Q Consensus       204 ~-~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l  282 (399)
                      . +....|+..      ...+|+|+||+++......    ...+++++|+||||++.+. .+..    +...+ +..+++
T Consensus       159 ~~v~~~~g~~~------~~~~Ivv~T~~~l~~~~~~----~~~~~~liIvDEaH~~~~~-~~~~----~~~~~-~~~~~l  222 (472)
T 2fwr_A          159 EYVGEFSGRIK------ELKPLTVSTYDSAYVNAEK----LGNRFMLLIFDEVHHLPAE-SYVQ----IAQMS-IAPFRL  222 (472)
T ss_dssp             GGEEEBSSSCB------CCCSEEEEEHHHHHHTHHH----HTTTCSEEEEETGGGTTST-TTHH----HHHTC-CCSEEE
T ss_pred             cceEEECCCcC------CcCCEEEEEcHHHHHHHHH----hcCCCCEEEEECCcCCCCh-HHHH----HHHhc-CCCeEE
Confidence            4 555555442      2467999999998776432    1246899999999998754 4443    44444 467899


Q ss_pred             EEEeeCCh-------------------hHHHHHHhhCCCCeEEec--c--cccc----------------------cccc
Q psy11867        283 LFSATYDK-------------------EVMEFAQDMVPNPLIIKL--K--REEE----------------------SLDN  317 (399)
Q Consensus       283 ~~SAT~~~-------------------~v~~~~~~~~~~p~~i~~--~--~~~~----------------------~~~~  317 (399)
                      ++|||...                   ....+...++..+....+  .  ....                      ....
T Consensus       223 ~lSATp~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  302 (472)
T 2fwr_A          223 GLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAED  302 (472)
T ss_dssp             EEESCCCCTTSGGGSHHHHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCTTTCCSS
T ss_pred             EEecCccCCCCHHHHHHHHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCccccchhh
Confidence            99999762                   233332333333222111  0  0000                      0000


Q ss_pred             eeEEEE--------------------EeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCC
Q psy11867        318 IKQHYV--------------------MCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGE  377 (399)
Q Consensus       318 i~~~~~--------------------~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~  377 (399)
                      +.+.+.                    .......|...+.+++.....+++||||++++.++.+++.|.     +..+||+
T Consensus       303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~  377 (472)
T 2fwr_A          303 FNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHR  377 (472)
T ss_dssp             STTTTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSS
T ss_pred             HHHHHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHhC-----cceeeCC
Confidence            000000                    001124577888888888777899999999999999999883     6789999


Q ss_pred             CCHHHHHHHHHHHhcCCCcccC
Q psy11867        378 LTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       378 ~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++..+|.+++++|++|+++|||
T Consensus       378 ~~~~~R~~~~~~F~~g~~~vLv  399 (472)
T 2fwr_A          378 TSREEREEILEGFRTGRFRAIV  399 (472)
T ss_dssp             SCSHHHHTHHHHHHHSSCSBCB
T ss_pred             CCHHHHHHHHHHHhCCCCCEEE
Confidence            9999999999999999999986

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.95  E-value=3.1e-28  Score=246.46  Aligned_cols=225  Identities=17%  Similarity=0.163  Sum_probs=158.4

Q ss_pred             ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEE
Q psy11867        126 PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV  205 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~  205 (399)
                      +.++|..+++.+..  +++++++||||||||.+|.+|+++.      +.++||++|||+||.|+++.+.+...    ..+
T Consensus       218 ~~~~q~~i~~~L~~--~~~vlv~ApTGSGKT~a~~l~ll~~------g~~vLVl~PTReLA~Qia~~l~~~~g----~~v  285 (666)
T 3o8b_A          218 VFTDNSSPPAVPQS--FQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAHG----IDP  285 (666)
T ss_dssp             SCCCCCSCCCCCSS--CEEEEEECCTTSCTTTHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHHS----CCC
T ss_pred             cHHHHHHHHHHHHc--CCeEEEEeCCchhHHHHHHHHHHHC------CCeEEEEcchHHHHHHHHHHHHHHhC----CCe
Confidence            33445554454444  7999999999999999999999862      45799999999999999988776542    233


Q ss_pred             EEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCc--EEE
Q psy11867        206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ--IML  283 (399)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q--~l~  283 (399)
                      ...+|+..    .....+|+|+||++|+.    ...+.++++++|||||||++. . ++...+..+++.++...|  +++
T Consensus       286 g~~vG~~~----~~~~~~IlV~TPGrLl~----~~~l~l~~l~~lVlDEAH~l~-~-~~~~~l~~Il~~l~~~~~~llil  355 (666)
T 3o8b_A          286 NIRTGVRT----ITTGAPVTYSTYGKFLA----DGGCSGGAYDIIICDECHSTD-S-TTILGIGTVLDQAETAGARLVVL  355 (666)
T ss_dssp             EEECSSCE----ECCCCSEEEEEHHHHHH----TTSCCTTSCSEEEETTTTCCS-H-HHHHHHHHHHHHTTTTTCSEEEE
T ss_pred             eEEECcEe----ccCCCCEEEECcHHHHh----CCCcccCcccEEEEccchhcC-c-cHHHHHHHHHHhhhhcCCceEEE
Confidence            44455543    24567899999999843    356678899999999998763 2 566667788888887776  778


Q ss_pred             EEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHH
Q psy11867        284 FSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEK  363 (399)
Q Consensus       284 ~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~  363 (399)
                      ||||++..+.      ...|....+.....  ..+ ..+   .. ...       +.....+++||||++++.|+.+++.
T Consensus       356 ~SAT~~~~i~------~~~p~i~~v~~~~~--~~i-~~~---~~-~~~-------l~~~~~~~vLVFv~Tr~~ae~la~~  415 (666)
T 3o8b_A          356 ATATPPGSVT------VPHPNIEEVALSNT--GEI-PFY---GK-AIP-------IEAIRGGRHLIFCHSKKKCDELAAK  415 (666)
T ss_dssp             EESSCTTCCC------CCCTTEEEEECBSC--SSE-EET---TE-EEC-------GGGSSSSEEEEECSCHHHHHHHHHH
T ss_pred             ECCCCCcccc------cCCcceEEEeeccc--chh-HHH---Hh-hhh-------hhhccCCcEEEEeCCHHHHHHHHHH
Confidence            8999987421      12222211111000  000 000   00 000       1223568999999999999999999


Q ss_pred             HHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        364 MSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       364 L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      |++.|+++..+||+|++++       |+++..+|||
T Consensus       416 L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLV  444 (666)
T 3o8b_A          416 LSGLGINAVAYYRGLDVSV-------IPTIGDVVVV  444 (666)
T ss_dssp             HHTTTCCEEEECTTSCGGG-------SCSSSCEEEE
T ss_pred             HHhCCCcEEEecCCCCHHH-------HHhCCCcEEE
Confidence            9999999999999999875       4556668875

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.94  E-value=3e-27  Score=231.91  Aligned_cols=220  Identities=16%  Similarity=0.180  Sum_probs=148.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |+++++++|||||||++|++|+++.+..  .+.+++|++||++||.|+++.++       ++.+.+..++..  ......
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~--~g~~~lvl~Pt~~La~Q~~~~~~-------~~~v~~~~~~~~--~~~~~~   70 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVK--KRLRTVILAPTRVVASEMYEALR-------GEPIRYMTPAVQ--SERTGN   70 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT-------TSCEEEC-----------CC
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHh--CCCCEEEECcHHHHHHHHHHHhC-------CCeEEEEecCcc--ccCCCC
Confidence            7999999999999999999999966543  45689999999999999998775       233443333311  111122


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHh-CCCCCcEEEEEeeCChhHHHHHHhhC
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR-LPSDCQIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~-l~~~~q~l~~SAT~~~~v~~~~~~~~  300 (399)
                      .-+.+.|.+.+.+.+..  ...+++++++|+||||++. . ++......+... .+..+|+++||||+++.+..+...  
T Consensus        71 ~~~~~~~~~~l~~~l~~--~~~~~~l~~vViDEaH~~~-~-~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~~~--  144 (431)
T 2v6i_A           71 EIVDFMCHSTFTMKLLQ--GVRVPNYNLYIMDEAHFLD-P-ASVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPPS--  144 (431)
T ss_dssp             CSEEEEEHHHHHHHHHH--TCCCCCCSEEEEESTTCCS-H-HHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSCCC--
T ss_pred             ceEEEEchHHHHHHHhc--CccccCCCEEEEeCCccCC-c-cHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhcCC--
Confidence            34677788888765544  3458899999999999972 1 233333333333 256899999999998753222111  


Q ss_pred             CCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCH
Q psy11867        301 PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTV  380 (399)
Q Consensus       301 ~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~  380 (399)
                      ..|+. .+..             ...  ..+...+..++... .+++||||++++.|+.+++.|++.|+++..+||+   
T Consensus       145 ~~~i~-~~~~-------------~~~--~~~~~~~~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~---  204 (431)
T 2v6i_A          145 NSPII-DEET-------------RIP--DKAWNSGYEWITEF-DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK---  204 (431)
T ss_dssp             SSCCE-EEEC-------------CCC--SSCCSSCCHHHHSC-SSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT---
T ss_pred             CCcee-eccc-------------cCC--HHHHHHHHHHHHcC-CCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc---
Confidence            11111 1100             000  00111122233332 5799999999999999999999999999999997   


Q ss_pred             HHHHHHHHHHhcCCCcccC
Q psy11867        381 EQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       381 ~~R~~v~~~F~~G~~~ILV  399 (399)
                       +|.++++.|++|+++|||
T Consensus       205 -~r~~~~~~f~~g~~~vLV  222 (431)
T 2v6i_A          205 -TFESEYPKCKSEKWDFVI  222 (431)
T ss_dssp             -THHHHTTHHHHSCCSEEE
T ss_pred             -cHHHHHHhhcCCCCeEEE
Confidence             688999999999999986

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.94  E-value=5.2e-29  Score=244.94  Aligned_cols=213  Identities=16%  Similarity=0.159  Sum_probs=137.1

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |+|++++||||||||++|++|++..+..  .+++++|++||++||.|+++.++.+       .+.+..  ..+       
T Consensus         8 g~~vlv~a~TGSGKT~~~l~~~l~~~~~--~~~~~lil~Ptr~La~Q~~~~l~~~-------~v~~~~--~~~-------   69 (440)
T 1yks_A            8 GMTTVLDFHPGAGKTRRFLPQILAECAR--RRLRTLVLAPTRVVLSEMKEAFHGL-------DVKFHT--QAF-------   69 (440)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTTS-------CEEEES--SCC-------
T ss_pred             CCCEEEEcCCCCCHHHHHHHHHHHHHHh--cCCeEEEEcchHHHHHHHHHHHhcC-------CeEEec--ccc-------
Confidence            7999999999999999999999987654  3568999999999999999988743       122111  100       


Q ss_pred             CcEEEeCchhHHHhhhcc-------ccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC-CCCCcEEEEEeeCChhHH
Q psy11867        222 EQIIIGTPGKVLDWGLKY-------RFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL-PSDCQIMLFSATYDKEVM  293 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~-------~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~l~~SAT~~~~v~  293 (399)
                        -.|+||+++++++...       ....+++++++|+||||++ +. .+...+..+...+ +.++|+++||||+++.+.
T Consensus        70 --~~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~-~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~  145 (440)
T 1yks_A           70 --SAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DP-ASIAARGWAAHRARANESATILMTATPPGTSD  145 (440)
T ss_dssp             --CCCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SH-HHHHHHHHHHHHHHTTSCEEEEECSSCTTCCC
T ss_pred             --eeccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-Cc-chHHHHHHHHHHhccCCceEEEEeCCCCchhh
Confidence              1378888776543221       1123789999999999998 21 2222222222222 367999999999987644


Q ss_pred             HHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEE
Q psy11867        294 EFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGL  373 (399)
Q Consensus       294 ~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~  373 (399)
                      .+...  ..++..              ....+.. ..+...+..+..  ..+++||||++++.|+.+++.|+..|+++..
T Consensus       146 ~~~~~--~~~~~~--------------~~~~~~~-~~~~~~~~~l~~--~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~  206 (440)
T 1yks_A          146 EFPHS--NGEIED--------------VQTDIPS-EPWNTGHDWILA--DKRPTAWFLPSIRAANVMAASLRKAGKSVVV  206 (440)
T ss_dssp             SSCCC--SSCEEE--------------EECCCCS-SCCSSSCHHHHH--CCSCEEEECSCHHHHHHHHHHHHHTTCCEEE
T ss_pred             hhhhc--CCCeeE--------------eeeccCh-HHHHHHHHHHHh--cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEE
Confidence            33221  111111              0001111 000011111222  2479999999999999999999999999999


Q ss_pred             EcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        374 LSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       374 lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +||    ++|..+++.|++|+++|||
T Consensus       207 lhg----~~R~~~~~~F~~g~~~vLV  228 (440)
T 1yks_A          207 LNR----KTFEREYPTIKQKKPDFIL  228 (440)
T ss_dssp             CCS----SSCC--------CCCSEEE
T ss_pred             ecc----hhHHHHHhhhcCCCceEEE
Confidence            999    4799999999999999986

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.94  E-value=1.5e-26  Score=236.28  Aligned_cols=258  Identities=16%  Similarity=0.160  Sum_probs=145.9

Q ss_pred             CCChHHHHHHhhhhhc---CCCCcEEEEccCCCCceehhHHHHHHhhCCC------CCCCeEEEEeCcHHHHHHHH-HHH
Q psy11867        124 YAPSKIQETALPTLLA---DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS------IQEPQVLCLAPTYELAIQIG-EVV  193 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~---~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~------~~~~~~lil~Pt~~La~Q~~-~~~  193 (399)
                      ..|+++|.++++.++.   ..+++++++++||||||++++..+...+...      ...+++|||+||++|+.|++ +.+
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            3699999999999875   1157799999999999999765554444322      15678999999999999999 777


Q ss_pred             HHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhc---cccccCCceeEEEEechhhHhhcCCchHHHHH
Q psy11867        194 AKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLK---YRFFDLSKIKVFVLDEADVMIATQGHQDFSIR  270 (399)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~---~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~  270 (399)
                      +.++..     +....++     ......+|+|+||++|......   .+.+...++++||+||||++...  .......
T Consensus       257 ~~~~~~-----~~~~~~~-----~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~--~~~~~~~  324 (590)
T 3h1t_A          257 TPFGDA-----RHKIEGG-----KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSAR--DNSNWRE  324 (590)
T ss_dssp             TTTCSS-----EEECCC-------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC-----------CHH
T ss_pred             Hhcchh-----hhhhhcc-----CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCcccccc--chHHHHH
Confidence            766432     1111111     1234568999999999876432   23445678999999999998642  1233455


Q ss_pred             HHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEE------------------eccccccccc--------------ce
Q psy11867        271 IQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII------------------KLKREEESLD--------------NI  318 (399)
Q Consensus       271 i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i------------------~~~~~~~~~~--------------~i  318 (399)
                      ++..++ ..++++||||...........++..++..                  .+.... ...              .+
T Consensus       325 il~~~~-~~~~l~lTATP~~~~~~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  402 (590)
T 3h1t_A          325 ILEYFE-PAFQIGMTATPLREDNRDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEV-DAAGWRPSKGDVDRFGREI  402 (590)
T ss_dssp             HHHHST-TSEEEEEESSCSCTTTHHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETT-CC-----------------
T ss_pred             HHHhCC-cceEEEeccccccccchhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeee-ecccccccccccccccccc
Confidence            666665 57899999996643222222223222211                  111000 000              00


Q ss_pred             eEEEEEeCCh----------hhHHHHHHHHhcc-CCCCcEEEEecchHhHHHHHHHHHHCCC--------eEEEEcCCCC
Q psy11867        319 KQHYVMCKNI----------DEKFEAVSNIYGV-VTIGQAMIFCHTRKTAAWLAEKMSKEGL--------NVGLLSGELT  379 (399)
Q Consensus       319 ~~~~~~~~~~----------~~k~~~l~~ll~~-~~~~k~IIF~~s~~~a~~l~~~L~~~g~--------~v~~lhg~~~  379 (399)
                      ..........          ......+..++.. ...+++||||+++++|+.+++.|.+.+.        .+..+||+++
T Consensus       403 ~~~~~~~~~~~~~~~~~~r~~~i~~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~  482 (590)
T 3h1t_A          403 PDGEYQTKDFERVIALKARTDAFAKHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEG  482 (590)
T ss_dssp             ------CCSHHHHHHHHHTHHHHHHHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTH
T ss_pred             ccccCCHHHhhhHhcChHHHHHHHHHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCCh
Confidence            0000000000          0011223333433 3447999999999999999999987543        3788999986


Q ss_pred             HHHHHHHHHHHhcCCCc
Q psy11867        380 VEQRLSILDRFREGEFK  396 (399)
Q Consensus       380 ~~~R~~v~~~F~~G~~~  396 (399)
                      + +|..++++|++|+.+
T Consensus       483 ~-~r~~~l~~F~~~~~~  498 (590)
T 3h1t_A          483 K-IGKGHLSRFQELETS  498 (590)
T ss_dssp             H-HHHHHHHHHHCTTCC
T ss_pred             H-HHHHHHHHHhCCCCC
Confidence            4 799999999998865

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.93  E-value=4.2e-27  Score=232.64  Aligned_cols=222  Identities=18%  Similarity=0.234  Sum_probs=148.9

Q ss_pred             hhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchh
Q psy11867        135 PTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL  214 (399)
Q Consensus       135 ~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  214 (399)
                      +.++.+ +++++++||||||||++|++|++..+..  .+.++||++||++||.|+++.++.       ..+....+.  .
T Consensus        15 ~~~l~~-~~~vlv~a~TGsGKT~~~~l~il~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~g-------~~v~~~~~~--~   82 (459)
T 2z83_A           15 PNMLRK-RQMTVLDLHPGSGKTRKILPQIIKDAIQ--QRLRTAVLAPTRVVAAEMAEALRG-------LPVRYQTSA--V   82 (459)
T ss_dssp             CGGGST-TCEEEECCCTTSCTTTTHHHHHHHHHHH--TTCCEEEEECSHHHHHHHHHHTTT-------SCEEECC-----
T ss_pred             HHHHhc-CCcEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEECchHHHHHHHHHHhcC-------ceEeEEecc--c
Confidence            444444 7999999999999999999999987753  356899999999999999998862       222221111  1


Q ss_pred             hhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH-----hhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        215 ERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM-----IATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       215 ~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l-----~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      ........-+.+.|.+.+...+..  ...++++++|||||||++     ... ++..   .+.  ..+..|+++||||++
T Consensus        83 ~~~~t~~~~i~~~~~~~l~~~l~~--~~~l~~~~~iViDEaH~~~~~~~~~~-~~~~---~~~--~~~~~~~il~SAT~~  154 (459)
T 2z83_A           83 QREHQGNEIVDVMCHATLTHRLMS--PNRVPNYNLFVMDEAHFTDPASIAAR-GYIA---TKV--ELGEAAAIFMTATPP  154 (459)
T ss_dssp             -----CCCSEEEEEHHHHHHHHHS--CC-CCCCSEEEESSTTCCSHHHHHHH-HHHH---HHH--HTTSCEEEEECSSCT
T ss_pred             ccCCCCCcEEEEEchHHHHHHhhc--cccccCCcEEEEECCccCCchhhHHH-HHHH---HHh--ccCCccEEEEEcCCC
Confidence            111112234777888887766543  345889999999999983     321 1211   111  236899999999998


Q ss_pred             hhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCC
Q psy11867        290 KEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGL  369 (399)
Q Consensus       290 ~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~  369 (399)
                      ..+..+...  ..|+......    ..        ..........+    ... .+++||||++++.|+.+++.|...|+
T Consensus       155 ~~~~~~~~~--~~pi~~~~~~----~~--------~~~~~~~~~~l----~~~-~~~~LVF~~s~~~~~~l~~~L~~~g~  215 (459)
T 2z83_A          155 GTTDPFPDS--NAPIHDLQDE----IP--------DRAWSSGYEWI----TEY-AGKTVWFVASVKMGNEIAMCLQRAGK  215 (459)
T ss_dssp             TCCCSSCCC--SSCEEEEECC----CC--------SSCCSSCCHHH----HHC-CSCEEEECSCHHHHHHHHHHHHHTTC
T ss_pred             cchhhhccC--CCCeEEeccc----CC--------cchhHHHHHHH----Hhc-CCCEEEEeCChHHHHHHHHHHHhcCC
Confidence            764332211  2333221100    00        00001111222    222 57999999999999999999999999


Q ss_pred             eEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        370 NVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       370 ~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+..+||+    +|..+++.|++|+.+|||
T Consensus       216 ~v~~lh~~----~R~~~~~~f~~g~~~iLV  241 (459)
T 2z83_A          216 KVIQLNRK----SYDTEYPKCKNGDWDFVI  241 (459)
T ss_dssp             CEEEESTT----CCCCCGGGSSSCCCSEEE
T ss_pred             cEEecCHH----HHHHHHhhccCCCceEEE
Confidence            99999995    788999999999999986

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.91  E-value=5.8e-25  Score=224.81  Aligned_cols=219  Identities=15%  Similarity=0.126  Sum_probs=149.9

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh-cc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK-KI  220 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~  220 (399)
                      |++++++||||||||+.++    ..+...   ..++|++||++||.|+++.++++     ++.+....|+....... ..
T Consensus       155 rk~vlv~apTGSGKT~~al----~~l~~~---~~gl~l~PtR~LA~Qi~~~l~~~-----g~~v~lltG~~~~iv~TpGr  222 (677)
T 3rc3_A          155 RKIIFHSGPTNSGKTYHAI----QKYFSA---KSGVYCGPLKLLAHEIFEKSNAA-----GVPCDLVTGEERVTVQPNGK  222 (677)
T ss_dssp             CEEEEEECCTTSSHHHHHH----HHHHHS---SSEEEEESSHHHHHHHHHHHHHT-----TCCEEEECSSCEECCSTTCC
T ss_pred             CCEEEEEcCCCCCHHHHHH----HHHHhc---CCeEEEeCHHHHHHHHHHHHHhc-----CCcEEEEECCeeEEecCCCc
Confidence            7999999999999998333    333222   23699999999999999999886     44566666665431110 11


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC-CCCcEEEEEeeCChhHHHHHHhh
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP-SDCQIMLFSATYDKEVMEFAQDM  299 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~l~~SAT~~~~v~~~~~~~  299 (399)
                      ..+++++|++.+.         ....++++||||||++.+. ++...+..++..++ ...+++++|||.+ .+..+....
T Consensus       223 ~~~il~~T~e~~~---------l~~~v~lvVIDEaH~l~d~-~~g~~~~~~l~~l~~~~i~il~~SAT~~-~i~~l~~~~  291 (677)
T 3rc3_A          223 QASHVSCTVEMCS---------VTTPYEVAVIDEIQMIRDP-ARGWAWTRALLGLCAEEVHLCGEPAAID-LVMELMYTT  291 (677)
T ss_dssp             CCSEEEEEGGGCC---------SSSCEEEEEECSGGGGGCT-TTHHHHHHHHHHCCEEEEEEEECGGGHH-HHHHHHHHH
T ss_pred             ccceeEecHhHhh---------hcccCCEEEEecceecCCc-cchHHHHHHHHccCccceEEEeccchHH-HHHHHHHhc
Confidence            2356666664321         2467899999999999764 66666677777776 7889999999953 344444433


Q ss_pred             CCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCC
Q psy11867        300 VPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT  379 (399)
Q Consensus       300 ~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~  379 (399)
                       ..+..+......   ...  .+  ...   .   + ..+... ....||||++++.++.+++.|.+.|+.+..+||+|+
T Consensus       292 -~~~~~v~~~~r~---~~l--~~--~~~---~---l-~~l~~~-~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~  355 (677)
T 3rc3_A          292 -GEEVEVRDYKRL---TPI--SV--LDH---A---L-ESLDNL-RPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLP  355 (677)
T ss_dssp             -TCCEEEEECCCS---SCE--EE--CSS---C---C-CSGGGC-CTTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSC
T ss_pred             -CCceEEEEeeec---chH--HH--HHH---H---H-HHHHhc-CCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCC
Confidence             333333211100   000  00  000   0   0 011112 245689999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhc--CCCcccC
Q psy11867        380 VEQRLSILDRFRE--GEFKIYS  399 (399)
Q Consensus       380 ~~~R~~v~~~F~~--G~~~ILV  399 (399)
                      +.+|..+++.|++  |+.+|||
T Consensus       356 ~~~R~~~~~~F~~~~g~~~VLV  377 (677)
T 3rc3_A          356 PGTKLAQAKKFNDPNDPCKILV  377 (677)
T ss_dssp             HHHHHHHHHHHHCTTSSCCEEE
T ss_pred             HHHHHHHHHHHHccCCCeEEEE
Confidence            9999999999999  9899986

>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=99.91  E-value=4e-24  Score=192.75  Aligned_cols=181  Identities=21%  Similarity=0.225  Sum_probs=130.2

Q ss_pred             HHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC--CCCeEEEEeCcHHHHHHH
Q psy11867        112 PELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI--QEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       112 ~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~--~~~~~lil~Pt~~La~Q~  189 (399)
                      +.+.+.+...+...++++|.++++.+..  |++++++||||||||+++.++++.......  ...++++++|+++|+.|+
T Consensus        48 ~~~~~~~~~~~~~p~~~~q~~~i~~i~~--g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~  125 (235)
T 3llm_A           48 HDLQAILQERELLPVKKFESEILEAISQ--NSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSV  125 (235)
T ss_dssp             HHHHHHHHHHHTSGGGGGHHHHHHHHHH--CSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHH
T ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhc--CCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHH
Confidence            3333334444455689999999999998  799999999999999999999887654332  245899999999999999


Q ss_pred             HHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH-hhcCCch-HH
Q psy11867        190 GEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM-IATQGHQ-DF  267 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l-~~~~~~~-~~  267 (399)
                      .+.+........+..+.+.......  ......+|+|+|||+|++++..    .+++++++|+||||++ ++. ++. ..
T Consensus       126 ~~~~~~~~~~~~~~~~g~~~~~~~~--~~~~~~~Ivv~Tpg~l~~~l~~----~l~~~~~lVlDEah~~~~~~-~~~~~~  198 (235)
T 3llm_A          126 AERVAFERGEEPGKSCGYSVRFESI--LPRPHASIMFCTVGVLLRKLEA----GIRGISHVIVDEIHERDINT-DFLLVV  198 (235)
T ss_dssp             HHHHHHTTTCCTTSSEEEEETTEEE--CCCSSSEEEEEEHHHHHHHHHH----CCTTCCEEEECCTTSCCHHH-HHHHHH
T ss_pred             HHHHHHHhccccCceEEEeechhhc--cCCCCCeEEEECHHHHHHHHHh----hhcCCcEEEEECCccCCcch-HHHHHH
Confidence            9888765543223333333322211  1124578999999999998754    4889999999999986 443 344 44


Q ss_pred             HHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCe
Q psy11867        268 SIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPL  304 (399)
Q Consensus       268 ~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~  304 (399)
                      +..+.... ++.|+++||||++...  +.+.+...|+
T Consensus       199 l~~i~~~~-~~~~~il~SAT~~~~~--~~~~~~~~pv  232 (235)
T 3llm_A          199 LRDVVQAY-PEVRIVLMSATIDTSM--FCEYFFNCPI  232 (235)
T ss_dssp             HHHHHHHC-TTSEEEEEECSSCCHH--HHHHTTSCCC
T ss_pred             HHHHHhhC-CCCeEEEEecCCCHHH--HHHHcCCCCE
Confidence            55555554 5799999999999876  5555555554

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=99.91  E-value=2.5e-24  Score=230.01  Aligned_cols=270  Identities=15%  Similarity=0.155  Sum_probs=179.6

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..|+|+|.+++..++...+.+++++++||+|||++++..+...+..+ ...++|||||+ .|+.|+.+.+.+..    ++
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g-~~~rvLIVvP~-sLl~Qw~~E~~~~f----~l  225 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG-AAERVLIIVPE-TLQHQWLVEMLRRF----NL  225 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS-SCCCEEEECCT-TTHHHHHHHHHHHS----CC
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEeCH-HHHHHHHHHHHHHh----CC
Confidence            47999999999999876567899999999999999988777666543 34579999999 99999999986654    23


Q ss_pred             EEEEEEcCchhhh-----hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhC-CC
Q psy11867        204 SVRYAVRGENLER-----NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL-PS  277 (399)
Q Consensus       204 ~~~~~~~~~~~~~-----~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l-~~  277 (399)
                      .+....++.....     ......+|+|+|++.+.........+...++++||+||||++............++..+ ..
T Consensus       226 ~v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~  305 (968)
T 3dmq_A          226 RFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEH  305 (968)
T ss_dssp             CCEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTT
T ss_pred             CEEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhc
Confidence            3333333322111     11235689999999886542222334566899999999999864322221222233322 24


Q ss_pred             CCcEEEEEeeCCh----hHHHHHHhhCCCC--------------------------------------------------
Q psy11867        278 DCQIMLFSATYDK----EVMEFAQDMVPNP--------------------------------------------------  303 (399)
Q Consensus       278 ~~q~l~~SAT~~~----~v~~~~~~~~~~p--------------------------------------------------  303 (399)
                      ..+++++|||.-.    ++..+.....++.                                                  
T Consensus       306 ~~~~L~LTATPi~n~~~el~sll~~L~p~~~~~~~~f~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~L~~~l~~~~~~~l  385 (968)
T 3dmq_A          306 VPGVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYCPVADAVAMLLAGNKLSNDELNMLGEMIGEQDIEPL  385 (968)
T ss_dssp             CSSEEESCSSCSSSCSSCTHHHHHHHCTTTCSSTHHHHHHHHHHHHHHHHHHTTTTSCCCCGGGTTSSTTTTCTTCSSTT
T ss_pred             CCcEEEEEcCCccCCHHHHHHHHHhcCccccCCHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHhcchhhHHH
Confidence            5679999999521    1111111110000                                                  


Q ss_pred             ------------------------------eEEeccccc-cc--ccceeEEEE---------------------------
Q psy11867        304 ------------------------------LIIKLKREE-ES--LDNIKQHYV---------------------------  323 (399)
Q Consensus       304 ------------------------------~~i~~~~~~-~~--~~~i~~~~~---------------------------  323 (399)
                                                    ..+.-.... ..  .........                           
T Consensus       386 ~~~~~~~~~~~~~~~~~~i~~lld~~g~~~~l~r~~r~~i~~~p~r~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  465 (968)
T 3dmq_A          386 LQAANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGARKSAEDRAR  465 (968)
T ss_dssp             GGGTCCCSSCSTTTHHHHHHHHGGGCTTTTTEECCCTTTCCCCCCCCCCEEEECCCHHHHHHHHHHHHTTCCSSGGGGTH
T ss_pred             HhcccchhhhhHHHHHHHHHHHHHhhCcchhhhhhhhhhhcccChhheEeeecCCCHHHHHHHHHHhhhhhhhhhHHHHh
Confidence                                          000000000 00  000000000                           


Q ss_pred             -----------------EeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHH-CCCeEEEEcCCCCHHHHHH
Q psy11867        324 -----------------MCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSK-EGLNVGLLSGELTVEQRLS  385 (399)
Q Consensus       324 -----------------~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~-~g~~v~~lhg~~~~~~R~~  385 (399)
                                       .......|...+..++.....+++||||++++.++.++..|.. .|+++..+||+|++.+|..
T Consensus       466 ~~l~pe~~~~~l~~~~~~~~~~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~  545 (968)
T 3dmq_A          466 DMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDR  545 (968)
T ss_dssp             HHHCSGGGTTTTTSSSCCTTTTSHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHH
T ss_pred             hhcChHHHHHHhhhhhhcccCccHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHH
Confidence                             0112245888899999887788999999999999999999985 5999999999999999999


Q ss_pred             HHHHHhcCC--CcccC
Q psy11867        386 ILDRFREGE--FKIYS  399 (399)
Q Consensus       386 v~~~F~~G~--~~ILV  399 (399)
                      ++++|++|+  ++|||
T Consensus       546 ~l~~F~~g~~~~~vLv  561 (968)
T 3dmq_A          546 AAAWFAEEDTGAQVLL  561 (968)
T ss_dssp             HHHHHHSTTSSCEEEE
T ss_pred             HHHHHhCCCCcccEEE
Confidence            999999998  98886

>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=99.90  E-value=2.3e-24  Score=191.22  Aligned_cols=163  Identities=17%  Similarity=0.069  Sum_probs=115.5

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC---CCCCeEEEEeCcHHHHHH-HHHHHHHH
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS---IQEPQVLCLAPTYELAIQ-IGEVVAKM  196 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~---~~~~~~lil~Pt~~La~Q-~~~~~~~~  196 (399)
                      .+...|+++|.++++.++.  ++++++++|||+|||++|+++++..+...   ..+.++||++|+++|+.| +.+.++.+
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~--~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~  106 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALE--GKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPF  106 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHT--TCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHH
T ss_pred             cCCCCchHHHHHHHHHHhc--CCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHH
Confidence            4556899999999999998  69999999999999999999998776431   235689999999999999 78888888


Q ss_pred             hccCCCcEEEEEEcCchhhh---hhccCCcEEEeCchhHHHhhhcccc-----ccCCceeEEEEechhhHhhcCCchHHH
Q psy11867        197 GKHITDLSVRYAVRGENLER---NKKITEQIIIGTPGKVLDWGLKYRF-----FDLSKIKVFVLDEADVMIATQGHQDFS  268 (399)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~IlV~Tp~~l~~~~~~~~~-----~~~~~~~~lViDEah~l~~~~~~~~~~  268 (399)
                      ...  ++.+....|+.....   .....++|+|+||++|...+.....     +.+.+++++|+||||++.+...+...+
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            764  456666666543322   1123578999999999988655432     567889999999999997643344433


Q ss_pred             HHHHHhC-------------CCCCcEEEEEee
Q psy11867        269 IRIQKRL-------------PSDCQIMLFSAT  287 (399)
Q Consensus       269 ~~i~~~l-------------~~~~q~l~~SAT  287 (399)
                      ..+....             .+..+++++|||
T Consensus       185 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          185 RHYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHHHHhcccccccccccCCCCcceEEEeecC
Confidence            3332221             157899999998

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.90  E-value=8.3e-23  Score=204.39  Aligned_cols=259  Identities=17%  Similarity=0.174  Sum_probs=170.9

Q ss_pred             CCChHHHHHHhhhhhc--CCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        124 YAPSKIQETALPTLLA--DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~--~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      ..|+|+|.++++.+..  ..+++++++++||+|||++++..+.... ......++|||||+ .|+.|+.++++++..   
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~-~~~~~~~~LIv~P~-~l~~qw~~e~~~~~~---  110 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAK-KENELTPSLVICPL-SVLKNWEEELSKFAP---  110 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHH-HTTCCSSEEEEECS-TTHHHHHHHHHHHCT---
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHH-hcCCCCCEEEEccH-HHHHHHHHHHHHHCC---
Confidence            3699999999987742  1268999999999999999765544443 22344679999995 689999999998864   


Q ss_pred             CcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcE
Q psy11867        202 DLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQI  281 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~  281 (399)
                      .+.+....++..  +......+|+|+|++++.....    +....++++|+||||++...   .......+..++ ..+.
T Consensus       111 ~~~v~~~~g~~~--~~~~~~~~ivi~t~~~l~~~~~----l~~~~~~~vIvDEaH~~kn~---~~~~~~~l~~l~-~~~~  180 (500)
T 1z63_A          111 HLRFAVFHEDRS--KIKLEDYDIILTTYAVLLRDTR----LKEVEWKYIVIDEAQNIKNP---QTKIFKAVKELK-SKYR  180 (500)
T ss_dssp             TSCEEECSSSTT--SCCGGGSSEEEEEHHHHTTCHH----HHTCCEEEEEEETGGGGSCT---TSHHHHHHHTSC-EEEE
T ss_pred             CceEEEEecCch--hccccCCcEEEeeHHHHhccch----hcCCCcCEEEEeCccccCCH---hHHHHHHHHhhc-cCcE
Confidence            345544444432  2223456899999999865421    34457899999999998532   223344555553 4678


Q ss_pred             EEEEeeCCh-h---HHHHHHhhCC--------------------------------CCeEEeccccc----ccccceeEE
Q psy11867        282 MLFSATYDK-E---VMEFAQDMVP--------------------------------NPLIIKLKREE----ESLDNIKQH  321 (399)
Q Consensus       282 l~~SAT~~~-~---v~~~~~~~~~--------------------------------~p~~i~~~~~~----~~~~~i~~~  321 (399)
                      +++|||... .   +..++....+                                .|..++-...+    ..++.....
T Consensus       181 l~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~~l~~~~lrr~k~~~~~~~~lp~~~~~  260 (500)
T 1z63_A          181 IALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTKYDKAIINDLPDKIET  260 (500)
T ss_dssp             EEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHHHHTTTEECCCTTCHHHHTTSCSEEEE
T ss_pred             EEEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHHHHhhHeeeecccccchhhcCCCCeEE
Confidence            999999632 1   2211111111                                22222211110    112222222


Q ss_pred             EEEeCC--------------------------------------------------------hhhHHHHHHHHhccC--C
Q psy11867        322 YVMCKN--------------------------------------------------------IDEKFEAVSNIYGVV--T  343 (399)
Q Consensus       322 ~~~~~~--------------------------------------------------------~~~k~~~l~~ll~~~--~  343 (399)
                      .+.+.-                                                        ...|...+.+++...  .
T Consensus       261 ~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~s~K~~~l~~~l~~~~~~  340 (500)
T 1z63_A          261 NVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLKGGEQSVRRSGKMIRTMEIIEEALDE  340 (500)
T ss_dssp             EEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHHHCSCCCSTTCHHHHHHHHHHHHHHTT
T ss_pred             EEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHhcCccchhhcchhHHHHHHHHHHHHcc
Confidence            233321                                                        123444455555443  4


Q ss_pred             CCcEEEEecchHhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcC-CCcc
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKE-GLNVGLLSGELTVEQRLSILDRFREG-EFKI  397 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~-g~~v~~lhg~~~~~~R~~v~~~F~~G-~~~I  397 (399)
                      ..++||||+++..++.++..|... |..+..+||+++..+|.+++++|++| ..++
T Consensus       341 ~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~v  396 (500)
T 1z63_A          341 GDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKF  396 (500)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCC
T ss_pred             CCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCE
Confidence            579999999999999999999885 99999999999999999999999998 5653

>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=99.90  E-value=8.1e-24  Score=224.98  Aligned_cols=152  Identities=18%  Similarity=0.100  Sum_probs=112.6

