Psyllid ID: psy576

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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-------16
Protein Sequence
MAVDFNHTNPALKRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHccccEEEEEccccccHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHcccccEEEEEHHHccccccccccEEEEccccccccccEEccccccccccccEEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHHHHcccccEEEEEEccHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHcccccEEEEEHHHHcccccccEEEEEEEcccccHHHHEEEEcccccccccEEEEEEEccccccccc
Coil and Loop (DISEMBL)
mavdfnhtnpalKRRVKSNLARMYretegagspvqaqdetillgieppvlVFVQSKERAQELYNELIydginvdvihsdrtqkqrDNVVRSFRTGRIWILITTELlgrgidfrtvrlvvnydfpssaiSYIHRIgragrggregkavtfftkqdapllr
Flexible Loop (DISEMBL)
mavdfnhtnpalkrrvKSNLARMYREtegagspvqaqDETILLGIEPPVLVFVQSKERAQELYNELIYDGINvdvihsdrtqkqrdnvvrsfrtgriwilittellgrgidfRTVRLVVNYDFPSSAISYIHRIGragrggregkavtfftkqdapllr
Low Complexity Region (SEG)
MAVDFNHTNPALKRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHrigragrggregKAVTFFTKQDAPLLR
Disordered region (IsUnstruct)
**************************************ETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF*********
Disordered Region (DISOPRED)
MAVDFNHTNPALKRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL*
Disordered Region (DISEMBL)
MAVDFNHTNPALKRRVKSNLARMYRE*********AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR
Disordered Region (DISPRO)
*AVDFNHTNPALKRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVDFNHTNPALKRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR
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	159	2.2.26 [Sep-21-2011]
A5D7C1	596	Probable ATP-dependent RN	yes	N/A	0.779	0.208	0.693	4e-48
Q9Y2R4	599	Probable ATP-dependent RN	yes	N/A	0.779	0.207	0.677	1e-47
Q8K301	598	Probable ATP-dependent RN	yes	N/A	0.779	0.207	0.685	2e-47
Q99PT0	598	Probable ATP-dependent RN	yes	N/A	0.779	0.207	0.685	2e-47
Q86IZ9	668	Probable ATP-dependent RN	yes	N/A	0.773	0.184	0.601	5e-41
A5DIX5	537	ATP-dependent RNA helicas	N/A	N/A	0.685	0.202	0.587	3e-38
Q5K5B6	540	DEAD-box ATP-dependent RN	yes	N/A	0.723	0.212	0.582	3e-38
A3GHW9	558	ATP-dependent RNA helicas	yes	N/A	0.685	0.195	0.577	4e-38
Q6BP45	550	ATP-dependent RNA helicas	yes	N/A	0.685	0.198	0.605	6e-38
Q9Y7C4	578	ATP-dependent RNA helicas	N/A	N/A	0.685	0.188	0.605	1e-37

>sp|A5D7C1|DDX52_BOVIN Probable ATP-dependent RNA helicase DDX52 OS=Bos taurus GN=DDX52 PE=2 SV=1

 Score =  190 bits (482), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 86/124 (69%), Positives = 102/124 (82%)

Query: 36  AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
           A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH+DRTQ+QRDN V SFR G
Sbjct: 400 AMRELVKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAG 459

Query: 96  RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIHRIGR GR G +GKAVTFFT+ D 
Sbjct: 460 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGHKGKAVTFFTEDDK 519

Query: 156 PLLR 159
           PLLR
Sbjct: 520 PLLR 523

Bos taurus (taxid: 9913)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q9Y2R4|DDX52_HUMAN Probable ATP-dependent RNA helicase DDX52 OS=Homo sapiens GN=DDX52 PE=1 SV=3

 Score =  188 bits (477), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 84/124 (67%), Positives = 102/124 (82%)

Query: 36  AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
           A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH++RTQ+QRDN V SFR G
Sbjct: 402 AMRELVKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHAERTQQQRDNTVHSFRAG 461

Query: 96  RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIHRIGR GR G +GKA+TFFT+ D 
Sbjct: 462 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGNKGKAITFFTEDDK 521

Query: 156 PLLR 159
           PLLR
Sbjct: 522 PLLR 525

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8K301|DDX52_MOUSE Probable ATP-dependent RNA helicase DDX52 OS=Mus musculus GN=Ddx52 PE=2 SV=2

 Score =  188 bits (477), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 85/124 (68%), Positives = 102/124 (82%)

Query: 36  AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
           A  E +  G +PPVLVFVQS ERA+EL++ELIY+GINVDVIH++RTQ+QRDN V SFR G
Sbjct: 403 AMRELVKKGFKPPVLVFVQSIERAKELFHELIYEGINVDVIHAERTQQQRDNTVHSFRAG 462

Query: 96  RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIHRIGR GR G  GKAVTFFT+ D 
Sbjct: 463 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGNRGKAVTFFTEDDK 522

Query: 156 PLLR 159
           PLLR
Sbjct: 523 PLLR 526

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q99PT0|DDX52_RAT Probable ATP-dependent RNA helicase DDX52 OS=Rattus norvegicus GN=Ddx52 PE=2 SV=1

 Score =  187 bits (476), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 85/124 (68%), Positives = 101/124 (81%)

Query: 36  AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
           A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH++RTQ+QRDN V SFR G
Sbjct: 403 AMRELVKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHAERTQQQRDNTVHSFRAG 462

Query: 96  RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIHRIGR GR G  GKAVTFFT+ D 
Sbjct: 463 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGNRGKAVTFFTEDDK 522

Query: 156 PLLR 159
           PLLR
Sbjct: 523 PLLR 526

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q86IZ9|DDX52_DICDI Probable ATP-dependent RNA helicase ddx52 OS=Dictyostelium discoideum GN=ddx52 PE=3 SV=1

 Score =  166 bits (420), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 74/123 (60%), Positives = 94/123 (76%)

Query: 36  AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
           A  + I  G+EPP+L+F QSKERA +L+ ELI+DGINVDVIHS+RTQ QRD +V+ FR G
Sbjct: 430 AVRQLIQKGLEPPILIFTQSKERAHDLFQELIFDGINVDVIHSERTQFQRDTIVKKFRMG 489

Query: 96  RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           +IW+LI TEL+ RG+DF+ V  V+N+DFP +  SYIHRIGR GR GR G A T +T  D 
Sbjct: 490 KIWVLICTELMARGMDFKGVNFVINFDFPHTLASYIHRIGRTGRAGRPGVAYTLYTDADT 549

Query: 156 PLL 158
           P+L
Sbjct: 550 PML 552

ATP-binding RNA helicase which may be involved in the ribosome biogenesis.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DIX5|ROK1_PICGU ATP-dependent RNA helicase ROK1 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=ROK1 PE=3 SV=2

 Score =  157 bits (397), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 64/109 (58%), Positives = 91/109 (83%)

Query: 46  EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
           +PP+++F+QS  RA+ L++ELIYD +NV+VIH++RT KQR+  +R F+ G  W+LITT++
Sbjct: 352 KPPIIIFLQSIPRAKALFHELIYDKLNVEVIHAERTPKQREEAIRRFKNGDAWVLITTDV 411

Query: 106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
           L RG+DF+ V LV+NYD P ++ +Y+HRIGR GRGG+EGKAVTFFTK+D
Sbjct: 412 LARGVDFKGVNLVINYDVPQTSQAYVHRIGRTGRGGKEGKAVTFFTKED 460

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5K5B6|RH57_ORYSJ DEAD-box ATP-dependent RNA helicase 57 OS=Oryza sativa subsp. japonica GN=Os07g0647900 PE=2 SV=2

 Score =  157 bits (396), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 67/115 (58%), Positives = 90/115 (78%)

Query: 45  IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE 104
           + PPVL+FVQSKERA+ELY EL +D +  DVIH+D  ++QR + V + R G+ W+LI TE
Sbjct: 384 LNPPVLIFVQSKERAKELYKELAFDDVRADVIHADLDEEQRQDAVDNLRAGKTWVLIATE 443

Query: 105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           ++ RG+DF+ V  V+NYDFP SA +YIHRIGR+GR GR G+A+TFFT++D P LR
Sbjct: 444 VIARGMDFKGVNCVINYDFPESASAYIHRIGRSGRAGRSGEAITFFTEEDKPFLR 498

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A3GHW9|ROK1_PICST ATP-dependent RNA helicase ROK1 OS=Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) GN=ROK1 PE=3 SV=1

 Score =  157 bits (396), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 63/109 (57%), Positives = 92/109 (84%)

Query: 46  EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
           +PP+++F+QS  RA+ L++EL+YD +NVDVIH++RT KQR+ V++ F+ G IW+LITT++
Sbjct: 368 KPPIIIFLQSIHRAKALFHELLYDKLNVDVIHAERTPKQREEVIKRFKNGDIWVLITTDV 427

Query: 106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
           L RG+DF+ V +V+NYD P +A +Y+HRIGR GRGG+ G+AVTFFTK+D
Sbjct: 428 LARGVDFKGVNMVINYDVPQTAQAYVHRIGRTGRGGKAGRAVTFFTKED 476

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6BP45|ROK1_DEBHA ATP-dependent RNA helicase ROK1 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=ROK1 PE=3 SV=2

 Score =  156 bits (394), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 66/109 (60%), Positives = 93/109 (85%)

Query: 46  EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
           +PP+++F+QS  RA+ L++EL+YD +NVDVIH++RT KQRD V++ F++G IW+LITT++
Sbjct: 361 KPPIIIFLQSITRAKALFHELLYDRLNVDVIHAERTPKQRDEVIKRFKSGDIWVLITTDV 420

Query: 106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
           + RG+DF+ V LV+NYD P SA +Y+HRIGR GRGG+ GKAVTFFTK+D
Sbjct: 421 IARGVDFKGVNLVINYDVPQSAQAYVHRIGRTGRGGKAGKAVTFFTKED 469

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9Y7C4|ROK1_CANAL ATP-dependent RNA helicase CHR1 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=CHR1 PE=3 SV=1

 Score =  155 bits (391), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 66/109 (60%), Positives = 92/109 (84%)

Query: 46  EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
           +PP+++F+QS  RA+ L++EL+YD +NVDVIH++RT KQR+ V++ F+ G IW+LITT++
Sbjct: 378 KPPIIIFLQSITRAKALFHELLYDRLNVDVIHAERTPKQREEVIKRFKNGDIWVLITTDV 437

Query: 106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
           L RG+DF+ V LV+NYD P SA +Y+HRIGR GRGG+ GKAVTFFTK+D
Sbjct: 438 LARGVDFKGVNLVINYDVPQSAQAYVHRIGRTGRGGKAGKAVTFFTKED 486

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

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	159
193632062	528	PREDICTED: probable ATP-dependent RNA he	0.729	0.219	0.758	1e-49
328789292	512	PREDICTED: probable ATP-dependent RNA he	0.729	0.226	0.784	2e-49
332020434	558	Putative ATP-dependent RNA helicase DDX5	0.729	0.207	0.784	3e-49
332374956	588	unknown [Dendroctonus ponderosae]	0.729	0.197	0.767	3e-49
242005744	1130	predicted protein [Pediculus humanus cor	0.698	0.098	0.783	4e-49
291242221	681	PREDICTED: probable ATP-dependent RNA he	0.729	0.170	0.784	6e-49
380019489	512	PREDICTED: probable ATP-dependent RNA he	0.729	0.226	0.775	9e-49
383855221	589	PREDICTED: probable ATP-dependent RNA he	0.811	0.219	0.713	1e-48
321466548	581	hypothetical protein DAPPUDRAFT_321368 [	0.811	0.222	0.705	1e-48
340715568	582	PREDICTED: probable ATP-dependent RNA he	0.729	0.199	0.758	2e-48

>gi|193632062|ref|XP_001950933.1| PREDICTED: probable ATP-dependent RNA helicase DDX52-like [Acyrthosiphon pisum]

 Score =  201 bits (510), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 88/116 (75%), Positives = 103/116 (88%)

Query: 44  GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
           G+ PPVL+F+QSKERA+EL++ELIYDGINVD IH+DRTQ+QRDN V++FR G+IW+LI T
Sbjct: 298 GLSPPVLIFLQSKERAKELFSELIYDGINVDAIHADRTQQQRDNTVKAFREGKIWVLICT 357

Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           EL+GRGIDF+ V LVVNYDFPSSAISYIHRIGR GR GR GKAVTFFT  D P+LR
Sbjct: 358 ELMGRGIDFKGVNLVVNYDFPSSAISYIHRIGRTGRAGRSGKAVTFFTNDDKPMLR 413

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328789292|ref|XP_001120427.2| PREDICTED: probable ATP-dependent RNA helicase DDX52-like, partial [Apis mellifera]

 Score =  200 bits (508), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 91/116 (78%), Positives = 102/116 (87%)

Query: 44  GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
           GI PPVLVFVQSKERAQEL+NELIYDGINVDVIH+DRTQ QRDNVVR FR G+IW+LI T
Sbjct: 322 GILPPVLVFVQSKERAQELFNELIYDGINVDVIHADRTQTQRDNVVRCFREGKIWVLICT 381

Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           EL+ RGIDF+ + LV+NYDFPSSAISYIHRIGR GR G +GKA+TFFT+QD   LR
Sbjct: 382 ELMARGIDFKGINLVINYDFPSSAISYIHRIGRTGRAGHKGKAITFFTEQDTTNLR 437

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332020434|gb|EGI60854.1| Putative ATP-dependent RNA helicase DDX52 [Acromyrmex echinatior]

 Score =  199 bits (506), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 91/116 (78%), Positives = 100/116 (86%)

Query: 44  GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
           GI PPVLVFVQSKERAQEL+NELIYDGINVDVIH+DRT  QRDN VR FR G+IW+LI T
Sbjct: 377 GISPPVLVFVQSKERAQELFNELIYDGINVDVIHADRTMTQRDNTVRCFREGKIWVLICT 436

Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           EL+GRGIDF+ V LV+NYDFP SAISYIHRIGR GR G +GKAVTFFT+QD   LR
Sbjct: 437 ELMGRGIDFKGVNLVINYDFPPSAISYIHRIGRTGRAGHKGKAVTFFTQQDTVNLR 492

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332374956|gb|AEE62619.1| unknown [Dendroctonus ponderosae]

 Score =  199 bits (506), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 89/116 (76%), Positives = 100/116 (86%)

Query: 44  GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
           GI PPVL+FVQSKERAQ+L+NELIYDGI VD IH+DRTQ QRDNVV+ FR G+IW+LI T
Sbjct: 363 GISPPVLIFVQSKERAQQLFNELIYDGIMVDAIHADRTQTQRDNVVKCFREGKIWVLICT 422

Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           EL+ RGIDF+ V LVVNYDFP S ISY+HRIGRAGR GR GKAVTFFT+ D PLLR
Sbjct: 423 ELMARGIDFKGVNLVVNYDFPPSTISYVHRIGRAGRAGRTGKAVTFFTQDDTPLLR 478

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242005744|ref|XP_002423722.1| predicted protein [Pediculus humanus corporis] gi|212506907|gb|EEB10984.1| predicted protein [Pediculus humanus corporis]

 Score =  199 bits (505), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 87/111 (78%), Positives = 101/111 (90%)

Query: 44   GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
            G+ PPVLVFVQSKERAQEL+NEL+YDGINVDVIHSDRTQKQRDNV+RSFR G+IW+LI T
Sbjct: 996  GLTPPVLVFVQSKERAQELFNELVYDGINVDVIHSDRTQKQRDNVIRSFREGKIWVLICT 1055

Query: 104  ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
            EL+GRGIDF+ V LVVNYDFP S++SYIHRIGR GR GR G+A+T+FT+ D
Sbjct: 1056 ELMGRGIDFKGVNLVVNYDFPPSSVSYIHRIGRTGRAGRPGRAITYFTQDD 1106

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291242221|ref|XP_002741008.1| PREDICTED: probable ATP-dependent RNA helicase DDX52-like [Saccoglossus kowalevskii]

 Score =  198 bits (504), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 91/116 (78%), Positives = 102/116 (87%)

Query: 44  GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
           G++PP+LVFVQSKERA+EL+ ELIYDGINVDVIH+DRTQ QRDNVVRSFR G+IWILI T
Sbjct: 414 GVQPPMLVFVQSKERAKELFLELIYDGINVDVIHADRTQTQRDNVVRSFRAGKIWILICT 473

Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           EL+GRGIDF+ V LVVNYDFPSSA+SYIHRIGR GR GR G+AVTFFT  D   LR
Sbjct: 474 ELMGRGIDFKGVNLVVNYDFPSSAVSYIHRIGRTGRAGRAGRAVTFFTHDDVTNLR 529

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|380019489|ref|XP_003693637.1| PREDICTED: probable ATP-dependent RNA helicase DDX52-like, partial [Apis florea]

 Score =  197 bits (502), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 90/116 (77%), Positives = 101/116 (87%)

Query: 44  GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
           GI PPVLVFVQSKERAQEL+NELIYDGINVDVIH+DRTQ QRDNVVR FR G+IW+LI T
Sbjct: 325 GILPPVLVFVQSKERAQELFNELIYDGINVDVIHADRTQTQRDNVVRCFREGKIWVLICT 384

Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           EL+ RGIDF+ + LV+NYDFP SAISYIHRIGR GR G +GKA+TFFT+QD   LR
Sbjct: 385 ELMARGIDFKGINLVINYDFPLSAISYIHRIGRTGRAGHKGKAITFFTEQDTTNLR 440

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383855221|ref|XP_003703115.1| PREDICTED: probable ATP-dependent RNA helicase DDX52-like [Megachile rotundata]

 Score =  197 bits (501), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 92/129 (71%), Positives = 104/129 (80%)

Query: 31  GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVR 90
           G  + A    I  G+ PPVLVFVQSKERAQEL+NELIYDGINVDVIH+DRTQ QRDNVVR
Sbjct: 370 GGKLVALRNIIQKGVLPPVLVFVQSKERAQELFNELIYDGINVDVIHADRTQTQRDNVVR 429

Query: 91  SFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF 150
            FR G+IW+LI TEL+ RGIDF+ V LV+NYDFP S ISY+HRIGR GR G +GKA+TFF
Sbjct: 430 CFREGKIWVLICTELMARGIDFKGVNLVINYDFPPSVISYVHRIGRTGRAGHKGKAITFF 489

Query: 151 TKQDAPLLR 159
           TKQD   LR
Sbjct: 490 TKQDTVNLR 498

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321466548|gb|EFX77543.1| hypothetical protein DAPPUDRAFT_321368 [Daphnia pulex]

 Score =  197 bits (500), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 91/129 (70%), Positives = 108/129 (83%)

Query: 31  GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVR 90
           G  + A    I+ G+ PPVLVFVQ+KERA+ELY EL+YDGINVDVIH++R+Q QRDNVV+
Sbjct: 368 GGKLMAFRNLIVEGLNPPVLVFVQTKERAKELYTELVYDGINVDVIHAERSQLQRDNVVK 427

Query: 91  SFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF 150
           SFR+G+IW+LI TEL+GRGIDF+ V LVVNYDFP SAISYIHRIGR GR GR GKA+TFF
Sbjct: 428 SFRSGQIWVLICTELMGRGIDFKGVNLVVNYDFPPSAISYIHRIGRTGRAGRPGKAITFF 487

Query: 151 TKQDAPLLR 159
           T+ DA  LR
Sbjct: 488 TESDAVYLR 496

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340715568|ref|XP_003396283.1| PREDICTED: probable ATP-dependent RNA helicase DDX52-like [Bombus terrestris]

 Score =  196 bits (499), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 88/116 (75%), Positives = 100/116 (86%)

Query: 44  GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
           G+ PPVLVFVQSKERAQEL+NELIYDG+NVDVIH+DRTQ QRDNVVR FR G+IW+LI T
Sbjct: 379 GVLPPVLVFVQSKERAQELFNELIYDGVNVDVIHADRTQTQRDNVVRCFREGKIWVLICT 438

Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           EL+ RGIDF+ V LV+NYDFP SAISY+HRIGR GR G +GKA+TFFT QD   LR
Sbjct: 439 ELMARGIDFKGVNLVINYDFPPSAISYVHRIGRTGRAGHKGKAITFFTVQDTTNLR 494

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

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	159
UNIPROTKB|I3LJA0	507	DDX52 "Uncharacterized protein	0.779	0.244	0.629	5.5e-38
UNIPROTKB|A5D7C1	596	DDX52 "Probable ATP-dependent	0.779	0.208	0.629	7.2e-38
UNIPROTKB|J9P4L6	598	DDX52 "Uncharacterized protein	0.779	0.207	0.629	7.6e-38
UNIPROTKB|E2RB54	601	DDX52 "Uncharacterized protein	0.779	0.206	0.629	8.1e-38
ZFIN|ZDB-GENE-060623-1	606	ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.792	0.207	0.619	8.9e-38
MGI|MGI:1925644	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.779	0.207	0.620	1.7e-37
UNIPROTKB|A8MTP9	491	DDX52 "Probable ATP-dependent	0.779	0.252	0.612	1.9e-37
RGD|621743	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.779	0.207	0.620	2.2e-37
UNIPROTKB|F1NQA6	603	DDX52 "Uncharacterized protein	0.779	0.205	0.620	2.4e-37
UNIPROTKB|E1C4M1	604	DDX52 "Uncharacterized protein	0.779	0.205	0.620	2.5e-37

UNIPROTKB|I3LJA0 DDX52 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 78/124 (62%), Positives = 93/124 (75%)

Query:    36 AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
             A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH+DRTQ+QRDN V SFR G
Sbjct:   310 AMRELVKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAG 369

Query:    96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDA 155
             +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIH            KAVTFFT+ D 
Sbjct:   370 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGHKGKAVTFFTEDDK 429

Query:   156 PLLR 159
             PLLR
Sbjct:   430 PLLR 433

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|A5D7C1 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Bos taurus (taxid:9913)]

 Score = 407 (148.3 bits), Expect = 7.2e-38, P = 7.2e-38
 Identities = 78/124 (62%), Positives = 93/124 (75%)

Query:    36 AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
             A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH+DRTQ+QRDN V SFR G
Sbjct:   400 AMRELVKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAG 459

Query:    96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDA 155
             +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIH            KAVTFFT+ D 
Sbjct:   460 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGHKGKAVTFFTEDDK 519

Query:   156 PLLR 159
             PLLR
Sbjct:   520 PLLR 523

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|J9P4L6 DDX52 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 407 (148.3 bits), Expect = 7.6e-38, P = 7.6e-38
 Identities = 78/124 (62%), Positives = 93/124 (75%)

Query:    36 AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
             A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH+DRTQ+QRDN V SFR G
Sbjct:   401 AMRELVKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAG 460

Query:    96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDA 155
             +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIH            KAVTFFT+ D 
Sbjct:   461 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGHKGKAVTFFTEDDK 520

Query:   156 PLLR 159
             PLLR
Sbjct:   521 PLLR 524

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E2RB54 DDX52 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 407 (148.3 bits), Expect = 8.1e-38, P = 8.1e-38
 Identities = 78/124 (62%), Positives = 93/124 (75%)

Query:    36 AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
             A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH+DRTQ+QRDN V SFR G
Sbjct:   404 AMRELVKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAG 463

Query:    96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDA 155
             +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIH            KAVTFFT+ D 
Sbjct:   464 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGHKGKAVTFFTEDDK 523

Query:   156 PLLR 159
             PLLR
Sbjct:   524 PLLR 527

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-060623-1 ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Danio rerio (taxid:7955)]

 Score = 407 (148.3 bits), Expect = 8.9e-38, P = 8.9e-38
 Identities = 78/126 (61%), Positives = 95/126 (75%)

Query:    34 VQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFR 93
             + A    I  G  PPVLVFVQS +RA+ELY+EL+Y+GINVDVIH+DRTQ+QRDNVV SFR
Sbjct:   402 ILAMRNLIKQGFLPPVLVFVQSIDRARELYHELVYEGINVDVIHADRTQQQRDNVVSSFR 461

Query:    94 TGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQ 153
             +G+IW+LI T LL RGIDF+ + LV+NYDFP+SA+ YIH            KAVTFFT+ 
Sbjct:   462 SGKIWVLICTALLARGIDFKGINLVINYDFPTSAVEYIHRIGRTGRAGHKGKAVTFFTED 521

Query:   154 DAPLLR 159
             D PLLR
Sbjct:   522 DKPLLR 527

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

MGI|MGI:1925644 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Mus musculus (taxid:10090)]

 Score = 404 (147.3 bits), Expect = 1.7e-37, P = 1.7e-37
 Identities = 77/124 (62%), Positives = 94/124 (75%)

Query:    36 AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
             A  E +  G +PPVLVFVQS ERA+EL++ELIY+GINVDVIH++RTQ+QRDN V SFR G
Sbjct:   403 AMRELVKKGFKPPVLVFVQSIERAKELFHELIYEGINVDVIHAERTQQQRDNTVHSFRAG 462

Query:    96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDA 155
             +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIH            KAVTFFT+ D 
Sbjct:   463 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGNRGKAVTFFTEDDK 522

Query:   156 PLLR 159
             PLLR
Sbjct:   523 PLLR 526

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|A8MTP9 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Homo sapiens (taxid:9606)]

 Score = 402 (146.6 bits), Expect = 1.9e-37, P = 1.9e-37
 Identities = 76/124 (61%), Positives = 93/124 (75%)

Query:    36 AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
             A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH++RTQ+QRDN V SFR G
Sbjct:   294 AMRELVKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHAERTQQQRDNTVHSFRAG 353

Query:    96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDA 155
             +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIH            KA+TFFT+ D 
Sbjct:   354 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGNKGKAITFFTEDDK 413

Query:   156 PLLR 159
             PLLR
Sbjct:   414 PLLR 417

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

RGD|621743 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Rattus norvegicus (taxid:10116)]

 Score = 403 (146.9 bits), Expect = 2.2e-37, P = 2.2e-37
 Identities = 77/124 (62%), Positives = 93/124 (75%)

Query:    36 AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
             A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH++RTQ+QRDN V SFR G
Sbjct:   403 AMRELVKKGFNPPVLVFVQSIERAKELFHELIYEGINVDVIHAERTQQQRDNTVHSFRAG 462

Query:    96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDA 155
             +IW+LI T LL RGIDF+ V LV+NYDFP+S++ YIH            KAVTFFT+ D 
Sbjct:   463 KIWVLICTALLARGIDFKGVNLVINYDFPTSSVEYIHRIGRTGRAGNRGKAVTFFTEDDK 522

Query:   156 PLLR 159
             PLLR
Sbjct:   523 PLLR 526

GO:0003723 "RNA binding" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=NAS

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005730 "nucleolus" evidence=IEA

GO:0006364 "rRNA processing" evidence=TAS

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

UNIPROTKB|F1NQA6 DDX52 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 403 (146.9 bits), Expect = 2.4e-37, P = 2.4e-37
 Identities = 77/124 (62%), Positives = 93/124 (75%)

Query:    36 AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
             A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH+D+TQ+QRDNVV SFR G
Sbjct:   396 AMRELVKKGFAPPVLVFVQSIERAKELFHELIYEGINVDVIHADKTQQQRDNVVHSFRAG 455

Query:    96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDA 155
             +IW+LI T LL RGIDF+ V +V+NYD P+SA+ YIH            KAVTFFT+ D 
Sbjct:   456 KIWVLICTALLARGIDFKGVNMVINYDLPTSAVEYIHRIGRTGRAGHTGKAVTFFTEDDK 515

Query:   156 PLLR 159
             PLLR
Sbjct:   516 PLLR 519

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|E1C4M1 DDX52 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 403 (146.9 bits), Expect = 2.5e-37, P = 2.5e-37
 Identities = 77/124 (62%), Positives = 93/124 (75%)

Query:    36 AQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG 95
             A  E +  G  PPVLVFVQS ERA+EL++ELIY+GINVDVIH+D+TQ+QRDNVV SFR G
Sbjct:   397 AMRELVKKGFAPPVLVFVQSIERAKELFHELIYEGINVDVIHADKTQQQRDNVVHSFRAG 456

Query:    96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDA 155
             +IW+LI T LL RGIDF+ V +V+NYD P+SA+ YIH            KAVTFFT+ D 
Sbjct:   457 KIWVLICTALLARGIDFKGVNMVINYDLPTSAVEYIHRIGRTGRAGHTGKAVTFFTEDDK 516

Query:   156 PLLR 159
             PLLR
Sbjct:   517 PLLR 520

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6BP45	ROK1_DEBHA	3, ., 6, ., 4, ., 1, 3	0.6055	0.6855	0.1981	yes	N/A
P0CR04	ROK1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.5535	0.7044	0.1806	yes	N/A
A5D7C1	DDX52_BOVIN	3, ., 6, ., 4, ., 1, 3	0.6935	0.7798	0.2080	yes	N/A
Q5K5B6	RH57_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.5826	0.7232	0.2129	yes	N/A
Q6FN65	ROK1_CANGA	3, ., 6, ., 4, ., 1, 3	0.5727	0.6918	0.1946	yes	N/A
Q6CDS6	ROK1_YARLI	3, ., 6, ., 4, ., 1, 3	0.6111	0.6792	0.1974	yes	N/A
Q9Y2R4	DDX52_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6774	0.7798	0.2070	yes	N/A
Q8K301	DDX52_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6854	0.7798	0.2073	yes	N/A
A3GHW9	ROK1_PICST	3, ., 6, ., 4, ., 1, 3	0.5779	0.6855	0.1953	yes	N/A
Q86IZ9	DDX52_DICDI	3, ., 6, ., 4, ., 1, 3	0.6016	0.7735	0.1841	yes	N/A
Q75AE1	ROK1_ASHGO	3, ., 6, ., 4, ., 1, 3	0.5963	0.6855	0.1915	yes	N/A
Q99PT0	DDX52_RAT	3, ., 6, ., 4, ., 1, 3	0.6854	0.7798	0.2073	yes	N/A
Q6CSW1	ROK1_KLULA	3, ., 6, ., 4, ., 1, 3	0.5818	0.6918	0.1899	yes	N/A
Q84TG1	RH57_ARATH	3, ., 6, ., 4, ., 1, 3	0.5739	0.7232	0.2125	yes	N/A
P45818	ROK1_YEAST	3, ., 6, ., 4, ., 1, 3	0.5909	0.6918	0.1950	yes	N/A
Q09775	ROK1_SCHPO	3, ., 6, ., 4, ., 1, 3	0.5391	0.7232	0.2390	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	0.691

---

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	159
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	8e-39
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	2e-36
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	6e-28
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	3e-27
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	4e-27
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-26
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-24
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	4e-22
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	9e-22
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	1e-20
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-20
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	1e-19
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-16
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-15
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	5e-15
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	6e-15
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	3e-12
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	1e-11
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	6e-11
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	9e-10
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	3e-09
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	4e-09
TIGR00631	655	TIGR00631, uvrb, excinuclease ABC, B subunit	2e-07
COG4098	441	COG4098, comFA, Superfamily II DNA/RNA helicase re	4e-07
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	9e-07
COG1205	851	COG1205, COG1205, Distinct helicase family with a	3e-06
TIGR00595	505	TIGR00595, priA, primosomal protein N'	8e-06
TIGR01587	358	TIGR01587, cas3_core, CRISPR-associated helicase C	3e-05
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	4e-05
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	5e-05
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	6e-05
PRK01172	674	PRK01172, PRK01172, ski2-like helicase; Provisiona	1e-04
cd09639	353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	1e-04
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	2e-04
PRK05580	679	PRK05580, PRK05580, primosome assembly protein Pri	4e-04
COG1200	677	COG1200, RecG, RecG-like helicase [DNA replication	4e-04
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	7e-04
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	7e-04
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	9e-04
PRK09401	1176	PRK09401, PRK09401, reverse gyrase; Reviewed	0.003

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

 Score =  137 bits (346), Expect = 8e-39
 Identities = 46/121 (38%), Positives = 70/121 (57%), Gaps = 3/121 (2%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           LL  E    V+VFV++K   +EL   L   G  V  +H D  Q++RD  +  F+ G + +
Sbjct: 267 LLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRV 326

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ-DAPLL 158
           L+ T++  RG+D   V  V+NYD P     Y+HRIGR GR GR+G A++F T++ +   L
Sbjct: 327 LVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKL 386

Query: 159 R 159
           +
Sbjct: 387 K 387

Length = 513

>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 =  121 bits (307), Expect = 2e-36
 Identities = 45/102 (44%), Positives = 65/102 (63%)

Query: 48  PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
            VL+F  SK+   EL   L   GI V  +H D +Q++R+ V++ FR G I +L+ T+++ 
Sbjct: 30  KVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIA 89

Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF 149
           RGID   V +V+NYD P S  SY+ RIGRAGR G++G A+  
Sbjct: 90  RGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131

Length = 131

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

 Score =  106 bits (266), Expect = 6e-28
 Identities = 47/110 (42%), Positives = 69/110 (62%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           +++  ++ +   L  ++      V  +H D  QK RD ++R FR+G   +LITT+LL RG
Sbjct: 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG 330

Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           ID + V LV+NYD P+S  +YIHRIGR+GR GR+G A+ F T  D   L+
Sbjct: 331 IDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLK 380

Length = 401

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

 Score = 96.8 bits (242), Expect = 3e-27
 Identities = 35/77 (45%), Positives = 49/77 (63%)

Query: 65  ELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFP 124
            L   GI V  +H   +Q++R+ ++  FR G+  +L+ T++ GRGID   V LV+NYD P
Sbjct: 2   LLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLP 61

Query: 125 SSAISYIHRIGRAGRGG 141
            +  SYI RIGRAGR G
Sbjct: 62  WNPASYIQRIGRAGRAG 78

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

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

 Score = 96.9 bits (242), Expect = 4e-27
 Identities = 35/82 (42%), Positives = 50/82 (60%)

Query: 60  QELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV 119
           +EL   L   GI V  +H   +Q++R+ ++  F  G+I +L+ T++  RG+D   V LV+
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 120 NYDFPSSAISYIHRIGRAGRGG 141
            YD P S  SYI RIGRAGR G
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score =  103 bits (259), Expect = 2e-26
 Identities = 44/105 (41%), Positives = 67/105 (63%)

Query: 47  PPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELL 106
             +L+FV++K+ A  L  EL  DG     IH D+ Q++R  V+  F+TG+  I+I T++ 
Sbjct: 378 DKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVA 437

Query: 107 GRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT 151
            RG+D + V+ V+N+DFP+    Y+HRIGR GR G +G + TF T
Sbjct: 438 SRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLT 482

Length = 545

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

 Score = 96.9 bits (242), Expect = 2e-24
 Identities = 43/108 (39%), Positives = 64/108 (59%)

Query: 51  VFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI 110
           VFV+++ER  EL   L   GIN   +  +  Q +R+  ++    GR+ +L+ T++  RGI
Sbjct: 250 VFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGI 309

Query: 111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL 158
           D   V  V+N+D P SA +Y+HRIGR GR GR+G A++     D  LL
Sbjct: 310 DIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLL 357

Length = 434

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

 Score = 91.4 bits (227), Expect = 4e-22
 Identities = 43/112 (38%), Positives = 69/112 (61%), Gaps = 1/112 (0%)

Query: 47  PPVLVFVQSKERAQELYNEL-IYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
           PP +VFV S+  A  L N + +  G+    IH +++ K+R  V++SF  G + +++ T +
Sbjct: 368 PPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGV 427

Query: 106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL 157
           LGRG+D   VR V+ +D P++   YIH+IGRA R G +G A+ F  ++D  L
Sbjct: 428 LGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNL 479

Length = 518

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

 Score = 89.9 bits (224), Expect = 9e-22
 Identities = 35/116 (30%), Positives = 60/116 (51%), Gaps = 2/116 (1%)

Query: 42  LLGIEPPV--LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           LL    P   +VF  +K+  QE+ + L   G +   +H D  Q+ RD V+  F      +
Sbjct: 236 LLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSV 295

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           L+ T++  RG+D + +  V+NY+       ++HRIGR GR G +G A++    ++ 
Sbjct: 296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEM 351

Length = 460

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

 Score = 86.9 bits (215), Expect = 1e-20
 Identities = 38/107 (35%), Positives = 59/107 (55%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           V+VF   K+  + +   L+ DGIN   +  D  Q +R   +  FR G+I +L+ T++ GR
Sbjct: 338 VMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGR 397

Query: 109 GIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           GI    +  V+N+  P     Y+HRIGR GR G  G +++F  + DA
Sbjct: 398 GIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDA 444

Length = 475

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

 Score = 86.1 bits (213), Expect = 2e-20
 Identities = 43/110 (39%), Positives = 65/110 (59%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++FV++K    E+   L  +G N   ++ D  Q  R+  +   + GR+ ILI T++  RG
Sbjct: 249 IIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARG 308

Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           +D   + LVVNYD P  + SY+HRIGR GR GR G+A+ F   ++  LLR
Sbjct: 309 LDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLR 358

Length = 629

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

 Score = 83.7 bits (207), Expect = 1e-19
 Identities = 41/111 (36%), Positives = 63/111 (56%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           VLVF ++K  A  L  +L  DGI    IH +++Q  R   +  F++G I +L+ T++  R
Sbjct: 248 VLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAAR 307

Query: 109 GIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           G+D   +  VVNY+ P+    Y+HRIGR GR    G+A++     +  LLR
Sbjct: 308 GLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLR 358

Length = 456

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

 Score = 75.4 bits (185), Expect = 1e-16
 Identities = 43/122 (35%), Positives = 68/122 (55%), Gaps = 5/122 (4%)

Query: 33  PVQAQDETILLGI-----EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDN 87
           P   + +T+LLG+         +VFV +K   + +   L   G  V V+  D  QK+R++
Sbjct: 239 PADEEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRES 298

Query: 88  VVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAV 147
           ++  F+ G++ IL+ T++  RG+    V+ V NYD P  A  Y+HRIGR  R G EG A+
Sbjct: 299 LLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAI 358

Query: 148 TF 149
           +F
Sbjct: 359 SF 360

Length = 572

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

 Score = 72.3 bits (178), Expect = 1e-15
 Identities = 35/100 (35%), Positives = 55/100 (55%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  +K R +E++  L  DG  V ++  D  QK+R  ++  F  G + IL+ T++  RG
Sbjct: 259 IIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARG 318

Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF 149
           +    V  V NYD P     Y+HRIGR GR G  G +++ 
Sbjct: 319 LHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358

Length = 423

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

 Score = 70.8 bits (174), Expect = 5e-15
 Identities = 36/116 (31%), Positives = 57/116 (49%), Gaps = 10/116 (8%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVI---HSDR------TQKQRDNVVRSFRTGRIWI 99
           V+VF + ++ A+E+ N L   GI   V     + R      +QK++  ++  FR G   +
Sbjct: 369 VIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNV 428

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           L+ T +   G+D   V LV+ Y+   S I  I R GR GR  R+G+ V   T+   
Sbjct: 429 LVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR-KRKGRVVVLVTEGTR 483

Length = 542

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

 Score = 70.4 bits (173), Expect = 6e-15
 Identities = 33/112 (29%), Positives = 60/112 (53%)

Query: 48  PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
             +++  ++++ +EL   L  +GI+    H+  + ++R+ V ++F    I +++ T   G
Sbjct: 232 SGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFG 291

Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
            GID   VR V++YD P S  SY    GRAGR G   +A+  ++ +D    R
Sbjct: 292 MGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQR 343

Length = 590

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

 Score = 62.8 bits (153), Expect = 3e-12
 Identities = 33/110 (30%), Positives = 55/110 (50%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           +++  S+++ +EL   L   GI+    H+  + K R      F    + +++ T   G G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287

Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           ID   VR V++YD P +  SY    GRAGR G   +A+  ++  D  LL+
Sbjct: 288 IDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLK 337

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

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

 Score = 61.4 bits (150), Expect = 1e-11
 Identities = 36/120 (30%), Positives = 61/120 (50%), Gaps = 11/120 (9%)

Query: 43  LGIEPP--VLVFVQSKERAQELYNELIYDGINVD--VIHSDR------TQKQRDNVVRSF 92
           LG  P   ++VF Q ++ A+++ + L  +GI     V  + +      +QK++  ++  F
Sbjct: 360 LGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKF 419

Query: 93  RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK 152
           R G   +L++T +   G+D  +V LV+ Y+   S I  I R GR GR   EG+ V    K
Sbjct: 420 RAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGR-QEEGRVVVLIAK 478

Length = 773

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

 Score = 59.0 bits (143), Expect = 6e-11
 Identities = 32/110 (29%), Positives = 53/110 (48%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           +++  S+++++++   L   GI     H+      RD+V   F+   I +++ T   G G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289

Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           I+   VR V++Y  P S  SY    GRAGR G   +   F+   D   LR
Sbjct: 290 INKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLR 339

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

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

 Score = 55.5 bits (134), Expect = 9e-10
 Identities = 32/110 (29%), Positives = 54/110 (49%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           +++  S+ + ++    L   GI+    H+      R +V  +F+   + I++ T   G G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299

Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           I+   VR VV++D P +  SY    GRAGR G   +A+ F+   D   LR
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR 349

Length = 607

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

 Score = 54.2 bits (131), Expect = 3e-09
 Identities = 26/97 (26%), Positives = 43/97 (44%), Gaps = 1/97 (1%)

Query: 48  PVLVFVQSKERAQELYNELIY-DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELL 106
             L+F  ++  A+ L   L       ++V H   +++ R  V    + G +  ++ T  L
Sbjct: 255 TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSL 314

Query: 107 GRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGRE 143
             GID   + LV+    P S   ++ RIGRAG    E
Sbjct: 315 ELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGE 351

Length = 814

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

 Score = 54.0 bits (130), Expect = 4e-09
 Identities = 28/106 (26%), Positives = 52/106 (49%), Gaps = 3/106 (2%)

Query: 48  PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
             L+F    E A E+    +  GI V+ I  +  +++R+ ++  FRTG I +L+T ++L 
Sbjct: 285 KTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLD 343

Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGR--GGREGKAVTFFT 151
            G+D     +++      S   +I R+GR  R   G+E      ++
Sbjct: 344 EGVDIPDADVLIILRPTGSRRLFIQRLGRGLRPAEGKEDTLALDYS 389

Length = 442

>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 36/104 (34%), Positives = 50/104 (48%), Gaps = 6/104 (5%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           VLV   +K+ A++L + L   GI V  +HS+    +R  ++R  R G   +L+   LL  
Sbjct: 445 VLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLRE 504

Query: 109 GIDFRTVRLVVNYD-----FPSSAISYIHRIGRAGRGGREGKAV 147
           G+D   V LV   D     F  S  S I  IGRA R    GK +
Sbjct: 505 GLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVN-GKVI 547

All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 655

>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

 Score = 47.8 bits (114), Expect = 4e-07
 Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 13/101 (12%)

Query: 48  PVLVFVQSKERAQELYNELI--YDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
           PVL+F    E  +++   L        +  +HS    + R   V +FR G+I +LITT +
Sbjct: 307 PVLIFFPEIETMEQVAAALKKKLPKETIASVHS--EDQHRKEKVEAFRDGKITLLITTTI 364

Query: 106 LGRGIDFRTVRLVV----NYDFPSSAISYIHRIGRAGRGGR 142
           L RG+ F  V + V    +  F  SA+  I     AGR GR
Sbjct: 365 LERGVTFPNVDVFVLGAEHRVFTESALVQI-----AGRVGR 400

Length = 441

>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

 Score = 46.8 bits (112), Expect = 9e-07
 Identities = 37/104 (35%), Positives = 49/104 (47%), Gaps = 6/104 (5%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           VLV   +K+ A++L   L   GI V  +HSD    +R  ++R  R G   +L+   LL  
Sbjct: 449 VLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE 508

Query: 109 GIDFRTVRLVVNYD-----FPSSAISYIHRIGRAGRGGREGKAV 147
           G+D   V LV   D     F  S  S I  IGRA R    GK +
Sbjct: 509 GLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVN-GKVI 551

Length = 663

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

 Score = 45.5 bits (108), Expect = 3e-06
 Identities = 31/105 (29%), Positives = 53/105 (50%), Gaps = 9/105 (8%)

Query: 49  VLVFVQSKERAQELYNELI-----YDGINVDVIHSDR---TQKQRDNVVRSFRTGRIWIL 100
            LVF +S+++ + LY           G  +D + + R    +++R  +   F+ G +  +
Sbjct: 309 TLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGV 368

Query: 101 ITTELLGRGIDFRTVRLVVNYDFPS-SAISYIHRIGRAGRGGREG 144
           I T  L  GID  ++  V+ Y +P  S +S+  R GRAGR G+E 
Sbjct: 369 IATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQES 413

Length = 851

>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'

 Score = 44.3 bits (105), Expect = 8e-06
 Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 14/86 (16%)

Query: 73  VDVIHSD--RTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV---------NY 121
           +  I SD    +   + ++  F  G+  ILI T+++ +G  F  V LV          + 
Sbjct: 287 IARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSP 346

Query: 122 DFPSS--AISYIHRI-GRAGRGGREG 144
           DF ++      + ++ GRAGR    G
Sbjct: 347 DFRAAERGFQLLTQVAGRAGRAEDPG 372

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) [DNA metabolism, DNA replication, recombination, and repair]. Length = 505

>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 22/101 (21%), Positives = 47/101 (46%), Gaps = 9/101 (8%)

Query: 48  PVLVFVQSKERAQELYNELIYDGIN--VDVIHSDRTQKQRDN----VVRSFRTGRIWILI 101
            + + V + +RAQE Y +L  +     + ++HS  T+K R      ++   +    ++++
Sbjct: 224 KIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIV 283

Query: 102 TTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGR 142
            T+++   +D     ++      +   S I R+GR  R GR
Sbjct: 284 ATQVIEASLDISADVMITE---LAPIDSLIQRLGRLHRYGR 321

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 [Mobile and extrachromosomal element functions, Other]. Length = 358

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

 Score = 42.3 bits (100), Expect = 4e-05
 Identities = 25/92 (27%), Positives = 46/92 (50%), Gaps = 3/92 (3%)

Query: 59  AQELYNEL--IYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVR 116
           A+ LY  L   +   NV ++H      +++ V+  FR G + IL+ T ++  G+D     
Sbjct: 469 AEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNAT 528

Query: 117 LVVNYDFPSSAISYIHRI-GRAGRGGREGKAV 147
           ++V  D     +S +H++ GR GRG  +   +
Sbjct: 529 VMVIEDAERFGLSQLHQLRGRVGRGDHQSYCL 560

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

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

 Score = 42.1 bits (99), Expect = 5e-05
 Identities = 28/100 (28%), Positives = 46/100 (46%), Gaps = 12/100 (12%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           +VF  S+ R  EL + L   G+     H+    K+R +V R+F    +  ++TT  L  G
Sbjct: 444 IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAG 503

Query: 110 IDFRTVRLVVNYDFPSSAI--------SYIHRIGRAGRGG 141
           +DF   +++    F S A+         +   +GRAGR  
Sbjct: 504 VDFPASQVI----FESLAMGIEWLSVREFQQMLGRAGRPD 539

Length = 830

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

 Score = 41.7 bits (98), Expect = 6e-05
 Identities = 30/107 (28%), Positives = 50/107 (46%), Gaps = 15/107 (14%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT----GRIWILITTE 104
           VLV V + +RA ELY +L   G  V ++HS  T K R+   R  +        +I++ T+
Sbjct: 443 VLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQ 502

Query: 105 LLGRGIDFRTVRLVVNYDF----PSSAISYIHRIGRAGRGGREGKAV 147
           ++  G+D       +++D      +   S I R GR  R G++    
Sbjct: 503 VIEAGVD-------IDFDVLITELAPIDSLIQRAGRVNRHGKKENGK 542

Length = 733

>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 33/127 (25%), Positives = 53/127 (41%), Gaps = 35/127 (27%)

Query: 49  VLVFVQSKERAQELYNELI------------------YDGINVDVI-------HSDRTQK 83
           VLVFV S++ A++    LI                  YD    +++       H+  + +
Sbjct: 239 VLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNE 298

Query: 84  QRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD---FPSSAISYI------HRI 134
           QR  +   FR   I +++ T  L  G++    RLV+  D   + +  I Y+        I
Sbjct: 299 QRRFIEEMFRNRYIKVIVATPTLAAGVNL-PARLVIVRDITRYGNGGIRYLSNMEIKQMI 357

Query: 135 GRAGRGG 141
           GRAGR G
Sbjct: 358 GRAGRPG 364

Length = 674

>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 25/101 (24%), Positives = 47/101 (46%), Gaps = 9/101 (8%)

Query: 48  PVLVFVQSKERAQELYNELIYDG--INVDVIHSDRTQKQRDN----VVRSFRTGRIWILI 101
            V + V + +RAQE Y +L   G    + +IHS  T+K R      ++  F+    ++++
Sbjct: 220 SVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKSEKFVIV 279

Query: 102 TTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGR 142
            T+++   +D     ++      +   S I R+GR  R G 
Sbjct: 280 ATQVIEASLDISVDVMITE---LAPIDSLIQRLGRLHRYGE 317

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I. Length = 353

>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 24/78 (30%), Positives = 35/78 (44%)

Query: 77  HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGR 136
           H      QR  V + +    I I+  T   G GI+   VR V+++  P S   Y    GR
Sbjct: 711 HGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGR 770

Query: 137 AGRGGREGKAVTFFTKQD 154
           AGR G+    V +++  D
Sbjct: 771 AGRDGQRSSCVLYYSYSD 788

Length = 1195

>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated

 Score = 39.4 bits (93), Expect = 4e-04
 Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 14/87 (16%)

Query: 75  VIHSD--RTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV---------NYDF 123
            I  D  R +   + ++  F  G   ILI T++L +G DF  V LV          + DF
Sbjct: 457 RIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDF 516

Query: 124 PSS--AISYIHRI-GRAGRGGREGKAV 147
            +S      + ++ GRAGR  + G+ +
Sbjct: 517 RASERTFQLLTQVAGRAGRAEKPGEVL 543

Length = 679

>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination, and repair / Transcription]

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 28/92 (30%), Positives = 50/92 (54%), Gaps = 9/92 (9%)

Query: 59  AQELYNEL--IYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDF--RT 114
           A+ELY EL      + V ++H      ++D V+ +F+ G I IL+ T ++  G+D    T
Sbjct: 494 AEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNAT 553

Query: 115 VRLVVNYD-FPSSAISYIHRI-GRAGRGGREG 144
           V ++ N + F    ++ +H++ GR GRG  + 
Sbjct: 554 VMVIENAERF---GLAQLHQLRGRVGRGDLQS 582

Length = 677

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

 Score = 38.6 bits (90), Expect = 7e-04
 Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 90  RSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF 149
           R+ R G +  + TT  L  G+D   +  VV   FP +  S   + GRAGR G+    V  
Sbjct: 323 RALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVV-- 380

Query: 150 FTKQDAPL 157
              +D PL
Sbjct: 381 LVARDDPL 388

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

>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr; Provisional

 Score = 38.8 bits (90), Expect = 7e-04
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 77  HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGR 136
           H   +++QR    ++ ++G +  ++ T  L  GID   V LV+    P S  S + RIGR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367

Query: 137 AG 138
           AG
Sbjct: 368 AG 369

Length = 1490

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

 Score = 38.3 bits (90), Expect = 9e-04
 Identities = 28/105 (26%), Positives = 46/105 (43%), Gaps = 9/105 (8%)

Query: 50  LVFVQSKERAQELYNELIYDGINVD---VI---HSDRTQKQRDNVVRSFRTGRIWILITT 103
           LVF  ++ +A+  +  L     N +    I   H    ++QR  V  +   GR+  ++ T
Sbjct: 251 LVFTNTRSQAELWFQALWE--ANPEFALPIALHHGSLDREQRRWVEAAMAAGRLRAVVCT 308

Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAG-RGGREGKAV 147
             L  G+DF  V LV+    P      + R GR+  R G   +A+
Sbjct: 309 SSLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPGEPSRAL 353

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

>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 27/88 (30%), Positives = 38/88 (43%), Gaps = 13/88 (14%)

Query: 50  LVFVQS---KERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE-- 104
           L+FV S   KE A+EL   L   GIN ++  S   +K        F  G + +L+     
Sbjct: 332 LIFVPSDKGKEYAEELAEYLEDLGINAELAISGFERKFEK-----FEEGEVDVLVGVASY 386

Query: 105 --LLGRGIDF-RTVRLVVNYDFPSSAIS 129
             +L RGID    +R  + Y  P    S
Sbjct: 387 YGVLVRGIDLPERIRYAIFYGVPKFKFS 414

Length = 1176

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	159
KOG0328|consensus	400		100.0
KOG0333|consensus	673		99.97
KOG0331|consensus	519		99.97
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.96
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.96
KOG0332|consensus	477		99.96
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.96
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.96
KOG0330|consensus	476		99.96
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.96
KOG0326|consensus	459		99.96
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.95
PTZ00110	545	helicase; Provisional	99.95
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.95
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.95
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.95
PTZ00424	401	helicase 45; Provisional	99.95
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.95
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.94
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.94
KOG0335|consensus	482		99.94
KOG0344|consensus	593		99.94
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.94
KOG0342|consensus	543		99.93
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.93
KOG0340|consensus	442		99.92
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.92
KOG0341|consensus	610		99.92
KOG0338|consensus	691		99.91
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.91
KOG0345|consensus	567		99.91
KOG0336|consensus	629		99.9
PRK04914	956	ATP-dependent helicase HepA; Validated	99.9
KOG0346|consensus	569		99.9
KOG0343|consensus	758		99.9
KOG0327|consensus	397		99.89
KOG0350|consensus	620		99.88
KOG0334|consensus	997		99.88
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.88
PRK13767	876	ATP-dependent helicase; Provisional	99.87
KOG4284|consensus	980		99.87
KOG0339|consensus	731		99.87
PHA02653	675	RNA helicase NPH-II; Provisional	99.87
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.87
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.87
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.87
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.87
KOG0347|consensus	731		99.87
KOG0348|consensus	708		99.86
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.86
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.86
PRK10689	1147	transcription-repair coupling factor; Provisional	99.86
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.86
KOG0351|consensus	941		99.86
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.85
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.85
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.84
PRK02362	737	ski2-like helicase; Provisional	99.84
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.84
PRK13766	773	Hef nuclease; Provisional	99.84
PHA02558	501	uvsW UvsW helicase; Provisional	99.83
PRK05298	652	excinuclease ABC subunit B; Provisional	99.83
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.82
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.82
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.81
COG1202	830	Superfamily II helicase, archaea-specific [General	99.81
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.81
PRK00254	720	ski2-like helicase; Provisional	99.8
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.79
KOG0354|consensus	746		99.79
PRK01172	674	ski2-like helicase; Provisional	99.78
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.77
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.77
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.75
KOG0349|consensus	725		99.75
KOG0352|consensus	641		99.74
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.74
KOG0337|consensus	529		99.74
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.71
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.71
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.7
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.68
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.65
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.64
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.64
KOG0353|consensus	695		99.64
PRK09694	878	helicase Cas3; Provisional	99.63
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.62
COG1204	766	Superfamily II helicase [General function predicti	99.61
PRK09401	1176	reverse gyrase; Reviewed	99.6
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.6
PRK14701	1638	reverse gyrase; Provisional	99.59
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.56
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.54
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.54
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.53
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.52
KOG0329|consensus	387		99.51
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.45
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.41
COG1205	851	Distinct helicase family with a unique C-terminal	99.4
KOG0384|consensus	1373		99.39
PRK05580	679	primosome assembly protein PriA; Validated	99.39
KOG0385|consensus	971		99.39
KOG0947|consensus	1248		99.38
KOG0951|consensus	1674		99.37
KOG0390|consensus	776		99.36
KOG0948|consensus	1041		99.36
KOG0950|consensus	1008		99.36
KOG0953|consensus	700		99.34
KOG0387|consensus	923		99.3
KOG4150|consensus	1034		99.29
KOG0952|consensus	1230		99.26
KOG0922|consensus	674		99.21
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.2
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.17
KOG0389|consensus	941		99.1
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.04
KOG0923|consensus	902		99.04
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	99.04
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.03
KOG0391|consensus	1958		99.03
KOG0388|consensus	1185		99.01
KOG0392|consensus	1549		99.0
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.0
KOG0920|consensus	924		98.98
KOG0924|consensus	1042		98.96
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.93
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.9
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.89
KOG0949|consensus	1330		98.87
KOG1015|consensus	1567		98.86
KOG1123|consensus	776		98.77
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.75
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.73
KOG0926|consensus	1172		98.72
KOG1000|consensus	689		98.72
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.71
COG4096	875	HsdR Type I site-specific restriction-modification	98.7
KOG0386|consensus	1157		98.65
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.61
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.58
KOG4439|consensus	901		98.54
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.46
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.46
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.45
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.44
KOG1002|consensus	791		98.41
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.39
KOG0925|consensus	699		98.3
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.27
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.25
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	98.24
COG4889	1518	Predicted helicase [General function prediction on	98.19
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	98.12
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	98.02
PF13871	278	Helicase_C_4: Helicase_C-like	98.01
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.98
KOG1016|consensus	1387		97.79
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.45
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.44
PRK05580	679	primosome assembly protein PriA; Validated	97.38
TIGR00595	505	priA primosomal protein N'. All proteins in this f	97.33
PRK14873	665	primosome assembly protein PriA; Provisional	97.26
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	97.23
COG1198	730	PriA Primosomal protein N' (replication factor Y)	97.14
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	96.88
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	96.86
KOG1001|consensus	674		96.81
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.8
KOG0951|consensus	1674		96.7
KOG2340|consensus	698		96.7
PRK14873	665	primosome assembly protein PriA; Provisional	96.57
KOG0921|consensus	1282		96.37
PRK10689	1147	transcription-repair coupling factor; Provisional	96.33
PRK14701	1638	reverse gyrase; Provisional	96.27
KOG0298|consensus	1394		96.0
KOG1133|consensus	821		95.9
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	95.72
KOG0701|consensus	1606		95.72
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	95.26
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	95.18
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	94.91
KOG0339|consensus	731		94.85
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	94.7
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	94.63
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	94.13
KOG1513|consensus	1300		94.04
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	93.93
KOG0347|consensus	731		93.54
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	92.29
KOG0338|consensus	691		92.15
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	91.91
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	91.72
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	91.53
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	91.47
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	91.23
PRK09401	1176	reverse gyrase; Reviewed	91.19
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	91.01
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	90.68
PF04364	137	DNA_pol3_chi: DNA polymerase III chi subunit, HolC	90.49
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	90.4
PRK15483	986	type III restriction-modification system StyLTI en	90.1
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	90.07
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	90.01
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	89.14
KOG0389|consensus	941		88.9
KOG0330|consensus	476		88.89
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	88.86
COG0610	962	Type I site-specific restriction-modification syst	88.74
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	88.37
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	88.29
PRK05728	142	DNA polymerase III subunit chi; Validated	88.05
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	87.98
PRK13766	773	Hef nuclease; Provisional	87.96
PTZ00110	545	helicase; Provisional	87.34
COG1205	851	Distinct helicase family with a unique C-terminal	87.32
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	86.97
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	86.41
KOG0329|consensus	387		86.36
cd01518	101	RHOD_YceA Member of the Rhodanese Homology Domain	86.15
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	85.7
cd01533	109	4RHOD_Repeat_2 Member of the Rhodanese Homology Do	85.55
cd01534	95	4RHOD_Repeat_3 Member of the Rhodanese Homology Do	85.53
PRK09200	790	preprotein translocase subunit SecA; Reviewed	85.51
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	85.1
TIGR00696	177	wecB_tagA_cpsF bacterial polymer biosynthesis prot	84.74
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	84.45
PF03808	172	Glyco_tran_WecB: Glycosyl transferase WecB/TagA/Cp	84.22
cd01521	110	RHOD_PspE2 Member of the Rhodanese Homology Domain	84.12
cd01527	99	RHOD_YgaP Member of the Rhodanese Homology Domain	84.03
KOG0331|consensus	519		83.97
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	83.9
KOG0343|consensus	758		83.88
cd01526	122	RHOD_ThiF Member of the Rhodanese Homology Domain	83.83
KOG0350|consensus	620		83.51
cd01532	92	4RHOD_Repeat_1 Member of the Rhodanese Homology Do	83.14
cd06533	171	Glyco_transf_WecG_TagA The glycosyltransferase Wec	83.03
COG3587	985	Restriction endonuclease [Defense mechanisms]	82.97
cd01449	118	TST_Repeat_2 Thiosulfate sulfurtransferase (TST),	82.56
KOG0334|consensus	997		82.46
PRK12904	830	preprotein translocase subunit SecA; Reviewed	82.31
PRK02362	737	ski2-like helicase; Provisional	81.99
KOG1132|consensus	945		81.93
cd00158	89	RHOD Rhodanese Homology Domain (RHOD); an alpha be	81.84
cd01444	96	GlpE_ST GlpE sulfurtransferase (ST) and homologs a	81.14
PRK10287	104	thiosulfate:cyanide sulfurtransferase; Provisional	81.03
PRK05320	257	rhodanese superfamily protein; Provisional	80.65
cd01528	101	RHOD_2 Member of the Rhodanese Homology Domain sup	80.52
PF11496	297	HDA2-3: Class II histone deacetylase complex subun	80.12
cd01525	105	RHOD_Kc Member of the Rhodanese Homology Domain su	80.12
KOG0383|consensus	696		80.09

>KOG0328|consensus

Probab=100.00  E-value=1.3e-32  Score=195.04  Aligned_cols=144  Identities=31%  Similarity=0.531  Sum_probs=137.1

Q ss_pred             hhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc
Q psy576           15 RVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      ...++|.++|+.++.++.|+..|..+-....-.+++|||+|+..++.+.+.+++.++.+...||+|+.++|.+++..|+.
T Consensus       235 ltlEgIKqf~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRs  314 (400)
T KOG0328|consen  235 LTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRS  314 (400)
T ss_pred             CchhhhhhheeeechhhhhHhHHHHHhhhhehheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhc
Confidence            44578999999999999999999999998888899999999999999999999999999999999999999999999999


Q ss_pred             CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcccc
Q psy576           95 GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL  158 (159)
Q Consensus        95 ~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~  158 (159)
                      |+.+|||+|+++++|+|+|.++.|||||.|.+.+.|+||+||.||+|++|.++.|+.+.|...+
T Consensus       315 g~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~l  378 (400)
T KOG0328|consen  315 GKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRIL  378 (400)
T ss_pred             CCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999887654

>KOG0333|consensus

Probab=99.97  E-value=6.9e-30  Score=193.41  Aligned_cols=139  Identities=35%  Similarity=0.610  Sum_probs=130.9

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      +.+.+.++.+.. +.|...|.++++.....++|||+++++.|+.+++.|.+.++++..+||+-.+++|+.+++.|+.|..
T Consensus       490 ~rveQ~v~m~~e-d~k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~  568 (673)
T KOG0333|consen  490 PRVEQKVEMVSE-DEKRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTG  568 (673)
T ss_pred             cchheEEEEecc-hHHHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCC
Confidence            456677777777 6779999999998888899999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      .|||||+++++|+|||++++||||+.+++..+|.||+||+||.|+.|.++.|++..|.+.
T Consensus       569 dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~v  628 (673)
T KOG0333|consen  569 DILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTAV  628 (673)
T ss_pred             CEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhHH
Confidence            999999999999999999999999999999999999999999999999999999988653

>KOG0331|consensus

Probab=99.97  E-value=3.1e-30  Score=197.81  Aligned_cols=140  Identities=34%  Similarity=0.633  Sum_probs=127.5

Q ss_pred             hhhccceeeeecCCCCChHHHHHHHHhc---CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHH
Q psy576           16 VKSNLARMYRETEGAGSPVQAQDETILL---GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        16 ~~~~i~~~~~~~~~~~~k~~~l~~~~~~---~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ...+|.+....++. ..|...|.+++..   ...+++||||+|++.|+++...++..++++..+||+.++.+|..+++.|
T Consensus       309 a~~~i~qive~~~~-~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~F  387 (519)
T KOG0331|consen  309 ANHNIRQIVEVCDE-TAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGF  387 (519)
T ss_pred             hhcchhhhhhhcCH-HHHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhc
Confidence            34577777777774 6788888777764   3567899999999999999999998889999999999999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      ++|+..|||||+++++|+|+|++++||||++|.+.++|.||+||+||.|+.|.++.|+...+..
T Consensus       388 reG~~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~  451 (519)
T KOG0331|consen  388 REGKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAK  451 (519)
T ss_pred             ccCCcceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999877654

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

Probab=99.96  E-value=1.2e-29  Score=198.94  Aligned_cols=138  Identities=33%  Similarity=0.603  Sum_probs=131.2

Q ss_pred             hhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC
Q psy576           16 VKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        16 ~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~   95 (159)
                      ..+.|.+++..+.....|+..|..++......++||||+++..++.++..|...++++..+||++++++|.++++.|++|
T Consensus       243 ~~~~i~q~~~~v~~~~~k~~~L~~ll~~~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g  322 (513)
T COG0513         243 TLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDG  322 (513)
T ss_pred             cccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcC
Confidence            45788899999988556999999999987777899999999999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576           96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus        96 ~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      +.+|||||+++++|+|+|++++|||||.|.+++.|.||+||+||.|..|.++.|+.+.
T Consensus       323 ~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~  380 (513)
T COG0513         323 ELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEE  380 (513)
T ss_pred             CCCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcH
Confidence            9999999999999999999999999999999999999999999999999999999874

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.96  E-value=4.7e-29  Score=194.03  Aligned_cols=137  Identities=26%  Similarity=0.486  Sum_probs=126.9

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .+.+.+..+.. ..|...+..++......++||||++++.++.+++.|.+.+..+..+||++++.+|..+++.|++|+.+
T Consensus       216 ~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~  294 (460)
T PRK11776        216 AIEQRFYEVSP-DERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCS  294 (460)
T ss_pred             CeeEEEEEeCc-HHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCc
Confidence            36677777766 45899999999877778899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      |||||+++++|+|+|++++||+++.|.+...|.||+||+||.|..|.++.++.+.|..
T Consensus       295 vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~  352 (460)
T PRK11776        295 VLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQ  352 (460)
T ss_pred             EEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHHH
Confidence            9999999999999999999999999999999999999999999999999999887643

>KOG0332|consensus

Probab=99.96  E-value=1.3e-28  Score=180.13  Aligned_cols=143  Identities=34%  Similarity=0.527  Sum_probs=135.2

Q ss_pred             HHhhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHH
Q psy576           13 KRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        13 ~~~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      +....++|.++|..|..++.|.+.|.++.....-++.+|||.|+..+..++..+.+.|-.+..+||.|..++|..+++.|
T Consensus       297 eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~F  376 (477)
T KOG0332|consen  297 EELALDNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRF  376 (477)
T ss_pred             hhccccchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHH
Confidence            44557899999999999999999999998888889999999999999999999999999999999999999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCC------CHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPS------SAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~------~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      +.|+.+|||+|++.++|+|++.+++|+|||.|.      +.+.|+||+||+||+|..|.++.++++.+.
T Consensus       377 r~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s  445 (477)
T KOG0332|consen  377 REGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDS  445 (477)
T ss_pred             hcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCc
Confidence            999999999999999999999999999999994      799999999999999999999999987754

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=6.2e-29  Score=191.59  Aligned_cols=135  Identities=27%  Similarity=0.506  Sum_probs=122.4

Q ss_pred             cceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeE
Q psy576           20 LARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI   99 (159)
Q Consensus        20 i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v   99 (159)
                      +.+.+..... ..|...|..++......++||||++.+.++.++..|.+.+.++..+||+++.++|.++++.|++|+.+|
T Consensus       230 i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~v  308 (423)
T PRK04837        230 IKEELFYPSN-EEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDI  308 (423)
T ss_pred             eeEEEEeCCH-HHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcE
Confidence            3444443333 578888888888767789999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       100 lv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      ||||+++++|+|+|++++||+|++|.+..+|.||+||+||.|..|.++.|+.+.|.
T Consensus       309 LVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~  364 (423)
T PRK04837        309 LVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYA  364 (423)
T ss_pred             EEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHH
Confidence            99999999999999999999999999999999999999999999999999987653

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.96  E-value=2.3e-28  Score=189.85  Aligned_cols=137  Identities=29%  Similarity=0.522  Sum_probs=123.4

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .+.+.+..++. ..|.+.+..++......++||||+++..++.+++.|.+.++++..+||+++..+|..+++.|++|+.+
T Consensus       219 ~i~~~~~~~~~-~~k~~~l~~l~~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~  297 (456)
T PRK10590        219 QVTQHVHFVDK-KRKRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIR  297 (456)
T ss_pred             ceeEEEEEcCH-HHHHHHHHHHHHcCCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCc
Confidence            34445544444 56777788888776778999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      |||||+++++|+|+|++++||+|++|.+..+|.||+||+||.|..|.++.++...|..
T Consensus       298 iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~  355 (456)
T PRK10590        298 VLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHK  355 (456)
T ss_pred             EEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHH
Confidence            9999999999999999999999999999999999999999999999999999877654

>KOG0330|consensus

Probab=99.96  E-value=1.3e-28  Score=180.92  Aligned_cols=141  Identities=30%  Similarity=0.436  Sum_probs=132.2

Q ss_pred             hhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC
Q psy576           16 VKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        16 ~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~   95 (159)
                      +-+.+.++|..+.. ..|...|..+++...+.++||||++-..+..++-.|+..++.+..+||.|+...|...++.|++|
T Consensus       271 tv~~lkQ~ylfv~~-k~K~~yLV~ll~e~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~  349 (476)
T KOG0330|consen  271 TVDHLKQTYLFVPG-KDKDTYLVYLLNELAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAG  349 (476)
T ss_pred             chHHhhhheEeccc-cccchhHHHHHHhhcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhcc
Confidence            34677788888888 78999999999988889999999999999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        96 ~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      ...||+||+++++|+|+|.+++|||||.|.+..+|+||+||++|.|.+|.++.+++.-|.+.
T Consensus       350 ~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~  411 (476)
T KOG0330|consen  350 ARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVEL  411 (476)
T ss_pred             CCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHH
Confidence            99999999999999999999999999999999999999999999999999999998766543

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.96  E-value=3.5e-28  Score=187.95  Aligned_cols=139  Identities=30%  Similarity=0.532  Sum_probs=127.6

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ..+.+++...+....|...|..++......++||||++++.++.++..|...++.+..+||+++..+|..+++.|++|+.
T Consensus       217 ~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~  296 (434)
T PRK11192        217 KKIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRV  296 (434)
T ss_pred             cCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCC
Confidence            45666666666667788999999886667889999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      +|||||+++++|+|+|++++||+++.|.+...|.||+||+||.|..|.++.++...|..
T Consensus       297 ~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~  355 (434)
T PRK11192        297 NVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHL  355 (434)
T ss_pred             cEEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecHHHHH
Confidence            99999999999999999999999999999999999999999999999999999876653

>KOG0326|consensus

Probab=99.96  E-value=9e-29  Score=178.14  Aligned_cols=144  Identities=30%  Similarity=0.477  Sum_probs=136.7

Q ss_pred             HHhhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHH
Q psy576           13 KRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        13 ~~~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      .+..+.++.++|..+.+ .+|+-.|..++.+.+-++.+|||+|...++-++..+.+.|+.+.++|+.|.++.|..++..|
T Consensus       290 ~eLtl~GvtQyYafV~e-~qKvhCLntLfskLqINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdF  368 (459)
T KOG0326|consen  290 EELTLKGVTQYYAFVEE-RQKVHCLNTLFSKLQINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDF  368 (459)
T ss_pred             hhhhhcchhhheeeech-hhhhhhHHHHHHHhcccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhh
Confidence            55667899999999998 79999999999988899999999999999999999999999999999999999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      ++|.++.||||+.+-+|+|++++++|||+|.|++.+.|++|+||.||+|..|.++.+++..|...
T Consensus       369 r~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~  433 (459)
T KOG0326|consen  369 RNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFN  433 (459)
T ss_pred             hccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999887643

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=2.1e-27  Score=185.42  Aligned_cols=136  Identities=29%  Similarity=0.544  Sum_probs=124.1

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .+.+.+..+.. ..|...+..++......++||||++++.++.+++.|...++.+..+||+++.++|.++++.|++|++.
T Consensus       309 ~~~~~~~~~~~-~~k~~~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~  387 (475)
T PRK01297        309 TVEQHVYAVAG-SDKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIR  387 (475)
T ss_pred             cccEEEEEecc-hhHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCc
Confidence            44455555554 67888888888876677999999999999999999998899999999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      +||||+++++|+|+|++++||+++.|.+..+|.||+||+||.|..|.++.|+.+.|.
T Consensus       388 vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~  444 (475)
T PRK01297        388 VLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDA  444 (475)
T ss_pred             EEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHH
Confidence            999999999999999999999999999999999999999999999999999987754

>PTZ00110 helicase; Provisional

Probab=99.95  E-value=1e-27  Score=189.41  Aligned_cols=137  Identities=34%  Similarity=0.532  Sum_probs=122.2

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcC--CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLG--IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~--~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      .+.+.+..+.. ..|...|.+++...  ...++||||++++.++.++..|...++++..+||+++.++|..+++.|++|+
T Consensus       349 ~i~q~~~~~~~-~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~  427 (545)
T PTZ00110        349 NIKQEVFVVEE-HEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGK  427 (545)
T ss_pred             CeeEEEEEEec-hhHHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCC
Confidence            34444444444 56777777777653  4678999999999999999999988999999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      ..|||||+++++|+|+|++++||++++|.+..+|.||+||+||.|..|.++.|+++.+..
T Consensus       428 ~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~  487 (545)
T PTZ00110        428 SPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYR  487 (545)
T ss_pred             CcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHH
Confidence            999999999999999999999999999999999999999999999999999999987654

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.95  E-value=1.7e-27  Score=190.15  Aligned_cols=136  Identities=32%  Similarity=0.552  Sum_probs=123.7

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .+.+.+..+.. ..|.+.|.+++......++||||+++..++++++.|.+.++.+..+||++++.+|..+++.|++|+.+
T Consensus       219 ~i~q~~~~v~~-~~k~~~L~~~L~~~~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~  297 (629)
T PRK11634        219 DISQSYWTVWG-MRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLD  297 (629)
T ss_pred             ceEEEEEEech-hhHHHHHHHHHHhcCCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCC
Confidence            34455554444 46888888888876778899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |||||+++++|+|+|++++||+|+.|.+...|.||+||+||.|..|.+++|+.+.|.
T Consensus       298 ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~  354 (629)
T PRK11634        298 ILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRER  354 (629)
T ss_pred             EEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechHHH
Confidence            999999999999999999999999999999999999999999999999999987654

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=1.4e-27  Score=189.38  Aligned_cols=136  Identities=29%  Similarity=0.458  Sum_probs=123.6

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .+.+.+..... ..|...+..++......++||||+++..++.+++.|...++.+..+||+++..+|.++++.|++|+.+
T Consensus       231 ~i~q~~~~~~~-~~k~~~L~~ll~~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~  309 (572)
T PRK04537        231 RVRQRIYFPAD-EEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLE  309 (572)
T ss_pred             ceeEEEEecCH-HHHHHHHHHHHhcccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCe
Confidence            34455554443 67888888888877778999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |||||+++++|+|+|++++||+|+.|.+..+|.||+||+||.|..|.+++|+.+.+.
T Consensus       310 VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~  366 (572)
T PRK04537        310 ILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYA  366 (572)
T ss_pred             EEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHH
Confidence            999999999999999999999999999999999999999999999999999987654

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

Probab=99.95  E-value=3.2e-27  Score=185.85  Aligned_cols=136  Identities=32%  Similarity=0.562  Sum_probs=118.9

Q ss_pred             cceeeeecCCCCChHHHHHHHHhcC--CCCCEEEEecchHHHHHHHHHHHh-CCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           20 LARMYRETEGAGSPVQAQDETILLG--IEPPVLVFVQSKERAQELYNELIY-DGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        20 i~~~~~~~~~~~~k~~~l~~~~~~~--~~~~~lif~~~~~~~~~l~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      +.+.+..+.. ..|...+.+++...  ...++||||+++..++.+++.|.. .++++..+||+++..+|..+++.|++|+
T Consensus       340 v~q~~~~~~~-~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~  418 (518)
T PLN00206        340 VKQLAIWVET-KQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGE  418 (518)
T ss_pred             eeEEEEeccc-hhHHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCC
Confidence            4455555554 45666777777642  235799999999999999999975 5889999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      .+|||||+++++|+|+|++++||+|++|.+..+|.||+||+||.|..|.+++|+...+..
T Consensus       419 ~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~  478 (518)
T PLN00206        419 VPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRN  478 (518)
T ss_pred             CCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHH
Confidence            999999999999999999999999999999999999999999999999999999877643

>PTZ00424 helicase 45; Provisional

Probab=99.95  E-value=2.7e-27  Score=181.31  Aligned_cols=139  Identities=35%  Similarity=0.585  Sum_probs=124.6

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      +.+.+++........+...+..++......++||||++++.++.+++.|...+..+..+||+++..+|..+++.|++|+.
T Consensus       239 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~  318 (401)
T PTZ00424        239 EGIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGST  318 (401)
T ss_pred             CCceEEEEecChHHHHHHHHHHHHHhcCCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCC
Confidence            34555665555545577777777776667789999999999999999999889999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      +|||||+++++|+|+|++++||++++|.+...|.||+||+||.|..|.|+.++.+.+.+
T Consensus       319 ~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~  377 (401)
T PTZ00424        319 RVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIE  377 (401)
T ss_pred             CEEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHHHHH
Confidence            99999999999999999999999999999999999999999999999999999877654

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.95  E-value=9.3e-27  Score=181.50  Aligned_cols=125  Identities=25%  Similarity=0.395  Sum_probs=114.3

Q ss_pred             ChHHHHHHHHh-cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccccc
Q psy576           32 SPVQAQDETIL-LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI  110 (159)
Q Consensus        32 ~k~~~l~~~~~-~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~  110 (159)
                      ...+.+.+++. ...++.+||||+++++++.++..|.+.++.+..+||+|++++|..+++.|.+|+.+|||||+++++|+
T Consensus       211 ~~~~~l~~~l~~~~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GI  290 (470)
T TIGR00614       211 KILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGI  290 (470)
T ss_pred             cHHHHHHHHHHHhcCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccC
Confidence            44555666665 33455679999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576          111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus       111 ~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      |+|++++||++++|.+...|.||+||+||.|..|.|++++.+.|..
T Consensus       291 D~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~  336 (470)
T TIGR00614       291 NKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADIN  336 (470)
T ss_pred             CcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechhHHH
Confidence            9999999999999999999999999999999999999999987654

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

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.94  E-value=1.5e-26  Score=184.84  Aligned_cols=125  Identities=25%  Similarity=0.446  Sum_probs=116.3

Q ss_pred             ChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccc
Q psy576           32 SPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGID  111 (159)
Q Consensus        32 ~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~  111 (159)
                      .+...+...+....+.++||||+++++++.++..|.+.++++..+||+|++++|.++++.|.+|+.+|||||+++++|+|
T Consensus       222 ~~~~~l~~~l~~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GID  301 (607)
T PRK11057        222 KPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGIN  301 (607)
T ss_pred             chHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCC
Confidence            45566667776667789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576          112 FRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus       112 i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      +|++++||+++.|.+..+|.|++||+||.|.+|.|++++++.|..
T Consensus       302 ip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~  346 (607)
T PRK11057        302 KPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMA  346 (607)
T ss_pred             CCCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHH
Confidence            999999999999999999999999999999999999999887753

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

Probab=99.94  E-value=2.6e-26  Score=188.68  Aligned_cols=122  Identities=24%  Similarity=0.368  Sum_probs=111.9

Q ss_pred             HHHHHHHHhc-CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccccccc
Q psy576           34 VQAQDETILL-GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDF  112 (159)
Q Consensus        34 ~~~l~~~~~~-~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i  112 (159)
                      ...+.+++.. ..+.+.||||.+++.++.++..|...++++..+||+|++++|..+++.|.+|+++|||||+++++|+|+
T Consensus       667 le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDk  746 (1195)
T PLN03137        667 LEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINK  746 (1195)
T ss_pred             HHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCc
Confidence            4455566653 235679999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          113 RTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       113 ~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |++++|||++.|.+++.|.|++||+||.|..+.|++|+...|.
T Consensus       747 PDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~  789 (1195)
T PLN03137        747 PDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDY  789 (1195)
T ss_pred             cCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHH
Confidence            9999999999999999999999999999999999999987654

>KOG0335|consensus

Probab=99.94  E-value=4.2e-26  Score=172.96  Aligned_cols=154  Identities=31%  Similarity=0.494  Sum_probs=132.7

Q ss_pred             cccccccchhhHHhhh----------------hccceeeeecCCCCChHHHHHHHHhcCC----CC-----CEEEEecch
Q psy576            2 AVDFNHTNPALKRRVK----------------SNLARMYRETEGAGSPVQAQDETILLGI----EP-----PVLVFVQSK   56 (159)
Q Consensus         2 ~~~~~~~~~~~~~~~~----------------~~i~~~~~~~~~~~~k~~~l~~~~~~~~----~~-----~~lif~~~~   56 (159)
                      |++|+.....+...+.                +++.+....+.+ ..|...|.+++....    ..     .++|||.++
T Consensus       269 SAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~-~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~  347 (482)
T KOG0335|consen  269 SATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNE-MEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETK  347 (482)
T ss_pred             eccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecc-hhhHHHHHHHhhcccCCcccCCcccceEEEEeecc
Confidence            7777777666654443                356677777777 466666666665322    33     799999999


Q ss_pred             HHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhh
Q psy576           57 ERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGR  136 (159)
Q Consensus        57 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR  136 (159)
                      +.++.+..+|...+++...+||..+..+|...+..|+.|+..+||||+++++|+|+|++++||+||.|.+..+|.||+||
T Consensus       348 ~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGR  427 (482)
T KOG0335|consen  348 RGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGR  427 (482)
T ss_pred             chhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCcceEEEEecCCCcc
Q psy576          137 AGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus       137 ~~R~g~~g~~~~~~~~~~~~  156 (159)
                      +||.|+.|.+..|++..+..
T Consensus       428 TGR~Gn~G~atsf~n~~~~~  447 (482)
T KOG0335|consen  428 TGRVGNGGRATSFFNEKNQN  447 (482)
T ss_pred             cccCCCCceeEEEeccccch
Confidence            99999999999999965543

>KOG0344|consensus

Probab=99.94  E-value=6.3e-26  Score=173.70  Aligned_cols=142  Identities=56%  Similarity=0.969  Sum_probs=133.2

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHH-HhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNEL-IYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l-~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      ..+.|-.+.+..+..|...+.+++..+-..|++||+.+.+.|.+++..| .-.++++.++||..++.+|.+++++|+.|+
T Consensus       359 ~~V~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~  438 (593)
T KOG0344|consen  359 ETVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGK  438 (593)
T ss_pred             hhhhhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccC
Confidence            4566777777778899999999999998999999999999999999999 666899999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccccC
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR  159 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~~  159 (159)
                      ++|||||+++++|+|+.+++.|||||.|.+.-+|++|+||+||.|+.|.++.|+.+.|.+.++
T Consensus       439 IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir  501 (593)
T KOG0344|consen  439 IWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIR  501 (593)
T ss_pred             eeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhh
Confidence            999999999999999999999999999999999999999999999999999999999887654

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.94  E-value=7.3e-26  Score=180.80  Aligned_cols=125  Identities=25%  Similarity=0.422  Sum_probs=116.8

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccccc
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI  110 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~  110 (159)
                      ..+...+.+.+....+.++||||++++.++.+++.|...++++..+||+|+.++|..+++.|.+|+.+|||||+++++|+
T Consensus       209 ~~~~~~l~~~l~~~~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GI  288 (591)
T TIGR01389       209 NNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGI  288 (591)
T ss_pred             CCHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccC
Confidence            45677778888766678899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       111 ~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |+|++++||++++|.+..+|.|++||+||.|..+.|+++++..|.
T Consensus       289 D~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~  333 (591)
T TIGR01389       289 DKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADI  333 (591)
T ss_pred             cCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHHH
Confidence            999999999999999999999999999999999999999887764

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.

