Psyllid ID: psy15610

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------
Protein Sequence
LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSSQNSNAPDWWNDK
Secondary Structure (PSIPRED)
ccHHHHHcccccEEEccccccccccccEEEEEEccccccHHcccccHHHHHHHHccccEEcccccccHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHcccccEEEEEcccccHHHHHHHHHHcccccEEccccccHHHHHHHHHHHHcccccEEEEEHHHccccccccccEEEccccccccccccccccccccccccccEEEccccccccHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHccccEEEEcccHHHHHHHccEEEEcHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccHHHHHcccEEEEEccccEEEEEEcHHHHHHHHHHHHHccccccEEEEEcccHHHHHHHHHHHHcccccHEEcccccHHHHHHHHHHHHcccccEEEEHHHHHcccccccccEEEEEcccccHHHHEEEEcccccccccEEEEEEEccccHHHHHHHHHHHcccHHHHHcc
Coil and Loop (DISEMBL)
LLAKEFLYRYIFLAIGrvgstseniTQRIAWVDEQDKRSClldllsspsqeelgdEALTLVFVETKKGADQLEDFlhhhgypvtsihgdrtQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFlhhhgypvtsihgdrTQKEREEALRRFRSGETPILVATAVAargldiphvkhvinfdlpsdvEEYVHRIgrtgrmgnldfpfsynqpgyggsyggsssqnsnapdwwndk
Flexible Loop (DISEMBL)
LLAKEFLYRYIFLaigrvgstsenITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHgypvtsihgdrtqKEREEALRrfrsgetpiLVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSyggsssqnsnapdwwndk
Low Complexity Region (SEG)
LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFsynqpgyggsyggsssqnsnAPDWWNDK
Disordered region (IsUnstruct)
***KEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLL*********DEALTLVFVETKKGADQLEDFLHHHGYPVTSIH***********QQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIH*****************GETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQ************************
Disordered Region (DISOPRED)
LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSSQNSNAPDWW***
Disordered Region (DISEMBL)
LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTS************AQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTS***********EALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG*******************
Disordered Region (DISPRO)
LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSSQNSNAPDW****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSSQNSNAPDWWNDK
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	237	2.2.26 [Sep-21-2011]
Q9VHP0	798	ATP-dependent RNA helicas	yes	N/A	0.670	0.199	0.590	1e-57
P24346	697	Putative ATP-dependent RN	N/A	N/A	0.649	0.220	0.521	1e-50
Q62167	662	ATP-dependent RNA helicas	yes	N/A	0.649	0.232	0.521	2e-50
O00571	662	ATP-dependent RNA helicas	yes	N/A	0.649	0.232	0.516	6e-50
P16381	660	Putative ATP-dependent RN	no	N/A	0.649	0.233	0.511	3e-49
Q0UWA6	696	ATP-dependent RNA helicas	N/A	N/A	0.616	0.209	0.5	1e-48
Q62095	658	ATP-dependent RNA helicas	no	N/A	0.649	0.234	0.516	3e-48
O15523	660	ATP-dependent RNA helicas	no	N/A	0.649	0.233	0.511	3e-48
Q5RF43	658	ATP-dependent RNA helicas	no	N/A	0.649	0.234	0.511	4e-48
Q6GVM6	660	ATP-dependent RNA helicas	yes	N/A	0.649	0.233	0.511	5e-48

>sp|Q9VHP0|DDX3_DROME ATP-dependent RNA helicase bel OS=Drosophila melanogaster GN=bel PE=1 SV=1

 Score =  223 bits (567), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 124/210 (59%), Positives = 136/210 (64%), Gaps = 51/210 (24%)

Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLV 61
           LA +FL  YIFLA+GRVGSTSENITQ I WV E DKRS LLDLLSS              
Sbjct: 504 LASDFLSNYIFLAVGRVGSTSENITQTILWVYEPDKRSYLLDLLSS-------------- 549

Query: 62  FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA 121
               + G +  +D                                  +LTL+FVETKKGA
Sbjct: 550 ---IRDGPEYTKD----------------------------------SLTLIFVETKKGA 572

Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
           D LE+FL+   +PVTSIHGDRTQKEREEALR FRSG+ PILVATAVAARGLDIPHVKHVI
Sbjct: 573 DSLEEFLYQCNHPVTSIHGDRTQKEREEALRCFRSGDCPILVATAVAARGLDIPHVKHVI 632

Query: 182 NFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           NFDLPSDVEEYVHRIGRTGRMGNL    S+
Sbjct: 633 NFDLPSDVEEYVHRIGRTGRMGNLGVATSF 662

ATP-dependent RNA helicase that is essential and required for cellular function, larval growth, and for male and female fertility. Also required for RNA interference (RNAi), double-stranded RNA induces potent and specific gene silencing, by acting downstream of dsRNA internalization. RNAi is mediated by the RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys or silences messenger RNAs homologous to the silencing trigger.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|P24346|DDX3_XENLA Putative ATP-dependent RNA helicase an3 OS=Xenopus laevis GN=an3 PE=2 SV=1

 Score =  199 bits (506), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 110/211 (52%), Positives = 132/211 (62%), Gaps = 57/211 (27%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ++ WV                  EE+   +  L
Sbjct: 432 ILARDFLDEYIFLAVGRVGSTSENITQKVVWV------------------EEMDKRSFLL 473

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                        D L+  G                           ++LTLVFVETKKG
Sbjct: 474 -------------DLLNATG--------------------------KDSLTLVFVETKKG 494

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAVAARGLDI +VKHV
Sbjct: 495 ADALEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHV 554

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSD+EEYVHRIGRTGR+GNL    S+
Sbjct: 555 INFDLPSDIEEYVHRIGRTGRVGNLGLATSF 585

Putative ATP-dependent RNA helicase.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q62167|DDX3X_MOUSE ATP-dependent RNA helicase DDX3X OS=Mus musculus GN=Ddx3x PE=1 SV=3

 Score =  199 bits (505), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 110/211 (52%), Positives = 132/211 (62%), Gaps = 57/211 (27%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ++ WV                  EE+   +  L
Sbjct: 391 MLARDFLDEYIFLAVGRVGSTSENITQKVVWV------------------EEIDKRSFLL 432

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                        D L+  G                           ++LTLVFVETKKG
Sbjct: 433 -------------DLLNATG--------------------------KDSLTLVFVETKKG 453

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAVAARGLDI +VKHV
Sbjct: 454 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHV 513

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSD+EEYVHRIGRTGR+GNL    S+
Sbjct: 514 INFDLPSDIEEYVHRIGRTGRVGNLGLATSF 544

Putative ATP-dependent RNA helicase. It may play a role in translational activation of mRNA in the oocyte and early embryo.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O00571|DDX3X_HUMAN ATP-dependent RNA helicase DDX3X OS=Homo sapiens GN=DDX3X PE=1 SV=3

 Score =  197 bits (500), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 109/211 (51%), Positives = 129/211 (61%), Gaps = 57/211 (27%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ++ W                             
Sbjct: 391 MLARDFLDEYIFLAVGRVGSTSENITQKVVW----------------------------- 421

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
             VE       L D L+  G                           ++LTLVFVETKKG
Sbjct: 422 --VEESDKRSFLLDLLNATG--------------------------KDSLTLVFVETKKG 453

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAVAARGLDI +VKHV
Sbjct: 454 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHV 513

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSD+EEYVHRIGRTGR+GNL    S+
Sbjct: 514 INFDLPSDIEEYVHRIGRTGRVGNLGLATSF 544

ATP-dependent RNA helicase. Acts as a cofactor for XPO1-mediated nuclear export of incompletely spliced HIV-1 Rev RNAs. Also involved in HIV-1 replication. Interacts specifically with hepatitis C virus core protein resulting in a change in intracellular location.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P16381|DDX3L_MOUSE Putative ATP-dependent RNA helicase Pl10 OS=Mus musculus GN=D1Pas1 PE=1 SV=1

 Score =  195 bits (495), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 108/211 (51%), Positives = 128/211 (60%), Gaps = 57/211 (27%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ++ W                             
Sbjct: 390 MLARDFLDEYIFLAVGRVGSTSENITQKVVW----------------------------- 420

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
             VE       L D L+  G                           ++L LVFVETKKG
Sbjct: 421 --VEEADKRSFLLDLLNATG--------------------------KDSLILVFVETKKG 452

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAVAARGLDI +VKHV
Sbjct: 453 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHV 512

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSD+EEYVHRIGRTGR+GNL    S+
Sbjct: 513 INFDLPSDIEEYVHRIGRTGRVGNLGLATSF 543

Putative ATP-dependent RNA helicase. Possible role in a key step of the spermatogenic process.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0UWA6|DED1_PHANO ATP-dependent RNA helicase DED1 OS=Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) GN=DED1 PE=3 SV=1

 Score =  193 bits (490), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 102/204 (50%), Positives = 126/204 (61%), Gaps = 58/204 (28%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFL++GRVGSTSENITQ+I +V++ DKRS LLD+L               
Sbjct: 411 MLARDFLKEYIFLSVGRVGSTSENITQKIEYVEDADKRSVLLDIL--------------- 455

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                           H HG                             L+L+FVETK+ 
Sbjct: 456 ----------------HTHG---------------------------AGLSLIFVETKRM 472

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD L DFL + G+P TSIHGDRTQ+ERE+AL  FRSG  PILVATAVAARGLDIP+V HV
Sbjct: 473 ADSLSDFLINQGFPATSIHGDRTQREREKALEMFRSGRCPILVATAVAARGLDIPNVTHV 532

Query: 181 INFDLPSDVEEYVHRIGRTGRMGN 204
           +N+DLP+D+++YVHRIGRTGR GN
Sbjct: 533 VNYDLPTDIDDYVHRIGRTGRAGN 556

ATP-binding RNA helicase involved in translation initiation. Remodels RNA in response to ADP and ATP concentrations by facilitating disruption, but also formation of RNA duplexes.

Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (taxid: 321614)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q62095|DDX3Y_MOUSE ATP-dependent RNA helicase DDX3Y OS=Mus musculus GN=Ddx3y PE=1 SV=2

 Score =  191 bits (486), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 109/211 (51%), Positives = 127/211 (60%), Gaps = 57/211 (27%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ++ WV                  EEL   +  L
Sbjct: 390 MLARDFLDEYIFLAVGRVGSTSENITQKVVWV------------------EELDKRSFLL 431

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                        D L+  G                           ++LTLVFVETKKG
Sbjct: 432 -------------DLLNATG--------------------------KDSLTLVFVETKKG 452

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LE+FL    Y  TSIHGDR+QK+REEAL +FRSG  PILVATAVAARGLDI +VKHV
Sbjct: 453 ADSLENFLFQERYACTSIHGDRSQKDREEALHQFRSGRKPILVATAVAARGLDISNVKHV 512

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSD+EEYVHRIGRTGR+GNL    S+
Sbjct: 513 INFDLPSDIEEYVHRIGRTGRVGNLGLATSF 543

Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O15523|DDX3Y_HUMAN ATP-dependent RNA helicase DDX3Y OS=Homo sapiens GN=DDX3Y PE=1 SV=2

 Score =  191 bits (485), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 108/211 (51%), Positives = 129/211 (61%), Gaps = 57/211 (27%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ++                               
Sbjct: 389 MLARDFLDEYIFLAVGRVGSTSENITQKV------------------------------- 417

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
           V+VE       L D L   G                           ++LTLVFVETKKG
Sbjct: 418 VWVEDLDKRSFLLDILGATG--------------------------SDSLTLVFVETKKG 451

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAVAARGLDI +V+HV
Sbjct: 452 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVRHV 511

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSD+EEYVHRIGRTGR+GNL    S+
Sbjct: 512 INFDLPSDIEEYVHRIGRTGRVGNLGLATSF 542

Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5RF43|DDX3Y_PONAB ATP-dependent RNA helicase DDX3Y OS=Pongo abelii GN=DDX3Y PE=2 SV=1

 Score =  191 bits (485), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 108/211 (51%), Positives = 129/211 (61%), Gaps = 57/211 (27%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ++                               
Sbjct: 389 MLARDFLDEYIFLAVGRVGSTSENITQKV------------------------------- 417

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
           V+VE       L D L   G                           ++LTLVFVETKKG
Sbjct: 418 VWVEDLDKRSFLLDLLGATGR--------------------------DSLTLVFVETKKG 451

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAVAARGLDI +V+HV
Sbjct: 452 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVRHV 511

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSD+EEYVHRIGRTGR+GNL    S+
Sbjct: 512 INFDLPSDIEEYVHRIGRTGRVGNLGLATSF 542

Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6GVM6|DDX3Y_PANTR ATP-dependent RNA helicase DDX3Y OS=Pan troglodytes GN=DDX3Y PE=2 SV=1

 Score =  191 bits (484), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 108/211 (51%), Positives = 129/211 (61%), Gaps = 57/211 (27%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ++                               
Sbjct: 389 MLARDFLDEYIFLAVGRVGSTSENITQKV------------------------------- 417

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
           V+VE       L D L   G                           ++LTLVFVETKKG
Sbjct: 418 VWVEDLDKRSFLLDILGAAG--------------------------TDSLTLVFVETKKG 451

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAVAARGLDI +V+HV
Sbjct: 452 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVRHV 511

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSD+EEYVHRIGRTGR+GNL    S+
Sbjct: 512 INFDLPSDIEEYVHRIGRTGRVGNLGLATSF 542

Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Pan troglodytes (taxid: 9598)

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	237
357612893	717	ATP-dependent RNA helicase belle-like pr	0.679	0.224	0.597	2e-60
350408815	700	PREDICTED: putative ATP-dependent RNA he	0.670	0.227	0.597	3e-60
283767232	485	PL10A [Macrobrachium nipponense]	0.734	0.358	0.590	1e-59
283767234	709	PL10B [Macrobrachium nipponense]	0.734	0.245	0.590	2e-59
321459317	738	hypothetical protein DAPPUDRAFT_328137 [	0.708	0.227	0.601	3e-59
340719243	700	PREDICTED: putative ATP-dependent RNA he	0.670	0.227	0.592	3e-59
383847715	711	PREDICTED: putative ATP-dependent RNA he	0.670	0.223	0.587	3e-59
349806887	709	PL10-like protein [Macrobrachium nippone	0.734	0.245	0.590	6e-59
145974737	660	PL10A [Fenneropenaeus chinensis]	0.734	0.263	0.595	1e-58
380017597	701	PREDICTED: LOW QUALITY PROTEIN: putative	0.670	0.226	0.582	2e-58

>gi|357612893|gb|EHJ68220.1| ATP-dependent RNA helicase belle-like protein [Danaus plexippus]

 Score =  238 bits (606), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 126/211 (59%), Positives = 146/211 (69%), Gaps = 50/211 (23%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL+ Y+FLA+GRVGSTSENITQ++ WV+EQDKRS LLDLL++             
Sbjct: 442 VLAQDFLHNYVFLAVGRVGSTSENITQKVVWVEEQDKRSFLLDLLNA------------- 488

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                                       +  Q+  EE Q          LTLVFVETKKG
Sbjct: 489 ---------------------------SNLLQRNNEEDQ----------LTLVFVETKKG 511

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           ADQLEDFL+  GYPVTSIHGDRTQ+ERE+ALRRFR+G+TPILVATAVAARGLDIPHV+HV
Sbjct: 512 ADQLEDFLYADGYPVTSIHGDRTQREREDALRRFRTGQTPILVATAVAARGLDIPHVRHV 571

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSDVEEYVHRIGRTGRMGNL    S+
Sbjct: 572 INFDLPSDVEEYVHRIGRTGRMGNLGVATSF 602

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350408815|ref|XP_003488524.1| PREDICTED: putative ATP-dependent RNA helicase Pl10-like [Bombus impatiens]

 Score =  237 bits (604), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 126/211 (59%), Positives = 141/211 (66%), Gaps = 52/211 (24%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ+I WV+E DKRS LLDLL               
Sbjct: 429 MLARDFLSNYIFLAVGRVGSTSENITQKIVWVEEHDKRSYLLDLL--------------- 473

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                                               +A  Y+  S  E+LTLVFVETKKG
Sbjct: 474 ------------------------------------QAGNYSDSSA-ESLTLVFVETKKG 496

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LE++LHH GYPVTSIHGDRTQ+EREEALRRFR+G+ PILVATAVAARGLDIPHVKHV
Sbjct: 497 ADMLEEYLHHMGYPVTSIHGDRTQREREEALRRFRAGKAPILVATAVAARGLDIPHVKHV 556

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLP DVEEYVHRIGRTGRMGNL    S+
Sbjct: 557 INFDLPGDVEEYVHRIGRTGRMGNLGLATSF 587

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|283767232|gb|ADB28895.1| PL10A [Macrobrachium nipponense]

 Score =  235 bits (599), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 124/210 (59%), Positives = 146/210 (69%), Gaps = 36/210 (17%)

Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLV 61
           LA++FL  YIFLA+GRVGSTSENITQ+I WV E DKRS LLD+L++              
Sbjct: 192 LAQDFLDNYIFLAVGRVGSTSENITQKIVWVAEDDKRSFLLDILNA-------------- 237

Query: 62  FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA 121
                 G D+L +    +   + +                 L   +E+LTLVFVETKKGA
Sbjct: 238 -----AGLDRLSNANKDNKLAIVA-----------------LPPQEESLTLVFVETKKGA 275

Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
           D LE+FL+ HGYPVTSIHGDR+Q+ERE+ALR FRSG+ PILVATAVAARGLDIPHVKHVI
Sbjct: 276 DALEEFLYRHGYPVTSIHGDRSQREREDALRVFRSGQCPILVATAVAARGLDIPHVKHVI 335

Query: 182 NFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           NFDLPSD+EEYVHRIGRTGRMGNL    S+
Sbjct: 336 NFDLPSDIEEYVHRIGRTGRMGNLGLATSF 365

Source: Macrobrachium nipponense

Species: Macrobrachium nipponense

Genus: Macrobrachium

Family: Palaemonidae

Order: Decapoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|283767234|gb|ADB28896.1| PL10B [Macrobrachium nipponense]

 Score =  234 bits (598), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 124/210 (59%), Positives = 146/210 (69%), Gaps = 36/210 (17%)

Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLV 61
           LA++FL  YIFLA+GRVGSTSENITQ+I WV E DKRS LLD+L++              
Sbjct: 416 LAQDFLDNYIFLAVGRVGSTSENITQKIVWVAEDDKRSFLLDILNA-------------- 461

Query: 62  FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA 121
                 G D+L +    +   + +                 L   +E+LTLVFVETKKGA
Sbjct: 462 -----AGLDRLSNANKDNKLAIVA-----------------LPPQEESLTLVFVETKKGA 499

Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
           D LE+FL+ HGYPVTSIHGDR+Q+ERE+ALR FRSG+ PILVATAVAARGLDIPHVKHVI
Sbjct: 500 DALEEFLYRHGYPVTSIHGDRSQREREDALRVFRSGQCPILVATAVAARGLDIPHVKHVI 559

Query: 182 NFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           NFDLPSD+EEYVHRIGRTGRMGNL    S+
Sbjct: 560 NFDLPSDIEEYVHRIGRTGRMGNLGLATSF 589

Source: Macrobrachium nipponense

Species: Macrobrachium nipponense

Genus: Macrobrachium

Family: Palaemonidae

Order: Decapoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321459317|gb|EFX70372.1| hypothetical protein DAPPUDRAFT_328137 [Daphnia pulex]

 Score =  234 bits (596), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 127/211 (60%), Positives = 145/211 (68%), Gaps = 43/211 (20%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ+I WV+E DKRS LLDLL+              
Sbjct: 430 MLARDFLENYIFLAVGRVGSTSENITQKIVWVEEHDKRSFLLDLLN-------------- 475

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                   A  L  F               +Q E E  +        E LTLVFVETK+G
Sbjct: 476 --------ASGLNKF--------------NSQVETESTEH-------EQLTLVFVETKRG 506

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LE+FL+  GYPVTSIHGDR+Q+ERE+AL+RFRSG+TPILVATAVAARGLDIPHVKHV
Sbjct: 507 ADALEEFLYRDGYPVTSIHGDRSQREREDALKRFRSGKTPILVATAVAARGLDIPHVKHV 566

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLPSDVEEYVHRIGRTGRMGNL    S+
Sbjct: 567 INFDLPSDVEEYVHRIGRTGRMGNLGVATSF 597

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719243|ref|XP_003398065.1| PREDICTED: putative ATP-dependent RNA helicase Pl10-like [Bombus terrestris]

 Score =  234 bits (596), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 125/211 (59%), Positives = 140/211 (66%), Gaps = 52/211 (24%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ+I WV+E DKRS LLDLL               
Sbjct: 429 MLARDFLSNYIFLAVGRVGSTSENITQKIVWVEEHDKRSYLLDLL--------------- 473

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                                               +A  Y+  S  E+LTLVFVETKKG
Sbjct: 474 ------------------------------------QAGNYSDSSA-ESLTLVFVETKKG 496

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LE++LH  GYPVTSIHGDRTQ+EREEALRRFR+G+ PILVATAVAARGLDIPHVKHV
Sbjct: 497 ADMLEEYLHQMGYPVTSIHGDRTQREREEALRRFRAGKAPILVATAVAARGLDIPHVKHV 556

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLP DVEEYVHRIGRTGRMGNL    S+
Sbjct: 557 INFDLPGDVEEYVHRIGRTGRMGNLGLATSF 587

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847715|ref|XP_003699498.1| PREDICTED: putative ATP-dependent RNA helicase an3-like [Megachile rotundata]

 Score =  234 bits (596), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 124/211 (58%), Positives = 141/211 (66%), Gaps = 52/211 (24%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ+I WV+EQDKRS LLDLL               
Sbjct: 441 MLARDFLSNYIFLAVGRVGSTSENITQKIVWVEEQDKRSYLLDLL--------------- 485

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                                               +A  ++  S  E+LTLVFVETKKG
Sbjct: 486 ------------------------------------QASNFSDPSA-ESLTLVFVETKKG 508

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LE++LH  GYPVTSIHGDRTQ+ERE+ALRRFR+G+ PILVATAVAARGLDIPHVKHV
Sbjct: 509 ADMLEEYLHQMGYPVTSIHGDRTQREREDALRRFRAGKAPILVATAVAARGLDIPHVKHV 568

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLP DVEEYVHRIGRTGRMGNL    S+
Sbjct: 569 INFDLPGDVEEYVHRIGRTGRMGNLGLATSF 599

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|349806887|gb|AEQ19570.1| PL10-like protein [Macrobrachium nipponense]

 Score =  233 bits (593), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 124/210 (59%), Positives = 144/210 (68%), Gaps = 36/210 (17%)

Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLV 61
           LA+ FL  YIFLA+GRVGSTSENITQ+I WV E DKRS LLD+L++              
Sbjct: 416 LAQVFLDNYIFLAVGRVGSTSENITQKIVWVAEDDKRSFLLDILNA-------------- 461

Query: 62  FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA 121
                 G D+L +    +   + +                 L   +E+LTLVFVETKKGA
Sbjct: 462 -----AGVDRLSNANKDNKLAIVA-----------------LPPQEESLTLVFVETKKGA 499

Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
           D LE+FL+ HGYPVTSIHGDR+Q+ERE+ALR FRSG  PILVATAVAARGLDIPHVKHVI
Sbjct: 500 DALEEFLYRHGYPVTSIHGDRSQREREDALRVFRSGRCPILVATAVAARGLDIPHVKHVI 559

Query: 182 NFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           NFDLPSD+EEYVHRIGRTGRMGNL    S+
Sbjct: 560 NFDLPSDIEEYVHRIGRTGRMGNLGLATSF 589

Source: Macrobrachium nipponense

Species: Macrobrachium nipponense

Genus: Macrobrachium

Family: Palaemonidae

Order: Decapoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|145974737|gb|ABQ00072.1| PL10A [Fenneropenaeus chinensis]

 Score =  232 bits (591), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 125/210 (59%), Positives = 145/210 (69%), Gaps = 36/210 (17%)

Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLV 61
           LA++FL  YIFLA+GRVGSTSENITQ+I WV E DKRS LLD+L++   +          
Sbjct: 427 LAQDFLDNYIFLAVGRVGSTSENITQKIVWVSEDDKRSFLLDILNAAGLD---------- 476

Query: 62  FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA 121
                +  +  +D     G P            REE+           LTLVFVETKKGA
Sbjct: 477 -----RATEANKDEKMAMGVP----------PRREES-----------LTLVFVETKKGA 510

Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
           D LE+FL+ HGYPVTSIHGDR+Q+ERE+ALR FRSG+ PILVATAVAARGLDIPHVKHVI
Sbjct: 511 DALEEFLYRHGYPVTSIHGDRSQREREDALRVFRSGQCPILVATAVAARGLDIPHVKHVI 570

Query: 182 NFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           NFDLPSD+EEYVHRIGRTGRMGNL    S+
Sbjct: 571 NFDLPSDIEEYVHRIGRTGRMGNLGLATSF 600

Source: Fenneropenaeus chinensis

Species: Fenneropenaeus chinensis

Genus: Fenneropenaeus

Family: Penaeidae

Order: Decapoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380017597|ref|XP_003692739.1| PREDICTED: LOW QUALITY PROTEIN: putative ATP-dependent RNA helicase Pl10-like [Apis florea]

 Score =  231 bits (589), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 123/211 (58%), Positives = 140/211 (66%), Gaps = 52/211 (24%)

Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ+I WV+E DKRS LLDLL               
Sbjct: 429 MLARDFLSNYIFLAVGRVGSTSENITQKIVWVEEHDKRSYLLDLL--------------- 473

Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                                               +A  ++  S  E+LTLVFVETKKG
Sbjct: 474 ------------------------------------QASNFSDPSA-ESLTLVFVETKKG 496

Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LE++LH  GYPVTSIHGDRTQ+ERE+ALRRFR+G+ PILVATAVAARGLDIPHVKHV
Sbjct: 497 ADMLEEYLHQMGYPVTSIHGDRTQREREDALRRFRAGKAPILVATAVAARGLDIPHVKHV 556

Query: 181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY 211
           INFDLP DVEEYVHRIGRTGRMGNL    S+
Sbjct: 557 INFDLPGDVEEYVHRIGRTGRMGNLGLATSF 587

Source: Apis florea

Species: Apis florea

Genus: Apis

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	237
FB|FBgn0263231	798	bel "belle" [Drosophila melano	0.413	0.122	0.867	2.1e-42
UNIPROTKB|B4E132	407	DDX3Y "Uncharacterized protein	0.413	0.240	0.806	1.4e-39
UNIPROTKB|F1NIX2	636	DDX3X "Uncharacterized protein	0.413	0.154	0.816	1.6e-39
UNIPROTKB|F1NIX1	638	DDX3X "Uncharacterized protein	0.413	0.153	0.816	1.6e-39
UNIPROTKB|G5E631	661	DDX3X "Uncharacterized protein	0.413	0.148	0.816	1.7e-39
UNIPROTKB|F1RX16	661	DDX3X "Uncharacterized protein	0.413	0.148	0.816	1.7e-39
UNIPROTKB|J9P0V9	662	DDX3X "Uncharacterized protein	0.413	0.148	0.816	1.7e-39
UNIPROTKB|O00571	662	DDX3X "ATP-dependent RNA helic	0.413	0.148	0.816	1.7e-39
MGI|MGI:103064	662	Ddx3x "DEAD/H (Asp-Glu-Ala-Asp	0.413	0.148	0.816	1.7e-39
RGD|1564771	662	Ddx3x "DEAD (Asp-Glu-Ala-Asp)	0.413	0.148	0.816	1.7e-39

FB|FBgn0263231 bel "belle" [Drosophila melanogaster (taxid:7227)]

 Score = 441 (160.3 bits), Expect = 2.1e-42, Sum P(2) = 2.1e-42
 Identities = 85/98 (86%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTL+FVETKKGAD LE+FL+   +PVTSIHGDRTQKEREEALR FRSG+ PILVATAV
Sbjct:   559 DSLTLIFVETKKGADSLEEFLYQCNHPVTSIHGDRTQKEREEALRCFRSGDCPILVATAV 618

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL
Sbjct:   619 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 656

GO:0007286 "spermatid development" evidence=IMP

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

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0043186 "P granule" evidence=IDA

GO:0007283 "spermatogenesis" evidence=IMP

GO:0002168 "instar larval development" evidence=IMP

GO:0048477 "oogenesis" evidence=IMP

GO:0016442 "RNA-induced silencing complex" evidence=IDA

GO:0016246 "RNA interference" evidence=IMP

GO:0005811 "lipid particle" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0043025 "neuronal cell body" evidence=IDA

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0000070 "mitotic sister chromatid segregation" evidence=IMP

UNIPROTKB|B4E132 DDX3Y "Uncharacterized protein" [Homo sapiens (taxid:9606)]

 Score = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 79/98 (80%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTLVFVETKKGAD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAV
Sbjct:   186 DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV 245

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDI +V+HVINFDLPSD+EEYVHRIGRTGR+GNL
Sbjct:   246 AARGLDISNVRHVINFDLPSDIEEYVHRIGRTGRVGNL 283

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1NIX2 DDX3X "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 424 (154.3 bits), Expect = 1.6e-39, P = 1.6e-39
 Identities = 80/98 (81%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTLVFVETKKGAD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAV
Sbjct:   418 DSLTLVFVETKKGADALEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV 477

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDI +VKHVINFDLPSD+EEYVHRIGRTGR+GNL
Sbjct:   478 AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 515

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1NIX1 DDX3X "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 424 (154.3 bits), Expect = 1.6e-39, P = 1.6e-39
 Identities = 80/98 (81%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTLVFVETKKGAD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAV
Sbjct:   419 DSLTLVFVETKKGADALEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV 478

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDI +VKHVINFDLPSD+EEYVHRIGRTGR+GNL
Sbjct:   479 AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 516

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|G5E631 DDX3X "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 425 (154.7 bits), Expect = 1.7e-39, P = 1.7e-39
 Identities = 80/98 (81%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTLVFVETKKGAD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAV
Sbjct:   440 DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV 499

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDI +VKHVINFDLPSD+EEYVHRIGRTGR+GNL
Sbjct:   500 AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 537

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=IEA

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IEA

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IEA

GO:0071470 "cellular response to osmotic stress" evidence=IEA

GO:0071243 "cellular response to arsenic-containing substance" evidence=IEA

GO:0048027 "mRNA 5'-UTR binding" evidence=IEA

GO:0045948 "positive regulation of translational initiation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043024 "ribosomal small subunit binding" evidence=IEA

GO:0042256 "mature ribosome assembly" evidence=IEA

GO:0035613 "RNA stem-loop binding" evidence=IEA

GO:0034063 "stress granule assembly" evidence=IEA

GO:0031333 "negative regulation of protein complex assembly" evidence=IEA

GO:0030308 "negative regulation of cell growth" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=IEA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007243 "intracellular protein kinase cascade" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1RX16 DDX3X "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 425 (154.7 bits), Expect = 1.7e-39, P = 1.7e-39
 Identities = 80/98 (81%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTLVFVETKKGAD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAV
Sbjct:   441 DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV 500

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDI +VKHVINFDLPSD+EEYVHRIGRTGR+GNL
Sbjct:   501 AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 538

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=IEA

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IEA

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IEA

GO:0071470 "cellular response to osmotic stress" evidence=IEA

GO:0071243 "cellular response to arsenic-containing substance" evidence=IEA

GO:0048027 "mRNA 5'-UTR binding" evidence=IEA

GO:0045948 "positive regulation of translational initiation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043024 "ribosomal small subunit binding" evidence=IEA

GO:0042256 "mature ribosome assembly" evidence=IEA

GO:0035613 "RNA stem-loop binding" evidence=IEA

GO:0034063 "stress granule assembly" evidence=IEA

GO:0031333 "negative regulation of protein complex assembly" evidence=IEA

GO:0030308 "negative regulation of cell growth" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=IEA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007243 "intracellular protein kinase cascade" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|J9P0V9 DDX3X "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 425 (154.7 bits), Expect = 1.7e-39, P = 1.7e-39
 Identities = 80/98 (81%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTLVFVETKKGAD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAV
Sbjct:   441 DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV 500

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDI +VKHVINFDLPSD+EEYVHRIGRTGR+GNL
Sbjct:   501 AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 538

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|O00571 DDX3X "ATP-dependent RNA helicase DDX3X" [Homo sapiens (taxid:9606)]

 Score = 425 (154.7 bits), Expect = 1.7e-39, P = 1.7e-39
 Identities = 80/98 (81%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTLVFVETKKGAD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAV
Sbjct:   441 DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV 500

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDI +VKHVINFDLPSD+EEYVHRIGRTGR+GNL
Sbjct:   501 AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 538

GO:0005524 "ATP binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0005741 "mitochondrial outer membrane" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0030307 "positive regulation of cell growth" evidence=IMP

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IDA

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IMP

GO:0045948 "positive regulation of translational initiation" evidence=IMP

GO:0031333 "negative regulation of protein complex assembly" evidence=IDA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IDA

GO:0017148 "negative regulation of translation" evidence=IMP

GO:0034063 "stress granule assembly" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0071470 "cellular response to osmotic stress" evidence=IDA

GO:0071243 "cellular response to arsenic-containing substance" evidence=IDA

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=IMP

GO:0007059 "chromosome segregation" evidence=IMP

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0045727 "positive regulation of translation" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

GO:0031369 "translation initiation factor binding" evidence=IDA

GO:0042256 "mature ribosome assembly" evidence=IMP

GO:0043024 "ribosomal small subunit binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0016887 "ATPase activity" evidence=IDA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IDA

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

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IMP;IDA

GO:0009615 "response to virus" evidence=IDA

GO:0007243 "intracellular protein kinase cascade" evidence=IDA

GO:0032728 "positive regulation of interferon-beta production" evidence=TAS

GO:0045087 "innate immune response" evidence=IMP

GO:0071651 "positive regulation of chemokine (C-C motif) ligand 5 production" evidence=TAS

GO:0035613 "RNA stem-loop binding" evidence=IDA

GO:0010501 "RNA secondary structure unwinding" evidence=IDA

GO:0048027 "mRNA 5'-UTR binding" evidence=IDA

GO:0008134 "transcription factor binding" evidence=IDA

GO:0030308 "negative regulation of cell growth" evidence=IDA

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IMP

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IMP

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IMP

GO:0043065 "positive regulation of apoptotic process" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0006200 "ATP catabolic process" evidence=IDA

MGI|MGI:103064 Ddx3x "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked" [Mus musculus (taxid:10090)]

 Score = 425 (154.7 bits), Expect = 1.7e-39, P = 1.7e-39
 Identities = 80/98 (81%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTLVFVETKKGAD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAV
Sbjct:   441 DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV 500

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDI +VKHVINFDLPSD+EEYVHRIGRTGR+GNL
Sbjct:   501 AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 538

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=ISO

GO:0003723 "RNA binding" evidence=ISO

GO:0004003 "ATP-dependent DNA helicase activity" evidence=ISO

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

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005739 "mitochondrion" evidence=IEA

GO:0005741 "mitochondrial outer membrane" evidence=IEA

GO:0006200 "ATP catabolic process" evidence=IEA;ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0007059 "chromosome segregation" evidence=ISO

GO:0007243 "intracellular protein kinase cascade" evidence=ISO

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

GO:0008134 "transcription factor binding" evidence=ISO

GO:0008143 "poly(A) RNA binding" evidence=ISO

GO:0008152 "metabolic process" evidence=IEA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=ISO

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=ISO

GO:0009615 "response to virus" evidence=ISO

GO:0010494 "cytoplasmic stress granule" evidence=ISO

GO:0010501 "RNA secondary structure unwinding" evidence=ISO

GO:0016020 "membrane" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISO

GO:0017148 "negative regulation of translation" evidence=ISO

GO:0030307 "positive regulation of cell growth" evidence=ISO

GO:0030308 "negative regulation of cell growth" evidence=ISO

GO:0031333 "negative regulation of protein complex assembly" evidence=ISO

GO:0031369 "translation initiation factor binding" evidence=ISO

GO:0034063 "stress granule assembly" evidence=ISO

GO:0035613 "RNA stem-loop binding" evidence=ISO

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0042256 "mature ribosome assembly" evidence=ISO

GO:0043024 "ribosomal small subunit binding" evidence=ISO

GO:0043065 "positive regulation of apoptotic process" evidence=ISO

GO:0043066 "negative regulation of apoptotic process" evidence=ISO

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=ISO

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=ISO

GO:0045087 "innate immune response" evidence=ISO

GO:0045727 "positive regulation of translation" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0045948 "positive regulation of translational initiation" evidence=ISO

GO:0048027 "mRNA 5'-UTR binding" evidence=ISO

GO:0071243 "cellular response to arsenic-containing substance" evidence=ISO

GO:0071470 "cellular response to osmotic stress" evidence=ISO

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=ISO

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=ISO

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=ISO

RGD|1564771 Ddx3x "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked" [Rattus norvegicus (taxid:10116)]

 Score = 425 (154.7 bits), Expect = 1.7e-39, P = 1.7e-39
 Identities = 80/98 (81%), Positives = 92/98 (93%)

Query:   108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
             ++LTLVFVETKKGAD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAV
Sbjct:   441 DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAV 500

Query:   168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
             AARGLDI +VKHVINFDLPSD+EEYVHRIGRTGR+GNL
Sbjct:   501 AARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 538

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" 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)
Q6GVM6	DDX3Y_PANTR	3, ., 6, ., 4, ., 1, 3	0.5118	0.6497	0.2333	yes	N/A
P0CQ74	DED1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.5049	0.6202	0.2307	yes	N/A
Q9VHP0	DDX3_DROME	3, ., 6, ., 4, ., 1, 3	0.5904	0.6708	0.1992	yes	N/A
O00571	DDX3X_HUMAN	3, ., 6, ., 4, ., 1, 3	0.5165	0.6497	0.2326	yes	N/A
Q62167	DDX3X_MOUSE	3, ., 6, ., 4, ., 1, 3	0.5213	0.6497	0.2326	yes	N/A
Q75HJ0	RH37_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.5099	0.6371	0.2370	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	237
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	8e-43
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	4e-39
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-36
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-35
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	1e-35
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	2e-32
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-32
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	6e-28
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	2e-27
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-26
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-26
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	4e-25
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-23
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	6e-21
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	7e-16
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	1e-13
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	3e-13
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	1e-12
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	4e-09
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	1e-08
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	2e-08
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	3e-08
COG1110	1187	COG1110, COG1110, Reverse gyrase [DNA replication,	4e-08
PRK09401	1176	PRK09401, PRK09401, reverse gyrase; Reviewed	2e-07
COG0553	866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	2e-07
TIGR00631	655	TIGR00631, uvrb, excinuclease ABC, B subunit	4e-07
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	1e-06
COG1200	677	COG1200, RecG, RecG-like helicase [DNA replication	2e-06
PRK10917	681	PRK10917, PRK10917, ATP-dependent DNA helicase Rec	5e-06
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	1e-05
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	1e-05
COG1198	730	COG1198, PriA, Primosomal protein N' (replication	2e-05
TIGR01054	1171	TIGR01054, rgy, reverse gyrase	3e-05
COG1205	851	COG1205, COG1205, Distinct helicase family with a	4e-05
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	0.001
TIGR04095	451	TIGR04095, dnd_restrict_1, DNA phosphorothioation	0.001
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	0.001
PRK14701	1638	PRK14701, PRK14701, reverse gyrase; Provisional	0.002
pfam13307	165	pfam13307, Helicase_C_2, Helicase C-terminal domai	0.002
PRK05298	652	PRK05298, PRK05298, excinuclease ABC subunit B; Pr	0.002
TIGR00580	926	TIGR00580, mfd, transcription-repair coupling fact	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 =  151 bits (382), Expect = 8e-43
 Identities = 65/156 (41%), Positives = 90/156 (57%), Gaps = 11/156 (7%)

Query: 49  SQEELGDEALTLVFVETKKGA-DQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCD 107
           ++  L D     V VE  +    +++ F               +++E+ E     L   D
Sbjct: 223 ARRYLNDPVEIEVSVEKLERTLKKIKQFYLEV----------ESEEEKLELLLKLLKDED 272

Query: 108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
           E   +VFV TK+  ++L + L   G+ V ++HGD  Q+ER+ AL +F+ GE  +LVAT V
Sbjct: 273 EGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDV 332

Query: 168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           AARGLDIP V HVIN+DLP D E+YVHRIGRTGR G
Sbjct: 333 AARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAG 368

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 =  131 bits (332), Expect = 4e-39
 Identities = 47/94 (50%), Positives = 62/94 (65%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            L+F  +KK  D+L + L   G  V ++HGD +Q+EREE L+ FR GE  +LVAT V AR
Sbjct: 31  VLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIAR 90

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           G+D+P+V  VIN+DLP     Y+ RIGR GR G 
Sbjct: 91  GIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQ 124

Length = 131

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

 Score =  134 bits (340), Expect = 1e-36
 Identities = 55/103 (53%), Positives = 74/103 (71%)

Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           L+FVETKKGAD L   L   G+P   IHGD+ Q+ER   L  F++G++PI++AT VA+RG
Sbjct: 381 LIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRG 440

Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQP 214
           LD+  VK+VINFD P+ +E+YVHRIGRTGR G     +++  P
Sbjct: 441 LDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTP 483

Length = 545

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

 Score =  121 bits (305), Expect = 1e-35
 Identities = 39/78 (50%), Positives = 51/78 (65%)

Query: 126 DFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL 185
             L   G  V  +HG  +Q+EREE L  FR+G++ +LVAT VA RG+D+P V  VIN+DL
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60

Query: 186 PSDVEEYVHRIGRTGRMG 203
           P +   Y+ RIGR GR G
Sbjct: 61  PWNPASYIQRIGRAGRAG 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 =  120 bits (304), Expect = 1e-35
 Identities = 39/82 (47%), Positives = 52/82 (63%)

Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
           ++L + L   G  V  +HG  +Q+EREE L +F +G+  +LVAT VA RGLD+P V  VI
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 182 NFDLPSDVEEYVHRIGRTGRMG 203
            +DLP     Y+ RIGR GR G
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score =  122 bits (308), Expect = 2e-32
 Identities = 44/94 (46%), Positives = 63/94 (67%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            +VF  TKK   ++ D L+  G+   ++HGD  Q++R++ L RF +    +LVAT VAAR
Sbjct: 245 CVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAAR 304

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           GLDI  ++ VIN++L  D E +VHRIGRTGR G+
Sbjct: 305 GLDIKALEAVINYELARDPEVHVHRIGRTGRAGS 338

Length = 460

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

 Score =  121 bits (305), Expect = 4e-32
 Identities = 43/94 (45%), Positives = 59/94 (62%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           ++VFV T++   +L  +L   G     + G+  Q +R EA++R   G   +LVAT VAAR
Sbjct: 248 SIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAAR 307

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           G+DI  V HVINFD+P   + Y+HRIGRTGR G 
Sbjct: 308 GIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGR 341

Length = 434

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

 Score =  109 bits (274), Expect = 6e-28
 Identities = 47/93 (50%), Positives = 58/93 (62%)

Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           ++F  TK   +++   L   G+ V  + GD  QK+R   L  F  G+  ILVAT VAARG
Sbjct: 259 IIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARG 318

Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           L IP V HV N+DLP D E+YVHRIGRTGR G 
Sbjct: 319 LHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGA 351

Length = 423

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

 Score =  107 bits (269), Expect = 2e-27
 Identities = 48/114 (42%), Positives = 70/114 (61%), Gaps = 4/114 (3%)

Query: 94  EREEAQQYTLISCDEALTLV----FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           E+EE +  TL    E LT+     +  T++  D L   +H   + V+ +HGD  QK+R+ 
Sbjct: 249 EKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDL 308

Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
            +R FRSG T +L+ T + ARG+D+  V  VIN+DLP+  E Y+HRIGR+GR G
Sbjct: 309 IMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFG 362

Length = 401

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

 Score =  107 bits (268), Expect = 1e-26
 Identities = 53/95 (55%), Positives = 65/95 (68%)

Query: 109 ALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA 168
           A T+VFV TK   +++   L  HGY V  + GD  QK+RE  L RF+ G+  ILVAT VA
Sbjct: 258 ARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVA 317

Query: 169 ARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           ARGL I  VK+V N+DLP D E+YVHRIGRT R+G
Sbjct: 318 ARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLG 352

Length = 572

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

 Score =  106 bits (265), Expect = 2e-26
 Identities = 47/90 (52%), Positives = 64/90 (71%)

Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           LVF  TK GA+ L + L+  G    +IHG+++Q  R  AL  F+SG+  +LVAT +AARG
Sbjct: 249 LVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARG 308

Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGR 201
           LDI  + HV+N++LP+  E+YVHRIGRTGR
Sbjct: 309 LDIEELPHVVNYELPNVPEDYVHRIGRTGR 338

Length = 456

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

 Score =  102 bits (255), Expect = 4e-25
 Identities = 42/94 (44%), Positives = 63/94 (67%), Gaps = 1/94 (1%)

Query: 112 LVFVETKKGADQLEDFLH-HHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           +VFV ++ GAD L + +    G    SIHG+++ KER E ++ F  GE P++VAT V  R
Sbjct: 371 VVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGR 430

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           G+D+  V+ VI FD+P+ ++EY+H+IGR  RMG 
Sbjct: 431 GVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGE 464

Length = 518

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

 Score = 98.4 bits (245), Expect = 1e-23
 Identities = 43/93 (46%), Positives = 60/93 (64%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            ++FV TK    ++ + L  +GY   +++GD  Q  RE+ L R + G   IL+AT VAAR
Sbjct: 248 AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAAR 307

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           GLD+  +  V+N+D+P D E YVHRIGRTGR G
Sbjct: 308 GLDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340

Length = 629

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

 Score = 90.4 bits (224), Expect = 6e-21
 Identities = 42/92 (45%), Positives = 55/92 (59%)

Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           +VF   K    ++E+ L   G     + GD  Q +R + L  FR G+  +LVAT VA RG
Sbjct: 339 MVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRG 398

Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           + I  + HVINF LP D ++YVHRIGRTGR G
Sbjct: 399 IHIDGISHVINFTLPEDPDDYVHRIGRTGRAG 430

Length = 475

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

 Score = 75.8 bits (187), Expect = 7e-16
 Identities = 30/92 (32%), Positives = 51/92 (55%)

Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           +++  T+K  ++L ++L  +G    + H   + +ERE   + F + E  ++VAT     G
Sbjct: 234 IIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMG 293

Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           +D P V+ VI++DLP  +E Y    GR GR G
Sbjct: 294 IDKPDVRFVIHYDLPGSIESYYQETGRAGRDG 325

Length = 590

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

 Score = 69.3 bits (170), Expect = 1e-13
 Identities = 33/141 (23%), Positives = 59/141 (41%), Gaps = 27/141 (19%)

Query: 63  VETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGAD 122
           V+       L D+L               +K R ++             +++  ++K  +
Sbjct: 206 VKKNNKQKFLLDYL---------------KKHRGQS------------GIIYASSRKKVE 238

Query: 123 QLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN 182
           +L + L   G    + H   + K R E    F   +  ++VAT     G+D P+V+ VI+
Sbjct: 239 ELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIH 298

Query: 183 FDLPSDVEEYVHRIGRTGRMG 203
           +D+P ++E Y    GR GR G
Sbjct: 299 YDMPGNLESYYQEAGRAGRDG 319

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

 Score = 67.8 bits (166), Expect = 3e-13
 Identities = 37/105 (35%), Positives = 58/105 (55%), Gaps = 11/105 (10%)

Query: 107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSI---HGDR------TQKEREEALRRFRSG 157
            ++  +VF E +  A+++ +FL   G            R      +QKE++E + +FR G
Sbjct: 365 GDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKG 424

Query: 158 ETPILVATAVAARGLDIPHVKHVINFD-LPSDVEEYVHRIGRTGR 201
           E  +LVAT+V   GLDIP V  VI ++ +PS++   + R GRTGR
Sbjct: 425 EYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEI-RSIQRKGRTGR 468

Length = 542

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

 Score = 66.4 bits (163), Expect = 1e-12
 Identities = 39/99 (39%), Positives = 59/99 (59%), Gaps = 10/99 (10%)

Query: 112 LVFVETKKGADQLEDFLHHHGYPV------TSIHGDR--TQKEREEALRRFRSGETPILV 163
           +VF + +  A+++ D L   G          S  GD+  +QKE+ E L +FR+GE  +LV
Sbjct: 369 IVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLV 428

Query: 164 ATAVAARGLDIPHVKHVINFD-LPSDVEEYVHRIGRTGR 201
           +T+VA  GLDIP V  VI ++ +PS++   + R GRTGR
Sbjct: 429 STSVAEEGLDIPSVDLVIFYEPVPSEI-RSIQRKGRTGR 466

Length = 773

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

 Score = 56.1 bits (136), Expect = 4e-09
 Identities = 34/98 (34%), Positives = 45/98 (45%), Gaps = 9/98 (9%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            LV   TKK A+ L ++L   G  V  +H D    ER E +R  R GE  +LV   +   
Sbjct: 449 VLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE 508

Query: 171 GLDIPHVKHVINFDLPSDVEEY-------VHRIGRTGR 201
           GLD+P V  V   D  +D E +       +  IGR  R
Sbjct: 509 GLDLPEVSLVAILD--ADKEGFLRSERSLIQTIGRAAR 544

Length = 663

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

 Score = 54.8 bits (132), Expect = 1e-08
 Identities = 25/92 (27%), Positives = 47/92 (51%)

Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           +++  ++K ++Q+   L + G    + H       R++   +F+  E  ++VAT     G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289

Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           ++ P V+ VI++ LP  +E Y    GR GR G
Sbjct: 290 INKPDVRFVIHYSLPKSMESYYQESGRAGRDG 321

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

 Score = 53.8 bits (130), Expect = 2e-08
 Identities = 32/100 (32%), Positives = 45/100 (45%), Gaps = 17/100 (17%)

Query: 111 TLVFVETKKGADQL---------EDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI 161
           TL+F  T+ GA++L         +    HHG    S+   R    R E   R + GE   
Sbjct: 256 TLIFTNTRSGAERLAFRLKKLGPDIIEVHHG----SL--SREL--RLEVEERLKEGELKA 307

Query: 162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGR 201
           +VAT+    G+DI  +  VI    P  V  ++ RIGR G 
Sbjct: 308 VVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347

Length = 814

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

 Score = 53.2 bits (128), Expect = 3e-08
 Identities = 31/108 (28%), Positives = 48/108 (44%), Gaps = 3/108 (2%)

Query: 93  KEREEAQQYTLI--SCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA 150
            ER+ A    L+        TL+F    + A ++       G  V +I G+  ++ERE  
Sbjct: 266 SERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAI 324

Query: 151 LRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGR 198
           L RFR+G   +LV   V   G+DIP    +I          ++ R+GR
Sbjct: 325 LERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGR 372

Length = 442

>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and repair]

 Score = 53.2 bits (128), Expect = 4e-08
 Identities = 32/98 (32%), Positives = 48/98 (48%), Gaps = 18/98 (18%)