Q ss_pred             CChHHHHHHhhhhhcC------------CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLAD------------PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEV  192 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~------------~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~  192 (399)
                      .|+|+|..|++.++..            .+++++++++||||||+++ ++++..+.......++|||+|+++|+.|+.+.
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~  349 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDFIDKVFFVVDRKDLDYQTMKE  349 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTTCCEEEEEECGGGCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCCCceEEEEeCcHHHHHHHHHH
Confidence            5999999999998761            1478999999999999997 56666665544456899999999999999999


Q ss_pred             HHHHhccCCCcEEEEEEcCc---hhhhhh-ccCCcEEEeCchhHHHhhhcccc-ccCCceeEEEEechhhHhhcCCchHH
Q psy11867        193 VAKMGKHITDLSVRYAVRGE---NLERNK-KITEQIIIGTPGKVLDWGLKYRF-FDLSKIKVFVLDEADVMIATQGHQDF  267 (399)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~~~IlV~Tp~~l~~~~~~~~~-~~~~~~~~lViDEah~l~~~~~~~~~  267 (399)
                      ++.++...       ..++.   .+.... ....+|+|+||++|..++..... ..+....+||+||||++..    ...
T Consensus       350 f~~f~~~~-------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~----~~~  418 (1038)
T 2w00_A          350 YQRFSPDS-------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQF----GEA  418 (1038)
T ss_dssp             HHTTSTTC-------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHH----HHH
T ss_pred             HHHhcccc-------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcc----hHH
Confidence            98876431       11222   222222 34678999999999887543321 2355789999999999753    233


Q ss_pred             HHHHHHhCCCCCcEEEEEeeCC
Q psy11867        268 SIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       268 ~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      ...+...++ +.++++||||..
T Consensus       419 ~~~I~~~~p-~a~~lgfTATP~  439 (1038)
T 2w00_A          419 QKNLKKKFK-RYYQFGFTGTPI  439 (1038)
T ss_dssp             HHHHHHHCS-SEEEEEEESSCC
T ss_pred             HHHHHHhCC-cccEEEEeCCcc
Confidence            456667775 589999999975

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.89  E-value=7e-22  Score=201.29  Aligned_cols=130  Identities=19%  Similarity=0.185  Sum_probs=110.2

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      +|+ .|+++|..++|.++.  |+  |++++||+|||++|.+|++.....   +.+++|++||++||.|.++++..++.++
T Consensus        76 lG~-~Pt~VQ~~~ip~Llq--G~--IaeakTGeGKTLvf~Lp~~L~aL~---G~qv~VvTPTreLA~Qdae~m~~l~~~l  147 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHE--GK--IAEMKTGEGKTLVATLAVALNALT---GKGVHVVTVNDYLARRDAEWMGPVYRGL  147 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHT--TS--EEECCSTHHHHHHHHHHHHHHHTT---CSCCEEEESSHHHHHHHHHHHHHHHHTT
T ss_pred             hCC-CCcHHHHhhcccccC--Cc--eeeccCCCchHHHHHHHHHHHHHh---CCCEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            788 999999999999998  56  999999999999999999654433   3469999999999999999999999887


Q ss_pred             CCcEEEEEEcCchhhh-hhccCCcEEEeCchhH-HHhhhccc-----cccCC---ceeEEEEechhhHh
Q psy11867        201 TDLSVRYAVRGENLER-NKKITEQIIIGTPGKV-LDWGLKYR-----FFDLS---KIKVFVLDEADVMI  259 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~~-~~~~~~~IlV~Tp~~l-~~~~~~~~-----~~~~~---~~~~lViDEah~l~  259 (399)
                       ++++.+.+||..... .....++|+||||++| ++++...-     .+.++   .+.++|+||+|.|+
T Consensus       148 -GLsv~~i~Gg~~~~~r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          148 -GLSVGVIQHASTPAERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             -TCCEEECCTTCCHHHHHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             -CCeEEEEeCCCCHHHHHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence             799999998876432 2345789999999999 78776542     34577   89999999999987

>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=4.5e-23  Score=191.04  Aligned_cols=155  Identities=15%  Similarity=0.113  Sum_probs=122.5

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..|+++|.++++.+++  +++.++++|||+|||+++++++...+..  ...++||++||++|+.|+.+.+++++... ..
T Consensus       112 ~~l~~~Q~~ai~~~l~--~~~~ll~~~tGsGKT~~~~~~~~~~~~~--~~~~~lil~Pt~~L~~q~~~~l~~~~~~~-~~  186 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLV--NRRRILNLPTSAGRSLIQALLARYYLEN--YEGKILIIVPTTALTTQMADDFVDYRLFS-HA  186 (282)
T ss_dssp             CCCCHHHHHHHHHHHH--HSEEEECCCTTSCHHHHHHHHHHHHHHH--CSSEEEEECSSHHHHHHHHHHHHHHTSCC-GG
T ss_pred             cCccHHHHHHHHHHHh--cCCeEEEcCCCCCcHHHHHHHHHHHHHc--CCCeEEEEECCHHHHHHHHHHHHHhcccc-cc
Confidence            4899999999999998  4788999999999999999888876643  23479999999999999999999986543 45


Q ss_pred             EEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEE
Q psy11867        204 SVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIML  283 (399)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~  283 (399)
                      .+....++...........+|+|+||+++...    ....+.+++++|+||||++..     .....++..+....++++
T Consensus       187 ~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~----~~~~~~~~~~vIiDEaH~~~~-----~~~~~il~~~~~~~~~l~  257 (282)
T 1rif_A          187 MIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMMNDECHLATG-----KSISSIISGLNNCMFKFG  257 (282)
T ss_dssp             GEEECSTTCSSTTCCCTTCSEEEECHHHHTTS----CGGGGGGEEEEEEETGGGCCH-----HHHHHHTTTCTTCCEEEE
T ss_pred             eEEEEeCCCcchhhhccCCcEEEEchHHHHhh----HHHHHhhCCEEEEECCccCCc-----ccHHHHHHHhhcCCeEEE
Confidence            55666666544333335678999999987553    223467899999999999853     355677777777899999


Q ss_pred             EEeeCChhH
Q psy11867        284 FSATYDKEV  292 (399)
Q Consensus       284 ~SAT~~~~v  292 (399)
                      +|||.++..
T Consensus       258 lSATp~~~~  266 (282)
T 1rif_A          258 LSGSLRDGK  266 (282)
T ss_dssp             ECSSCCTTS
T ss_pred             EeCCCCCcc
Confidence            999987653

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.84  E-value=3.5e-20  Score=194.95  Aligned_cols=261  Identities=16%  Similarity=0.178  Sum_probs=173.7

Q ss_pred             CChHHHHHHhhhhhc--CCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        125 APSKIQETALPTLLA--DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~--~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      .++|+|.+++..++.  ..+++.|++.+||+|||+.++..+...+........+||||| ..|+.|+.+.++++.   +.
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~---p~  311 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWA---PD  311 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHS---TT
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHC---CC
Confidence            688999999987751  127899999999999999877666554433333455899999 678899999998876   35


Q ss_pred             cEEEEEEcCchhhhh---------------hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHH
Q psy11867        203 LSVRYAVRGENLERN---------------KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF  267 (399)
Q Consensus       203 ~~~~~~~~~~~~~~~---------------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~  267 (399)
                      +.+....|+......               .....+|+|+|++.+.....   .+....+++||+||||++-.   ....
T Consensus       312 ~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~---~l~~~~w~~vIvDEaH~lkn---~~s~  385 (800)
T 3mwy_W          312 LNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRA---ELGSIKWQFMAVDEAHRLKN---AESS  385 (800)
T ss_dssp             CCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHH---HHHTSEEEEEEETTGGGGCC---SSSH
T ss_pred             ceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHH---HHhcCCcceeehhhhhhhcC---chhH
Confidence            566666665433211               12356899999999976532   23334688999999999842   3334


Q ss_pred             HHHHHHhCCCCCcEEEEEeeCC----hhHHHHHHhhCCC-----------------------------CeEEeccccc--
Q psy11867        268 SIRIQKRLPSDCQIMLFSATYD----KEVMEFAQDMVPN-----------------------------PLIIKLKREE--  312 (399)
Q Consensus       268 ~~~i~~~l~~~~q~l~~SAT~~----~~v~~~~~~~~~~-----------------------------p~~i~~~~~~--  312 (399)
                      ....+..+. ....+++|||.-    .++..++....++                             |..++-....  
T Consensus       386 ~~~~l~~l~-~~~rl~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~p~~lRR~k~dv~  464 (800)
T 3mwy_W          386 LYESLNSFK-VANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVE  464 (800)
T ss_dssp             HHHHHTTSE-EEEEEEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHHHTTGGGEEECCGGGGT
T ss_pred             HHHHHHHhh-hccEEEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHHHHHhHHHhhhhHHhhh
Confidence            445555553 455789999951    2333333333222                             1111110000  


Q ss_pred             ccccceeEEEEEeCC-----------------------------------------------------------------
Q psy11867        313 ESLDNIKQHYVMCKN-----------------------------------------------------------------  327 (399)
Q Consensus       313 ~~~~~i~~~~~~~~~-----------------------------------------------------------------  327 (399)
                      ..++......+.+.-                                                                 
T Consensus       465 ~~LP~k~~~~v~v~ls~~q~~~Y~~i~~~~~~~l~~~~~~~~~~~l~~l~~Lrk~~~hp~l~~~~~~~~~~~~~~~~~~~  544 (800)
T 3mwy_W          465 KSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTR  544 (800)
T ss_dssp             TTSCCEEEEEEEECCCHHHHHHHHHHHHHCCC----------CTHHHHHHHHHHHHHCGGGSSSHHHHHCCCC----CCS
T ss_pred             hccCCcEEEEEEeCCCHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhcChhhhcchHHHHHHhcccccccH
Confidence            001111222222211                                                                 


Q ss_pred             ---------hhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc
Q psy11867        328 ---------IDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK  396 (399)
Q Consensus       328 ---------~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~  396 (399)
                               ...|...+..++...  ...++||||+....+..|...|...|+.+..+||+++..+|..++++|++|...
T Consensus       545 ~~~~~~l~~~s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~  624 (800)
T 3mwy_W          545 ENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSN  624 (800)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCS
T ss_pred             HHHHHHhhhcChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCC
Confidence                     123555566666543  346999999999999999999999999999999999999999999999997665

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=99.83  E-value=4.7e-19  Score=182.02  Aligned_cols=262  Identities=15%  Similarity=0.175  Sum_probs=167.5

Q ss_pred             CChHHHHHHhhhhhc-------CCCCcEEEEccCCCCceehhHHHHHHhhCCCC----CCCeEEEEeCcHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLA-------DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI----QEPQVLCLAPTYELAIQIGEVV  193 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~-------~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~----~~~~~lil~Pt~~La~Q~~~~~  193 (399)
                      .++|+|.+++..+..       ..+.+.|+..+||+|||+.++..+...+....    ...++|||+|+ +|+.|+.+++
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            689999999998852       22678999999999999998777666554322    23469999997 8899999999


Q ss_pred             HHHhccCCCcEEEEEEcCchhhhhh-----------ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC
Q psy11867        194 AKMGKHITDLSVRYAVRGENLERNK-----------KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ  262 (399)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~  262 (399)
                      +++...  .+.+....+|.......           ....+|+|+|++.+....   ..+....++++|+||||++-.  
T Consensus       134 ~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~---~~l~~~~~~~vI~DEaH~ikn--  206 (644)
T 1z3i_X          134 GKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA---EVLHKGKVGLVICDEGHRLKN--  206 (644)
T ss_dssp             HHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT---TTTTTSCCCEEEETTGGGCCT--
T ss_pred             HHHcCC--CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhH---HHhhcCCccEEEEECceecCC--
Confidence            998754  34444445553321110           124689999999987643   334445788999999999843  


Q ss_pred             CchHHHHHHHHhCCCCCcEEEEEeeCCh-h---HHH---------------HHHhhC-----------------------
Q psy11867        263 GHQDFSIRIQKRLPSDCQIMLFSATYDK-E---VME---------------FAQDMV-----------------------  300 (399)
Q Consensus       263 ~~~~~~~~i~~~l~~~~q~l~~SAT~~~-~---v~~---------------~~~~~~-----------------------  300 (399)
                       ........+..+. ....+++|||.-. .   ++.               |.+.+.                       
T Consensus       207 -~~~~~~~al~~l~-~~~rl~LTgTPiqN~l~El~sll~fl~p~~l~~~~~F~~~f~~pi~~~~~~~~~~~~~~~~~~~~  284 (644)
T 1z3i_X          207 -SDNQTYLALNSMN-AQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKL  284 (644)
T ss_dssp             -TCHHHHHHHHHHC-CSEEEEECSSCSGGGGGGCHHHHHHHHHHHHCCHHHHHHHTHHHHHHHHSTTCCSHHHHHHHHHH
T ss_pred             -hhhHHHHHHHhcc-cCcEEEEecCcccCCHHHHHHHHHhhCCCcCCCHHHHHHhhcchhhhcCCcCCCHHHHHHHHHHH
Confidence             2223333334443 4578999999421 0   000               000000                       


Q ss_pred             ------CCCeEEeccccc--ccccceeEEEEEeC----------------------------------------------
Q psy11867        301 ------PNPLIIKLKREE--ESLDNIKQHYVMCK----------------------------------------------  326 (399)
Q Consensus       301 ------~~p~~i~~~~~~--~~~~~i~~~~~~~~----------------------------------------------  326 (399)
                            -.|..++-....  ..++......+.|.                                              
T Consensus       285 ~~L~~~l~~~~lRR~k~~v~~~LP~k~~~~v~~~ls~~q~~lY~~~~~~~~~~~~~~~g~~~~~~l~~l~~Lrk~c~hp~  364 (644)
T 1z3i_X          285 QELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSITSLKKLCNHPA  364 (644)
T ss_dssp             HHHHHHHHHHEECCCGGGGGGTSCCEEEEEEEECCCHHHHHHHHHHHHHHCGGGSSCTTCCCHHHHHHHHHHHHHHHCTH
T ss_pred             HHHHHHHHHHHHHhhHHhHhhhCCCceEEEEEeCCCHHHHHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHhCCHH
Confidence                  000011000000  00111111111111                                              


Q ss_pred             -------------------------------ChhhHHHHHHHHhcc---CCCCcEEEEecchHhHHHHHHHHHHCCCeEE
Q psy11867        327 -------------------------------NIDEKFEAVSNIYGV---VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVG  372 (399)
Q Consensus       327 -------------------------------~~~~k~~~l~~ll~~---~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~  372 (399)
                                                     ....|...+..++..   ....++||||+.+..++.++..|...|+.+.
T Consensus       365 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~  444 (644)
T 1z3i_X          365 LIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYV  444 (644)
T ss_dssp             HHHHHHHHTCTTCTTGGGTSCSSCCSSSCCGGGSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHhcccchhhhHHhhccccccccccCcccChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEE
Confidence                                           012344444444433   2457999999999999999999999999999


Q ss_pred             EEcCCCCHHHHHHHHHHHhcCCCc
Q psy11867        373 LLSGELTVEQRLSILDRFREGEFK  396 (399)
Q Consensus       373 ~lhg~~~~~~R~~v~~~F~~G~~~  396 (399)
                      .+||+++..+|.+++++|++|...
T Consensus       445 ~l~G~~~~~~R~~~i~~F~~~~~~  468 (644)
T 1z3i_X          445 RLDGTMSIKKRAKIVERFNNPSSP  468 (644)
T ss_dssp             EECSSCCHHHHHHHHHHHHSTTCC
T ss_pred             EEeCCCCHHHHHHHHHHhcCCCCC
Confidence            999999999999999999999764

>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=99.81  E-value=1.8e-18  Score=173.41  Aligned_cols=262  Identities=14%  Similarity=0.120  Sum_probs=184.5

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      .|. .|+++|....-.+..  |+  |+...||+|||+++.+|++-....   +..+.|++||..||.|-.+++..+..++
T Consensus        72 lg~-r~~dvQligg~~L~~--G~--iaEM~TGEGKTLva~lp~~lnAL~---G~~vhVvT~ndyLA~rdae~m~~l~~~L  143 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHE--GK--VAEMKTGEGKTLAATMPIYLNALI---GKGVHLVTVNDYLARRDALWMGPVYLFL  143 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHT--TC--EEECCTTSCHHHHTHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             hCC-CCcHHHHHHHHHHhC--CC--hhhccCCCCccHHHHHHHHHHHhc---CCceEEEeccHHHHHhHHHHHHHHHHHh
Confidence            454 699999999998876  44  999999999999999999855443   3459999999999999999999999887


Q ss_pred             CCcEEEEEEcCc---------------------------------------------------hhhhhhccCCcEEEeCc
Q psy11867        201 TDLSVRYAVRGE---------------------------------------------------NLERNKKITEQIIIGTP  229 (399)
Q Consensus       201 ~~~~~~~~~~~~---------------------------------------------------~~~~~~~~~~~IlV~Tp  229 (399)
                       ++++.+.....                                                   ..++.....++|+.+|.
T Consensus       144 -glsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~aY~~DItYgTn  222 (822)
T 3jux_A          144 -GLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAYLCDVTYGTN  222 (822)
T ss_dssp             -TCCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHHHHSSEEEEEH
T ss_pred             -CCEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHHhcCCCEEccC
Confidence             78888877620                                                   11222234578999999


Q ss_pred             hhH-HHhhhcc-----ccccCCceeEEEEechhhHhhcC------------Cch--------------------------
Q psy11867        230 GKV-LDWGLKY-----RFFDLSKIKVFVLDEADVMIATQ------------GHQ--------------------------  265 (399)
Q Consensus       230 ~~l-~~~~~~~-----~~~~~~~~~~lViDEah~l~~~~------------~~~--------------------------  265 (399)
                      ..| .+++..+     ...-.+.+.+.|+||+|.++=..            ...                          
T Consensus       223 ~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~~~~~~~~y~~~~~~v~~l~~~~dy~vdek~~  302 (822)
T 3jux_A          223 NEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKAR  302 (822)
T ss_dssp             HHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECCCCSCHHHHHHHHHHTTSSCBTTTEEECCSSS
T ss_pred             cchhhHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCCCCCccHHHHHHHHHHHhcCcCCcEEEEcccC
Confidence            887 4444332     12235678999999999653100            000                          


Q ss_pred             ---------------------------HHHHHHHH------hCC------------------------------------
Q psy11867        266 ---------------------------DFSIRIQK------RLP------------------------------------  276 (399)
Q Consensus       266 ---------------------------~~~~~i~~------~l~------------------------------------  276 (399)
                                                 ..+..+..      .+.                                    
T Consensus       303 ~v~lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQai  382 (822)
T 3jux_A          303 TIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQAI  382 (822)
T ss_dssp             CEEECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSEEEETTEEEECSSSSCSCCCSCCCGGGHHHHH
T ss_pred             eEEECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcEEEECCEEEEEECCCCcCCCCCcCchHHHHHH
Confidence                                       00000000      000                                    


Q ss_pred             -------------------------CCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhH
Q psy11867        277 -------------------------SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEK  331 (399)
Q Consensus       277 -------------------------~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k  331 (399)
                                               --.++.+||+|.......+.+.|-.+  .+.+.. +.....+.+....+.....|
T Consensus       383 EaKEgv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te~~Ef~~iY~l~--vv~IPt-nkp~~R~d~~d~vy~t~~eK  459 (822)
T 3jux_A          383 EAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGME--VVVIPT-HKPMIRKDHDDLVFRTQKEK  459 (822)
T ss_dssp             HHHHSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGGHHHHHHHSCCC--EEECCC-SSCCCCEECCCEEESSHHHH
T ss_pred             HHHcCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchHHHHHHHHhCCe--EEEECC-CCCcceeecCcEEEecHHHH
Confidence                                     01268899999998888877766443  333332 23333444433344566789


Q ss_pred             HHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC
Q psy11867        332 FEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGE  394 (399)
Q Consensus       332 ~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~  394 (399)
                      ...+...+...  ...|+||||+|++.++.|+..|.+.|+++.++||+..+.+|..+.+.|+.|.
T Consensus       460 ~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g~  524 (822)
T 3jux_A          460 YEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKGM  524 (822)
T ss_dssp             HHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTTC
T ss_pred             HHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCCe
Confidence            89888887653  4568999999999999999999999999999999977777776777777774

>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=99.79  E-value=4.9e-19  Score=159.41  Aligned_cols=138  Identities=18%  Similarity=0.116  Sum_probs=106.1

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..|+++|.++++.+++  ++++++++|||+|||.+++.++...      +.+++|++|+++|+.|+++.++++     ++
T Consensus        92 ~~l~~~Q~~ai~~~~~--~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~-----~~  158 (237)
T 2fz4_A           92 ISLRDYQEKALERWLV--DKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF-----GE  158 (237)
T ss_dssp             CCCCHHHHHHHHHHTT--TSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG-----CG
T ss_pred             CCcCHHHHHHHHHHHh--CCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC-----CC
Confidence            4899999999999998  5789999999999999998887754      356999999999999999998874     33


Q ss_pred             E-EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEE
Q psy11867        204 S-VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM  282 (399)
Q Consensus       204 ~-~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l  282 (399)
                      . +....++..      ...+|+|+|++.+......    ...+++++||||||++.+. .+.    .+...++ ..+++
T Consensus       159 ~~v~~~~g~~~------~~~~i~v~T~~~l~~~~~~----~~~~~~llIiDEaH~l~~~-~~~----~i~~~~~-~~~~l  222 (237)
T 2fz4_A          159 EYVGEFSGRIK------ELKPLTVSTYDSAYVNAEK----LGNRFMLLIFDEVHHLPAE-SYV----QIAQMSI-APFRL  222 (237)
T ss_dssp             GGEEEESSSCB------CCCSEEEEEHHHHHHTHHH----HTTTCSEEEEECSSCCCTT-THH----HHHHTCC-CSEEE
T ss_pred             CeEEEEeCCCC------CcCCEEEEeHHHHHhhHHH----hcccCCEEEEECCccCCCh-HHH----HHHHhcc-CCEEE
Confidence            4 444444432      2457999999998765432    1346899999999998653 332    3455554 67899


Q ss_pred             EEEeeCCh
Q psy11867        283 LFSATYDK  290 (399)
Q Consensus       283 ~~SAT~~~  290 (399)
                      ++|||...
T Consensus       223 ~LSATp~r  230 (237)
T 2fz4_A          223 GLTATFER  230 (237)
T ss_dssp             EEEESCC-
T ss_pred             EEecCCCC
Confidence            99999764

>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=99.70  E-value=8.4e-16  Score=157.92  Aligned_cols=114  Identities=14%  Similarity=0.107  Sum_probs=76.6

Q ss_pred             CCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhcc-C-CCCcEEEEecch
Q psy11867        277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGV-V-TIGQAMIFCHTR  354 (399)
Q Consensus       277 ~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~-~-~~~k~IIF~~s~  354 (399)
                      ...|+++||||.+......    ........+........     .+.+.....+...+...+.. . ...++||||+++
T Consensus       379 ~~~q~i~~SAT~~~~~~~~----~~~~~~~~~r~~~l~~p-----~i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~  449 (664)
T 1c4o_A          379 RVSQVVFVSATPGPFELAH----SGRVVEQIIRPTGLLDP-----LVRVKPTENQILDLMEGIRERAARGERTLVTVLTV  449 (664)
T ss_dssp             TCSEEEEEESSCCHHHHHH----CSEEEEECSCTTCCCCC-----EEEEECSTTHHHHHHHHHHHHHHTTCEEEEECSSH
T ss_pred             hcCCEEEEecCCCHHHHHh----hhCeeeeeeccCCCCCC-----eEEEecccchHHHHHHHHHHHHhcCCEEEEEECCH
Confidence            3678999999988654222    11111111111110111     11122223344444333322 2 357999999999


Q ss_pred             HhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        355 KTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       355 ~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.|+.|++.|...|+++..+||+|++.+|..+++.|+.|+++|||
T Consensus       450 ~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLv  494 (664)
T 1c4o_A          450 RMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLV  494 (664)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEE
T ss_pred             HHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEE
Confidence            999999999999999999999999999999999999999999986

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.67  E-value=6.6e-17  Score=163.20  Aligned_cols=129  Identities=17%  Similarity=0.080  Sum_probs=97.1

Q ss_pred             CChHHHHHHhhhhhcC--CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        125 APSKIQETALPTLLAD--PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~--~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      .|+|.|.+++..+...  .|++++++||||+|||++|++|++.      .+++++|++||++|+.|+.+.++.+.... +
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~------~~~~v~i~~pt~~l~~q~~~~~~~l~~~~-~   75 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE------VKPKVLFVVRTHNEFYPIYRDLTKIREKR-N   75 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH------HCSEEEEEESSGGGHHHHHHHHTTCCCSS-C
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh------CCCeEEEEcCCHHHHHHHHHHHHHHhhhc-C
Confidence            7899999987755321  2799999999999999999999997      35689999999999999999999886654 5


Q ss_pred             cEEEEEEcCchhh------------------------------------------------------hhhccCCcEEEeC
Q psy11867        203 LSVRYAVRGENLE------------------------------------------------------RNKKITEQIIIGT  228 (399)
Q Consensus       203 ~~~~~~~~~~~~~------------------------------------------------------~~~~~~~~IlV~T  228 (399)
                      +++....|+..+.                                                      +......+|||+|
T Consensus        76 ~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~adIVV~~  155 (551)
T 3crv_A           76 ITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALT  155 (551)
T ss_dssp             CCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCSEEEEE
T ss_pred             ccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCCEEEeC
Confidence            5555554432210                                                      1112356899999


Q ss_pred             chhHHHhhhccccccCCceeEEEEechhhHhh
Q psy11867        229 PGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       229 p~~l~~~~~~~~~~~~~~~~~lViDEah~l~~  260 (399)
                      ++.|++...+..........++||||||.|.+
T Consensus       156 ~~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          156 YPYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             THHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             chHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            99999875443321224678999999998865

>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=99.64  E-value=1e-14  Score=149.70  Aligned_cols=114  Identities=16%  Similarity=0.209  Sum_probs=77.2

Q ss_pred             CCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHH-HhccC-CCCcEEEEecch
Q psy11867        277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSN-IYGVV-TIGQAMIFCHTR  354 (399)
Q Consensus       277 ~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~-ll~~~-~~~k~IIF~~s~  354 (399)
                      ...|+++||||.+.......    .......+.......+.    + .+.....+...+.. +.... ...++||||+++
T Consensus       385 ~~~q~i~~SAT~~~~~~~~~----~~~~~~~~r~~~l~~p~----i-~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~  455 (661)
T 2d7d_A          385 HMHNIVYVSATPGPYEIEHT----DEMVEQIIRPTGLLDPL----I-DVRPIEGQIDDLIGEIQARIERNERVLVTTLTK  455 (661)
T ss_dssp             TCSEEEEECSSCCHHHHHHC----SSCEEECCCTTCCCCCE----E-EEECSTTHHHHHHHHHHHHHTTTCEEEEECSSH
T ss_pred             cCCCEEEEecCCChhHHHhh----hCeeeeeecccCCCCCe----E-EEecccchHHHHHHHHHHHHhcCCeEEEEECCH
Confidence            46899999999886543221    11122211111111111    1 11222233333333 33322 346999999999


Q ss_pred             HhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        355 KTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       355 ~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.|+.|++.|...|+++..+||++++.+|..+++.|++|+++|||
T Consensus       456 ~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLV  500 (661)
T 2d7d_A          456 KMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLV  500 (661)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEE
T ss_pred             HHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEE
Confidence            999999999999999999999999999999999999999999986

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.57  E-value=2e-15  Score=151.92  Aligned_cols=126  Identities=15%  Similarity=0.154  Sum_probs=85.4

Q ss_pred             cCCCCChHHHHHHhhhhh---cCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        121 MGFYAPSKIQETALPTLL---ADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll---~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      .|| .|+|+|.+++..+.   .. |++++++||||+|||++|++|++..      +.+++|++||++|+.|+.+.+..+.
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~-~~~~~~~a~TGtGKT~~~l~~~~~~------~~~~~~~~~t~~l~~q~~~~~~~l~   75 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKH-GKTLLLNAKPGLGKTVFVEVLGMQL------KKKVLIFTRTHSQLDSIYKNAKLLG   75 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHT-TCEEEEECCTTSCHHHHHHHHHHHH------TCEEEEEESCHHHHHHHHHHHGGGT
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHc-CCCEEEEcCCCCcHHHHHHHHHHhC------CCcEEEEcCCHHHHHHHHHHHHhcC
Confidence            467 89999999876543   22 7999999999999999999999864      4679999999999999998887753


Q ss_pred             ccCCCcEEEEEEcCch--------------------------------------------------hhhhhccCCcEEEe
Q psy11867        198 KHITDLSVRYAVRGEN--------------------------------------------------LERNKKITEQIIIG  227 (399)
Q Consensus       198 ~~~~~~~~~~~~~~~~--------------------------------------------------~~~~~~~~~~IlV~  227 (399)
                      .     ++....|...                                                  ..+......+|||+
T Consensus        76 ~-----~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~adiVV~  150 (540)
T 2vl7_A           76 L-----KTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKDVIAM  150 (540)
T ss_dssp             C-----CEEEC---------------------------------------------------------CTTGGGCSEEEE
T ss_pred             C-----cEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcCCEEEE
Confidence            1     1111111000                                                  00111235689999


Q ss_pred             CchhHHHhhhccccc------cCCceeEEEEechhhHh
Q psy11867        228 TPGKVLDWGLKYRFF------DLSKIKVFVLDEADVMI  259 (399)
Q Consensus       228 Tp~~l~~~~~~~~~~------~~~~~~~lViDEah~l~  259 (399)
                      |++.|++........      .+....++||||||.|.
T Consensus       151 n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          151 TYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             ETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             ChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            999998754332111      23567899999999983

>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=99.36  E-value=3.8e-12  Score=108.76  Aligned_cols=87  Identities=54%  Similarity=0.963  Sum_probs=82.0

Q ss_pred             ccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhc
Q psy11867        313 ESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFRE  392 (399)
Q Consensus       313 ~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~  392 (399)
                      .++.++.|+|+.++..+.|...|..++.....+++||||++++.|+.++..|...|+.+..+||+|++.+|..+++.|++
T Consensus         3 ~~~~~i~q~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~   82 (175)
T 2rb4_A            3 LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRD   82 (175)
T ss_dssp             CCBCCEEEEEEECSSHHHHHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHT
T ss_pred             CccCCceEEEEEcCChHhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHc
Confidence            35678999999999877799999999998888899999999999999999999999999999999999999999999999


Q ss_pred             CCCcccC
Q psy11867        393 GEFKIYS  399 (399)
Q Consensus       393 G~~~ILV  399 (399)
                      |+.+|||
T Consensus        83 g~~~vLv   89 (175)
T 2rb4_A           83 GKEKVLI   89 (175)
T ss_dssp             TSCSEEE
T ss_pred             CCCeEEE
Confidence            9999986

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.35  E-value=2.6e-12  Score=111.34  Aligned_cols=101  Identities=14%  Similarity=0.184  Sum_probs=76.0

Q ss_pred             HhhCCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcC
Q psy11867        297 QDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSG  376 (399)
Q Consensus       297 ~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg  376 (399)
                      ..++.+|..+.+........++.|.++.+.. ..|...|.+++.... +++||||++++.++.++..|...|+.+..+||
T Consensus         9 ~~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~-~~K~~~L~~~l~~~~-~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg   86 (191)
T 2p6n_A            9 SGVDLGTENLYFQSMGAASLDVIQEVEYVKE-EAKMVYLLECLQKTP-PPVLIFAEKKADVDAIHEYLLLKGVEAVAIHG   86 (191)
T ss_dssp             -------------------CCSEEEEEECCG-GGHHHHHHHHHTTSC-SCEEEECSCHHHHHHHHHHHHHHTCCEEEECT
T ss_pred             ccccCCCEEEEECCCCCCCcCceEEEEEcCh-HHHHHHHHHHHHhCC-CCEEEEECCHHHHHHHHHHHHHcCCcEEEEeC
Confidence            4577889999988888888999999998865 679999999988753 68999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcccC
Q psy11867        377 ELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       377 ~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +|++.+|..+++.|++|+.+|||
T Consensus        87 ~~~~~~R~~~l~~F~~g~~~vLv  109 (191)
T 2p6n_A           87 GKDQEERTKAIEAFREGKKDVLV  109 (191)
T ss_dssp             TSCHHHHHHHHHHHHHTSCSEEE
T ss_pred             CCCHHHHHHHHHHHhcCCCEEEE
Confidence            99999999999999999999986

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.33  E-value=6.7e-13  Score=135.24  Aligned_cols=72  Identities=21%  Similarity=0.213  Sum_probs=60.3

Q ss_pred             CCChHHHHHHhhhh----hcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Q psy11867        124 YAPSKIQETALPTL----LADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH  199 (399)
Q Consensus       124 ~~p~~iQ~~ai~~l----l~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~  199 (399)
                      .+|++.|.+.+..+    .+  |++++++||||+|||++|++|++..+..  .+.+++|++||++|+.|+.+.++.+...
T Consensus         2 ~~~R~~Q~~~~~~v~~~l~~--~~~~~~~apTGtGKT~a~l~p~l~~~~~--~~~kvli~t~T~~l~~Qi~~el~~l~~~   77 (620)
T 4a15_A            2 YENRQYQVEAIDFLRSSLQK--SYGVALESPTGSGKTIMALKSALQYSSE--RKLKVLYLVRTNSQEEQVIKELRSLSST   77 (620)
T ss_dssp             ---CHHHHHHHHHHHHHHHH--SSEEEEECCTTSCHHHHHHHHHHHHHHH--HTCEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHc--CCCEEEECCCCCCHHHHHHHHHHHhhhh--cCCeEEEECCCHHHHHHHHHHHHHHhhc
Confidence            46899999998644    44  7999999999999999999999988754  3568999999999999999999988654

>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=99.29  E-value=1.3e-11  Score=105.13  Aligned_cols=85  Identities=24%  Similarity=0.359  Sum_probs=77.6

Q ss_pred             cccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC
Q psy11867        314 SLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREG  393 (399)
Q Consensus       314 ~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G  393 (399)
                      ++.++.|+|+.+.. +.|...|..+++....+++||||++++.|+.++..|...|+.+..+||+|++.+|..+++.|++|
T Consensus         2 ~~~~i~q~~~~~~~-~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g   80 (172)
T 1t5i_A            2 SLHGLQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF   80 (172)
T ss_dssp             ---CCEEEEEECCG-GGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             ccCCeEEEEEECCh-HHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCC
Confidence            35678999998875 67999999999988888999999999999999999999999999999999999999999999999


Q ss_pred             CCcccC
Q psy11867        394 EFKIYS  399 (399)
Q Consensus       394 ~~~ILV  399 (399)
                      +.+|||
T Consensus        81 ~~~vLv   86 (172)
T 1t5i_A           81 QRRILV   86 (172)
T ss_dssp             SCSEEE
T ss_pred             CCcEEE
Confidence            999986

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.29  E-value=1.5e-11  Score=103.96  Aligned_cols=84  Identities=30%  Similarity=0.597  Sum_probs=77.7

Q ss_pred             cceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        316 DNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       316 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                      .+++|+|+.+...+.|...|..++.....+++||||++++.++.++..|...|+.+..+||+|++.+|..+++.|++|+.
T Consensus         2 ~~i~~~~~~~~~~~~K~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   81 (165)
T 1fuk_A            2 EGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSS   81 (165)
T ss_dssp             --CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCcEEEEEECCcchhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCC
Confidence            46889999998766699999999998888999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy11867        396 KIYS  399 (399)
Q Consensus       396 ~ILV  399 (399)
                      +|||
T Consensus        82 ~vlv   85 (165)
T 1fuk_A           82 RILI   85 (165)
T ss_dssp             SEEE
T ss_pred             EEEE
Confidence            9986

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.28  E-value=1.5e-11  Score=103.69  Aligned_cols=86  Identities=19%  Similarity=0.474  Sum_probs=79.2

Q ss_pred             ccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhc
Q psy11867        313 ESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFRE  392 (399)
Q Consensus       313 ~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~  392 (399)
                      ....++.|.|+.+.. +.|...|..++.....+++||||++++.++.++..|...|+.+..+||+|++.+|..+++.|++
T Consensus         5 ~~~~~i~~~~~~~~~-~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~   83 (163)
T 2hjv_A            5 LTTRNIEHAVIQVRE-ENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKR   83 (163)
T ss_dssp             -CCCCEEEEEEECCG-GGHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             cCcccceEEEEECCh-HHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHc
Confidence            456789999998865 7799999999988888899999999999999999999999999999999999999999999999


Q ss_pred             CCCcccC
Q psy11867        393 GEFKIYS  399 (399)
Q Consensus       393 G~~~ILV  399 (399)
                      |+.+|||
T Consensus        84 g~~~vlv   90 (163)
T 2hjv_A           84 GEYRYLV   90 (163)
T ss_dssp             TSCSEEE
T ss_pred             CCCeEEE
Confidence            9999986

>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=99.20  E-value=3.4e-11  Score=103.74  Aligned_cols=89  Identities=21%  Similarity=0.320  Sum_probs=70.8

Q ss_pred             cccccccceeEEEEEeCChhhHHHHHHHHhccC-CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHH
Q psy11867        310 REEESLDNIKQHYVMCKNIDEKFEAVSNIYGVV-TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILD  388 (399)
Q Consensus       310 ~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~  388 (399)
                      ....+..++.|.|+.++. ..|...|.+++... ..+++||||++++.|+.++..|...|+.+..+||+|++.+|..+++
T Consensus        12 ~~~~~~~~i~q~~~~v~~-~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~   90 (185)
T 2jgn_A           12 FQGSTSENITQKVVWVEE-SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALH   90 (185)
T ss_dssp             ----CCTTEEEEEEECCG-GGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHH
T ss_pred             ccCCCCCCceEEEEEeCc-HHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHH
Confidence            344567899999999875 67999999999887 4679999999999999999999999999999999999999999999


Q ss_pred             HHhcCCCcccC
Q psy11867        389 RFREGEFKIYS  399 (399)
Q Consensus       389 ~F~~G~~~ILV  399 (399)
                      .|++|+.+|||
T Consensus        91 ~f~~g~~~vLv  101 (185)
T 2jgn_A           91 QFRSGKSPILV  101 (185)
T ss_dssp             HHHHTSSSEEE
T ss_pred             HHHcCCCeEEE
Confidence            99999999986

>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=98.62  E-value=2e-11  Score=103.77  Aligned_cols=84  Identities=20%  Similarity=0.375  Sum_probs=77.4