>KOG0342|consensus

Probab=99.93  E-value=1.1e-25  Score=169.42  Aligned_cols=143  Identities=28%  Similarity=0.395  Sum_probs=130.3

Q ss_pred             hhhhccceeeeecCCCCChHHHHHHHHhcCCC-CCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHh
Q psy576           15 RVKSNLARMYRETEGAGSPVQAQDETILLGIE-PPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~-~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      .+-+.+.+-|..+.. ..++..+..++..... .+++|||+|-..+..+++.|+...+++..+||+.++..|..+...|.
T Consensus       299 ~The~l~Qgyvv~~~-~~~f~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~  377 (543)
T KOG0342|consen  299 ETHERLEQGYVVAPS-DSRFSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFC  377 (543)
T ss_pred             chhhcccceEEeccc-cchHHHHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHh
Confidence            344677787777777 4568888888887666 78999999999999999999998999999999999999999999999


Q ss_pred             cCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcccc
Q psy576           94 TGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL  158 (159)
Q Consensus        94 ~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~  158 (159)
                      +.+.-||+||+++++|+|+|++++|+.+++|.++.+|+||+||++|.|..|.++.+..+.|..++
T Consensus       378 kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Fl  442 (543)
T KOG0342|consen  378 KAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFL  442 (543)
T ss_pred             hcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999998887654

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

Probab=99.93  E-value=2.8e-25  Score=173.37  Aligned_cols=143  Identities=26%  Similarity=0.449  Sum_probs=122.8

Q ss_pred             HHhhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHH
Q psy576           13 KRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        13 ~~~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      .+..+++|....+.......+...+.+ +.....++.||||.|++.++.++++|...++++..+|++|+.++|..+.++|
T Consensus       198 ~sfdRpNi~~~v~~~~~~~~q~~fi~~-~~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f  276 (590)
T COG0514         198 GSFDRPNLALKVVEKGEPSDQLAFLAT-VLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAF  276 (590)
T ss_pred             ecCCCchhhhhhhhcccHHHHHHHHHh-hccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHH
Confidence            334455666655555533444443333 2244566789999999999999999999999999999999999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      .+++..|+|||.+.++|+|-|++..||||+.|.++++|.|-+||+||+|.+..|++++.+.|..
T Consensus       277 ~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAGRDG~~a~aill~~~~D~~  340 (590)
T COG0514         277 LNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIR  340 (590)
T ss_pred             hcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhccCCCCcceEEEeeccccHH
Confidence            9999999999999999999999999999999999999999999999999999999999988854

>KOG0340|consensus

Probab=99.92  E-value=8.7e-25  Score=159.24  Aligned_cols=140  Identities=31%  Similarity=0.421  Sum_probs=126.4

Q ss_pred             hhccceeeeecCCCCChHHHHHHHHhcC---CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHh
Q psy576           17 KSNLARMYRETEGAGSPVQAQDETILLG---IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        17 ~~~i~~~~~~~~~~~~k~~~l~~~~~~~---~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      .+.+.+.|..++. ..|...|..++...   ..+.++||+++..+++.++..|+..++.+..+|+.|++++|...+..|+
T Consensus       223 vetL~q~yI~~~~-~vkdaYLv~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFr  301 (442)
T KOG0340|consen  223 VETLYQGYILVSI-DVKDAYLVHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFR  301 (442)
T ss_pred             hhhhhhheeecch-hhhHHHHHHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHh
Confidence            4556666777766 67888888888642   3567999999999999999999999999999999999999999999999


Q ss_pred             cCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           94 TGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        94 ~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      .+..+|||||+++++|+|||.+..|+|++.|.++.+|+||+||..|.|+.|.++.++..-|.+.
T Consensus       302 s~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l  365 (442)
T KOG0340|consen  302 SNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVEL  365 (442)
T ss_pred             hcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHH
Confidence            9999999999999999999999999999999999999999999999999999999999877654

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

Probab=99.92  E-value=1.2e-23  Score=137.31  Aligned_cols=118  Identities=40%  Similarity=0.670  Sum_probs=109.9

Q ss_pred             ChHHHHHHHHhcC--CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccc
Q psy576           32 SPVQAQDETILLG--IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG  109 (159)
Q Consensus        32 ~k~~~l~~~~~~~--~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g  109 (159)
                      .|...+.+++...  .++++||||++.+.++.+.+.|.+.+.++..+||++++.++..+++.|+++...+|++|+++++|
T Consensus        12 ~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G   91 (131)
T cd00079          12 EKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARG   91 (131)
T ss_pred             HHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcC
Confidence            7888888888764  36789999999999999999998888889999999999999999999999999999999999999


Q ss_pred             cccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       110 ~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      +|+|.+++|+.+++|++...+.|++||++|.|+.|.++++
T Consensus        92 ~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          92 IDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             cChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            9999999999999999999999999999999988887764

>KOG0341|consensus

Probab=99.92  E-value=8.3e-25  Score=161.41  Aligned_cols=122  Identities=33%  Similarity=0.666  Sum_probs=114.8

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccccc
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI  110 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~  110 (159)
                      +.|+-.|.+.+.+ ...|+||||..+..++.++++|.-.|..+..+||+-++++|...++.|+.|+.+|||+|++++.|+
T Consensus       407 EaKiVylLeCLQK-T~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGL  485 (610)
T KOG0341|consen  407 EAKIVYLLECLQK-TSPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGL  485 (610)
T ss_pred             hhhhhhHHHHhcc-CCCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccC
Confidence            5677777777776 567899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576          111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus       111 ~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      |+|++.+|||||.|...++|.+|+||+||.|..|.+.+|++..
T Consensus       486 DFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~  528 (610)
T KOG0341|consen  486 DFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKN  528 (610)
T ss_pred             CCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeeccc
Confidence            9999999999999999999999999999999999999999865

>KOG0338|consensus

Probab=99.91  E-value=2.1e-24  Score=163.50  Aligned_cols=130  Identities=32%  Similarity=0.540  Sum_probs=122.0

Q ss_pred             CCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccc
Q psy576           30 AGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG  109 (159)
Q Consensus        30 ~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g  109 (159)
                      +..+...|..++.......++||+.|++.|..+.-+|--.|++++-+||.+++.+|.+.++.|++.+++|||||+++++|
T Consensus       410 e~dRea~l~~l~~rtf~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRG  489 (691)
T KOG0338|consen  410 EGDREAMLASLITRTFQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRG  489 (691)
T ss_pred             ccccHHHHHHHHHHhcccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhcc
Confidence            35677788888888788899999999999999999888889999999999999999999999999999999999999999


Q ss_pred             cccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccccC
Q psy576          110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR  159 (159)
Q Consensus       110 ~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~~  159 (159)
                      +||+.+..||||..|.+...|+||+||+.|.|+.|..+.|+..+|.+++|
T Consensus       490 LDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK  539 (691)
T KOG0338|consen  490 LDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLK  539 (691)
T ss_pred             CCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHH
Confidence            99999999999999999999999999999999999999999999877653

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

Probab=99.91  E-value=3.7e-24  Score=173.92  Aligned_cols=118  Identities=23%  Similarity=0.284  Sum_probs=106.6

Q ss_pred             hHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC--------CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC
Q psy576           33 PVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYD--------GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE  104 (159)
Q Consensus        33 k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~  104 (159)
                      +...+..++..  +.++||||+|++.++.++..+++.        +.++..+||++++++|.+++++|++|++++||||+
T Consensus       260 ~~~~l~~l~~~--~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd  337 (742)
T TIGR03817       260 AADLLADLVAE--GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTN  337 (742)
T ss_pred             HHHHHHHHHHC--CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECc
Confidence            45556666653  578999999999999999988653        45688999999999999999999999999999999


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecC
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      ++++|+|+|++++||+++.|.+..+|.||+||+||.|..|.++++...
T Consensus       338 ~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~  385 (742)
T TIGR03817       338 ALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARD  385 (742)
T ss_pred             hHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCC
Confidence            999999999999999999999999999999999999999999988864

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.

>KOG0345|consensus

Probab=99.91  E-value=4.6e-24  Score=160.14  Aligned_cols=140  Identities=26%  Similarity=0.399  Sum_probs=127.7

Q ss_pred             hhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHh
Q psy576           16 VKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        16 ~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      .++.+..+|..+.. ..|...+..++......++|||++|=..++..+..+...  +.++..+||.|...+|.++++.|.
T Consensus       226 tPS~L~~~Y~v~~a-~eK~~~lv~~L~~~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~  304 (567)
T KOG0345|consen  226 TPSSLALEYLVCEA-DEKLSQLVHLLNNNKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFR  304 (567)
T ss_pred             CchhhcceeeEecH-HHHHHHHHHHHhccccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHH
Confidence            55667788888887 799999999999888899999999999999988887554  678999999999999999999999


Q ss_pred             cCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           94 TGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        94 ~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      +..-.+|+||+++++|+|||++++|+++|+|.++..|.||+||++|.|+.|.+++|..+.|.+
T Consensus       305 ~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~a  367 (567)
T KOG0345|consen  305 KLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEA  367 (567)
T ss_pred             hccCceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHH
Confidence            988889999999999999999999999999999999999999999999999999999886654

>KOG0336|consensus

Probab=99.90  E-value=5.6e-24  Score=157.91  Aligned_cols=138  Identities=29%  Similarity=0.568  Sum_probs=124.6

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcC-CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLG-IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~-~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      .+.+.+ .+..+.+|++.+...+..+ ...++||||.++-.|+.+..-|.-.++..-.+||.-.+.+|+..++.|+.|+.
T Consensus       438 sVkQ~i-~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~v  516 (629)
T KOG0336|consen  438 SVKQNI-IVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEV  516 (629)
T ss_pred             eeeeeE-EecccHHHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCce
Confidence            455666 4555578888888888754 55689999999999999999888889999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      +|||+|+.+++|+|+|+++||+|||+|.+.++|.||+||.||.|+.|..+.|.+..|.+.
T Consensus       517 rILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~  576 (629)
T KOG0336|consen  517 RILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSM  576 (629)
T ss_pred             EEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhHHH
Confidence            999999999999999999999999999999999999999999999999999999887654

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.90  E-value=4.5e-23  Score=169.68  Aligned_cols=123  Identities=22%  Similarity=0.255  Sum_probs=113.4

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHH-hCCCceEEEecCCCHHHHHHHHHHHhcC--CeeEEEEeCCcc
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELI-YDGINVDVIHSDRTQKQRDNVVRSFRTG--RIWILITTELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~-~~~~~~~~~~~~~~~~~r~~~~~~f~~~--~~~vlv~t~~~~  107 (159)
                      +.|.+.|.+++......++||||++...+..+.+.|+ ..|+++..+||+|+..+|.++++.|+++  ...|||||++++
T Consensus       478 d~Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgs  557 (956)
T PRK04914        478 DPRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGS  557 (956)
T ss_pred             CHHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhc
Confidence            5688899999987778899999999999999999994 5689999999999999999999999984  589999999999


Q ss_pred             cccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576          108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus       108 ~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      +|+|++.+++||+||.|+++..|.||+||++|.|+++.+.+++...
T Consensus       558 eGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~  603 (956)
T PRK04914        558 EGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYL  603 (956)
T ss_pred             cCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccC
Confidence            9999999999999999999999999999999999999887776543

>KOG0346|consensus

Probab=99.90  E-value=2.2e-23  Score=155.63  Aligned_cols=155  Identities=28%  Similarity=0.437  Sum_probs=139.2

Q ss_pred             CcccccccchhhHHhh----------------hhccceeeeecCCCCChHHHHHHHHh-cCCCCCEEEEecchHHHHHHH
Q psy576            1 MAVDFNHTNPALKRRV----------------KSNLARMYRETEGAGSPVQAQDETIL-LGIEPPVLVFVQSKERAQELY   63 (159)
Q Consensus         1 m~~~~~~~~~~~~~~~----------------~~~i~~~~~~~~~~~~k~~~l~~~~~-~~~~~~~lif~~~~~~~~~l~   63 (159)
                      ||||+++....+...+                .+++.++++.+++ ++|+.++..+++ ..-.++.|||+++.+.+..+.
T Consensus       207 mSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse-~DKflllyallKL~LI~gKsliFVNtIdr~YrLk  285 (569)
T KOG0346|consen  207 MSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSE-EDKFLLLYALLKLRLIRGKSLIFVNTIDRCYRLK  285 (569)
T ss_pred             ehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEecc-chhHHHHHHHHHHHHhcCceEEEEechhhhHHHH
Confidence            7888888776664432                3678899999995 899999998887 356789999999999999999


Q ss_pred             HHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC-----------------------------------Cccc
Q psy576           64 NELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE-----------------------------------LLGR  108 (159)
Q Consensus        64 ~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~-----------------------------------~~~~  108 (159)
                      -.|.+.|++.+++.|.+|.+.|..++++|+.|-++++|||+                                   -+.+
T Consensus       286 LfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsR  365 (569)
T KOG0346|consen  286 LFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSR  365 (569)
T ss_pred             HHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCccccccccCchhchhc
Confidence            99999999999999999999999999999999999999998                                   1468


Q ss_pred             ccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576          109 GIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus       109 g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      |+|+..+..|+|+|.|.+...|+||+||++|.+++|.++.|+.+.+..
T Consensus       366 GIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~  413 (569)
T KOG0346|consen  366 GIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEF  413 (569)
T ss_pred             cccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHh
Confidence            999999999999999999999999999999999999999999987653

>KOG0343|consensus

Probab=99.90  E-value=5.5e-23  Score=157.14  Aligned_cols=139  Identities=27%  Similarity=0.417  Sum_probs=131.8

Q ss_pred             hhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHH
Q psy576           15 RVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      -+++++.++|+.+.. ..|+..|.-.+......+.|||+.|-+++..+++.++..  |+++..+||+|++..|.+++..|
T Consensus       283 atP~~L~Q~y~~v~l-~~Ki~~L~sFI~shlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F  361 (758)
T KOG0343|consen  283 ATPSNLQQSYVIVPL-EDKIDMLWSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKF  361 (758)
T ss_pred             cChhhhhheEEEEeh-hhHHHHHHHHHHhccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHH
Confidence            457788999999988 799999999999988999999999999999999998765  88999999999999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      ...+--||+||+++++|+|+|.+++||.+|+|.++..|+||+||+.|.+..|.++++..+.|
T Consensus       362 ~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psE  423 (758)
T KOG0343|consen  362 VRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSE  423 (758)
T ss_pred             HHhcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchh
Confidence            99999999999999999999999999999999999999999999999999999999999887

>KOG0327|consensus

Probab=99.89  E-value=5.8e-23  Score=150.86  Aligned_cols=141  Identities=38%  Similarity=0.635  Sum_probs=132.2

Q ss_pred             hhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc
Q psy576           15 RVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      ...+.++++|...... .|+..|.++..  ...+.+|||++.+.++.+...|..+++.+..+||.|.+.+|..++..|+.
T Consensus       235 ltl~gikq~~i~v~k~-~k~~~l~dl~~--~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~  311 (397)
T KOG0327|consen  235 LTLEGIKQFYINVEKE-EKLDTLCDLYR--RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRS  311 (397)
T ss_pred             hhhhheeeeeeecccc-ccccHHHHHHH--hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhc
Confidence            5568999999999994 59999999999  66789999999999999999998899999999999999999999999999


Q ss_pred             CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcccc
Q psy576           95 GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL  158 (159)
Q Consensus        95 ~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~  158 (159)
                      |+.+|||+|+.+++|+|+..++.|++|+.|...++|.+|+||+||.|.+|.++.++...|...+
T Consensus       312 gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~l  375 (397)
T KOG0327|consen  312 GSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDL  375 (397)
T ss_pred             CCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHH
Confidence            9999999999999999999999999999999999999999999999999999999998776543

>KOG0350|consensus

Probab=99.88  E-value=1.7e-22  Score=152.81  Aligned_cols=139  Identities=32%  Similarity=0.436  Sum_probs=125.0

Q ss_pred             hhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHH-h---CCCceEEEecCCCHHHHHHHHHHH
Q psy576           17 KSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELI-Y---DGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        17 ~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~-~---~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ++.+.++.+.++. ..|...+..++......++|+|+++.+.+.++...|+ .   .+.++..++|+++...|.+.++.|
T Consensus       401 p~~l~~~~vv~~~-~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f  479 (620)
T KOG0350|consen  401 PSSLSHRLVVTEP-KFKPLAVYALITSNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKF  479 (620)
T ss_pred             Chhhhhceeeccc-ccchHhHHHHHHHhhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHH
Confidence            3455566666655 7899999999998888899999999999999999886 2   256777899999999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      ..|++.+||||+++++|+|+.+++.||+|++|.+...|.||+||++|+|+.|.|+.+....+..
T Consensus       480 ~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r  543 (620)
T KOG0350|consen  480 AKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKR  543 (620)
T ss_pred             hcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccch
Confidence            9999999999999999999999999999999999999999999999999999999999987653

>KOG0334|consensus

Probab=99.88  E-value=2.6e-22  Score=162.12  Aligned_cols=154  Identities=32%  Similarity=0.542  Sum_probs=138.0

Q ss_pred             cccccccchhhHH---------------hhhhccceeeeecCCCCChHHHHHHHHhc-CCCCCEEEEecchHHHHHHHHH
Q psy576            2 AVDFNHTNPALKR---------------RVKSNLARMYRETEGAGSPVQAQDETILL-GIEPPVLVFVQSKERAQELYNE   65 (159)
Q Consensus         2 ~~~~~~~~~~~~~---------------~~~~~i~~~~~~~~~~~~k~~~l~~~~~~-~~~~~~lif~~~~~~~~~l~~~   65 (159)
                      |++|+.....++.               .+-+.+.+.+..+..+..|+..|.+++.. ....+++|||...+.|+.+.+-
T Consensus       553 Satfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~  632 (997)
T KOG0334|consen  553 SATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRD  632 (997)
T ss_pred             hhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHH
Confidence            5666666554433               33357788889999779999999999973 4578999999999999999999


Q ss_pred             HHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcce
Q psy576           66 LIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGK  145 (159)
Q Consensus        66 l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~  145 (159)
                      |.+.++++..+||+.+..+|..++++|+++.+.+||+|+.+++|+|++.+..||||++|.+.++|.+|+||+||.|++|.
T Consensus       633 L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~  712 (997)
T KOG0334|consen  633 LQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGA  712 (997)
T ss_pred             HHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccce
Confidence            99999998889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCCCc
Q psy576          146 AVTFFTKQDA  155 (159)
Q Consensus       146 ~~~~~~~~~~  155 (159)
                      +++|..+.+.
T Consensus       713 AvtFi~p~q~  722 (997)
T KOG0334|consen  713 AVTFITPDQL  722 (997)
T ss_pred             eEEEeChHHh
Confidence            9999988543

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]

Probab=99.88  E-value=1.3e-21  Score=148.43  Aligned_cols=130  Identities=28%  Similarity=0.420  Sum_probs=113.2

Q ss_pred             eecCCCCChHHHHHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhCCCceE-EEe--------cCCCHHHHHHHHHH
Q psy576           25 RETEGAGSPVQAQDETIL----LGIEPPVLVFVQSKERAQELYNELIYDGINVD-VIH--------SDRTQKQRDNVVRS   91 (159)
Q Consensus        25 ~~~~~~~~k~~~l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~-~~~--------~~~~~~~r~~~~~~   91 (159)
                      ....-.+-|++.+.+++.    +..+.++|||++.+++++.+.++|.+.+.++. .+-        .||++.++.+++++
T Consensus       341 ~~~~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~  420 (542)
T COG1111         341 DESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQ  420 (542)
T ss_pred             ccccCCCccHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHH
Confidence            334445678888887775    34556899999999999999999998877663 333        36999999999999


Q ss_pred             HhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576           92 FRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus        92 f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |++|++.|||||+++++|+|||+++.||.|++..|+.-++||.||+||. .+|.+++++..+..
T Consensus       421 Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gtr  483 (542)
T COG1111         421 FRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGTR  483 (542)
T ss_pred             HhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCch
Confidence            9999999999999999999999999999999999999999999999999 78999999988743

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.87  E-value=1.8e-21  Score=160.98  Aligned_cols=97  Identities=26%  Similarity=0.384  Sum_probs=91.0

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC------CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD------GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLV  118 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~v  118 (159)
                      ..+++||||+|++.++.++..|++.      +..+..+||+++.++|..+++.|++|++++||||+++++|+|+|++++|
T Consensus       283 ~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~Vd~V  362 (876)
T PRK13767        283 EHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLV  362 (876)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCCCcEE
Confidence            3578999999999999999998763      3578999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCHHHHHHHHhhccCCC
Q psy576          119 VNYDFPSSAISYIHRIGRAGRGG  141 (159)
Q Consensus       119 i~~~~~~~~~~~~q~~GR~~R~g  141 (159)
                      |+++.|.+...|.||+||+||.+
T Consensus       363 I~~~~P~sv~~ylQRiGRaGR~~  385 (876)
T PRK13767        363 VLLGSPKSVSRLLQRIGRAGHRL  385 (876)
T ss_pred             EEeCCCCCHHHHHHhcccCCCCC
Confidence            99999999999999999999874

>KOG4284|consensus

Probab=99.87  E-value=3.9e-22  Score=154.92  Aligned_cols=137  Identities=33%  Similarity=0.447  Sum_probs=126.5

Q ss_pred             ccceeeeecCCCCC-------hHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHH
Q psy576           19 NLARMYRETEGAGS-------PVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        19 ~i~~~~~~~~~~~~-------k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      +|+++++.+.....       |++.|-+++..-+..++||||+....|+-++.+|...|+++.++.|.|++.+|..++++
T Consensus       238 GikQyv~~~~s~nnsveemrlklq~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~  317 (980)
T KOG4284|consen  238 GIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQ  317 (980)
T ss_pred             chhheeeeccCCcchHHHHHHHHHHHHHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHH
Confidence            77888888777433       77778888888788899999999999999999999999999999999999999999999


Q ss_pred             HhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576           92 FRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus        92 f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      ++.-..+|||+|+..++|+|-+.++.|||.|+|-+-..|+||+||+||+|..|.+++|+-..+.
T Consensus       318 lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  318 LRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             hhhceEEEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchh
Confidence            9999999999999999999999999999999999999999999999999999999999876654

>KOG0339|consensus

Probab=99.87  E-value=5.8e-22  Score=150.42  Aligned_cols=140  Identities=31%  Similarity=0.541  Sum_probs=130.0

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhc-CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILL-GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~-~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      +.|.+.+..+.....|+..|.+-|-. ...+++|+|+..+..++++...|+..++++..+||++.+.+|.+++..|+++.
T Consensus       439 ~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~  518 (731)
T KOG0339|consen  439 EDITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKR  518 (731)
T ss_pred             cchhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcC
Confidence            57888888888888899887766654 45579999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      ..|||+|+++.+|+|||++..|++||.-.+.+.+.||+||.||.|..|.++.|+++.|.++
T Consensus       519 ~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~f  579 (731)
T KOG0339|consen  519 KPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEF  579 (731)
T ss_pred             CceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechhhHHH
Confidence            9999999999999999999999999999999999999999999999999999999988764

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.87  E-value=1.8e-21  Score=155.88  Aligned_cols=108  Identities=23%  Similarity=0.281  Sum_probs=95.7

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHH-hcCCeeEEEEeCCcccccccCCCcEEEEe
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSF-RTGRIWILITTELLGRGIDFRTVRLVVNY  121 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f-~~~~~~vlv~t~~~~~g~~i~~~~~vi~~  121 (159)
                      .++++||||+++++++.+.+.|.+.  ++.+..+||++++.  ++.++.| ++|+.+|||||+++++|+|+|++++||++
T Consensus       394 ~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~  471 (675)
T PHA02653        394 KGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDT  471 (675)
T ss_pred             cCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEEC
Confidence            3468999999999999999999876  68899999999874  4566776 68999999999999999999999999999


Q ss_pred             c---CCC---------CHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          122 D---FPS---------SAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       122 ~---~~~---------~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      +   .|.         |.++|.||+||+||. .+|.|+.+++..+.
T Consensus       472 G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        472 GRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             CCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHh
Confidence            8   554         888999999999999 78999999987653

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.87  E-value=6.5e-21  Score=144.21  Aligned_cols=121  Identities=19%  Similarity=0.342  Sum_probs=99.3

Q ss_pred             CChHHHHHHHHhc-CCCCCEEEEecchHHHHHHHHHHHhCCC--ceEEEecCCCHHHHHHH----HHHHhcCCeeEEEEe
Q psy576           31 GSPVQAQDETILL-GIEPPVLVFVQSKERAQELYNELIYDGI--NVDVIHSDRTQKQRDNV----VRSFRTGRIWILITT  103 (159)
Q Consensus        31 ~~k~~~l~~~~~~-~~~~~~lif~~~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~~r~~~----~~~f~~~~~~vlv~t  103 (159)
                      ..+...+.+++.. ..++++||||+++++++.++..|++.+.  .+..+||++++.+|.+.    ++.|++++..|||||
T Consensus       206 ~~~~~~l~~l~~~~~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT  285 (358)
T TIGR01587       206 VGEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVAT  285 (358)
T ss_pred             ccCHHHHHHHHHHhhCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEEC
Confidence            3556666666653 3467899999999999999999987654  58999999999999764    888999999999999


Q ss_pred             CCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCc----ceEEEEecCCC
Q psy576          104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGRE----GKAVTFFTKQD  154 (159)
Q Consensus       104 ~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~----g~~~~~~~~~~  154 (159)
                      +++++|+|++ +++++++..|  ..+|.||+||+||.|..    |.++++....+
T Consensus       286 ~~~~~GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~~  337 (358)
T TIGR01587       286 QVIEASLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAPE  337 (358)
T ss_pred             cchhceeccC-CCEEEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecCC
Confidence            9999999996 7778887655  88999999999998843    36777766543

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.87  E-value=2.4e-21  Score=153.73  Aligned_cols=128  Identities=22%  Similarity=0.212  Sum_probs=108.7

Q ss_pred             eeecCCCCChHHHHHHHHhcC--CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEE
Q psy576           24 YRETEGAGSPVQAQDETILLG--IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILI  101 (159)
Q Consensus        24 ~~~~~~~~~k~~~l~~~~~~~--~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  101 (159)
                      ++.+.. ..|...|.+++...  .+.++||||+|.+.++.++..|.+.++++..+||.++  +++..+..+..++..|+|
T Consensus       450 ~v~~t~-~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~--~rE~~ii~~ag~~g~VlV  526 (656)
T PRK12898        450 EVFLTA-AAKWAAVAARVRELHAQGRPVLVGTRSVAASERLSALLREAGLPHQVLNAKQD--AEEAAIVARAGQRGRITV  526 (656)
T ss_pred             EEEeCH-HHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcH--HHHHHHHHHcCCCCcEEE
Confidence            333443 57888888888653  3578999999999999999999999999999999865  445555666666667999


Q ss_pred             EeCCcccccccC---CCc-----EEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          102 TTELLGRGIDFR---TVR-----LVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       102 ~t~~~~~g~~i~---~~~-----~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      ||+++++|+||+   .+.     +||+++.|.+...|.|++||+||.|.+|.++.+++..|
T Consensus       527 ATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD  587 (656)
T PRK12898        527 ATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLED  587 (656)
T ss_pred             EccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhH
Confidence            999999999999   555     99999999999999999999999999999999998755

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.87  E-value=4.4e-21  Score=158.24  Aligned_cols=110  Identities=18%  Similarity=0.275  Sum_probs=101.8

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEec
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD  122 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~  122 (159)
                      .++++++||++.+.++.+++.|++.  +.++..+||+|+.++|.+++++|.+|+.+|||||+++++|+|+|++++||+++
T Consensus       659 ~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~~  738 (926)
T TIGR00580       659 RGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIER  738 (926)
T ss_pred             cCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEEec
Confidence            4678999999999999999999874  67899999999999999999999999999999999999999999999999998


Q ss_pred             CCC-CHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          123 FPS-SAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       123 ~~~-~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      .|. ...+|.|++||+||.|..|.|++++.+.+
T Consensus       739 a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~~  771 (926)
T TIGR00580       739 ADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQK  771 (926)
T ss_pred             CCCCCHHHHHHHhcCCCCCCCCeEEEEEECCcc
Confidence            864 67899999999999999999999987643

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.

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=99.87  E-value=1.2e-21  Score=117.45  Aligned_cols=78  Identities=46%  Similarity=0.767  Sum_probs=75.1

Q ss_pred             HHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCC
Q psy576           64 NELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGG  141 (159)
Q Consensus        64 ~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g  141 (159)
                      +.|++.++++..+||+++..+|.++++.|++++..|||||+++++|+|+|.+++|+++++|++...|.|++||++|.|
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            357888999999999999999999999999999999999999999999999999999999999999999999999986

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 ....

>KOG0347|consensus

Probab=99.87  E-value=1.8e-22  Score=154.19  Aligned_cols=114  Identities=30%  Similarity=0.411  Sum_probs=109.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFP  124 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~  124 (159)
                      ..++.||||++.+.+.+++.+|+..+++...+|+.|.+..|.+-++.|++....|||||+++++|+|||.+.|||||-+|
T Consensus       462 yPGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVP  541 (731)
T KOG0347|consen  462 YPGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVP  541 (731)
T ss_pred             cCCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHhhccCCCCcceEEEEecCCCcccc
Q psy576          125 SSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL  158 (159)
Q Consensus       125 ~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~  158 (159)
                      .+.+-|.||.||+.|.+..|..++++.+.|...|
T Consensus       542 rtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~  575 (731)
T KOG0347|consen  542 RTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPL  575 (731)
T ss_pred             CccceeEecccccccccCCCeEEEEeChHHhHHH
Confidence            9999999999999999999999999999886544

>KOG0348|consensus

Probab=99.86  E-value=2.8e-21  Score=147.40  Aligned_cols=141  Identities=26%  Similarity=0.461  Sum_probs=120.6

Q ss_pred             hhhccceeeeecCCCCChHHHHHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhC----------------------
Q psy576           16 VKSNLARMYRETEGAGSPVQAQDETIL----LGIEPPVLVFVQSKERAQELYNELIYD----------------------   69 (159)
Q Consensus        16 ~~~~i~~~~~~~~~~~~k~~~l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~----------------------   69 (159)
                      .++.+.+.|..+.. +-++-.|..++.    .....++|||+.+.+.++.-+..+...                      
T Consensus       392 iPeqL~qry~vVPp-KLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~  470 (708)
T KOG0348|consen  392 IPEQLLQRYTVVPP-KLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFM  470 (708)
T ss_pred             CcHHhhhceEecCC-chhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhh
Confidence            46677788888877 555555555553    345568999999999999887776432                      


Q ss_pred             CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576           70 GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus        70 ~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      +.++..+||+|.+++|..+++.|..+.-.||+||+++++|+|+|++.+||.|++|.+.++|+||+||+.|.|..|.++.|
T Consensus       471 ~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLf  550 (708)
T KOG0348|consen  471 DLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLF  550 (708)
T ss_pred             cceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEE
Confidence            23478899999999999999999999888999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCccc
Q psy576          150 FTKQDAPL  157 (159)
Q Consensus       150 ~~~~~~~~  157 (159)
                      ..+.|.+.
T Consensus       551 L~P~Eaey  558 (708)
T KOG0348|consen  551 LLPSEAEY  558 (708)
T ss_pred             ecccHHHH
Confidence            99988763

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.86  E-value=9.3e-21  Score=153.33  Aligned_cols=108  Identities=23%  Similarity=0.378  Sum_probs=96.7

Q ss_pred             CCCCEEEEecch--------HHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCC
Q psy576           45 IEPPVLVFVQSK--------ERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRT  114 (159)
Q Consensus        45 ~~~~~lif~~~~--------~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~  114 (159)
                      .+++++|||+..        ..+..+++.|.+.  +.++..+||+|+.++|..++++|++|+.+|||||+++++|+|+|+
T Consensus       470 ~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~  549 (681)
T PRK10917        470 KGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPN  549 (681)
T ss_pred             cCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccCC
Confidence            567899999854        4566777877665  468999999999999999999999999999999999999999999


Q ss_pred             CcEEEEecCCC-CHHHHHHHHhhccCCCCcceEEEEecC
Q psy576          115 VRLVVNYDFPS-SAISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       115 ~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      +++||+++.|. ....+.|++||+||.|..|.|++++..
T Consensus       550 v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~  588 (681)
T PRK10917        550 ATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKD  588 (681)
T ss_pred             CcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECC
Confidence            99999999886 578899999999999999999999963

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=4.6e-21  Score=154.91  Aligned_cols=122  Identities=23%  Similarity=0.314  Sum_probs=109.7

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+..  ..+.|+||||+|.+.++.++..|.+.++++..+||.+..+++..+...+..|  .|+|||+++++
T Consensus       411 ~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgR  488 (790)
T PRK09200        411 DEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGR  488 (790)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhc
Confidence            5688888887764  3678999999999999999999999999999999999888887777776666  69999999999


Q ss_pred             cccc---CCCc-----EEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          109 GIDF---RTVR-----LVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       109 g~~i---~~~~-----~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |+||   |.+.     +||+++.|.+...|.|++||+||.|.+|.++.|++..|
T Consensus       489 G~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD  542 (790)
T PRK09200        489 GTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLED  542 (790)
T ss_pred             CcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchH
Confidence            9999   6888     99999999999999999999999999999999998655

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.86  E-value=8.8e-21  Score=159.30  Aligned_cols=109  Identities=17%  Similarity=0.210  Sum_probs=99.4

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEec
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD  122 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~  122 (159)
                      .+++++|||++.+.++.+++.|.+.  +.++..+||+|+.++|.+++.+|++|+.+|||||+++++|+|+|++++||..+
T Consensus       808 r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~  887 (1147)
T PRK10689        808 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIER  887 (1147)
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEec
Confidence            4578999999999999999999876  67899999999999999999999999999999999999999999999999665


Q ss_pred             CC-CCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576          123 FP-SSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus       123 ~~-~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      .. .+...|.|++||+||.|..|.|++++...
T Consensus       888 ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~  919 (1147)
T PRK10689        888 ADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  919 (1147)
T ss_pred             CCCCCHHHHHHHhhccCCCCCceEEEEEeCCC
Confidence            43 57788999999999999999999988654

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.86  E-value=3.7e-21  Score=157.19  Aligned_cols=117  Identities=16%  Similarity=0.317  Sum_probs=102.9

Q ss_pred             HHHHHhcCCCCCEEEEecchHHHHHHHHHHHh---CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccC
Q psy576           37 QDETILLGIEPPVLVFVQSKERAQELYNELIY---DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFR  113 (159)
Q Consensus        37 l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~  113 (159)
                      +..++.. ..+++|||+++.++++.+++.|.+   .++.+..+||+++.++|.++++.|.+|+.+|||||+++++|++||
T Consensus       201 l~~~l~~-~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp  279 (819)
T TIGR01970       201 VEHALAS-ETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIE  279 (819)
T ss_pred             HHHHHHh-cCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhccccc
Confidence            3344433 467899999999999999999976   368899999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCC------------------CHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          114 TVRLVVNYDFPS------------------SAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       114 ~~~~vi~~~~~~------------------~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      ++++||+++.+.                  |.+++.||.||+||. .+|.|+.+++..+.
T Consensus       280 ~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~  338 (819)
T TIGR01970       280 GIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQH  338 (819)
T ss_pred             CceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHH
Confidence            999999998774                  345699999999999 79999999987653

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.

>KOG0351|consensus

Probab=99.86  E-value=2.3e-21  Score=158.85  Aligned_cols=146  Identities=22%  Similarity=0.355  Sum_probs=126.6

Q ss_pred             hHHhhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHH
Q psy576           12 LKRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        12 ~~~~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..+..++++...+..-.....-...+............||||.++.+++.++..|+..+....++|++|++.+|..+..+
T Consensus       451 ~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~  530 (941)
T KOG0351|consen  451 KSSFNRPNLKYEVSPKTDKDALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKA  530 (941)
T ss_pred             cccCCCCCceEEEEeccCccchHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHH
Confidence            34455566666655555434444445555556677889999999999999999999999999999999999999999999


Q ss_pred             HhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           92 FRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        92 f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      |..++++|+|||=+.++|+|-|++..||||+.|++.+.|.|-+||+||.|....|++|+...|...
T Consensus       531 w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~  596 (941)
T KOG0351|consen  531 WMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADISE  596 (941)
T ss_pred             HhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEecchhHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999887643

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.85  E-value=4.7e-21  Score=156.70  Aligned_cols=133  Identities=20%  Similarity=0.312  Sum_probs=109.6

Q ss_pred             cceeeeecCCCCChHH-----HHHHHHhcCCCCCEEEEecchHHHHHHHHHHHh---CCCceEEEecCCCHHHHHHHHHH
Q psy576           20 LARMYRETEGAGSPVQ-----AQDETILLGIEPPVLVFVQSKERAQELYNELIY---DGINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        20 i~~~~~~~~~~~~k~~-----~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      +.++|..... ..+.+     .+..++.. ..+.+|||+++.++++.+++.|.+   .++.+..+||+++.+++.++++.
T Consensus       183 V~~~y~~~~~-~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~  260 (812)
T PRK11664        183 VERRYQPLPA-HQRFDEAVARATAELLRQ-ESGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILP  260 (812)
T ss_pred             ceEEeccCch-hhhHHHHHHHHHHHHHHh-CCCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhcc
Confidence            4455554443 33332     34444443 467899999999999999999986   46789999999999999999999


Q ss_pred             HhcCCeeEEEEeCCcccccccCCCcEEEEecCCC------------------CHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576           92 FRTGRIWILITTELLGRGIDFRTVRLVVNYDFPS------------------SAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus        92 f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~------------------~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      |.+|+.+|+|||+++++|++||++++||+++.+.                  |.++|.||.||+||. .+|.|+.+++..
T Consensus       261 ~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~  339 (812)
T PRK11664        261 APAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKE  339 (812)
T ss_pred             ccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHH
Confidence            9999999999999999999999999999987664                  346899999999999 699999999876


Q ss_pred             Cc
Q psy576          154 DA  155 (159)
Q Consensus       154 ~~  155 (159)
                      +.
T Consensus       340 ~~  341 (812)
T PRK11664        340 QA  341 (812)
T ss_pred             HH
Confidence            43

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.85  E-value=2.5e-20  Score=149.85  Aligned_cols=108  Identities=22%  Similarity=0.364  Sum_probs=96.4

Q ss_pred             CCCCEEEEecch--------HHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCC
Q psy576           45 IEPPVLVFVQSK--------ERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRT  114 (159)
Q Consensus        45 ~~~~~lif~~~~--------~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~  114 (159)
                      .+++++|||+..        ..++.+++.|.+.  +.++..+||+|++++|..+++.|++|+.+|||||+++++|+|+|+
T Consensus       447 ~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~  526 (630)
T TIGR00643       447 KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN  526 (630)
T ss_pred             hCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccCC
Confidence            467899999865        4566777777653  678999999999999999999999999999999999999999999


Q ss_pred             CcEEEEecCCC-CHHHHHHHHhhccCCCCcceEEEEecC
Q psy576          115 VRLVVNYDFPS-SAISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       115 ~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      +++||+++.|. ....|.|++||+||.|..|.|++++..
T Consensus       527 v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~~  565 (630)
T TIGR00643       527 ATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKN  565 (630)
T ss_pred             CcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEECC
Confidence            99999999885 688999999999999999999999843

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.84  E-value=4e-20  Score=148.33  Aligned_cols=125  Identities=31%  Similarity=0.409  Sum_probs=111.4

Q ss_pred             CCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcc
Q psy576           30 AGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG  107 (159)
Q Consensus        30 ~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~  107 (159)
                      ..++++.|.+.+..  ..+.+++|||++++.++.+++.|.+.++++..+||+++..+|.++++.|++|++.|+|||+.++
T Consensus       424 ~~~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~  503 (655)
T TIGR00631       424 TDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLR  503 (655)
T ss_pred             ccchHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhc
Confidence            34566666666653  3567899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCcEEEEec-----CCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          108 RGIDFRTVRLVVNYD-----FPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       108 ~g~~i~~~~~vi~~~-----~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      +|+|+|++++|++++     .|.+..+|+|++||+||. ..|.+++|.+..+.
T Consensus       504 rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~  555 (655)
T TIGR00631       504 EGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITD  555 (655)
T ss_pred             CCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCH
Confidence            999999999999987     788999999999999998 58999999887653

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

>PRK02362 ski2-like helicase; Provisional

Probab=99.84  E-value=2.4e-20  Score=152.39  Aligned_cols=109  Identities=27%  Similarity=0.413  Sum_probs=96.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC------------------------------------CCceEEEecCCCHHHHHHH
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD------------------------------------GINVDVIHSDRTQKQRDNV   88 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~------------------------------------~~~~~~~~~~~~~~~r~~~   88 (159)
                      .++++||||++++.++.++..|...                                    ...+.++||++++.+|..+
T Consensus       242 ~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~v  321 (737)
T PRK02362        242 EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELV  321 (737)
T ss_pred             cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHH
Confidence            5678999999999999888777532                                    1257899999999999999


Q ss_pred             HHHHhcCCeeEEEEeCCcccccccCCCcEEEE----ec-----CCCCHHHHHHHHhhccCCCC--cceEEEEecCC
Q psy576           89 VRSFRTGRIWILITTELLGRGIDFRTVRLVVN----YD-----FPSSAISYIHRIGRAGRGGR--EGKAVTFFTKQ  153 (159)
Q Consensus        89 ~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~~-----~~~~~~~~~q~~GR~~R~g~--~g~~~~~~~~~  153 (159)
                      ++.|++|.++|||||+++++|+|+|..++||+    |+     .|.+..+|.||+||+||.|.  .|.++++....
T Consensus       322 e~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~  397 (737)
T PRK02362        322 EDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSY  397 (737)
T ss_pred             HHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCc
Confidence            99999999999999999999999999999986    54     57899999999999999984  49999998764

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.84  E-value=3.5e-20  Score=148.90  Aligned_cols=122  Identities=21%  Similarity=0.360  Sum_probs=107.9

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+..  ..+.|+||||+|.+.++.+...|.+.++++..+||.++.+++..+..+++.|  .|+|||+++++
T Consensus       407 ~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgR  484 (762)
T TIGR03714       407 PEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGR  484 (762)
T ss_pred             HHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEcccccc
Confidence            4688888777754  4678999999999999999999999999999999999988887776666666  69999999999


Q ss_pred             ccccC---------CCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          109 GIDFR---------TVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       109 g~~i~---------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |+|||         .+.+|++++.|....+ .|++||+||.|.+|.++.|++..|.
T Consensus       485 GtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       485 GTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             ccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchh
Confidence            99999         8999999999987766 9999999999999999999987653

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.

>PRK13766 Hef nuclease; Provisional

Probab=99.84  E-value=1.1e-19  Score=149.46  Aligned_cols=125  Identities=26%  Similarity=0.427  Sum_probs=111.8

Q ss_pred             CCCChHHHHHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecC--------CCHHHHHHHHHHHhcCC
Q psy576           29 GAGSPVQAQDETILL----GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSD--------RTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        29 ~~~~k~~~l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~--------~~~~~r~~~~~~f~~~~   96 (159)
                      ....|...|.+++..    ....++||||.+...++.+++.|...++++..+||.        ++..+|..+++.|++|+
T Consensus       344 ~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~  423 (773)
T PRK13766        344 IEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGE  423 (773)
T ss_pred             cCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCC
Confidence            345688888888754    467789999999999999999998888888899886        89999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      ..+||+|+++++|+|+|.+++||+|++|++...|.||+||+||.|. |.+++++..+.
T Consensus       424 ~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~t  480 (773)
T PRK13766        424 FNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKGT  480 (773)
T ss_pred             CCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCCC
Confidence            9999999999999999999999999999999999999999999865 77888877554

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.83  E-value=1.1e-19  Score=142.79  Aligned_cols=115  Identities=17%  Similarity=0.175  Sum_probs=100.4

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEe-CCcc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT-ELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t-~~~~  107 (159)
                      ..+...+.+++..  ..+.+++|||.+.++++.+++.|++.+.++..+||+++.++|..+++.|++++..||||| ++++
T Consensus       327 ~~Rn~~I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~  406 (501)
T PHA02558        327 TKRNKWIANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFS  406 (501)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceec
Confidence            3455555555432  245678999999999999999999999999999999999999999999999999999998 8999


Q ss_pred             cccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcce
Q psy576          108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGK  145 (159)
Q Consensus       108 ~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~  145 (159)
                      +|+|+|++++||.+.++.+...|.||+||++|.+..+.
T Consensus       407 eG~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K~  444 (501)
T PHA02558        407 TGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKS  444 (501)
T ss_pred             cccccccccEEEEecCCcchhhhhhhhhccccCCCCCc
Confidence            99999999999999999999999999999999885543

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.83  E-value=1.6e-19  Score=145.42  Aligned_cols=122  Identities=32%  Similarity=0.383  Sum_probs=108.7

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      .+++..+.+.+..  ..+.+++|||++.+.++.+.+.|...++++..+||+++..+|..+++.|+.|+..|+|||+.+++
T Consensus       429 ~~q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~r  508 (652)
T PRK05298        429 KGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE  508 (652)
T ss_pred             cccHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhC
Confidence            4556666665543  24668999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCcEEEEecC-----CCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576          109 GIDFRTVRLVVNYDF-----PSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus       109 g~~i~~~~~vi~~~~-----~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      |+|+|++++|++++.     |.+...|.||+||+||. ..|.++.|++..
T Consensus       509 Gfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~  557 (652)
T PRK05298        509 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKI  557 (652)
T ss_pred             CccccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCC
Confidence            999999999998764     78999999999999997 689999999854

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.82  E-value=1.8e-19  Score=144.17  Aligned_cols=122  Identities=25%  Similarity=0.289  Sum_probs=110.0

Q ss_pred             CChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+.  ...+.|+||||++.+.++.++..|.+.+++...+|+.  ..+|+..+..|..+...|+|||++++|
T Consensus       388 ~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgR  465 (745)
T TIGR00963       388 EEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGR  465 (745)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccC
Confidence            456666666552  3467899999999999999999999999999999997  778999999999999999999999999


Q ss_pred             ccccCC-------CcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          109 GIDFRT-------VRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       109 g~~i~~-------~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |+||+.       ..+||+++.|.+...|.|++||+||.|.+|.+..|++..|
T Consensus       466 GtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD  518 (745)
T TIGR00963       466 GTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLED  518 (745)
T ss_pred             CcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccH
Confidence            999998       5599999999999999999999999999999999998765

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.82  E-value=7.4e-20  Score=155.43  Aligned_cols=107  Identities=27%  Similarity=0.332  Sum_probs=92.9

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCC---------------------------------CceEEEecCCCHHHHHHHHHH
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDG---------------------------------INVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~---------------------------------~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      .+.++||||+|++.++.++..|++..                                 ..+..+||+++.++|..+++.
T Consensus       243 ~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~  322 (1490)
T PRK09751        243 RHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQA  322 (1490)
T ss_pred             cCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHHHH
Confidence            45789999999999999999886531                                 125688999999999999999


Q ss_pred             HhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCC-CcceEEEEec
Q psy576           92 FRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGG-REGKAVTFFT  151 (159)
Q Consensus        92 f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g-~~g~~~~~~~  151 (159)
                      |++|++++||||+.+++|+|++++++||+++.|.+..+|+||+||+||.. ..+.++++..
T Consensus       323 fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~  383 (1490)
T PRK09751        323 LKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPR  383 (1490)
T ss_pred             HHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeC
Confidence            99999999999999999999999999999999999999999999999963 3344554433

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.81  E-value=3.3e-19  Score=143.13  Aligned_cols=123  Identities=15%  Similarity=0.194  Sum_probs=104.5

Q ss_pred             CCCChHHHHHHHHhcC--CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC-CeeEEEEeCC
Q psy576           29 GAGSPVQAQDETILLG--IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG-RIWILITTEL  105 (159)
Q Consensus        29 ~~~~k~~~l~~~~~~~--~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vlv~t~~  105 (159)
                      .+..|+..+..++...  .++++||||.+...++.++..|.     +.++||.++..+|..+++.|+.+ +.++||+|++
T Consensus       477 ~np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkV  551 (732)
T TIGR00603       477 MNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKV  551 (732)
T ss_pred             hChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHHhCCCccEEEEecc
Confidence            3467888877777643  66799999999999998888773     46799999999999999999875 7899999999


Q ss_pred             cccccccCCCcEEEEecCC-CCHHHHHHHHhhccCCCCcceE-------EEEecCCCcc
Q psy576          106 LGRGIDFRTVRLVVNYDFP-SSAISYIHRIGRAGRGGREGKA-------VTFFTKQDAP  156 (159)
Q Consensus       106 ~~~g~~i~~~~~vi~~~~~-~~~~~~~q~~GR~~R~g~~g~~-------~~~~~~~~~~  156 (159)
                      +.+|+|+|++++||+++.| .+...|.||+||++|.+..|.+       +.+++.+..+
T Consensus       552 gdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E  610 (732)
T TIGR00603       552 GDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQE  610 (732)
T ss_pred             cccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchH
Confidence            9999999999999999987 4999999999999999866654       6677666543

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).

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

Probab=99.81  E-value=1.1e-19  Score=139.91  Aligned_cols=152  Identities=21%  Similarity=0.306  Sum_probs=124.5

Q ss_pred             cccccccchhhHHhhh---------hccceeeeecCCCCChHHHHHHHHhc--------CCCCCEEEEecchHHHHHHHH
Q psy576            2 AVDFNHTNPALKRRVK---------SNLARMYRETEGAGSPVQAQDETILL--------GIEPPVLVFVQSKERAQELYN   64 (159)
Q Consensus         2 ~~~~~~~~~~~~~~~~---------~~i~~~~~~~~~~~~k~~~l~~~~~~--------~~~~~~lif~~~~~~~~~l~~   64 (159)
                      |||+.++....+..-.         -.+......+..+.+|..++.++.+.        +..+++|||++|++.+.+++.
T Consensus       379 SATVgNp~elA~~l~a~lV~y~~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~  458 (830)
T COG1202         379 SATVGNPEELAKKLGAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELAD  458 (830)
T ss_pred             EeecCChHHHHHHhCCeeEeecCCCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHH
Confidence            5666665443332222         24445666667678999999988862        345789999999999999999


Q ss_pred             HHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE---ecCCC-CHHHHHHHHhhccCC
Q psy576           65 ELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN---YDFPS-SAISYIHRIGRAGRG  140 (159)
Q Consensus        65 ~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~---~~~~~-~~~~~~q~~GR~~R~  140 (159)
                      .|...|+++.++|++++..+|..+..+|.++++.++|+|-+++.|+|+|.-.+|+-   ++..| ++.+|.||.||+||.
T Consensus       459 ~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp  538 (830)
T COG1202         459 ALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRP  538 (830)
T ss_pred             HhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHHHHHcccccCCHHHHHHHhcccCCC
Confidence            99999999999999999999999999999999999999999999999998886652   34444 899999999999999


Q ss_pred             C--CcceEEEEecCC
Q psy576          141 G--REGKAVTFFTKQ  153 (159)
Q Consensus       141 g--~~g~~~~~~~~~  153 (159)
                      +  ..|.+++++.++
T Consensus       539 ~yHdrGkVyllvepg  553 (830)
T COG1202         539 DYHDRGKVYLLVEPG  553 (830)
T ss_pred             CcccCceEEEEecCC
Confidence            8  669898888765

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.81  E-value=5.7e-19  Score=142.39  Aligned_cols=122  Identities=25%  Similarity=0.328  Sum_probs=108.6

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+..  ..+.|+||||.|+..++.++..|.+.+++...+|+++...++..+..+++.|.  |+|||++++|
T Consensus       423 ~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGR  500 (796)
T PRK12906        423 DSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGR  500 (796)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccC
Confidence            4577777777743  36789999999999999999999999999999999988777777777777776  9999999999


Q ss_pred             ccccC---CCc-----EEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          109 GIDFR---TVR-----LVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       109 g~~i~---~~~-----~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |.||+   .+.     +||+++.|.+...|.|+.||+||.|.+|.+..+++..|
T Consensus       501 GtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD  554 (796)
T PRK12906        501 GTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLED  554 (796)
T ss_pred             CCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccc
Confidence            99995   788     99999999999999999999999999999999988765

>PRK00254 ski2-like helicase; Provisional

Probab=99.80  E-value=8.7e-19  Score=142.96  Aligned_cols=116  Identities=23%  Similarity=0.365  Sum_probs=95.1

Q ss_pred             HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC---------------------------------CCceEEEecCCCHH
Q psy576           37 QDETILLGIEPPVLVFVQSKERAQELYNELIYD---------------------------------GINVDVIHSDRTQK   83 (159)
Q Consensus        37 l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~---------------------------------~~~~~~~~~~~~~~   83 (159)
                      +.+.+.  .++++||||+|++.++.++..+...                                 ...+.++||+++++
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            344444  4678999999999998776555321                                 12488999999999


Q ss_pred             HHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE-------ecCC-CCHHHHHHHHhhccCCC--CcceEEEEecCC
Q psy576           84 QRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN-------YDFP-SSAISYIHRIGRAGRGG--REGKAVTFFTKQ  153 (159)
Q Consensus        84 ~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~-------~~~~-~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~  153 (159)
                      +|..+++.|++|.++|||||+++++|+|+|..++||.       ++.| .+..+|.||+||+||.|  ..|.++++....
T Consensus       309 eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~  388 (720)
T PRK00254        309 ERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTE  388 (720)
T ss_pred             HHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCc
Confidence            9999999999999999999999999999999999984       3333 36789999999999976  569999998765


Q ss_pred             C
Q psy576          154 D  154 (159)
Q Consensus       154 ~  154 (159)
                      +
T Consensus       389 ~  389 (720)
T PRK00254        389 E  389 (720)
T ss_pred             c
Confidence            4

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.79  E-value=9.1e-19  Score=105.22  Aligned_cols=81  Identities=43%  Similarity=0.735  Sum_probs=76.8

Q ss_pred             HHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCC
Q psy576           61 ELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRG  140 (159)
Q Consensus        61 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~  140 (159)
                      .+++.|.+.+..+..+||++++++|.++++.|+++...++|+|+++++|+|+|.+++|+.+++|++...|.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            46777888889999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q psy576          141 G  141 (159)
Q Consensus       141 g  141 (159)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            5

>KOG0354|consensus

Probab=99.79  E-value=3.5e-18  Score=135.86  Aligned_cols=124  Identities=29%  Similarity=0.500  Sum_probs=104.4

Q ss_pred             CCCCChHHHHHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhC---CCceEEEec--------CCCHHHHHHHHHHH
Q psy576           28 EGAGSPVQAQDETIL----LGIEPPVLVFVQSKERAQELYNELIYD---GINVDVIHS--------DRTQKQRDNVVRSF   92 (159)
Q Consensus        28 ~~~~~k~~~l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~---~~~~~~~~~--------~~~~~~r~~~~~~f   92 (159)
                      .....|++.+.+.+.    .....++||||.+++.|+.|..+|.+.   +++...+-|        +|+..++.+++++|
T Consensus       391 ~~~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~F  470 (746)
T KOG0354|consen  391 PKENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKF  470 (746)
T ss_pred             CccChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHH
Confidence            334678888887775    345568999999999999999999732   344444444        68999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      ++|++.|||||+++++|+||+.++.||-||...++..+.||+|| ||. +.|.|+.+++..
T Consensus       471 r~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa-~ns~~vll~t~~  529 (746)
T KOG0354|consen  471 RDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRA-RNSKCVLLTTGS  529 (746)
T ss_pred             hCCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-ccc-cCCeEEEEEcch
Confidence            99999999999999999999999999999999999999999999 998 567788777743

>PRK01172 ski2-like helicase; Provisional

Probab=99.78  E-value=3.7e-18  Score=138.55  Aligned_cols=109  Identities=28%  Similarity=0.375  Sum_probs=91.6

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC-----C--------------------CceEEEecCCCHHHHHHHHHHHhcCCeeE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD-----G--------------------INVDVIHSDRTQKQRDNVVRSFRTGRIWI   99 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~-----~--------------------~~~~~~~~~~~~~~r~~~~~~f~~~~~~v   99 (159)
                      .++++||||++++.++.++..|.+.     .                    ..+.++||+++.++|..+++.|++|.++|
T Consensus       235 ~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~V  314 (674)
T PRK01172        235 DGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKV  314 (674)
T ss_pred             CCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeE
Confidence            5678999999999999999887543     0                    13788999999999999999999999999


Q ss_pred             EEEeCCcccccccCCCcEEEEec---------CCCCHHHHHHHHhhccCCC--CcceEEEEecCCC
Q psy576          100 LITTELLGRGIDFRTVRLVVNYD---------FPSSAISYIHRIGRAGRGG--REGKAVTFFTKQD  154 (159)
Q Consensus       100 lv~t~~~~~g~~i~~~~~vi~~~---------~~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~~  154 (159)
                      ||||+++++|+|+|...+||. +         .|.+..+|.||+||+||.|  ..|.++++....+
T Consensus       315 LvaT~~la~Gvnipa~~VII~-~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~  379 (674)
T PRK01172        315 IVATPTLAAGVNLPARLVIVR-DITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPA  379 (674)
T ss_pred             EEecchhhccCCCcceEEEEc-CceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcc
Confidence            999999999999998765553 2         2458899999999999998  4577887766443

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

Probab=99.77  E-value=5.1e-18  Score=137.79  Aligned_cols=101  Identities=19%  Similarity=0.293  Sum_probs=86.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHH-----HHHHHHhc----CC-------eeEEEEeCCccc
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRD-----NVVRSFRT----GR-------IWILITTELLGR  108 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~-----~~~~~f~~----~~-------~~vlv~t~~~~~  108 (159)
                      ..+++||||+|++.++.+++.|.+.++  ..+||+|++.+|.     .+++.|++    ++       ..|||||+++++
T Consensus       271 ~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaer  348 (844)
T TIGR02621       271 SGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEV  348 (844)
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccchhhh
Confidence            457899999999999999999988775  8999999999999     77889987    43       679999999999


Q ss_pred             ccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCc-ceEEEEe
Q psy576          109 GIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGRE-GKAVTFF  150 (159)
Q Consensus       109 g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~-g~~~~~~  150 (159)
                      |+||+. ++||+...|  .++|+||+||+||.|.. +..+.++
T Consensus       349 GLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv  388 (844)
T TIGR02621       349 GVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVV  388 (844)
T ss_pred             cccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEE
Confidence            999986 788886655  79999999999999964 3334444

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.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.77  E-value=4.1e-18  Score=138.92  Aligned_cols=122  Identities=25%  Similarity=0.284  Sum_probs=108.9

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+..  ..+.|+||||.|++.++.++..|.+.++++..+|+  ...+|+..+.+|..+...|+|||++++|
T Consensus       581 ~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGR  658 (1025)
T PRK12900        581 REKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGR  658 (1025)
T ss_pred             HHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCC
Confidence            4688888888853  36789999999999999999999999999999997  5789999999999999999999999999


Q ss_pred             ccccC---CCc-----EEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          109 GIDFR---TVR-----LVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       109 g~~i~---~~~-----~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |+||+   .+.     +||....|.+...|.|++||+||.|.+|.+.+|++..|
T Consensus       659 GtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD  712 (1025)
T PRK12900        659 GTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLED  712 (1025)
T ss_pred             CCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhH
Confidence            99999   443     45788888999999999999999999999999998765

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

Probab=99.75  E-value=1.9e-17  Score=133.95  Aligned_cols=117  Identities=24%  Similarity=0.341  Sum_probs=102.2

Q ss_pred             hHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCC-CceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccc
Q psy576           33 PVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDG-INVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGID  111 (159)
Q Consensus        33 k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~-~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~  111 (159)
                      ....+.++++.  ...+|||+||+..++.++..|++.. ..+..+||.++.+.|.++.+.|++|+++.+|||+.++.|+|
T Consensus       242 ~~~~i~~~v~~--~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGID  319 (814)
T COG1201         242 LYERIAELVKK--HRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGID  319 (814)
T ss_pred             HHHHHHHHHhh--cCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccc
Confidence            44455566664  4489999999999999999998885 78999999999999999999999999999999999999999


Q ss_pred             cCCCcEEEEecCCCCHHHHHHHHhhccCCC-CcceEEEEec
Q psy576          112 FRTVRLVVNYDFPSSAISYIHRIGRAGRGG-REGKAVTFFT  151 (159)
Q Consensus       112 i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g-~~g~~~~~~~  151 (159)
                      +.+++.||+++.|.+...++||+||+|+.- .....+++..
T Consensus       320 iG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~  360 (814)
T COG1201         320 IGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAE  360 (814)
T ss_pred             cCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEec
Confidence            999999999999999999999999999854 3344555443

>KOG0349|consensus

Probab=99.75  E-value=1e-17  Score=125.86  Aligned_cols=113  Identities=25%  Similarity=0.467  Sum_probs=103.3

Q ss_pred             cCCCCCEEEEecchHHHHHHHHHHHhC---CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEE
Q psy576           43 LGIEPPVLVFVQSKERAQELYNELIYD---GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV  119 (159)
Q Consensus        43 ~~~~~~~lif~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi  119 (159)
                      .....++||||.++..++.+.+++.+.   .+.+.++||+..+.+|..-++.|++++.+.||||+++++|+||-.+..+|
T Consensus       502 ~h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~i  581 (725)
T KOG0349|consen  502 RHAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMI  581 (725)
T ss_pred             hhccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEE
Confidence            345679999999999999999999877   35789999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          120 NYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       120 ~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      +...|.+...|.+|+||+||..+-|.++.++.....
T Consensus       582 nvtlpd~k~nyvhrigrvgraermglaislvat~~e  617 (725)
T KOG0349|consen  582 NVTLPDDKTNYVHRIGRVGRAERMGLAISLVATVPE  617 (725)
T ss_pred             EEecCcccchhhhhhhccchhhhcceeEEEeeccch
Confidence            999999999999999999999888988888765433

>KOG0352|consensus

Probab=99.74  E-value=5.9e-18  Score=126.71  Aligned_cols=113  Identities=23%  Similarity=0.406  Sum_probs=107.7

Q ss_pred             CCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCCC
Q psy576           46 EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPS  125 (159)
Q Consensus        46 ~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~  125 (159)
                      .+..||||.|++.++.++-.|...|++...+|.++...+|.++.++|.+++..|+++|...++|+|-|++..|||.++|.
T Consensus       255 ~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~q  334 (641)
T KOG0352|consen  255 TGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQ  334 (641)
T ss_pred             CcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchh
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHhhccCCCCcceEEEEecCCCcccc
Q psy576          126 SAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL  158 (159)
Q Consensus       126 ~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~  158 (159)
                      +.+.|.|-.||+||.|...+|-.|+...|...+
T Consensus       335 n~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i  367 (641)
T KOG0352|consen  335 NLAGYYQESGRAGRDGKRSYCRLYYSRQDKNAL  367 (641)
T ss_pred             hhHHHHHhccccccCCCccceeeeecccchHHH
Confidence            999999999999999999999999998886543

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.74  E-value=1.8e-17  Score=139.24  Aligned_cols=109  Identities=17%  Similarity=0.295  Sum_probs=95.2

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCCc---eEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGIN---VDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN  120 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~~---~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~  120 (159)
                      ...+.+|||+++..+++.+++.|.+.+.+   +..+||+++.+++.++++.  .|..+|+|||+++++|+++|++++||+
T Consensus       284 ~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID  361 (1294)
T PRK11131        284 EGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVID  361 (1294)
T ss_pred             CCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEE
Confidence            35678999999999999999999887553   6789999999999999876  477899999999999999999999999


Q ss_pred             ecC---------------C---CCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          121 YDF---------------P---SSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       121 ~~~---------------~---~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      ++.               |   .|.++|.||.||+||. .+|.|+.+++..+.
T Consensus       362 ~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~  413 (1294)
T PRK11131        362 PGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDF  413 (1294)
T ss_pred             CCCccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHH
Confidence            852               2   3568999999999999 68999999987643

>KOG0337|consensus

Probab=99.74  E-value=1.8e-18  Score=128.95  Aligned_cols=142  Identities=27%  Similarity=0.384  Sum_probs=126.3

Q ss_pred             HhhhhccceeeeecCCCCChHHHHHHHHhcC-CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHH
Q psy576           14 RRVKSNLARMYRETEGAGSPVQAQDETILLG-IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        14 ~~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~-~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      +...+.+...|..+.. .+|...|..++... .+++.+|||.+..+++.+...|...+..+..++|.+++..|..-...|
T Consensus       229 tkise~lk~~f~~~~~-a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F  307 (529)
T KOG0337|consen  229 TKISELLKVRFFRVRK-AEKEAALLSILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDF  307 (529)
T ss_pred             hhcchhhhhheeeecc-HHHHHHHHHHHhccccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccc
Confidence            4555666666666666 67888777777643 345799999999999999999999999999999999999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      ..++..+||.|+.+++|+|||..+.||||+.|.+...|.+|+||+.|.|+.|..|-++.+.|..
T Consensus       308 ~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~  371 (529)
T KOG0337|consen  308 RGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDP  371 (529)
T ss_pred             cCCccceEEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecccch
Confidence            9999999999999999999999999999999999999999999999999999999999887764

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.71  E-value=1.7e-16  Score=131.87  Aligned_cols=120  Identities=23%  Similarity=0.301  Sum_probs=106.9

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC---CeeEEEEeCC
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG---RIWILITTEL  105 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~---~~~vlv~t~~  105 (159)
                      ..|+..|.+++..  ..+.++|||+.....++.|..+|...++....++|+++..+|..+++.|++.   ...+|++|.+
T Consensus       470 SgKl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrA  549 (1033)
T PLN03142        470 SGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRA  549 (1033)
T ss_pred             hhHHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccc
Confidence            5788888887763  3567999999999999999999999999999999999999999999999863   3467889999


Q ss_pred             cccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       106 ~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      ++.|+|+..+++||+|+++|++....|++||++|.|+...|.+|.
T Consensus       550 GGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyR  594 (1033)
T PLN03142        550 GGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFR  594 (1033)
T ss_pred             cccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEE
Confidence            999999999999999999999999999999999999887766553

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

Probab=99.71  E-value=2.1e-16  Score=124.36  Aligned_cols=135  Identities=22%  Similarity=0.296  Sum_probs=109.7

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchH--------HHHHHHHHHHhC--CCceEEEecCCCHHHHHH
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKE--------RAQELYNELIYD--GINVDVIHSDRTQKQRDN   87 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~--------~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~   87 (159)
                      ..|.-++......+.-.+.+.+.+.  .++++.+.|+=.+        .+.++++.|+..  +.++..+||+|++.++..
T Consensus       447 kpI~T~~i~~~~~~~v~e~i~~ei~--~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~  524 (677)
T COG1200         447 KPITTVVIPHERRPEVYERIREEIA--KGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDA  524 (677)
T ss_pred             CceEEEEeccccHHHHHHHHHHHHH--cCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHH
Confidence            4555565555544445555555555  5678888888543        556777777743  567999999999999999


Q ss_pred             HHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCC-CCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           88 VVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFP-SSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        88 ~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~-~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      +++.|++|+.+|||||.+.+-|+|+|+++++++.+.- .-.+++.|..||+||.+..+.|+.++++..
T Consensus       525 vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         525 VMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             HHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            9999999999999999999999999999998887644 578999999999999999999999998775

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.70  E-value=1e-16  Score=135.10  Aligned_cols=108  Identities=16%  Similarity=0.258  Sum_probs=93.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCC---CceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEe
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDG---INVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNY  121 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~---~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~  121 (159)
                      ..+.+|||+++..+++.+.+.|.+.+   ..+..+||+++.+++.++++.+  +..+|+|||+++++|++||++++||++
T Consensus       278 ~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDs  355 (1283)
T TIGR01967       278 GPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDT  355 (1283)
T ss_pred             CCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeC
Confidence            45789999999999999999998763   4588999999999999886543  346899999999999999999999998


Q ss_pred             cCC------------------CCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          122 DFP------------------SSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       122 ~~~------------------~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      +.+                  -|.++|.||.||+||.| +|.|+.+++..+.
T Consensus       356 Gl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~  406 (1283)
T TIGR01967       356 GTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDF  406 (1283)
T ss_pred             CCccccccccccCccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHH
Confidence            743                  36689999999999997 9999999986543

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.

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

Probab=99.68  E-value=1.4e-15  Score=117.93  Aligned_cols=109  Identities=26%  Similarity=0.433  Sum_probs=99.2

Q ss_pred             CChHHHHHHHHhcC-CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccc
Q psy576           31 GSPVQAQDETILLG-IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG  109 (159)
Q Consensus        31 ~~k~~~l~~~~~~~-~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g  109 (159)
                      +.+...+..++... ...+++|||.+..++.+++..+...+. +..+++..+..+|..+++.|+.|++.+|+++.++.+|
T Consensus       267 ~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EG  345 (442)
T COG1061         267 ERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEG  345 (442)
T ss_pred             HHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccce
Confidence            45666666666654 467899999999999999999987776 7899999999999999999999999999999999999


Q ss_pred             cccCCCcEEEEecCCCCHHHHHHHHhhccCC
Q psy576          110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRG  140 (159)
Q Consensus       110 ~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~  140 (159)
                      +|+|+++++|...++.|...|.||+||..|.
T Consensus       346 vDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR~  376 (442)
T COG1061         346 VDIPDADVLIILRPTGSRRLFIQRLGRGLRP  376 (442)
T ss_pred             ecCCCCcEEEEeCCCCcHHHHHHHhhhhccC
Confidence            9999999999999999999999999999993

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.65  E-value=1.5e-15  Score=114.89  Aligned_cols=85  Identities=21%  Similarity=0.358  Sum_probs=73.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCC--CceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEec
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDG--INVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD  122 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~--~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~  122 (159)
                      .++++||||++.+.++.++..|++.+  ..+..+||.++..+|.+.      ++..|||||+++++|+|+|.. +|| ++
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~  342 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS  342 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC
Confidence            45789999999999999999998753  578889999999888654      378899999999999999986 455 44


Q ss_pred             CCCCHHHHHHHHhhcc
Q psy576          123 FPSSAISYIHRIGRAG  138 (159)
Q Consensus       123 ~~~~~~~~~q~~GR~~  138 (159)
                       |.+..+|.||+||+|
T Consensus       343 -p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       343 -ARDAAAFWQRLGRLG  357 (357)
T ss_pred             -CCCHHHHhhhcccCC
Confidence             889999999999986

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.