Query: 111 TLVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA- 166
            L+FV    G   A++L ++L  HG     IH      E+EEAL  F  GE  +LV  A 
Sbjct: 338 GLIFVPIDYGREKAEELAEYLRSHGINAELIH-----AEKEEALEDFEEGEVDVLVGVAS 392

Query: 167 ---VAARGLDIPH-VKHVINFDLPS-----DVEEYVHR 195
              V  RGLD+PH +++ + + +P       +EE   +
Sbjct: 393 YYGVLVRGLDLPHRIRYAVFYGVPKFRFRLTLEESDPK 430

Length = 1187

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

 Score = 51.1 bits (123), Expect = 2e-07
 Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 13/84 (15%)

Query: 112 LVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA-- 166
           L+FV + KG   A++L ++L   G               E    +F  GE  +LV  A  
Sbjct: 332 LIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDVLVGVASY 386

Query: 167 --VAARGLDIPH-VKHVINFDLPS 187
             V  RG+D+P  +++ I + +P 
Sbjct: 387 YGVLVRGIDLPERIRYAIFYGVPK 410

Length = 1176

>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

 Score = 50.9 bits (121), Expect = 2e-07
 Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 5/96 (5%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            L+F +     D LED+L   G     + G    K R+E + RF + E   +   ++ A 
Sbjct: 714 VLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAG 773

Query: 171 GLDIP-----HVKHVINFDLPSDVEEYVHRIGRTGR 201
           GL +       V     +  P+   + + R  R G+
Sbjct: 774 GLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQ 809

Length = 866

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

 Score = 50.0 bits (120), Expect = 4e-07
 Identities = 32/96 (33%), Positives = 41/96 (42%), Gaps = 5/96 (5%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            LV   TKK A+ L D+L   G  V  +H +    ER E +R  R GE  +LV   +   
Sbjct: 445 VLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLRE 504

Query: 171 GLDIPHVKHVINFD-----LPSDVEEYVHRIGRTGR 201
           GLD+P V  V   D             +  IGR  R
Sbjct: 505 GLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 540

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

 Score = 48.6 bits (116), Expect = 1e-06
 Identities = 35/120 (29%), Positives = 46/120 (38%), Gaps = 6/120 (5%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           T+VF  +++   +L D L   G      H     KER+   R F + E   +V TA  A 
Sbjct: 443 TIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAA 502

Query: 171 GLDIPHVKHVINFDLPS-----DVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS 225
           G+D P    VI   L        V E+   +GR GR    D    Y     G  Y  S  
Sbjct: 503 GVDFP-ASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGKKYHASME 561

Length = 830

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

 Score = 47.6 bits (114), Expect = 2e-06
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 8/77 (10%)

Query: 101 YTLISCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGE 158
             LI   E L L      + A++L + L        V  +HG     E++  +  F+ GE
Sbjct: 480 CPLIEESEKLEL------QAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGE 533

Query: 159 TPILVATAVAARGLDIP 175
             ILVAT V   G+D+P
Sbjct: 534 IDILVATTVIEVGVDVP 550

Length = 677

>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional

 Score = 46.7 bits (112), Expect = 5e-06
 Identities = 28/109 (25%), Positives = 48/109 (44%), Gaps = 21/109 (19%)

Query: 82  PVTSIHGDRTQKE------REEAQQ-------YTLISCDEALTLVFVETKKGADQLEDFL 128
           P+T++    ++++      REE  +         LI   E L L      + A++  + L
Sbjct: 446 PITTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEESEKLDL------QSAEETYEEL 499

Query: 129 HHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP 175
                   V  +HG     E++  +  F++GE  ILVAT V   G+D+P
Sbjct: 500 QEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP 548

Length = 681

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

 Score = 45.5 bits (108), Expect = 1e-05
 Identities = 23/92 (25%), Positives = 43/92 (46%)

Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           +++  ++   +     L   G    + H       R +    F+  +  I+VAT     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299

Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           ++ P+V+ V++FD+P ++E Y    GR GR G
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331

Length = 607

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

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 19/43 (44%), Positives = 24/43 (55%)

Query: 133 YPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP 175
           Y V  +HG     E+E  +  FR GE  ILVAT V   G+D+P
Sbjct: 483 YNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVP 525

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

>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

 Score = 44.6 bits (106), Expect = 2e-05
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 104 ISCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGD--RTQKEREEALRRFRSGET 159
            SC E  +        G +++E+ L     G  +  I  D  R +   E+ L +F +GE 
Sbjct: 476 QSCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEA 535

Query: 160 PILVATAVAARGLDIPHVKHV 180
            IL+ T + A+G D P+V  V
Sbjct: 536 DILIGTQMIAKGHDFPNVTLV 556

Length = 730

>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase

 Score = 44.4 bits (105), Expect = 3e-05
 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 12/84 (14%)

Query: 112 LVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA-- 166
           +V+V    G   A+++ +FL +HG    + H      + +E   +F  GE  +L+  A  
Sbjct: 330 IVYVSIDYGKEKAEEIAEFLENHGVKAVAYHA----TKPKEDYEKFAEGEIDVLIGVASY 385

Query: 167 --VAARGLDIPH-VKHVINFDLPS 187
                RGLD+P  V++ +   +P 
Sbjct: 386 YGTLVRGLDLPERVRYAVFLGVPK 409

This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 1171

>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 = 43.9 bits (104), Expect = 4e-05
 Identities = 27/103 (26%), Positives = 41/103 (39%), Gaps = 9/103 (8%)

Query: 111 TLVFVETKKGADQLEDFL--------HHHGYPVTSIHGDRTQKEREEALRRFRSGETPIL 162
           TLVF  ++K  + L                  V++      ++ER      F+ GE   +
Sbjct: 309 TLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGV 368

Query: 163 VATAVAARGLDIPHVKHVINFDLPSD-VEEYVHRIGRTGRMGN 204
           +AT     G+DI  +  VI +  P   V  +  R GR GR G 
Sbjct: 369 IATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQ 411

Length = 851

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

 Score = 39.9 bits (93), Expect = 0.001
 Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 118 KKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV 177
           +K A++L++F H   +     HG     +R    +++   E  I+ AT     G++ P V
Sbjct: 694 EKVAERLQEFGHKAAF----YHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDV 749

Query: 178 KHVINFDLPSDVEEYVHRIGRTGRMG 203
           + VI+  LP  +E Y    GR GR G
Sbjct: 750 RFVIHHSLPKSIEGYHQECGRAGRDG 775

Length = 1195

>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system restriction enzyme

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 2/103 (1%)

Query: 101 YTLISC-DEALTLVFVETKKGADQLEDFL-HHHGYPVTSIHGDRTQKEREEALRRFRSGE 158
           +TL  C D +      E  +  D +   L +  G  V +   + +++EREE LR+F SG 
Sbjct: 280 HTLFYCGDGSTEDGSDEEDRQIDAVVRLLGNELGMRVNTFTAEESKEEREELLRQFESGL 339

Query: 159 TPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGR 201
              LVA      G+DIP  +        S+  +++ R GR  R
Sbjct: 340 LQGLVAIRCLDEGVDIPATRTAYILASSSNPRQFIQRRGRVLR 382

The DNA phosphorothioate modification system dnd (DNA instability during electrophoresis) recently has been shown to provide a modification essential to a restriction system. This protein family was detected by Partial Phylogenetic Profiling as linked to dnd, and its members usually are clustered with the dndABCDE genes. Length = 451

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

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 22/64 (34%), Positives = 33/64 (51%)

Query: 137 SIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRI 196
           S HG  ++++R    +  +SGE   +VAT+    G+D+  V  VI    P  V   + RI
Sbjct: 306 SHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRI 365

Query: 197 GRTG 200
           GR G
Sbjct: 366 GRAG 369

Length = 1490

>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional

 Score = 38.7 bits (90), Expect = 0.002
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 13/83 (15%)

Query: 112 LVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA-- 166
           L+FV   +G   A+++E +L   G+ +  +       + ++    F  GE   L+  A  
Sbjct: 334 LIFVPIDEGAEKAEEIEKYLLEDGFKIELVSA-----KNKKGFDLFEEGEIDYLIGVATY 388

Query: 167 --VAARGLDIPH-VKHVINFDLP 186
                RGLD+P  ++  + + +P
Sbjct: 389 YGTLVRGLDLPERIRFAVFYGVP 411

Length = 1638

>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 15/65 (23%), Positives = 25/65 (38%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            LV   +    +Q+ + L             + +  RE+ L RF+ G+  IL        
Sbjct: 12  VLVLFPSYSLLEQVAELLASELLEKGIELLVQGEGSREKLLERFKKGKGAILFGVGSFWE 71

Query: 171 GLDIP 175
           G+D P
Sbjct: 72  GIDFP 76

This domain is the second of two tandem AAA domains found in a wide variety of helicase enzymes. Length = 165

>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional

 Score = 38.5 bits (91), Expect = 0.002
 Identities = 27/67 (40%), Positives = 34/67 (50%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            LV   TK+ A+ L D+L   G  V  +H D    ER E +R  R GE  +LV   +   
Sbjct: 449 VLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE 508

Query: 171 GLDIPHV 177
           GLDIP V
Sbjct: 509 GLDIPEV 515

Length = 652

>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd)

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 138 IHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI-----NFDLPSDVEEY 192
            HG  T+ E EE +  F  GE  +LV T +   G+DIP+   +I      F L + + + 
Sbjct: 692 AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGL-AQLYQL 750

Query: 193 VHRIGRTGRMG 203
             R+GR+ +  
Sbjct: 751 RGRVGRSKKKA 761

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 transcribed 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 926

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	237
KOG0333|consensus	673		99.97
KOG0328|consensus	400		99.97
KOG0331|consensus	519		99.97
KOG0326|consensus	459		99.97
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.96
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.95
KOG0330|consensus	476		99.95
KOG0332|consensus	477		99.95
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.95
PTZ00110	545	helicase; Provisional	99.94
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.94
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.94
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.94
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.94
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.94
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.94
KOG0335|consensus	482		99.94
KOG0345|consensus	567		99.93
KOG0342|consensus	543		99.93
PTZ00424	401	helicase 45; Provisional	99.93
KOG0343|consensus	758		99.92
KOG0327|consensus	397		99.92
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.92
KOG0336|consensus	629		99.92
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.92
KOG0340|consensus	442		99.91
KOG0341|consensus	610		99.91
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.9
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.9
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.9
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.9
KOG0346|consensus	569		99.88
KOG0344|consensus	593		99.88
KOG4284|consensus	980		99.88
KOG0347|consensus	731		99.88
KOG0348|consensus	708		99.88
KOG0338|consensus	691		99.87
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.86
PRK13767	876	ATP-dependent helicase; Provisional	99.85
KOG0334|consensus	997		99.85
PRK04914	956	ATP-dependent helicase HepA; Validated	99.85
KOG0339|consensus	731		99.84
PRK02362	737	ski2-like helicase; Provisional	99.84
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.84
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.84
PHA02653	675	RNA helicase NPH-II; Provisional	99.83
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.82
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.81
KOG0350|consensus	620		99.81
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.8
PRK10689	1147	transcription-repair coupling factor; Provisional	99.8
PRK00254	720	ski2-like helicase; Provisional	99.8
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.79
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.79
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.79
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.78
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.78
KOG0351|consensus	941		99.78
PRK01172	674	ski2-like helicase; Provisional	99.78
COG1202	830	Superfamily II helicase, archaea-specific [General	99.78
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.78
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.77
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.77
PRK13766	773	Hef nuclease; Provisional	99.75
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.74
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.74
KOG0337|consensus	529		99.73
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.73
PRK05298	652	excinuclease ABC subunit B; Provisional	99.72
PHA02558	501	uvsW UvsW helicase; Provisional	99.72
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.72
KOG0352|consensus	641		99.7
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.69
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.69
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.67
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.67
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.67
KOG0354|consensus	746		99.66
COG1204	766	Superfamily II helicase [General function predicti	99.66
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.65
KOG0349|consensus	725		99.65
KOG0329|consensus	387		99.64
PRK14701	1638	reverse gyrase; Provisional	99.63
KOG0948|consensus	1041		99.61
KOG0353|consensus	695		99.61
KOG0951|consensus	1674		99.61
PRK09401	1176	reverse gyrase; Reviewed	99.59
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.53
KOG0392|consensus	1549		99.53
KOG0952|consensus	1230		99.53
KOG0385|consensus	971		99.51
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.5
KOG0922|consensus	674		99.48
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.48
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.47
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.47
KOG0950|consensus	1008		99.47
PRK09694	878	helicase Cas3; Provisional	99.47
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.46
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.45
KOG0947|consensus	1248		99.45
COG1205	851	Distinct helicase family with a unique C-terminal	99.43
KOG0384|consensus	1373		99.42
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.4
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.37
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.37
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.35
KOG0923|consensus	902		99.32
KOG0391|consensus	1958		99.3
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.29
KOG0387|consensus	923		99.28
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.28
PRK05580	679	primosome assembly protein PriA; Validated	99.26
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.23
KOG0388|consensus	1185		99.21
KOG0390|consensus	776		99.15
KOG0389|consensus	941		99.13
KOG4150|consensus	1034		99.12
KOG0924|consensus	1042		99.12
KOG0953|consensus	700		99.11
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.1
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.97
KOG0920|consensus	924		98.91
KOG1000|consensus	689		98.9
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.87
KOG0386|consensus	1157		98.85
KOG0949|consensus	1330		98.83
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.81
KOG1015|consensus	1567		98.73
KOG1123|consensus	776		98.69
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.64
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.62
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.59
COG4096	875	HsdR Type I site-specific restriction-modification	98.59
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.57
KOG1002|consensus	791		98.48
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.42
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.35
KOG4439|consensus	901		98.3
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.27
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.27
KOG0925|consensus	699		98.25
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.14
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.12
KOG1016|consensus	1387		98.1
KOG0926|consensus	1172		98.03
KOG0951|consensus	1674		97.9
COG4889	1518	Predicted helicase [General function prediction on	97.86
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.84
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.83
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.75
PF13871	278	Helicase_C_4: Helicase_C-like	97.69
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.58
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	97.56
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.55
KOG0331|consensus	519		97.54
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.5
KOG1001|consensus	674		97.43
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	97.26
KOG0332|consensus	477		97.2
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	97.09
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.09
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.04
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	96.91
KOG0326|consensus	459		96.86
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.57
KOG0333|consensus	673		96.56
PRK05580	679	primosome assembly protein PriA; Validated	96.33
KOG0328|consensus	400		96.29
TIGR00595	505	priA primosomal protein N'. All proteins in this f	96.25
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	96.05
COG1202	830	Superfamily II helicase, archaea-specific [General	95.97
PRK14873	665	primosome assembly protein PriA; Provisional	95.96
PRK14873	665	primosome assembly protein PriA; Provisional	95.75
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	95.64
COG1198	730	PriA Primosomal protein N' (replication factor Y)	95.44
PRK10689	1147	transcription-repair coupling factor; Provisional	95.28
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	95.1
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	95.04
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	94.91
KOG0342|consensus	543		94.64
PRK14701	1638	reverse gyrase; Provisional	94.32
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	94.26
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	94.2
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	94.02
KOG0298|consensus	1394		94.02
KOG4284|consensus	980		94.02
KOG0701|consensus	1606		93.88
KOG1513|consensus	1300		93.56
KOG0335|consensus	482		93.47
PTZ00110	545	helicase; Provisional	93.38
PHA02653	675	RNA helicase NPH-II; Provisional	93.27
KOG0330|consensus	476		93.17
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	92.82
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	92.72
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	92.71
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	92.38
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	92.35
KOG0327|consensus	397		92.32
KOG0347|consensus	731		92.24
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	92.19
KOG0340|consensus	442		91.96
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	91.89
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	91.78
KOG2340|consensus	698		91.65
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	91.28
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	91.22
KOG0921|consensus	1282		90.4
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	90.4
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	89.86
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	89.15
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	88.18
KOG0338|consensus	691		88.12
KOG0341|consensus	610		87.86
PTZ00424	401	helicase 45; Provisional	87.36
PRK09200	790	preprotein translocase subunit SecA; Reviewed	87.08
PRK09401	1176	reverse gyrase; Reviewed	86.32
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	85.89
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	85.77
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	85.53
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	85.53
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	84.75
KOG0383|consensus	696		84.17
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	83.77
KOG0343|consensus	758		83.41
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	83.39
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	83.04
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	81.09
KOG1133|consensus	821		81.02
KOG0349|consensus	725		80.5
PRK04914	956	ATP-dependent helicase HepA; Validated	80.47
PRK05298	652	excinuclease ABC subunit B; Provisional	80.13

>KOG0333|consensus

Probab=99.97  E-value=1.9e-30  Score=218.85  Aligned_cols=163  Identities=42%  Similarity=0.735  Sum_probs=155.1

Q ss_pred             ChHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          1 LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         1 ~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      .||+.||.+|+.+.+...+.+...++|.++.+++++|...|..+|....                               
T Consensus       468 rlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~k~kkL~eil~~~~-------------------------------  516 (673)
T KOG0333|consen  468 RLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDEKRKKLIEILESNF-------------------------------  516 (673)
T ss_pred             HHHHHHhhCCeEEEeccCCCCccchheEEEEecchHHHHHHHHHHHhCC-------------------------------
Confidence            3899999999999998888999999999999999999999999998772                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++|||+|+.+.|+.+++.|.+.|+.+..+||+-++++|+..+..|++|..+
T Consensus       517 ---------------------------~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~d  569 (673)
T KOG0333|consen  517 ---------------------------DPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGD  569 (673)
T ss_pred             ---------------------------CCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCC
Confidence                                       47899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYG  221 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  221 (237)
                      |||||+++++|+|+|++.+||+||++++.+.|.||+||+||.|+.|.+++|+.+.+...|-
T Consensus       570 IlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~v~y  630 (673)
T KOG0333|consen  570 ILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTAVFY  630 (673)
T ss_pred             EEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhHHHH
Confidence            9999999999999999999999999999999999999999999999999999999866443

>KOG0328|consensus

Probab=99.97  E-value=8.3e-31  Score=206.27  Aligned_cols=159  Identities=33%  Similarity=0.569  Sum_probs=150.8

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechh-HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQD-KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      +.++||+||+.|-+.+.+.++++|+++|+.+++++ |.+.|.+|-+....                              
T Consensus       217 mt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtLcdLYd~LtI------------------------------  266 (400)
T KOG0328|consen  217 MTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTI------------------------------  266 (400)
T ss_pred             HHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhHhHHHHHhhhheh------------------------------
Confidence            46799999999999999999999999999999887 99999999998853                              


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                  .+++|||+|+..++-+.+-+....+.+...||+|++++|+++...|++|..+
T Consensus       267 ----------------------------tQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~Sr  318 (400)
T KOG0328|consen  267 ----------------------------TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSR  318 (400)
T ss_pred             ----------------------------heEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCce
Confidence                                        5799999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      ||++||+-++|+|+|.+++||+||.|.+.+.|+||+||+||.|++|.++-|+...+..
T Consensus       319 vLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~  376 (400)
T KOG0328|consen  319 VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLR  376 (400)
T ss_pred             EEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHH
Confidence            9999999999999999999999999999999999999999999999999999877654

>KOG0331|consensus

Probab=99.97  E-value=8.9e-31  Score=224.93  Aligned_cols=162  Identities=43%  Similarity=0.689  Sum_probs=150.5

Q ss_pred             ChHHHHhhcceeEEEeecc--CCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhh
Q psy15610          1 LLAKEFLYRYIFLAIGRVG--STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHH   78 (237)
Q Consensus         1 ~~~~~~l~~~~~i~~~~~~--~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~   78 (237)
                      .||++||.+|+.+.+....  ..+.+|.|....+++..|...|.++|.....                            
T Consensus       287 ~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~lL~~~~~----------------------------  338 (519)
T KOG0331|consen  287 QLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGKLLEDISS----------------------------  338 (519)
T ss_pred             HHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHHHHHHHhc----------------------------
Confidence            4899999999999997543  7889999999999999999999999987642                            


Q ss_pred             cCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610         79 HGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                                                 .++.++||||.|.+.|++++..++..++++..+||+.++.+|+.+++.|++|.
T Consensus       339 ---------------------------~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~  391 (519)
T KOG0331|consen  339 ---------------------------DSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGK  391 (519)
T ss_pred             ---------------------------cCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCC
Confidence                                       22679999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        159 TPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       159 ~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ..|||||+++++|+|+|++++||+||+|.+.+.|+||+||+||.|+.|.+++|+...+.
T Consensus       392 ~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~  450 (519)
T KOG0331|consen  392 SPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNA  450 (519)
T ss_pred             cceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHH
Confidence            99999999999999999999999999999999999999999999999999999987654

>KOG0326|consensus

Probab=99.97  E-value=1.6e-30  Score=207.82  Aligned_cols=159  Identities=30%  Similarity=0.485  Sum_probs=152.1

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      ++.+||++|+.|+++ ++.++.++.|+|..|++++|..+|..|+.+.+                                
T Consensus       275 Fm~~~l~kPy~INLM-~eLtl~GvtQyYafV~e~qKvhCLntLfskLq--------------------------------  321 (459)
T KOG0326|consen  275 FMDRHLKKPYEINLM-EELTLKGVTQYYAFVEERQKVHCLNTLFSKLQ--------------------------------  321 (459)
T ss_pred             HHHHhccCcceeehh-hhhhhcchhhheeeechhhhhhhHHHHHHHhc--------------------------------
Confidence            688999999999998 77899999999999999999999999999987                                


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                -+++||||++...++.++.-+.+.|+++.++|+.|.+++|-+++..|++|..+.
T Consensus       322 --------------------------INQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crn  375 (459)
T KOG0326|consen  322 --------------------------INQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRN  375 (459)
T ss_pred             --------------------------ccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccce
Confidence                                      368999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGS  219 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~  219 (237)
                      |||||.+.+|+|+|.+++||+||.|.+++.|+||+||+||.|-.|.++.++..++.-.
T Consensus       376 LVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~  433 (459)
T KOG0326|consen  376 LVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFN  433 (459)
T ss_pred             eeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhh
Confidence            9999999999999999999999999999999999999999999999999999877643

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

Probab=99.96  E-value=3.3e-29  Score=221.26  Aligned_cols=157  Identities=43%  Similarity=0.671  Sum_probs=148.2

Q ss_pred             ChHHHHhhcceeEEEeeccC--CCCCceeEEEEeechh-HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhh
Q psy15610          1 LLAKEFLYRYIFLAIGRVGS--TSENITQRIAWVDEQD-KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLH   77 (237)
Q Consensus         1 ~~~~~~l~~~~~i~~~~~~~--~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~   77 (237)
                      +|+++||.+|..+.+..+..  +...|.|+|+.++..+ |+..|..+|....                            
T Consensus       221 ~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~~----------------------------  272 (513)
T COG0513         221 ELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDED----------------------------  272 (513)
T ss_pred             HHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHHhcCC----------------------------
Confidence            37899999999998875555  8899999999999876 9999999999874                            


Q ss_pred             hcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC
Q psy15610         78 HHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG  157 (237)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g  157 (237)
                                                    ..++||||+|...++.++..|...|+.+..+||++++++|.+.++.|++|
T Consensus       273 ------------------------------~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g  322 (513)
T COG0513         273 ------------------------------EGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDG  322 (513)
T ss_pred             ------------------------------CCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcC
Confidence                                          35799999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        158 ETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       158 ~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      ..+||||||++++|+|+|++++||+||.|.+++.|+||+||+||.|..|.++.|+.+.
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            9999999999999999999999999999999999999999999999999999999974

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=8.1e-28  Score=209.03  Aligned_cols=158  Identities=36%  Similarity=0.554  Sum_probs=143.6

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      ++..++.+|..+.+.+.......+.+.+..+...+|...|.+++....                                
T Consensus       207 ~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~--------------------------------  254 (423)
T PRK04837        207 LAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRLLQTLIEEEW--------------------------------  254 (423)
T ss_pred             HHHHHCCCCEEEEEcCCCcCCCceeEEEEeCCHHHHHHHHHHHHHhcC--------------------------------
Confidence            456788899988887666677788888877777889888888886542                                


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..++||||+++..++.++..|...++.+..+||+|++.+|..+++.|++|+.+|
T Consensus       255 --------------------------~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~v  308 (423)
T PRK04837        255 --------------------------PDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDI  308 (423)
T ss_pred             --------------------------CCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcE
Confidence                                      468999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||||+++++|+|+|++++||+||+|.+...|+||+||+||.|+.|.+++|+.+.+.
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            99999999999999999999999999999999999999999999999999987643

>KOG0330|consensus

Probab=99.95  E-value=4e-28  Score=198.39  Aligned_cols=161  Identities=32%  Similarity=0.497  Sum_probs=149.3

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      |...-+++|..+.+...-.+.+.++|.|+.++...|..+|+.+|+...                                
T Consensus       252 L~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K~~yLV~ll~e~~--------------------------------  299 (476)
T KOG0330|consen  252 LQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDTYLVYLLNELA--------------------------------  299 (476)
T ss_pred             HHhhccCCCeEEeccchhcchHHhhhheEeccccccchhHHHHHHhhc--------------------------------
Confidence            344567899999887666888999999999999999999999999764                                


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                +.++||||+|....+.++-+|+.+|+.+..+||.|+++.|.-.++.|++|...|
T Consensus       300 --------------------------g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~i  353 (476)
T KOG0330|consen  300 --------------------------GNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSI  353 (476)
T ss_pred             --------------------------CCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcE
Confidence                                      689999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSY  220 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~  220 (237)
                      |+|||++++|+|+|.+++|||||.|.+..+|+||+||++|.|.+|.++.+++.-+.+.|
T Consensus       354 Lv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~  412 (476)
T KOG0330|consen  354 LVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELV  412 (476)
T ss_pred             EEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHH
Confidence            99999999999999999999999999999999999999999999999999987554433

>KOG0332|consensus

Probab=99.95  E-value=2.1e-27  Score=193.25  Aligned_cols=158  Identities=32%  Similarity=0.499  Sum_probs=146.7

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeech-hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQ-DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      +|.+++++|..+-+.++..++.+|.|+|+.|..+ +|.+.|.+|-...-                               
T Consensus       281 Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~t-------------------------------  329 (477)
T KOG0332|consen  281 FALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLT-------------------------------  329 (477)
T ss_pred             HHHHhcCCCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhhh-------------------------------
Confidence            6889999999999999999999999999999964 69999999665542                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 -+++||||.|++.+..++..+...|..+..+||.|.-++|..+++.|++|..+
T Consensus       330 ---------------------------igqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~k  382 (477)
T KOG0332|consen  330 ---------------------------IGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEK  382 (477)
T ss_pred             ---------------------------hhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcce
Confidence                                       37899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCC------CHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      |||+|+++++|+|++.+++||+||.|.      +.+.|+||+||+||+|+.|.++.|+..+..
T Consensus       383 VLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s  445 (477)
T KOG0332|consen  383 VLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDS  445 (477)
T ss_pred             EEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCc
Confidence            999999999999999999999999995      789999999999999999999999876543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.95  E-value=6e-27  Score=205.60  Aligned_cols=157  Identities=34%  Similarity=0.519  Sum_probs=143.7

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      +++.|+.+|..+.+... .....+.+.++.++..+|...|..++....                                
T Consensus       195 l~~~~~~~~~~i~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~--------------------------------  241 (460)
T PRK11776        195 ISQRFQRDPVEVKVEST-HDLPAIEQRFYEVSPDERLPALQRLLLHHQ--------------------------------  241 (460)
T ss_pred             HHHHhcCCCEEEEECcC-CCCCCeeEEEEEeCcHHHHHHHHHHHHhcC--------------------------------
Confidence            57788999999887543 345669999999998889999999887542                                


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..++||||+++..++.+++.|...++.+..+||+|++.+|+.+++.|++|..+|
T Consensus       242 --------------------------~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~v  295 (460)
T PRK11776        242 --------------------------PESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSV  295 (460)
T ss_pred             --------------------------CCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcE
Confidence                                      468999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||||+++++|+|+|++++||+++.|.++..|+||+||+||.|..|.+++|+.+.+.
T Consensus       296 LVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~  351 (460)
T PRK11776        296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEM  351 (460)
T ss_pred             EEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHH
Confidence            99999999999999999999999999999999999999999999999999988754

>PTZ00110 helicase; Provisional

Probab=99.94  E-value=2.2e-26  Score=205.00  Aligned_cols=161  Identities=43%  Similarity=0.706  Sum_probs=143.6

Q ss_pred             hHHHHhh-cceeEEEeecc-CCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhc
Q psy15610          2 LAKEFLY-RYIFLAIGRVG-STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHH   79 (237)
Q Consensus         2 ~~~~~l~-~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~   79 (237)
                      +++.++. +|+.+.+.... ....++.+.+..+++.+|...|.++|.....                             
T Consensus       325 l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~-----------------------------  375 (545)
T PTZ00110        325 LARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMR-----------------------------  375 (545)
T ss_pred             HHHHHhccCCEEEEECCCccccCCCeeEEEEEEechhHHHHHHHHHHHhcc-----------------------------
Confidence            5667776 68888776444 4567889998888888899988888876421                             


Q ss_pred             CCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCC
Q psy15610         80 GYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGET  159 (237)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~  159 (237)
                                                 +..++||||++++.++.++..|...++.+..+||++++++|+.+++.|++|..
T Consensus       376 ---------------------------~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~  428 (545)
T PTZ00110        376 ---------------------------DGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKS  428 (545)
T ss_pred             ---------------------------cCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCC
Confidence                                       15799999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        160 PILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       160 ~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      +|||||+++++|+|+|++++||+||+|.++..|+||+||+||.|..|.+++|+.+.+..
T Consensus       429 ~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~  487 (545)
T PTZ00110        429 PIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYR  487 (545)
T ss_pred             cEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHH
Confidence            99999999999999999999999999999999999999999999999999999987653

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.94  E-value=2.1e-26  Score=201.79  Aligned_cols=158  Identities=39%  Similarity=0.614  Sum_probs=142.1

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      ++.+++.+|..+.+.........+.+.+..++..+|...|..++....                                
T Consensus       197 l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~l~~~~~--------------------------------  244 (456)
T PRK10590        197 LAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQMIGKGN--------------------------------  244 (456)
T ss_pred             HHHHHcCCCeEEEEecccccccceeEEEEEcCHHHHHHHHHHHHHcCC--------------------------------
Confidence            567888899888877666667788888888888888877777765432                                


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..++||||+++..++.+++.|...++.+..+||+|++.+|.++++.|++|.++|
T Consensus       245 --------------------------~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~i  298 (456)
T PRK10590        245 --------------------------WQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRV  298 (456)
T ss_pred             --------------------------CCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcE
Confidence                                      468999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||||+++++|+|+|++++||+|++|.++..|+||+||+||.|..|.+++|+...+.
T Consensus       299 LVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~  354 (456)
T PRK10590        299 LVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEH  354 (456)
T ss_pred             EEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHH
Confidence            99999999999999999999999999999999999999999999999999976653

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=1.9e-26  Score=206.25  Aligned_cols=157  Identities=44%  Similarity=0.620  Sum_probs=141.6

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      ++..+|.+|..+.+..+......+.+.++.+...+|...|..++....                                
T Consensus       209 l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~--------------------------------  256 (572)
T PRK04537        209 LAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLLLGLLSRSE--------------------------------  256 (572)
T ss_pred             HHHHHhcCCcEEEeccccccccceeEEEEecCHHHHHHHHHHHHhccc--------------------------------
Confidence            466788888777766566667788888888887888888888886542                                


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..++||||+|+..++.+++.|...++.+..+||+|++.+|..+++.|++|.++|
T Consensus       257 --------------------------~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~V  310 (572)
T PRK04537        257 --------------------------GARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEI  310 (572)
T ss_pred             --------------------------CCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeE
Confidence                                      468999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      ||||+++++|+|+|++++||+|+.|.+...|+||+||+||.|..|.+++|+.+.+
T Consensus       311 LVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~  365 (572)
T PRK04537        311 LVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERY  365 (572)
T ss_pred             EEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHH
Confidence            9999999999999999999999999999999999999999999999999997653

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.94  E-value=3e-26  Score=199.94  Aligned_cols=158  Identities=34%  Similarity=0.548  Sum_probs=143.2

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeec-hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDE-QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      ++..++.+|+.+.+.+......++.+++..++. ..|...|..++....                               
T Consensus       196 ~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~-------------------------------  244 (434)
T PRK11192        196 FAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQPE-------------------------------  244 (434)
T ss_pred             HHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHhcCC-------------------------------
Confidence            567788899999887766777889998887775 568888888887542                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++||||+++..++.++..|...++.+..+||+|++.+|..+++.|++|.++
T Consensus       245 ---------------------------~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~  297 (434)
T PRK11192        245 ---------------------------VTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVN  297 (434)
T ss_pred             ---------------------------CCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCc
Confidence                                       47899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      |||||+++++|+|+|++++||+|++|.+...|+||+||+||.|..|.+++|+...+.
T Consensus       298 vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~  354 (434)
T PRK11192        298 VLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDH  354 (434)
T ss_pred             EEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecHHHH
Confidence            999999999999999999999999999999999999999999999999999976554

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.94  E-value=2.6e-26  Score=206.73  Aligned_cols=158  Identities=33%  Similarity=0.517  Sum_probs=146.3

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      ++++|+.+|..+.+.........+.+.|+.+...+|...|..+|....                                
T Consensus       197 i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~~~k~~~L~~~L~~~~--------------------------------  244 (629)
T PRK11634        197 ITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAED--------------------------------  244 (629)
T ss_pred             HHHHHcCCCeEEEccCccccCCceEEEEEEechhhHHHHHHHHHHhcC--------------------------------
Confidence            578899999999887666777889999999988899999998887542                                


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..++||||+|+..++.+++.|...++.+..+||+|++.+|+++++.|++|.++|
T Consensus       245 --------------------------~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~I  298 (629)
T PRK11634        245 --------------------------FDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDI  298 (629)
T ss_pred             --------------------------CCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCE
Confidence                                      468999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||||+++++|+|+|++++||+||.|.++..|+||+||+||.|..|.+++|+.+.+.
T Consensus       299 LVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~  354 (629)
T PRK11634        299 LIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRER  354 (629)
T ss_pred             EEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechHHH
Confidence            99999999999999999999999999999999999999999999999999987654

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

Probab=99.94  E-value=2.9e-26  Score=203.45  Aligned_cols=164  Identities=33%  Similarity=0.612  Sum_probs=145.4

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      +++.++.+++.+.+.........+.+.++.++..+|...|.+++......                              
T Consensus       317 l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~~k~~~l~~~l~~~~~~------------------------------  366 (518)
T PLN00206        317 FASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHF------------------------------  366 (518)
T ss_pred             HHHHhCCCCEEEEeCCCCCCCcceeEEEEeccchhHHHHHHHHHHhhccc------------------------------
Confidence            57788889999988766677788889888888888888888888654211                              


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhh-CCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHH-HGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~-~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                ..++||||+++..++.++..|.. .++.+..+||++++.+|..+++.|++|..+
T Consensus       367 --------------------------~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~  420 (518)
T PLN00206        367 --------------------------KPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVP  420 (518)
T ss_pred             --------------------------CCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCC
Confidence                                      25799999999999999999975 588999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYG  221 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  221 (237)
                      |||||+++++|+|+|++++||+|++|.+...|+||+||+||.|..|.+++|+...+...+.
T Consensus       421 ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~  481 (518)
T PLN00206        421 VIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFP  481 (518)
T ss_pred             EEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999987754443

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=7.4e-26  Score=199.37  Aligned_cols=157  Identities=34%  Similarity=0.537  Sum_probs=141.2

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      +++.++.+|..+.+..+.....++.+.+..+...+|...|.+++....                                
T Consensus       287 ~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~ll~~~~--------------------------------  334 (475)
T PRK01297        287 LAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQNP--------------------------------  334 (475)
T ss_pred             HHHHhccCCEEEEeccCcCCCCcccEEEEEecchhHHHHHHHHHHhcC--------------------------------
Confidence            567788888888777666666778888777777888888887776432                                


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..++||||+++..++.+++.|...++.+..+||++++++|..+++.|++|.+++
T Consensus       335 --------------------------~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~v  388 (475)
T PRK01297        335 --------------------------WERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRV  388 (475)
T ss_pred             --------------------------CCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcE
Confidence                                      468999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      ||||+++++|+|+|++++||++++|.+...|+||+||+||.|..|.+++|+...+
T Consensus       389 LvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d  443 (475)
T PRK01297        389 LVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDD  443 (475)
T ss_pred             EEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHH
Confidence            9999999999999999999999999999999999999999999999999998664

>KOG0335|consensus

Probab=99.94  E-value=2.9e-26  Score=194.33  Aligned_cols=186  Identities=56%  Similarity=0.870  Sum_probs=162.2

Q ss_pred             hHHHHhhc-ceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYR-YIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~-~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      ++..|+.+ .+++.+..-+.+..+|.|.+..|.+.+|...|+++|.......            +.              
T Consensus       279 l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~------------~~--------------  332 (482)
T KOG0335|consen  279 LAADFLKDNYIFLAVGRVGSTSENITQKILFVNEMEKRSKLLDLLNKDDGPP------------SD--------------  332 (482)
T ss_pred             hHHHHhhccceEEEEeeeccccccceeEeeeecchhhHHHHHHHhhcccCCc------------cc--------------
Confidence            67788886 9999999999999999999999999999999999998663110            00              


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                             .......++|||.|.+.+..++.+|...++++..+||..++.+|++.++.|++|...
T Consensus       333 -----------------------~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~p  389 (482)
T KOG0335|consen  333 -----------------------GEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAP  389 (482)
T ss_pred             -----------------------CCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcc
Confidence                                   000124899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCC----CCCCCCCCCCCccC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGG----SSSQNSNAPDWWND  236 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~  236 (237)
                      +||||+++++|+|+|++++||+||+|.+...|+||+||+||.|+.|.+..|++......-..    +..+....|+|+.+
T Consensus       390 vlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L~~~l~ea~q~vP~wl~~  469 (482)
T KOG0335|consen  390 VLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIAKALVEILTEANQEVPQWLSE  469 (482)
T ss_pred             eEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhHHHHHHHHHHhcccCcHHHHh
Confidence            99999999999999999999999999999999999999999999999999999555543333    55567778888764

>KOG0345|consensus

Probab=99.93  E-value=7.1e-26  Score=189.11  Aligned_cols=160  Identities=29%  Similarity=0.429  Sum_probs=146.7

Q ss_pred             ChHHHHhhcceeEEEeeccC--CCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhh
Q psy15610          1 LLAKEFLYRYIFLAIGRVGS--TSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHH   78 (237)
Q Consensus         1 ~~~~~~l~~~~~i~~~~~~~--~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~   78 (237)
                      +|++..|.||+.|.+..++.  +...+.-.|+.|+..+|+..|+.+|....                             
T Consensus       204 dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~~L~~~~-----------------------------  254 (567)
T KOG0345|consen  204 DLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNNNK-----------------------------  254 (567)
T ss_pred             HHHHhhccCceeeeecccccccCchhhcceeeEecHHHHHHHHHHHHhccc-----------------------------
Confidence            37888999999999976664  67779999999999999999999998864                             


Q ss_pred             cCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhc
Q psy15610         79 HGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRS  156 (237)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~  156 (237)
                                                   ..++|||.+|...++.....+...  ...+..+||.|.+..|.++++.|++
T Consensus       255 -----------------------------~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~  305 (567)
T KOG0345|consen  255 -----------------------------DKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRK  305 (567)
T ss_pred             -----------------------------cccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHh
Confidence                                         578999999999999998888765  6789999999999999999999999


Q ss_pred             CCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        157 GETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       157 g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      ..-.+|+|||++++|+|+|++++||+||+|.+++.|+||+||++|.|+.|.+++|+.+.+..
T Consensus       306 ~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~a  367 (567)
T KOG0345|consen  306 LSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEA  367 (567)
T ss_pred             ccCceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHH
Confidence            88899999999999999999999999999999999999999999999999999999995543

>KOG0342|consensus

Probab=99.93  E-value=8.3e-26  Score=189.61  Aligned_cols=167  Identities=32%  Similarity=0.440  Sum_probs=151.3

Q ss_pred             hHHHHhh-cceeEEEeecc--CCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhh
Q psy15610          2 LAKEFLY-RYIFLAIGRVG--STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHH   78 (237)
Q Consensus         2 ~~~~~l~-~~~~i~~~~~~--~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~   78 (237)
                      |+.--|+ +|++|++..++  .+...+.|-|++++...++..+..+|.+...                            
T Consensus       278 l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~ll~~~LKk~~~----------------------------  329 (543)
T KOG0342|consen  278 LARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSRFSLLYTFLKKNIK----------------------------  329 (543)
T ss_pred             HHHHhhcCCceEeecCCCCCcchhhcccceEEeccccchHHHHHHHHHHhcC----------------------------
Confidence            3444444 69999997665  6778999999999999999999999988741                            


Q ss_pred             cCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610         79 HGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                                                   ..++||||+|......++++|....+++.-+||++++..|..+...|++.+
T Consensus       330 -----------------------------~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kae  380 (543)
T KOG0342|consen  330 -----------------------------RYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAE  380 (543)
T ss_pred             -----------------------------CceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcc
Confidence                                         268999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCCC
Q psy15610        159 TPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS  225 (237)
Q Consensus       159 ~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  225 (237)
                      ..||+|||++++|+|+|++++||+|++|.++.+|+||+||+||.|..|.+++|..|.+.......++
T Consensus       381 sgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK~  447 (543)
T KOG0342|consen  381 SGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLKK  447 (543)
T ss_pred             cceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999999999999999999998877666554

>PTZ00424 helicase 45; Provisional

Probab=99.93  E-value=8.5e-25  Score=188.98  Aligned_cols=166  Identities=31%  Similarity=0.524  Sum_probs=139.0

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeech-hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQ-DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      +..+|+.+|..+.+........++.+.+..++.. .+...+.+++....                               
T Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------------------------------  266 (401)
T PTZ00424        218 LTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLT-------------------------------  266 (401)
T ss_pred             HHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHHhcC-------------------------------
Confidence            3456777777766554455666777777666542 35555665554331                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++||||+++..++.++..|...++.+..+||++++.+|..+++.|++|.++
T Consensus       267 ---------------------------~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~  319 (401)
T PTZ00424        267 ---------------------------ITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTR  319 (401)
T ss_pred             ---------------------------CCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCC
Confidence                                       46899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS  225 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  225 (237)
                      |||||+++++|+|+|++++||+++.|.+...|+||+||+||.|..|.|+.|+.+.+...+....+
T Consensus       320 vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~e~  384 (401)
T PTZ00424        320 VLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIER  384 (401)
T ss_pred             EEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999998887665555433

>KOG0343|consensus

Probab=99.92  E-value=8.2e-25  Score=185.95  Aligned_cols=159  Identities=31%  Similarity=0.461  Sum_probs=148.0

Q ss_pred             ChHHHHhhcceeEEEeec--cCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhh
Q psy15610          1 LLAKEFLYRYIFLAIGRV--GSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHH   78 (237)
Q Consensus         1 ~~~~~~l~~~~~i~~~~~--~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~   78 (237)
                      +||+--|+||..|.+-..  .++..++.|+|++++..+|+.+|...|..+.                             
T Consensus       262 dLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~shl-----------------------------  312 (758)
T KOG0343|consen  262 DLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIKSHL-----------------------------  312 (758)
T ss_pred             HHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHHHHHHHHHHhcc-----------------------------
Confidence            467778899999998633  3778899999999999999999999998874                             


Q ss_pred             cCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhc
Q psy15610         79 HGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRS  156 (237)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~  156 (237)
                                                   ..++|||..|.+++..+.+.+.+.  |+++..+||.|++..|..+...|-.
T Consensus       313 -----------------------------k~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~  363 (758)
T KOG0343|consen  313 -----------------------------KKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVR  363 (758)
T ss_pred             -----------------------------ccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHH
Confidence                                         578999999999999999999875  8999999999999999999999999


Q ss_pred             CCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        157 GETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       157 g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ....||+|||++++|+|||.+++||++|+|.+...|+||+||+.|.+..|.+++++.|.+.
T Consensus       364 ~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEe  424 (758)
T KOG0343|consen  364 KRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEE  424 (758)
T ss_pred             hcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhH
Confidence            9999999999999999999999999999999999999999999999999999999999874

>KOG0327|consensus

Probab=99.92  E-value=3.8e-25  Score=180.86  Aligned_cols=162  Identities=33%  Similarity=0.581  Sum_probs=152.9

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      ++++||.+|+.+.+...+.++.+|+|+|+.+.+.+|+.+|.++.+.                                  
T Consensus       217 vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~k~~~l~dl~~~----------------------------------  262 (397)
T KOG0327|consen  217 VTKKFMREPVRILVKKDELTLEGIKQFYINVEKEEKLDTLCDLYRR----------------------------------  262 (397)
T ss_pred             HHHHhccCceEEEecchhhhhhheeeeeeeccccccccHHHHHHHh----------------------------------
Confidence            6789999999999998889999999999999999999999999982                                  


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..+++|||||+..++.+.+.|...++.+..+||.|.+.+|..+.+.|+.|..+|
T Consensus       263 --------------------------~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrv  316 (397)
T KOG0327|consen  263 --------------------------VTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRV  316 (397)
T ss_pred             --------------------------hhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceE
Confidence                                      368999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGS  223 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~  223 (237)
                      ||+|+.+++|+|+..+..|++|+.|.+.+.|+||.||+||.|.+|.++.|+...+....+..
T Consensus       317 lIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk~i  378 (397)
T KOG0327|consen  317 LITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDI  378 (397)
T ss_pred             EeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHHhH
Confidence            99999999999999999999999999999999999999999999999999998776655543

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.92  E-value=3.2e-24  Score=188.60  Aligned_cols=166  Identities=19%  Similarity=0.301  Sum_probs=129.4

Q ss_pred             cccceeEEeecccc--hhhHHHHhhhcCCCcee----------ecCCcchhhHHHHhhhhhhccCCceEEEEeecccchH
Q psy15610         55 DEALTLVFVETKKG--ADQLEDFLHHHGYPVTS----------IHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGAD  122 (237)
Q Consensus        55 ~~~~~i~f~~t~~~--~~~~~~~l~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~  122 (237)
                      ++.+++++++|...  .+++.+.+.-.......          ...............+.....++.++||||+|++.++
T Consensus       161 ~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~~r~nl~~~v~~~~~~~~~~l~~~l~~~~~~~~~IIF~~s~~~~e  240 (470)
T TIGR00614       161 PNVPIMALTATASPSVREDILRQLNLKNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKSE  240 (470)
T ss_pred             CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCCCCCCCcEEEEEeCCccHHHHHHHHHHHhcCCCceEEEECcHHHHH
Confidence            45679999999876  34566655332211110          0000000111111112222344566799999999999


Q ss_pred             HHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccC
Q psy15610        123 QLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRM  202 (237)
Q Consensus       123 ~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~  202 (237)
                      .++..|...++.+..+||+|++++|..+++.|++|.++|||||+++++|+|+|++++||++++|.|.+.|+||+||+||.
T Consensus       241 ~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~  320 (470)
T TIGR00614       241 QVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRD  320 (470)
T ss_pred             HHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHHhhhcCcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCceEEeecCCCCCCC
Q psy15610        203 GNLDFPFSYNQPGYGGSY  220 (237)
Q Consensus       203 g~~~~~~~~~~~~~~~~~  220 (237)
                      |.+|.|++|+.+.+....
T Consensus       321 G~~~~~~~~~~~~d~~~~  338 (470)
T TIGR00614       321 GLPSECHLFYAPADINRL  338 (470)
T ss_pred             CCCceEEEEechhHHHHH
Confidence            999999999998765433

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

>KOG0336|consensus

Probab=99.92  E-value=1.1e-24  Score=179.68  Aligned_cols=167  Identities=34%  Similarity=0.543  Sum_probs=149.7

Q ss_pred             ChHHHHhhcceeEEEeecc-CCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhc
Q psy15610          1 LLAKEFLYRYIFLAIGRVG-STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHH   79 (237)
Q Consensus         1 ~~~~~~l~~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~   79 (237)
                      +||..||++|+.+-+..-. .....++|.+++-.+.+|+..+..++...+.                             
T Consensus       414 rLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~~ms~-----------------------------  464 (629)
T KOG0336|consen  414 RLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVANMSS-----------------------------  464 (629)
T ss_pred             HHHHHhhhCceEEEecccceeeeeeeeeeEEecccHHHHHHHHHHHHhcCC-----------------------------
Confidence            4899999999999876555 5566888888777788899888888776642                             


Q ss_pred             CCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCC
Q psy15610         80 GYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGET  159 (237)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~  159 (237)
                                                  ..++||||.....++.+...|.-.|+..-.+||+-++.+|+..++.|++|..
T Consensus       465 ----------------------------ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~v  516 (629)
T KOG0336|consen  465 ----------------------------NDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEV  516 (629)
T ss_pred             ----------------------------CceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCce
Confidence                                        4799999999999999998888889999999999999999999999999999


Q ss_pred             CEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCC
Q psy15610        160 PILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSS  224 (237)
Q Consensus       160 ~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~  224 (237)
                      +|||+||++++|+|+|++++|++||.|.+.+.|+||+||.||.|+.|..+.|+...+....+.++
T Consensus       517 rILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~a~eLI  581 (629)
T KOG0336|consen  517 RILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEELI  581 (629)
T ss_pred             EEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999988876665543

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

Probab=99.92  E-value=4.1e-24  Score=197.37  Aligned_cols=164  Identities=18%  Similarity=0.241  Sum_probs=128.4

Q ss_pred             cccceeEEeecccc--hhhHHHHhhhcCCCceeecCCcch-----------hhHHHHhhhhhhccCCceEEEEeecccch
Q psy15610         55 DEALTLVFVETKKG--ADQLEDFLHHHGYPVTSIHGDRTQ-----------KEREEAQQYTLISCDEALTLVFVETKKGA  121 (237)
Q Consensus        55 ~~~~~i~f~~t~~~--~~~~~~~l~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~iIF~~t~~~~  121 (237)
                      +..++++|++|...  .+++...|.-.+.. ....+..+.           .....+..+........+.||||.|++.+
T Consensus       615 p~vPilALTATAT~~V~eDI~~~L~l~~~~-vfr~Sf~RpNL~y~Vv~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~  693 (1195)
T PLN03137        615 PNIPVLALTATATASVKEDVVQALGLVNCV-VFRQSFNRPNLWYSVVPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDC  693 (1195)
T ss_pred             CCCCeEEEEecCCHHHHHHHHHHcCCCCcE-EeecccCccceEEEEeccchhHHHHHHHHHHhcccCCCceeEeCchhHH
Confidence            35678999999665  34566666433211 111111111           11111111222222356799999999999