Q ss_pred             cceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        316 DNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       316 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                      +++.|.|+.++..+.|...|..+++....+++||||++++.|+.++..|...|+.+..+||+|++.+|..+++.|++|+.
T Consensus         2 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~   81 (170)
T 2yjt_D            2 KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRV   81 (170)
Confidence            46788888887657899999999988777899999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy11867        396 KIYS  399 (399)
Q Consensus       396 ~ILV  399 (399)
                      +|||
T Consensus        82 ~vLv   85 (170)
T 2yjt_D           82 NVLV   85 (170)
Confidence            9986

>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=99.01  E-value=6.5e-10  Score=97.85  Aligned_cols=81  Identities=23%  Similarity=0.397  Sum_probs=73.3

Q ss_pred             eeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcc
Q psy11867        318 IKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI  397 (399)
Q Consensus       318 i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~I  397 (399)
                      +.+.++.+.. ..|...+..++.....+++||||++++.++.++..|...|+.+..+||+|++.+|..+++.|++|+.+|
T Consensus         6 ~~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~v   84 (212)
T 3eaq_A            6 YEEEAVPAPV-RGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRV   84 (212)
T ss_dssp             BCCEEEECCT-TSHHHHHHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCE
T ss_pred             eeeeEEeCCH-HHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeE
Confidence            3455555544 679999999999888899999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q psy11867        398 YS  399 (399)
Q Consensus       398 LV  399 (399)
                      ||
T Consensus        85 lv   86 (212)
T 3eaq_A           85 LV   86 (212)
T ss_dssp             EE
T ss_pred             EE
Confidence            86

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.00  E-value=6.6e-10  Score=102.85  Aligned_cols=82  Identities=21%  Similarity=0.385  Sum_probs=75.7

Q ss_pred             ceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc
Q psy11867        317 NIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK  396 (399)
Q Consensus       317 ~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~  396 (399)
                      .+.++++.+.. ..|...+..++.....+++||||++++.++.++..|...|+.+..+||+|++.+|..+++.|++|+.+
T Consensus         2 ~v~~~~i~~~~-~~K~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~   80 (300)
T 3i32_A            2 TYEEEAVPAPV-RGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVR   80 (300)
T ss_dssp             CSEEEEEECCS-SSHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCC
T ss_pred             ceEEEEEECCH-HHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCce
Confidence            35677887766 67999999999888889999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q psy11867        397 IYS  399 (399)
Q Consensus       397 ILV  399 (399)
                      |||
T Consensus        81 vLV   83 (300)
T 3i32_A           81 VLV   83 (300)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            986

>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=98.98  E-value=7.8e-10  Score=112.50  Aligned_cols=145  Identities=20%  Similarity=0.269  Sum_probs=92.6

Q ss_pred             hHHHHHHhhhhhcCCCCcEEEEccCCCCce--ehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        127 SKIQETALPTLLADPPHNMIAQSQSGTGKT--AAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       127 ~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT--~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      ++.|..|++.++.  ++.++++|++|||||  ++++++.+..+... .+.++++++||..+|.++.+.+......+ ++.
T Consensus       151 ~~~Q~~Ai~~~l~--~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~-~~~~vll~APTg~AA~~L~e~~~~~~~~l-~l~  226 (608)
T 1w36_D          151 INWQKVAAAVALT--RRISVISGGPGTGKTTTVAKLLAALIQMADG-ERCRIRLAAPTGKAAARLTESLGKALRQL-PLT  226 (608)
T ss_dssp             CCHHHHHHHHHHT--BSEEEEECCTTSTHHHHHHHHHHHHHHTCSS-CCCCEEEEBSSHHHHHHHHHHHTHHHHHS-SCC
T ss_pred             CHHHHHHHHHHhc--CCCEEEEeCCCCCHHHHHHHHHHHHHHhhhc-CCCeEEEEeCChhHHHHHHHHHHHHHhcC-CCC
Confidence            7899999999997  699999999999999  77888888765332 45689999999999999998887765443 111


Q ss_pred             EEEEEcCchhhhhhccCCc-EEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEE
Q psy11867        205 VRYAVRGENLERNKKITEQ-IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIML  283 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~-IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~  283 (399)
                      .... .  .... .....| ++-.+|+.. .+ .. .......++++|||||+++ +    ...+..++..++..+|+++
T Consensus       227 ~~~~-~--~~~~-~~~Tih~ll~~~~~~~-~~-~~-~~~~~l~~d~lIIDEAsml-~----~~~~~~Ll~~l~~~~~liL  294 (608)
T 1w36_D          227 DEQK-K--RIPE-DASTLHRLLGAQPGSQ-RL-RH-HAGNPLHLDVLVVDEASMI-D----LPMMSRLIDALPDHARVIF  294 (608)
T ss_dssp             SCCC-C--SCSC-CCBTTTSCC--------------CTTSCCSCSEEEECSGGGC-B----HHHHHHHHHTCCTTCEEEE
T ss_pred             HHHH-h--ccch-hhhhhHhhhccCCCch-HH-Hh-ccCCCCCCCEEEEechhhC-C----HHHHHHHHHhCCCCCEEEE
Confidence            0000 0  0000 001112 222233321 11 11 1112237899999999943 2    4566778888998999998


Q ss_pred             EEee
Q psy11867        284 FSAT  287 (399)
Q Consensus       284 ~SAT  287 (399)
                      +.=.
T Consensus       295 vGD~  298 (608)
T 1w36_D          295 LGDR  298 (608)
T ss_dssp             EECT
T ss_pred             Ecch
Confidence            8644

>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=98.22  E-value=4.6e-06  Score=81.91  Aligned_cols=140  Identities=16%  Similarity=0.198  Sum_probs=78.8

Q ss_pred             HcCCCCChHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        120 EMGFYAPSKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       120 ~~g~~~p~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      .+.|..+++-|.+|+..++..   +...+++.|+.|||||.+.. .++..+... ....+++++||...+..+.+.+.  
T Consensus        20 p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~-~~~~~l~~~-~~~~il~~a~T~~Aa~~l~~~~~--   95 (459)
T 3upu_A           20 HMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTK-FIIEALIST-GETGIILAAPTHAAKKILSKLSG--   95 (459)
T ss_dssp             -CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHH-HHHHHHHHT-TCCCEEEEESSHHHHHHHHHHHS--
T ss_pred             CCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHH-HHHHHHHhc-CCceEEEecCcHHHHHHHHhhhc--
Confidence            366889999999999977542   12499999999999996543 334333322 22469999999988876655441  


Q ss_pred             hccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC
Q psy11867        197 GKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP  276 (399)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~  276 (399)
                            ........-.............+           .......+...+++|+||++.+.     ......+...++
T Consensus        96 ------~~~~T~h~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~iiiDE~~~~~-----~~~~~~l~~~~~  153 (459)
T 3upu_A           96 ------KEASTIHSILKINPVTYEENVLF-----------EQKEVPDLAKCRVLICDEVSMYD-----RKLFKILLSTIP  153 (459)
T ss_dssp             ------SCEEEHHHHHTEEEEECSSCEEE-----------EECSCCCCSSCSEEEESCGGGCC-----HHHHHHHHHHSC
T ss_pred             ------cchhhHHHHhccCcccccccchh-----------cccccccccCCCEEEEECchhCC-----HHHHHHHHHhcc
Confidence                  11111000000000000000000           00112245678999999999753     234555666666


Q ss_pred             CCCcEEEEE
Q psy11867        277 SDCQIMLFS  285 (399)
Q Consensus       277 ~~~q~l~~S  285 (399)
                      ...+++++.
T Consensus       154 ~~~~~~~vG  162 (459)
T 3upu_A          154 PWCTIIGIG  162 (459)
T ss_dssp             TTCEEEEEE
T ss_pred             CCCEEEEEC
Confidence            566666554

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=98.12  E-value=3.1e-06  Score=77.05  Aligned_cols=70  Identities=21%  Similarity=0.283  Sum_probs=62.8

Q ss_pred             hhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcC-CCcc
Q psy11867        328 IDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKE-GLNVGLLSGELTVEQRLSILDRFREG-EFKI  397 (399)
Q Consensus       328 ~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~-g~~v~~lhg~~~~~~R~~v~~~F~~G-~~~I  397 (399)
                      ...|...+.+++...  ...++||||+++..++.++..|... |+.+..+||++++.+|..++++|++| ..+|
T Consensus        94 ~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v  167 (271)
T 1z5z_A           94 RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKF  167 (271)
T ss_dssp             TCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCE
T ss_pred             cCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCE
Confidence            367888888888765  5689999999999999999999885 99999999999999999999999999 7774

>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=98.12  E-value=7.8e-06  Score=82.29  Aligned_cols=123  Identities=20%  Similarity=0.333  Sum_probs=79.0

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .+++.|..++..++.  ++.+++.|+.|||||.... .++..+..  .+.++++++||...+..+.+...   .     .
T Consensus       189 ~L~~~Q~~Av~~~~~--~~~~~I~G~pGTGKTt~i~-~l~~~l~~--~g~~Vl~~ApT~~Aa~~L~e~~~---~-----~  255 (574)
T 3e1s_A          189 GLSEEQASVLDQLAG--HRLVVLTGGPGTGKSTTTK-AVADLAES--LGLEVGLCAPTGKAARRLGEVTG---R-----T  255 (574)
T ss_dssp             TCCHHHHHHHHHHTT--CSEEEEECCTTSCHHHHHH-HHHHHHHH--TTCCEEEEESSHHHHHHHHHHHT---S-----C
T ss_pred             CCCHHHHHHHHHHHh--CCEEEEEcCCCCCHHHHHH-HHHHHHHh--cCCeEEEecCcHHHHHHhHhhhc---c-----c
Confidence            578999999999987  5899999999999996532 33333332  34569999999998877765431   0     0


Q ss_pred             EEEEEcCchhhhhhccCCcEEEeCchhHHHhh---hccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcE
Q psy11867        205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWG---LKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQI  281 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~---~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~  281 (399)
                                           ..|-.+++...   ...........+++|||||+++.     ...+..+++.++...++
T Consensus       256 ---------------------a~Tih~ll~~~~~~~~~~~~~~~~~dvlIIDEasml~-----~~~~~~Ll~~~~~~~~l  309 (574)
T 3e1s_A          256 ---------------------ASTVHRLLGYGPQGFRHNHLEPAPYDLLIVDEVSMMG-----DALMLSLLAAVPPGARV  309 (574)
T ss_dssp             ---------------------EEEHHHHTTEETTEESCSSSSCCSCSEEEECCGGGCC-----HHHHHHHHTTSCTTCEE
T ss_pred             ---------------------HHHHHHHHcCCcchhhhhhcccccCCEEEEcCccCCC-----HHHHHHHHHhCcCCCEE
Confidence                                 00111111000   00111123467899999999863     34566777888777777


Q ss_pred             EEEEe
Q psy11867        282 MLFSA  286 (399)
Q Consensus       282 l~~SA  286 (399)
                      +++.=
T Consensus       310 ilvGD  314 (574)
T 3e1s_A          310 LLVGD  314 (574)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            77643

>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=98.11  E-value=0.00019  Score=73.42  Aligned_cols=70  Identities=13%  Similarity=0.172  Sum_probs=55.8

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ..+++-|.+|+...    ...++|.|+.|||||.+.+--+...+.. .....++|++++|+..+.++.+.+.++.
T Consensus         8 ~~Ln~~Q~~av~~~----~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            8 DSLNDKQREAVAAP----RSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TTCCHHHHHHHTCC----SSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHhCC----CCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            46899999999732    5789999999999998776656655544 2234579999999999999999998874

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.99  E-value=1.3e-05  Score=82.03  Aligned_cols=69  Identities=26%  Similarity=0.272  Sum_probs=54.2

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      .+++-|.+|+..++.. ..-.+|+||+|||||.+..-.+.+.+..   +.++|+++||..-+.++.+.+...+
T Consensus       189 ~LN~~Q~~AV~~al~~-~~~~lI~GPPGTGKT~ti~~~I~~l~~~---~~~ILv~a~TN~AvD~i~erL~~~~  257 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQ-KELAIIHGPPGTGKTTTVVEIILQAVKQ---GLKVLCCAPSNIAVDNLVERLALCK  257 (646)
T ss_dssp             TCCHHHHHHHHHHHHC-SSEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHhcC-CCceEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEcCchHHHHHHHHHHHhcC
Confidence            5789999999998873 2357899999999998765555555543   4579999999999999988876653

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=97.99  E-value=2.7e-05  Score=79.41  Aligned_cols=71  Identities=24%  Similarity=0.215  Sum_probs=55.1

Q ss_pred             CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        123 FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      +..+++.|..|+..++.  +...+++||+|||||....-.+...+..  .+.++|+++||..-+.++.+.+.+.+
T Consensus       178 ~~~ln~~Q~~av~~~l~--~~~~li~GppGTGKT~~~~~~i~~l~~~--~~~~ilv~a~tn~A~~~l~~~l~~~~  248 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQ--RPLSLIQGPPGTGKTVTSATIVYHLARQ--GNGPVLVCAPSNIAVDQLTEKIHQTG  248 (624)
T ss_dssp             SCCCCHHHHHHHHHHHT--CSEEEEECCTTSCHHHHHHHHHHHHHTS--SSCCEEEEESSHHHHHHHHHHHHTTT
T ss_pred             cCCCCHHHHHHHHHHhc--CCCeEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEEEeCcHHHHHHHHHHHHhcC
Confidence            45689999999999887  4788999999999997654333333321  34579999999999999988877643

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.92  E-value=3.2e-05  Score=80.78  Aligned_cols=71  Identities=20%  Similarity=0.256  Sum_probs=54.8

Q ss_pred             CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        123 FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      +..+++.|.+|+..++.  +.-.+++||+|||||....-.+...+..  .+.++|+++||..-+.++.+.+.+.+
T Consensus       358 ~~~Ln~~Q~~Av~~~l~--~~~~lI~GppGTGKT~~i~~~i~~l~~~--~~~~ILv~a~tn~A~d~l~~rL~~~g  428 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQ--RPLSLIQGPPGTGKTVTSATIVYHLSKI--HKDRILVCAPSNVAVDHLAAKLRDLG  428 (802)
T ss_dssp             SCCCCHHHHHHHHHHTT--CSEEEEECSTTSSHHHHHHHHHHHHHHH--HCCCEEEEESSHHHHHHHHHHHHHTT
T ss_pred             cccCCHHHHHHHHHHhc--CCCEEEECCCCCCHHHHHHHHHHHHHhC--CCCeEEEEcCcHHHHHHHHHHHHhhC
Confidence            45678999999999987  4678999999999997654333222221  34579999999999999999888753

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=97.90  E-value=6.4e-05  Score=78.46  Aligned_cols=71  Identities=24%  Similarity=0.239  Sum_probs=54.6

Q ss_pred             CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        123 FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ...+++.|.+|+..++.  +.-.+++||+|||||.+..- ++..+... .+.++++++||..-+.++.+.+...+
T Consensus       354 ~~~Ln~~Q~~Av~~~l~--~~~~lI~GppGTGKT~ti~~-~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~g  424 (800)
T 2wjy_A          354 LPDLNHSQVYAVKTVLQ--RPLSLIQGPPGTGKTVTSAT-IVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQTG  424 (800)
T ss_dssp             SCCCCHHHHHHHHHHHT--SSEEEEECCTTSCHHHHHHH-HHHHHHTT-CSSCEEEEESSHHHHHHHHHHHHTTT
T ss_pred             ccCCCHHHHHHHHHhcc--CCeEEEEcCCCCCHHHHHHH-HHHHHHHc-CCCcEEEEcCcHHHHHHHHHHHHHhC
Confidence            44678999999999887  47889999999999976543 33333221 45579999999999999988877643

>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=97.42  E-value=0.00055  Score=65.03  Aligned_cols=74  Identities=12%  Similarity=0.065  Sum_probs=57.7

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      .++|+|...+..+..  .+-+++..+-+.|||.+....++..+.. ..+..+++++|+++.|..+.+.++.+....+
T Consensus       163 ~L~p~Qk~il~~l~~--~R~~vi~~sRq~GKT~l~a~~~l~~a~~-~~g~~v~~vA~t~~qA~~vf~~i~~mi~~~P  236 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSS--KRMTVCNLSRQLGKTTVVAIFLAHFVCF-NKDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (385)
T ss_dssp             CCCHHHHHHHHHHHH--SSEEEEEECSSSCHHHHHHHHHHHHHHS-SSSCEEEEEESSHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHHhhcc--CcEEEEEEcCcCChhHHHHHHHHHHHHh-CCCCeEEEEeCCHHHHHHHHHHHHHHHHhCh
Confidence            689999999987754  4778999999999998776655553332 2456799999999999988888888776544

>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=97.26  E-value=0.0012  Score=66.80  Aligned_cols=74  Identities=12%  Similarity=0.082  Sum_probs=58.1

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      .++|+|...+..+..  .+.+++..+-|+|||.+....++..+... .+..+++++|+++.|..+.+.++.+....+
T Consensus       163 ~l~p~Q~~i~~~l~~--~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~-~~~~i~~va~t~~qA~~~~~~i~~~i~~~p  236 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSS--KRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (592)
T ss_dssp             CCCHHHHHHHHHHHH--CSEEEEEECSSSCHHHHHHHHHHHHHHTS-SSCEEEEEESSHHHHHHHHHHHHHHHTTSC
T ss_pred             cCCHHHHHHHHhhcc--ccEEEEEEcCccChHHHHHHHHHHHHHhC-CCCeEEEEECCHHHHHHHHHHHHHHHHhCh
Confidence            579999999987743  57899999999999987665444444332 355799999999999999988888876654

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.07  E-value=0.0022  Score=61.70  Aligned_cols=85  Identities=24%  Similarity=0.216  Sum_probs=52.9

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCC
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE  222 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (399)
                      +=.++.|+.|+|||....    ..+..    ...+|++||++++..+.+.+.+.+..                    ...
T Consensus       162 ~v~~I~G~aGsGKTt~I~----~~~~~----~~~lVlTpT~~aa~~l~~kl~~~~~~--------------------~~~  213 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEIL----SRVNF----EEDLILVPGRQAAEMIRRRANASGII--------------------VAT  213 (446)
T ss_dssp             EEEEEEECTTSCHHHHHH----HHCCT----TTCEEEESCHHHHHHHHHHHTTTSCC--------------------CCC
T ss_pred             cEEEEEcCCCCCHHHHHH----HHhcc----CCeEEEeCCHHHHHHHHHHhhhcCcc--------------------ccc
Confidence            456789999999996432    22221    24799999999998888766432110                    011


Q ss_pred             cEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       223 ~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      +.-|.|.+.++-.   ......-..+++|||||-.+
T Consensus       214 ~~~V~T~dsfL~~---~~~~~~~~~d~liiDE~sm~  246 (446)
T 3vkw_A          214 KDNVRTVDSFLMN---YGKGARCQFKRLFIDEGLML  246 (446)
T ss_dssp             TTTEEEHHHHHHT---TTSSCCCCCSEEEEETGGGS
T ss_pred             cceEEEeHHhhcC---CCCCCCCcCCEEEEeCcccC
Confidence            2346676665432   22222234789999999754

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=96.59  E-value=0.0023  Score=53.83  Aligned_cols=19  Identities=21%  Similarity=0.237  Sum_probs=16.6

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      |+.+++.||+|+|||....
T Consensus        38 g~~~~l~G~~G~GKTtL~~   56 (180)
T 3ec2_A           38 GKGLTFVGSPGVGKTHLAV   56 (180)
T ss_dssp             CCEEEECCSSSSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            7899999999999996543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.44  E-value=0.013  Score=54.02  Aligned_cols=26  Identities=8%  Similarity=0.101  Sum_probs=20.3

Q ss_pred             hhhhcCCCCcEEEEccCCCCceehhH
Q psy11867        135 PTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       135 ~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.+..+.+.++++.||+|+|||++.-
T Consensus        38 ~~i~~~~~~~lli~GpPGTGKT~~v~   63 (318)
T 3te6_A           38 DSLMSSQNKLFYITNADDSTKFQLVN   63 (318)
T ss_dssp             HHHHTTCCCEEEEECCCSHHHHHHHH
T ss_pred             HHhcCCCCCeEEEECCCCCCHHHHHH
Confidence            44444468999999999999997654

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.42  E-value=0.0018  Score=54.98  Aligned_cols=39  Identities=13%  Similarity=0.051  Sum_probs=26.4

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      |+-.++.|+.|+|||...+--+.....   .+.+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~---~g~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKL---GKKKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHH---TTCEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEeecc
Confidence            567889999999999876543333322   234688888874

>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=96.31  E-value=0.024  Score=48.57  Aligned_cols=39  Identities=28%  Similarity=0.422  Sum_probs=24.4

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ..-.++||||+|.+..  .....+..++...+.+..+++.|
T Consensus       101 ~~~~vliiDe~~~l~~--~~~~~l~~~l~~~~~~~~~i~~~  139 (226)
T 2chg_A          101 APFKIIFLDEADALTA--DAQAALRRTMEMYSKSCRFILSC  139 (226)
T ss_dssp             CSCEEEEEETGGGSCH--HHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             cCceEEEEeChhhcCH--HHHHHHHHHHHhcCCCCeEEEEe
Confidence            4567999999999853  23344455555555555555544

>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=96.26  E-value=0.0039  Score=54.61  Aligned_cols=18  Identities=11%  Similarity=0.139  Sum_probs=16.0

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      ++.+++.||+|+|||...
T Consensus        52 ~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           52 VQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             CSEEEEECSTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            689999999999999654

>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=96.21  E-value=0.0091  Score=55.23  Aligned_cols=19  Identities=26%  Similarity=0.338  Sum_probs=16.2

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +..+++.||+|+|||...-
T Consensus        37 ~~~lll~G~~GtGKT~la~   55 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQ   55 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHH
Confidence            5789999999999996543

>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=96.13  E-value=0.0027  Score=55.56  Aligned_cols=91  Identities=13%  Similarity=0.165  Sum_probs=51.3

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhcc
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI  220 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (399)
                      +|.-+++.|++|+|||.+.+-.+.....   .+.+++++.|...-  . .  ...+...+          |..       
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~---~g~kVli~~~~~d~--r-~--~~~i~srl----------G~~-------   65 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEY---ADVKYLVFKPKIDT--R-S--IRNIQSRT----------GTS-------   65 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHH---TTCCEEEEEECCCG--G-G--CSSCCCCC----------CCS-------
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHh---cCCEEEEEEeccCc--h-H--HHHHHHhc----------CCC-------
Confidence            3678889999999999876544443333   23458888776521  0 0  00111111          000       


Q ss_pred             CCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       221 ~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      ...+-+.+...+++.+...  ..-...++|||||++.+
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            0123456666676654321  22345789999999975

>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=96.13  E-value=0.0046  Score=63.46  Aligned_cols=70  Identities=17%  Similarity=0.145  Sum_probs=55.0

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      .+++-|.+++...    +.+++|.|+.|||||.+..--+...+.. .....++|+|+.|+..|.++.+.+.....
T Consensus         2 ~L~~~Q~~av~~~----~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEFV----TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHCC----SSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhCC----CCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            4789999999752    5889999999999998766555555543 22445799999999999999999887643

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.13  E-value=0.0091  Score=60.40  Aligned_cols=115  Identities=18%  Similarity=0.216  Sum_probs=73.4

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .+|.-|.+++..++.-.....++.|+-|.|||.+..+.+-.. ..     .++|.+|+.+=+..+.+...+         
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~~-~~-----~~~vtAP~~~a~~~l~~~~~~---------  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISRI-AG-----RAIVTAPAKASTDVLAQFAGE---------  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHHS-SS-----CEEEECSSCCSCHHHHHHHGG---------
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHHH-Hh-----CcEEECCCHHHHHHHHHHhhC---------
Confidence            689999999998886423457999999999996665544433 22     378999998866544332211         


Q ss_pred             EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEE
Q psy11867        205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLF  284 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~  284 (399)
                                        .|-+..|+.+...        ....+++|||||=.+.     ...+..++.    ....++|
T Consensus       240 ------------------~i~~~~Pd~~~~~--------~~~~dlliVDEAAaIp-----~pll~~ll~----~~~~v~~  284 (671)
T 2zpa_A          240 ------------------KFRFIAPDALLAS--------DEQADWLVVDEAAAIP-----APLLHQLVS----RFPRTLL  284 (671)
T ss_dssp             ------------------GCCBCCHHHHHHS--------CCCCSEEEEETGGGSC-----HHHHHHHHT----TSSEEEE
T ss_pred             ------------------CeEEeCchhhhhC--------cccCCEEEEEchhcCC-----HHHHHHHHh----hCCeEEE
Confidence                              0223356554321        2358899999997753     233444443    3346888


Q ss_pred             EeeCC
Q psy11867        285 SATYD  289 (399)
Q Consensus       285 SAT~~  289 (399)
                      |.|..
T Consensus       285 ~tTv~  289 (671)
T 2zpa_A          285 TTTVQ  289 (671)
T ss_dssp             EEEBS
T ss_pred             EecCC
Confidence            88853

>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=96.10  E-value=0.0072  Score=66.33  Aligned_cols=67  Identities=18%  Similarity=0.256  Sum_probs=54.8

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCC---CCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI---QEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~---~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      .+|+-|.++|..-    +++++|.|..|||||.+.+--++..+....   ...++|+|++|+..|..+.+.+..
T Consensus        10 ~~t~eQ~~~i~~~----~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~   79 (1232)
T 3u4q_A           10 TWTDDQWNAIVST----GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAE   79 (1232)
T ss_dssp             CCCHHHHHHHHCC----SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC----CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHH
Confidence            6799999998642    589999999999999887777777776533   445799999999999998877765

>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=96.09  E-value=0.0085  Score=51.78  Aligned_cols=40  Identities=8%  Similarity=0.073  Sum_probs=27.4

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      |+=.++.++.|+|||.+.+--+.....   .+.+++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~---~g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQF---AKQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHH---TTCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHH---CCCEEEEEEeccC
Confidence            566678999999999876554444433   3446999998763

>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=96.03  E-value=0.0088  Score=61.92  Aligned_cols=70  Identities=20%  Similarity=0.193  Sum_probs=55.6

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      ..+++-|.+|+...    +.+++|.|+.|||||.+..--+...+.. .....++|+|+.|+..|.++.+.+..+.
T Consensus        10 ~~Ln~~Q~~av~~~----~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           10 AHLNKEQQEAVRTT----EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             TTSCHHHHHHHHCC----SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhCC----CCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            46899999999752    4789999999999998776666666643 2244579999999999999998888764

>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=95.96  E-value=0.013  Score=49.87  Aligned_cols=39  Identities=8%  Similarity=0.071  Sum_probs=27.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      |+=.++.|++|||||.+.+--+.....   .+.+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~~~---~g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRAKI---AKQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHH---TTCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHH---CCCEEEEEEecc
Confidence            677888999999999776544433332   345699998874

>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=95.90  E-value=0.051  Score=48.70  Aligned_cols=20  Identities=25%  Similarity=0.361  Sum_probs=16.7

Q ss_pred             CCCcEEEEccCCCCceehhH
Q psy11867        141 PPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~  160 (399)
                      +..++++.||+|+|||..+.
T Consensus        63 ~~~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           63 PLVSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             SEEEEEEECSTTSSHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHH
Confidence            35789999999999997653

>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=95.83  E-value=0.012  Score=54.81  Aligned_cols=36  Identities=19%  Similarity=0.210  Sum_probs=24.8

Q ss_pred             ChHHHHHHhhhhhc----CC-CCcEEEEccCCCCceehhHH
Q psy11867        126 PSKIQETALPTLLA----DP-PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       126 p~~iQ~~ai~~ll~----~~-g~~vi~~a~TGsGKT~~~~l  161 (399)
                      .+|+|..++..+..    +. ++.+++.||.|+|||.....
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~   43 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYA   43 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHH
Confidence            35777777665542    22 34599999999999976553

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.76  E-value=0.0052  Score=50.13  Aligned_cols=18  Identities=17%  Similarity=0.307  Sum_probs=16.0

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      |..+++.+|+|+|||...
T Consensus        36 g~~~~l~G~~G~GKTtL~   53 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLL   53 (149)
T ss_dssp             CSEEEEESSSTTTTCHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            799999999999999643

>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=95.61  E-value=0.047  Score=51.21  Aligned_cols=52  Identities=17%  Similarity=0.227  Sum_probs=30.0

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhc---CCCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLA---DPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~---~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+|+++.-.+...+.|...-.   .|   .-.|.+..   .+++++++.||+|+|||+.+-
T Consensus        48 ~~~~di~G~~~~~~~l~~~v~---~~---~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~  102 (355)
T 2qp9_X           48 VKWEDVAGLEGAKEALKEAVI---LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYLAK  102 (355)
T ss_dssp             CCGGGSCCGGGHHHHHHHHTH---HH---HHCGGGGCSSCCCCCCEEEECSTTSCHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHH---HH---HhCHHHHhcCCCCCceEEEECCCCCcHHHHHH
Confidence            457777655556666654210   00   11122221   135789999999999997653

>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=95.57  E-value=0.043  Score=50.69  Aligned_cols=52  Identities=17%  Similarity=0.225  Sum_probs=32.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+|+++.-.....+.|...-.   .|   ...|.+...   +++++++.||+|+|||..+-
T Consensus        15 ~~~~di~G~~~~~~~l~~~i~---~~---~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~   69 (322)
T 3eie_A           15 VKWEDVAGLEGAKEALKEAVI---LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYLAK   69 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTH---HH---HHCGGGCCTTCCCCCEEEEECSSSSCHHHHHH
T ss_pred             CCHHHhcChHHHHHHHHHHHH---HH---HhCHHHHhcCCCCCCeEEEECCCCCcHHHHHH
Confidence            458888777777777765411   11   112222221   35789999999999997543

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.57  E-value=0.014  Score=47.20  Aligned_cols=19  Identities=16%  Similarity=0.190  Sum_probs=16.7

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.++++.|++|+|||..+-
T Consensus        24 ~~~vll~G~~GtGKt~lA~   42 (145)
T 3n70_A           24 DIAVWLYGAPGTGRMTGAR   42 (145)
T ss_dssp             CSCEEEESSTTSSHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHH
Confidence            7899999999999997653

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=95.42  E-value=0.012  Score=53.76  Aligned_cols=19  Identities=32%  Similarity=0.345  Sum_probs=16.3

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.++++.||+|+|||..+-
T Consensus        67 ~~~vll~G~~GtGKT~la~   85 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVAL   85 (309)
T ss_dssp             CCEEEEEECTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            6789999999999997653

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=95.39  E-value=0.017  Score=49.05  Aligned_cols=45  Identities=9%  Similarity=-0.012  Sum_probs=27.0

Q ss_pred             hhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        135 PTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       135 ~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      |......|+=.++.|++|||||.-.+-.+-.....   +.+++++.|.
T Consensus        13 ~~~~~~~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~---~~kvl~~kp~   57 (195)
T 1w4r_A           13 PRGSKTRGQIQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYA   57 (195)
T ss_dssp             ------CCEEEEEEECTTSCHHHHHHHHHHHHHHT---TCCEEEEEET
T ss_pred             ccCCCCceEEEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEccc
Confidence            33333347888999999999995544433333332   3558888886

>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=95.36  E-value=0.033  Score=48.64  Aligned_cols=39  Identities=8%  Similarity=-0.032  Sum_probs=28.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      |+=.++.|+.|+|||.+.+--+.....   .+.+++++-|..
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~---~g~kvli~kp~~   57 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQI---AQYKCLVIKYAK   57 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHT---TTCCEEEEEETT
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHH---CCCeEEEEeecC
Confidence            677888999999999776655554443   345688888875

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.13  E-value=0.078  Score=43.89  Aligned_cols=19  Identities=37%  Similarity=0.447  Sum_probs=16.2

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.++++.||+|+|||....
T Consensus        43 ~~~vll~G~~G~GKT~la~   61 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVE   61 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            6789999999999996543

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=95.11  E-value=0.31  Score=44.90  Aligned_cols=52  Identities=17%  Similarity=0.201  Sum_probs=31.7

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhc---CCCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLA---DPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~---~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+|++++=.+...+.|...-.   .|.   -.|.+..   .+++.+++.||+|+|||..+-
T Consensus         9 ~~~~di~G~~~~k~~l~~~v~---~p~---~~~~~~~~~~~~~~~iLL~GppGtGKT~la~   63 (322)
T 1xwi_A            9 VKWSDVAGLEGAKEALKEAVI---LPI---KFPHLFTGKRTPWRGILLFGPPGTGKSYLAK   63 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHH---HHH---HCGGGSCTTCCCCSEEEEESSSSSCHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHH---HHH---hCHHHHhCCCCCCceEEEECCCCccHHHHHH
Confidence            468888766777777654210   011   1122222   235899999999999996543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.96  E-value=0.029  Score=45.08  Aligned_cols=18  Identities=6%  Similarity=0.097  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      +.++++.|++|+|||..+
T Consensus        27 ~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           27 TSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             SSCEEEEEETTCCHHHHH
T ss_pred             CCcEEEECCCCccHHHHH
Confidence            689999999999999543

>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=0.11  Score=47.40  Aligned_cols=53  Identities=19%  Similarity=0.272  Sum_probs=31.1

Q ss_pred             cccccCCCCHHHHHHHHHcC---CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMG---FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g---~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+|+++.-.+...+.|...-   ...|..+....    + .+++.+++.||+|+|||+.+-
T Consensus        12 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~----~-~~~~~vLL~Gp~GtGKT~la~   67 (301)
T 3cf0_A           12 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFG----M-TPSKGVLFYGPPGCGKTLLAK   67 (301)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC----C-CCCSEEEEECSSSSSHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcC----C-CCCceEEEECCCCcCHHHHHH
Confidence            45777766666666665420   11111111110    1 237899999999999997553

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=94.90  E-value=0.053  Score=52.46  Aligned_cols=19  Identities=21%  Similarity=0.256  Sum_probs=16.1

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +..+++.||+|+|||....
T Consensus       130 ~~~lll~Gp~G~GKTtLa~  148 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQ  148 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4789999999999997553

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=94.79  E-value=0.079  Score=44.97  Aligned_cols=18  Identities=22%  Similarity=0.353  Sum_probs=15.8

Q ss_pred             CcEEEEccCCCCceehhH
Q psy11867        143 HNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~  160 (399)
                      .++++.||+|+|||....
T Consensus        55 ~~~~l~G~~GtGKT~la~   72 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLA   72 (202)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            789999999999997643

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.70  E-value=0.13  Score=46.28  Aligned_cols=55  Identities=18%  Similarity=0.254  Sum_probs=31.3

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      .+|+++.-.+...+.|...-. .|. ...+.+..+-...++++++.||+|+|||...
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~-~~~-~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVE-LPL-KHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTH-HHH-HCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHH-HHh-hCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            457888767777777765310 000 0011111111123689999999999999654

>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=94.66  E-value=0.074  Score=51.17  Aligned_cols=134  Identities=16%  Similarity=0.184  Sum_probs=67.1

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe--CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA--PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKK  219 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~--Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (399)
                      +.-+++.+++|+|||.....-+.... .  .+.+++++.  +.+.-+   .+.+..++... ++.+.....+.       
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~-~--~G~kVllv~~D~~r~~a---~eqL~~~~~~~-gv~~~~~~~~~-------  162 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYK-K--RGYKVGLVAADVYRPAA---YDQLLQLGNQI-GVQVYGEPNNQ-------  162 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHH-H--TTCCEEEEEECCSCHHH---HHHHHHHHHTT-TCCEECCTTCS-------
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-H--cCCeEEEEecCccchhH---HHHHHHHHHhc-CCceeeccccC-------
Confidence            57788899999999976543222222 2  234465555  333322   22333333322 22211111110       


Q ss_pred             cCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh--hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHH
Q psy11867        220 ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI--ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ  297 (399)
Q Consensus       220 ~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~--~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~  297 (399)
                              .|..+.....  ......+.+++++|++-++.  ........+..+...+.+..-++.++|+........++
T Consensus       163 --------dp~~i~~~al--~~a~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~~a~  232 (433)
T 3kl4_A          163 --------NPIEIAKKGV--DIFVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLAS  232 (433)
T ss_dssp             --------CHHHHHHHHH--HHTTTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHHHHH
T ss_pred             --------CHHHHHHHHH--HHHHhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHHHHHH
Confidence                    1222221111  11223467889999987653  22234445555555555666677888887665555554


Q ss_pred             hh
Q psy11867        298 DM  299 (399)
Q Consensus       298 ~~  299 (399)
                      .+
T Consensus       233 ~f  234 (433)
T 3kl4_A          233 RF  234 (433)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=94.63  E-value=0.032  Score=48.16  Aligned_cols=98  Identities=15%  Similarity=0.167  Sum_probs=51.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |.=.++.++.|+|||...+--+ .+...  .+.+++++.|...--   + --..+....          |.       ..
T Consensus        28 G~I~vitG~M~sGKTT~Llr~~-~r~~~--~g~kvli~kp~~D~R---~-~~~~I~Sr~----------G~-------~~   83 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEELIRRL-RRGIY--AKQKVVVFKPAIDDR---Y-HKEKVVSHN----------GN-------AI   83 (219)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH-HHHHH--TTCCEEEEEEC---------------CBT----------TB-------CC
T ss_pred             ceEEEEECCCCCCHHHHHHHHH-HHHHH--cCCceEEEEeccCCc---c-hhhhHHHhc----------CC-------ce
Confidence            6778899999999997554443 33322  235589998865311   0 001111111          10       01


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHH
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQ  272 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~  272 (399)
                      ..+.|..+..+.+.+       ..+.++|+||||+.+.+  ...+++..+.
T Consensus        84 ~a~~v~~~~di~~~i-------~~~~dvV~IDEaQFf~~--~~v~~l~~la  125 (219)
T 3e2i_A           84 EAINISKASEIMTHD-------LTNVDVIGIDEVQFFDD--EIVSIVEKLS  125 (219)
T ss_dssp             EEEEESSGGGGGGSC-------CTTCSEEEECCGGGSCT--HHHHHHHHHH
T ss_pred             eeEEeCCHHHHHHHH-------hcCCCEEEEechhcCCH--HHHHHHHHHH
Confidence            124455554443321       24678999999999742  2444454554

>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=94.62  E-value=0.082  Score=49.69  Aligned_cols=19  Identities=26%  Similarity=0.242  Sum_probs=16.2

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++.+++.||+|+|||....
T Consensus        45 ~~~vll~G~~G~GKT~la~   63 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVSK   63 (384)
T ss_dssp             CCEEEEEECTTSSHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHH
Confidence            5789999999999997653