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

Probab=99.64  E-value=4.6e-15  Score=122.55  Aligned_cols=111  Identities=17%  Similarity=0.219  Sum_probs=101.1

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEe
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNY  121 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~  121 (159)
                      .+++++-..++.+++.+.+.+.|++.  ..++.+.||.|+..+-++++..|.+|+.+|||||...+.|+|||+++.+|..
T Consensus       801 ~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe  880 (1139)
T COG1197         801 LRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIE  880 (1139)
T ss_pred             hcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEe
Confidence            46789988999999999999999876  6689999999999999999999999999999999999999999999988876


Q ss_pred             cCC-CCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          122 DFP-SSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       122 ~~~-~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      +.. .-.+++.|..||+||....+.|+.++.+.+
T Consensus       881 ~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~k  914 (1139)
T COG1197         881 RADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQK  914 (1139)
T ss_pred             ccccccHHHHHHhccccCCccceEEEEEeecCcc
Confidence            554 478999999999999999999999998654

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.64  E-value=3.8e-15  Score=121.00  Aligned_cols=122  Identities=25%  Similarity=0.258  Sum_probs=108.4

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+..  ..+.|+||||.|++.++.++..|.+.++++..+|+.  ..+|+..+.+|..+...|+|||++++|
T Consensus       413 ~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGR  490 (830)
T PRK12904        413 KEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGR  490 (830)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccC
Confidence            5688888888854  567899999999999999999999999999999995  778999999999999999999999999


Q ss_pred             ccccCCC--------------------------------------cEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          109 GIDFRTV--------------------------------------RLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       109 g~~i~~~--------------------------------------~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      |+||+--                                      -+||....+.|..---|..||+||.|.+|.+.+|+
T Consensus       491 GtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~l  570 (830)
T PRK12904        491 GTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYL  570 (830)
T ss_pred             CcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEEE
Confidence            9999753                                      26777778889988999999999999999999988


Q ss_pred             cCCC
Q psy576          151 TKQD  154 (159)
Q Consensus       151 ~~~~  154 (159)
                      +-.|
T Consensus       571 SleD  574 (830)
T PRK12904        571 SLED  574 (830)
T ss_pred             EcCc
Confidence            8654

>KOG0353|consensus

Probab=99.64  E-value=6.3e-16  Score=114.79  Aligned_cols=141  Identities=21%  Similarity=0.352  Sum_probs=119.8

Q ss_pred             hhhhccceeeeecCCC-CChHHHHHHHHhc-CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHH
Q psy576           15 RVKSNLARMYRETEGA-GSPVQAQDETILL-GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~-~~k~~~l~~~~~~-~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ..++++.+.++..++. ++-.+-+.++++. ..++..||||-+.+.++.++..|+..|+....+|..|.|.++..+-+.|
T Consensus       284 fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w  363 (695)
T KOG0353|consen  284 FNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGW  363 (695)
T ss_pred             cCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccc
Confidence            4455666555555443 3344445555553 3456689999999999999999999999999999999999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHH----------------------------------------
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIH----------------------------------------  132 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q----------------------------------------  132 (159)
                      ..|+++|+|+|-..++|+|-|+++.||+.+.|++.+.|.|                                        
T Consensus       364 ~a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavf  443 (695)
T KOG0353|consen  364 IAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVF  443 (695)
T ss_pred             cccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeee
Confidence            9999999999999999999999999999999999999999                                        


Q ss_pred             ---HHhhccCCCCcceEEEEecCCCc
Q psy576          133 ---RIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       133 ---~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                         -.||+||.+.+..|+.|+.-.|+
T Consensus       444 sekesgragrd~~~a~cilyy~~~di  469 (695)
T KOG0353|consen  444 SEKESGRAGRDDMKADCILYYGFADI  469 (695)
T ss_pred             cchhccccccCCCcccEEEEechHHH
Confidence               67999999999999999876554

>PRK09694 helicase Cas3; Provisional

Probab=99.63  E-value=1.2e-14  Score=119.72  Aligned_cols=95  Identities=24%  Similarity=0.423  Sum_probs=81.5

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCC---CceEEEecCCCHHHHH----HHHHHH-hcCC---eeEEEEeCCcccccccC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDG---INVDVIHSDRTQKQRD----NVVRSF-RTGR---IWILITTELLGRGIDFR  113 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~---~~~~~~~~~~~~~~r~----~~~~~f-~~~~---~~vlv~t~~~~~g~~i~  113 (159)
                      .+++++|||+|++.+.++++.|++..   .++..+||+++..+|.    ++++.| ++++   ..|||+|+++++|+|+ 
T Consensus       559 ~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-  637 (878)
T PRK09694        559 AGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-  637 (878)
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-
Confidence            56789999999999999999998753   5789999999999884    566777 5555   4799999999999999 


Q ss_pred             CCcEEEEecCCCCHHHHHHHHhhccCCCC
Q psy576          114 TVRLVVNYDFPSSAISYIHRIGRAGRGGR  142 (159)
Q Consensus       114 ~~~~vi~~~~~~~~~~~~q~~GR~~R~g~  142 (159)
                      +++++|....|  .+.++||+||++|.+.
T Consensus       638 d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        638 DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            57988887666  7899999999999874

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

Probab=99.62  E-value=6.6e-15  Score=107.79  Aligned_cols=117  Identities=26%  Similarity=0.383  Sum_probs=96.8

Q ss_pred             HHHHHHhcC--CCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccc
Q psy576           36 AQDETILLG--IEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGID  111 (159)
Q Consensus        36 ~l~~~~~~~--~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~  111 (159)
                      .|..+++..  .+.|++||+++.+.++.++..|++.  ...+..+|+.  ...|.+..++|++|++.+||+|..+++|+.
T Consensus       293 kl~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVT  370 (441)
T COG4098         293 KLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVT  370 (441)
T ss_pred             HHHHHHHHHHhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccc
Confidence            467777753  4479999999999999999999654  4466889984  678999999999999999999999999999


Q ss_pred             cCCCcEEEEec--CCCCHHHHHHHHhhccCCC--CcceEEEEecCCC
Q psy576          112 FRTVRLVVNYD--FPSSAISYIHRIGRAGRGG--REGKAVTFFTKQD  154 (159)
Q Consensus       112 i~~~~~vi~~~--~~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~~  154 (159)
                      +|.+++.+.-.  .-.+.+.+.|..||+||.-  +.|.++.|.....
T Consensus       371 fp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~G~s  417 (441)
T COG4098         371 FPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYGKS  417 (441)
T ss_pred             cccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEeccch
Confidence            99999877643  3368999999999999966  5687777765443

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.61  E-value=6.4e-15  Score=120.03  Aligned_cols=110  Identities=29%  Similarity=0.476  Sum_probs=93.0

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHh----C---------------------------------CCceEEEecCCCHHHHHH
Q psy576           45 IEPPVLVFVQSKERAQELYNELIY----D---------------------------------GINVDVIHSDRTQKQRDN   87 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~----~---------------------------------~~~~~~~~~~~~~~~r~~   87 (159)
                      .+++++|||+|++.+...+..+..    .                                 ...+.++|++++.+.|..
T Consensus       252 ~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~  331 (766)
T COG1204         252 EGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQL  331 (766)
T ss_pred             cCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHHH
Confidence            567999999999999988887762    0                                 011689999999999999


Q ss_pred             HHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----ec-----CCCCHHHHHHHHhhccCCC--CcceEEEEecCCC
Q psy576           88 VVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----YD-----FPSSAISYIHRIGRAGRGG--REGKAVTFFTKQD  154 (159)
Q Consensus        88 ~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~~-----~~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~~  154 (159)
                      +.+.|+.|.++||+||+++++|+|+|.-++||-    ++     .+-+.-++.||.||+||.|  ..|..+++....+
T Consensus       332 vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~~~~~  409 (766)
T COG1204         332 VEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSHD  409 (766)
T ss_pred             HHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEEecCcc
Confidence            999999999999999999999999999998873    45     3457899999999999999  6688888885443

>PRK09401 reverse gyrase; Reviewed

Probab=99.60  E-value=6.2e-15  Score=124.74  Aligned_cols=113  Identities=26%  Similarity=0.302  Sum_probs=96.1

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHH---HHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKER---AQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~---~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      .++.+.|....   .+...|.+++... +.++||||++...   ++.++..|...|+++..+||++     .+.+++|++
T Consensus       304 rnI~~~yi~~~---~k~~~L~~ll~~l-~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~  374 (1176)
T PRK09401        304 RNIVDSYIVDE---DSVEKLVELVKRL-GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEE  374 (1176)
T ss_pred             CCceEEEEEcc---cHHHHHHHHHHhc-CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHC
Confidence            45666666554   5777888888764 4689999999777   9999999999999999999998     234599999


Q ss_pred             CCeeEEEE----eCCcccccccCC-CcEEEEecCCC------CHHHHHHHHhhccC
Q psy576           95 GRIWILIT----TELLGRGIDFRT-VRLVVNYDFPS------SAISYIHRIGRAGR  139 (159)
Q Consensus        95 ~~~~vlv~----t~~~~~g~~i~~-~~~vi~~~~~~------~~~~~~q~~GR~~R  139 (159)
                      |+.+||||    |+++++|+|+|+ +++|||++.|.      ....+.+++||+..
T Consensus       375 G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~~  430 (1176)
T PRK09401        375 GEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLLS  430 (1176)
T ss_pred             CCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHHh
Confidence            99999999    689999999999 89999999998      66788999999864

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.60  E-value=2.3e-14  Score=116.92  Aligned_cols=122  Identities=25%  Similarity=0.266  Sum_probs=105.6

Q ss_pred             CChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+.  ...+.|+||||.|++.++.++..|.+.+++...+|+.++..++..+.++|+.|.  |+|||+++++
T Consensus       427 ~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNmAGR  504 (896)
T PRK13104        427 ADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNMAGR  504 (896)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCCc--EEEeccCccC
Confidence            457766666663  346789999999999999999999999999999999999999999999999995  9999999999


Q ss_pred             ccccCCC--------------------------------------cEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          109 GIDFRTV--------------------------------------RLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       109 g~~i~~~--------------------------------------~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      |+||.--                                      -+||-...+.|..---|..||+||.|.+|.+-+|+
T Consensus       505 GtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~l  584 (896)
T PRK13104        505 GTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYL  584 (896)
T ss_pred             CcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEE
Confidence            9999621                                      26776677788888899999999999999999888


Q ss_pred             cCCC
Q psy576          151 TKQD  154 (159)
Q Consensus       151 ~~~~  154 (159)
                      +-.|
T Consensus       585 SleD  588 (896)
T PRK13104        585 SLED  588 (896)
T ss_pred             EcCc
Confidence            7554

>PRK14701 reverse gyrase; Provisional

Probab=99.59  E-value=6.7e-15  Score=127.25  Aligned_cols=121  Identities=23%  Similarity=0.280  Sum_probs=98.4

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHH---HHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKER---AQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~---~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      .++.+.|...+. ..+ ..+.+++... +.++||||++.+.   ++++++.|.+.|+++..+||+     |.+.++.|++
T Consensus       305 r~i~~~yi~~~~-~~k-~~L~~ll~~~-g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~~F~~  376 (1638)
T PRK14701        305 RNIVDVYLNPEK-IIK-EHVRELLKKL-GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFDLFEE  376 (1638)
T ss_pred             CCcEEEEEECCH-HHH-HHHHHHHHhC-CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHHHHHc
Confidence            356666665543 233 4677777664 5689999999875   589999999999999999994     8889999999


Q ss_pred             CCeeEEEEe----CCcccccccCC-CcEEEEecCCC---CHHHHHHHH-------------hhccCCCCcceE
Q psy576           95 GRIWILITT----ELLGRGIDFRT-VRLVVNYDFPS---SAISYIHRI-------------GRAGRGGREGKA  146 (159)
Q Consensus        95 ~~~~vlv~t----~~~~~g~~i~~-~~~vi~~~~~~---~~~~~~q~~-------------GR~~R~g~~g~~  146 (159)
                      |+.+|||||    +++++|+|+|+ +++||++++|+   +...|.|-.             ||++|.|....+
T Consensus       377 G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~  449 (1638)
T PRK14701        377 GEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEG  449 (1638)
T ss_pred             CCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchh
Confidence            999999999    48999999999 99999999998   777665544             999999866554

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.56  E-value=6e-14  Score=114.31  Aligned_cols=122  Identities=25%  Similarity=0.293  Sum_probs=105.4

Q ss_pred             CChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+.  ...+.|+||||.|.+.++.++..|...+++...+|+.++..++..+.++|+.|.  |+|||+++++
T Consensus       432 ~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGR  509 (908)
T PRK13107        432 DEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGR  509 (908)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCC
Confidence            456666655554  246789999999999999999999999999999999999999999999999999  9999999999


Q ss_pred             ccccCC-------------------------------------CcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEec
Q psy576          109 GIDFRT-------------------------------------VRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       109 g~~i~~-------------------------------------~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      |.||.-                                     --+||-...+.|..---|..||+||.|.+|.+.+|++
T Consensus       510 GTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lS  589 (908)
T PRK13107        510 GTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLS  589 (908)
T ss_pred             CcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEE
Confidence            999962                                     1267777778888888999999999999999998887


Q ss_pred             CCC
Q psy576          152 KQD  154 (159)
Q Consensus       152 ~~~  154 (159)
                      -.|
T Consensus       590 lED  592 (908)
T PRK13107        590 MED  592 (908)
T ss_pred             eCc
Confidence            654

>TIGR00595 priA primosomal protein N'

Probab=99.54  E-value=6.9e-14  Score=109.98  Aligned_cols=98  Identities=28%  Similarity=0.428  Sum_probs=80.4

Q ss_pred             HHHHHHHHHhC--CCceEEEecCCCHHHH--HHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecC------CC---
Q psy576           59 AQELYNELIYD--GINVDVIHSDRTQKQR--DNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDF------PS---  125 (159)
Q Consensus        59 ~~~l~~~l~~~--~~~~~~~~~~~~~~~r--~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~------~~---  125 (159)
                      .+.+.+.|.+.  +.++..+|++++...+  +++++.|.+|+.+|||+|+++++|+|+|+++.|+.++.      |+   
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra  350 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRA  350 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccch
Confidence            35677777665  6789999999876655  88999999999999999999999999999998865433      22   


Q ss_pred             ---CHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576          126 ---SAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus       126 ---~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                         ..+.|.|++||+||.+..|.+++.....+..
T Consensus       351 ~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~~~  384 (505)
T TIGR00595       351 AERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHP  384 (505)
T ss_pred             HHHHHHHHHHHHhccCCCCCCCEEEEEeCCCCCH
Confidence               2467899999999999999999887766653

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).

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.54  E-value=1.3e-13  Score=112.70  Aligned_cols=106  Identities=29%  Similarity=0.463  Sum_probs=89.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHh----cCCeeEEEEeCCcccccccCCCcEEEE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFR----TGRIWILITTELLGRGIDFRTVRLVVN  120 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~----~~~~~vlv~t~~~~~g~~i~~~~~vi~  120 (159)
                      .+.+++|.|+|++.|.++++.|+..+.++..+||.+...+|.+.++.+.    .+...|+|+|++++.|+|+. .+++|-
T Consensus       439 ~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-fd~mIT  517 (733)
T COG1203         439 EGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-FDVLIT  517 (733)
T ss_pred             cCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-cCeeee
Confidence            5578999999999999999999988778999999999999998888654    46788999999999999984 666665


Q ss_pred             ecCCCCHHHHHHHHhhccCCC--CcceEEEEecCC
Q psy576          121 YDFPSSAISYIHRIGRAGRGG--REGKAVTFFTKQ  153 (159)
Q Consensus       121 ~~~~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~  153 (159)
                      =  +.+..+++||+||++|.|  ..|.++++....
T Consensus       518 e--~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~~  550 (733)
T COG1203         518 E--LAPIDSLIQRAGRVNRHGKKENGKIYVYNDEE  550 (733)
T ss_pred             c--CCCHHHHHHHHHHHhhcccccCCceeEeeccc
Confidence            3  345899999999999999  567777666544

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

Probab=99.53  E-value=2.2e-13  Score=104.82  Aligned_cols=108  Identities=34%  Similarity=0.458  Sum_probs=100.2

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecC
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDF  123 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~  123 (159)
                      ..+.+++|-+-|++.++.+.++|.+.|+++.++|++..--+|.+++.+++.|+++|||.-+.+-+|+|+|.++.|..+|.
T Consensus       444 ~~~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDA  523 (663)
T COG0556         444 AKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDA  523 (663)
T ss_pred             hcCCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeec
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             C-----CCHHHHHHHHhhccCCCCcceEEEEecC
Q psy576          124 P-----SSAISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       124 ~-----~~~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      .     .|..+++|-+||+.|. -.|.+++|.+.
T Consensus       524 DKeGFLRse~SLIQtIGRAARN-~~GkvIlYAD~  556 (663)
T COG0556         524 DKEGFLRSERSLIQTIGRAARN-VNGKVILYADK  556 (663)
T ss_pred             CccccccccchHHHHHHHHhhc-cCCeEEEEchh
Confidence            4     5899999999999998 57889888764

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

Probab=99.52  E-value=3.8e-13  Score=113.57  Aligned_cols=96  Identities=27%  Similarity=0.330  Sum_probs=82.4

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC------CC---ceEEEecCCCHHHHHHHHHHHhcCCe-eEEEEeCCcccccccCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD------GI---NVDVIHSDRTQKQRDNVVRSFRTGRI-WILITTELLGRGIDFRT  114 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~------~~---~~~~~~~~~~~~~r~~~~~~f~~~~~-~vlv~t~~~~~g~~i~~  114 (159)
                      ..+++||||.+.++|+.+.+.|.+.      +.   .+..+||+.+  ++..+++.|++++. .|+|+++++.+|+|+|.
T Consensus       697 ~~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~  774 (1123)
T PRK11448        697 GEGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPS  774 (1123)
T ss_pred             CCCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCccc
Confidence            3478999999999999999887652      12   3556888764  46779999999876 69999999999999999


Q ss_pred             CcEEEEecCCCCHHHHHHHHhhccCCCC
Q psy576          115 VRLVVNYDFPSSAISYIHRIGRAGRGGR  142 (159)
Q Consensus       115 ~~~vi~~~~~~~~~~~~q~~GR~~R~g~  142 (159)
                      +.+|+.+.++.|...|.||+||+.|...
T Consensus       775 v~~vVf~rpvkS~~lf~QmIGRgtR~~~  802 (1123)
T PRK11448        775 ICNLVFLRRVRSRILYEQMLGRATRLCP  802 (1123)
T ss_pred             ccEEEEecCCCCHHHHHHHHhhhccCCc
Confidence            9999999999999999999999999653

>KOG0329|consensus

Probab=99.51  E-value=8.9e-15  Score=103.47  Aligned_cols=106  Identities=31%  Similarity=0.570  Sum_probs=92.1

Q ss_pred             HHhhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHH
Q psy576           13 KRRVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        13 ~~~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      .+....++.++|..+.+ .+|+..+.+++.....++++||+.+.....                               |
T Consensus       251 ~KLtLHGLqQ~YvkLke-~eKNrkl~dLLd~LeFNQVvIFvKsv~Rl~-------------------------------f  298 (387)
T KOG0329|consen  251 AKLTLHGLQQYYVKLKE-NEKNRKLNDLLDVLEFNQVVIFVKSVQRLS-------------------------------F  298 (387)
T ss_pred             hhhhhhhHHHHHHhhhh-hhhhhhhhhhhhhhhhcceeEeeehhhhhh-------------------------------h
Confidence            34556788899999988 799999999999888999999999887510                               2


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                         +.+ +|+|+..++|+||..++.++|||.|.++..|++|+||+||.|.+|.++.|++..+
T Consensus       299 ---~kr-~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~  356 (387)
T KOG0329|consen  299 ---QKR-LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  356 (387)
T ss_pred             ---hhh-hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchh
Confidence               122 7899999999999999999999999999999999999999999999999988654

>TIGR01054 rgy reverse gyrase

Probab=99.45  E-value=9.9e-13  Score=111.66  Aligned_cols=100  Identities=26%  Similarity=0.344  Sum_probs=83.2

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecch---HHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSK---ERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~---~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      .++.+.+.....   +...|.+++... +.++||||++.   +.+++++..|.+.|+++..+||+++.    ..++.|++
T Consensus       302 r~I~~~~~~~~~---~~~~L~~ll~~l-~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l~~Fr~  373 (1171)
T TIGR01054       302 RNVVDVYVEDED---LKETLLEIVKKL-GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDYEKFAE  373 (1171)
T ss_pred             cceEEEEEeccc---HHHHHHHHHHHc-CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHHHHHHc
Confidence            355555553322   245566777653 46799999999   99999999999999999999999863    68999999


Q ss_pred             CCeeEEEEe----CCcccccccCC-CcEEEEecCCC
Q psy576           95 GRIWILITT----ELLGRGIDFRT-VRLVVNYDFPS  125 (159)
Q Consensus        95 ~~~~vlv~t----~~~~~g~~i~~-~~~vi~~~~~~  125 (159)
                      |+.+|||||    +++++|+|+|+ +++||++++|.
T Consensus       374 G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       374 GEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             CCCCEEEEeccccCcccccCCCCccccEEEEECCCC
Confidence            999999994    89999999999 89999999996

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.

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

Probab=99.41  E-value=6.6e-13  Score=108.56  Aligned_cols=111  Identities=19%  Similarity=0.300  Sum_probs=96.6

Q ss_pred             cCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEE
Q psy576           43 LGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLV  118 (159)
Q Consensus        43 ~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~v  118 (159)
                      ....+.+|||.+..++.+...+.|.+    ....+.++||.++.+++.++++.-..++-+|+++|++++.++.||++.+|
T Consensus       256 ~~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~V  335 (845)
T COG1643         256 REGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYV  335 (845)
T ss_pred             cCCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEE
Confidence            34578899999999999999999987    35678999999999999998888888877799999999999999999999


Q ss_pred             EEecC------------------CCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          119 VNYDF------------------PSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       119 i~~~~------------------~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |.-+.                  |-|-++..||.||+||- .+|.|+-+|+..+
T Consensus       336 IDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~-~pGicyRLyse~~  388 (845)
T COG1643         336 IDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRT-GPGICYRLYSEED  388 (845)
T ss_pred             ecCCcccccccccccCceeeeEEEechhhhhhhccccccC-CCceEEEecCHHH
Confidence            96432                  23788899999999999 4899999998654

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

Probab=99.40  E-value=2.8e-12  Score=105.99  Aligned_cols=121  Identities=27%  Similarity=0.473  Sum_probs=100.8

Q ss_pred             ChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHH----HHHhCC----CceEEEecCCCHHHHHHHHHHHhcCCeeEEE
Q psy576           32 SPVQAQDETILL--GIEPPVLVFVQSKERAQELYN----ELIYDG----INVDVIHSDRTQKQRDNVVRSFRTGRIWILI  101 (159)
Q Consensus        32 ~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~----~l~~~~----~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  101 (159)
                      .+...+..+...  ..+-++|+|+.+.+.++.++.    .+...+    ..+...++++.+.+|.++...|+.|++.+++
T Consensus       290 s~~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~  369 (851)
T COG1205         290 SALAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVI  369 (851)
T ss_pred             chHHHHHHHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEe
Confidence            444444444432  256789999999999999973    333334    5688999999999999999999999999999


Q ss_pred             EeCCcccccccCCCcEEEEecCCC-CHHHHHHHHhhccCCCCcceEEEEecC
Q psy576          102 TTELLGRGIDFRTVRLVVNYDFPS-SAISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       102 ~t~~~~~g~~i~~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      +|.+++.|+|+.+++.||..+.|. +..++.|+.||+||.++....+.....
T Consensus       370 st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~  421 (851)
T COG1205         370 ATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRS  421 (851)
T ss_pred             cchhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCC
Confidence            999999999999999999999999 899999999999999977766666653

>KOG0384|consensus

Probab=99.39  E-value=7.9e-13  Score=109.33  Aligned_cols=125  Identities=19%  Similarity=0.207  Sum_probs=109.5

Q ss_pred             CCCCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc---CCeeEEEE
Q psy576           28 EGAGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT---GRIWILIT  102 (159)
Q Consensus        28 ~~~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~---~~~~vlv~  102 (159)
                      -...+|+-+|-++|..  ..+++||||..-+...+-++++|..++++.-.+.|.+..+.|...++.|+.   .++..|+|
T Consensus       679 I~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLS  758 (1373)
T KOG0384|consen  679 IQSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLS  758 (1373)
T ss_pred             HHhcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEe
Confidence            3346788777788764  356799999999999999999999999999999999999999999999987   35779999


Q ss_pred             eCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceE--EEEecC
Q psy576          103 TELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKA--VTFFTK  152 (159)
Q Consensus       103 t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~--~~~~~~  152 (159)
                      |.+.+.|||+-.++.||+||..|+++.=+|...||.|.|++..|  |-|++.
T Consensus       759 TRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk  810 (1373)
T KOG0384|consen  759 TRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTK  810 (1373)
T ss_pred             cccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecC
Confidence            99999999999999999999999999999999999999977544  444544

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.39  E-value=2.2e-12  Score=104.80  Aligned_cols=99  Identities=27%  Similarity=0.340  Sum_probs=82.6

Q ss_pred             HHHHHHHHHHhC--CCceEEEecCCC--HHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCC--C------
Q psy576           58 RAQELYNELIYD--GINVDVIHSDRT--QKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFP--S------  125 (159)
Q Consensus        58 ~~~~l~~~l~~~--~~~~~~~~~~~~--~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~--~------  125 (159)
                      -++.+.+.|.+.  +.++..+|+++.  ..+++++++.|.+|+.+|||+|+++++|+|+|+++.|+.++..  .      
T Consensus       438 G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfr  517 (679)
T PRK05580        438 GTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFR  517 (679)
T ss_pred             cHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccc
Confidence            455777777665  678999999986  4678999999999999999999999999999999988765433  2      


Q ss_pred             ----CHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576          126 ----SAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus       126 ----~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                          ..+.|.|++||+||.+..|.+++.....+..
T Consensus       518 a~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~~~  552 (679)
T PRK05580        518 ASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHP  552 (679)
T ss_pred             hHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCCCH
Confidence                2367999999999999999999988877654

>KOG0385|consensus

Probab=99.39  E-value=3.7e-12  Score=101.51  Aligned_cols=120  Identities=18%  Similarity=0.282  Sum_probs=107.8

Q ss_pred             CCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC---CeeEEEEeC
Q psy576           30 AGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG---RIWILITTE  104 (159)
Q Consensus        30 ~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~---~~~vlv~t~  104 (159)
                      ..+|+.+|-+++..  ..++++|||..-....+-+..++.-+++....+.|.++-++|...++.|+..   ..-.|++|.
T Consensus       469 nSGKm~vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTR  548 (971)
T KOG0385|consen  469 NSGKMLVLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTR  548 (971)
T ss_pred             cCcceehHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEecc
Confidence            36888888888863  4778999999999999999999988899999999999999999999999873   356788999


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      +++.|+|+-.+++||.||..|+++.=+|.+.|+.|.|+..+|.+|
T Consensus       549 AGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~  593 (971)
T KOG0385|consen  549 AGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVY  593 (971)
T ss_pred             ccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEE
Confidence            999999999999999999999999999999999999987766655

>KOG0947|consensus

Probab=99.38  E-value=3.6e-12  Score=103.57  Aligned_cols=111  Identities=25%  Similarity=0.318  Sum_probs=91.5

Q ss_pred             cCCCCCEEEEecchHHHHHHHHHHHhCCCc---------------------------------------eEEEecCCCHH
Q psy576           43 LGIEPPVLVFVQSKERAQELYNELIYDGIN---------------------------------------VDVIHSDRTQK   83 (159)
Q Consensus        43 ~~~~~~~lif~~~~~~~~~l~~~l~~~~~~---------------------------------------~~~~~~~~~~~   83 (159)
                      ...--|+++||-+++.|++-+++|...+..                                       +.++||++-|-
T Consensus       564 k~~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPi  643 (1248)
T KOG0947|consen  564 KKNLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPI  643 (1248)
T ss_pred             hcccCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHH
Confidence            334558999999999999888877543221                                       78999999999


Q ss_pred             HHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecC--------CCCHHHHHHHHhhccCCC--CcceEEEEecCC
Q psy576           84 QRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDF--------PSSAISYIHRIGRAGRGG--REGKAVTFFTKQ  153 (159)
Q Consensus        84 ~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~--------~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~  153 (159)
                      -++-+.-.|+.|-.+||.||...++|+|.|.-++|+.--.        --.+.+|.||.||+||.|  ..|.++++....
T Consensus       644 vKE~VE~LFqrGlVKVLFATETFAMGVNMPARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~  723 (1248)
T KOG0947|consen  644 VKEVVELLFQRGLVKVLFATETFAMGVNMPARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDS  723 (1248)
T ss_pred             HHHHHHHHHhcCceEEEeehhhhhhhcCCCceeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecCC
Confidence            9998889999999999999999999999999998874211        126899999999999999  679888887654

>KOG0951|consensus

Probab=99.37  E-value=7.4e-12  Score=104.08  Aligned_cols=117  Identities=22%  Similarity=0.377  Sum_probs=93.7

Q ss_pred             HHHhcCCCCCEEEEecchHHHHHHHHHHHhC-------------------------------------CCceEEEecCCC
Q psy576           39 ETILLGIEPPVLVFVQSKERAQELYNELIYD-------------------------------------GINVDVIHSDRT   81 (159)
Q Consensus        39 ~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~-------------------------------------~~~~~~~~~~~~   81 (159)
                      +.++...++++|||+-++++..+.++.++..                                     ...++++|.||+
T Consensus       539 KVm~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~  618 (1674)
T KOG0951|consen  539 KVLEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLN  618 (1674)
T ss_pred             HHHHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCC
Confidence            4444445689999999998877766665410                                     123789999999


Q ss_pred             HHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----ecCC------CCHHHHHHHHhhccCCC--CcceEEEE
Q psy576           82 QKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----YDFP------SSAISYIHRIGRAGRGG--REGKAVTF  149 (159)
Q Consensus        82 ~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~~~~------~~~~~~~q~~GR~~R~g--~~g~~~~~  149 (159)
                      ..+|....+.|.+|.++|+++|-.+++|+|+|+=+++|-    |++-      -++.+..||.||+||.+  ..|..++.
T Consensus       619 R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiii  698 (1674)
T KOG0951|consen  619 RKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIII  698 (1674)
T ss_pred             cchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeec
Confidence            999999999999999999999999999999999998873    4432      37899999999999988  45777777


Q ss_pred             ecCCCc
Q psy576          150 FTKQDA  155 (159)
Q Consensus       150 ~~~~~~  155 (159)
                      ....|.
T Consensus       699 t~~se~  704 (1674)
T KOG0951|consen  699 TDHSEL  704 (1674)
T ss_pred             cCchHh
Confidence            665554

>KOG0390|consensus

Probab=99.36  E-value=1.4e-11  Score=99.41  Aligned_cols=120  Identities=13%  Similarity=0.158  Sum_probs=94.5

Q ss_pred             CChHHHHHHHHhc---CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC---eeEEEEeC
Q psy576           31 GSPVQAQDETILL---GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR---IWILITTE  104 (159)
Q Consensus        31 ~~k~~~l~~~~~~---~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~---~~vlv~t~  104 (159)
                      .+|+..|..++..   ....++++..+-+...+-+...++-.|..+..+||.++..+|..+++.|++..   .-.|.+|.
T Consensus       577 s~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsK  656 (776)
T KOG0390|consen  577 SGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSK  656 (776)
T ss_pred             hhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecc
Confidence            4566667777632   12223444445555555555555556999999999999999999999999843   33555778


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      +.+.|+++-+++.+|.+|++|+++.-.|.++|++|.|++.+|++|-
T Consensus       657 Agg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iYr  702 (776)
T KOG0390|consen  657 AGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIYR  702 (776)
T ss_pred             cccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEEE
Confidence            9999999999999999999999999999999999999999998873

>KOG0948|consensus

Probab=99.36  E-value=1.3e-12  Score=103.95  Aligned_cols=115  Identities=24%  Similarity=0.336  Sum_probs=93.1

Q ss_pred             HHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCc---------------------------------------eEEEecC
Q psy576           39 ETILLGIEPPVLVFVQSKERAQELYNELIYDGIN---------------------------------------VDVIHSD   79 (159)
Q Consensus        39 ~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~---------------------------------------~~~~~~~   79 (159)
                      +.+-..+..|+|||+-++++|+..+-.+.+..++                                       ++++|+|
T Consensus       376 kmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHHsG  455 (1041)
T KOG0948|consen  376 KMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHHSG  455 (1041)
T ss_pred             HHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHhcccccccc
Confidence            3333447789999999999999766655443222                                       7899999


Q ss_pred             CCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEe----cCC----CCHHHHHHHHhhccCCC--CcceEEEE
Q psy576           80 RTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNY----DFP----SSAISYIHRIGRAGRGG--REGKAVTF  149 (159)
Q Consensus        80 ~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~----~~~----~~~~~~~q~~GR~~R~g--~~g~~~~~  149 (159)
                      +-|--++-+.=.|+.|-+++|.||...+.|+|.|+-++|+..    |-.    -+..+|+||.||+||.|  ..|.|+++
T Consensus       456 LLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlm  535 (1041)
T KOG0948|consen  456 LLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILM  535 (1041)
T ss_pred             chHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccCCcceeeecccceEEecccccccCCCCCceEEEE
Confidence            999888888889999999999999999999999999987743    111    16889999999999999  56989888


Q ss_pred             ecCC
Q psy576          150 FTKQ  153 (159)
Q Consensus       150 ~~~~  153 (159)
                      ++..
T Consensus       536 iDek  539 (1041)
T KOG0948|consen  536 IDEK  539 (1041)
T ss_pred             ecCc
Confidence            8754

>KOG0950|consensus

Probab=99.36  E-value=2.5e-12  Score=104.39  Aligned_cols=111  Identities=24%  Similarity=0.444  Sum_probs=91.9

Q ss_pred             CCEEEEecchHHHHHHHHHHHhC--------------------------------------CCceEEEecCCCHHHHHHH
Q psy576           47 PPVLVFVQSKERAQELYNELIYD--------------------------------------GINVDVIHSDRTQKQRDNV   88 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~--------------------------------------~~~~~~~~~~~~~~~r~~~   88 (159)
                      .++||||++++.++.++..+...                                      ...+.++|.+++.++|+.+
T Consensus       461 ~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER~~i  540 (1008)
T KOG0950|consen  461 SSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEEREII  540 (1008)
T ss_pred             CeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchHHHH
Confidence            45999999999888665433210                                      1127899999999999999


Q ss_pred             HHHHhcCCeeEEEEeCCcccccccCCCcEEEEe----cCCCCHHHHHHHHhhccCCC--CcceEEEEecCCCccc
Q psy576           89 VRSFRTGRIWILITTELLGRGIDFRTVRLVVNY----DFPSSAISYIHRIGRAGRGG--REGKAVTFFTKQDAPL  157 (159)
Q Consensus        89 ~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~----~~~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~~~~~  157 (159)
                      ...|++|-..|++||+.++.|+|.|...+++-.    ....+.-.|.||+||+||.|  -.|.+++.+...|++.
T Consensus       541 E~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e~~~  615 (1008)
T KOG0950|consen  541 EAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSEKKR  615 (1008)
T ss_pred             HHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccchhH
Confidence            999999999999999999999999999988853    23357889999999999998  4598999999888754

>KOG0953|consensus

Probab=99.34  E-value=2.4e-11  Score=94.10  Aligned_cols=109  Identities=19%  Similarity=0.256  Sum_probs=85.7

Q ss_pred             hcCCCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCCCHHHHHHHHHHHhc--CCeeEEEEeCCcccccccCCCcEE
Q psy576           42 LLGIEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDRTQKQRDNVVRSFRT--GRIWILITTELLGRGIDFRTVRLV  118 (159)
Q Consensus        42 ~~~~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~~~~~r~~~~~~f~~--~~~~vlv~t~~~~~g~~i~~~~~v  118 (159)
                      .....+.|+|. -|++..-.+...+.+.+. ++.+++|++||+.|......|++  ++.+|||||++.++|+|+ +++-|
T Consensus       353 ~nlk~GDCvV~-FSkk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRi  430 (700)
T KOG0953|consen  353 SNLKPGDCVVA-FSKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRI  430 (700)
T ss_pred             ccCCCCCeEEE-eehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEE
Confidence            33456677554 355667777777877755 49999999999999999999998  889999999999999998 66667


Q ss_pred             EEecCC---------CCHHHHHHHHhhccCCC---CcceEEEEecC
Q psy576          119 VNYDFP---------SSAISYIHRIGRAGRGG---REGKAVTFFTK  152 (159)
Q Consensus       119 i~~~~~---------~~~~~~~q~~GR~~R~g---~~g~~~~~~~~  152 (159)
                      |.++..         -+..+..|..||+||.|   ..|.+..+..+
T Consensus       431 iF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~e  476 (700)
T KOG0953|consen  431 IFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHSE  476 (700)
T ss_pred             EEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeHh
Confidence            766543         36778899999999988   45766666543

>KOG0387|consensus

Probab=99.30  E-value=2.9e-11  Score=96.78  Aligned_cols=120  Identities=19%  Similarity=0.203  Sum_probs=105.5

Q ss_pred             CCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHH-hCCCceEEEecCCCHHHHHHHHHHHhcCC--eeEEEEeC
Q psy576           30 AGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELI-YDGINVDVIHSDRTQKQRDNVVRSFRTGR--IWILITTE  104 (159)
Q Consensus        30 ~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~-~~~~~~~~~~~~~~~~~r~~~~~~f~~~~--~~vlv~t~  104 (159)
                      ..+|++.+.+++..  .+++++++|..++...+-+...|. ..++....+.|..+...|..+++.|++++  .-.|++|.
T Consensus       528 ~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTr  607 (923)
T KOG0387|consen  528 RSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTR  607 (923)
T ss_pred             hcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEec
Confidence            36799998888873  466789999999999988888887 67999999999999999999999999865  34677999


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      +.+.|+|+-.++-||.|||.|++..=.|..-|++|.|++..|++|
T Consensus       608 vGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VY  652 (923)
T KOG0387|consen  608 VGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVY  652 (923)
T ss_pred             ccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEE
Confidence            999999999999999999999999999999999999987655554

>KOG4150|consensus

Probab=99.29  E-value=2.2e-11  Score=94.97  Aligned_cols=108  Identities=19%  Similarity=0.235  Sum_probs=91.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC----CC----ceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCc
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD----GI----NVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVR  116 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~  116 (159)
                      .+-++|.||.+++-|+-+....+..    +.    .+..+.|+...++|+++...+-.|++.-+|+|.+++.|+||..++
T Consensus       524 ~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LD  603 (1034)
T KOG4150|consen  524 HGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLD  603 (1034)
T ss_pred             cCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccce
Confidence            4568999999999888765544332    11    255678999999999999999999999999999999999999999


Q ss_pred             EEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecC
Q psy576          117 LVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       117 ~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      .|+++++|.+.+.+.|+.||+||..++..+++....
T Consensus       604 AVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~  639 (1034)
T KOG4150|consen  604 AVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFL  639 (1034)
T ss_pred             eEEEccCchhHHHHHHHhccccccCCCceEEEEEec
Confidence            999999999999999999999998766666655543

>KOG0952|consensus

Probab=99.26  E-value=4.5e-11  Score=98.05  Aligned_cols=111  Identities=24%  Similarity=0.425  Sum_probs=90.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC----C-------------------CceEEEecCCCHHHHHHHHHHHhcCCeeEEE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD----G-------------------INVDVIHSDRTQKQRDNVVRSFRTGRIWILI  101 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~----~-------------------~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  101 (159)
                      .+++++|||.+++...+.++.|.+.    +                   ...++.|.||..++|.-+.+.|+.|-++||+
T Consensus       348 ~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~  427 (1230)
T KOG0952|consen  348 EGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIKVLC  427 (1230)
T ss_pred             cCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCceEEE
Confidence            6789999999999888887777542    1                   1267899999999999999999999999999


Q ss_pred             EeCCcccccccCCCcEEEE----ecCCC------CHHHHHHHHhhccCCC--CcceEEEEecCCCc
Q psy576          102 TTELLGRGIDFRTVRLVVN----YDFPS------SAISYIHRIGRAGRGG--REGKAVTFFTKQDA  155 (159)
Q Consensus       102 ~t~~~~~g~~i~~~~~vi~----~~~~~------~~~~~~q~~GR~~R~g--~~g~~~~~~~~~~~  155 (159)
                      ||..+++|+|+|+--++|.    |+...      ..-+.+|..||+||.+  ..|.+++..+.+..
T Consensus       428 cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl  493 (1230)
T KOG0952|consen  428 CTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKL  493 (1230)
T ss_pred             ecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHH
Confidence            9999999999998777764    22221      4667899999999977  66888887776544

>KOG0922|consensus

Probab=99.21  E-value=1e-10  Score=92.20  Aligned_cols=118  Identities=22%  Similarity=0.297  Sum_probs=98.0

Q ss_pred             HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC----CC----ceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           37 QDETILLGIEPPVLVFVQSKERAQELYNELIYD----GI----NVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        37 l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..++-...+.+.+|||....++++...+.|.+.    +.    -+.++||+++.+++.++++.--.|.-+|+++|++++.
T Consensus       249 v~~Ih~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAET  328 (674)
T KOG0922|consen  249 VIQIHLTEPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAET  328 (674)
T ss_pred             HHHHHccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeee
Confidence            333333457778999999999999999988764    11    2578999999999999999888899999999999999


Q ss_pred             ccccCCCcEEEEecC------------------CCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          109 GIDFRTVRLVVNYDF------------------PSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       109 g~~i~~~~~vi~~~~------------------~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      .+.||.+..||+-+.                  |-|-++-.||.||+||.| +|.|+-++...+.
T Consensus       329 SlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRLYte~~~  392 (674)
T KOG0922|consen  329 SLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRTG-PGKCYRLYTESAY  392 (674)
T ss_pred             eEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCCC-CceEEEeeeHHHH
Confidence            999999999985332                  347888999999999995 8999999987654

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.20  E-value=2.8e-10  Score=92.83  Aligned_cols=121  Identities=23%  Similarity=0.314  Sum_probs=94.5

Q ss_pred             CChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC-CeeEEEEeCCcc
Q psy576           31 GSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG-RIWILITTELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vlv~t~~~~  107 (159)
                      ..|...+.+.+.  ...+.|+||.|.|.+..+.++..|.+.+++..+++..-.  +++.-+-. +.| .-.|.|||++++
T Consensus       409 ~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~--e~EA~IIa-~AG~~GaVTIATNMAG  485 (925)
T PRK12903        409 HAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQN--AREAEIIA-KAGQKGAITIATNMAG  485 (925)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccch--hhHHHHHH-hCCCCCeEEEeccccc
Confidence            456666665554  246789999999999999999999999999888888633  33222222 345 457999999999


Q ss_pred             cccccCCCc--------EEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          108 RGIDFRTVR--------LVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       108 ~g~~i~~~~--------~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      +|.||.--.        +||....+.|..---|..||+||.|.+|.+.+|.+-.|
T Consensus       486 RGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD  540 (925)
T PRK12903        486 RGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDD  540 (925)
T ss_pred             CCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecch
Confidence            999996332        78888888888888899999999999999888887554

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.17  E-value=8.3e-10  Score=88.87  Aligned_cols=121  Identities=26%  Similarity=0.313  Sum_probs=93.6

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC-CeeEEEEeCCcc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG-RIWILITTELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vlv~t~~~~  107 (159)
                      ..|...+.+.+..  ..+.|+||.+.|.+..+.+...|.+.+++...+++.-...+ .+++.  +.| .-.|.|||++++
T Consensus       410 ~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~E-A~IIa--~AG~~gaVTIATNMAG  486 (764)
T PRK12326        410 AEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEE-ARIIA--EAGKYGAVTVSTQMAG  486 (764)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhH-HHHHH--hcCCCCcEEEEecCCC
Confidence            3566666555542  46789999999999999999999999999888887644332 22222  223 345999999999


Q ss_pred             cccccCC---------------CcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          108 RGIDFRT---------------VRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       108 ~g~~i~~---------------~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      +|.||.-               --+||-...+.|..--.|..||+||.|.+|.+.+|++-.|
T Consensus       487 RGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleD  548 (764)
T PRK12326        487 RGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLED  548 (764)
T ss_pred             CccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            9999962               2378888888999999999999999999999988887554

>KOG0389|consensus

Probab=99.10  E-value=1.2e-09  Score=87.75  Aligned_cols=119  Identities=18%  Similarity=0.187  Sum_probs=104.5

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC--eeEEEEeCCc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR--IWILITTELL  106 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~--~~vlv~t~~~  106 (159)
                      .+|...|..++..  ..++++|||..-....+-+...|.-.++....+.|......|..+++.|...+  .-.|++|.+.
T Consensus       760 SgK~r~L~~LLp~~k~~G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAG  839 (941)
T KOG0389|consen  760 SGKCRKLKELLPKIKKKGDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAG  839 (941)
T ss_pred             hhhHhHHHHHHHHHhhcCCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccC
Confidence            6789999988874  35578999999888888888888888999999999999999999999999865  3477799999


Q ss_pred             ccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          107 GRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       107 ~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      +.|+|+-.+++||.+|...++-+=.|.--||.|.|+..+|.++
T Consensus       840 G~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~  882 (941)
T KOG0389|consen  840 GFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVY  882 (941)
T ss_pred             cceecccccceEEEeecCCCCcccchhHHHHHhhCCcceeEEE
Confidence            9999999999999999999999999999999999977665543

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

Probab=99.04  E-value=4.6e-09  Score=87.65  Aligned_cols=119  Identities=22%  Similarity=0.234  Sum_probs=104.4

Q ss_pred             ChHHHHHHHH-h--cCCCC--CEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC--CeeEEEEeC
Q psy576           32 SPVQAQDETI-L--LGIEP--PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG--RIWILITTE  104 (159)
Q Consensus        32 ~k~~~l~~~~-~--~~~~~--~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~--~~~vlv~t~  104 (159)
                      .|...+.+++ .  ...+.  ++++|+......+-+...+...++....++|.++.+.|...++.|+++  ..-.++++.
T Consensus       692 ~k~~~l~~ll~~~~~~~~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~k  771 (866)
T COG0553         692 GKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLK  771 (866)
T ss_pred             hHHHHHHHHHHHHHHhhcccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEec
Confidence            6788877777 2  33445  899999999999999999988888899999999999999999999995  455667888


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      +++.|+|+-.+++|+++++.|++....|...|+.|.|+...+.++-
T Consensus       772 agg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r  817 (866)
T COG0553         772 AGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYR  817 (866)
T ss_pred             ccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEE
Confidence            9999999999999999999999999999999999999887776654

>KOG0923|consensus

Probab=99.04  E-value=8.9e-10  Score=87.15  Aligned_cols=108  Identities=22%  Similarity=0.346  Sum_probs=92.1

Q ss_pred             cCCCCCEEEEecchHHHHHHHHHHHhC---------CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccC
Q psy576           43 LGIEPPVLVFVQSKERAQELYNELIYD---------GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFR  113 (159)
Q Consensus        43 ~~~~~~~lif~~~~~~~~~l~~~l~~~---------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~  113 (159)
                      ..+.+.+|||....++.+...+.|.+.         .+-+.++|+.+|...+.++++..-+|--+|++||++++..+.|+
T Consensus       470 tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTId  549 (902)
T KOG0923|consen  470 TQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTID  549 (902)
T ss_pred             ccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeec
Confidence            345678999999999888877776543         44578999999999999999998889999999999999999999


Q ss_pred             CCcEEEEecC------------------CCCHHHHHHHHhhccCCCCcceEEEEec
Q psy576          114 TVRLVVNYDF------------------PSSAISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       114 ~~~~vi~~~~------------------~~~~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      ++..||.-+.                  |-|.++-.||.||+||-| +|.|+-+++
T Consensus       550 gI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt  604 (902)
T KOG0923|consen  550 GIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYT  604 (902)
T ss_pred             CeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeec
Confidence            9999995332                  346788899999999996 789999987

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=99.04  E-value=2.7e-09  Score=88.48  Aligned_cols=122  Identities=25%  Similarity=0.240  Sum_probs=93.1

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+..  ..+.|+||-+.|++..+.+++.|...+++.-++.......+-.-+.+  .-..-.|.|||++++|
T Consensus       611 ~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~--AG~~GaVTIATNMAGR  688 (1112)
T PRK12901        611 REKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAE--AGQPGTVTIATNMAGR  688 (1112)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHh--cCCCCcEEEeccCcCC
Confidence            4566666655542  46789999999999999999999999888777777544333222212  2223459999999999


Q ss_pred             ccccC--------CCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          109 GIDFR--------TVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       109 g~~i~--------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |.||.        .--+||-...+.|..---|..||+||.|.+|.+.+|++-.|
T Consensus       689 GTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLED  742 (1112)
T PRK12901        689 GTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLED  742 (1112)
T ss_pred             CcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEccc
Confidence            99996        22477877888999999999999999999999888887554

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.03  E-value=4.7e-09  Score=86.56  Aligned_cols=121  Identities=21%  Similarity=0.259  Sum_probs=92.0

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC-eeEEEEeCCcc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR-IWILITTELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~vlv~t~~~~  107 (159)
                      ..|...+.+.+..  ..+.|+||-|.|.+..+.++..|.+.+++...++..-...+-. ++.  ..|+ -.|.|||++++
T Consensus       551 ~~k~~ai~~ei~~~~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak~~~~Ea~-iia--~AG~~g~VTIATNmAG  627 (970)
T PRK12899        551 REKYHAIVAEIASIHRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAKNHAQEAE-IIA--GAGKLGAVTVATNMAG  627 (970)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccchhhhHHH-HHH--hcCCCCcEEEeecccc
Confidence            3555555544432  3667999999999999999999999999888888753322222 221  2233 56999999999


Q ss_pred             cccccCCC--------cEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          108 RGIDFRTV--------RLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       108 ~g~~i~~~--------~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      +|.||.--        -+||....+.|..--.|..||+||.|.+|.+..|++-.|
T Consensus       628 RGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlED  682 (970)
T PRK12899        628 RGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFED  682 (970)
T ss_pred             CCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            99999522        267878888999999999999999999999988887554

>KOG0391|consensus

Probab=99.03  E-value=4.1e-09  Score=87.84  Aligned_cols=121  Identities=20%  Similarity=0.215  Sum_probs=103.4

Q ss_pred             CCCChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC--eeEEEEeC
Q psy576           29 GAGSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR--IWILITTE  104 (159)
Q Consensus        29 ~~~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~--~~vlv~t~  104 (159)
                      .+-+|++.|+-++.  +..++++|||+.-.+..+-+.++|..+|+--..+.|....++|...++.|+...  +..|++|.
T Consensus      1257 yDcGKLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTr 1336 (1958)
T KOG0391|consen 1257 YDCGKLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTR 1336 (1958)
T ss_pred             cccchHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEecc
Confidence            34567777666664  246789999999999999999999999999999999999999999999999854  45677999


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      ..+.|+|+-.++.||.||..|++.--.|.-.||.|.|+...+++|
T Consensus      1337 SggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIY 1381 (1958)
T KOG0391|consen 1337 SGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIY 1381 (1958)
T ss_pred             CCccccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEE
Confidence            999999999999999999999998888988899998876555554

>KOG0388|consensus

Probab=99.01  E-value=3.1e-09  Score=84.92  Aligned_cols=117  Identities=21%  Similarity=0.296  Sum_probs=103.9

Q ss_pred             CCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe-eEEEEeCCc
Q psy576           30 AGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI-WILITTELL  106 (159)
Q Consensus        30 ~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~-~vlv~t~~~  106 (159)
                      +.+|+..|-+++.+  ..++++|+|+.-.+..+-+.++|.-++++...+.|.....+|.+++.+|+..++ -.|++|.+.
T Consensus      1026 dSgKL~~LDeLL~kLkaegHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAG 1105 (1185)
T KOG0388|consen 1026 DSGKLVVLDELLPKLKAEGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAG 1105 (1185)
T ss_pred             cccceeeHHHHHHHhhcCCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccC
Confidence            36787777777763  356789999999999999999999999999999999999999999999999765 467799999


Q ss_pred             ccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceE
Q psy576          107 GRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKA  146 (159)
Q Consensus       107 ~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~  146 (159)
                      +.|+|+-.++.||.|+..|++..-.|.+.|+.|.|+...+
T Consensus      1106 GLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdv 1145 (1185)
T KOG0388|consen 1106 GLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDV 1145 (1185)
T ss_pred             cccccccccceEEEecCCCCcchhhHHHHHHHhccCccce
Confidence            9999999999999999999999999999999999976443

>KOG0392|consensus

Probab=99.00  E-value=7.2e-09  Score=86.60  Aligned_cols=115  Identities=18%  Similarity=0.250  Sum_probs=97.0

Q ss_pred             CChHHHHHHHHhc----------------CCCCCEEEEecchHHHHHHHHHHHhC---CCceEEEecCCCHHHHHHHHHH
Q psy576           31 GSPVQAQDETILL----------------GIEPPVLVFVQSKERAQELYNELIYD---GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        31 ~~k~~~l~~~~~~----------------~~~~~~lif~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      .-|+..|.+++..                ..++++||||.-++.++-+.+-|.+.   .+.-..+.|..++..|.++.+.
T Consensus      1309 spKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~ 1388 (1549)
T KOG0392|consen 1309 SPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVER 1388 (1549)
T ss_pred             chhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHH
Confidence            5688888888852                13568999999999999988766554   3334478999999999999999


Q ss_pred             HhcC-CeeEEE-EeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcce
Q psy576           92 FRTG-RIWILI-TTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGK  145 (159)
Q Consensus        92 f~~~-~~~vlv-~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~  145 (159)
                      |+++ .++||+ +|.+.+.|+|+-.++.||.+.-.|++-.=+|.+.|+.|.|++..
T Consensus      1389 FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrv 1444 (1549)
T KOG0392|consen 1389 FNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRV 1444 (1549)
T ss_pred             hcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCcee
Confidence            9997 778776 77999999999999999999999999888999999999997653

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.00  E-value=4.9e-09  Score=86.23  Aligned_cols=121  Identities=25%  Similarity=0.320  Sum_probs=93.0

Q ss_pred             CChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC-CeeEEEEeCCcc
Q psy576           31 GSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG-RIWILITTELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vlv~t~~~~  107 (159)
                      ..|...+.+.+.  ...+.|+||-+.|++..+.+++.|.+.+++.-++.......+-. ++.  +.| .-.|.|||++++
T Consensus       432 ~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk~~~~EA~-IIa--~AG~~GaVTIATNMAG  508 (913)
T PRK13103        432 EEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAKYHEKEAE-IIA--QAGRPGALTIATNMAG  508 (913)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccccchhHHH-HHH--cCCCCCcEEEeccCCC
Confidence            456666666555  24678999999999999999999999988877777754332222 222  234 456999999999


Q ss_pred             cccccC-------------------------------------CCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          108 RGIDFR-------------------------------------TVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       108 ~g~~i~-------------------------------------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      +|.||.                                     .--+||--..+.|..---|..||+||.|.+|.+-+|+
T Consensus       509 RGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~l  588 (913)
T PRK13103        509 RGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYL  588 (913)
T ss_pred             CCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEE
Confidence            999994                                     1226777778888888899999999999999999988


Q ss_pred             cCCC
Q psy576          151 TKQD  154 (159)
Q Consensus       151 ~~~~  154 (159)
                      +-.|
T Consensus       589 SlED  592 (913)
T PRK13103        589 SLED  592 (913)
T ss_pred             EcCc
Confidence            8654

>KOG0920|consensus

Probab=98.98  E-value=1.2e-09  Score=90.03  Aligned_cols=110  Identities=24%  Similarity=0.308  Sum_probs=93.5

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC-------CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD-------GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRL  117 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~  117 (159)
                      ..+.+|||.+..+++..+.+.|...       .+-+.++|+.|+..++..+....-.|..+|+++|..++.++.|+++-+
T Consensus       412 ~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNIAETSITIdDVvy  491 (924)
T KOG0920|consen  412 FEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETSITIDDVVY  491 (924)
T ss_pred             CCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhhhHhhcccccCeEE
Confidence            4578999999999999999998643       245789999999999999998888899999999999999999999999


Q ss_pred             EEEec--------CC----------CCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          118 VVNYD--------FP----------SSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       118 vi~~~--------~~----------~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      ||..+        +-          -+.++-.||.||+||- ..|.|+-++.....
T Consensus       492 VIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~  546 (924)
T KOG0920|consen  492 VIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRY  546 (924)
T ss_pred             EEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhh
Confidence            99643        22          1566789999999998 68999999986543

>KOG0924|consensus

Probab=98.96  E-value=1.3e-09  Score=86.66  Aligned_cols=108  Identities=20%  Similarity=0.323  Sum_probs=89.3

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHh----C------CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccC
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIY----D------GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFR  113 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~----~------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~  113 (159)
                      ...+.+|||....+..+.....+..    .      ++.+..+++.++..-+.++++.-..|.-+++|+|++++..+.+|
T Consensus       561 ~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~  640 (1042)
T KOG0924|consen  561 GPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIP  640 (1042)
T ss_pred             CCCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeec
Confidence            3557899999988776655544432    1      56789999999999999998888889999999999999999999


Q ss_pred             CCcEEEEecC------------------CCCHHHHHHHHhhccCCCCcceEEEEecC
Q psy576          114 TVRLVVNYDF------------------PSSAISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       114 ~~~~vi~~~~------------------~~~~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      .+.+||..+.                  |-|.++--||.||+||.| +|.|+-+|+.
T Consensus       641 gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe  696 (1042)
T KOG0924|consen  641 GIRYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTE  696 (1042)
T ss_pred             ceEEEEecCceeeeecccccccceeEEEechhccchhhccccCCCC-Ccceeeehhh
Confidence            9999996543                  346777889999999995 8999999876

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

Probab=98.93  E-value=8.9e-09  Score=70.17  Aligned_cols=111  Identities=26%  Similarity=0.354  Sum_probs=74.8

Q ss_pred             HHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCC--ceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC--CcccccccC
Q psy576           38 DETILLGIEPPVLVFVQSKERAQELYNELIYDGI--NVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE--LLGRGIDFR  113 (159)
Q Consensus        38 ~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~--~~~~g~~i~  113 (159)
                      .+++.. .++.++||++|.+.++.+.+.+.....  ....+..  ...+..++++.|+.++-.||+++.  ...+|+|+|
T Consensus         2 ~~l~~~-~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~   78 (167)
T PF13307_consen    2 LELISA-VPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFP   78 (167)
T ss_dssp             HHHHHC-CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--E
T ss_pred             hHHHhc-CCCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCC
Confidence            345555 458899999999999999999876531  2233333  366788899999999999999998  999999999


Q ss_pred             C--CcEEEEecCCCC------------------------------HHHHHHHHhhccCCCCcceEEEEec
Q psy576          114 T--VRLVVNYDFPSS------------------------------AISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       114 ~--~~~vi~~~~~~~------------------------------~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      +  ++.||..+.|..                              .....|.+||+-|..+.--++++.+
T Consensus        79 ~~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD  148 (167)
T PF13307_consen   79 GDLLRAVIIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLD  148 (167)
T ss_dssp             CESEEEEEEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEES
T ss_pred             CchhheeeecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEc
Confidence            6  778888777742                              1124788999999875543444443

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=98.90  E-value=8.8e-09  Score=85.87  Aligned_cols=111  Identities=23%  Similarity=0.288  Sum_probs=88.2

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhC----------------------------CCc-------------eEEEecCCCH
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYD----------------------------GIN-------------VDVIHSDRTQ   82 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~----------------------------~~~-------------~~~~~~~~~~   82 (159)
                      .+.-|+++|+-++..|+..+..+...                            +++             +.++|+++-|
T Consensus       377 ~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP  456 (1041)
T COG4581         377 DNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLP  456 (1041)
T ss_pred             hcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccch
Confidence            35668999999999988655544310                            111             5688999999


Q ss_pred             HHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----ec----CCCCHHHHHHHHhhccCCC--CcceEEEEecC
Q psy576           83 KQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----YD----FPSSAISYIHRIGRAGRGG--REGKAVTFFTK  152 (159)
Q Consensus        83 ~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~~----~~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~  152 (159)
                      ..+..+...|+.|-.+|+.+|.+.+.|+|.|.-++|+-    ++    ..-++.+|.|+.||+||.|  ..|.+++...+
T Consensus       457 ~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~  536 (1041)
T COG4581         457 AIKELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPP  536 (1041)
T ss_pred             HHHHHHHHHHhccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCC
Confidence            99999999999999999999999999999999887763    21    1237999999999999999  34888877555


Q ss_pred             CC
Q psy576          153 QD  154 (159)
Q Consensus       153 ~~  154 (159)
                      .+
T Consensus       537 ~~  538 (1041)
T COG4581         537 FE  538 (1041)
T ss_pred             CC
Confidence            44

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=98.89  E-value=3.5e-08  Score=82.56  Aligned_cols=106  Identities=22%  Similarity=0.283  Sum_probs=77.5

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCc--EEEE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVR--LVVN  120 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~--~vi~  120 (159)
                      .+++++||++|.+.++.++..|...  ......+..+.. ..|.++++.|++++..||++|+...+|+|+|+..  .||.
T Consensus       673 ~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI  751 (850)
T TIGR01407       673 TSPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVI  751 (850)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHhhhccccCceEEecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEE
Confidence            5578999999999999999998752  112223334333 5788899999999999999999999999999755  5565


Q ss_pred             ecCCCC------------------------------HHHHHHHHhhccCCCCcceEEEEec
Q psy576          121 YDFPSS------------------------------AISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       121 ~~~~~~------------------------------~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      ...|..                              ...+.|.+||+-|.....-++++.+
T Consensus       752 ~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD  812 (850)
T TIGR01407       752 PRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILD  812 (850)
T ss_pred             eCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEEc
Confidence            555531                              1225788999999875433455544

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.

>KOG0949|consensus

Probab=98.87  E-value=5.8e-09  Score=85.66  Aligned_cols=77  Identities=32%  Similarity=0.478  Sum_probs=66.9

Q ss_pred             eEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEec-CCCCHHHHHHHHhhccCCC--CcceEEEE
Q psy576           73 VDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD-FPSSAISYIHRIGRAGRGG--REGKAVTF  149 (159)
Q Consensus        73 ~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~-~~~~~~~~~q~~GR~~R~g--~~g~~~~~  149 (159)
                      ++++|++++..+|..+.-.|+.|.+.||++|..++.|+|.|.-++|+--| .--++-.|-||.||+||.|  -.|.++.+
T Consensus       965 iG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~Fm 1044 (1330)
T KOG0949|consen  965 IGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVFM 1044 (1330)
T ss_pred             ccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEEE
Confidence            78999999999999999999999999999999999999999888776554 3357889999999999998  34666554

>KOG1015|consensus

Probab=98.86  E-value=1.7e-08  Score=82.88  Aligned_cols=136  Identities=18%  Similarity=0.105  Sum_probs=113.6

Q ss_pred             hhhhccceeeeecCCCCChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhC----------------------C
Q psy576           15 RVKSNLARMYRETEGAGSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYD----------------------G   70 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~----------------------~   70 (159)
                      ++.+.+...-.....+.+|+-+|.+++.  ..-+.++|||..+....+-|-.+|.--                      |
T Consensus      1109 w~kd~v~e~d~~v~~~SgKmiLLleIL~mceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~G 1188 (1567)
T KOG1015|consen 1109 WYKDFVTEADAEVLEHSGKMILLLEILRMCEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRG 1188 (1567)
T ss_pred             hHHhhhhhhhhhhhhcCcceehHHHHHHHHHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecC
Confidence            5556666666666677899999999986  346789999999999999988887421                      2


Q ss_pred             CceEEEecCCCHHHHHHHHHHHhcCC----eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceE
Q psy576           71 INVDVIHSDRTQKQRDNVVRSFRTGR----IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKA  146 (159)
Q Consensus        71 ~~~~~~~~~~~~~~r~~~~~~f~~~~----~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~  146 (159)
                      ..-..+.|......|....+.|++-.    .-.||+|.+.+.|+|+-+++-||++|..|++..-.|.+=|++|+|+..+|
T Consensus      1189 kDyyriDGst~s~~R~k~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPv 1268 (1567)
T KOG1015|consen 1189 KDYYRLDGSTTSQSRKKWAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPV 1268 (1567)
T ss_pred             CceEEecCcccHHHHHHHHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCce
Confidence            33567788899999999999998732    34899999999999999999999999999999999999999999999999


Q ss_pred             EEEe
Q psy576          147 VTFF  150 (159)
Q Consensus       147 ~~~~  150 (159)
                      ++|=
T Consensus      1269 yiYR 1272 (1567)
T KOG1015|consen 1269 YIYR 1272 (1567)
T ss_pred             eehh
Confidence            8873

>KOG1123|consensus

Probab=98.77  E-value=1.8e-07  Score=72.55  Aligned_cols=130  Identities=16%  Similarity=0.146  Sum_probs=93.6

Q ss_pred             ccchhhHHhhhhccceeeeecCCCCChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHH
Q psy576            7 HTNPALKRRVKSNLARMYRETEGAGSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQ   84 (159)
Q Consensus         7 ~~~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~   84 (159)
                      .+..++++.++++.+......--+..|+..-.=++.  ..++.++|||....-   ++.++-.+.+  -.+++|..++.+
T Consensus       502 Mt~eFy~eYL~~~t~kr~lLyvMNP~KFraCqfLI~~HE~RgDKiIVFsDnvf---ALk~YAikl~--KpfIYG~Tsq~E  576 (776)
T KOG1123|consen  502 MTPEFYREYLRENTRKRMLLYVMNPNKFRACQFLIKFHERRGDKIIVFSDNVF---ALKEYAIKLG--KPFIYGPTSQNE  576 (776)
T ss_pred             CCHHHHHHHHhhhhhhhheeeecCcchhHHHHHHHHHHHhcCCeEEEEeccHH---HHHHHHHHcC--CceEECCCchhH
Confidence            344566666666555433333333566665333333  347789999987765   4444433332  358999999999


Q ss_pred             HHHHHHHHhc-CCeeEEEEeCCcccccccCCCcEEEEecCC-CCHHHHHHHHhhccCCC
Q psy576           85 RDNVVRSFRT-GRIWILITTELLGRGIDFRTVRLVVNYDFP-SSAISYIHRIGRAGRGG  141 (159)
Q Consensus        85 r~~~~~~f~~-~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~-~~~~~~~q~~GR~~R~g  141 (159)
                      |.++++.|+- .+..-+..+.++...+|+|.++++|..+.- .|..+-.||.||..|..
T Consensus       577 Rm~ILqnFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAK  635 (776)
T KOG1123|consen  577 RMKILQNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAK  635 (776)
T ss_pred             HHHHHHhcccCCccceEEEeeccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHh
Confidence            9999999987 467788888999999999999999987654 47788899999999976

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=98.75  E-value=4.8e-08  Score=79.51  Aligned_cols=97  Identities=31%  Similarity=0.429  Sum_probs=75.0

Q ss_pred             HHHHHHHhC--CCceEEEecCCCH--HHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCC------C-----
Q psy576           61 ELYNELIYD--GINVDVIHSDRTQ--KQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFP------S-----  125 (159)
Q Consensus        61 ~l~~~l~~~--~~~~~~~~~~~~~--~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~------~-----  125 (159)
                      ++.+.|...  +.++..+.++...  ..-+..++.|.+|+.+|||.|+++..|.|+|+++.|...+..      +     
T Consensus       495 rieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~E  574 (730)
T COG1198         495 RIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASE  574 (730)
T ss_pred             HHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchHH
Confidence            444444433  5567777777644  335678999999999999999999999999999987755432      1     


Q ss_pred             -CHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576          126 -SAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus       126 -~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                       ....+.|-.||+||.+.+|.+++.....|...
T Consensus       575 r~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~  607 (730)
T COG1198         575 RTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPA  607 (730)
T ss_pred             HHHHHHHHHHhhhccCCCCCeEEEEeCCCCcHH
Confidence             35567889999999999999999998888654

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.73  E-value=2.7e-07  Score=75.99  Aligned_cols=82  Identities=20%  Similarity=0.220  Sum_probs=58.8

Q ss_pred             CChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCC-CHHHHHHHHHHHhcCCeeEEEEeCCcc
Q psy576           31 GSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDR-TQKQRDNVVRSFRTGRIWILITTELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~-~~~~r~~~~~~f~~~~~~vlv~t~~~~  107 (159)
                      ..|...+.+.+.  ...+.|+||-|.|.+..+.++..|.+.+++.-+++... ..+.-.+++.. .-..-.|.|||++++
T Consensus       407 ~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIA~-AG~~G~VTIATNMAG  485 (870)
T CHL00122        407 LSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPENVRRESEIVAQ-AGRKGSITIATNMAG  485 (870)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCccchhHHHHHHh-cCCCCcEEEeccccC
Confidence            345555554443  24678999999999999999999999999988888863 21222223332 223456999999999


Q ss_pred             cccccC
Q psy576          108 RGIDFR  113 (159)
Q Consensus       108 ~g~~i~  113 (159)
                      ||.||.
T Consensus       486 RGTDI~  491 (870)
T CHL00122        486 RGTDII  491 (870)
T ss_pred             CCcCee
Confidence            999984

>KOG0926|consensus

Probab=98.72  E-value=5e-08  Score=79.00  Aligned_cols=80  Identities=21%  Similarity=0.294  Sum_probs=63.1

Q ss_pred             eEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCCC------------------CHHHHHHHH
Q psy576           73 VDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPS------------------SAISYIHRI  134 (159)
Q Consensus        73 ~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~------------------~~~~~~q~~  134 (159)
                      +.++|+=++.+.+.++++.--.|..-++|+|++++..+.||++.+|+..+.-+                  |-++--||+
T Consensus       607 vLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRA  686 (1172)
T KOG0926|consen  607 VLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRA  686 (1172)
T ss_pred             EeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhc
Confidence            45556666666666666666678878999999999999999999999755321                  456678999


Q ss_pred             hhccCCCCcceEEEEecCC
Q psy576          135 GRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus       135 GR~~R~g~~g~~~~~~~~~  153 (159)
                      ||+||.| +|.||.+|+..
T Consensus       687 GRAGRtg-pGHcYRLYSSA  704 (1172)
T KOG0926|consen  687 GRAGRTG-PGHCYRLYSSA  704 (1172)
T ss_pred             cccCCCC-CCceeehhhhH
Confidence            9999996 78999998753

>KOG1000|consensus

Probab=98.72  E-value=1.1e-07  Score=73.41  Aligned_cols=119  Identities=18%  Similarity=0.209  Sum_probs=99.9

Q ss_pred             ChHHHHHHHHhc------CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC-CeeEEE-Ee
Q psy576           32 SPVQAQDETILL------GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG-RIWILI-TT  103 (159)
Q Consensus        32 ~k~~~l~~~~~~------~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vlv-~t  103 (159)
                      .|...+.+.+..      ....+.+|||--....+.|...+.++++....+.|..++.+|....+.|+.+ +..|-| +.
T Consensus       472 aK~~av~eyi~~~~~l~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsI  551 (689)
T KOG1000|consen  472 AKAAAVCEYILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSI  551 (689)
T ss_pred             cccHHHHHHHHhCcccccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEE
Confidence            444445555542      3456899999999999999999999999999999999999999999999985 455544 66


Q ss_pred             CCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       104 ~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      .+++.|+++...+.|+....+|++..++|.=.|+.|.|++..+.+++
T Consensus       552 tA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQkssV~v~y  598 (689)
T KOG1000|consen  552 TAAGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSSVFVQY  598 (689)
T ss_pred             eecccceeeeccceEEEEEecCCCceEEechhhhhhccccceeeEEE
Confidence            88999999999999999999999999999999999999776554443

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=98.71  E-value=2.5e-07  Score=75.64  Aligned_cols=105  Identities=17%  Similarity=0.139  Sum_probs=77.6

Q ss_pred             CCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHH---------------------HHHHHHHHHhc-CCee
Q psy576           46 EPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQK---------------------QRDNVVRSFRT-GRIW   98 (159)
Q Consensus        46 ~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~---------------------~r~~~~~~f~~-~~~~   98 (159)
                      ..+++|||.++..|..+++.|.+.     +.....+++..+..                     ....+++.|++ +.++
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            478999999999999999887554     23344555543322                     22467888876 6789


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCC-C---CcceEEEEec
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRG-G---REGKAVTFFT  151 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~-g---~~g~~~~~~~  151 (159)
                      |||+++++..|+|.|.+++++...+..+. .++|++||+.|. .   ..|.++-|+.
T Consensus       594 ilIVvdmllTGFDaP~l~tLyldKplk~h-~LlQai~R~nR~~~~~K~~g~IvDy~g  649 (667)
T TIGR00348       594 LLIVVDMLLTGFDAPILNTLYLDKPLKYH-GLLQAIARTNRIDGKDKTFGLIVDYRG  649 (667)
T ss_pred             EEEEEcccccccCCCccceEEEecccccc-HHHHHHHHhccccCCCCCCEEEEECcC
Confidence            99999999999999999988887665554 579999999993 3   2354554443

Members of this family are assumed to differ from each other in DNA site specificity.

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

Probab=98.70  E-value=1.6e-07  Score=76.38  Aligned_cols=94  Identities=23%  Similarity=0.296  Sum_probs=75.6

Q ss_pred             CCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHHHhc--CCeeEEEEeCCcccccccCCCcEE
Q psy576           46 EPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRSFRT--GRIWILITTELLGRGIDFRTVRLV  118 (159)
Q Consensus        46 ~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~--~~~~vlv~t~~~~~g~~i~~~~~v  118 (159)
                      .+++||||.+..+|+.+...|.+.     +--+..++|.-  ++-...++.|..  .-..|.|+.+++..|+|+|.+..+
T Consensus       426 ~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~--~~~q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nl  503 (875)
T COG4096         426 IGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDA--EQAQALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNL  503 (875)
T ss_pred             cCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccc--hhhHHHHHHHHhcCCCCceEEehhhhhcCCCchheeee
Confidence            468999999999999999999765     23366777753  233334555544  346799999999999999999999


Q ss_pred             EEecCCCCHHHHHHHHhhccCCC
Q psy576          119 VNYDFPSSAISYIHRIGRAGRGG  141 (159)
Q Consensus       119 i~~~~~~~~~~~~q~~GR~~R~g  141 (159)
                      +.+..-.|...|.||+||.-|..
T Consensus       504 VF~r~VrSktkF~QMvGRGTRl~  526 (875)
T COG4096         504 VFDRKVRSKTKFKQMVGRGTRLC  526 (875)
T ss_pred             eehhhhhhHHHHHHHhcCccccC
Confidence            99988899999999999999954

>KOG0386|consensus

Probab=98.65  E-value=8.9e-08  Score=78.92  Aligned_cols=121  Identities=17%  Similarity=0.194  Sum_probs=107.2

Q ss_pred             CCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC---eeEEEEeC
Q psy576           30 AGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR---IWILITTE  104 (159)
Q Consensus        30 ~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~---~~vlv~t~  104 (159)
                      ..+|+++|-+++.+  ..+++++.||.-+.-.+-+-.+|.-.++.-..+.|.....+|-..++.|+...   ...|.+|.
T Consensus       708 ~sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~Fllstr  787 (1157)
T KOG0386|consen  708 VSGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTR  787 (1157)
T ss_pred             hccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeec
Confidence            47899999998874  35689999999999888889999888888999999999999999999999843   45677999


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      ..+.|+|++.++.||.+|..|++....|+--|+.|.|+...+-++.
T Consensus       788 agglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~r  833 (1157)
T KOG0386|consen  788 AGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLR  833 (1157)
T ss_pred             ccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeee
Confidence            9999999999999999999999999999999999999877766654

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

Probab=98.61  E-value=8.2e-07  Score=75.06  Aligned_cols=107  Identities=19%  Similarity=0.236  Sum_probs=78.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC--ceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCC--CcEEEE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI--NVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRT--VRLVVN  120 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~--~~~vi~  120 (159)
                      .+++++|+++|.+.++.+++.|.....  ....+.-+++...|.++++.|++++-.||++|....+|+|+|+  ++.||.
T Consensus       751 ~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI  830 (928)
T PRK08074        751 TKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVI  830 (928)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEE
Confidence            567899999999999999999875422  1223333444456788999999988889999999999999996  477777


Q ss_pred             ecCCC----C--------------------------HHHHHHHHhhccCCCCcceEEEEec
Q psy576          121 YDFPS----S--------------------------AISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       121 ~~~~~----~--------------------------~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      ...|.    +                          ...+.|.+||+-|.....-++++.+
T Consensus       831 ~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD  891 (928)
T PRK08074        831 VRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLD  891 (928)
T ss_pred             ecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEec
Confidence            66553    1                          1225788999999874433455444

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

Probab=98.58  E-value=1.4e-06  Score=71.29  Aligned_cols=111  Identities=21%  Similarity=0.299  Sum_probs=79.6

Q ss_pred             HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCc-eEEEecCCCHHHHHHHHHHHhcCCe-eEEEEeCCcccccccCC
Q psy576           37 QDETILLGIEPPVLVFVQSKERAQELYNELIYDGIN-VDVIHSDRTQKQRDNVVRSFRTGRI-WILITTELLGRGIDFRT  114 (159)
Q Consensus        37 l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~r~~~~~~f~~~~~-~vlv~t~~~~~g~~i~~  114 (159)
                      +.+++.. .+++++||++|.+.+..+.+.+...... ....+|   ...+.+.++.|..+.- .++|++..+.+|+|+|+
T Consensus       471 i~~~~~~-~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~---~~~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g  546 (654)
T COG1199         471 LREILKA-SPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQG---EDEREELLEKFKASGEGLILVGGGSFWEGVDFPG  546 (654)
T ss_pred             HHHHHhh-cCCCEEEEeccHHHHHHHHHHHhhcCccceeeecC---CCcHHHHHHHHHHhcCCeEEEeeccccCcccCCC
Confidence            3334444 4558999999999999999999876542 334444   3444588899888654 89999999999999986


Q ss_pred             --CcEEEEecCCCC------------------------------HHHHHHHHhhccCCCCcceEEEEec
Q psy576          115 --VRLVVNYDFPSS------------------------------AISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       115 --~~~vi~~~~~~~------------------------------~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                        +..||..+.|..                              .....|.+||+-|.-+..-++++.+
T Consensus       547 ~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD  615 (654)
T COG1199         547 DALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLD  615 (654)
T ss_pred             CCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEec
Confidence              467777766642                              3346899999999764433444444

>KOG4439|consensus

Probab=98.54  E-value=1.3e-06  Score=70.03  Aligned_cols=105  Identities=14%  Similarity=0.159  Sum_probs=87.0

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc--CCeeEEE-EeCCcccccccCCCcEEEEe
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT--GRIWILI-TTELLGRGIDFRTVRLVVNY  121 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~--~~~~vlv-~t~~~~~g~~i~~~~~vi~~  121 (159)
                      .+.+++|...=.+...-+...+++.+.....+||.....+|.++++.|+.  |..+|++ +=.+.+-|+|+-..+|++..
T Consensus       745 skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHlilv  824 (901)
T KOG4439|consen  745 SKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLILV  824 (901)
T ss_pred             ccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEEEE
Confidence            44555554444444555667888889999999999999999999999976  5466665 44889999999999999999


Q ss_pred             cCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          122 DFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       122 ~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      |.-|+++.-.|.+.|..|.|++..++++
T Consensus       825 DlHWNPaLEqQAcDRIYR~GQkK~V~Ih  852 (901)
T KOG4439|consen  825 DLHWNPALEQQACDRIYRMGQKKDVFIH  852 (901)
T ss_pred             ecccCHHHHHHHHHHHHHhcccCceEEE
Confidence            9999999999999999999998887765

>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=98.46  E-value=9.2e-06  Score=62.94  Aligned_cols=141  Identities=18%  Similarity=0.196  Sum_probs=110.3

Q ss_pred             hhhhccceeeeecCCC------CChHHHHHH-----HHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHH
Q psy576           15 RVKSNLARMYRETEGA------GSPVQAQDE-----TILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQK   83 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~------~~k~~~l~~-----~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~   83 (159)
                      ....+++|.|...+..      +.+++...+     +......+.+|||++|--+--.+..+|++.++..+.+++..+..
T Consensus       258 ~v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~  337 (442)
T PF06862_consen  258 QVVVQVRQVFQRFDCSSPADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNS  337 (442)
T ss_pred             ccccCCceEEEEecCCCcchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHH
Confidence            3455777888775442      334444332     22234557899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCeeEEEEeCC--cccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCC------cceEEEEecCCCc
Q psy576           84 QRDNVVRSFRTGRIWILITTEL--LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGR------EGKAVTFFTKQDA  155 (159)
Q Consensus        84 ~r~~~~~~f~~~~~~vlv~t~~--~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~------~g~~~~~~~~~~~  155 (159)
                      +..+....|..|+..+|+.|.=  .-+-..+.++..||.|++|..+.=|...++-.+....      ...|.++++.-|.
T Consensus       338 ~isRAR~~F~~G~~~iLL~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~  417 (442)
T PF06862_consen  338 DISRARSQFFHGRKPILLYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDA  417 (442)
T ss_pred             HHHHHHHHHHcCCceEEEEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHH
Confidence            9999999999999999999963  4455677889999999999999999998876665543      4678888776553

; GO: 0005634 nucleus

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

Probab=98.46  E-value=4.4e-06  Score=69.82  Aligned_cols=105  Identities=21%  Similarity=0.290  Sum_probs=75.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCC--CcEEEEec
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRT--VRLVVNYD  122 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~--~~~vi~~~  122 (159)
                      .+++++|+++|.+.++.+++.|.....++ ...|...  .+.++++.|++++-.||++|....+|+|+|.  ...+|...
T Consensus       646 ~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~k  722 (820)
T PRK07246        646 LQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVITR  722 (820)
T ss_pred             cCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEec
Confidence            56889999999999999999987654443 5555322  3456899999988889999999999999973  44455544


Q ss_pred             CCC----C--------------------------HHHHHHHHhhccCCCCcceEEEEecC
Q psy576          123 FPS----S--------------------------AISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       123 ~~~----~--------------------------~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      .|.    +                          ...+.|.+||+-|.....-++++.++
T Consensus       723 LPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~  782 (820)
T PRK07246        723 LPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDR  782 (820)
T ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECC
Confidence            442    2                          22268899999998743324555443

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.45  E-value=4.4e-06  Score=69.16  Aligned_cols=82  Identities=23%  Similarity=0.256  Sum_probs=59.3

Q ss_pred             CChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHH-HHHHHHhcCCeeEEEEeCCcc
Q psy576           31 GSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRD-NVVRSFRTGRIWILITTELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~-~~~~~f~~~~~~vlv~t~~~~  107 (159)
                      ..|...+.+.+.  ...+.|+||-+.|.+..+.++..|.+.+++..+++......+++ +++.. .-..-.|.|||++++
T Consensus       422 ~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIa~-AG~~GaVTIATNMAG  500 (939)
T PRK12902        422 IAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAKPENVEREAEIVAQ-AGRKGAVTIATNMAG  500 (939)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCCCcchHhHHHHHHh-cCCCCcEEEeccCCC
Confidence            356666555554  24678999999999999999999999999988888862222222 23322 222356999999999


Q ss_pred             cccccC
Q psy576          108 RGIDFR  113 (159)
Q Consensus       108 ~g~~i~  113 (159)
                      +|.||.
T Consensus       501 RGTDIk  506 (939)
T PRK12902        501 RGTDII  506 (939)
T ss_pred             CCcCEe
Confidence            999884

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.44  E-value=5.9e-06  Score=67.98  Aligned_cols=105  Identities=20%  Similarity=0.302  Sum_probs=73.7

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc----CCeeEEEEeCCcccccccCC--CcEE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT----GRIWILITTELLGRGIDFRT--VRLV  118 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~----~~~~vlv~t~~~~~g~~i~~--~~~v  118 (159)
                      ..+.++||++|.+.++.++..|....-.....+|.   ..+..+++.|++    ++-.||++|....+|+|+|+  ++.|
T Consensus       533 ~~gg~LVlFtSy~~l~~v~~~l~~~~~~~ll~Q~~---~~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~v  609 (697)
T PRK11747        533 KHKGSLVLFASRRQMQKVADLLPRDLRLMLLVQGD---QPRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQV  609 (697)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHhcCCcEEEeCC---chHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEE
Confidence            34558999999999999999886432123455664   246677776664    67789999999999999986  6788


Q ss_pred             EEecCCC----CH--------------------------HHHHHHHhhccCCCCcceEEEEecC
Q psy576          119 VNYDFPS----SA--------------------------ISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       119 i~~~~~~----~~--------------------------~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      |....|.    ++                          ..+.|.+||+-|....--++++.++
T Consensus       610 II~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~  673 (697)
T PRK11747        610 IITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDR  673 (697)
T ss_pred             EEEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEcc
Confidence            8766553    11                          1257888999998644334444443

>KOG1002|consensus

Probab=98.41  E-value=2.8e-06  Score=65.99  Aligned_cols=116  Identities=14%  Similarity=0.113  Sum_probs=97.3

Q ss_pred             CChHHHHHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC-CeeEEE-EeC
Q psy576           31 GSPVQAQDETIL----LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG-RIWILI-TTE  104 (159)
Q Consensus        31 ~~k~~~l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vlv-~t~  104 (159)
                      .-|.+.|.+.+-    ....-+.|||..-.+..+-+.=.|.+.|+.++-+-|+|++..|...++.|.+. .+.|++ +-.
T Consensus       619 STKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLk  698 (791)
T KOG1002|consen  619 STKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLK  698 (791)
T ss_pred             hhHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEec
Confidence            456777666553    33334789999999999988888989999999999999999999999999884 566554 558


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceE
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKA  146 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~  146 (159)
                      +.+..+|+-.+++|+++|+=|+++.-.|...|..|.|+..++
T Consensus       699 AGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPv  740 (791)
T KOG1002|consen  699 AGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPV  740 (791)
T ss_pred             cCceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccce
Confidence            898999999999999999999999999999999999965544

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.39  E-value=3e-06  Score=70.54  Aligned_cols=88  Identities=28%  Similarity=0.495  Sum_probs=73.6

Q ss_pred             ChHHHHHHHHhcCCCCCEEEEecc---hHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEe----C
Q psy576           32 SPVQAQDETILLGIEPPVLVFVQS---KERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT----E  104 (159)
Q Consensus        32 ~k~~~l~~~~~~~~~~~~lif~~~---~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t----~  104 (159)
                      ...+.+.+++... +.-.|||++.   .+.+++++++|+..|+++..+|+.     ..+.++.|..|+.++||+.    .
T Consensus       322 ~~~e~~~elvk~l-G~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG  395 (1187)
T COG1110         322 ESLEKVVELVKKL-GDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KEEALEDFEEGEVDVLVGVASYYG  395 (1187)
T ss_pred             ccHHHHHHHHHHh-CCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----chhhhhhhccCceeEEEEeccccc
Confidence            4555566666653 3368999999   999999999999999999999983     2678999999999999976    4


Q ss_pred             CcccccccCC-CcEEEEecCCC
Q psy576          105 LLGRGIDFRT-VRLVVNYDFPS  125 (159)
Q Consensus       105 ~~~~g~~i~~-~~~vi~~~~~~  125 (159)
                      ++-+|+|+|. +..+|.+++|+
T Consensus       396 ~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         396 VLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             ceeecCCchhheeEEEEecCCc
Confidence            6999999997 78999999994

>KOG0925|consensus

Probab=98.30  E-value=6.7e-06  Score=63.82  Aligned_cols=118  Identities=21%  Similarity=0.365  Sum_probs=85.0

Q ss_pred             CChHHHHHHHH----hcCCCCCEEEEecchHHHHHHHHHHHhC---------CCceEEEecCCCHHHHHHHHHHHhc---
Q psy576           31 GSPVQAQDETI----LLGIEPPVLVFVQSKERAQELYNELIYD---------GINVDVIHSDRTQKQRDNVVRSFRT---   94 (159)
Q Consensus        31 ~~k~~~l~~~~----~~~~~~~~lif~~~~~~~~~l~~~l~~~---------~~~~~~~~~~~~~~~r~~~~~~f~~---   94 (159)
                      .+.++...+.+    .....+.+++|..+.++.+...+.+...         ..++..+|    +.+...+++....   
T Consensus       234 rDylEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~  309 (699)
T KOG0925|consen  234 RDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRN  309 (699)
T ss_pred             hhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccC
Confidence            45555433333    2456788999999999988887776532         34677777    4444444444322   


Q ss_pred             C--CeeEEEEeCCcccccccCCCcEEEEecC------------------CCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576           95 G--RIWILITTELLGRGIDFRTVRLVVNYDF------------------PSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus        95 ~--~~~vlv~t~~~~~g~~i~~~~~vi~~~~------------------~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      |  ..+|+|+|..++..+.++.+.+||.-++                  |-|..+-.||.||+||. ++|.|+.++...
T Consensus       310 ~~~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~  387 (699)
T KOG0925|consen  310 GAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEE  387 (699)
T ss_pred             CCccceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHH
Confidence            2  3579999999999999999999985332                  34678889999999998 789999999754

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.27  E-value=1.4e-05  Score=66.03  Aligned_cols=107  Identities=20%  Similarity=0.330  Sum_probs=76.7

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-------ceEEEecCCCHHHHHHHHHHHhc----CCeeEEEEe--CCcccccc
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-------NVDVIHSDRTQKQRDNVVRSFRT----GRIWILITT--ELLGRGID  111 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-------~~~~~~~~~~~~~r~~~~~~f~~----~~~~vlv~t--~~~~~g~~  111 (159)
                      .++.++||++|.+.++.+.+.+.+.+.       +..+.-+ -...++.++++.|+.    ++-.||.++  ..+++|+|
T Consensus       521 ~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~-~~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGID  599 (705)
T TIGR00604       521 IPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVET-KDAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGID  599 (705)
T ss_pred             CCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeC-CCcchHHHHHHHHHHHHhcCCceEEEEecCCcccCccc
Confidence            457899999999999999998865421       2233333 233577889999965    455699988  89999999


Q ss_pred             cCC--CcEEEEecCCCC-H------------------------------HHHHHHHhhccCCCCcceEEEEecC
Q psy576          112 FRT--VRLVVNYDFPSS-A------------------------------ISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       112 i~~--~~~vi~~~~~~~-~------------------------------~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      +++  ++.||..+.|.. +                              ....|.+||+-|..+.--++++.+.
T Consensus       600 f~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~~~D~G~iillD~  673 (705)
T TIGR00604       600 FCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQDFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDK  673 (705)
T ss_pred             cCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHHHHhCccccCcCceEEEEEEeh
Confidence            986  678888887751 0                              1246889999998755435555553

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).