Q ss_pred             HHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhccccc
Q psy15610        122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGR  201 (237)
Q Consensus       122 ~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R  201 (237)
                      +.++..|...|+.+..|||+|++++|..+++.|.+|+++|||||+++++|||+|++++||+|++|.+.+.|+|++|||||
T Consensus       694 E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGR  773 (1195)
T PLN03137        694 EKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGR  773 (1195)
T ss_pred             HHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCceEEeecCCCCCC
Q psy15610        202 MGNLDFPFSYNQPGYGGS  219 (237)
Q Consensus       202 ~g~~~~~~~~~~~~~~~~  219 (237)
                      .|.++.|++|++..+...
T Consensus       774 DG~~g~cILlys~~D~~~  791 (1195)
T PLN03137        774 DGQRSSCVLYYSYSDYIR  791 (1195)
T ss_pred             CCCCceEEEEecHHHHHH
Confidence            999999999998765533

>KOG0340|consensus

Probab=99.91  E-value=5.2e-24  Score=172.61  Aligned_cols=153  Identities=36%  Similarity=0.478  Sum_probs=139.3

Q ss_pred             ceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCC
Q psy15610         10 YIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGD   89 (237)
Q Consensus        10 ~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~   89 (237)
                      +.+++..+...+.+.+.+.|+.++...|-.+|..+|......                                      
T Consensus       211 a~~~e~~~~vstvetL~q~yI~~~~~vkdaYLv~~Lr~~~~~--------------------------------------  252 (442)
T KOG0340|consen  211 AFELEVIDGVSTVETLYQGYILVSIDVKDAYLVHLLRDFENK--------------------------------------  252 (442)
T ss_pred             ceEEeccCCCCchhhhhhheeecchhhhHHHHHHHHhhhhhc--------------------------------------
Confidence            344555445577889999999999999999999999887521                                      


Q ss_pred             cchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccc
Q psy15610         90 RTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA  169 (237)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~  169 (237)
                                       ....++||+++...|+.++..|...++++..+|+-|++.+|...+.+|+++..+||||||+++
T Consensus       253 -----------------~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAs  315 (442)
T KOG0340|consen  253 -----------------ENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVAS  315 (442)
T ss_pred             -----------------cCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhh
Confidence                             147899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       170 ~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +|+|+|.++.|+++|.|.+|..|+||+||..|.|+.|.++.|+.+.+-
T Consensus       316 RGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv  363 (442)
T KOG0340|consen  316 RGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDV  363 (442)
T ss_pred             cCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhH
Confidence            999999999999999999999999999999999999999999986553

>KOG0341|consensus

Probab=99.91  E-value=2e-24  Score=177.06  Aligned_cols=158  Identities=36%  Similarity=0.677  Sum_probs=146.4

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      +|+.-|-.|+.|++.+.++..-++.|.+-+|....|+-+|++-|.+.                                 
T Consensus       374 FAkSALVKPvtvNVGRAGAAsldViQevEyVkqEaKiVylLeCLQKT---------------------------------  420 (610)
T KOG0341|consen  374 FAKSALVKPVTVNVGRAGAASLDVIQEVEYVKQEAKIVYLLECLQKT---------------------------------  420 (610)
T ss_pred             HHHhhcccceEEecccccccchhHHHHHHHHHhhhhhhhHHHHhccC---------------------------------
Confidence            56777889999999999988888888877778888988888888776                                 


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..+++|||.....++.+.+||.-+|..+..+||+.++++|...++.|+.|+-+|
T Consensus       421 --------------------------~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDV  474 (610)
T KOG0341|consen  421 --------------------------SPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDV  474 (610)
T ss_pred             --------------------------CCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCce
Confidence                                      489999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      ||+||+++.|+|||++.+||+||+|...+.|+||+||.||.|..|.+-+|++.....
T Consensus       475 LVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~~e  531 (610)
T KOG0341|consen  475 LVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQEE  531 (610)
T ss_pred             EEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccchH
Confidence            999999999999999999999999999999999999999999999999999876543

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

Probab=99.90  E-value=2.1e-23  Score=191.21  Aligned_cols=188  Identities=18%  Similarity=0.202  Sum_probs=138.7

Q ss_pred             EEEeechhHHH-----HHHHhhcCch--hhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcc----------
Q psy15610         29 IAWVDEQDKRS-----CLLDLLSSPS--QEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRT----------   91 (237)
Q Consensus        29 ~~~~~~~~k~~-----~l~~ll~~~~--~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~----------   91 (237)
                      +++++|.+++.     .+..+++...  ....+.+.+.++||+|..+..++++.+....+.  .+..+..          
T Consensus       160 ~vViDEah~~~g~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~~~~~l~g~~~~--~i~~~~~~~~~~~~~~~  237 (742)
T TIGR03817       160 YVVIDECHSYRGVFGSHVALVLRRLRRLCARYGASPVFVLASATTADPAAAASRLIGAPVV--AVTEDGSPRGARTVALW  237 (742)
T ss_pred             EEEEeChhhccCccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHHHHHHHcCCCeE--EECCCCCCcCceEEEEe
Confidence            67788877542     2222332221  112345678999999999988888777554322  1111100          


Q ss_pred             -h---------------h-hHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhC--------CCceEEEeCCCCHHH
Q psy15610         92 -Q---------------K-EREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHH--------GYPVTSIHGDRTQKE  146 (237)
Q Consensus        92 -~---------------~-~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~--------~~~~~~~h~~~~~~~  146 (237)
                       .               . ..............+.++||||+|++.++.++..+...        +..+..+||++++++
T Consensus       238 ~p~~~~~~~~~~~~~r~~~~~~~~~~l~~l~~~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~e  317 (742)
T TIGR03817       238 EPPLTELTGENGAPVRRSASAEAADLLADLVAEGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPED  317 (742)
T ss_pred             cCCccccccccccccccchHHHHHHHHHHHHHCCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHH
Confidence             0               0 00111111111124679999999999999999987653        567889999999999


Q ss_pred             HHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        147 REEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       147 r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      |.++++.|++|++++||||+++++|+|+|++++||+++.|.+...|+||+||+||.|..|.++++......+
T Consensus       318 R~~ie~~f~~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d  389 (742)
T TIGR03817       318 RRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLD  389 (742)
T ss_pred             HHHHHHHHHcCCceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHH
Confidence            999999999999999999999999999999999999999999999999999999999999999988754443

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.90  E-value=1.4e-23  Score=189.33  Aligned_cols=115  Identities=21%  Similarity=0.409  Sum_probs=109.2

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      ..+.++||||+|++.++.++..|...++.+..+||+|++++|..+++.|++|.++|||||+++++|+|+|++++||++++
T Consensus       234 ~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~  313 (607)
T PRK11057        234 QRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDI  313 (607)
T ss_pred             cCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCC
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHhhcccccCCCCCceEEeecCCCCCCC
Q psy15610        186 PSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSY  220 (237)
Q Consensus       186 p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~  220 (237)
                      |.|.+.|+||+||+||.|.+|.|++|+++.+...+
T Consensus       314 P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~  348 (607)
T PRK11057        314 PRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWL  348 (607)
T ss_pred             CCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHH
Confidence            99999999999999999999999999998775443

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

Probab=99.90  E-value=1.1e-22  Score=178.20  Aligned_cols=162  Identities=22%  Similarity=0.326  Sum_probs=133.8

Q ss_pred             ccceeEEeecccc--hhhHHHHhhhcCCCceeecCCcchhhHHHHhh-------hhhh----ccCCceEEEEeecccchH
Q psy15610         56 EALTLVFVETKKG--ADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ-------YTLI----SCDEALTLVFVETKKGAD  122 (237)
Q Consensus        56 ~~~~i~f~~t~~~--~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~----~~~~~~~iIF~~t~~~~~  122 (237)
                      +-+++.+++|-..  ..++.+.|.-... ...+.+..+++.+-.+..       ..++    .....+.||||.|++.++
T Consensus       166 ~~p~~AlTATA~~~v~~DI~~~L~l~~~-~~~~~sfdRpNi~~~v~~~~~~~~q~~fi~~~~~~~~~~GIIYc~sRk~~E  244 (590)
T COG0514         166 NPPVLALTATATPRVRDDIREQLGLQDA-NIFRGSFDRPNLALKVVEKGEPSDQLAFLATVLPQLSKSGIIYCLTRKKVE  244 (590)
T ss_pred             CCCEEEEeCCCChHHHHHHHHHhcCCCc-ceEEecCCCchhhhhhhhcccHHHHHHHHHhhccccCCCeEEEEeeHHhHH
Confidence            5579999777544  6677777765543 233334444443322222       1122    344566899999999999


Q ss_pred             HHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccC
Q psy15610        123 QLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRM  202 (237)
Q Consensus       123 ~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~  202 (237)
                      .++++|+..|+.+..||++|+.++|+.+.++|.+++++|+|||.++++|+|-|++.+||||+.|.|.+.|+|-+|||||.
T Consensus       245 ~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAGRD  324 (590)
T COG0514         245 ELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRD  324 (590)
T ss_pred             HHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCceEEeecCCCCC
Q psy15610        203 GNLDFPFSYNQPGYGG  218 (237)
Q Consensus       203 g~~~~~~~~~~~~~~~  218 (237)
                      |.+..|++|+++.+..
T Consensus       325 G~~a~aill~~~~D~~  340 (590)
T COG0514         325 GLPAEAILLYSPEDIR  340 (590)
T ss_pred             CCcceEEEeeccccHH
Confidence            9999999999998853

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.90  E-value=5.2e-23  Score=185.71  Aligned_cols=113  Identities=25%  Similarity=0.438  Sum_probs=107.7

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS  187 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~  187 (237)
                      +.++||||+|++.++.+++.|...++++..+||+|+.++|..+++.|.+|.++|||||+++++|+|+|++++||++++|.
T Consensus       224 ~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~  303 (591)
T TIGR01389       224 GQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPG  303 (591)
T ss_pred             CCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCC
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHhhcccccCCCCCceEEeecCCCCCCC
Q psy15610        188 DVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSY  220 (237)
Q Consensus       188 s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~  220 (237)
                      |.+.|+|++||+||.|.++.|++|+++.+...+
T Consensus       304 s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~  336 (591)
T TIGR01389       304 NLESYYQEAGRAGRDGLPAEAILLYSPADIALL  336 (591)
T ss_pred             CHHHHhhhhccccCCCCCceEEEecCHHHHHHH
Confidence            999999999999999999999999988765443

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.

>KOG0346|consensus

Probab=99.88  E-value=1.6e-22  Score=167.97  Aligned_cols=164  Identities=29%  Similarity=0.420  Sum_probs=148.9

Q ss_pred             hHHHHhhcceeEEEeecc-CCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVG-STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      |-+.||.+|+.+.+..++ ....++.|+++.|++.+|+..+..+|.-.-+                              
T Consensus       218 LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~DKflllyallKL~LI------------------------------  267 (569)
T KOG0346|consen  218 LKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEEDKFLLLYALLKLRLI------------------------------  267 (569)
T ss_pred             HHHHhccCCeEEEeccccCCCcccceEEEEEeccchhHHHHHHHHHHHHh------------------------------
Confidence            557899999999998666 5567999999999999999999988876532                              


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 .+++|||+||.+.|..+.=+|..-|++..+++|++|..-|..++.+|+.|.++
T Consensus       268 ---------------------------~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~Yd  320 (569)
T KOG0346|consen  268 ---------------------------RGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYD  320 (569)
T ss_pred             ---------------------------cCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCccee
Confidence                                       37999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcC-----------------------------------ccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCC
Q psy15610        161 ILVATA-----------------------------------VAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL  205 (237)
Q Consensus       161 vlv~T~-----------------------------------~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~  205 (237)
                      ++|+||                                   -+.+|+||.++.+|++||+|.+...|+||+||++|.+++
T Consensus       321 ivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~  400 (569)
T KOG0346|consen  321 IVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNK  400 (569)
T ss_pred             EEEEccCccchhhhhccccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCC
Confidence            999998                                   146899999999999999999999999999999999999


Q ss_pred             CceEEeecCCCCCCCCC
Q psy15610        206 DFPFSYNQPGYGGSYGG  222 (237)
Q Consensus       206 ~~~~~~~~~~~~~~~~~  222 (237)
                      |.++.|+.|.+.-+..+
T Consensus       401 GtalSfv~P~e~~g~~~  417 (569)
T KOG0346|consen  401 GTALSFVSPKEEFGKES  417 (569)
T ss_pred             CceEEEecchHHhhhhH
Confidence            99999999987765543

>KOG0344|consensus

Probab=99.88  E-value=2.3e-22  Score=172.34  Aligned_cols=166  Identities=31%  Similarity=0.462  Sum_probs=146.2

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeec-hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDE-QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      .++..+.+++.|-+..-++....|.|..+.|.. ..|+-.+.+++..--                               
T Consensus       338 ~~~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g~-------------------------------  386 (593)
T KOG0344|consen  338 WAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALRQLVASGF-------------------------------  386 (593)
T ss_pred             HHHHhhccceeEEEecchhHhhhhhhhheeeecchhHHHHHHHHHhccC-------------------------------
Confidence            456677788888776666667888888777765 458888888887652                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHH-hhCCCceEEEeCCCCHHHHHHHHHHhhcCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFL-HHHGYPVTSIHGDRTQKEREEALRRFRSGET  159 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L-~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~  159 (237)
                                                 ..+++||+.+.+.|..+...| ...++++.++||+.++.+|+.++++|+.|.+
T Consensus       387 ---------------------------~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~I  439 (593)
T KOG0344|consen  387 ---------------------------KPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKI  439 (593)
T ss_pred             ---------------------------CCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCe
Confidence                                       478999999999999999999 6778999999999999999999999999999


Q ss_pred             CEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCCC
Q psy15610        160 PILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS  225 (237)
Q Consensus       160 ~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  225 (237)
                      ++|+||+++++|+|+.+++.||+||.|.+...|+||+||+||.|+.|.+|+|+...+.+..+..++
T Consensus       440 wvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae  505 (593)
T KOG0344|consen  440 WVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAE  505 (593)
T ss_pred             eEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHH
Confidence            999999999999999999999999999999999999999999999999999999977776665443

>KOG4284|consensus

Probab=99.88  E-value=9e-23  Score=176.36  Aligned_cols=164  Identities=28%  Similarity=0.368  Sum_probs=145.9

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeec--------hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHH
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDE--------QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLE   73 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~--------~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~   73 (237)
                      +..+||.+|..|........+-+|+|+|+.+..        +.|++.|..+++...                        
T Consensus       216 ~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~ip------------------------  271 (980)
T KOG4284|consen  216 LLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSIP------------------------  271 (980)
T ss_pred             HHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHHHhhCc------------------------
Confidence            456899999999887667889999999876543        237777777776652                        


Q ss_pred             HHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHH
Q psy15610         74 DFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRR  153 (237)
Q Consensus        74 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~  153 (237)
                                                        ..++||||+....|+-++.+|...|+++.++.|.|++.+|....+.
T Consensus       272 ----------------------------------y~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~  317 (980)
T KOG4284|consen  272 ----------------------------------YVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQ  317 (980)
T ss_pred             ----------------------------------hHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHH
Confidence                                              4689999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC-CCCCCC
Q psy15610        154 FRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG-GSYGGS  223 (237)
Q Consensus       154 f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~-~~~~~~  223 (237)
                      +++-..+|||+||..++|+|-+++++||+.|+|.+.+.|+||+|||||+|..|.+++|+..++. ..|.++
T Consensus       318 lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e~~~f~~m  388 (980)
T KOG4284|consen  318 LRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERELKGFTAM  388 (980)
T ss_pred             hhhceEEEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchhhhhhHHH
Confidence            9999999999999999999999999999999999999999999999999999999999987766 665554

>KOG0347|consensus

Probab=99.88  E-value=8e-24  Score=179.88  Aligned_cols=156  Identities=29%  Similarity=0.430  Sum_probs=147.2

Q ss_pred             hcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeec
Q psy15610          8 YRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIH   87 (237)
Q Consensus         8 ~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~   87 (237)
                      -.|.+|++.+.+.+...+.+..+.|+..+|--+|..+|..+                                       
T Consensus       422 ~kpkiiD~t~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~ry---------------------------------------  462 (731)
T KOG0347|consen  422 GKPKIIDLTPQSATASTLTESLIECPPLEKDLYLYYFLTRY---------------------------------------  462 (731)
T ss_pred             CCCeeEecCcchhHHHHHHHHhhcCCccccceeEEEEEeec---------------------------------------
Confidence            36799999989999999999999999889998888888877                                       


Q ss_pred             CCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc
Q psy15610         88 GDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV  167 (237)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~  167 (237)
                                          ++++|||||+.+.+..++-+|...+++...+|+.|.+.+|.+.++.|++....||||||+
T Consensus       463 --------------------PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDV  522 (731)
T KOG0347|consen  463 --------------------PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDV  522 (731)
T ss_pred             --------------------CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeehh
Confidence                                589999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCC
Q psy15610        168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGG  222 (237)
Q Consensus       168 ~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~  222 (237)
                      +++|+|+|.+.+||+|..|.+.+.|+||.||+.|.+..|..+.++.|.+-..|..
T Consensus       523 AARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~K  577 (731)
T KOG0347|consen  523 AARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKK  577 (731)
T ss_pred             hhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHHHH
Confidence            9999999999999999999999999999999999999999999999998766654

>KOG0348|consensus

Probab=99.88  E-value=2.7e-22  Score=170.16  Aligned_cols=167  Identities=25%  Similarity=0.397  Sum_probs=133.9

Q ss_pred             ChHHHHhhcceeEEEeec-------------------------cCCCCCceeEEEEeechhHHHHHHHhhcCchhhhccc
Q psy15610          1 LLAKEFLYRYIFLAIGRV-------------------------GSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGD   55 (237)
Q Consensus         1 ~~~~~~l~~~~~i~~~~~-------------------------~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~   55 (237)
                      +||+--|+||+.|.+...                         -...+++.|.|.+|+.+-++-+|..+|......    
T Consensus       347 rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~----  422 (708)
T KOG0348|consen  347 RLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKF----  422 (708)
T ss_pred             HHhhccccCceeeeccchhhhcCcchhhhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhh----
Confidence            467777888888872211                         122345677888888888888888888765322    


Q ss_pred             ccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhC----
Q psy15610         56 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHH----  131 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~----  131 (237)
                                                                        ....++|||..+.+.++..++.|...    
T Consensus       423 --------------------------------------------------~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~  452 (708)
T KOG0348|consen  423 --------------------------------------------------EEKQKMIVFFSCSDSVEFHYSLFSEALLSH  452 (708)
T ss_pred             --------------------------------------------------hhhceeEEEEechhHHHHHHHHHHhhhhcc
Confidence                                                              11346777777777777666655321    


Q ss_pred             ------------------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHH
Q psy15610        132 ------------------GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYV  193 (237)
Q Consensus       132 ------------------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~  193 (237)
                                        +.++..+||+|++++|..++..|....-.||+|||++++|+|+|++++||+||+|.++.+|+
T Consensus       453 ~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adyl  532 (708)
T KOG0348|consen  453 LEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYL  532 (708)
T ss_pred             cccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHH
Confidence                              34688999999999999999999999888999999999999999999999999999999999


Q ss_pred             HhhcccccCCCCCceEEeecCCCCCCCC
Q psy15610        194 HRIGRTGRMGNLDFPFSYNQPGYGGSYG  221 (237)
Q Consensus       194 Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  221 (237)
                      ||+||..|.|..|..++|..|.+.++.+
T Consensus       533 HRvGRTARaG~kG~alLfL~P~Eaey~~  560 (708)
T KOG0348|consen  533 HRVGRTARAGEKGEALLFLLPSEAEYVN  560 (708)
T ss_pred             HHhhhhhhccCCCceEEEecccHHHHHH
Confidence            9999999999999999999999987433

>KOG0338|consensus

Probab=99.87  E-value=5.1e-22  Score=167.69  Aligned_cols=163  Identities=33%  Similarity=0.478  Sum_probs=144.9

Q ss_pred             ChHHHHhhcceeEEEeeccCCCCCceeEEEEee-ch--hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhh
Q psy15610          1 LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVD-EQ--DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLH   77 (237)
Q Consensus         1 ~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~-~~--~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~   77 (237)
                      +|++--|+.|+.|-+.+.......+.|-|+-+- .+  ++-..|..|+....                            
T Consensus       374 dL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf----------------------------  425 (691)
T KOG0338|consen  374 DLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLITRTF----------------------------  425 (691)
T ss_pred             HHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHHHHHHhc----------------------------
Confidence            367788999999988877788888888876444 33  47788888887653                            


Q ss_pred             hcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC
Q psy15610         78 HHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG  157 (237)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g  157 (237)
                                                    ...++||+.|.++|..|.-+|--.|+.+.-+||++++++|...++.|+++
T Consensus       426 ------------------------------~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~  475 (691)
T KOG0338|consen  426 ------------------------------QDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKE  475 (691)
T ss_pred             ------------------------------ccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhc
Confidence                                          36799999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCC
Q psy15610        158 ETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYG  221 (237)
Q Consensus       158 ~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  221 (237)
                      ++++|||||++++|+|++.+.+||+|++|.+...|+||+||..|.|+.|..++|+...+....+
T Consensus       476 eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK  539 (691)
T KOG0338|consen  476 EIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLK  539 (691)
T ss_pred             cCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999987664443

>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=99.86  E-value=9.4e-21  Score=138.27  Aligned_cols=104  Identities=45%  Similarity=0.753  Sum_probs=99.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS  187 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~  187 (237)
                      +.++||||++...++.+.+.|...+.++..+||++++.+|..+.+.|+++...++++|..+++|+|+|.+++||.+++|+
T Consensus        28 ~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G~d~~~~~~vi~~~~~~  107 (131)
T cd00079          28 GGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPW  107 (131)
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcCcChhhCCEEEEeCCCC
Confidence            57899999999999999999998888999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHhhcccccCCCCCceEEe
Q psy15610        188 DVEEYVHRIGRTGRMGNLDFPFSY  211 (237)
Q Consensus       188 s~~~~~Q~~GR~~R~g~~~~~~~~  211 (237)
                      +...+.|++||++|.|+.|.+++|
T Consensus       108 ~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079         108 SPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             CHHHheecccccccCCCCceEEeC
Confidence            999999999999999998887654

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.85  E-value=1.6e-20  Score=175.43  Aligned_cols=159  Identities=19%  Similarity=0.271  Sum_probs=121.4

Q ss_pred             cccceeEEeecccchhhHHHHhhhcC-----CCceeecCCcch-------------------hhHHHHhh-hhhhccCCc
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHG-----YPVTSIHGDRTQ-------------------KEREEAQQ-YTLISCDEA  109 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~-----~~~~~~~~~~~~-------------------~~~~~~~~-~~~~~~~~~  109 (237)
                      ...+.|.+|+|..+.+++++++....     -++..+.....+                   ........ ..-...+..
T Consensus       206 ~~~q~IglSATl~~~~~va~~L~~~~~~~~~r~~~iv~~~~~k~~~i~v~~p~~~l~~~~~~~~~~~l~~~L~~~i~~~~  285 (876)
T PRK13767        206 GEFVRIGLSATIEPLEEVAKFLVGYEDDGEPRDCEIVDARFVKPFDIKVISPVDDLIHTPAEEISEALYETLHELIKEHR  285 (876)
T ss_pred             CCCeEEEEecccCCHHHHHHHhcCccccCCCCceEEEccCCCccceEEEeccCccccccccchhHHHHHHHHHHHHhcCC
Confidence            45678999999999999999997641     122222111000                   00000011 111123467


Q ss_pred             eEEEEeecccchHHHHHHHhhC------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEe
Q psy15610        110 LTLVFVETKKGADQLEDFLHHH------GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       110 ~~iIF~~t~~~~~~l~~~L~~~------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      ++||||+|+..++.++..|...      +..+..+||++++++|..+++.|++|.+++||||+++++|+|+|++++||++
T Consensus       286 ~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~Vd~VI~~  365 (876)
T PRK13767        286 TTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLL  365 (876)
T ss_pred             CEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCCCcEEEEe
Confidence            8999999999999999999763      4679999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccC-CCCCceEEeec
Q psy15610        184 DLPSDVEEYVHRIGRTGRM-GNLDFPFSYNQ  213 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~-g~~~~~~~~~~  213 (237)
                      +.|.+...|+||+||+||. |..+.++++..
T Consensus       366 ~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~  396 (876)
T PRK13767        366 GSPKSVSRLLQRIGRAGHRLGEVSKGRIIVV  396 (876)
T ss_pred             CCCCCHHHHHHhcccCCCCCCCCCcEEEEEc
Confidence            9999999999999999986 44455555543

>KOG0334|consensus

Probab=99.85  E-value=7.9e-21  Score=172.10  Aligned_cols=158  Identities=34%  Similarity=0.590  Sum_probs=149.2

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEee-chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVD-EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      ||.+.|+-|+.+-+...+.....+.+.+.++. +.+|...|+.||.....                              
T Consensus       563 la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e------------------------------  612 (997)
T KOG0334|consen  563 LARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYE------------------------------  612 (997)
T ss_pred             HHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHHHHHHHhh------------------------------
Confidence            68899999999999877888999999999999 89999999999988753                              


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++||||.....|+.+.+-|++.|+++..+||+.++.+|..++..|+++...
T Consensus       613 ---------------------------~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~  665 (997)
T KOG0334|consen  613 ---------------------------DGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVN  665 (997)
T ss_pred             ---------------------------cCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCce
Confidence                                       37999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      +|++|+++++|+|+++..+||+|+.|...+.|+||+||+||.|..|.+++|+.+.+
T Consensus       666 LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q  721 (997)
T KOG0334|consen  666 LLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQ  721 (997)
T ss_pred             EEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChHH
Confidence            99999999999999999999999999999999999999999999999999999843

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.85  E-value=1.2e-20  Score=174.99  Aligned_cols=110  Identities=24%  Similarity=0.294  Sum_probs=101.9

Q ss_pred             CCceEEEEeecccchHHHHHHH-hhCCCceEEEeCCCCHHHHHHHHHHhhcC--CCCEEEEcCccccccCCCCCcEEEEe
Q psy15610        107 DEALTLVFVETKKGADQLEDFL-HHHGYPVTSIHGDRTQKEREEALRRFRSG--ETPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L-~~~~~~~~~~h~~~~~~~r~~~~~~f~~g--~~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      ...++||||+++..+..+++.| ...|+++..+||+|++.+|.+.++.|+++  ..+|||||+++++|+|++.+++||+|
T Consensus       492 ~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgseGlNlq~a~~VInf  571 (956)
T PRK04914        492 RSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSEGRNFQFASHLVLF  571 (956)
T ss_pred             CCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhccCCCcccccEEEEe
Confidence            3679999999999999999999 45699999999999999999999999974  58999999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      |.||++..|.||+||++|.|+++.+.+++....
T Consensus       572 DlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~  604 (956)
T PRK04914        572 DLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLE  604 (956)
T ss_pred             cCCCCHHHHHHHhcccccCCCCceEEEEEccCC
Confidence            999999999999999999999998877775444

>KOG0339|consensus

Probab=99.84  E-value=1.1e-20  Score=159.63  Aligned_cols=177  Identities=37%  Similarity=0.579  Sum_probs=154.9

Q ss_pred             ChHHHHhhcceeEEEeeccCCCCCceeEEEEeec-hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhc
Q psy15610          1 LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDE-QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHH   79 (237)
Q Consensus         1 ~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~   79 (237)
                      +||..+|.+|+.+-....+.....|.|.+.+++. ..|+.+|+.-|....                              
T Consensus       417 ~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~------------------------------  466 (731)
T KOG0339|consen  417 KLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEFS------------------------------  466 (731)
T ss_pred             HHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhhc------------------------------
Confidence            3789999999999776666778899999887775 569999887776653                              


Q ss_pred             CCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCC
Q psy15610         80 GYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGET  159 (237)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~  159 (237)
                                                 +.+++|||+.....++.++..|.-.++++..+||+|.+.+|-.++..|+.+..
T Consensus       467 ---------------------------S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~  519 (731)
T KOG0339|consen  467 ---------------------------SEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRK  519 (731)
T ss_pred             ---------------------------cCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCC
Confidence                                       24799999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCCC----CCCCCCCCc
Q psy15610        160 PILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS----QNSNAPDWW  234 (237)
Q Consensus       160 ~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~  234 (237)
                      .||++||+..+|+|+|.+..||+||.-.+.+.+.||+||.||.|..|..++++...+...-+.+.+    ..-++||-|
T Consensus       520 ~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~fAG~LVnnLe~agQnVP~~l  598 (731)
T KOG0339|consen  520 PVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHLVNNLEGAGQNVPDEL  598 (731)
T ss_pred             ceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechhhHHHhhHHHHHHhhccccCChHH
Confidence            999999999999999999999999999999999999999999999999999999998875554333    233455544

>PRK02362 ski2-like helicase; Provisional

Probab=99.84  E-value=3e-20  Score=171.50  Aligned_cols=161  Identities=20%  Similarity=0.286  Sum_probs=122.4

Q ss_pred             cccceeEEeecccchhhHHHHhhhcCCCce-------e-e--------cC---CcchhhHHHHhhhhh-hccCCceEEEE
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHGYPVT-------S-I--------HG---DRTQKEREEAQQYTL-ISCDEALTLVF  114 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~-------~-~--------~~---~~~~~~~~~~~~~~~-~~~~~~~~iIF  114 (237)
                      ++.+++.+|+|..+.+++++|+...-+...       . +        ..   .+............. ...++.++|||
T Consensus       170 ~~~qii~lSATl~n~~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LVF  249 (737)
T PRK02362        170 PDLQVVALSATIGNADELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDTLNLVLDTLEEGGQCLVF  249 (737)
T ss_pred             CCCcEEEEcccCCCHHHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccchHHHHHHHHHHHcCCCeEEE
Confidence            457899999999999999999975432110       0 0        00   000000011111111 12356899999


Q ss_pred             eecccchHHHHHHHhhC------------------------------------CCceEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610        115 VETKKGADQLEDFLHHH------------------------------------GYPVTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus       115 ~~t~~~~~~l~~~L~~~------------------------------------~~~~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                      |+|+..++.++..|...                                    ...+.++|++|++++|..+++.|++|.
T Consensus       250 ~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~ve~~Fr~G~  329 (737)
T PRK02362        250 VSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRL  329 (737)
T ss_pred             EeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHHHHHHHcCC
Confidence            99999999888777532                                    136889999999999999999999999


Q ss_pred             CCEEEEcCccccccCCCCCcEEEE----ec-----CCCCHHHHHHhhcccccCCCC--CceEEeecCC
Q psy15610        159 TPILVATAVAARGLDIPHVKHVIN----FD-----LPSDVEEYVHRIGRTGRMGNL--DFPFSYNQPG  215 (237)
Q Consensus       159 ~~vlv~T~~~~~Gvdl~~~~~Vi~----~~-----~p~s~~~~~Q~~GR~~R~g~~--~~~~~~~~~~  215 (237)
                      ++|||||+.+++|+|+|..++||.    |+     .|.+...|.||+|||||.|..  |.+++++...
T Consensus       330 i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~  397 (737)
T PRK02362        330 IKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSY  397 (737)
T ss_pred             CeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCc
Confidence            999999999999999999999996    65     578999999999999998865  8889988764

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.84  E-value=7.1e-20  Score=175.14  Aligned_cols=158  Identities=24%  Similarity=0.302  Sum_probs=118.4

Q ss_pred             ccccceeEEeecccchhhHHHHhhhcCCCceeec---------------CCcchh-------------hHH-----HHh-
Q psy15610         54 GDEALTLVFVETKKGADQLEDFLHHHGYPVTSIH---------------GDRTQK-------------ERE-----EAQ-   99 (237)
Q Consensus        54 ~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~---------------~~~~~~-------------~~~-----~~~-   99 (237)
                      +.+.+.|.+|+|..+.++++++|..... +..+.               .++.+.             .+.     ... 
T Consensus       157 ~~~~QrIgLSATI~n~eevA~~L~g~~p-v~Iv~~~~~r~~~l~v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~  235 (1490)
T PRK09751        157 HTSAQRIGLSATVRSASDVAAFLGGDRP-VTVVNPPAMRHPQIRIVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIET  235 (1490)
T ss_pred             CCCCeEEEEEeeCCCHHHHHHHhcCCCC-EEEECCCCCcccceEEEEecCchhhccccccccccccchhhhhhhhHHHHH
Confidence            3567899999999999999999965311 11110               000000             000     000 


Q ss_pred             hhhhhccCCceEEEEeecccchHHHHHHHhhCC---------------------------------CceEEEeCCCCHHH
Q psy15610        100 QYTLISCDEALTLVFVETKKGADQLEDFLHHHG---------------------------------YPVTSIHGDRTQKE  146 (237)
Q Consensus       100 ~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~---------------------------------~~~~~~h~~~~~~~  146 (237)
                      ..........++||||||+..|+.++..|++..                                 ..+..|||+++.++
T Consensus       236 ~il~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkee  315 (1490)
T PRK09751        236 GILDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQ  315 (1490)
T ss_pred             HHHHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHH
Confidence            011112346789999999999999998887531                                 12568999999999


Q ss_pred             HHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccC-CCCCceEEee
Q psy15610        147 REEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRM-GNLDFPFSYN  212 (237)
Q Consensus       147 r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~-g~~~~~~~~~  212 (237)
                      |..+++.|++|.+++||||+.+++|||++++++||+++.|.+...|+||+||+||. |..+.++++.
T Consensus       316 R~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p  382 (1490)
T PRK09751        316 RAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFP  382 (1490)
T ss_pred             HHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEe
Confidence            99999999999999999999999999999999999999999999999999999995 4445555443

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.84  E-value=4.1e-20  Score=164.76  Aligned_cols=156  Identities=18%  Similarity=0.171  Sum_probs=127.1

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      |.+.|..+++.|...  ......+.+.++.+.+.+|...|.+++......                              
T Consensus       425 l~~~y~l~vv~IPt~--kp~~r~~~~~~v~~t~~~K~~aL~~~i~~~~~~------------------------------  472 (656)
T PRK12898        425 LWSVYGLPVVRIPTN--RPSQRRHLPDEVFLTAAAKWAAVAARVRELHAQ------------------------------  472 (656)
T ss_pred             HHHHHCCCeEEeCCC--CCccceecCCEEEeCHHHHHHHHHHHHHHHHhc------------------------------
Confidence            456677787777432  222334556677788888999999988764211                              


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                +.++||||+|...++.++..|.+.|+++..+||+++  +|+..+..+..+...|
T Consensus       473 --------------------------~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~--~rE~~ii~~ag~~g~V  524 (656)
T PRK12898        473 --------------------------GRPVLVGTRSVAASERLSALLREAGLPHQVLNAKQD--AEEAAIVARAGQRGRI  524 (656)
T ss_pred             --------------------------CCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcH--HHHHHHHHHcCCCCcE
Confidence                                      468999999999999999999999999999999865  4555555566566679


Q ss_pred             EEEcCccccccCCC---CCc-----EEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        162 LVATAVAARGLDIP---HVK-----HVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       162 lv~T~~~~~Gvdl~---~~~-----~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +|||+++++|+|++   ++.     +||+++.|.|...|.|++||+||.|.+|.+++|++..+.
T Consensus       525 lVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        525 TVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             EEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhHH
Confidence            99999999999999   555     899999999999999999999999999999999997664

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.83  E-value=7.5e-20  Score=164.94  Aligned_cols=186  Identities=16%  Similarity=0.303  Sum_probs=127.7

Q ss_pred             EEEeechhHHHHHHHhhcCchhhhcccccceeEEeeccc-chhhHHHHhhhcC---------CCceeec--CCcc-----
Q psy15610         29 IAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKK-GADQLEDFLHHHG---------YPVTSIH--GDRT-----   91 (237)
Q Consensus        29 ~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~-~~~~~~~~l~~~~---------~~~~~~~--~~~~-----   91 (237)
                      +++++|.+.+....+++........+...++++||+|.. .++.+.+++....         +++....  ....     
T Consensus       294 ~VVIDEaHEr~~~~DllL~llk~~~~~~rq~ILmSATl~~dv~~l~~~~~~p~~I~I~grt~~pV~~~yi~~~~~~~~~~  373 (675)
T PHA02653        294 TVIIDEVHEHDQIGDIIIAVARKHIDKIRSLFLMTATLEDDRDRIKEFFPNPAFVHIPGGTLFPISEVYVKNKYNPKNKR  373 (675)
T ss_pred             EEEccccccCccchhHHHHHHHHhhhhcCEEEEEccCCcHhHHHHHHHhcCCcEEEeCCCcCCCeEEEEeecCcccccch
Confidence            566677655433333332211111223347999999986 3677777664211         1111111  1000     


Q ss_pred             ---hhhHHHHhhhhh--hccCCceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHh-hcCCCCEEE
Q psy15610         92 ---QKEREEAQQYTL--ISCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRF-RSGETPILV  163 (237)
Q Consensus        92 ---~~~~~~~~~~~~--~~~~~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f-~~g~~~vlv  163 (237)
                         ............  ....++++|||+++...++.+.+.|.+.  ++.+..+||++++.  ++.++.| ++|+.+|||
T Consensus       374 ~y~~~~k~~~l~~L~~~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILV  451 (675)
T PHA02653        374 AYIEEEKKNIVTALKKYTPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIII  451 (675)
T ss_pred             hhhHHHHHHHHHHHHHhhcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEe
Confidence               001111111111  1224568999999999999999999876  68999999999985  4666676 789999999


Q ss_pred             EcCccccccCCCCCcEEEEec---CCC---------CHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        164 ATAVAARGLDIPHVKHVINFD---LPS---------DVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       164 ~T~~~~~Gvdl~~~~~Vi~~~---~p~---------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||+++++|+|+|++++||+++   .|.         |.+.|.||+||+||. ++|.|+.|++....
T Consensus       452 ATdIAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        452 STPYLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             ccChhhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHh
Confidence            999999999999999999998   554         888999999999999 79999999987654

>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=99.82  E-value=8e-20  Score=121.72  Aligned_cols=78  Identities=50%  Similarity=0.905  Sum_probs=75.4

Q ss_pred             HHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCC
Q psy15610        126 DFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG  203 (237)
Q Consensus       126 ~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g  203 (237)
                      .+|+..++++..+||+++..+|..+++.|+++...+||||+++++|+|+|.+++||++++|+++..|.|++||++|.|
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            367888999999999999999999999999999999999999999999999999999999999999999999999987

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 ....

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

Probab=99.81  E-value=2.1e-19  Score=152.33  Aligned_cols=111  Identities=32%  Similarity=0.474  Sum_probs=100.4

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCceE--EE-------eCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCC
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYPVT--SI-------HGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPH  176 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~--~~-------h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~  176 (237)
                      .++.++|||++.++.++.+.++|.+.+..+.  ++       ..||++.++..+++.|++|..+|||||+++++|+|+|+
T Consensus       364 ~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~  443 (542)
T COG1111         364 NGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPE  443 (542)
T ss_pred             CCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCc
Confidence            3457999999999999999999998877663  33       25799999999999999999999999999999999999


Q ss_pred             CcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        177 VKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       177 ~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +|.||+|++-.|+..++||.||+||. ++|.+++++..+..
T Consensus       444 vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gtr  483 (542)
T COG1111         444 VDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGTR  483 (542)
T ss_pred             ccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCch
Confidence            99999999999999999999999998 78999998887733

>KOG0350|consensus

Probab=99.81  E-value=7.1e-20  Score=154.44  Aligned_cols=148  Identities=26%  Similarity=0.454  Sum_probs=130.3

Q ss_pred             CCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHh
Q psy15610         20 STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQ   99 (237)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   99 (237)
                      .....+.++++.++..-|.-++..++....                                                  
T Consensus       399 slp~~l~~~~vv~~~~~kpl~~~~lI~~~k--------------------------------------------------  428 (620)
T KOG0350|consen  399 SLPSSLSHRLVVTEPKFKPLAVYALITSNK--------------------------------------------------  428 (620)
T ss_pred             ecChhhhhceeecccccchHhHHHHHHHhh--------------------------------------------------
Confidence            445567777777777777777777776653                                                  


Q ss_pred             hhhhhccCCceEEEEeecccchHHHHHHHh----hCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCC
Q psy15610        100 QYTLISCDEALTLVFVETKKGADQLEDFLH----HHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP  175 (237)
Q Consensus       100 ~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~----~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~  175 (237)
                              ..++|+|+++...+..+...|.    .....+..+.|+++...|-+.++.|+.|.+++|||||++++|+|+-
T Consensus       429 --------~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~  500 (620)
T KOG0350|consen  429 --------LNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVN  500 (620)
T ss_pred             --------cceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCccc
Confidence                    5799999999999999998887    2355667789999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCCC
Q psy15610        176 HVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS  225 (237)
Q Consensus       176 ~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  225 (237)
                      ++++||+||+|.+...|+||+||.+|.|+.|.++++....+...|..+..
T Consensus       501 ~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~  550 (620)
T KOG0350|consen  501 DVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLK  550 (620)
T ss_pred             ccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHHHHHHH
Confidence            99999999999999999999999999999999999999999988877544

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.80  E-value=9.9e-19  Score=162.68  Aligned_cols=110  Identities=21%  Similarity=0.316  Sum_probs=102.5

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      .+++++|||++.+.++.+++.|.+.  +.++..+||+|++.+|+++++.|++|+.+|||||+++++|+|+|++++||+++
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            3678999999999999999999875  78899999999999999999999999999999999999999999999999999


Q ss_pred             CCC-CHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        185 LPS-DVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       185 ~p~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      .|. +...|+||+||+||.|..|.|++++.+..
T Consensus       739 a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~~  771 (926)
T TIGR00580       739 ADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQK  771 (926)
T ss_pred             CCCCCHHHHHHHhcCCCCCCCCeEEEEEECCcc
Confidence            875 78899999999999999999999997654

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

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.80  E-value=1.5e-18  Score=164.57  Aligned_cols=108  Identities=17%  Similarity=0.252  Sum_probs=99.3

Q ss_pred             CceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      +++++|||++.+.++.+++.|.+.  +.++..+||+|++.+|++++..|++|+++|||||+++++|+|+|++++||..+.
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~a  888 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERA  888 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEecC
Confidence            578999999999999999999886  788999999999999999999999999999999999999999999999997655


Q ss_pred             C-CCHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        186 P-SDVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       186 p-~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      + .+..+|+|++||+||.|..|.|++++...
T Consensus       889 d~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~  919 (1147)
T PRK10689        889 DHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  919 (1147)
T ss_pred             CCCCHHHHHHHhhccCCCCCceEEEEEeCCC
Confidence            3 46788999999999999999999988654

>PRK00254 ski2-like helicase; Provisional

Probab=99.80  E-value=5.3e-19  Score=162.88  Aligned_cols=162  Identities=20%  Similarity=0.192  Sum_probs=117.9

Q ss_pred             cccceeEEeecccchhhHHHHhhhcCCCceee----------cCCc------chhhHHHHhh-hhhhccCCceEEEEeec
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHGYPVTSI----------HGDR------TQKEREEAQQ-YTLISCDEALTLVFVET  117 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~----------~~~~------~~~~~~~~~~-~~~~~~~~~~~iIF~~t  117 (237)
                      ...+++.+|+|..+.+++++|+....+.....          .+..      .......... ..-....+.++||||+|
T Consensus       168 ~~~qiI~lSATl~n~~~la~wl~~~~~~~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~vLVF~~s  247 (720)
T PRK00254        168 GRAQILGLSATVGNAEELAEWLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDAVKKGKGALVFVNT  247 (720)
T ss_pred             cCCcEEEEEccCCCHHHHHHHhCCccccCCCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHHHHHhCCCEEEEEcC
Confidence            45789999999999999999997543321100          0000      0000000000 00011246789999999


Q ss_pred             ccchHHHHHHHhh---------------------------------CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEE
Q psy15610        118 KKGADQLEDFLHH---------------------------------HGYPVTSIHGDRTQKEREEALRRFRSGETPILVA  164 (237)
Q Consensus       118 ~~~~~~l~~~L~~---------------------------------~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~  164 (237)
                      +..++.++..|..                                 ....+.++|++|++++|..+++.|++|.++||||
T Consensus       248 r~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~F~~G~i~VLva  327 (720)
T PRK00254        248 RRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITA  327 (720)
T ss_pred             hHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHHHHCCCCeEEEe
Confidence            9999877655531                                 1235899999999999999999999999999999


Q ss_pred             cCccccccCCCCCcEEEE-------ecCCC-CHHHHHHhhcccccCC--CCCceEEeecCCC
Q psy15610        165 TAVAARGLDIPHVKHVIN-------FDLPS-DVEEYVHRIGRTGRMG--NLDFPFSYNQPGY  216 (237)
Q Consensus       165 T~~~~~Gvdl~~~~~Vi~-------~~~p~-s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~  216 (237)
                      |+.+++|+|+|..++||.       ++.|. +...|.||+|||||.|  ..|.+++++...+
T Consensus       328 T~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        328 TPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             CcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcc
Confidence            999999999999999984       44433 5779999999999965  6689999987654

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

Probab=99.79  E-value=8.1e-19  Score=159.11  Aligned_cols=159  Identities=24%  Similarity=0.368  Sum_probs=129.5

Q ss_pred             ccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhh------------------HHHHhhhhhhccCCceEEEEeec
Q psy15610         56 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKE------------------REEAQQYTLISCDEALTLVFVET  117 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~------------------~~~~~~~~~~~~~~~~~iIF~~t  117 (237)
                      +.+.|..|+|..+.+++++||...+.++..+.....+..                  ............+...++||+||
T Consensus       183 ~~qRIGLSATV~~~~~varfL~g~~~~~~Iv~~~~~k~~~i~v~~p~~~~~~~~~~~~~~~~~i~~~v~~~~ttLIF~NT  262 (814)
T COG1201         183 DFQRIGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEELWAALYERIAELVKKHRTTLIFTNT  262 (814)
T ss_pred             ccEEEeehhccCCHHHHHHHhcCCCCceEEEEcccCCcceEEEEecCCccccccchhHHHHHHHHHHHhhcCcEEEEEeC
Confidence            788999999999999999999988743333321111111                  11111111223334589999999


Q ss_pred             ccchHHHHHHHhhCC-CceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhh
Q psy15610        118 KKGADQLEDFLHHHG-YPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRI  196 (237)
Q Consensus       118 ~~~~~~l~~~L~~~~-~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~  196 (237)
                      +..++.++..|.+.. ..+..+||+++.++|..++++|++|.++++|||+.++.|+|+.+++.||+++.|.+...++||+
T Consensus       263 R~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdlVIq~~SP~sV~r~lQRi  342 (814)
T COG1201         263 RSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRI  342 (814)
T ss_pred             hHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCceEEEEeCCcHHHHHHhHhc
Confidence            999999999999885 8999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc-CCCCCceEEeecC
Q psy15610        197 GRTGR-MGNLDFPFSYNQP  214 (237)
Q Consensus       197 GR~~R-~g~~~~~~~~~~~  214 (237)
                      ||+|. .|....++++...
T Consensus       343 GRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         343 GRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             cccccccCCcccEEEEecC
Confidence            99996 6666777777654

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.79  E-value=4.8e-18  Score=155.20  Aligned_cols=108  Identities=21%  Similarity=0.321  Sum_probs=96.5

Q ss_pred             cCCceEEEEeeccc--------chHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCC
Q psy15610        106 CDEALTLVFVETKK--------GADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP  175 (237)
Q Consensus       106 ~~~~~~iIF~~t~~--------~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~  175 (237)
                      .++.+++|||+..+        .++.+++.|.+.  ++++..+||+|++.+|..+++.|++|+++|||||+++++|+|+|
T Consensus       469 ~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip  548 (681)
T PRK10917        469 AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP  548 (681)
T ss_pred             HcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccC
Confidence            46789999999654        345566666654  57899999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCC-CHHHHHHhhcccccCCCCCceEEeec
Q psy15610        176 HVKHVINFDLPS-DVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       176 ~~~~Vi~~~~p~-s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      ++++||+++.|. +...+.|+.||+||.|..|.|++++.
T Consensus       549 ~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~  587 (681)
T PRK10917        549 NATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYK  587 (681)
T ss_pred             CCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEEC
Confidence            999999999986 68899999999999999999999995

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.79  E-value=1.5e-18  Score=159.85  Aligned_cols=109  Identities=18%  Similarity=0.302  Sum_probs=99.4

Q ss_pred             CceEEEEeecccchHHHHHHHhh---CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec
Q psy15610        108 EALTLVFVETKKGADQLEDFLHH---HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~---~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      .+++|||+++...++.+.+.|.+   .++.+..+||+|++++|.++++.|++|..+|+|||+++++|+++|++++||+++
T Consensus       209 ~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~G  288 (819)
T TIGR01970       209 TGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSG  288 (819)
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcC
Confidence            57899999999999999999986   378899999999999999999999999999999999999999999999999998


Q ss_pred             CCC------------------CHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        185 LPS------------------DVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       185 ~p~------------------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      .|.                  |..++.||+||+||. .+|.||.+++..+.
T Consensus       289 l~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~  338 (819)
T TIGR01970       289 LARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQH  338 (819)
T ss_pred             cccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHH
Confidence            764                  345689999999999 79999999987643

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.