>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=94.53  E-value=0.063  Score=49.40  Aligned_cols=39  Identities=28%  Similarity=0.361  Sum_probs=23.9

Q ss_pred             CceeEEEEechhhHh-hcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMI-ATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~-~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ...++++|||+|.+. .  .....+..++...+.++++++.+
T Consensus       104 ~~~~vliiDEi~~l~~~--~~~~~L~~~le~~~~~~~iI~~~  143 (324)
T 3u61_B          104 GRQKVIVIDEFDRSGLA--ESQRHLRSFMEAYSSNCSIIITA  143 (324)
T ss_dssp             SCEEEEEEESCCCGGGH--HHHHHHHHHHHHHGGGCEEEEEE
T ss_pred             CCCeEEEEECCcccCcH--HHHHHHHHHHHhCCCCcEEEEEe
Confidence            367899999999985 3  23334444444444456655533

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=94.39  E-value=0.042  Score=48.19  Aligned_cols=51  Identities=18%  Similarity=0.204  Sum_probs=31.8

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      |.-+++.|++|+|||...+--+......   +..++++.-. +-..++.+.+..+
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~~~~~---~~~v~~~~~e-~~~~~~~~~~~~~   73 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWNGLKM---GEPGIYVALE-EHPVQVRQNMAQF   73 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHHHHT---TCCEEEEESS-SCHHHHHHHHHTT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEcc-CCHHHHHHHHHHc
Confidence            7889999999999997654333333322   3347777643 3345555555544

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=94.32  E-value=0.098  Score=49.06  Aligned_cols=20  Identities=40%  Similarity=0.526  Sum_probs=16.9

Q ss_pred             CCCcEEEEccCCCCceehhH
Q psy11867        141 PPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+.++++.||+|+|||...-
T Consensus        43 ~~~~vll~G~~G~GKT~l~~   62 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVAR   62 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHHH
Confidence            37899999999999997543

>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=94.12  E-value=0.32  Score=45.07  Aligned_cols=41  Identities=12%  Similarity=0.304  Sum_probs=25.5

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEee
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSAT  287 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT  287 (399)
                      .+.+++|+||+|.|- . .....+..++...+.++.+++.|-.
T Consensus       133 ~~~~vlilDE~~~L~-~-~~~~~L~~~le~~~~~~~~Il~t~~  173 (354)
T 1sxj_E          133 HRYKCVIINEANSLT-K-DAQAALRRTMEKYSKNIRLIMVCDS  173 (354)
T ss_dssp             -CCEEEEEECTTSSC-H-HHHHHHHHHHHHSTTTEEEEEEESC
T ss_pred             CCCeEEEEeCccccC-H-HHHHHHHHHHHhhcCCCEEEEEeCC
Confidence            467899999999953 2 3344455666665656555555543

>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=94.00  E-value=0.098  Score=47.85  Aligned_cols=39  Identities=26%  Similarity=0.368  Sum_probs=24.2

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ..-.++|+||+|.+..  .....+..++...+..+.+++.+
T Consensus       109 ~~~~vliiDe~~~l~~--~~~~~L~~~le~~~~~~~~i~~~  147 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQ--DAQQALRRTMEMFSSNVRFILSC  147 (327)
T ss_dssp             CSCEEEEEETGGGSCH--HHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCCeEEEEeCCCcCCH--HHHHHHHHHHHhcCCCCeEEEEe
Confidence            4567999999999843  23334445555555555555543

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=93.93  E-value=0.049  Score=50.03  Aligned_cols=19  Identities=16%  Similarity=0.289  Sum_probs=16.4

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.++++.||+|+|||....
T Consensus       152 ~~~lll~G~~GtGKT~La~  170 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLA  170 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5899999999999996554

>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=93.71  E-value=0.27  Score=45.84  Aligned_cols=20  Identities=40%  Similarity=0.624  Sum_probs=16.8

Q ss_pred             CCCcEEEEccCCCCceehhH
Q psy11867        141 PPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+..+++.||+|+|||...-
T Consensus        44 ~~~~vli~G~~G~GKTtl~~   63 (386)
T 2qby_A           44 KPNNIFIYGLTGTGKTAVVK   63 (386)
T ss_dssp             CCCCEEEEECTTSSHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            36899999999999997543

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=93.62  E-value=0.15  Score=44.06  Aligned_cols=52  Identities=12%  Similarity=0.049  Sum_probs=28.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      |.-+++.||+|+|||.....-+.....   .+..++++.... ...++...+..++
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~~~---~~~~v~~~~~~~-~~~~~~~~~~~~~   74 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKGLR---DGDPCIYVTTEE-SRDSIIRQAKQFN   74 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHH---HTCCEEEEESSS-CHHHHHHHHHHTT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHH---CCCeEEEEEccc-CHHHHHHHHHHhc
Confidence            788999999999999654332222221   123466665322 2344444444443

>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=93.45  E-value=0.16  Score=46.55  Aligned_cols=44  Identities=11%  Similarity=0.086  Sum_probs=25.4

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChh
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKE  291 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~  291 (399)
                      ...+++||||||+|...  ..+.+...+..-++.+.++++ ++.+..
T Consensus        81 ~~~kvviIdead~lt~~--a~naLLk~LEep~~~t~fIl~-t~~~~k  124 (305)
T 2gno_A           81 YTRKYVIVHDCERMTQQ--AANAFLKALEEPPEYAVIVLN-TRRWHY  124 (305)
T ss_dssp             SSSEEEEETTGGGBCHH--HHHHTHHHHHSCCTTEEEEEE-ESCGGG
T ss_pred             CCceEEEeccHHHhCHH--HHHHHHHHHhCCCCCeEEEEE-ECChHh
Confidence            45789999999998532  233334444544444555544 454433

>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=93.41  E-value=0.13  Score=47.64  Aligned_cols=39  Identities=28%  Similarity=0.324  Sum_probs=24.6

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ...+++++||+|.+...  ....+..++...+....+++.+
T Consensus       132 ~~~~vliiDE~~~l~~~--~~~~Ll~~le~~~~~~~~il~~  170 (353)
T 1sxj_D          132 PPYKIIILDEADSMTAD--AQSALRRTMETYSGVTRFCLIC  170 (353)
T ss_dssp             CSCEEEEETTGGGSCHH--HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCceEEEEECCCccCHH--HHHHHHHHHHhcCCCceEEEEe
Confidence            35579999999998532  3344455555555556566544

>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=93.34  E-value=0.47  Score=41.71  Aligned_cols=18  Identities=28%  Similarity=0.412  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      ++.+++.||+|+|||...
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            688999999999999654

>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=93.27  E-value=0.42  Score=44.72  Aligned_cols=35  Identities=14%  Similarity=0.256  Sum_probs=21.8

Q ss_pred             cEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe
Q psy11867        144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA  180 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  180 (399)
                      .+++.||+|+|||...- .+...+.... +..++++.
T Consensus        46 ~~li~G~~G~GKTtl~~-~l~~~~~~~~-~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLR-KLWELYKDKT-TARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHHH-HHHHHHTTSC-CCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHhhhc-CeeEEEEe
Confidence            89999999999997653 3334443321 23455554

>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=93.09  E-value=0.5  Score=40.49  Aligned_cols=17  Identities=29%  Similarity=0.458  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCceehh
Q psy11867        143 HNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~  159 (399)
                      +.+++.||+|+|||...
T Consensus        46 ~~~ll~G~~G~GKT~l~   62 (250)
T 1njg_A           46 HAYLFSGTRGVGKTSIA   62 (250)
T ss_dssp             SEEEEECSTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            47899999999999654

>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=92.95  E-value=0.091  Score=47.98  Aligned_cols=38  Identities=29%  Similarity=0.308  Sum_probs=23.4

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      .-.++||||+|.+...  ....+..++...+....+++.|
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            4679999999998532  2233344555555556666654

>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=92.89  E-value=0.24  Score=47.69  Aligned_cols=42  Identities=17%  Similarity=0.110  Sum_probs=25.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe--CcHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA--PTYELA  186 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~--Pt~~La  186 (399)
                      +.-+++++++|+|||....--+.. +..  .+.+++++.  |.+.-+
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~-l~~--~G~kVllv~~D~~R~aa  143 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARY-FQK--RGYKVGVVCSDTWRPGA  143 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH-HHT--TTCCEEEEECCCSSTHH
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHH-HHH--CCCeEEEEeCCCcchhH
Confidence            567889999999999765433322 222  234566655  444433

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=92.83  E-value=0.11  Score=47.37  Aligned_cols=42  Identities=19%  Similarity=0.268  Sum_probs=26.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      .+|+++--.+...+.+... +              ..+...++++.||+|+|||...
T Consensus        14 ~~~~~~~g~~~~~~~l~~~-l--------------~~~~~~~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           14 RTLDEVVGQDEVIQRLKGY-V--------------ERKNIPHLLFSGPPGTGKTATA   55 (319)
T ss_dssp             SSGGGSCSCHHHHHHHHTT-T--------------TTTCCCCEEEESSSSSSHHHHH
T ss_pred             CCHHHHhCCHHHHHHHHHH-H--------------hCCCCCeEEEECcCCcCHHHHH
Confidence            4566665566666666542 1              1121346999999999999654

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=92.15  E-value=0.28  Score=49.59  Aligned_cols=113  Identities=11%  Similarity=0.086  Sum_probs=65.8

Q ss_pred             CCCcEEEEEeeCChhHHHHHHhhCCCCeEEecccccccccceeEEEEEeCC--------hhh----HHHHHHHHhccCCC
Q psy11867        277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKN--------IDE----KFEAVSNIYGVVTI  344 (399)
Q Consensus       277 ~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~~~~~~~~~i~~~~~~~~~--------~~~----k~~~l~~ll~~~~~  344 (399)
                      ....+|++|||+.+ ...+....-.+...+.+..... ..+.  ....+..        ...    -...+..++.. .+
T Consensus       374 ~~~~~il~SaTL~p-~~~~~~~lGl~~~~~~~~spf~-~~~~--~~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~-~~  448 (620)
T 4a15_A          374 KESKTIHMSGTLDP-FDFYSDITGFEIPFKKIGEIFP-PENR--YIAYYDGVSSKYDTLDEKELDRMATVIEDIILK-VK  448 (620)
T ss_dssp             GGSEEEEEESSCCS-HHHHHHHHCCCCCEEECCCCSC-GGGE--EEEEECCC-------CHHHHHHHHHHHHHHHHH-HC
T ss_pred             hCCeEEEEccCCCc-HHHHHHHhCCCceeeecCCCCC-HHHe--EEEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHh-CC
Confidence            55678999999986 3444444332233333332211 1122  1111111        011    12223344433 34


Q ss_pred             CcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        345 GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       345 ~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                      +.++||++|.+..+.+++.|...+.+   ...+++..+|..++++|+ |+-.||
T Consensus       449 g~~lvlF~Sy~~l~~v~~~l~~~~~~---~~q~~~~~~~~~ll~~f~-~~~~vL  498 (620)
T 4a15_A          449 KNTIVYFPSYSLMDRVENRVSFEHMK---EYRGIDQKELYSMLKKFR-RDHGTI  498 (620)
T ss_dssp             SCEEEEESCHHHHHHHTSSCCSCCEE---CCTTCCSHHHHHHHHHHT-TSCCEE
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhcchh---ccCCCChhHHHHHHHHhc-cCCcEE
Confidence            78999999999999999888632222   555677789999999999 766655

>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=92.13  E-value=0.41  Score=40.54  Aligned_cols=141  Identities=16%  Similarity=0.168  Sum_probs=73.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH-HHHHHHHHHHHHhccCCCcEEEEEEcCchh--hhhh
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE-LAIQIGEVVAKMGKHITDLSVRYAVRGENL--ERNK  218 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~-La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~  218 (399)
                      ...+++..++|.|||.+++--++..+..   +.+++|+.-.+. .-..-.+.++++     .+.  +...|..+  ....
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~---G~rV~~vQF~Kg~~~~gE~~~l~~L-----~v~--~~~~g~gf~~~~~~   97 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGH---GKNVGVVQFIKGTWPNGERNLLEPH-----GVE--FQVMATGFTWETQN   97 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHT---TCCEEEEESSCCSSCCHHHHHHGGG-----TCE--EEECCTTCCCCGGG
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEEeeCCCCCccHHHHHHhC-----CcE--EEEcccccccCCCC
Confidence            4689999999999999988777777754   345877743221 000001222222     122  22222111  0000


Q ss_pred             ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC-CchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHH
Q psy11867        219 KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ-GHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ  297 (399)
Q Consensus       219 ~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~-~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~  297 (399)
                      ... +..  .....+....  +.+.-..+++||+||+-..+..+ --.+.+..++...+....+|+.+--.|+.+.+.+.
T Consensus        98 ~~~-~~~--~a~~~l~~a~--~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e~AD  172 (196)
T 1g5t_A           98 REA-DTA--ACMAVWQHGK--RMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLAD  172 (196)
T ss_dssp             HHH-HHH--HHHHHHHHHH--HHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHCS
T ss_pred             cHH-HHH--HHHHHHHHHH--HHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHHhCc
Confidence            000 000  0011122211  22233678999999997754431 13344556667667677777777767777766653

>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=92.04  E-value=0.45  Score=46.55  Aligned_cols=20  Identities=35%  Similarity=0.602  Sum_probs=16.9

Q ss_pred             CCCcEEEEccCCCCceehhH
Q psy11867        141 PPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++.++++.||+|+|||+.+-
T Consensus       237 ~~~~vLL~GppGtGKT~lAr  256 (489)
T 3hu3_A          237 PPRGILLYGPPGTGKTLIAR  256 (489)
T ss_dssp             CCCEEEEECSTTSSHHHHHH
T ss_pred             CCCcEEEECcCCCCHHHHHH
Confidence            36889999999999997653

>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=91.58  E-value=0.31  Score=45.09  Aligned_cols=39  Identities=26%  Similarity=0.428  Sum_probs=25.4

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                      ...+++|+||+|.|..  .....+..++...+..+.+++.+
T Consensus       109 ~~~~viiiDe~~~l~~--~~~~~L~~~le~~~~~~~~il~~  147 (340)
T 1sxj_C          109 KGFKLIILDEADAMTN--AAQNALRRVIERYTKNTRFCVLA  147 (340)
T ss_dssp             CSCEEEEETTGGGSCH--HHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCH--HHHHHHHHHHhcCCCCeEEEEEe
Confidence            3478999999999853  23344555666666666666543

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=91.52  E-value=0.33  Score=46.16  Aligned_cols=57  Identities=14%  Similarity=0.180  Sum_probs=51.7

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHH---CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSK---EGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~---~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+++||.++++.-+.++++.+..   .|+++..+||+.+..+|....+.+..|+.+|+|
T Consensus        63 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv  122 (414)
T 3oiy_A           63 KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILV  122 (414)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEE
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEE
Confidence            457899999999999999999988   588999999999999999999999999888875

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=91.46  E-value=0.13  Score=47.43  Aligned_cols=19  Identities=21%  Similarity=0.335  Sum_probs=16.1

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      ..++++.||+|+|||..+.
T Consensus        55 ~~~vll~G~~GtGKT~la~   73 (338)
T 3pfi_A           55 LDHILFSGPAGLGKTTLAN   73 (338)
T ss_dssp             CCCEEEECSTTSSHHHHHH
T ss_pred             CCeEEEECcCCCCHHHHHH
Confidence            4789999999999996543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=90.79  E-value=0.22  Score=56.56  Aligned_cols=90  Identities=14%  Similarity=0.158  Sum_probs=52.7

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhcc
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI  220 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (399)
                      +|+++++.+|+|+|||..+...+.....   .+.+++++..-..+... +  ++.++..+..+                 
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~---~G~~v~Fi~~e~~~~~l-~--a~~~G~dl~~l----------------- 1482 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDAEHALDPI-Y--ARKLGVDIDNL----------------- 1482 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHT---TTCCEEEECTTSCCCHH-H--HHHTTCCTTTC-----------------
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEEEcccccCHH-H--HHHcCCCchhc-----------------
Confidence            3799999999999999877655554443   34568888765443322 2  55555444332                 


Q ss_pred             CCcEEEeCch---hHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        221 TEQIIIGTPG---KVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       221 ~~~IlV~Tp~---~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                          .|..|.   +++..+..  ...-..+++|||||.+-+.
T Consensus      1483 ----~v~~~~~~E~~l~~~~~--lvr~~~~~lVVIDsi~al~ 1518 (2050)
T 3cmu_A         1483 ----LCSQPDTGEQALEICDA--LARSGAVDVIVVDSVAALT 1518 (2050)
T ss_dssp             ----EEECCSSHHHHHHHHHH--HHHHTCCSEEEESCGGGCC
T ss_pred             ----eeecCChHHHHHHHHHH--HHhcCCCCEEEEcChhHhc
Confidence                222232   23222111  1112468899999998553

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=90.67  E-value=0.2  Score=48.47  Aligned_cols=19  Identities=42%  Similarity=0.492  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      ..++++.||+|+|||..+-
T Consensus        50 ~~~vLL~GppGtGKTtlAr   68 (447)
T 3pvs_A           50 LHSMILWGPPGTGKTTLAE   68 (447)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CcEEEEECCCCCcHHHHHH
Confidence            3579999999999997553

>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=90.46  E-value=0.37  Score=49.91  Aligned_cols=26  Identities=31%  Similarity=0.359  Sum_probs=19.2

Q ss_pred             hhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        134 LPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       134 i~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      +..+....+.++++.||+|+|||...
T Consensus       199 ~~~l~~~~~~~vlL~G~~GtGKT~la  224 (758)
T 1r6b_X          199 IQVLCRRRKNNPLLVGESGVGKTAIA  224 (758)
T ss_dssp             HHHHTSSSSCEEEEECCTTSSHHHHH
T ss_pred             HHHHhccCCCCeEEEcCCCCCHHHHH
Confidence            33333334789999999999999654

>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=90.44  E-value=1.4  Score=36.13  Aligned_cols=71  Identities=15%  Similarity=0.084  Sum_probs=50.1

Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccC
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDL  244 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~  244 (399)
                      ...++||.++++..+..+++.+...     ++.+....|+......       ..+..+|+|+|.-       -...+++
T Consensus        33 ~~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~-------~~~Gid~  100 (175)
T 2rb4_A           33 TIGQAIIFCQTRRNAKWLTVEMIQD-----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV-------CARGIDV  100 (175)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCS-------CCTTTCC
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecc-------hhcCCCc
Confidence            4568999999999999998888764     4556666666443221       1456789999942       2356788


Q ss_pred             CceeEEEEec
Q psy11867        245 SKIKVFVLDE  254 (399)
Q Consensus       245 ~~~~~lViDE  254 (399)
                      ..++++|.-+
T Consensus       101 ~~~~~Vi~~d  110 (175)
T 2rb4_A          101 KQVTIVVNFD  110 (175)
T ss_dssp             TTEEEEEESS
T ss_pred             ccCCEEEEeC
Confidence            8899988533

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=90.28  E-value=0.094  Score=43.78  Aligned_cols=61  Identities=16%  Similarity=0.155  Sum_probs=45.8

Q ss_pred             ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHH
Q psy11867        126 PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQ  188 (399)
Q Consensus       126 p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q  188 (399)
                      ..+-|..++..++....+-.++.+.-|++|+...+-.++.....  .+.++.+|+|+..-...
T Consensus        35 ~~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~--~Gr~V~vLAp~~~s~~~   95 (189)
T 2l8b_A           35 RTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMARE--QGREVQIIAADRRSQMN   95 (189)
T ss_dssp             CHHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHH--TTCCEEEECSTTHHHHH
T ss_pred             cCccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHh--cCeEEEEEcCchHHHHH
Confidence            44679999999987656788889999999998865555544433  56679999999765543

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=90.27  E-value=0.61  Score=40.42  Aligned_cols=40  Identities=15%  Similarity=0.018  Sum_probs=25.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCC---CCCCeEEEEeC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPS---IQEPQVLCLAP  181 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~---~~~~~~lil~P  181 (399)
                      |.-+.+.+|+|+|||.....-+...+...   .....++++.-
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~   66 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDT   66 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEEC
Confidence            78899999999999976554433322211   01345677764

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=89.99  E-value=0.32  Score=42.40  Aligned_cols=53  Identities=15%  Similarity=0.136  Sum_probs=30.9

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      +|.-+++.|++|+|||...+--+.+....  .+..++|++-. +-..++.+.+..+
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~--~~~~v~~~s~E-~~~~~~~~~~~~~   81 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEE--YGEPGVFVTLE-ERARDLRREMASF   81 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHH--HCCCEEEEESS-SCHHHHHHHHHTT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHh--cCCCceeeccc-CCHHHHHHHHHHc
Confidence            37889999999999996544333332222  12236776633 3345555555443

>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=88.97  E-value=0.49  Score=44.71  Aligned_cols=19  Identities=37%  Similarity=0.382  Sum_probs=15.8

Q ss_pred             CCcEEE--EccCCCCceehhH
Q psy11867        142 PHNMIA--QSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~--~a~TGsGKT~~~~  160 (399)
                      +..+++  .|+.|+|||....
T Consensus        50 ~~~~li~i~G~~G~GKT~L~~   70 (412)
T 1w5s_A           50 DVNMIYGSIGRVGIGKTTLAK   70 (412)
T ss_dssp             CEEEEEECTTCCSSSHHHHHH
T ss_pred             CCEEEEeCcCcCCCCHHHHHH
Confidence            578888  9999999997543

>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=88.77  E-value=0.55  Score=48.70  Aligned_cols=56  Identities=20%  Similarity=0.195  Sum_probs=50.3

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKE----GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~----g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+++|.++++.-|.+.++.+.+.    |+++..+||+++..+|..+++.+.+|..+|+|
T Consensus       417 g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvV  476 (780)
T 1gm5_A          417 GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVI  476 (780)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEE
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEE
Confidence            468999999999999888887654    78999999999999999999999999999875

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=88.63  E-value=1.2  Score=36.16  Aligned_cols=70  Identities=16%  Similarity=0.160  Sum_probs=49.0

Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCC
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLS  245 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~  245 (399)
                      +.++||.++++.-+..+++.++..     ++.+....|+......       ..+..+|+|+|.  +     -...+++.
T Consensus        35 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~--~-----~~~Gld~~  102 (163)
T 2hjv_A           35 PDSCIIFCRTKEHVNQLTDELDDL-----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD--V-----AARGIDIE  102 (163)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG--G-----GTTTCCCS
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC--h-----hhcCCchh
Confidence            457999999999999999988875     4556666666433221       145668999993  1     12467788


Q ss_pred             ceeEEEEec
Q psy11867        246 KIKVFVLDE  254 (399)
Q Consensus       246 ~~~~lViDE  254 (399)
                      .++++|.-+
T Consensus       103 ~~~~Vi~~~  111 (163)
T 2hjv_A          103 NISLVINYD  111 (163)
T ss_dssp             CCSEEEESS
T ss_pred             cCCEEEEeC
Confidence            888888643

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=88.38  E-value=0.73  Score=42.83  Aligned_cols=18  Identities=28%  Similarity=0.429  Sum_probs=15.0

Q ss_pred             CcEEEEccCCCCceehhH
Q psy11867        143 HNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~  160 (399)
                      +.+++.||.|+|||....
T Consensus        39 ~~~ll~G~~G~GKT~la~   56 (373)
T 1jr3_A           39 HAYLFSGTRGVGKTSIAR   56 (373)
T ss_dssp             SEEEEESCTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            458999999999997653

>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=88.15  E-value=0.51  Score=46.02  Aligned_cols=51  Identities=12%  Similarity=0.226  Sum_probs=38.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      +....+.+-||||||++..- +....     +..+|||+|+...|.|+++.++.+..
T Consensus        14 ~~~~~l~g~~gs~ka~~~a~-l~~~~-----~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           14 GEQRLLGELTGAACATLVAE-IAERH-----AGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TCEEEEECCCTTHHHHHHHH-HHHHS-----SSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCeEEEeCCCchHHHHHHHH-HHHHh-----CCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            67889999999999965332 22221     12389999999999999999998753

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.60  E-value=0.24  Score=47.59  Aligned_cols=53  Identities=17%  Similarity=0.269  Sum_probs=37.0

Q ss_pred             ccccccCCCCHHHHHHHHHc---CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        102 VKTFEALHLKPELLKGVYEM---GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~---g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      -.+|++.+-.+...+.|...   -+.+|--++...++     +++.+++.||+|+|||+.+
T Consensus       177 ~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~-----~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          177 TETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIR-----APKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCC-----CCCEEEEESCTTSSHHHHH
T ss_pred             CCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCC-----CCCeeEEECcCCCCHHHHH
Confidence            45799998778888777653   23344444443332     3689999999999999654

>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=87.59  E-value=0.37  Score=50.68  Aligned_cols=27  Identities=30%  Similarity=0.423  Sum_probs=19.3

Q ss_pred             hhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867        134 LPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       134 i~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      +..+......++++.||+|+|||...-
T Consensus       183 ~~~l~~~~~~~vlL~G~pG~GKT~la~  209 (854)
T 1qvr_A          183 IQILLRRTKNNPVLIGEPGVGKTAIVE  209 (854)
T ss_dssp             HHHHHCSSCCCCEEEECTTSCHHHHHH
T ss_pred             HHHHhcCCCCceEEEcCCCCCHHHHHH
Confidence            333334346789999999999996543

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=87.52  E-value=1.9  Score=34.98  Aligned_cols=71  Identities=11%  Similarity=0.097  Sum_probs=49.0

Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccC
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDL  244 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~  244 (399)
                      ...++||.++++.-+..+++.++..     ++.+....++......       ..+...|+|+|.-       -...+++
T Consensus        29 ~~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-------~~~G~d~   96 (165)
T 1fuk_A           29 SVTQAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL-------LARGIDV   96 (165)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG-------GTTTCCC
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcCh-------hhcCCCc
Confidence            3457999999999999999888875     4455666666443221       1456689999942       1246678


Q ss_pred             CceeEEEEec
Q psy11867        245 SKIKVFVLDE  254 (399)
Q Consensus       245 ~~~~~lViDE  254 (399)
                      ..++++|.-+
T Consensus        97 ~~~~~Vi~~~  106 (165)
T 1fuk_A           97 QQVSLVINYD  106 (165)
T ss_dssp             CSCSEEEESS
T ss_pred             ccCCEEEEeC
Confidence            8888887643

>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=87.10  E-value=1  Score=44.48  Aligned_cols=56  Identities=16%  Similarity=0.278  Sum_probs=52.2

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+++||.++++.-+...++.|...|..+..+||+.+..++..++..++.|..+||+
T Consensus        65 ~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv  120 (523)
T 1oyw_A           65 NGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLY  120 (523)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEE
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEE
Confidence            47899999999999999999999999999999999999999999999999988874

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=87.06  E-value=0.81  Score=49.45  Aligned_cols=57  Identities=14%  Similarity=0.180  Sum_probs=51.9

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHH---CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSK---EGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~---~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...++||.++++.-|.++++.|..   .++.+..+||+++..+|...++.++.|..+|+|
T Consensus       120 ~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV  179 (1104)
T 4ddu_A          120 KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILV  179 (1104)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEE
T ss_pred             cCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEE
Confidence            456899999999999999999988   467999999999999999999999999988875

>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=86.89  E-value=0.5  Score=43.28  Aligned_cols=92  Identities=11%  Similarity=0.051  Sum_probs=53.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      | -+.+.+|+|+|||...+-.+...... ..+.+++++..-..+...   .+++++-...                    
T Consensus        29 G-iteI~G~pGsGKTtL~Lq~~~~~~~~-g~g~~vlyId~E~s~~~~---ra~~lGvd~d--------------------   83 (333)
T 3io5_A           29 G-LLILAGPSKSFKSNFGLTMVSSYMRQ-YPDAVCLFYDSEFGITPA---YLRSMGVDPE--------------------   83 (333)
T ss_dssp             E-EEEEEESSSSSHHHHHHHHHHHHHHH-CTTCEEEEEESSCCCCHH---HHHHTTCCGG--------------------
T ss_pred             C-eEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEeccchhhHH---HHHHhCCCHH--------------------
Confidence            5 68999999999997665544443322 124578998876555332   3555543221                    


Q ss_pred             CcEEEeCchhHHHh----hhccccccCCceeEEEEechhhHh
Q psy11867        222 EQIIIGTPGKVLDW----GLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~----~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                       ++++..|..+-+.    +.....+.-..++++|||-+..|.
T Consensus        84 -~llv~~~~~~E~~~l~i~~~l~~i~~~~~~lvVIDSI~aL~  124 (333)
T 3io5_A           84 -RVIHTPVQSLEQLRIDMVNQLDAIERGEKVVVFIDSLGNLA  124 (333)
T ss_dssp             -GEEEEECSBHHHHHHHHHHHHHTCCTTCCEEEEEECSTTCB
T ss_pred             -HeEEEcCCCHHHHHHHHHHHHHHhhccCceEEEEecccccc
Confidence             2455544443222    111111233468999999999875

>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=86.60  E-value=1.7  Score=37.14  Aligned_cols=68  Identities=9%  Similarity=0.119  Sum_probs=48.6

Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCC
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLS  245 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~  245 (399)
                      +.++||.++++.-+..+++.+...     ++.+....|+......       ..+..+|+|+|.-       -...+++.
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~-------~~~Gidi~   98 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDV-------AARGLDIP   98 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHH-----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTT-------TTCSSSCC
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecCh-------hhcCCCCc
Confidence            457999999999999999988876     4556666776443221       2456789999942       22567888


Q ss_pred             ceeEEEE
Q psy11867        246 KIKVFVL  252 (399)
Q Consensus       246 ~~~~lVi  252 (399)
                      ++++||.
T Consensus        99 ~v~~Vi~  105 (212)
T 3eaq_A           99 QVDLVVH  105 (212)
T ss_dssp             CBSEEEE
T ss_pred             cCcEEEE
Confidence            8888884

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=86.59  E-value=5.1  Score=33.41  Aligned_cols=68  Identities=18%  Similarity=0.207  Sum_probs=48.1

Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCC
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLS  245 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~  245 (399)
                      +.++||.++++.-+..+++.++..     ++.+....|+......       ..+...|+|+|.  +..     ..+++.
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~--~~~-----~Gldi~  121 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLLK-----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD--VAS-----KGLDFP  121 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH--HHH-----TTCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC--chh-----cCCCcc
Confidence            357999999999999999988876     4455666666433221       145678999993  222     466788


Q ss_pred             ceeEEEE
Q psy11867        246 KIKVFVL  252 (399)
Q Consensus       246 ~~~~lVi  252 (399)
                      +++++|.
T Consensus       122 ~v~~VI~  128 (191)
T 2p6n_A          122 AIQHVIN  128 (191)
T ss_dssp             CCSEEEE
T ss_pred             cCCEEEE
Confidence            8888876

>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=86.33  E-value=2  Score=35.22  Aligned_cols=71  Identities=15%  Similarity=0.221  Sum_probs=49.5

Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccC
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDL  244 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~  244 (399)
                      ...++||.|+++.-+..+++.+...     ++.+....|+......       ..+...|+|+|.-       -...+++
T Consensus        30 ~~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~-------~~~Gldi   97 (172)
T 1t5i_A           30 EFNQVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL-------FGRGMDI   97 (172)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC-------CSTTCCG
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCc-------hhcCcch
Confidence            3457999999999999999988875     4555666666433221       1456789999952       2246678


Q ss_pred             CceeEEEEec
Q psy11867        245 SKIKVFVLDE  254 (399)
Q Consensus       245 ~~~~~lViDE  254 (399)
                      ..++++|.-+
T Consensus        98 ~~~~~Vi~~d  107 (172)
T 1t5i_A           98 ERVNIAFNYD  107 (172)
T ss_dssp             GGCSEEEESS
T ss_pred             hhCCEEEEEC
Confidence            8888888644

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=85.99  E-value=1  Score=33.88  Aligned_cols=37  Identities=22%  Similarity=0.276  Sum_probs=32.9

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCH
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTV  380 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~  380 (399)
                      ..++++||.+-..+...+..|...|+++..+.||+..
T Consensus        55 ~~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~~~   91 (108)
T 3gk5_A           55 DKKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGIQS   91 (108)
T ss_dssp             TSCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHHHH
T ss_pred             CCeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcHHH
Confidence            3689999999888999999999999999999999654

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=85.79  E-value=2.4  Score=42.57  Aligned_cols=19  Identities=21%  Similarity=0.323  Sum_probs=16.8

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      |..+++.+|+|+|||..+-
T Consensus        60 g~~vll~Gp~GtGKTtlar   78 (604)
T 3k1j_A           60 KRHVLLIGEPGTGKSMLGQ   78 (604)
T ss_dssp             TCCEEEECCTTSSHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHH
Confidence            7999999999999997653

>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=85.63  E-value=0.82  Score=43.70  Aligned_cols=39  Identities=18%  Similarity=0.407  Sum_probs=24.3

Q ss_pred             HHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC
Q psy11867        130 QETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP  169 (399)
Q Consensus       130 Q~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~  169 (399)
                      +..++..++..+|.-+++.||||||||... -.++..+..
T Consensus       155 ~~~~L~~l~~~~ggii~I~GpnGSGKTTlL-~allg~l~~  193 (418)
T 1p9r_A          155 NHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELNS  193 (418)
T ss_dssp             HHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHCC
T ss_pred             HHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHhhcCC
Confidence            344444444444678899999999999643 234444443

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=84.76  E-value=0.44  Score=39.22  Aligned_cols=18  Identities=33%  Similarity=0.466  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      +.++++.||+|+|||...
T Consensus        43 ~~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            588999999999999654

>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=84.55  E-value=1.8  Score=43.43  Aligned_cols=56  Identities=13%  Similarity=0.187  Sum_probs=50.7

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHH--hcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRF--REGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F--~~G~~~ILV  399 (399)
                      .+++||.++++.-+...++.|...|+.+..++|+++..++..++..+  ..|..+|||
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv  141 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIY  141 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEE
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEE
Confidence            47899999999999999999999999999999999999999999988  567887764

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=84.51  E-value=1.7  Score=44.87  Aligned_cols=17  Identities=29%  Similarity=0.384  Sum_probs=14.6

Q ss_pred             cEEEEccCCCCceehhH
Q psy11867        144 NMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~  160 (399)
                      ++++.||||+|||..+-
T Consensus       523 ~~Ll~Gp~GtGKT~lA~  539 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELAR  539 (758)
T ss_dssp             EEEEESCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            69999999999996553

>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=84.40  E-value=0.49  Score=45.40  Aligned_cols=43  Identities=14%  Similarity=0.306  Sum_probs=30.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI  187 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~  187 (399)
                      ..|+++.|+||||||... ..++..+..  .+..++|+=|..++..
T Consensus        53 ~~h~~i~G~tGsGKs~~~-~~li~~~~~--~g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLL-RELAYTGLL--RGDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGCEEEEECTTSSHHHHH-HHHHHHHHH--TTCEEEEEEETTHHHH
T ss_pred             cceEEEECCCCCCHHHHH-HHHHHHHHH--CCCcEEEEeCCCchhH
Confidence            589999999999999874 333433322  3456888889888764

>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=84.20  E-value=1.6  Score=40.14  Aligned_cols=54  Identities=19%  Similarity=0.183  Sum_probs=32.1

Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhh
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDM  299 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~  299 (399)
                      ..+++++|.+-++.........+..+.+.+.+...++.+.++....+.+.++.+
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            345677887766432223334444455555566677788888777666666554

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=84.08  E-value=0.94  Score=42.46  Aligned_cols=38  Identities=8%  Similarity=-0.047  Sum_probs=25.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      |.-+++.+++|+|||...+-.+......   +..++|+..-
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~---g~~vlyi~~E  111 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAE  111 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESS
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHC---CCeEEEEECC
Confidence            7889999999999996554433333322   3357777754

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=83.99  E-value=1.2  Score=50.71  Aligned_cols=54  Identities=13%  Similarity=0.033  Sum_probs=36.7

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      +|+++++.+++|+|||......+.+....   +.+++++. ..++..+++  .+.++-.+
T Consensus      1080 ~g~~vll~G~~GtGKT~la~~~~~ea~k~---Ge~~~Fit-~ee~~~~L~--a~~~G~dl 1133 (2050)
T 3cmu_A         1080 MGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFID-AEHALDPIY--ARKLGVDI 1133 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEEC-TTSCCCHHH--HHHTTCCT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEE-ccccHHHHH--HHHcCCCh
Confidence            38999999999999998777666666554   34577776 344455555  35555444

>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=83.92  E-value=8.3  Score=34.98  Aligned_cols=17  Identities=18%  Similarity=0.188  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCCceehh
Q psy11867        143 HNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~  159 (399)
                      ..+++.|+.|+|||...
T Consensus        31 ~~v~i~G~~G~GKT~L~   47 (357)
T 2fna_A           31 PITLVLGLRRTGKSSII   47 (357)
T ss_dssp             SEEEEEESTTSSHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            58999999999999654

>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=83.74  E-value=2.6  Score=35.05  Aligned_cols=84  Identities=17%  Similarity=0.191  Sum_probs=48.3

Q ss_pred             CCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhh-------hhccCCcEE
Q psy11867        153 TGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER-------NKKITEQII  225 (399)
Q Consensus       153 sGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~Il  225 (399)
                      +.|- .+++-++...   ..+.++||.++++.-+..+.+.++..     ++.+....|+.....       -..+...|+
T Consensus        30 ~~K~-~~L~~ll~~~---~~~~k~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vL  100 (185)
T 2jgn_A           30 SDKR-SFLLDLLNAT---GKDSLTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPIL  100 (185)
T ss_dssp             GGHH-HHHHHHHHHC----CCSCEEEEESCHHHHHHHHHHHHHT-----TCCEEEEC--------CHHHHHHHHTSSSEE
T ss_pred             HHHH-HHHHHHHHhc---CCCCeEEEEECCHHHHHHHHHHHHHc-----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEE
Confidence            4453 3344444442   24567999999999999999888875     345555555543211       124567899


Q ss_pred             EeCchhHHHhhhccccccCCceeEEEE
Q psy11867        226 IGTPGKVLDWGLKYRFFDLSKIKVFVL  252 (399)
Q Consensus       226 V~Tp~~l~~~~~~~~~~~~~~~~~lVi  252 (399)
                      |+|.  +..     ..+++..++++|.
T Consensus       101 vaT~--~~~-----~Gldi~~~~~VI~  120 (185)
T 2jgn_A          101 VATA--VAA-----RGLDISNVKHVIN  120 (185)
T ss_dssp             EEEC-------------CCCSBSEEEE
T ss_pred             EEcC--hhh-----cCCCcccCCEEEE
Confidence            9994  222     3567778888876