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

Probab=98.25  E-value=2.4e-05  Score=63.46  Aligned_cols=115  Identities=13%  Similarity=0.076  Sum_probs=80.5

Q ss_pred             HHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC----CeeEEEEeCCccccc
Q psy576           35 QAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG----RIWILITTELLGRGI  110 (159)
Q Consensus        35 ~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~----~~~vlv~t~~~~~g~  110 (159)
                      +.+.+++.. .++.++|.+.|.+.+..+++.+...-.-...+.|..+  .+..+++.|+..    +-.||++|..+.+|+
T Consensus       460 ~~~~~~~~~-~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGv  536 (636)
T TIGR03117       460 LSTAAILRK-AQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGI  536 (636)
T ss_pred             HHHHHHHHH-cCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCcccccc
Confidence            445555555 5678999999999999999998664223356666432  445678888874    688999999999999


Q ss_pred             cc--------C--CCcEEEEecCCCC-------------------------HHHHHHHHhhccCCCCc--ceEEEEecC
Q psy576          111 DF--------R--TVRLVVNYDFPSS-------------------------AISYIHRIGRAGRGGRE--GKAVTFFTK  152 (159)
Q Consensus       111 ~i--------~--~~~~vi~~~~~~~-------------------------~~~~~q~~GR~~R~g~~--g~~~~~~~~  152 (159)
                      |+        |  .++.||+...|..                         .-.+.|-+||.-|....  .-++.+.++
T Consensus       537 Dv~~~~~~p~~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~  615 (636)
T TIGR03117       537 DLTHKPVSPDKDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDG  615 (636)
T ss_pred             ccCCccCCCCCCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeC
Confidence            99        2  3778887665532                         22267889999998743  334444443

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.

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=98.24  E-value=4.6e-05  Score=50.46  Aligned_cols=93  Identities=19%  Similarity=0.290  Sum_probs=61.1

Q ss_pred             HHHHHHHHHhCCC------ceEEEecCCCHHHHHHHHHHHhcCC-eeEEEEeCCcccccccCC--CcEEEEecCCCC---
Q psy576           59 AQELYNELIYDGI------NVDVIHSDRTQKQRDNVVRSFRTGR-IWILITTELLGRGIDFRT--VRLVVNYDFPSS---  126 (159)
Q Consensus        59 ~~~l~~~l~~~~~------~~~~~~~~~~~~~r~~~~~~f~~~~-~~vlv~t~~~~~g~~i~~--~~~vi~~~~~~~---  126 (159)
                      ++.+...+...+.      ....+..+....+...+++.|.+.. -.||+++....+|+|+|+  ++.||..+.|..   
T Consensus         4 m~~v~~~~~~~~~~~~l~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPfp~~~   83 (141)
T smart00492        4 MESFVQYWKENGILENINKNLLLLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPFPYPD   83 (141)
T ss_pred             HHHHHHHHHHcCchhhHhcCCeEEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCCCCCC
Confidence            4455555554432      2344555556667888999998754 379999977999999986  567777666531   


Q ss_pred             ----------------------------HHHHHHHHhhccCCCCcceEEEEec
Q psy576          127 ----------------------------AISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       127 ----------------------------~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                                                  .....|.+||+-|..+.--++++.+
T Consensus        84 d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~l~D  136 (141)
T smart00492       84 SPILKARLELLRDKGQIRPFDFVSLPDAMRTLAQCVGRLIRGANDYGVVVIAD  136 (141)
T ss_pred             CHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHhCccccCcCceEEEEEEe
Confidence                                        1225788899999875433444443

>COG4889 Predicted helicase [General function prediction only]

Probab=98.19  E-value=1.1e-06  Score=72.24  Aligned_cols=104  Identities=17%  Similarity=0.321  Sum_probs=79.7

Q ss_pred             CCEEEEecchHHHHHHHHHHHh-----------C--CC--ceEEEecCCCHHHHHHHHHH---HhcCCeeEEEEeCCccc
Q psy576           47 PPVLVFVQSKERAQELYNELIY-----------D--GI--NVDVIHSDRTQKQRDNVVRS---FRTGRIWILITTELLGR  108 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~-----------~--~~--~~~~~~~~~~~~~r~~~~~~---f~~~~~~vlv~t~~~~~  108 (159)
                      ++++.||.+.++...+++.+..           .  ++  .+..+.|.|+.-+|++....   |...+++||-...++.+
T Consensus       461 ~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSE  540 (1518)
T COG4889         461 QRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSE  540 (1518)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhhhc
Confidence            3678899988877766554421           1  23  35567788998888555543   34578899999999999


Q ss_pred             ccccCCCcEEEEecCCCCHHHHHHHHhhccCCC---CcceEEEEe
Q psy576          109 GIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGG---REGKAVTFF  150 (159)
Q Consensus       109 g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g---~~g~~~~~~  150 (159)
                      |+|+|.++.||.+++..+.-+..|.+||+-|-.   ..|..+.-+
T Consensus       541 GVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILPI  585 (1518)
T COG4889         541 GVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILPI  585 (1518)
T ss_pred             CCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEEe
Confidence            999999999999999999999999999999954   335555443

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=98.12  E-value=8.8e-05  Score=49.19  Aligned_cols=94  Identities=19%  Similarity=0.281  Sum_probs=59.9

Q ss_pred             HHHHHHHHHHhCCC---ceEEEecCCCHHHHHHHHHHHhcCCe---eEEEEeCC--cccccccCC--CcEEEEecCCCC-
Q psy576           58 RAQELYNELIYDGI---NVDVIHSDRTQKQRDNVVRSFRTGRI---WILITTEL--LGRGIDFRT--VRLVVNYDFPSS-  126 (159)
Q Consensus        58 ~~~~l~~~l~~~~~---~~~~~~~~~~~~~r~~~~~~f~~~~~---~vlv~t~~--~~~g~~i~~--~~~vi~~~~~~~-  126 (159)
                      .++.+++.+.+.+.   ....+..+....+..++++.|++...   .||+++.-  ..+|+|+|+  ++.||..+.|.. 
T Consensus         3 ~m~~v~~~~~~~~~~~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~   82 (142)
T smart00491        3 YLEQVVEYWKENGILEINKPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPN   82 (142)
T ss_pred             HHHHHHHHHHhcCccccCceEEEECCCCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCCCC
Confidence            34566666665432   22333333344455788899987543   68888766  999999987  567877776631 


Q ss_pred             ------------------------------HHHHHHHHhhccCCCCcceEEEEec
Q psy576          127 ------------------------------AISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       127 ------------------------------~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                                                    .....|.+||+-|..+.--++++.+
T Consensus        83 ~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~Qa~GR~iR~~~D~g~i~l~D  137 (142)
T smart00491       83 PDSPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLD  137 (142)
T ss_pred             CCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHhCccccCccceEEEEEEe
Confidence                                          1224788999999875433555544

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

Probab=98.02  E-value=8.8e-06  Score=66.96  Aligned_cols=120  Identities=24%  Similarity=0.238  Sum_probs=83.6

Q ss_pred             CChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      +.|+..+.+.+.  ...++|+||-+.+.+..+.+.+.|.+.+++..++......++  .-+-+..-..-.|-|||+++++
T Consensus       412 ~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h~~E--A~Iia~AG~~gaVTiATNMAGR  489 (822)
T COG0653         412 EEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNHARE--AEIIAQAGQPGAVTIATNMAGR  489 (822)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccHHHH--HHHHhhcCCCCccccccccccC
Confidence            456666555554  357789999999999999999999999988878877655333  2222333233468999999999


Q ss_pred             ccccCCCc-----------EEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecC
Q psy576          109 GIDFRTVR-----------LVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       109 g~~i~~~~-----------~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      |-||.--.           +||--.--.|..-=-|..||+||+|.+|....|.+-
T Consensus       490 GTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSl  544 (822)
T COG0653         490 GTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSL  544 (822)
T ss_pred             CcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhh
Confidence            99995332           233222223333345999999999988877776653

>PF13871 Helicase_C_4: Helicase_C-like

Probab=98.01  E-value=3.7e-05  Score=56.20  Aligned_cols=68  Identities=21%  Similarity=0.312  Sum_probs=55.2

Q ss_pred             HHHHHHHHhcCCeeEEEEeCCcccccccCC--------CcEEEEecCCCCHHHHHHHHhhccCCCCc-ceEEEEecC
Q psy576           85 RDNVVRSFRTGRIWILITTELLGRGIDFRT--------VRLVVNYDFPSSAISYIHRIGRAGRGGRE-GKAVTFFTK  152 (159)
Q Consensus        85 r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~--------~~~vi~~~~~~~~~~~~q~~GR~~R~g~~-g~~~~~~~~  152 (159)
                      .....+.|.+|+..|+|.|++++.|+.+.+        ..+-|.+.+||+....+|..||+.|.++. .+.+.++..
T Consensus        50 N~~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t  126 (278)
T PF13871_consen   50 NIAEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVT  126 (278)
T ss_pred             cHHHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeec
Confidence            335677899999999999999999997752        34667789999999999999999999964 555665543

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=97.98  E-value=9.9e-05  Score=62.40  Aligned_cols=91  Identities=22%  Similarity=0.221  Sum_probs=67.2

Q ss_pred             EEEEecchHHHHHHHHHHHhC------CCceEEEecCCCHHHHHHHHHHH----------------------hc----CC
Q psy576           49 VLVFVQSKERAQELYNELIYD------GINVDVIHSDRTQKQRDNVVRSF----------------------RT----GR   96 (159)
Q Consensus        49 ~lif~~~~~~~~~l~~~l~~~------~~~~~~~~~~~~~~~r~~~~~~f----------------------~~----~~   96 (159)
                      .+|-..+++.+-.+++.|...      .+...++|+..+...|..+.+..                      .+    +.
T Consensus       759 GliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~  838 (1110)
T TIGR02562       759 GLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNH  838 (1110)
T ss_pred             EEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCC
Confidence            566677777777777776543      23477889999877776666543                      12    35


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCC
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGR  142 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~  142 (159)
                      ..|+|+|++.+.|+|+ +.+++|-  .|.+..+.+|++||+.|.|.
T Consensus       839 ~~i~v~Tqv~E~g~D~-dfd~~~~--~~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       839 LFIVLATPVEEVGRDH-DYDWAIA--DPSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             CeEEEEeeeEEEEecc-cCCeeee--ccCcHHHHHHHhhccccccc
Confidence            6799999999999998 4555554  35679999999999999873

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.

>KOG1016|consensus

Probab=97.79  E-value=9.7e-05  Score=60.56  Aligned_cols=106  Identities=15%  Similarity=0.209  Sum_probs=87.7

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCc------------------eEEEecCCCHHHHHHHHHHHhcC-Ce--eEEEEe
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGIN------------------VDVIHSDRTQKQRDNVVRSFRTG-RI--WILITT  103 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~------------------~~~~~~~~~~~~r~~~~~~f~~~-~~--~vlv~t  103 (159)
                      .+.++|||.......+.|.+.|.++.++                  -.-+.|..+..+|++.+.+|+.. .+  -++++|
T Consensus       718 ~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllst  797 (1387)
T KOG1016|consen  718 IGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLST  797 (1387)
T ss_pred             cCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehh
Confidence            3468999999999999988888765221                  23567778889999999999872 22  477789


Q ss_pred             CCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       104 ~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      .....|+|+-..+-++.++..|++-.-.|.+.|+.|.|+..+|++|-
T Consensus       798 rag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYR  844 (1387)
T KOG1016|consen  798 RAGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYR  844 (1387)
T ss_pred             ccccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEe
Confidence            99999999999998999999999988899999999999999998874

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=97.45  E-value=0.003  Score=52.42  Aligned_cols=103  Identities=17%  Similarity=0.177  Sum_probs=73.9

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCC--CcEEEEec
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRT--VRLVVNYD  122 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~--~~~vi~~~  122 (159)
                      .++++-||+.|.+.++.+.+.......++..++|.-+..   ++ +.  =++.+|+|-|+++..|+++..  .+-++-|=
T Consensus       281 ~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~---dv-~~--W~~~~VviYT~~itvG~Sf~~~HF~~~f~yv  354 (824)
T PF02399_consen  281 AGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLE---DV-ES--WKKYDVVIYTPVITVGLSFEEKHFDSMFAYV  354 (824)
T ss_pred             CCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCcc---cc-cc--ccceeEEEEeceEEEEeccchhhceEEEEEe
Confidence            455677899999999999998877777888888865443   22 11  257889999999999999864  34444331


Q ss_pred             CC----CCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          123 FP----SSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       123 ~~----~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      -|    .+..+..|++||+-.. ..+..+++++...
T Consensus       355 k~~~~gpd~~s~~Q~lgRvR~l-~~~ei~v~~d~~~  389 (824)
T PF02399_consen  355 KPMSYGPDMVSVYQMLGRVRSL-LDNEIYVYIDASG  389 (824)
T ss_pred             cCCCCCCcHHHHHHHHHHHHhh-ccCeEEEEEeccc
Confidence            12    3566789999999544 5677888877653

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

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.44  E-value=0.00091  Score=55.98  Aligned_cols=39  Identities=10%  Similarity=0.069  Sum_probs=29.6

Q ss_pred             CCChHHHHHHHHhc-----------CCCCCEEEEecchHHHHHHHHHHHh
Q psy576           30 AGSPVQAQDETILL-----------GIEPPVLVFVQSKERAQELYNELIY   68 (159)
Q Consensus        30 ~~~k~~~l~~~~~~-----------~~~~~~lif~~~~~~~~~l~~~l~~   68 (159)
                      +.=|...|.+++..           ...+++||||....+|..+.++|..
T Consensus       268 e~PKw~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       268 ENPKWEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             cCCCHHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHh
Confidence            35677777777642           2346799999999999999998855

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

>PRK05580 primosome assembly protein PriA; Validated

Probab=97.38  E-value=0.0038  Score=51.63  Aligned_cols=92  Identities=16%  Similarity=0.191  Sum_probs=70.5

Q ss_pred             CCCCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhC-CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC
Q psy576           28 EGAGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYD-GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE  104 (159)
Q Consensus        28 ~~~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~  104 (159)
                      ....+|.+.....+..  ..+.++||.+++.+.+..+.+.+++. +..+..+||+++..++.+.+.....|+.+|+|+|.
T Consensus       170 ~TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTr  249 (679)
T PRK05580        170 VTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGAR  249 (679)
T ss_pred             CCCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEecc
Confidence            3346787776554431  23568999999999999999998764 67899999999999999999999999999999997


Q ss_pred             CcccccccCCCcEEEE
Q psy576          105 LLGRGIDFRTVRLVVN  120 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~  120 (159)
                      .... ..+.++..||.
T Consensus       250 sal~-~p~~~l~liVv  264 (679)
T PRK05580        250 SALF-LPFKNLGLIIV  264 (679)
T ss_pred             HHhc-ccccCCCEEEE
Confidence            4332 34456666654

>TIGR00595 priA primosomal protein N'

Probab=97.33  E-value=0.0028  Score=50.62  Aligned_cols=89  Identities=20%  Similarity=0.323  Sum_probs=69.4

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhC-CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYD-GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~  107 (159)
                      .+|.+....++..  ..++++++.+++..-+..+++.|++. +..+..+||+++..+|.+.+....+|+..|+|+|..+.
T Consensus         8 sGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsal   87 (505)
T TIGR00595         8 SGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSAL   87 (505)
T ss_pred             CCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHH
Confidence            5777776555532  24567999999999999999999765 66789999999999999999999999999999997543


Q ss_pred             cccccCCCcEEEE
Q psy576          108 RGIDFRTVRLVVN  120 (159)
Q Consensus       108 ~g~~i~~~~~vi~  120 (159)
                      . ..++++..||.
T Consensus        88 f-~p~~~l~lIIV   99 (505)
T TIGR00595        88 F-LPFKNLGLIIV   99 (505)
T ss_pred             c-CcccCCCEEEE
Confidence            2 34456666664

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).

>PRK14873 primosome assembly protein PriA; Provisional

Probab=97.26  E-value=0.0024  Score=52.49  Aligned_cols=76  Identities=14%  Similarity=0.067  Sum_probs=66.0

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhC-C-CceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYD-G-INVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELL  106 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~-~-~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~  106 (159)
                      .+|.+...+++..  ..++++||.++.......+.+.|++. + ..+..+|+++++.+|.+.+....+|+.+|+|.|..+
T Consensus       171 SGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSA  250 (665)
T PRK14873        171 EDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSA  250 (665)
T ss_pred             CcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEccee
Confidence            5888888888863  24668999999999999999999765 3 678999999999999999999999999999999654

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=97.23  E-value=0.0059  Score=50.55  Aligned_cols=99  Identities=15%  Similarity=0.250  Sum_probs=73.3

Q ss_pred             eeeeecCCCCChHHHHH-HHHh-cCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcC
Q psy576           22 RMYRETEGAGSPVQAQD-ETIL-LGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~-~~~~-~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~   95 (159)
                      ......+...+|..... .++. ...+.++++.++|..-+...++.+++    .++++..+||+++..++.+.++.+.+|
T Consensus       284 ~~Ll~~~TGSGKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g  363 (681)
T PRK10917        284 NRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASG  363 (681)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCC
Confidence            34444455567766532 2222 22456899999999999888777654    368899999999999999999999999


Q ss_pred             CeeEEEEeCC-cccccccCCCcEEEE
Q psy576           96 RIWILITTEL-LGRGIDFRTVRLVVN  120 (159)
Q Consensus        96 ~~~vlv~t~~-~~~g~~i~~~~~vi~  120 (159)
                      +..|+|+|.. +...+.++.+.+||.
T Consensus       364 ~~~IvVgT~~ll~~~v~~~~l~lvVI  389 (681)
T PRK10917        364 EADIVIGTHALIQDDVEFHNLGLVII  389 (681)
T ss_pred             CCCEEEchHHHhcccchhcccceEEE
Confidence            9999999964 444566777777664

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=97.14  E-value=0.0016  Score=53.72  Aligned_cols=77  Identities=25%  Similarity=0.261  Sum_probs=67.2

Q ss_pred             CCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhC-CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCc
Q psy576           30 AGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYD-GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELL  106 (159)
Q Consensus        30 ~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~  106 (159)
                      ..+|.++..+++..  ..++++|+.++.......+.+.++.. +.++..+|+++++.+|.+.+.+..+|+.+|+|.|..+
T Consensus       227 GSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSA  306 (730)
T COG1198         227 GSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSA  306 (730)
T ss_pred             CCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEechh
Confidence            37999998888873  35678999999999888888888765 7889999999999999999999999999999999654

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=96.88  E-value=0.016  Score=47.56  Aligned_cols=97  Identities=18%  Similarity=0.314  Sum_probs=71.4

Q ss_pred             eeecCCCCChHHHHH-HHHh-cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           24 YRETEGAGSPVQAQD-ETIL-LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        24 ~~~~~~~~~k~~~l~-~~~~-~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ....+...+|..... .++. ...+.++++.++|..-+..+++.+++.    ++++..+||+++..++...++...+|+.
T Consensus       260 Ll~g~TGSGKT~va~l~il~~~~~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~  339 (630)
T TIGR00643       260 LLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQI  339 (630)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHcCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCC
Confidence            444444567766532 2222 224568999999999999887766543    6889999999999999999999999999


Q ss_pred             eEEEEeCCc-ccccccCCCcEEEE
Q psy576           98 WILITTELL-GRGIDFRTVRLVVN  120 (159)
Q Consensus        98 ~vlv~t~~~-~~g~~i~~~~~vi~  120 (159)
                      .|+|+|... ...+.+.++.+||.
T Consensus       340 ~IiVgT~~ll~~~~~~~~l~lvVI  363 (630)
T TIGR00643       340 HLVVGTHALIQEKVEFKRLALVII  363 (630)
T ss_pred             CEEEecHHHHhccccccccceEEE
Confidence            999999653 33456667776664

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=96.86  E-value=0.007  Score=51.36  Aligned_cols=73  Identities=23%  Similarity=0.284  Sum_probs=58.3

Q ss_pred             hHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC----C-CceEE-EecCCCHHHHHHHHHHHhcCCeeEEEEeCC
Q psy576           33 PVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYD----G-INVDV-IHSDRTQKQRDNVVRSFRTGRIWILITTEL  105 (159)
Q Consensus        33 k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~----~-~~~~~-~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~  105 (159)
                      .+..+..+....+++++++.++|..-+...++.|.+.    + ..+.. +|+.++.+++++.+++|.+|+.+|||+|..
T Consensus       112 Tfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         112 TFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             HHHHHHHHHHHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            3444455555556788999999999999888888654    2 44444 899999999999999999999999999864

>KOG1001|consensus

Probab=96.81  E-value=0.00018  Score=58.92  Aligned_cols=102  Identities=17%  Similarity=0.153  Sum_probs=88.6

Q ss_pred             CCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC-ee-EEEEeCCcccccccCCCcEEEEecCC
Q psy576           47 PPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR-IW-ILITTELLGRGIDFRTVRLVVNYDFP  124 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~-~~-vlv~t~~~~~g~~i~~~~~vi~~~~~  124 (159)
                      .+++||+.-..-++-+...+...++....+.|.|+...|.+.+..|..+. .. .+++..+.+-|+|+-.+++|+..++=
T Consensus       540 ~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~  619 (674)
T KOG1001|consen  540 PKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPW  619 (674)
T ss_pred             CceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchh
Confidence            48999999888888888877777888889999999999999999998643 33 44567899999999999999999999


Q ss_pred             CCHHHHHHHHhhccCCCCcceEEE
Q psy576          125 SSAISYIHRIGRAGRGGREGKAVT  148 (159)
Q Consensus       125 ~~~~~~~q~~GR~~R~g~~g~~~~  148 (159)
                      |++....|.+-|+.|.|+..++.+
T Consensus       620 wnp~~eeQaidR~hrigq~k~v~v  643 (674)
T KOG1001|consen  620 WNPAVEEQAIDRAHRIGQTKPVKV  643 (674)
T ss_pred             cChHHHHHHHHHHHHhcccceeee
Confidence            999999999999999998777665

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.80  E-value=0.019  Score=49.06  Aligned_cols=98  Identities=16%  Similarity=0.246  Sum_probs=72.5

Q ss_pred             eeeecCCCCChHHHHHH-HHh-cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           23 MYRETEGAGSPVQAQDE-TIL-LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        23 ~~~~~~~~~~k~~~l~~-~~~-~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      .....+...+|...... ++. ...+.+++|.++|..-|...++.+++.    ++++..++|..+..++.++++.+.+|+
T Consensus       475 ~Ll~adTGsGKT~val~a~l~al~~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~  554 (926)
T TIGR00580       475 RLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGK  554 (926)
T ss_pred             EEEECCCCccHHHHHHHHHHHHHHhCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCC
Confidence            34444555677765332 222 124578999999999999998877653    567888999999999999999999999


Q ss_pred             eeEEEEeCC-cccccccCCCcEEEE
Q psy576           97 IWILITTEL-LGRGIDFRTVRLVVN  120 (159)
Q Consensus        97 ~~vlv~t~~-~~~g~~i~~~~~vi~  120 (159)
                      .+|+|+|.. +...+.+.++.++|.
T Consensus       555 ~dIVIGTp~ll~~~v~f~~L~llVI  579 (926)
T TIGR00580       555 IDILIGTHKLLQKDVKFKDLGLLII  579 (926)
T ss_pred             ceEEEchHHHhhCCCCcccCCEEEe
Confidence            999999963 444566777776664

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.

>KOG0951|consensus

Probab=96.70  E-value=0.011  Score=51.23  Aligned_cols=111  Identities=20%  Similarity=0.330  Sum_probs=79.3

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHH----------------h------CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEE
Q psy576           44 GIEPPVLVFVQSKERAQELYNELI----------------Y------DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILI  101 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~----------------~------~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  101 (159)
                      ..+++.+||+++++++..++--+-                .      ...+.++-|.+++..+..-+-..|..|.+.|+|
T Consensus      1357 ~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v 1436 (1674)
T KOG0951|consen 1357 GNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCV 1436 (1674)
T ss_pred             cCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEE
Confidence            467889999999998886533221                0      123344448899998888888889999999999


Q ss_pred             EeCCcccccccCCCcEEEE----ec------CCCCHHHHHHHHhhccCCCCcceEEEEecCCCcccc
Q psy576          102 TTELLGRGIDFRTVRLVVN----YD------FPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL  158 (159)
Q Consensus       102 ~t~~~~~g~~i~~~~~vi~----~~------~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~  158 (159)
                      .+.- ..|+....--+|+.    ||      .+.+.++.+||+|++.|.   |.|+++.+..+...|
T Consensus      1437 ~s~~-~~~~~~~~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~~---~k~vi~~~~~~k~yy 1499 (1674)
T KOG0951|consen 1437 MSRD-CYGTKLKAHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASGA---GKCVIMCHTPKKEYY 1499 (1674)
T ss_pred             EEcc-cccccccceEEEEecceeecccccccccCchhHHHHHhhhhcCC---ccEEEEecCchHHHH
Confidence            7755 66666543333331    22      345799999999999984   789999888776544

>KOG2340|consensus

Probab=96.70  E-value=0.012  Score=46.77  Aligned_cols=109  Identities=21%  Similarity=0.236  Sum_probs=85.1

Q ss_pred             CCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC--cccccccCCCcEEEEecC
Q psy576           46 EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL--LGRGIDFRTVRLVVNYDF  123 (159)
Q Consensus        46 ~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~--~~~g~~i~~~~~vi~~~~  123 (159)
                      ...+||+.++--.--++..++++..+....+++..+...-....+.|..|...+|+-|.=  .-+-.+|..+..||.|.+
T Consensus       552 ~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfYqp  631 (698)
T KOG2340|consen  552 ESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFYQP  631 (698)
T ss_pred             cCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEecC
Confidence            345899999999999999999998888888888878888888899999999999999964  456778899999999999


Q ss_pred             CCCHHHHHHH---HhhccCCC----CcceEEEEecCCC
Q psy576          124 PSSAISYIHR---IGRAGRGG----REGKAVTFFTKQD  154 (159)
Q Consensus       124 ~~~~~~~~q~---~GR~~R~g----~~g~~~~~~~~~~  154 (159)
                      |..+.=|.-.   .+|..-.|    ..-.|.+++.+-|
T Consensus       632 P~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD  669 (698)
T KOG2340|consen  632 PNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYD  669 (698)
T ss_pred             CCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechh
Confidence            9887666554   44443333    2245666666544

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.57  E-value=0.014  Score=48.21  Aligned_cols=61  Identities=10%  Similarity=0.086  Sum_probs=43.7

Q ss_pred             HHHHHHhcCCeeEEEEeC----CcccccccCCCcEEEEecC------CC------CHHHHHHHHhhccCCCCcceEEEEe
Q psy576           87 NVVRSFRTGRIWILITTE----LLGRGIDFRTVRLVVNYDF------PS------SAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus        87 ~~~~~f~~~~~~vlv~t~----~~~~g~~i~~~~~vi~~~~------~~------~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      .+++.|. ++.+|||+|+    ++.     ++++.|..+|.      |+      ....+.|-.||+||.+..|.+++..
T Consensus       463 ~~l~~~~-~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfRA~Er~~qll~qvagragr~~~~G~V~iq~  536 (665)
T PRK14873        463 QVVDTVD-AGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVVA  536 (665)
T ss_pred             HHHHhhc-cCCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcChHHHHHHHHHHHHHhhcCCCCCCEEEEEe
Confidence            4788886 5999999999    555     35566655442      21      2455678899999998889999885


Q ss_pred             cCCC
Q psy576          151 TKQD  154 (159)
Q Consensus       151 ~~~~  154 (159)
                       ..+
T Consensus       537 -~p~  539 (665)
T PRK14873        537 -ESS  539 (665)
T ss_pred             -CCC
Confidence             444

>KOG0921|consensus

Probab=96.37  E-value=0.0044  Score=51.97  Aligned_cols=106  Identities=25%  Similarity=0.344  Sum_probs=84.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC-------CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD-------GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRL  117 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~  117 (159)
                      -.+-+++|.+.......+..++...       ...+...|+.....+..++.+....|..+++++|..++..+.+.++..
T Consensus       642 i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~  721 (1282)
T KOG0921|consen  642 IDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVY  721 (1282)
T ss_pred             CccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeE
Confidence            3456999999999999988887543       346889999999999999999999999999999999999998888666


Q ss_pred             EEEecCC------------------CCHHHHHHHHhhccCCCCcceEEEEec
Q psy576          118 VVNYDFP------------------SSAISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       118 vi~~~~~------------------~~~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      |+..+.-                  .+..+..|+.||+||. ++|.|..+.+
T Consensus       722 vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~lcs  772 (1282)
T KOG0921|consen  722 VIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFHLCS  772 (1282)
T ss_pred             EEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccccccH
Confidence            6532211                  1455678999999997 6777777654

>PRK10689 transcription-repair coupling factor; Provisional

Probab=96.33  E-value=0.036  Score=48.52  Aligned_cols=98  Identities=16%  Similarity=0.230  Sum_probs=70.6

Q ss_pred             eeeecCCCCChHHHHHHH--HhcCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           23 MYRETEGAGSPVQAQDET--ILLGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        23 ~~~~~~~~~~k~~~l~~~--~~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      .....+...+|.......  .....+.+++|.++|..-+..+++.+.+.    ++++..++|..+..++..+++.+.+|.
T Consensus       624 ~Ll~a~TGsGKT~val~aa~~~~~~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~  703 (1147)
T PRK10689        624 RLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGK  703 (1147)
T ss_pred             EEEEcCCCcCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCC
Confidence            344444457777642211  11224678999999999999998888653    457788999999999999999999999


Q ss_pred             eeEEEEeCC-cccccccCCCcEEEE
Q psy576           97 IWILITTEL-LGRGIDFRTVRLVVN  120 (159)
Q Consensus        97 ~~vlv~t~~-~~~g~~i~~~~~vi~  120 (159)
                      .+|+|+|.. +...+.+.++.++|.
T Consensus       704 ~dIVVgTp~lL~~~v~~~~L~lLVI  728 (1147)
T PRK10689        704 IDILIGTHKLLQSDVKWKDLGLLIV  728 (1147)
T ss_pred             CCEEEECHHHHhCCCCHhhCCEEEE
Confidence            999999964 333455566666653

>PRK14701 reverse gyrase; Provisional

Probab=96.27  E-value=0.057  Score=48.90  Aligned_cols=82  Identities=11%  Similarity=0.083  Sum_probs=61.5

Q ss_pred             eeecCCCCChHHHHH--HHHhcCCCCCEEEEecchHHHHHHHHHHHhC------CCceEEEecCCCHHHHHHHHHHHhcC
Q psy576           24 YRETEGAGSPVQAQD--ETILLGIEPPVLVFVQSKERAQELYNELIYD------GINVDVIHSDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        24 ~~~~~~~~~k~~~l~--~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~------~~~~~~~~~~~~~~~r~~~~~~f~~~   95 (159)
                      ........+|.....  .+.....+.+++|.++|++-+..+.+.++..      +..+..+||+++..++.+.++.+.+|
T Consensus        98 li~APTGsGKTl~~~~~al~~~~~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g  177 (1638)
T PRK14701         98 SIVAPTGMGKSTFGAFIALFLALKGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENG  177 (1638)
T ss_pred             EEEEcCCCCHHHHHHHHHHHHHhcCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcC
Confidence            344444467776322  2222224557999999999999988888652      45678899999999999999999999


Q ss_pred             CeeEEEEeCC
Q psy576           96 RIWILITTEL  105 (159)
Q Consensus        96 ~~~vlv~t~~  105 (159)
                      +.+|||+|+-
T Consensus       178 ~~dILV~TPg  187 (1638)
T PRK14701        178 DFDILVTTAQ  187 (1638)
T ss_pred             CCCEEEECCc
Confidence            9999999974

>KOG0298|consensus

Probab=96.00  E-value=0.014  Score=50.51  Aligned_cols=100  Identities=16%  Similarity=0.139  Sum_probs=73.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee-EEEEeCCcccccccCCCcEEEEecC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW-ILITTELLGRGIDFRTVRLVVNYDF  123 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~-vlv~t~~~~~g~~i~~~~~vi~~~~  123 (159)
                      ...++|+|+.-....+.+...+...++....--+   -++..+.+..|+.  ++ .++-+...+.|+|+-.+.+|+..++
T Consensus      1220 ~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~---t~d~~dc~~~fk~--I~clll~~~~~~~GLNL~eA~Hvfl~eP 1294 (1394)
T KOG0298|consen 1220 EQEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGE---TEDFDDCIICFKS--IDCLLLFVSKGSKGLNLIEATHVFLVEP 1294 (1394)
T ss_pred             cCceEEEEEehHHHHHHHHHHHHhhhhHhhhccC---Ccchhhhhhhccc--ceEEEEEeccCcccccHHhhhhhheecc
Confidence            4457888888777777777777666544322222   2234445666665  43 5557788899999999999999999


Q ss_pred             CCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          124 PSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       124 ~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      --++..-.|.+||+.|.|+.-+..+.
T Consensus      1295 iLN~~~E~QAigRvhRiGQ~~pT~V~ 1320 (1394)
T KOG0298|consen 1295 ILNPGDEAQAIGRVHRIGQKRPTFVH 1320 (1394)
T ss_pred             ccCchHHHhhhhhhhhcccccchhhh
Confidence            99999999999999999977665543

>KOG1133|consensus

Probab=95.90  E-value=0.37  Score=39.86  Aligned_cols=105  Identities=24%  Similarity=0.319  Sum_probs=68.9

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-------ceEEEecCCCHHHHHHHHHHHhc----CCeeEEEEe--CCcccccc
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-------NVDVIHSDRTQKQRDNVVRSFRT----GRIWILITT--ELLGRGID  111 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-------~~~~~~~~~~~~~r~~~~~~f~~----~~~~vlv~t--~~~~~g~~  111 (159)
                      -++-+++|++|.+-...+.+.+.+.|+       +..+.-..-+   -+.+++.|..    |.-.+|.+.  ..+++|+|
T Consensus       628 VPgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~---~~dvl~~Ya~a~~~g~GaiLlaVVGGKlSEGIN  704 (821)
T KOG1133|consen  628 VPGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDT---VEDVLEGYAEAAERGRGAILLAVVGGKLSEGIN  704 (821)
T ss_pred             CCCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCccc---HHHHHHHHHHHhhcCCCeEEEEEeccccccccc
Confidence            347799999999999999998876543       2233332222   3455666543    444566554  78999999


Q ss_pred             cCC--CcEEEEecCCCC--------------------------------HHHHHHHHhhccCCCCcceEEEEecC
Q psy576          112 FRT--VRLVVNYDFPSS--------------------------------AISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       112 i~~--~~~vi~~~~~~~--------------------------------~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      +.+  ++.|+..+.|.+                                ...--|.+||+-|..+.=.++++.+.
T Consensus       705 F~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkAVNQsIGRAIRH~~DYA~i~LlD~  779 (821)
T KOG1133|consen  705 FSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKAVNQSIGRAIRHRKDYASIYLLDK  779 (821)
T ss_pred             cccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHhhhccceeEEEehh
Confidence            975  677888777753                                01135888999998655555665553

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

Probab=95.72  E-value=0.13  Score=42.22  Aligned_cols=77  Identities=21%  Similarity=0.280  Sum_probs=61.8

Q ss_pred             CCCCCEEEEecchHHHH----HHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCc-ccccccCCCcEE
Q psy576           44 GIEPPVLVFVQSKERAQ----ELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELL-GRGIDFRTVRLV  118 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~----~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~-~~g~~i~~~~~v  118 (159)
                      ..+.++....+|.=-|+    .+.++|...++.+..++|.+...+|.++++...+|+.+++|.|.++ -..+++.++-.|
T Consensus       309 ~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLV  388 (677)
T COG1200         309 EAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLV  388 (677)
T ss_pred             HcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeEE
Confidence            35678999999875444    5556666668999999999999999999999999999999999765 446777666655


Q ss_pred             EE
Q psy576          119 VN  120 (159)
Q Consensus       119 i~  120 (159)
                      |.
T Consensus       389 Ii  390 (677)
T COG1200         389 II  390 (677)
T ss_pred             EE
Confidence            54

>KOG0701|consensus

Probab=95.72  E-value=0.011  Score=52.60  Aligned_cols=93  Identities=26%  Similarity=0.365  Sum_probs=76.4

Q ss_pred             CEEEEecchHHHHHHHHHHHhC-CCceEEEecCCC-----------HHHHHHHHHHHhcCCeeEEEEeCCcccccccCCC
Q psy576           48 PVLVFVQSKERAQELYNELIYD-GINVDVIHSDRT-----------QKQRDNVVRSFRTGRIWILITTELLGRGIDFRTV  115 (159)
Q Consensus        48 ~~lif~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~-----------~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~  115 (159)
                      ..++|++....+....+.++.. ...+..+.|.+.           ...+.+++..|...++.+|+.|.++.+|+|++.+
T Consensus       294 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~  373 (1606)
T KOG0701|consen  294 SGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKC  373 (1606)
T ss_pred             hheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhh
Confidence            4678999999998888887665 334555666542           2235667888888999999999999999999999


Q ss_pred             cEEEEecCCCCHHHHHHHHhhccCC
Q psy576          116 RLVVNYDFPSSAISYIHRIGRAGRG  140 (159)
Q Consensus       116 ~~vi~~~~~~~~~~~~q~~GR~~R~  140 (159)
                      +.++.++.|....+|.|..||+-+.
T Consensus       374 ~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  374 NLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhheeccCcchHHHHHHhhcccccc
Confidence            9999999999999999999999654

>TIGR01054 rgy reverse gyrase

Probab=95.26  E-value=0.2  Score=44.19  Aligned_cols=82  Identities=13%  Similarity=0.118  Sum_probs=59.2

Q ss_pred             eeecCCCCChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhC----CCc---eEEEecCCCHHHHHHHHHHHhc
Q psy576           24 YRETEGAGSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYD----GIN---VDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        24 ~~~~~~~~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~---~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      ........+|.....-+..  ...+.+++|.++|++-+..+++.+...    ++.   +..+||+++..++.+.++.+.+
T Consensus        97 vi~ApTGsGKT~f~l~~~~~l~~~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~  176 (1171)
T TIGR01054        97 AIIAPTGVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIEN  176 (1171)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhcCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhc
Confidence            3334444677764332221  224567999999999999988877653    333   3358999999999999999999


Q ss_pred             CCeeEEEEeCC
Q psy576           95 GRIWILITTEL  105 (159)
Q Consensus        95 ~~~~vlv~t~~  105 (159)
                      +..+|+|+|+.
T Consensus       177 ~~~dIlV~Tp~  187 (1171)
T TIGR01054       177 GDFDILITTTM  187 (1171)
T ss_pred             CCCCEEEECHH
Confidence            99999999974

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.

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

Probab=95.18  E-value=0.15  Score=44.25  Aligned_cols=89  Identities=19%  Similarity=0.343  Sum_probs=68.8

Q ss_pred             CChHHHH-HHHHh-cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEe-
Q psy576           31 GSPVQAQ-DETIL-LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT-  103 (159)
Q Consensus        31 ~~k~~~l-~~~~~-~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t-  103 (159)
                      -+|.++- +.... -+.++++.|.++|+=-|+.-++.++++    ++++..+..=.+.++...+++..++|+.+|+|.| 
T Consensus       626 FGKTEVAmRAAFkAV~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTH  705 (1139)
T COG1197         626 FGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTH  705 (1139)
T ss_pred             CcHHHHHHHHHHHHhcCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEech
Confidence            3566653 33333 245678999999998888888888765    5567777777789999999999999999999999 


Q ss_pred             CCcccccccCCCcEEE
Q psy576          104 ELLGRGIDFRTVRLVV  119 (159)
Q Consensus       104 ~~~~~g~~i~~~~~vi  119 (159)
                      ..+..++.+.++-.+|
T Consensus       706 rLL~kdv~FkdLGLlI  721 (1139)
T COG1197         706 RLLSKDVKFKDLGLLI  721 (1139)
T ss_pred             HhhCCCcEEecCCeEE
Confidence            5677778888777665

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=94.91  E-value=0.52  Score=37.46  Aligned_cols=82  Identities=18%  Similarity=0.231  Sum_probs=64.8

Q ss_pred             eeeeecCCCCChHHH-HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEE
Q psy576           22 RMYRETEGAGSPVQA-QDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL  100 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vl  100 (159)
                      ..+...+...+|-.. +...+.  ..+.+||.+++++-+......|...++++..++++.+..++..++..+..++.+++
T Consensus        28 dvlv~apTGsGKTl~y~lp~l~--~~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il  105 (470)
T TIGR00614        28 DCFVVMPTGGGKSLCYQLPALC--SDGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLL  105 (470)
T ss_pred             CEEEEcCCCCcHhHHHHHHHHH--cCCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEE
Confidence            455556666677653 233332  35679999999999988888888889999999999999999999999999999999


Q ss_pred             EEeCC
Q psy576          101 ITTEL  105 (159)
Q Consensus       101 v~t~~  105 (159)
                      ++|+-
T Consensus       106 ~~TPe  110 (470)
T TIGR00614       106 YVTPE  110 (470)
T ss_pred             EECHH
Confidence            99863

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

>KOG0339|consensus

Probab=94.85  E-value=0.25  Score=39.52  Aligned_cols=70  Identities=16%  Similarity=0.264  Sum_probs=52.8

Q ss_pred             CC-EEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC------CcccccccCCC
Q psy576           47 PP-VLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE------LLGRGIDFRTV  115 (159)
Q Consensus        47 ~~-~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~------~~~~g~~i~~~  115 (159)
                      +| .+|.|+|++-+..++...++.    ++++..+||+.+.-++.+-++    -...++|||+      +--.++|+..+
T Consensus       296 gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTPgRlid~VkmKatn~~rv  371 (731)
T KOG0339|consen  296 GPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK----EGAEIVVATPGRLIDMVKMKATNLSRV  371 (731)
T ss_pred             CCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh----cCCeEEEechHHHHHHHHhhcccceee
Confidence            45 667899999999988776554    788999999999877766555    4566899997      23457788777


Q ss_pred             cEEEE
Q psy576          116 RLVVN  120 (159)
Q Consensus       116 ~~vi~  120 (159)
                      ++++.
T Consensus       372 S~LV~  376 (731)
T KOG0339|consen  372 SYLVL  376 (731)
T ss_pred             eEEEE
Confidence            77664

>cd00268 DEADc DEAD-box helicases

Probab=94.70  E-value=0.67  Score=32.06  Aligned_cols=96  Identities=15%  Similarity=0.133  Sum_probs=59.8

Q ss_pred             ceeeeecCCCCChHHH-HHHH---HhcC---CCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHH
Q psy576           21 ARMYRETEGAGSPVQA-QDET---ILLG---IEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVV   89 (159)
Q Consensus        21 ~~~~~~~~~~~~k~~~-l~~~---~~~~---~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~   89 (159)
                      +..+.......+|... +..+   +...   .+.+++|.+++...+......+...    +..+..++|+.+..+..+.+
T Consensus        37 ~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (203)
T cd00268          37 RDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKL  116 (203)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh
Confidence            3455555555677544 2222   2222   3457999999999888877666443    66788899988765544333


Q ss_pred             HHHhcCCeeEEEEeCC-----c-ccccccCCCcEEEE
Q psy576           90 RSFRTGRIWILITTEL-----L-GRGIDFRTVRLVVN  120 (159)
Q Consensus        90 ~~f~~~~~~vlv~t~~-----~-~~g~~i~~~~~vi~  120 (159)
                      +    +...|+|+|.-     + ....++++++.+|.
T Consensus       117 ~----~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIv  149 (203)
T cd00268         117 K----RGPHIVVATPGRLLDLLERGKLDLSKVKYLVL  149 (203)
T ss_pred             c----CCCCEEEEChHHHHHHHHcCCCChhhCCEEEE
Confidence            2    56789999952     1 22245567776664

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=94.63  E-value=0.69  Score=37.88  Aligned_cols=82  Identities=11%  Similarity=0.177  Sum_probs=64.8

Q ss_pred             eeeeecCCCCChHHHH-HHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEE
Q psy576           22 RMYRETEGAGSPVQAQ-DETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL  100 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l-~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vl  100 (159)
                      ..+.......+|-... ...+.  ..+.++|.+++.+-+..-...|++.++++..+|+..+..++..++.....+..+++
T Consensus        30 dvlv~~PTG~GKTl~y~lpal~--~~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il  107 (591)
T TIGR01389        30 DVLVVMPTGGGKSLCYQVPALL--LKGLTVVISPLISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLL  107 (591)
T ss_pred             CEEEEcCCCccHhHHHHHHHHH--cCCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEE
Confidence            4556666666776652 22222  35678999999999888888888889999999999999999999999999999999


Q ss_pred             EEeCC
Q psy576          101 ITTEL  105 (159)
Q Consensus       101 v~t~~  105 (159)
                      +.|+-
T Consensus       108 ~~tpe  112 (591)
T TIGR01389       108 YVAPE  112 (591)
T ss_pred             EEChh
Confidence            88753

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.

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

Probab=94.13  E-value=0.38  Score=34.78  Aligned_cols=91  Identities=19%  Similarity=0.225  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHHhC---CCceEEEecCCCHHHHHHHHHHHhcCC----eeEEEEeCCcccccccCCCcEEEEecCCCCHHH
Q psy576           57 ERAQELYNELIYD---GINVDVIHSDRTQKQRDNVVRSFRTGR----IWILITTELLGRGIDFRTVRLVVNYDFPSSAIS  129 (159)
Q Consensus        57 ~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~----~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~  129 (159)
                      ...+++...|...   ++.+..+.++.+...     -.|.++.    ..|+|+-+.+++|+.++.+.+.+....+...+.
T Consensus        94 ~s~~ei~~~l~~~~~~~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DT  168 (239)
T PF10593_consen   94 PSWEEIKPELPKAISDGIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDT  168 (239)
T ss_pred             cCHHHHHHHHHHHHhcCceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHH
Confidence            3344554444322   588899997655433     3344433    789999999999999999999999888888888


Q ss_pred             HHHHHhhcc-CCCCcceEEEEecC
Q psy576          130 YIHRIGRAG-RGGREGKAVTFFTK  152 (159)
Q Consensus       130 ~~q~~GR~~-R~g~~g~~~~~~~~  152 (159)
                      +.||.-..| |.|-.+.|-+|.++
T Consensus       169 L~QmgRwFGYR~gY~dl~Ri~~~~  192 (239)
T PF10593_consen  169 LMQMGRWFGYRPGYEDLCRIYMPE  192 (239)
T ss_pred             HHHHhhcccCCcccccceEEecCH
Confidence            888775544 33335666666643

This domain is found associated with a helicase domain of superfamily type II [].

>KOG1513|consensus

Probab=94.04  E-value=0.072  Score=44.64  Aligned_cols=62  Identities=24%  Similarity=0.427  Sum_probs=48.8

Q ss_pred             HHHHhcCCeeEEEEeCCcccccccCCCc--------EEEEecCCCCHHHHHHHHhhccCCCC-cceEEEEe
Q psy576           89 VRSFRTGRIWILITTELLGRGIDFRTVR--------LVVNYDFPSSAISYIHRIGRAGRGGR-EGKAVTFF  150 (159)
Q Consensus        89 ~~~f~~~~~~vlv~t~~~~~g~~i~~~~--------~vi~~~~~~~~~~~~q~~GR~~R~g~-~g~~~~~~  150 (159)
                      -+.|..|+..|-|-+.++.-|+.++.-.        +=|.+..||+..--+|+.||+.|..+ +++-++|.
T Consensus       850 KqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFl  920 (1300)
T KOG1513|consen  850 KQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFL  920 (1300)
T ss_pred             HhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEE
Confidence            4568899999999999999999887543        34567899999999999999999864 24444443

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

Probab=93.93  E-value=0.48  Score=38.20  Aligned_cols=68  Identities=25%  Similarity=0.427  Sum_probs=51.4

Q ss_pred             EEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC-----Ccccc-cccCCCcE
Q psy576           49 VLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE-----LLGRG-IDFRTVRL  117 (159)
Q Consensus        49 ~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~-----~~~~g-~~i~~~~~  117 (159)
                      +||+++|++-|..+++.+...     ++.+..++|+.+...+.   +.++.| .+|+|+|+     .+.++ +++..+.+
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~---~~l~~~-~~ivVaTPGRllD~i~~~~l~l~~v~~  177 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQI---EALKRG-VDIVVATPGRLLDLIKRGKLDLSGVET  177 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHH---HHHhcC-CCEEEECccHHHHHHHcCCcchhhcCE
Confidence            999999999999998877542     46788999998877666   444446 89999997     34444 67777776


Q ss_pred             EEE
Q psy576          118 VVN  120 (159)
Q Consensus       118 vi~  120 (159)
                      +|.
T Consensus       178 lVl  180 (513)
T COG0513         178 LVL  180 (513)
T ss_pred             EEe
Confidence            663

>KOG0347|consensus

Probab=93.54  E-value=0.26  Score=39.79  Aligned_cols=52  Identities=21%  Similarity=0.256  Sum_probs=45.5

Q ss_pred             EEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC
Q psy576           49 VLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE  104 (159)
Q Consensus        49 ~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~  104 (159)
                      .||+.+|++-|..+.+.|.+.    ++.+..+.||++.+.+.+++.+    ...|+|||+
T Consensus       266 ~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATP  321 (731)
T KOG0347|consen  266 ALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATP  321 (731)
T ss_pred             eEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc----CCCEEEecc
Confidence            899999999999999988664    7889999999999887777766    677999997

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=92.29  E-value=4.7  Score=31.94  Aligned_cols=69  Identities=14%  Similarity=0.181  Sum_probs=48.1

Q ss_pred             CEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC------cccccccCCCcE
Q psy576           48 PVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL------LGRGIDFRTVRL  117 (159)
Q Consensus        48 ~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~------~~~g~~i~~~~~  117 (159)
                      ++||.+++++-+..+.+.+...    ++.+..++|+.+.......   + .+..+|+|+|+-      ....+++..+.+
T Consensus        77 ~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l-~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~  152 (456)
T PRK10590         77 RALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK---L-RGGVDVLVATPGRLLDLEHQNAVKLDQVEI  152 (456)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHH---H-cCCCcEEEEChHHHHHHHHcCCcccccceE
Confidence            5999999999998888877543    5677888998876554322   2 356789999962      223445666776


Q ss_pred             EEE
Q psy576          118 VVN  120 (159)
Q Consensus       118 vi~  120 (159)
                      +|.
T Consensus       153 lVi  155 (456)
T PRK10590        153 LVL  155 (456)
T ss_pred             EEe
Confidence            664

>KOG0338|consensus

Probab=92.15  E-value=0.95  Score=36.39  Aligned_cols=70  Identities=23%  Similarity=0.236  Sum_probs=51.4

Q ss_pred             CCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC-------cccccccCCC
Q psy576           47 PPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL-------LGRGIDFRTV  115 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~-------~~~g~~i~~~  115 (159)
                      -++||.|+|++-+..++...++.    .+.++..-||++-..++.++.    ...+|+|+|+=       =..++|+.++
T Consensus       253 TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LR----s~PDIVIATPGRlIDHlrNs~sf~ldsi  328 (691)
T KOG0338|consen  253 TRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLR----SRPDIVIATPGRLIDHLRNSPSFNLDSI  328 (691)
T ss_pred             eeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHh----hCCCEEEecchhHHHHhccCCCccccce
Confidence            47999999999888877765443    678889999999887665554    45889999972       2345666666


Q ss_pred             cEEEE
Q psy576          116 RLVVN  120 (159)
Q Consensus       116 ~~vi~  120 (159)
                      .++|.
T Consensus       329 EVLvl  333 (691)
T KOG0338|consen  329 EVLVL  333 (691)
T ss_pred             eEEEe
Confidence            66554

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=91.91  E-value=3.1  Score=34.30  Aligned_cols=81  Identities=19%  Similarity=0.261  Sum_probs=62.0

Q ss_pred             eeeeecCCCCChHHH-HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEE
Q psy576           22 RMYRETEGAGSPVQA-QDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL  100 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vl  100 (159)
                      ..+.......+|-.. +.-.+.  ..+.+||.+++.+-+......++..++.+..+++..+..+...+++....++.+++
T Consensus        42 dvlv~apTGsGKTl~y~lpal~--~~g~tlVisPl~sL~~dqv~~l~~~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il  119 (607)
T PRK11057         42 DCLVVMPTGGGKSLCYQIPALV--LDGLTLVVSPLISLMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTGQIKLL  119 (607)
T ss_pred             CEEEEcCCCchHHHHHHHHHHH--cCCCEEEEecHHHHHHHHHHHHHHcCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEE
Confidence            344555555666553 222222  34679999999999988888888889999999999999988888888889999998


Q ss_pred             EEeC
Q psy576          101 ITTE  104 (159)
Q Consensus       101 v~t~  104 (159)
                      ++|+
T Consensus       120 ~~tP  123 (607)
T PRK11057        120 YIAP  123 (607)
T ss_pred             EECh
Confidence            8874

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=91.72  E-value=1.2  Score=34.87  Aligned_cols=95  Identities=13%  Similarity=0.147  Sum_probs=59.4

Q ss_pred             eeeeecCCCCChHHH-HHHHH----hc----CCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETI----LL----GIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNV   88 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~----~~----~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~   88 (159)
                      ..+.......+|... +.-++    ..    ....++||.+++.+-+..+++.+..    .+.++..++|+.+.......
T Consensus        40 d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~  119 (434)
T PRK11192         40 DVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEV  119 (434)
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHH
Confidence            444455555677654 22222    11    1234699999999988887765543    36789999999887665443


Q ss_pred             HHHHhcCCeeEEEEeCC------cccccccCCCcEEEE
Q psy576           89 VRSFRTGRIWILITTEL------LGRGIDFRTVRLVVN  120 (159)
Q Consensus        89 ~~~f~~~~~~vlv~t~~------~~~g~~i~~~~~vi~  120 (159)
                      +    .+..+|+|+|+-      ....++...+.++|.
T Consensus       120 l----~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lVi  153 (434)
T PRK11192        120 F----SENQDIVVATPGRLLQYIKEENFDCRAVETLIL  153 (434)
T ss_pred             h----cCCCCEEEEChHHHHHHHHcCCcCcccCCEEEE
Confidence            3    345679999962      123455666776664

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

Probab=91.53  E-value=3.7  Score=36.45  Aligned_cols=82  Identities=11%  Similarity=0.106  Sum_probs=60.4

Q ss_pred             eeeeecCCCCChHHH-HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc--CCee
Q psy576           22 RMYRETEGAGSPVQA-QDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT--GRIW   98 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~--~~~~   98 (159)
                      ..+..+....+|-.. +.-.+.  ..+.+||.+++++-+..-...|...++++..+.++++..++.+++..+..  ++++
T Consensus       477 DVLVimPTGSGKSLcYQLPAL~--~~GiTLVISPLiSLmqDQV~~L~~~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~  554 (1195)
T PLN03137        477 DVFVLMPTGGGKSLTYQLPALI--CPGITLVISPLVSLIQDQIMNLLQANIPAASLSAGMEWAEQLEILQELSSEYSKYK  554 (1195)
T ss_pred             CEEEEcCCCccHHHHHHHHHHH--cCCcEEEEeCHHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHHHHHhcCCCCC
Confidence            344445555555554 222222  34679999999998875555566778999999999999999999998876  8899


Q ss_pred             EEEEeCC
Q psy576           99 ILITTEL  105 (159)
Q Consensus        99 vlv~t~~  105 (159)
                      ||++|+-
T Consensus       555 ILyvTPE  561 (1195)
T PLN03137        555 LLYVTPE  561 (1195)
T ss_pred             EEEEChH
Confidence            9999963

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=91.47  E-value=1.6  Score=36.14  Aligned_cols=95  Identities=16%  Similarity=0.120  Sum_probs=58.3

Q ss_pred             eeeeecCCCCChHHHH-HHHH---h-cCCCCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQ-DETI---L-LGIEPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l-~~~~---~-~~~~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..+.....-.+|.... .-++   . .....++||.|++++-+..+++.+...     ++.+..+||+.+.......+  
T Consensus        45 dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l--  122 (629)
T PRK11634         45 DVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL--  122 (629)
T ss_pred             CEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHh--
Confidence            3444444556676542 2222   2 223457999999999998887766432     67888999998765443322  


Q ss_pred             HhcCCeeEEEEeCC-----ccc-ccccCCCcEEEE
Q psy576           92 FRTGRIWILITTEL-----LGR-GIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~-----~~~-g~~i~~~~~vi~  120 (159)
                        .....|+|+|+-     +.+ .+++..+..||.
T Consensus       123 --~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVl  155 (629)
T PRK11634        123 --RQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVL  155 (629)
T ss_pred             --cCCCCEEEECHHHHHHHHHcCCcchhhceEEEe
Confidence              245779999952     222 345666666553

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=91.23  E-value=1.7  Score=34.41  Aligned_cols=95  Identities=14%  Similarity=0.134  Sum_probs=60.5

Q ss_pred             eeeeecCCCCChHHH-HHHHHh---cC-CCCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETIL---LG-IEPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~---~~-~~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..+...+...+|... +.-++.   .. ...+++|.++|++-+..+.+.++..     +..+..++|+.+...+...++ 
T Consensus        43 dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~-  121 (460)
T PRK11776         43 DVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE-  121 (460)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc-
Confidence            455555555677754 223332   11 2336899999999999888877542     567888999988765543332 


Q ss_pred             HhcCCeeEEEEeCC-----c-ccccccCCCcEEEE
Q psy576           92 FRTGRIWILITTEL-----L-GRGIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~-----~-~~g~~i~~~~~vi~  120 (159)
                         ...+|+|+|+-     + ...+++.++..+|.
T Consensus       122 ---~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lVi  153 (460)
T PRK11776        122 ---HGAHIIVGTPGRILDHLRKGTLDLDALNTLVL  153 (460)
T ss_pred             ---CCCCEEEEChHHHHHHHHcCCccHHHCCEEEE
Confidence               45779999952     2 13456667776664

>PRK09401 reverse gyrase; Reviewed

Probab=91.19  E-value=3  Score=37.21  Aligned_cols=81  Identities=14%  Similarity=0.125  Sum_probs=56.0

Q ss_pred             eeecCCCCChHHHHHHHH--hcCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEe--cCCCHHHHHHHHHHHhcC
Q psy576           24 YRETEGAGSPVQAQDETI--LLGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIH--SDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        24 ~~~~~~~~~k~~~l~~~~--~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~--~~~~~~~r~~~~~~f~~~   95 (159)
                      ........+|...+.-..  ....+.+++|.++|++-+..+++.++..    +..+..+.  +.++..++.+..+.+.++
T Consensus        99 ~i~ApTGsGKT~f~l~~~~~l~~~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~  178 (1176)
T PRK09401         99 AIIAPTGVGKTTFGLVMSLYLAKKGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEG  178 (1176)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcC
Confidence            344444567775533222  1224578999999999999998888654    34444444  445567788888889999


Q ss_pred             CeeEEEEeC
Q psy576           96 RIWILITTE  104 (159)
Q Consensus        96 ~~~vlv~t~  104 (159)
                      ..+|+|+|+
T Consensus       179 ~~~IlV~Tp  187 (1176)
T PRK09401        179 DFDILVTTS  187 (1176)
T ss_pred             CCCEEEECH
Confidence            999999995

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=91.01  E-value=0.6  Score=27.92  Aligned_cols=37  Identities=14%  Similarity=0.180  Sum_probs=30.7

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRT   81 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~   81 (159)
                      ...++++||.+-..+...+..|+..|+++..+.|++.
T Consensus        50 ~~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~   86 (90)
T cd01524          50 KDKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYK   86 (90)
T ss_pred             CCCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHH
Confidence            4568999999877888888889888888888999863

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.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=90.68  E-value=1.2  Score=36.48  Aligned_cols=70  Identities=11%  Similarity=0.254  Sum_probs=48.7

Q ss_pred             CCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC-----ccc--ccccCCC
Q psy576           47 PPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL-----LGR--GIDFRTV  115 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~-----~~~--g~~i~~~  115 (159)
                      .++||.+++++-+..+++.+...    ++.+..++|+.+.....+.+    .+..+|+|+|+-     +..  .+++..+
T Consensus        85 ~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l----~~~~dIiV~TP~rL~~~l~~~~~~~l~~v  160 (572)
T PRK04537         85 PRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELL----QQGVDVIIATPGRLIDYVKQHKVVSLHAC  160 (572)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHH----hCCCCEEEECHHHHHHHHHhccccchhhe
Confidence            47999999999999888876543    66788999998876554433    345789999952     221  2455556


Q ss_pred             cEEEE
Q psy576          116 RLVVN  120 (159)
Q Consensus       116 ~~vi~  120 (159)
                      .++|.
T Consensus       161 ~~lVi  165 (572)
T PRK04537        161 EICVL  165 (572)
T ss_pred             eeeEe
Confidence            65553

>PF04364 DNA_pol3_chi: DNA polymerase III chi subunit, HolC; InterPro: IPR007459 The DNA polymerase III holoenzyme (2

Probab=90.49  E-value=2  Score=28.20  Aligned_cols=80  Identities=16%  Similarity=0.011  Sum_probs=41.7

Q ss_pred             HHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccc
Q psy576           34 VQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGID  111 (159)
Q Consensus        34 ~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~  111 (159)
                      ...+.+++.+  ..+.+++|+|.+.+.++.+-+.|.......-+.|+-....         ....-.|+|+++...  -.
T Consensus        15 ~~~~c~L~~k~~~~g~rv~V~~~d~~~a~~lD~~LW~~~~~sFlPH~~~~~~---------~~~~~PV~i~~~~~~--~~   83 (137)
T PF04364_consen   15 ERFACRLAEKAYRQGQRVLVLCPDEEQAEALDELLWTFSPDSFLPHGLAGEP---------PAARQPVLITWDQEA--NP   83 (137)
T ss_dssp             HHHHHHHHHHHHHTT--EEEE-SSHHHHHHHHHHTTTSSTT----EEETT-S---------STT--SEEEE-TTS-----
T ss_pred             HHHHHHHHHHHHHcCCeEEEEeCCHHHHHHHHHHHHCCCCCCCCCCcccCCC---------CCCCCeEEEecCccc--CC
Confidence            4566666653  3567899999999999999999987755555556542221         111246888886642  12


Q ss_pred             cCCCcEEEEecCC
Q psy576          112 FRTVRLVVNYDFP  124 (159)
Q Consensus       112 i~~~~~vi~~~~~  124 (159)
                      .+..+++||++..
T Consensus        84 ~~~~~vLinL~~~   96 (137)
T PF04364_consen   84 NNHADVLINLSGE   96 (137)
T ss_dssp             -S--SEEEE--SS
T ss_pred             CCCCCEEEECCCC
Confidence            2336778887543

7.7.7 from EC) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either the tau or gamma product of gene dnax, complexed to delta.delta and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3SXU_A 1EM8_C.

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=90.40  E-value=0.5  Score=28.84  Aligned_cols=37  Identities=19%  Similarity=0.170  Sum_probs=31.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRT   81 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~   81 (159)
                      ..++++++|.+-..+...+..|...|+.+..+.|++.
T Consensus        60 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~~l~GG~~   96 (100)
T cd01523          60 DDQEVTVICAKEGSSQFVAELLAERGYDVDYLAGGMK   96 (100)
T ss_pred             CCCeEEEEcCCCCcHHHHHHHHHHcCceeEEeCCcHH
Confidence            4568999999888888899999999988888888863

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=90.10  E-value=0.36  Score=41.61  Aligned_cols=46  Identities=22%  Similarity=0.167  Sum_probs=42.2

Q ss_pred             CeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCC
Q psy576           96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGG  141 (159)
Q Consensus        96 ~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g  141 (159)
                      ..+.+++.+++.+|+|.|.+-+++.+....|...-.|.+||..|.-
T Consensus       501 ~~~fifs~~al~egwd~~~~~~~~~l~~~~s~~~~~q~~gr~lr~~  546 (986)
T PRK15483        501 TRRFLFSKWTLREGWDNPNVFQIAKLRSSGSETSKLQEVGRGLRLP  546 (986)
T ss_pred             CeEEEEEhHHhhhcCCCCCeEEEEEeccCCchHHHHHHhccceecc
Confidence            5679999999999999999999999998889999999999999954

>smart00450 RHOD Rhodanese Homology Domain

Probab=90.07  E-value=1.1  Score=26.70  Aligned_cols=39  Identities=23%  Similarity=0.289  Sum_probs=31.6

Q ss_pred             cCCCCCEEEEecchHHHHHHHHHHHhCCCc-eEEEecCCC
Q psy576           43 LGIEPPVLVFVQSKERAQELYNELIYDGIN-VDVIHSDRT   81 (159)
Q Consensus        43 ~~~~~~~lif~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~   81 (159)
                      .....+++++|.+...+..++..|.+.+.+ +..+.|++.
T Consensus        53 ~~~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~   92 (100)
T smart00450       53 LDKDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYK   92 (100)
T ss_pred             CCCCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHH
Confidence            345568999999988999999999888876 778888863

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=90.01  E-value=5.1  Score=33.45  Aligned_cols=86  Identities=16%  Similarity=0.068  Sum_probs=56.0

Q ss_pred             ecCCCCChHHH--HHHHHhcCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCeeE
Q psy576           26 ETEGAGSPVQA--QDETILLGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRIWI   99 (159)
Q Consensus        26 ~~~~~~~k~~~--l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v   99 (159)
                      .+...++|...  +..+.....+.+++|.+++..-|...++.+..    .++.+..+.|+++++++....      ..+|
T Consensus       122 e~~TGeGKTla~~lp~~~~al~G~~v~VvTptreLA~qdae~~~~l~~~lGlsv~~i~gg~~~~~r~~~y------~~dI  195 (656)
T PRK12898        122 EMQTGEGKTLTATLPAGTAALAGLPVHVITVNDYLAERDAELMRPLYEALGLTVGCVVEDQSPDERRAAY------GADI  195 (656)
T ss_pred             eeeCCCCcHHHHHHHHHHHhhcCCeEEEEcCcHHHHHHHHHHHHHHHhhcCCEEEEEeCCCCHHHHHHHc------CCCE
Confidence            33333555544  22333344567899999999988877776644    488999999999877655432      4578


Q ss_pred             EEEeCCcccccccCCCcEE
Q psy576          100 LITTELLGRGIDFRTVRLV  118 (159)
Q Consensus       100 lv~t~~~~~g~~i~~~~~v  118 (159)
                      +++|.. +-|+|.-.-+.+
T Consensus       196 vygT~~-e~~FDyLrd~~~  213 (656)
T PRK12898        196 TYCTNK-ELVFDYLRDRLA  213 (656)
T ss_pred             EEECCC-chhhhhcccccc
Confidence            888854 347776444433

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=89.14  E-value=3.7  Score=34.73  Aligned_cols=74  Identities=16%  Similarity=-0.008  Sum_probs=52.7

Q ss_pred             ecCCCCChHHH--HHHHHhcCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCeeE
Q psy576           26 ETEGAGSPVQA--QDETILLGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRIWI   99 (159)
Q Consensus        26 ~~~~~~~k~~~--l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v   99 (159)
                      .....++|...  +...+....+.++.|.+++..-|...++.+..    .|+.+..++|+++.+++...+.      .+|
T Consensus        75 em~TGeGKTLva~lpa~l~aL~G~~V~VvTpt~~LA~qdae~~~~l~~~LGLsv~~i~g~~~~~~r~~~y~------~dI  148 (745)
T TIGR00963        75 EMKTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAEWMGQVYRFLGLSVGLILSGMSPEERREAYA------CDI  148 (745)
T ss_pred             eecCCCccHHHHHHHHHHHHHhCCCEEEEcCCHHHHHHHHHHHHHHhccCCCeEEEEeCCCCHHHHHHhcC------CCE
Confidence            33444555544  22334444566899999999988888877654    3789999999999887765553      689


Q ss_pred             EEEeCC
Q psy576          100 LITTEL  105 (159)
Q Consensus       100 lv~t~~  105 (159)
                      +++|..
T Consensus       149 vyGT~~  154 (745)
T TIGR00963       149 TYGTNN  154 (745)
T ss_pred             EEECCC
Confidence            999976

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.

>KOG0389|consensus

Probab=88.90  E-value=4.2  Score=34.54  Aligned_cols=67  Identities=24%  Similarity=0.208  Sum_probs=46.5

Q ss_pred             HHHHHhcCCCCCEEEEecchHHHHHHHHHHHh-----CCCceEEEecCCCHHHHHHHHHHHhcC--CeeEEEEeCCcccc
Q psy576           37 QDETILLGIEPPVLVFVQSKERAQELYNELIY-----DGINVDVIHSDRTQKQRDNVVRSFRTG--RIWILITTELLGRG  109 (159)
Q Consensus        37 l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~-----~~~~~~~~~~~~~~~~r~~~~~~f~~~--~~~vlv~t~~~~~g  109 (159)
                      |.-+...+..+|=||.|++..    +-.|+++     ..+.+..+||  +..+|+++...+..+  .++||++|--+..+
T Consensus       439 layLkq~g~~gpHLVVvPsST----leNWlrEf~kwCPsl~Ve~YyG--Sq~ER~~lR~~i~~~~~~ydVllTTY~la~~  512 (941)
T KOG0389|consen  439 LAYLKQIGNPGPHLVVVPSST----LENWLREFAKWCPSLKVEPYYG--SQDERRELRERIKKNKDDYDVLLTTYNLAAS  512 (941)
T ss_pred             HHHHHHcCCCCCcEEEecchh----HHHHHHHHHHhCCceEEEeccC--cHHHHHHHHHHHhccCCCccEEEEEeecccC
Confidence            444445566788888888732    3333332     2567889999  579999999999885  78899999554433

>KOG0330|consensus

Probab=88.89  E-value=4.1  Score=31.76  Aligned_cols=79  Identities=18%  Similarity=0.198  Sum_probs=53.4

Q ss_pred             HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC-------
Q psy576           37 QDETILLGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL-------  105 (159)
Q Consensus        37 l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~-------  105 (159)
                      |..++..-..-.++|.++|++-+..|++-+...    |..+..+-||++......  +  ...+..|||||+=       
T Consensus       120 l~~LL~~p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~--~--L~kkPhilVaTPGrL~dhl~  195 (476)
T KOG0330|consen  120 LQRLLQEPKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQAN--Q--LSKKPHILVATPGRLWDHLE  195 (476)
T ss_pred             HHHHHcCCCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHH--H--hhcCCCEEEeCcHHHHHHHH
Confidence            444555433345999999999999998887665    678899999987653221  1  2246778999972       


Q ss_pred             cccccccCCCcEEE
Q psy576          106 LGRGIDFRTVRLVV  119 (159)
Q Consensus       106 ~~~g~~i~~~~~vi  119 (159)
                      -..|+++..+.+++
T Consensus       196 ~Tkgf~le~lk~LV  209 (476)
T KOG0330|consen  196 NTKGFSLEQLKFLV  209 (476)
T ss_pred             hccCccHHHhHHHh
Confidence            13566666665544

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=88.86  E-value=2  Score=33.56  Aligned_cols=70  Identities=19%  Similarity=0.261  Sum_probs=47.9

Q ss_pred             CCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC-----c-ccccccCCCc
Q psy576           47 PPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL-----L-GRGIDFRTVR  116 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~-----~-~~g~~i~~~~  116 (159)
                      .++||.+++++-|..+++.+..    .++++..++|+.+.......   + ....+|+|+|+-     + ...+++..+.
T Consensus        84 ~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~---l-~~~~~IlV~TP~~l~~~l~~~~~~l~~v~  159 (423)
T PRK04837         84 PRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV---L-ESGVDILIGTTGRLIDYAKQNHINLGAIQ  159 (423)
T ss_pred             ceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHH---h-cCCCCEEEECHHHHHHHHHcCCccccccc
Confidence            4699999999999988776543    36788899998765544332   2 235689999962     1 2245566677


Q ss_pred             EEEE
Q psy576          117 LVVN  120 (159)
Q Consensus       117 ~vi~  120 (159)
                      ++|.
T Consensus       160 ~lVi  163 (423)
T PRK04837        160 VVVL  163 (423)
T ss_pred             EEEE
Confidence            6664

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

Probab=88.74  E-value=1.2  Score=38.69  Aligned_cols=56  Identities=25%  Similarity=0.267  Sum_probs=42.8

Q ss_pred             CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCC----CcceEEEEec
Q psy576           95 GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGG----REGKAVTFFT  151 (159)
Q Consensus        95 ~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g----~~g~~~~~~~  151 (159)
                      ..+++||.++++-.|+|.|.++.+. .|-|--.-.++|.+.|+.|.-    ..|.++.|..
T Consensus       592 d~~kilIV~dmlLTGFDaP~L~TmY-vDK~Lk~H~L~QAisRtNR~~~~~K~~G~IVDf~g  651 (962)
T COG0610         592 DPLDLLIVVDMLLTGFDAPCLNTLY-VDKPLKYHNLIQAISRTNRVFPGKKKFGLIVDFRG  651 (962)
T ss_pred             CCCCEEEEEccccccCCccccceEE-eccccccchHHHHHHHhccCCCCCCCCcEEEECcc
Confidence            5689999999999999999998554 456666677899999999944    2355555443

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

Probab=88.37  E-value=5.5  Score=26.34  Aligned_cols=96  Identities=19%  Similarity=0.236  Sum_probs=61.3

Q ss_pred             ceeeeecCCCCChHHHHHHH----HhcCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHH-HHHHHHHH
Q psy576           21 ARMYRETEGAGSPVQAQDET----ILLGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQK-QRDNVVRS   91 (159)
Q Consensus        21 ~~~~~~~~~~~~k~~~l~~~----~~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~-~r~~~~~~   91 (159)
                      .+.+.......+|-....-.    +.......+++.+++.+.+....+.+...    +.++..++++.+.. +....+  
T Consensus        15 ~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--   92 (169)
T PF00270_consen   15 KNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVL--   92 (169)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHH--
T ss_pred             CCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeecccccccccccccccccccccccccccccccccccccccc--
Confidence            44555556667777764422    22333458999999999999998887654    35788889987744 222222  


Q ss_pred             HhcCCeeEEEEeCC-cc-----cccccCCCcEEEE
Q psy576           92 FRTGRIWILITTEL-LG-----RGIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~-~~-----~g~~i~~~~~vi~  120 (159)
                        .++..|+|+|.. +.     ...++..++++|.
T Consensus        93 --~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iVi  125 (169)
T PF00270_consen   93 --SNQADILVTTPEQLLDLISNGKINISRLSLIVI  125 (169)
T ss_dssp             --HTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEE
T ss_pred             --cccccccccCcchhhccccccccccccceeecc
Confidence              667889999852 11     2235556776664

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 ....