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

Probab=99.78  E-value=2.5e-18  Score=156.64  Aligned_cols=102  Identities=27%  Similarity=0.388  Sum_probs=88.0

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHH-----HHHHHhhc----CC-------CCEEEEcCccccc
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKERE-----EALRRFRS----GE-------TPILVATAVAARG  171 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~-----~~~~~f~~----g~-------~~vlv~T~~~~~G  171 (237)
                      +.++||||+|++.++.+++.|.+.++  ..+||.|++.+|.     ++++.|++    +.       ..|||||+++++|
T Consensus       272 g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerG  349 (844)
T TIGR02621       272 GGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVG  349 (844)
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccchhhhc
Confidence            57899999999999999999988775  8999999999999     77889987    43       6799999999999


Q ss_pred             cCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCce-EEeecC
Q psy15610        172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFP-FSYNQP  214 (237)
Q Consensus       172 vdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~-~~~~~~  214 (237)
                      +|++. ++||+...|  .+.|+||+||+||.|..+.+ +.++..
T Consensus       350 LDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~~  390 (844)
T TIGR02621       350 VNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVHL  390 (844)
T ss_pred             ccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEee
Confidence            99986 888887777  78999999999999976443 555543

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.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.78  E-value=1.1e-18  Score=158.74  Aligned_cols=108  Identities=21%  Similarity=0.251  Sum_probs=101.1

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCC---CCCc-----E
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDI---PHVK-----H  179 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl---~~~~-----~  179 (237)
                      +.++||||+|.+.++.++..|.+.++++..+||.+.+.++..+...++.|  .|+|||++++||+|+   |.+.     +
T Consensus       428 ~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~  505 (790)
T PRK09200        428 GRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGLA  505 (790)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCcE
Confidence            57999999999999999999999999999999999998888888887765  799999999999999   6888     9


Q ss_pred             EEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        180 VINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       180 Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||+++.|.+...|.||+||+||.|.+|.+++|++..+.
T Consensus       506 VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD~  543 (790)
T PRK09200        506 VIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLEDD  543 (790)
T ss_pred             EEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchHH
Confidence            99999999999999999999999999999999997665

>KOG0351|consensus

Probab=99.78  E-value=1.4e-18  Score=160.35  Aligned_cols=164  Identities=18%  Similarity=0.252  Sum_probs=133.9

Q ss_pred             cceeEEeecc--cchhhHHHHhhhcCCCc-----------eeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHH
Q psy15610         57 ALTLVFVETK--KGADQLEDFLHHHGYPV-----------TSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQ  123 (237)
Q Consensus        57 ~~~i~f~~t~--~~~~~~~~~l~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~  123 (237)
                      .++|..++|-  ...+++.+.|+-.+...           .+.+....+..................+||||.++..|+.
T Consensus       421 vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~  500 (941)
T KOG0351|consen  421 VPFIALTATATERVREDVIRSLGLRNPELFKSSFNRPNLKYEVSPKTDKDALLDILEESKLRHPDQSGIIYCLSRKECEQ  500 (941)
T ss_pred             CCeEEeehhccHHHHHHHHHHhCCCCcceecccCCCCCceEEEEeccCccchHHHHHHhhhcCCCCCeEEEeCCcchHHH
Confidence            6788888886  55788888886655331           1111111111111122233334557789999999999999


Q ss_pred             HHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCC
Q psy15610        124 LEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG  203 (237)
Q Consensus       124 l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g  203 (237)
                      ++..|...++....||+||++.+|+.+.+.|..++++|+++|-++++|+|.|++..||+|+.|.+.+.|+|-+|||||.|
T Consensus       501 vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG  580 (941)
T KOG0351|consen  501 VSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDG  580 (941)
T ss_pred             HHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCcCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCceEEeecCCCCCCC
Q psy15610        204 NLDFPFSYNQPGYGGSY  220 (237)
Q Consensus       204 ~~~~~~~~~~~~~~~~~  220 (237)
                      ....|++|+...+....
T Consensus       581 ~~s~C~l~y~~~D~~~l  597 (941)
T KOG0351|consen  581 LPSSCVLLYGYADISEL  597 (941)
T ss_pred             CcceeEEecchhHHHHH
Confidence            99999999998865433

>PRK01172 ski2-like helicase; Provisional

Probab=99.78  E-value=2.3e-18  Score=157.85  Aligned_cols=161  Identities=23%  Similarity=0.286  Sum_probs=116.8

Q ss_pred             ccccceeEEeecccchhhHHHHhhhcCCCcee---------ecCC-c-c-hhhHH--HHhhh-hhhccCCceEEEEeecc
Q psy15610         54 GDEALTLVFVETKKGADQLEDFLHHHGYPVTS---------IHGD-R-T-QKERE--EAQQY-TLISCDEALTLVFVETK  118 (237)
Q Consensus        54 ~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~---------~~~~-~-~-~~~~~--~~~~~-~~~~~~~~~~iIF~~t~  118 (237)
                      +.+.++|++|+|..+.+++++|+....+....         .+.. . . ...+.  ..... .....++.++||||+++
T Consensus       167 ~~~~riI~lSATl~n~~~la~wl~~~~~~~~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~vLVF~~sr  246 (674)
T PRK01172        167 NPDARILALSATVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYERSQVDINSLIKETVNDGGQVLVFVSSR  246 (674)
T ss_pred             CcCCcEEEEeCccCCHHHHHHHhCCCccCCCCCCCCeEEEEEecCeeeecccccccccHHHHHHHHHhCCCcEEEEeccH
Confidence            35678999999999999999999654332110         0000 0 0 00000  00011 11124567999999999


Q ss_pred             cchHHHHHHHhhC-------------------------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccC
Q psy15610        119 KGADQLEDFLHHH-------------------------GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLD  173 (237)
Q Consensus       119 ~~~~~l~~~L~~~-------------------------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvd  173 (237)
                      +.++.++..|...                         ...+.++||++++++|..+++.|++|.++|||||+++++|+|
T Consensus       247 ~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~VLvaT~~la~Gvn  326 (674)
T PRK01172        247 KNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVN  326 (674)
T ss_pred             HHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeEEEecchhhccCC
Confidence            9999998888542                         124789999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEec---------CCCCHHHHHHhhcccccCCC--CCceEEeecCC
Q psy15610        174 IPHVKHVINFD---------LPSDVEEYVHRIGRTGRMGN--LDFPFSYNQPG  215 (237)
Q Consensus       174 l~~~~~Vi~~~---------~p~s~~~~~Q~~GR~~R~g~--~~~~~~~~~~~  215 (237)
                      +|...+|| .+         .|.+..+|.||+|||||.|.  .|.+++++...
T Consensus       327 ipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~  378 (674)
T PRK01172        327 LPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASP  378 (674)
T ss_pred             CcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCc
Confidence            99875555 33         25688999999999999884  56677776544

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

Probab=99.78  E-value=1.6e-18  Score=148.72  Aligned_cols=177  Identities=21%  Similarity=0.262  Sum_probs=134.8

Q ss_pred             HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCcee----------ecCCcchhhHHHHhh--hhh-
Q psy15610         37 KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTS----------IHGDRTQKEREEAQQ--YTL-  103 (237)
Q Consensus        37 k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~----------~~~~~~~~~~~~~~~--~~~-  103 (237)
                      +++-|..=|++..     ++.|.|-+|+|..+.++++..|+..-..+..          +...-.+..+.....  ..+ 
T Consensus       358 RLdGLI~RLr~l~-----~~AQ~i~LSATVgNp~elA~~l~a~lV~y~~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~  432 (830)
T COG1202         358 RLDGLIGRLRYLF-----PGAQFIYLSATVGNPEELAKKLGAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFS  432 (830)
T ss_pred             chhhHHHHHHHhC-----CCCeEEEEEeecCChHHHHHHhCCeeEeecCCCCChhHeeeeecCchHHHHHHHHHHHHHHh
Confidence            6666666666653     3567999999999999999999654332111          111112222211111  112 


Q ss_pred             -hccC--CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEE
Q psy15610        104 -ISCD--EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV  180 (237)
Q Consensus       104 -~~~~--~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~V  180 (237)
                       .++.  .+++|||++++..|..++++|..+|+++..||+|+++.+|..+.+.|.++.+.++|+|-+++.|+|||...+|
T Consensus       433 ~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVI  512 (830)
T COG1202         433 TESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVI  512 (830)
T ss_pred             hhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHH
Confidence             1222  3689999999999999999999999999999999999999999999999999999999999999999987655


Q ss_pred             EE---ecCCC-CHHHHHHhhcccccCC--CCCceEEeecCCCCC
Q psy15610        181 IN---FDLPS-DVEEYVHRIGRTGRMG--NLDFPFSYNQPGYGG  218 (237)
Q Consensus       181 i~---~~~p~-s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~~~  218 (237)
                      +-   .+..| |+..|.||+|||||-+  ..|++++++.++..-
T Consensus       513 FEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg~~Y  556 (830)
T COG1202         513 FESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGKKY  556 (830)
T ss_pred             HHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCChhh
Confidence            42   44455 8999999999999966  678888888887653

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.78  E-value=9.5e-18  Score=143.00  Aligned_cols=107  Identities=22%  Similarity=0.325  Sum_probs=91.6

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCC--ceEEEeCCCCHHHHHHH----HHHhhcCCCCEEEEcCccccccCCCCCcE
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGY--PVTSIHGDRTQKEREEA----LRRFRSGETPILVATAVAARGLDIPHVKH  179 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~--~~~~~h~~~~~~~r~~~----~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~  179 (237)
                      .++.++||||+|.+.++.++..|.+.+.  .+..+||++++.+|.+.    ++.|+++...+||||+++++|+|++ ++.
T Consensus       220 ~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~  298 (358)
T TIGR01587       220 KKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADV  298 (358)
T ss_pred             hCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCE
Confidence            3568999999999999999999987765  48999999999999774    7889999999999999999999996 788


Q ss_pred             EEEecCCCCHHHHHHhhcccccCCCCC----ceEEeecCC
Q psy15610        180 VINFDLPSDVEEYVHRIGRTGRMGNLD----FPFSYNQPG  215 (237)
Q Consensus       180 Vi~~~~p~s~~~~~Q~~GR~~R~g~~~----~~~~~~~~~  215 (237)
                      ||++..|  +..|+||+||+||.|...    .+++|....
T Consensus       299 vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~  336 (358)
T TIGR01587       299 MITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAP  336 (358)
T ss_pred             EEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecC
Confidence            8888766  889999999999988543    455555543

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.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.77  E-value=2e-17  Score=150.16  Aligned_cols=108  Identities=26%  Similarity=0.384  Sum_probs=96.1

Q ss_pred             cCCceEEEEeeccc--------chHHHHHHHhh--CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCC
Q psy15610        106 CDEALTLVFVETKK--------GADQLEDFLHH--HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP  175 (237)
Q Consensus       106 ~~~~~~iIF~~t~~--------~~~~l~~~L~~--~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~  175 (237)
                      .++.+++|||+..+        .++.+++.|..  .++.+..+||+|++++|..+++.|++|+.+|||||+++++|+|+|
T Consensus       446 ~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP  525 (630)
T TIGR00643       446 AKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVP  525 (630)
T ss_pred             HhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccC
Confidence            35678999998764        34556666654  367899999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCC-CHHHHHHhhcccccCCCCCceEEeec
Q psy15610        176 HVKHVINFDLPS-DVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       176 ~~~~Vi~~~~p~-s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      ++++||+++.|. +...|.|++||+||.|..|.|++++.
T Consensus       526 ~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       526 NATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             CCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            999999999986 78899999999999999999999983

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.77  E-value=2e-18  Score=159.23  Aligned_cols=109  Identities=17%  Similarity=0.284  Sum_probs=99.3

Q ss_pred             CceEEEEeecccchHHHHHHHhh---CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec
Q psy15610        108 EALTLVFVETKKGADQLEDFLHH---HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~---~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      .+++|||+++...++.+++.|..   .++.+..+||++++++|.+.+..|++|..+|+|||+++++|+++|++++||+++
T Consensus       212 ~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~G  291 (812)
T PRK11664        212 SGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSG  291 (812)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECC
Confidence            57899999999999999999986   477899999999999999999999999999999999999999999999999977


Q ss_pred             CCC------------------CHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        185 LPS------------------DVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       185 ~p~------------------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      .+.                  |..++.||+||+||. .+|.||.+++....
T Consensus       292 l~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~  341 (812)
T PRK11664        292 LERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQA  341 (812)
T ss_pred             CcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHHHH
Confidence            653                  446899999999999 59999999986644

>PRK13766 Hef nuclease; Provisional

Probab=99.75  E-value=1.2e-17  Score=155.47  Aligned_cols=110  Identities=33%  Similarity=0.492  Sum_probs=101.7

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCC--------CCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCc
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGD--------RTQKEREEALRRFRSGETPILVATAVAARGLDIPHVK  178 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~--------~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~  178 (237)
                      ++.++||||+++..++.+.++|...++.+..+||.        |++.+|..++..|++|..++||+|+++++|+|+|.++
T Consensus       364 ~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~  443 (773)
T PRK13766        364 PDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVD  443 (773)
T ss_pred             CCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCC
Confidence            46899999999999999999999889998889886        9999999999999999999999999999999999999


Q ss_pred             EEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        179 HVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       179 ~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +||+||+|+++..|+||+||+||.|. |.+++++..+..
T Consensus       444 ~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~t~  481 (773)
T PRK13766        444 LVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKGTR  481 (773)
T ss_pred             EEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCCCh
Confidence            99999999999999999999999874 778888776554

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.74  E-value=1.5e-17  Score=150.30  Aligned_cols=107  Identities=19%  Similarity=0.248  Sum_probs=99.2

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCC---------CCc
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP---------HVK  178 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~---------~~~  178 (237)
                      +.++||||+|.+.++.++..|.+.|+++.++||.+.+.++..+..+++.|  .|+|||+++++|+|++         .+.
T Consensus       424 ~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~  501 (762)
T TIGR03714       424 GQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLA  501 (762)
T ss_pred             CCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeE
Confidence            57999999999999999999999999999999999999988887777766  7999999999999999         889


Q ss_pred             EEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        179 HVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       179 ~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +|+++++|..... .|+.||+||.|.+|.+++|++..+.
T Consensus       502 vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       502 VIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             EEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchh
Confidence            9999999988766 9999999999999999999998665

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.74  E-value=2.7e-17  Score=148.67  Aligned_cols=108  Identities=31%  Similarity=0.399  Sum_probs=102.5

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec---
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD---  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~---  184 (237)
                      +.+++|||+|...++.++++|...|+++..+||+++..+|..+++.|++|.+.|+|||+.+.+|+|+|++++|++++   
T Consensus       442 g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP~v~lVvi~Dadi  521 (655)
T TIGR00631       442 NERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADK  521 (655)
T ss_pred             CCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeCCCcEEEEeCccc
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999988   


Q ss_pred             --CCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        185 --LPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       185 --~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                        .|.+...|+||+||+||. ..|.+++|+....
T Consensus       522 fG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~  554 (655)
T TIGR00631       522 EGFLRSERSLIQTIGRAARN-VNGKVIMYADKIT  554 (655)
T ss_pred             ccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCC
Confidence              788999999999999998 5899999988653

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

>KOG0337|consensus

Probab=99.73  E-value=4.1e-18  Score=141.29  Aligned_cols=165  Identities=32%  Similarity=0.435  Sum_probs=150.3

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      +|+.=+.+|..|.+.-+......++..+..+.+.+|..+|+.++.....                               
T Consensus       212 fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~K~aaLl~il~~~~~-------------------------------  260 (529)
T KOG0337|consen  212 FAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAEKEAALLSILGGRIK-------------------------------  260 (529)
T ss_pred             HHHccCCCCceEEeehhhhcchhhhhheeeeccHHHHHHHHHHHhcccc-------------------------------
Confidence            4555677898888877778888899999999999999999999987631                               


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..+++|||+|..+++.+...|...|+....++|+++++-|..-...|+.+...+
T Consensus       261 --------------------------~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~  314 (529)
T KOG0337|consen  261 --------------------------DKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSI  314 (529)
T ss_pred             --------------------------ccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccce
Confidence                                      358999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGS  223 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~  223 (237)
                      +|.|+++.+|+|+|..+.||+||.|.+..-|+||+||+.|.|+.|..|.++.+.+.++.--.
T Consensus       315 lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~yl~DL  376 (529)
T KOG0337|consen  315 LVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPYLLDL  376 (529)
T ss_pred             EEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecccchhhhhh
Confidence            99999999999999999999999999999999999999999999999999999888765443

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.73  E-value=3e-17  Score=109.75  Aligned_cols=81  Identities=48%  Similarity=0.828  Sum_probs=77.2

Q ss_pred             HHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccC
Q psy15610        123 QLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRM  202 (237)
Q Consensus       123 ~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~  202 (237)
                      .+++.|...++.+..+||++++.+|...++.|+++...++++|+++++|+|+|.++.||.+++|++...|.|++||++|.
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            46778888899999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             C
Q psy15610        203 G  203 (237)
Q Consensus       203 g  203 (237)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            6

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.72  E-value=5.2e-17  Score=147.49  Aligned_cols=106  Identities=32%  Similarity=0.417  Sum_probs=100.8

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC--
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL--  185 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~--  185 (237)
                      +.+++|||+|...++.+++.|...|+++..+||++++.+|..++..|++|.+.|+|||+.+++|+|+|++++||+++.  
T Consensus       446 g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp~v~lVii~d~ei  525 (652)
T PRK05298        446 GERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADK  525 (652)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccccCCcEEEEeCCcc
Confidence            678999999999999999999999999999999999999999999999999999999999999999999999999885  


Q ss_pred             ---CCCHHHHHHhhcccccCCCCCceEEeecC
Q psy15610        186 ---PSDVEEYVHRIGRTGRMGNLDFPFSYNQP  214 (237)
Q Consensus       186 ---p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  214 (237)
                         |.+...|+||+||+||. ..|.+++|+..
T Consensus       526 fG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~  556 (652)
T PRK05298        526 EGFLRSERSLIQTIGRAARN-VNGKVILYADK  556 (652)
T ss_pred             cccCCCHHHHHHHhccccCC-CCCEEEEEecC
Confidence               67999999999999996 68999999984

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.72  E-value=6.3e-17  Score=143.41  Aligned_cols=111  Identities=20%  Similarity=0.170  Sum_probs=99.4

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEc-CccccccCCCCCcEEEEecC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT-AVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T-~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      .+.+.+|||.+.++++.+++.|.+.+.++..+||+++.++|..+++.|++|...+||+| +.+++|+|+|.+++||++.+
T Consensus       343 ~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~p  422 (501)
T PHA02558        343 KGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHP  422 (501)
T ss_pred             cCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEEEecC
Confidence            35788999999999999999999999999999999999999999999999999999998 89999999999999999999


Q ss_pred             CCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        186 PSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       186 p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +.|...|+||+||++|.+..+...++++-.+.
T Consensus       423 ~~s~~~~~QriGR~~R~~~~K~~~~i~D~vD~  454 (501)
T PHA02558        423 SKSKIIVLQSIGRVLRKHGSKSIATVWDIIDD  454 (501)
T ss_pred             CcchhhhhhhhhccccCCCCCceEEEEEeecc
Confidence            99999999999999998866555555544443

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.72  E-value=1e-16  Score=144.12  Aligned_cols=108  Identities=21%  Similarity=0.231  Sum_probs=103.0

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCC-------CcEE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPH-------VKHV  180 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~-------~~~V  180 (237)
                      +.++||||+|...++.++..|.+.|++...+|++  +.+|+..+..|+.+...|+|||++++||.|++.       ..+|
T Consensus       405 grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~V  482 (745)
T TIGR00963       405 GQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYV  482 (745)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEE
Confidence            6899999999999999999999999999999998  889999999999999999999999999999998       5599


Q ss_pred             EEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       181 i~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      |+++.|.|...+.|+.||+||.|.+|.+.+|++..+.
T Consensus       483 I~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD~  519 (745)
T TIGR00963       483 IGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLEDN  519 (745)
T ss_pred             EecCCCCcHHHHHHHhccccCCCCCcceEEEEeccHH
Confidence            9999999999999999999999999999999998765

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.

>KOG0352|consensus

Probab=99.70  E-value=2.2e-17  Score=137.36  Aligned_cols=113  Identities=25%  Similarity=0.441  Sum_probs=108.1

Q ss_pred             ceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCC
Q psy15610        109 ALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSD  188 (237)
Q Consensus       109 ~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s  188 (237)
                      +-.||||.|++.|++++..|...|+++..||.|+...+|..+.+.+-++++.|+++|..+++|+|-|++..||++++|.|
T Consensus       256 GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn  335 (641)
T KOG0352|consen  256 GCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQN  335 (641)
T ss_pred             cceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchhh
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcccccCCCCCceEEeecCCCCCCCC
Q psy15610        189 VEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYG  221 (237)
Q Consensus       189 ~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  221 (237)
                      ...|+|-.|||||.|.++.|-+|++..+.+..+
T Consensus       336 ~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~  368 (641)
T KOG0352|consen  336 LAGYYQESGRAGRDGKRSYCRLYYSRQDKNALN  368 (641)
T ss_pred             hHHHHHhccccccCCCccceeeeecccchHHHH
Confidence            999999999999999999999999988776543

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.69  E-value=1.8e-16  Score=143.74  Aligned_cols=108  Identities=25%  Similarity=0.281  Sum_probs=101.0

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCC---CCc-----E
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP---HVK-----H  179 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~---~~~-----~  179 (237)
                      +.++||||.|...++.++..|.+.+++...+|+++...+++.+..+++.|.  |+|+|++++||.|++   ++.     +
T Consensus       440 g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLh  517 (796)
T PRK12906        440 GQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLA  517 (796)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcE
Confidence            689999999999999999999999999999999999888888888887776  999999999999995   788     9


Q ss_pred             EEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        180 VINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       180 Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||+++.|.|...+.|+.||+||.|.+|.+.+|++..+.
T Consensus       518 VI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD~  555 (796)
T PRK12906        518 VIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  555 (796)
T ss_pred             EEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccch
Confidence            99999999999999999999999999999999998865

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.69  E-value=1.9e-16  Score=143.06  Aligned_cols=109  Identities=19%  Similarity=0.259  Sum_probs=95.0

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC-CCCEEEEcCccccccCCCCCcEEEEecC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG-ETPILVATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g-~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      .+.++||||.+...++.++..|   +  +.++||+++..+|.++++.|+++ .+++||+|+++++|+|+|++++||+++.
T Consensus       495 ~g~kiLVF~~~~~~l~~~a~~L---~--~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgdeGIDlP~a~vvI~~s~  569 (732)
T TIGR00603       495 RGDKIIVFSDNVFALKEYAIKL---G--KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQISS  569 (732)
T ss_pred             cCCeEEEEeCCHHHHHHHHHHc---C--CceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccccCCCCCCEEEEeCC
Confidence            3689999999999888888877   2  45799999999999999999975 7899999999999999999999999998


Q ss_pred             CC-CHHHHHHhhcccccCCCCCce-------EEeecCCCCCCC
Q psy15610        186 PS-DVEEYVHRIGRTGRMGNLDFP-------FSYNQPGYGGSY  220 (237)
Q Consensus       186 p~-s~~~~~Q~~GR~~R~g~~~~~-------~~~~~~~~~~~~  220 (237)
                      |. |..+|+||+||++|.+..+.+       |.+++++..+.+
T Consensus       570 ~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E~~  612 (732)
T TIGR00603       570 HYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMY  612 (732)
T ss_pred             CCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchHHH
Confidence            85 999999999999998866554       777877766544

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.67  E-value=3.4e-16  Score=148.01  Aligned_cols=106  Identities=21%  Similarity=0.300  Sum_probs=94.1

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCc---eEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYP---VTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~---~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      .+.+|||+++...++.+++.|...+++   +..+||++++++|.++++.  .|..+|+|||+++++|+++|++++||+++
T Consensus       286 ~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~G  363 (1294)
T PRK11131        286 PGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPG  363 (1294)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEECC
Confidence            578999999999999999999887654   6789999999999999876  47789999999999999999999999985


Q ss_pred             ---------------CC---CCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        185 ---------------LP---SDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       185 ---------------~p---~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                                     .|   .|..+|.||+||+||. .+|.||.+++..+
T Consensus       364 l~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d  412 (1294)
T PRK11131        364 TARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDD  412 (1294)
T ss_pred             CccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHH
Confidence                           23   4668999999999999 6999999998654

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.67  E-value=7.7e-16  Score=146.01  Aligned_cols=158  Identities=16%  Similarity=0.247  Sum_probs=117.9

Q ss_pred             cccceeEEeecccchhhHHHHhhhc--------CCCceeecCCcch-------hhHHHHhh--hhhhccCCceEEEEeec
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHH--------GYPVTSIHGDRTQ-------KEREEAQQ--YTLISCDEALTLVFVET  117 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~--------~~~~~~~~~~~~~-------~~~~~~~~--~~~~~~~~~~~iIF~~t  117 (237)
                      ++.++|+||+|.. .+.+++++...        .+++...+.....       .....+..  ..+.....+.+|||+++
T Consensus       210 pdLKlIlmSATld-~~~fa~~F~~apvI~V~Gr~~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg  288 (1283)
T TIGR01967       210 PDLKIIITSATID-PERFSRHFNNAPIIEVSGRTYPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPG  288 (1283)
T ss_pred             CCCeEEEEeCCcC-HHHHHHHhcCCCEEEECCCcccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCC
Confidence            5678999999996 57788888532        2333332222111       01111111  11122356789999999


Q ss_pred             ccchHHHHHHHhhCC---CceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC---------
Q psy15610        118 KKGADQLEDFLHHHG---YPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL---------  185 (237)
Q Consensus       118 ~~~~~~l~~~L~~~~---~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~---------  185 (237)
                      ...++.+.+.|...+   ..+..+||++++++|.++++.+  +..+|++||+++++|+++|++++||+++.         
T Consensus       289 ~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~  366 (1283)
T TIGR01967       289 EREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYR  366 (1283)
T ss_pred             HHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccc
Confidence            999999999998764   4588999999999999886654  23689999999999999999999999873         


Q ss_pred             ---------CCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        186 ---------PSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       186 ---------p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                               |.|..++.||+||+||.| +|.||.+++..+
T Consensus       367 ~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~  405 (1283)
T TIGR01967       367 TKVQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEED  405 (1283)
T ss_pred             cCccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHH
Confidence                     336789999999999998 999999998654

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.

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.67  E-value=3.4e-16  Score=146.26  Aligned_cols=106  Identities=21%  Similarity=0.357  Sum_probs=97.3

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC---CCEEEEcCccccccCCCCCcEEEEe
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE---TPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~---~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      .+.++|||+.....++.++++|...++.+..++|+++..+|...++.|++..   ..+|++|.+++.|+|++.+++||+|
T Consensus       486 ~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINLt~Ad~VIiy  565 (1033)
T PLN03142        486 RDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVILY  565 (1033)
T ss_pred             cCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCchhhCCEEEEe
Confidence            4689999999999999999999999999999999999999999999998643   3578999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEee
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSYN  212 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~  212 (237)
                      |+||+|....|+.||++|+|+...+.+|.
T Consensus       566 D~dWNP~~d~QAidRaHRIGQkk~V~VyR  594 (1033)
T PLN03142        566 DSDWNPQVDLQAQDRAHRIGQKKEVQVFR  594 (1033)
T ss_pred             CCCCChHHHHHHHHHhhhcCCCceEEEEE
Confidence            99999999999999999999987665543

>KOG0354|consensus

Probab=99.66  E-value=5.6e-16  Score=138.16  Aligned_cols=107  Identities=37%  Similarity=0.517  Sum_probs=91.3

Q ss_pred             ccCCceEEEEeecccchHHHHHHHhh-C--CCceEEE--------eCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccC
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHH-H--GYPVTSI--------HGDRTQKEREEALRRFRSGETPILVATAVAARGLD  173 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~-~--~~~~~~~--------h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvd  173 (237)
                      ..+..++||||.++..+..+..+|.. .  +++...+        ..+|++.+...++++|++|+++|||||+++++|+|
T Consensus       410 ~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLD  489 (746)
T KOG0354|consen  410 QNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLD  489 (746)
T ss_pred             cCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCC
Confidence            45567899999999999999998873 2  2232222        24799999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeec
Q psy15610        174 IPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       174 l~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      +++|+.||.||.-.|+..++||+|| ||.. .|.++++..
T Consensus       490 I~ec~lVIcYd~~snpIrmIQrrGR-gRa~-ns~~vll~t  527 (746)
T KOG0354|consen  490 IGECNLVICYDYSSNPIRMVQRRGR-GRAR-NSKCVLLTT  527 (746)
T ss_pred             cccccEEEEecCCccHHHHHHHhcc-cccc-CCeEEEEEc
Confidence            9999999999999999999999999 9984 677777776

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.66  E-value=5.6e-16  Score=141.80  Aligned_cols=160  Identities=21%  Similarity=0.231  Sum_probs=119.5

Q ss_pred             ccceeEEeecccchhhHHHHhhhcCCCc-eeecCCcchh-------------------hHHHHhh-hhhhccCCceEEEE
Q psy15610         56 EALTLVFVETKKGADQLEDFLHHHGYPV-TSIHGDRTQK-------------------EREEAQQ-YTLISCDEALTLVF  114 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~~~~~~l~~~~~~~-~~~~~~~~~~-------------------~~~~~~~-~~~~~~~~~~~iIF  114 (237)
                      ..+++..|+|.+++++++.|++...+.. ....+.+++.                   ..+.... ......++++++||
T Consensus       180 ~~rivgLSATlpN~~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~~qvLvF  259 (766)
T COG1204         180 LIRIVGLSATLPNAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVF  259 (766)
T ss_pred             ceEEEEEeeecCCHHHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHHHHhcCCeEEEE
Confidence            3689999999999999999998875411 1111111111                   1111111 22234567899999


Q ss_pred             eecccchHHHHHHHhhC-------------------------------------CCceEEEeCCCCHHHHHHHHHHhhcC
Q psy15610        115 VETKKGADQLEDFLHHH-------------------------------------GYPVTSIHGDRTQKEREEALRRFRSG  157 (237)
Q Consensus       115 ~~t~~~~~~l~~~L~~~-------------------------------------~~~~~~~h~~~~~~~r~~~~~~f~~g  157 (237)
                      |+++..+...+..+...                                     ...+.++|++++.++|..+.+.|++|
T Consensus       260 v~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~vE~~Fr~g  339 (766)
T COG1204         260 VHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDAFRKG  339 (766)
T ss_pred             EecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHHHHHHHHhcC
Confidence            99999988887777620                                     12478999999999999999999999


Q ss_pred             CCCEEEEcCccccccCCCCCcEEEE----ec-----CCCCHHHHHHhhcccccCC--CCCceEEeecCC
Q psy15610        158 ETPILVATAVAARGLDIPHVKHVIN----FD-----LPSDVEEYVHRIGRTGRMG--NLDFPFSYNQPG  215 (237)
Q Consensus       158 ~~~vlv~T~~~~~Gvdl~~~~~Vi~----~~-----~p~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~  215 (237)
                      .++||+||+.+++|+|+|.-.+||-    |+     .+.+.-++.||.|||||.|  ..|.++++....
T Consensus       340 ~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~~~~  408 (766)
T COG1204         340 KIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSH  408 (766)
T ss_pred             CceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEEecCc
Confidence            9999999999999999999888773    55     3457889999999999987  446666666333

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.65  E-value=7e-16  Score=141.19  Aligned_cols=108  Identities=19%  Similarity=0.219  Sum_probs=100.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCC---CCc-----E
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP---HVK-----H  179 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~---~~~-----~  179 (237)
                      +.++||||+|...++.++.+|...+++..++|+  .+.+|+..+..|..+...|+|||++++||.|++   .+.     +
T Consensus       598 grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~  675 (1025)
T PRK12900        598 GQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLF  675 (1025)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhCCce
Confidence            689999999999999999999999999999997  688999999999999999999999999999999   343     4


Q ss_pred             EEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        180 VINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       180 Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||.++.|.|...|.|+.||+||.|.+|.+++|++..+.
T Consensus       676 VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~  713 (1025)
T PRK12900        676 ILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDE  713 (1025)
T ss_pred             eeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHH
Confidence            58889999999999999999999999999999998765

>KOG0349|consensus

Probab=99.65  E-value=2.9e-15  Score=125.19  Aligned_cols=196  Identities=24%  Similarity=0.361  Sum_probs=140.2

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeec-hh-HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhh-
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDE-QD-KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHH-   78 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~-k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~-   78 (237)
                      ++++.|-=|..+++..+....+.+.|....+.. -+ -...|...|.....   ...--...--.++++..+-...|.. 
T Consensus       418 ~~ervmhfptwVdLkgeD~vpetvHhvv~lv~p~~d~sw~~lr~~i~td~v---h~kdn~~pg~~Spe~~s~a~kilkgE  494 (725)
T KOG0349|consen  418 VGERVMHFPTWVDLKGEDLVPETVHHVVKLVCPSVDGSWCDLRQFIETDKV---HTKDNLLPGQVSPENPSSATKILKGE  494 (725)
T ss_pred             hhhhhccCceeEecccccccchhhccceeecCCccCccHHHHhhhhccCCc---ccccccccccCCCCChhhhhHHhcCc
Confidence            567788889999998888888888888765443 22 33444444443321   0000111112222222222221111 


Q ss_pred             cCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhC---CCceEEEeCCCCHHHHHHHHHHhh
Q psy15610         79 HGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFR  155 (237)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~---~~~~~~~h~~~~~~~r~~~~~~f~  155 (237)
                      .+..+                   +..-...++||||.|...|+.+++++...   .+.+.++||+..|.+|.+.++.|+
T Consensus       495 y~v~a-------------------i~~h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fk  555 (725)
T KOG0349|consen  495 YGVVA-------------------IRRHAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFK  555 (725)
T ss_pred             hhhhh-------------------hhhhccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhh
Confidence            11110                   11122578999999999999999999886   468899999999999999999999


Q ss_pred             cCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCC
Q psy15610        156 SGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGS  219 (237)
Q Consensus       156 ~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~  219 (237)
                      .+..+.||||+++++|+|+..+-++|+...|.+...|+||+||+||..+-|.+|.++.......
T Consensus       556 k~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgraermglaislvat~~ekv  619 (725)
T KOG0349|consen  556 KFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVATVPEKV  619 (725)
T ss_pred             hcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhhhcceeEEEeeccchhe
Confidence            9999999999999999999999999999999999999999999999877788888776554433

>KOG0329|consensus

Probab=99.64  E-value=3.9e-17  Score=127.74  Aligned_cols=123  Identities=28%  Similarity=0.477  Sum_probs=106.8

Q ss_pred             hHHHHhhcceeEEEeecc-CCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVG-STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      +.++||.||+.|-+..|. .+++++.|+|+...+++|...|.+||+...                               
T Consensus       234 vC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~Le-------------------------------  282 (387)
T KOG0329|consen  234 VCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLE-------------------------------  282 (387)
T ss_pred             HHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhh-------------------------------
Confidence            468999999999888777 889999999999999998888888888764                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 .++++||+.+...       |                       . |.   -+
T Consensus       283 ---------------------------FNQVvIFvKsv~R-------l-----------------------~-f~---kr  301 (387)
T KOG0329|consen  283 ---------------------------FNQVVIFVKSVQR-------L-----------------------S-FQ---KR  301 (387)
T ss_pred             ---------------------------hcceeEeeehhhh-------h-----------------------h-hh---hh
Confidence                                       5789999988764       0                       0 21   12


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                       +++|+.+++|+|+-.++.+++||+|.++..|+||+|||||.|..|.++.|++....
T Consensus       302 -~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~d  357 (387)
T KOG0329|consen  302 -LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEND  357 (387)
T ss_pred             -hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhh
Confidence             78999999999999999999999999999999999999999999999999986543

>PRK14701 reverse gyrase; Provisional

Probab=99.63  E-value=2.5e-15  Score=146.37  Aligned_cols=140  Identities=20%  Similarity=0.321  Sum_probs=117.4

Q ss_pred             HHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCc
Q psy15610          4 KEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPV   83 (237)
Q Consensus         4 ~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~   83 (237)
                      .+++.++..+.+........+|.|.|+.++..+| ..|.+++...                                   
T Consensus       286 ~~l~~~~l~f~v~~~~~~lr~i~~~yi~~~~~~k-~~L~~ll~~~-----------------------------------  329 (1638)
T PRK14701        286 VKLYRELLGFEVGSGRSALRNIVDVYLNPEKIIK-EHVRELLKKL-----------------------------------  329 (1638)
T ss_pred             HHHhhcCeEEEecCCCCCCCCcEEEEEECCHHHH-HHHHHHHHhC-----------------------------------
Confidence            3556788888877666778889999887766555 5677777654                                   


Q ss_pred             eeecCCcchhhHHHHhhhhhhccCCceEEEEeecccc---hHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         84 TSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~---~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                              +.++||||+|++.   ++.++..|...|+++..+||+     |...++.|++|+.+
T Consensus       330 ------------------------g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~~F~~G~~~  380 (1638)
T PRK14701        330 ------------------------GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFDLFEEGEID  380 (1638)
T ss_pred             ------------------------CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHHHHHcCCCC
Confidence                                    3679999999886   489999999999999999995     88999999999999


Q ss_pred             EEEEc----CccccccCCCC-CcEEEEecCCC---CHHHHHHhh-------------cccccCCCCCce
Q psy15610        161 ILVAT----AVAARGLDIPH-VKHVINFDLPS---DVEEYVHRI-------------GRTGRMGNLDFP  208 (237)
Q Consensus       161 vlv~T----~~~~~Gvdl~~-~~~Vi~~~~p~---s~~~~~Q~~-------------GR~~R~g~~~~~  208 (237)
                      |||+|    ++++||+|+|+ +++||++++|.   +.+.|.|-.             ||++|.|.+..+
T Consensus       381 VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~  449 (1638)
T PRK14701        381 YLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEG  449 (1638)
T ss_pred             EEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchh
Confidence            99999    58999999999 99999999999   777666655             999999977666

>KOG0948|consensus

Probab=99.61  E-value=4.7e-16  Score=136.99  Aligned_cols=182  Identities=19%  Similarity=0.198  Sum_probs=134.3

Q ss_pred             cccccceeEEeecccchhhHHHHhhh-cCCCceeecCCcchhhHHHHhh-------------------------------
Q psy15610         53 LGDEALTLVFVETKKGADQLEDFLHH-HGYPVTSIHGDRTQKEREEAQQ-------------------------------  100 (237)
Q Consensus        53 ~~~~~~~i~f~~t~~~~~~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~-------------------------------  100 (237)
                      +|.+-+.+.+|+|.+++.++++|+.. +..+|.....+.+..+..+-+.                               
T Consensus       263 lP~~vr~VFLSATiPNA~qFAeWI~~ihkQPcHVVYTdyRPTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~  342 (1041)
T KOG0948|consen  263 LPDNVRFVFLSATIPNARQFAEWICHIHKQPCHVVYTDYRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRK  342 (1041)
T ss_pred             ccccceEEEEeccCCCHHHHHHHHHHHhcCCceEEeecCCCCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhc
Confidence            46678899999999999999999977 4556666666655555433322                               


Q ss_pred             ---------------------------------hhhhccCCceEEEEeecccchHHHHHHHhhCC---------------
Q psy15610        101 ---------------------------------YTLISCDEALTLVFVETKKGADQLEDFLHHHG---------------  132 (237)
Q Consensus       101 ---------------------------------~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~---------------  132 (237)
                                                       ..+...+..++|||+-+++.|+..+--+.+..               
T Consensus       343 ~~~~~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~  422 (1041)
T KOG0948|consen  343 AGESDGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFN  422 (1041)
T ss_pred             cCCCccccccccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHH
Confidence                                             11123345789999999999998855443321               


Q ss_pred             ------------------------CceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE----ec
Q psy15610        133 ------------------------YPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN----FD  184 (237)
Q Consensus       133 ------------------------~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~----~~  184 (237)
                                              ..++++|+|+-|--++-+.-.|++|-+++|++|..++.|+|+|.-++|+-    ||
T Consensus       423 nAi~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfD  502 (1041)
T KOG0948|consen  423 NAIDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFD  502 (1041)
T ss_pred             HHHHhcChhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccC
Confidence                                    24889999999999999999999999999999999999999998877764    33


Q ss_pred             CC----CCHHHHHHhhcccccCC--CCCceEEeecCCCCCCCCCCCCCCCCCCCCccC
Q psy15610        185 LP----SDVEEYVHRIGRTGRMG--NLDFPFSYNQPGYGGSYGGSSSQNSNAPDWWND  236 (237)
Q Consensus       185 ~p----~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  236 (237)
                      -.    .|..+|+||.|||||-|  ..|.||++++....  +.-.++-.+|.+|.+++
T Consensus       503 G~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDekm~--~~~ak~m~kG~aD~LnS  558 (1041)
T KOG0948|consen  503 GKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEKME--PQVAKDMLKGSADPLNS  558 (1041)
T ss_pred             CcceeeecccceEEecccccccCCCCCceEEEEecCcCC--HHHHHHHhcCCCcchhh
Confidence            22    16788999999999988  45777777765443  33333445555665554

>KOG0353|consensus

Probab=99.61  E-value=1.4e-15  Score=125.23  Aligned_cols=114  Identities=23%  Similarity=0.363  Sum_probs=107.6

Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEe
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      ....++..||||-+++.++.++..|+.+|+.+..||..|.|+++.-..+.+..|+++|+|+|-++++|+|-|+++.||+.
T Consensus       313 ~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihh  392 (695)
T KOG0353|consen  313 GDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHH  392 (695)
T ss_pred             cccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEec
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHH-------------------------------------------hhcccccCCCCCceEEeecCCCC
Q psy15610        184 DLPSDVEEYVH-------------------------------------------RIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       184 ~~p~s~~~~~Q-------------------------------------------~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ++|.|.+.|+|                                           -.||+||.|.+..|++|+.-++.
T Consensus       393 sl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~di  469 (695)
T KOG0353|consen  393 SLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFADI  469 (695)
T ss_pred             ccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEechHHH
Confidence            99999999999                                           67999999999999999875543

>KOG0951|consensus

Probab=99.61  E-value=1.9e-15  Score=139.14  Aligned_cols=179  Identities=18%  Similarity=0.202  Sum_probs=140.6

Q ss_pred             cccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhh--------------------HHHHhhhhhhccCCceEEEE
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKE--------------------REEAQQYTLISCDEALTLVF  114 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~~iIF  114 (237)
                      .+.+.+.+|+|.++.++++.+|.......+++.+..++.+                    -+...+.++...+.+++|||
T Consensus       473 e~~RlVGLSATLPNy~DV~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~~~~~qamNe~~yeKVm~~agk~qVLVF  552 (1674)
T KOG0951|consen  473 EGSRLVGLSATLPNYEDVASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLKRFQAMNEACYEKVLEHAGKNQVLVF  552 (1674)
T ss_pred             cCceeeeecccCCchhhhHHHhccCcccccccCcccCcCCccceEeccccCCchHHHHHHHHHHHHHHHHhCCCCcEEEE
Confidence            3678899999999999999988776633333322222211                    12333356667788999999


Q ss_pred             eecccchHHHHHHHhhC-------------------------------------CCceEEEeCCCCHHHHHHHHHHhhcC
Q psy15610        115 VETKKGADQLEDFLHHH-------------------------------------GYPVTSIHGDRTQKEREEALRRFRSG  157 (237)
Q Consensus       115 ~~t~~~~~~l~~~L~~~-------------------------------------~~~~~~~h~~~~~~~r~~~~~~f~~g  157 (237)
                      +.+++.....++.++..                                     .+.++.+|+||+..+|..+.+.|++|
T Consensus       553 VHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R~dR~~~EdLf~~g  632 (1674)
T KOG0951|consen  553 VHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNRKDRELVEDLFADG  632 (1674)
T ss_pred             EEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCcchHHHHHHHHhcC
Confidence            99999777665555410                                     24689999999999999999999999


Q ss_pred             CCCEEEEcCccccccCCCCCcEEEE----ecC------CCCHHHHHHhhcccccCC--CCCceEEeecCCCCCCCCCCCC
Q psy15610        158 ETPILVATAVAARGLDIPHVKHVIN----FDL------PSDVEEYVHRIGRTGRMG--NLDFPFSYNQPGYGGSYGGSSS  225 (237)
Q Consensus       158 ~~~vlv~T~~~~~Gvdl~~~~~Vi~----~~~------p~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~~~~~~~~~~  225 (237)
                      .++|+++|..++||+|+|.-+++|-    |++      +.++.+.+||.|||||.+  +.|.+++.....+.++|-+.-+
T Consensus       633 ~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~~se~qyyls~mn  712 (1674)
T KOG0951|consen  633 HIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSELQYYLSLMN  712 (1674)
T ss_pred             ceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeeccCchHhhhhHHhhh
Confidence            9999999999999999999888884    554      338999999999999955  6788999999999999999877


Q ss_pred             CCCCCCCC
Q psy15610        226 QNSNAPDW  233 (237)
Q Consensus       226 ~~~~~~~~  233 (237)
                      .+.+.++.
T Consensus       713 ~qLpiesq  720 (1674)
T KOG0951|consen  713 QQLPIESQ  720 (1674)
T ss_pred             hcCCChHH
Confidence            77776544

>PRK09401 reverse gyrase; Reviewed

Probab=99.59  E-value=1.2e-14  Score=138.53  Aligned_cols=131  Identities=22%  Similarity=0.340  Sum_probs=109.3

Q ss_pred             HHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCce
Q psy15610          5 EFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVT   84 (237)
Q Consensus         5 ~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~   84 (237)
                      .++.+++.+.+........+|.|.|+.++  +|...|..++...                                    
T Consensus       286 ~l~~~ll~~~v~~~~~~~rnI~~~yi~~~--~k~~~L~~ll~~l------------------------------------  327 (1176)
T PRK09401        286 KLFRELLGFEVGSPVFYLRNIVDSYIVDE--DSVEKLVELVKRL------------------------------------  327 (1176)
T ss_pred             HHhhccceEEecCcccccCCceEEEEEcc--cHHHHHHHHHHhc------------------------------------
Confidence            34567777777666667788888887665  5667777777654                                    


Q ss_pred             eecCCcchhhHHHHhhhhhhccCCceEEEEeecccc---hHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         85 SIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~---~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                             +.++||||+++..   ++.++.+|...|+++..+||+|     .+.++.|++|+++|
T Consensus       328 -----------------------~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~~~V  379 (1176)
T PRK09401        328 -----------------------GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDV  379 (1176)
T ss_pred             -----------------------CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCCCCE
Confidence                                   3579999999888   9999999999999999999999     23459999999999


Q ss_pred             EEE----cCccccccCCCC-CcEEEEecCCC------CHHHHHHhhccccc
Q psy15610        162 LVA----TAVAARGLDIPH-VKHVINFDLPS------DVEEYVHRIGRTGR  201 (237)
Q Consensus       162 lv~----T~~~~~Gvdl~~-~~~Vi~~~~p~------s~~~~~Q~~GR~~R  201 (237)
                      ||+    |++++||+|+|+ +++||+|+.|.      ....+.++.||...
T Consensus       380 LVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~~  430 (1176)
T PRK09401        380 LVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLLS  430 (1176)
T ss_pred             EEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHHh
Confidence            999    689999999999 89999999998      56778899998853

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

Probab=99.53  E-value=1.5e-13  Score=121.37  Aligned_cols=182  Identities=19%  Similarity=0.232  Sum_probs=126.2

Q ss_pred             EEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCc-------------eeecCCcchhhH
Q psy15610         29 IAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPV-------------TSIHGDRTQKER   95 (237)
Q Consensus        29 ~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~-------------~~~~~~~~~~~~   95 (237)
                      +++++|.++.-+.....-...-.+   .-=.++|++|+=+-.-....++..+.+.             ..+.........
T Consensus       387 LVIiDEQHRFGV~QR~~L~~KG~~---~Ph~LvMTATPIPRTLAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~  463 (677)
T COG1200         387 LVIIDEQHRFGVHQRLALREKGEQ---NPHVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVY  463 (677)
T ss_pred             EEEEeccccccHHHHHHHHHhCCC---CCcEEEEeCCCchHHHHHHHhccccchhhccCCCCCCceEEEEeccccHHHHH
Confidence            467788776644443322211000   1127899999655333333333333332             222222222222


Q ss_pred             HHHhhhhhhccCCceEEEEeecccch--------HHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEc
Q psy15610         96 EEAQQYTLISCDEALTLVFVETKKGA--------DQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVAT  165 (237)
Q Consensus        96 ~~~~~~~~~~~~~~~~iIF~~t~~~~--------~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T  165 (237)
                      ..+   .-...++.++.+.|+-.+..        ..+.+.|...  +.++..+||.|++.+++.+.+.|++|+++|||||
T Consensus       464 e~i---~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaT  540 (677)
T COG1200         464 ERI---REEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVAT  540 (677)
T ss_pred             HHH---HHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEe
Confidence            211   11234688899999876644        4455666533  6679999999999999999999999999999999


Q ss_pred             CccccccCCCCCcEEEEecCCC-CHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        166 AVAARGLDIPHVKHVINFDLPS-DVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       166 ~~~~~Gvdl~~~~~Vi~~~~p~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      .+.+.|||+|+++++|..+... ..+++.|-.||+||.+..+.|++++.+..
T Consensus       541 TVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         541 TVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             eEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            9999999999999988888764 79999999999999999999999998877

>KOG0392|consensus

Probab=99.53  E-value=8.2e-14  Score=128.29  Aligned_cols=168  Identities=17%  Similarity=0.256  Sum_probs=131.9

Q ss_pred             HHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCc-eeecCCcchhhHHHHhhhhhhcc----------
Q psy15610         38 RSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPV-TSIHGDRTQKEREEAQQYTLISC----------  106 (237)
Q Consensus        38 ~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~----------  106 (237)
                      ++++.++++++          .++.+.-.+....+...+...+-.. ...|+......++....+.+..+          
T Consensus      1268 LqYlrKLcnHp----------aLvlt~~hp~la~i~~~l~~~~~~LHdi~hspKl~AL~qLL~eCGig~~~~~~~g~~s~ 1337 (1549)
T KOG0392|consen 1268 LQYLRKLCNHP----------ALVLTPVHPDLAAIVSHLAHFNSSLHDIQHSPKLSALKQLLSECGIGNNSDSEVGTPSD 1337 (1549)
T ss_pred             HHHHHHhcCCc----------ceeeCCCcchHHHHHHHHHHhhhhHHHhhhchhHHHHHHHHHHhCCCCCCcccccCcch
Confidence            55666666655          6777766666777777776666555 34466666777777766666422          


Q ss_pred             -CCceEEEEeecccchHHHHHHHhhC---CCceEEEeCCCCHHHHHHHHHHhhcC-CCCEE-EEcCccccccCCCCCcEE
Q psy15610        107 -DEALTLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSG-ETPIL-VATAVAARGLDIPHVKHV  180 (237)
Q Consensus       107 -~~~~~iIF~~t~~~~~~l~~~L~~~---~~~~~~~h~~~~~~~r~~~~~~f~~g-~~~vl-v~T~~~~~Gvdl~~~~~V  180 (237)
                       .+++++|||.-...++.+++-|.+.   ......+.|+.++.+|.++.++|+++ .++|| ++|.+++.|+|+..+|.|
T Consensus      1338 vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTV 1417 (1549)
T KOG0392|consen 1338 VSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTV 1417 (1549)
T ss_pred             hccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceE
Confidence             4678999999999999998888665   34456899999999999999999998 67876 567999999999999999


Q ss_pred             EEecCCCCHHHHHHhhcccccCCCCCce--EEeecCC
Q psy15610        181 INFDLPSDVEEYVHRIGRTGRMGNLDFP--FSYNQPG  215 (237)
Q Consensus       181 i~~~~p~s~~~~~Q~~GR~~R~g~~~~~--~~~~~~~  215 (237)
                      |+++.+|+|..-+|.+.||+|.||+..+  |-++..+
T Consensus      1418 VFvEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlItrG 1454 (1549)
T KOG0392|consen 1418 VFVEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLITRG 1454 (1549)
T ss_pred             EEEecCCCchhhHHHHHHHHhhcCceeeeeeeehhcc
Confidence            9999999999999999999999998663  4444443

>KOG0952|consensus

Probab=99.53  E-value=2.1e-14  Score=130.68  Aligned_cols=198  Identities=15%  Similarity=0.187  Sum_probs=142.3

Q ss_pred             hHHHHHHHhhcCchhhh--cccccceeEEeecccchhhHHHHhhhcCC-CceeecCCcchhh------------------
Q psy15610         36 DKRSCLLDLLSSPSQEE--LGDEALTLVFVETKKGADQLEDFLHHHGY-PVTSIHGDRTQKE------------------   94 (237)
Q Consensus        36 ~k~~~l~~ll~~~~~~~--~~~~~~~i~f~~t~~~~~~~~~~l~~~~~-~~~~~~~~~~~~~------------------   94 (237)
                      ++=..|-.++.......  -+..-+++..|+|.++.+++++||.-... -..++....++.+                  
T Consensus       253 ~RGpvlEtiVaRtlr~vessqs~IRivgLSATlPN~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~  332 (1230)
T KOG0952|consen  253 DRGPVLETIVARTLRLVESSQSMIRIVGLSATLPNYEDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKK  332 (1230)
T ss_pred             cccchHHHHHHHHHHHHHhhhhheEEEEeeccCCCHHHHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhh
Confidence            34444444444333111  13467899999999999999999987521 2222222222211                  


Q ss_pred             --HHHHhh-hhhhccCCceEEEEeecccchHHHHHHHhhC-----------------------CCceEEEeCCCCHHHHH
Q psy15610         95 --REEAQQ-YTLISCDEALTLVFVETKKGADQLEDFLHHH-----------------------GYPVTSIHGDRTQKERE  148 (237)
Q Consensus        95 --~~~~~~-~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~-----------------------~~~~~~~h~~~~~~~r~  148 (237)
                        .+.... ..-....+.+++|||.++......++.|.+.                       ...+.++|+||..++|.
T Consensus       333 ~~d~~~~~kv~e~~~~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~  412 (1230)
T KOG0952|consen  333 NIDEVCYDKVVEFLQEGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQ  412 (1230)
T ss_pred             hHHHHHHHHHHHHHHcCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHH
Confidence              111111 1223456899999999999888888777532                       13478999999999999


Q ss_pred             HHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE----ecCCC------CHHHHHHhhccccc--CCCCCceEEeecCCC
Q psy15610        149 EALRRFRSGETPILVATAVAARGLDIPHVKHVIN----FDLPS------DVEEYVHRIGRTGR--MGNLDFPFSYNQPGY  216 (237)
Q Consensus       149 ~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~----~~~p~------s~~~~~Q~~GR~~R--~g~~~~~~~~~~~~~  216 (237)
                      -..+.|..|.++||+||..++||+|+|+--++|-    ||...      +.-+.+|..|||||  .+..|.++++.....
T Consensus       413 l~E~~F~~G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dk  492 (1230)
T KOG0952|consen  413 LVEKEFKEGHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDK  492 (1230)
T ss_pred             HHHHHHhcCCceEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccH
Confidence            9999999999999999999999999998776663    44432      56688999999999  557899999999999


Q ss_pred             CCCCCCCCCCCCCCCCC
Q psy15610        217 GGSYGGSSSQNSNAPDW  233 (237)
Q Consensus       217 ~~~~~~~~~~~~~~~~~  233 (237)
                      ...|-.+..+....++.
T Consensus       493 l~~Y~sLl~~~~piES~  509 (1230)
T KOG0952|consen  493 LDHYESLLTGQNPIESQ  509 (1230)
T ss_pred             HHHHHHHHcCCChhHHH
Confidence            99998877776665543

>KOG0385|consensus

Probab=99.51  E-value=4.1e-14  Score=125.24  Aligned_cols=106  Identities=23%  Similarity=0.382  Sum_probs=98.4

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC---CCEEEEcCccccccCCCCCcEEEE
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE---TPILVATAVAARGLDIPHVKHVIN  182 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~---~~vlv~T~~~~~Gvdl~~~~~Vi~  182 (237)
                      .++.+++||..-....+.+.+|+.-.++.+..+.|+++.++|...++.|.+..   +-.|++|.+++.|+|+..+++||.
T Consensus       485 ~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGINL~aADtVIl  564 (971)
T KOG0385|consen  485 EQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGINLTAADTVIL  564 (971)
T ss_pred             hCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccccccccccccccEEEE
Confidence            34799999999999999999999999999999999999999999999998765   457899999999999999999999


Q ss_pred             ecCCCCHHHHHHhhcccccCCCCCceEEe
Q psy15610        183 FDLPSDVEEYVHRIGRTGRMGNLDFPFSY  211 (237)
Q Consensus       183 ~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~  211 (237)
                      ||..|+|..-+|.+.||+|+|+..-+.+|
T Consensus       565 yDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~  593 (971)
T KOG0385|consen  565 YDSDWNPQVDLQAMDRAHRIGQKKPVVVY  593 (971)
T ss_pred             ecCCCCchhhhHHHHHHHhhCCcCceEEE
Confidence            99999999999999999999998766555

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.50  E-value=2e-13  Score=116.23  Aligned_cols=84  Identities=26%  Similarity=0.464  Sum_probs=73.5

Q ss_pred             CceEEEEeecccchHHHHHHHhhCC--CceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHG--YPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~--~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      +.+++|||+|...++.++..|...+  ..+..+||.+++.+|++.      ++..+||||+++++|+|++.. +|| ++ 
T Consensus       272 ~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~-  342 (357)
T TIGR03158       272 GERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS-  342 (357)
T ss_pred             CCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC-
Confidence            5789999999999999999998764  567889999999988754      378999999999999999976 555 45 


Q ss_pred             CCCHHHHHHhhcccc
Q psy15610        186 PSDVEEYVHRIGRTG  200 (237)
Q Consensus       186 p~s~~~~~Q~~GR~~  200 (237)
                      |.+.+.|+||+||+|
T Consensus       343 p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       343 ARDAAAFWQRLGRLG  357 (357)
T ss_pred             CCCHHHHhhhcccCC
Confidence            889999999999987

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.