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=83.71  E-value=0.88  Score=33.62  Aligned_cols=35  Identities=17%  Similarity=0.349  Sum_probs=31.8

Q ss_pred             CcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCC
Q psy11867        345 GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT  379 (399)
Q Consensus       345 ~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~  379 (399)
                      .++++||.+-..+...+..|...|+++..+.||+.
T Consensus        57 ~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~   91 (100)
T 3foj_A           57 ETYYIICKAGGRSAQVVQYLEQNGVNAVNVEGGMD   91 (100)
T ss_dssp             SEEEEECSSSHHHHHHHHHHHTTTCEEEEETTHHH
T ss_pred             CcEEEEcCCCchHHHHHHHHHHCCCCEEEecccHH
Confidence            58999999998999999999999999999999854

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=83.55  E-value=0.88  Score=42.46  Aligned_cols=41  Identities=12%  Similarity=0.040  Sum_probs=26.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      |.-+++.+|+|+|||...+. ++..+..  .+..++++..-..+
T Consensus        61 G~i~~I~GppGsGKSTLal~-la~~~~~--~gg~VlyId~E~s~  101 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALH-AIAEAQK--MGGVAAFIDAEHAL  101 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHH-HHHHHHH--TTCCEEEEESSCCC
T ss_pred             CcEEEEECCCCCCHHHHHHH-HHHHHHh--cCCeEEEEeccccc
Confidence            78899999999999965443 3332222  23457888754433

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=82.93  E-value=1  Score=32.81  Aligned_cols=35  Identities=20%  Similarity=0.265  Sum_probs=31.5

Q ss_pred             CcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCC
Q psy11867        345 GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT  379 (399)
Q Consensus       345 ~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~  379 (399)
                      .++++||.+-..+...+..|...|+.+..+.||+.
T Consensus        54 ~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~   88 (94)
T 1wv9_A           54 RPLLLVCEKGLLSQVAALYLEAEGYEAMSLEGGLQ   88 (94)
T ss_dssp             SCEEEECSSSHHHHHHHHHHHHHTCCEEEETTGGG
T ss_pred             CCEEEEcCCCChHHHHHHHHHHcCCcEEEEcccHH
Confidence            68999999988899999999999999888999875

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.90  E-value=0.46  Score=45.05  Aligned_cols=52  Identities=21%  Similarity=0.316  Sum_probs=33.6

Q ss_pred             cccccCCCCHHHHHHHHHc---CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        103 KTFEALHLKPELLKGVYEM---GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~---g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      -+|++.+=.+...+.|.+.   -+.+|--++...+     .+++.+++.||+|+|||+.+
T Consensus       145 v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi-----~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          145 STYDMVGGLTKQIKEIKEVIELPVKHPELFESLGI-----AQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTC-----CCCCCEEEESCSSSSHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCC-----CCCCceEEeCCCCCCHHHHH
Confidence            4688887556666666653   1233333333322     23689999999999999654

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=82.71  E-value=5.8  Score=29.46  Aligned_cols=50  Identities=16%  Similarity=0.312  Sum_probs=43.0

Q ss_pred             EEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc
Q psy11867        347 AMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK  396 (399)
Q Consensus       347 ~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~  396 (399)
                      .+||...-+....+.+.+...|..+..+.++.....|..-++.|...-+.
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqgvd   54 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVD   54 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTCE
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCCc
Confidence            36777888888889999999999999999999999999999999765443

>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=82.53  E-value=4.6  Score=39.84  Aligned_cols=76  Identities=16%  Similarity=0.114  Sum_probs=54.2

Q ss_pred             CCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhcccccc
Q psy11867        171 IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFD  243 (399)
Q Consensus       171 ~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~  243 (399)
                      ..+.++||.|+|+.-+..+++.++.....  ++.+....++......       ..+..+|+|||.-       -...++
T Consensus       337 ~~~~~~iVF~~s~~~~~~l~~~L~~~~~~--~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~-------~~~GiD  407 (563)
T 3i5x_A          337 DSNYKAIIFAPTVKFTSFLCSILKNEFKK--DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV-------GARGMD  407 (563)
T ss_dssp             TTCCEEEEECSCHHHHHHHHHHHHHHHTT--TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGG-------GTSSCC
T ss_pred             CCCCcEEEEcCcHHHHHHHHHHHHHhccC--CceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcch-------hhcCCC
Confidence            35668999999999999999999887542  4566666776543221       1456789999962       225678


Q ss_pred             CCceeEEEEech
Q psy11867        244 LSKIKVFVLDEA  255 (399)
Q Consensus       244 ~~~~~~lViDEa  255 (399)
                      +.++++||.-..
T Consensus       408 ip~v~~VI~~~~  419 (563)
T 3i5x_A          408 FPNVHEVLQIGV  419 (563)
T ss_dssp             CTTCCEEEEESC
T ss_pred             cccCCEEEEECC
Confidence            888999886553

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=81.66  E-value=0.64  Score=45.71  Aligned_cols=40  Identities=18%  Similarity=0.132  Sum_probs=25.9

Q ss_pred             HHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceeh
Q psy11867        116 KGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAA  158 (399)
Q Consensus       116 ~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~  158 (399)
                      ..|.+.|..  ++.+..-+...... |.++++.||||||||..
T Consensus       237 ~~l~~~G~~--~~~~l~~l~~~v~~-g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          237 IDLIEKGTV--PSGVLAYLWLAIEH-KFSAIVVGETASGKTTT  276 (511)
T ss_dssp             HHHHHTTSS--CHHHHHHHHHHHHT-TCCEEEEESTTSSHHHH
T ss_pred             hhHHhcCCC--CHHHHHHHHHHHhC-CCEEEEECCCCCCHHHH
Confidence            445556632  33344444444444 78999999999999964

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.38  E-value=0.47  Score=45.58  Aligned_cols=52  Identities=25%  Similarity=0.412  Sum_probs=31.8

Q ss_pred             cccccCCCCHHHHHHHHHc---CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        103 KTFEALHLKPELLKGVYEM---GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~---g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      -+|++.+=.+...+.|...   -+.+|--++...+     .+++.+++.||+|+|||+.+
T Consensus       178 v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~-----~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          178 ITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGI-----KPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             SCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCC-----CCCCEEEEESCTTSSHHHHH
T ss_pred             CChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCC-----CCCCeEEEECCCCCcHHHHH
Confidence            3577776555666666542   1223333333222     23799999999999999654

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=81.17  E-value=1.2  Score=40.05  Aligned_cols=53  Identities=15%  Similarity=0.157  Sum_probs=30.5

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHH-HHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQ-ETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ-~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      .+|+++.=.+...+.+...-.   .+.. .+.+..+ ..+++.+++.||+|+|||..+
T Consensus        18 ~~~~~i~G~~~~~~~l~~~i~---~~~~~~~~~~~~-~~~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           18 VEWTDIAGQDVAKQALQEMVI---LPSVRPELFTGL-RAPAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CCGGGSCCCHHHHHHHHHHTH---HHHHCGGGSCGG-GCCCSEEEEESSSSSCHHHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHH---hhhhCHHHHhcC-CCCCCeEEEECcCCCCHHHHH
Confidence            457777666677776654310   0000 0011111 123689999999999999654

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=80.70  E-value=1.1  Score=43.26  Aligned_cols=52  Identities=17%  Similarity=0.206  Sum_probs=31.1

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhh---cCCCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLL---ADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll---~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      .+|+++.=.....+.|...-.   .|..   .|.+.   ..+++.+++.||+|+|||+.+-
T Consensus       131 ~~~~di~G~~~~k~~l~~~v~---~p~~---~~~~~~~~~~~~~~vLL~GppGtGKT~lA~  185 (444)
T 2zan_A          131 VKWSDVAGLEGAKEALKEAVI---LPIK---FPHLFTGKRTPWRGILLFGPPGTGKSYLAK  185 (444)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHT---HHHH---CTTTTSGGGCCCSEEEEECSTTSSHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHH---HHhh---CHHHhhccCCCCceEEEECCCCCCHHHHHH
Confidence            467887666677777664310   0111   11111   1236899999999999997553

>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=80.25  E-value=4.5  Score=34.22  Aligned_cols=51  Identities=20%  Similarity=0.405  Sum_probs=39.1

Q ss_pred             CcEEEEecchHhHHHHHHHHHHC-----CCeEEEEcCCCCHHHHHHHHHHHhcCCCccc
Q psy11867        345 GQAMIFCHTRKTAAWLAEKMSKE-----GLNVGLLSGELTVEQRLSILDRFREGEFKIY  398 (399)
Q Consensus       345 ~k~IIF~~s~~~a~~l~~~L~~~-----g~~v~~lhg~~~~~~R~~v~~~F~~G~~~IL  398 (399)
                      .++||.|+++.-+.++++.+.+.     +..+..++|+.+..++...+   ..+..+|+
T Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~---~~~~~~i~  138 (220)
T 1t6n_A           83 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL---KKNCPHIV  138 (220)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHH---HHSCCSEE
T ss_pred             EEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHH---hcCCCCEE
Confidence            48999999999999998887764     68899999999877665433   34444554

---

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	399
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	8e-40
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	1e-39
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-37
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	2e-36
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	3e-34
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	5e-31
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	7e-31
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	3e-29
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	2e-24
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-24
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	2e-18
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	4e-16
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	1e-15
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	1e-13
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	1e-11
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	2e-10
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	2e-09
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	3e-06
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	2e-05
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	4e-05
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	9e-05
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	1e-04
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	2e-04
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	4e-04
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	0.004

>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 =  139 bits (350), Expect = 8e-40
 Identities = 74/212 (34%), Positives = 122/212 (57%), Gaps = 7/212 (3%)

Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           V +F+ ++L   LL+G+Y  GF  PS IQ+ A+   +    +++IAQ+QSGTGKTA F +
Sbjct: 11  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKG--YDVIAQAQSGTGKTATFAI 68

Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI- 220
           ++L ++   ++  Q L LAPT ELA QI +VV  +G ++                 +K+ 
Sbjct: 69  SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 128

Query: 221 --TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSD 278
                II+GTPG+ +   L  R+     IK+FVLDEAD  + ++G +D    I ++L S+
Sbjct: 129 MEAPHIIVGTPGR-VFDMLNRRYLSPKYIKMFVLDEAD-EMLSRGFKDQIYDIFQKLNSN 186

Query: 279 CQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR 310
            Q++L SAT   +V+E  +  + +P+ I +K+
Sbjct: 187 TQVVLLSATMPSDVLEVTKKFMRDPIRILVKK 218

>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 =  138 bits (349), Expect = 1e-39
 Identities = 56/206 (27%), Positives = 99/206 (48%), Gaps = 3/206 (1%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
            F  L+L   +L  +   GF  P+ IQ   +P  L D  +N++AQ+++G+GKTA+F + +
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDE-YNIVAQARTGSGKTASFAIPL 63

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQ 223
           +  VN +     ++             E+ +  G     ++  Y  +    +        
Sbjct: 64  IELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNAN 123

Query: 224 IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIML 283
           I++GTPG++LD  +     +L  +K F+LDEAD M+   G      +I      D +I+L
Sbjct: 124 IVVGTPGRILDH-INRGTLNLKNVKYFILDEADEML-NMGFIKDVEKILNACNKDKRILL 181

Query: 284 FSATYDKEVMEFAQDMVPNPLIIKLK 309
           FSAT  +E++  A+  + +   IK K
Sbjct: 182 FSATMPREILNLAKKYMGDYSFIKAK 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 =  131 bits (331), Expect = 4e-37
 Identities = 76/206 (36%), Positives = 120/206 (58%), Gaps = 5/206 (2%)

Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
           V  F+ + L   LL+GV+  GF  PS IQ+ A+  ++    H+++AQ+QSGTGKT  F++
Sbjct: 9   VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEG--HDVLAQAQSGTGKTGTFSI 66

Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT 221
             L R++ S++ PQ L LAPT ELA+QI +VV  +  H+             +E  + + 
Sbjct: 67  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 126

Query: 222 E-QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
           + QI++GTPG+V    ++ R F   KIK+F+LDEAD  + + G ++   +I   LP   Q
Sbjct: 127 DAQIVVGTPGRV-FDNIQRRRFRTDKIKMFILDEAD-EMLSSGFKEQIYQIFTLLPPTTQ 184

Query: 281 IMLFSATYDKEVMEFAQDMVPNPLII 306
           ++L SAT   +V+E     + NP+ I
Sbjct: 185 VVLLSATMPNDVLEVTTKFMRNPVRI 210

>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 =  130 bits (327), Expect = 2e-36
 Identities = 71/212 (33%), Positives = 118/212 (55%), Gaps = 6/212 (2%)

Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
              TF+ + L+ +LL+G+Y  GF  PS IQ+ A+  ++     ++IAQSQSGTGKTA F+
Sbjct: 15  VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKG--RDVIAQSQSGTGKTATFS 72

Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKH--ITDLSVRYAVRGENLERNK 218
           +++L  ++  ++E Q L LAPT ELA+QI + +  +G +  +   +           R  
Sbjct: 73  ISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL 132

Query: 219 KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSD 278
              + ++ GTPG+V D   + R      IK+ VLDEAD  +  +G ++    + + LP  
Sbjct: 133 DYGQHVVAGTPGRVFDMI-RRRSLRTRAIKMLVLDEAD-EMLNKGFKEQIYDVYRYLPPA 190

Query: 279 CQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR 310
            Q++L SAT   E++E     + +P+ I +KR
Sbjct: 191 TQVVLISATLPHEILEMTNKFMTDPIRILVKR 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 =  124 bits (311), Expect = 3e-34
 Identities = 63/207 (30%), Positives = 106/207 (51%), Gaps = 7/207 (3%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
            F    LKPELL+ + + GF  PS++Q   +P  +     +++ Q++SG GKTA F L  
Sbjct: 2   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG--MDVLCQAKSGMGKTAVFVLAT 59

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD----LSVRYAVRGENLERNKK 219
           L ++ P   +  VL +  T ELA QI +   +  K++ +    +        ++ E  KK
Sbjct: 60  LQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK 119

Query: 220 ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
               I++GTPG++L    + +  +L  IK F+LDE D M+     +     I +  P + 
Sbjct: 120 NCPHIVVGTPGRILALA-RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEK 178

Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLII 306
           Q+M+FSAT  KE+    +  + +P+ I
Sbjct: 179 QVMMFSATLSKEIRPVCRKFMQDPMEI 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 =  115 bits (288), Expect = 5e-31
 Identities = 69/208 (33%), Positives = 102/208 (49%), Gaps = 8/208 (3%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
           TFE  +LK ELL G++E GF  PS IQE A+P  +     +++A++++GTGKTAAF +  
Sbjct: 2   TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITG--RDILARAKNGTGKTAAFVIPT 59

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRY---AVRGENLERNKKI 220
           L +V P + + Q L + PT E        V +       +S           +       
Sbjct: 60  LEKVKPKLNKIQALIMVPTRE-LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNE 118

Query: 221 TEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ 280
           T  I++GTPG+V       +  DLS   +F++DEAD M++         +I   LP   Q
Sbjct: 119 TVHILVGTPGRV-LDLASRKVADLSDCSLFIMDEADKMLSRDFKTII-EQILSFLPPTHQ 176

Query: 281 IMLFSATYDKEVMEFAQDMVPNPLIIKL 308
            +LFSAT+   V EF    +  P  I L
Sbjct: 177 SLLFSATFPLTVKEFMVKHLHKPYEINL 204

>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 =  115 bits (287), Expect = 7e-31
 Identities = 65/207 (31%), Positives = 112/207 (54%), Gaps = 7/207 (3%)

Query: 103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLT 162
             FE   LK ELL G++EMG+  PS IQE ++P  L+    +++A++++GTGK+ A+ + 
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSG--RDILARAKNGTGKSGAYLIP 60

Query: 163 MLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---K 219
           +L R++      Q + + PT ELA+Q+ ++  ++ KH+    V     G NL  +     
Sbjct: 61  LLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD 120

Query: 220 ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
            T  ++I TPG+ +   +K     +  +++ VLDEAD +++    Q     I   LP + 
Sbjct: 121 DTVHVVIATPGR-ILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIME-DIILTLPKNR 178

Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLII 306
           QI+L+SAT+   V +F    +  P  I
Sbjct: 179 QILLYSATFPLSVQKFMNSHLEKPYEI 205

>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 =  111 bits (279), Expect = 3e-29
 Identities = 57/235 (24%), Positives = 102/235 (43%), Gaps = 18/235 (7%)

Query: 87  ELEIQRKDPHSPLYS-VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNM 145
            + +    P     + ++ F+ L L P +   +    +  P+ IQ+ A+P +L     ++
Sbjct: 4   SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEH--RDI 61

Query: 146 IAQSQSGTGKTAAFTLTMLSRV---------NPSIQEPQVLCLAPTYELAIQIGEVVAKM 196
           +A +Q+G+GKTAAF + +++ +               P+ L LAPT ELAIQI     K 
Sbjct: 62  MACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKF 121

Query: 197 GKH--ITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDE 254
             +  +    V       +  R  ++   +++ TP   L   ++     L   K  VLDE
Sbjct: 122 SLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATP-GRLVDFIEKNKISLEFCKYIVLDE 180

Query: 255 ADVMIATQGHQDFSI---RIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII 306
           AD M+                     + Q ++FSAT+ KE+ + A D + N + +
Sbjct: 181 ADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFM 235

>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 = 97.4 bits (241), Expect = 2e-24
 Identities = 58/209 (27%), Positives = 102/209 (48%), Gaps = 8/209 (3%)

Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
            F     +P +++ +  + FY P++IQE  +P  L     +M+ QSQ+GTGKT A+ L +
Sbjct: 2   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRG--ESMVGQSQTGTGKTHAYLLPI 59

Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQ 223
           + ++ P   E Q +  APT ELA QI     K+ K      +  A         +K  E+
Sbjct: 60  MEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEK 119

Query: 224 -----IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSD 278
                 I+      ++  ++ +  D+    + V+DEAD+M+      D   +I  R+P D
Sbjct: 120 LNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVD-QIAARMPKD 178

Query: 279 CQIMLFSATYDKEVMEFAQDMVPNPLIIK 307
            Q+++FSAT  +++  F +  + NP  + 
Sbjct: 179 LQMLVFSATIPEKLKPFLKKYMENPTFVH 207

>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 = 99.6 bits (247), Expect = 3e-24
 Identities = 32/253 (12%), Positives = 71/253 (28%), Gaps = 33/253 (13%)

Query: 144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL 203
             I     G GKT  +   ++       +  + L LAPT  +A ++ E +  +       
Sbjct: 11  LTIMDLHPGAGKTKRYLPAIVREAIK--RGLRTLILAPTRVVAAEMEEALRGLPIRY--- 65

Query: 204 SVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQG 263
                 +   +       E + +                 +    + ++DEA        
Sbjct: 66  ------QTPAIRAEHTGREIVDLMCHATFTM--RLLSPIRVPNYNLIIMDEAHFTDP-AS 116

Query: 264 HQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYV 323
                    +    +   +  +AT       F Q   P                 ++  +
Sbjct: 117 IAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAP--------------IMDEEREI 162

Query: 324 MCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQR 383
             ++ +   E V++       G+ + F  + K    +A  + K G  V  LS +    + 
Sbjct: 163 PERSWNSGHEWVTD-----FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEY 217

Query: 384 LSILDRFREGEFK 396
           +       +    
Sbjct: 218 IKTRTNDWDFVVT 230

>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 = 81.5 bits (200), Expect = 2e-18
 Identities = 28/201 (13%), Positives = 54/201 (26%), Gaps = 24/201 (11%)

Query: 112 PELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSI 171
            +     +      P  IQ+     +L     +  A + +G GKT+      L       
Sbjct: 30  LKEFVEFFRKCVGEPRAIQKMWAKRILRK--ESFAATAPTGVGKTSFGLAMSLFLAL--- 84

Query: 172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGK 231
           +  +   + PT  L IQ  E + K  +      V                E+       +
Sbjct: 85  KGKRCYVIFPTSLLVIQAAETIRKYAEK---AGVGTENLIGYYHGRIPKREKENFMQNLR 141

Query: 232 VLDW------GLKYRFFDLSKIKVFVLDEADVMIATQGHQDFS----------IRIQKRL 275
                      L   + +L       +D+ D ++    + D                   
Sbjct: 142 NFKIVITTTQFLSKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVG 201

Query: 276 PSDCQIMLFSATYDKEVMEFA 296
            +   +M+ +AT  K      
Sbjct: 202 EARGCLMVSTATAKKGKKAEL 222

>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 = 74.3 bits (181), Expect = 4e-16
 Identities = 30/212 (14%), Positives = 70/212 (33%), Gaps = 21/212 (9%)

Query: 104 TFEALHLKP---ELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
             E L+L+    ++L+  +  G+      QE  + T+L+    + +    +G GK+  + 
Sbjct: 3   QAEVLNLESGAKQVLQETF--GYQQFRPGQEEIIDTVLSG--RDCLVVMPTGGGKSLCYQ 58

Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVR--YAVRGENLERNK 218
           +  L            + ++P   L     + +   G     L+       + E +   +
Sbjct: 59  IPALLLN------GLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCR 112

Query: 219 KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRL--- 275
               +++   P +++               +  +DEA  +               +L   
Sbjct: 113 TGQIRLLYIAPERLMLDN-FLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQR 171

Query: 276 PSDCQIMLFSATYDKEVMEFAQDM--VPNPLI 305
                 M  +AT D    +    +  + +PLI
Sbjct: 172 FPTLPFMALTATADDTTRQDIVRLLGLNDPLI 203

>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 = 73.1 bits (178), Expect = 1e-15
 Identities = 36/198 (18%), Positives = 76/198 (38%), Gaps = 13/198 (6%)

Query: 104 TFEALH--LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
             E L   +    +  + E G       Q  A+  + +    N++    +  GK     L
Sbjct: 2   KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSG--KNLLLAMPTAAGK---TLL 56

Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT 221
             ++ V  +I+  + L + P   LA +  E   K  K    + +     G+   R++ + 
Sbjct: 57  AEMAMVREAIKGGKSLYVVPLRALAGEKYESFKKWEKIGLRIGIST---GDYESRDEHLG 113

Query: 222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFS--IRIQKRLPSDC 279
           +  II T  +  D  ++ R   +  +   V+DE  ++ + +        +   +R+    
Sbjct: 114 DCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKAL 173

Query: 280 QIMLFSATYDKEVMEFAQ 297
           +++  SAT    V E A+
Sbjct: 174 RVIGLSATAP-NVTEIAE 190

>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 = 67.1 bits (162), Expect = 1e-13
 Identities = 38/204 (18%), Positives = 71/204 (34%), Gaps = 7/204 (3%)

Query: 118 VYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVL 177
           V       P   QE            N +    +G GKT    +    R+       +VL
Sbjct: 2   VLRRDLIQPRIYQEVIYAKCKE---TNCLIVLPTGLGKTLIAMMIAEYRLTK--YGGKVL 56

Query: 178 CLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGL 237
            LAPT  L +Q  E   ++     +  V         ER+K      +I    + ++  L
Sbjct: 57  MLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDL 116

Query: 238 KYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ 297
                 L  + + V DEA   +    +     R  KR   +  ++  +A+      E   
Sbjct: 117 LAGRISLEDVSLIVFDEAHRAVGNYAYVFI-AREYKRQAKNPLVIGLTASPGSTP-EKIM 174

Query: 298 DMVPNPLIIKLKREEESLDNIKQH 321
           +++ N  I  ++   E+  +++ +
Sbjct: 175 EVINNLGIEHIEYRSENSPDVRPY 198

>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 = 60.7 bits (146), Expect = 1e-11
 Identities = 25/80 (31%), Positives = 47/80 (58%)

Query: 318 IKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGE 377
           IKQ YV  +  + K+E ++++Y  +++ QA+IFC+TR+    L  K+  +   V  +  +
Sbjct: 1   IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 60

Query: 378 LTVEQRLSILDRFREGEFKI 397
           L  ++R +I+  FR G  +I
Sbjct: 61  LPQQERDTIMKEFRSGSSRI 80

>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 = 56.9 bits (136), Expect = 2e-10
 Identities = 30/87 (34%), Positives = 54/87 (62%)

Query: 311 EEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLN 370
           +E +L+ IKQ +V  +  + KF+ + ++Y  +TI QA+IFC+T++   WL EKM +    
Sbjct: 1   DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFT 60

Query: 371 VGLLSGELTVEQRLSILDRFREGEFKI 397
           V  + G++  ++R SI+  FR G  ++
Sbjct: 61  VSSMHGDMPQKERESIMKEFRSGASRV 87

>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 = 46.5 bits (110), Expect = 3e-06
 Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 10/63 (15%)

Query: 345 GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLS----------ILDRFREGE 394
           G+ +IFCH++K    LA K+   G+N       L V    +           L     G+
Sbjct: 37  GRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGD 96

Query: 395 FKI 397
           F  
Sbjct: 97  FDS 99

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {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: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (99), Expect = 2e-05
 Identities = 12/47 (25%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 318 IKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKM 364
           ++Q+YV  K+ +EK   + ++  V+   Q +IF  + +    LA+ +
Sbjct: 2   LQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLL 47

>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 = 42.5 bits (99), Expect = 4e-05
 Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 8/80 (10%)

Query: 318 IKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGE 377
           ++    +  N DE    +S+I   +     +I+  T + A  + E +  +          
Sbjct: 1   VRNVEDVAVN-DESISTLSSILEKLG-TGGIIYARTGEEAEEIYESLKNK------FRIG 52

Query: 378 LTVEQRLSILDRFREGEFKI 397
           +    +    ++F EGE   
Sbjct: 53  IVTATKKGDYEKFVEGEIDH 72

>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 = 41.4 bits (96), Expect = 9e-05
 Identities = 33/156 (21%), Positives = 58/156 (37%), Gaps = 23/156 (14%)

Query: 251 VLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKR 310
            L  A  ++ TQG         K+L  + +     A+      E   D      I  L +
Sbjct: 81  KLHHAIELLETQGLSALR-AYIKKLYEEAKAGSTKAS-----KEIFSDKRMKKAISLLVQ 134

Query: 311 -EEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGL 369
            +E  LD+ K        +D+  E +          + ++F + R+TA  +  ++ K+G+
Sbjct: 135 AKEIGLDHPK--------MDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGI 186

Query: 370 NVGLLSGELTVEQRL--------SILDRFREGEFKI 397
                 G+ + E            ILD F  GEF +
Sbjct: 187 KAKRFVGQASKENDRGLSQREQKLILDEFARGEFNV 222

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} 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: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 40.4 bits (93), Expect = 1e-04
 Identities = 12/81 (14%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 317 NIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSG 376
           NI   Y++ +   +  + +            +I+C++R      A ++  +G++      
Sbjct: 6   NI--RYMLMEK-FKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHA 62

Query: 377 ELTVEQRLSILDRFREGEFKI 397
            L    R  + ++F+  + +I
Sbjct: 63  GLENNVRADVQEKFQRDDLQI 83

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

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 = 39.6 bits (91), Expect = 2e-04
 Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 312 EESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKM 364
           E +L  I Q+Y   +   +K   ++ ++  + I QA+IFC++      LA+K+
Sbjct: 1   ELTLKGITQYYAFVEE-RQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKI 52

>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 = 38.4 bits (88), Expect = 4e-04
 Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 317 NIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKM 364
           NI+Q YV     +E+FEA+  +         ++FC T++    LA  +
Sbjct: 3   NIEQSYVEVNE-NERFEALCRLLKNKEF-YGLVFCKTKRDTKELASML 48

>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 = 35.1 bits (80), Expect = 0.004
 Identities = 23/93 (24%), Positives = 34/93 (36%), Gaps = 14/93 (15%)

Query: 299 MVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAA 358
            VP+P I     EE +L    +     K I  +             G+ +IFCH++K   
Sbjct: 4   TVPHPNI-----EEVALSTTGEIPFYGKAIPLEVIK---------GGRHLIFCHSKKKCD 49

Query: 359 WLAEKMSKEGLNVGLLSGELTVEQRLSILDRFR 391
            LA K+   G+N       L V    +  D   
Sbjct: 50  ELAAKLVALGINAVAYYRGLDVSVIPTNGDVVV 82

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	399
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.95
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.94
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.94
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.93
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.9
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.77
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.77
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.75
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.73
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.71
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.67
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.47
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.44
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.43
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.42
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.4
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.3
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.18
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.18
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.17
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.09
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.04
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.78
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.71
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	98.41
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	98.33
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	98.25
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	98.25
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.22
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.12
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.02
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	98.01
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.55
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.53
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	97.4
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.28
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.2
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	97.11
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.83
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.82
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.67
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.43
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.4
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.36
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.14
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.01
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.85
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.84
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	95.66
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	95.61
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	95.33
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.27
d1okkd2	207	GTPase domain of the signal recognition particle r	95.09
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	94.96
d1vmaa2	213	GTPase domain of the signal recognition particle r	94.94
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.91
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	94.81
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	94.73
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	94.41
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	94.3
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.22
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	94.06
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	93.38
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	92.74
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	92.53
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	92.49
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	92.08
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	91.59
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	91.35
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	90.7
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	90.59
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	90.28
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	89.61
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	89.42
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	89.39
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	88.78
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	88.62
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	87.96
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	87.81
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	87.6
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	87.57
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	87.55
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	87.31
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	87.13
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	87.05
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	87.03
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	86.88
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	86.1
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	85.97
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	85.67
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	85.07
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	84.68
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	84.35
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	84.06
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	83.91
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	83.8
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	83.6
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	83.54
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	83.17
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	82.98
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	81.75
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	81.55
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	81.48
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	81.44
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	81.18
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	81.08
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	80.6

>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=1e-45  Score=327.43  Aligned_cols=205  Identities=35%  Similarity=0.599  Sum_probs=187.6

Q ss_pred             ccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEE
Q psy11867        100 YSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCL  179 (399)
Q Consensus       100 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil  179 (399)
                      ....+|++++|++.++++|+++||..|||+|..|||.+++  |+|++++||||||||+||++|+++.+......++++|+
T Consensus        14 ~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~--g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil   91 (222)
T d2j0sa1          14 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIK--GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALIL   91 (222)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEE
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHC--CCCeEEEcCcchhhhhhhcccccccccccccCceeEEe
Confidence            3456899999999999999999999999999999999998  79999999999999999999999999888888999999


Q ss_pred             eCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechh
Q psy11867        180 APTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD  256 (399)
Q Consensus       180 ~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah  256 (399)
                      +||+|||.|+++.+++++... ++++....|+.......   ..+++|+|+|||+|.+++. .+.+.+++++++|+||||
T Consensus        92 ~PtreLa~Qi~~~~~~l~~~~-~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~-~~~~~~~~l~~lVlDEaD  169 (222)
T d2j0sa1          92 APTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR-RRSLRTRAIKMLVLDEAD  169 (222)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHH-TTSSCCTTCCEEEEETHH
T ss_pred             cchHHHHHHHHHHHHHHhCcc-ceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhccc-ccccccccceeeeecchh
Confidence            999999999999999998875 78888888887655443   4578999999999999854 466789999999999999


Q ss_pred             hHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc
Q psy11867        257 VMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       257 ~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~  309 (399)
                      +|++. +|...+..|++.+++++|+++||||+++++.++++.++.+|+.|.++
T Consensus       170 ~ll~~-~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         170 EMLNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             HHTST-TTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             Hhhhc-CcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEEe
Confidence            99975 89999999999999999999999999999999999999999998765

>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=2.9e-44  Score=315.50  Aligned_cols=200  Identities=33%  Similarity=0.557  Sum_probs=183.4

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      .+|++++|++.++++|.++||..|||+|.+|||.+++  |+|++++||||||||+||++|+++++.....+++++|++||
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~--g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt   80 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALS--GRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPT   80 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHT--TCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSC
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHc--CCCEEeeccCccccccccccchhhcccccccCcceEEEeec
Confidence            5799999999999999999999999999999999998  79999999999999999999999999888889999999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      ++|+.|+++.++.+.............|+.......   ...++|+|+||+++.+++. .+.+.+++++++|+||||+|+
T Consensus        81 ~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~-~~~~~~~~l~~lVlDEaD~ll  159 (206)
T d1veca_          81 RELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIK-KGVAKVDHVQMIVLDEADKLL  159 (206)
T ss_dssp             HHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHH-TTCSCCTTCCEEEEETHHHHT
T ss_pred             chhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCcccccccc-chhccccccceEEEecccccc
Confidence            999999999999998877677777777776554433   5678999999999999854 466789999999999999999


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEE
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLII  306 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i  306 (399)
                      +. +|...+..|++.+++++|+++||||+++.+.++++.++.+|+.|
T Consensus       160 ~~-~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         160 SQ-DFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             ST-TTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             cc-chHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            75 89999999999999999999999999999999999999999876

>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=2.1e-44  Score=316.60  Aligned_cols=202  Identities=31%  Similarity=0.540  Sum_probs=184.1

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      .|++++|++.++++|.++||.+|||+|.+|||.+++  |+|++++||||||||+||++|+++.+.....+++++|++||+
T Consensus         2 ~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~--g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~Ptr   79 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAIL--GMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTR   79 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHT--TCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCH
T ss_pred             CccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHc--CCCeEEEeccccccccccccceeeeecccCCCceEEEEeccc
Confidence            699999999999999999999999999999999999  799999999999999999999999999888889999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh----ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        184 ELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK----KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       184 ~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      +||.|+++.++.+......+......|+.......    ...++|+|+||+++.+++. .+.+++++++++|+||||+|+
T Consensus        80 eL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~-~~~~~l~~l~~lVlDEaD~ll  158 (207)
T d1t6na_          80 ELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALAR-NKSLNLKHIKHFILDECDKML  158 (207)
T ss_dssp             HHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHH-TTSSCCTTCCEEEEESHHHHH
T ss_pred             hhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhcc-CCceeccccceeehhhhhhhh
Confidence            99999999999999887777777778876554332    4578999999999999865 467789999999999999999


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEec
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKL  308 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~  308 (399)
                      +..++...+..+.+.+++++|+++||||+++++.++++.++++|+.|.+
T Consensus       159 ~~~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~V  207 (207)
T d1t6na_         159 EQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  207 (207)
T ss_dssp             SSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             hcCCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEeC
Confidence            7547888899999999999999999999999999999999999988753

>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=2.6e-43  Score=311.61  Aligned_cols=204  Identities=38%  Similarity=0.624  Sum_probs=182.0

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe
Q psy11867        101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA  180 (399)
Q Consensus       101 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  180 (399)
                      .+.+|++++|++.++++|.++||.+||++|..|||.++.  |+|++++||||||||++|++|+++++.....++++||++
T Consensus        10 ~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~--g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~   87 (218)
T d2g9na1          10 IVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIK--GYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLA   87 (218)
T ss_dssp             CCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHH--TCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             ccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHc--CCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEc
Confidence            367899999999999999999999999999999999999  799999999999999999999999998888899999999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh----hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechh
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD  256 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah  256 (399)
                      ||++||.|+++.++.+.... .+......++......    ....++|+|+||+++.+++.+ +...+++++++|+||||
T Consensus        88 Pt~eL~~Q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~-~~~~~~~l~~lVlDEaD  165 (218)
T d2g9na1          88 PTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLDEAD  165 (218)
T ss_dssp             SSHHHHHHHHHHHHHHHTTT-TCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHT-TSSCSTTCCEEEEESHH
T ss_pred             ccchhhhhHHHHHhhhcccc-ceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhc-CCcccccceEEEeeecc
Confidence            99999999999999998876 5555555554433222    245679999999999999754 56789999999999999


Q ss_pred             hHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc
Q psy11867        257 VMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       257 ~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~  309 (399)
                      +|++. +|...+..+++.+++++|+++||||+++.+.++++.++++|+.+.++
T Consensus       166 ~ll~~-~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         166 EMLSR-GFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             HHHHT-TCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             hhhcC-chHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            99985 89999999999999999999999999999999999999999998775

>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=1.7e-42  Score=305.14  Aligned_cols=201  Identities=40%  Similarity=0.668  Sum_probs=178.1

Q ss_pred             ccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeC
Q psy11867        102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAP  181 (399)
Q Consensus       102 ~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  181 (399)
                      +.+|++++|++.++++|.++||.+||++|.+|||.++.  |+|++++||||||||++|++|+++++.....+++++|++|
T Consensus         9 ~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~--g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~p   86 (212)
T d1qdea_           9 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIE--GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAP   86 (212)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             ccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHc--CCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcc
Confidence            67899999999999999999999999999999999999  7999999999999999999999999998889999999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh--ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        182 TYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK--KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       182 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      |++|+.|++..+..+.... ........++.....+.  ..+++|+|+||+++.+++.+ +.+.+++++++|+||||+|+
T Consensus        87 t~el~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~IvI~TP~~l~~~~~~-~~~~l~~l~~lVlDEad~ll  164 (212)
T d1qdea_          87 TRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDEADEML  164 (212)
T ss_dssp             SHHHHHHHHHHHHHHTTTS-CCCEEEECC----------CTTCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEETHHHHH
T ss_pred             cHHHhhhhhhhhccccccc-ccceeeEeeccchhHHHHHhcCCcEEEECCCcccccccc-CceecCcceEEeehhhhhhc
Confidence            9999999999999988765 55666666655443332  34679999999999998654 56789999999999999999


Q ss_pred             hcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEe
Q psy11867        260 ATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIK  307 (399)
Q Consensus       260 ~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~  307 (399)
                      +. +|...+..+++.+++++|+++||||+++.+.++++.++++|+.|.
T Consensus       165 d~-~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~  211 (212)
T d1qdea_         165 SS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRIL  211 (212)
T ss_dssp             HT-TCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC
T ss_pred             cc-chHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            85 899999999999999999999999999999999999999998875

>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=2e-41  Score=303.63  Aligned_cols=206  Identities=29%  Similarity=0.460  Sum_probs=180.1

Q ss_pred             CccccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC---------
Q psy11867         99 LYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP---------  169 (399)
Q Consensus        99 ~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~---------  169 (399)
                      ...+.+|++++|++.++++|.++||..||++|..|||.+++  |+|++++||||||||+||++|+++++..         
T Consensus        17 ~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~--g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~   94 (238)
T d1wrba1          17 TNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILE--HRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYS   94 (238)
T ss_dssp             CSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------
T ss_pred             CCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhC--CCCEEEECCCCCCcceeeHHHHHHHHHhccccccccc
Confidence            34578999999999999999999999999999999999998  7999999999999999999999998743         