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=88.29  E-value=3.8  Score=35.35  Aligned_cols=69  Identities=14%  Similarity=0.025  Sum_probs=49.6

Q ss_pred             CChHHH--HHHHHhcCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC
Q psy576           31 GSPVQA--QDETILLGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE  104 (159)
Q Consensus        31 ~~k~~~--l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~  104 (159)
                      ++|...  |..++....+..+.|.+++..-|...++++..    .|+.+..++|++++.++...+      ..+|+++|+
T Consensus       106 eGKTL~a~Lpa~~~al~G~~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~~i~gg~~~~~r~~~y------~~dIvygT~  179 (896)
T PRK13104        106 EGKTLVATLPAYLNAISGRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGVIYPDMSHKEKQEAY------KADIVYGTN  179 (896)
T ss_pred             CCchHHHHHHHHHHHhcCCCEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCHHHHHHHh------CCCEEEECC
Confidence            444443  23333334556799999999999888887754    378899999999988876554      467999986


Q ss_pred             C
Q psy576          105 L  105 (159)
Q Consensus       105 ~  105 (159)
                      .
T Consensus       180 g  180 (896)
T PRK13104        180 N  180 (896)
T ss_pred             h
Confidence            4

>PRK05728 DNA polymerase III subunit chi; Validated

Probab=88.05  E-value=3.8  Score=27.09  Aligned_cols=80  Identities=18%  Similarity=0.013  Sum_probs=51.5

Q ss_pred             CCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEE-eCCc
Q psy576           30 AGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILIT-TELL  106 (159)
Q Consensus        30 ~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~-t~~~  106 (159)
                      ...+...+.+++.+  ..+.+++|.|.+.+.++.+-+.|.......-+.|+.....         ......|+|+ ++..
T Consensus        11 ~~~~~~~~c~L~~ka~~~g~rv~I~~~d~~~a~~lD~~LW~~~~~sFlPH~~~~~~---------~~~~~PV~l~~~~~~   81 (142)
T PRK05728         11 LSALEALLCELAEKALRAGWRVLVQCEDEEQAEALDEALWTFRDESFLPHGLAGEG---------PAAGQPVLLTWPGKR   81 (142)
T ss_pred             chhHHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHHHHhcCCCCCcCCCCCcCCCC---------CCCCCCEEEEcCCCC
Confidence            35677778888864  4678899999999999999999977654455556632211         0123467776 2211


Q ss_pred             ccccccCCCcEEEEec
Q psy576          107 GRGIDFRTVRLVVNYD  122 (159)
Q Consensus       107 ~~g~~i~~~~~vi~~~  122 (159)
                          +.+..+++||++
T Consensus        82 ----~~~~~~~LinL~   93 (142)
T PRK05728         82 ----NANHRDLLINLD   93 (142)
T ss_pred             ----CCCCCcEEEECC
Confidence                334456677664

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=87.98  E-value=1.7  Score=26.26  Aligned_cols=37  Identities=16%  Similarity=0.103  Sum_probs=29.7

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      ....+++++|.+...+...+..|+..|. ++..+.|++
T Consensus        54 ~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~GG~   91 (96)
T cd01529          54 GRATRYVLTCDGSLLARFAAQELLALGGKPVALLDGGT   91 (96)
T ss_pred             CCCCCEEEEeCChHHHHHHHHHHHHcCCCCEEEeCCCH
Confidence            3566899999998888888888888777 577788876

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.

>PRK13766 Hef nuclease; Provisional

Probab=87.96  E-value=6.5  Score=33.36  Aligned_cols=93  Identities=11%  Similarity=0.095  Sum_probs=59.6

Q ss_pred             eeeeecCCCCChHHH----HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC-C---CceEEEecCCCHHHHHHHHHHHh
Q psy576           22 RMYRETEGAGSPVQA----QDETILLGIEPPVLVFVQSKERAQELYNELIYD-G---INVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~----l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~-~---~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      ......+...+|...    +...+. ..++++|+.|++...+....+.+++. +   .++..++|+.+..+|.+.+.   
T Consensus        31 n~lv~~ptG~GKT~~a~~~i~~~l~-~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~r~~~~~---  106 (773)
T PRK13766         31 NTLVVLPTGLGKTAIALLVIAERLH-KKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWE---  106 (773)
T ss_pred             CeEEEcCCCccHHHHHHHHHHHHHH-hCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEEeCCCCHHHHHHHHh---
Confidence            455555665777763    333332 35678999999998887777766543 2   36788999988877765443   


Q ss_pred             cCCeeEEEEeCC-c-----ccccccCCCcEEEE
Q psy576           94 TGRIWILITTEL-L-----GRGIDFRTVRLVVN  120 (159)
Q Consensus        94 ~~~~~vlv~t~~-~-----~~g~~i~~~~~vi~  120 (159)
                        +..|+|+|+- +     ..-++...++.||.
T Consensus       107 --~~~iiv~T~~~l~~~l~~~~~~~~~~~liVv  137 (773)
T PRK13766        107 --KAKVIVATPQVIENDLIAGRISLEDVSLLIF  137 (773)
T ss_pred             --CCCEEEECHHHHHHHHHcCCCChhhCcEEEE
Confidence              2468888853 1     22334455666664

>PTZ00110 helicase; Provisional

Probab=87.34  E-value=3.6  Score=33.51  Aligned_cols=70  Identities=23%  Similarity=0.269  Sum_probs=47.2

Q ss_pred             CCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC-----Ccccc-cccCCCc
Q psy576           47 PPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE-----LLGRG-IDFRTVR  116 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~-----~~~~g-~~i~~~~  116 (159)
                      ..+||.+++++-|..+.+.+.+.    ++.+..++|+.+.......   +.+ ...|+|+|+     .+..+ +++..++
T Consensus       204 p~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~---l~~-~~~IlVaTPgrL~d~l~~~~~~l~~v~  279 (545)
T PTZ00110        204 PIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYA---LRR-GVEILIACPGRLIDFLESNVTNLRRVT  279 (545)
T ss_pred             cEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHH---HHc-CCCEEEECHHHHHHHHHcCCCChhhCc
Confidence            35899999999999888877654    4667888998776544332   222 467999996     23222 4556677


Q ss_pred             EEEE
Q psy576          117 LVVN  120 (159)
Q Consensus       117 ~vi~  120 (159)
                      ++|.
T Consensus       280 ~lVi  283 (545)
T PTZ00110        280 YLVL  283 (545)
T ss_pred             EEEe
Confidence            6654

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

Probab=87.32  E-value=7.1  Score=33.74  Aligned_cols=126  Identities=14%  Similarity=0.098  Sum_probs=80.3

Q ss_pred             ceeeeecCCCCChHHH-HHHHH---hcCCCCCEEEEecch----HHHHHHHHHHHhCC--CceEEEecCCCHHHHHHHHH
Q psy576           21 ARMYRETEGAGSPVQA-QDETI---LLGIEPPVLVFVQSK----ERAQELYNELIYDG--INVDVIHSDRTQKQRDNVVR   90 (159)
Q Consensus        21 ~~~~~~~~~~~~k~~~-l~~~~---~~~~~~~~lif~~~~----~~~~~l~~~l~~~~--~~~~~~~~~~~~~~r~~~~~   90 (159)
                      ++..+......+|-+. +.-++   ...+..++|++.+++    ++++++.+++...+  +.+..++|+.++++|.    
T Consensus        86 ~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~----  161 (851)
T COG1205          86 RNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERR----  161 (851)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHhhHHHHHHHHHHhCCCcceeeeecCCCChHHHH----
Confidence            6777777777788776 22333   233555789999987    46667777776665  7889999999998876    


Q ss_pred             HHhcCCeeEEEEeC-Cccccccc---------CCCcEEEE-----ec--CCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576           91 SFRTGRIWILITTE-LLGRGIDF---------RTVRLVVN-----YD--FPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus        91 ~f~~~~~~vlv~t~-~~~~g~~i---------~~~~~vi~-----~~--~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      .+..+..+||+++. ++..-+--         ..+.+||.     |.  .=.+++..+-|..|..|..++...++..
T Consensus       162 ~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~vA~llRRL~~~~~~~~~~~q~i~~  238 (851)
T COG1205         162 AIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRRLRRYGSPLQIICT  238 (851)
T ss_pred             HHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhHHHHHHHHHHHHHhccCCCceEEEE
Confidence            56667888999874 44332211         13445543     11  1135666777777666655555555444

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=86.97  E-value=16  Score=30.74  Aligned_cols=109  Identities=20%  Similarity=0.226  Sum_probs=70.9

Q ss_pred             eeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC-CCc-eEEE-------------------------
Q psy576           24 YRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYD-GIN-VDVI-------------------------   76 (159)
Q Consensus        24 ~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~-~~~-~~~~-------------------------   76 (159)
                      +.-+.+ .+|.-.++.++.. .+.++||.+++...|..++.-|+.. +-+ +.++                         
T Consensus        34 l~Gvtg-s~kt~~~a~~~~~-~~~p~Lvi~~n~~~A~ql~~el~~f~p~~~V~~f~sy~d~y~pe~y~P~~d~~~~k~~~  111 (655)
T TIGR00631        34 LLGVTG-SGKTFTMANVIAQ-VNRPTLVIAHNKTLAAQLYNEFKEFFPENAVEYFVSYYDYYQPEAYVPSKDTYIEKDAS  111 (655)
T ss_pred             EECCCC-cHHHHHHHHHHHH-hCCCEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeeecccCCccccCCCccccccccCC
Confidence            333444 6788888888876 4678999999999999999988665 223 4433                         


Q ss_pred             ecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCC----CcEEEEecCCCCHHHHHHHH
Q psy576           77 HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRT----VRLVVNYDFPSSAISYIHRI  134 (159)
Q Consensus        77 ~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~----~~~vi~~~~~~~~~~~~q~~  134 (159)
                      .+.--...|..++..+..++..|+|+|-.+..|+--|.    ....+..+...+...+..+.
T Consensus       112 ~~~~i~~~R~~al~~L~~~~~~ivVasv~~i~~l~~p~~~~~~~~~l~~G~~i~~~~l~~~L  173 (655)
T TIGR00631       112 INDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEVGKEIDRRELLRRL  173 (655)
T ss_pred             CChHHHHHHHHHHHHHHhCCCeEEEEcHHHhcCCCCHHHHHhccEEEeCCCCcCHHHHHHHH
Confidence            11112455677777777777778888755577776554    23444455555666655443

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

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

Probab=86.41  E-value=8.4  Score=32.75  Aligned_cols=78  Identities=15%  Similarity=0.108  Sum_probs=52.2

Q ss_pred             eeeeecCCCCChHHH-HHHH---HhcCCCCCEEEEecchHHHHHHHHHHHhC---CCceEEEecCCCHHHHHHHHHHHhc
Q psy576           22 RMYRETEGAGSPVQA-QDET---ILLGIEPPVLVFVQSKERAQELYNELIYD---GINVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~---~~~~~~~~~lif~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      +.........+|... +.-+   +......++|+.+++++-+......+++.   ++.+..++|+.+..++..+    + 
T Consensus        53 nvvv~apTGSGKTla~~LPiL~~l~~~~~~~aL~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~~i----~-  127 (742)
T TIGR03817        53 HVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERRWA----R-  127 (742)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHhhCCCcEEEEEcChHHHHHHHHHHHHHhccCCeEEEEEeCCCCHHHHHHH----h-
Confidence            455555555667665 2222   22234557999999999999888887654   5678889999887665332    2 


Q ss_pred             CCeeEEEEeC
Q psy576           95 GRIWILITTE  104 (159)
Q Consensus        95 ~~~~vlv~t~  104 (159)
                      ...+|+|+|+
T Consensus       128 ~~~~IivtTP  137 (742)
T TIGR03817       128 EHARYVLTNP  137 (742)
T ss_pred             cCCCEEEECh
Confidence            2367999995

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.

>KOG0329|consensus

Probab=86.36  E-value=2.2  Score=31.37  Aligned_cols=69  Identities=20%  Similarity=0.327  Sum_probs=49.9

Q ss_pred             CEEEEecchHHHHHHHHHHHh-----CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC------CcccccccCCCc
Q psy576           48 PVLVFVQSKERAQELYNELIY-----DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE------LLGRGIDFRTVR  116 (159)
Q Consensus        48 ~~lif~~~~~~~~~l~~~l~~-----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~------~~~~g~~i~~~~  116 (159)
                      .++|.|.+++-|-.+......     .+.++.+++|+++.+.-++.++.    -..|+|+|+      +-++.+++..+.
T Consensus       112 svlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~----~PhivVgTPGrilALvr~k~l~lk~vk  187 (387)
T KOG0329|consen  112 SVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN----CPHIVVGTPGRILALVRNRSLNLKNVK  187 (387)
T ss_pred             EEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhC----CCeEEEcCcHHHHHHHHhccCchhhcc
Confidence            588999999998888665432     26789999999987765555443    567889987      345566777777


Q ss_pred             EEEE
Q psy576          117 LVVN  120 (159)
Q Consensus       117 ~vi~  120 (159)
                      +.+.
T Consensus       188 hFvl  191 (387)
T KOG0329|consen  188 HFVL  191 (387)
T ss_pred             eeeh
Confidence            6654

>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily

Probab=86.15  E-value=2.2  Score=25.97  Aligned_cols=38  Identities=16%  Similarity=0.097  Sum_probs=29.2

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCCc-eEEEecCCC
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGIN-VDVIHSDRT   81 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~   81 (159)
                      .++.+++++|.+-..+...+.+|...|+. +..+.|++.
T Consensus        59 ~~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~   97 (101)
T cd01518          59 LKGKKVLMYCTGGIRCEKASAYLKERGFKNVYQLKGGIL   97 (101)
T ss_pred             cCCCEEEEECCCchhHHHHHHHHHHhCCcceeeechhHH
Confidence            35567999999877777788888888874 777888753

This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=85.70  E-value=4.8  Score=32.07  Aligned_cols=71  Identities=15%  Similarity=0.205  Sum_probs=49.2

Q ss_pred             CCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC------cccccccCCCc
Q psy576           47 PPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL------LGRGIDFRTVR  116 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~------~~~g~~i~~~~  116 (159)
                      .++|+.+++++-+..+++.++..    +.++..++|+.+....   .+.+..+..+|+|+|+-      ....+.+..++
T Consensus       163 ~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~---~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~  239 (475)
T PRK01297        163 PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQ---LKQLEARFCDILVATPGRLLDFNQRGEVHLDMVE  239 (475)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHH---HHHHhCCCCCEEEECHHHHHHHHHcCCcccccCc
Confidence            46999999999999888876543    6778888998765433   34555677889999963      12234455666


Q ss_pred             EEEE
Q psy576          117 LVVN  120 (159)
Q Consensus       117 ~vi~  120 (159)
                      +||.
T Consensus       240 ~lVi  243 (475)
T PRK01297        240 VMVL  243 (475)
T ss_pred             eEEe
Confidence            6654

>cd01533 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2

Probab=85.55  E-value=2.7  Score=26.04  Aligned_cols=37  Identities=22%  Similarity=0.325  Sum_probs=29.5

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-c-eEEEecCCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-N-VDVIHSDRT   81 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-~-~~~~~~~~~   81 (159)
                      .+.++++||.+-..+...+..|+..|+ + +..+.|+++
T Consensus        65 ~~~~ivv~C~~G~rs~~a~~~L~~~G~~~~v~~l~gG~~  103 (109)
T cd01533          65 PRTPIVVNCAGRTRSIIGAQSLINAGLPNPVAALRNGTQ  103 (109)
T ss_pred             CCCeEEEECCCCchHHHHHHHHHHCCCCcceeEecCCHH
Confidence            356899999988777778888888888 3 778888873

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue.

>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3

Probab=85.53  E-value=1.7  Score=26.25  Aligned_cols=36  Identities=17%  Similarity=0.048  Sum_probs=29.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~   80 (159)
                      .+.+++++|.+-..+...+..|...|+++..+.|++
T Consensus        55 ~~~~iv~~c~~G~rs~~aa~~L~~~G~~v~~l~GG~   90 (95)
T cd01534          55 RGARIVLADDDGVRADMTASWLAQMGWEVYVLEGGL   90 (95)
T ss_pred             CCCeEEEECCCCChHHHHHHHHHHcCCEEEEecCcH
Confidence            356799999988778888888888888876778876

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=85.51  E-value=7.5  Score=33.27  Aligned_cols=75  Identities=15%  Similarity=0.064  Sum_probs=51.7

Q ss_pred             eeecCCCCChHHH--HHHHHhcCCCCCEEEEecchHHHHHHHHHHH----hCCCceEEEecCCC-HHHHHHHHHHHhcCC
Q psy576           24 YRETEGAGSPVQA--QDETILLGIEPPVLVFVQSKERAQELYNELI----YDGINVDVIHSDRT-QKQRDNVVRSFRTGR   96 (159)
Q Consensus        24 ~~~~~~~~~k~~~--l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~----~~~~~~~~~~~~~~-~~~r~~~~~~f~~~~   96 (159)
                      .......++|...  +..++....+..+.|.+++..-|...++.+.    ..|+.+..+.|+++ +.++....      .
T Consensus        95 Iaem~TGeGKTL~a~lp~~l~al~G~~v~VvTpt~~LA~qd~e~~~~l~~~lGl~v~~i~g~~~~~~~r~~~y------~  168 (790)
T PRK09200         95 IAEMQTGEGKTLTATMPLYLNALEGKGVHLITVNDYLAKRDAEEMGQVYEFLGLTVGLNFSDIDDASEKKAIY------E  168 (790)
T ss_pred             eeeecCCCcchHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCcHHHHHHhc------C
Confidence            3444444566554  2333344567789999999988887776654    34889999999998 77766432      3


Q ss_pred             eeEEEEeC
Q psy576           97 IWILITTE  104 (159)
Q Consensus        97 ~~vlv~t~  104 (159)
                      .+|+++|.
T Consensus       169 ~dIvygT~  176 (790)
T PRK09200        169 ADIIYTTN  176 (790)
T ss_pred             CCEEEECC
Confidence            67888884

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

Probab=85.10  E-value=16  Score=28.31  Aligned_cols=122  Identities=15%  Similarity=0.147  Sum_probs=78.8

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHh
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      +........+.+ .+|.+.+.+-++.  .+++.+.|-.+..+.+-+++..|++.  +..+..+||+-++.-        +
T Consensus       115 ~k~~~lv~AV~G-aGKTEMif~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~~~~I~~Lyg~S~~~f--------r  185 (441)
T COG4098         115 QKEDTLVWAVTG-AGKTEMIFQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFSNCDIDLLYGDSDSYF--------R  185 (441)
T ss_pred             hcCcEEEEEecC-CCchhhhHHHHHHHHhcCCeEEEecCcccchHHHHHHHHHhhccCCeeeEecCCchhc--------c
Confidence            344444555555 6888888877763  35677888999999999999999775  578999999865532        2


Q ss_pred             cCCeeEEEEeCCcccccccCCCcEEEEe---cCCCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576           94 TGRIWILITTELLGRGIDFRTVRLVVNY---DFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus        94 ~~~~~vlv~t~~~~~g~~i~~~~~vi~~---~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                         -.++|||.---.-+. ...+.+|.-   ..|.+-+..+|.+-+-.|- ..|..+++....
T Consensus       186 ---~plvVaTtHQLlrFk-~aFD~liIDEVDAFP~~~d~~L~~Av~~ark-~~g~~IylTATp  243 (441)
T COG4098         186 ---APLVVATTHQLLRFK-QAFDLLIIDEVDAFPFSDDQSLQYAVKKARK-KEGATIYLTATP  243 (441)
T ss_pred             ---ccEEEEehHHHHHHH-hhccEEEEeccccccccCCHHHHHHHHHhhc-ccCceEEEecCC
Confidence               356777743211111 245555542   3677777777777666665 345555554443

>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family

Probab=84.74  E-value=11  Score=26.04  Aligned_cols=67  Identities=12%  Similarity=0.144  Sum_probs=47.3

Q ss_pred             HHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEE
Q psy576           35 QAQDETILL--GIEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILI  101 (159)
Q Consensus        35 ~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv  101 (159)
                      ++...++..  ..+.++-++-.+...++.+.+.|++.  +..+...||.+++++...+++..+....++++
T Consensus        35 dl~~~l~~~~~~~~~~vfllG~~~~v~~~~~~~l~~~yP~l~i~g~~g~f~~~~~~~i~~~I~~s~~dil~  105 (177)
T TIGR00696        35 DLMEELCQRAGKEKLPIFLYGGKPDVLQQLKVKLIKEYPKLKIVGAFGPLEPEERKAALAKIARSGAGIVF  105 (177)
T ss_pred             HHHHHHHHHHHHcCCeEEEECCCHHHHHHHHHHHHHHCCCCEEEEECCCCChHHHHHHHHHHHHcCCCEEE
Confidence            444455543  23346767777788888999998776  66666668999888888888988887665444

The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.

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

Probab=84.45  E-value=5  Score=33.03  Aligned_cols=81  Identities=16%  Similarity=0.229  Sum_probs=60.8

Q ss_pred             ceeeeecCCCCChHHH--HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           21 ARMYRETEGAGSPVQA--QDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        21 ~~~~~~~~~~~~k~~~--l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      ...+..+....+|-..  +..++.   .+.+||..+=.+-+..=.+.|+..|+.+..+++.++.+++..++..+..|+++
T Consensus        33 ~d~lvvmPTGgGKSlCyQiPAll~---~G~TLVVSPLiSLM~DQV~~l~~~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~k  109 (590)
T COG0514          33 KDTLVVMPTGGGKSLCYQIPALLL---EGLTLVVSPLISLMKDQVDQLEAAGIRAAYLNSTLSREERQQVLNQLKSGQLK  109 (590)
T ss_pred             CcEEEEccCCCCcchHhhhHHHhc---CCCEEEECchHHHHHHHHHHHHHcCceeehhhcccCHHHHHHHHHHHhcCcee
Confidence            3444444444444333  333333   56888998888877777777888899999999999999999999999999999


Q ss_pred             EEEEeC
Q psy576           99 ILITTE  104 (159)
Q Consensus        99 vlv~t~  104 (159)
                      +|.-++
T Consensus       110 lLyisP  115 (590)
T COG0514         110 LLYISP  115 (590)
T ss_pred             EEEECc
Confidence            887664

>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli

Probab=84.22  E-value=11  Score=25.71  Aligned_cols=58  Identities=10%  Similarity=0.142  Sum_probs=44.6

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC--CCceE-EEecCCCHHHHHHHHHHHhcCCeeEEEE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD--GINVD-VIHSDRTQKQRDNVVRSFRTGRIWILIT  102 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~-~~~~~~~~~~r~~~~~~f~~~~~~vlv~  102 (159)
                      .+.++-++-.+.+.++++.+.|++.  ++.+. ..+|-+++.+...+++..+....++++.
T Consensus        47 ~~~~ifllG~~~~~~~~~~~~l~~~yP~l~ivg~~~g~f~~~~~~~i~~~I~~~~pdiv~v  107 (172)
T PF03808_consen   47 RGKRIFLLGGSEEVLEKAAANLRRRYPGLRIVGYHHGYFDEEEEEAIINRINASGPDIVFV  107 (172)
T ss_pred             cCCeEEEEeCCHHHHHHHHHHHHHHCCCeEEEEecCCCCChhhHHHHHHHHHHcCCCEEEE
Confidence            4457777888888889999999876  55555 5566678889999999999877765553

Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process

>cd01521 RHOD_PspE2 Member of the Rhodanese Homology Domain superfamily

Probab=84.12  E-value=2.4  Score=26.38  Aligned_cols=36  Identities=17%  Similarity=0.111  Sum_probs=28.7

Q ss_pred             CCCCEEEEecch--HHHHHHHHHHHhCCCceEEEecCC
Q psy576           45 IEPPVLVFVQSK--ERAQELYNELIYDGINVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~--~~~~~l~~~l~~~~~~~~~~~~~~   80 (159)
                      .+.+++++|.+.  ..+..++..|...|.++..+.|++
T Consensus        63 ~~~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l~GG~  100 (110)
T cd01521          63 KEKLFVVYCDGPGCNGATKAALKLAELGFPVKEMIGGL  100 (110)
T ss_pred             CCCeEEEEECCCCCchHHHHHHHHHHcCCeEEEecCCH
Confidence            456899999975  367788888888888888888876

This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins.

>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily

Probab=84.03  E-value=2.8  Score=25.36  Aligned_cols=36  Identities=14%  Similarity=0.068  Sum_probs=28.7

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      .+.+++++|.+-..+...+..|.+.+. ++..+.|++
T Consensus        53 ~~~~iv~~c~~g~~s~~~~~~L~~~g~~~v~~l~gG~   89 (99)
T cd01527          53 GANAIIFHCRSGMRTQQNAERLAAISAGEAYVLEGGL   89 (99)
T ss_pred             CCCcEEEEeCCCchHHHHHHHHHHcCCccEEEeeCCH
Confidence            456899999998888888888887766 576788875

This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.

>KOG0331|consensus

Probab=83.97  E-value=4.8  Score=32.56  Aligned_cols=69  Identities=20%  Similarity=0.268  Sum_probs=46.7

Q ss_pred             CCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC-----Ccccc-cccCCCc
Q psy576           47 PPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE-----LLGRG-IDFRTVR  116 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~-----~~~~g-~~i~~~~  116 (159)
                      ..+||.++|++-|..+.+.+.+.    .+...+++|+.+...+.+-++   + ...|+|+|+     .++.| +++..++
T Consensus       166 P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~---~-gvdiviaTPGRl~d~le~g~~~l~~v~  241 (519)
T KOG0331|consen  166 PIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLE---R-GVDVVIATPGRLIDLLEEGSLNLSRVT  241 (519)
T ss_pred             CeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHh---c-CCcEEEeCChHHHHHHHcCCcccccee
Confidence            45999999999999998887664    445889999988765443332   2 356888886     22222 3555566


Q ss_pred             EEE
Q psy576          117 LVV  119 (159)
Q Consensus       117 ~vi  119 (159)
                      +++
T Consensus       242 ylV  244 (519)
T KOG0331|consen  242 YLV  244 (519)
T ss_pred             EEE
Confidence            655

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=83.90  E-value=13  Score=32.42  Aligned_cols=75  Identities=13%  Similarity=0.023  Sum_probs=50.3

Q ss_pred             eecCCCCChHHH-HHHHH-hcCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           25 RETEGAGSPVQA-QDETI-LLGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        25 ~~~~~~~~k~~~-l~~~~-~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .......+|... +.-++ ....+.+++|.+++..-|...++++...    ++.+..+.|+++..++...+      ..+
T Consensus       112 AeaqTGeGKTLAf~LP~l~~aL~g~~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y------~~D  185 (970)
T PRK12899        112 TEMQTGEGKTLTAVMPLYLNALTGKPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY------QCD  185 (970)
T ss_pred             EEeCCCCChHHHHHHHHHHHHhhcCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc------CCC
Confidence            333443555444 33333 2223346888999999999888877543    77899999999988776443      367


Q ss_pred             EEEEeCC
Q psy576           99 ILITTEL  105 (159)
Q Consensus        99 vlv~t~~  105 (159)
                      |+++|+-
T Consensus       186 IVygTPg  192 (970)
T PRK12899        186 VVYGTAS  192 (970)
T ss_pred             EEEECCC
Confidence            9999964

>KOG0343|consensus

Probab=83.88  E-value=3.3  Score=33.83  Aligned_cols=54  Identities=19%  Similarity=0.200  Sum_probs=40.9

Q ss_pred             CCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC
Q psy576           46 EPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE  104 (159)
Q Consensus        46 ~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~  104 (159)
                      +-.+||..+|++-|..+++.|.+.    ++.++.+-||....     .+.-+-+...|||||+
T Consensus       141 GlGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k-----~E~eRi~~mNILVCTP  198 (758)
T KOG0343|consen  141 GLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVK-----FELERISQMNILVCTP  198 (758)
T ss_pred             CceeEEecchHHHHHHHHHHHHHHhhccccccceeecCchhH-----HHHHhhhcCCeEEech
Confidence            346999999999999999998764    66788888886543     2333346788999997

>cd01526 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily

Probab=83.83  E-value=1.6  Score=27.81  Aligned_cols=36  Identities=19%  Similarity=0.194  Sum_probs=30.4

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC--ceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI--NVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~--~~~~~~~~~   80 (159)
                      .+.+++++|.+-..+...+..|...|+  ++..+.|++
T Consensus        71 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~v~~l~GG~  108 (122)
T cd01526          71 KDSPIYVVCRRGNDSQTAVRKLKELGLERFVRDIIGGL  108 (122)
T ss_pred             CCCcEEEECCCCCcHHHHHHHHHHcCCccceeeecchH
Confidence            456899999987788888889998888  688889987

This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.

>KOG0350|consensus

Probab=83.51  E-value=4.4  Score=32.67  Aligned_cols=102  Identities=16%  Similarity=0.164  Sum_probs=63.7

Q ss_pred             cceeeeecCCCCChHHH----HHHHHhcC--CCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHH-HHHH
Q psy576           20 LARMYRETEGAGSPVQA----QDETILLG--IEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQ-RDNV   88 (159)
Q Consensus        20 i~~~~~~~~~~~~k~~~----l~~~~~~~--~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~-r~~~   88 (159)
                      .+..++......+|...    +.+++...  +.-+++|.++++.-+-.++..+...    |..++...|.-+-+. ....
T Consensus       183 ~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL  262 (620)
T KOG0350|consen  183 PRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQL  262 (620)
T ss_pred             CCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHH
Confidence            45566666666666544    33444332  2236999999999999888887654    566666776543322 2222


Q ss_pred             HHHHhcCCeeEEEEeCC-------cccccccCCCcEEEEe
Q psy576           89 VRSFRTGRIWILITTEL-------LGRGIDFRTVRLVVNY  121 (159)
Q Consensus        89 ~~~f~~~~~~vlv~t~~-------~~~g~~i~~~~~vi~~  121 (159)
                      ...-.....+|||+|+-       .-.|+++.++.++|.-
T Consensus       263 ~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVID  302 (620)
T KOG0350|consen  263 ASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVID  302 (620)
T ss_pred             hcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEec
Confidence            22223356799999973       3578888888877753

>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1

Probab=83.14  E-value=2.9  Score=25.04  Aligned_cols=37  Identities=16%  Similarity=0.288  Sum_probs=27.3

Q ss_pred             CCCCEEEEecc--hHHHHHHHHHHHhCCC-ceEEEecCCC
Q psy576           45 IEPPVLVFVQS--KERAQELYNELIYDGI-NVDVIHSDRT   81 (159)
Q Consensus        45 ~~~~~lif~~~--~~~~~~l~~~l~~~~~-~~~~~~~~~~   81 (159)
                      +..+++++|.+  ...+...+..|...++ ++..+.|++.
T Consensus        49 ~~~~ivl~c~~G~~~~s~~aa~~L~~~G~~~v~~l~GG~~   88 (92)
T cd01532          49 RDTPIVVYGEGGGEDLAPRAARRLSELGYTDVALLEGGLQ   88 (92)
T ss_pred             CCCeEEEEeCCCCchHHHHHHHHHHHcCccCEEEccCCHH
Confidence            35689999998  3446777778887776 5777888763

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.

>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins

Probab=83.03  E-value=12  Score=25.44  Aligned_cols=58  Identities=12%  Similarity=0.123  Sum_probs=43.6

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC--CCceEE-EecCCCHHHHHHHHHHHhcCCeeEEEE
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD--GINVDV-IHSDRTQKQRDNVVRSFRTGRIWILIT  102 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~-~~~~~~~~~r~~~~~~f~~~~~~vlv~  102 (159)
                      .+.++-++-.+.+.++.+.+.+++.  +..+.. .||-+...+..++++..+....++++.
T Consensus        45 ~~~~v~llG~~~~~~~~~~~~l~~~yp~l~i~g~~~g~~~~~~~~~i~~~I~~~~pdiv~v  105 (171)
T cd06533          45 KGLRVFLLGAKPEVLEKAAERLRARYPGLKIVGYHHGYFGPEEEEEIIERINASGADILFV  105 (171)
T ss_pred             cCCeEEEECCCHHHHHHHHHHHHHHCCCcEEEEecCCCCChhhHHHHHHHHHHcCCCEEEE
Confidence            3567777888888888988888776  566554 788888888777888888877665553

E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=82.97  E-value=1.3  Score=37.68  Aligned_cols=45  Identities=22%  Similarity=0.254  Sum_probs=41.5

Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCC
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGG  141 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g  141 (159)
                      .+.|.+-.++-+|+|-|++=.++-+....|..+=.|.+||..|..
T Consensus       484 lRFIFS~waLrEGWDNPNVFtIckL~~S~SeiSK~QeVGRGLRLa  528 (985)
T COG3587         484 LRFIFSKWALREGWDNPNVFTICKLRSSGSEISKLQEVGRGLRLA  528 (985)
T ss_pred             ceeeeehhHHhhcCCCCCeeEEEEecCCCcchHHHHHhccceeee
Confidence            578889999999999999999999999999999999999999954

>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain

Probab=82.56  E-value=4.2  Score=25.40  Aligned_cols=36  Identities=28%  Similarity=0.278  Sum_probs=28.8

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      +..+++++|.+-..+..++..|...|. ++..+.|++
T Consensus        77 ~~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~l~GG~  113 (118)
T cd01449          77 PDKPVIVYCGSGVTACVLLLALELLGYKNVRLYDGSW  113 (118)
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHHcCCCCeeeeCChH
Confidence            466899999998888888888988887 466777765

TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.

>KOG0334|consensus

Probab=82.46  E-value=5.2  Score=34.77  Aligned_cols=54  Identities=20%  Similarity=0.307  Sum_probs=42.2

Q ss_pred             CC-EEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC
Q psy576           47 PP-VLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE  104 (159)
Q Consensus        47 ~~-~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~  104 (159)
                      +| ++|.++|++.+..|.+.++..    ++.+..++|+...   ..-+...+.| ..|+|||.
T Consensus       438 GPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~---~~qiaelkRg-~eIvV~tp  496 (997)
T KOG0334|consen  438 GPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGI---SQQIAELKRG-AEIVVCTP  496 (997)
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccH---HHHHHHHhcC-CceEEecc
Confidence            44 888999999999998877543    7788899997644   4456777788 77888885

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=82.31  E-value=9.4  Score=32.84  Aligned_cols=70  Identities=16%  Similarity=0.010  Sum_probs=49.7

Q ss_pred             CCChHHH--HHHHHhcCCCCCEEEEecchHHHHHHHHHHH----hCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEe
Q psy576           30 AGSPVQA--QDETILLGIEPPVLVFVQSKERAQELYNELI----YDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT  103 (159)
Q Consensus        30 ~~~k~~~--l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~----~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t  103 (159)
                      .++|...  +...+....+..+-|.+++..-|...++.+.    ..|+++..+.|+++..++...++      .+|+++|
T Consensus       104 GeGKTLva~lpa~l~aL~G~~V~IvTpn~yLA~rd~e~~~~l~~~LGlsv~~i~~~~~~~er~~~y~------~dI~ygT  177 (830)
T PRK12904        104 GEGKTLVATLPAYLNALTGKGVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGVILSGMSPEERREAYA------ADITYGT  177 (830)
T ss_pred             CCCcHHHHHHHHHHHHHcCCCEEEEecCHHHHHHHHHHHHHHHhhcCCeEEEEcCCCCHHHHHHhcC------CCeEEEC
Confidence            3455444  3333444456678899999987777766654    34889999999999998887753      6788888


Q ss_pred             CC
Q psy576          104 EL  105 (159)
Q Consensus       104 ~~  105 (159)
                      ..
T Consensus       178 ~~  179 (830)
T PRK12904        178 NN  179 (830)
T ss_pred             Cc
Confidence            63

>PRK02362 ski2-like helicase; Provisional

Probab=81.99  E-value=10  Score=32.07  Aligned_cols=77  Identities=16%  Similarity=0.180  Sum_probs=52.4

Q ss_pred             ceeeeecCCCCChHHHHH-HHHhc-CCCCCEEEEecchHHHHHHHHHHHhC---CCceEEEecCCCHHHHHHHHHHHhcC
Q psy576           21 ARMYRETEGAGSPVQAQD-ETILL-GIEPPVLVFVQSKERAQELYNELIYD---GINVDVIHSDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        21 ~~~~~~~~~~~~k~~~l~-~~~~~-~~~~~~lif~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~   95 (159)
                      .+.+.......+|..... .++.. ..++++++.+++++-+.+.+..++..   +.++..++|+.+....     .+  +
T Consensus        40 ~nvlv~APTGSGKTlia~lail~~l~~~~kal~i~P~raLa~q~~~~~~~~~~~g~~v~~~tGd~~~~~~-----~l--~  112 (737)
T PRK02362         40 KNLLAAIPTASGKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEFERFEELGVRVGISTGDYDSRDE-----WL--G  112 (737)
T ss_pred             CcEEEECCCcchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHHHHhhcCCCEEEEEeCCcCcccc-----cc--C
Confidence            355555566677776632 22221 25678999999999999998888754   7788899998754321     11  3


Q ss_pred             CeeEEEEeC
Q psy576           96 RIWILITTE  104 (159)
Q Consensus        96 ~~~vlv~t~  104 (159)
                      ..+|+|||+
T Consensus       113 ~~~IiV~Tp  121 (737)
T PRK02362        113 DNDIIVATS  121 (737)
T ss_pred             CCCEEEECH
Confidence            467999995

>KOG1132|consensus

Probab=81.93  E-value=34  Score=29.74  Aligned_cols=80  Identities=18%  Similarity=0.303  Sum_probs=49.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC-------CCceEEEecCCCHHHHHHHHHHHhc--------CCeeEEEEeCCcccc
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD-------GINVDVIHSDRTQKQRDNVVRSFRT--------GRIWILITTELLGRG  109 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~--------~~~~vlv~t~~~~~g  109 (159)
                      -...+|+|+++-...+.+.+.++..       +.+-.++ +=-+..+-.+++..|.+        |-.-.-||=...++|
T Consensus       560 Vp~G~L~FfPSY~vmdk~~tfw~~~~~we~~~~vk~l~v-EPr~k~~f~e~m~~y~~~i~~pes~ga~~~aVcRGKVSEG  638 (945)
T KOG1132|consen  560 VPYGLLIFFPSYPVMDKLITFWQNRGLWERMEKVKKLVV-EPRSKSEFTEVMSRYYNAIADPESSGAVFFAVCRGKVSEG  638 (945)
T ss_pred             cccceEEeccchHHHHHHHHHHHcchHHHHhhcccCcee-ccCCccchHHHHHHHHHHhhCccccceEEEEEecccccCC
Confidence            3445999999998888886655432       2222222 21134444455555543        223466677899999


Q ss_pred             cccCC--CcEEEEecCCC
Q psy576          110 IDFRT--VRLVVNYDFPS  125 (159)
Q Consensus       110 ~~i~~--~~~vi~~~~~~  125 (159)
                      +|+-+  .+.||..+.|.
T Consensus       639 lDFsD~~~RaVI~tGlPy  656 (945)
T KOG1132|consen  639 LDFSDDNGRAVIITGLPY  656 (945)
T ss_pred             CCccccCCceeEEecCCC
Confidence            99965  55777776663

>cd00158 RHOD Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein

Probab=81.84  E-value=4.2  Score=23.59  Aligned_cols=38  Identities=21%  Similarity=0.260  Sum_probs=29.6

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCCC
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDRT   81 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~~   81 (159)
                      ....+++++|.+...+..++..|...|. ++..+.|++.
T Consensus        48 ~~~~~vv~~c~~~~~a~~~~~~l~~~G~~~v~~l~gG~~   86 (89)
T cd00158          48 DKDKPIVVYCRSGNRSARAAKLLRKAGGTNVYNLEGGML   86 (89)
T ss_pred             CCCCeEEEEeCCCchHHHHHHHHHHhCcccEEEecCChh
Confidence            3567899999998888999999988854 5667777753

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 certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.

>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily

Probab=81.14  E-value=3.4  Score=24.66  Aligned_cols=36  Identities=19%  Similarity=0.310  Sum_probs=29.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      ...+++++|.+-..+...+..|...|. ++..+.|++
T Consensus        55 ~~~~ivv~c~~g~~s~~a~~~l~~~G~~~v~~l~gG~   91 (96)
T cd01444          55 RDRPVVVYCYHGNSSAQLAQALREAGFTDVRSLAGGF   91 (96)
T ss_pred             CCCCEEEEeCCCChHHHHHHHHHHcCCceEEEcCCCH
Confidence            556899999998899999999988876 466777765

Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.

>PRK10287 thiosulfate:cyanide sulfurtransferase; Provisional

Probab=81.03  E-value=7.4  Score=24.21  Aligned_cols=36  Identities=8%  Similarity=-0.006  Sum_probs=28.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~   80 (159)
                      ...+++++|.+-..+...+..|.+.|++.....|++
T Consensus        59 ~~~~IVlyC~~G~rS~~aa~~L~~~G~~~v~~~GG~   94 (104)
T PRK10287         59 KNDTVKLYCNAGRQSGQAKEILSEMGYTHAENAGGL   94 (104)
T ss_pred             CCCeEEEEeCCChHHHHHHHHHHHcCCCeEEecCCH
Confidence            345699999998888888899988887665666764

>PRK05320 rhodanese superfamily protein; Provisional

Probab=80.65  E-value=4.7  Score=29.53  Aligned_cols=37  Identities=16%  Similarity=0.139  Sum_probs=32.0

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCc-eEEEecCCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGIN-VDVIHSDRT   81 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~   81 (159)
                      .+.++++||.+-..+...+.+|++.|++ +..+.|++.
T Consensus       174 kdk~IvvyC~~G~Rs~~Aa~~L~~~Gf~~V~~L~GGi~  211 (257)
T PRK05320        174 AGKTVVSFCTGGIRCEKAAIHMQEVGIDNVYQLEGGIL  211 (257)
T ss_pred             CCCeEEEECCCCHHHHHHHHHHHHcCCcceEEeccCHH
Confidence            5678999999999999999999999884 778899873

>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2

Probab=80.52  E-value=4  Score=24.83  Aligned_cols=37  Identities=16%  Similarity=0.258  Sum_probs=29.4

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDRT   81 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~~   81 (159)
                      ...+++++|.+-..+...+..|.+.|+ ++..+.|++.
T Consensus        57 ~~~~vv~~c~~g~rs~~~~~~l~~~G~~~v~~l~GG~~   94 (101)
T cd01528          57 PDKDIVVLCHHGGRSMQVAQWLLRQGFENVYNLQGGID   94 (101)
T ss_pred             CCCeEEEEeCCCchHHHHHHHHHHcCCccEEEecCCHH
Confidence            356899999998888888888888877 4778888753

Subgroup 2 includes uncharacterized putative rhodanese-related domains.

>PF11496 HDA2-3: Class II histone deacetylase complex subunits 2 and 3; InterPro: IPR021006 This entry contains the class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi

Probab=80.12  E-value=20  Score=26.90  Aligned_cols=123  Identities=14%  Similarity=0.145  Sum_probs=59.8

Q ss_pred             CCCChHHHHHHHHhcC-----C--CCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHH------------
Q psy576           29 GAGSPVQAQDETILLG-----I--EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVV------------   89 (159)
Q Consensus        29 ~~~~k~~~l~~~~~~~-----~--~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~------------   89 (159)
                      ...+|+.+|.+++...     .  +-.++|.+...+..+-+-.+|...+++.-.+.|..-..+....-            
T Consensus        93 ~tS~KF~~L~~Li~~li~~~~~~~~~~ilIv~~~~k~ldllE~~llGk~~~~kr~sg~~l~~~~~~~~~~~~~~~~~~~~  172 (297)
T PF11496_consen   93 YTSGKFQFLNDLIDSLIDRDRREYPLHILIVSRSGKELDLLEGLLLGKKLNYKRYSGESLYDEKHKVPKNGNTESNSSNN  172 (297)
T ss_dssp             HT-HHHHHHHHHHHHH-----TTSSEEEEEEE-STHHHHHHHHHHTTSSSEEEESSS--S--S---S-------------
T ss_pred             HcCchHHHHHHHHHHHHhhhcccCCceEEEEecCccHHHHHHHHHccCCeeEEecCCCCCcCccccCCcccccccccccc
Confidence            3478999998888643     2  33699999999999999999988887777777765443333222            


Q ss_pred             HH-Hhc--CCeeEEEEeCC-cccc----cccCCCcEEEEecCCCCH-HHHHHHHhhccCCCCcceEEEEec
Q psy576           90 RS-FRT--GRIWILITTEL-LGRG----IDFRTVRLVVNYDFPSSA-ISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus        90 ~~-f~~--~~~~vlv~t~~-~~~g----~~i~~~~~vi~~~~~~~~-~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      .. -.+  ....|-++|+. +...    ..-..++.||-+|+..+. ....|++-...|.++.-+++.++.
T Consensus       173 ~~~~~~~~~~~~i~L~ts~~l~~~~~~~~~~~~~d~IIsfD~~~d~~~p~i~~lR~~~~~~~~~PiirLv~  243 (297)
T PF11496_consen  173 SKKKDKGSLSVWIHLITSDQLYNNKPPLLSNYNFDLIISFDPSFDTSLPSIEQLRTQNRRNRLCPIIRLVP  243 (297)
T ss_dssp             ---------SEEEEEEESS---TTTS--TT-S-EEEEEE-SST--TTSHHHHHHH-------S--EEEEEE
T ss_pred             cccccccccceEEEEecCccccccCCCccccCCcCEEEEecCCCCCCChHHHHHHhhcCCCCCCcEEEEee
Confidence            01 111  23445455544 3221    222356788888876432 234454433333323455555554

The member from Schizosaccharomyces pombe (Fission yeast) is referred to as Ccq1 in Q10432 from SWISSPROT. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C terminus []. ; PDB: 3HGQ_C 3HGT_B.

>cd01525 RHOD_Kc Member of the Rhodanese Homology Domain superfamily

Probab=80.12  E-value=4.9  Score=24.48  Aligned_cols=36  Identities=14%  Similarity=0.183  Sum_probs=28.4

Q ss_pred             CCCEEEEecchHHHHHHHHHHHhCCCc-eEEEecCCC
Q psy576           46 EPPVLVFVQSKERAQELYNELIYDGIN-VDVIHSDRT   81 (159)
Q Consensus        46 ~~~~lif~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~   81 (159)
                      ..+++++|.+-..+...+..|...|.. +..+.|++.
T Consensus        65 ~~~vv~~c~~g~~s~~~a~~L~~~G~~~v~~l~GG~~  101 (105)
T cd01525          65 GKIIVIVSHSHKHAALFAAFLVKCGVPRVCILDGGIN  101 (105)
T ss_pred             CCeEEEEeCCCccHHHHHHHHHHcCCCCEEEEeCcHH
Confidence            567999998877788888888888874 677888863

Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD.

>KOG0383|consensus

Probab=80.09  E-value=1.3  Score=36.92  Aligned_cols=78  Identities=21%  Similarity=0.270  Sum_probs=60.9

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc---CCeeEEEEeCC
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT---GRIWILITTEL  105 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~---~~~~vlv~t~~  105 (159)
                      .+|...|...+..  ..+++++||..-....+-+..++...+ ....+.|.....+|...++.|+.   .....|.+|..
T Consensus       614 ~~k~~~l~~~~~~l~~~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~~~~rq~ai~~~n~~~~~~~cfllstra  692 (696)
T KOG0383|consen  614 SGKLTLLLKMLKKLKSSGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPITGPERQAAIDRFNAPGSNQFCFLLSTRA  692 (696)
T ss_pred             HHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCccchhhhhhccccCCCCccceEEEeeccc
Confidence            3455555555543  356799999988888888888887776 77788999999999999999985   35778899998


Q ss_pred             cccc
Q psy576          106 LGRG  109 (159)
Q Consensus       106 ~~~g  109 (159)
                      .+.|
T Consensus       693 ~g~g  696 (696)
T KOG0383|consen  693 GGLG  696 (696)
T ss_pred             ccCC
Confidence            8765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	159
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		3e-17
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		4e-17
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-16
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		4e-15
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		4e-15
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		5e-15
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		5e-15
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		2e-14
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-14
2jgn_A	185	Ddx3 Helicase Domain Length = 185		3e-14
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		5e-14
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		5e-14
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		6e-14
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		5e-13
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		1e-12
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		2e-12
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		9e-12
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		1e-11
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-11
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-11
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		2e-11
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		2e-11
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-11
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-11
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-11
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-11
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		5e-11
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		5e-11
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		1e-10
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-08
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-08
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-08
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		2e-08
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-08
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		2e-08
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-08
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		3e-08
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		3e-07
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		1e-06
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		1e-06
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		1e-06
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		1e-06
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		1e-06
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		1e-06
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		4e-05
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		5e-05
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		1e-04
3v4r_A	667	Crystal Structure Of A Uvrb Dimer-Dna Complex Lengt		5e-04
2d7d_A	661	Structural Insights Into The Cryptic Dna Dependent		5e-04
3uwx_B	683	Crystal Structure Of Uvra-Uvrb Complex Length = 683		7e-04
1d9x_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Le		7e-04
1t5l_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Po		7e-04
2fdc_A	658	Structural Basis Of Dna Damage Recognition And Proc		8e-04
1d9z_A	657	Crystal Structure Of The Dna Repair Protein Uvrb In		8e-04

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 84.0 bits (206), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 40/110 (36%), Positives = 64/110 (58%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  ++ + +EL  +L  D   V  I+SD  Q++RD +++ FR+G   ILI+T+LL RG
Sbjct: 264 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 323
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           ID + V LV+NYD P++  +YIH             A+ F T +D   +R
Sbjct: 324 IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMR 373

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 84.0 bits (206), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 40/110 (36%), Positives = 64/110 (58%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  ++ + +EL  +L  D   V  I+SD  Q++RD +++ FR+G   ILI+T+LL RG
Sbjct: 34  VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           ID + V LV+NYD P++  +YIH             A+ F T +D   +R
Sbjct: 94  IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMR 143

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/110 (36%), Positives = 62/110 (56%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  ++ + +EL  +L  D   V  I+SD  Q++RD + + FR+G   ILI+T+LL RG
Sbjct: 263 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARG 322
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           ID + V LV+NYD P++  +YIH             A+ F T +D    R
Sbjct: 323 IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAXR 372

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 77.0 bits (188), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/110 (34%), Positives = 61/110 (55%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F+ ++ +   L  ++      V  +H D  QK+RD ++R FR+G   +LITT+LL RG
Sbjct: 284 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 343
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           ID + V LV+NYD P++  +YIH             A+   T++D   LR
Sbjct: 344 IDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLR 393

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 77.0 bits (188), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/110 (34%), Positives = 61/110 (55%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F+ ++ +   L  ++      V  +H D  QK+RD ++R FR+G   +LITT+LL RG
Sbjct: 258 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARG 317
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           ID + V LV+NYD P++  +YIH             A+   T++D   LR
Sbjct: 318 IDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLR 367

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 76.6 bits (187), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 38/89 (42%), Positives = 55/89 (61%), Gaps = 6/89 (6%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++FV +K+ A  LY +L  +G  V ++H D   ++RD ++  FR GR  +LITT +L RG
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 306
Query: 110 IDFRTVRLVVNYDFPSSA------ISYIH 132
           ID  TV +VVNYD P+ A       +YIH
Sbjct: 307 IDIPTVSMVVNYDLPTLANGQADPATYIH 335

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 76.6 bits (187), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 38/89 (42%), Positives = 55/89 (61%), Gaps = 6/89 (6%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++FV +K+ A  LY +L  +G  V ++H D   ++RD ++  FR GR  +LITT +L RG
Sbjct: 247 IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 306
Query: 110 IDFRTVRLVVNYDFPSSA------ISYIH 132
           ID  TV +VVNYD P+ A       +YIH
Sbjct: 307 IDIPTVSMVVNYDLPTLANGQADPATYIH 335

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 74.7 bits (182), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/89 (42%), Positives = 55/89 (61%), Gaps = 6/89 (6%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++FV +K+ A  LY +L  +G  V ++H D   ++RD ++  FR GR  +LITT +L RG
Sbjct: 39  IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 98
Query: 110 IDFRTVRLVVNYDFPSSA------ISYIH 132
           ID  TV +VVNYD P+ A       +YIH
Sbjct: 99  IDIPTVSMVVNYDLPTLANGQADPATYIH 127

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 74.7 bits (182), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 60/111 (54%)
Query: 44  GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
           G +   LVFV++K+ A  L + L ++G     IH DR+Q+ R+  +  FR+G+  IL+ T
Sbjct: 274 GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVAT 333
Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQD 154
            +  RG+D   V+ V+N+D PS    Y+H             A +FF +++
Sbjct: 334 AVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERN 384

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 74.3 bits (181), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 60/111 (54%)
Query: 44  GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT 103
           G +   LVFV++K+ A  L + L ++G     IH DR+Q+ R+  +  FR+G+  IL+ T
Sbjct: 44  GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVAT 103
Query: 104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQD 154
            +  RG+D   V+ V+N+D PS    Y+H             A +FF +++
Sbjct: 104 AVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERN 154

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 73.6 bits (179), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 31/106 (29%), Positives = 54/106 (50%)
Query: 47  PPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELL 106
           PPVL+F + K     ++  L+  G+    IH  + Q++R   + +FR G+  +L+ T++ 
Sbjct: 55  PPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVA 114
Query: 107 GRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTK 152
            +G+DF  ++ V+NYD P    +Y+H             A TF  K
Sbjct: 115 SKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINK 160

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 73.2 bits (178), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 38/89 (42%), Positives = 54/89 (60%), Gaps = 6/89 (6%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++FV +K+ A  LY +L  +G  V ++H D   ++RD ++  FR GR  +LITT +L RG
Sbjct: 41  IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 100
Query: 110 IDFRTVRLVVNYDFPSSA------ISYIH 132
           ID  TV  VVNYD P+ A       +YIH
Sbjct: 101 IDIPTVSXVVNYDLPTLANGQADPATYIH 129

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 73.2 bits (178), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 38/89 (42%), Positives = 54/89 (60%), Gaps = 6/89 (6%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++FV +K+ A  LY +L  +G  V ++H D   ++RD ++  FR GR  +LITT +L RG
Sbjct: 40  IIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG 99
Query: 110 IDFRTVRLVVNYDFPSSA------ISYIH 132
           ID  TV  VVNYD P+ A       +YIH
Sbjct: 100 IDIPTVSXVVNYDLPTLANGQADPATYIH 128

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 37/110 (33%), Positives = 56/110 (50%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           LVF ++K   +EL + L   G     IH D +Q QR+ V+R F+  +I ILI T++  RG
Sbjct: 242 LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRG 301
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           ID   +  V+NY  P +  SY H            KA++   +++   LR
Sbjct: 302 IDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLR 351

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 68.9 bits (167), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 52/101 (51%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           +VFV++K  A  L + L         IH DR Q QR+  +R F+ G + +LI T +  RG
Sbjct: 304 IVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRG 363
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFF 150
           +D + ++ V+NYD PS    Y+H            +A +FF
Sbjct: 364 LDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFF 404

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 2/112 (1%)
Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           +L  E P   ++F ++KE   +L +EL   G   D IH    Q+ R +V+  F+ G    
Sbjct: 29  VLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRY 88
Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFT 151
           L+ T++  RGID   + LV+NYD P    SY+H            KA++F T
Sbjct: 89  LVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVT 140

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 65.9 bits (159), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 61/111 (54%), Gaps = 4/111 (3%)
Query: 26  ETEGAGSPVQAQDETI--LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRT 81
           E E   +PV+ + E +  LL +  P   +VF ++K   +E+   L+  G     +H D +
Sbjct: 4   EEEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMS 63
Query: 82  QKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIH 132
           Q +R+ V+ +FR G + +L+ T++  RG+D   V LVV+Y  P  A +Y H
Sbjct: 64  QGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQH 114

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 61/111 (54%), Gaps = 4/111 (3%)
Query: 26  ETEGAGSPVQAQDETI--LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRT 81
           E E   +PV+ + E +  LL +  P   +VF ++K   +E+   L+  G     +H D +
Sbjct: 7   EEEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLS 66
Query: 82  QKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIH 132
           Q +R+ V+ +FR G + +L+ T++  RG+D   V LVV+Y  P  A +Y H
Sbjct: 67  QGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQH 117

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/110 (30%), Positives = 57/110 (51%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  +K +   L  ++      V  +H D  QK+R+++++ FR+G   +LI+T++  RG
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 303
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           +D   V L++NYD P++   YIH             AV F    D  +LR
Sbjct: 304 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLR 353

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 65.1 bits (157), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 33/110 (30%), Positives = 57/110 (51%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  +K +   L  ++      V  +H D  QK+R+++++ FR+G   +LI+T++  RG
Sbjct: 244 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 303
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           +D   V L++NYD P++   YIH             AV F    D  +LR
Sbjct: 304 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLR 353

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 65.1 bits (157), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 50/83 (60%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  S  R + L  ++   G +    H+   Q++R+ V   FR G++  L+ ++LL RG
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG 321
Query: 110 IDFRTVRLVVNYDFPSSAISYIH 132
           ID + V +V+N+DFP +A +Y+H
Sbjct: 322 IDIQAVNVVINFDFPKTAETYLH 344

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 65.1 bits (157), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 53/109 (48%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           +VFV+ +ER  EL N L   GIN   +  +  Q +R+  ++    GR+ +L+ T++  RG
Sbjct: 34  IVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARG 93
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLL 158
           ID   V  V N+D P S  +Y+H             A++     D  LL
Sbjct: 94  IDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLL 142

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 65.1 bits (157), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 57/110 (51%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  +K +   L  ++      V  +H D  QK+R+++++ FR+G   +LI+T++  RG
Sbjct: 280 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 339
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           +D   V L++NYD P++   YIH             A+ F    D  +LR
Sbjct: 340 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILR 389

>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 = 65.1 bits (157), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 57/110 (51%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  +K +   L  ++      V  +H D  QK+R+++++ FR+G   +LI+T++  RG
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           +D   V L++NYD P++   YIH             A+ F    D  +LR
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILR 390

>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 = 65.1 bits (157), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 57/110 (51%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  +K +   L  ++      V  +H D  QK+R+++++ FR+G   +LI+T++  RG
Sbjct: 281 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 340
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           +D   V L++NYD P++   YIH             A+ F    D  +LR
Sbjct: 341 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILR 390

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 57/110 (51%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  +K +   L  ++      V  +H D  QK+R+++++ FR+G   +LI+T++  RG
Sbjct: 259 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG 318
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           +D   V L++NYD P++   YIH             A+ F    D  +LR
Sbjct: 319 LDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILR 368

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 63.5 bits (153), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 49/75 (65%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F Q++  A+ L  E+I DG  V ++  + T +QR ++++ FR G+  +LITT +  RG
Sbjct: 38  IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97
Query: 110 IDFRTVRLVVNYDFP 124
           ID + V +VVN+D P
Sbjct: 98  IDVKQVTIVVNFDLP 112

>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 = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 47/83 (56%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  S +R + L  ++   G +   IH+   Q+ R+ V   FR G    L+ T+L  RG
Sbjct: 48  IIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRG 107
Query: 110 IDFRTVRLVVNYDFPSSAISYIH 132
           ID + V +V+N+DFP  A +Y+H
Sbjct: 108 IDIQAVNVVINFDFPKLAETYLH 130

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 43/76 (56%)
Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
            ++F  +++ A  L  EL  +G  V ++  +   +QR  V+  FR G+  +L+TT +  R
Sbjct: 336 AMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCAR 395
Query: 109 GIDFRTVRLVVNYDFP 124
           GID   V +V+N+D P
Sbjct: 396 GIDVEQVSVVINFDLP 411

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 54/111 (48%), Gaps = 1/111 (0%)
Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           V++FV+S +R   L   L+        IH    Q++R +  + F+  +  IL+ T L GR
Sbjct: 253 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 312
Query: 109 GIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQ-DAPLL 158
           G+D   V +  NYD P  + +Y+H             A+TF + + DA +L
Sbjct: 313 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 363

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 54/111 (48%), Gaps = 1/111 (0%)
Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           V++FV+S +R   L   L+        IH    Q++R +  + F+  +  IL+ T L GR
Sbjct: 253 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 312
Query: 109 GIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQ-DAPLL 158
           G+D   V +  NYD P  + +Y+H             A+TF + + DA +L
Sbjct: 313 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 363

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 54/111 (48%), Gaps = 1/111 (0%)
Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           V++FV+S +R   L   L+        IH    Q++R +  + F+  +  IL+ T L GR
Sbjct: 252 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 311
Query: 109 GIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQ-DAPLL 158
           G+D   V +  NYD P  + +Y+H             A+TF + + DA +L
Sbjct: 312 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 362

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 43/75 (57%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  +++ A  L  EL  +G  V ++  +   +QR  V+  FR G+  +L+TT +  RG
Sbjct: 270 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 329
Query: 110 IDFRTVRLVVNYDFP 124
           ID   V +V+N+D P
Sbjct: 330 IDVEQVSVVINFDLP 344

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 43/76 (56%)
Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
            ++F  +++ A  L  EL  +G  V ++  +   +QR  V+  FR G+  +L+TT +  R
Sbjct: 306 AMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCAR 365
Query: 109 GIDFRTVRLVVNYDFP 124
           GID   V +V+N+D P
Sbjct: 366 GIDVEQVSVVINFDLP 381

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 43/75 (57%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F  +++ A  L  EL  +G  V ++  +   +QR  V+  FR G+  +L+TT +  RG
Sbjct: 286 MIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG 345
Query: 110 IDFRTVRLVVNYDFP 124
           ID   V +V+N+D P
Sbjct: 346 IDVEQVSVVINFDLP 360

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 54/111 (48%), Gaps = 1/111 (0%)
Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           V++FV+S +R   L   L+        IH    Q++R +  + F+  +  IL+ T L GR
Sbjct: 34  VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 93
Query: 109 GIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQ-DAPLL 158
           G+D   V +  NYD P  + +Y+H             A+TF + + DA +L
Sbjct: 94  GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 144

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 38/122 (31%), Positives = 59/122 (48%), Gaps = 8/122 (6%)
Query: 32  SPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRS 91
           S VQA  E    G    V+VFV+++ R  +L    ++D  N   +  D  Q  R+  + +
Sbjct: 210 SKVQALRENKDKG----VIVFVRTRNRVAKLVR--LFD--NAIELRGDLPQSVRNRNIDA 261
Query: 92  FRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFT 151
           FR G   +LITT++  RG+D   V  V+N+D P    +YIH            +A+TF  
Sbjct: 262 FREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL 321
Query: 152 KQ 153
            +
Sbjct: 322 NE 323

>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 = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 39/83 (46%)
Query: 77  HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXX 136
           H   TQ +R ++V+ F+     IL+ T++  RG+DF  V  V+    PS   +YIH    
Sbjct: 322 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGR 381
Query: 137 XXXXXXXXKAVTFFTKQDAPLLR 159
                    +V F  K + P +R
Sbjct: 382 TARSGKEGSSVLFICKDELPFVR 404

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 39/83 (46%)
Query: 77  HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXX 136
           H   TQ +R ++V+ F+     IL+ T++  RG+DF  V  V+    PS   +YIH    
Sbjct: 67  HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGR 126
Query: 137 XXXXXXXXKAVTFFTKQDAPLLR 159
                    +V F  K + P +R
Sbjct: 127 TARSGKEGSSVLFICKDELPFVR 149

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 39/83 (46%)
Query: 77  HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXX 136
           H   TQ +R ++V+ F+     IL+ T++  RG+DF  V  V+    PS   +YIH    
Sbjct: 67  HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGR 126
Query: 137 XXXXXXXXKAVTFFTKQDAPLLR 159
                    +V F  K + P +R
Sbjct: 127 TARSGKEGSSVLFICKDELPFVR 149

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 39/83 (46%)
Query: 77  HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXX 136
           H   TQ +R ++V+ F+     IL+ T++  RG+DF  V  V+    PS   +YIH    
Sbjct: 67  HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGR 126
Query: 137 XXXXXXXXKAVTFFTKQDAPLLR 159
                    +V F  K + P +R
Sbjct: 127 TARSGKEGSSVLFICKDELPFVR 149

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 39/83 (46%)
Query: 77  HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXX 136
           H   TQ +R ++V+ F+     IL+ T++  RG+DF  V  V+    PS   +YIH    
Sbjct: 322 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGR 381
Query: 137 XXXXXXXXKAVTFFTKQDAPLLR 159
                    +V F  K + P +R
Sbjct: 382 TARSGKEGSSVLFICKDELPFVR 404

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 39/83 (46%)
Query: 77  HSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHXXXX 136
           H   TQ +R ++V+ F+     IL+ T++  RG+DF  V  V+    PS   +YIH    
Sbjct: 373 HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGR 432
Query: 137 XXXXXXXXKAVTFFTKQDAPLLR 159
                    +V F  K + P +R
Sbjct: 433 TARSGKEGSSVLFICKDELPFVR 455

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/110 (23%), Positives = 47/110 (42%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           +++  S+ + ++    L   GI+    H+      R +V   F+   + I++ T   G G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           I+   VR VV++D P +  SY              +A+ F+   D   LR
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR 349

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/110 (23%), Positives = 46/110 (41%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           +++  S+ + ++    L   GI+    H+      R +V   F+   + I++ T   G G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXG 299
Query: 110 IDFRTVRLVVNYDFPSSAISYIHXXXXXXXXXXXXKAVTFFTKQDAPLLR 159
           I+   VR VV++D P +  SY              +A  F+   D   LR
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWLR 349

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 8/92 (8%)
Query: 49  VLVFVQSKERAQELYNELIYDGINVDVI------HSDRTQKQRDN--VVRSFRTGRIWIL 100
           ++VF   +E A+++ NEL+ DGI            +DR   QR+   ++  F  G   +L
Sbjct: 364 IIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVL 423
Query: 101 ITTELLGRGIDFRTVRLVVNYDFPSSAISYIH 132
           + T +   G+D   V LVV Y+   SAI  I 
Sbjct: 424 VATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQ 455

>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex Length = 667

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%)
Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           VLV   +K+ +++L + L   GI V+ +HS+    +R  ++R  R G+  +L+   LL  
Sbjct: 454 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 513
Query: 109 GIDFRTVRLVVNYD 122
           G+D   V LV   D
Sbjct: 514 GLDIPEVSLVAILD 527

>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase Activity Of Uvrb Length = 661

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%)
Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
           VLV   +K+ +++L + L   GI V+ +HS+    +R  ++R  R G+  +L+   LL  
Sbjct: 448 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 109 GIDFRTVRLVVNYD 122
           G+D   V LV   D
Sbjct: 508 GLDIPEVSLVAILD 521

>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex Length = 683

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           LV   +K+ A++L + L   GI V  +HS+    +R  ++R  R G+  +L+   LL  G
Sbjct: 474 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 533
Query: 110 IDFRTVRLVVNYD 122
           +D   V LV   D
Sbjct: 534 LDIPEVSLVAILD 546

>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Length = 658

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           LV   +K+ A++L + L   GI V  +HS+    +R  ++R  R G+  +L+   LL  G
Sbjct: 449 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 508
Query: 110 IDFRTVRLVVNYD 122
           +D   V LV   D
Sbjct: 509 LDIPEVSLVAILD 521

>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point Mutant Y96a Revealing A Novel Fold For Domain 2 Length = 658

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           LV   +K+ A++L + L   GI V  +HS+    +R  ++R  R G+  +L+   LL  G
Sbjct: 449 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 508
Query: 110 IDFRTVRLVVNYD 122
           +D   V LV   D
Sbjct: 509 LDIPEVSLVAILD 521

>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX Length = 658

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           LV   +K+ A++L + L   GI V  +HS+    +R  ++R  R G+  +L+   LL  G
Sbjct: 449 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 508
Query: 110 IDFRTVRLVVNYD 122
           +D   V LV   D
Sbjct: 509 LDIPEVSLVAILD 521

>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In Complex With Atp Length = 657

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           LV   +K+ A++L + L   GI V  +HS+    +R  ++R  R G+  +L+   LL  G
Sbjct: 448 LVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG 507
Query: 110 IDFRTVRLVVNYD 122
           +D   V LV   D
Sbjct: 508 LDIPEVSLVAILD 520

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	159
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	3e-45
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	3e-44
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	5e-44
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	8e-44
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	9e-44
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	3e-42
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	3e-42
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	4e-42
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	9e-42
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	3e-41
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	8e-41
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	8e-41
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-40
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	4e-39
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	6e-39
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-38
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-38
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	1e-37
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	3e-37
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-36
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	8e-36
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-35
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	9e-35
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	2e-31
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	2e-31
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-21
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	5e-13
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-13
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	9e-13
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	3e-12
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	6e-12
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	6e-11
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	3e-10
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	2e-09
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	1e-07
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	8e-07
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	5e-05
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	7e-05
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	1e-04
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	9e-04
1yks_A	440	Genome polyprotein [contains: flavivirin protease	9e-04

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  145 bits (367), Expect = 3e-45
 Identities = 49/111 (44%), Positives = 74/111 (66%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
            ++F  ++ + +EL  +L  D   V  I+SD  Q++RD +++ FR+G   ILI+T+LL R
Sbjct: 33  AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLAR 92

Query: 109 GIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           GID + V LV+NYD P++  +YIHRIGR GR GR+G A+ F T +D   +R
Sbjct: 93  GIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMR 143

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  143 bits (362), Expect = 3e-44
 Identities = 41/120 (34%), Positives = 65/120 (54%), Gaps = 1/120 (0%)

Query: 41  ILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL 100
            L    PPVL+F + K     ++  L+  G+    IH  + Q++R   + +FR G+  +L
Sbjct: 49  CLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVL 108

Query: 101 ITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK-QDAPLLR 159
           + T++  +G+DF  ++ V+NYD P    +Y+HRIGR G  G  G A TF  K  D  +L 
Sbjct: 109 VATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLM 168

>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 =  141 bits (358), Expect = 8e-44
 Identities = 42/121 (34%), Positives = 66/121 (54%), Gaps = 3/121 (2%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           LL +     V++FV+S +R   L   L+        IH    Q++R +  + F+  +  I
Sbjct: 25  LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 84

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT-KQDAPLL 158
           L+ T L GRG+D   V +  NYD P  + +Y+HR+ RAGR G +G A+TF + + DA +L
Sbjct: 85  LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 144

Query: 159 R 159
            
Sbjct: 145 N 145

>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 =  141 bits (359), Expect = 9e-44
 Identities = 44/121 (36%), Positives = 70/121 (57%), Gaps = 2/121 (1%)

Query: 41  ILLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW 98
           +L         LVFV++K+ A  L + L ++G     IH DR+Q+ R+  +  FR+G+  
Sbjct: 39  LLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP 98

Query: 99  ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL 158
           IL+ T +  RG+D   V+ V+N+D PS    Y+HRIGR GR G  G A +FF +++  + 
Sbjct: 99  ILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINIT 158

Query: 159 R 159
           +
Sbjct: 159 K 159

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  144 bits (365), Expect = 3e-42
 Identities = 44/121 (36%), Positives = 70/121 (57%), Gaps = 2/121 (1%)

Query: 41  ILLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW 98
           +L         LVFV++K+ A  L + L ++G     IH DR+Q+ R+  +  FR+G+  
Sbjct: 269 LLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSP 328

Query: 99  ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL 158
           IL+ T +  RG+D   V+ V+N+D PS    Y+HRIGR GR G  G A +FF +++  + 
Sbjct: 329 ILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINIT 388

Query: 159 R 159
           +
Sbjct: 389 K 389

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  137 bits (347), Expect = 3e-42
 Identities = 45/120 (37%), Positives = 66/120 (55%), Gaps = 2/120 (1%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           +L  E P   ++F ++KE   +L +EL   G   D IH    Q+ R +V+  F+ G    
Sbjct: 29  VLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRY 88

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           L+ T++  RGID   + LV+NYD P    SY+HR GR GR G +GKA++F T  +   L 
Sbjct: 89  LVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLA 148

>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 =  137 bits (347), Expect = 4e-42
 Identities = 42/116 (36%), Positives = 67/116 (57%), Gaps = 6/116 (5%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           ++F Q++  A+ L  E+I DG  V ++  + T +QR ++++ FR G+  +LITT +  RG
Sbjct: 38  IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97

Query: 110 IDFRTVRLVVNYDFPSSAI------SYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           ID + V +VVN+D P          +Y+HRIGR GR G++G A       + P L 
Sbjct: 98  IDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLM 153

>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 =  142 bits (360), Expect = 9e-42
 Identities = 50/120 (41%), Positives = 75/120 (62%), Gaps = 2/120 (1%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           L         ++F  ++ + +EL  +L  D   V  I+SD  Q++RD +++ FR+G   I
Sbjct: 253 LYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI 312

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           LI+T+LL RGID + V LV+NYD P++  +YIHRIGR GR GR+G A+ F T +D   +R
Sbjct: 313 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMR 372

>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 =  141 bits (357), Expect = 3e-41
 Identities = 48/120 (40%), Positives = 72/120 (60%), Gaps = 2/120 (1%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           L         ++F+ ++ +   L  ++      V  +H D  QK+RD ++R FR+G   +
Sbjct: 274 LYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRV 333

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           LITT+LL RGID + V LV+NYD P++  +YIHRIGR GR GR+G A+   T++D   LR
Sbjct: 334 LITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLR 393

>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 =  140 bits (354), Expect = 8e-41
 Identities = 40/120 (33%), Positives = 64/120 (53%), Gaps = 2/120 (1%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           L         ++F  S  R + L  ++   G +    H+   Q++R+ V   FR G++  
Sbjct: 252 LFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRT 311

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           L+ ++LL RGID + V +V+N+DFP +A +Y+HRIGR+GR G  G A+      D   L 
Sbjct: 312 LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLY 371

>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 =  140 bits (354), Expect = 8e-41
 Identities = 42/120 (35%), Positives = 69/120 (57%), Gaps = 2/120 (1%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           L         ++F  +K +   L  ++      V  +H D  QK+R+++++ FR+G   +
Sbjct: 270 LYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRV 329

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           LI+T++  RG+D   V L++NYD P++   YIHRIGR+GR GR+G A+ F    D  +LR
Sbjct: 330 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILR 389

>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 =  139 bits (354), Expect = 1e-40
 Identities = 45/120 (37%), Positives = 65/120 (54%), Gaps = 1/120 (0%)

Query: 41  ILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL 100
           IL       +VFV++K  A  L + L         IH DR Q QR+  +R F+ G + +L
Sbjct: 295 ILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVL 354

Query: 101 ITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK-QDAPLLR 159
           I T +  RG+D + ++ V+NYD PS    Y+HRIGR GR G  G+A +FF   +D  +  
Sbjct: 355 IATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAA 414

>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 =  135 bits (342), Expect = 4e-39
 Identities = 42/121 (34%), Positives = 66/121 (54%), Gaps = 3/121 (2%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           LL +     V++FV+S +R   L   L+        IH    Q++R +  + F+  +  I
Sbjct: 244 LLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI 303

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT-KQDAPLL 158
           L+ T L GRG+D   V +  NYD P  + +Y+HR+ RAGR G +G A+TF + + DA +L
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 363

Query: 159 R 159
            
Sbjct: 364 N 364

>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 =  135 bits (342), Expect = 6e-39
 Identities = 41/127 (32%), Positives = 63/127 (49%), Gaps = 9/127 (7%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           L G       ++F  +++ A  L  EL  +G  V ++  +   +QR  V+  FR G+  +
Sbjct: 260 LYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKV 319

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAI------SYIHRIGRAGRGGREGKAVTFFT-K 152
           L+TT +  RGID   V +V+N+D P          +Y+HRIGR GR G+ G AV     K
Sbjct: 320 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSK 379

Query: 153 QDAPLLR 159
               +L 
Sbjct: 380 HSMNILN 386

>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 =  134 bits (339), Expect = 1e-38
 Identities = 53/127 (41%), Positives = 75/127 (59%), Gaps = 9/127 (7%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           L G+      ++FV +K+ A  LY +L  +G  V ++H D   ++RD ++  FR GR  +
Sbjct: 237 LYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKV 296

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAI------SYIHRIGRAGRGGREGKAVTFFT-K 152
           LITT +L RGID  TV +VVNYD P+ A       +YIHRIGR GR GR+G A++F   K
Sbjct: 297 LITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK 356

Query: 153 QDAPLLR 159
               +L 
Sbjct: 357 NSFNILS 363

>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 =  135 bits (341), Expect = 2e-38
 Identities = 41/127 (32%), Positives = 63/127 (49%), Gaps = 9/127 (7%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           L G       ++F  +++ A  L  EL  +G  V ++  +   +QR  V+  FR G+  +
Sbjct: 327 LYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKV 386

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAI------SYIHRIGRAGRGGREGKAVTFFT-K 152
           L+TT +  RGID   V +V+N+D P          +Y+HRIGR GR G+ G AV     K
Sbjct: 387 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSK 446

Query: 153 QDAPLLR 159
               +L 
Sbjct: 447 HSMNILN 453

>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 =  127 bits (320), Expect = 1e-37
 Identities = 40/120 (33%), Positives = 66/120 (55%), Gaps = 2/120 (1%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           LL +  P   +VF ++K   +E+   L+  G     +H D +Q +R+ V+ +FR G + +
Sbjct: 25  LLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRV 84

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           L+ T++  RG+D   V LVV+Y  P  A +Y HR GR GR GR G+ V  +  ++   + 
Sbjct: 85  LVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVE 144

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score =  124 bits (315), Expect = 3e-37
 Identities = 44/120 (36%), Positives = 64/120 (53%), Gaps = 2/120 (1%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           LL        +VFV+ +ER  EL N L   GIN   +  +  Q +R+  ++    GR+ +
Sbjct: 24  LLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNV 83

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           L+ T++  RGID   V  V N+D P S  +Y+HRIGR  R GR+G A++     D  LL 
Sbjct: 84  LVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLG 143

>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 =  128 bits (324), Expect = 1e-36
 Identities = 45/110 (40%), Positives = 68/110 (61%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           LVF ++K   +EL + L   G     IH D +Q QR+ V+R F+  +I ILI T+++ RG
Sbjct: 242 LVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRG 301

Query: 110 IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           ID   +  V+NY  P +  SY+HRIGR GR G++GKA++   +++   LR
Sbjct: 302 IDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLR 351

>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 =  124 bits (314), Expect = 8e-36
 Identities = 40/120 (33%), Positives = 66/120 (55%), Gaps = 2/120 (1%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
           LL +  P   +VF ++K   +E+   L+  G     +H D +Q +R+ V+ +FR G + +
Sbjct: 22  LLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRV 81

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           L+ T++  RG+D   V LVV+Y  P  A +Y HR GR GR GR G+ V  +  ++   + 
Sbjct: 82  LVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVE 141

>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 =  128 bits (324), Expect = 1e-35
 Identities = 35/123 (28%), Positives = 58/123 (47%), Gaps = 5/123 (4%)

Query: 42  LLGIEPP--VLVFVQSKERAQELY---NELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR 96
           +   +     ++F  + +    L           + +   H   TQ +R ++V+ F+   
Sbjct: 333 IKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDE 392