>KOG0922|consensus

Probab=99.48  E-value=1.9e-13  Score=119.81  Aligned_cols=208  Identities=16%  Similarity=0.263  Sum_probs=149.5

Q ss_pred             HhhcceeEEEeeccCCCCCceeE-EEEeechhHH----HHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhh--
Q psy15610          6 FLYRYIFLAIGRVGSTSENITQR-IAWVDEQDKR----SCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHH--   78 (237)
Q Consensus         6 ~l~~~~~i~~~~~~~~~~~i~~~-~~~~~~~~k~----~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~--   78 (237)
                      ||+|-+.+   +|......++++ +++++|.+-+    +.|+.+|++..  +-.+++++|+.|+|.+ ++.+.++|..  
T Consensus       145 ymTDG~LL---RE~l~Dp~LskYsvIIlDEAHERsl~TDiLlGlLKki~--~~R~~LklIimSATld-a~kfS~yF~~a~  218 (674)
T KOG0922|consen  145 YMTDGMLL---REILKDPLLSKYSVIILDEAHERSLHTDILLGLLKKIL--KKRPDLKLIIMSATLD-AEKFSEYFNNAP  218 (674)
T ss_pred             EecchHHH---HHHhcCCccccccEEEEechhhhhhHHHHHHHHHHHHH--hcCCCceEEEEeeeec-HHHHHHHhcCCc
Confidence            44444444   244444556666 5677776543    45555555432  2246789999999987 6677777755  


Q ss_pred             ------cCCCceeecCCc-chhhHHHHhhhhh---hccCCceEEEEeecccchHHHHHHHhhC----C--C--ceEEEeC
Q psy15610         79 ------HGYPVTSIHGDR-TQKEREEAQQYTL---ISCDEALTLVFVETKKGADQLEDFLHHH----G--Y--PVTSIHG  140 (237)
Q Consensus        79 ------~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~iIF~~t~~~~~~l~~~L~~~----~--~--~~~~~h~  140 (237)
                            ..|++..+...- ...+........+   ...+.+.++||...+++.+.+.+.|.+.    +  .  -+..+||
T Consensus       219 i~~i~GR~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~  298 (674)
T KOG0922|consen  219 ILTIPGRTFPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYG  298 (674)
T ss_pred             eEeecCCCCceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecc
Confidence                  556776555442 3333333322222   2366778999999999998888888654    1  1  2568999


Q ss_pred             CCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec------------------CCCCHHHHHHhhcccccC
Q psy15610        141 DRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD------------------LPSDVEEYVHRIGRTGRM  202 (237)
Q Consensus       141 ~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~------------------~p~s~~~~~Q~~GR~~R~  202 (237)
                      +++.++..++++.-..|.-+|+++|++++..+.++.+.+||..+                  .|.|..+-.||.|||||.
T Consensus       299 aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt  378 (674)
T KOG0922|consen  299 ALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRT  378 (674)
T ss_pred             cCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCC
Confidence            99999999999888889999999999999999999999999633                  256889999999999999


Q ss_pred             CCCCceEEeecCCCCCCC
Q psy15610        203 GNLDFPFSYNQPGYGGSY  220 (237)
Q Consensus       203 g~~~~~~~~~~~~~~~~~  220 (237)
                      | +|.||-+++..+-+.+
T Consensus       379 ~-pGkcyRLYte~~~~~~  395 (674)
T KOG0922|consen  379 G-PGKCYRLYTESAYDKM  395 (674)
T ss_pred             C-CceEEEeeeHHHHhhc
Confidence            7 9999999987665433

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

Probab=99.48  E-value=4.8e-13  Score=124.17  Aligned_cols=112  Identities=20%  Similarity=0.326  Sum_probs=103.3

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEe
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      ..++++-...|..+..+.+++.|...  ..++.+.||-|++.+-+.++..|.+|.++|||||.+.+.|+|+|+++.+|.-
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            45789888899999999999999987  6789999999999999999999999999999999999999999999999987


Q ss_pred             cCCC-CHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        184 DLPS-DVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       184 ~~p~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +... ..++++|..||+||....+.||+++.+.+.
T Consensus       881 ~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~k~  915 (1139)
T COG1197         881 RADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQKA  915 (1139)
T ss_pred             ccccccHHHHHHhccccCCccceEEEEEeecCccc
Confidence            7764 899999999999999999999999987554

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.47  E-value=6.8e-13  Score=121.20  Aligned_cols=108  Identities=23%  Similarity=0.242  Sum_probs=100.5

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC----------
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV----------  177 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~----------  177 (237)
                      +.++||||+|...++.++..|...+++...+|+.  +.+|+..+..|+.+...|+|||++++||+|++--          
T Consensus       430 grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~  507 (830)
T PRK12904        430 GQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAAL  507 (830)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhh
Confidence            6899999999999999999999999999999995  7899999999999999999999999999999763          


Q ss_pred             ----------------------------cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        178 ----------------------------KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       178 ----------------------------~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                                                  -+||....|.|...-.|-.||+||.|.+|.+-+|++..+.
T Consensus       508 ~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~lSleD~  575 (830)
T PRK12904        508 LEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  575 (830)
T ss_pred             hhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEEEEcCcH
Confidence                                        3688888999999999999999999999999999997765

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

Probab=99.47  E-value=5.2e-13  Score=116.56  Aligned_cols=94  Identities=30%  Similarity=0.509  Sum_probs=90.6

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLP  186 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p  186 (237)
                      .+.+++|||.+..+++.++..+...+. +..+.++.+..+|+.+++.|+.|.+++|+++.++.+|+|+|+++++|...+.
T Consensus       282 ~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t  360 (442)
T COG1061         282 RGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPT  360 (442)
T ss_pred             CCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEEEEeCCC
Confidence            467999999999999999999988877 8899999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHhhccccc
Q psy15610        187 SDVEEYVHRIGRTGR  201 (237)
Q Consensus       187 ~s~~~~~Q~~GR~~R  201 (237)
                      .|+..|.||+||..|
T Consensus       361 ~S~~~~~Q~lGR~LR  375 (442)
T COG1061         361 GSRRLFIQRLGRGLR  375 (442)
T ss_pred             CcHHHHHHHhhhhcc
Confidence            999999999999999

>KOG0950|consensus

Probab=99.47  E-value=6e-13  Score=120.49  Aligned_cols=164  Identities=25%  Similarity=0.321  Sum_probs=121.3

Q ss_pred             cceeEEeecccchhhHHHHhhhcCCC----ceee-----------cCCcchhhHHHHhh----------------hhhhc
Q psy15610         57 ALTLVFVETKKGADQLEDFLHHHGYP----VTSI-----------HGDRTQKEREEAQQ----------------YTLIS  105 (237)
Q Consensus        57 ~~~i~f~~t~~~~~~~~~~l~~~~~~----~~~~-----------~~~~~~~~~~~~~~----------------~~~~~  105 (237)
                      .++|.+|+|.++++.+..||..--+.    .+.+           .....+..++....                +....
T Consensus       378 ~~iIGMSATi~N~~lL~~~L~A~~y~t~fRPv~L~E~ik~G~~i~~~~r~~~lr~ia~l~~~~~g~~dpD~~v~L~tet~  457 (1008)
T KOG0950|consen  378 VQIIGMSATIPNNSLLQDWLDAFVYTTRFRPVPLKEYIKPGSLIYESSRNKVLREIANLYSSNLGDEDPDHLVGLCTETA  457 (1008)
T ss_pred             eeEeeeecccCChHHHHHHhhhhheecccCcccchhccCCCcccccchhhHHHHHhhhhhhhhcccCCCcceeeehhhhh
Confidence            67999999999999999999743221    1111           11112222222210                11223


Q ss_pred             cCCceEEEEeecccchHHHHHHHhhC--------------------------------------CCceEEEeCCCCHHHH
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHH--------------------------------------GYPVTSIHGDRTQKER  147 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~--------------------------------------~~~~~~~h~~~~~~~r  147 (237)
                      ..+.++||||++++.|+.++..+...                                      ...++++|+|++.++|
T Consensus       458 ~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER  537 (1008)
T KOG0950|consen  458 PEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEER  537 (1008)
T ss_pred             hcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchH
Confidence            34667999999999998875443210                                      1358999999999999


Q ss_pred             HHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC----CCCHHHHHHhhcccccCC--CCCceEEeecCCCCCCC
Q psy15610        148 EEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL----PSDVEEYVHRIGRTGRMG--NLDFPFSYNQPGYGGSY  220 (237)
Q Consensus       148 ~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~----p~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~~~~~  220 (237)
                      ..+...|++|.+.|+++|+.+..|+|+|...+++-+.+    ..+.-.|.||+|||||.|  ..|.+++++.+.+...+
T Consensus       538 ~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e~~~~  616 (1008)
T KOG0950|consen  538 EIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSEKKRV  616 (1008)
T ss_pred             HHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccchhHH
Confidence            99999999999999999999999999999998886432    347889999999999987  56889999998886433

>PRK09694 helicase Cas3; Provisional

Probab=99.47  E-value=2.2e-12  Score=119.70  Aligned_cols=96  Identities=25%  Similarity=0.349  Sum_probs=82.8

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCC---CceEEEeCCCCHHHHH----HHHHHh-hcCC---CCEEEEcCccccccCC
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHG---YPVTSIHGDRTQKERE----EALRRF-RSGE---TPILVATAVAARGLDI  174 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~---~~~~~~h~~~~~~~r~----~~~~~f-~~g~---~~vlv~T~~~~~Gvdl  174 (237)
                      .++.+++|||||.+.++.+++.|.+..   ..+..+||.++..+|.    ++++.| ++|.   ..|||+|+++++|+|+
T Consensus       558 ~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI  637 (878)
T PRK09694        558 NAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL  637 (878)
T ss_pred             hcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec
Confidence            457789999999999999999998764   5799999999999994    456677 5565   4699999999999999


Q ss_pred             CCCcEEEEecCCCCHHHHHHhhcccccCCC
Q psy15610        175 PHVKHVINFDLPSDVEEYVHRIGRTGRMGN  204 (237)
Q Consensus       175 ~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~  204 (237)
                       +.+++|....|  ...++||+||++|.+.
T Consensus       638 -d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        638 -DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             -CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence             57988887778  7899999999999875

>TIGR01054 rgy reverse gyrase

Probab=99.46  E-value=6.8e-13  Score=126.89  Aligned_cols=76  Identities=26%  Similarity=0.583  Sum_probs=70.7

Q ss_pred             CceEEEEeecc---cchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEE----cCccccccCCCC-CcE
Q psy15610        108 EALTLVFVETK---KGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVA----TAVAARGLDIPH-VKH  179 (237)
Q Consensus       108 ~~~~iIF~~t~---~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~----T~~~~~Gvdl~~-~~~  179 (237)
                      +.++||||+++   +.++.++..|.+.|+++..+||+++.    ..++.|++|+++|||+    |+++++|+|+|+ +++
T Consensus       326 ~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~  401 (1171)
T TIGR01054       326 GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRY  401 (1171)
T ss_pred             CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHHHHHHcCCCCEEEEeccccCcccccCCCCccccE
Confidence            36799999999   99999999999999999999999973    6899999999999999    489999999999 899


Q ss_pred             EEEecCCC
Q psy15610        180 VINFDLPS  187 (237)
Q Consensus       180 Vi~~~~p~  187 (237)
                      ||+|++|.
T Consensus       402 vI~~~~P~  409 (1171)
T TIGR01054       402 AVFLGVPK  409 (1171)
T ss_pred             EEEECCCC
Confidence            99999996

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.

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.45  E-value=9.8e-13  Score=120.48  Aligned_cols=108  Identities=20%  Similarity=0.185  Sum_probs=100.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC----------
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV----------  177 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~----------  177 (237)
                      +.++||||.|.+.++.++.+|.+.|++..++|+.+.+.+++.+.++|+.|  .|+|||+++++|+|+.--          
T Consensus       444 g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G--~VtIATNmAGRGtDI~Lggn~~~~~~~~  521 (896)
T PRK13104        444 KQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPG--AVTIATNMAGRGTDIVLGGSLAADLANL  521 (896)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCC--cEEEeccCccCCcceecCCchhhhhhcc
Confidence            78999999999999999999999999999999999999999999999999  499999999999998632          


Q ss_pred             ----------------------------cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        178 ----------------------------KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       178 ----------------------------~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                                                  -+||....+.|...-.|-.||+||.|.+|.+-+|++-.+.
T Consensus       522 ~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~  589 (896)
T PRK13104        522 PADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDN  589 (896)
T ss_pred             ccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence                                        3688888999999999999999999999999999997765

>KOG0947|consensus

Probab=99.45  E-value=5.3e-13  Score=120.67  Aligned_cols=106  Identities=25%  Similarity=0.290  Sum_probs=88.5

Q ss_pred             ceEEEEeecccchHHHHHHHhhCC---------------------------------------CceEEEeCCCCHHHHHH
Q psy15610        109 ALTLVFVETKKGADQLEDFLHHHG---------------------------------------YPVTSIHGDRTQKEREE  149 (237)
Q Consensus       109 ~~~iIF~~t~~~~~~l~~~L~~~~---------------------------------------~~~~~~h~~~~~~~r~~  149 (237)
                      -++||||-+++.|++.+++|....                                       ..++++|||.-|--++-
T Consensus       568 LP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~  647 (1248)
T KOG0947|consen  568 LPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEV  647 (1248)
T ss_pred             CceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHH
Confidence            478999999999999988886431                                       23899999999999999


Q ss_pred             HHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC--------CCCHHHHHHhhcccccCC--CCCceEEeecC
Q psy15610        150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL--------PSDVEEYVHRIGRTGRMG--NLDFPFSYNQP  214 (237)
Q Consensus       150 ~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~--------p~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~  214 (237)
                      +.-.|+.|-++||++|..+++|+|+|.-++|+..-.        -..|.+|.||+|||||-|  ..|.+++.+..
T Consensus       648 VE~LFqrGlVKVLFATETFAMGVNMPARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~  722 (1248)
T KOG0947|consen  648 VELLFQRGLVKVLFATETFAMGVNMPARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKD  722 (1248)
T ss_pred             HHHHHhcCceEEEeehhhhhhhcCCCceeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecC
Confidence            999999999999999999999999998887775221        237899999999999988  44666655543

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

Probab=99.43  E-value=1.8e-12  Score=120.49  Aligned_cols=165  Identities=22%  Similarity=0.291  Sum_probs=128.5

Q ss_pred             cccceeEEeecccchhhHHHHhhhcCCCce-eecC----------Ccc-----------hhhHHHHhhhhhhccCCceEE
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHGYPVT-SIHG----------DRT-----------QKEREEAQQYTLISCDEALTL  112 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~-~~~~----------~~~-----------~~~~~~~~~~~~~~~~~~~~i  112 (237)
                      ...++|..|+|..+..+.++-+....+... ...+          ...           +..............++-++|
T Consensus       231 ~~~q~i~~SAT~~np~e~~~~l~~~~f~~~v~~~g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~~~~~~~~~~~tL  310 (851)
T COG1205         231 SPLQIICTSATLANPGEFAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTL  310 (851)
T ss_pred             CCceEEEEeccccChHHHHHHhcCCcceeeccCCCCCCCceEEEEeCCcchhhhhhcccchHHHHHHHHHHHHHcCceEE
Confidence            567899999999999998888877777652 1111          011           111122222334455788999


Q ss_pred             EEeecccchHHHH----HHHhhCC----CceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec
Q psy15610        113 VFVETKKGADQLE----DFLHHHG----YPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       113 IF~~t~~~~~~l~----~~L~~~~----~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      +|+.++..++.+.    ..+...+    ..+..+++++.+++|.++.+.|++|++.++++|.+++.|+|+..++.||.++
T Consensus       311 ~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ldavi~~g  390 (851)
T COG1205         311 VFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYG  390 (851)
T ss_pred             EEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehhhhhHhhcC
Confidence            9999999999986    3333334    5789999999999999999999999999999999999999999999999999


Q ss_pred             CCC-CHHHHHHhhcccccCCCCCceEEeecCCCCCC
Q psy15610        185 LPS-DVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGS  219 (237)
Q Consensus       185 ~p~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~  219 (237)
                      .|. +..++.|+.||+||.++.+..+........+.
T Consensus       391 ~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~d~  426 (851)
T COG1205         391 YPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPLDS  426 (851)
T ss_pred             CCCchHHHHHHhhhhccCCCCCceEEEEeCCCccch
Confidence            999 89999999999999997777666666444433

>KOG0384|consensus

Probab=99.42  E-value=3.1e-13  Score=124.74  Aligned_cols=109  Identities=20%  Similarity=0.376  Sum_probs=100.0

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC---CCCEEEEcCccccccCCCCCcEEEEe
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG---ETPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g---~~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      +++++|||..-+...+.+++||...++++-.+.|++..+.|.+.++.|.+.   .+..|+||.+++.|||+..++.||.|
T Consensus       698 ~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLatADTVIIF  777 (1373)
T KOG0384|consen  698 GGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLATADTVIIF  777 (1373)
T ss_pred             CCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccccceEEEe
Confidence            479999999999999999999999999999999999999999999999865   46689999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCc--eEEeecCC
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDF--PFSYNQPG  215 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~--~~~~~~~~  215 (237)
                      |..|+|+.-+|..-||+|+||...  +|-|++.+
T Consensus       778 DSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~  811 (1373)
T KOG0384|consen  778 DSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKN  811 (1373)
T ss_pred             CCCCCcchHHHHHHHHHhhcccceEEEEEEecCC
Confidence            999999999999999999998865  45555543

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.40  E-value=2.8e-12  Score=117.29  Aligned_cols=108  Identities=20%  Similarity=0.212  Sum_probs=100.9

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC----------
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV----------  177 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~----------  177 (237)
                      +.++||||.|...++.++.+|...+++...+|+.++..+++.+.++|+.|.  |+|||+++++|.|+.--          
T Consensus       449 GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~  526 (908)
T PRK13107        449 GQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEAL  526 (908)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhh
Confidence            789999999999999999999999999999999999999999999999988  99999999999998632          


Q ss_pred             ---------------------------cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        178 ---------------------------KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       178 ---------------------------~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                                                 -+||....+.|...-.|-.||+||.|.+|...+|++..+.
T Consensus       527 ~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        527 ENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             cchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCcH
Confidence                                       3688899999999999999999999999999999997776

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

Probab=99.37  E-value=3.6e-12  Score=117.00  Aligned_cols=185  Identities=18%  Similarity=0.308  Sum_probs=135.6

Q ss_pred             EEEeechhHH----HHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhh--------cCCCceeec-CCcchhhH
Q psy15610         29 IAWVDEQDKR----SCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHH--------HGYPVTSIH-GDRTQKER   95 (237)
Q Consensus        29 ~~~~~~~~k~----~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~--------~~~~~~~~~-~~~~~~~~   95 (237)
                      .++++|-+-.    +.++.++.... ....+++++|++|+|... +.++++|..        ..|++.... .......+
T Consensus       165 ~vIiDEaHERSl~tDilLgllk~~~-~~rr~DLKiIimSATld~-~rfs~~f~~apvi~i~GR~fPVei~Y~~~~~~d~~  242 (845)
T COG1643         165 VVIIDEAHERSLNTDILLGLLKDLL-ARRRDDLKLIIMSATLDA-ERFSAYFGNAPVIEIEGRTYPVEIRYLPEAEADYI  242 (845)
T ss_pred             EEEEcchhhhhHHHHHHHHHHHHHH-hhcCCCceEEEEecccCH-HHHHHHcCCCCEEEecCCccceEEEecCCCCcchh
Confidence            3456664433    34444443321 223557999999999874 567777763        557776665 33322221


Q ss_pred             --HHHhh--hhhhccCCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc
Q psy15610         96 --EEAQQ--YTLISCDEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV  167 (237)
Q Consensus        96 --~~~~~--~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~  167 (237)
                        .....  ........+.++||.+-....+...+.|++    ....+..+||.++.++..++++.-..|.-+|+++|++
T Consensus       243 l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNI  322 (845)
T COG1643         243 LLDAIVAAVDIHLREGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNI  322 (845)
T ss_pred             HHHHHHHHHHHhccCCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccc
Confidence              11111  222345578999999999999999999987    3477899999999999999888888887779999999


Q ss_pred             cccccCCCCCcEEEEec------------------CCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        168 AARGLDIPHVKHVINFD------------------LPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       168 ~~~Gvdl~~~~~Vi~~~------------------~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      ++.++.+|++.+||..+                  .|.|..+..||.|||||.+ +|.||-+|+..+
T Consensus       323 AETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~-pGicyRLyse~~  388 (845)
T COG1643         323 AETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTG-PGICYRLYSEED  388 (845)
T ss_pred             cccceeeCCeEEEecCCcccccccccccCceeeeEEEechhhhhhhccccccCC-CceEEEecCHHH
Confidence            99999999999999733                  2558889999999999996 999999998643

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

Probab=99.37  E-value=1.3e-11  Score=105.97  Aligned_cols=157  Identities=24%  Similarity=0.311  Sum_probs=122.5

Q ss_pred             ccceeEEeecccchh-hHHH-Hh-----hhcCC--CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHH
Q psy15610         56 EALTLVFVETKKGAD-QLED-FL-----HHHGY--PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLED  126 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~-~~~~-~l-----~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~  126 (237)
                      -.++|..|+|+...| +.+. .+     +..|.  +...+.+...|.. +....+......+.+++|-+-|.+.++.+.+
T Consensus       386 ~~q~i~VSATPg~~E~e~s~~~vveQiIRPTGLlDP~ievRp~~~Qvd-DL~~EI~~r~~~~eRvLVTtLTKkmAEdLT~  464 (663)
T COG0556         386 IPQTIYVSATPGDYELEQSGGNVVEQIIRPTGLLDPEIEVRPTKGQVD-DLLSEIRKRVAKNERVLVTTLTKKMAEDLTE  464 (663)
T ss_pred             cCCEEEEECCCChHHHHhccCceeEEeecCCCCCCCceeeecCCCcHH-HHHHHHHHHHhcCCeEEEEeehHHHHHHHHH
Confidence            477899999998854 2221 11     22222  3333333333332 2222233334556899999999999999999


Q ss_pred             HHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC-----CHHHHHHhhccccc
Q psy15610        127 FLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS-----DVEEYVHRIGRTGR  201 (237)
Q Consensus       127 ~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~-----s~~~~~Q~~GR~~R  201 (237)
                      +|.+.|+++..+|++...-+|..+++.++.|.++|||.-+.+-+|+|+|.+..|..+|..+     |-.+++|-+|||.|
T Consensus       465 Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAAR  544 (663)
T COG0556         465 YLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAAR  544 (663)
T ss_pred             HHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999999999999999999888654     88999999999999


Q ss_pred             CCCCCceEEeecC
Q psy15610        202 MGNLDFPFSYNQP  214 (237)
Q Consensus       202 ~g~~~~~~~~~~~  214 (237)
                      -- .|.++.|.+.
T Consensus       545 N~-~GkvIlYAD~  556 (663)
T COG0556         545 NV-NGKVILYADK  556 (663)
T ss_pred             cc-CCeEEEEchh
Confidence            73 7888888753

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

Probab=99.35  E-value=5.8e-12  Score=102.79  Aligned_cols=110  Identities=20%  Similarity=0.334  Sum_probs=88.9

Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEE-
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI-  181 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi-  181 (237)
                      ...+.+++||.++.+..+.+++.|+..  ...+..+|+.  ...|....++|++|.+++||+|.++++|+.+|++++.+ 
T Consensus       302 ~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vl  379 (441)
T COG4098         302 RKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVL  379 (441)
T ss_pred             HhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEe
Confidence            445789999999999999999999543  3456788874  45688889999999999999999999999999999854 


Q ss_pred             EecCC-CCHHHHHHhhcccccCCC--CCceEEeecCCC
Q psy15610        182 NFDLP-SDVEEYVHRIGRTGRMGN--LDFPFSYNQPGY  216 (237)
Q Consensus       182 ~~~~p-~s~~~~~Q~~GR~~R~g~--~~~~~~~~~~~~  216 (237)
                      ....+ .+.+.++|.+||+||.-.  .|.+++|.....
T Consensus       380 gaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~G~s  417 (441)
T COG4098         380 GAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYGKS  417 (441)
T ss_pred             cCCcccccHHHHHHHhhhccCCCcCCCCcEEEEeccch
Confidence            44443 488999999999999542  477777765443

>KOG0923|consensus

Probab=99.32  E-value=1.2e-11  Score=108.39  Aligned_cols=183  Identities=21%  Similarity=0.278  Sum_probs=136.8

Q ss_pred             EEEeechhHHHHHHHhhcCchhh--hcccccceeEEeecccchhhHHHHhhh--------cCCCceeecCCcc-hhhHHH
Q psy15610         29 IAWVDEQDKRSCLLDLLSSPSQE--ELGDEALTLVFVETKKGADQLEDFLHH--------HGYPVTSIHGDRT-QKEREE   97 (237)
Q Consensus        29 ~~~~~~~~k~~~l~~ll~~~~~~--~~~~~~~~i~f~~t~~~~~~~~~~l~~--------~~~~~~~~~~~~~-~~~~~~   97 (237)
                      ++++++.+-...-.++|-.....  ...++++.++-|+|.+ ++++..+|..        ..+++..+...-. -.+...
T Consensus       381 ViiiDEAHERTL~TDILfgLvKDIar~RpdLKllIsSAT~D-AekFS~fFDdapIF~iPGRRyPVdi~Yt~~PEAdYldA  459 (902)
T KOG0923|consen  381 VIIVDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMD-AEKFSAFFDDAPIFRIPGRRYPVDIFYTKAPEADYLDA  459 (902)
T ss_pred             EEEeehhhhhhhhhhHHHHHHHHHHhhCCcceEEeeccccC-HHHHHHhccCCcEEeccCcccceeeecccCCchhHHHH
Confidence            67788877665555555444322  2357888999999876 5677777743        3456655544333 333333


Q ss_pred             Hhhhhh---hccCCceEEEEeecccchHHHHHHHhhC---------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEc
Q psy15610         98 AQQYTL---ISCDEALTLVFVETKKGADQLEDFLHHH---------GYPVTSIHGDRTQKEREEALRRFRSGETPILVAT  165 (237)
Q Consensus        98 ~~~~~~---~~~~~~~~iIF~~t~~~~~~l~~~L~~~---------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T  165 (237)
                      ++.-++   ...+.+.+|||..-.+..+.+.+.|..+         .+-+..+|+.+|.+...++++.--+|--+|+++|
T Consensus       460 ai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLAT  539 (902)
T KOG0923|consen  460 AIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLAT  539 (902)
T ss_pred             HHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEee
Confidence            333222   2445688999999999888887777643         3457899999999999999999999999999999


Q ss_pred             CccccccCCCCCcEEEEec------------------CCCCHHHHHHhhcccccCCCCCceEEeec
Q psy15610        166 AVAARGLDIPHVKHVINFD------------------LPSDVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       166 ~~~~~Gvdl~~~~~Vi~~~------------------~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      ++++..+.++++.+||.-+                  .|.|..+-.||+|||||.| +|+|+-++.
T Consensus       540 NIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt  604 (902)
T KOG0923|consen  540 NIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYT  604 (902)
T ss_pred             cchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeec
Confidence            9999999999999999633                  2668888999999999998 999999988

>KOG0391|consensus

Probab=99.30  E-value=1.1e-11  Score=114.04  Aligned_cols=107  Identities=21%  Similarity=0.352  Sum_probs=97.7

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC--CCEEEEcCccccccCCCCCcEEEEecC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE--TPILVATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~--~~vlv~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      +++++||+.-.+..+-++.+|+.+|+-+..+.|...-++|+...++|+.+.  +..+++|...+.|||+..+|.||+||.
T Consensus      1276 ghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggvGiNLtgADTVvFYDs 1355 (1958)
T KOG0391|consen 1276 GHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGVGINLTGADTVVFYDS 1355 (1958)
T ss_pred             CceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCccccccccCceEEEecC
Confidence            689999999999999999999999999999999999999999999999875  456788999999999999999999999


Q ss_pred             CCCHHHHHHhhcccccCCCCCce--EEeecC
Q psy15610        186 PSDVEEYVHRIGRTGRMGNLDFP--FSYNQP  214 (237)
Q Consensus       186 p~s~~~~~Q~~GR~~R~g~~~~~--~~~~~~  214 (237)
                      +|++..-.|.-.|++|+|+...+  |-|++.
T Consensus      1356 DwNPtMDaQAQDrChRIGqtRDVHIYRLISe 1386 (1958)
T KOG0391|consen 1356 DWNPTMDAQAQDRCHRIGQTRDVHIYRLISE 1386 (1958)
T ss_pred             CCCchhhhHHHHHHHhhcCccceEEEEeecc
Confidence            99999999999999999987654  444443

>TIGR00595 priA primosomal protein N'

Probab=99.29  E-value=1.1e-11  Score=109.76  Aligned_cols=159  Identities=20%  Similarity=0.243  Sum_probs=105.0

Q ss_pred             ccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh---hhhh-----ccCCceEEEEeecccchHHHH
Q psy15610         54 GDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ---YTLI-----SCDEALTLVFVETKKGADQLE  125 (237)
Q Consensus        54 ~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-----~~~~~~~iIF~~t~~~~~~l~  125 (237)
                      ..+.++|+|++++.....+...-...-..|......+.-........   +...     ..+....--+.....-.+.++
T Consensus       196 ~~g~qvLvflnrrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~  275 (505)
T TIGR00595       196 AAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVE  275 (505)
T ss_pred             HcCCcEEEEEeCCcCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHH
Confidence            44568999999988765555444444444444444433221111110   0000     000000101222223457777


Q ss_pred             HHHhhC--CCceEEEeCCCCHHHH--HHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC------------CH
Q psy15610        126 DFLHHH--GYPVTSIHGDRTQKER--EEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS------------DV  189 (237)
Q Consensus       126 ~~L~~~--~~~~~~~h~~~~~~~r--~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~------------s~  189 (237)
                      +.|.+.  +.++..+|++++...+  +.+++.|++|+++|||+|+++++|+|+|++++|+.++.+.            ..
T Consensus       276 e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~  355 (505)
T TIGR00595       276 EELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGF  355 (505)
T ss_pred             HHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHH
Confidence            777765  7889999999987766  8899999999999999999999999999999886544431            24


Q ss_pred             HHHHHhhcccccCCCCCceEEee
Q psy15610        190 EEYVHRIGRTGRMGNLDFPFSYN  212 (237)
Q Consensus       190 ~~~~Q~~GR~~R~g~~~~~~~~~  212 (237)
                      +.|+|++||+||.+..|.+++..
T Consensus       356 ~ll~q~~GRagR~~~~g~viiqt  378 (505)
T TIGR00595       356 QLLTQVAGRAGRAEDPGQVIIQT  378 (505)
T ss_pred             HHHHHHHhccCCCCCCCEEEEEe
Confidence            67899999999999888887543

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).

>KOG0387|consensus

Probab=99.28  E-value=1.1e-11  Score=110.49  Aligned_cols=105  Identities=26%  Similarity=0.379  Sum_probs=96.3

Q ss_pred             CCceEEEEeecccchHHHHHHHh-hCCCceEEEeCCCCHHHHHHHHHHhhcCCC-C-EEEEcCccccccCCCCCcEEEEe
Q psy15610        107 DEALTLVFVETKKGADQLEDFLH-HHGYPVTSIHGDRTQKEREEALRRFRSGET-P-ILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~-~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~-~-vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      .+.+++.|..++...+.++.+|. ..++.+..+.|..+...|..+++.|+++.. . .|++|.+++.|+|+..++.||.|
T Consensus       545 qg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTrvGGLGlNLTgAnRVIIf  624 (923)
T KOG0387|consen  545 QGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTRVGGLGLNLTGANRVIIF  624 (923)
T ss_pred             CCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEecccccccccccCceEEEE
Confidence            36799999999999999999999 589999999999999999999999998763 3 56889999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEe
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSY  211 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~  211 (237)
                      |+.|+|+.-.|..-||-|+|++..+.+|
T Consensus       625 DPdWNPStD~QAreRawRiGQkkdV~VY  652 (923)
T KOG0387|consen  625 DPDWNPSTDNQARERAWRIGQKKDVVVY  652 (923)
T ss_pred             CCCCCCccchHHHHHHHhhcCccceEEE
Confidence            9999999999999999999998776554

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

Probab=99.28  E-value=2.4e-11  Score=115.79  Aligned_cols=95  Identities=24%  Similarity=0.411  Sum_probs=82.3

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC------C---CceEEEeCCCCHHHHHHHHHHhhcCCC-CEEEEcCccccccCCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH------G---YPVTSIHGDRTQKEREEALRRFRSGET-PILVATAVAARGLDIPH  176 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~------~---~~~~~~h~~~~~~~r~~~~~~f~~g~~-~vlv~T~~~~~Gvdl~~  176 (237)
                      ...++||||.+.++|+.+.+.|.+.      +   ..+..++|+++  ++..+++.|+++.. .|+|+++++.+|+|+|.
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            3479999999999999998887642      2   24567888875  46789999999886 58999999999999999


Q ss_pred             CcEEEEecCCCCHHHHHHhhcccccCC
Q psy15610        177 VKHVINFDLPSDVEEYVHRIGRTGRMG  203 (237)
Q Consensus       177 ~~~Vi~~~~p~s~~~~~Q~~GR~~R~g  203 (237)
                      +.+||++.++.|...|.||+||+.|..
T Consensus       775 v~~vVf~rpvkS~~lf~QmIGRgtR~~  801 (1123)
T PRK11448        775 ICNLVFLRRVRSRILYEQMLGRATRLC  801 (1123)
T ss_pred             ccEEEEecCCCCHHHHHHHHhhhccCC
Confidence            999999999999999999999999964

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.26  E-value=2.6e-11  Score=110.98  Aligned_cols=163  Identities=21%  Similarity=0.192  Sum_probs=112.8

Q ss_pred             cccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh---hhh-----hccCCceEEEEeecccchHHH
Q psy15610         53 LGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ---YTL-----ISCDEALTLVFVETKKGADQL  124 (237)
Q Consensus        53 ~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~---~~~-----~~~~~~~~iIF~~t~~~~~~l  124 (237)
                      +..+.++++|++++.....+...-...-..|......+.-........   +..     ..++......|......++.+
T Consensus       363 l~~g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~  442 (679)
T PRK05580        363 LERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERL  442 (679)
T ss_pred             HHcCCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHH
Confidence            345668999999988765555555554444444443332111100000   000     001112223466667788889


Q ss_pred             HHHHhhC--CCceEEEeCCCC--HHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCC--CC----------
Q psy15610        125 EDFLHHH--GYPVTSIHGDRT--QKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLP--SD----------  188 (237)
Q Consensus       125 ~~~L~~~--~~~~~~~h~~~~--~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p--~s----------  188 (237)
                      ++.|.+.  +.++..+|++++  ..+++++++.|++|+.+|||+|+++++|+|+|+++.|+.++.+  .+          
T Consensus       443 ~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra~Er~  522 (679)
T PRK05580        443 EEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERT  522 (679)
T ss_pred             HHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccchHHHH
Confidence            9999875  789999999987  4679999999999999999999999999999999998665543  22          


Q ss_pred             HHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        189 VEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       189 ~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      ...|+|++||+||.+..|.+++.....
T Consensus       523 ~~~l~q~~GRagR~~~~g~viiqT~~p  549 (679)
T PRK05580        523 FQLLTQVAGRAGRAEKPGEVLIQTYHP  549 (679)
T ss_pred             HHHHHHHHhhccCCCCCCEEEEEeCCC
Confidence            367999999999999999888665443

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.23  E-value=1.9e-10  Score=106.34  Aligned_cols=160  Identities=26%  Similarity=0.281  Sum_probs=113.4

Q ss_pred             cccceeEEeecccc--hhhHHHHhhhcCCCcee-------ecCCcchh----hHHH-----HhhhhhhccCCceEEEEee
Q psy15610         55 DEALTLVFVETKKG--ADQLEDFLHHHGYPVTS-------IHGDRTQK----EREE-----AQQYTLISCDEALTLVFVE  116 (237)
Q Consensus        55 ~~~~~i~f~~t~~~--~~~~~~~l~~~~~~~~~-------~~~~~~~~----~~~~-----~~~~~~~~~~~~~~iIF~~  116 (237)
                      .+.++|+.++|.+.  .+.+-..+...+.....       -.....+.    ....     ..........+.+++|.||
T Consensus       369 ~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kvlvI~N  448 (733)
T COG1203         369 AGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELISEEVKEGKKVLVIVN  448 (733)
T ss_pred             CCCCEEEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhhhhhHhhhhcchhhhccCCcEEEEEe
Confidence            47889999999998  33455555444332221       01111111    1111     1111223456789999999


Q ss_pred             cccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhh----cCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHH
Q psy15610        117 TKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFR----SGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEY  192 (237)
Q Consensus       117 t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~----~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~  192 (237)
                      |+..|..+++.|+..+..+..+||.++..+|...++.+.    .+...|+|+|.+.+.|+|+. .+++|-=-.|  ...+
T Consensus       449 TV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-fd~mITe~aP--idSL  525 (733)
T COG1203         449 TVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-FDVLITELAP--IDSL  525 (733)
T ss_pred             cHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-cCeeeecCCC--HHHH
Confidence            999999999999998767999999999999999988655    45778999999999999985 6666554344  8999


Q ss_pred             HHhhcccccCC--CCCceEEeecCCCC
Q psy15610        193 VHRIGRTGRMG--NLDFPFSYNQPGYG  217 (237)
Q Consensus       193 ~Q~~GR~~R~g--~~~~~~~~~~~~~~  217 (237)
                      +||+||++|-|  ..|..+++......
T Consensus       526 IQR~GRv~R~g~~~~~~~~v~~~~~~~  552 (733)
T COG1203         526 IQRAGRVNRHGKKENGKIYVYNDEERG  552 (733)
T ss_pred             HHHHHHHhhcccccCCceeEeecccCC
Confidence            99999999999  55666666554444

>KOG0388|consensus

Probab=99.21  E-value=2.5e-11  Score=107.14  Aligned_cols=104  Identities=20%  Similarity=0.374  Sum_probs=96.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC-CCEEEEcCccccccCCCCCcEEEEecCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE-TPILVATAVAARGLDIPHVKHVINFDLP  186 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p  186 (237)
                      ++++++|..-.+..+.+++||...++....+.|+....+|..+++.|+... +-.|++|.+++.|+|+..++.||+||..
T Consensus      1044 gHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLGINLTAADTViFYdSD 1123 (1185)
T KOG0388|consen 1044 GHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLGINLTAADTVIFYDSD 1123 (1185)
T ss_pred             CceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCcccccccccceEEEecCC
Confidence            789999999999999999999999999999999999999999999999855 4567899999999999999999999999


Q ss_pred             CCHHHHHHhhcccccCCCCCceEEe
Q psy15610        187 SDVEEYVHRIGRTGRMGNLDFPFSY  211 (237)
Q Consensus       187 ~s~~~~~Q~~GR~~R~g~~~~~~~~  211 (237)
                      |+|..-.|.+.||+|.|+...+-+|
T Consensus      1124 WNPT~D~QAMDRAHRLGQTrdvtvy 1148 (1185)
T KOG0388|consen 1124 WNPTADQQAMDRAHRLGQTRDVTVY 1148 (1185)
T ss_pred             CCcchhhHHHHHHHhccCccceeee
Confidence            9999999999999999988665443

>KOG0390|consensus

Probab=99.15  E-value=2.8e-10  Score=103.10  Aligned_cols=103  Identities=20%  Similarity=0.366  Sum_probs=86.4

Q ss_pred             EEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC---EEEEcCccccccCCCCCcEEEEecCCC
Q psy15610        111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP---ILVATAVAARGLDIPHVKHVINFDLPS  187 (237)
Q Consensus       111 ~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~---vlv~T~~~~~Gvdl~~~~~Vi~~~~p~  187 (237)
                      +.+..|-....+.++....-.|+.+..+||.|+..+|+++++.|++....   .|.+|.+++.|+|+-.++.||.+|++|
T Consensus       598 ~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dW  677 (776)
T KOG0390|consen  598 SVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDW  677 (776)
T ss_pred             EEEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCC
Confidence            33334444556666666666799999999999999999999999975433   567789999999999999999999999


Q ss_pred             CHHHHHHhhcccccCCCCCceEEeec
Q psy15610        188 DVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       188 s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      +|+.-.|++.||-|.||...|++|--
T Consensus       678 NPa~d~QAmaR~~RdGQKk~v~iYrL  703 (776)
T KOG0390|consen  678 NPAVDQQAMARAWRDGQKKPVYIYRL  703 (776)
T ss_pred             CchhHHHHHHHhccCCCcceEEEEEe
Confidence            99999999999999999988877643

>KOG0389|consensus

Probab=99.13  E-value=1.9e-10  Score=102.63  Aligned_cols=108  Identities=19%  Similarity=0.286  Sum_probs=97.6

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC--CCEEEEcCccccccCCCCCcEEEEecC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE--TPILVATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~--~~vlv~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      +.+++||.......+.++-+|..+++.+..+.|++.-.+|+.+++.|.+.+  +-.|++|.+++.|+|+..+++||.+|.
T Consensus       777 G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~  856 (941)
T KOG0389|consen  777 GDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDI  856 (941)
T ss_pred             CCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEEeec
Confidence            689999999999999999999999999999999999999999999999765  346788999999999999999999999


Q ss_pred             CCCHHHHHHhhcccccCCCCCc--eEEeecCC
Q psy15610        186 PSDVEEYVHRIGRTGRMGNLDF--PFSYNQPG  215 (237)
Q Consensus       186 p~s~~~~~Q~~GR~~R~g~~~~--~~~~~~~~  215 (237)
                      ..+|-.-.|.-.||+|.|+...  ++-+++.+
T Consensus       857 dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~  888 (941)
T KOG0389|consen  857 DFNPYDDKQAEDRCHRVGQTKPVTVYRLITKS  888 (941)
T ss_pred             CCCCcccchhHHHHHhhCCcceeEEEEEEecC
Confidence            9999999999999999997654  44555544

>KOG4150|consensus

Probab=99.12  E-value=1.5e-10  Score=100.37  Aligned_cols=179  Identities=16%  Similarity=0.202  Sum_probs=125.4

Q ss_pred             hhHHHHHHHhhcCchhhhcccccceeEEeecc-cchhhHHHHhhhcCCCceeecCC--------------cchhhH----
Q psy15610         35 QDKRSCLLDLLSSPSQEELGDEALTLVFVETK-KGADQLEDFLHHHGYPVTSIHGD--------------RTQKER----   95 (237)
Q Consensus        35 ~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~-~~~~~~~~~l~~~~~~~~~~~~~--------------~~~~~~----   95 (237)
                      ...+..|.+|+....++   -+.+++-=+++- ..+....+.++-.......+.+.              ..+..+    
T Consensus       433 ~~~~R~L~~L~~~F~~~---~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DGSPs~~K~~V~WNP~~~P~~~~~~~~  509 (1034)
T KOG4150|consen  433 QDQLRALSDLIKGFEAS---INMGVYDGDTPYKDRTRLRSELANLSELELVTIDGSPSSEKLFVLWNPSAPPTSKSEKSS  509 (1034)
T ss_pred             HHHHHHHHHHHHHHHhh---cCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecCCCCccceEEEeCCCCCCcchhhhhh
Confidence            35677788887765433   244444444443 33555555554443333222221              122222    


Q ss_pred             ---HHHhhhhhhccCCceEEEEeecccchHHHHHHHhh----CC----CceEEEeCCCCHHHHHHHHHHhhcCCCCEEEE
Q psy15610         96 ---EEAQQYTLISCDEALTLVFVETKKGADQLEDFLHH----HG----YPVTSIHGDRTQKEREEALRRFRSGETPILVA  164 (237)
Q Consensus        96 ---~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~----~~----~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~  164 (237)
                         +....+.-....+-++|-||++++.|+.+-...++    .+    -.+..|.||...++|.++.+.+=-|.+.-+|+
T Consensus       510 ~i~E~s~~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIa  589 (1034)
T KOG4150|consen  510 KVVEVSHLFAEMVQHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIA  589 (1034)
T ss_pred             HHHHHHHHHHHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEe
Confidence               11212333345678999999999999987444332    22    24678899999999999999988899999999


Q ss_pred             cCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        165 TAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       165 T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      |.+++.|+|+...+.|+..+.|.|...+.|+.|||||-..++..++.++...
T Consensus       590 TNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~P  641 (1034)
T KOG4150|consen  590 TNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGP  641 (1034)
T ss_pred             cchhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccc
Confidence            9999999999999999999999999999999999999988877766665443

>KOG0924|consensus

Probab=99.12  E-value=2.2e-10  Score=100.96  Aligned_cols=203  Identities=20%  Similarity=0.287  Sum_probs=138.2

Q ss_pred             HHhhcceeEEEeeccCCCCCceeE-EEEeechh----HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhh--
Q psy15610          5 EFLYRYIFLAIGRVGSTSENITQR-IAWVDEQD----KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLH--   77 (237)
Q Consensus         5 ~~l~~~~~i~~~~~~~~~~~i~~~-~~~~~~~~----k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~--   77 (237)
                      +||.|.+.+   +|......+.++ +++.++.+    -.+.|+.+|+...+.  ..+++.|+.++|.. +++++.+|+  
T Consensus       449 kymTDGiLL---rEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~lar--RrdlKliVtSATm~-a~kf~nfFgn~  522 (1042)
T KOG0924|consen  449 KYMTDGILL---RESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLAR--RRDLKLIVTSATMD-AQKFSNFFGNC  522 (1042)
T ss_pred             EEeccchHH---HHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHHHh--hccceEEEeecccc-HHHHHHHhCCC
Confidence            345555544   344444555555 33444433    235555555544322  34788899998875 678888887  