Q ss_pred             CCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhh---hhccCCcEEEeCchhHHHhhhccccccCCc
Q psy11867        170 SIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER---NKKITEQIIIGTPGKVLDWGLKYRFFDLSK  246 (399)
Q Consensus       170 ~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~  246 (399)
                      ...++++|||+||++||.|+++.+..++... .+++....|+.....   ....++||+|+||++|.+++.. +.+.+.+
T Consensus        95 ~~~~~~alil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~-~~~~l~~  172 (238)
T d1wrba1          95 KTAYPKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEK-NKISLEF  172 (238)
T ss_dssp             CCBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHT-TSBCCTT
T ss_pred             CCCCceEEEeccchhhhcchheeeeecccCC-CcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHcc-Cceeccc
Confidence            2346889999999999999999999998876 677777777765432   3356789999999999998644 5678999


Q ss_pred             eeEEEEechhhHhhcCCchHHHHHHHHhCC----CCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc
Q psy11867        247 IKVFVLDEADVMIATQGHQDFSIRIQKRLP----SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       247 ~~~lViDEah~l~~~~~~~~~~~~i~~~l~----~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~  309 (399)
                      ++++|+||||+|++. +|...+..+++.+.    .++|+++||||++..+.++++.++.+|+.+.++
T Consensus       173 v~~lViDEaD~ll~~-~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~vg  238 (238)
T d1wrba1         173 CKYIVLDEADRMLDM-GFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG  238 (238)
T ss_dssp             CCEEEEETHHHHHHT-TCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             cceeeeehhhhhhhh-ccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEeC
Confidence            999999999999975 89999999988654    367999999999999999999999999988653

>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=8.5e-41  Score=293.93  Aligned_cols=202  Identities=31%  Similarity=0.515  Sum_probs=179.9

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      .+|++++|++.++++|.++||.+|||+|.++||.++++ +.|++++||||||||++|++|+++..... .++++||++||
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g-~~d~iv~a~TGsGKT~~~~l~~~~~~~~~-~~~~~lil~pt   81 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLND-EYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPT   81 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHT-CSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSC
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcC-CCCeeeechhcccccceeecccccccccc-cCcceEEEeec
Confidence            48999999999999999999999999999999999984 46999999999999999999999987654 77899999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh--ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhh
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK--KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~  260 (399)
                      ++||.|+++.++.+.... +..+....|+.....+.  ..+++|+|+||++|.+++. .+.+++++++++|+||||+|++
T Consensus        82 ~~l~~q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~l~~~~IlV~TP~~l~~~l~-~~~~~~~~l~~lViDEad~l~~  159 (208)
T d1hv8a1          82 RELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHIN-RGTLNLKNVKYFILDEADEMLN  159 (208)
T ss_dssp             HHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHH-TTCSCTTSCCEEEEETHHHHHT
T ss_pred             cccchhhhhhhhhhcccC-CeEEEEeeCCCChHHHHHhcCCCCEEEEChHHHHHHHH-cCCCCcccCcEEEEEChHHhhc
Confidence            999999999999998776 56777777776554432  3468999999999999864 4677899999999999999987


Q ss_pred             cCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc
Q psy11867        261 TQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       261 ~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~  309 (399)
                      . ++...+..+++.+++++|+++||||+++.+.++++.+++||..|++.
T Consensus       160 ~-~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~~  207 (208)
T d1hv8a1         160 M-GFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAK  207 (208)
T ss_dssp             T-TTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECC
T ss_pred             C-CChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEEE
Confidence            5 78888999999999999999999999999999999999999988753

>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=1.3e-40  Score=292.58  Aligned_cols=201  Identities=40%  Similarity=0.637  Sum_probs=184.8

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      +|++++|++.++++|+++||.+|||+|.+|||.+++  |+|++++||||||||++|++|+++.+.....++++++++|+.
T Consensus         2 sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~--g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~   79 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAIT--GRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTR   79 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHH--TCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             ChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHc--CCCEEEecCCcchhhhhhccccccccccccccccceeeccch
Confidence            799999999999999999999999999999999999  799999999999999999999999998888889999999999


Q ss_pred             HHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh---ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhh
Q psy11867        184 ELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK---KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       184 ~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~  260 (399)
                      +++.|....+..+.... ++++....|+.......   ...++|+|+||++|.+++. ...+.+.+++++|+||||+|++
T Consensus        80 ~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~-~~~~~l~~l~~lV~DEaD~l~~  157 (206)
T d1s2ma1          80 ELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLAS-RKVADLSDCSLFIMDEADKMLS  157 (206)
T ss_dssp             HHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHH-TTCSCCTTCCEEEEESHHHHSS
T ss_pred             hhhhhhhhhhhhccccc-CeeEEeecCccchhhHHHHhcccceEEEECCcccccccc-cceeecccceEEEeechhhhhh
Confidence            99999999999988775 78888888887654433   5678999999999999965 4667899999999999999997


Q ss_pred             cCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEecc
Q psy11867        261 TQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLK  309 (399)
Q Consensus       261 ~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~~  309 (399)
                      . +|...+..|++.+++.+|+++||||+++.+.++++.++.+|..+.+.
T Consensus       158 ~-~f~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~~  205 (206)
T d1s2ma1         158 R-DFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM  205 (206)
T ss_dssp             H-HHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCC
T ss_pred             h-hhHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEee
Confidence            5 79999999999999999999999999999999999999999998765

>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=4.4e-38  Score=277.21  Aligned_cols=201  Identities=31%  Similarity=0.552  Sum_probs=176.6

Q ss_pred             ccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      +|++++|++.++++|+++||.+||++|.+|||.+++  |+|++++||||||||+||++|+++.+......+..++++|+.
T Consensus         2 ~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~--G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~   79 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALR--GESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTR   79 (209)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHH--TCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             ccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHC--CCCeEeecccccccceeeeeeecccccccccccccccccccc
Confidence            699999999999999999999999999999999999  799999999999999999999999998887888999999999


Q ss_pred             HHHHHHHHHHHHHhccCC---CcEEEEEEcCchhhhh---hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhh
Q psy11867        184 ELAIQIGEVVAKMGKHIT---DLSVRYAVRGENLERN---KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADV  257 (399)
Q Consensus       184 ~La~Q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~---~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~  257 (399)
                      +++.+.+..+........   ........++......   ...+++|+|+||+++.+++.+ ....+.+++++|+||||+
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~-~~~~~~~l~~lViDEad~  158 (209)
T d1q0ua_          80 ELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIRE-QALDVHTAHILVVDEADL  158 (209)
T ss_dssp             HHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHT-TCCCGGGCCEEEECSHHH
T ss_pred             chhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhh-hccccccceEEEEeeccc
Confidence            999999988887765442   2344455555544333   245789999999999998654 456789999999999999


Q ss_pred             HhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCeEEec
Q psy11867        258 MIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKL  308 (399)
Q Consensus       258 l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~~i~~  308 (399)
                      +++. +|...+..+++.+++++|+++||||+++++.++++.++++|..+.+
T Consensus       159 ll~~-~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         159 MLDM-GFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             HHHT-TCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             cccc-ccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            9985 7999999999999999999999999999999999999999998864

>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=99.95  E-value=3.4e-28  Score=212.25  Aligned_cols=184  Identities=17%  Similarity=0.132  Sum_probs=138.4

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQI  189 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~  189 (399)
                      +++.+...|.+.||.+|+|+|.++++.+++  |+|+++++|||||||.+|.++++..+..   ++++|||+|+++|+.|+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~--~~~~il~apTGsGKT~~a~l~i~~~~~~---~~~vl~l~P~~~L~~q~   84 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFS--GKNLLLAMPTAAGKTLLAEMAMVREAIK---GGKSLYVVPLRALAGEK   84 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTT--CSCEEEECSSHHHHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHc--CCCEEEEcCCCCchhHHHHHHHHHHhhc---cCcceeecccHHHHHHH
Confidence            668888999999999999999999999998  7999999999999999999999987754   34699999999999999


Q ss_pred             HHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHH--
Q psy11867        190 GEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF--  267 (399)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~--  267 (399)
                      ++.++++....  ..+....++............|+++||..+...+.+ ....+.+++++|+||+|++.+. .....  
T Consensus        85 ~~~~~~~~~~~--~~v~~~~~~~~~~~~~~~~~~ii~~~~~~~~~~~~~-~~~~~~~~~~ii~DE~h~~~~~-~r~~~~~  160 (202)
T d2p6ra3          85 YESFKKWEKIG--LRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRN-RASWIKAVSCLVVDEIHLLDSE-KRGATLE  160 (202)
T ss_dssp             HHHHTTTTTTT--CCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHT-TCSGGGGCCEEEETTGGGGGCT-TTHHHHH
T ss_pred             HHHHHHHhhcc--ccceeeccCcccccccccccceeeeccHHHHHHHhc-cchhhhhhhhccccHHHHhccc-ccchHHH
Confidence            99998876543  333344444333333345678999999999877544 4456889999999999998754 22222  


Q ss_pred             -HHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhCCCCe
Q psy11867        268 -SIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPL  304 (399)
Q Consensus       268 -~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~~~p~  304 (399)
                       ....++..++++|+++||||+++ ..++. .++..+.
T Consensus       161 ~~l~~i~~~~~~~~~l~lSATl~n-~~~~~-~~l~~~~  196 (202)
T d2p6ra3         161 ILVTKMRRMNKALRVIGLSATAPN-VTEIA-EWLDADY  196 (202)
T ss_dssp             HHHHHHHHHCTTCEEEEEECCCTT-HHHHH-HHTTCEE
T ss_pred             HHHHHHHhcCCCCcEEEEcCCCCc-HHHHH-HHcCCCe
Confidence             23334455678999999999976 45555 4454433

>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=5.1e-28  Score=211.79  Aligned_cols=186  Identities=15%  Similarity=0.173  Sum_probs=139.7

Q ss_pred             ccccCCCCHHHHHHHHHc-CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCc
Q psy11867        104 TFEALHLKPELLKGVYEM-GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPT  182 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~-g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt  182 (399)
                      ..+.++|++...+.|++. ||..++|+|.+|++.+++  |+|+++++|||||||++|.+|++..      ..++++++|+
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~--g~~vlv~apTGsGKT~~~~~~~~~~------~~~~~~v~P~   74 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLS--GRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPL   74 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHT--TCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSC
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHc--CCCEEEEcCCCCCCcchhhhhhhhc------cCceEEeccc
Confidence            467889999999999986 999999999999999998  7999999999999999999999853      3569999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCcEEEEEEcC-chh------hhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEech
Q psy11867        183 YELAIQIGEVVAKMGKHITDLSVRYAVRG-ENL------ERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEA  255 (399)
Q Consensus       183 ~~La~Q~~~~~~~~~~~~~~~~~~~~~~~-~~~------~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEa  255 (399)
                      ++|+.|+.+.++.++...     ...... ...      ........+|+++||.++..... .......+++++|+|||
T Consensus        75 ~~L~~q~~~~l~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~-~~~~~~~~v~~lviDEa  148 (206)
T d1oywa2          75 ISLMKDQVDQLQANGVAA-----ACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNF-LEHLAHWNPVLLAVDEA  148 (206)
T ss_dssp             HHHHHHHHHHHHHTTCCE-----EEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTH-HHHHTTSCEEEEEESSG
T ss_pred             hhhhhhHHHHHHhhcccc-----cccccccccccchhHHHHHhcCCceEEEEechhhhchhh-cccchhheeeeeeeeee
Confidence            999999999998875432     111111 111      11124567899999998765432 23456778999999999


Q ss_pred             hhHhhcCCc-hH---HHHHHHHhCCCCCcEEEEEeeCChhHHH-HHHhh-CCCCe
Q psy11867        256 DVMIATQGH-QD---FSIRIQKRLPSDCQIMLFSATYDKEVME-FAQDM-VPNPL  304 (399)
Q Consensus       256 h~l~~~~~~-~~---~~~~i~~~l~~~~q~l~~SAT~~~~v~~-~~~~~-~~~p~  304 (399)
                      |++.+.+.. ..   ....+...+ +++|+++||||+++.+.+ +++.+ +.+|+
T Consensus       149 H~~~~~~~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         149 HCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             GGGCTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             eeeeccccchHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            998754221 11   122344444 479999999999998765 44543 78885

>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=99.94  E-value=2.1e-27  Score=212.42  Aligned_cols=182  Identities=18%  Similarity=0.153  Sum_probs=129.4

Q ss_pred             cccccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe
Q psy11867        101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA  180 (399)
Q Consensus       101 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  180 (399)
                      +...|.+..+.+.+ ..+.+.++.+|+++|+.+++.++.  |+|++++||||+|||++|+++++.....   +.++|||+
T Consensus        20 ~~~~~~~~~~~~~~-~~~~~~~~~~p~~~Q~~~i~~~l~--g~~~~i~apTGsGKT~~~~~~~~~~~~~---~~rvliv~   93 (237)
T d1gkub1          20 SLCLFPEDFLLKEF-VEFFRKCVGEPRAIQKMWAKRILR--KESFAATAPTGVGKTSFGLAMSLFLALK---GKRCYVIF   93 (237)
T ss_dssp             CCSCCTTHHHHHHH-HHHHHTTTCSCCHHHHHHHHHHHT--TCCEECCCCBTSCSHHHHHHHHHHHHTT---SCCEEEEE
T ss_pred             ccccCccchhHHHH-HHHHHhccCCCCHHHHHHHHHHHC--CCCEEEEecCCChHHHHHHHHHHHHHHh---cCeEEEEe
Confidence            34455554444454 456667889999999999999998  7999999999999999999999887764   45799999


Q ss_pred             CcHHHHHHHHHHHHHHhccCCCcE----EEEEEcCchhhh-h----hccCCcEEEeCchhHHHhhhccccccCCceeEEE
Q psy11867        181 PTYELAIQIGEVVAKMGKHITDLS----VRYAVRGENLER-N----KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFV  251 (399)
Q Consensus       181 Pt~~La~Q~~~~~~~~~~~~~~~~----~~~~~~~~~~~~-~----~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lV  251 (399)
                      ||++|+.|+++.++++...+ ++.    .....++..... .    ....++|+|+||++|.+..     ..+++++++|
T Consensus        94 Pt~~La~Q~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~-----~~~~~~~~vV  167 (237)
T d1gkub1          94 PTSLLVIQAAETIRKYAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHY-----RELGHFDFIF  167 (237)
T ss_dssp             SCHHHHHHHHHHHHHHHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCS-----TTSCCCSEEE
T ss_pred             ccHHHHHHHHHHHHHHHHHc-CCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhh-----hhcCCCCEEE
Confidence            99999999999999987654 222    222222221111 1    1345689999999987642     2467889999


Q ss_pred             EechhhHhhcCCchHHHHHHH----------HhCCCCCcEEEEEeeCChhHHH
Q psy11867        252 LDEADVMIATQGHQDFSIRIQ----------KRLPSDCQIMLFSATYDKEVME  294 (399)
Q Consensus       252 iDEah~l~~~~~~~~~~~~i~----------~~l~~~~q~l~~SAT~~~~v~~  294 (399)
                      +||||.|++.....+....++          ...+...|++++|||+++.+..
T Consensus       168 vDE~d~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~  220 (237)
T d1gkub1         168 VDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKA  220 (237)
T ss_dssp             ESCHHHHHTSTHHHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTH
T ss_pred             EEChhhhhhcccchhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHH
Confidence            999999975311111111111          1124567899999999876543

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.93  E-value=6e-27  Score=217.03  Aligned_cols=219  Identities=15%  Similarity=0.107  Sum_probs=143.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |+++++.||||||||++|+.+++.....  .+.++||++||++||.|+++.++.++........         .......
T Consensus         9 ~~~~lv~~~TGsGKT~~~l~~~~~~~~~--~~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~---------~~~~~~~   77 (305)
T d2bmfa2           9 KRLTIMDLHPGAGKTKRYLPAIVREAIK--RGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAI---------RAEHTGR   77 (305)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHHHH--HTCCEEEEESSHHHHHHHHHHTTTSCCBCCC-----------------CC
T ss_pred             CCcEEEEECCCCCHHHHHHHHHHHHHHh--cCCEEEEEccHHHHHHHHHHHHhcCCcceeeeEE---------eecccCc
Confidence            8999999999999999998888876543  3567999999999999999988766433221111         1112234


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHh--CCCCCcEEEEEeeCChhHHHHHHhh
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR--LPSDCQIMLFSATYDKEVMEFAQDM  299 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~--l~~~~q~l~~SAT~~~~v~~~~~~~  299 (399)
                      ..|+++|++.|..+...  ...+.+++++|+||||++... ++.  ...++..  .....+++++|||.+.....+..  
T Consensus        78 ~~i~~~t~~~l~~~~~~--~~~~~~~~~vViDE~H~~~~~-~~~--~~~~l~~~~~~~~~~~v~~SAT~~~~~~~~~~--  150 (305)
T d2bmfa2          78 EIVDLMCHATFTMRLLS--PIRVPNYNLIIMDEAHFTDPA-SIA--ARGYISTRVEMGEAAGIFMTATPPGSRDPFPQ--  150 (305)
T ss_dssp             CSEEEEEHHHHHHHHTS--SSCCCCCSEEEEESTTCCSHH-HHH--HHHHHHHHHHHTSCEEEEECSSCTTCCCSSCC--
T ss_pred             cccccCCcHHHHHHHhc--CccccceeEEEeeeeeecchh-hHH--HHHHHHHhhccccceEEEeecCCCcceeeecc--
Confidence            56999999988776443  345788999999999998543 111  1112211  13578999999998753211100  


Q ss_pred             CCCCeEEecccccccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCC
Q psy11867        300 VPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT  379 (399)
Q Consensus       300 ~~~p~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~  379 (399)
                      ...|+...              ....... .+...+..+  ....+++||||++++.++.+++.|.+.|+.+..+||++.
T Consensus       151 ~~~~~~~~--------------~~~~~~~-~~~~~~~~~--~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~  213 (305)
T d2bmfa2         151 SNAPIMDE--------------EREIPER-SWNSGHEWV--TDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTF  213 (305)
T ss_dssp             CSSCEEEE--------------ECCCCCS-CCSSCCHHH--HSSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCH
T ss_pred             cCCcceEE--------------EEeccHH-HHHHHHHHH--HhhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcCh
Confidence            00111110              0000000 000001111  123478999999999999999999999999999999997


Q ss_pred             HHHHHHHHHHHhcCCCcccC
Q psy11867        380 VEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       380 ~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +..|    ..|++|..++||
T Consensus       214 ~~~~----~~~~~~~~~~lv  229 (305)
T d2bmfa2         214 DSEY----IKTRTNDWDFVV  229 (305)
T ss_dssp             HHHG----GGGGTSCCSEEE
T ss_pred             HHHH----hhhhccchhhhh
Confidence            6554    468899888875

>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=99.90  E-value=7e-24  Score=184.17  Aligned_cols=164  Identities=20%  Similarity=0.178  Sum_probs=123.1

Q ss_pred             CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        123 FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       123 ~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      +.+|+++|.+++..+..   +|+++++|||+|||+++++++...+..  .+.++||++|+++|+.|+++.++++.... +
T Consensus         7 ~~~pr~~Q~~~~~~~~~---~n~lv~~pTGsGKT~i~~~~~~~~~~~--~~~~il~i~P~~~L~~q~~~~~~~~~~~~-~   80 (200)
T d1wp9a1           7 LIQPRIYQEVIYAKCKE---TNCLIVLPTGLGKTLIAMMIAEYRLTK--YGGKVLMLAPTKPLVLQHAESFRRLFNLP-P   80 (200)
T ss_dssp             HHCCCHHHHHHHHHGGG---SCEEEECCTTSCHHHHHHHHHHHHHHH--SCSCEEEECSSHHHHHHHHHHHHHHBCSC-G
T ss_pred             CCCCCHHHHHHHHHHhc---CCeEEEeCCCCcHHHHHHHHHHHHHHh--cCCcEEEEcCchHHHHHHHHHHHHhhccc-c
Confidence            44899999999998875   789999999999999999888776654  34579999999999999999999987654 5


Q ss_pred             cEEEEEEcCchhhhh--hccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCc
Q psy11867        203 LSVRYAVRGENLERN--KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQ  280 (399)
Q Consensus       203 ~~~~~~~~~~~~~~~--~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q  280 (399)
                      ..+....++......  .....+|+++||+.+.+.+. ...+.+++++++|+||||++... ...............+.+
T Consensus        81 ~~v~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~-~~~~~~~~~~~vIiDE~H~~~~~-~~~~~~~~~~~~~~~~~~  158 (200)
T d1wp9a1          81 EKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLL-AGRISLEDVSLIVFDEAHRAVGN-YAYVFIAREYKRQAKNPL  158 (200)
T ss_dssp             GGEEEECSCSCHHHHHHHHHHCSEEEECHHHHHHHHH-TTSCCTTSCSEEEEETGGGCSTT-CHHHHHHHHHHHHCSSCC
T ss_pred             cceeeeecccchhHHHHhhhcccccccccchhHHHHh-hhhhhccccceEEEEehhhhhcc-hhHHHHHHHHHhcCCCCc
Confidence            555555554433222  13456899999999988754 45667889999999999998654 222223333333456789


Q ss_pred             EEEEEeeCChhHHH
Q psy11867        281 IMLFSATYDKEVME  294 (399)
Q Consensus       281 ~l~~SAT~~~~v~~  294 (399)
                      +++||||.+.....
T Consensus       159 ~l~~SATp~~~~~~  172 (200)
T d1wp9a1         159 VIGLTASPGSTPEK  172 (200)
T ss_dssp             EEEEESCSCSSHHH
T ss_pred             EEEEEecCCCcHHH
Confidence            99999997654443

>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=99.77  E-value=6e-18  Score=147.80  Aligned_cols=173  Identities=19%  Similarity=0.180  Sum_probs=131.5

Q ss_pred             CCHHHHHHHHHcCCCCChHHHHHHhhhhhcC----CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        110 LKPELLKGVYEMGFYAPSKIQETALPTLLAD----PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       110 l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~----~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      .+....+.+.+.-...+|+-|..++..+.+.    ...+.+++|.||||||.+|+.++...+..   +.++++++||..|
T Consensus        40 ~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~---g~qv~~l~Pt~~L  116 (233)
T d2eyqa3          40 HDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVPTTLL  116 (233)
T ss_dssp             CCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECSSHHH
T ss_pred             CCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc---CCceEEEccHHHh
Confidence            4567777777665668999999999888543    35689999999999999999999988864   5679999999999


Q ss_pred             HHHHHHHHHHHhccCCCcEEEEEEcCchhhh-------hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        186 AIQIGEVVAKMGKHITDLSVRYAVRGENLER-------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       186 a~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      +.|+++.++++...+ +..+....++.....       ...+..+|+|||...+.      ..+.+++++++|+||-|++
T Consensus       117 a~Q~~~~~~~~~~~~-~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~------~~~~f~~LgLiIiDEeH~f  189 (233)
T d2eyqa3         117 AQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ------SDVKFKDLGLLIVDEEHRF  189 (233)
T ss_dssp             HHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH------SCCCCSSEEEEEEESGGGS
T ss_pred             HHHHHHHHHHHHhhC-CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc------cCCccccccceeeechhhh
Confidence            999999999987776 567777777654322       22567799999987554      2455789999999999996


Q ss_pred             hhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHh
Q psy11867        259 IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQD  298 (399)
Q Consensus       259 ~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~  298 (399)
                          ++... ..+ +....++.++++|||.-+....++..
T Consensus       190 ----g~kQ~-~~l-~~~~~~~~~l~~SATPiprtl~~~~~  223 (233)
T d2eyqa3         190 ----GVRHK-ERI-KAMRANVDILTLTATPIPRTLNMAMS  223 (233)
T ss_dssp             ----CHHHH-HHH-HHHHTTSEEEEEESSCCCHHHHHHHT
T ss_pred             ----hhHHH-HHH-HhhCCCCCEEEEecchhHHHHHHHHH
Confidence                33322 222 22335789999999976665555543

>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=99.77  E-value=6e-19  Score=160.41  Aligned_cols=154  Identities=16%  Similarity=0.117  Sum_probs=111.5

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCc
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL  203 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~  203 (399)
                      ..|+++|.+|+..++.  .++.++.+|||+|||+.....+......  ...++|||+|+++|+.|+++.+.+++... ..
T Consensus       112 ~~~rdyQ~~av~~~l~--~~~~il~~pTGsGKT~i~~~i~~~~~~~--~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~-~~  186 (282)
T d1rifa_         112 IEPHWYQKDAVFEGLV--NRRRILNLPTSAGRSLIQALLARYYLEN--YEGKILIIVPTTALTTQMADDFVDYRLFS-HA  186 (282)
T ss_dssp             CCCCHHHHHHHHHHHH--HSEEEECCCTTSCHHHHHHHHHHHHHHH--CSSEEEEECSSHHHHHHHHHHHHHHTSCC-GG
T ss_pred             cccchHHHHHHHHHHh--cCCceeEEEcccCccHHHHHHHHHhhhc--ccceEEEEEcCchhHHHHHHHHHHhhccc-cc
Confidence            4799999999999998  4788999999999998866544333322  34579999999999999999999987543 33


Q ss_pred             EEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEE
Q psy11867        204 SVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIML  283 (399)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~  283 (399)
                      .+....+|............|+|+|++.+...    ....++++++||+||||++.+     .....++..+.+....++
T Consensus       187 ~~~~~~~g~~~~~~~~~~~~i~i~t~qs~~~~----~~~~~~~f~~VIvDEaH~~~a-----~~~~~il~~~~~~~~rlG  257 (282)
T d1rifa_         187 MIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMMNDECHLATG-----KSISSIISGLNNCMFKFG  257 (282)
T ss_dssp             GEEECSTTCSSTTCCCTTCSEEEECHHHHTTS----CGGGGGGEEEEEEETGGGCCH-----HHHHHHTTTCTTCCEEEE
T ss_pred             cceeecceecccccccccceEEEEeeehhhhh----cccccCCCCEEEEECCCCCCc-----hhHHHHHHhccCCCeEEE
Confidence            34444455444333344567999999887544    223467899999999999642     334556666654455689


Q ss_pred             EEeeCChh
Q psy11867        284 FSATYDKE  291 (399)
Q Consensus       284 ~SAT~~~~  291 (399)
                      ||||++..
T Consensus       258 lTaT~~~~  265 (282)
T d1rifa_         258 LSGSLRDG  265 (282)
T ss_dssp             ECSSCCTT
T ss_pred             EEeecCCC
Confidence            99998643

>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=99.75  E-value=6.3e-18  Score=150.42  Aligned_cols=170  Identities=19%  Similarity=0.186  Sum_probs=124.1

Q ss_pred             HHHHHHHHHcCCCCChHHHHHHhhhhhcC----CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHH
Q psy11867        112 PELLKGVYEMGFYAPSKIQETALPTLLAD----PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI  187 (399)
Q Consensus       112 ~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~----~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~  187 (399)
                      ..+.+.+.+.--..+|.-|.+|+..+..+    .+.+.+++|.||||||.+|+.+++..+..   +.++++++||..||.
T Consensus        70 ~~l~~~f~~~LPFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~---g~q~~~m~Pt~~La~  146 (264)
T d1gm5a3          70 GKLAEEFIKSLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILAI  146 (264)
T ss_dssp             THHHHHHHHHSSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHHH
T ss_pred             hHHHHHHHhhccccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc---ccceeEEeehHhhhH
Confidence            34555554433347999999999998642    36788999999999999999999888765   356999999999999


Q ss_pred             HHHHHHHHHhccCCCcEEEEEEcCchhhh-------hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhh
Q psy11867        188 QIGEVVAKMGKHITDLSVRYAVRGENLER-------NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA  260 (399)
Q Consensus       188 Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~  260 (399)
                      |.++.++++...+ ++.+....++.....       ...+..+|+|||..-+.+      .+.+++++++|+||-|++.-
T Consensus       147 Qh~~~~~~~f~~~-~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~------~~~f~~LglviiDEqH~fgv  219 (264)
T d1gm5a3         147 QHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE------DVHFKNLGLVIIDEQHRFGV  219 (264)
T ss_dssp             HHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH------CCCCSCCCEEEEESCCCC--
T ss_pred             HHHHHHHHhhhhc-cccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC------CCCccccceeeeccccccch
Confidence            9999999998776 677777777654322       225678999999875543      34567999999999999743


Q ss_pred             cCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHH
Q psy11867        261 TQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQ  297 (399)
Q Consensus       261 ~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~  297 (399)
                      .+.      ..+.....+++++++|||.-+....++.
T Consensus       220 ~Qr------~~l~~~~~~~~~l~~SATPiprtl~~~~  250 (264)
T d1gm5a3         220 KQR------EALMNKGKMVDTLVMSATPIPRSMALAF  250 (264)
T ss_dssp             ---------CCCCSSSSCCCEEEEESSCCCHHHHHHH
T ss_pred             hhH------HHHHHhCcCCCEEEEECCCCHHHHHHHH
Confidence            221      1112223468899999996555544443

>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=99.73  E-value=1.8e-18  Score=140.21  Aligned_cols=137  Identities=17%  Similarity=0.208  Sum_probs=90.8

Q ss_pred             hhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhh
Q psy11867        137 LLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER  216 (399)
Q Consensus       137 ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  216 (399)
                      +++. |+++++++|||||||.+++.+++.....  .+.++++++|+++++.|.++.+....     ..  ......  ..
T Consensus         3 ~l~~-~~~~il~~~tGsGKT~~~~~~~~~~~~~--~~~~vli~~p~~~l~~q~~~~~~~~~-----~~--~~~~~~--~~   70 (140)
T d1yksa1           3 MLKK-GMTTVLDFHPGAGKTRRFLPQILAECAR--RRLRTLVLAPTRVVLSEMKEAFHGLD-----VK--FHTQAF--SA   70 (140)
T ss_dssp             TTST-TCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTTSC-----EE--EESSCC--CC
T ss_pred             HHHc-CCcEEEEcCCCCChhHHHHHHHHHHhhh--cCceeeeeecchhHHHHHHHHhhhhh-----hh--hccccc--cc
Confidence            4444 8999999999999999887777766644  34679999999999999987664321     11  111111  11


Q ss_pred             hhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCC-chHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        217 NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQG-HQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       217 ~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~-~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      .......+.+.|...+....  .....+.+++++|+||||.+..... ....... +.. .++.++++||||.|
T Consensus        71 ~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~-~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          71 HGSGREVIDAMCHATLTYRM--LEPTRVVNWEVIIMDEAHFLDPASIAARGWAAH-RAR-ANESATILMTATPP  140 (140)
T ss_dssp             CCCSSCCEEEEEHHHHHHHH--TSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHH-HHH-TTSCEEEEECSSCT
T ss_pred             ccccccchhhhhHHHHHHHH--hccccccceeEEEEccccccChhhHHHHHHHHH-Hhh-CCCCCEEEEEcCCC
Confidence            11233457778887776643  2455688999999999998743211 1111222 222 35899999999976

>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=99.71  E-value=6.5e-18  Score=146.63  Aligned_cols=137  Identities=20%  Similarity=0.163  Sum_probs=98.2

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcE
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS  204 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~  204 (399)
                      .|+++|.+++..+++  +++.++.+|||+|||++++..+ ..+     +.++||+||+++|+.|+.+.++.++..    .
T Consensus        70 ~Lr~yQ~eav~~~~~--~~~~ll~~~tG~GKT~~a~~~~-~~~-----~~~~Liv~p~~~L~~q~~~~~~~~~~~----~  137 (206)
T d2fz4a1          70 SLRDYQEKALERWLV--DKRGCIVLPTGSGKTHVAMAAI-NEL-----STPTLIVVPTLALAEQWKERLGIFGEE----Y  137 (206)
T ss_dssp             CCCHHHHHHHHHHTT--TSEEEEEESSSTTHHHHHHHHH-HHS-----CSCEEEEESSHHHHHHHHHHHGGGCGG----G
T ss_pred             CcCHHHHHHHHHHHh--CCCcEEEeCCCCCceehHHhHH-HHh-----cCceeEEEcccchHHHHHHHHHhhccc----c
Confidence            689999999999998  4788899999999998876544 333     235999999999999999999877543    1


Q ss_pred             EEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEE
Q psy11867        205 VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLF  284 (399)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~  284 (399)
                      +....++.      .....|+|+|...+......    ...++++||+||||++.+.     ....++..++ ....+++
T Consensus       138 ~~~~~~~~------~~~~~i~i~t~~~~~~~~~~----~~~~~~lvIiDEaH~~~a~-----~~~~i~~~~~-~~~~lgL  201 (206)
T d2fz4a1         138 VGEFSGRI------KELKPLTVSTYDSAYVNAEK----LGNRFMLLIFDEVHHLPAE-----SYVQIAQMSI-APFRLGL  201 (206)
T ss_dssp             EEEESSSC------BCCCSEEEEEHHHHHHTHHH----HTTTCSEEEEECSSCCCTT-----THHHHHHTCC-CSEEEEE
T ss_pred             hhhccccc------ccccccccceehhhhhhhHh----hCCcCCEEEEECCeeCCcH-----HHHHHHhccC-CCcEEEE
Confidence            22222221      22346999999987665322    2457889999999997432     2334555543 4567899


Q ss_pred             EeeCC
Q psy11867        285 SATYD  289 (399)
Q Consensus       285 SAT~~  289 (399)
                      |||+.
T Consensus       202 TATl~  206 (206)
T d2fz4a1         202 TATFE  206 (206)
T ss_dssp             EESCC
T ss_pred             ecCCC
Confidence            99973

>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=99.67  E-value=8.7e-17  Score=129.91  Aligned_cols=126  Identities=17%  Similarity=0.108  Sum_probs=85.3

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      .+..++.+|||||||..+...++      ..+.+++|++|+++|++|+.+.+.+......    ....++...    ...
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~------~~~~~vli~~P~~~l~~q~~~~~~~~~~~~~----~~~~~~~~~----~~~   73 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYA------AQGYKVLVLNPSVAATLGFGAYMSKAHGVDP----NIRTGVRTI----TTG   73 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHH------TTTCCEEEEESCHHHHHHHHHHHHHHHSCCC----EEECSSCEE----CCC
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHH------HcCCcEEEEcChHHHHHHHHHHHHHHhhccc----ccccccccc----ccc
Confidence            57889999999999976543332      1355799999999999999999988754321    222222211    223


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC--CCCcEEEEEee
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP--SDCQIMLFSAT  287 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~--~~~q~l~~SAT  287 (399)
                      ..++++|.+.+...    ....+++++++|+||+|++...  ....+..+++.+.  +..+++++|||
T Consensus        74 ~~~~~~~~~~~~~~----~~~~~~~~~~vIiDE~H~~~~~--~~~~~~~~l~~~~~~~~~~~l~~TAT  135 (136)
T d1a1va1          74 SPITYSTYGKFLAD----GGCSGGAYDIIICDECHSTDAT--SILGIGTVLDQAETAGARLVVLATAT  135 (136)
T ss_dssp             CSEEEEEHHHHHHT----TGGGGCCCSEEEEETTTCCSHH--HHHHHHHHHHHTTTTTCSEEEEEESS
T ss_pred             cceEEEeeeeeccc----cchhhhcCCEEEEecccccCHH--HHHHHHHHHHHHHHCCCCcEEEEeCC
Confidence            45889998877554    2335789999999999987432  1122334444443  46678999999

>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=99.44  E-value=1.5e-13  Score=114.39  Aligned_cols=88  Identities=34%  Similarity=0.686  Sum_probs=83.7

Q ss_pred             cccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHh
Q psy11867        312 EESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFR  391 (399)
Q Consensus       312 ~~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~  391 (399)
                      +.++++++|+|+.|++.+.|+..|..+++.....++||||++++.|+.++..|...|+.+..+||++++.+|..+++.|+
T Consensus         2 ~~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk   81 (168)
T d2j0sa2           2 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFR   81 (168)
T ss_dssp             GCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCcEEEEEEecChHHHHHHHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHh
Confidence            45779999999999988889999999999988899999999999999999999999999999999999999999999999


Q ss_pred             cCCCcccC
Q psy11867        392 EGEFKIYS  399 (399)
Q Consensus       392 ~G~~~ILV  399 (399)
                      +|+++|||
T Consensus        82 ~g~~~iLv   89 (168)
T d2j0sa2          82 SGASRVLI   89 (168)
T ss_dssp             HTSSCEEE
T ss_pred             cCCccEEe
Confidence            99999986

>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=99.43  E-value=2.7e-13  Score=112.89  Aligned_cols=82  Identities=22%  Similarity=0.346  Sum_probs=77.9

Q ss_pred             ceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc
Q psy11867        317 NIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK  396 (399)
Q Consensus       317 ~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~  396 (399)
                      +++|+|+.+.. ++|.+.|.+++.....+++||||++++.++.|++.|.+.|+++..+||+|++.+|..+++.|++|+.+
T Consensus         1 ~l~q~~v~~~~-~~K~~~L~~ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~   79 (168)
T d1t5ia_           1 GLQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR   79 (168)
T ss_dssp             CCEEEEEECCG-GGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             CcEEEEEEeCh-HHHHHHHHHHHHhCCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccce
Confidence            47899999975 78999999999999889999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q psy11867        397 IYS  399 (399)
Q Consensus       397 ILV  399 (399)
                      |||
T Consensus        80 iLv   82 (168)
T d1t5ia_          80 ILV   82 (168)
T ss_dssp             EEE
T ss_pred             eee
Confidence            986

>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=99.42  E-value=4.1e-13  Score=111.03  Aligned_cols=82  Identities=30%  Similarity=0.599  Sum_probs=78.8

Q ss_pred             eeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcc
Q psy11867        318 IKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI  397 (399)
Q Consensus       318 i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~I  397 (399)
                      |+|+|+.|...+.|++.|..+++.....++||||++++.++.++..|...|+.+..+||+|++.+|..+++.|+.|+.+|
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~i   80 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI   80 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSE
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccce
Confidence            57999999888889999999999998899999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q psy11867        398 YS  399 (399)
Q Consensus       398 LV  399 (399)
                      ||
T Consensus        81 Lv   82 (162)
T d1fuka_          81 LI   82 (162)
T ss_dssp             EE
T ss_pred             ee
Confidence            86

>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=99.40  E-value=3.9e-13  Score=112.35  Aligned_cols=86  Identities=22%  Similarity=0.487  Sum_probs=81.3