Query: 97  IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP 156
             IL+ T++  RG+DF  V  V+    PS   +YIHRIGR  R G+EG +V F  K + P
Sbjct: 393 SGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELP 452

Query: 157 LLR 159
            +R
Sbjct: 453 FVR 455

>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 =  126 bits (317), Expect = 9e-35
 Identities = 36/123 (29%), Positives = 60/123 (48%), Gaps = 5/123 (4%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNEL---IYDGINVDVIHSDRTQKQRDNVVRSFRTGR 96
           +   +     ++F  + +    L + L       + +   H   TQ +R ++V+ F+   
Sbjct: 282 IKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDE 341

Query: 97  IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP 156
             IL+ T++  RG+DF  V  V+    PS   +YIHRIGR  R G+EG +V F  K + P
Sbjct: 342 SGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELP 401

Query: 157 LLR 159
            +R
Sbjct: 402 FVR 404

>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 =  114 bits (287), Expect = 2e-31
 Identities = 42/120 (35%), Positives = 63/120 (52%), Gaps = 7/120 (5%)

Query: 42  LLGIEPP--VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI 99
            L       V+VFV+++ R  +L         N   +  D  Q  R+  + +FR G   +
Sbjct: 214 ALRENKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDM 269

Query: 100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           LITT++  RG+D   V  V+N+D P    +YIHRIGR GR GR+G+A+TF    +  L +
Sbjct: 270 LITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFILN-EYWLEK 328

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  115 bits (289), Expect = 2e-31
 Identities = 33/124 (26%), Positives = 54/124 (43%), Gaps = 14/124 (11%)

Query: 45  IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE 104
               +L+F Q++E  +ELY  L     NV    S+  +   D     F+ G+I ILI  +
Sbjct: 251 FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFED-----FKVGKINILIGVQ 305

Query: 105 ----LLGRGIDFR-TVRLVVNYDFPSS--AISYIHRIGRAGRGGREG--KAVTFFTKQDA 155
                L RG+D    ++ V+ +  PS     +YI   GR+ R       K V+   ++D 
Sbjct: 306 AYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDE 365

Query: 156 PLLR 159
            +  
Sbjct: 366 EIFE 369

>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 = 88.7 bits (219), Expect = 2e-21
 Identities = 33/112 (29%), Positives = 53/112 (47%), Gaps = 9/112 (8%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDR--------TQKQRDNVVRSFRTGRIWIL 100
           ++VF   +E A+++ NEL+ DGI                 +Q+++  ++  F  G   +L
Sbjct: 364 IIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVL 423

Query: 101 ITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK 152
           + T +   G+D   V LVV Y+   SAI  I R GR GR    G+ +    K
Sbjct: 424 VATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR-HMPGRVIILMAK 474

>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 = 64.6 bits (156), Expect = 5e-13
 Identities = 24/119 (20%), Positives = 45/119 (37%), Gaps = 15/119 (12%)

Query: 49  VLVFVQSKERAQELYNELI----YDGINVDVIH--------SDRTQKQRDNVVRSFRTGR 96
            L+F +++     L   +      + I   V+         +  T   +  V+ +F+T +
Sbjct: 634 TLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSK 693

Query: 97  I-WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
              +LI T +   GID     LVV Y++  +    I   GR        K +   +K +
Sbjct: 694 DNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRA--AGSKCILVTSKTE 750

>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 = 64.6 bits (156), Expect = 6e-13
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 13/106 (12%)

Query: 49  VLVFVQSKERAQELYNEL----IYDGINVDVI--------HSDRTQKQRDNVVRSFRTGR 96
            L+F +++     L   +    I + I   V+         +  T   +  V+ +F+T +
Sbjct: 393 TLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSK 452

Query: 97  I-WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGG 141
              +LI T +   GID     LVV Y++  +    I   GR    G
Sbjct: 453 DNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAG 498

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Length = 936

 Score = 63.8 bits (154), Expect = 9e-13
 Identities = 23/117 (19%), Positives = 42/117 (35%), Gaps = 15/117 (12%)

Query: 49  VLVFVQSKERAQELYNEL------------IYDGINVDVIHSDRTQKQRDNVVRSFRTGR 96
            L+F +++     L   +            +  G       +  T   +  V+ +F+T +
Sbjct: 634 TLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSK 693

Query: 97  I-WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK 152
              +LI T +   GID     LVV Y++  +    I   GR        K +   +K
Sbjct: 694 DNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRA--AGSKCILVTSK 748

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 62.6 bits (151), Expect = 3e-12
 Identities = 27/122 (22%), Positives = 45/122 (36%), Gaps = 15/122 (12%)

Query: 46  EPPVLVFVQSKERAQELYNELIYD------------GINVDVIHSDRTQKQRDNVVRSFR 93
           E   ++FV+++     L   +  +            G       +  T   +  V+ +FR
Sbjct: 389 ETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFR 448

Query: 94  T-GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTK 152
             G   ILI T +   GID     LV+ Y++  + I  I   GR     R+ K     + 
Sbjct: 449 ASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGRGRA--RDSKCFLLTSS 506

Query: 153 QD 154
            D
Sbjct: 507 AD 508

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 61.5 bits (148), Expect = 6e-12
 Identities = 23/118 (19%), Positives = 46/118 (38%), Gaps = 15/118 (12%)

Query: 50  LVFVQSKERAQELYNEL----IYDGINVDVI--------HSDRTQKQRDNVVRSFR-TGR 96
           ++FV+++     L N +        +   ++        ++  T   +  ++ +F+ +G 
Sbjct: 402 ILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGD 461

Query: 97  IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
             ILI T +   GID     LV+ Y++  + I  I   GR     R  K     +   
Sbjct: 462 HNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRA--RGSKCFLLTSNAG 517

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A* Length = 591

 Score = 58.5 bits (142), Expect = 6e-11
 Identities = 24/109 (22%), Positives = 50/109 (45%)

Query: 51  VFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI 110
           ++  S++ ++++   L   GI+    H++   + +  V R +    I +++ T   G GI
Sbjct: 272 IYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGI 331

Query: 111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           D   VR V+++    S  +Y    GRAGR   +   + ++   D   + 
Sbjct: 332 DKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRIS 380

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A* Length = 523

 Score = 56.4 bits (137), Expect = 3e-10
 Identities = 32/109 (29%), Positives = 52/109 (47%)

Query: 51  VFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI 110
           ++  S+ + ++    L   GI+    H+      R +V   F+   + I++ T   G GI
Sbjct: 241 IYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGI 300

Query: 111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           +   VR VV++D P +  SY    GRAGR G   +A+ F+   D   LR
Sbjct: 301 NKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR 349

>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 = 54.3 bits (130), Expect = 2e-09
 Identities = 32/132 (24%), Positives = 48/132 (36%), Gaps = 10/132 (7%)

Query: 20  LARMYRETEGAGSPVQAQD-------ETILLGIEPPVLVFVQSKERAQELYNELIYD-GI 71
             R+Y+E EG  +     D         +       VLV       A +L   L    GI
Sbjct: 470 PERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGI 529

Query: 72  NVDVIHSDRTQKQRDNVVRSFRT--GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAIS 129
              V H   +  +RD     F        +L+ +E+   G +F+    +V +D P +   
Sbjct: 530 RAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDL 589

Query: 130 YIHRIGRAGRGG 141
              RIGR  R G
Sbjct: 590 LEQRIGRLDRIG 601

>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 = 49.1 bits (117), Expect = 1e-07
 Identities = 23/106 (21%), Positives = 47/106 (44%), Gaps = 5/106 (4%)

Query: 46  EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
           +  +++F +  E    +          +  I    ++++R+ ++  FRTGR   ++++++
Sbjct: 349 KDKIIIFTRHNELVYRISKVF-----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQV 403

Query: 106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT 151
           L  GID     + V      SA  YI R+GR  R  +  K    + 
Sbjct: 404 LDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYE 449

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 46.4 bits (109), Expect = 8e-07
 Identities = 16/103 (15%), Positives = 37/103 (35%), Gaps = 1/103 (0%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT-ELLG 107
             V  +     + +++ +  +   V  +  +   + R+ +      G+  I++ +  +  
Sbjct: 350 AFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFS 409

Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF 150
            GI  + +  VV      S I  +  IGR  R        T +
Sbjct: 410 TGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVW 452

>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 = 41.3 bits (97), Expect = 5e-05
 Identities = 35/146 (23%), Positives = 51/146 (34%), Gaps = 39/146 (26%)

Query: 48  PVLVFVQSK----ERAQELYNELIYDGIN--------------------------VDVIH 77
            VLVF  ++    + A +L         N                              H
Sbjct: 244 GVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHH 303

Query: 78  SDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDF--RTV--RLVVNYDFPSSAIS---Y 130
           +     QR  V  +FR G I +++ T  L  G++   R V  R +  +D  S  I    Y
Sbjct: 304 AGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEY 363

Query: 131 IHRIGRAGRGG--REGKAVTFFTKQD 154
               GRAGR G    G+A+    K+D
Sbjct: 364 KQMAGRAGRPGMDERGEAIIIVGKRD 389

>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 = 41.0 bits (96), Expect = 7e-05
 Identities = 30/151 (19%), Positives = 50/151 (33%), Gaps = 43/151 (28%)

Query: 48  PVLVFVQSKERAQ-----------------------ELYNELIYDGIN----------VD 74
             L+FV  + +A+                       EL + L  +  N          V 
Sbjct: 239 GALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVA 298

Query: 75  VIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDF--RTVRLVVNYDFPSSAISYIH 132
             H+   + +R  V  +FR G I  ++ T  L  GI+     V +   + +    +  I 
Sbjct: 299 FHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIP 358

Query: 133 R------IGRAGRGG--REGKAVTFFTKQDA 155
                  +GRAGR      G+ +   T  D 
Sbjct: 359 IIEVHQMLGRAGRPKYDEVGEGIIVSTSDDP 389

>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 = 40.4 bits (94), Expect = 1e-04
 Identities = 30/128 (23%), Positives = 43/128 (33%), Gaps = 29/128 (22%)

Query: 50  LVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRG 109
           L+F  SK++  EL  +L   GIN    +                T    +++ T+ L  G
Sbjct: 400 LIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTG 452

Query: 110 --------IDFRTVRL-VVNYDF-----------PSSAISYIHRIGRAGRGGREGKAVTF 149
                   ID  T     V++             P  A+S   R GR GRG        F
Sbjct: 453 YTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRG--RRGIYRF 510

Query: 150 FTKQDAPL 157
            T  + P 
Sbjct: 511 VTPGERPS 518

>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* Length = 664

 Score = 37.6 bits (88), Expect = 9e-04
 Identities = 32/96 (33%), Positives = 43/96 (44%), Gaps = 5/96 (5%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
            LV V +   A+EL + L+  GI    +H +    +R  ++R  R G    L+   LL  
Sbjct: 442 TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLRE 501

Query: 109 GIDFRTVRLVVNYD-----FPSSAISYIHRIGRAGR 139
           G+D   V LV   D     F  S  S I  IGRA R
Sbjct: 502 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 537

>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 = 37.5 bits (87), Expect = 9e-04
 Identities = 21/125 (16%), Positives = 43/125 (34%), Gaps = 23/125 (18%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
              F+ S   A  +   L   G +V V++  +T ++      + +  +   ++ T++   
Sbjct: 180 TAWFLPSIRAANVMAASLRKAGKSVVVLNR-KTFER---EYPTIKQKKPDFILATDIAEM 235

Query: 109 G--IDFRTV----------------RLVVNYDFPSSAISYIHRIGRAGR-GGREGKAVTF 149
           G  +    V                ++ +      SA S   R GR GR   R+G +  +
Sbjct: 236 GANLCVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYY 295

Query: 150 FTKQD 154
                
Sbjct: 296 SEPTS 300

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	159
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	100.0
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	100.0
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	100.0
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	100.0
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.98
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.97
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.97
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.97
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.94
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.95
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.95
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.95
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.95
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.95
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.94
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.94
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.94
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.94
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.94
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.93
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.93
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.93
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.92
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.92
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.92
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.91
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.91
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.9
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.9
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.88
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.88
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.88
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.88
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.88
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.88
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.88
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.88
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.87
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.87
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.87
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.87
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.87
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.87
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.86
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.86
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.86
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.86
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.86
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.85
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.85
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.85
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.85
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.85
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.84
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.84
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.84
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.83
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.83
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.83
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.82
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.82
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.81
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.81
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.81
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.8
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.79
3h1t_A	590	Type I site-specific restriction-modification syst	99.78
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.77
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.75
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.47
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.82
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.79
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.66
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.34
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	97.87
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	96.85
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	96.69
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	96.18
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	95.64
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	95.18
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	94.58
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	93.77
2l82_A	162	Designed protein OR32; structural genomics, northe	93.7
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	93.54
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	93.21
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	92.29
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	92.26
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	91.5
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	91.38
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	90.77
3bor_A	237	Human initiation factor 4A-II; translation initiat	90.75
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	90.46
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	90.44
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	90.13
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	90.04
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	90.0
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	89.71
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	89.54
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	89.39
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	89.22
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	89.11
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	89.02
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	88.96
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	88.96
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	88.76
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	88.57
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	88.49
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	88.28
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	88.21
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	87.92
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	87.82
2jtq_A	85	Phage shock protein E; solution structure rhodanes	87.15
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	87.14
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	86.99
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	86.36
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	86.31
2k0z_A	110	Uncharacterized protein HP1203; A/B domain, struct	86.01
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	85.49
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	85.45
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	85.09
3nhv_A	144	BH2092 protein; alpha-beta protein, structural gen	84.8
1tq1_A	129	AT5G66040, senescence-associated family protein; C	83.55
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	83.32
2fsx_A	148	RV0390, COG0607: rhodanese-related sulfurtransfera	83.31
1gmx_A	108	GLPE protein; transferase, rhodanese, sulfurtransf	83.26
1qxn_A	137	SUD, sulfide dehydrogenase; polysulfide-sulfur tra	82.36
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	82.33
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	81.95
2hhg_A	139	Hypothetical protein RPA3614; MCSG, structural gen	80.97
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	80.46
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	80.17

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=100.00  E-value=6.1e-33  Score=187.60  Aligned_cols=142  Identities=30%  Similarity=0.526  Sum_probs=132.4

Q ss_pred             hhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc
Q psy576           15 RVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      ..++++.+.+..+.. +.|...|.+++.....+++||||++.+.++.+++.|.+.++++..+||++++.+|..+++.|++
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            446778999998887 7899999999987777899999999999999999999999999999999999999999999999


Q ss_pred             CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           95 GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        95 ~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      |+..|||||+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.++.++...|...
T Consensus        84 g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~  146 (163)
T 2hjv_A           84 GEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRF  146 (163)
T ss_dssp             TSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHH
T ss_pred             CCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999998776543

>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=100.00  E-value=9.5e-33  Score=188.61  Aligned_cols=141  Identities=33%  Similarity=0.517  Sum_probs=128.6

Q ss_pred             hhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC
Q psy576           16 VKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        16 ~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~   95 (159)
                      ..+++.++|..++....|...|.+++.....+++||||++.+.++.++..|.+.+..+..+||++++.+|..+++.|++|
T Consensus         4 ~~~~i~q~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g   83 (175)
T 2rb4_A            4 TLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDG   83 (175)
T ss_dssp             CBCCEEEEEEECSSHHHHHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTT
T ss_pred             ccCCceEEEEEcCChHhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence            45789999999988666999999999887778999999999999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeCCcccccccCCCcEEEEecCC------CCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           96 RIWILITTELLGRGIDFRTVRLVVNYDFP------SSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        96 ~~~vlv~t~~~~~g~~i~~~~~vi~~~~~------~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      +..|||||+++++|+|+|++++||+++.|      .+..+|.||+||+||.|+.|.+++++.+.+.+
T Consensus        84 ~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~  150 (175)
T 2rb4_A           84 KEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELP  150 (175)
T ss_dssp             SCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHH
T ss_pred             CCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHH
Confidence            99999999999999999999999999999      89999999999999999999999999887644

>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=100.00  E-value=7.2e-32  Score=183.84  Aligned_cols=136  Identities=29%  Similarity=0.454  Sum_probs=128.2

Q ss_pred             hhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           17 KSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        17 ~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      ++++.++|..+.. +.|...|.+++.....+++||||++.+.++.++..|...++++..+||++++.+|..+++.|++|+
T Consensus         3 ~~~i~q~~~~~~~-~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~   81 (172)
T 1t5i_A            3 LHGLQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQ   81 (172)
T ss_dssp             --CCEEEEEECCG-GGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             cCCeEEEEEECCh-HHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCC
Confidence            4678899998887 789999999999877889999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      ..|||||+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++++.+.
T Consensus        82 ~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~  138 (172)
T 1t5i_A           82 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE  138 (172)
T ss_dssp             CSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSH
T ss_pred             CcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcCh
Confidence            999999999999999999999999999999999999999999999999999999764

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=100.00  E-value=1.5e-32  Score=186.01  Aligned_cols=139  Identities=36%  Similarity=0.610  Sum_probs=125.2

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      +++.++|..++..+.|.+.|.+++.....+++||||++.+.++.++..|.+.+..+..+||+++..+|..+++.|++|+.
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            46888999998855599999999998778899999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      .|||||+++++|+|+|++++||++++|++...|.||+||+||.|+.|.+++++.+.+..
T Consensus        82 ~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~  140 (165)
T 1fuk_A           82 RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVG  140 (165)
T ss_dssp             SEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHH
T ss_pred             EEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHH
Confidence            99999999999999999999999999999999999999999999999999999988754

>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=99.98  E-value=7e-32  Score=185.90  Aligned_cols=143  Identities=31%  Similarity=0.531  Sum_probs=118.4

Q ss_pred             HhhhhccceeeeecCCCCChHHHHHHHHhcC-CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHH
Q psy576           14 RRVKSNLARMYRETEGAGSPVQAQDETILLG-IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        14 ~~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~-~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ....++|.+.+..+.. ..|...|.+++... ...++||||++.+.++.++..|...++.+..+||+++..+|..+++.|
T Consensus        14 ~~~~~~i~q~~~~v~~-~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f   92 (185)
T 2jgn_A           14 GSTSENITQKVVWVEE-SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQF   92 (185)
T ss_dssp             --CCTTEEEEEEECCG-GGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHH
T ss_pred             CCCCCCceEEEEEeCc-HHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHH
Confidence            3456789999998887 68999999999875 567899999999999999999999999999999999999999999999


Q ss_pred             hcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           93 RTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        93 ~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      ++|+..|||||+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++++.+.+...
T Consensus        93 ~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~  157 (185)
T 2jgn_A           93 RSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINI  157 (185)
T ss_dssp             HHTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGG
T ss_pred             HcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999877654

>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=99.97  E-value=4.7e-31  Score=185.37  Aligned_cols=134  Identities=28%  Similarity=0.534  Sum_probs=122.8

Q ss_pred             ceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEE
Q psy576           21 ARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL  100 (159)
Q Consensus        21 ~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vl  100 (159)
                      .+.+..+.. ..|.+.|.+++.....+++||||++++.++.+++.|.+.++.+..+||++++.+|..+++.|++|+.+||
T Consensus         7 ~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vl   85 (212)
T 3eaq_A            7 EEEAVPAPV-RGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVL   85 (212)
T ss_dssp             CCEEEECCT-TSHHHHHHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEE
T ss_pred             eeeEEeCCH-HHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEE
Confidence            344444444 7999999999987778899999999999999999999989999999999999999999999999999999


Q ss_pred             EEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          101 ITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       101 v~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |||+++++|+|+|++++||+++.|++...|.||+||+||.|+.|.|+.++...+.
T Consensus        86 vaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~  140 (212)
T 3eaq_A           86 VATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRER  140 (212)
T ss_dssp             EECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGH
T ss_pred             EecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHH
Confidence            9999999999999999999999999999999999999999999999999988763

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.97  E-value=9.7e-31  Score=181.00  Aligned_cols=137  Identities=28%  Similarity=0.556  Sum_probs=124.0

Q ss_pred             hhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc
Q psy576           15 RVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      ...+++.+.+..+.. ..|...|.+++.. ..+++||||++++.++.+++.|...++++..+||++++.+|..+++.|++
T Consensus        25 ~~~~~i~q~~~~~~~-~~K~~~L~~~l~~-~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~  102 (191)
T 2p6n_A           25 AASLDVIQEVEYVKE-EAKMVYLLECLQK-TPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFRE  102 (191)
T ss_dssp             ---CCSEEEEEECCG-GGHHHHHHHHHTT-SCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCCcCceEEEEEcCh-HHHHHHHHHHHHh-CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhc
Confidence            456789999988877 6899999999986 35689999999999999999999889999999999999999999999999


Q ss_pred             CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576           95 GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus        95 ~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      |+..|||||+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++|+.+.
T Consensus       103 g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~  161 (191)
T 2p6n_A          103 GKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKA  161 (191)
T ss_dssp             TSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTT
T ss_pred             CCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCc
Confidence            99999999999999999999999999999999999999999999999999999999876

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.97  E-value=2.8e-30  Score=189.59  Aligned_cols=135  Identities=27%  Similarity=0.530  Sum_probs=122.9

Q ss_pred             cceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeE
Q psy576           20 LARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI   99 (159)
Q Consensus        20 i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v   99 (159)
                      +.+++..+.. ..|++.|.+++.....+++||||++++.++.+++.|.+.++.+..+||++++.+|..+++.|++|+.+|
T Consensus         3 v~~~~i~~~~-~~K~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~v   81 (300)
T 3i32_A            3 YEEEAVPAPV-RGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRV   81 (300)
T ss_dssp             SEEEEEECCS-SSHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCE
T ss_pred             eEEEEEECCH-HHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceE
Confidence            5677777777 789999999998767889999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       100 lv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      ||||+++++|+|+|++++||+++.|++...|.||+||+||.|+.|.|+.++...+.
T Consensus        82 LVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~  137 (300)
T 3i32_A           82 LVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRER  137 (300)
T ss_dssp             EEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTH
T ss_pred             EEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHH
Confidence            99999999999999999999999999999999999999999999999999998774

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=99.94  E-value=1.1e-32  Score=187.52  Aligned_cols=142  Identities=30%  Similarity=0.521  Sum_probs=131.7

Q ss_pred             hhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           17 KSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        17 ~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      ++++.+.+..+.....|...|.+++.....+++||||++.+.++.+++.|...++.+..+||++++.+|..+++.|++|+
T Consensus         1 R~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~   80 (170)
T 2yjt_D            1 RKKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGR   80 (170)
Confidence            35678888888876789999999998767789999999999999999999988999999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcccc
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL  158 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~  158 (159)
                      ..|||||+++++|+|+|++++||++++|++...|.||+||+||.|+.|.+++++...|...+
T Consensus        81 ~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~  142 (170)
T 2yjt_D           81 VNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLL  142 (170)
Confidence            99999999999999999999999999999999999999999999999999999988876543

>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=99.95  E-value=1.8e-27  Score=182.84  Aligned_cols=135  Identities=33%  Similarity=0.548  Sum_probs=122.4

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      .++.+.+..+.. ..|...|.+++.... .++||||++++.++.+++.|.+.++++..+||+++..+|..+++.|++|+.
T Consensus       274 ~~i~~~~~~~~~-~~k~~~l~~~l~~~~-~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~  351 (434)
T 2db3_A          274 SDVKQTIYEVNK-YAKRSKLIEILSEQA-DGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSM  351 (434)
T ss_dssp             TTEEEEEEECCG-GGHHHHHHHHHHHCC-TTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSC
T ss_pred             cccceEEEEeCc-HHHHHHHHHHHHhCC-CCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCC
Confidence            345566666655 578888888887644 459999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      .|||||+++++|+|+|++++||+++.|.+..+|.||+||+||.|+.|.++.|+++.+
T Consensus       352 ~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~  408 (434)
T 2db3_A          352 KVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEK  408 (434)
T ss_dssp             SEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTT
T ss_pred             cEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccc
Confidence            999999999999999999999999999999999999999999999999999998543

>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=99.95  E-value=6.2e-28  Score=183.54  Aligned_cols=140  Identities=29%  Similarity=0.522  Sum_probs=129.5

Q ss_pred             hhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           17 KSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        17 ~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      .+.+.+.+..+.....|...+.+++.....+++||||++.+.++.+++.|.+.+..+..+||+++..+|.++++.|++|+
T Consensus       247 ~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  326 (410)
T 2j0s_A          247 LEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGA  326 (410)
T ss_dssp             CTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTS
T ss_pred             CCCceEEEEEeCcHHhHHHHHHHHHHhcCCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCC
Confidence            34667777777776668999999988767789999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      .+|||||+++++|+|+|++++||++++|++...|.||+||+||.|+.|.+++++.+.|..
T Consensus       327 ~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~  386 (410)
T 2j0s_A          327 SRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIR  386 (410)
T ss_dssp             SCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHH
T ss_pred             CCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHHH
Confidence            999999999999999999999999999999999999999999999999999999987754

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.95  E-value=2.1e-27  Score=180.70  Aligned_cols=139  Identities=32%  Similarity=0.549  Sum_probs=124.0

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcC-CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLG-IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~-~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      +.+.+.+..+.. ..|...+.+++... ..+++||||++++.++.+++.|.+.+..+..+||+++.++|.++++.|++|+
T Consensus       248 ~~i~~~~~~~~~-~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  326 (417)
T 2i4i_A          248 ENITQKVVWVEE-SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGK  326 (417)
T ss_dssp             SSEEEEEEECCG-GGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTS
T ss_pred             cCceEEEEEecc-HhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCC
Confidence            345555555555 67888888888865 4668999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      .+|||||+++++|+|+|++++||++++|.+...|.||+||+||.|+.|.+++++.+.|.+.
T Consensus       327 ~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~  387 (417)
T 2i4i_A          327 SPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINI  387 (417)
T ss_dssp             SCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGG
T ss_pred             CCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHH
Confidence            9999999999999999999999999999999999999999999999999999999887654

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.95  E-value=1.4e-27  Score=181.43  Aligned_cols=139  Identities=34%  Similarity=0.587  Sum_probs=115.4

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ..+.+.+........+...+.+++.....+++||||++++.++.+++.|.+.+..+..+||+++..+|.++++.|++|+.
T Consensus       252 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~  331 (414)
T 3eiq_A          252 EGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSS  331 (414)
T ss_dssp             TSCCEEEEECSSSTTHHHHHHHHHHSSCCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC--
T ss_pred             CCceEEEEEeChHHhHHHHHHHHHHhCCCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCC
Confidence            45667777777777899999999998888899999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      +|||||+++++|+|+|++++||+++.|.+...|.||+||+||.|+.|.|++++.+.|..
T Consensus       332 ~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~  390 (414)
T 3eiq_A          332 RVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKR  390 (414)
T ss_dssp             -CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHHH
T ss_pred             cEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHH
Confidence            99999999999999999999999999999999999999999999999999999987654

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.95  E-value=5.1e-27  Score=177.87  Aligned_cols=137  Identities=29%  Similarity=0.508  Sum_probs=124.9

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .+.+++..... ..|...+..++.....+++||||++.+.++.+++.|.+.+..+..+||+++..+|..+++.|++|+..
T Consensus       232 ~~~~~~~~~~~-~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~  310 (400)
T 1s2m_A          232 GITQYYAFVEE-RQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVR  310 (400)
T ss_dssp             TEEEEEEECCG-GGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSS
T ss_pred             CceeEEEEech-hhHHHHHHHHHhhcCCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCc
Confidence            44455555544 67888888888877778999999999999999999998899999999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      |||||+++++|+|+|++++||++++|++...|.||+||+||.|+.|.|+++++..|..
T Consensus       311 vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~  368 (400)
T 1s2m_A          311 TLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRF  368 (400)
T ss_dssp             EEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHH
T ss_pred             EEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHH
Confidence            9999999999999999999999999999999999999999999999999999887653

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.94  E-value=2e-26  Score=173.91  Aligned_cols=135  Identities=29%  Similarity=0.468  Sum_probs=123.2

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .+.+.+..... ..|...+.+++.....+++||||++.+.++.+++.|.+.+..+..+||+++..+|.++++.|++|+..
T Consensus       224 ~~~~~~~~~~~-~~~~~~l~~~l~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  302 (391)
T 1xti_A          224 GLQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR  302 (391)
T ss_dssp             TCEEEEEECCG-GGHHHHHHHHHHHSCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCS
T ss_pred             cceEEEEEcCc-hhHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCc
Confidence            34445555444 67888888888877788999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |||||+++++|+|+|++++||+++.|++...|.||+||+||.|+.|.+++++.+.+
T Consensus       303 vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  358 (391)
T 1xti_A          303 ILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  358 (391)
T ss_dssp             EEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHH
T ss_pred             EEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccc
Confidence            99999999999999999999999999999999999999999999999999998653

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.94  E-value=1e-26  Score=175.35  Aligned_cols=137  Identities=37%  Similarity=0.670  Sum_probs=125.6

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ..+.+.+........+...+..++.....+++||||++++.++.+++.|++.+..+..+||+++..+|.++++.|++|+.
T Consensus       215 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~  294 (395)
T 3pey_A          215 DAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRS  294 (395)
T ss_dssp             TTEEEEEEECSSHHHHHHHHHHHHTTTTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             ccccEEEEEcCchHHHHHHHHHHHHhccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCC
Confidence            45556666666666788888888887778899999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCC------CHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPS------SAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~------~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      +|||||+++++|+|+|++++||+++.|+      +..+|.||+||+||.|+.|.+++++.+.+
T Consensus       295 ~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  357 (395)
T 3pey_A          295 KVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN  357 (395)
T ss_dssp             CEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             CEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechH
Confidence            9999999999999999999999999998      99999999999999999999999998643

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.94  E-value=1e-26  Score=182.32  Aligned_cols=125  Identities=25%  Similarity=0.431  Sum_probs=118.0

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccccc
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI  110 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~  110 (159)
                      ..+...+.+++....++++||||++++.++.+++.|.+.++.+..+||++++++|..+++.|.+|+..|||||+++++|+
T Consensus       221 ~~~~~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~Gi  300 (523)
T 1oyw_A          221 FKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGI  300 (523)
T ss_dssp             SSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTT
T ss_pred             CCHHHHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCC
Confidence            56778888888876778999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       111 ~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |+|++++||+++.|.+...|.|++||+||.|.+|.+++++.+.|.
T Consensus       301 D~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~  345 (523)
T 1oyw_A          301 NKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADM  345 (523)
T ss_dssp             CCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHH
T ss_pred             CccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHH
Confidence            999999999999999999999999999999999999999977654

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.94  E-value=1.1e-26  Score=176.22  Aligned_cols=138  Identities=29%  Similarity=0.476  Sum_probs=125.3

Q ss_pred             hhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           17 KSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        17 ~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      ...+.+.+........+...+.+++.....+++||||++.+.++.+++.|.+.+..+..+||+++..+|..+++.|++|+
T Consensus       237 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~  316 (412)
T 3fht_A          237 LDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGK  316 (412)
T ss_dssp             CTTEEEEEEECSSHHHHHHHHHHHHHHHSSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             ccCceEEEEEcCChHHHHHHHHHHHhhcCCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCC
Confidence            34556666666666778888888888777789999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCC------CCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFP------SSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~------~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      .+|||||+++++|+|+|++++||+++.|      .+..+|.||+||+||.|+.|.++++++..+
T Consensus       317 ~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  380 (412)
T 3fht_A          317 EKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  380 (412)
T ss_dssp             CSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             CcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChh
Confidence            9999999999999999999999999999      467999999999999999999999997653

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.94  E-value=4.3e-26  Score=170.44  Aligned_cols=136  Identities=35%  Similarity=0.590  Sum_probs=123.6

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .+.+.+..... ..+...+.+++.. ...++||||++.+.++.+++.|.+.+..+..+||+++..+|.++++.|++|+..
T Consensus       213 ~~~~~~~~~~~-~~~~~~l~~~l~~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  290 (367)
T 1hv8_A          213 NIEQSYVEVNE-NERFEALCRLLKN-KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIR  290 (367)
T ss_dssp             SSEEEEEECCG-GGHHHHHHHHHCS-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSS
T ss_pred             CceEEEEEeCh-HHHHHHHHHHHhc-CCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCe
Confidence            44555555554 6788888888874 677899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      |||||+++++|+|+|++++||+++.|++..+|.||+||+||.|+.|.++.++++.|..
T Consensus       291 vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~  348 (367)
T 1hv8_A          291 ILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYK  348 (367)
T ss_dssp             EEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHH
T ss_pred             EEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHHH
Confidence            9999999999999999999999999999999999999999999999999999988754

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.93  E-value=4.7e-26  Score=180.68  Aligned_cols=123  Identities=20%  Similarity=0.321  Sum_probs=112.9

Q ss_pred             hHHHHHHHHhc-CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccc
Q psy576           33 PVQAQDETILL-GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGID  111 (159)
Q Consensus        33 k~~~l~~~~~~-~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~  111 (159)
                      +...+.+++.. ..++++||||++++.++.+++.|.+.++.+..+||+|++.+|..+++.|.+|+..|||||+++++|+|
T Consensus       253 ~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID  332 (591)
T 2v1x_A          253 FIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGID  332 (591)
T ss_dssp             HHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCC
T ss_pred             HHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCC
Confidence            34556666653 35678999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          112 FRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       112 i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      +|++++||++++|.+...|.|++||+||.|.+|.|++++...|.
T Consensus       333 ~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~  376 (591)
T 2v1x_A          333 KPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDI  376 (591)
T ss_dssp             CSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHH
T ss_pred             cccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHH
Confidence            99999999999999999999999999999999999999987654

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.93  E-value=1.5e-25  Score=176.76  Aligned_cols=114  Identities=31%  Similarity=0.532  Sum_probs=107.6

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhC---CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYD---GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN  120 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~  120 (159)
                      ....++||||++++.++.++..|.+.   +..+..+||++++.+|..+++.|++|+..|||||+++++|+|+|++++||+
T Consensus       337 ~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~VI~  416 (563)
T 3i5x_A          337 DSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQ  416 (563)
T ss_dssp             TTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEE
T ss_pred             CCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCCcccCCEEEE
Confidence            45678999999999999999999876   888999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576          121 YDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus       121 ~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      +++|.+...|.||+||+||.|..|.+++++.+.|...
T Consensus       417 ~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~  453 (563)
T 3i5x_A          417 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPF  453 (563)
T ss_dssp             ESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHH
T ss_pred             ECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHH
Confidence            9999999999999999999999999999999877543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.93  E-value=2.6e-25  Score=176.26  Aligned_cols=113  Identities=31%  Similarity=0.531  Sum_probs=107.3

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhC---CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYD---GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN  120 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~  120 (159)
                      ....++||||++.+.++.+++.|.+.   +..+..+||+++..+|..+++.|++|+..|||||+++++|+|+|++++||+
T Consensus       286 ~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~VI~  365 (579)
T 3sqw_A          286 DSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQ  365 (579)
T ss_dssp             TTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEE
T ss_pred             CCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCCcccCCEEEE
Confidence            45678999999999999999999876   888999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576          121 YDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus       121 ~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      +++|.+...|.||+||+||.|+.|.|++++.+.|..
T Consensus       366 ~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~  401 (579)
T 3sqw_A          366 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDELP  401 (579)
T ss_dssp             ESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHH
T ss_pred             cCCCCCHHHhhhhccccccCCCCceEEEEEcccHHH
Confidence            999999999999999999999999999999987754

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.92  E-value=3.5e-27  Score=178.10  Aligned_cols=141  Identities=35%  Similarity=0.605  Sum_probs=0.0

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      +.+.+.+..+.....+...+.+++.....+++||||++++.++.+++.|++.+..+..+||+++..+|.++++.|++|+.
T Consensus       231 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~  310 (394)
T 1fuu_A          231 EGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSS  310 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCceEEEEEcCchhhHHHHHHHHHhcCCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCC
Confidence            34455555555555577778888877677899999999999999999999888999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcccc
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLL  158 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~~  158 (159)
                      .|||||+++++|+|+|++++||++++|.+...|.||+||+||.|+.|.|++++.+.|...+
T Consensus       311 ~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~  371 (394)
T 1fuu_A          311 RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAM  371 (394)
T ss_dssp             -------------------------------------------------------------
T ss_pred             cEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHH
Confidence            9999999999999999999999999999999999999999999999999999998876543

>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=99.92  E-value=7.7e-27  Score=181.10  Aligned_cols=138  Identities=29%  Similarity=0.473  Sum_probs=0.0

Q ss_pred             hhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           17 KSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        17 ~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      ...+.+.+..+.....+...+..++.....+++||||++.+.++.++..|...+..+..+||+++..+|..+++.|++|+
T Consensus       304 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~  383 (479)
T 3fmp_B          304 LDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGK  383 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCCceEEEEEeCCHHHHHHHHHHHHhhccCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCC
Confidence            34555666666666778888888887767789999999999999999999988999999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCC------CHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPS------SAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~------~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      .+|||||+++++|+|+|++++||++++|.      +...|.||+||+||.|..|.+++++++.+
T Consensus       384 ~~iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~  447 (479)
T 3fmp_B          384 EKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  447 (479)
T ss_dssp             ----------------------------------------------------------------
T ss_pred             CcEEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcc
Confidence            99999999999999999999999999994      56899999999999999999999998665

>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=99.92  E-value=1.9e-24  Score=166.21  Aligned_cols=126  Identities=28%  Similarity=0.421  Sum_probs=114.7

Q ss_pred             CCCChHHHHHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEec--------CCCHHHHHHHHHHHhcCC
Q psy576           29 GAGSPVQAQDETILL----GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHS--------DRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        29 ~~~~k~~~l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~~~   96 (159)
                      ....|...+.+++..    ..++++||||++++.++.+++.|...++++..+||        +++..+|.++++.|++|+
T Consensus       340 ~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~  419 (494)
T 1wp9_A          340 LDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE  419 (494)
T ss_dssp             CSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTS
T ss_pred             CCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCC
Confidence            446788888888875    57889999999999999999999999999999999        999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      ..|||||+++++|+|+|++++||++++|+++..|.||+||+||.|+ |.++.++..++.
T Consensus       420 ~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~  477 (494)
T 1wp9_A          420 FNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTR  477 (494)
T ss_dssp             CSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSH
T ss_pred             ceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCH
Confidence            9999999999999999999999999999999999999999999998 999999987753

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.91  E-value=9.6e-24  Score=156.18  Aligned_cols=128  Identities=32%  Similarity=0.552  Sum_probs=110.4

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      .+.+.+...... .  ....+.+.....+++||||++.+.++.+++.|.    ++..+||+++..+|.++++.|++|+.+
T Consensus       196 ~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~  268 (337)
T 2z0m_A          196 NVEHKFVHVKDD-W--RSKVQALRENKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYD  268 (337)
T ss_dssp             GEEEEEEECSSS-S--HHHHHHHHTCCCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             CceEEEEEeChH-H--HHHHHHHHhCCCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCc
Confidence            444445444442 2  223355666677899999999999999999886    478999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |||||+++++|+|+|++++||++++|++...|.||+||+||.|+.|.+++|+. .|
T Consensus       269 vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~  323 (337)
T 2z0m_A          269 MLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL-NE  323 (337)
T ss_dssp             EEEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES-SC
T ss_pred             EEEEcCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe-Cc
Confidence            99999999999999999999999999999999999999999999999999998 44

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.90  E-value=9.8e-24  Score=153.00  Aligned_cols=124  Identities=15%  Similarity=0.208  Sum_probs=97.2

Q ss_pred             CCCChHHHHHHHHhcC--CCCCEEEEecchHHHHHHHHHHHhC-CCceEEEecCCCHHHHHHHHHHHhcC-Cee-EEEEe
Q psy576           29 GAGSPVQAQDETILLG--IEPPVLVFVQSKERAQELYNELIYD-GINVDVIHSDRTQKQRDNVVRSFRTG-RIW-ILITT  103 (159)
Q Consensus        29 ~~~~k~~~l~~~~~~~--~~~~~lif~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~-vlv~t  103 (159)
                      ....|+..|.+++...  .+.++||||.+...++.+...|.+. ++++..+||+++..+|.++++.|+++ +.. +|++|
T Consensus        93 ~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st  172 (271)
T 1z5z_A           93 RRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSV  172 (271)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEEC
T ss_pred             ccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEeh
Confidence            3467999988888754  6789999999999999999999875 88999999999999999999999998 666 78899


Q ss_pred             CCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceE--EEEecC
Q psy576          104 ELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKA--VTFFTK  152 (159)
Q Consensus       104 ~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~--~~~~~~  152 (159)
                      +++++|+|++.+++||++++||++..|.|++||++|.|+.+.+  +.++..
T Consensus       173 ~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~  223 (271)
T 1z5z_A          173 KAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISV  223 (271)
T ss_dssp             CTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEET
T ss_pred             hhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeC
Confidence            9999999999999999999999999999999999999987765  444443

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.90  E-value=6.6e-24  Score=166.60  Aligned_cols=123  Identities=20%  Similarity=0.287  Sum_probs=68.6

Q ss_pred             CCChHHHHHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC------------CCceEEEecCCCHHHHHHHHHHHh
Q psy576           30 AGSPVQAQDETILL----GIEPPVLVFVQSKERAQELYNELIYD------------GINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        30 ~~~k~~~l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~------------~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      ...|...|.+++..    ..+.++||||++++.++.+++.|.+.            |.....+||+++..+|.++++.|+
T Consensus       370 ~~~K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~  449 (556)
T 4a2p_A          370 ENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK  449 (556)
T ss_dssp             CCHHHHHHHHHHHHHHHHCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC--------------------------
T ss_pred             CChHHHHHHHHHHHHhcCCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhc
Confidence            36788888888863    56789999999999999999999765            444556678899999999999999


Q ss_pred             c-CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           94 T-GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        94 ~-~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      + |+.+|||||+++++|+|+|++++||+|++|+++..|.||+|| ||. ..|.++.++...+
T Consensus       450 ~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~  509 (556)
T 4a2p_A          450 TSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTE  509 (556)
T ss_dssp             ----CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHH
T ss_pred             ccCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcc
Confidence            9 999999999999999999999999999999999999999999 999 7899999987654

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.88  E-value=2.1e-22  Score=153.54  Aligned_cols=112  Identities=28%  Similarity=0.433  Sum_probs=101.3

Q ss_pred             ChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceE-EEecCCCHHHHHHHHHHHhcCCeeEEEE----eCCc
Q psy576           32 SPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVD-VIHSDRTQKQRDNVVRSFRTGRIWILIT----TELL  106 (159)
Q Consensus        32 ~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~-~~~~~~~~~~r~~~~~~f~~~~~~vlv~----t~~~  106 (159)
                      .+...+.+++.. .++++||||++++.++.++..|...++++. .+||.    +|.  ++.|++|+.+||||    |+++
T Consensus       239 ~~~~~l~~~l~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s~T~~~  311 (414)
T 3oiy_A          239 RSKEKLVELLEI-FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQAYYGKL  311 (414)
T ss_dssp             CCHHHHHHHHHH-HCSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECCTTCCC
T ss_pred             CHHHHHHHHHHH-cCCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecCcCchh
Confidence            467777777776 458999999999999999999999999998 88984    333  99999999999999    9999


Q ss_pred             ccccccCC-CcEEEEecCC--CCHHHHHHHHhhccCCC----CcceEEEEe
Q psy576          107 GRGIDFRT-VRLVVNYDFP--SSAISYIHRIGRAGRGG----REGKAVTFF  150 (159)
Q Consensus       107 ~~g~~i~~-~~~vi~~~~~--~~~~~~~q~~GR~~R~g----~~g~~~~~~  150 (159)
                      ++|+|+|+ +++||+++.|  .+..+|.||+||+||.|    ..|.+++++
T Consensus       312 ~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~  362 (414)
T 3oiy_A          312 TRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE  362 (414)
T ss_dssp             CCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC
T ss_pred             hccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE
Confidence            99999999 9999999999  99999999999999988    479999988

>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=99.88  E-value=1.9e-22  Score=162.58  Aligned_cols=121  Identities=21%  Similarity=0.378  Sum_probs=96.7

Q ss_pred             CChHHHHHHHHh----cCC-CCCEEEEecchHHHHHHHHHHHhC------CCceEEEecC--------CCHHHHHHHHHH
Q psy576           31 GSPVQAQDETIL----LGI-EPPVLVFVQSKERAQELYNELIYD------GINVDVIHSD--------RTQKQRDNVVRS   91 (159)
Q Consensus        31 ~~k~~~l~~~~~----~~~-~~~~lif~~~~~~~~~l~~~l~~~------~~~~~~~~~~--------~~~~~r~~~~~~   91 (159)
                      ..|...|.+++.    ... .+++||||++++.++.++++|...      ++++..+||+        |+..+|.++++.
T Consensus       380 ~~k~~~L~~~L~~~~~~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~  459 (699)
T 4gl2_A          380 NEKLTKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISK  459 (699)
T ss_dssp             --CSSCSHHHHHHHHHHSSSCCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhcCCCCCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHH
Confidence            345555555544    223 789999999999999999999876      7899999999        999999999999


Q ss_pred             HhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576           92 FRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus        92 f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      |++|+.+|||||+++++|+|+|++++||+|++|+++..|.||+||+||.|  +.++++....
T Consensus       460 F~~g~~~VLVaT~~~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRArr~g--~~~~l~~~~~  519 (699)
T 4gl2_A          460 FRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADE--STYVLVAHSG  519 (699)
T ss_dssp             HCC---CCSEEECSCCTTSCCCSCCCCEEESCCCCHHHHHHHHTTSCSSS--CEEEEEEESS
T ss_pred             HhcCCCcEEEEccccccCCccccCCEEEEeCCCCCHHHHHHHcCCCCCCC--ceEEEEEeCC
Confidence            99999999999999999999999999999999999999999999976654  4444444433

>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=99.88  E-value=3.5e-23  Score=159.32  Aligned_cols=107  Identities=22%  Similarity=0.293  Sum_probs=89.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----  120 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----  120 (159)
                      .+++++|||++++.++.+++.|++.+.++..+||    ++|.++++.|++|+.+|||||+++++|+|+| +++||+    
T Consensus       176 ~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~  250 (440)
T 1yks_A          176 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTA  250 (440)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCcc
Confidence            3678999999999999999999999999999999    3678899999999999999999999999999 999886    


Q ss_pred             ---------------ecCCCCHHHHHHHHhhccCC-CCcceEEEEe---cCCCcc
Q psy576          121 ---------------YDFPSSAISYIHRIGRAGRG-GREGKAVTFF---TKQDAP  156 (159)
Q Consensus       121 ---------------~~~~~~~~~~~q~~GR~~R~-g~~g~~~~~~---~~~~~~  156 (159)
                                     ++.|.+..+|.||+||+||. |.+|.|++++   .+.|..
T Consensus       251 ~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~  305 (440)
T 1yks_A          251 FKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAH  305 (440)
T ss_dssp             EEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTT
T ss_pred             ceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhh
Confidence                           88899999999999999998 5789999997   444443

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.88  E-value=1.5e-23  Score=164.39  Aligned_cols=123  Identities=23%  Similarity=0.341  Sum_probs=88.5

Q ss_pred             CCChHHHHHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhCC----C--------ceEEEecCCCHHHHHHHHHHHh
Q psy576           30 AGSPVQAQDETILL----GIEPPVLVFVQSKERAQELYNELIYDG----I--------NVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        30 ~~~k~~~l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~~----~--------~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      ...|...|.+++..    ...+++||||++++.++.++..|...+    +        ....+||+|+..+|.++++.|+
T Consensus       369 ~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~  448 (555)
T 3tbk_A          369 ENPKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFR  448 (555)
T ss_dssp             CCHHHHHHHHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-----------------------
T ss_pred             CCHHHHHHHHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHh
Confidence            46788888877764    466899999999999999999998763    2        3445566999999999999999


Q ss_pred             c-CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           94 T-GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        94 ~-~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      + |+.+|||||+++++|+|+|++++||+|++|+++..|.||+|| ||. ..|.++.++.+.+
T Consensus       449 ~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~  508 (555)
T 3tbk_A          449 ASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSAD  508 (555)
T ss_dssp             ---CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHH
T ss_pred             cCCCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCC
Confidence            9 999999999999999999999999999999999999999999 898 8899999987654

>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=99.88  E-value=2.3e-22  Score=167.03  Aligned_cols=121  Identities=22%  Similarity=0.255  Sum_probs=112.9

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHh-CCCceEEEecCCCHHHHHHHHHHHhcCC--eeEEEEeCCcc
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIY-DGINVDVIHSDRTQKQRDNVVRSFRTGR--IWILITTELLG  107 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~-~~~~~~~~~~~~~~~~r~~~~~~f~~~~--~~vlv~t~~~~  107 (159)
                      ..|...|.+++....++++||||++++.++.++..|.. .++++..+||+|+..+|..+++.|++|+  ..|||||++++
T Consensus       488 ~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~  567 (968)
T 3dmq_A          488 DPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGS  567 (968)
T ss_dssp             SHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTT
T ss_pred             cHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhh
Confidence            56899999999887788999999999999999999985 4899999999999999999999999998  99999999999


Q ss_pred             cccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEec
Q psy576          108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       108 ~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      +|+|+|.+++||++++|+++..|.|++||+||.|+.+.++++..
T Consensus       568 ~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~  611 (968)
T 3dmq_A          568 EGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVP  611 (968)
T ss_dssp             CSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEE
T ss_pred             cCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEe
Confidence            99999999999999999999999999999999998887666643

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.88  E-value=1.7e-23  Score=168.60  Aligned_cols=124  Identities=21%  Similarity=0.343  Sum_probs=79.5

Q ss_pred             CCChHHHHHHHHhcC----CCCCEEEEecchHHHHHHHHHHHhCC----CceEEE--------ecCCCHHHHHHHHHHHh
Q psy576           30 AGSPVQAQDETILLG----IEPPVLVFVQSKERAQELYNELIYDG----INVDVI--------HSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        30 ~~~k~~~l~~~~~~~----~~~~~lif~~~~~~~~~l~~~l~~~~----~~~~~~--------~~~~~~~~r~~~~~~f~   93 (159)
                      ...|...|.+++...    .++++||||++++.++.+++.|...+    +++..+        ||+|+.++|.++++.|+
T Consensus       378 ~~~k~~~L~~ll~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~  457 (696)
T 2ykg_A          378 ENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFK  457 (696)
T ss_dssp             CCHHHHHHHHHHHHHHTTCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC--------------------------
T ss_pred             CCHHHHHHHHHHHHHhccCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHH
Confidence            467888888888653    56789999999999999999999886    788888        55999999999999999


Q ss_pred             c-CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576           94 T-GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus        94 ~-~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      + |+.+|||||+++++|+|+|++++||+|++|+++..|.||+|| ||. +.|.++.++...+.
T Consensus       458 ~~g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~  518 (696)
T 2ykg_A          458 ASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGV  518 (696)
T ss_dssp             ---CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC-----------CCCEEEEEESCHHH
T ss_pred             hcCCccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCH
Confidence            8 999999999999999999999999999999999999999999 998 78899998876543

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.88  E-value=8.3e-23  Score=167.04  Aligned_cols=123  Identities=20%  Similarity=0.287  Sum_probs=74.4

Q ss_pred             CCChHHHHHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC------------CCceEEEecCCCHHHHHHHHHHHh
Q psy576           30 AGSPVQAQDETILL----GIEPPVLVFVQSKERAQELYNELIYD------------GINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        30 ~~~k~~~l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~------------~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      ...|...|.+++..    ..+.++||||++++.++.++.+|.+.            |.....+||+|+..+|.++++.|+
T Consensus       611 ~~~K~~~L~~lL~~~~~~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~  690 (797)
T 4a2q_A          611 ENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK  690 (797)
T ss_dssp             CCHHHHHHHHHHHHHHHHCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC-------------------------
T ss_pred             CChHHHHHHHHHHHHhccCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhh
Confidence            36788888888864    56789999999999999999999763            445566788899999999999999


Q ss_pred             c-CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           94 T-GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        94 ~-~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      + |+.+|||||+++++|+|+|++++||+|++|+++..|.||+|| ||. ..|.++.++...+
T Consensus       691 ~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~  750 (797)
T 4a2q_A          691 TSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTE  750 (797)
T ss_dssp             ---CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHH
T ss_pred             ccCCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCc
Confidence            9 999999999999999999999999999999999999999999 999 7899999987654

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.88  E-value=2.6e-22  Score=162.03  Aligned_cols=123  Identities=23%  Similarity=0.280  Sum_probs=108.1

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+++..  ..+.++||||+|++.++.++..|.+.++++..+||+++..++..+.++++.|  .|+|||+++++
T Consensus       415 ~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgR  492 (844)
T 1tf5_A          415 EGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGR  492 (844)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSST
T ss_pred             HHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCcccc
Confidence            5677777777753  2467899999999999999999999999999999998877776555555555  69999999999


Q ss_pred             ccccC--------CCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          109 GIDFR--------TVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       109 g~~i~--------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |+||+        +..+||+++.|.+...|.||+||+||.|.+|.++.|++..|.
T Consensus       493 G~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          493 GTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             TCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             CcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            99999        788999999999999999999999999999999999987763

>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=99.87  E-value=1.3e-21  Score=157.10  Aligned_cols=124  Identities=29%  Similarity=0.390  Sum_probs=110.1

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      .++...+...+..  ..+.++||||+|+..++.+++.|.+.++++..+||+++..+|.++++.|++|+..|||||+++++
T Consensus       428 ~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~  507 (661)
T 2d7d_A          428 EGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE  507 (661)
T ss_dssp             TTHHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCST
T ss_pred             cchHHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhC
Confidence            3444444444432  25678999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCcEEEEecC-----CCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          109 GIDFRTVRLVVNYDF-----PSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       109 g~~i~~~~~vi~~~~-----~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |+|+|++++||+++.     |.+..+|.||+||+||. ..|.+++++++.+.
T Consensus       508 GlDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~  558 (661)
T 2d7d_A          508 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-AEGRVIMYADKITK  558 (661)
T ss_dssp             TCCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCCH
T ss_pred             CcccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCCH
Confidence            999999999999987     89999999999999998 68999999987654

>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=99.87  E-value=1.3e-21  Score=157.17  Aligned_cols=124  Identities=27%  Similarity=0.335  Sum_probs=109.8

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      .++...+...+..  ..+.++||||+|+..++.+++.|.+.++++..+||+++..+|.++++.|++|+..|||||+++++
T Consensus       422 ~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~  501 (664)
T 1c4o_A          422 ENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLRE  501 (664)
T ss_dssp             TTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCT
T ss_pred             cchHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhc
Confidence            3445555444432  24678999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCcEEEEecC-----CCCHHHHHHHHhhccCCCCcceEEEEecCCCc
Q psy576          109 GIDFRTVRLVVNYDF-----PSSAISYIHRIGRAGRGGREGKAVTFFTKQDA  155 (159)
Q Consensus       109 g~~i~~~~~vi~~~~-----~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~  155 (159)
                      |+|+|++++||+++.     |.+..+|.||+||+||.+ .|.++++++..+.
T Consensus       502 GlDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~~  552 (664)
T 1c4o_A          502 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSE  552 (664)
T ss_dssp             TCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCH
T ss_pred             CccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCCH
Confidence            999999999999987     889999999999999995 7999999887654

>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=99.87  E-value=2.4e-22  Score=155.13  Aligned_cols=104  Identities=22%  Similarity=0.263  Sum_probs=94.8

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEec--
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD--  122 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~--  122 (159)
                      ..+++||||++++.++.+++.|.+.++.+..+||++.    .++++.|++|+.+|||||+++++|+|+|+ ++||+++  
T Consensus       187 ~~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~  261 (451)
T 2jlq_A          187 YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRC  261 (451)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEE
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCc
Confidence            3568999999999999999999999999999999753    46899999999999999999999999999 9999988  


Q ss_pred             ------------------CCCCHHHHHHHHhhccCCCC-cceEEEEecCC
Q psy576          123 ------------------FPSSAISYIHRIGRAGRGGR-EGKAVTFFTKQ  153 (159)
Q Consensus       123 ------------------~~~~~~~~~q~~GR~~R~g~-~g~~~~~~~~~  153 (159)
                                        .|.+..+|.||+||+||.|. +|.+++|....
T Consensus       262 ~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~~  311 (451)
T 2jlq_A          262 LKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDP  311 (451)
T ss_dssp             EEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             ccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCCc
Confidence                              99999999999999999997 78888887544

>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=99.87  E-value=3.1e-22  Score=159.49  Aligned_cols=107  Identities=23%  Similarity=0.260  Sum_probs=96.5

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEE------
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLV------  118 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~v------  118 (159)
                      ..+++||||++++.++.+++.|.+.+.++..+||.    +|.++++.|++|+.+|||||+++++|+|+| +++|      
T Consensus       354 ~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~  428 (618)
T 2whx_A          354 YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRC  428 (618)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEE
T ss_pred             CCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcce
Confidence            36789999999999999999999999999999984    677899999999999999999999999997 8877      


Q ss_pred             --------------EEecCCCCHHHHHHHHhhccCCCC-cceEEEEec---CCCcc
Q psy576          119 --------------VNYDFPSSAISYIHRIGRAGRGGR-EGKAVTFFT---KQDAP  156 (159)
Q Consensus       119 --------------i~~~~~~~~~~~~q~~GR~~R~g~-~g~~~~~~~---~~~~~  156 (159)
                                    ++++.|.+..+|.||+||+||.|. .|.+++|+.   +.|..
T Consensus       429 ~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~  484 (618)
T 2whx_A          429 LKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDED  484 (618)
T ss_dssp             EEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTT
T ss_pred             ecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHH
Confidence                          777889999999999999999974 899999997   55543

>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=99.87  E-value=1.3e-22  Score=156.94  Aligned_cols=103  Identities=22%  Similarity=0.259  Sum_probs=93.3

Q ss_pred             CCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE-----
Q psy576           46 EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN-----  120 (159)
Q Consensus        46 ~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~-----  120 (159)
                      .+++||||++++.++.+++.|+..+.++..+||.    +|.++++.|++|+.+|||||+++++|+|+|+ ++||+     
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~  264 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSV  264 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEEC
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCccc
Confidence            6789999999999999999999999999999985    6777899999999999999999999999999 99998     


Q ss_pred             ---------------ecCCCCHHHHHHHHhhccCCCC-cceEEEEecCC
Q psy576          121 ---------------YDFPSSAISYIHRIGRAGRGGR-EGKAVTFFTKQ  153 (159)
Q Consensus       121 ---------------~~~~~~~~~~~q~~GR~~R~g~-~g~~~~~~~~~  153 (159)
                                     ++.|.+..+|.||+||+||.|. .|.+++|+...
T Consensus       265 ~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          265 KPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             CEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             ccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence                           6699999999999999999996 89999999876

>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=99.87  E-value=4.3e-22  Score=165.05  Aligned_cols=123  Identities=20%  Similarity=0.287  Sum_probs=75.1

Q ss_pred             CCChHHHHHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC------------CCceEEEecCCCHHHHHHHHHHHh
Q psy576           30 AGSPVQAQDETILL----GIEPPVLVFVQSKERAQELYNELIYD------------GINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        30 ~~~k~~~l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~------------~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      ...|...|.+++..    ..+.++||||++++.++.++++|.+.            |.....+||+|+..+|.++++.|+
T Consensus       611 ~~~K~~~L~~lL~~~~~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr  690 (936)
T 4a2w_A          611 ENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK  690 (936)
T ss_dssp             CCHHHHHHHHHHHHTTTSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC-------------------------
T ss_pred             CCHHHHHHHHHHHHHhccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhh
Confidence            46788888888864    45689999999999999999999876            444556688899999999999999


Q ss_pred             c-CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           94 T-GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        94 ~-~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      + |+.+|||||+++++|+|+|++++||+|++|+++..|.||+|| ||. ..|.++.++...+
T Consensus       691 ~~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t  750 (936)
T 4a2w_A          691 TSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTE  750 (936)
T ss_dssp             ---CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHH
T ss_pred             ccCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCC
Confidence            9 999999999999999999999999999999999999999999 998 6788998887643

>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=99.86  E-value=2.9e-21  Score=153.75  Aligned_cols=122  Identities=26%  Similarity=0.327  Sum_probs=106.0

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+..  ..+.|+||||+|++.++.++..|.+.++++..+||+....++..+..+++.|  .|+|||+++++
T Consensus       457 ~eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgR  534 (822)
T 3jux_A          457 KEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGR  534 (822)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTT
T ss_pred             HHHHHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhC
Confidence            5688888877764  2567999999999999999999999999999999986555555555556555  59999999999


Q ss_pred             ccccC--------CCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          109 GIDFR--------TVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       109 g~~i~--------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |+||+        +..+||+++.|.+...|.|++||+||.|.+|.++.|++..|
T Consensus       535 GtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD  588 (822)
T 3jux_A          535 GTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLED  588 (822)
T ss_dssp             TCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTS
T ss_pred             CcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhH
Confidence            99998        56799999999999999999999999999999999998876

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.86  E-value=3.9e-21  Score=155.58  Aligned_cols=121  Identities=20%  Similarity=0.341  Sum_probs=101.5

Q ss_pred             ChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCC------------------------------------CceEE
Q psy576           32 SPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDG------------------------------------INVDV   75 (159)
Q Consensus        32 ~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~------------------------------------~~~~~   75 (159)
                      .+...+.+.+.  .++++||||+++++++.++..|.+..                                    ..+.+
T Consensus       240 ~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~  317 (715)
T 2va8_A          240 AIIAYTLDSLS--KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAY  317 (715)
T ss_dssp             HHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEE
T ss_pred             HHHHHHHHHHh--cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEE
Confidence            34444555554  56899999999999999999987541                                    24899


Q ss_pred             EecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----ec-------CCCCHHHHHHHHhhccCCC--C
Q psy576           76 IHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----YD-------FPSSAISYIHRIGRAGRGG--R  142 (159)
Q Consensus        76 ~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~~-------~~~~~~~~~q~~GR~~R~g--~  142 (159)
                      +||+++.++|..+++.|.+|+.+|||||+++++|+|+|++++||+    |+       .|.+..+|.||+||+||.|  .
T Consensus       318 ~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~  397 (715)
T 2va8_A          318 HHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQ  397 (715)
T ss_dssp             ECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCS
T ss_pred             ECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCC
Confidence            999999999999999999999999999999999999999999998    88       7899999999999999988  4


Q ss_pred             cceEEEEecCCC
Q psy576          143 EGKAVTFFTKQD  154 (159)
Q Consensus       143 ~g~~~~~~~~~~  154 (159)
                      .|.|++++...+
T Consensus       398 ~G~~~~l~~~~~  409 (715)
T 2va8_A          398 IGESIVVVRDKE  409 (715)
T ss_dssp             CEEEEEECSCGG
T ss_pred             CceEEEEeCCch
Confidence            799999987665

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.86  E-value=6.2e-22  Score=158.87  Aligned_cols=101  Identities=22%  Similarity=0.260  Sum_probs=94.4

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----  120 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----  120 (159)
                      ..+++||||++++.++.+++.|++.+.++..+||+    +|.++++.|++|+.+|||||+++++|+|+| +++||+    
T Consensus       409 ~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~  483 (673)
T 2wv9_A          409 YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRKS  483 (673)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCEE
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCCc
Confidence            56799999999999999999999999999999993    788899999999999999999999999999 999997    


Q ss_pred             ----------------ecCCCCHHHHHHHHhhccCC-CCcceEEEEe
Q psy576          121 ----------------YDFPSSAISYIHRIGRAGRG-GREGKAVTFF  150 (159)
Q Consensus       121 ----------------~~~~~~~~~~~q~~GR~~R~-g~~g~~~~~~  150 (159)
                                      ++.|.+.++|.||+||+||. |++|.|++|+
T Consensus       484 ~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~  530 (673)
T 2wv9_A          484 VKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYG  530 (673)
T ss_dssp             CCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEEC
T ss_pred             ccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEE
Confidence                            56889999999999999999 6889999996

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.86  E-value=3.8e-21  Score=155.73  Aligned_cols=122  Identities=25%  Similarity=0.323  Sum_probs=106.6

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC---------------------------------CCceEEEe
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYD---------------------------------GINVDVIH   77 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~---------------------------------~~~~~~~~   77 (159)
                      ..+...+.+.+.  .++++||||++++.++.++..|.+.                                 ...+.++|
T Consensus       224 ~~~~~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h  301 (720)
T 2zj8_A          224 SSWEELVYDAIR--KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHH  301 (720)
T ss_dssp             SSTTHHHHHHHH--TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEEC
T ss_pred             hHHHHHHHHHHh--CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeec
Confidence            455666666665  4689999999999999999888642                                 12489999


Q ss_pred             cCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----ec----CCCCHHHHHHHHhhccCCC--CcceEE
Q psy576           78 SDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----YD----FPSSAISYIHRIGRAGRGG--REGKAV  147 (159)
Q Consensus        78 ~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~~----~~~~~~~~~q~~GR~~R~g--~~g~~~  147 (159)
                      |++++++|..+++.|++|+.+|||||+++++|+|+|++++||+    |+    .|.+..+|.||+||+||.|  ..|.|+
T Consensus       302 ~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~  381 (720)
T 2zj8_A          302 AGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGI  381 (720)
T ss_dssp             TTSCHHHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEE
T ss_pred             CCCCHHHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEE
Confidence            9999999999999999999999999999999999999999998    55    5889999999999999988  478999


Q ss_pred             EEecCCC
Q psy576          148 TFFTKQD  154 (159)
Q Consensus       148 ~~~~~~~  154 (159)
                      +++...+
T Consensus       382 ~l~~~~~  388 (720)
T 2zj8_A          382 IVSTSDD  388 (720)
T ss_dssp             EECSSSC
T ss_pred             EEecCcc
Confidence            9998776

>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=99.86  E-value=4.8e-22  Score=153.84  Aligned_cols=118  Identities=21%  Similarity=0.408  Sum_probs=104.9

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccccc
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI  110 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~  110 (159)
                      ..|...+.+++....++++||||++.+.++.+++.|.     +..+||+++..+|.++++.|++|+.+|||||+++++|+
T Consensus       334 ~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gl  408 (472)
T 2fwr_A          334 KNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGI  408 (472)
T ss_dssp             SHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSS
T ss_pred             hHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCc
Confidence            4677888888887778899999999999999999884     56899999999999999999999999999999999999


Q ss_pred             ccCCCcEEEEecCCCCHHHHHHHHhhccCCCCc-ceEE--EEecCC
Q psy576          111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGRE-GKAV--TFFTKQ  153 (159)
Q Consensus       111 ~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~-g~~~--~~~~~~  153 (159)
                      |+|++++||+++.|+++..|.|++||+||.|+. +.++  .++..+
T Consensus       409 dlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          409 DVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             CSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             ccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCC
Confidence            999999999999999999999999999999854 4444  445443

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.85  E-value=6.1e-21  Score=153.93  Aligned_cols=123  Identities=26%  Similarity=0.285  Sum_probs=110.6

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+..  ..+.|+||||.|++.++.++..|.+.++++..+||++...++..+.++|+.|  .|+|||++++|
T Consensus       424 ~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgR  501 (853)
T 2fsf_A          424 AEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGR  501 (853)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSS
T ss_pred             HHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccC
Confidence            5788888887753  3567899999999999999999999999999999998888887777888888  69999999999


Q ss_pred             ccccCCC-------------------------------------cEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEec
Q psy576          109 GIDFRTV-------------------------------------RLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       109 g~~i~~~-------------------------------------~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      |+||+..                                     .+||+++.|.+...|.|++||+||.|.+|.++.|++
T Consensus       502 GtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls  581 (853)
T 2fsf_A          502 GTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLS  581 (853)
T ss_dssp             CSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEE
T ss_pred             CcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEec
Confidence            9999873                                     599999999999999999999999999999999998


Q ss_pred             CCCc
Q psy576          152 KQDA  155 (159)
Q Consensus       152 ~~~~  155 (159)
                      ..|.
T Consensus       582 ~eD~  585 (853)
T 2fsf_A          582 MEDA  585 (853)
T ss_dssp             TTSG
T ss_pred             ccHH
Confidence            7763

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.85  E-value=5.4e-21  Score=159.18  Aligned_cols=119  Identities=24%  Similarity=0.308  Sum_probs=104.0

Q ss_pred             HHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCC---------------------------------------ceEE
Q psy576           35 QAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGI---------------------------------------NVDV   75 (159)
Q Consensus        35 ~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~---------------------------------------~~~~   75 (159)
                      ..+.+.+......++||||++++.++.++..|...++                                       .+.+
T Consensus       332 ~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~  411 (1010)
T 2xgj_A          332 YKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGI  411 (1010)
T ss_dssp             HHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEE
T ss_pred             HHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeE
Confidence            3344545444566999999999999999998865332                                       2789


Q ss_pred             EecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----ecC----CCCHHHHHHHHhhccCCCC--cce
Q psy576           76 IHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----YDF----PSSAISYIHRIGRAGRGGR--EGK  145 (159)
Q Consensus        76 ~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~~~----~~~~~~~~q~~GR~~R~g~--~g~  145 (159)
                      +||++++.+|..+++.|++|.++|||||+++++|+|+|++++||+    |+.    |.++.+|.||+||+||.|.  .|.
T Consensus       412 ~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~  491 (1010)
T 2xgj_A          412 HHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGI  491 (1010)
T ss_dssp             ESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEE
T ss_pred             ECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceE
Confidence            999999999999999999999999999999999999999999998    888    8899999999999999995  599


Q ss_pred             EEEEecCC
Q psy576          146 AVTFFTKQ  153 (159)
Q Consensus       146 ~~~~~~~~  153 (159)
                      |++++.+.
T Consensus       492 vi~l~~~~  499 (1010)
T 2xgj_A          492 VIMMIDEK  499 (1010)
T ss_dssp             EEEEECSC
T ss_pred             EEEEECCC
Confidence            99999865

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.85  E-value=5.7e-21  Score=154.34  Aligned_cols=120  Identities=27%  Similarity=0.376  Sum_probs=104.9

Q ss_pred             hHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC------------------------------CCceEEEecCCCH
Q psy576           33 PVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYD------------------------------GINVDVIHSDRTQ   82 (159)
Q Consensus        33 k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~------------------------------~~~~~~~~~~~~~   82 (159)
                      +...+.+.+.  .++++||||++++.++.++..|.+.                              +..+.++||++++
T Consensus       231 ~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~  308 (702)
T 2p6r_A          231 FEELVEECVA--ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  308 (702)
T ss_dssp             HHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHHh--cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCH
Confidence            4555666665  5689999999999999999888642                              1347899999999


Q ss_pred             HHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----ec---CCCCHHHHHHHHhhccCCC--CcceEEEEecCC
Q psy576           83 KQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----YD---FPSSAISYIHRIGRAGRGG--REGKAVTFFTKQ  153 (159)
Q Consensus        83 ~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~~---~~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~  153 (159)
                      ++|..+++.|++|+.+|||||+++++|+|+|++++||+    |+   .|.+..+|.||+||+||.|  ..|.|++++...
T Consensus       309 ~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~  388 (702)
T 2p6r_A          309 GQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKR  388 (702)
T ss_dssp             HHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGG
T ss_pred             HHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCc
Confidence            99999999999999999999999999999999999998    55   6889999999999999998  479999998876


Q ss_pred             C
Q psy576          154 D  154 (159)
Q Consensus       154 ~  154 (159)
                      +
T Consensus       389 ~  389 (702)
T 2p6r_A          389 D  389 (702)
T ss_dssp             G
T ss_pred             c
Confidence            5

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.85  E-value=3e-21  Score=148.20  Aligned_cols=108  Identities=20%  Similarity=0.235  Sum_probs=92.1

Q ss_pred             HHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcE
Q psy576           38 DETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRL  117 (159)
Q Consensus        38 ~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~  117 (159)
                      .+++.. ..++++|||++++.++.+++.|++.+.++..+||+    +|.++++.|++|+.+|||||+++++|+|+|...+
T Consensus       164 ~~~l~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip~~~V  238 (431)
T 2v6i_A          164 YEWITE-FDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFKADRV  238 (431)
T ss_dssp             CHHHHS-CSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCCCSEE
T ss_pred             HHHHHc-CCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccCCcEE
Confidence            344544 36689999999999999999999989999999996    5778999999999999999999999999994332


Q ss_pred             ----------------EEEecCCCCHHHHHHHHhhccCCCC-cceEEEEe
Q psy576          118 ----------------VVNYDFPSSAISYIHRIGRAGRGGR-EGKAVTFF  150 (159)
Q Consensus       118 ----------------vi~~~~~~~~~~~~q~~GR~~R~g~-~g~~~~~~  150 (159)
                                      +++++.|.+..+|.||+||+||.|. ++.++++.
T Consensus       239 I~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          239 IDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             EECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             EecCccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence                            5778899999999999999999985 45555554

>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=99.85  E-value=8.7e-22  Score=160.27  Aligned_cols=115  Identities=19%  Similarity=0.311  Sum_probs=103.6

Q ss_pred             HHHhcCCCCCEEEEecchHHHHHHHHHHHh-----------CCCceEEEecCCCHHHHHHHHHHHh-----cCCeeEEEE
Q psy576           39 ETILLGIEPPVLVFVQSKERAQELYNELIY-----------DGINVDVIHSDRTQKQRDNVVRSFR-----TGRIWILIT  102 (159)
Q Consensus        39 ~~~~~~~~~~~lif~~~~~~~~~l~~~l~~-----------~~~~~~~~~~~~~~~~r~~~~~~f~-----~~~~~vlv~  102 (159)
                      ++......+++||||+++++++.+++.|.+           .++.+..+||+++.++|..+++.|.     +|+.+||||
T Consensus       296 ~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVA  375 (773)
T 2xau_A          296 QIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVIS  375 (773)
T ss_dssp             HHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEE
T ss_pred             HHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEe
Confidence            333344678999999999999999999875           4678999999999999999999999     999999999


Q ss_pred             eCCcccccccCCCcEEEEecC------------------CCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          103 TELLGRGIDFRTVRLVVNYDF------------------PSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       103 t~~~~~g~~i~~~~~vi~~~~------------------~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |+++++|+|+|++++||+++.                  |.+..+|.||+||+||. ..|.|+.++...+
T Consensus       376 T~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~  444 (773)
T 2xau_A          376 TNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEA  444 (773)
T ss_dssp             CTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHH
T ss_pred             CcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHH
Confidence            999999999999999999777                  88999999999999999 7899999987654

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.84  E-value=7.1e-21  Score=159.64  Aligned_cols=118  Identities=25%  Similarity=0.290  Sum_probs=98.1

Q ss_pred             HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCc---------------------------------------eEEEe
Q psy576           37 QDETILLGIEPPVLVFVQSKERAQELYNELIYDGIN---------------------------------------VDVIH   77 (159)
Q Consensus        37 l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~---------------------------------------~~~~~   77 (159)
                      +...+......++||||++++.++.++..|...++.                                       +.++|
T Consensus       432 li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~H  511 (1108)
T 3l9o_A          432 IVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHH  511 (1108)
T ss_dssp             HHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEEC
T ss_pred             HHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeec
Confidence            334444446679999999999999999887542211                                       78999


Q ss_pred             cCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecC--------CCCHHHHHHHHhhccCCC--CcceEE
Q psy576           78 SDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDF--------PSSAISYIHRIGRAGRGG--REGKAV  147 (159)
Q Consensus        78 ~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~--------~~~~~~~~q~~GR~~R~g--~~g~~~  147 (159)
                      |+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||+++.        |.+..+|.||+||+||.|  ..|.|+
T Consensus       512 g~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~i  591 (1108)
T 3l9o_A          512 SGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVI  591 (1108)
T ss_dssp             SCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEE
T ss_pred             CCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEE
Confidence            9999999999999999999999999999999999999999996554        337888999999999999  679999


Q ss_pred             EEecCCC
Q psy576          148 TFFTKQD  154 (159)
Q Consensus       148 ~~~~~~~  154 (159)
                      +++.+..
T Consensus       592 ll~~~~~  598 (1108)
T 3l9o_A          592 MMIDEKM  598 (1108)
T ss_dssp             EEECCCC
T ss_pred             EEecCCc
Confidence            9887653

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.84  E-value=4.4e-21  Score=149.74  Aligned_cols=119  Identities=14%  Similarity=0.163  Sum_probs=100.1

Q ss_pred             ChHHHHHHHHhcC---CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEe-CCcc
Q psy576           32 SPVQAQDETILLG---IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT-ELLG  107 (159)
Q Consensus        32 ~k~~~l~~~~~~~---~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t-~~~~  107 (159)
                      .+...+.+++...   ..++++|||. .++++.+++.|.+.+.++..+||+++..+|.++++.|++|+.+||||| ++++
T Consensus       331 ~~~~~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~  409 (510)
T 2oca_A          331 KRNKWIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFS  409 (510)
T ss_dssp             HHHHHHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhh
Confidence            3444455555432   3345666666 899999999999887789999999999999999999999999999999 9999


Q ss_pred             cccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEec
Q psy576          108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       108 ~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      +|+|+|++++||++++|+++..|.|++||+||.|+.+.++++++
T Consensus       410 ~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          410 TGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             HSCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             cccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            99999999999999999999999999999999997764444433

>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=99.84  E-value=1.5e-20  Score=146.47  Aligned_cols=118  Identities=16%  Similarity=0.228  Sum_probs=101.6

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhC-CCceEEEecCCCHHHHHHHHHHHhcC-Cee-EEEEeCC
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYD-GINVDVIHSDRTQKQRDNVVRSFRTG-RIW-ILITTEL  105 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~-vlv~t~~  105 (159)
                      ..|...+.+++..  ..+.++||||.+.+.++.+...|... +..+..+||+++..+|.++++.|+++ +.. +|++|++
T Consensus       324 s~K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~  403 (500)
T 1z63_A          324 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKA  403 (500)
T ss_dssp             CHHHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCC
T ss_pred             chhHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEeccc
Confidence            5677777777764  35679999999999999999999875 88899999999999999999999998 554 7889999


Q ss_pred             cccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEE
Q psy576          106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVT  148 (159)
Q Consensus       106 ~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~  148 (159)
                      +++|+|+|.+++||++++|+++..|.|++||++|.|+.+.+.+
T Consensus       404 ~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v  446 (500)
T 1z63_A          404 GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIV  446 (500)
T ss_dssp             C-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEE
T ss_pred             ccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEE
Confidence            9999999999999999999999999999999999998776644

>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=99.83  E-value=3.4e-20  Score=150.12  Aligned_cols=122  Identities=21%  Similarity=0.254  Sum_probs=108.1

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|...+.+.+..  ..+.|+||||.|++.++.++..|.+.++++..+||+....++..+.++|+.|  .|+|||+++++
T Consensus       443 ~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgR  520 (922)
T 1nkt_A          443 EAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGR  520 (922)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCST
T ss_pred             HHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhc
Confidence            5688888777753  2567899999999999999999999999999999998777776677777777  69999999999


Q ss_pred             ccccCCC----------------------------------------------------cEEEEecCCCCHHHHHHHHhh
Q psy576          109 GIDFRTV----------------------------------------------------RLVVNYDFPSSAISYIHRIGR  136 (159)
Q Consensus       109 g~~i~~~----------------------------------------------------~~vi~~~~~~~~~~~~q~~GR  136 (159)
                      |+||+..                                                    .+||+++.|.+...|.|++||
T Consensus       521 GtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GR  600 (922)
T 1nkt_A          521 GTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGR  600 (922)
T ss_dssp             TCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHT
T ss_pred             CccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcc
Confidence            9999964                                                    599999999999999999999


Q ss_pred             ccCCCCcceEEEEecCCC
Q psy576          137 AGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       137 ~~R~g~~g~~~~~~~~~~  154 (159)
                      +||.|.+|.++.|++..|
T Consensus       601 TGRqGdpG~s~fflSleD  618 (922)
T 1nkt_A          601 SGRQGDPGESRFYLSLGD  618 (922)
T ss_dssp             SSGGGCCEEEEEEEETTS
T ss_pred             cccCCCCeeEEEEechhH
Confidence            999999999999998765