Q ss_pred             ------hcCCCceeecCCc-chhhHHHHhh-hhh--hccCCceEEEEeecccchHHH----HHHHhhC------CCceEE
Q psy15610         78 ------HHGYPVTSIHGDR-TQKEREEAQQ-YTL--ISCDEALTLVFVETKKGADQL----EDFLHHH------GYPVTS  137 (237)
Q Consensus        78 ------~~~~~~~~~~~~~-~~~~~~~~~~-~~~--~~~~~~~~iIF~~t~~~~~~l----~~~L~~~------~~~~~~  137 (237)
                            ...|++..++... .+.+...+.. ..-  .....+..+||..-.+..+-.    .+.|.+.      ++.+..
T Consensus       523 p~f~IpGRTyPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlp  602 (1042)
T KOG0924|consen  523 PQFTIPGRTYPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLP  602 (1042)
T ss_pred             ceeeecCCccceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEe
Confidence                  3445666555433 2333332222 111  233457799999888765544    4444332      567889


Q ss_pred             EeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC------------------CCCHHHHHHhhccc
Q psy15610        138 IHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL------------------PSDVEEYVHRIGRT  199 (237)
Q Consensus       138 ~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~------------------p~s~~~~~Q~~GR~  199 (237)
                      +++-++..-..+++..-..|.-+++|+|.+++..+.+|.+.+||..+.                  |.|...--||+|||
T Consensus       603 iYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRA  682 (1042)
T KOG0924|consen  603 IYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRA  682 (1042)
T ss_pred             ehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeeecccccccceeEEEechhccchhhcccc
Confidence            999999999998888888888899999999999999999999997442                  66778888999999


Q ss_pred             ccCCCCCceEEeecC
Q psy15610        200 GRMGNLDFPFSYNQP  214 (237)
Q Consensus       200 ~R~g~~~~~~~~~~~  214 (237)
                      ||.| +|.||-+|..
T Consensus       683 GRt~-pG~cYRlYTe  696 (1042)
T KOG0924|consen  683 GRTG-PGTCYRLYTE  696 (1042)
T ss_pred             CCCC-Ccceeeehhh
Confidence            9997 9999998875

>KOG0953|consensus

Probab=99.11  E-value=7.4e-10  Score=95.67  Aligned_cols=144  Identities=21%  Similarity=0.263  Sum_probs=101.5

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhh-HHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCc-eE
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKE-REEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYP-VT  136 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~-~~  136 (237)
                      .|..|..+..+.-+...+.-.|-.+...+=+..... ......-.+...+.+.+ |.|-+++..-.+...+.+.+.. +.
T Consensus       307 EiHLCGepsvldlV~~i~k~TGd~vev~~YeRl~pL~v~~~~~~sl~nlk~GDC-vV~FSkk~I~~~k~kIE~~g~~k~a  385 (700)
T KOG0953|consen  307 EIHLCGEPSVLDLVRKILKMTGDDVEVREYERLSPLVVEETALGSLSNLKPGDC-VVAFSKKDIFTVKKKIEKAGNHKCA  385 (700)
T ss_pred             hhhccCCchHHHHHHHHHhhcCCeeEEEeecccCcceehhhhhhhhccCCCCCe-EEEeehhhHHHHHHHHHHhcCcceE
Confidence            467787777777776666655554433322111111 11111111222233434 5677888888888888877654 99


Q ss_pred             EEeCCCCHHHHHHHHHHhhc--CCCCEEEEcCccccccCCCCCcEEEEecC---------CCCHHHHHHhhcccccCCC
Q psy15610        137 SIHGDRTQKEREEALRRFRS--GETPILVATAVAARGLDIPHVKHVINFDL---------PSDVEEYVHRIGRTGRMGN  204 (237)
Q Consensus       137 ~~h~~~~~~~r~~~~~~f~~--g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~---------p~s~~~~~Q~~GR~~R~g~  204 (237)
                      +++|++||+.|.+-...|++  ++.+|||+||+.++|+|+ +++.||+++.         |.+..+..|.+|||||.|.
T Consensus       386 VIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s  463 (700)
T KOG0953|consen  386 VIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGS  463 (700)
T ss_pred             EEecCCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhccccccc
Confidence            99999999999999999997  789999999999999998 5677777765         3368899999999999874

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

Probab=99.10  E-value=1.7e-10  Score=107.29  Aligned_cols=151  Identities=19%  Similarity=0.194  Sum_probs=102.6

Q ss_pred             cccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccch-HHHHHHHhhCCC
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA-DQLEDFLHHHGY  133 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~-~~l~~~L~~~~~  133 (237)
                      +..++|.|+-++..|++.+..+...+.....-...-   .+..+ ...+..        +..+.... -.+..+..-+..
T Consensus       378 ~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~---i~~ii-~~~i~~--------L~~ed~~lp~~~~~~~~~L~R  445 (1041)
T COG4581         378 NLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERA---IREII-DHAIGD--------LAEEDRELPLQILEISALLLR  445 (1041)
T ss_pred             cCCceEEEEEchhhHHHHHHHhcccccccCCcHHHH---HHHHH-HHHHhh--------cChhhhcCcccHHHHHHHHhh
Confidence            357899999999999999999987665443322110   11111 100111        11122212 122222222234


Q ss_pred             ceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE----ec----CCCCHHHHHHhhcccccCCCC
Q psy15610        134 PVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN----FD----LPSDVEEYVHRIGRTGRMGNL  205 (237)
Q Consensus       134 ~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~----~~----~p~s~~~~~Q~~GR~~R~g~~  205 (237)
                      .++++|+||-|..++.+...|..|..+|+++|..++.|+|+|.-++|+-    ++    ...++.+|.|+.|||||-|.+
T Consensus       446 GiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD  525 (1041)
T COG4581         446 GIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLD  525 (1041)
T ss_pred             hhhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhcccccc
Confidence            4569999999999999999999999999999999999999998777663    22    234799999999999998855


Q ss_pred             --CceEEeecCCCC
Q psy15610        206 --DFPFSYNQPGYG  217 (237)
Q Consensus       206 --~~~~~~~~~~~~  217 (237)
                        |.+++...+...
T Consensus       526 ~~G~vI~~~~~~~~  539 (1041)
T COG4581         526 VLGTVIVIEPPFES  539 (1041)
T ss_pred             ccceEEEecCCCCC
Confidence              666666554444

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

Probab=98.97  E-value=3.8e-09  Score=99.77  Aligned_cols=104  Identities=26%  Similarity=0.360  Sum_probs=95.3

Q ss_pred             eEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC--CCCEEEEcCccccccCCCCCcEEEEecCCC
Q psy15610        110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG--ETPILVATAVAARGLDIPHVKHVINFDLPS  187 (237)
Q Consensus       110 ~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g--~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~  187 (237)
                      +++||++.....+.+..++...++.+..++|+++..+|...++.|.++  ....++++.+++.|+|+..++.||.+|+.|
T Consensus       713 kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~~d~~w  792 (866)
T COG0553         713 KVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWW  792 (866)
T ss_pred             cEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEEecccc
Confidence            899999999999999999999998999999999999999999999986  344667789999999999999999999999


Q ss_pred             CHHHHHHhhcccccCCCCCceEEeec
Q psy15610        188 DVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       188 s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      ++....|...|++|.|+...+.++-.
T Consensus       793 np~~~~Qa~dRa~RigQ~~~v~v~r~  818 (866)
T COG0553         793 NPAVELQAIDRAHRIGQKRPVKVYRL  818 (866)
T ss_pred             ChHHHHHHHHHHHHhcCcceeEEEEe
Confidence            99999999999999998877655543

>KOG0920|consensus

Probab=98.91  E-value=2.1e-08  Score=92.70  Aligned_cols=190  Identities=23%  Similarity=0.308  Sum_probs=134.7

Q ss_pred             cCCCCCceeEEE-Eeechh-----HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcch
Q psy15610         19 GSTSENITQRIA-WVDEQD-----KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQ   92 (237)
Q Consensus        19 ~~~~~~i~~~~~-~~~~~~-----k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~   92 (237)
                      .....++.|.++ .+.+++     -+-++..+|...      +++++|++|+|.. ++.+..+++  +.++..+.+..-.
T Consensus       282 ~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~------p~LkvILMSAT~d-ae~fs~YF~--~~pvi~i~grtfp  352 (924)
T KOG0920|consen  282 DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRN------PDLKVILMSATLD-AELFSDYFG--GCPVITIPGRTFP  352 (924)
T ss_pred             CcccccCceeeeeeEEEccCCcccHHHHHHHHhhhC------CCceEEEeeeecc-hHHHHHHhC--CCceEeecCCCcc
Confidence            345556666643 344433     334444444443      7889999999998 888888886  3232222221100


Q ss_pred             ---------------------------------------------hhHHHHhhhhhhccCCceEEEEeecccchHHHHHH
Q psy15610         93 ---------------------------------------------KEREEAQQYTLISCDEALTLVFVETKKGADQLEDF  127 (237)
Q Consensus        93 ---------------------------------------------~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~  127 (237)
                                                                   ................+.+|||.+....+..+...
T Consensus       353 V~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~Li~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~  432 (924)
T KOG0920|consen  353 VKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDLIEDLIEYIDEREFEGAILVFLPGWEEILQLKEL  432 (924)
T ss_pred             hHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHHHHHHHHhcccCCCCceEEEEcCCHHHHHHHHHH
Confidence                                                         01111111222334567899999999999999888


Q ss_pred             HhhC-------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE--------ecCC------
Q psy15610        128 LHHH-------GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN--------FDLP------  186 (237)
Q Consensus       128 L~~~-------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~--------~~~p------  186 (237)
                      |...       ..-+..+|+.|+.++...+...--.|.-+|+++|.+++..+.++++-+||.        ||+-      
T Consensus       433 L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l  512 (924)
T KOG0920|consen  433 LEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCL  512 (924)
T ss_pred             hhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchh
Confidence            8642       256788999999999999999999999999999999999999999999997        3331      


Q ss_pred             ----CCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        187 ----SDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       187 ----~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                          .|...-.||.|||||. .+|.||-+++....+
T Consensus       513 ~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~~  547 (924)
T KOG0920|consen  513 LLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRYE  547 (924)
T ss_pred             heeeccccchHHhcccccCc-cCCeeEEeechhhhh
Confidence                2666778999999998 599999998866543

>KOG1000|consensus

Probab=98.90  E-value=9.6e-09  Score=87.88  Aligned_cols=109  Identities=17%  Similarity=0.190  Sum_probs=96.6

Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC-CCCEE-EEcCccccccCCCCCcEEE
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG-ETPIL-VATAVAARGLDIPHVKHVI  181 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g-~~~vl-v~T~~~~~Gvdl~~~~~Vi  181 (237)
                      ...++.+.+|||.-....+.+..++.++++....+.|+.++.+|....+.|+.. +..|. ++-.+++.|+++..+++|+
T Consensus       488 ~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VV  567 (689)
T KOG1000|consen  488 PDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVV  567 (689)
T ss_pred             ccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEE
Confidence            356778999999999999999999999999999999999999999999999965 45554 4558899999999999999


Q ss_pred             EecCCCCHHHHHHhhcccccCCCCCceEEee
Q psy15610        182 NFDLPSDVEEYVHRIGRTGRMGNLDFPFSYN  212 (237)
Q Consensus       182 ~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~  212 (237)
                      +...+|+|..++|.-.|++|.|++..+.+.+
T Consensus       568 FaEL~wnPgvLlQAEDRaHRiGQkssV~v~y  598 (689)
T KOG1000|consen  568 FAELHWNPGVLLQAEDRAHRIGQKSSVFVQY  598 (689)
T ss_pred             EEEecCCCceEEechhhhhhccccceeeEEE
Confidence            9999999999999999999999886644433

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.87  E-value=1.4e-08  Score=92.81  Aligned_cols=107  Identities=22%  Similarity=0.290  Sum_probs=90.2

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC-CCEEEEcCccccccCCCCCc--------
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE-TPILVATAVAARGLDIPHVK--------  178 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~~Gvdl~~~~--------  178 (237)
                      ++++||.|.|.+..+.++.+|.+.|++..++++...  +++..+-. ++|. -.|.|+|..++||.|+.--.        
T Consensus       426 gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~--e~EA~IIa-~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGL  502 (925)
T PRK12903        426 GQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQN--AREAEIIA-KAGQKGAITIATNMAGRGTDIKLSKEVLELGGL  502 (925)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccch--hhHHHHHH-hCCCCCeEEEecccccCCcCccCchhHHHcCCc
Confidence            689999999999999999999999999999988643  33333322 4564 45889999999999996433        


Q ss_pred             EEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        179 HVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       179 ~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +||....|.|...--|..||+||.|.+|.+.+|++-.+.
T Consensus       503 hVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD~  541 (925)
T PRK12903        503 YVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDDQ  541 (925)
T ss_pred             EEEecccCchHHHHHHHhcccccCCCCCcceEEEecchH
Confidence            899999999999999999999999999999999997765

>KOG0386|consensus

Probab=98.85  E-value=4.8e-09  Score=95.99  Aligned_cols=106  Identities=23%  Similarity=0.329  Sum_probs=98.0

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCC---CEEEEcCccccccCCCCCcEEEEec
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGET---PILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~---~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      +++++.|+.-..-...++++|.-.++.+..+.|....++|-..++.|.....   ..|.+|.+.+.|+|++.++.||.||
T Consensus       726 gHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadtviifd  805 (1157)
T KOG0386|consen  726 GHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADTVIIFD  805 (1157)
T ss_pred             CcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeecccccccchhhcceEEEec
Confidence            7899999999999999999999999999999999999999999999997653   4778999999999999999999999


Q ss_pred             CCCCHHHHHHhhcccccCCCCCceEEeec
Q psy15610        185 LPSDVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       185 ~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      ..|+|....|+-.||+|.|+...+-++..
T Consensus       806 sdwnp~~d~qaqdrahrigq~~evRv~rl  834 (1157)
T KOG0386|consen  806 SDWNPHQDLQAQDRAHRIGQKKEVRVLRL  834 (1157)
T ss_pred             CCCCchhHHHHHHHHHHhhchhheeeeee
Confidence            99999999999999999998877766543

>KOG0949|consensus

Probab=98.83  E-value=6.6e-09  Score=94.96  Aligned_cols=79  Identities=27%  Similarity=0.296  Sum_probs=68.0

Q ss_pred             ceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC-CCCHHHHHHhhcccccCCC--CCceEE
Q psy15610        134 PVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL-PSDVEEYVHRIGRTGRMGN--LDFPFS  210 (237)
Q Consensus       134 ~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~-p~s~~~~~Q~~GR~~R~g~--~~~~~~  210 (237)
                      .+.++|++++...|..++-.|+.|...||++|..++.|+|+|.-++|+.-|. -.++-.|.||+|||||-|-  .|.+++
T Consensus       964 GiG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~F 1043 (1330)
T KOG0949|consen  964 GIGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVF 1043 (1330)
T ss_pred             cccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEE
Confidence            5789999999999999999999999999999999999999998877776654 3478999999999999883  355554


Q ss_pred             ee
Q psy15610        211 YN  212 (237)
Q Consensus       211 ~~  212 (237)
                      +-
T Consensus      1044 mg 1045 (1330)
T KOG0949|consen 1044 MG 1045 (1330)
T ss_pred             Ee
Confidence            43

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.81  E-value=5e-08  Score=88.06  Aligned_cols=109  Identities=20%  Similarity=0.185  Sum_probs=90.3

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC---------
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV---------  177 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~---------  177 (237)
                      .+.++||.|.+....+.++..|.+.+++..++++.-...+-+.+.++-+  .-.|.|+|..+++|.|+.--         
T Consensus       426 ~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa~AG~--~gaVTIATNMAGRGTDIkLg~~~~~~~~~  503 (764)
T PRK12326        426 TGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEEARIIAEAGK--YGAVTVSTQMAGRGTDIRLGGSDEADRDR  503 (764)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhHHHHHHhcCC--CCcEEEEecCCCCccCeecCCCcccchHH
Confidence            3789999999999999999999999999999998755444333333322  23588999999999998632         


Q ss_pred             ------cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        178 ------KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       178 ------~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                            -+||....|.|...-.|-.||+||.|.+|.+.+|++-.+.
T Consensus       504 V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleDd  549 (764)
T PRK12326        504 VAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLEDD  549 (764)
T ss_pred             HHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcchh
Confidence                  3799999999999999999999999999999999997765

>KOG1015|consensus

Probab=98.73  E-value=3.8e-08  Score=89.91  Aligned_cols=107  Identities=23%  Similarity=0.302  Sum_probs=93.9

Q ss_pred             CceEEEEeecccchHHHHHHHhhC----------------------CCceEEEeCCCCHHHHHHHHHHhhcCC---C-CE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH----------------------GYPVTSIHGDRTQKEREEALRRFRSGE---T-PI  161 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~----------------------~~~~~~~h~~~~~~~r~~~~~~f~~g~---~-~v  161 (237)
                      +.+.|||..+....+.|..+|...                      |.....+.|+....+|.++...|++..   . -.
T Consensus      1142 GDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~~~~FNdp~NlRaRl~ 1221 (1567)
T KOG1015|consen 1142 GDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKWAEEFNDPTNLRARLF 1221 (1567)
T ss_pred             cceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHHHHHhcCcccceeEEE
Confidence            678999999999999999888531                      456889999999999999999998753   2 27


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQP  214 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  214 (237)
                      ||+|.+++.|+|+-.++.||.||..|+|+.-.|.+=|+-|+|+..-||+|=.-
T Consensus      1222 LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYRfi 1274 (1567)
T KOG1015|consen 1222 LISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYRFI 1274 (1567)
T ss_pred             EEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehhhh
Confidence            89999999999999999999999999999999999999999998888776443

>KOG1123|consensus

Probab=98.69  E-value=8.3e-08  Score=82.46  Aligned_cols=112  Identities=19%  Similarity=0.283  Sum_probs=85.7

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC-CCCEEEEcCccccccCCCCCcEEEEecCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG-ETPILVATAVAARGLDIPHVKHVINFDLP  186 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g-~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p  186 (237)
                      +.++|||..+.-.....+-.|   +  -.+++|..++.+|.++++.|+.. .++.++.+.++...+|+|.++++|+.+..
T Consensus       543 gDKiIVFsDnvfALk~YAikl---~--KpfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQISSH  617 (776)
T KOG1123|consen  543 GDKIIVFSDNVFALKEYAIKL---G--KPFIYGPTSQNERMKILQNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQISSH  617 (776)
T ss_pred             CCeEEEEeccHHHHHHHHHHc---C--CceEECCCchhHHHHHHHhcccCCccceEEEeeccCccccCCcccEEEEEccc
Confidence            789999999877666655544   2  34789999999999999999955 68899999999999999999999998876


Q ss_pred             C-CHHHHHHhhcccccCC---CCCceEEee---cCCCCCCCCCCC
Q psy15610        187 S-DVEEYVHRIGRTGRMG---NLDFPFSYN---QPGYGGSYGGSS  224 (237)
Q Consensus       187 ~-s~~~~~Q~~GR~~R~g---~~~~~~~~~---~~~~~~~~~~~~  224 (237)
                      . |..+-.||.||..|.-   .++.-.+|+   +....+.|-+.+
T Consensus       618 ~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~DTqEM~YStK  662 (776)
T KOG1123|consen  618 GGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKDTQEMYYSTK  662 (776)
T ss_pred             ccchHHHHHHHHHHHHHhhcCccccceeeeeeeecchHHHHhhhh
Confidence            4 7888899999988842   233334444   444444444433

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.64  E-value=1.5e-07  Score=87.60  Aligned_cols=115  Identities=22%  Similarity=0.165  Sum_probs=94.6

Q ss_pred             hhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCC----
Q psy15610        101 YTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPH----  176 (237)
Q Consensus       101 ~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~----  176 (237)
                      ..-....++++||-|.|.+..+.++++|...|++..++++.....+-+.+.++-+.  -.|-|+|..++||.|+.-    
T Consensus       621 i~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~--GaVTIATNMAGRGTDIkLg~~V  698 (1112)
T PRK12901        621 ITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQP--GTVTIATNMAGRGTDIKLSPEV  698 (1112)
T ss_pred             HHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCC--CcEEEeccCcCCCcCcccchhh
Confidence            44446789999999999999999999999999998888886554444444443332  358889999999999862    


Q ss_pred             ----CcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        177 ----VKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       177 ----~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                          =-+||....+.|...-.|-.||+||.|.+|.+.+|++..+.
T Consensus       699 ~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDd  743 (1112)
T PRK12901        699 KAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDN  743 (1112)
T ss_pred             HHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccH
Confidence                24789999999999999999999999999999999997765

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.62  E-value=2.2e-07  Score=85.84  Aligned_cols=108  Identities=23%  Similarity=0.231  Sum_probs=89.5

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC-CCEEEEcCccccccCCCC---------
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE-TPILVATAVAARGLDIPH---------  176 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~~Gvdl~~---------  176 (237)
                      .+.++||-|.|.+..+.++.+|...+++..+++......+-+.+.   +.|. -.|.|+|..++||.|+.-         
T Consensus       448 ~GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk~~~~EA~IIa---~AG~~GaVTIATNMAGRGTDIkLg~n~~~~~~  524 (913)
T PRK13103        448 LGRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAKYHEKEAEIIA---QAGRPGALTIATNMAGRGTDILLGGNWEVEVA  524 (913)
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccccchhHHHHHH---cCCCCCcEEEeccCCCCCCCEecCCchHHHHH
Confidence            378999999999999999999999999988888765444333333   3453 458899999999999841         


Q ss_pred             ----------------------------CcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        177 ----------------------------VKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       177 ----------------------------~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                                                  =-+||....+.|...-.|-.||+||.|.+|.+-+|++..+.
T Consensus       525 ~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED~  593 (913)
T PRK13103        525 ALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDS  593 (913)
T ss_pred             hhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence                                        13788899999999999999999999999999999998665

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.59  E-value=3.4e-07  Score=84.85  Aligned_cols=114  Identities=20%  Similarity=0.161  Sum_probs=93.4

Q ss_pred             hhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC-CCEEEEcCccccccCCCCC--
Q psy15610        101 YTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE-TPILVATAVAARGLDIPHV--  177 (237)
Q Consensus       101 ~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~~Gvdl~~~--  177 (237)
                      .......+.+++|-|.+....+.++..|...|++..+++..-...+-+.+.+   +|. -.|.|+|..+++|.|+.--  
T Consensus       561 i~~~~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak~~~~Ea~iia~---AG~~g~VTIATNmAGRGTDIkl~~~  637 (970)
T PRK12899        561 IASIHRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAKNHAQEAEIIAG---AGKLGAVTVATNMAGRGTDIKLDEE  637 (970)
T ss_pred             HHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccchhhhHHHHHHh---cCCCCcEEEeeccccCCcccccCch
Confidence            3334567899999999999999999999999999999988644443333333   343 4588999999999998532  


Q ss_pred             ------cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        178 ------KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       178 ------~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                            -+||....|.|...-.|-.||+||.|.+|.+.+|++..+.
T Consensus       638 v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlEDd  683 (970)
T PRK12899        638 AVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFEDR  683 (970)
T ss_pred             HHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcchH
Confidence                  3688899999999999999999999999999999997765

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

Probab=98.59  E-value=2.3e-07  Score=84.14  Aligned_cols=93  Identities=19%  Similarity=0.353  Sum_probs=75.1

Q ss_pred             CceEEEEeecccchHHHHHHHhhC-----CCceEEEeCCCCHHHHHHHHHHhhc--CCCCEEEEcCccccccCCCCCcEE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH-----GYPVTSIHGDRTQKEREEALRRFRS--GETPILVATAVAARGLDIPHVKHV  180 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~--g~~~vlv~T~~~~~Gvdl~~~~~V  180 (237)
                      ..++||||.+..+|+.|...|.+.     +--+..+.|+-  ++-.+.++.|..  .-..|.++.+.+..|+|+|.|.++
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            479999999999999999998764     33355666643  334445566654  346788999999999999999999


Q ss_pred             EEecCCCCHHHHHHhhcccccC
Q psy15610        181 INFDLPSDVEEYVHRIGRTGRM  202 (237)
Q Consensus       181 i~~~~p~s~~~~~Q~~GR~~R~  202 (237)
                      +++..-.|...|.||+||+-|.
T Consensus       504 VF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         504 VFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             eehhhhhhHHHHHHHhcCcccc
Confidence            9999989999999999999994

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

Probab=98.57  E-value=1.7e-07  Score=85.55  Aligned_cols=158  Identities=23%  Similarity=0.272  Sum_probs=108.6

Q ss_pred             cccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhh-----------hccCCceEEEEeecccch
Q psy15610         53 LGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTL-----------ISCDEALTLVFVETKKGA  121 (237)
Q Consensus        53 ~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~iIF~~t~~~~  121 (237)
                      +..+.++|+|.+.+.....+...=...-..|......+.-........+-.           -.+. ...|+++..  -.
T Consensus       417 l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cg-s~~L~~~G~--Gt  493 (730)
T COG1198         417 LERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECG-SEHLRAVGP--GT  493 (730)
T ss_pred             HhcCCeEEEEEccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCC-CCeeEEecc--cH
Confidence            356778999999998876665555555555655555554433332222111           1112 224555443  45


Q ss_pred             HHHHHHHhhC--CCceEEEeCCCCHHH--HHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC----------
Q psy15610        122 DQLEDFLHHH--GYPVTSIHGDRTQKE--REEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS----------  187 (237)
Q Consensus       122 ~~l~~~L~~~--~~~~~~~h~~~~~~~--r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~----------  187 (237)
                      +.+++.|...  +.++..+.++.+...  -+..+..|.+|+.+|||.|.++..|.|+|+++.|...+.+.          
T Consensus       494 erieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~  573 (730)
T COG1198         494 ERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRAS  573 (730)
T ss_pred             HHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchH
Confidence            6777777654  778888888766533  56779999999999999999999999999999877655432          


Q ss_pred             --CHHHHHHhhcccccCCCCCceEEeec
Q psy15610        188 --DVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       188 --s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                        ....++|-+|||||.+.+|.+++=..
T Consensus       574 Er~fqll~QvaGRAgR~~~~G~VvIQT~  601 (730)
T COG1198         574 ERTFQLLMQVAGRAGRAGKPGEVVIQTY  601 (730)
T ss_pred             HHHHHHHHHHHhhhccCCCCCeEEEEeC
Confidence              45677899999999988887765443

>KOG1002|consensus

Probab=98.48  E-value=4.8e-07  Score=77.80  Aligned_cols=107  Identities=17%  Similarity=0.221  Sum_probs=94.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC-CCE-EEEcCccccccCCCCCcEEEEecC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE-TPI-LVATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~-~~v-lv~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      ..++|||.......+.+.=.|.+.|+.+..+.|+|++..|...++.|.+.. ..| |++-.+++..+|+..+..|+..|+
T Consensus       638 t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmDP  717 (791)
T KOG1002|consen  638 TAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMDP  717 (791)
T ss_pred             chhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeecc
Confidence            468999999999999999999999999999999999999999999999875 444 455699999999999999999999


Q ss_pred             CCCHHHHHHhhcccccCCCC--CceEEeecC
Q psy15610        186 PSDVEEYVHRIGRTGRMGNL--DFPFSYNQP  214 (237)
Q Consensus       186 p~s~~~~~Q~~GR~~R~g~~--~~~~~~~~~  214 (237)
                      -|++..-.|...|.+|+|+.  -.++.|+-.
T Consensus       718 WWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iE  748 (791)
T KOG1002|consen  718 WWNPAVEWQAQDRIHRIGQYRPVKVVRFCIE  748 (791)
T ss_pred             cccHHHHhhhhhhHHhhcCccceeEEEeehh
Confidence            99999999999999999964  455666543

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

Probab=98.42  E-value=2.2e-06  Score=81.07  Aligned_cols=110  Identities=19%  Similarity=0.175  Sum_probs=81.5

Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcE--E
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKH--V  180 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~--V  180 (237)
                      ....++++||+++.+.++.++..|...  .....++..+.. ..|.++++.|+++...||++|+.+.+|+|+|+...  |
T Consensus       671 ~~~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~v  749 (850)
T TIGR01407       671 AITSPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCL  749 (850)
T ss_pred             HhcCCCEEEEeCCHHHHHHHHHHHhhhccccCceEEecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEE
Confidence            345678999999999999999998752  112334444433 57889999999999999999999999999998764  5


Q ss_pred             EEecCCC----C--------------------------HHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        181 INFDLPS----D--------------------------VEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       181 i~~~~p~----s--------------------------~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      |....|.    +                          ...+.|.+||.-|..+...++++++..
T Consensus       750 iI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~R  814 (850)
T TIGR01407       750 VIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDRR  814 (850)
T ss_pred             EEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEEccc
Confidence            5555442    1                          134578999999988776666666654

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.

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.35  E-value=5.9e-06  Score=76.31  Aligned_cols=114  Identities=20%  Similarity=0.181  Sum_probs=88.6

Q ss_pred             hhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCC--HHHHHHHHHHhhcCC-CCEEEEcCccccccCCCCC
Q psy15610        101 YTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRT--QKEREEALRRFRSGE-TPILVATAVAARGLDIPHV  177 (237)
Q Consensus       101 ~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~--~~~r~~~~~~f~~g~-~~vlv~T~~~~~Gvdl~~~  177 (237)
                      .......+.+++|-|.|.+..+.++..|...|++..++++.-.  ..|-+.+.+   +|. -.|.|+|..++||.|+.--
T Consensus       417 i~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIA~---AG~~G~VTIATNMAGRGTDI~Lg  493 (870)
T CHL00122        417 CLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPENVRRESEIVAQ---AGRKGSITIATNMAGRGTDIILG  493 (870)
T ss_pred             HHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCccchhHHHHHHh---cCCCCcEEEeccccCCCcCeecC
Confidence            3344667899999999999999999999999999999998642  333333333   344 4588999999999876321


Q ss_pred             --------------------------------------------------------------------------------
Q psy15610        178 --------------------------------------------------------------------------------  177 (237)
Q Consensus       178 --------------------------------------------------------------------------------  177 (237)
                                                                                                      
T Consensus       494 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  573 (870)
T CHL00122        494 GNPEFKLKKELYDLLLSYKSNEKISTISQNFLNILNSLKNDLKFLSLSDFENLKILNEASEISIPKNSYQLSLRFLYNEL  573 (870)
T ss_pred             CchhHHHHHHHhhhhcccccccccccccccchhhhhhcccchhhhcccccccccccccccccccccchhhhhhhhHHHHH
Confidence                                                                                            


Q ss_pred             --------------------cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        178 --------------------KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       178 --------------------~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                                          -+||......|...--|-.||+||.|.+|..-+|++-.+.
T Consensus       574 ~~~~~~~~~~e~e~V~~~GGL~VIgTErheSrRIDnQLrGRaGRQGDPG~s~f~lSLED~  633 (870)
T CHL00122        574 LEKYKKLQEKEKKIVKKLGGLYVIGTERHESRRIDNQLRGRAGRQGDPGSSRFFLSLEDN  633 (870)
T ss_pred             HHHHHHHhhhhHHHHHHcCCCEEEecCcCchHHHHHHHhccccCCCCCCcceEEEEeccH
Confidence                                1355556666777888999999999999999999997765

>KOG4439|consensus

Probab=98.30  E-value=4.9e-06  Score=74.35  Aligned_cols=108  Identities=19%  Similarity=0.271  Sum_probs=94.6

Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhc--CCCCEEE-EcCccccccCCCCCcEE
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRS--GETPILV-ATAVAARGLDIPHVKHV  180 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~--g~~~vlv-~T~~~~~Gvdl~~~~~V  180 (237)
                      ..+...+++|...-......+...|.+.|.....+||.....+|+.+++.|..  |..+|++ +-.+.+.|+|+...+++
T Consensus       742 ~~~skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHl  821 (901)
T KOG4439|consen  742 LTSSKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHL  821 (901)
T ss_pred             hhcccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceE
Confidence            45667788888888888888999999999999999999999999999999974  4456654 45889999999999999


Q ss_pred             EEecCCCCHHHHHHhhcccccCCCCCceEEe
Q psy15610        181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSY  211 (237)
Q Consensus       181 i~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~  211 (237)
                      |..|+.|+|.---|.+.|..|+|+...+++.
T Consensus       822 ilvDlHWNPaLEqQAcDRIYR~GQkK~V~Ih  852 (901)
T KOG4439|consen  822 ILVDLHWNPALEQQACDRIYRMGQKKDVFIH  852 (901)
T ss_pred             EEEecccCHHHHHHHHHHHHHhcccCceEEE
Confidence            9999999999999999999999999877654

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.27  E-value=2.6e-06  Score=78.96  Aligned_cols=75  Identities=36%  Similarity=0.710  Sum_probs=67.1

Q ss_pred             CceEEEEeec---ccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEc----CccccccCCCC-CcE
Q psy15610        108 EALTLVFVET---KKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT----AVAARGLDIPH-VKH  179 (237)
Q Consensus       108 ~~~~iIF~~t---~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T----~~~~~Gvdl~~-~~~  179 (237)
                      +.-.|||+++   ++.+++++++|...|+++..+|++     .+..++.|..|++++||..    ..+.+|+|+|. +.+
T Consensus       335 G~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirY  409 (1187)
T COG1110         335 GDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRY  409 (1187)
T ss_pred             CCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----chhhhhhhccCceeEEEEecccccceeecCCchhheeE
Confidence            5679999999   889999999999999999999984     3678899999999999875    57999999998 678


Q ss_pred             EEEecCCC
Q psy15610        180 VINFDLPS  187 (237)
Q Consensus       180 Vi~~~~p~  187 (237)
                      +|+++.|.
T Consensus       410 aIF~GvPk  417 (1187)
T COG1110         410 AVFYGVPK  417 (1187)
T ss_pred             EEEecCCc
Confidence            99999984

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

Probab=98.27  E-value=6.2e-06  Score=75.91  Aligned_cols=94  Identities=15%  Similarity=0.221  Sum_probs=73.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhC-----CCceEEEeCCCCHH---------------------HHHHHHHHhhc-CCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH-----GYPVTSIHGDRTQK---------------------EREEALRRFRS-GETP  160 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~---------------------~r~~~~~~f~~-g~~~  160 (237)
                      ..+++|||.++.+|..+.+.|.+.     +....+++++.+.+                     ....++++|++ +.++
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            478999999999999998887654     23455666554332                     12467888876 5789


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRM  202 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~  202 (237)
                      +||+++.+..|+|.|.+++++...+-.+. .++|++||+.|.
T Consensus       594 ilIVvdmllTGFDaP~l~tLyldKplk~h-~LlQai~R~nR~  634 (667)
T TIGR00348       594 LLIVVDMLLTGFDAPILNTLYLDKPLKYH-GLLQAIARTNRI  634 (667)
T ss_pred             EEEEEcccccccCCCccceEEEecccccc-HHHHHHHHhccc
Confidence            99999999999999999988877665554 489999999994

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

>KOG0925|consensus

Probab=98.25  E-value=1.2e-05  Score=69.17  Aligned_cols=202  Identities=17%  Similarity=0.207  Sum_probs=124.2

Q ss_pred             HHhhcceeEEEeeccCCCCCceeE-EEEeechhHHHHHHHhhcCchhhh--cccccceeEEeecccchhhHHHHhhhc--
Q psy15610          5 EFLYRYIFLAIGRVGSTSENITQR-IAWVDEQDKRSCLLDLLSSPSQEE--LGDEALTLVFVETKKGADQLEDFLHHH--   79 (237)
Q Consensus         5 ~~l~~~~~i~~~~~~~~~~~i~~~-~~~~~~~~k~~~l~~ll~~~~~~~--~~~~~~~i~f~~t~~~~~~~~~~l~~~--   79 (237)
                      +|+.|.+.+   +|.-+..-+..+ +++.++.+.+....++|.-.-...  ..+++++|++++|.. ++++..++...  
T Consensus       140 ky~tDgmLl---rEams~p~l~~y~viiLDeahERtlATDiLmGllk~v~~~rpdLk~vvmSatl~-a~Kfq~yf~n~Pl  215 (699)
T KOG0925|consen  140 KYCTDGMLL---REAMSDPLLGRYGVIILDEAHERTLATDILMGLLKEVVRNRPDLKLVVMSATLD-AEKFQRYFGNAPL  215 (699)
T ss_pred             HHhcchHHH---HHHhhCcccccccEEEechhhhhhHHHHHHHHHHHHHHhhCCCceEEEeecccc-hHHHHHHhCCCCe
Confidence            455555544   234334444444 456666655544444444332222  246889999998865 45666666443  


Q ss_pred             -----CCCceeecCC-cchhhHHHHhhhhhh---ccCCceEEEEeecccchHHHHHHHh----hC-----CCceEEEeCC
Q psy15610         80 -----GYPVTSIHGD-RTQKEREEAQQYTLI---SCDEALTLVFVETKKGADQLEDFLH----HH-----GYPVTSIHGD  141 (237)
Q Consensus        80 -----~~~~~~~~~~-~~~~~~~~~~~~~~~---~~~~~~~iIF~~t~~~~~~l~~~L~----~~-----~~~~~~~h~~  141 (237)
                           .+++..+... .....-+.++..++.   ....+.+++|....+..+..-+.+.    ..     ...+..+|  
T Consensus       216 l~vpg~~PvEi~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy--  293 (699)
T KOG0925|consen  216 LAVPGTHPVEIFYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY--  293 (699)
T ss_pred             eecCCCCceEEEecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC--
Confidence                 2345444433 333333333332222   3347789999999886655544443    22     24566677  


Q ss_pred             CCHHHHHHHHHHhhc---C--CCCEEEEcCccccccCCCCCcEEEEec------------------CCCCHHHHHHhhcc
Q psy15610        142 RTQKEREEALRRFRS---G--ETPILVATAVAARGLDIPHVKHVINFD------------------LPSDVEEYVHRIGR  198 (237)
Q Consensus       142 ~~~~~r~~~~~~f~~---g--~~~vlv~T~~~~~Gvdl~~~~~Vi~~~------------------~p~s~~~~~Q~~GR  198 (237)
                        |.+..++++.-..   |  .-+|+|+|.+++..+.++.+.+||.-+                  .|.|..+-.||.||
T Consensus       294 --P~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gr  371 (699)
T KOG0925|consen  294 --PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGR  371 (699)
T ss_pred             --chhhccccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhh
Confidence              5555555444332   2  246999999999999999999999633                  36788889999999


Q ss_pred             cccCCCCCceEEeecCC
Q psy15610        199 TGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       199 ~~R~g~~~~~~~~~~~~  215 (237)
                      +||. .+|+|+-++...
T Consensus       372 agrt-~pGkcfrLYte~  387 (699)
T KOG0925|consen  372 AGRT-RPGKCFRLYTEE  387 (699)
T ss_pred             ccCC-CCCceEEeecHH
Confidence            9998 589999888743

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.14  E-value=2.9e-05  Score=71.92  Aligned_cols=65  Identities=25%  Similarity=0.377  Sum_probs=51.1

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCC--HHHHHHHHHHhhcCC-CCEEEEcCccccccCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRT--QKEREEALRRFRSGE-TPILVATAVAARGLDIP  175 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~--~~~r~~~~~~f~~g~-~~vlv~T~~~~~Gvdl~  175 (237)
                      +.+++|-|.|.+..+.++..|...|++..+++....  ..+-+.+.+   +|. -.|-|+|..++||.|+.
T Consensus       439 GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIa~---AG~~GaVTIATNMAGRGTDIk  506 (939)
T PRK12902        439 GRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAKPENVEREAEIVAQ---AGRKGAVTIATNMAGRGTDII  506 (939)
T ss_pred             CCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCCCcchHhHHHHHHh---cCCCCcEEEeccCCCCCcCEe
Confidence            789999999999999999999999999999998633  233333333   454 35889999999997763

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

Probab=98.12  E-value=1e-05  Score=61.56  Aligned_cols=105  Identities=26%  Similarity=0.313  Sum_probs=72.6

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCC--ceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC--ccccccCCCC--CcEEE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGY--PVTSIHGDRTQKEREEALRRFRSGETPILVATA--VAARGLDIPH--VKHVI  181 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~--~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~--~~~~Gvdl~~--~~~Vi  181 (237)
                      ++.++||+++...++.+.+.+.....  .+.++.-  ...++...++.|+++.-.||+++.  .+.+|+|+|+  +..||
T Consensus         9 ~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~vi   86 (167)
T PF13307_consen    9 PGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAVI   86 (167)
T ss_dssp             SSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhheee
Confidence            68899999999999999999976532  2233333  355678889999999989999998  9999999996  66788


Q ss_pred             EecCCC----CH--------------------------HHHHHhhcccccCCCCCceEEeecC
Q psy15610        182 NFDLPS----DV--------------------------EEYVHRIGRTGRMGNLDFPFSYNQP  214 (237)
Q Consensus       182 ~~~~p~----s~--------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~  214 (237)
                      ....|.    ++                          ..+.|.+||+-|..++-.++++++.
T Consensus        87 i~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~  149 (167)
T PF13307_consen   87 IVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDS  149 (167)
T ss_dssp             EES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESG
T ss_pred             ecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcC
Confidence            877663    21                          1335889999998877666666654

>KOG1016|consensus

Probab=98.10  E-value=1.6e-05  Score=71.93  Aligned_cols=105  Identities=20%  Similarity=0.312  Sum_probs=91.1

Q ss_pred             CceEEEEeecccchHHHHHHHhhCC------------------CceEEEeCCCCHHHHHHHHHHhhcCCC---CEEEEcC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHG------------------YPVTSIHGDRTQKEREEALRRFRSGET---PILVATA  166 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~------------------~~~~~~h~~~~~~~r~~~~~~f~~g~~---~vlv~T~  166 (237)
                      +.++|||..+....+.+++.|.+..                  .....+.|..+..+|++++.+|.+..-   -++++|.
T Consensus       719 g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllstr  798 (1387)
T KOG1016|consen  719 GEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLSTR  798 (1387)
T ss_pred             CceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehhc
Confidence            6789999999999999999997652                  235577889999999999999987542   3678899


Q ss_pred             ccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEee
Q psy15610        167 VAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYN  212 (237)
Q Consensus       167 ~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~  212 (237)
                      +.+.|+|+-.++.++.|+..|++---.|.+-|+.|.|+..-|++|-
T Consensus       799 ag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYR  844 (1387)
T KOG1016|consen  799 AGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYR  844 (1387)
T ss_pred             cccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEe
Confidence            9999999999999999999999999999999999999999988764

>KOG0926|consensus

Probab=98.03  E-value=2.3e-06  Score=77.43  Aligned_cols=80  Identities=24%  Similarity=0.304  Sum_probs=67.6

Q ss_pred             eEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec--------C---------CC-CHHHHHHhh
Q psy15610        135 VTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD--------L---------PS-DVEEYVHRI  196 (237)
Q Consensus       135 ~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~--------~---------p~-s~~~~~Q~~  196 (237)
                      +..+++-++.+...+++..-..|.--++|+|.+++..+.+|++.+||..+        .         .| |..+--||+
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            67778889999999998888888888999999999999999999999733        2         22 555667999


Q ss_pred             cccccCCCCCceEEeecCC
Q psy15610        197 GRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       197 GR~~R~g~~~~~~~~~~~~  215 (237)
                      |||||.| +|.||-+|+..
T Consensus       687 GRAGRtg-pGHcYRLYSSA  704 (1172)
T KOG0926|consen  687 GRAGRTG-PGHCYRLYSSA  704 (1172)
T ss_pred             cccCCCC-CCceeehhhhH
Confidence            9999998 99999988753

>KOG0951|consensus

Probab=97.90  E-value=2.4e-05  Score=74.01  Aligned_cols=169  Identities=13%  Similarity=0.062  Sum_probs=113.8

Q ss_pred             ccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh---------------------hhhhccCCceEE
Q psy15610         54 GDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ---------------------YTLISCDEALTL  112 (237)
Q Consensus        54 ~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~i  112 (237)
                      .+.-+++..+.+..++.++   ++.....++.+.+..+..+-..-++                     ...-.....+++
T Consensus      1287 ~k~ir~v~ls~~lana~d~---ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~~~ 1363 (1674)
T KOG0951|consen 1287 EKKIRVVALSSSLANARDL---IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKPAI 1363 (1674)
T ss_pred             HhheeEEEeehhhccchhh---ccccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCCeE
Confidence            3445566666666666665   3333344455555555544322222                     111234567899


Q ss_pred             EEeecccchHHHHHHHhhC----------------------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCcccc
Q psy15610        113 VFVETKKGADQLEDFLHHH----------------------GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR  170 (237)
Q Consensus       113 IF~~t~~~~~~l~~~L~~~----------------------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~  170 (237)
                      ||+++++++..++.-+...                      ..+..+-|-+++..+...+...|..|.++|+|.+.. ++
T Consensus      1364 vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~s~~-~~ 1442 (1674)
T KOG0951|consen 1364 VFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CY 1442 (1674)
T ss_pred             EEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEEEcc-cc
Confidence            9999999998874433210                      123333389999999999999999999999999877 88


Q ss_pred             ccCCCCCcEEEE----ecC------CCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCCCCCCC
Q psy15610        171 GLDIPHVKHVIN----FDL------PSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSSQNSN  229 (237)
Q Consensus       171 Gvdl~~~~~Vi~----~~~------p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (237)
                      |+....--+|+.    ||.      +.....++||+|+|+|   .|.|++++...++.+|+.-...-.+
T Consensus      1443 ~~~~~~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~vi~~~~~~k~yykkfl~e~lP 1508 (1674)
T KOG0951|consen 1443 GTKLKAHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AGKCVIMCHTPKKEYYKKFLYEPLP 1508 (1674)
T ss_pred             cccccceEEEEecceeecccccccccCchhHHHHHhhhhcC---CccEEEEecCchHHHHHHhccCcCc
Confidence            887654444442    332      3468999999999998   5689999999999988875554333

>COG4889 Predicted helicase [General function prediction only]

Probab=97.86  E-value=6.7e-06  Score=75.31  Aligned_cols=109  Identities=21%  Similarity=0.344  Sum_probs=81.1

Q ss_pred             ceEEEEeecccchHHHHHHHh---------------hCCCceEEEeCCCCHHHHHHHHHH---hhcCCCCEEEEcCcccc
Q psy15610        109 ALTLVFVETKKGADQLEDFLH---------------HHGYPVTSIHGDRTQKEREEALRR---FRSGETPILVATAVAAR  170 (237)
Q Consensus       109 ~~~iIF~~t~~~~~~l~~~L~---------------~~~~~~~~~h~~~~~~~r~~~~~~---f~~g~~~vlv~T~~~~~  170 (237)
                      .++|-||.+.+....+++.+.               .+.+.+..+.|.|+..+|++.+..   |...+.+||---.++.+
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            566777777776665544432               124456677799999999776654   45566777777789999


Q ss_pred             ccCCCCCcEEEEecCCCCHHHHHHhhcccccCC-CCCceEEeecCCCC
Q psy15610        171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG-NLDFPFSYNQPGYG  217 (237)
Q Consensus       171 Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g-~~~~~~~~~~~~~~  217 (237)
                      |+|+|..+-||++++-.+....+|.+||+.|-. ++..+|++.+-.-.
T Consensus       541 GVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILPIalp  588 (1518)
T COG4889         541 GVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILPIALP  588 (1518)
T ss_pred             CCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEEeccC
Confidence            999999999999999999999999999999954 34456666654333

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

Probab=97.84  E-value=0.00015  Score=66.98  Aligned_cols=156  Identities=17%  Similarity=0.177  Sum_probs=103.1

Q ss_pred             cceeEEeecccchhhHHHHhhhcCCCcee--e--cC--------------Ccch----hhHHHHhh--hhhhccCCceEE
Q psy15610         57 ALTLVFVETKKGADQLEDFLHHHGYPVTS--I--HG--------------DRTQ----KEREEAQQ--YTLISCDEALTL  112 (237)
Q Consensus        57 ~~~i~f~~t~~~~~~~~~~l~~~~~~~~~--~--~~--------------~~~~----~~~~~~~~--~~~~~~~~~~~i  112 (237)
                      ..+|++|+|......+..++...+.....  +  .+              ....    ........  ..+....++.++
T Consensus       404 ~~~vl~SaTL~~~~~f~~~~~~~~~~~~~~~~~~~spf~~~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~l  483 (654)
T COG1199         404 ASVVLTSATLSPLDSFSSLLGLLGLEEKLRFLSLPSPFNYEEQGQLYVPTDLPEPREPELLAKLAAYLREILKASPGGVL  483 (654)
T ss_pred             CcEEEeeeeccCCCcHHHHHHHcCCccccceeccCCCCChhhcceEeccccCCCCCChHHHHHHHHHHHHHHhhcCCCEE
Confidence            45899999999988888877766654332  1  11              0000    01111111  222344455899


Q ss_pred             EEeecccchHHHHHHHhhCCCc-eEEEeCCCCHHHHHHHHHHhhcCCC-CEEEEcCccccccCCCCC--cEEEEecCCC-
Q psy15610        113 VFVETKKGADQLEDFLHHHGYP-VTSIHGDRTQKEREEALRRFRSGET-PILVATAVAARGLDIPHV--KHVINFDLPS-  187 (237)
Q Consensus       113 IF~~t~~~~~~l~~~L~~~~~~-~~~~h~~~~~~~r~~~~~~f~~g~~-~vlv~T~~~~~Gvdl~~~--~~Vi~~~~p~-  187 (237)
                      ||+++-+.++.+.+.+...... ....+|..+.+   ..++.|.++.- .++|+|..+.+|+|+|.-  ..||....|. 
T Consensus       484 vlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~~~---~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI~~lPfp  560 (654)
T COG1199         484 VLFPSYEYLKRVAERLKDERSTLPVLTQGEDERE---ELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLPFP  560 (654)
T ss_pred             EEeccHHHHHHHHHHHhhcCccceeeecCCCcHH---HHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEEEecCCC
Confidence            9999999999999999876542 34455554444   67777776555 899999999999999985  5566655432 


Q ss_pred             -----------------------------CHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        188 -----------------------------DVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       188 -----------------------------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                                                   -...+.|.+||+-|.-+....+++++..
T Consensus       561 ~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~R  617 (654)
T COG1199         561 NPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKR  617 (654)
T ss_pred             CCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEeccc
Confidence                                         2335679999999976665566666543

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.83  E-value=0.0002  Score=66.58  Aligned_cols=126  Identities=18%  Similarity=0.283  Sum_probs=87.4

Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhCCC-------ceEEEeCCCCHHHHHHHHHHhhc----CCCCEEEEc--Cccccc
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHHGY-------PVTSIHGDRTQKEREEALRRFRS----GETPILVAT--AVAARG  171 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~~~-------~~~~~h~~~~~~~r~~~~~~f~~----g~~~vlv~T--~~~~~G  171 (237)
                      ..-++.++||.++-...+.+.+.+...+.       ...++-+. ...++..+++.|++    +.-.||+++  ..+.+|
T Consensus       519 ~~~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~-~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEG  597 (705)
T TIGR00604       519 KIIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETK-DAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEG  597 (705)
T ss_pred             hcCCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCC-CcchHHHHHHHHHHHHhcCCceEEEEecCCcccCc
Confidence            33457799999999999998888765432       12233232 22577888999964    455699998  889999


Q ss_pred             cCCCC--CcEEEEecCCC----CH---------------------------HHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        172 LDIPH--VKHVINFDLPS----DV---------------------------EEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       172 vdl~~--~~~Vi~~~~p~----s~---------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      +|+++  +..||..+.|.    ++                           ..+.|.+||+-|--.+-.++++++..-..
T Consensus       598 IDf~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~~~D~G~iillD~R~~~  677 (705)
T TIGR00604       598 IDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQDFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYAR  677 (705)
T ss_pred             cccCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHHHHhCccccCcCceEEEEEEehhcCC
Confidence            99997  57788887764    11                           13458899999987776677777655222


Q ss_pred             CCCCCCCCCCCCCCCccC
Q psy15610        219 SYGGSSSQNSNAPDWWND  236 (237)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~  236 (237)
                           .+..+..|+||..
T Consensus       678 -----~~~~~~lp~W~~~  690 (705)
T TIGR00604       678 -----SNKRKKLPKWIQD  690 (705)
T ss_pred             -----cchhhhcCHHHHh
Confidence                 2345667888854

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).