Q ss_pred             ccccceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhc
Q psy11867        313 ESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFRE  392 (399)
Q Consensus       313 ~~~~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~  392 (399)
                      -++++++|+|+.++. .+|...|.++++....+++||||+++++|+.++..|...|+.+..+||+|++.+|..+++.|++
T Consensus         2 ~tl~~i~q~yi~v~~-~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~   80 (171)
T d1s2ma2           2 LTLKGITQYYAFVEE-RQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQ   80 (171)
T ss_dssp             CBCTTEEEEEEECCG-GGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CCccceEEEEEEcCH-HHHHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhccc
Confidence            367889999999976 6899999999999988999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccC
Q psy11867        393 GEFKIYS  399 (399)
Q Consensus       393 G~~~ILV  399 (399)
                      |+.+|||
T Consensus        81 ~~~~ilv   87 (171)
T d1s2ma2          81 GKVRTLV   87 (171)
T ss_dssp             TSSSEEE
T ss_pred             Ccccccc
Confidence            9999986

>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=99.30  E-value=6.1e-12  Score=103.18  Aligned_cols=82  Identities=27%  Similarity=0.511  Sum_probs=76.4

Q ss_pred             cceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        316 DNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       316 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                      ++++|.|+.++. ++|++.|..+++.. ..++||||+++++|+.++..|+..|+.+..+||++++.+|..+++.|++|+.
T Consensus         2 ~nI~~~~i~v~~-~~K~~~L~~ll~~~-~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~   79 (155)
T d1hv8a2           2 ANIEQSYVEVNE-NERFEALCRLLKNK-EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI   79 (155)
T ss_dssp             SSSEEEEEECCG-GGHHHHHHHHHCST-TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSS
T ss_pred             CCeEEEEEEeCh-HHHHHHHHHHHccC-CCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccc
Confidence            578999999966 78999999999865 4689999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy11867        396 KIYS  399 (399)
Q Consensus       396 ~ILV  399 (399)
                      +|||
T Consensus        80 ~ilv   83 (155)
T d1hv8a2          80 RILI   83 (155)
T ss_dssp             SEEE
T ss_pred             eeee
Confidence            9986

>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=99.18  E-value=1.1e-10  Score=106.14  Aligned_cols=154  Identities=16%  Similarity=0.126  Sum_probs=97.6

Q ss_pred             CChHHHHHHhhhhhc-------CCCCcEEEEccCCCCceehhHHHHHHhhCCC----CCCCeEEEEeCcHHHHHHHHHHH
Q psy11867        125 APSKIQETALPTLLA-------DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS----IQEPQVLCLAPTYELAIQIGEVV  193 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~-------~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~----~~~~~~lil~Pt~~La~Q~~~~~  193 (399)
                      .+.|+|.+++..+..       ..+..+|++-.+|.|||+..+-.+...+...    ....++|||||.. |..|+.+++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccch-hhHHHHHHH
Confidence            578999999987632       1266799999999999976443222222221    1234699999985 888999999


Q ss_pred             HHHhccCCCcEEEEEEcCchhhhhh-----------ccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcC
Q psy11867        194 AKMGKHITDLSVRYAVRGENLERNK-----------KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ  262 (399)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~  262 (399)
                      +++...  ........++.......           ....+++|+|.+.+....   ..+.-.+++++|+||+|++-.. 
T Consensus       134 ~k~~~~--~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~---~~l~~~~~~~vI~DEaH~ikn~-  207 (298)
T d1z3ix2         134 GKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA---EVLHKGKVGLVICDEGHRLKNS-  207 (298)
T ss_dssp             HHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT---TTTTTSCCCEEEETTGGGCCTT-
T ss_pred             HhhcCC--ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccch---hcccccceeeeecccccccccc-
Confidence            988754  23333444443221110           123469999998876543   2333346789999999998432 


Q ss_pred             CchHHHHHHHHhCCCCCcEEEEEeeC
Q psy11867        263 GHQDFSIRIQKRLPSDCQIMLFSATY  288 (399)
Q Consensus       263 ~~~~~~~~i~~~l~~~~q~l~~SAT~  288 (399)
                        ..........+ .....+++|||.
T Consensus       208 --~s~~~~a~~~l-~~~~rllLTGTP  230 (298)
T d1z3ix2         208 --DNQTYLALNSM-NAQRRVLISGTP  230 (298)
T ss_dssp             --CHHHHHHHHHH-CCSEEEEECSSC
T ss_pred             --cchhhhhhhcc-ccceeeeecchH
Confidence              22223333334 345678999995

>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=99.18  E-value=3.5e-11  Score=99.29  Aligned_cols=57  Identities=18%  Similarity=0.260  Sum_probs=54.9

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...++||||+++++|+.|+..|.+.|+++..+||+|++.+|.+++++|++|+++|||
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLV   86 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLV   86 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEE
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEE
Confidence            456899999999999999999999999999999999999999999999999999997

>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=99.17  E-value=4.2e-11  Score=104.78  Aligned_cols=149  Identities=17%  Similarity=0.115  Sum_probs=95.8

Q ss_pred             CChHHHHHHhhhhhc--CCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCC
Q psy11867        125 APSKIQETALPTLLA--DPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD  202 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~--~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~  202 (399)
                      .+.|+|.+++..+..  ..+..+|+..++|.|||+..+..+ ..+.......++|||||. .+..|+.+++.++....  
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~-~~~~~~~~~~~~LIv~p~-~l~~~W~~e~~~~~~~~--   87 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVF-SDAKKENELTPSLVICPL-SVLKNWEEELSKFAPHL--   87 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHH-HHHHHTTCCSSEEEEECS-TTHHHHHHHHHHHCTTS--
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhh-hhhhhcccccccceecch-hhhhHHHHHHHhhcccc--
Confidence            578999999986643  125678999999999999875444 333333344569999995 67788888888876432  


Q ss_pred             cEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEE
Q psy11867        203 LSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIM  282 (399)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l  282 (399)
                       .+....  ...........+|+|+|.+.+...    ..+.--..+++|+||+|.+...   ..........+. ....+
T Consensus        88 -~~~~~~--~~~~~~~~~~~~vvi~~~~~~~~~----~~l~~~~~~~vI~DEah~~k~~---~s~~~~~~~~l~-a~~r~  156 (230)
T d1z63a1          88 -RFAVFH--EDRSKIKLEDYDIILTTYAVLLRD----TRLKEVEWKYIVIDEAQNIKNP---QTKIFKAVKELK-SKYRI  156 (230)
T ss_dssp             -CEEECS--SSTTSCCGGGSSEEEEEHHHHTTC----HHHHTCCEEEEEEETGGGGSCT---TSHHHHHHHTSC-EEEEE
T ss_pred             -cceeec--cccchhhccCcCEEEeeHHHHHhH----HHHhcccceEEEEEhhhccccc---chhhhhhhhhhc-cceEE
Confidence             222221  111122234457999999877543    1222335788999999998542   222333344443 34578


Q ss_pred             EEEeeC
Q psy11867        283 LFSATY  288 (399)
Q Consensus       283 ~~SAT~  288 (399)
                      ++|||.
T Consensus       157 ~LTgTP  162 (230)
T d1z63a1         157 ALTGTP  162 (230)
T ss_dssp             EECSSC
T ss_pred             EEecch
Confidence            999995

>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=99.09  E-value=1.7e-10  Score=98.18  Aligned_cols=81  Identities=14%  Similarity=0.311  Sum_probs=71.9

Q ss_pred             cceeEEEEEeCChhhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q psy11867        316 DNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEF  395 (399)
Q Consensus       316 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~  395 (399)
                      +|+.+  .+++. .+|.+.|..+++.....++||||+|++.++.|+..|...|+.+..+||++++++|..+++.|++|++
T Consensus         5 pNi~y--~v~~~-~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~   81 (200)
T d1oywa3           5 PNIRY--MLMEK-FKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDL   81 (200)
T ss_dssp             TTEEE--EEEEC-SSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCcEE--EEEcC-CcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccc
Confidence            45543  33333 4588999999998888899999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy11867        396 KIYS  399 (399)
Q Consensus       396 ~ILV  399 (399)
                      +|||
T Consensus        82 ~ilv   85 (200)
T d1oywa3          82 QIVV   85 (200)
T ss_dssp             SEEE
T ss_pred             eEEE
Confidence            9986

>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=99.04  E-value=1.9e-10  Score=96.07  Aligned_cols=57  Identities=21%  Similarity=0.416  Sum_probs=54.7

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...++||||+++++++.++..|...|+++..+||+|++.+|..++++|++|+++|||
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLV   86 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLV   86 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEE
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEE
Confidence            346899999999999999999999999999999999999999999999999999997

>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=98.78  E-value=2.5e-08  Score=86.45  Aligned_cols=168  Identities=18%  Similarity=0.166  Sum_probs=119.7

Q ss_pred             cCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccC
Q psy11867        121 MGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHI  200 (399)
Q Consensus       121 ~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  200 (399)
                      .|. +|+++|...--.+..  |  -|+...||-|||++..+|+.-....++   .+=|++.+--||..=.+++..+...+
T Consensus        77 lG~-RhyDVQLiGgi~L~~--G--~iaem~TGEGKTL~a~l~a~l~al~g~---~vhvvTvNdyLA~RDae~m~~iy~~l  148 (273)
T d1tf5a3          77 TGM-FPFKVQLMGGVALHD--G--NIAEMKTGEGKTLTSTLPVYLNALTGK---GVHVVTVNEYLASRDAEQMGKIFEFL  148 (273)
T ss_dssp             HSC-CCCHHHHHHHHHHHT--T--SEEECCTTSCHHHHHHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             hce-EEehhHHHHHHHHHh--h--hheeecCCCcchhHHHHHHHHHHhcCC---CceEEecCccccchhhhHHhHHHHHc
Confidence            344 789999988887765  3  589999999999999988877665543   38899999999999999999999887


Q ss_pred             CCcEEEEEEcCchhh-hhhccCCcEEEeCchhH-HHhhhcc-----ccccCCceeEEEEechhhHhhcCCchH-------
Q psy11867        201 TDLSVRYAVRGENLE-RNKKITEQIIIGTPGKV-LDWGLKY-----RFFDLSKIKVFVLDEADVMIATQGHQD-------  266 (399)
Q Consensus       201 ~~~~~~~~~~~~~~~-~~~~~~~~IlV~Tp~~l-~~~~~~~-----~~~~~~~~~~lViDEah~l~~~~~~~~-------  266 (399)
                       ++++.+...+.... +.....++|+.+|...+ .+++..+     .....+.+.+.|+||+|.++=......       
T Consensus       149 -Glsvg~~~~~~~~~~r~~~Y~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpliisg~~  227 (273)
T d1tf5a3         149 -GLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQS  227 (273)
T ss_dssp             -TCCEEECCTTSCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEE
T ss_pred             -CCCccccccccCHHHHHHHhhCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEeccCc
Confidence             88888877665443 33456789999999887 3444322     222367789999999998862211110       


Q ss_pred             ------HHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhhC
Q psy11867        267 ------FSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDMV  300 (399)
Q Consensus       267 ------~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~~  300 (399)
                            ....+.+   --.++.+||.|......++.+-|-
T Consensus       228 ~~~a~it~q~~f~---~y~~l~gmtgta~~~~~e~~~iy~  264 (273)
T d1tf5a3         228 MTLATITFQNYFR---MYEKLAGMTGTAKTEEEEFRNIYN  264 (273)
T ss_dssp             EEEEEEEHHHHHT---TSSEEEEEESCCGGGHHHHHHHHC
T ss_pred             cchhhhhHHHHHH---HHHHHhCCccccHHHHHHHHhccC
Confidence                  0112222   234677888887766666666554

>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=98.41  E-value=6.8e-08  Score=81.86  Aligned_cols=66  Identities=27%  Similarity=0.277  Sum_probs=54.1

Q ss_pred             HHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHC------------------------------CCeEEEEcCCCCHH
Q psy11867        332 FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKE------------------------------GLNVGLLSGELTVE  381 (399)
Q Consensus       332 ~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~------------------------------g~~v~~lhg~~~~~  381 (399)
                      .+.+.+++..  .+++||||+||+.|+.+|..|...                              ...++++||+|++.
T Consensus        30 ~~l~~~~i~~--~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~  107 (201)
T d2p6ra4          30 EELVEECVAE--NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNG  107 (201)
T ss_dssp             HHHHHHHHHT--TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHH
T ss_pred             HHHHHHHHHc--CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhh
Confidence            3444555553  468999999999999999888652                              12388999999999


Q ss_pred             HHHHHHHHHhcCCCcccC
Q psy11867        382 QRLSILDRFREGEFKIYS  399 (399)
Q Consensus       382 ~R~~v~~~F~~G~~~ILV  399 (399)
                      +|..+++.|++|.++|||
T Consensus       108 ~r~~ie~~f~~g~i~vlv  125 (201)
T d2p6ra4         108 QRRVVEDAFRRGNIKVVV  125 (201)
T ss_dssp             HHHHHHHHHHTTSCCEEE
T ss_pred             hHHHHHHHHhCCCceEEE
Confidence            999999999999999986

>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=98.33  E-value=6.9e-08  Score=76.45  Aligned_cols=51  Identities=25%  Similarity=0.354  Sum_probs=45.7

Q ss_pred             CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        342 VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       342 ~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ...+++||||+|++.|+.|++.|.+.|+.+..+||+|+++       .|++|+.+|||
T Consensus        33 ~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~-------~~~~~~~~vlv   83 (138)
T d1jr6a_          33 IKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS-------VIPTNGDVVVV   83 (138)
T ss_dssp             HTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSC-------CCTTSSCEEEE
T ss_pred             cCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhh-------hhhhhhcceee
Confidence            3457999999999999999999999999999999999854       57899999886

>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=98.25  E-value=1.1e-07  Score=83.57  Aligned_cols=56  Identities=29%  Similarity=0.342  Sum_probs=49.2

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHH----------HHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQR----------LSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R----------~~v~~~F~~G~~~ILV  399 (399)
                      .+++||||+|++.|+.|+..|++.|+++..+||+++++.|          ..+++.|+.|+.+++|
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVV  101 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVI  101 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEE
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEE
Confidence            4799999999999999999999999999999999999987          5688999999999875

>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=98.25  E-value=2.9e-08  Score=87.25  Aligned_cols=64  Identities=19%  Similarity=0.296  Sum_probs=57.3

Q ss_pred             hhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ++|+..|..+++... +++||||++++.|+.|++.|...      +||++++.+|..+++.|++|+++|||
T Consensus        11 ~~~~~~l~~~l~~~~-~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLV   74 (248)
T d1gkub2          11 DESISTLSSILEKLG-TGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLI   74 (248)
T ss_dssp             CCCTTTTHHHHTTSC-SCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEE
T ss_pred             chHHHHHHHHHHHhC-CCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEE
Confidence            567888889988654 67999999999999999999753      89999999999999999999999987

>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=98.22  E-value=2e-07  Score=78.87  Aligned_cols=66  Identities=18%  Similarity=0.316  Sum_probs=59.6

Q ss_pred             hhHHHHHHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        329 DEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       329 ~~k~~~l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..|+..+.+++......++||||++...++.|++.|     .+..+||+++..+|..+++.|++|+++|||
T Consensus        78 ~~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l-----~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv  143 (200)
T d2fwra1          78 KNKIRKLREILERHRKDKIIIFTRHNELVYRISKVF-----LIPAITHRTSREEREEILEGFRTGRFRAIV  143 (200)
T ss_dssp             SHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHT-----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCB
T ss_pred             HHHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhc-----CcceeeCCCCHHHHHHHHHHhhcCCeeeee
Confidence            468889999999988889999999999999998877     355689999999999999999999999986

>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=98.12  E-value=1.6e-06  Score=77.34  Aligned_cols=65  Identities=23%  Similarity=0.430  Sum_probs=54.2

Q ss_pred             HHHHhccCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcC--------CCCHHHHHHHHHHHhcCCCcccC
Q psy11867        335 VSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSG--------ELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       335 l~~ll~~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg--------~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      |..++......++||||+++.+|+.+++.|.+.|+++..+||        ++++.+|..+++.|++|+++|||
T Consensus       152 l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv  224 (286)
T d1wp9a2         152 IREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLV  224 (286)
T ss_dssp             HHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEE
T ss_pred             HHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEE
Confidence            334445567789999999999999999999999999988866        57777999999999999999986

>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=98.02  E-value=1.1e-05  Score=74.05  Aligned_cols=142  Identities=19%  Similarity=0.193  Sum_probs=83.8

Q ss_pred             CCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH--HHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCC
Q psy11867        124 YAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT--LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHIT  201 (399)
Q Consensus       124 ~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~--l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~  201 (399)
                      ......|..|+..++.  ++-++++|+.|||||....  +..+..... ..+.++++.+||-.-|..+.+.+......+.
T Consensus       147 ~~~~~~Q~~A~~~al~--~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~-~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~  223 (359)
T d1w36d1         147 SDEINWQKVAAAVALT--RRISVISGGPGTGKTTTVAKLLAALIQMAD-GERCRIRLAAPTGKAAARLTESLGKALRQLP  223 (359)
T ss_dssp             TTSCCHHHHHHHHHHT--BSEEEEECCTTSTHHHHHHHHHHHHHHTCS-SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSS
T ss_pred             cccccHHHHHHHHHHc--CCeEEEEcCCCCCceehHHHHHHHHHHHHh-ccCCeEEEecCcHHHHHHHHHHHHHHHhhcC
Confidence            3457899999999998  5899999999999997642  222322222 3566799999999888887776655433221


Q ss_pred             CcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhh-----hccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCC
Q psy11867        202 DLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWG-----LKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP  276 (399)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~-----~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~  276 (399)
                      ....     ..       .....-..|..+++...     ..........++++|||||-.+-     ...+..++..++
T Consensus       224 ~~~~-----~~-------~~~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~-----~~l~~~ll~~~~  286 (359)
T d1w36d1         224 LTDE-----QK-------KRIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID-----LPMMSRLIDALP  286 (359)
T ss_dssp             CCSC-----CC-------CSCSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCB-----HHHHHHHHHTCC
T ss_pred             chhh-----hh-------hhhhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccC-----HHHHHHHHHHhc
Confidence            1000     00       00000011111111110     01112234568899999997752     345567788888


Q ss_pred             CCCcEEEEE
Q psy11867        277 SDCQIMLFS  285 (399)
Q Consensus       277 ~~~q~l~~S  285 (399)
                      ..+++|++.
T Consensus       287 ~~~~lILvG  295 (359)
T d1w36d1         287 DHARVIFLG  295 (359)
T ss_dssp             TTCEEEEEE
T ss_pred             CCCEEEEEC
Confidence            888877764

>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=98.01  E-value=8.7e-06  Score=68.02  Aligned_cols=57  Identities=12%  Similarity=0.251  Sum_probs=53.1

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~~--g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+++.+.|+..+..+.++..+.+.  ++++.++||.|+.++++.++++|++|+++|||
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv   88 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLV   88 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEE
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEE
Confidence            4579999999999999999999875  78999999999999999999999999999997

>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=97.55  E-value=3.5e-05  Score=68.65  Aligned_cols=70  Identities=17%  Similarity=0.137  Sum_probs=52.0

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC-CCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP-SIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~-~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      +++|-|.+|+..  .  ..+++|.|+.|||||.+.+.-+...+.. .....++||+++|+.+|..+...+.++..
T Consensus         1 ~L~~eQ~~av~~--~--~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           1 RLNPGQQQAVEF--V--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCCHHHHHHHHC--C--SSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CcCHHHHHHHhC--C--CCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            468999999964  1  4679999999999998765444333322 12345799999999999999888877653

>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=97.53  E-value=5.2e-05  Score=65.57  Aligned_cols=70  Identities=21%  Similarity=0.287  Sum_probs=59.0

Q ss_pred             hhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcCC-Cccc
Q psy11867        329 DEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKE-GLNVGLLSGELTVEQRLSILDRFREGE-FKIY  398 (399)
Q Consensus       329 ~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~-g~~v~~lhg~~~~~~R~~v~~~F~~G~-~~IL  398 (399)
                      ..|+..+.+++...  ...++||||+.....+.+...+.+. |..+..+||+++..+|..++++|.++. .+||
T Consensus        68 S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vl  141 (244)
T d1z5za1          68 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFI  141 (244)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEE
T ss_pred             hhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhc
Confidence            45888888887653  4569999999999999998888655 889999999999999999999998764 5665

>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=97.40  E-value=1.5e-05  Score=66.94  Aligned_cols=57  Identities=30%  Similarity=0.461  Sum_probs=41.7

Q ss_pred             CCCcEEEEecchHhHH--------HHHHHHHHC---CCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAA--------WLAEKMSKE---GLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~--------~l~~~L~~~---g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      ..+++.+.|+..+..+        ..++.|.+.   ++++..+||+|++++|++++++|++|+++|||
T Consensus        28 ~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLV   95 (206)
T d1gm5a4          28 RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILV   95 (206)
T ss_dssp             TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCC
T ss_pred             cCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEE
Confidence            3468888888765443        334444433   67899999999999999999999999999997

>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=97.28  E-value=0.00022  Score=63.76  Aligned_cols=69  Identities=20%  Similarity=0.208  Sum_probs=53.2

Q ss_pred             CChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCC-CCCCeEEEEeCcHHHHHHHHHHHHHHh
Q psy11867        125 APSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPS-IQEPQVLCLAPTYELAIQIGEVVAKMG  197 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~-~~~~~~lil~Pt~~La~Q~~~~~~~~~  197 (399)
                      .+++-|.+++...    +..++|.|+.|||||.+.+--+...+... ....+++++++|+..+..+...+....
T Consensus        11 ~L~~eQ~~~v~~~----~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~   80 (318)
T d1pjra1          11 HLNKEQQEAVRTT----EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLL   80 (318)
T ss_dssp             TSCHHHHHHHHCC----SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhCC----CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhc
Confidence            4789999999742    46799999999999988766555555332 233479999999999999988887654

>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=97.20  E-value=0.00034  Score=63.41  Aligned_cols=68  Identities=15%  Similarity=0.240  Sum_probs=59.4

Q ss_pred             hhHHHHHHHHhcc---CCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc
Q psy11867        329 DEKFEAVSNIYGV---VTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK  396 (399)
Q Consensus       329 ~~k~~~l~~ll~~---~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~  396 (399)
                      ..|+..|..++..   ....|+|||++.....+.|...|...|+.+..++|+++..+|..++++|+++...
T Consensus       100 S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~  170 (346)
T d1z3ix1         100 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSP  170 (346)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCC
T ss_pred             CHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhccccc
Confidence            5688777777654   3457999999999999999999999999999999999999999999999987643

>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=97.11  E-value=0.00016  Score=64.05  Aligned_cols=52  Identities=13%  Similarity=0.114  Sum_probs=41.5

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .++++|||++.+.++.++..|++.|.+|..+||.+...++.    .|++|+.+|||
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~   87 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFIL   87 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEE
Confidence            57999999999999999999999999999999999988855    57899998875

>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=96.83  E-value=0.00047  Score=63.75  Aligned_cols=68  Identities=24%  Similarity=0.269  Sum_probs=51.3

Q ss_pred             CChHHHHHHhhhhhcC---CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        125 APSKIQETALPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      .|+.-|-+||..+.++   +.++.++.|-||||||++.. .++.....     .+|||+|+..+|.|+++.++.+..
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~~r-----p~LVVt~n~~~A~qL~~dL~~~l~   81 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQVNK-----PTLVIAHNKTLAGQLYSELKEFFP   81 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHHTC-----CEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHhCC-----CEEEEeCCHHHHHHHHHHHHHHcC
Confidence            5777888888777653   24678999999999995433 33333322     289999999999999999999864

>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=96.82  E-value=0.00039  Score=58.25  Aligned_cols=38  Identities=18%  Similarity=0.176  Sum_probs=26.3

Q ss_pred             ChHHHHHHhhhhhc----CC-CCcEEEEccCCCCceehhHHHH
Q psy11867        126 PSKIQETALPTLLA----DP-PHNMIAQSQSGTGKTAAFTLTM  163 (399)
Q Consensus       126 p~~iQ~~ai~~ll~----~~-g~~vi~~a~TGsGKT~~~~l~i  163 (399)
                      .+|||..++..+..    +. ++.+++.||.|+|||..+..-+
T Consensus         3 ~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a   45 (207)
T d1a5ta2           3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALS   45 (207)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHH
T ss_pred             CCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHH
Confidence            34777777766532    22 3459999999999998765533

>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=0.0025  Score=52.70  Aligned_cols=113  Identities=13%  Similarity=0.079  Sum_probs=61.4

Q ss_pred             HHHHhhhhhcC-CCCcEEEEccCCCCceehhHHHHHHhh-CCCCCCCeEEEEeCcHH--HHHHHHHHHHHHhccCCCcEE
Q psy11867        130 QETALPTLLAD-PPHNMIAQSQSGTGKTAAFTLTMLSRV-NPSIQEPQVLCLAPTYE--LAIQIGEVVAKMGKHITDLSV  205 (399)
Q Consensus       130 Q~~ai~~ll~~-~g~~vi~~a~TGsGKT~~~~l~il~~l-~~~~~~~~~lil~Pt~~--La~Q~~~~~~~~~~~~~~~~~  205 (399)
                      |.+.+..+.+. .+.++++.||.|+|||..+.... ..+ ......+-.+++.|...  -+.|+.+              
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~-~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~--------------   66 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELP-EYVEKFPPKASDVLEIDPEGENIGIDDIRT--------------   66 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHH-HHHHTSCCCTTTEEEECCSSSCBCHHHHHH--------------
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH-HHHhccccCCCCEEEEeCCcCCCCHHHHHH--------------
Confidence            44555555443 47899999999999997654322 222 12223344566655311  0122211              


Q ss_pred             EEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEE
Q psy11867        206 RYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFS  285 (399)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~S  285 (399)
                                                +.+.+.. .. .....+++|+||||+|-.  .....+..++..-|.++.++++|
T Consensus        67 --------------------------i~~~~~~-~~-~~~~~KviIId~ad~l~~--~aqNaLLK~LEEPp~~t~fiLit  116 (198)
T d2gnoa2          67 --------------------------IKDFLNY-SP-ELYTRKYVIVHDCERMTQ--QAANAFLKALEEPPEYAVIVLNT  116 (198)
T ss_dssp             --------------------------HHHHHTS-CC-SSSSSEEEEETTGGGBCH--HHHHHTHHHHHSCCTTEEEEEEE
T ss_pred             --------------------------HHHHHhh-Cc-ccCCCEEEEEeCccccch--hhhhHHHHHHhCCCCCceeeecc
Confidence                                      2222111 11 134568999999999953  23444445555556677777765


Q ss_pred             ee
Q psy11867        286 AT  287 (399)
Q Consensus       286 AT  287 (399)
                      ..
T Consensus       117 ~~  118 (198)
T d2gnoa2         117 RR  118 (198)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=96.40  E-value=0.0037  Score=52.25  Aligned_cols=47  Identities=11%  Similarity=0.134  Sum_probs=26.7

Q ss_pred             CCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCCh
Q psy11867        244 LSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDK  290 (399)
Q Consensus       244 ~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~  290 (399)
                      +...++++||++|.+.........+..+...+......+++|+..++
T Consensus        95 ~~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p  141 (213)
T d1l8qa2          95 YKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHP  141 (213)
T ss_dssp             HHTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCG
T ss_pred             HhhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcc
Confidence            34678999999999864323333344444443333334555665443

>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=96.36  E-value=0.0032  Score=52.29  Aligned_cols=133  Identities=17%  Similarity=0.120  Sum_probs=62.0

Q ss_pred             Cc-EEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe--CcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhc
Q psy11867        143 HN-MIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA--PTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKK  219 (399)
Q Consensus       143 ~~-vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~--Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (399)
                      ++ +++++|||+|||....--+......   +.++.+++  ..|.-|.++.+.+.+..    ++.+............  
T Consensus        10 ~~vi~lvGp~GvGKTTTiaKLA~~~~~~---g~kV~lit~Dt~R~gA~eQL~~~a~~l----~v~~~~~~~~~~~~~~--   80 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTTTAAKLALYYKGK---GRRPLLVAADTQRPAAREQLRLLGEKV----GVPVLEVMDGESPESI--   80 (207)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHT---TCCEEEEECCSSCHHHHHHHHHHHHHH----TCCEEECCTTCCHHHH--
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEecccccchHHHHHHHHHHhc----CCccccccccchhhHH--
Confidence            44 4568999999986654323222222   23455555  34555543333333322    3333333322222110  


Q ss_pred             cCCcEEEeCchhHHHhhhccccccCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCChhHHHHHHhh
Q psy11867        220 ITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDM  299 (399)
Q Consensus       220 ~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~~~v~~~~~~~  299 (399)
                                   .....  .....++.+++++|=+-+..........+..+.+...+..-++.++|+...+..+.+..+
T Consensus        81 -------------~~~~~--~~~~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~~~~f  145 (207)
T d1ls1a2          81 -------------RRRVE--EKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAF  145 (207)
T ss_dssp             -------------HHHHH--HHHHHHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHHHHHH
T ss_pred             -------------HHHHH--HHHhhccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchhHHHHHHHH
Confidence                         00000  001123445555655555321111223334455555556667788888887766665544

>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=96.14  E-value=0.004  Score=52.26  Aligned_cols=45  Identities=24%  Similarity=0.241  Sum_probs=28.8

Q ss_pred             cCCceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        243 DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       243 ~~~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      ......++|+||+|.+...  ....+...+...+..+.+++.+....
T Consensus        98 ~~~~~kviiiDe~d~~~~~--~~~~ll~~~e~~~~~~~~i~~~~~~~  142 (224)
T d1sxjb2          98 PPGKHKIVILDEADSMTAG--AQQALRRTMELYSNSTRFAFACNQSN  142 (224)
T ss_dssp             CTTCCEEEEEESGGGSCHH--HHHTTHHHHHHTTTTEEEEEEESCGG
T ss_pred             CCcceEEEEEecccccchh--HHHHHhhhccccccceeeeeccCchh
Confidence            3456679999999998643  33334445555566667777666543

>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=96.01  E-value=0.021  Score=48.18  Aligned_cols=44  Identities=23%  Similarity=0.267  Sum_probs=30.4

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcC-CCCcEEEEccCCCCceehhHH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLAD-PPHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~-~g~~vi~~a~TGsGKT~~~~l  161 (399)
                      ++|+++-.++.+.+.|...               +.++ .++.+++.||+|+|||.++.+
T Consensus         9 ~~~~dlig~~~~~~~L~~~---------------i~~~~~~~~~Ll~Gp~G~GKtt~a~~   53 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANG---------------LSLGRIHHAYLFSGTRGVGKTSIARL   53 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHH---------------HHTTCCCSEEEEECSTTSSHHHHHHH
T ss_pred             CCHHHccChHHHHHHHHHH---------------HHcCCCCeeEEEECCCCCcHHHHHHH
Confidence            4678887778877777542               1111 135589999999999987654

>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=95.85  E-value=0.0075  Score=50.01  Aligned_cols=18  Identities=22%  Similarity=0.346  Sum_probs=14.1

Q ss_pred             cEEEEccCCCCceehhHH
Q psy11867        144 NMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~~l  161 (399)
                      -+++++|||+|||....=
T Consensus        11 vi~lvGptGvGKTTTiAK   28 (211)
T d2qy9a2          11 VILMVGVNGVGKTTTIGK   28 (211)
T ss_dssp             EEEEECCTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            355789999999977654

>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=0.013  Score=48.85  Aligned_cols=43  Identities=19%  Similarity=0.290  Sum_probs=29.1

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++|+++-.++.+.+.|...               +.++.-.++++.||+|+|||.+.-
T Consensus        11 ~~~~divg~~~~~~~L~~~---------------i~~~~~~~lLl~Gp~G~GKttl~~   53 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKF---------------VDEGKLPHLLFYGPPGTGKTSTIV   53 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHH---------------HHTTCCCCEEEECSSSSSHHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH---------------HHcCCCCeEEEECCCCCChhHHHH
Confidence            5677776777777776542               112213469999999999996543

>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=95.66  E-value=0.066  Score=45.33  Aligned_cols=52  Identities=25%  Similarity=0.341  Sum_probs=32.0

Q ss_pred             cccccCCCCHHHHHHHHHc-C-CCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        103 KTFEALHLKPELLKGVYEM-G-FYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~-g-~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      .+|++++-.+...+.|.+. . +..|..++..-     ....+.+++.||+|+|||...
T Consensus         6 ~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g-----~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           6 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMG-----ARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTT-----CCCCSEEEEECCTTSSHHHHH
T ss_pred             CcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcC-----CCCCceEEEecCCCCChhHHH
Confidence            4788887667776666542 0 22222222211     122578999999999999654

>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=95.61  E-value=0.02  Score=47.83  Aligned_cols=43  Identities=14%  Similarity=0.240  Sum_probs=29.6

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++|+++-.++...+.|...               +-.+...++++.||+|+|||.++-
T Consensus        21 ~~~~diig~~~~~~~l~~~---------------i~~~~~~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          21 QRLDDIVGQEHIVKRLKHY---------------VKTGSMPHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             CSTTTCCSCHHHHHHHHHH---------------HHHTCCCEEEEESCTTSSHHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH---------------HHcCCCCeEEEECCCCCcHHHHHH
Confidence            4677776677777776542               112224679999999999996643

>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=95.33  E-value=0.012  Score=50.50  Aligned_cols=56  Identities=20%  Similarity=0.170  Sum_probs=50.1

Q ss_pred             CCcEEEEecchHhHHHHHHHHHH----CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSK----EGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~----~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      +.++++.+++.--|.+.+..+.+    .|..+..+||+++..+|..++...++|+++|+|
T Consensus       132 g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiI  191 (264)
T d1gm5a3         132 GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVI  191 (264)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEE
T ss_pred             ccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEE
Confidence            36899999999988888877665    378999999999999999999999999999986

>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=95.27  E-value=0.012  Score=49.98  Aligned_cols=45  Identities=20%  Similarity=0.211  Sum_probs=31.8

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l  161 (399)
                      ++|+++--++.+.+.|..+ +..             .....++++.||.|+|||.....
T Consensus         8 ~~~~diig~~~~~~~L~~~-~~~-------------~~~~~~lll~Gp~G~GKTt~~~~   52 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSL-SDQ-------------PRDLPHLLLYGPNGTGKKTRCMA   52 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTT-TTC-------------TTCCCCEEEECSTTSSHHHHHHT
T ss_pred             CCHHHccCcHHHHHHHHHH-HHc-------------CCCCCeEEEECCCCCCHHHHHHH
Confidence            5688888888888888653 110             01135799999999999976543

>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=95.09  E-value=0.018  Score=47.51  Aligned_cols=49  Identities=14%  Similarity=-0.035  Sum_probs=27.2

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEe-C-cHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLA-P-TYELAIQIGEVV  193 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~-P-t~~La~Q~~~~~  193 (399)
                      ++-++++||||+|||....=-+......   +.++.+++ - .|.=|.++.+.+
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~---g~kV~lit~Dt~R~gA~eQL~~~   56 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNL---GKKVMFCAGDTFRAAGGTQLSEW   56 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTT---TCCEEEECCCCSSTTHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEEeccccccchhhHhhc
Confidence            5667889999999997754333333222   23344444 3 355554333333

>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=94.96  E-value=0.0054  Score=51.66  Aligned_cols=43  Identities=26%  Similarity=0.269  Sum_probs=24.9

Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEEEeeCC
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD  289 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~SAT~~  289 (399)
                      ....++|+||+|.+...  ....+..+....+..+.+++++....
T Consensus       107 ~~~~viiiDe~d~l~~~--~~~~l~~~~~~~~~~~~~i~~~~~~~  149 (237)
T d1sxjd2         107 PPYKIIILDEADSMTAD--AQSALRRTMETYSGVTRFCLICNYVT  149 (237)
T ss_dssp             CSCEEEEETTGGGSCHH--HHHHHHHHHHHTTTTEEEEEEESCGG
T ss_pred             cCceEEEEecccccCHH--HHHHHhhccccccccccccccccccc
Confidence            34568999999998542  23334444455455555555444433

>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=94.94  E-value=0.014  Score=48.38  Aligned_cols=41  Identities=27%  Similarity=0.324  Sum_probs=23.6

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYE  184 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~  184 (399)
                      +.-++++||||+|||....=-+......  ....+||-+-|.-
T Consensus        11 p~vi~lvGptGvGKTTTiAKLAa~~~~~--~~kV~lit~Dt~R   51 (213)
T d1vmaa2          11 PFVIMVVGVNGTGKTTSCGKLAKMFVDE--GKSVVLAAADTFR   51 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT--TCCEEEEEECTTC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHC--CCceEEEeecccc
Confidence            4556789999999997654323222322  2334555555443

>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=94.91  E-value=0.015  Score=51.64  Aligned_cols=65  Identities=23%  Similarity=0.320  Sum_probs=43.6

Q ss_pred             HHHHHcCCCC---ChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHH
Q psy11867        116 KGVYEMGFYA---PSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYEL  185 (399)
Q Consensus       116 ~~l~~~g~~~---p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  185 (399)
                      ..+.+.|+..   ..+-+...+..+... ++|++++|+||||||.. +-+++..+..   ..+++.+--+.||
T Consensus       138 ~~l~~~g~~~~~~~~~~~~~~l~~~v~~-~~nili~G~tgSGKTT~-l~al~~~i~~---~~rivtiEd~~El  205 (323)
T d1g6oa_         138 SFFEEQGFYNLLDNKEQAISAIKDGIAI-GKNVIVCGGTGSGKTTY-IKSIMEFIPK---EERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHTTTTTTCSSHHHHHHHHHHHHHH-TCCEEEEESTTSSHHHH-HHHHGGGSCT---TCCEEEEESSCCC
T ss_pred             HHHHHHhhhcccccHHHHHHHHHHHHHh-CCCEEEEeeccccchHH-HHHHhhhccc---ccceeeccchhhh
Confidence            3445555543   345556666666655 79999999999999964 4455555533   3468888788886

>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=94.81  E-value=0.033  Score=46.72  Aligned_cols=57  Identities=16%  Similarity=0.176  Sum_probs=52.0

Q ss_pred             CCCcEEEEecchHhHHHHHHHHHH----CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcccC
Q psy11867        343 TIGQAMIFCHTRKTAAWLAEKMSK----EGLNVGLLSGELTVEQRLSILDRFREGEFKIYS  399 (399)
Q Consensus       343 ~~~k~IIF~~s~~~a~~l~~~L~~----~g~~v~~lhg~~~~~~R~~v~~~F~~G~~~ILV  399 (399)
                      .+.++++.+++.--+.+.++.+++    .+.++..+||.++..+|..+.+.+.+|+.+|+|
T Consensus       103 ~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~ivi  163 (233)
T d2eyqa3         103 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILI  163 (233)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEE
T ss_pred             cCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEE
Confidence            346899999999999999999986    478999999999999999999999999999985

>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=94.73  E-value=0.015  Score=46.23  Aligned_cols=71  Identities=14%  Similarity=0.193  Sum_probs=53.4