>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=99.83  E-value=1.4e-20  Score=158.53  Aligned_cols=109  Identities=17%  Similarity=0.209  Sum_probs=102.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEec
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD  122 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~  122 (159)
                      .+++++|||++++.++.+++.|++.  +..+..+||+|+..+|.++++.|.+|+.+|||||+++++|+|+|++++||+++
T Consensus       811 ~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~~  890 (1151)
T 2eyq_A          811 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIER  890 (1151)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEeC
Confidence            5678999999999999999999876  77899999999999999999999999999999999999999999999999988


Q ss_pred             C-CCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576          123 F-PSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus       123 ~-~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      . +++...|.|++||+||.|+.|.|++++.+.
T Consensus       891 ~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          891 ADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             TTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             CCCCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            7 578999999999999999999999998764

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.83  E-value=4.4e-20  Score=153.65  Aligned_cols=122  Identities=22%  Similarity=0.250  Sum_probs=104.8

Q ss_pred             CCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCC-------------------------------------
Q psy576           29 GAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGI-------------------------------------   71 (159)
Q Consensus        29 ~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~-------------------------------------   71 (159)
                      ....+...+.+.+......++||||.+++.++.++..|...++                                     
T Consensus       319 ~~~~~~~~li~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l  398 (997)
T 4a4z_A          319 PSKKTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLL  398 (997)
T ss_dssp             CCTTHHHHHHHHHHHTTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHh
Confidence            3356777788888877778999999999999999998866444                                     


Q ss_pred             --ceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCCC---------CHHHHHHHHhhccCC
Q psy576           72 --NVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPS---------SAISYIHRIGRAGRG  140 (159)
Q Consensus        72 --~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~---------~~~~~~q~~GR~~R~  140 (159)
                        .+..+||++++.+|..+++.|.+|+.+|||||+++++|+|+|+.+ ||+++.++         +..+|.||+||+||.
T Consensus       399 ~~gi~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~~~-VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~  477 (997)
T 4a4z_A          399 ERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRT-VIFSSIRKHDGNGLRELTPGEFTQMAGRAGRR  477 (997)
T ss_dssp             TTTEEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCCSE-EEESCSEEEETTEEEECCHHHHHHHHGGGCCT
T ss_pred             hcCeeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCCce-EEEeccccccCccCCCCCHHHHhHHhcccccC
Confidence              478999999999999999999999999999999999999999955 55544444         999999999999999


Q ss_pred             C--CcceEEEEec
Q psy576          141 G--REGKAVTFFT  151 (159)
Q Consensus       141 g--~~g~~~~~~~  151 (159)
                      |  ..|.|++++.
T Consensus       478 G~~~~G~vi~l~~  490 (997)
T 4a4z_A          478 GLDSTGTVIVMAY  490 (997)
T ss_dssp             TTCSSEEEEEECC
T ss_pred             CCCcceEEEEecC
Confidence            8  5688888874

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.82  E-value=8e-20  Score=146.55  Aligned_cols=104  Identities=21%  Similarity=0.359  Sum_probs=94.9

Q ss_pred             CCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc--CCeeEEEEeCCcccccccCCCcEEEEecC-
Q psy576           47 PPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT--GRIWILITTELLGRGIDFRTVRLVVNYDF-  123 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~--~~~~vlv~t~~~~~g~~i~~~~~vi~~~~-  123 (159)
                      ...+|||.++++++.+++.|.+.+..+..+||+|++++|..+++.|++  |+.+|||||+++++|+|+ +++.||+++. 
T Consensus       321 ~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~  399 (677)
T 3rc3_A          321 PGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLI  399 (677)
T ss_dssp             TTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSB
T ss_pred             CCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCcc
Confidence            345789999999999999999999999999999999999999999999  889999999999999999 8999999998 


Q ss_pred             -------------CCCHHHHHHHHhhccCCCCc---ceEEEEec
Q psy576          124 -------------PSSAISYIHRIGRAGRGGRE---GKAVTFFT  151 (159)
Q Consensus       124 -------------~~~~~~~~q~~GR~~R~g~~---g~~~~~~~  151 (159)
                                   |.+..+|.||+||+||.|..   |.|+.++.
T Consensus       400 k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~~  443 (677)
T 3rc3_A          400 KPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNH  443 (677)
T ss_dssp             C-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESST
T ss_pred             ccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEec
Confidence                         77899999999999999954   66666544

>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=99.82  E-value=1.5e-19  Score=144.88  Aligned_cols=119  Identities=11%  Similarity=0.133  Sum_probs=105.9

Q ss_pred             CChHHHHHHHHhc---CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe---eEEEEeC
Q psy576           31 GSPVQAQDETILL---GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI---WILITTE  104 (159)
Q Consensus        31 ~~k~~~l~~~~~~---~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~---~vlv~t~  104 (159)
                      ..|...+..++..   ..++++||||...+.++.+...|...++.+..+||+++..+|.++++.|++++.   .+|++|.
T Consensus       398 s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~  477 (644)
T 1z3i_X          398 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK  477 (644)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG
T ss_pred             ChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecc
Confidence            4566777666653   356799999999999999999999999999999999999999999999999765   4899999


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      ++++|+|++.+++||++++||++..+.|++||++|.|+...|.++
T Consensus       478 a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~  522 (644)
T 1z3i_X          478 AGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIY  522 (644)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEE
T ss_pred             cccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEE
Confidence            999999999999999999999999999999999999987665543

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.81  E-value=5.3e-20  Score=154.04  Aligned_cols=118  Identities=22%  Similarity=0.354  Sum_probs=97.5

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEE----eCCc
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILIT----TELL  106 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~----t~~~  106 (159)
                      ..|...|.+++... ++++||||++++.++.+++.|... +++..+||++.     .+++.|++|+.+||||    |+++
T Consensus       261 ~~k~~~L~~ll~~~-~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~~-----~~l~~F~~G~~~VLVaTas~Tdv~  333 (1054)
T 1gku_B          261 DESISTLSSILEKL-GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATKK-----GDYEKFVEGEIDHLIGTAHYYGTL  333 (1054)
T ss_dssp             CCCTTTTHHHHTTS-CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSSS-----HHHHHHHHTSCSEEEEECC-----
T ss_pred             hhHHHHHHHHHhhc-CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccHH-----HHHHHHHcCCCcEEEEecCCCCee
Confidence            56777777888764 578999999999999999999887 89999999983     6789999999999999    8999


Q ss_pred             ccccccCCC-cEEEEecCC-------------------------------------------------------------
Q psy576          107 GRGIDFRTV-RLVVNYDFP-------------------------------------------------------------  124 (159)
Q Consensus       107 ~~g~~i~~~-~~vi~~~~~-------------------------------------------------------------  124 (159)
                      ++|+|+|++ ++||+++.|                                                             
T Consensus       334 ~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  413 (1054)
T 1gku_B          334 VRGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKD  413 (1054)
T ss_dssp             -CCSCCTTTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSS
T ss_pred             EeccccCCcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence            999999995 999999999                                                             


Q ss_pred             ----------CCHHHHHHHHhhccCCCCcc--eEEEEecCCCc
Q psy576          125 ----------SSAISYIHRIGRAGRGGREG--KAVTFFTKQDA  155 (159)
Q Consensus       125 ----------~~~~~~~q~~GR~~R~g~~g--~~~~~~~~~~~  155 (159)
                                .+..+|.||+||+||.|..|  .++.++...|.
T Consensus       414 ~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~  456 (1054)
T 1gku_B          414 VVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDS  456 (1054)
T ss_dssp             SEEETTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECSCH
T ss_pred             eeEeecceecCcHHHHhhhhchhhhccCCCCceEEEEEEecCH
Confidence                      78999999999999987665  36666655554

>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=99.81  E-value=7.3e-20  Score=145.93  Aligned_cols=104  Identities=28%  Similarity=0.333  Sum_probs=92.6

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEE----
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV----  119 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi----  119 (159)
                      ...+++||||++++.++.+++.|++.++++..+||++++++       |.++..+|||||+++++|+|+| +++||    
T Consensus       394 ~~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl  465 (666)
T 3o8b_A          394 IRGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNT  465 (666)
T ss_dssp             SSSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCE
T ss_pred             ccCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCc
Confidence            35678999999999999999999999999999999998875       4556669999999999999997 99888    


Q ss_pred             ------Eec-----------CCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576          120 ------NYD-----------FPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus       120 ------~~~-----------~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                            |||           .|.+.++|.||+||+|| |.+|. +.|+.+.|...
T Consensus       466 ~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~  518 (666)
T 3o8b_A          466 CVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGERPS  518 (666)
T ss_dssp             EEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCCBCS
T ss_pred             ccccccccccccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecchhhc
Confidence                  566           89999999999999999 88898 89988887654

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.81  E-value=1.9e-19  Score=147.32  Aligned_cols=119  Identities=22%  Similarity=0.254  Sum_probs=107.6

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe---eEEEEeCC
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI---WILITTEL  105 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~---~vlv~t~~  105 (159)
                      ..|+..|.+++..  ..++++||||.....++.+..+|...++++..+||+++..+|..+++.|+++..   .+|++|.+
T Consensus       555 s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~a  634 (800)
T 3mwy_W          555 SGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRA  634 (800)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHH
T ss_pred             ChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEeccc
Confidence            5688888888864  356799999999999999999999999999999999999999999999998554   59999999


Q ss_pred             cccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       106 ~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      ++.|+|++.+++||++++|+++..+.|++||++|.|+...|.++
T Consensus       635 gg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vy  678 (800)
T 3mwy_W          635 GGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVY  678 (800)
T ss_dssp             HTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEE
T ss_pred             ccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEE
Confidence            99999999999999999999999999999999999977665543

>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=99.80  E-value=5.2e-21  Score=155.41  Aligned_cols=108  Identities=24%  Similarity=0.351  Sum_probs=95.6

Q ss_pred             CCCCEEEEecchH--------HHHHHHHHHHh---CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccC
Q psy576           45 IEPPVLVFVQSKE--------RAQELYNELIY---DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFR  113 (159)
Q Consensus        45 ~~~~~lif~~~~~--------~~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~  113 (159)
                      .+++++|||+..+        .++.+++.|.+   .+..+..+||+|+..+|..+++.|++|+.+|||||+++++|+|+|
T Consensus       577 ~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDiP  656 (780)
T 1gm5_A          577 RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVP  656 (780)
T ss_dssp             TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCT
T ss_pred             cCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccccCC
Confidence            5678999999664        46788888877   367899999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCC-CHHHHHHHHhhccCCCCcceEEEEecC
Q psy576          114 TVRLVVNYDFPS-SAISYIHRIGRAGRGGREGKAVTFFTK  152 (159)
Q Consensus       114 ~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~g~~~~~~~~  152 (159)
                      ++++||+++.|. +...|.|++||+||.|..|.|++++.+
T Consensus       657 ~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~  696 (780)
T 1gm5_A          657 RANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD  696 (780)
T ss_dssp             TCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             CCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECC
Confidence            999999999985 788999999999999999999999873

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.79  E-value=2.9e-19  Score=149.95  Aligned_cols=96  Identities=27%  Similarity=0.426  Sum_probs=82.7

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceE-EEecCCCHHHHHHHHHHHhcCCe
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVD-VIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~-~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ++.+.+..+    .+...|.+++.. .++++||||++++.++.++..|...++++. .+||     +|.+ ++.|++|+.
T Consensus       287 ~i~~~~~~~----~k~~~L~~ll~~-~~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg-----~rr~-l~~F~~G~~  355 (1104)
T 4ddu_A          287 NITHVRISS----RSKEKLVELLEI-FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSE-----FEKN-FEDFKVGKI  355 (1104)
T ss_dssp             CEEEEEESC----CCHHHHHHHHHH-HCSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSS-----HHHH-HHHHHHTSC
T ss_pred             CceeEEEec----CHHHHHHHHHHh-cCCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecC-----cHHH-HHHHHCCCC
Confidence            444554444    467777777776 458999999999999999999999999998 9998     2555 999999999


Q ss_pred             eEEEE----eCCcccccccCC-CcEEEEecCCC
Q psy576           98 WILIT----TELLGRGIDFRT-VRLVVNYDFPS  125 (159)
Q Consensus        98 ~vlv~----t~~~~~g~~i~~-~~~vi~~~~~~  125 (159)
                      +||||    |+++++|+|+|+ +++||++++|.
T Consensus       356 ~VLVatas~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          356 NILIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             SEEEEETTTHHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             CEEEEecCCCCeeEecCcCCCCCCEEEEECCCC
Confidence            99999    999999999999 99999999998

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.78  E-value=1e-18  Score=138.67  Aligned_cols=98  Identities=24%  Similarity=0.242  Sum_probs=86.3

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCC--------ceEEEecCCCHHHHHHHHHHHhcCCee---EEEEeCCccccccc
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGI--------NVDVIHSDRTQKQRDNVVRSFRTGRIW---ILITTELLGRGIDF  112 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~--------~~~~~~~~~~~~~r~~~~~~f~~~~~~---vlv~t~~~~~g~~i  112 (159)
                      ...+++||||+++++++.+++.|.+.+.        .+..+||.++ ++|.++++.|++++..   |||||+++++|+|+
T Consensus       437 ~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~-~~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDi  515 (590)
T 3h1t_A          437 DRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEG-KIGKGHLSRFQELETSTPVILTTSQLLTTGVDA  515 (590)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTH-HHHHHHHHHHHCTTCCCCCEEEESSTTTTTCCC
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCCh-HHHHHHHHHHhCCCCCCCEEEEECChhhcCccc
Confidence            3457899999999999999999976432        2678899875 4799999999998755   88899999999999


Q ss_pred             CCCcEEEEecCCCCHHHHHHHHhhccCCCC
Q psy576          113 RTVRLVVNYDFPSSAISYIHRIGRAGRGGR  142 (159)
Q Consensus       113 ~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~  142 (159)
                      |.+++||++++|++...|.||+||++|.+.
T Consensus       516 p~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          516 PTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             TTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             hheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            999999999999999999999999999874

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.77  E-value=1.5e-18  Score=150.38  Aligned_cols=114  Identities=21%  Similarity=0.345  Sum_probs=97.3

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhC-------------------------------------CCceEEEecCCCHHHHH
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYD-------------------------------------GINVDVIHSDRTQKQRD   86 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~-------------------------------------~~~~~~~~~~~~~~~r~   86 (159)
                      ..++++||||+|++.++.+++.|.+.                                     ...+.++||+|+..+|.
T Consensus       315 ~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~  394 (1724)
T 4f92_B          315 AGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRT  394 (1724)
T ss_dssp             CSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHH
T ss_pred             hcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHH
Confidence            45678999999998888877766421                                     12378999999999999


Q ss_pred             HHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE----ec------CCCCHHHHHHHHhhccCCC--CcceEEEEecCCC
Q psy576           87 NVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN----YD------FPSSAISYIHRIGRAGRGG--REGKAVTFFTKQD  154 (159)
Q Consensus        87 ~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~~------~~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~~  154 (159)
                      .+++.|++|.++|||||+++++|+|+|..++||.    ++      .|.+..+|.||+||+||.|  ..|.++++....+
T Consensus       395 ~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~  474 (1724)
T 4f92_B          395 LVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGE  474 (1724)
T ss_dssp             HHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTT
T ss_pred             HHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchh
Confidence            9999999999999999999999999999999985    33      3458999999999999988  5699999998887


Q ss_pred             ccc
Q psy576          155 APL  157 (159)
Q Consensus       155 ~~~  157 (159)
                      ...
T Consensus       475 ~~~  477 (1724)
T 4f92_B          475 LQY  477 (1724)
T ss_dssp             CCH
T ss_pred             HHH
Confidence            653

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.75  E-value=3.1e-18  Score=148.34  Aligned_cols=114  Identities=19%  Similarity=0.313  Sum_probs=96.5

Q ss_pred             cCCCCCEEEEecchHHHHHHHHHHHhC----------------------------------CCceEEEecCCCHHHHHHH
Q psy576           43 LGIEPPVLVFVQSKERAQELYNELIYD----------------------------------GINVDVIHSDRTQKQRDNV   88 (159)
Q Consensus        43 ~~~~~~~lif~~~~~~~~~l~~~l~~~----------------------------------~~~~~~~~~~~~~~~r~~~   88 (159)
                      ....++++|||++++.++.++..|...                                  ...+.++||+|++.+|..+
T Consensus      1152 ~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~V 1231 (1724)
T 4f92_B         1152 HSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLV 1231 (1724)
T ss_dssp             HCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHH
T ss_pred             hcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHH
Confidence            356789999999999998876655221                                  1238899999999999999


Q ss_pred             HHHHhcCCeeEEEEeCCcccccccCCCcEEEE----e------cCCCCHHHHHHHHhhccCCCC--cceEEEEecCCCcc
Q psy576           89 VRSFRTGRIWILITTELLGRGIDFRTVRLVVN----Y------DFPSSAISYIHRIGRAGRGGR--EGKAVTFFTKQDAP  156 (159)
Q Consensus        89 ~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~----~------~~~~~~~~~~q~~GR~~R~g~--~g~~~~~~~~~~~~  156 (159)
                      ++.|++|.++|||||+.+++|+|+|+..+||.    +      ..|.+..+|.||+||+||.|.  .|.+++++.+.+..
T Consensus      1232 E~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~~~~ 1311 (1724)
T 4f92_B         1232 EQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKD 1311 (1724)
T ss_dssp             HHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGGGHH
T ss_pred             HHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecchHHH
Confidence            99999999999999999999999999998883    2      235789999999999999994  69999998876654

>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=99.47  E-value=3e-13  Score=112.94  Aligned_cols=105  Identities=16%  Similarity=0.161  Sum_probs=84.3

Q ss_pred             CCCEEEEecchHHHHHHHHHHHhCC------------CceE-EEecC----------C----------CH----------
Q psy576           46 EPPVLVFVQSKERAQELYNELIYDG------------INVD-VIHSD----------R----------TQ----------   82 (159)
Q Consensus        46 ~~~~lif~~~~~~~~~l~~~l~~~~------------~~~~-~~~~~----------~----------~~----------   82 (159)
                      +.++||||.++..|..+++.|.+.+            .++. .+||.          +          +.          
T Consensus       537 g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I  616 (1038)
T 2w00_A          537 GFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAI  616 (1038)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHH
Confidence            3579999999999999999886542            4454 44542          2          21          


Q ss_pred             -------------------HHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCc
Q psy576           83 -------------------KQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGRE  143 (159)
Q Consensus        83 -------------------~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~  143 (159)
                                         .+|.++++.|++|+++|||+|+++.+|+|+|.+ .+++++.|.+...|.|++||++|.++.
T Consensus       617 ~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~  695 (1038)
T 2w00_A          617 REYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDA  695 (1038)
T ss_dssp             HHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCT
T ss_pred             HHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCC
Confidence                               147788999999999999999999999999999 577889999999999999999998753


Q ss_pred             ----ceEEEEec
Q psy576          144 ----GKAVTFFT  151 (159)
Q Consensus       144 ----g~~~~~~~  151 (159)
                          |.++.|..
T Consensus       696 ~K~~G~IVdf~~  707 (1038)
T 2w00_A          696 TKTFGNIVTFRD  707 (1038)
T ss_dssp             TCCSEEEEESSC
T ss_pred             CCCcEEEEEccc
Confidence                66665554

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.82  E-value=1.4e-08  Score=79.96  Aligned_cols=108  Identities=19%  Similarity=0.252  Sum_probs=67.2

Q ss_pred             HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEE--EeCCcccccccCC
Q psy576           37 QDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILI--TTELLGRGIDFRT  114 (159)
Q Consensus        37 l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv--~t~~~~~g~~i~~  114 (159)
                      +.+++.. ..+.++||++|.+.++.+++.|...   ..+.+|..  .++.++++.|+++. .||+  +|..+.+|+|+|+
T Consensus       376 l~~~~~~-~~g~~lvff~S~~~~~~v~~~l~~~---~~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~  448 (540)
T 2vl7_A          376 LKRIYEN-SSKSVLVFFPSYEMLESVRIHLSGI---PVIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFRE  448 (540)
T ss_dssp             HHHHHHT-CSSEEEEEESCHHHHHHHHTTCTTS---CEEESTTT--CCHHHHHHHHHTSC-CEEEEEC------------
T ss_pred             HHHHHHh-CCCCEEEEeCCHHHHHHHHHHhccC---ceEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCC
Confidence            3344443 5678999999999999999888642   34566653  46788999998864 5666  8899999999997


Q ss_pred             ----CcEEEEecCCCCH------------------------------HHHHHHHhhccCCCCcceEEEEec
Q psy576          115 ----VRLVVNYDFPSSA------------------------------ISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       115 ----~~~vi~~~~~~~~------------------------------~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                          +++||+.+.|...                              ..+.|.+||+.|....--++++.+
T Consensus       449 ~~~~~~~Vii~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD  519 (540)
T 2vl7_A          449 KENLFESLVLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCD  519 (540)
T ss_dssp             ---CEEEEEEESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEES
T ss_pred             CcccccEEEEECCCCCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEc
Confidence                7889999888421                              235689999999764322444443

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.79  E-value=5e-08  Score=79.96  Aligned_cols=122  Identities=25%  Similarity=0.272  Sum_probs=89.3

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHH-----------------------------------------
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELI-----------------------------------------   67 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~-----------------------------------------   67 (159)
                      ..|...+.+.+..  ..+.|+||+|.|.+..+.++++|+                                         
T Consensus       426 ~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE~LS~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  505 (997)
T 2ipc_A          426 KGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLSQMLKEPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQL  505 (997)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCEEEECSSHHHHHHHHHHHHCGGGGHHHHHHHHHHHHHHHTTCCSHHHHHHHHHTSSSTTC
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHHHHHHHHhhccccchhhhhhhhhhhhhhhhccccchhhhhhhhhccccc
Confidence            5667666655542  357899999999999999999998                                         


Q ss_pred             -----------------------------------hCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccccccc
Q psy576           68 -----------------------------------YDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDF  112 (159)
Q Consensus        68 -----------------------------------~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i  112 (159)
                                                         +.+++.-++.....  +++.-+-+-....-.|.|||+++++|.||
T Consensus       506 ~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gI~H~VLNAK~h--e~EAeIIAqAG~~GaVTIATNMAGRGTDI  583 (997)
T 2ipc_A          506 KDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVLRQGIPHQVLNAKHH--AREAEIVAQAGRSKTVTIATNMAGRGTDI  583 (997)
T ss_dssp             SHHHHSGGGGGCCSSHHHHHHHHHHHHHHHHHHHHHHCCCCCEECSSSH--HHHHHHHHTTTSTTCEEEECSSTTTTSCC
T ss_pred             cccccccccccccccccccccccccchhhhhhHHHHcCCCeeeccccch--HHHHHHHHhcCCCCeEEEEecccCCCcCe
Confidence                                               34566666666533  23221111112234699999999999999


Q ss_pred             CCC-------------------c-------------------------------------------------------EE
Q psy576          113 RTV-------------------R-------------------------------------------------------LV  118 (159)
Q Consensus       113 ~~~-------------------~-------------------------------------------------------~v  118 (159)
                      .--                   .                                                       +|
T Consensus       584 kLggn~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~V~e~GGLhV  663 (997)
T 2ipc_A          584 KLGGNPEYLAAALLEKEGFDRYEWKVELFIKKMVAGKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLFI  663 (997)
T ss_dssp             CSSCCHHHHHHHTTSSSCSSTTHHHHHHHHHHHHHTCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTCCCCE
T ss_pred             ecCCCHHHHHHHHHHhhcccccccccccccccccccchhhccccchhhhhhhhHHHHHHHhhhhhhhhhhHHHhcCCeEE
Confidence            532                   1                                                       67


Q ss_pred             EEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          119 VNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       119 i~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |--..+.|..---|..||+||.|.+|...+|.+-.|
T Consensus       664 IGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeD  699 (997)
T 2ipc_A          664 IGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDD  699 (997)
T ss_dssp             EESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSS
T ss_pred             EeccCCchHHHHHHHhcccccCCCCCCeEEEEECCh
Confidence            777778888888999999999999999988877554

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=98.66  E-value=1.6e-07  Score=68.98  Aligned_cols=119  Identities=8%  Similarity=-0.001  Sum_probs=86.1

Q ss_pred             CCChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcc
Q psy576           30 AGSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG  107 (159)
Q Consensus        30 ~~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~  107 (159)
                      ..+|+.+|.+++..  ..+++++||+...+..+-+..++...+++...+.|..... +.+    -.++...+.+.|...+
T Consensus       107 ~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~-~~k----~~~~~~~i~Lltsag~  181 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKS-AAA----ANDFSCTVHLFSSEGI  181 (328)
T ss_dssp             TCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCC
T ss_pred             cCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhh-hhh----cccCCceEEEEECCCC
Confidence            37899999988873  3567899999999999999999999999999999884432 211    1245556666677777


Q ss_pred             cccc-----cCCCcEEEEecCCCCHHHH-HHHHhhccCCC----CcceEEEEecCC
Q psy576          108 RGID-----FRTVRLVVNYDFPSSAISY-IHRIGRAGRGG----REGKAVTFFTKQ  153 (159)
Q Consensus       108 ~g~~-----i~~~~~vi~~~~~~~~~~~-~q~~GR~~R~g----~~g~~~~~~~~~  153 (159)
                      -|+|     ...++.||.+|..|++..- +|.+-|+.|.|    +.-.++.++...
T Consensus       182 ~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~  237 (328)
T 3hgt_A          182 NFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAIN  237 (328)
T ss_dssp             CTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETT
T ss_pred             CCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCC
Confidence            7776     5689999999999998875 89888988873    234666666543

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.34  E-value=3.7e-06  Score=67.25  Aligned_cols=108  Identities=19%  Similarity=0.270  Sum_probs=70.9

Q ss_pred             HHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeC--CcccccccCC--
Q psy576           39 ETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTE--LLGRGIDFRT--  114 (159)
Q Consensus        39 ~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~--~~~~g~~i~~--  114 (159)
                      +++.. .++.++||++|...++.+++.|.  ..... ...+++..++..+++.|+ ++-.||+++.  ...+|+|+|+  
T Consensus       442 ~l~~~-~~g~~lvlF~Sy~~l~~v~~~l~--~~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~  516 (620)
T 4a15_A          442 DIILK-VKKNTIVYFPSYSLMDRVENRVS--FEHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNE  516 (620)
T ss_dssp             HHHHH-HCSCEEEEESCHHHHHHHTSSCC--SCCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CC
T ss_pred             HHHHh-CCCCEEEEeCCHHHHHHHHHHHH--hcchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCc
Confidence            33333 45679999999999999998876  22222 444455678999999999 8888999974  9999999985  


Q ss_pred             CcEEEEecCCCCH-----------------------------HHHHHHHhhccCCCCcceEEEEec
Q psy576          115 VRLVVNYDFPSSA-----------------------------ISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       115 ~~~vi~~~~~~~~-----------------------------~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      ++.||..+.|...                             ....|.+||+-|....--++++.+
T Consensus       517 l~~viI~~lPfp~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD  582 (620)
T 4a15_A          517 LEMIILAGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILD  582 (620)
T ss_dssp             CCEEEESSCCCCCCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEEC
T ss_pred             eEEEEEEcCCCCCCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEc
Confidence            6788887777421                             113689999999865433454444

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=97.87  E-value=0.00037  Score=54.93  Aligned_cols=100  Identities=20%  Similarity=0.264  Sum_probs=67.8

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEec-CCCHHHHHHHHHHHhcCCeeEEEEe--CCcccccccC-----CCc
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHS-DRTQKQRDNVVRSFRTGRIWILITT--ELLGRGIDFR-----TVR  116 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~-~~~~~~r~~~~~~f~~~~~~vlv~t--~~~~~g~~i~-----~~~  116 (159)
                      .++.++||++|.+.++.+++.   .+.+ .+..+ +++   +.+.++.|+...-.||+++  ....+|+|+|     .++
T Consensus       392 ~~g~~lvlF~Sy~~l~~v~~~---~~~~-v~~q~~~~~---~~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~  464 (551)
T 3crv_A          392 AKANVLVVFPSYEIMDRVMSR---ISLP-KYVESEDSS---VEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLIS  464 (551)
T ss_dssp             CSSEEEEEESCHHHHHHHHTT---CCSS-EEECCSSCC---HHHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEE
T ss_pred             CCCCEEEEecCHHHHHHHHHh---cCCc-EEEcCCCCC---HHHHHHHHHhcCCeEEEEEecceecccccccccCCccee
Confidence            566899999999999998873   2322 33443 334   3457778854444799998  6999999999     477


Q ss_pred             EEEEecCCCC--------------------H----------HHHHHHHhhccCCCCcceEEEEec
Q psy576          117 LVVNYDFPSS--------------------A----------ISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       117 ~vi~~~~~~~--------------------~----------~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                      .||..+.|..                    .          ....|.+||+-|..+.--++++.+
T Consensus       465 ~viI~~lPfp~~dp~~~ar~~~~~~~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD  529 (551)
T 3crv_A          465 DVVIVGIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLD  529 (551)
T ss_dssp             EEEEESCCCCCCSHHHHHHHHHTTCCSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEES
T ss_pred             EEEEEcCCCCCCCHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEee
Confidence            8887776641                    1          113588999999864433455444

>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=96.85  E-value=0.008  Score=49.41  Aligned_cols=100  Identities=15%  Similarity=0.208  Sum_probs=73.3

Q ss_pred             eeeeecCCCCChHHHHHHHH-hc-CCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcC
Q psy576           22 RMYRETEGAGSPVQAQDETI-LL-GIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~~~~-~~-~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~   95 (159)
                      ......+...+|.......+ .. ..+.++++.+++..-+...++.+.+.    ++++..+||+++..++...++.+.+|
T Consensus       391 ~~Ll~a~TGSGKTlvall~il~~l~~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g  470 (780)
T 1gm5_A          391 NRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNG  470 (780)
T ss_dssp             CCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSS
T ss_pred             cEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcC
Confidence            34444455567766633222 11 13568999999999888877766543    68899999999999999999999999


Q ss_pred             CeeEEEEeCC-cccccccCCCcEEEEe
Q psy576           96 RIWILITTEL-LGRGIDFRTVRLVVNY  121 (159)
Q Consensus        96 ~~~vlv~t~~-~~~g~~i~~~~~vi~~  121 (159)
                      +.+|+|+|.. +...+.+.++..||.-
T Consensus       471 ~~~IvVgT~~ll~~~~~~~~l~lVVID  497 (780)
T 1gm5_A          471 QIDVVIGTHALIQEDVHFKNLGLVIID  497 (780)
T ss_dssp             CCCEEEECTTHHHHCCCCSCCCEEEEE
T ss_pred             CCCEEEECHHHHhhhhhccCCceEEec
Confidence            9999999964 3345666777777653

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=96.69  E-value=0.014  Score=43.88  Aligned_cols=99  Identities=7%  Similarity=0.054  Sum_probs=72.5

Q ss_pred             eeeeecCCCCChHHHHH-HHHh-cCCCCCEEEEecchHHHHHHHHHHHh---CCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           22 RMYRETEGAGSPVQAQD-ETIL-LGIEPPVLVFVQSKERAQELYNELIY---DGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~-~~~~-~~~~~~~lif~~~~~~~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      ..........+|..... .++. ...+.+++|.++++.-+..+++.+++   .++++..++|+.+..++...++.+..++
T Consensus        38 ~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~  117 (414)
T 3oiy_A           38 SFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDD  117 (414)
T ss_dssp             CEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTC
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCC
Confidence            44444555567776422 2222 23567899999999999999999887   5778999999999999888999999999


Q ss_pred             eeEEEEeCCcc----cccccCCCcEEEE
Q psy576           97 IWILITTELLG----RGIDFRTVRLVVN  120 (159)
Q Consensus        97 ~~vlv~t~~~~----~g~~i~~~~~vi~  120 (159)
                      .+|+|+|+-.-    .-++...+++||.
T Consensus       118 ~~Iiv~Tp~~l~~~l~~~~~~~~~~iVi  145 (414)
T 3oiy_A          118 YHILVFSTQFVSKNREKLSQKRFDFVFV  145 (414)
T ss_dssp             CSEEEEEHHHHHHCHHHHTTCCCSEEEE
T ss_pred             CCEEEECHHHHHHHHHHhccccccEEEE
Confidence            99999996321    1244456776665

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=96.18  E-value=0.045  Score=46.75  Aligned_cols=99  Identities=9%  Similarity=0.058  Sum_probs=73.8

Q ss_pred             eeeeecCCCCChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHh---CCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           22 RMYRETEGAGSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIY---DGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      ..........+|.......+.  ...+.++||.+++++-+..+++.+.+   .++++..+||+.+..++...++.+.++.
T Consensus        95 dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~  174 (1104)
T 4ddu_A           95 SFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDD  174 (1104)
T ss_dssp             CEEECCSTTCCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSC
T ss_pred             CEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCC
Confidence            444555555777775333222  23567899999999999999999987   4678999999999989999999999999


Q ss_pred             eeEEEEeCCcc----cccccCCCcEEEE
Q psy576           97 IWILITTELLG----RGIDFRTVRLVVN  120 (159)
Q Consensus        97 ~~vlv~t~~~~----~g~~i~~~~~vi~  120 (159)
                      .+|+|+|+-.-    .-++...+.++|.
T Consensus       175 ~~IlV~Tp~rL~~~l~~l~~~~l~~lVi  202 (1104)
T 4ddu_A          175 YHILVFSTQFVSKNREKLSQKRFDFVFV  202 (1104)
T ss_dssp             CSEEEEEHHHHHHSHHHHHTSCCSEEEE
T ss_pred             CCEEEECHHHHHHHHHhhcccCcCEEEE
Confidence            99999995321    1144567787775

>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=95.64  E-value=0.12  Score=44.41  Aligned_cols=99  Identities=18%  Similarity=0.246  Sum_probs=72.2

Q ss_pred             eeeeecCCCCChHHHHH-HHH-hcCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcC
Q psy576           22 RMYRETEGAGSPVQAQD-ETI-LLGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~-~~~-~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~   95 (159)
                      ......+...+|..... ..+ ....+.+++|.+++..-+...++.+.+.    +.++..+++..+..++...++.+..|
T Consensus       626 d~ll~~~TGsGKT~val~aa~~~~~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g  705 (1151)
T 2eyq_A          626 DRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEG  705 (1151)
T ss_dssp             EEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcC
Confidence            34444555567776532 221 2235568999999999888888877643    56788999999999999999999999


Q ss_pred             CeeEEEEeCC-cccccccCCCcEEEE
Q psy576           96 RIWILITTEL-LGRGIDFRTVRLVVN  120 (159)
Q Consensus        96 ~~~vlv~t~~-~~~g~~i~~~~~vi~  120 (159)
                      +.+|+|+|.. +...+.+.++.+||.
T Consensus       706 ~~dIvV~T~~ll~~~~~~~~l~lvIi  731 (1151)
T 2eyq_A          706 KIDILIGTHKLLQSDVKFKDLGLLIV  731 (1151)
T ss_dssp             CCSEEEECTHHHHSCCCCSSEEEEEE
T ss_pred             CCCEEEECHHHHhCCccccccceEEE
Confidence            9999999953 444466667776664

>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=95.18  E-value=0.16  Score=40.48  Aligned_cols=81  Identities=11%  Similarity=0.122  Sum_probs=62.8

Q ss_pred             eeeeecCCCCChHHH-HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHH--hcCCee
Q psy576           22 RMYRETEGAGSPVQA-QDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSF--RTGRIW   98 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f--~~~~~~   98 (159)
                      ..+...+...+|-.. +.-.+.  ..+.+||.+++.+-+....+.|.+.++++..++|+.+..++..++..+  ..+..+
T Consensus        61 d~lv~~pTGsGKTl~~~lpal~--~~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~  138 (591)
T 2v1x_A           61 EVFLVMPTGGGKSLCYQLPALC--SDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELK  138 (591)
T ss_dssp             CEEEECCTTSCTTHHHHHHHHT--SSSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCC
T ss_pred             CEEEEECCCChHHHHHHHHHHH--cCCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCC
Confidence            345555555666653 222222  356899999999999999999988899999999999999998888888  467889


Q ss_pred             EEEEeC
Q psy576           99 ILITTE  104 (159)
Q Consensus        99 vlv~t~  104 (159)
                      |+++|+
T Consensus       139 Ilv~Tp  144 (591)
T 2v1x_A          139 LIYVTP  144 (591)
T ss_dssp             EEEECH
T ss_pred             EEEECh
Confidence            999996

>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=94.58  E-value=0.12  Score=40.34  Aligned_cols=81  Identities=19%  Similarity=0.243  Sum_probs=62.7

Q ss_pred             eeeeecCCCCChHHH-HHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEE
Q psy576           22 RMYRETEGAGSPVQA-QDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL  100 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vl  100 (159)
                      ..+.......+|-.. +.-.+.  ..+.+||.++++.-+....+.+.+.++++..++|+.+..++...+..+..+..+|+
T Consensus        42 d~lv~apTGsGKTl~~~lp~l~--~~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~il  119 (523)
T 1oyw_A           42 DCLVVMPTGGGKSLCYQIPALL--LNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLL  119 (523)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHH--SSSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEE
T ss_pred             CEEEECCCCcHHHHHHHHHHHH--hCCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEE
Confidence            344444444556542 222222  34679999999999999999999889999999999999999999999999999999


Q ss_pred             EEeC
Q psy576          101 ITTE  104 (159)
Q Consensus       101 v~t~  104 (159)
                      ++|+
T Consensus       120 v~Tp  123 (523)
T 1oyw_A          120 YIAP  123 (523)
T ss_dssp             EECH
T ss_pred             EECH
Confidence            9885

>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=93.77  E-value=0.92  Score=30.64  Aligned_cols=96  Identities=13%  Similarity=0.164  Sum_probs=61.9

Q ss_pred             eeeeecCCCCChHHHHH-HHHhc---C-CCCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQD-ETILL---G-IEPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~-~~~~~---~-~~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..........+|..... -++..   . ...+++|.+++++-+..+++.+++.     +.++..++|+.+.....   +.
T Consensus        53 ~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~---~~  129 (220)
T 1t6n_A           53 DVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE---EV  129 (220)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHH---HH
T ss_pred             CEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHH---HH
Confidence            34444555567765432 22222   1 2347999999999998888777553     67889999988765543   34


Q ss_pred             HhcCCeeEEEEeCC-c-----ccccccCCCcEEEE
Q psy576           92 FRTGRIWILITTEL-L-----GRGIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~-~-----~~g~~i~~~~~vi~  120 (159)
                      +.++..+|+|+|.- +     ...++...++++|.
T Consensus       130 ~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lVi  164 (220)
T 1t6n_A          130 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFIL  164 (220)
T ss_dssp             HHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             HhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEE
Confidence            45567789999952 1     12345667777665

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=93.70  E-value=0.68  Score=28.27  Aligned_cols=49  Identities=24%  Similarity=0.436  Sum_probs=38.5

Q ss_pred             EEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           49 VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        49 ~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      .++|.+..+-..++...++..|..+..++++.+...|.+-++.|.+...
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqgv   53 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGV   53 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTC
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCC
Confidence            4568888888888888888888888888888888888888888765433

>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=93.54  E-value=0.61  Score=31.93  Aligned_cols=94  Identities=10%  Similarity=0.136  Sum_probs=60.5

Q ss_pred             eeeeecCCCCChHHH-HHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETIL----LGIEPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..........+|... +.-++.    .....++||.+++++-+..+++.++..     +.++..++|+.+..+....+  
T Consensus        63 ~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~--  140 (230)
T 2oxc_A           63 DLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL--  140 (230)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT--
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc--
Confidence            344455555777765 333332    223468999999999999888877653     56788999998776554332  


Q ss_pred             HhcCCeeEEEEeCC-c-----ccccccCCCcEEEE
Q psy576           92 FRTGRIWILITTEL-L-----GRGIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~-~-----~~g~~i~~~~~vi~  120 (159)
                         ...+|+|+|.- +     ...++...++++|.
T Consensus       141 ---~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lVi  172 (230)
T 2oxc_A          141 ---KKCHIAVGSPGRIKQLIELDYLNPGSIRLFIL  172 (230)
T ss_dssp             ---TSCSEEEECHHHHHHHHHTTSSCGGGCCEEEE
T ss_pred             ---cCCCEEEECHHHHHHHHhcCCcccccCCEEEe
Confidence               35789999963 1     12345556666664

>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=93.21  E-value=0.92  Score=31.60  Aligned_cols=95  Identities=17%  Similarity=0.183  Sum_probs=60.3

Q ss_pred             eeeeecCCCCChHHHHH-----HHHhcCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQD-----ETILLGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~-----~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ..+.......+|.....     .+.......+++|.+++++-+..+++.++..    +..+..++|+.+.......+   
T Consensus        82 ~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---  158 (249)
T 3ber_A           82 DIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL---  158 (249)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH---
T ss_pred             CEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh---
Confidence            44444555567765522     2222333457999999999888888776543    77889999988765443322   


Q ss_pred             hcCCeeEEEEeCC-c------ccccccCCCcEEEE
Q psy576           93 RTGRIWILITTEL-L------GRGIDFRTVRLVVN  120 (159)
Q Consensus        93 ~~~~~~vlv~t~~-~------~~g~~i~~~~~vi~  120 (159)
                       .+..+|+|+|.- +      ..++++..++++|.
T Consensus       159 -~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lVi  192 (249)
T 3ber_A          159 -AKKPHIIIATPGRLIDHLENTKGFNLRALKYLVM  192 (249)
T ss_dssp             -HTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEE
T ss_pred             -cCCCCEEEECHHHHHHHHHcCCCcCccccCEEEE
Confidence             246789999952 1      13456667776664

>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=92.29  E-value=1.9  Score=29.64  Aligned_cols=95  Identities=17%  Similarity=0.121  Sum_probs=61.2

Q ss_pred             eeeeecCCCCChHHH-HHHHHh---c------CCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETIL---L------GIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDN   87 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~---~------~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~   87 (159)
                      ..+.......+|... +.-++.   .      ..+.+++|.+++++-+..+++.++.    .+..+..++|+.+......
T Consensus        68 ~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  147 (242)
T 3fe2_A           68 DMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR  147 (242)
T ss_dssp             CEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHH
T ss_pred             CEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHH
Confidence            455555555777655 222222   1      2355799999999998888776654    3788999999988766554


Q ss_pred             HHHHHhcCCeeEEEEeCC-----cc-cccccCCCcEEEE
Q psy576           88 VVRSFRTGRIWILITTEL-----LG-RGIDFRTVRLVVN  120 (159)
Q Consensus        88 ~~~~f~~~~~~vlv~t~~-----~~-~g~~i~~~~~vi~  120 (159)
                      .+..    ..+|+|+|+-     +. ..+++..+.++|.
T Consensus       148 ~~~~----~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lVi  182 (242)
T 3fe2_A          148 DLER----GVEICIATPGRLIDFLECGKTNLRRTTYLVL  182 (242)
T ss_dssp             HHHH----CCSEEEECHHHHHHHHHHTSCCCTTCCEEEE
T ss_pred             HhcC----CCCEEEECHHHHHHHHHcCCCCcccccEEEE
Confidence            4332    4679999952     11 2345667776664

>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=92.26  E-value=0.68  Score=39.43  Aligned_cols=97  Identities=11%  Similarity=0.105  Sum_probs=65.4

Q ss_pred             eeeeecCCCCChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhC----CC----ceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYD----GI----NVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~----~~----~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..+.......+|.....-++.  ...+.+++|.++++.-+..+++.++..    +.    .+..++|+.+..++.+..+.
T Consensus        73 dvlv~apTGSGKTl~~lp~l~~~~~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~  152 (1054)
T 1gku_B           73 SFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQN  152 (1054)
T ss_dssp             CEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHS
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhh
Confidence            444444555677654333332  235678999999999999888877643    55    78999999999888777777


Q ss_pred             HhcCCeeEEEEeCC-cccccc-cCCCcEEEE
Q psy576           92 FRTGRIWILITTEL-LGRGID-FRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~-~~~g~~-i~~~~~vi~  120 (159)
                      +.+  .+|+|+|+- +..-+. +..++++|.
T Consensus       153 l~~--~~IlV~TP~~L~~~l~~L~~l~~lVi  181 (1054)
T 1gku_B          153 LRN--FKIVITTTQFLSKHYRELGHFDFIFV  181 (1054)
T ss_dssp             GGG--CSEEEEEHHHHHHCSTTSCCCSEEEE
T ss_pred             ccC--CCEEEEcHHHHHHHHHHhccCCEEEE
Confidence            777  889999962 211111 445666664

>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=91.50  E-value=2.2  Score=31.23  Aligned_cols=96  Identities=13%  Similarity=0.170  Sum_probs=61.9

Q ss_pred             eeeeecCCCCChHHHH-HHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQ-DETILL----GIEPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l-~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ......+...+|.... .-++..    ....++||.|+++.-+..+++.+.+.     +.++..++|+.+......   .
T Consensus        47 ~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~  123 (391)
T 1xti_A           47 DVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE---V  123 (391)
T ss_dssp             CEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHH---H
T ss_pred             cEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHH---H
Confidence            4455555556777653 333322    13457999999999998888777553     678899999987665443   3


Q ss_pred             HhcCCeeEEEEeCC-c-----ccccccCCCcEEEE
Q psy576           92 FRTGRIWILITTEL-L-----GRGIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~-~-----~~g~~i~~~~~vi~  120 (159)
                      +..+..+|+|+|.- +     ...++...+++||.
T Consensus       124 ~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vVi  158 (391)
T 1xti_A          124 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFIL  158 (391)
T ss_dssp             HHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEE
T ss_pred             HhcCCCCEEEECHHHHHHHHHcCCccccccCEEEE
Confidence            44566789999953 2     12244566676664

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=91.38  E-value=1.9  Score=29.45  Aligned_cols=94  Identities=16%  Similarity=0.162  Sum_probs=57.2

Q ss_pred             eeeeecCCCCChHHHH-H---HHHhc-----CCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQ-D---ETILL-----GIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNV   88 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l-~---~~~~~-----~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~   88 (159)
                      ..........+|.... .   +.+..     ..+.+++|.+++++-+..+++.++..    +..+..++|+.+.......
T Consensus        64 ~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  143 (236)
T 2pl3_A           64 DVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAER  143 (236)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHH
T ss_pred             CEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHh
Confidence            3444555556777642 2   22211     23567999999999999888877653    4678889998765543332


Q ss_pred             HHHHhcCCeeEEEEeCC-c----cc--ccccCCCcEEEE
Q psy576           89 VRSFRTGRIWILITTEL-L----GR--GIDFRTVRLVVN  120 (159)
Q Consensus        89 ~~~f~~~~~~vlv~t~~-~----~~--g~~i~~~~~vi~  120 (159)
                      +     +..+|+|+|.- +    ..  .++...++++|.
T Consensus       144 ~-----~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lVi  177 (236)
T 2pl3_A          144 I-----NNINILVCTPGRLLQHMDETVSFHATDLQMLVL  177 (236)
T ss_dssp             H-----TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEE
T ss_pred             C-----CCCCEEEECHHHHHHHHHhcCCcccccccEEEE
Confidence            2     45789999952 2    11  245556666664

>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=90.77  E-value=1.8  Score=35.90  Aligned_cols=75  Identities=11%  Similarity=-0.027  Sum_probs=52.3

Q ss_pred             eeecCCCCChHHH-HH-HHHhcCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           24 YRETEGAGSPVQA-QD-ETILLGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        24 ~~~~~~~~~k~~~-l~-~~~~~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ........+|... +. -++....+..++|.++|.+-|..+++++..    .++.+..+.|+++.+++....      ..
T Consensus       100 Iaea~TGeGKTlaf~LP~~l~aL~g~~vlVltptreLA~qd~e~~~~l~~~lgl~v~~i~gg~~~~~r~~~~------~~  173 (844)
T 1tf5_A          100 IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAY------AA  173 (844)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTSCHHHHHHHH------HS
T ss_pred             EEEccCCcHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHhc------CC
Confidence            4444444666554 22 233444566899999999999888776643    488999999999987665432      26


Q ss_pred             eEEEEeC
Q psy576           98 WILITTE  104 (159)
Q Consensus        98 ~vlv~t~  104 (159)
                      +|+++|+
T Consensus       174 dIv~gTp  180 (844)
T 1tf5_A          174 DITYSTN  180 (844)
T ss_dssp             SEEEEEH
T ss_pred             CEEEECc
Confidence            7999995

>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=90.75  E-value=0.91  Score=31.23  Aligned_cols=96  Identities=13%  Similarity=0.172  Sum_probs=52.9

Q ss_pred             eeeeecCCCCChHHH-HHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETILL----GIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ..+.......+|... +.-++..    ....+++|.+++++-+..+++.++..    +..+..++|+.+...   ..+.+
T Consensus        69 ~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~---~~~~l  145 (237)
T 3bor_A           69 DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRN---EMQKL  145 (237)
T ss_dssp             CEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC--------------
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHH---HHHHH
Confidence            344444444566654 3333332    23458999999999999888887653    456777888754332   33445


Q ss_pred             hcCCeeEEEEeC-----Cccc-ccccCCCcEEEE
Q psy576           93 RTGRIWILITTE-----LLGR-GIDFRTVRLVVN  120 (159)
Q Consensus        93 ~~~~~~vlv~t~-----~~~~-g~~i~~~~~vi~  120 (159)
                      ..+...|+|+|.     .+.. .++...++++|.
T Consensus       146 ~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lVi  179 (237)
T 3bor_A          146 QAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVL  179 (237)
T ss_dssp             --CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEE
T ss_pred             hcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEE
Confidence            566788999994     2222 245556776664

>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=90.46  E-value=1.4  Score=29.25  Aligned_cols=95  Identities=13%  Similarity=0.098  Sum_probs=58.5

Q ss_pred             eeeeecCCCCChHHH-HHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETILL----GIEPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..........+|... +.-++..    ....++++.++++.-+..+++.+...     +..+..++|+.+..+...   .
T Consensus        42 ~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~  118 (206)
T 1vec_A           42 DILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM---R  118 (206)
T ss_dssp             CEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHH---H
T ss_pred             CEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHH---h
Confidence            444445555666654 3333332    23457999999999988888877542     567888999877654332   2


Q ss_pred             HhcCCeeEEEEeCC-c----cc-ccccCCCcEEEE
Q psy576           92 FRTGRIWILITTEL-L----GR-GIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~-~----~~-g~~i~~~~~vi~  120 (159)
                      + .+..+|+|+|.- +    .. .++...++++|.
T Consensus       119 ~-~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lVi  152 (206)
T 1vec_A          119 L-DDTVHVVIATPGRILDLIKKGVAKVDHVQMIVL  152 (206)
T ss_dssp             T-TSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEE
T ss_pred             c-CCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEE
Confidence            2 346789999962 1    12 234556776664

>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=90.44  E-value=0.74  Score=31.17  Aligned_cols=94  Identities=11%  Similarity=0.134  Sum_probs=54.5

Q ss_pred             eeeeecCCCCChHHH-HHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETIL----LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ..........+|... +..++.    .....++++.++++.-+..+++.+...    +..+..++|+.+..+...   .+
T Consensus        53 ~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~  129 (224)
T 1qde_A           53 DVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAE---GL  129 (224)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-------------C
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHh---cC
Confidence            445555555777765 333333    234458999999999988888877543    677888898866544332   22


Q ss_pred             hcCCeeEEEEeCCc------ccccccCCCcEEEE
Q psy576           93 RTGRIWILITTELL------GRGIDFRTVRLVVN  120 (159)
Q Consensus        93 ~~~~~~vlv~t~~~------~~g~~i~~~~~vi~  120 (159)
                      .  ..+|+|+|.-.      ...++...++++|.
T Consensus       130 ~--~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iVi  161 (224)
T 1qde_A          130 R--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFIL  161 (224)
T ss_dssp             T--TCSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             C--CCCEEEECHHHHHHHHHhCCcchhhCcEEEE
Confidence            2  37799998521      22344556666664

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=90.13  E-value=0.31  Score=29.42  Aligned_cols=36  Identities=14%  Similarity=0.090  Sum_probs=31.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~   80 (159)
                      ++.+++++|.+-..+...+..|.+.|+++..+.|++
T Consensus        54 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~   89 (108)
T 3gk5_A           54 RDKKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGI   89 (108)
T ss_dssp             TTSCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHH
T ss_pred             CCCeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcH
Confidence            456799999999999999999999888888888875

>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=90.04  E-value=2  Score=35.70  Aligned_cols=75  Identities=12%  Similarity=-0.082  Sum_probs=51.2

Q ss_pred             eeecCCCCChHHH-HHHHH-hcCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           24 YRETEGAGSPVQA-QDETI-LLGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        24 ~~~~~~~~~k~~~-l~~~~-~~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ........+|... +.-++ ....+.+++|.++|..-|..+++.+..    .++.+..++|+++.+.+....      ..
T Consensus        91 Iaem~TGsGKTlaf~LP~l~~~l~g~~vlVltPTreLA~Q~~e~~~~l~~~lgl~v~~i~GG~~~~~r~~~~------~~  164 (853)
T 2fsf_A           91 IAEMRTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAENNRPLFEFLGLTVGINLPGMPAPAKREAY------AA  164 (853)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHTTSSCCEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHHHHHH------HS
T ss_pred             eeeecCCchHHHHHHHHHHHHHHcCCcEEEEcCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHhc------CC
Confidence            4444444566554 22322 334566899999999988887776643    488999999999987555433      26


Q ss_pred             eEEEEeC
Q psy576           98 WILITTE  104 (159)
Q Consensus        98 ~vlv~t~  104 (159)
                      +|+|+|+
T Consensus       165 dIvvgTp  171 (853)
T 2fsf_A          165 DITYGTN  171 (853)
T ss_dssp             SEEEEEH
T ss_pred             CEEEECC
Confidence            7899886

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=90.00  E-value=1.4  Score=33.87  Aligned_cols=79  Identities=10%  Similarity=-0.041  Sum_probs=51.1

Q ss_pred             eeeeecCCCCChHHHHH----HHHhcCC---CCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQD----ETILLGI---EPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVR   90 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~----~~~~~~~---~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~   90 (159)
                      ......+...+|.....    +.+....   ..++||.++++.-+....+.+...    ++.+..++|+.+...+...+.
T Consensus        21 ~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  100 (555)
T 3tbk_A           21 NTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNIASISGATSDSVSVQHII  100 (555)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECTTTGGGSCHHHHH
T ss_pred             CEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEEEEEcCCCcchhhHHHHh
Confidence            44555555567776522    2333323   678999999998888777766543    788999999986554432221


Q ss_pred             HHhcCCeeEEEEeC
Q psy576           91 SFRTGRIWILITTE  104 (159)
Q Consensus        91 ~f~~~~~~vlv~t~  104 (159)
                          +..+|+|+|.
T Consensus       101 ----~~~~i~v~T~  110 (555)
T 3tbk_A          101 ----EDNDIIILTP  110 (555)
T ss_dssp             ----HHCSEEEECH
T ss_pred             ----cCCCEEEECH
Confidence                1366889885

>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=89.71  E-value=2.6  Score=35.27  Aligned_cols=75  Identities=15%  Similarity=-0.016  Sum_probs=52.6

Q ss_pred             eeecCCCCChHHH--HHHHHhcCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           24 YRETEGAGSPVQA--QDETILLGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        24 ~~~~~~~~~k~~~--l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ........+|...  |.-++....+.+++|.+++..-|...++++..    .++.+..+.|+++++++....      ..
T Consensus       128 Iaem~TGeGKTLa~~LP~~l~aL~g~~v~VvTpTreLA~Qdae~m~~l~~~lGLsv~~i~gg~~~~~r~~~y------~~  201 (922)
T 1nkt_A          128 VAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDYLAKRDSEWMGRVHRFLGLQVGVILATMTPDERRVAY------NA  201 (922)
T ss_dssp             EEECCTTSCHHHHTHHHHHHHHTTTSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHHHHHH------HS
T ss_pred             EEEecCCCccHHHHHHHHHHHHHhCCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHhc------CC
Confidence            4444444666655  22334444567899999999988887776643    488999999999987665543      26


Q ss_pred             eEEEEeC
Q psy576           98 WILITTE  104 (159)
Q Consensus        98 ~vlv~t~  104 (159)
                      +|+++|+
T Consensus       202 DIvygTp  208 (922)
T 1nkt_A          202 DITYGTN  208 (922)
T ss_dssp             SEEEEEH
T ss_pred             CEEEECc
Confidence            7999985

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=89.54  E-value=0.31  Score=28.91  Aligned_cols=36  Identities=11%  Similarity=0.178  Sum_probs=30.9

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~   80 (159)
                      ++.+++++|.+-..+...+..|.+.|+++..+.|++
T Consensus        55 ~~~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~   90 (100)
T 3foj_A           55 DNETYYIICKAGGRSAQVVQYLEQNGVNAVNVEGGM   90 (100)
T ss_dssp             TTSEEEEECSSSHHHHHHHHHHHTTTCEEEEETTHH
T ss_pred             CCCcEEEEcCCCchHHHHHHHHHHCCCCEEEecccH
Confidence            456799999999999999999998888888888874

>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=89.39  E-value=3.3  Score=27.38  Aligned_cols=95  Identities=16%  Similarity=0.127  Sum_probs=60.3

Q ss_pred             eeeeecCCCCChHHH-HHHHHhc-------CCCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETILL-------GIEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~-------~~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..........+|... +.-++..       ....++++.++++.-+..+++.+...  ..++..++|+.+.......+. 
T Consensus        40 ~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  118 (207)
T 2gxq_A           40 DLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL-  118 (207)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH-
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh-
Confidence            344555555777765 3333332       23557999999999999998888765  467888999876654433322 


Q ss_pred             HhcCCeeEEEEeCC-----cc-cccccCCCcEEEE
Q psy576           92 FRTGRIWILITTEL-----LG-RGIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~-----~~-~g~~i~~~~~vi~  120 (159)
                         ...+|+|+|.-     +. ..++...++++|.
T Consensus       119 ---~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iVi  150 (207)
T 2gxq_A          119 ---RGADAVVATPGRALDYLRQGVLDLSRVEVAVL  150 (207)
T ss_dssp             ---HCCSEEEECHHHHHHHHHHTSSCCTTCSEEEE
T ss_pred             ---CCCCEEEECHHHHHHHHHcCCcchhhceEEEE
Confidence               24679999952     11 2345566776664

>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=89.22  E-value=2.7  Score=31.41  Aligned_cols=94  Identities=11%  Similarity=0.088  Sum_probs=60.9

Q ss_pred             eeeeecCCCCChHHHHHHHHhc---CCCCCEEEEecchHHHHHHHHHHHhC-CC---ceEEEecCCCHHHHHHHHHHHhc
Q psy576           22 RMYRETEGAGSPVQAQDETILL---GIEPPVLVFVQSKERAQELYNELIYD-GI---NVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~~~~~~---~~~~~~lif~~~~~~~~~l~~~l~~~-~~---~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      ......+...+|.......+..   ....++||.|++..-+....+.+.+. +.   .+..++|+....++.....    
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~----  100 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA----  100 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHH----
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhcc----
Confidence            3444445556777665444332   25678999999999888888887654 44   7899999988876554432    


Q ss_pred             CCeeEEEEeCC-ccc-----ccccCCCcEEEE
Q psy576           95 GRIWILITTEL-LGR-----GIDFRTVRLVVN  120 (159)
Q Consensus        95 ~~~~vlv~t~~-~~~-----g~~i~~~~~vi~  120 (159)
                       ...|+|+|.- +..     .+.....++||.
T Consensus       101 -~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIi  131 (494)
T 1wp9_A          101 -RAKVIVATPQTIENDLLAGRISLEDVSLIVF  131 (494)
T ss_dssp             -HCSEEEECHHHHHHHHHTTSCCTTSCSEEEE
T ss_pred             -CCCEEEecHHHHHHHHhcCCcchhhceEEEE
Confidence             3568888842 221     234455666654

>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=89.11  E-value=4.6  Score=29.07  Aligned_cols=94  Identities=9%  Similarity=0.103  Sum_probs=58.7

Q ss_pred             eeeeecCCCCChHHHHHH-HHh---cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHh
Q psy576           22 RMYRETEGAGSPVQAQDE-TIL---LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~~-~~~---~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      ..+...+...+|...... ++.   .....++++.+++..-+..+++.+.+.    +..+..++|+.........+.   
T Consensus        46 ~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~---  122 (367)
T 1hv8_A           46 NIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK---  122 (367)
T ss_dssp             EEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH---
T ss_pred             CEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC---
Confidence            444555555777765332 222   234568999999999888888877653    567888899877655433332   


Q ss_pred             cCCeeEEEEeCC-cc-----cccccCCCcEEEE
Q psy576           94 TGRIWILITTEL-LG-----RGIDFRTVRLVVN  120 (159)
Q Consensus        94 ~~~~~vlv~t~~-~~-----~g~~i~~~~~vi~  120 (159)
                        ..+|+|+|.- +.     ..+++...++||.
T Consensus       123 --~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIi  153 (367)
T 1hv8_A          123 --NANIVVGTPGRILDHINRGTLNLKNVKYFIL  153 (367)
T ss_dssp             --TCSEEEECHHHHHHHHHTTCSCTTSCCEEEE
T ss_pred             --CCCEEEecHHHHHHHHHcCCcccccCCEEEE
Confidence              4678898852 11     1234456666654

>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=88.96  E-value=3.9  Score=27.64  Aligned_cols=95  Identities=15%  Similarity=0.171  Sum_probs=56.0

Q ss_pred             eeeeecCCCCChHHH-HHHHHh---c-------CCCCCEEEEecchHHHHHHHHHHHhC---CCceEEEecCCCHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETIL---L-------GIEPPVLVFVQSKERAQELYNELIYD---GINVDVIHSDRTQKQRDN   87 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~---~-------~~~~~~lif~~~~~~~~~l~~~l~~~---~~~~~~~~~~~~~~~r~~   87 (159)
                      ..........+|... +.-++.   .       ..+.++++.+++++-+..+++.+...   +..+..++|+.+......
T Consensus        59 ~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  138 (228)
T 3iuy_A           59 DLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIE  138 (228)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHH
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHH
Confidence            445555555777654 222221   1       24567999999999999998888763   677888888866544332


Q ss_pred             HHHHHhcCCeeEEEEeCC------cccccccCCCcEEEE
Q psy576           88 VVRSFRTGRIWILITTEL------LGRGIDFRTVRLVVN  120 (159)
Q Consensus        88 ~~~~f~~~~~~vlv~t~~------~~~g~~i~~~~~vi~  120 (159)
                         .+. ...+|+|+|.-      ....+++..++++|.
T Consensus       139 ---~~~-~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~lVi  173 (228)
T 3iuy_A          139 ---DIS-KGVDIIIATPGRLNDLQMNNSVNLRSITYLVI  173 (228)
T ss_dssp             ---HHH-SCCSEEEECHHHHHHHHHTTCCCCTTCCEEEE
T ss_pred             ---Hhc-CCCCEEEECHHHHHHHHHcCCcCcccceEEEE
Confidence               222 34789999952      122345667776664

>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=88.96  E-value=3.6  Score=31.07  Aligned_cols=95  Identities=17%  Similarity=0.218  Sum_probs=59.9

Q ss_pred             eeeeecCCCCChHHH-HH----HHHhcC-----CCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QD----ETILLG-----IEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDN   87 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~----~~~~~~-----~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~   87 (159)
                      ..........+|... +.    .++...     ...++||.+++++-+..+++.+++.    +..+..++|+.+......
T Consensus        95 d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~  174 (434)
T 2db3_A           95 DLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNE  174 (434)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHH
T ss_pred             CEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHH
Confidence            445555555777764 22    222221     2457999999999999998877653    567889999988765443


Q ss_pred             HHHHHhcCCeeEEEEeCC-----ccc-ccccCCCcEEEE
Q psy576           88 VVRSFRTGRIWILITTEL-----LGR-GIDFRTVRLVVN  120 (159)
Q Consensus        88 ~~~~f~~~~~~vlv~t~~-----~~~-g~~i~~~~~vi~  120 (159)
                      .+    ....+|+|+|.-     +.. .+++..++++|.
T Consensus       175 ~l----~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVl  209 (434)
T 2db3_A          175 CI----TRGCHVVIATPGRLLDFVDRTFITFEDTRFVVL  209 (434)
T ss_dssp             HH----TTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEE
T ss_pred             Hh----hcCCCEEEEChHHHHHHHHhCCcccccCCeEEE
Confidence            22    235789999952     122 234556776664

>3iwh_A Rhodanese-like domain protein; alpha-beta-alpha sandwich, structural genomics, C structural genomics of infectious diseases, csgid; 2.00A {Staphylococcus aureus subsp} PDB: 3mzz_A

Probab=88.76  E-value=0.3  Score=29.40  Aligned_cols=36  Identities=11%  Similarity=0.114  Sum_probs=30.5

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~   80 (159)
                      ++.+++++|.+-..+...+..|.+.|++...+.||+
T Consensus        55 ~~~~ivv~C~~G~rS~~aa~~L~~~G~~~~~l~GG~   90 (103)
T 3iwh_A           55 KNEIYYIVCAGGVRSAKVVEYLEANGIDAVNVEGGM   90 (103)
T ss_dssp             TTSEEEEECSSSSHHHHHHHHHHTTTCEEEEETTHH
T ss_pred             CCCeEEEECCCCHHHHHHHHHHHHcCCCEEEecChH
Confidence            456799999998888999999999999888787764

>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=88.57  E-value=2.2  Score=32.87  Aligned_cols=95  Identities=12%  Similarity=0.032  Sum_probs=55.5

Q ss_pred             eeeeecCCCCChHHHHH----HHHhcCC---CCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQD----ETILLGI---EPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVR   90 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~----~~~~~~~---~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~   90 (159)
                      ......+...+|.....    +.+....   ..++||.++++.-+....+.+...    ++.+..++|+.+...+...+.
T Consensus        24 ~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  103 (556)
T 4a2p_A           24 NALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI  103 (556)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEECCCC-----CHHHHH
T ss_pred             CEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCcchhHHHhh
Confidence            44555555567766532    2333323   678999999999888877776553    788999999886554332221


Q ss_pred             HHhcCCeeEEEEeCC-cc----cc-c-ccCCCcEEEE
Q psy576           91 SFRTGRIWILITTEL-LG----RG-I-DFRTVRLVVN  120 (159)
Q Consensus        91 ~f~~~~~~vlv~t~~-~~----~g-~-~i~~~~~vi~  120 (159)
                          ...+|+|+|.- +.    .+ + .+..+++||.
T Consensus       104 ----~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vVi  136 (556)
T 4a2p_A          104 ----EDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIF  136 (556)
T ss_dssp             ----HHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEE
T ss_pred             ----CCCCEEEECHHHHHHHHHhCcccccccCCEEEE
Confidence                13668998853 21    11 2 4456666664

>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=88.49  E-value=1.9  Score=29.80  Aligned_cols=70  Identities=16%  Similarity=0.162  Sum_probs=47.4

Q ss_pred             CCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC-c-----ccccccCCCc
Q psy576           47 PPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL-L-----GRGIDFRTVR  116 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~-~-----~~g~~i~~~~  116 (159)
                      .++||.+++++-+..+++.++..    +..+..++|+.+.......   + ....+|+|+|.- +     ...+++..++
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~  176 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIRE---V-QMGCHLLVATPGRLVDFIEKNKISLEFCK  176 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHH---H-SSCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHH---h-CCCCCEEEECHHHHHHHHHcCCCChhhCC
Confidence            57999999999998888777543    5678888998766544322   2 245789999953 1     1224556667


Q ss_pred             EEEE
Q psy576          117 LVVN  120 (159)
Q Consensus       117 ~vi~  120 (159)
                      ++|.
T Consensus       177 ~lVi  180 (253)
T 1wrb_A          177 YIVL  180 (253)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6664

>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=88.28  E-value=3.3  Score=33.97  Aligned_cols=79  Identities=10%  Similarity=-0.040  Sum_probs=48.6

Q ss_pred             eeeeecCCCCChHHHHHH----HHhcCC---CCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQDE----TILLGI---EPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVR   90 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~~----~~~~~~---~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~   90 (159)
                      ..........+|......    .+....   +.++||.|++..-+......+++.    ++++..++|+.+...+...+.
T Consensus       265 ~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~  344 (797)
T 4a2q_A          265 NALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI  344 (797)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECCC-----CHHHHH
T ss_pred             CEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhcccCCceEEEEeCCcchhhhHHHhh
Confidence            444555555677765332    222222   678999999999888877766553    789999999986554332221


Q ss_pred             HHhcCCeeEEEEeC
Q psy576           91 SFRTGRIWILITTE  104 (159)
Q Consensus        91 ~f~~~~~~vlv~t~  104 (159)
                          +..+|+|+|.
T Consensus       345 ----~~~~Ivv~Tp  354 (797)
T 4a2q_A          345 ----EDSDIIVVTP  354 (797)
T ss_dssp             ----HTCSEEEECH
T ss_pred             ----CCCCEEEEch
Confidence                2467999984

>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=88.21  E-value=2  Score=31.44  Aligned_cols=78  Identities=12%  Similarity=0.135  Sum_probs=51.5

Q ss_pred             eeeeecCCCCChHHH-HHHHHh----cCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETIL----LGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ..+...+...+|... +.-++.    .....++++.++++.-+..+++.+.+    .+..+..++|+.+..+....+.  
T Consensus        60 ~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--  137 (394)
T 1fuu_A           60 DVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR--  137 (394)
T ss_dssp             CEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH--
T ss_pred             CEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC--
Confidence            344444555667655 333332    22456899999999999888887754    3678889999988766554433  


Q ss_pred             hcCCeeEEEEeC
Q psy576           93 RTGRIWILITTE  104 (159)
Q Consensus        93 ~~~~~~vlv~t~  104 (159)
                         ..+|+|+|.
T Consensus       138 ---~~~i~v~T~  146 (394)
T 1fuu_A          138 ---DAQIVVGTP  146 (394)
T ss_dssp             ---HCSEEEECH
T ss_pred             ---CCCEEEECH
Confidence               356888884

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=87.92  E-value=0.56  Score=27.38  Aligned_cols=35  Identities=14%  Similarity=0.089  Sum_probs=30.0

Q ss_pred             CCEEEEecchHHHHHHHHHHHhCCCceEEEecCCC
Q psy576           47 PPVLVFVQSKERAQELYNELIYDGINVDVIHSDRT   81 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~   81 (159)
                      .+++++|.+-..+...+..|.+.|+++..+.|++.
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            78999999998899999999888888777888763

>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=87.82  E-value=5.3  Score=27.84  Aligned_cols=95  Identities=14%  Similarity=0.159  Sum_probs=59.6

Q ss_pred             eeeeecCCCCChHHH-HHHHHh---c-----CCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETIL---L-----GIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNV   88 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~---~-----~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~   88 (159)
                      ..........+|... +.-++.   .     ..+.++++.+++++-+..+++.+++.    +..+..++|+........ 
T Consensus        93 ~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~-  171 (262)
T 3ly5_A           93 DLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQ-  171 (262)
T ss_dssp             CCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHH-
T ss_pred             cEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHH-
Confidence            344555555677765 222221   1     13567999999999999988887653    567788899876654432 


Q ss_pred             HHHHhcCCeeEEEEeCC-----cc--cccccCCCcEEEE
Q psy576           89 VRSFRTGRIWILITTEL-----LG--RGIDFRTVRLVVN  120 (159)
Q Consensus        89 ~~~f~~~~~~vlv~t~~-----~~--~g~~i~~~~~vi~  120 (159)
                        .+..+ .+|+|+|+-     +.  .++++..+.++|.
T Consensus       172 --~~~~~-~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lVi  207 (262)
T 3ly5_A          172 --KLGNG-INIIVATPGRLLDHMQNTPGFMYKNLQCLVI  207 (262)
T ss_dssp             --HHHHC-CSEEEECHHHHHHHHHHCTTCCCTTCCEEEE
T ss_pred             --HhcCC-CCEEEEcHHHHHHHHHccCCcccccCCEEEE
Confidence              23333 789999941     11  2356667776664

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=87.15  E-value=2.3  Score=24.06  Aligned_cols=36  Identities=14%  Similarity=0.111  Sum_probs=28.5

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCc-eEEEecCCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGIN-VDVIHSDRT   81 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~   81 (159)
                      +..+++++|.+-..+...+..|.+.|++ +..+ |++.
T Consensus        40 ~~~~ivv~C~~g~rs~~aa~~L~~~G~~~v~~l-GG~~   76 (85)
T 2jtq_A           40 KNDTVKVYCNAGRQSGQAKEILSEMGYTHVENA-GGLK   76 (85)
T ss_dssp             TTSEEEEEESSSHHHHHHHHHHHHTTCSSEEEE-EETT
T ss_pred             CCCcEEEEcCCCchHHHHHHHHHHcCCCCEEec-cCHH
Confidence            5567999999988899999999988875 4455 7653

>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=87.14  E-value=4.3  Score=28.89  Aligned_cols=77  Identities=16%  Similarity=0.113  Sum_probs=52.9

Q ss_pred             eeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           22 RMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ..+...+...+|.......+.. ...++++.++++.-+...++.+.+.    +..+..++|+.+.......   +.  ..
T Consensus        33 ~~lv~~~TGsGKT~~~~~~~~~-~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~--~~  106 (337)
T 2z0m_A           33 NVVVRAKTGSGKTAAYAIPILE-LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINR---VR--NA  106 (337)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH-HTCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHH---HT--TC
T ss_pred             CEEEEcCCCCcHHHHHHHHHHh-hcCCEEEEeCCHHHHHHHHHHHHHHhhhcCCcEEEEECCcchHHHHhh---cC--CC
Confidence            4555555557777654443333 3678999999999999888888642    5678899998876654332   22  36


Q ss_pred             eEEEEeC
Q psy576           98 WILITTE  104 (159)
Q Consensus        98 ~vlv~t~  104 (159)
                      +|+|+|.
T Consensus       107 ~i~v~T~  113 (337)
T 2z0m_A          107 DIVVATP  113 (337)
T ss_dssp             SEEEECH
T ss_pred             CEEEECH
Confidence            7899884

>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=86.99  E-value=2.8  Score=30.11  Aligned_cols=92  Identities=12%  Similarity=0.040  Sum_probs=57.2

Q ss_pred             eeeeecCCCCChHHH-HHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETILL----GIEPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..+.......+|... +..++..    ....++||.+++++-+..++..+...     +..+...+|+.......     
T Consensus       133 ~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-----  207 (300)
T 3fmo_B          133 NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ-----  207 (300)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC-----
T ss_pred             eEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh-----
Confidence            444444555677654 3344432    23346999999999999988777543     46677777765432211     


Q ss_pred             HhcCCeeEEEEeCCc------c-cccccCCCcEEEE
Q psy576           92 FRTGRIWILITTELL------G-RGIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~~------~-~g~~i~~~~~vi~  120 (159)
                        ....+|+|+|+-.      . ..+++..+.++|.
T Consensus       208 --~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVl  241 (300)
T 3fmo_B          208 --KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVL  241 (300)
T ss_dssp             --CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEE
T ss_pred             --cCCCCEEEECHHHHHHHHHhcCCCChhhceEEEE
Confidence              3456799999632      1 2456677887765

>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp, NSR437I, NESG, structural genomics, PSI-2, protein structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A

Probab=86.36  E-value=0.74  Score=27.57  Aligned_cols=36  Identities=17%  Similarity=0.218  Sum_probs=30.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCc-eEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGIN-VDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~-~~~~~~~~   80 (159)
                      ...+++++|.+-..+...+..|...|+. +..+.|++
T Consensus        51 ~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~   87 (106)
T 3hix_A           51 KSRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGL   87 (106)
T ss_dssp             TTSCEEEECSSHHHHHHHHHHHHHTTCSCEEECTTHH
T ss_pred             CCCeEEEEECCCChHHHHHHHHHHcCCcCEEEecCCH
Confidence            4567999999998999999999998884 77778874

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=86.31  E-value=3  Score=35.12  Aligned_cols=72  Identities=14%  Similarity=-0.013  Sum_probs=49.9

Q ss_pred             cCCCCChHHH--HHHHHhcCCCCCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCeeEE
Q psy576           27 TEGAGSPVQA--QDETILLGIEPPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL  100 (159)
Q Consensus        27 ~~~~~~k~~~--l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vl  100 (159)
                      .....+|...  +.-++....+.+++|.++|..-|...++.+..    .++.+..+.|+++.+++....      ..+|+
T Consensus        99 akTGeGKTLvf~Lp~~L~aL~G~qv~VvTPTreLA~Qdae~m~~l~~~lGLsv~~i~Gg~~~~~r~~ay------~~DIv  172 (997)
T 2ipc_A           99 MKTGEGKTLVATLAVALNALTGKGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGVIQHASTPAERRKAY------LADVT  172 (997)
T ss_dssp             CCSTHHHHHHHHHHHHHHHTTCSCCEEEESSHHHHHHHHHHHHHHHHTTTCCEEECCTTCCHHHHHHHH------TSSEE
T ss_pred             ccCCCchHHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHc------CCCEE
Confidence            3333455443  22333444566899999999988887776643    488999999999987766544      36788


Q ss_pred             EEeC
Q psy576          101 ITTE  104 (159)
Q Consensus       101 v~t~  104 (159)
                      ++|+
T Consensus       173 yGTp  176 (997)
T 2ipc_A          173 YVTN  176 (997)
T ss_dssp             EEEH
T ss_pred             EECc
Confidence            8885

>2k0z_A Uncharacterized protein HP1203; A/B domain, structural genomics, unknown function, PSI-2, PR structure initiative; NMR {Helicobacter pylori}

Probab=86.01  E-value=1.4  Score=26.53  Aligned_cols=38  Identities=13%  Similarity=0.101  Sum_probs=31.4

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCC
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRT   81 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~   81 (159)
                      .+..+++++|.+-..+...+..|...|+....+.|++.
T Consensus        54 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~~~~l~GG~~   91 (110)
T 2k0z_A           54 HKDKKVLLHCRAGRRALDAAKSMHELGYTPYYLEGNVY   91 (110)
T ss_dssp             CSSSCEEEECSSSHHHHHHHHHHHHTTCCCEEEESCGG
T ss_pred             CCCCEEEEEeCCCchHHHHHHHHHHCCCCEEEecCCHH
Confidence            35678999999999999999999998875577888863

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=85.49  E-value=0.91  Score=30.72  Aligned_cols=95  Identities=15%  Similarity=0.162  Sum_probs=55.3

Q ss_pred             eeeeecCCCCChHHH-HHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC--------CCceEEEecCCCHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETILL----GIEPPVLVFVQSKERAQELYNELIYD--------GINVDVIHSDRTQKQRDNV   88 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~--------~~~~~~~~~~~~~~~r~~~   88 (159)
                      ..........+|... +.-++..    ....+++|.+++++-+..+++.+++.        +..+..++|+.+.....  
T Consensus        43 ~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~--  120 (219)
T 1q0u_A           43 SMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKAL--  120 (219)
T ss_dssp             CEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTT--
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHH--
Confidence            344444554566654 3333322    23457999999999988887776542        56778888876443211  


Q ss_pred             HHHHhcCCeeEEEEeCC-----ccc-ccccCCCcEEEE
Q psy576           89 VRSFRTGRIWILITTEL-----LGR-GIDFRTVRLVVN  120 (159)
Q Consensus        89 ~~~f~~~~~~vlv~t~~-----~~~-g~~i~~~~~vi~  120 (159)
                       +.+ ....+|+|+|.-     +.. .++...++++|.
T Consensus       121 -~~~-~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lVi  156 (219)
T 1q0u_A          121 -EKL-NVQPHIVIGTPGRINDFIREQALDVHTAHILVV  156 (219)
T ss_dssp             -CCC-SSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEE
T ss_pred             -HHc-CCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEE
Confidence             111 235679999952     111 234556666654