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

Probab=97.75  E-value=0.00016  Score=69.17  Aligned_cols=117  Identities=18%  Similarity=0.162  Sum_probs=83.4

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCC--ceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC--cEEE
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGY--PVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV--KHVI  181 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~--~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~--~~Vi  181 (237)
                      ..++.++||.++.+..+.+++.|.....  ....+.=+++...|.++++.|+++.-.||++|..+.+|||+|+-  .+||
T Consensus       750 ~~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~vi  829 (928)
T PRK08074        750 ATKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLV  829 (928)
T ss_pred             hCCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEE
Confidence            3467899999999999999999875421  12233324444557889999999888899999999999999975  5677


Q ss_pred             EecCCC----C--------------------------HHHHHHhhcccccCCCCCceEEeecCC-CCCCCCC
Q psy15610        182 NFDLPS----D--------------------------VEEYVHRIGRTGRMGNLDFPFSYNQPG-YGGSYGG  222 (237)
Q Consensus       182 ~~~~p~----s--------------------------~~~~~Q~~GR~~R~g~~~~~~~~~~~~-~~~~~~~  222 (237)
                      ....|.    +                          ...+.|.+||.-|..+...++++++.. ....|+.
T Consensus       830 I~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~R~~~k~Yg~  901 (928)
T PRK08074        830 IVRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLDRRLTTTSYGK  901 (928)
T ss_pred             EecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEecCccccchHHH
Confidence            655442    1                          224478889999988665566666655 2344543

>PF13871 Helicase_C_4: Helicase_C-like

Probab=97.69  E-value=0.00014  Score=59.28  Aligned_cols=67  Identities=18%  Similarity=0.413  Sum_probs=54.7

Q ss_pred             HHHHHHHhhcCCCCEEEEcCccccccCCCC--------CcEEEEecCCCCHHHHHHhhcccccCCCCCce-EEeec
Q psy15610        147 REEALRRFRSGETPILVATAVAARGLDIPH--------VKHVINFDLPSDVEEYVHRIGRTGRMGNLDFP-FSYNQ  213 (237)
Q Consensus       147 r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~--------~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~-~~~~~  213 (237)
                      .....+.|.+|+..|+|.|++++.|+.++.        -.+-|...+|||....+|..||++|.|+.... |.++.
T Consensus        50 N~~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~  125 (278)
T PF13871_consen   50 NIAEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLV  125 (278)
T ss_pred             cHHHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEee
Confidence            345668999999999999999999998874        24677899999999999999999999986443 44333

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

Probab=97.58  E-value=0.00037  Score=65.70  Aligned_cols=107  Identities=21%  Similarity=0.190  Sum_probs=77.8

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCC--CcEEEEe
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPH--VKHVINF  183 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~--~~~Vi~~  183 (237)
                      ..+++++|+.+|.+..+.+++.|......+ ...|...  .+.++++.|+++.-.||++|..+.+|+|+|.  ...||..
T Consensus       645 ~~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~  721 (820)
T PRK07246        645 QLQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVIT  721 (820)
T ss_pred             hcCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEe
Confidence            456789999999999999999997655444 4545322  2456899999988899999999999999974  4445554


Q ss_pred             cCC----CC--------------------------HHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        184 DLP----SD--------------------------VEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       184 ~~p----~s--------------------------~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      ..|    .+                          ...+.|.+||.-|......++++++..
T Consensus       722 kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~R  783 (820)
T PRK07246        722 RLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRR  783 (820)
T ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECCc
Confidence            433    22                          224678899999987665566666655

>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=97.56  E-value=0.0011  Score=57.58  Aligned_cols=111  Identities=18%  Similarity=0.211  Sum_probs=92.5

Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC--ccccccCCCCCcEEEE
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA--VAARGLDIPHVKHVIN  182 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~--~~~~Gvdl~~~~~Vi~  182 (237)
                      ......++||+++--.--.+..+|.+.++.+..+|.-.+..+..+.-..|..|+.++|+.|.  ..=+-..+..+..||+
T Consensus       297 ~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~irGi~~viF  376 (442)
T PF06862_consen  297 DSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIRGIRHVIF  376 (442)
T ss_pred             ccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceecCCcEEEE
Confidence            45567899999999999999999999999999999999999999999999999999999995  3334556778999999


Q ss_pred             ecCCCCHHHHHHhhcccccCCC------CCceEEeecCC
Q psy15610        183 FDLPSDVEEYVHRIGRTGRMGN------LDFPFSYNQPG  215 (237)
Q Consensus       183 ~~~p~s~~~~~Q~~GR~~R~g~------~~~~~~~~~~~  215 (237)
                      |++|..+.-|...++..+...+      ...|.++++.-
T Consensus       377 Y~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~  415 (442)
T PF06862_consen  377 YGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKY  415 (442)
T ss_pred             ECCCCChhHHHHHHhhhcccccccccccCceEEEEecHh
Confidence            9999999999888865554433      45666666643

; GO: 0005634 nucleus

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.55  E-value=0.00091  Score=62.13  Aligned_cols=105  Identities=21%  Similarity=0.330  Sum_probs=74.7

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC-CCceEEEeCCCCHHHHHHHHHHhh----cCCCCEEEEcCccccccCCCC--CcE
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH-GYPVTSIHGDRTQKEREEALRRFR----SGETPILVATAVAARGLDIPH--VKH  179 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~r~~~~~~f~----~g~~~vlv~T~~~~~Gvdl~~--~~~  179 (237)
                      ..+.++||.++....+.++..|... +.. ...+|..   .+.++++.|+    .+.-.||++|..+.+|||+|+  +.+
T Consensus       533 ~~gg~LVlFtSy~~l~~v~~~l~~~~~~~-ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~  608 (697)
T PRK11747        533 KHKGSLVLFASRRQMQKVADLLPRDLRLM-LLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQ  608 (697)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHhcCCc-EEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEE
Confidence            3445899999999999999988643 333 3445643   4566776666    466779999999999999987  567


Q ss_pred             EEEecCCC----CH--------------------------HHHHHhhcccccCCCCCceEEeecCC
Q psy15610        180 VINFDLPS----DV--------------------------EEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       180 Vi~~~~p~----s~--------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      ||....|.    ++                          ..+.|.+||.-|...+..+++++++.
T Consensus       609 vII~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~R  674 (697)
T PRK11747        609 VIITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRR  674 (697)
T ss_pred             EEEEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEccc
Confidence            87765442    22                          13468889999987665566666654

>KOG0331|consensus

Probab=97.54  E-value=0.00011  Score=64.70  Aligned_cols=97  Identities=31%  Similarity=0.424  Sum_probs=77.0

Q ss_pred             ccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHH
Q psy15610         18 VGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE   97 (237)
Q Consensus        18 ~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   97 (237)
                      .+.....|....-...+..|+..++.-.......+      +||||+|+..++++.+.+...++++..+|++.+|..|..
T Consensus       309 a~~~i~qive~~~~~~K~~~l~~lL~~~~~~~~~K------vIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~  382 (519)
T KOG0331|consen  309 ANHNIRQIVEVCDETAKLRKLGKLLEDISSDSEGK------VIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDW  382 (519)
T ss_pred             hhcchhhhhhhcCHHHHHHHHHHHHHHHhccCCCc------EEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHH
Confidence            44455566666667788888866666665444443      999999999999999999999999999999999999998


Q ss_pred             HhhhhhhccCCceEEEEeecccchHHH
Q psy15610         98 AQQYTLISCDEALTLVFVETKKGADQL  124 (237)
Q Consensus        98 ~~~~~~~~~~~~~~iIF~~t~~~~~~l  124 (237)
                      .    +..+..++.-|.+.|...++.+
T Consensus       383 ~----L~~FreG~~~vLVATdVAaRGL  405 (519)
T KOG0331|consen  383 V----LKGFREGKSPVLVATDVAARGL  405 (519)
T ss_pred             H----HHhcccCCcceEEEcccccccC
Confidence            8    5557778888888887766654

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

Probab=97.50  E-value=0.00039  Score=64.29  Aligned_cols=114  Identities=21%  Similarity=0.183  Sum_probs=86.6

Q ss_pred             hhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCc--
Q psy15610        101 YTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVK--  178 (237)
Q Consensus       101 ~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~--  178 (237)
                      .......++++||-+.+.+..+.+.+.|.+.|++..++...-...+-+.+..+-+  .-.|-|+|..+++|-|+.--.  
T Consensus       422 I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h~~EA~Iia~AG~--~gaVTiATNMAGRGTDIkLg~~~  499 (822)
T COG0653         422 IKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNHAREAEIIAQAGQ--PGAVTIATNMAGRGTDIKLGGNP  499 (822)
T ss_pred             HHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccHHHHHHHHhhcCC--CCccccccccccCCcccccCCCH
Confidence            4455678999999999999999999999999999888887655433333333222  234778999999999985433  


Q ss_pred             ---------EEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        179 ---------HVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       179 ---------~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                               +||-.....|..---|-.||+||.|-+|...+|++..+
T Consensus       500 ~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSleD  546 (822)
T COG0653         500 EFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  546 (822)
T ss_pred             HHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhhHH
Confidence                     46666666666666699999999999999888887544

>KOG1001|consensus

Probab=97.43  E-value=1.4e-05  Score=73.03  Aligned_cols=102  Identities=18%  Similarity=0.205  Sum_probs=91.5

Q ss_pred             ceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCC-C-EEEEcCccccccCCCCCcEEEEecCC
Q psy15610        109 ALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGET-P-ILVATAVAARGLDIPHVKHVINFDLP  186 (237)
Q Consensus       109 ~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~-~-vlv~T~~~~~Gvdl~~~~~Vi~~~~p  186 (237)
                      .+++||+.-...+..+...|...++....+.|.|+...|.+.+..|.++.. . .+++..+++.|+|+..+.+|+..|+-
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            489999999999999999998889999999999999999999999996653 3 44667999999999999999999999


Q ss_pred             CCHHHHHHhhcccccCCCCCceEE
Q psy15610        187 SDVEEYVHRIGRTGRMGNLDFPFS  210 (237)
Q Consensus       187 ~s~~~~~Q~~GR~~R~g~~~~~~~  210 (237)
                      |++...-|.+.|++|.|+...+.+
T Consensus       620 wnp~~eeQaidR~hrigq~k~v~v  643 (674)
T KOG1001|consen  620 WNPAVEEQAIDRAHRIGQTKPVKV  643 (674)
T ss_pred             cChHHHHHHHHHHHHhcccceeee
Confidence            999999999999999998765544

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=97.26  E-value=0.0048  Score=45.49  Aligned_cols=79  Identities=24%  Similarity=0.224  Sum_probs=54.6

Q ss_pred             EEEeCCCCHHHHHHHHHHhhcCCC-CEEEEcCccccccCCCCC--cEEEEecCCC----C--------------------
Q psy15610        136 TSIHGDRTQKEREEALRRFRSGET-PILVATAVAARGLDIPHV--KHVINFDLPS----D--------------------  188 (237)
Q Consensus       136 ~~~h~~~~~~~r~~~~~~f~~g~~-~vlv~T~~~~~Gvdl~~~--~~Vi~~~~p~----s--------------------  188 (237)
                      ..+.-+....+...+++.|++..- .||+++..+.+|+|+|+-  ..||....|.    +                    
T Consensus        25 ~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~  104 (141)
T smart00492       25 LLLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPFPYPDSPILKARLELLRDKGQIRPFD  104 (141)
T ss_pred             eEEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhCCCCchh
Confidence            444444566667888999987543 799999889999999974  5677766542    1                    


Q ss_pred             -------HHHHHHhhcccccCCCCCceEEeecC
Q psy15610        189 -------VEEYVHRIGRTGRMGNLDFPFSYNQP  214 (237)
Q Consensus       189 -------~~~~~Q~~GR~~R~g~~~~~~~~~~~  214 (237)
                             ...+.|.+||+-|...+-.++++++.
T Consensus       105 ~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~l~D~  137 (141)
T smart00492      105 FVSLPDAMRTLAQCVGRLIRGANDYGVVVIADK  137 (141)
T ss_pred             HHHHHHHHHHHHHHhCccccCcCceEEEEEEec
Confidence                   12345888999997766556666544

>KOG0332|consensus

Probab=97.20  E-value=0.0019  Score=54.27  Aligned_cols=104  Identities=23%  Similarity=0.339  Sum_probs=80.3

Q ss_pred             HHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccc
Q psy15610         41 LLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG  120 (237)
Q Consensus        41 l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~  120 (237)
                      |..++.--+         .||||.|+..+..++..+...|+.+..+|+++....|..+    +..++.++.-|...|..-
T Consensus       324 lyg~~tigq---------siIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~i----i~~Fr~g~~kVLitTnV~  390 (477)
T KOG0332|consen  324 LYGLLTIGQ---------SIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAI----IDRFREGKEKVLITTNVC  390 (477)
T ss_pred             HHhhhhhhh---------eEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHH----HHHHhcCcceEEEEechh
Confidence            555555555         8999999999999999999999999999999999998877    444445555555555554


Q ss_pred             hHHH-----------------------HHHHhhC---------CCceEEEeCCCCHHHHHHHHHHhhcC
Q psy15610        121 ADQL-----------------------EDFLHHH---------GYPVTSIHGDRTQKEREEALRRFRSG  157 (237)
Q Consensus       121 ~~~l-----------------------~~~L~~~---------~~~~~~~h~~~~~~~r~~~~~~f~~g  157 (237)
                      ++.+                       +.||++.         |..+.++|.+-+.+.-.++.+.|...
T Consensus       391 ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~  459 (477)
T KOG0332|consen  391 ARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMK  459 (477)
T ss_pred             hcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhc
Confidence            4444                       6777754         55678899999998888888988653

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=97.09  E-value=0.0042  Score=45.89  Aligned_cols=93  Identities=22%  Similarity=0.303  Sum_probs=58.0

Q ss_pred             HHHHHHHhhCCC---ceEEEeCCCCHHHHHHHHHHhhcCCC---CEEEEcCc--cccccCCCC--CcEEEEecCCC----
Q psy15610        122 DQLEDFLHHHGY---PVTSIHGDRTQKEREEALRRFRSGET---PILVATAV--AARGLDIPH--VKHVINFDLPS----  187 (237)
Q Consensus       122 ~~l~~~L~~~~~---~~~~~h~~~~~~~r~~~~~~f~~g~~---~vlv~T~~--~~~Gvdl~~--~~~Vi~~~~p~----  187 (237)
                      +.+.+.+...+.   ...++.-+....+...+++.|++..-   .||+++.-  +.+|+|+|+  ++.||....|.    
T Consensus         5 ~~v~~~~~~~~~~~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~~~   84 (142)
T smart00491        5 EQVVEYWKENGILEINKPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPNPD   84 (142)
T ss_pred             HHHHHHHHhcCccccCceEEEECCCCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCCCCCC
Confidence            444555544332   22233323333345678888886543   58888866  999999998  46777766552    


Q ss_pred             CH---------------------------HHHHHhhcccccCCCCCceEEeecC
Q psy15610        188 DV---------------------------EEYVHRIGRTGRMGNLDFPFSYNQP  214 (237)
Q Consensus       188 s~---------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~  214 (237)
                      ++                           ..+.|.+||+-|..++-.++++++.
T Consensus        85 d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~Qa~GR~iR~~~D~g~i~l~D~  138 (142)
T smart00491       85 SPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDK  138 (142)
T ss_pred             CHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHhCccccCccceEEEEEEec
Confidence            11                           2345888999998777666666654

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

Probab=97.09  E-value=0.0067  Score=55.42  Aligned_cols=115  Identities=16%  Similarity=0.140  Sum_probs=80.1

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC----CCCEEEEcCccccccCC-------
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG----ETPILVATAVAARGLDI-------  174 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g----~~~vlv~T~~~~~Gvdl-------  174 (237)
                      ..++.++|.+.+...++.+++.|...---...+.|+.+  .+..+++.|++.    .-.||++|+.+.+|+|+       
T Consensus       468 ~~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~p  545 (636)
T TIGR03117       468 KAQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSP  545 (636)
T ss_pred             HcCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCCC
Confidence            34678999999999999999998654223345556443  345577888764    68899999999999999       


Q ss_pred             -CC--CcEEEEecCCC-------------------------CHHHHHHhhcccccCCCC--CceEEeecCCCCCCCCC
Q psy15610        175 -PH--VKHVINFDLPS-------------------------DVEEYVHRIGRTGRMGNL--DFPFSYNQPGYGGSYGG  222 (237)
Q Consensus       175 -~~--~~~Vi~~~~p~-------------------------s~~~~~Q~~GR~~R~g~~--~~~~~~~~~~~~~~~~~  222 (237)
                       |.  +.+||....|.                         ..-.+.|-+||.-|....  ...+.++++.-...|+.
T Consensus       546 ~~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~R~~~~yg~  623 (636)
T TIGR03117       546 DKDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGRIHWPYME  623 (636)
T ss_pred             CCCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeCCCCchhHH
Confidence             22  66777655441                         122456888998887766  56667777665555654

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.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.04  E-value=0.0018  Score=60.67  Aligned_cols=46  Identities=28%  Similarity=0.403  Sum_probs=31.2

Q ss_pred             echhHHHHHHHhhcCchhh-----hcccccceeEEeecccchhhHHHHhhh
Q psy15610         33 DEQDKRSCLLDLLSSPSQE-----ELGDEALTLVFVETKKGADQLEDFLHH   78 (237)
Q Consensus        33 ~~~~k~~~l~~ll~~~~~~-----~~~~~~~~i~f~~t~~~~~~~~~~l~~   78 (237)
                      ++..|...|.++|..-...     ...++.++|+||.....+.++.++|..
T Consensus       267 Ee~PKw~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       267 EENPKWEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             ccCCCHHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHh
Confidence            5677888888888553222     113456688888888888888887743

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

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=96.91  E-value=0.006  Score=58.06  Aligned_cols=91  Identities=23%  Similarity=0.228  Sum_probs=65.0

Q ss_pred             EEEEeecccchHHHHHHHhhC------CCceEEEeCCCCHHHHHHHHHHh----------------------hc----CC
Q psy15610        111 TLVFVETKKGADQLEDFLHHH------GYPVTSIHGDRTQKEREEALRRF----------------------RS----GE  158 (237)
Q Consensus       111 ~iIF~~t~~~~~~l~~~L~~~------~~~~~~~h~~~~~~~r~~~~~~f----------------------~~----g~  158 (237)
                      .+|=.++.+.+-.++..|...      .+.+.+||+..+-..|..+++..                      .+    +.
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            345566666676776666543      24578899999877777766543                      11    35


Q ss_pred             CCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCC
Q psy15610        159 TPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN  204 (237)
Q Consensus       159 ~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~  204 (237)
                      ..|+|+|.+.+.|+|+ +.+++|-  -|.+...++|++||+.|-|.
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            6799999999999996 3444443  45669999999999999774

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.

>KOG0326|consensus

Probab=96.86  E-value=0.0013  Score=54.26  Aligned_cols=58  Identities=17%  Similarity=0.298  Sum_probs=50.6

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +-.=+..|+.-|.-.+         .|+||++...+|.++..+.+.|++|+++|..|.|..|+++++
T Consensus       309 KvhCLntLfskLqINQ---------sIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFH  366 (459)
T KOG0326|consen  309 KVHCLNTLFSKLQINQ---------SIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFH  366 (459)
T ss_pred             hhhhHHHHHHHhcccc---------eEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhh
Confidence            3344566776676677         899999999999999999999999999999999999999976

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.57  E-value=0.0091  Score=55.48  Aligned_cols=76  Identities=25%  Similarity=0.284  Sum_probs=63.9

Q ss_pred             CCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-cccccCCCCCcEEE
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-AARGLDIPHVKHVI  181 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~~~Gvdl~~~~~Vi  181 (237)
                      .+.+++|.+||+.-+.++++.+.+    .++++..+||+++..+|...+....+|..+|+|+|.. +...+.+.++.+||
T Consensus       309 ~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvV  388 (681)
T PRK10917        309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI  388 (681)
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEE
Confidence            467899999999988887776654    4789999999999999999999999999999999965 44466788888766


Q ss_pred             E
Q psy15610        182 N  182 (237)
Q Consensus       182 ~  182 (237)
                      .
T Consensus       389 I  389 (681)
T PRK10917        389 I  389 (681)
T ss_pred             E
Confidence            4

>KOG0333|consensus

Probab=96.56  E-value=0.004  Score=54.58  Aligned_cols=78  Identities=33%  Similarity=0.527  Sum_probs=60.0

Q ss_pred             echhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEE
Q psy15610         33 DEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTL  112 (237)
Q Consensus        33 ~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  112 (237)
                      ++..|+.-+++-...+.         +|+|+|++.+++.++..|...++.+..+|+...|..|..++    ..+..+..=
T Consensus       503 ~k~kkL~eil~~~~~pp---------iIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL----~~fr~~t~d  569 (673)
T KOG0333|consen  503 EKRKKLIEILESNFDPP---------IIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENAL----ADFREGTGD  569 (673)
T ss_pred             HHHHHHHHHHHhCCCCC---------EEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHH----HHHHhcCCC
Confidence            44566655555444444         99999999999999999999999999999999999998884    444455566


Q ss_pred             EEeecccchHH
Q psy15610        113 VFVETKKGADQ  123 (237)
Q Consensus       113 IF~~t~~~~~~  123 (237)
                      ||+.|...++.
T Consensus       570 IlVaTDvAgRG  580 (673)
T KOG0333|consen  570 ILVATDVAGRG  580 (673)
T ss_pred             EEEEecccccC
Confidence            77777665443

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.33  E-value=0.022  Score=52.97  Aligned_cols=75  Identities=21%  Similarity=0.293  Sum_probs=62.2

Q ss_pred             CCceEEEEeecccchHHHHHHHhh-CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH-HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN  182 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~-~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~  182 (237)
                      .+.+++|.+|+...+.++.+.+.+ .+..+..+||+++..+|.+.+....+|..+|+|+|.... -..+.+...||.
T Consensus       189 ~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal-~~p~~~l~liVv  264 (679)
T PRK05580        189 QGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSAL-FLPFKNLGLIIV  264 (679)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHh-cccccCCCEEEE
Confidence            467899999999999999888876 477899999999999999999999999999999997432 244566666664

>KOG0328|consensus

Probab=96.29  E-value=0.0056  Score=49.78  Aligned_cols=56  Identities=29%  Similarity=0.498  Sum_probs=45.7

Q ss_pred             eEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeeccc
Q psy15610         60 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKK  119 (237)
Q Consensus        60 i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~  119 (237)
                      ++||+|+..+..+.+.+...+|.+...|+++.|.+|+.+    ...+..+++-|...|..
T Consensus       270 vIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~i----m~dFRsg~SrvLitTDV  325 (400)
T KOG0328|consen  270 VIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKI----MNDFRSGKSRVLITTDV  325 (400)
T ss_pred             EEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHH----HHHhhcCCceEEEEech
Confidence            789999999999999999999999999999999999877    44444455445555544

>TIGR00595 priA primosomal protein N'

Probab=96.25  E-value=0.022  Score=51.03  Aligned_cols=74  Identities=22%  Similarity=0.280  Sum_probs=61.3

Q ss_pred             CceEEEEeecccchHHHHHHHhhC-CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH-GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN  182 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~  182 (237)
                      +.+++|.+|+...+.++.+.|.+. +..+.++||+++..+|........+|..+|+|+|...-. ..+++...||.
T Consensus        25 g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~lIIV   99 (505)
T TIGR00595        25 GKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGLIIV   99 (505)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCEEEE
Confidence            578999999999999998888754 678999999999999999999999999999999965332 34566666664

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).

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=96.05  E-value=0.021  Score=52.71  Aligned_cols=76  Identities=22%  Similarity=0.254  Sum_probs=63.2

Q ss_pred             CCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCcc-ccccCCCCCcEEE
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA-ARGLDIPHVKHVI  181 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~-~~Gvdl~~~~~Vi  181 (237)
                      .+.++++.+||+.-+.++++.+.+    .++++..++|+++..+|...++...+|..+|+|+|..+ ...+.+.++.+||
T Consensus       283 ~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvV  362 (630)
T TIGR00643       283 AGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVI  362 (630)
T ss_pred             cCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEE
Confidence            466899999999998888776654    37899999999999999999999999999999999653 3456777777766


Q ss_pred             E
Q psy15610        182 N  182 (237)
Q Consensus       182 ~  182 (237)
                      .
T Consensus       363 I  363 (630)
T TIGR00643       363 I  363 (630)
T ss_pred             E
Confidence            4

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

Probab=95.97  E-value=0.094  Score=47.00  Aligned_cols=75  Identities=21%  Similarity=0.353  Sum_probs=62.7

Q ss_pred             CceeEEEEee-chhHHHHHHHhhcCchhhh--cccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHH
Q psy15610         24 NITQRIAWVD-EQDKRSCLLDLLSSPSQEE--LGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        24 ~i~~~~~~~~-~~~k~~~l~~ll~~~~~~~--~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   98 (237)
                      .++...+.+. +.+|.+.+..|.+....+.  -+..+|.|+|++++.++.+++..|...|.++.-.|..+....|..+
T Consensus       405 plErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~v  482 (830)
T COG1202         405 PLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSV  482 (830)
T ss_pred             ChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHH
Confidence            4444455555 6789999999998765444  4678999999999999999999999999999999999998888766

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.96  E-value=0.025  Score=52.22  Aligned_cols=142  Identities=12%  Similarity=0.074  Sum_probs=84.4

Q ss_pred             ccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh---hhh-------hccCCceEEEEeecccchHH
Q psy15610         54 GDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ---YTL-------ISCDEALTLVFVETKKGADQ  123 (237)
Q Consensus        54 ~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~---~~~-------~~~~~~~~iIF~~t~~~~~~  123 (237)
                      ..+ ++|+|.+.+.....+...=...-..|......+.-........   +..       -.+++.   -|-....-.+.
T Consensus       367 ~~g-qvll~lnRrGyap~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~---~l~~~g~Gter  442 (665)
T PRK14873        367 EHG-PVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD---RLRAVVVGARR  442 (665)
T ss_pred             hcC-cEEEEecCCCCCCeeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC---cceeeeccHHH
Confidence            345 9999999999877655555555555555554444322111111   111       111111   12233345667


Q ss_pred             HHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC----ccccccCCCCCcEEEEecC------CC----
Q psy15610        124 LEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATA----VAARGLDIPHVKHVINFDL------PS----  187 (237)
Q Consensus       124 l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~----~~~~Gvdl~~~~~Vi~~~~------p~----  187 (237)
                      +++.|.+.  +.++....+       ..+++.|. ++.+|||+|.    ++.     ++++.|+..|.      |.    
T Consensus       443 ~eeeL~~~FP~~~V~r~d~-------d~~l~~~~-~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfRA~  509 (665)
T PRK14873        443 TAEELGRAFPGVPVVTSGG-------DQVVDTVD-AGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLRAA  509 (665)
T ss_pred             HHHHHHHHCCCCCEEEECh-------HHHHHhhc-cCCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcChH
Confidence            77777654  555655443       24788887 5899999998    444     35566665443      21    


Q ss_pred             --CHHHHHHhhcccccCCCCCceEEee
Q psy15610        188 --DVEEYVHRIGRTGRMGNLDFPFSYN  212 (237)
Q Consensus       188 --s~~~~~Q~~GR~~R~g~~~~~~~~~  212 (237)
                        ....++|.+||+||.+..|.+++-.
T Consensus       510 Er~~qll~qvagragr~~~~G~V~iq~  536 (665)
T PRK14873        510 EDTLRRWMAAAALVRPRADGGQVVVVA  536 (665)
T ss_pred             HHHHHHHHHHHHhhcCCCCCCEEEEEe
Confidence              3556789999999988888887764

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.75  E-value=0.05  Score=50.29  Aligned_cols=75  Identities=20%  Similarity=0.180  Sum_probs=61.2

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC-C-CceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH-G-YPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN  182 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~-~-~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~  182 (237)
                      .+.++||.++......++.+.|... + ..+.++|+++++.+|.+.+....+|+.+|+|.|..+- =.-+++.-.||.
T Consensus       187 ~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAv-FaP~~~LgLIIv  263 (665)
T PRK14873        187 AGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAV-FAPVEDLGLVAI  263 (665)
T ss_pred             cCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeE-EeccCCCCEEEE
Confidence            4678999999999999998888764 4 6799999999999999999999999999999996542 123445555554

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=95.64  E-value=0.04  Score=52.84  Aligned_cols=76  Identities=22%  Similarity=0.256  Sum_probs=63.2

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-cccccCCCCCcEEE
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-AARGLDIPHVKHVI  181 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~~~Gvdl~~~~~Vi  181 (237)
                      .+.+++|.+||+.-+.++.+.+.+.    ++++..++|..+..++.+..+.+++|..+|+|+|.. +...+.+.++.++|
T Consensus       499 ~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llV  578 (926)
T TIGR00580       499 DGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLI  578 (926)
T ss_pred             hCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEE
Confidence            4578999999999999988877653    667889999999999999999999999999999964 44456777887766


Q ss_pred             E
Q psy15610        182 N  182 (237)
Q Consensus       182 ~  182 (237)
                      .
T Consensus       579 I  579 (926)
T TIGR00580       579 I  579 (926)
T ss_pred             e
Confidence            4

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.

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

Probab=95.44  E-value=0.046  Score=50.76  Aligned_cols=74  Identities=26%  Similarity=0.287  Sum_probs=59.5

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC-CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEE
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH-GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI  181 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi  181 (237)
                      ++.++||.+|......++...+... +.++..+|+++++.+|...+.+..+|+.+|+|.|..+- =.-+++.-.||
T Consensus       244 ~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl-F~Pf~~LGLII  318 (730)
T COG1198         244 QGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSAL-FLPFKNLGLII  318 (730)
T ss_pred             cCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhh-cCchhhccEEE
Confidence            3689999999999888887777654 88999999999999999999999999999999996431 12334444444

>PRK10689 transcription-repair coupling factor; Provisional

Probab=95.28  E-value=0.067  Score=52.52  Aligned_cols=77  Identities=19%  Similarity=0.167  Sum_probs=62.2

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhC----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-cccccCCCCCcEE
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHH----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-AARGLDIPHVKHV  180 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~~~Gvdl~~~~~V  180 (237)
                      .++.+++|.+||+..+.++...+.+.    ++.+..++|..+..++.++++..++|..+|+|+|.. +...+.+.++.++
T Consensus       647 ~~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lL  726 (1147)
T PRK10689        647 ENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLL  726 (1147)
T ss_pred             HcCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEE
Confidence            35678999999999999998877642    467788999999999999999999999999999964 3334566677765


Q ss_pred             EE
Q psy15610        181 IN  182 (237)
Q Consensus       181 i~  182 (237)
                      |.
T Consensus       727 VI  728 (1147)
T PRK10689        727 IV  728 (1147)
T ss_pred             EE
Confidence            53

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=95.10  E-value=0.061  Score=51.07  Aligned_cols=64  Identities=30%  Similarity=0.376  Sum_probs=52.8

Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhC----C-CceEE-EeCCCCHHHHHHHHHHhhcCCCCEEEEcCc
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHH----G-YPVTS-IHGDRTQKEREEALRRFRSGETPILVATAV  167 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~----~-~~~~~-~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~  167 (237)
                      ...++.++.+.+||..-+.+..+-|...    + ..+.+ ||+.++..+++...++|.+|.++|+|+|..
T Consensus       121 ~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         121 LAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             HHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            3455789999999999888887777654    2 44433 999999999999999999999999999964

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

Probab=95.04  E-value=0.023  Score=51.09  Aligned_cols=79  Identities=29%  Similarity=0.406  Sum_probs=61.9

Q ss_pred             echhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEE
Q psy15610         33 DEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTL  112 (237)
Q Consensus        33 ~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  112 (237)
                      ++.+-+..+++.....+         +|+||+|+..++.++..|...|+.+..+|+++.|..|.....    .+..++.-
T Consensus       259 ~k~~~L~~ll~~~~~~~---------~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~----~F~~g~~~  325 (513)
T COG0513         259 EKLELLLKLLKDEDEGR---------VIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALE----KFKDGELR  325 (513)
T ss_pred             HHHHHHHHHHhcCCCCe---------EEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHH----HHHcCCCC
Confidence            46677777777776666         899999999999999999999999999999999999998844    33345555


Q ss_pred             EEeecccchHHH
Q psy15610        113 VFVETKKGADQL  124 (237)
Q Consensus       113 IF~~t~~~~~~l  124 (237)
                      |.+.|...++.+
T Consensus       326 vLVaTDvaaRGi  337 (513)
T COG0513         326 VLVATDVAARGL  337 (513)
T ss_pred             EEEEechhhccC
Confidence            555565554443

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

Probab=94.91  E-value=0.17  Score=46.27  Aligned_cols=78  Identities=24%  Similarity=0.286  Sum_probs=64.8

Q ss_pred             ccCCceEEEEeecccchH----HHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCcc-ccccCCCCCcE
Q psy15610        105 SCDEALTLVFVETKKGAD----QLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA-ARGLDIPHVKH  179 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~----~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~-~~Gvdl~~~~~  179 (237)
                      ...+.++...+||---|+    .+.++|...++++..+.|++....|..++....+|.++++|.|.++ ...+++.+.-+
T Consensus       308 i~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgL  387 (677)
T COG1200         308 IEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGL  387 (677)
T ss_pred             HHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeE
Confidence            455778999999966555    4556666679999999999999999999999999999999999875 45888888777


Q ss_pred             EEE
Q psy15610        180 VIN  182 (237)
Q Consensus       180 Vi~  182 (237)
                      ||.
T Consensus       388 VIi  390 (677)
T COG1200         388 VII  390 (677)
T ss_pred             EEE
Confidence            665

>KOG0342|consensus

Probab=94.64  E-value=0.027  Score=49.14  Aligned_cols=73  Identities=23%  Similarity=0.281  Sum_probs=57.5

Q ss_pred             HHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecc
Q psy15610         39 SCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETK  118 (237)
Q Consensus        39 ~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~  118 (237)
                      ..|.+-+..+.         +|+|+.|...+..+++.|...+.++.+||+...|+.|+..    ...+......|.+.|.
T Consensus       322 ~~LKk~~~~~K---------iiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~----~~~F~kaesgIL~cTD  388 (543)
T KOG0342|consen  322 TFLKKNIKRYK---------IIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTST----FFEFCKAESGILVCTD  388 (543)
T ss_pred             HHHHHhcCCce---------EEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchH----HHHHhhcccceEEecc
Confidence            45566666344         9999999999999999999999999999999999999877    3334455566666676


Q ss_pred             cchHHH
Q psy15610        119 KGADQL  124 (237)
Q Consensus       119 ~~~~~l  124 (237)
                      ..|+.+
T Consensus       389 VaARGl  394 (543)
T KOG0342|consen  389 VAARGL  394 (543)
T ss_pred             hhhccC
Confidence            666655

>PRK14701 reverse gyrase; Provisional

Probab=94.32  E-value=0.14  Score=51.90  Aligned_cols=61  Identities=25%  Similarity=0.292  Sum_probs=53.1

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH------GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV  167 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~  167 (237)
                      ++.+++|.+||+.-+.++.+.+...      +..+..+||+++..++...++.+.+|..+|+|+|+-
T Consensus       121 ~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        121 KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            5668999999999999888887752      456788999999999999999999999999999964

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=94.26  E-value=0.23  Score=46.48  Aligned_cols=104  Identities=15%  Similarity=0.165  Sum_probs=74.9

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCc--EEEEec
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVK--HVINFD  184 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~--~Vi~~~  184 (237)
                      .+..+-||+.|...++.++++....+..+..+++..+..+.+    .  =++.+|++=|.++..|+++-+..  -++.|=
T Consensus       281 ~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv~----~--W~~~~VviYT~~itvG~Sf~~~HF~~~f~yv  354 (824)
T PF02399_consen  281 AGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDVE----S--WKKYDVVIYTPVITVGLSFEEKHFDSMFAYV  354 (824)
T ss_pred             CCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccccc----c--ccceeEEEEeceEEEEeccchhhceEEEEEe
Confidence            456677999999999999999998888888888876665321    1  24688999999999999886543  344442


Q ss_pred             CC----CCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        185 LP----SDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       185 ~p----~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      -|    .+..+..|++||+-... ....++++++...
T Consensus       355 k~~~~gpd~~s~~Q~lgRvR~l~-~~ei~v~~d~~~~  390 (824)
T PF02399_consen  355 KPMSYGPDMVSVYQMLGRVRSLL-DNEIYVYIDASGA  390 (824)
T ss_pred             cCCCCCCcHHHHHHHHHHHHhhc-cCeEEEEEecccc
Confidence            22    24556789999997765 4566677765433

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

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

Probab=94.20  E-value=0.2  Score=48.51  Aligned_cols=77  Identities=19%  Similarity=0.255  Sum_probs=66.4

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhC----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEc-CccccccCCCCCcEE
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHH----GYPVTSIHGDRTQKEREEALRRFRSGETPILVAT-AVAARGLDIPHVKHV  180 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T-~~~~~Gvdl~~~~~V  180 (237)
                      .++.++.|.+||.--+++..+-+.++    .+++..++.-.+..+...+++..++|.++|+|.| ..+..++.+.+.-.+
T Consensus       641 ~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLl  720 (1139)
T COG1197         641 MDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLL  720 (1139)
T ss_pred             cCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeE
Confidence            45789999999999998887777654    6678899999999999999999999999999999 567888888888776


Q ss_pred             EE
Q psy15610        181 IN  182 (237)
Q Consensus       181 i~  182 (237)
                      |.
T Consensus       721 II  722 (1139)
T COG1197         721 II  722 (1139)
T ss_pred             EE
Confidence            64

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

Probab=94.02  E-value=0.15  Score=47.95  Aligned_cols=57  Identities=23%  Similarity=0.372  Sum_probs=43.9

Q ss_pred             hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhc--------CCCceeecCCcchhhHHHHhh
Q psy15610         36 DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHH--------GYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        36 ~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~--------~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      ++...+.+++..        +.++|+||+|+..++.+++.+...        +..+..+|+.+.+..|..+..
T Consensus       259 ~~~~~l~~l~~~--------~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~  323 (742)
T TIGR03817       259 EAADLLADLVAE--------GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELER  323 (742)
T ss_pred             HHHHHHHHHHHC--------CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHH
Confidence            355556555542        357999999999999999988653        567788999999999887744

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.

>KOG0298|consensus

Probab=94.02  E-value=0.067  Score=51.77  Aligned_cols=96  Identities=17%  Similarity=0.167  Sum_probs=69.8

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEE-EEcCccccccCCCCCcEEEEecC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPIL-VATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vl-v~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      ...++|+|+.-....+-++..+.-.++....--+   -++-...+..|++  ++++ +-+...+-|+|+-++.+|+..++
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            3467999999888888777766544433222211   1223344555554  6554 55788899999999999999999


Q ss_pred             CCCHHHHHHhhcccccCCCCCc
Q psy15610        186 PSDVEEYVHRIGRTGRMGNLDF  207 (237)
Q Consensus       186 p~s~~~~~Q~~GR~~R~g~~~~  207 (237)
                      -.++..-.|.+||++|.|+..-
T Consensus      1295 iLN~~~E~QAigRvhRiGQ~~p 1316 (1394)
T KOG0298|consen 1295 ILNPGDEAQAIGRVHRIGQKRP 1316 (1394)
T ss_pred             ccCchHHHhhhhhhhhcccccc
Confidence            9999999999999999997643

>KOG4284|consensus

Probab=94.02  E-value=0.038  Score=49.98  Aligned_cols=80  Identities=23%  Similarity=0.238  Sum_probs=66.0

Q ss_pred             eechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceE
Q psy15610         32 VDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALT  111 (237)
Q Consensus        32 ~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  111 (237)
                      ..+-+++.-+++-|-..+         +|+||.....++.++..|...|+++..+.+.|.|+.|..+..    ......+
T Consensus       257 rlklq~L~~vf~~ipy~Q---------AlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~----~lr~f~~  323 (980)
T KOG4284|consen  257 RLKLQKLTHVFKSIPYVQ---------ALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVD----QLRAFRV  323 (980)
T ss_pred             HHHHHHHHHHHhhCchHH---------HHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHH----HhhhceE
Confidence            456789999999999999         899999999999999999999999999999999999987733    3334556


Q ss_pred             EEEeecccchHHH
Q psy15610        112 LVFVETKKGADQL  124 (237)
Q Consensus       112 iIF~~t~~~~~~l  124 (237)
                      -|.+.|.-.++.+
T Consensus       324 rILVsTDLtaRGI  336 (980)
T KOG4284|consen  324 RILVSTDLTARGI  336 (980)
T ss_pred             EEEEecchhhccC
Confidence            6666666655554

>KOG0701|consensus

Probab=93.88  E-value=0.039  Score=54.96  Aligned_cols=95  Identities=28%  Similarity=0.446  Sum_probs=76.7

Q ss_pred             ceEEEEeecccchHHHHHHHhhC-CCceEEEeCCCCH-----------HHHHHHHHHhhcCCCCEEEEcCccccccCCCC
Q psy15610        109 ALTLVFVETKKGADQLEDFLHHH-GYPVTSIHGDRTQ-----------KEREEALRRFRSGETPILVATAVAARGLDIPH  176 (237)
Q Consensus       109 ~~~iIF~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~-----------~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~  176 (237)
                      -..++||+.+..+....+.+.+. ...+..+-|.+.+           ..+..++..|......+|+.|.++.+|+|++.
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~  372 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPK  372 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhh
Confidence            46889999998888877777654 2333345554332           33667788899999999999999999999999


Q ss_pred             CcEEEEecCCCCHHHHHHhhcccccCC
Q psy15610        177 VKHVINFDLPSDVEEYVHRIGRTGRMG  203 (237)
Q Consensus       177 ~~~Vi~~~~p~s~~~~~Q~~GR~~R~g  203 (237)
                      ++.++.++.|.....|+|..||+-+.+
T Consensus       373 ~~~~~~~~~~~~~~~~vq~~~r~~~~~  399 (1606)
T KOG0701|consen  373 CNLVVLFDAPTYYRSYVQKKGRARAAD  399 (1606)
T ss_pred             hhhheeccCcchHHHHHHhhcccccch
Confidence            999999999999999999999997764

>KOG1513|consensus

Probab=93.56  E-value=0.079  Score=49.14  Aligned_cols=56  Identities=23%  Similarity=0.490  Sum_probs=47.1

Q ss_pred             HHHHhhcCCCCEEEEcCccccccCCCCCcE--------EEEecCCCCHHHHHHhhcccccCCCC
Q psy15610        150 ALRRFRSGETPILVATAVAARGLDIPHVKH--------VINFDLPSDVEEYVHRIGRTGRMGNL  205 (237)
Q Consensus       150 ~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~--------Vi~~~~p~s~~~~~Q~~GR~~R~g~~  205 (237)
                      --++|-.|+-.|.|-+.+++-|+.++.-..        -|-+..|||...-+|..||.+|..+.
T Consensus       849 EKqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQV  912 (1300)
T KOG1513|consen  849 EKQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQV  912 (1300)
T ss_pred             HHhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhccccccccc
Confidence            345788899899999999999999886544        45588999999999999999998754

>KOG0335|consensus

Probab=93.47  E-value=0.14  Score=45.06  Aligned_cols=91  Identities=42%  Similarity=0.540  Sum_probs=64.7

Q ss_pred             EEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccC
Q psy15610         28 RIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCD  107 (237)
Q Consensus        28 ~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  107 (237)
                      ++..-++..++-.++.-..-.....-+....+++|++|+..+.+++.+|...++++..+|++..|..|...    +-.+.
T Consensus       309 ~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~a----l~~Fr  384 (482)
T KOG0335|consen  309 FVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQA----LNDFR  384 (482)
T ss_pred             eecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHH----HHHhh
Confidence            44455666666555554442222223344469999999999999999999999999999999999999877    45555


Q ss_pred             CceEEEEeecccchH
Q psy15610        108 EALTLVFVETKKGAD  122 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~  122 (237)
                      ..+.-|++.|.-.++
T Consensus       385 ~g~~pvlVaT~VaaR  399 (482)
T KOG0335|consen  385 NGKAPVLVATNVAAR  399 (482)
T ss_pred             cCCcceEEEehhhhc
Confidence            666667776654433

>PTZ00110 helicase; Provisional

Probab=93.38  E-value=0.089  Score=47.72  Aligned_cols=76  Identities=33%  Similarity=0.475  Sum_probs=54.6

Q ss_pred             eechhHHHHHHHhhc-CchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCce
Q psy15610         32 VDEQDKRSCLLDLLS-SPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEAL  110 (237)
Q Consensus        32 ~~~~~k~~~l~~ll~-~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (237)
                      .++..++..++.-+. ...        ++|+||+|+..++.+++.|...++++..+|+++.+..|..+..    .+..++
T Consensus       360 ~~k~~~L~~ll~~~~~~~~--------k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~----~F~~G~  427 (545)
T PTZ00110        360 HEKRGKLKMLLQRIMRDGD--------KILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLN----EFKTGK  427 (545)
T ss_pred             hhHHHHHHHHHHHhcccCC--------eEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHH----HHhcCC
Confidence            355566655555443 222        2899999999999999999999999999999999999987643    333344


Q ss_pred             EEEEeeccc
Q psy15610        111 TLVFVETKK  119 (237)
Q Consensus       111 ~iIF~~t~~  119 (237)
                      .-|.+.|..
T Consensus       428 ~~ILVaTdv  436 (545)
T PTZ00110        428 SPIMIATDV  436 (545)
T ss_pred             CcEEEEcch
Confidence            445555543

>PHA02653 RNA helicase NPH-II; Provisional

Probab=93.27  E-value=0.52  Score=43.81  Aligned_cols=84  Identities=21%  Similarity=0.285  Sum_probs=58.3

Q ss_pred             HHHhhcceeEEEeeccCCCCCceeEEEEeec----------hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHH
Q psy15610          4 KEFLYRYIFLAIGRVGSTSENITQRIAWVDE----------QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLE   73 (237)
Q Consensus         4 ~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~----------~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~   73 (237)
                      ++|+.+|..+.+.  +.+..+|++.|+....          .++...+ ..+....   ......+|+|+++...++.++
T Consensus       339 ~~~~~~p~~I~I~--grt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l-~~L~~~~---~~~~g~iLVFlpg~~ei~~l~  412 (675)
T PHA02653        339 KEFFPNPAFVHIP--GGTLFPISEVYVKNKYNPKNKRAYIEEEKKNIV-TALKKYT---PPKGSSGIVFVASVSQCEEYK  412 (675)
T ss_pred             HHHhcCCcEEEeC--CCcCCCeEEEEeecCcccccchhhhHHHHHHHH-HHHHHhh---cccCCcEEEEECcHHHHHHHH
Confidence            4788899888874  4456788888875331          1222222 2222110   112357999999999999999


Q ss_pred             HHhhhc--CCCceeecCCcchh
Q psy15610         74 DFLHHH--GYPVTSIHGDRTQK   93 (237)
Q Consensus        74 ~~l~~~--~~~~~~~~~~~~~~   93 (237)
                      +.|...  ++.+..+|+.+.+.
T Consensus       413 ~~L~~~~~~~~v~~LHG~Lsq~  434 (675)
T PHA02653        413 KYLEKRLPIYDFYIIHGKVPNI  434 (675)
T ss_pred             HHHHhhcCCceEEeccCCcCHH
Confidence            999887  68999999999875

>KOG0330|consensus

Probab=93.17  E-value=0.15  Score=43.50  Aligned_cols=59  Identities=24%  Similarity=0.332  Sum_probs=46.4

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccch
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA  121 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~  121 (237)
                      +|+||+|..+...++-.|...|+.+..+|++|.|..|.-.    +..++.+..=|.+.|.-..
T Consensus       303 ~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~----l~~Fk~~~r~iLv~TDVaS  361 (476)
T KOG0330|consen  303 VIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGA----LNKFKAGARSILVCTDVAS  361 (476)
T ss_pred             EEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHH----HHHHhccCCcEEEecchhc
Confidence            8999999999999999999999999999999999998766    3333344333444444433

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=92.82  E-value=0.12  Score=45.88  Aligned_cols=57  Identities=28%  Similarity=0.429  Sum_probs=46.8

Q ss_pred             hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         35 QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        35 ~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      .+.+..++.......         +|+||+|+..++.+++.|...++.+..+|+.+.+..|..+..
T Consensus       230 ~~~l~~ll~~~~~~~---------~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~  286 (460)
T PRK11776        230 LPALQRLLLHHQPES---------CVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLV  286 (460)
T ss_pred             HHHHHHHHHhcCCCc---------eEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHH
Confidence            344545555554445         899999999999999999999999999999999999887744

>TIGR01054 rgy reverse gyrase

Probab=92.72  E-value=0.29  Score=48.37  Aligned_cols=62  Identities=19%  Similarity=0.277  Sum_probs=51.0

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhC----CCc---eEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHH----GYP---VTSIHGDRTQKEREEALRRFRSGETPILVATAV  167 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~----~~~---~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~  167 (237)
                      .++.+++|.+||+.-+.++.+.+...    ++.   +..+||+++..++....+.+.+|..+|+|+|+.
T Consensus       119 ~~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~  187 (1171)
T TIGR01054       119 KKGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTM  187 (1171)
T ss_pred             hcCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHH
Confidence            34678999999999999988777653    333   346899999999999899999999999999963

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.