Q ss_pred             EeCChhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC
Q psy11867        324 MCKNIDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGE  394 (399)
Q Consensus       324 ~~~~~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~R~~v~~~F~~G~  394 (399)
                      .+.....|+.++.+-+...  ...|+||+|.|.+.++.++..|.+.|++..++++.....+-+-+-+.-..|.
T Consensus        12 vf~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~Ag~~g~   84 (175)
T d1tf5a4          12 IYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGA   84 (175)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTTC
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhccCCCc
Confidence            3446678888887766443  2368999999999999999999999999999999876555544444444443

>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=94.41  E-value=0.07  Score=45.39  Aligned_cols=51  Identities=27%  Similarity=0.296  Sum_probs=30.4

Q ss_pred             ccccCCCCHHHHHHHHHc--CCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehh
Q psy11867        104 TFEALHLKPELLKGVYEM--GFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       104 ~f~~~~l~~~l~~~l~~~--g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~  159 (399)
                      +|++.+-.+...+.|.+.  -+..|..+|..-+     ..++.+++.||+|+|||...
T Consensus        10 t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~-----~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_          10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGG-----KIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC----------CCCCEEEEECCTTSCHHHHH
T ss_pred             CHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCC-----CCCCeEEeeCCCCCCccHHH
Confidence            688887777777666542  1222222222111     13688999999999999654

>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=94.30  E-value=0.39  Score=37.90  Aligned_cols=111  Identities=10%  Similarity=0.135  Sum_probs=71.5

Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccC
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDL  244 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~  244 (399)
                      .+.++||.|+|+.-|..+.+.+.+.     ++......|+......       ..+..+|+|+|.-       -.+.++.
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~-----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v-------~~~GiDi   97 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINL-------LREGLDI   97 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCC-------CCTTCCC
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhc-----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeeee-------eeeeccC
Confidence            4668999999999999999988875     6777888887654322       2567799999962       2367899


Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCCC-CCcEEEEEeeCChhHHH
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLPS-DCQIMLFSATYDKEVME  294 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~-~~q~l~~SAT~~~~v~~  294 (399)
                      .+++++|+=.++...-.......+.++-+..+. +...+++.......+..
T Consensus        98 p~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~~  148 (174)
T d1c4oa2          98 PEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQR  148 (174)
T ss_dssp             TTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHH
T ss_pred             CCCcEEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHHHHH
Confidence            999999997766532111223344444444433 23444444334444433

>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=94.22  E-value=0.075  Score=43.72  Aligned_cols=19  Identities=26%  Similarity=0.385  Sum_probs=10.8

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.-+++.||||+|||....
T Consensus        12 p~vi~lvGptGvGKTTTiA   30 (211)
T d1j8yf2          12 PYVIMLVGVQGTGKATTAG   30 (211)
T ss_dssp             SEEEEEECSCCC----HHH
T ss_pred             CEEEEEECCCCCCHHHHHH
Confidence            3446668999999997754

>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=94.06  E-value=0.33  Score=38.61  Aligned_cols=100  Identities=10%  Similarity=0.111  Sum_probs=67.5

Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCC
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLS  245 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~  245 (399)
                      +.+++|.|+++.-+..++..++..     ++.+....|+......       ..+..+|+|||.-       -.+.++..
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~-----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv-------~~rGiDip   98 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEA-----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINL-------LREGLDIP   98 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCC-------CSSSCCCT
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhC-----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhH-------HHccCCCC
Confidence            457999999999998888888765     6677888887654332       2567899999962       33678999


Q ss_pred             ceeEEEEechhhHhhcCCchHHHHHHHHhCCCCCcEEEE
Q psy11867        246 KIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLF  284 (399)
Q Consensus       246 ~~~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~l~~  284 (399)
                      ++++||.-++........+...+.++-+.-.......++
T Consensus        99 ~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~~~  137 (181)
T d1t5la2          99 EVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM  137 (181)
T ss_dssp             TEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEE
T ss_pred             CCCEEEEecCCcccccccHHHHHHHHHhhccccCceeEe
Confidence            999999988876321123444445555544433333333

>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=93.38  E-value=0.09  Score=43.02  Aligned_cols=90  Identities=12%  Similarity=0.079  Sum_probs=65.9

Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccC
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDL  244 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~  244 (399)
                      ++.++.||||..+-....++.++++.   +..++...+|.......       ..+..+|+|||.=  .     ...++.
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~---p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Ttv--I-----EvGiDv   99 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELV---PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTI--I-----ETGIDI   99 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHC---TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESST--T-----GGGSCC
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhC---CceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehh--h-----hhccCC
Confidence            56789999999988888887777764   56788888877543322       2567799999972  2     246789


Q ss_pred             CceeEEEEechhhHhhcCCchHHHHHHHHhCC
Q psy11867        245 SKIKVFVLDEADVMIATQGHQDFSIRIQKRLP  276 (399)
Q Consensus       245 ~~~~~lViDEah~l~~~~~~~~~~~~i~~~l~  276 (399)
                      .+..++||..||++.     ..++..+..+..
T Consensus       100 pnA~~iiI~~a~rfG-----LaQLhQLRGRVG  126 (211)
T d2eyqa5         100 PTANTIIIERADHFG-----LAQLHQLRGRVG  126 (211)
T ss_dssp             TTEEEEEETTTTSSC-----HHHHHHHHTTCC
T ss_pred             CCCcEEEEecchhcc-----ccccccccceee
Confidence            999999999999963     345666665553

>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=92.74  E-value=0.12  Score=39.40  Aligned_cols=89  Identities=16%  Similarity=0.228  Sum_probs=48.8

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCC
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE  222 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (399)
                      .=-++.||..||||.-.+ -.+.+...  .+.+++++-|...-         +...   .+  . ...|       ....
T Consensus         3 ~L~~i~GpMfsGKTteLi-~~~~~~~~--~~~kv~~ikp~~D~---------R~~~---~i--~-s~~g-------~~~~   57 (139)
T d2b8ta1           3 WIEFITGPMFAGKTAELI-RRLHRLEY--ADVKYLVFKPKIDT---------RSIR---NI--Q-SRTG-------TSLP   57 (139)
T ss_dssp             EEEEEECSTTSCHHHHHH-HHHHHHHH--TTCCEEEEEECCCG---------GGCS---SC--C-CCCC-------CSSC
T ss_pred             EEEEEEccccCHHHHHHH-HHHHHHHH--CCCcEEEEEEcccc---------cccc---eE--E-cccC-------ceee
Confidence            345778999999996433 33333322  23358888887431         0000   00  0 0011       1122


Q ss_pred             cEEEeCchhHHHhhhccccccCCceeEEEEechhhH
Q psy11867        223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM  258 (399)
Q Consensus       223 ~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l  258 (399)
                      .+.+.+...+.+......  ...+.+++.||||+.+
T Consensus        58 ~~~~~~~~~~~~~~~~~~--~~~~~dvI~IDE~QFf   91 (139)
T d2b8ta1          58 SVEVESAPEILNYIMSNS--FNDETKVIGIDEVQFF   91 (139)
T ss_dssp             CEEESSTHHHHHHHHSTT--SCTTCCEEEECSGGGS
T ss_pred             eEEeccchhhHHHHHhhc--cccCcCEEEechhhhc
Confidence            366666666666543322  2357899999999986

>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=92.53  E-value=0.078  Score=48.36  Aligned_cols=68  Identities=24%  Similarity=0.305  Sum_probs=47.6

Q ss_pred             CChHHHHHHhhhhhcC--CC-CcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhc
Q psy11867        125 APSKIQETALPTLLAD--PP-HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGK  198 (399)
Q Consensus       125 ~p~~iQ~~ai~~ll~~--~g-~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~  198 (399)
                      .|+.-|-+||..++++  .| +.+.+.|-+||||+++.. .+......     -+|||+|+...|.++++.++.+..
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~~r-----p~LvVt~~~~~A~~l~~dL~~~l~   78 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEALGR-----PALVLAPNKILAAQLAAEFRELFP   78 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHHTC-----CEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHhCC-----CEEEEeCCHHHHHHHHHHHHHhcC
Confidence            4556677777766432  14 457888999999995322 22333222     289999999999999999998864

>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=92.49  E-value=0.044  Score=50.03  Aligned_cols=41  Identities=17%  Similarity=0.351  Sum_probs=28.0

Q ss_pred             HHHHHHhhhhhcCCCCcEEEEccCCCCceehhHHHHHHhhCC
Q psy11867        128 KIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNP  169 (399)
Q Consensus       128 ~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~l~il~~l~~  169 (399)
                      +.|.+.+..++..+..-++++||||||||.... .++..+..
T Consensus       144 ~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~-~~l~~~~~  184 (401)
T d1p9ra_         144 AHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLY-AGLQELNS  184 (401)
T ss_dssp             HHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHH-HHHHHHCC
T ss_pred             HHHHHHHHHHHhhhhceEEEEcCCCCCccHHHH-HHhhhhcC
Confidence            445555555665556789999999999997643 45555543

>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=92.08  E-value=0.3  Score=41.50  Aligned_cols=24  Identities=33%  Similarity=0.382  Sum_probs=18.0

Q ss_pred             hhhhcCCCCcEEEEccCCCCceeh
Q psy11867        135 PTLLADPPHNMIAQSQSGTGKTAA  158 (399)
Q Consensus       135 ~~ll~~~g~~vi~~a~TGsGKT~~  158 (399)
                      ..+.+....|+++.|+.|.|||..
T Consensus        32 ~iL~r~~k~n~lLVG~~GvGKTal   55 (268)
T d1r6bx2          32 QVLCRRRKNNPLLVGESGVGKTAI   55 (268)
T ss_dssp             HHHTSSSSCEEEEECCTTSSHHHH
T ss_pred             HHHhcCccCCcEEECCCCCcHHHH
Confidence            334444468999999999999953

>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=91.59  E-value=0.19  Score=38.18  Aligned_cols=66  Identities=9%  Similarity=0.134  Sum_probs=49.8

Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccCCcEEEeCchhHHHhhhccccccCCceeEEE
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFV  251 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lV  251 (399)
                      +.++||.|+|+.-|.++++.+++.     ++.+....++...........+|+|||--      .. ..++ .++++||
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~-----G~~~~~~H~~~~~~~~~~~~~~vlvaTd~------~~-~GiD-~~v~~Vi  100 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVAL-----GINAVAYYRGLDVSVIPTNGDVVVVATDA------LM-TGFT-GDFDSVI  100 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHH-----TCEEEEECTTCCSCCCTTSSCEEEEESSS------SC-SSSC-CCBSEEE
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhcc-----ccchhhhhccchhhhhhhhhcceeehhHH------HH-hccc-cccceEE
Confidence            446999999999999999999877     56667777887776666778889999962      12 3455 4676765

>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=91.35  E-value=0.31  Score=37.95  Aligned_cols=71  Identities=11%  Similarity=0.087  Sum_probs=51.7

Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhh-------ccCCcEEEeCchhHHHhhhccccccC
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNK-------KITEQIIIGTPGKVLDWGLKYRFFDL  244 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~IlV~Tp~~l~~~~~~~~~~~~  244 (399)
                      ...++||.|.++.-+.++++.+...     ++.+....|+.......       .+..+|+|+|--       -.+.+++
T Consensus        26 ~~~k~iIF~~s~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv-------~~rGiDi   93 (162)
T d1fuka_          26 SVTQAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL-------LARGIDV   93 (162)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG-------GTTTCCC
T ss_pred             CCCcEEEEEEEEchHHHHHHHHhhc-----CceEEEeccCCchhhHHHHHHHHhhcccceeecccc-------ccccccC
Confidence            3456999999999999998888765     45566677765443221       456789999963       2367889


Q ss_pred             CceeEEEEec
Q psy11867        245 SKIKVFVLDE  254 (399)
Q Consensus       245 ~~~~~lViDE  254 (399)
                      .++++||.=+
T Consensus        94 ~~v~~VI~~d  103 (162)
T d1fuka_          94 QQVSLVINYD  103 (162)
T ss_dssp             CSCSEEEESS
T ss_pred             CCceEEEEec
Confidence            9999998744

>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=90.70  E-value=0.032  Score=51.62  Aligned_cols=19  Identities=32%  Similarity=0.562  Sum_probs=16.7

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++|+++.||||+|||+.+-
T Consensus        49 ksNILliGPTGvGKTlLAr   67 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIAR   67 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             cccEEEECCCCCCHHHHHH
Confidence            6899999999999997654

>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=90.59  E-value=0.038  Score=43.71  Aligned_cols=25  Identities=16%  Similarity=0.280  Sum_probs=18.6

Q ss_pred             CcEEEEccCCCCceehhHHHHHHhhC
Q psy11867        143 HNMIAQSQSGTGKTAAFTLTMLSRVN  168 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~l~il~~l~  168 (399)
                      +++++.||+|+|||.... .++..+.
T Consensus         2 k~v~ItG~~GtGKTtl~~-~i~~~l~   26 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIH-KASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHH-HHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHH-HHHHHHH
Confidence            789999999999997433 4444443

>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=90.28  E-value=0.57  Score=36.64  Aligned_cols=72  Identities=10%  Similarity=0.098  Sum_probs=52.2

Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccC
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDL  244 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~  244 (399)
                      ...++||.|+++.-+..++..+...     ++.+....|+......       ..+..+|+|||.-       -.+.+++
T Consensus        31 ~~~k~iVF~~~~~~~~~l~~~L~~~-----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~-------~~~Gid~   98 (171)
T d1s2ma2          31 QINQAIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL-------LTRGIDI   98 (171)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC-------SSSSCCC
T ss_pred             CCCceEEEEeeeehhhHhHHhhhcc-----cccccccccccchhhhhhhhhhcccCccccccchhH-------hhhcccc
Confidence            4568999999999999999888876     4555666666543221       1456789999973       2367889


Q ss_pred             CceeEEEEech
Q psy11867        245 SKIKVFVLDEA  255 (399)
Q Consensus       245 ~~~~~lViDEa  255 (399)
                      .+++++|.=++
T Consensus        99 ~~v~~VI~~d~  109 (171)
T d1s2ma2          99 QAVNVVINFDF  109 (171)
T ss_dssp             TTEEEEEESSC
T ss_pred             ceeEEEEecCC
Confidence            99999996544

>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=89.61  E-value=0.048  Score=47.87  Aligned_cols=19  Identities=32%  Similarity=0.567  Sum_probs=16.4

Q ss_pred             CCCcEEEEccCCCCceehh
Q psy11867        141 PPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~  159 (399)
                      +++++++.||||+|||..+
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4789999999999999544

>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=89.42  E-value=0.1  Score=46.78  Aligned_cols=19  Identities=26%  Similarity=0.413  Sum_probs=16.2

Q ss_pred             CCCcEEEEccCCCCceehh
Q psy11867        141 PPHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~  159 (399)
                      +..|+++.||||+|||..+
T Consensus        67 p~~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCcceeeeCCCCccHHHHH
Confidence            4689999999999999544

>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=89.39  E-value=0.31  Score=37.03  Aligned_cols=87  Identities=15%  Similarity=0.268  Sum_probs=46.7

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhhhccC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKIT  221 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (399)
                      |.=-++.||..||||.-. +-.+.+...  .+.+++++-|...-         ++..   + .+ ....|..       .
T Consensus         7 G~l~lI~GpMfSGKTteL-i~~~~~~~~--~g~~vl~i~~~~D~---------Ry~~---~-~i-~sh~g~~-------~   62 (141)
T d1xx6a1           7 GWVEVIVGPMYSGKSEEL-IRRIRRAKI--AKQKIQVFKPEIDN---------RYSK---E-DV-VSHMGEK-------E   62 (141)
T ss_dssp             CEEEEEECSTTSSHHHHH-HHHHHHHHH--TTCCEEEEEEC-------------------C-EE-ECTTSCE-------E
T ss_pred             eeEEEEEeccccHHHHHH-HHHHHHhhh--cCCcEEEEEecccc---------cccc---c-ee-eecccce-------E
Confidence            566678899999999653 344444332  23458999997531         0110   0 11 1111111       1


Q ss_pred             CcEEEeCchhHHHhhhccccccCCceeEEEEechhhHh
Q psy11867        222 EQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI  259 (399)
Q Consensus       222 ~~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah~l~  259 (399)
                      ..+.+.+...+....       ..+.+++.||||+.+.
T Consensus        63 ~a~~~~~~~~~~~~~-------~~~~dvI~IDE~QFf~   93 (141)
T d1xx6a1          63 QAVAIKNSREILKYF-------EEDTEVIAIDEVQFFD   93 (141)
T ss_dssp             ECEEESSSTHHHHHC-------CTTCSEEEECSGGGSC
T ss_pred             EEEEecchhhhhhhh-------cccccEEEEeehhhcc
Confidence            125555554444431       3467899999999874

>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=88.78  E-value=0.26  Score=45.26  Aligned_cols=54  Identities=15%  Similarity=0.125  Sum_probs=38.8

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCC---------CCCeEEEEeCcHHHHHHHHHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSI---------QEPQVLCLAPTYELAIQIGEVVAK  195 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~---------~~~~~lil~Pt~~La~Q~~~~~~~  195 (399)
                      ...++|.|.-|||||.+..--++..+....         ....+|+|+=|+.=|..+.+.+..
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~   78 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHH
Confidence            467999999999999776666666654321         123589999998877777666544

>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=87.96  E-value=0.15  Score=46.56  Aligned_cols=43  Identities=14%  Similarity=0.350  Sum_probs=29.5

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAI  187 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~  187 (399)
                      .+|+++.|+||||||......+.+.+.   .+..++|+=|.-++..
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~---~g~~~iiiD~kge~~~   92 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLL---RGDRMVIVDPNGDMLS   92 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHH---TTCEEEEEEETTHHHH
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHh---CCCCEEEEeCChhHHH
Confidence            589999999999999764333333333   2345777788876643

>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=87.81  E-value=0.052  Score=45.72  Aligned_cols=57  Identities=9%  Similarity=0.002  Sum_probs=32.4

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhh-h--cCCCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTL-L--ADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~l-l--~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++|+++-..+...+.|...= ...-......+... .  .+..+++++.||+|+|||.+.-
T Consensus        11 ~~~~dlig~~~~~~~L~~~l-~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2          11 TNLQQVCGNKGSVMKLKNWL-ANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             SSGGGCCSCHHHHHHHHHHH-HTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHH-HhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHH
Confidence            46888888888888776520 00000011111111 0  1124689999999999996543

>d1qvra3 c.37.1.20 (A:536-850) 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=87.60  E-value=0.12  Score=45.37  Aligned_cols=16  Identities=25%  Similarity=0.387  Sum_probs=13.3

Q ss_pred             cEEEEccCCCCceehh
Q psy11867        144 NMIAQSQSGTGKTAAF  159 (399)
Q Consensus       144 ~vi~~a~TGsGKT~~~  159 (399)
                      .++++||||+|||..+
T Consensus        55 ~~lf~Gp~G~GKt~la   70 (315)
T d1qvra3          55 SFLFLGPTGVGKTELA   70 (315)
T ss_dssp             EEEEBSCSSSSHHHHH
T ss_pred             EEEEECCCcchHHHHH
Confidence            6788899999999543

>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=87.57  E-value=0.74  Score=35.84  Aligned_cols=71  Identities=15%  Similarity=0.210  Sum_probs=50.3

Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCC
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLS  245 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~  245 (399)
                      ..++||.|+++.-+..+.+.+.+.     +..+....|+......       ..+...|+|+|--       -...+++.
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~~-----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~-------~~~Gid~~   94 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL-------FGRGMDIE   94 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC-------CSTTCCGG
T ss_pred             CCeEEEEEeeeecchhhhhhhccc-----cccccccccccchhhhhhhhhhhccccceeeecccc-------ccchhhcc
Confidence            456999999999999888888775     4556667777544322       2456789999953       22566788


Q ss_pred             ceeEEEEech
Q psy11867        246 KIKVFVLDEA  255 (399)
Q Consensus       246 ~~~~lViDEa  255 (399)
                      .++++|.=+.
T Consensus        95 ~~~~vi~~~~  104 (168)
T d1t5ia_          95 RVNIAFNYDM  104 (168)
T ss_dssp             GCSEEEESSC
T ss_pred             cchhhhhhhc
Confidence            8888887554

>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=87.55  E-value=0.77  Score=36.94  Aligned_cols=69  Identities=9%  Similarity=-0.004  Sum_probs=49.9

Q ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccC
Q psy11867        172 QEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDL  244 (399)
Q Consensus       172 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~  244 (399)
                      .+.++||.++|+.-+..+++.++..     ++.+....|+......       ..+..+|+|+|-.       -...+++
T Consensus        29 ~~~~~IIF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~-------~~~GiD~   96 (200)
T d1oywa3          29 RGKSGIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA-------FGMGINK   96 (200)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT-------SCTTTCC
T ss_pred             CCCCEEEEEeeehhhHHhhhhhccC-----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecch-------hhhccCC
Confidence            3456999999999999988888775     4556666666543222       1456789999973       2357788


Q ss_pred             CceeEEEE
Q psy11867        245 SKIKVFVL  252 (399)
Q Consensus       245 ~~~~~lVi  252 (399)
                      .++++||.
T Consensus        97 p~v~~VI~  104 (200)
T d1oywa3          97 PNVRFVVH  104 (200)
T ss_dssp             TTCCEEEE
T ss_pred             CCCCEEEE
Confidence            89999885

>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=87.31  E-value=0.76  Score=41.12  Aligned_cols=27  Identities=30%  Similarity=0.422  Sum_probs=19.6

Q ss_pred             HHhhhhhcCCCCcEEEEccCCCCceeh
Q psy11867        132 TALPTLLADPPHNMIAQSQSGTGKTAA  158 (399)
Q Consensus       132 ~ai~~ll~~~g~~vi~~a~TGsGKT~~  158 (399)
                      +.+..+......|+++.|+.|.|||..
T Consensus        33 ~~~~~L~r~~k~n~llvG~~GvGKtai   59 (387)
T d1qvra2          33 RVIQILLRRTKNNPVLIGEPGVGKTAI   59 (387)
T ss_dssp             HHHHHHHCSSCCCCEEEECTTSCHHHH
T ss_pred             HHHHHHhcCCCCCCeEECCCCCCHHHH
Confidence            344444444467899999999999954

>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=87.13  E-value=0.27  Score=41.19  Aligned_cols=27  Identities=19%  Similarity=0.217  Sum_probs=20.0

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCC
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNP  169 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~  169 (399)
                      +.++++.||+|+|||.+.- .+...+..
T Consensus        43 ~~~lll~GppGtGKT~l~~-~l~~~l~~   69 (276)
T d1fnna2          43 YPRATLLGRPGTGKTVTLR-KLWELYKD   69 (276)
T ss_dssp             CCEEEEECCTTSSHHHHHH-HHHHHHTT
T ss_pred             CCceEEECCCCCCHHHHHH-HHHHHHhc
Confidence            5799999999999997653 34555543

>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=87.05  E-value=0.32  Score=36.59  Aligned_cols=39  Identities=10%  Similarity=0.082  Sum_probs=25.9

Q ss_pred             CCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTY  183 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  183 (399)
                      |.=-++.||..||||.- ++-.+.+...  .+.+++++-|..
T Consensus         2 G~L~li~GpMfsGKTt~-Li~~~~~~~~--~g~~v~~ikp~~   40 (133)
T d1xbta1           2 GQIQVILGPMFSGKSTE-LMRRVRRFQI--AQYKCLVIKYAK   40 (133)
T ss_dssp             CEEEEEECCTTSCHHHH-HHHHHHHHHT--TTCCEEEEEETT
T ss_pred             cEEEEEEecccCHHHHH-HHHHHHHHHH--cCCcEEEEeccc
Confidence            44467889999999974 4444444433  234588888864

>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=87.03  E-value=1.7  Score=34.62  Aligned_cols=32  Identities=9%  Similarity=-0.073  Sum_probs=21.5

Q ss_pred             EEEeCchhHHHhhhccccccCCceeEEEEechh
Q psy11867        224 IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD  256 (399)
Q Consensus       224 IlV~Tp~~l~~~~~~~~~~~~~~~~~lViDEah  256 (399)
                      |.-+||+.+..++.+... -.+.+..+-++|-+
T Consensus       155 IgatT~eey~~~~e~d~a-L~rrF~~I~V~Ep~  186 (195)
T d1jbka_         155 VGATTLDEYRQYIEKDAA-LERRFQKVFVAEPS  186 (195)
T ss_dssp             EEEECHHHHHHHTTTCHH-HHTTEEEEECCCCC
T ss_pred             EecCCHHHHHHHHHcCHH-HHhcCCEeecCCCC
Confidence            555788888776544332 25678888888864

>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=86.88  E-value=0.093  Score=43.70  Aligned_cols=48  Identities=13%  Similarity=0.204  Sum_probs=29.6

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhcCCCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++|+++--.+.+.+.|...       ++.   .........++++.||+|+|||.++-
T Consensus         6 ~~~~divGqe~~~~~l~~~-------i~~---~~~~~~~~~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLA-------LEA---AKMRGEVLDHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHH-------HHH---HHHHTCCCCCEEEESSTTSSHHHHHH
T ss_pred             CcHHHcCChHHHHHHHHHH-------HHH---HHhcCCCCCeEEEECCCCCcHHHHHH
Confidence            4678876667776666532       000   00111124689999999999997653

>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=86.10  E-value=0.1  Score=40.77  Aligned_cols=19  Identities=32%  Similarity=0.434  Sum_probs=16.3

Q ss_pred             CCcEEEEccCCCCceehhH
Q psy11867        142 PHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~  160 (399)
                      +.++++.|++|||||...-
T Consensus         5 ~~~I~i~G~~GsGKTT~~~   23 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAE   23 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHH
Confidence            5789999999999997653

>d1yt8a4 c.46.1.2 (A:243-372) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=85.97  E-value=0.56  Score=34.83  Aligned_cols=39  Identities=18%  Similarity=0.149  Sum_probs=34.0

Q ss_pred             cCCCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCC
Q psy11867        341 VVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELT  379 (399)
Q Consensus       341 ~~~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~  379 (399)
                      .....++++||.+-..+...+..|.+.|+++..+.||+.
T Consensus        77 ~~~~~~ivl~C~~G~rS~~aa~~L~~~G~~v~~l~GG~~  115 (130)
T d1yt8a4          77 SVRGARLVLVDDDGVRANMSASWLAQMGWQVAVLDGLSE  115 (130)
T ss_dssp             CSBTCEEEEECSSSSHHHHHHHHHHHTTCEEEEECSCCG
T ss_pred             CCccceEEeecCCCccHHHHHHHHHHcCCCeEEEcCchH
Confidence            344568999999988899999999999999999999974

>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=85.67  E-value=0.14  Score=39.29  Aligned_cols=20  Identities=20%  Similarity=0.247  Sum_probs=16.8

Q ss_pred             CCcEEEEccCCCCceehhHH
Q psy11867        142 PHNMIAQSQSGTGKTAAFTL  161 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~~l  161 (399)
                      .+++++.|++|||||..+-.
T Consensus         2 ~k~I~l~G~~GsGKSTvak~   21 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQ   21 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            37899999999999976653

>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=85.07  E-value=1.6  Score=33.26  Aligned_cols=68  Identities=13%  Similarity=0.138  Sum_probs=47.8

Q ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCCcEEEeCchhHHHhhhccccccCC
Q psy11867        173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITEQIIIGTPGKVLDWGLKYRFFDLS  245 (399)
Q Consensus       173 ~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~Tp~~l~~~~~~~~~~~~~  245 (399)
                      ..++||.|++++-|.++++.+++.     ++.+....++......       ..+...|+|||--  ..     +.+++.
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~-----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~--~~-----~Gid~~   95 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV--MS-----RGIDVN   95 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT--HH-----HHCCCS
T ss_pred             CCCEEEEECchHHHHHHHhhhccc-----ccccccccccchhhhhhhhhhhhhcccceeeeehhH--Hh-----hhhhhc
Confidence            457999999999999999888876     4455666666443222       1456689999952  22     466788


Q ss_pred             ceeEEEE
Q psy11867        246 KIKVFVL  252 (399)
Q Consensus       246 ~~~~lVi  252 (399)
                      .++++|.
T Consensus        96 ~v~~Vi~  102 (155)
T d1hv8a2          96 DLNCVIN  102 (155)
T ss_dssp             CCSEEEE
T ss_pred             cCcEEEE
Confidence            8888885

>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=84.68  E-value=0.15  Score=42.33  Aligned_cols=46  Identities=22%  Similarity=0.255  Sum_probs=29.0

Q ss_pred             cccccCCCCHHHHHHHHHcCCCCChHHHHHHhhhhhc--CCCCcEEEEccCCCCceehhH
Q psy11867        103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLA--DPPHNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       103 ~~f~~~~l~~~l~~~l~~~g~~~p~~iQ~~ai~~ll~--~~g~~vi~~a~TGsGKT~~~~  160 (399)
                      ++|+++--.+.+.+.|...            +.....  ....++++.||+|+|||..+-
T Consensus         6 ~~~ddivGq~~~~~~L~~~------------i~~~~~~~~~~~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2           6 KTLDEYIGQERLKQKLRVY------------LEAAKARKEPLEHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CSGGGSCSCHHHHHHHHHH------------HHHHTTSSSCCCCEEEECCTTSCHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHH------------HHHHHhcCCCCCeEEEECCCCCCHHHHHH
Confidence            4677775566666666432            111111  125789999999999996653

>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=84.35  E-value=1.3  Score=35.71  Aligned_cols=59  Identities=14%  Similarity=0.192  Sum_probs=47.3

Q ss_pred             EeCChhhHHHHHHHHhccC--CCCcEEEEecchHhHHHHHHHHHHCCCeEEEEcCCCCHHH
Q psy11867        324 MCKNIDEKFEAVSNIYGVV--TIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQ  382 (399)
Q Consensus       324 ~~~~~~~k~~~l~~ll~~~--~~~k~IIF~~s~~~a~~l~~~L~~~g~~v~~lhg~~~~~~  382 (399)
                      .+.....|+.++.+-+...  ...|+||.+.|.+..+.|...|.+.|++..+|++.--..|
T Consensus        12 Vy~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herE   72 (219)
T d1nkta4          12 IYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQE   72 (219)
T ss_dssp             EESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHH
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHH
Confidence            3456678888877766543  3368999999999999999999999999999999854433

>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=84.06  E-value=0.13  Score=43.33  Aligned_cols=18  Identities=33%  Similarity=0.553  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      ++.+++.||+|+|||..+
T Consensus        32 P~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          32 PTAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             CEEEEEECCTTSCTHHHH
T ss_pred             CEEEEEECCCCCCHHHHH
Confidence            567999999999999765

>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=83.91  E-value=0.43  Score=39.31  Aligned_cols=59  Identities=17%  Similarity=0.146  Sum_probs=35.9

Q ss_pred             hhhhhcC---CCCcEEEEccCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHH
Q psy11867        134 LPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKM  196 (399)
Q Consensus       134 i~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~  196 (399)
                      +..++.+   +|.-+++.|++|+|||...+--+.+.+..   +..+++++-. +-..++.+.+..+
T Consensus        15 LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~~~~---~~~~~~is~e-~~~~~~~~~~~~~   76 (242)
T d1tf7a2          15 LDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACAN---KERAILFAYE-ESRAQLLRNAYSW   76 (242)
T ss_dssp             HHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTT---TCCEEEEESS-SCHHHHHHHHHTT
T ss_pred             HHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHh---ccccceeecc-CCHHHHHHHHHHc
Confidence            3444443   47899999999999997665555554433   3447777643 2234444544444

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.80  E-value=0.11  Score=44.05  Aligned_cols=17  Identities=35%  Similarity=0.608  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCCCceeh
Q psy11867        142 PHNMIAQSQSGTGKTAA  158 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~  158 (399)
                      ++.+++.||+|+|||..
T Consensus        38 ~~giLL~GppGtGKT~l   54 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CceeEEecCCCCCchHH
Confidence            57899999999999964

>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=83.60  E-value=1.4  Score=34.19  Aligned_cols=87  Identities=10%  Similarity=0.052  Sum_probs=57.3

Q ss_pred             cCCCCceehhHHHHHHhhCCCCCCCeEEEEeCcHHHHHHHHHHHHHHhccCCCcEEEEEEcCchhhhh-------hccCC
Q psy11867        150 QSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN-------KKITE  222 (399)
Q Consensus       150 ~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~  222 (399)
                      +....|. .++..++...    ...++||.|.++.-+..+++.++..+     +.+....++......       ..+..
T Consensus        16 ~~~~~K~-~~L~~ll~~~----~~~k~iiF~~~~~~~~~~~~~l~~~~-----~~~~~~~~~~~~~~r~~~~~~fk~g~~   85 (168)
T d2j0sa2          16 EREEWKF-DTLCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREAN-----FTVSSMHGDMPQKERESIMKEFRSGAS   85 (168)
T ss_dssp             SSTTHHH-HHHHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHTT-----CCCEEECTTSCHHHHHHHHHHHHHTSS
T ss_pred             cChHHHH-HHHHHHHHhC----CCCceEEEeeeHHHHHHHHHHhhhcc-----cchhhhhhhhhHHHHHHHHHHHhcCCc
Confidence            3333452 3344455443    34579999999999999998888763     444556666443222       14567


Q ss_pred             cEEEeCchhHHHhhhccccccCCceeEEEEe
Q psy11867        223 QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLD  253 (399)
Q Consensus       223 ~IlV~Tp~~l~~~~~~~~~~~~~~~~~lViD  253 (399)
                      +|+|||--       -.+.+++.++++||.=
T Consensus        86 ~iLv~Td~-------~~rGiDi~~v~~VIn~  109 (168)
T d2j0sa2          86 RVLISTDV-------WARGLDVPQVSLIINY  109 (168)
T ss_dssp             CEEEECGG-------GSSSCCCTTEEEEEES
T ss_pred             cEEeccch-------hcccccccCcceEEEe
Confidence            89999963       2367889999999863

>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=83.54  E-value=0.14  Score=38.96  Aligned_cols=17  Identities=18%  Similarity=0.282  Sum_probs=13.9

Q ss_pred             CcEEEEccCCCCceehh
Q psy11867        143 HNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~  159 (399)
                      +-++++|++|||||..+
T Consensus         3 klIii~G~pGsGKTTla   19 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            45788999999999753

>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=83.17  E-value=0.43  Score=39.13  Aligned_cols=40  Identities=15%  Similarity=0.032  Sum_probs=24.8

Q ss_pred             CCCcEEEEccCCCCceehhHHHHHHhhCC---CCCCCeEEEEe
Q psy11867        141 PPHNMIAQSQSGTGKTAAFTLTMLSRVNP---SIQEPQVLCLA  180 (399)
Q Consensus       141 ~g~~vi~~a~TGsGKT~~~~l~il~~l~~---~~~~~~~lil~  180 (399)
                      +|+-+++.|++|+|||...+--+......   ...+..++++.
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~   75 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID   75 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEE
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEe
Confidence            37899999999999996544333322211   12344566665

>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=82.98  E-value=0.16  Score=39.42  Aligned_cols=18  Identities=28%  Similarity=0.386  Sum_probs=15.2

Q ss_pred             CcEEEEccCCCCceehhH
Q psy11867        143 HNMIAQSQSGTGKTAAFT  160 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~~  160 (399)
                      .++++.|++|||||...-
T Consensus         5 ~~I~i~G~pGsGKTTia~   22 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGK   22 (173)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            678999999999997553

>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=81.75  E-value=0.18  Score=38.97  Aligned_cols=17  Identities=24%  Similarity=0.397  Sum_probs=14.4

Q ss_pred             CcEEEEccCCCCceehh
Q psy11867        143 HNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       143 ~~vi~~a~TGsGKT~~~  159 (399)
                      +-+++.|++|||||..+
T Consensus         3 klI~i~G~~GsGKTTva   19 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45889999999999754

>d1tq1a_ c.46.1.3 (A:) Thiosulfate sulfurtransferase/Senescence-associated protein {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Thiosulfate sulfurtransferase/Senescence-associated protein
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=81.55  E-value=0.4  Score=35.05  Aligned_cols=38  Identities=11%  Similarity=0.183  Sum_probs=32.6

Q ss_pred             CCcEEEEecchHhHHHHHHHHHHCCC-eEEEEcCCCCHH
Q psy11867        344 IGQAMIFCHTRKTAAWLAEKMSKEGL-NVGLLSGELTVE  381 (399)
Q Consensus       344 ~~k~IIF~~s~~~a~~l~~~L~~~g~-~v~~lhg~~~~~  381 (399)
                      ..++|+||++-..+...+..|.+.|+ +|..|.||+..-
T Consensus        72 ~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~~~W  110 (119)
T d1tq1a_          72 SDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYSAW  110 (119)
T ss_dssp             TSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHHHH
T ss_pred             CcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChHHHH
Confidence            36799999998889999999999998 699999997543

>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=81.48  E-value=0.15  Score=42.88  Aligned_cols=18  Identities=22%  Similarity=0.250  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      .+.+++.||+|+|||...
T Consensus        40 ~~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          40 LVSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECcCCCCHHHHH
Confidence            467999999999999654

>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=81.44  E-value=0.14  Score=40.13  Aligned_cols=18  Identities=11%  Similarity=0.217  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      .+.+++.|++|+|||...
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            378999999999999654

>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=81.18  E-value=0.19  Score=39.12  Aligned_cols=18  Identities=17%  Similarity=0.377  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      |+-+++.|++|||||...
T Consensus         4 g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TEEEEEEECTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            678899999999999754

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic 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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.08  E-value=0.45  Score=38.02  Aligned_cols=33  Identities=21%  Similarity=0.093  Sum_probs=22.9

Q ss_pred             hhhhhcC---CCCcEEEEccCCCCceehhHHHHHHh
Q psy11867        134 LPTLLAD---PPHNMIAQSQSGTGKTAAFTLTMLSR  166 (399)
Q Consensus       134 i~~ll~~---~g~~vi~~a~TGsGKT~~~~l~il~~  166 (399)
                      +..++.+   +|+-+++.|++|+|||...+--+.+.
T Consensus        12 LD~ll~GGi~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          12 LDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             HHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHHhhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3445543   47899999999999997655444443

>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=80.60  E-value=0.21  Score=38.85  Aligned_cols=18  Identities=17%  Similarity=0.176  Sum_probs=16.0

Q ss_pred             CCcEEEEccCCCCceehh
Q psy11867        142 PHNMIAQSQSGTGKTAAF  159 (399)
Q Consensus       142 g~~vi~~a~TGsGKT~~~  159 (399)
                      |.-++++|++|||||..+
T Consensus         6 g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           6 GFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             CEEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            688899999999999765