>3g5j_A Putative ATP/GTP binding protein; N-terminal domain of ATP/GTP binding protein, PSI, MCSG, STR genomics, protein structure initiative; HET: PGE; 1.76A {Clostridium difficile}

Probab=85.45  E-value=0.88  Score=28.13  Aligned_cols=35  Identities=17%  Similarity=0.277  Sum_probs=29.6

Q ss_pred             CCEEEEe-cchHHHHHHHHHHHhCCCceEEEecCCC
Q psy576           47 PPVLVFV-QSKERAQELYNELIYDGINVDVIHSDRT   81 (159)
Q Consensus        47 ~~~lif~-~~~~~~~~l~~~l~~~~~~~~~~~~~~~   81 (159)
                      .+++++| .+-..+...+..|...|+++..+.|++.
T Consensus        90 ~~ivvyC~~~G~rs~~a~~~L~~~G~~v~~l~GG~~  125 (134)
T 3g5j_A           90 DNIVIYCARGGMRSGSIVNLLSSLGVNVYQLEGGYK  125 (134)
T ss_dssp             SEEEEECSSSSHHHHHHHHHHHHTTCCCEEETTHHH
T ss_pred             CeEEEEECCCChHHHHHHHHHHHcCCceEEEeCcHH
Confidence            6899999 5777888889999998888889998864

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=85.09  E-value=7.4  Score=28.69  Aligned_cols=70  Identities=20%  Similarity=0.227  Sum_probs=47.5

Q ss_pred             CCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC-c----c-cccccCCCc
Q psy576           47 PPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL-L----G-RGIDFRTVR  116 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~-~----~-~g~~i~~~~  116 (159)
                      .++||.+++++-+..+++.+.+    .+..+..++|+.+..+...   .+. ...+|+|+|.- +    . ..+++..++
T Consensus       102 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~-~~~~I~v~Tp~~l~~~l~~~~~~~~~~~  177 (417)
T 2i4i_A          102 PISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIR---DLE-RGCHLLVATPGRLVDMMERGKIGLDFCK  177 (417)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHH---HHT-TCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHH---Hhh-CCCCEEEEChHHHHHHHHcCCcChhhCc
Confidence            4699999999999988887754    3677889999887655433   222 34679999962 1    1 123455666


Q ss_pred             EEEE
Q psy576          117 LVVN  120 (159)
Q Consensus       117 ~vi~  120 (159)
                      +||.
T Consensus       178 ~iVi  181 (417)
T 2i4i_A          178 YLVL  181 (417)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6664

>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 2.50A {Bacillus halodurans} PDB: 3o3w_A

Probab=84.80  E-value=0.84  Score=29.11  Aligned_cols=36  Identities=11%  Similarity=0.116  Sum_probs=30.3

Q ss_pred             CCCCEEEEecch--HHHHHHHHHHHhCCCceEEEecCC
Q psy576           45 IEPPVLVFVQSK--ERAQELYNELIYDGINVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~--~~~~~l~~~l~~~~~~~~~~~~~~   80 (159)
                      ++.++++||.+-  ..+...+..|...|+++..+.|++
T Consensus        71 ~~~~ivvyC~~g~~~rs~~aa~~L~~~G~~v~~l~GG~  108 (144)
T 3nhv_A           71 KEKVIITYCWGPACNGATKAAAKFAQLGFRVKELIGGI  108 (144)
T ss_dssp             TTSEEEEECSCTTCCHHHHHHHHHHHTTCEEEEEESHH
T ss_pred             CCCeEEEEECCCCccHHHHHHHHHHHCCCeEEEeCCcH
Confidence            456799999987  578888999999999988899975

>1tq1_A AT5G66040, senescence-associated family protein; CESG, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} SCOP: c.46.1.3

Probab=83.55  E-value=1  Score=28.04  Aligned_cols=36  Identities=22%  Similarity=0.215  Sum_probs=30.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      .+.+++++|.+-..+...+..|.+.|+ ++..+.|++
T Consensus        81 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~  117 (129)
T 1tq1_A           81 QSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGY  117 (129)
T ss_dssp             TTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCH
T ss_pred             CCCeEEEECCCCcHHHHHHHHHHHcCCCCeEEeCCcH
Confidence            456899999998888899999988887 477888886

>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=83.32  E-value=9.9  Score=27.93  Aligned_cols=95  Identities=13%  Similarity=0.145  Sum_probs=59.1

Q ss_pred             eeeecCCCCChHHH-HHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHh
Q psy576           23 MYRETEGAGSPVQA-QDETILL----GIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        23 ~~~~~~~~~~k~~~-l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      .+.......+|... +.-++..    ....+++|.++++.-+..+++.+...    +..+...+|+.....   ..+.+.
T Consensus        80 ~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~  156 (414)
T 3eiq_A           80 VIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRA---EVQKLQ  156 (414)
T ss_dssp             EEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHH---HHHHHT
T ss_pred             EEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHH---HHHHHh
Confidence            44445555677655 3333332    24567999999999988888877653    566777777765433   344556


Q ss_pred             cCCeeEEEEeCC-----ccc-ccccCCCcEEEE
Q psy576           94 TGRIWILITTEL-----LGR-GIDFRTVRLVVN  120 (159)
Q Consensus        94 ~~~~~vlv~t~~-----~~~-g~~i~~~~~vi~  120 (159)
                      .+...|+|+|.-     +.. .++...+++||.
T Consensus       157 ~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vVi  189 (414)
T 3eiq_A          157 MEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVL  189 (414)
T ss_dssp             TTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEE
T ss_pred             cCCCCEEEECHHHHHHHHHcCCcccccCcEEEE
Confidence            677889999942     112 234455665554

>2fsx_A RV0390, COG0607: rhodanese-related sulfurtransferase; RV0390 BR SAD DATA with FBAR, structural genomics, PSI; 1.80A {Mycobacterium tuberculosis}

Probab=83.31  E-value=1.3  Score=28.15  Aligned_cols=37  Identities=19%  Similarity=0.156  Sum_probs=30.0

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDRT   81 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~~   81 (159)
                      +..++++||.+-..+...+..|...|+ ++..+.|++.
T Consensus        79 ~~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~  116 (148)
T 2fsx_A           79 HERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFE  116 (148)
T ss_dssp             --CCEEEECSSSSTHHHHHHHHHHTTCCSEEEETTTTT
T ss_pred             CCCEEEEEcCCChhHHHHHHHHHHcCCcceEEEcCChh
Confidence            457899999998888888999999888 5888889873

>1gmx_A GLPE protein; transferase, rhodanese, sulfurtransferase, glycerol metabolism; 1.1A {Escherichia coli} SCOP: c.46.1.3 PDB: 1gn0_A

Probab=83.26  E-value=0.83  Score=27.37  Aligned_cols=36  Identities=19%  Similarity=0.258  Sum_probs=30.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      ++.+++++|.+-..+...+..|...|+ ++..+.|++
T Consensus        57 ~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~   93 (108)
T 1gmx_A           57 FDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGF   93 (108)
T ss_dssp             TTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHH
T ss_pred             CCCCEEEEcCCCchHHHHHHHHHHcCCceEEEecCCH
Confidence            456899999998888999999988888 477888875

>1qxn_A SUD, sulfide dehydrogenase; polysulfide-sulfur transferase, homodimer; NMR {Wolinella succinogenes} SCOP: c.46.1.3

Probab=82.36  E-value=0.88  Score=28.72  Aligned_cols=37  Identities=24%  Similarity=0.232  Sum_probs=30.9

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      .+..+++++|.+-..+...+..|.+.|+ ++..+.|++
T Consensus        80 ~~~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~  117 (137)
T 1qxn_A           80 DPEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGM  117 (137)
T ss_dssp             CTTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCH
T ss_pred             CCCCeEEEEcCCCcHHHHHHHHHHHcCCcceEEEcCcH
Confidence            3567899999998888889999988888 578888885

>3flh_A Uncharacterized protein LP_1913; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.00A {Lactobacillus plantarum} PDB: 3fnj_A 3i3u_A

Probab=82.33  E-value=0.52  Score=29.17  Aligned_cols=44  Identities=9%  Similarity=-0.040  Sum_probs=32.3

Q ss_pred             HHHHHhcC-CCCCEEEEecchHH--HHHHHHHHHhCCCceEEEecCC
Q psy576           37 QDETILLG-IEPPVLVFVQSKER--AQELYNELIYDGINVDVIHSDR   80 (159)
Q Consensus        37 l~~~~~~~-~~~~~lif~~~~~~--~~~l~~~l~~~~~~~~~~~~~~   80 (159)
                      +.+.+... ++.+++++|.+-..  +...+..|...|+++..+.|++
T Consensus        61 l~~~~~~l~~~~~ivvyC~~g~r~~s~~a~~~L~~~G~~v~~l~GG~  107 (124)
T 3flh_A           61 LATRIGELDPAKTYVVYDWTGGTTLGKTALLVLLSAGFEAYELAGAL  107 (124)
T ss_dssp             HHHHGGGSCTTSEEEEECSSSSCSHHHHHHHHHHHHTCEEEEETTHH
T ss_pred             HHHHHhcCCCCCeEEEEeCCCCchHHHHHHHHHHHcCCeEEEeCCcH
Confidence            33444333 45579999998776  7888889988899877888875

>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=81.95  E-value=12  Score=27.31  Aligned_cols=95  Identities=16%  Similarity=0.081  Sum_probs=58.8

Q ss_pred             eeeeecCCCCChHHHH-HHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQ-DETILL----GIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l-~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ..+...+...+|.... .-++..    ..+.++++.++++.-+...++.+...    +..+..++|+.........    
T Consensus        60 ~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----  135 (400)
T 1s2m_A           60 DILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR----  135 (400)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHH----
T ss_pred             CEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHH----
Confidence            3455555557777643 333322    13457999999999988888777643    6678888998765433211    


Q ss_pred             hcCCeeEEEEeCC-----ccc-ccccCCCcEEEE
Q psy576           93 RTGRIWILITTEL-----LGR-GIDFRTVRLVVN  120 (159)
Q Consensus        93 ~~~~~~vlv~t~~-----~~~-g~~i~~~~~vi~  120 (159)
                      ..+..+|+|+|.-     +.. ..++..+++||.
T Consensus       136 ~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIi  169 (400)
T 1s2m_A          136 LNETVHILVGTPGRVLDLASRKVADLSDCSLFIM  169 (400)
T ss_dssp             TTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEE
T ss_pred             hcCCCCEEEEchHHHHHHHHhCCcccccCCEEEE
Confidence            2356789999942     222 234556676664

>2hhg_A Hypothetical protein RPA3614; MCSG, structural genomics, rohopseudom palustris, PSI-2, protein structure initiative; 1.20A {Rhodopseudomonas palustris}

Probab=80.97  E-value=1.1  Score=28.08  Aligned_cols=36  Identities=11%  Similarity=0.062  Sum_probs=30.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCc-eEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGIN-VDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~-~~~~~~~~   80 (159)
                      .+.++++||.+-..+...+..|...|+. +..+.|++
T Consensus        85 ~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~  121 (139)
T 2hhg_A           85 EDKKFVFYCAGGLRSALAAKTAQDMGLKPVAHIEGGF  121 (139)
T ss_dssp             SSSEEEEECSSSHHHHHHHHHHHHHTCCSEEEETTHH
T ss_pred             CCCeEEEECCCChHHHHHHHHHHHcCCCCeEEecCCH
Confidence            4567999999988888899999888884 88888875

>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=80.46  E-value=6.5  Score=33.03  Aligned_cols=79  Identities=10%  Similarity=-0.050  Sum_probs=47.8

Q ss_pred             eeeeecCCCCChHHHHHHHHhc----CC---CCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQAQDETILL----GI---EPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVR   90 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~~~~~~----~~---~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~   90 (159)
                      ..........+|.......+..    ..   +.++||.+++..-+...+..+++.    ++.+..++|+.+...+...+.
T Consensus       265 ~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~G~~~~~~~~~~~~  344 (936)
T 4a2w_A          265 NALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI  344 (936)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECCC-----CCHHHH
T ss_pred             CEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEECCcchhhHHHHhc
Confidence            3444455556777664433321    12   668999999998888877766553    788999999886554322221


Q ss_pred             HHhcCCeeEEEEeC
Q psy576           91 SFRTGRIWILITTE  104 (159)
Q Consensus        91 ~f~~~~~~vlv~t~  104 (159)
                          ...+|+|+|.
T Consensus       345 ----~~~~IvI~Tp  354 (936)
T 4a2w_A          345 ----EDSDIIVVTP  354 (936)
T ss_dssp             ----HHCSEEEECH
T ss_pred             ----cCCCEEEecH
Confidence                1357899884

>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=80.17  E-value=19  Score=27.95  Aligned_cols=96  Identities=11%  Similarity=0.009  Sum_probs=58.7

Q ss_pred             eeeeecCCCCChHHH----HHHHHhcCC-----CCCEEEEecchHHHHHHHHHHHhC--------CCceEEEecCCCHHH
Q psy576           22 RMYRETEGAGSPVQA----QDETILLGI-----EPPVLVFVQSKERAQELYNELIYD--------GINVDVIHSDRTQKQ   84 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~----l~~~~~~~~-----~~~~lif~~~~~~~~~l~~~l~~~--------~~~~~~~~~~~~~~~   84 (159)
                      ..+.......+|...    +.+.+....     ..++||.+++++-+..+++.+++.        ...+..++|+.+...
T Consensus       113 ~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  192 (563)
T 3i5x_A          113 DVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRA  192 (563)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHH
T ss_pred             eEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHH
Confidence            445555555777764    222222211     247999999999999888877652        345677778765443


Q ss_pred             HHHHHHHHhcCCeeEEEEeCCcc-----c--ccccCCCcEEEE
Q psy576           85 RDNVVRSFRTGRIWILITTELLG-----R--GIDFRTVRLVVN  120 (159)
Q Consensus        85 r~~~~~~f~~~~~~vlv~t~~~~-----~--g~~i~~~~~vi~  120 (159)
                         .++.+..+..+|+|+|+-..     .  ...+..+.+||.
T Consensus       193 ---~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lVi  232 (563)
T 3i5x_A          193 ---AMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVL  232 (563)
T ss_dssp             ---HHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEE
T ss_pred             ---HHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEE
Confidence               34555556778999996321     1  224456776664

---

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	159
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	2e-28
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	5e-23
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-20
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	4e-20
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	6e-20
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-17
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	4e-16
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	1e-15
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	2e-15
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	6e-15
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-14
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	6e-13
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	3e-12
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	2e-09
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	2e-09
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	2e-08
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	3e-08
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	2e-06
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	2e-04

>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 =  103 bits (259), Expect = 2e-28
 Identities = 23/119 (19%), Positives = 37/119 (31%), Gaps = 14/119 (11%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQR----------DNVVRSFRTGRIW 98
            L+F  SK++  EL  +L+  GIN    +                   + + +  TG   
Sbjct: 39  HLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFD 98

Query: 99  ILITTELLGRG---IDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
            +I                   +     P  A+S   R GR GR G+ G        + 
Sbjct: 99  SVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPGER 156

>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 = 90.0 bits (222), Expect = 5e-23
 Identities = 32/114 (28%), Positives = 51/114 (44%), Gaps = 9/114 (7%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQR--------DNVVRSFRTGRIWIL 100
           ++VF   +E A+++ NEL+ DGI         +++            ++  F  G   +L
Sbjct: 164 IIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVL 223

Query: 101 ITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
           + T +   G+D   V LVV Y+   SAI  I R GR GR    G+ +    K  
Sbjct: 224 VATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGT 276

>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 = 79.6 bits (195), Expect = 3e-20
 Identities = 49/112 (43%), Positives = 74/112 (66%)

Query: 48  PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
             ++F  ++ + +EL  +L  D   V  I+SD  Q++RD +++ FR+G   ILI+T+LL 
Sbjct: 29  QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLA 88

Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           RGID + V LV+NYD P++  +YIHRIGR GR GR+G A+ F T +D   +R
Sbjct: 89  RGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMR 140

>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 = 79.2 bits (194), Expect = 4e-20
 Identities = 47/119 (39%), Positives = 71/119 (59%)

Query: 41  ILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL 100
           +L   E   LVF ++K   +EL + L   G     IH D +Q QR+ V+R F+  +I IL
Sbjct: 23  LLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRIL 82

Query: 101 ITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           I T+++ RGID   +  V+NY  P +  SY+HRIGR GR G++GKA++   +++   LR
Sbjct: 83  IATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLR 141

>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 = 81.0 bits (199), Expect = 6e-20
 Identities = 22/124 (17%), Positives = 41/124 (33%), Gaps = 15/124 (12%)

Query: 41  ILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWIL 100
           IL  +    +++ ++ E A+E+Y  L       +          +      F  G I  L
Sbjct: 20  ILEKLGTGGIIYARTGEEAEEIYESL------KNKFRIGIVTATKKGDYEKFVEGEIDHL 73

Query: 101 ITTE----LLGRGIDF-RTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           I T      L RG+D    +R  V    P    S+   I        +   +  +  ++ 
Sbjct: 74  IGTAHYYGTLVRGLDLPERIRFAVFVGCP----SFRVTIEDIDSLSPQMVKLLAYLYRNV 129

Query: 156 PLLR 159
             + 
Sbjct: 130 DEIE 133

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 73.8 bits (180), Expect = 1e-17
 Identities = 24/106 (22%), Positives = 47/106 (44%), Gaps = 5/106 (4%)

Query: 46  EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
           +  +++F +  E         I     +  I    ++++R+ ++  FRTGR   ++++++
Sbjct: 93  KDKIIIFTRHNELV-----YRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQV 147

Query: 106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFT 151
           L  GID     + V      SA  YI R+GR  R  +  K    + 
Sbjct: 148 LDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYE 193

>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 = 69.2 bits (168), Expect = 4e-16
 Identities = 41/112 (36%), Positives = 68/112 (60%)

Query: 48  PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
             ++F  +K +   L  ++      V  +H D  QK+R+++++ FR+G   +LI+T++  
Sbjct: 36  QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 95

Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           RG+D   V L++NYD P++   YIHRIGR+GR GR+G A+ F    D  +LR
Sbjct: 96  RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILR 147

>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 = 66.7 bits (162), Expect = 2e-15
 Identities = 24/109 (22%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
            L+F  SK++  EL  +L+  GIN    +                     +++ T+ L  
Sbjct: 38  HLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTN-------GDVVVVATDALMT 90

Query: 109 GIDFRT---VRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
           G        +    +   P  A+S   R GR GR G+ G    F    +
Sbjct: 91  GFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR-GKPG-IYRFVAPGE 137

>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 = 67.0 bits (162), Expect = 6e-15
 Identities = 32/112 (28%), Positives = 53/112 (47%)

Query: 48  PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
             +++  S+ + ++    L   GI+    H+      R +V   F+   + I++ T   G
Sbjct: 32  SGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFG 91

Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
            GI+   VR VV++D P +  SY    GRAGR G   +A+ F+   D   LR
Sbjct: 92  MGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR 143

>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 = 67.3 bits (163), Expect = 1e-14
 Identities = 21/132 (15%), Positives = 42/132 (31%), Gaps = 23/132 (17%)

Query: 42  LLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILI 101
           +   +   + FV S +   ++   L  +G  V  +       +        RT     ++
Sbjct: 174 VTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYIK----TRTNDWDFVV 229

Query: 102 TTELLGRGIDF---------RTVRLVVNYDFPS----------SAISYIHRIGRAGRGGR 142
           TT++   G +F         R ++ V+  D             +  S   R GR GR  +
Sbjct: 230 TTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPK 289

Query: 143 EGKAVTFFTKQD 154
                  +  + 
Sbjct: 290 NENDQYIYMGEP 301

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

 Score = 61.0 bits (147), Expect = 6e-13
 Identities = 33/99 (33%), Positives = 47/99 (47%), Gaps = 5/99 (5%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
            LV   +K+ A++L + L   GI V  +HS+    +R  ++R  R G+  +L+   LL  
Sbjct: 34  TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 93

Query: 109 GIDFRTVRLVVNYD-----FPSSAISYIHRIGRAGRGGR 142
           G+D   V LV   D     F  S  S I  IGRA R   
Sbjct: 94  GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN 132

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

 Score = 59.3 bits (143), Expect = 3e-12
 Identities = 34/112 (30%), Positives = 47/112 (41%), Gaps = 5/112 (4%)

Query: 49  VLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR 108
            LV V +   A+EL + L+  GI    +H +    +R  ++R  R G    L+   LL  
Sbjct: 34  TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLRE 93

Query: 109 GIDFRTVRLVVNYD-----FPSSAISYIHRIGRAGRGGREGKAVTFFTKQDA 155
           G+D   V LV   D     F  S  S I  IGRA R  R    +      +A
Sbjct: 94  GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEA 145

>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 = 51.6 bits (122), Expect = 2e-09
 Identities = 39/112 (34%), Positives = 63/112 (56%)

Query: 48  PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
             ++F  S  R + L  ++   G +    H+   Q++R+ V   FR G++  L+ ++LL 
Sbjct: 34  QAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLT 93

Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           RGID + V +V+N+DFP +A +Y+HRIGR+GR G  G A+      D   L 
Sbjct: 94  RGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLY 145

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 201

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 = 51.8 bits (123), Expect = 2e-09
 Identities = 31/150 (20%), Positives = 49/150 (32%), Gaps = 39/150 (26%)

Query: 48  PVLVFVQSKERAQELYNELIYDGIN------------------------------VDVIH 77
            VLVF  ++  A++   +L                                        H
Sbjct: 42  GVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHH 101

Query: 78  SDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV-------NYDFPSSAISY 130
           +     QR  V  +FR G I +++ T  L  G++    R++V        Y        Y
Sbjct: 102 AGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEY 161

Query: 131 IHRIGRAGRGGR--EGKAVTFFTKQDAPLL 158
               GRAGR G    G+A+    K+D  + 
Sbjct: 162 KQMAGRAGRPGMDERGEAIIIVGKRDREIA 191

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} 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: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 22/88 (25%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 68  YDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFPSSA 127
           +    + ++H   +Q+++D V+  F  GR  IL++T ++  GID     ++V  +     
Sbjct: 62  FPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFG 121

Query: 128 ISYIHR-IGRAGRGGREGKAVTFFTKQD 154
           ++ +H+  GR GRGG+E           
Sbjct: 122 LAQLHQLRGRVGRGGQEAYCFLVVGDVG 149

>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 = 48.1 bits (113), Expect = 3e-08
 Identities = 37/107 (34%), Positives = 60/107 (56%)

Query: 48  PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
            V++FV+S +R   L   L+        IH    Q++R +  + F+  +  IL+ T L G
Sbjct: 29  QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 88

Query: 108 RGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD 154
           RG+D   V +  NYD P  + +Y+HR+ RAGR G +G A+TF + ++
Sbjct: 89  RGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 135

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]} Length = 175

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]

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 27/120 (22%), Positives = 48/120 (40%), Gaps = 11/120 (9%)

Query: 48  PVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLG 107
           PVLV   + E ++ +   L   GI   V+++   +++   +  + + G +   I T + G
Sbjct: 36  PVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAV--TIATNMAG 93

Query: 108 RGIDFRTVRLVVNYD--------FPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPLLR 159
           RG D +    V               S        GR+GR G  G    + + +D  L+R
Sbjct: 94  RGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED-ELMR 152

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 24/126 (19%), Positives = 43/126 (34%), Gaps = 22/126 (17%)

Query: 46  EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL 105
           + P   F+ S   A  +   L   G +V V++     K  +    + +  +   ++ T++
Sbjct: 36  KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDI 91

Query: 106 LGRG--------IDFRTVRLVVNYD----------FPSSAISYIHRIGRAGRGGREGKAV 147
              G        +D RT    V  D             SA S   R GR GR        
Sbjct: 92  AEMGANLCVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDS 151

Query: 148 TFFTKQ 153
            ++++ 
Sbjct: 152 YYYSEP 157

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	159
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	100.0
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	100.0
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.96
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.96
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.93
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.93
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.91
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.9
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.87
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.87
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.86
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.84
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.79
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.75
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.67
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.66
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.59
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	99.21
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.8
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.66
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	96.49
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	94.04
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	91.36
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	90.07
d2b2na1	308	Transcription-repair coupling factor, TRCF {Escher	89.45
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	88.56
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	87.74
d1qxna_	137	Polysulfide-sulfur transferase (sulfide dehydrogen	87.62
d1wmaa1	275	Carbonyl reductase/20beta-hydroxysteroid dehydroge	86.32
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	86.25
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	86.02
d1em8a_	147	DNA polymerase III chi subunit {Escherichia coli [	85.39
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	84.97
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	84.29
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	83.93
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	83.76
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	83.16
d1yt8a1	136	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	82.97
d1urha2	120	3-mercaptopyruvate sulfurtransferase {Escherichia	80.41

>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=100.00  E-value=2.4e-36  Score=203.42  Aligned_cols=142  Identities=28%  Similarity=0.510  Sum_probs=135.5

Q ss_pred             hhhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhc
Q psy576           15 RVKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRT   94 (159)
Q Consensus        15 ~~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~   94 (159)
                      .+.++|+|+|+.++.++.|+..|.+++......++||||++.+.++.++..|...++++..+||+++.++|..+++.|++
T Consensus         3 ~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~   82 (168)
T d2j0sa2           3 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRS   82 (168)
T ss_dssp             CSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCcEEEEEEecChHHHHHHHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhc
Confidence            45789999999999988899999999988788899999999999999999999999999999999999999999999999


Q ss_pred             CCeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           95 GRIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        95 ~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      |+.++||||+++++|+|+|++++||+|++|++...|.||+||+||.|+.|.++.++.+.|..
T Consensus        83 g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~  144 (168)
T d2j0sa2          83 GASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIR  144 (168)
T ss_dssp             TSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHH
T ss_pred             CCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999887754

>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=100.00  E-value=9.1e-36  Score=199.49  Aligned_cols=137  Identities=36%  Similarity=0.617  Sum_probs=126.2

Q ss_pred             cceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeE
Q psy576           20 LARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWI   99 (159)
Q Consensus        20 i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v   99 (159)
                      |.|+|..+...+.|++.|.++++.....++||||+++..++.++..|...++++..+||+++.++|..+++.|+.|+.+|
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            57889999887889999999999888899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576          100 LITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus       100 lv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      ||||+++++|+|+|++++||+|++|+++..|.||+||+||.|+.|.++.++++.|..
T Consensus        81 Lv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~  137 (162)
T d1fuka_          81 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVG  137 (162)
T ss_dssp             EEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHH
T ss_pred             eeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHH
Confidence            999999999999999999999999999999999999999999999999999987754

>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=100.00  E-value=2.2e-35  Score=199.43  Aligned_cols=141  Identities=28%  Similarity=0.482  Sum_probs=133.9

Q ss_pred             hhhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcC
Q psy576           16 VKSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTG   95 (159)
Q Consensus        16 ~~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~   95 (159)
                      ..++|.|+|..++. +.|...|.+++...+.+++||||++++.++.++..|...++.+..+||+++.++|..+++.|++|
T Consensus         3 tl~~i~q~yi~v~~-~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~   81 (171)
T d1s2ma2           3 TLKGITQYYAFVEE-RQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQG   81 (171)
T ss_dssp             BCTTEEEEEEECCG-GGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CccceEEEEEEcCH-HHHHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccC
Confidence            46789999999987 78999999999988888999999999999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           96 RIWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        96 ~~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      +..+||||+++++|+|+|.+++||+|++|+++..|.||+||+||.|+.|.++.|+.+.|...
T Consensus        82 ~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~  143 (171)
T d1s2ma2          82 KVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFN  143 (171)
T ss_dssp             SSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHH
T ss_pred             ccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999998876543

>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=100.00  E-value=9.3e-35  Score=193.42  Aligned_cols=138  Identities=35%  Similarity=0.579  Sum_probs=130.2

Q ss_pred             hccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe
Q psy576           18 SNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI   97 (159)
Q Consensus        18 ~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~   97 (159)
                      ++|.|+|..++. ++|++.|.+++.. .+.++||||+++++++.+++.|++.++.+..+||+++..+|..+++.|++|+.
T Consensus         2 ~nI~~~~i~v~~-~~K~~~L~~ll~~-~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~   79 (155)
T d1hv8a2           2 ANIEQSYVEVNE-NERFEALCRLLKN-KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI   79 (155)
T ss_dssp             SSSEEEEEECCG-GGHHHHHHHHHCS-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSS
T ss_pred             CCeEEEEEEeCh-HHHHHHHHHHHcc-CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccc
Confidence            578999999987 7999999999976 56689999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCccc
Q psy576           98 WILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAPL  157 (159)
Q Consensus        98 ~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~~  157 (159)
                      .+||||+++++|+|+|.+++||++++|+++..|.||+||+||.|+.|.++.++.+.|...
T Consensus        80 ~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~  139 (155)
T d1hv8a2          80 RILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKK  139 (155)
T ss_dssp             SEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHH
T ss_pred             eeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHH
Confidence            999999999999999999999999999999999999999999999999999999887543

>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=100.00  E-value=1.3e-33  Score=190.08  Aligned_cols=134  Identities=29%  Similarity=0.466  Sum_probs=128.1

Q ss_pred             ccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCee
Q psy576           19 NLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        19 ~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~   98 (159)
                      ++.++|+.+.. +.|...|.+++......++||||++++.++.+++.|.+.++++..+||+|+.++|..+++.|++|+..
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            46889999987 79999999999988888999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      +||||+++++|+|+|.+++|+++++|.++..|.||+||+||.|+.|.|+.++++.
T Consensus        80 iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~  134 (168)
T d1t5ia_          80 ILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDE  134 (168)
T ss_dssp             EEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSH
T ss_pred             eeeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECch
Confidence            9999999999999999999999999999999999999999999999999998764

>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=100.00  E-value=6.6e-33  Score=191.08  Aligned_cols=137  Identities=25%  Similarity=0.426  Sum_probs=125.0

Q ss_pred             hhccceeeeecCCCCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCC
Q psy576           17 KSNLARMYRETEGAGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGR   96 (159)
Q Consensus        17 ~~~i~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~   96 (159)
                      +++|.+.+.  + ..+|++.|.+++......++||||+|.+.++.++..|...++.+..+||+++.++|..+++.|++|+
T Consensus         4 RpNi~y~v~--~-~~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~   80 (200)
T d1oywa3           4 RPNIRYMLM--E-KFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDD   80 (200)
T ss_dssp             CTTEEEEEE--E-CSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CCCcEEEEE--c-CCcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhccc
Confidence            455654432  2 3578999999998878889999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCCcc
Q psy576           97 IWILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQDAP  156 (159)
Q Consensus        97 ~~vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~~~  156 (159)
                      .+|||||+++++|+|+|++++||++++|.++..|.||+||+||.|.+|.+++|+.+.|..
T Consensus        81 ~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~  140 (200)
T d1oywa3          81 LQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMA  140 (200)
T ss_dssp             CSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHH
T ss_pred             ceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHH
Confidence            999999999999999999999999999999999999999999999999999999876543

>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=99.96  E-value=1.5e-28  Score=164.44  Aligned_cols=109  Identities=30%  Similarity=0.404  Sum_probs=99.9

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecC
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDF  123 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~  123 (159)
                      ..+.++||||.++++++.++..|.+.|+++..+||+++..+|.+++++|++|+++|||||+++++|+|+|++++|+++++
T Consensus        29 ~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~  108 (174)
T d1c4oa2          29 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDA  108 (174)
T ss_dssp             HTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTT
T ss_pred             hcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEecc
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CC-----CHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576          124 PS-----SAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus       124 ~~-----~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      |.     +..+|.|++||+||.|. |.++++....
T Consensus       109 ~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~  142 (174)
T d1c4oa2         109 DKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRV  142 (174)
T ss_dssp             TSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSC
T ss_pred             ccccccchhHHHHHHhhhhhhcCC-CeeEEeecCC
Confidence            75     56889999999999875 6666666543

>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=99.96  E-value=2.5e-28  Score=165.32  Aligned_cols=105  Identities=30%  Similarity=0.425  Sum_probs=96.6

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDFP  124 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~~  124 (159)
                      .+.++||||+++++++.++..|+..++++..+||+|++.+|.++++.|++|+.+|||||+++++|+|+|++++||+|++|
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p  109 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD  109 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEEETTTT
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEEEecCC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C-----CHHHHHHHHhhccCCCCcceEEEEe
Q psy576          125 S-----SAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       125 ~-----~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      .     +...|.||+||+||.|... ++++.
T Consensus       110 ~~~~~~s~~~yi~R~GRagR~g~~~-~~~~~  139 (181)
T d1t5la2         110 KEGFLRSERSLIQTIGRAARNANGH-VIMYA  139 (181)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTSTTCE-EEEEC
T ss_pred             cccccccHHHHHHHHHhhccccCce-eEeec
Confidence            5     6889999999999997543 33333

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.93  E-value=9.2e-27  Score=151.07  Aligned_cols=102  Identities=25%  Similarity=0.355  Sum_probs=91.4

Q ss_pred             cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEec
Q psy576           43 LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD  122 (159)
Q Consensus        43 ~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~  122 (159)
                      ....+++||||+|++.++.+++.|.+.++++..+|++++.+       .|++++..+||||+++++|+| |+++.||+++
T Consensus        32 ~~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~  103 (138)
T d1jr6a_          32 VIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVIDCN  103 (138)
T ss_dssp             HHTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEECS
T ss_pred             hcCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhh-------hhhhhhcceeehhHHHHhccc-cccceEEEEE
Confidence            34667899999999999999999999999999999999854       477899999999999999999 9999999854


Q ss_pred             ----CCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          123 ----FPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       123 ----~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                          +|.+..+|.||+||+|| |++|. +.|+.+.|
T Consensus       104 ~~~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         104 TSDGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             EETTEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             ecCCCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence                69999999999999999 88884 66777765

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.93  E-value=2.3e-25  Score=161.04  Aligned_cols=123  Identities=28%  Similarity=0.448  Sum_probs=106.7

Q ss_pred             CChHHHHHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEec--------CCCHHHHHHHHHHHhcCCee
Q psy576           31 GSPVQAQDETIL----LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHS--------DRTQKQRDNVVRSFRTGRIW   98 (159)
Q Consensus        31 ~~k~~~l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~~~~~   98 (159)
                      ..|++.|.+++.    ...+.++||||++...++.+++.|.+.++++..++|        +++..++.++++.|++|++.
T Consensus       142 ~pK~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~  221 (286)
T d1wp9a2         142 HPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFN  221 (286)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCS
T ss_pred             CcHHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCc
Confidence            457776666653    456789999999999999999999999998888876        46667899999999999999


Q ss_pred             EEEEeCCcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576           99 ILITTELLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus        99 vlv~t~~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |||||+++++|+|+|++++||+|++|+++..|.||+||+||.+ +|.++.|+..+.
T Consensus       222 vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~  276 (286)
T d1wp9a2         222 VLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGT  276 (286)
T ss_dssp             EEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTS
T ss_pred             EEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCC
Confidence            9999999999999999999999999999999999999999975 677888887764

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.91  E-value=1.6e-24  Score=149.09  Aligned_cols=121  Identities=26%  Similarity=0.367  Sum_probs=101.9

Q ss_pred             hHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC------------------------------CCceEEEecCCCH
Q psy576           33 PVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYD------------------------------GINVDVIHSDRTQ   82 (159)
Q Consensus        33 k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~------------------------------~~~~~~~~~~~~~   82 (159)
                      ..+++.+.+.  .++++||||+|++.++.++..|...                              ...+.++||+|++
T Consensus        29 ~~~l~~~~i~--~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          29 FEELVEECVA--ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHHH--cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            3455566666  4678999999999998887776531                              0127899999999


Q ss_pred             HHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEE-------ecCCCCHHHHHHHHhhccCCC--CcceEEEEecCC
Q psy576           83 KQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVN-------YDFPSSAISYIHRIGRAGRGG--REGKAVTFFTKQ  153 (159)
Q Consensus        83 ~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~-------~~~~~~~~~~~q~~GR~~R~g--~~g~~~~~~~~~  153 (159)
                      .+|..+++.|++|.++|||||+.+++|+|+|..++||.       .+.|.+..+|.||+||+||.|  ..|.+++++...
T Consensus       107 ~~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~  186 (201)
T d2p6ra4         107 GQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKR  186 (201)
T ss_dssp             HHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGG
T ss_pred             hhHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCC
Confidence            99999999999999999999999999999999999885       456789999999999999998  468899888776


Q ss_pred             Cc
Q psy576          154 DA  155 (159)
Q Consensus       154 ~~  155 (159)
                      +.
T Consensus       187 ~~  188 (201)
T d2p6ra4         187 DR  188 (201)
T ss_dssp             GH
T ss_pred             Ch
Confidence            54

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.90  E-value=1.1e-24  Score=149.91  Aligned_cols=108  Identities=21%  Similarity=0.409  Sum_probs=100.3

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccccc
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI  110 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~  110 (159)
                      ..|++.|.+++....+.++||||.+...++.+.+.|.     +..+||+++..+|..+++.|++|+.+|||||+++++|+
T Consensus        78 ~~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gi  152 (200)
T d2fwra1          78 KNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGI  152 (200)
T ss_dssp             SHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSS
T ss_pred             HHHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhccc
Confidence            5688899999998788899999999999999988774     44689999999999999999999999999999999999


Q ss_pred             ccCCCcEEEEecCCCCHHHHHHHHhhccCCCCc
Q psy576          111 DFRTVRLVVNYDFPSSAISYIHRIGRAGRGGRE  143 (159)
Q Consensus       111 ~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~  143 (159)
                      |+|.+++||++++|+++..|.|++||++|.|+.
T Consensus       153 dl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~  185 (200)
T d2fwra1         153 DVPDANVGVIMSGSGSAREYIQRLGRILRPSKG  185 (200)
T ss_dssp             CSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTT
T ss_pred             CCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCC
Confidence            999999999999999999999999999999864

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.87  E-value=3.3e-22  Score=136.44  Aligned_cols=110  Identities=17%  Similarity=0.195  Sum_probs=101.6

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhC--CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEe
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYD--GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNY  121 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~--~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~  121 (159)
                      ..++++-+.|+..+..+.+.+.+++.  +.++..+||.|+++++++++..|.+|+.+|||||++++.|+|+|+++++|..
T Consensus        29 ~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~iiI~  108 (211)
T d2eyqa5          29 LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIE  108 (211)
T ss_dssp             TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEET
T ss_pred             HcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcEEEEe
Confidence            36788999999999999999988774  6789999999999999999999999999999999999999999999999988


Q ss_pred             cCC-CCHHHHHHHHhhccCCCCcceEEEEecCC
Q psy576          122 DFP-SSAISYIHRIGRAGRGGREGKAVTFFTKQ  153 (159)
Q Consensus       122 ~~~-~~~~~~~q~~GR~~R~g~~g~~~~~~~~~  153 (159)
                      +.. .-.+++.|..||+||.+..+.|+.++...
T Consensus       109 ~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5         109 RADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             TTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             cchhccccccccccceeeecCccceEEEEecCC
Confidence            776 58999999999999999999999998654

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.87  E-value=4.8e-24  Score=146.43  Aligned_cols=122  Identities=22%  Similarity=0.320  Sum_probs=95.0

Q ss_pred             hHHHHHHHHh--cCCCCCEEEEecchHHHH--------HHHHHHHhC---CCceEEEecCCCHHHHHHHHHHHhcCCeeE
Q psy576           33 PVQAQDETIL--LGIEPPVLVFVQSKERAQ--------ELYNELIYD---GINVDVIHSDRTQKQRDNVVRSFRTGRIWI   99 (159)
Q Consensus        33 k~~~l~~~~~--~~~~~~~lif~~~~~~~~--------~l~~~l~~~---~~~~~~~~~~~~~~~r~~~~~~f~~~~~~v   99 (159)
                      +...+.+.+.  ...++++-+.|+..+..+        +.++.|.+.   +.++..+||+|+++++++++++|.+|+.+|
T Consensus        14 ~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~i   93 (206)
T d1gm5a4          14 RVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDI   93 (206)
T ss_dssp             THHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSB
T ss_pred             cHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEE
Confidence            4444444443  235667878888665443        334444333   567889999999999999999999999999


Q ss_pred             EEEeCCcccccccCCCcEEEEecCCC-CHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          100 LITTELLGRGIDFRTVRLVVNYDFPS-SAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       100 lv~t~~~~~g~~i~~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      ||||++++.|+|+|+++++|+++.|. ..+.+.|..||+||.|..|.|++++++.+
T Consensus        94 LVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~  149 (206)
T d1gm5a4          94 LVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVG  149 (206)
T ss_dssp             CCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCC
T ss_pred             EEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeecccc
Confidence            99999999999999999999998885 78889999999999999999999987643

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.86  E-value=3.4e-24  Score=151.97  Aligned_cols=114  Identities=18%  Similarity=0.227  Sum_probs=97.4

Q ss_pred             CCChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEe----CC
Q psy576           30 AGSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT----EL  105 (159)
Q Consensus        30 ~~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t----~~  105 (159)
                      ++.|++.|..++... +.++||||++++.++.++++|...      +||+++..+|.+++++|++|+++|||||    ++
T Consensus        10 ~~~~~~~l~~~l~~~-~~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v   82 (248)
T d1gkub2          10 NDESISTLSSILEKL-GTGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGT   82 (248)
T ss_dssp             SCCCTTTTHHHHTTS-CSCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEEEECC----
T ss_pred             CchHHHHHHHHHHHh-CCCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccch
Confidence            478999999999864 467999999999999999999653      7999999999999999999999999999    67


Q ss_pred             cccccccCC-CcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          106 LGRGIDFRT-VRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       106 ~~~g~~i~~-~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      +++|+|+|+ +++||+|++|+    |.|++||+||.|..|.++.++...+
T Consensus        83 ~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~  128 (248)
T d1gkub2          83 LVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRN  128 (248)
T ss_dssp             --CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSC
T ss_pred             hhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhh
Confidence            999999996 99999999996    7799999999998877766655443

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.84  E-value=1.1e-21  Score=139.54  Aligned_cols=102  Identities=23%  Similarity=0.248  Sum_probs=88.9

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHH----------HHHHHHHhcCCeeEEEEeCCccc---ccc
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQR----------DNVVRSFRTGRIWILITTELLGR---GID  111 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r----------~~~~~~f~~~~~~vlv~t~~~~~---g~~  111 (159)
                      +++++||||+|++.+++++..|++.++++..+|++++.+.|          .++++.|.+|+.+++|+|+.+.+   |+|
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giD  114 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFS  114 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCC
Confidence            46789999999999999999999999999999999998876          45788899999999999999888   566


Q ss_pred             cCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEE
Q psy576          112 FRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAV  147 (159)
Q Consensus       112 i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~  147 (159)
                      ++.+.+|++++.|.+..+|+||+||+|| |.+|...
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~  149 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYR  149 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEE
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEE
Confidence            7777899999999999999999999999 7777554

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.79  E-value=8.7e-19  Score=129.06  Aligned_cols=120  Identities=11%  Similarity=0.123  Sum_probs=106.1

Q ss_pred             CChHHHHHHHHhc---CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCe---eEEEEeC
Q psy576           31 GSPVQAQDETILL---GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRI---WILITTE  104 (159)
Q Consensus        31 ~~k~~~l~~~~~~---~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~---~vlv~t~  104 (159)
                      ..|+..|.+++..   ..++++|||+.....++.+...|...+++...++|.++..+|..+++.|+++..   -+|++|.
T Consensus       100 S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~  179 (346)
T d1z3ix1         100 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK  179 (346)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG
T ss_pred             CHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecch
Confidence            4588887777752   356799999999999999999999999999999999999999999999998643   3677889


Q ss_pred             CcccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEe
Q psy576          105 LLGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFF  150 (159)
Q Consensus       105 ~~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~  150 (159)
                      +++.|+|++.++.||+++++|++..+.|++||++|.|+...|.++.
T Consensus       180 agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~r  225 (346)
T d1z3ix1         180 AGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYR  225 (346)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEE
T ss_pred             hhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEE
Confidence            9999999999999999999999999999999999999887766553

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.75  E-value=4e-18  Score=120.05  Aligned_cols=119  Identities=15%  Similarity=0.213  Sum_probs=89.3

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhC-CCceEEEecCCCHHHHHHHHHHHhcC-CeeEEEE-eCC
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYD-GINVDVIHSDRTQKQRDNVVRSFRTG-RIWILIT-TEL  105 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~~~~r~~~~~~f~~~-~~~vlv~-t~~  105 (159)
                      ..|+..+.+++..  ..++++||||......+.+...+... +..+..+||+++..+|..+++.|+++ ...++++ +.+
T Consensus        68 S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~  147 (244)
T d1z5za1          68 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKA  147 (244)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCT
T ss_pred             hhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccc
Confidence            4588888888863  35779999999999999999888654 78888999999999999999999886 4666654 588


Q ss_pred             cccccccCCCcEEEEecCCCCHHHHHHHHhhccCCCCcceEEEE
Q psy576          106 LGRGIDFRTVRLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTF  149 (159)
Q Consensus       106 ~~~g~~i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~  149 (159)
                      .+.|+|++.+++||++++||++..+.|+.||+.|.|+...+.++
T Consensus       148 ~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~  191 (244)
T d1z5za1         148 GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVH  191 (244)
T ss_dssp             TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEE
T ss_pred             cccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEE
Confidence            99999999999999999999999999999999999976555543

>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=99.67  E-value=1.2e-16  Score=115.07  Aligned_cols=105  Identities=20%  Similarity=0.272  Sum_probs=86.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEE-----
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVV-----  119 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi-----  119 (159)
                      ..++++|||+++++++++++.|.+.+.++..+||++....    ...|.+++..++|+|+++++|+|++ ++.|+     
T Consensus       177 ~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~  251 (305)
T d2bmfa2         177 FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRC  251 (305)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEE
T ss_pred             hCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCc
Confidence            5678999999999999999999999999999999986543    4568899999999999999999995 44443     


Q ss_pred             -----Eec----------CCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          120 -----NYD----------FPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       120 -----~~~----------~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                           +++          .|-|..+|.||+||+||.|+.+...+++....
T Consensus       252 ~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~~  301 (305)
T d2bmfa2         252 MKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGEP  301 (305)
T ss_dssp             EEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECSCC
T ss_pred             eeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECCCC
Confidence                 222          34589999999999999998877766665443

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.66  E-value=4.6e-16  Score=111.86  Aligned_cols=102  Identities=20%  Similarity=0.270  Sum_probs=81.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEecC-
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYDF-  123 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~~-  123 (159)
                      ..+++++||++.+++.++++.|++.+.++..+||++..+++.    .|.+++.+++|||++++.|+++ ++.+||+.+. 
T Consensus        35 ~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~  109 (299)
T d1yksa2          35 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTA  109 (299)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCce
Confidence            467899999999999999999999999999999999877644    5788999999999999999999 5888885442 


Q ss_pred             ------------------CCCHHHHHHHHhhccCCCCcceEEEEec
Q psy576          124 ------------------PSSAISYIHRIGRAGRGGREGKAVTFFT  151 (159)
Q Consensus       124 ------------------~~~~~~~~q~~GR~~R~g~~g~~~~~~~  151 (159)
                                        |-+.++..||.||+||.+....+++++.
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         110 FKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             eceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                              2378899999999999875555655554

>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=99.59  E-value=1.1e-14  Score=96.04  Aligned_cols=122  Identities=23%  Similarity=0.286  Sum_probs=96.3

Q ss_pred             CChHHHHHHHHhc--CCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETILL--GIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~~--~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      .+|+..+.+.+..  ..+.|+||++.|.+..+.++.+|.+.+++..+++.....++- +++ ...-..-.|.|+|+++++
T Consensus        17 ~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea-~II-~~Ag~~g~VtIATNmAGR   94 (175)
T d1tf5a4          17 EGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREA-QII-EEAGQKGAVTIATNMAGR   94 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHH-HHH-TTTTSTTCEEEEETTSST
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHH-HHH-HhccCCCceeehhhHHHc
Confidence            4677776666642  356899999999999999999999999999999987543322 222 222233469999999999


Q ss_pred             ccccCC---C-----cEEEEecCCCCHHHHHHHHhhccCCCCcceEEEEecCCC
Q psy576          109 GIDFRT---V-----RLVVNYDFPSSAISYIHRIGRAGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       109 g~~i~~---~-----~~vi~~~~~~~~~~~~q~~GR~~R~g~~g~~~~~~~~~~  154 (159)
                      |.||+-   +     -+||....|.+..-..|..||+||.|.+|...+|++-.|
T Consensus        95 GtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          95 GTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             TCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             CCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            999952   2     278888899999999999999999999999988887655

>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=99.21  E-value=3.1e-10  Score=76.14  Aligned_cols=122  Identities=20%  Similarity=0.249  Sum_probs=94.7

Q ss_pred             CChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc
Q psy576           31 GSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR  108 (159)
Q Consensus        31 ~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~  108 (159)
                      ..|+..+.+.+.  ...+.|+||.+.|++..+.+...|.+.+++..+++....  +++.-+=+-.-..-.|.|+|+++++
T Consensus        17 ~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~h--erEAeIIAqAG~~GaVTIATNMAGR   94 (219)
T d1nkta4          17 EAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYH--EQEATIIAVAGRRGGVTVATNMAGR   94 (219)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCH--HHHHHHHHTTTSTTCEEEEETTCST
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhH--HHHHHHHHhcccCCcEEeeccccCC
Confidence            467777666664  246789999999999999999999999999999998743  3333333322334569999999999


Q ss_pred             ccccCC----------------------------------------------------CcEEEEecCCCCHHHHHHHHhh
Q psy576          109 GIDFRT----------------------------------------------------VRLVVNYDFPSSAISYIHRIGR  136 (159)
Q Consensus       109 g~~i~~----------------------------------------------------~~~vi~~~~~~~~~~~~q~~GR  136 (159)
                      |.||.-                                                    --+||-...-.|..-=-|..||
T Consensus        95 GTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRGR  174 (219)
T d1nkta4          95 GTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGR  174 (219)
T ss_dssp             TCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHT
T ss_pred             CCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEecccccccccccccccc
Confidence            999932                                                    1256766667787778899999


Q ss_pred             ccCCCCcceEEEEecCCC
Q psy576          137 AGRGGREGKAVTFFTKQD  154 (159)
Q Consensus       137 ~~R~g~~g~~~~~~~~~~  154 (159)
                      +||+|.+|...+|++-.|
T Consensus       175 sGRQGDPGsSrFflSLeD  192 (219)
T d1nkta4         175 SGRQGDPGESRFYLSLGD  192 (219)
T ss_dssp             SSGGGCCEEEEEEEETTS
T ss_pred             ccccCCCccceeEEeccH
Confidence            999999999999988655

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.80  E-value=6.1e-05  Score=52.29  Aligned_cols=104  Identities=17%  Similarity=0.256  Sum_probs=74.9

Q ss_pred             CCChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEe
Q psy576           30 AGSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT  103 (159)
Q Consensus        30 ~~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t  103 (159)
                      ..+|..+....+.  ...+.++++.+++.--+...++.+.+.    ++.+..+||+++..+|.+++...++|+.+|+|+|
T Consensus       114 GSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGT  193 (264)
T d1gm5a3         114 GSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGT  193 (264)
T ss_dssp             SSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEEC
T ss_pred             cccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEee
Confidence            3677777554442  235678999999998888877766543    6789999999999999999999999999999999


Q ss_pred             CCccc-ccccCCCcEEEEecCCCCHHHHHHHHh
Q psy576          104 ELLGR-GIDFRTVRLVVNYDFPSSAISYIHRIG  135 (159)
Q Consensus       104 ~~~~~-g~~i~~~~~vi~~~~~~~~~~~~q~~G  135 (159)
                      ..+-. .+.+.++..||.-.  .+...+.||-+
T Consensus       194 hsl~~~~~~f~~LglviiDE--qH~fgv~Qr~~  224 (264)
T d1gm5a3         194 HALIQEDVHFKNLGLVIIDE--QHRFGVKQREA  224 (264)
T ss_dssp             TTHHHHCCCCSCCCEEEEES--CCCC-----CC
T ss_pred             hHHhcCCCCccccceeeecc--ccccchhhHHH
Confidence            76544 57777777666543  23445566643

>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=97.66  E-value=0.00044  Score=46.96  Aligned_cols=104  Identities=18%  Similarity=0.270  Sum_probs=79.3

Q ss_pred             CCChHHHHHHHHh--cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEe
Q psy576           30 AGSPVQAQDETIL--LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFRTGRIWILITT  103 (159)
Q Consensus        30 ~~~k~~~l~~~~~--~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t  103 (159)
                      ..+|.++....+.  ...+.++++.+++.--+...++.+++.    +.++..+||..+..++.+++..+.+|+.+|+|.|
T Consensus        86 GsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGt  165 (233)
T d2eyqa3          86 GFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGT  165 (233)
T ss_dssp             CTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEEC
T ss_pred             CCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEee
Confidence            3678887665553  246778999999999999988888763    6788999999999999999999999999999999


Q ss_pred             CCccc-ccccCCCcEEEEecCCCCHHHHHHHHh
Q psy576          104 ELLGR-GIDFRTVRLVVNYDFPSSAISYIHRIG  135 (159)
Q Consensus       104 ~~~~~-g~~i~~~~~vi~~~~~~~~~~~~q~~G  135 (159)
                      ..+.. .+.++++-.||.-.  .+-..|-|+.+
T Consensus       166 hs~l~~~~~f~~LgLiIiDE--eH~fg~kQ~~~  196 (233)
T d2eyqa3         166 HKLLQSDVKFKDLGLLIVDE--EHRFGVRHKER  196 (233)
T ss_dssp             THHHHSCCCCSSEEEEEEES--GGGSCHHHHHH
T ss_pred             hhhhccCCccccccceeeec--hhhhhhHHHHH
Confidence            86554 57777777666532  22333445543

>d2eyqa2 c.37.1.19 (A:349-465) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.49  E-value=0.0041  Score=37.38  Aligned_cols=78  Identities=17%  Similarity=0.089  Sum_probs=58.9

Q ss_pred             CChHHHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccccc
Q psy576           31 GSPVQAQDETILLGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGI  110 (159)
Q Consensus        31 ~~k~~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~  110 (159)
                      .+-++.|..+++. ...++|++|.+....+.+.+.|...++++..+.+.          ..+.++.  +.|+...+..|+
T Consensus        20 ~~p~~~L~~~i~~-~~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~~----------~~~~~~~--~~i~~~~l~~GF   86 (117)
T d2eyqa2          20 KAPLDALRKFLET-FDGPVVFSVESEGRREALGELLARIKIAPQRIMRL----------DEASDRG--RYLMIGAAEHGF   86 (117)
T ss_dssp             SSTTHHHHHHHTT-CCSCCCEEESSHHHHHHHHHHHGGGTCCCEECSSG----------GGCCTTC--CEEEECCCCSCE
T ss_pred             hcHHHHHHHHHHh-CCCeEEEEECCccHHHHHHHHHHHcCCCceEecCh----------hhhcCce--EEEEEecCcccc
Confidence            4556778888875 45689999999999999999999998887655442          1233334  556677899999


Q ss_pred             ccCCCcEEEEe
Q psy576          111 DFRTVRLVVNY  121 (159)
Q Consensus       111 ~i~~~~~vi~~  121 (159)
                      -+|+...++.-
T Consensus        87 ~~~~~~l~vIt   97 (117)
T d2eyqa2          87 VDTVRNLALIC   97 (117)
T ss_dssp             EETTTTEEEEE
T ss_pred             ccCCCCEEEEE
Confidence            99999888764

>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=94.04  E-value=0.2  Score=32.43  Aligned_cols=94  Identities=9%  Similarity=0.123  Sum_probs=61.7

Q ss_pred             eeeeecCCCCChHHHHH-HHHh---cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHHh
Q psy576           22 RMYRETEGAGSPVQAQD-ETIL---LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSFR   93 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~l~-~~~~---~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~   93 (159)
                      ..........+|..... -.+.   ...+.+++|.|++++.+..+.+.+...    +..+...+|+.+..+..+.+   +
T Consensus        44 d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l---~  120 (208)
T d1hv8a1          44 NIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL---K  120 (208)
T ss_dssp             EEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH---H
T ss_pred             CeeeechhcccccceeecccccccccccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc---C
Confidence            34444445566665533 2222   334457999999999999988877553    56788899988776655433   2


Q ss_pred             cCCeeEEEEeCC-----c-ccccccCCCcEEEE
Q psy576           94 TGRIWILITTEL-----L-GRGIDFRTVRLVVN  120 (159)
Q Consensus        94 ~~~~~vlv~t~~-----~-~~g~~i~~~~~vi~  120 (159)
                        ..+|+|+|+-     + ...+++..+.++|.
T Consensus       121 --~~~IlV~TP~~l~~~l~~~~~~~~~l~~lVi  151 (208)
T d1hv8a1         121 --NANIVVGTPGRILDHINRGTLNLKNVKYFIL  151 (208)
T ss_dssp             --TCSEEEECHHHHHHHHHTTCSCTTSCCEEEE
T ss_pred             --CCCEEEEChHHHHHHHHcCCCCcccCcEEEE
Confidence              3679999952     2 33557778887775

>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=91.36  E-value=0.42  Score=31.35  Aligned_cols=95  Identities=9%  Similarity=0.092  Sum_probs=61.8

Q ss_pred             eeeeecCCCCChHH-HHHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQ-AQDETILL----GIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        22 ~~~~~~~~~~~k~~-~l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ..........+|.. .+.-++..    ....+++|++++++-+..+++.+...    ++.+..+.|+.+..+....++  
T Consensus        56 dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~--  133 (222)
T d2j0sa1          56 DVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD--  133 (222)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH--
T ss_pred             CeEEEcCcchhhhhhhcccccccccccccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhc--
Confidence            44444444455544 34444442    23346999999999999998877543    567888899887765544432  


Q ss_pred             hcCCeeEEEEeCC------cccccccCCCcEEEE
Q psy576           93 RTGRIWILITTEL------LGRGIDFRTVRLVVN  120 (159)
Q Consensus        93 ~~~~~~vlv~t~~------~~~g~~i~~~~~vi~  120 (159)
                       . ..+|+|+|+-      ....+++..+.++|.
T Consensus       134 -~-~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVl  165 (222)
T d2j0sa1         134 -Y-GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVL  165 (222)
T ss_dssp             -H-CCSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             -c-CCeEEeCCCCcHHhcccccccccccceeeee
Confidence             2 3579999952      244556677887775

>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=90.07  E-value=0.27  Score=29.37  Aligned_cols=39  Identities=15%  Similarity=0.000  Sum_probs=33.5

Q ss_pred             cCCCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCC
Q psy576           43 LGIEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRT   81 (159)
Q Consensus        43 ~~~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~   81 (159)
                      ...++++++||.+-..+...+..|.+.|+++..+.|++.
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            345678999999988899999999999999889999864

>d2b2na1 c.37.1.19 (A:26-333) 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=89.45  E-value=0.93  Score=31.27  Aligned_cols=97  Identities=14%  Similarity=-0.046  Sum_probs=59.4

Q ss_pred             HHHHHHHhcCCCCCEEEEecchHHHHHHHHHHHhC-CCceEEEec-------CC-----CHHHHHHHHHHHhcCCeeEEE
Q psy576           35 QAQDETILLGIEPPVLVFVQSKERAQELYNELIYD-GINVDVIHS-------DR-----TQKQRDNVVRSFRTGRIWILI  101 (159)
Q Consensus        35 ~~l~~~~~~~~~~~~lif~~~~~~~~~l~~~l~~~-~~~~~~~~~-------~~-----~~~~r~~~~~~f~~~~~~vlv  101 (159)
                      ..+.++... ..+++||.|++...|+.+++.|+.. +..+..+-+       ..     ...+|.+++..+.+++..|+|
T Consensus         4 ~~~a~~~~~-~~~p~lvv~~~~~~A~~l~~~L~~~~~~~v~~fP~~e~lpyd~~s~~~~i~~~R~~~L~~l~~~~~~iii   82 (308)
T d2b2na1           4 TLVAEIAER-HAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLI   82 (308)
T ss_dssp             HHHHHHHHH-CSSCEEEEESSHHHHHHHHHHHHTTCSSCEEECCCCCSCTTCSSCCCHHHHHHHHHHHHHGGGCCSSEEE
T ss_pred             HHHHHHHHh-hCCCEEEEcCCHHHHHHHHHHHHhcCCCceEEcCCcccCccccCCCChHHHHHHHHHHHHHhhcCCceEE
Confidence            345666665 5788999999999999999999764 333333322       11     134677888888888888888


Q ss_pred             EeCCcccccccCC-----CcEEEEecCCCCHHHHHH
Q psy576          102 TTELLGRGIDFRT-----VRLVVNYDFPSSAISYIH  132 (159)
Q Consensus       102 ~t~~~~~g~~i~~-----~~~vi~~~~~~~~~~~~q  132 (159)
                      +|-.+...--.|.     ....+..+...+...+..
T Consensus        83 ts~~al~~~~~p~~~~~~~~~~l~~g~~~~~~~l~~  118 (308)
T d2b2na1          83 VPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRT  118 (308)
T ss_dssp             EEHHHHTBCCCCHHHHHHHCEEEETTCBCCHHHHHH
T ss_pred             eechhhhhhcccHHHHHHHHHhhhhhccccHHHHHH
Confidence            8743332322221     123445555555554433

>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=88.56  E-value=0.19  Score=29.57  Aligned_cols=46  Identities=20%  Similarity=0.185  Sum_probs=34.5

Q ss_pred             HHHHHHHhc-CCCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           35 QAQDETILL-GIEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        35 ~~l~~~~~~-~~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      ..+.++... .++.+++++|.+-..+...+..|.+.|+ ++..+.||+
T Consensus        60 ~~~~~~~~~~~~~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~  107 (119)
T d1tq1a_          60 DFLEQVSSHFGQSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGY  107 (119)
T ss_dssp             THHHHHTTTCCTTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCH
T ss_pred             HHHHHHHHhcCCCcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChH
Confidence            334444332 2456799999998889999999988877 688889986

>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=87.74  E-value=1.5  Score=28.11  Aligned_cols=97  Identities=12%  Similarity=0.143  Sum_probs=61.4

Q ss_pred             eeeeecCCCCChHHH-HHHHHhc----CCCCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETILL----GIEPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~~----~~~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..........+|... +.-++..    ....+++|.+++++-+..+.+.+...     ......++|+.+.....   ..
T Consensus        40 dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~  116 (207)
T d1t6na_          40 DVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE---EV  116 (207)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHH---HH
T ss_pred             CeEEEeccccccccccccceeeeecccCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHH---HH
Confidence            444444444555544 4444442    23346999999999999988887543     23567778887665443   33


Q ss_pred             HhcCCeeEEEEeCC------cccccccCCCcEEEEe
Q psy576           92 FRTGRIWILITTEL------LGRGIDFRTVRLVVNY  121 (159)
Q Consensus        92 f~~~~~~vlv~t~~------~~~g~~i~~~~~vi~~  121 (159)
                      +.....+|+|+|+-      -...+++.++.+++.-
T Consensus       117 l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlD  152 (207)
T d1t6na_         117 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILD  152 (207)
T ss_dssp             HHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEE
T ss_pred             HHhcCCCEEEeCcchhhhhccCCceeccccceeehh
Confidence            44566789999973      2234567778877753

>d1qxna_ c.46.1.3 (A:) Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud) {Wolinella succinogenes [TaxId: 844]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud)
species: Wolinella succinogenes [TaxId: 844]

Probab=87.62  E-value=0.29  Score=29.57  Aligned_cols=38  Identities=26%  Similarity=0.261  Sum_probs=31.5

Q ss_pred             cCCCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           43 LGIEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        43 ~~~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      ..++.+++++|.+-..+...+..|.+.|+ ++..+.||+
T Consensus        79 ~~~~~~ivvyC~~G~rs~~aa~~L~~~G~~nV~~l~GG~  117 (137)
T d1qxna_          79 LDPEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGM  117 (137)
T ss_dssp             CCTTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCH
T ss_pred             cCcccceeeeecccchHHHHHHHHHHcCCCcEEEecCHH
Confidence            34567899999998889999999988888 577888884

>d1wmaa1 c.2.1.2 (A:2-276) Carbonyl reductase/20beta-hydroxysteroid dehydrogenase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Tyrosine-dependent oxidoreductases
domain: Carbonyl reductase/20beta-hydroxysteroid dehydrogenase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.32  E-value=2.8  Score=27.87  Aligned_cols=58  Identities=16%  Similarity=0.203  Sum_probs=44.1

Q ss_pred             CCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHH-HHHHHHHHHhc--CCeeEEEEe
Q psy576           46 EPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQK-QRDNVVRSFRT--GRIWILITT  103 (159)
Q Consensus        46 ~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~-~r~~~~~~f~~--~~~~vlv~t  103 (159)
                      ...+++.+.+.+.++++.+.|++.+.++.++..+++.. .-.+..+.+.+  |.+++||..
T Consensus        28 g~~Vi~~~r~~~~~~~~~~~l~~~~~~~~~~~~Dvs~~~sv~~~~~~~~~~~g~iDiLVnN   88 (275)
T d1wmaa1          28 SGDVVLTARDVTRGQAAVQQLQAEGLSPRFHQLDIDDLQSIRALRDFLRKEYGGLDVLVNN   88 (275)
T ss_dssp             SSEEEEEESSHHHHHHHHHHHHHTTCCCEEEECCTTCHHHHHHHHHHHHHHHSSEEEEEEC
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhcCCcEEEEEEecCCHHHHHHHHHHHHHhcCCcEEEEEc
Confidence            45788899999999999999988877788888887544 33444455543  789999975

>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=86.25  E-value=1.5  Score=28.03  Aligned_cols=95  Identities=12%  Similarity=0.034  Sum_probs=58.1

Q ss_pred             eeeeecCCCCChH-HHHHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhC-----CCceEEEecCCCHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPV-QAQDETIL----LGIEPPVLVFVQSKERAQELYNELIYD-----GINVDVIHSDRTQKQRDNVVRS   91 (159)
Q Consensus        22 ~~~~~~~~~~~k~-~~l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~   91 (159)
                      ..........+|. ..+.-++.    ......++|.+++++.+..+++.+...     +..+....|+.........   
T Consensus        42 dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---  118 (206)
T d1veca_          42 DILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR---  118 (206)
T ss_dssp             CEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH---
T ss_pred             CEEeeccCccccccccccchhhcccccccCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHH---
Confidence            3334443434444 44555554    234456999999999999998877542     3456677777666543332   


Q ss_pred             HhcCCeeEEEEeCC------cccccccCCCcEEEE
Q psy576           92 FRTGRIWILITTEL------LGRGIDFRTVRLVVN  120 (159)
Q Consensus        92 f~~~~~~vlv~t~~------~~~g~~i~~~~~vi~  120 (159)
                       .....+|+|+|+-      ....++...+.++|.
T Consensus       119 -l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVl  152 (206)
T d1veca_         119 -LDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVL  152 (206)
T ss_dssp             -TTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEE
T ss_pred             -HHhccCeEEeCCccccccccchhccccccceEEE
Confidence             2456789999952      223345667777764

>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=86.02  E-value=1.2  Score=28.74  Aligned_cols=94  Identities=10%  Similarity=0.091  Sum_probs=53.7

Q ss_pred             eeeeecCCCCChHHH-HHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETIL----LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ..........+|... +.-.+.    ......++|.+++.+.+..+...+...    .......+++....++...    
T Consensus        49 dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  124 (212)
T d1qdea_          49 DVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG----  124 (212)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC--------------
T ss_pred             CEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHH----
Confidence            344444444555554 334433    234457999999999999998887543    3455666665444333221    


Q ss_pred             hcCCeeEEEEeCC------cccccccCCCcEEEE
Q psy576           93 RTGRIWILITTEL------LGRGIDFRTVRLVVN  120 (159)
Q Consensus        93 ~~~~~~vlv~t~~------~~~g~~i~~~~~vi~  120 (159)
                       ....+|+|+|+-      ...++++..+.+++.
T Consensus       125 -~~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVl  157 (212)
T d1qdea_         125 -LRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFIL  157 (212)
T ss_dssp             -CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             -hcCCcEEEECCCccccccccCceecCcceEEee
Confidence             134679999962      344567778887775

>d1em8a_ c.128.1.1 (A:) DNA polymerase III chi subunit {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: DNA polymerase III chi subunit
superfamily: DNA polymerase III chi subunit
family: DNA polymerase III chi subunit
domain: DNA polymerase III chi subunit
species: Escherichia coli [TaxId: 562]

Probab=85.39  E-value=2.3  Score=25.75  Aligned_cols=66  Identities=14%  Similarity=0.037  Sum_probs=40.6

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCcccccccCCCcEEEEec
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGRGIDFRTVRLVVNYD  122 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~g~~i~~~~~vi~~~  122 (159)
                      .+.+++|+|++.+.++.+-+.|.......-..|+-....         ......|+++++-..   ..+..+++|+.+
T Consensus        35 ~g~ri~I~~~d~~~~~~lD~~LWt~~~~sFiPH~~~~~~---------~~~~~PI~l~~~~~~---~~~~~dvlinl~  100 (147)
T d1em8a_          35 SGKRVLIACEDEKQAYRLDEALWARPAESFVPHNLAGEG---------PRGGAPVEIAWPQKR---SSSRRDILISLR  100 (147)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHCSTTCCCCEEETTCS---------STTCCSEEEECTTSC---CCSCCSEEEECC
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHhCCCCcccccccccCCC---------ccCCCCEEecCCCCC---CCccceEEEECC
Confidence            577899999999999999999977643333444422111         012345777764321   123456677764

>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=84.97  E-value=1.5  Score=28.77  Aligned_cols=70  Identities=14%  Similarity=0.132  Sum_probs=49.4

Q ss_pred             CCEEEEecchHHHHHHHHHHHh----CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCC------cccccccCCCc
Q psy576           47 PPVLVFVQSKERAQELYNELIY----DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTEL------LGRGIDFRTVR  116 (159)
Q Consensus        47 ~~~lif~~~~~~~~~l~~~l~~----~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~------~~~g~~i~~~~  116 (159)
                      .+++|.+++++.+..+.+.+..    .++++..+.|+.......+    ......+|+|+|+-      -...+++..+.
T Consensus        99 ~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~----~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~  174 (238)
T d1wrba1          99 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIR----EVQMGCHLLVATPGRLVDFIEKNKISLEFCK  174 (238)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHH----HHSSCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHh----hcccCCceeecCHHHHHhHHccCceeccccc
Confidence            4699999999999998876643    2677888888776654432    23456789999963      23355667777


Q ss_pred             EEEE
Q psy576          117 LVVN  120 (159)
Q Consensus       117 ~vi~  120 (159)
                      +++.
T Consensus       175 ~lVi  178 (238)
T d1wrba1         175 YIVL  178 (238)
T ss_dssp             EEEE
T ss_pred             eeee
Confidence            7765

>d1gmxa_ c.46.1.3 (A:) Sulfurtransferase GlpE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Sulfurtransferase GlpE
species: Escherichia coli [TaxId: 562]

Probab=84.29  E-value=0.69  Score=26.42  Aligned_cols=46  Identities=15%  Similarity=0.161  Sum_probs=34.7

Q ss_pred             HHHHHHHhc-CCCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCC
Q psy576           35 QAQDETILL-GIEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDR   80 (159)
Q Consensus        35 ~~l~~~~~~-~~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~   80 (159)
                      ..+.+.+.. .++.+++++|.+-..+...+..|.+.|+ ++..+.|++
T Consensus        46 ~~l~~~~~~~~~~~~ivv~c~~g~rs~~~a~~L~~~G~~~v~~l~GG~   93 (108)
T d1gmxa_          46 DTLGAFMRDNDFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGF   93 (108)
T ss_dssp             HHHHHHHHHSCTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHH
T ss_pred             hhHHHHhhhccccCcccccCCCChHHHHHHHHHHHcCCCCEEEEcChH
Confidence            334444443 3566799999999999999999998888 577788875

>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=83.93  E-value=3.6  Score=26.02  Aligned_cols=95  Identities=15%  Similarity=0.084  Sum_probs=60.8

Q ss_pred             eeeeecCCCCChHHH-HHHHHh----cCCCCCEEEEecchHHHHHHHHHHHhC----CCceEEEecCCCHHHHHHHHHHH
Q psy576           22 RMYRETEGAGSPVQA-QDETIL----LGIEPPVLVFVQSKERAQELYNELIYD----GINVDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        22 ~~~~~~~~~~~k~~~-l~~~~~----~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f   92 (159)
                      ..........+|... +..++.    .......++.+++...+......+...    ++.+...+|+.........+   
T Consensus        40 dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l---  116 (206)
T d1s2ma1          40 DILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRL---  116 (206)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHT---
T ss_pred             CEEEecCCcchhhhhhccccccccccccccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHh---
Confidence            444445554555544 333343    234456888999999888777766432    67889999988776554332   


Q ss_pred             hcCCeeEEEEeCC------cccccccCCCcEEEE
Q psy576           93 RTGRIWILITTEL------LGRGIDFRTVRLVVN  120 (159)
Q Consensus        93 ~~~~~~vlv~t~~------~~~g~~i~~~~~vi~  120 (159)
                       .....|+|+|+-      -...+++..+.++|.
T Consensus       117 -~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~  149 (206)
T d1s2ma1         117 -NETVHILVGTPGRVLDLASRKVADLSDCSLFIM  149 (206)
T ss_dssp             -TSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEE
T ss_pred             -cccceEEEECCcccccccccceeecccceEEEe
Confidence             455789999963      233456677877775

>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=83.76  E-value=3.4  Score=26.61  Aligned_cols=96  Identities=11%  Similarity=0.134  Sum_probs=57.0

Q ss_pred             eeeecCCCCChHHHHHHHH--hcCCCCCEEEEecchHHHHHHHHHHHhC----CCc----eEEEecCCCHHHHHHHHHHH
Q psy576           23 MYRETEGAGSPVQAQDETI--LLGIEPPVLVFVQSKERAQELYNELIYD----GIN----VDVIHSDRTQKQRDNVVRSF   92 (159)
Q Consensus        23 ~~~~~~~~~~k~~~l~~~~--~~~~~~~~lif~~~~~~~~~l~~~l~~~----~~~----~~~~~~~~~~~~r~~~~~~f   92 (159)
                      .........+|.....-..  ....+.++++.++++.-+...++.+++.    +++    ....++.....++.+.++..
T Consensus        61 ~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  140 (237)
T d1gkub1          61 FAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNL  140 (237)
T ss_dssp             EECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSG
T ss_pred             EEEEecCCChHHHHHHHHHHHHHHhcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccc
Confidence            3444444567775432222  2235678999999999999888877542    332    44556666666665555433


Q ss_pred             hcCCeeEEEEeC-Ccccc-cccCCCcEEEE
Q psy576           93 RTGRIWILITTE-LLGRG-IDFRTVRLVVN  120 (159)
Q Consensus        93 ~~~~~~vlv~t~-~~~~g-~~i~~~~~vi~  120 (159)
                      .  ...|+|+|. .+... .+...+++||.
T Consensus       141 ~--~~~Ilv~Tp~~l~~~~~~~~~~~~vVv  168 (237)
T d1gkub1         141 R--NFKIVITTTQFLSKHYRELGHFDFIFV  168 (237)
T ss_dssp             G--GCSEEEEEHHHHHHCSTTSCCCSEEEE
T ss_pred             c--ccceeccChHHHHHhhhhcCCCCEEEE
Confidence            3  356899884 33332 24456776665

>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=83.16  E-value=0.2  Score=31.95  Aligned_cols=90  Identities=18%  Similarity=0.206  Sum_probs=51.1

Q ss_pred             ecchHHHHHHHHHHHh---CCCceEEEecCCCHHHHHHHHHHHhcCCeeEEEEeCCccc--------ccccCCCcEEEEe
Q psy576           53 VQSKERAQELYNELIY---DGINVDVIHSDRTQKQRDNVVRSFRTGRIWILITTELLGR--------GIDFRTVRLVVNY  121 (159)
Q Consensus        53 ~~~~~~~~~l~~~l~~---~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~t~~~~~--------g~~i~~~~~vi~~  121 (159)
                      -++....+.+...+.+   .+..+.++..  ....-..+.+.+++....+...+.-...        .+.-...++++--
T Consensus        11 rp~~~qvd~ll~~i~~~~~~~~~~iif~~--~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaT   88 (181)
T d1t5la2          11 RPTKGQIDDLIGEIRERVERNERTLVTTL--TKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGI   88 (181)
T ss_dssp             ECSTTHHHHHHHHHHHHHHTTCEEEEECS--SHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEES
T ss_pred             EECCCcHHHHHHHHHHHHhcCCeEEEEee--hhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEeh
Confidence            3445555555554443   3445555554  3555566666777766666555433221        2222355666642


Q ss_pred             -------cCCC-------CHH------HHHHHHhhccCCCCcc
Q psy576          122 -------DFPS-------SAI------SYIHRIGRAGRGGREG  144 (159)
Q Consensus       122 -------~~~~-------~~~------~~~q~~GR~~R~g~~g  144 (159)
                             |.|.       +..      ++.|.+||+||.|+.|
T Consensus        89 dv~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g  131 (181)
T d1t5la2          89 NLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA  131 (181)
T ss_dssp             CCCSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST
T ss_pred             hHHHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhcccc
Confidence                   4442       444      4789999999999876

>d1yt8a1 c.46.1.2 (A:107-242) 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=82.97  E-value=0.97  Score=27.03  Aligned_cols=36  Identities=22%  Similarity=0.270  Sum_probs=29.9

Q ss_pred             CCCCEEEEecchHHHHHHHHHHHhCCC-c-eEEEecCC
Q psy576           45 IEPPVLVFVQSKERAQELYNELIYDGI-N-VDVIHSDR   80 (159)
Q Consensus        45 ~~~~~lif~~~~~~~~~l~~~l~~~~~-~-~~~~~~~~   80 (159)
                      +..++++||.+-..+...+..|...++ + +..+.|++
T Consensus        79 ~~~~iV~~C~~g~rs~~aa~~L~~~G~~~~V~~L~GG~  116 (136)
T d1yt8a1          79 PRTRVIVNCAGRTRSIIGTQSLLNAGIPNPVAALRNGT  116 (136)
T ss_dssp             TTSEEEEECSSSHHHHHHHHHHHHTTCSSCEEEETTHH
T ss_pred             ccceEEEEcCCCCchHHHHHHHHHcCCCceEEEeCCcH
Confidence            455799999999999999999999887 3 77788874

>d1urha2 c.46.1.2 (A:149-268) 3-mercaptopyruvate sulfurtransferase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: 3-mercaptopyruvate sulfurtransferase
species: Escherichia coli [TaxId: 562]

Probab=80.41  E-value=1.7  Score=24.90  Aligned_cols=38  Identities=18%  Similarity=0.201  Sum_probs=30.0

Q ss_pred             CCCCCEEEEecchHHHHHHHHHHHhCCC-ceEEEecCCC
Q psy576           44 GIEPPVLVFVQSKERAQELYNELIYDGI-NVDVIHSDRT   81 (159)
Q Consensus        44 ~~~~~~lif~~~~~~~~~l~~~l~~~~~-~~~~~~~~~~   81 (159)
                      ....++++||.+-..+....-.|+..|+ ++..+.|++.
T Consensus        80 ~~~~~ii~yC~sG~~A~~~~~~L~~lG~~~v~~y~Gs~~  118 (120)
T d1urha2          80 SYDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWS  118 (120)
T ss_dssp             CSSSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCC
T ss_pred             CccCceEEEccchhHHHHHHHHHHHcCCCCceEcCCChh
Confidence            3556899999998888888888887877 5777788764