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

Probab=92.71  E-value=0.26  Score=48.03  Aligned_cols=68  Identities=12%  Similarity=0.192  Sum_probs=50.8

Q ss_pred             EEEEeechhH-HHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         28 RIAWVDEQDK-RSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        28 ~~~~~~~~~k-~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      .|..+++..+ ...+.+++....     .+...||||.|+..++.++..|...++.+..+|+.+.+..|..++.
T Consensus       656 ~y~Vv~k~kk~le~L~~~I~~~~-----~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe  724 (1195)
T PLN03137        656 WYSVVPKTKKCLEDIDKFIKENH-----FDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQK  724 (1195)
T ss_pred             EEEEeccchhHHHHHHHHHHhcc-----cCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHH
Confidence            3444444333 345555554321     2345899999999999999999999999999999999999988755

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=92.38  E-value=0.15  Score=44.70  Aligned_cols=42  Identities=26%  Similarity=0.404  Sum_probs=38.9

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +|+||+|+..++.+++.|...++.+..+|+++.+..|..+..
T Consensus       258 ~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~  299 (423)
T PRK04837        258 AIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILE  299 (423)
T ss_pred             EEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHH
Confidence            899999999999999999999999999999999998877643

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=92.35  E-value=0.34  Score=41.30  Aligned_cols=84  Identities=20%  Similarity=0.179  Sum_probs=56.1

Q ss_pred             hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC--CceeecCCcchhhHHHHhhhhhhccCCceEEE
Q psy15610         36 DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY--PVTSIHGDRTQKEREEAQQYTLISCDEALTLV  113 (237)
Q Consensus        36 ~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iI  113 (237)
                      .+...+..++...     ..+.++|+|++|+..++.+++.|...+.  .+..+|+.+.+..|.......+...+.++.-|
T Consensus       207 ~~~~~l~~l~~~~-----~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~i  281 (358)
T TIGR01587       207 GEISSLERLLEFI-----KKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFV  281 (358)
T ss_pred             cCHHHHHHHHHHh-----hCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeE
Confidence            4555666555322     2356899999999999999999988766  48899999999888765333333333444445


Q ss_pred             EeecccchHHH
Q psy15610        114 FVETKKGADQL  124 (237)
Q Consensus       114 F~~t~~~~~~l  124 (237)
                      .+.|......+
T Consensus       282 lvaT~~~~~Gi  292 (358)
T TIGR01587       282 IVATQVIEASL  292 (358)
T ss_pred             EEECcchhcee
Confidence            55554433333

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.

>KOG0327|consensus

Probab=92.32  E-value=0.2  Score=42.57  Aligned_cols=40  Identities=40%  Similarity=0.761  Sum_probs=38.3

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHH
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   98 (237)
                      .++|+||+..+..+..+|..+++.+..+|+++.|..|...
T Consensus       266 ~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~  305 (397)
T KOG0327|consen  266 AVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTL  305 (397)
T ss_pred             ceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHH
Confidence            5899999999999999999999999999999999999877

>KOG0347|consensus

Probab=92.24  E-value=0.29  Score=43.71  Aligned_cols=52  Identities=29%  Similarity=0.363  Sum_probs=45.7

Q ss_pred             EEEEeecccchHHHHHHHhhC----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC
Q psy15610        111 TLVFVETKKGADQLEDFLHHH----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATA  166 (237)
Q Consensus       111 ~iIF~~t~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~  166 (237)
                      ++|+++|++-+-++...|...    ++.+..+.||++....++++..    ..+|+|+|+
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            999999999999988877653    8999999999999888888777    688999997

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=92.19  E-value=0.54  Score=41.83  Aligned_cols=60  Identities=18%  Similarity=0.309  Sum_probs=53.9

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV  167 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~  167 (237)
                      ...+||.+|+++-+......|...++.+..++++.+..++..+......+..+++++|+.
T Consensus        51 ~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe  110 (470)
T TIGR00614        51 DGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPE  110 (470)
T ss_pred             CCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHH
Confidence            467999999999988888888888999999999999999999999999999999999863

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

>KOG0340|consensus

Probab=91.96  E-value=0.19  Score=42.41  Aligned_cols=61  Identities=25%  Similarity=0.311  Sum_probs=49.8

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHH
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQ  123 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~  123 (237)
                      +++|++|...++.++..|...++.+..+|+.+.|.+|...    +..+..+.+-|...|....+.
T Consensus       257 imIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~a----LsrFrs~~~~iliaTDVAsRG  317 (442)
T KOG0340|consen  257 IMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAA----LSRFRSNAARILIATDVASRG  317 (442)
T ss_pred             EEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHH----HHHHhhcCccEEEEechhhcC
Confidence            8999999999999999999999999999999999999877    444445555566666554443

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=91.89  E-value=0.19  Score=44.09  Aligned_cols=42  Identities=29%  Similarity=0.527  Sum_probs=39.3

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +|+||+++..++.+++.|...++.+..+|+++.+..|.....
T Consensus       248 ~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~  289 (434)
T PRK11192        248 SIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIK  289 (434)
T ss_pred             EEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHH
Confidence            899999999999999999999999999999999999987744

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=91.78  E-value=0.2  Score=45.77  Aligned_cols=42  Identities=40%  Similarity=0.596  Sum_probs=39.1

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +|+||+|+..++.+++.|...++.+..+|+.+.+..|.....
T Consensus       260 ~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~  301 (572)
T PRK04537        260 TMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLN  301 (572)
T ss_pred             EEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHH
Confidence            899999999999999999999999999999999999877644

>KOG2340|consensus

Probab=91.65  E-value=0.51  Score=42.00  Aligned_cols=110  Identities=16%  Similarity=0.193  Sum_probs=84.1

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC--ccccccCCCCCcEEEEecC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA--VAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~--~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      ..-++||.|+--.--.+..++.+.++.+..+|.-.+.+.-.+.-..|-.|+..+|+-|.  ..-+-.++..+..||+|.+
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            34579999999988999999999888888888777777777778889999999999885  3445678889999999999


Q ss_pred             CCCHHHH---HHhhcccccCCC----CCceEEeecCCCC
Q psy15610        186 PSDVEEY---VHRIGRTGRMGN----LDFPFSYNQPGYG  217 (237)
Q Consensus       186 p~s~~~~---~Q~~GR~~R~g~----~~~~~~~~~~~~~  217 (237)
                      |..|.=|   +.|.+|+.-.|+    ...|.++++.-+.
T Consensus       632 P~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~  670 (698)
T KOG2340|consen  632 PNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDR  670 (698)
T ss_pred             CCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhh
Confidence            9987654   556666554442    2346666665444

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=91.28  E-value=0.2  Score=44.35  Aligned_cols=57  Identities=30%  Similarity=0.447  Sum_probs=46.6

Q ss_pred             hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         35 QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        35 ~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      .+-+..++.-.....         +|+||+|+..++.+++.|...++.+..+|+.+.+..|.....
T Consensus       233 ~~~l~~l~~~~~~~~---------~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~  289 (456)
T PRK10590        233 RELLSQMIGKGNWQQ---------VLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALA  289 (456)
T ss_pred             HHHHHHHHHcCCCCc---------EEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHH
Confidence            344445555555445         899999999999999999999999999999999999887744

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=91.22  E-value=0.23  Score=45.83  Aligned_cols=58  Identities=22%  Similarity=0.410  Sum_probs=47.4

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+.+..+++......         +|+||+|+..++++++.|...++.+..+|+++.+..|..+..
T Consensus       232 k~~~L~~~L~~~~~~~---------~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~  289 (629)
T PRK11634        232 KNEALVRFLEAEDFDA---------AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLE  289 (629)
T ss_pred             HHHHHHHHHHhcCCCC---------EEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHH
Confidence            4444555555555444         899999999999999999999999999999999999887754

>KOG0921|consensus

Probab=90.40  E-value=0.39  Score=45.37  Aligned_cols=105  Identities=25%  Similarity=0.351  Sum_probs=79.1

Q ss_pred             CceEEEEeecccchHHHHHHHhhC-------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH-------GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV  180 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~-------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~V  180 (237)
                      .+.+++|.+--...-.+-.++...       .+.+...|+-.+-.+..++.+....|..+++++|.+....+.+-++..|
T Consensus       643 ~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~v  722 (1282)
T KOG0921|consen  643 DGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVYV  722 (1282)
T ss_pred             ccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeEE
Confidence            456788888877766666665432       4578888998888888899999999999999999998888877776665


Q ss_pred             EEec------------------CCCCHHHHHHhhcccccCCCCCceEEeec
Q psy15610        181 INFD------------------LPSDVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       181 i~~~------------------~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      +..+                  .-.+.....|+.||+||. ++|.|+..++
T Consensus       723 id~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~lcs  772 (1282)
T KOG0921|consen  723 IDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFHLCS  772 (1282)
T ss_pred             EeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccccccH
Confidence            5422                  112677888999999997 4777766554

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=90.40  E-value=1.1  Score=41.12  Aligned_cols=60  Identities=18%  Similarity=0.228  Sum_probs=53.2

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV  167 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~  167 (237)
                      .+.++|.+|+..-+....+.|...|+.+..+|++++..++..+.+....|..++++.|+.
T Consensus        53 ~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe  112 (591)
T TIGR01389        53 KGLTVVISPLISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPE  112 (591)
T ss_pred             CCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChh
Confidence            456899999999888888888888999999999999999999999999999999988853

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.

>cd00268 DEADc DEAD-box helicases

Probab=89.86  E-value=1.8  Score=33.41  Aligned_cols=72  Identities=24%  Similarity=0.283  Sum_probs=49.4

Q ss_pred             CCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----c-ccccCCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----A-ARGLDIPH  176 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~-~~Gvdl~~  176 (237)
                      ++.+++|.+++...+.++...+..    .++.+..++|+.+..+.....   . +...|+|+|..     + ....++++
T Consensus        68 ~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~iiv~T~~~l~~~l~~~~~~~~~  143 (203)
T cd00268          68 DGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKL---K-RGPHIVVATPGRLLDLLERGKLDLSK  143 (203)
T ss_pred             CCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh---c-CCCCEEEEChHHHHHHHHcCCCChhh
Confidence            356899999999988887666544    367788899998876554332   2 56789999952     2 22245666


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      .+.+|.
T Consensus       144 l~~lIv  149 (203)
T cd00268         144 VKYLVL  149 (203)
T ss_pred             CCEEEE
Confidence            777664

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.

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

Probab=89.15  E-value=0.71  Score=41.97  Aligned_cols=46  Identities=24%  Similarity=0.440  Sum_probs=42.2

Q ss_pred             cccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      .....|++|.|+..+++++++|...|+.+...|+.+....|...++
T Consensus       229 ~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~  274 (590)
T COG0514         229 LSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQ  274 (590)
T ss_pred             cCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHH
Confidence            3456899999999999999999999999999999999999988866

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=88.18  E-value=0.57  Score=41.73  Aligned_cols=40  Identities=25%  Similarity=0.445  Sum_probs=37.5

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHH
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   98 (237)
                      +|+||+++..++.+++.|...++.+..+++.+.+..|...
T Consensus       338 ~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~  377 (475)
T PRK01297        338 VMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKT  377 (475)
T ss_pred             EEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHH
Confidence            8999999999999999999999999999999999888766

>KOG0338|consensus

Probab=88.12  E-value=2.3  Score=37.90  Aligned_cols=71  Identities=21%  Similarity=0.265  Sum_probs=54.9

Q ss_pred             CceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC-------ccccccCCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA-------VAARGLDIPH  176 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-------~~~~Gvdl~~  176 (237)
                      -.++||.|||++.+.++.....+    ..+.+...-||++-...++.++.    ..+|+|+|+       --+.++|+.+
T Consensus       252 ~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs----~PDIVIATPGRlIDHlrNs~sf~lds  327 (691)
T KOG0338|consen  252 ATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRS----RPDIVIATPGRLIDHLRNSPSFNLDS  327 (691)
T ss_pred             ceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhh----CCCEEEecchhHHHHhccCCCccccc
Confidence            46799999999988877666554    37889999999999888877664    478999996       2456777777


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      +.+.|.
T Consensus       328 iEVLvl  333 (691)
T KOG0338|consen  328 IEVLVL  333 (691)
T ss_pred             eeEEEe
Confidence            776664

>KOG0341|consensus

Probab=87.86  E-value=3.6  Score=35.50  Aligned_cols=42  Identities=31%  Similarity=0.597  Sum_probs=39.5

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +++|+..+..++.+.++|.-.|.++..+|+...|..|...+.
T Consensus       424 VLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~  465 (610)
T KOG0341|consen  424 VLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIE  465 (610)
T ss_pred             eEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHH
Confidence            799999999999999999999999999999999999987754

>PTZ00424 helicase 45; Provisional

Probab=87.36  E-value=0.69  Score=40.00  Aligned_cols=42  Identities=26%  Similarity=0.593  Sum_probs=38.5

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +|+||+|...++.+++.+...++.+..+|+++.+..|..+..
T Consensus       270 ~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~  311 (401)
T PTZ00424        270 AIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMR  311 (401)
T ss_pred             EEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHH
Confidence            799999999999999999999999999999999998877644

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=87.08  E-value=1  Score=42.53  Aligned_cols=119  Identities=18%  Similarity=0.227  Sum_probs=80.2

Q ss_pred             EEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCC
Q psy15610         29 IAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDE  108 (237)
Q Consensus        29 ~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (237)
                      .+.+...+|...+.+.+....    ....++|+||+|+..++.++..|...++++..+|+.+.+..+......    ...
T Consensus       405 ~i~~~~~~K~~al~~~i~~~~----~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~a----g~~  476 (790)
T PRK09200        405 KVFVTLDEKYKAVIEEVKERH----ETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEA----GQK  476 (790)
T ss_pred             eEEcCHHHHHHHHHHHHHHHH----hcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHc----CCC
Confidence            455677889999998886531    236789999999999999999999999999999999877665544222    122


Q ss_pred             ceEEEEeecccchHHHHHHH----hhCCCceEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610        109 ALTLVFVETKKGADQLEDFL----HHHGYPVTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus       109 ~~~iIF~~t~~~~~~l~~~L----~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                      ++  |.+.|.-.++.+.-.|    .+.| ...+++-+++...|.-....-++|+
T Consensus       477 g~--VlIATdmAgRG~DI~l~~~V~~~G-GL~VI~~d~p~s~r~y~qr~GRtGR  527 (790)
T PRK09200        477 GA--VTVATNMAGRGTDIKLGEGVHELG-GLAVIGTERMESRRVDLQLRGRSGR  527 (790)
T ss_pred             Ce--EEEEccchhcCcCCCccccccccc-CcEEEeccCCCCHHHHHHhhccccC
Confidence            23  5555655555443322    1112 2367777777766666666555554

>PRK09401 reverse gyrase; Reviewed

Probab=86.32  E-value=5.8  Score=39.60  Aligned_cols=62  Identities=27%  Similarity=0.385  Sum_probs=48.3

Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhC----CCceEE--EeCCCCHHHHHHHHHHhhcCCCCEEEEcC
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHH----GYPVTS--IHGDRTQKEREEALRRFRSGETPILVATA  166 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~----~~~~~~--~h~~~~~~~r~~~~~~f~~g~~~vlv~T~  166 (237)
                      ..++.+++|.+||+.-+.++.+.+...    +..+..  .|++++..++......+..+..+|+|+|+
T Consensus       120 ~~~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp  187 (1176)
T PRK09401        120 AKKGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTS  187 (1176)
T ss_pred             HhcCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECH
Confidence            345678999999999999998888764    334433  35556677888888899989999999995

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

Probab=85.89  E-value=1.2  Score=42.35  Aligned_cols=91  Identities=13%  Similarity=0.082  Sum_probs=66.4

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      +++.++.++..+.+.........+.++ +.++...|+..+...+.....   ....++|+||+|+..++.+++.|...++
T Consensus       222 l~~~~~~~p~~i~V~~~~l~a~ki~q~-v~v~~e~Kl~~lv~~L~~ll~---e~g~~vLVF~NTv~~Aq~L~~~L~~~g~  297 (844)
T TIGR02621       222 RTTLLSAEDYKHPVLKKRLAAKKIVKL-VPPSDEKFLSTMVKELNLLMK---DSGGAILVFCRTVKHVRKVFAKLPKEKF  297 (844)
T ss_pred             HHHHHccCCceeecccccccccceEEE-EecChHHHHHHHHHHHHHHHh---hCCCcEEEEECCHHHHHHHHHHHHhcCC
Confidence            456788888877776666677777775 344555566555544432211   1346799999999999999999998887


Q ss_pred             CceeecCCcchhhHHHH
Q psy15610         82 PVTSIHGDRTQKEREEA   98 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~   98 (237)
                        ..+|+.+.+..|...
T Consensus       298 --~lLHG~m~q~dR~~~  312 (844)
T TIGR02621       298 --ELLTGTLRGAERDDL  312 (844)
T ss_pred             --eEeeCCCCHHHHhhH
Confidence              899999999999843

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.

>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=85.77  E-value=2.8  Score=33.76  Aligned_cols=82  Identities=17%  Similarity=0.187  Sum_probs=60.7

Q ss_pred             CCceEEEeCCCCHHHHHHHHHHhhcCC----CCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccc-cCCCCC
Q psy15610        132 GYPVTSIHGDRTQKEREEALRRFRSGE----TPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTG-RMGNLD  206 (237)
Q Consensus       132 ~~~~~~~h~~~~~~~r~~~~~~f~~g~----~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~-R~g~~~  206 (237)
                      ++.+..++++.+...     -.+.++.    ..|+|.=..+++|+.+....+-.+...+.....++||.-=-| |.|-..
T Consensus       110 ~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgRwFGYR~gY~d  184 (239)
T PF10593_consen  110 GIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGRWFGYRPGYED  184 (239)
T ss_pred             CceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhhcccCCccccc
Confidence            688999997765543     3343333    678888899999999999999999998988888888874443 555566


Q ss_pred             ceEEeecCCCCC
Q psy15610        207 FPFSYNQPGYGG  218 (237)
Q Consensus       207 ~~~~~~~~~~~~  218 (237)
                      .|-+|.++.-..
T Consensus       185 l~Ri~~~~~l~~  196 (239)
T PF10593_consen  185 LCRIYMPEELYD  196 (239)
T ss_pred             ceEEecCHHHHH
Confidence            788877654433

This domain is found associated with a helicase domain of superfamily type II [].

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=85.53  E-value=1.2  Score=41.12  Aligned_cols=93  Identities=17%  Similarity=0.193  Sum_probs=61.2

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHH----hhCCCc
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFL----HHHGYP  134 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L----~~~~~~  134 (237)
                      +|+||+|+..++.++..|...++++..+|+...+..+...      ...+.+.-|.+.|.-.++.+.-.+    .+.| .
T Consensus       476 vLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~~rE~~ii------~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~G-G  548 (656)
T PRK12898        476 VLVGTRSVAASERLSALLREAGLPHQVLNAKQDAEEAAIV------ARAGQRGRITVATNMAGRGTDIKLEPGVAARG-G  548 (656)
T ss_pred             EEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcHHHHHHHH------HHcCCCCcEEEEccchhcccCcCCccchhhcC-C
Confidence            8999999999999999999999999999998654444332      122222235566665555543322    1112 2


Q ss_pred             eEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610        135 VTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus       135 ~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                      ..+++-+++...|.-....=++|+
T Consensus       549 LhVI~~d~P~s~r~y~hr~GRTGR  572 (656)
T PRK12898        549 LHVILTERHDSARIDRQLAGRCGR  572 (656)
T ss_pred             CEEEEcCCCCCHHHHHHhcccccC
Confidence            357777787776666655555554

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=85.53  E-value=3.2  Score=38.33  Aligned_cols=59  Identities=20%  Similarity=0.290  Sum_probs=52.6

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA  166 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~  166 (237)
                      ...+||.+|++.-+....+.+...++.+..++++.+.++...+.....+|.++++++|+
T Consensus        65 ~g~tlVisPl~sL~~dqv~~l~~~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tP  123 (607)
T PRK11057         65 DGLTLVVSPLISLMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAP  123 (607)
T ss_pred             CCCEEEEecHHHHHHHHHHHHHHcCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEECh
Confidence            35789999999998888888888899999999999999999888889999999998884

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=84.75  E-value=1.8  Score=40.50  Aligned_cols=118  Identities=20%  Similarity=0.275  Sum_probs=78.7

Q ss_pred             EEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCc
Q psy15610         30 AWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEA  109 (237)
Q Consensus        30 ~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  109 (237)
                      +...+.+|...+.+.+....    ..+.++|+||+|....+.++..|...+++...+++.  +..++..    +....++
T Consensus       383 i~~t~~~k~~ai~~~i~~~~----~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~----ii~~ag~  452 (745)
T TIGR00963       383 VYKTEEEKWKAVVDEIKERH----AKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NHEREAE----IIAQAGR  452 (745)
T ss_pred             EEcCHHHHHHHHHHHHHHHH----hcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hHHHHHH----HHHhcCC
Confidence            34456678888877664432    357899999999999999999999999999999988  4444433    4444455


Q ss_pred             eEEEEeecccchHHHHHHH---hhCCCceEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610        110 LTLVFVETKKGADQLEDFL---HHHGYPVTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus       110 ~~iIF~~t~~~~~~l~~~L---~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                      +.-|.+.|.-..+.+.-.+   .+.| ...+++-.++.+.|......=++|+
T Consensus       453 ~g~VtIATnmAgRGtDI~l~~V~~~G-Gl~VI~t~~p~s~ri~~q~~GRtGR  503 (745)
T TIGR00963       453 KGAVTIATNMAGRGTDIKLEEVKELG-GLYVIGTERHESRRIDNQLRGRSGR  503 (745)
T ss_pred             CceEEEEeccccCCcCCCccchhhcC-CcEEEecCCCCcHHHHHHHhccccC
Confidence            5555555655444433222   2222 3466777777777776666666543

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.

>KOG0383|consensus

Probab=84.17  E-value=0.52  Score=43.58  Aligned_cols=65  Identities=29%  Similarity=0.405  Sum_probs=57.1

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC---CCCEEEEcCccccc
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG---ETPILVATAVAARG  171 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g---~~~vlv~T~~~~~G  171 (237)
                      ..+.+++||..-....+.+++++...+ .+..+.|..+-.+|...+..|+..   .+..|.+|.+.+.|
T Consensus       629 ~~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~~~~rq~ai~~~n~~~~~~~cfllstra~g~g  696 (696)
T KOG0383|consen  629 SSGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPITGPERQAAIDRFNAPGSNQFCFLLSTRAGGLG  696 (696)
T ss_pred             hcchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCccchhhhhhccccCCCCccceEEEeecccccCC
Confidence            347899999999999999999999888 899999999999999999999843   45688999988765

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=83.77  E-value=1.1  Score=38.29  Aligned_cols=74  Identities=18%  Similarity=0.197  Sum_probs=50.0

Q ss_pred             CceeEEEEeechhHHHHHHHhhcCchhhh-cccccceeEEeecccchhhHHHHhhhcC--CCceeecCCcchhhHHHH
Q psy15610         24 NITQRIAWVDEQDKRSCLLDLLSSPSQEE-LGDEALTLVFVETKKGADQLEDFLHHHG--YPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        24 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~-~~~~~~~i~f~~t~~~~~~~~~~l~~~~--~~~~~~~~~~~~~~~~~~   98 (237)
                      .+.+.+.. ....|...+..++....... ...+.++++|++|+..++.+++.|...+  +.+..+++.+.+..|...
T Consensus       240 ~i~~~~~~-~~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~  316 (357)
T TIGR03158       240 PVELELIP-APDFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA  316 (357)
T ss_pred             ceEEEEEe-CCchhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh
Confidence            45555544 33445555544444332111 1245679999999999999999999864  567889999999888755

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.

>KOG0343|consensus

Probab=83.41  E-value=5.9  Score=35.83  Aligned_cols=99  Identities=20%  Similarity=0.372  Sum_probs=67.9

Q ss_pred             eeEEeecccchhhHHHHhhh--cCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEe----------------ecccc
Q psy15610         59 TLVFVETKKGADQLEDFLHH--HGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFV----------------ETKKG  120 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~----------------~t~~~  120 (237)
                      .|+|..|...+..+++.+..  .|.+...+|+.+.|..|..+...-.   ....++.||                -..+.
T Consensus       316 ~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~---~~~~~vLF~TDv~aRGLDFpaVdwViQ~DC  392 (758)
T KOG0343|consen  316 SIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFV---RKRAVVLFCTDVAARGLDFPAVDWVIQVDC  392 (758)
T ss_pred             eEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHH---HhcceEEEeehhhhccCCCcccceEEEecC
Confidence            79999999999999999966  6678899999999999877754110   012233333                33444


Q ss_pred             hHHHHHHHhhCCCceEEEeCC-----CCHHHHHHHHHHhhcCCCC
Q psy15610        121 ADQLEDFLHHHGYPVTSIHGD-----RTQKEREEALRRFRSGETP  160 (237)
Q Consensus       121 ~~~l~~~L~~~~~~~~~~h~~-----~~~~~r~~~~~~f~~g~~~  160 (237)
                      .+.+..|++..|..+.....|     +.|.+.+..+..+++..+.
T Consensus       393 Pedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~k~I~  437 (758)
T KOG0343|consen  393 PEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQKKKIP  437 (758)
T ss_pred             chhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHHcCCC
Confidence            567788888877655544444     4577777777777765433

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=83.39  E-value=2.1  Score=28.42  Aligned_cols=36  Identities=14%  Similarity=0.290  Sum_probs=30.9

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRT  143 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~  143 (237)
                      ..++++||.+...+...+..|...|+.+..+.||++
T Consensus        51 ~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~   86 (90)
T cd01524          51 DKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYK   86 (90)
T ss_pred             CCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHH
Confidence            467899999887888889999999988888999874

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.

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=83.04  E-value=3.1  Score=39.39  Aligned_cols=118  Identities=18%  Similarity=0.202  Sum_probs=78.9

Q ss_pred             EEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCc
Q psy15610         30 AWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEA  109 (237)
Q Consensus        30 ~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  109 (237)
                      +...+.+|...+.+.+....    ....++|+||+|....+.+++.|...+++...+++...+..+..+.    .....+
T Consensus       418 i~~t~~~K~~al~~~i~~~~----~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~----~ag~~g  489 (796)
T PRK12906        418 LYPTLDSKFNAVVKEIKERH----AKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIM----NAGQRG  489 (796)
T ss_pred             EEcCHHHHHHHHHHHHHHHH----hCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHH----hcCCCc
Confidence            44566789999988885432    2467899999999999999999999999999999987766655442    222233


Q ss_pred             eEEEEeecccchHHHHHHH----hhCCCceEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610        110 LTLVFVETKKGADQLEDFL----HHHGYPVTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus       110 ~~iIF~~t~~~~~~l~~~L----~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                      .  |.+.|.-.++.+.-.|    .+.| ...+++-.++...|......=++|+
T Consensus       490 ~--VtIATnmAGRGtDI~l~~~V~~~G-GLhVI~te~pes~ri~~Ql~GRtGR  539 (796)
T PRK12906        490 A--VTIATNMAGRGTDIKLGPGVKELG-GLAVIGTERHESRRIDNQLRGRSGR  539 (796)
T ss_pred             e--EEEEeccccCCCCCCCCcchhhhC-CcEEEeeecCCcHHHHHHHhhhhcc
Confidence            3  5555544444433222    2222 3466667777766666666555543

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=81.09  E-value=1.7  Score=40.36  Aligned_cols=62  Identities=27%  Similarity=0.306  Sum_probs=49.1

Q ss_pred             hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         35 QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        35 ~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      ..++..|.+-|....    ..+.++++|++|+..++.+++.|...++++..+|+++.+..|.....
T Consensus       425 ~~qi~~Ll~eI~~~~----~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~  486 (655)
T TIGR00631       425 DGQVDDLLSEIRQRV----ARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIR  486 (655)
T ss_pred             cchHHHHHHHHHHHH----cCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHH
Confidence            346666666555432    34567999999999999999999999999999999998887766644

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

>KOG1133|consensus

Probab=81.02  E-value=45  Score=31.29  Aligned_cols=107  Identities=20%  Similarity=0.230  Sum_probs=70.2

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCC-------ceEEEeCCCCHHHHHHHHHHhh----cCCCCEEEEc--CccccccCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGY-------PVTSIHGDRTQKEREEALRRFR----SGETPILVAT--AVAARGLDI  174 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~-------~~~~~h~~~~~~~r~~~~~~f~----~g~~~vlv~T--~~~~~Gvdl  174 (237)
                      ++-+++|.++-+-...+.+.....|+       +..++....+   -+.+++.|.    .|.-.+|++-  .=+++|+||
T Consensus       629 PgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~---~~dvl~~Ya~a~~~g~GaiLlaVVGGKlSEGINF  705 (821)
T KOG1133|consen  629 PGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDT---VEDVLEGYAEAAERGRGAILLAVVGGKLSEGINF  705 (821)
T ss_pred             CCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCccc---HHHHHHHHHHHhhcCCCeEEEEEecccccccccc
Confidence            46799999999988888887765543       3344444444   344555554    4554566664  668899999


Q ss_pred             CC--CcEEEEecCCCC----HH----------------------------HHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        175 PH--VKHVINFDLPSD----VE----------------------------EYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       175 ~~--~~~Vi~~~~p~s----~~----------------------------~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      .+  ++.|+..++|..    ++                            ..-|-+|||-|=-.+-.++++++..-.
T Consensus       706 ~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkAVNQsIGRAIRH~~DYA~i~LlD~RY~  782 (821)
T KOG1133|consen  706 SDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKAVNQSIGRAIRHRKDYASIYLLDKRYA  782 (821)
T ss_pred             ccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHhhhccceeEEEehhhhc
Confidence            87  667887776541    11                            234788888887667777777765443

>KOG0349|consensus

Probab=80.50  E-value=3.2  Score=36.33  Aligned_cols=42  Identities=33%  Similarity=0.704  Sum_probs=35.5

Q ss_pred             cceeEEeecccchhhHHHHhhhcC---CCceeecCCcchhhHHHH
Q psy15610         57 ALTLVFVETKKGADQLEDFLHHHG---YPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        57 ~~~i~f~~t~~~~~~~~~~l~~~~---~~~~~~~~~~~~~~~~~~   98 (237)
                      -+.|+||.|+..++.+.+++.+.+   +.|..+|++....+|..-
T Consensus       506 dkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~n  550 (725)
T KOG0349|consen  506 DKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKAN  550 (725)
T ss_pred             CceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHH
Confidence            359999999999999999998766   588999999977776654

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=80.47  E-value=3  Score=40.47  Aligned_cols=60  Identities=27%  Similarity=0.314  Sum_probs=50.8

Q ss_pred             hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHh-hhcCCCceeecCCcchhhHHHHhh
Q psy15610         35 QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFL-HHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        35 ~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.|...|.++|....      ..++|+||+++..+..+.+.| ...|+++..+|+++.+..|.....
T Consensus       478 d~Ki~~L~~~L~~~~------~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~  538 (956)
T PRK04914        478 DPRVEWLIDFLKSHR------SEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAA  538 (956)
T ss_pred             CHHHHHHHHHHHhcC------CCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHH
Confidence            457888888887542      457999999999999999999 567999999999999999987754

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=80.13  E-value=1.9  Score=40.14  Aligned_cols=62  Identities=27%  Similarity=0.312  Sum_probs=48.9

Q ss_pred             hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         35 QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        35 ~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      ..++..|.+-|....    ..+.++++||+|+..++.+++.|...++++..+|+++.+..|..+..
T Consensus       429 ~~q~~~L~~~L~~~~----~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~  490 (652)
T PRK05298        429 KGQVDDLLSEIRKRV----AKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIR  490 (652)
T ss_pred             cccHHHHHHHHHHHH----hCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHH
Confidence            345666666665432    24567999999999999999999999999999999999887776544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	237
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		9e-55
2jgn_A	185	Ddx3 Helicase Domain Length = 185		3e-48
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		8e-34
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		5e-24
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-23
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-23
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-23
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-23
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-23
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-23
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		5e-21
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		5e-19
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		5e-19
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		8e-19
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		9e-19
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		1e-18
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		1e-18
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		1e-18
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		2e-18
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		1e-17
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		9e-17
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-16
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-16
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-16
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-16
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		2e-16
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		8e-15
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		8e-15
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		1e-14
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		1e-14
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		3e-14
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		3e-14
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		3e-14
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		3e-14
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		3e-14
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		3e-14
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		5e-14
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		2e-13
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		2e-13
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-13
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		1e-12
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-12
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		1e-12
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-12
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		2e-07
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		2e-07
1d9x_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Le		6e-07
1t5l_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Po		6e-07
1d9z_A	657	Crystal Structure Of The Dna Repair Protein Uvrb In		6e-07
2fdc_A	658	Structural Basis Of Dna Damage Recognition And Proc		6e-07
3uwx_B	683	Crystal Structure Of Uvra-Uvrb Complex Length = 683		7e-07
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		9e-07
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		8e-06
3v4r_A	667	Crystal Structure Of A Uvrb Dimer-Dna Complex Lengt		3e-05
2d7d_A	661	Structural Insights Into The Cryptic Dna Dependent		3e-05
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		3e-05
4i1s_A	243	Melanoma Differentiation Associated Protein-5 Helic		5e-05
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-04

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  209 bits (533), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 113/205 (55%), Positives = 133/205 (64%), Gaps = 57/205 (27%)
Query: 1   LLAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTL 60
           +LA++FL  YIFLA+GRVGSTSENITQ++ WV+E DKRS LL                  
Sbjct: 226 MLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLL------------------ 267
Query: 61  VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
                        D L+  G                           ++LTLVFVETKKG
Sbjct: 268 -------------DLLNATG--------------------------KDSLTLVFVETKKG 288
Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV 180
           AD LEDFL+H GY  TSIHGDR+Q++REEAL +FRSG++PILVATAVAARGLDI +VKHV
Sbjct: 289 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHV 348
Query: 181 INFDLPSDVEEYVHRIGRTGRMGNL 205
           INFDLPSD+EEYVHRIGRTGR+GNL
Sbjct: 349 INFDLPSDIEEYVHRIGRTGRVGNL 373

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score =  188 bits (477), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 102/187 (54%), Positives = 119/187 (63%), Gaps = 57/187 (30%)
Query: 19  GSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHH 78
           GSTSENITQ++ WV+E DKRS LLDLL++      G ++LTLVFVETKKGAD LEDFL+H
Sbjct: 14  GSTSENITQKVVWVEESDKRSFLLDLLNAT-----GKDSLTLVFVETKKGADSLEDFLYH 68
Query: 79  HGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSI 138
            GY  TSIHGDR+Q++REEA                                        
Sbjct: 69  EGYACTSIHGDRSQRDREEA---------------------------------------- 88
Query: 139 HGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGR 198
                       L +FRSG++PILVATAVAARGLDI +VKHVINFDLPSD+EEYVHRIGR
Sbjct: 89  ------------LHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGR 136
Query: 199 TGRMGNL 205
           TGR+GNL
Sbjct: 137 TGRVGNL 143

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  140 bits (352), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 81/203 (39%), Positives = 110/203 (54%), Gaps = 59/203 (29%)
Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLV 61
           +A EFL  Y+F+AIG VG    ++ Q I  V++  KRS L+++LS     E  D   T+V
Sbjct: 253 MAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILS-----EQADG--TIV 305
Query: 62  FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA 121
           FVETK+GAD L  FL    +P TSIHGDR Q +RE+A                       
Sbjct: 306 FVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQA----------------------- 342
Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
                                        LR F++G   +L+AT+VA+RGLDI ++KHVI
Sbjct: 343 -----------------------------LRDFKNGSMKVLIATSVASRGLDIKNIKHVI 373
Query: 182 NFDLPSDVEEYVHRIGRTGRMGN 204
           N+D+PS +++YVHRIGRTGR+GN
Sbjct: 374 NYDMPSKIDDYVHRIGRTGRVGN 396

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score =  107 bits (267), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 50/113 (44%), Positives = 73/113 (64%), Gaps = 3/113 (2%)
Query: 95  REEAQQYTLISCDEAL---TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAL 151
           +EEA+   L+ C +      L+F E K   D + ++L   G    +IHG + Q+ER +A+
Sbjct: 38  KEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAI 97
Query: 152 RRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
             FR G+  +LVAT VA++GLD P ++HVIN+D+P ++E YVHRIGRTG  GN
Sbjct: 98  EAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGN 150

>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 =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/114 (45%), Positives = 75/114 (65%), Gaps = 4/114 (3%)
Query: 94  EREEAQQYTLISCDEALTL----VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           EREE +  TL    + LT+    +F  TK+  D L + +    + V+S+HGD  QKERE 
Sbjct: 259 EREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 318
Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
            ++ FRSG + +L++T V ARGLD+P V  +IN+DLP++ E Y+HRIGR+GR G
Sbjct: 319 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 372

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/114 (45%), Positives = 75/114 (65%), Gaps = 4/114 (3%)
Query: 94  EREEAQQYTLISCDEALTL----VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           EREE +  TL    + LT+    +F  TK+  D L + +    + V+S+HGD  QKERE 
Sbjct: 222 EREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 281
Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
            ++ FRSG + +L++T V ARGLD+P V  +IN+DLP++ E Y+HRIGR+GR G
Sbjct: 282 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 335

>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 =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/114 (45%), Positives = 75/114 (65%), Gaps = 4/114 (3%)
Query: 94  EREEAQQYTLISCDEALTL----VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           EREE +  TL    + LT+    +F  TK+  D L + +    + V+S+HGD  QKERE 
Sbjct: 259 EREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 318
Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
            ++ FRSG + +L++T V ARGLD+P V  +IN+DLP++ E Y+HRIGR+GR G
Sbjct: 319 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 372

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/114 (45%), Positives = 75/114 (65%), Gaps = 4/114 (3%)
Query: 94  EREEAQQYTLISCDEALTL----VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           EREE +  TL    + LT+    +F  TK+  D L + +    + V+S+HGD  QKERE 
Sbjct: 258 EREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 317
Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
            ++ FRSG + +L++T V ARGLD+P V  +IN+DLP++ E Y+HRIGR+GR G
Sbjct: 318 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 371

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/114 (45%), Positives = 75/114 (65%), Gaps = 4/114 (3%)
Query: 94  EREEAQQYTLISCDEALTL----VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           EREE +  TL    + LT+    +F  TK+  D L + +    + V+S+HGD  QKERE 
Sbjct: 222 EREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 281
Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
            ++ FRSG + +L++T V ARGLD+P V  +IN+DLP++ E Y+HRIGR+GR G
Sbjct: 282 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 335

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/114 (45%), Positives = 75/114 (65%), Gaps = 4/114 (3%)
Query: 94  EREEAQQYTLISCDEALTL----VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           EREE +  TL    + LT+    +F  TK+  D L + +    + V+S+HGD  QKERE 
Sbjct: 237 EREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 296
Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
            ++ FRSG + +L++T V ARGLD+P V  +IN+DLP++ E Y+HRIGR+GR G
Sbjct: 297 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 350

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 97.4 bits (241), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 47/94 (50%), Positives = 61/94 (64%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            ++F  TK+  +QL D L   GYP   IHG   Q++R + +  F+ GE   LVAT VAAR
Sbjct: 38  CIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAAR 97
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           G+DI ++  VIN+DLP + E YVHR GRTGR GN
Sbjct: 98  GIDIENISLVINYDLPLEKESYVHRTGRTGRAGN 131

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 90.9 bits (224), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 44/99 (44%), Positives = 62/99 (62%), Gaps = 6/99 (6%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           +++FV TKK A+ L   L   G+ V+ +HGD   +ER+  +  FR G + +L+ T V AR
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 171 GLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMG 203
           G+DIP V  V+N+DLP+      D   Y+HRIGRTGR G
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFG 344

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 90.9 bits (224), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 44/99 (44%), Positives = 62/99 (62%), Gaps = 6/99 (6%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           +++FV TKK A+ L   L   G+ V+ +HGD   +ER+  +  FR G + +L+ T V AR
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 171 GLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMG 203
           G+DIP V  V+N+DLP+      D   Y+HRIGRTGR G
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFG 344

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 90.1 bits (222), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 44/99 (44%), Positives = 62/99 (62%), Gaps = 6/99 (6%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           +++FV TKK A+ L   L   G+ V+ +HGD   +ER+  +  FR G + +L+ T V AR
Sbjct: 38  SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 97
Query: 171 GLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMG 203
           G+DIP V  V+N+DLP+      D   Y+HRIGRTGR G
Sbjct: 98  GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFG 136

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 47/113 (41%), Positives = 67/113 (59%), Gaps = 1/113 (0%)
Query: 91  TQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA 150
            + ER EA    L+   E   LVF +TK+   +L   L   G+   +IHGD +Q +RE+ 
Sbjct: 222 NENERFEAL-CRLLKNKEFYGLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKV 280
Query: 151 LRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           +R F+  +  IL+AT V +RG+D+  +  VIN+ LP + E Y HRIGRTGR G
Sbjct: 281 IRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAG 333

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 44/99 (44%), Positives = 62/99 (62%), Gaps = 6/99 (6%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           +++FV TKK A+ L   L   G+ V+ +HGD   +ER+  +  FR G + +L+ T V AR
Sbjct: 40  SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 99
Query: 171 GLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMG 203
           G+DIP V  V+N+DLP+      D   Y+HRIGRTGR G
Sbjct: 100 GIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFG 138

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 44/99 (44%), Positives = 62/99 (62%), Gaps = 6/99 (6%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           +++FV TKK A+ L   L   G+ V+ +HGD   +ER+  +  FR G + +L+ T V AR
Sbjct: 39  SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 98
Query: 171 GLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMG 203
           G+DIP V  V+N+DLP+      D   Y+HRIGRTGR G
Sbjct: 99  GIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFG 137

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 89.4 bits (220), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 44/106 (41%), Positives = 68/106 (64%), Gaps = 4/106 (3%)
Query: 94  EREEAQQYTLISCDEALTL----VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           EREE +  TL    E LT+    +F+ T++  D L + +H   + V+++HGD  QKER+ 
Sbjct: 236 EREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDV 295
Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHR 195
            +R FRSG + +L+ T + ARG+D+  V  VIN+DLP++ E Y+HR
Sbjct: 296 IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHR 341

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 89.0 bits (219), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/106 (41%), Positives = 68/106 (64%), Gaps = 4/106 (3%)
Query: 94  EREEAQQYTLISCDEALTL----VFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           EREE +  TL    E LT+    +F+ T++  D L + +H   + V+++HGD  QKER+ 
Sbjct: 262 EREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDV 321
Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHR 195
            +R FRSG + +L+ T + ARG+D+  V  VIN+DLP++ E Y+HR
Sbjct: 322 IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHR 367

>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 = 86.7 bits (213), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/93 (44%), Positives = 58/93 (62%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           ++VFV  ++   +L ++L   G     + G+  Q +R EA++R   G   +LVAT VAAR
Sbjct: 33  SIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAAR 92
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           G+DIP V HV NFD+P   + Y+HRIGRT R G
Sbjct: 93  GIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAG 125

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 83.6 bits (205), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 40/104 (38%), Positives = 61/104 (58%), Gaps = 6/104 (5%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           ++F +T++ A  L   +   G+ V+ + G+ T ++R   ++RFR G+  +L+ T V ARG
Sbjct: 38  IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97
Query: 172 LDIPHVKHVINFDLP------SDVEEYVHRIGRTGRMGNLDFPF 209
           +D+  V  V+NFDLP       D E Y+HRIGRTGR G     F
Sbjct: 98  IDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAF 141

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 43/101 (42%), Positives = 57/101 (56%), Gaps = 6/101 (5%)
Query: 109 ALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA 168
           A  ++F  T+K A  L   L   G+ V  + G+   ++R   + RFR G+  +LV T V 
Sbjct: 334 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC 393
Query: 169 ARGLDIPHVKHVINFDLP------SDVEEYVHRIGRTGRMG 203
           ARG+D+  V  VINFDLP       D E Y+HRIGRTGR G
Sbjct: 394 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 434

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 43/101 (42%), Positives = 57/101 (56%), Gaps = 6/101 (5%)
Query: 109 ALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA 168
           A  ++F  T+K A  L   L   G+ V  + G+   ++R   + RFR G+  +LV T V 
Sbjct: 304 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC 363
Query: 169 ARGLDIPHVKHVINFDLP------SDVEEYVHRIGRTGRMG 203
           ARG+D+  V  VINFDLP       D E Y+HRIGRTGR G
Sbjct: 364 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 404

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 43/101 (42%), Positives = 57/101 (56%), Gaps = 6/101 (5%)
Query: 109 ALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA 168
           A  ++F  T+K A  L   L   G+ V  + G+   ++R   + RFR G+  +LV T V 
Sbjct: 283 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC 342
Query: 169 ARGLDIPHVKHVINFDLP------SDVEEYVHRIGRTGRMG 203
           ARG+D+  V  VINFDLP       D E Y+HRIGRTGR G
Sbjct: 343 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 383

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 82.8 bits (203), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 43/101 (42%), Positives = 57/101 (56%), Gaps = 6/101 (5%)
Query: 109 ALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA 168
           A  ++F  T+K A  L   L   G+ V  + G+   ++R   + RFR G+  +LV T V 
Sbjct: 267 AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC 326
Query: 169 ARGLDIPHVKHVINFDLP------SDVEEYVHRIGRTGRMG 203
           ARG+D+  V  VINFDLP       D E Y+HRIGRTGR G
Sbjct: 327 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 367

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 82.4 bits (202), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/93 (45%), Positives = 54/93 (58%), Gaps = 4/93 (4%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            +VFV T+    +L     +       + GD  Q  R   +  FR GE  +L+ T VA+R
Sbjct: 223 VIVFVRTRNRVAKLVRLFDN----AIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASR 278
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           GLDIP V+ VINFD P D+  Y+HRIGRTGRMG
Sbjct: 279 GLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMG 311

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 77.0 bits (188), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 36/95 (37%), Positives = 62/95 (65%), Gaps = 2/95 (2%)
Query: 101 YTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP 160
           Y  IS  +A+  +F  T++  ++L   L +  + V++I+ D  Q+ER+  ++ FRSG + 
Sbjct: 25  YDSISVTQAV--IFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSR 82
Query: 161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHR 195
           IL++T + ARG+D+  V  VIN+DLP++ E Y+HR
Sbjct: 83  ILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 117

>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 = 77.0 bits (188), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 39/84 (46%), Positives = 51/84 (60%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            +VF  TK   +++   L   G+P  ++HGD +Q ERE  L  FR GE  +LVAT VAAR
Sbjct: 34  AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAAR 93
Query: 171 GLDIPHVKHVINFDLPSDVEEYVH 194
           GLDIP V  V+++ LP   E Y H
Sbjct: 94  GLDIPQVDLVVHYRLPDRAEAYQH 117

>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 = 76.6 bits (187), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/92 (43%), Positives = 55/92 (59%), Gaps = 2/92 (2%)
Query: 103 LISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPIL 162
           + S D A+  VF  TK   +++   L   G+P  ++HGD +Q ERE  +  FR GE  +L
Sbjct: 25  VASPDRAM--VFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVL 82
Query: 163 VATAVAARGLDIPHVKHVINFDLPSDVEEYVH 194
           VAT VAARGLDIP V  V+++ +P   E Y H
Sbjct: 83  VATDVAARGLDIPQVDLVVHYRMPDRAEAYQH 114

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 76.6 bits (187), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 36/95 (37%), Positives = 62/95 (65%), Gaps = 2/95 (2%)
Query: 101 YTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP 160
           Y  IS  +A+  +F  T++  ++L   L +  + V++I+ D  Q+ER+  ++ FRSG + 
Sbjct: 255 YDSISVTQAV--IFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSR 312
Query: 161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHR 195
           IL++T + ARG+D+  V  VIN+DLP++ E Y+HR
Sbjct: 313 ILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 347

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 75.5 bits (184), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 53/97 (54%), Gaps = 3/97 (3%)
Query: 111 TLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
            ++F  T K    L   L +      P+   HG  TQ +R   ++RF+  E+ ILV T V
Sbjct: 36  AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 95
Query: 168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
            ARG+D P+V  V+   +PS++  Y+HRIGRT R G 
Sbjct: 96  GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGK 132

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 75.1 bits (183), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 53/97 (54%), Gaps = 3/97 (3%)
Query: 111 TLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
            ++F  T K    L   L +      P+   HG  TQ +R   ++RF+  E+ ILV T V
Sbjct: 36  AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 95
Query: 168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
            ARG+D P+V  V+   +PS++  Y+HRIGRT R G 
Sbjct: 96  GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGK 132

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 75.1 bits (183), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 53/97 (54%), Gaps = 3/97 (3%)
Query: 111 TLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
            ++F  T K    L   L +      P+   HG  TQ +R   ++RF+  E+ ILV T V
Sbjct: 36  AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 95
Query: 168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
            ARG+D P+V  V+   +PS++  Y+HRIGRT R G 
Sbjct: 96  GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGK 132

>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 = 75.1 bits (183), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 53/96 (55%), Gaps = 3/96 (3%)
Query: 111 TLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
            ++F  T K    L   L +      P+   HG  TQ +R   ++RF+  E+ ILV T V
Sbjct: 291 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 350
Query: 168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
            ARG+D P+V  V+   +PS++  Y+HRIGRT R G
Sbjct: 351 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 386

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 75.1 bits (183), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 53/96 (55%), Gaps = 3/96 (3%)
Query: 111 TLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
            ++F  T K    L   L +      P+   HG  TQ +R   ++RF+  E+ ILV T V
Sbjct: 291 AIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV 350
Query: 168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
            ARG+D P+V  V+   +PS++  Y+HRIGRT R G
Sbjct: 351 GARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 386

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 75.1 bits (183), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/95 (38%), Positives = 53/95 (55%), Gaps = 3/95 (3%)
Query: 112 LVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA 168
           ++F  T K    L   L +      P+   HG  TQ +R   ++RF+  E+ ILV T V 
Sbjct: 343 IIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVG 402
Query: 169 ARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           ARG+D P+V  V+   +PS++  Y+HRIGRT R G
Sbjct: 403 ARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG 437

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 74.7 bits (182), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/95 (37%), Positives = 61/95 (64%), Gaps = 2/95 (2%)
Query: 101 YTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP 160
           Y  IS  +A+  +F  T++  ++L   L +  + V++I+ D  Q+ER+   + FRSG + 
Sbjct: 254 YDSISVTQAV--IFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSR 311
Query: 161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHR 195
           IL++T + ARG+D+  V  VIN+DLP++ E Y+HR
Sbjct: 312 ILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 346

>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 = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/95 (37%), Positives = 50/95 (52%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           +++F  + +  + L   +   GY    IH    Q+ R      FR+G    LV T +  R
Sbjct: 47  SIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTR 106
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
           G+DI  V  VINFD P   E Y+HRIGR+GR G+L
Sbjct: 107 GIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHL 141

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 72.4 bits (176), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 49/94 (52%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           ++F  +    + L   +   GY     H    Q+ER +    FR G+   LV + +  RG
Sbjct: 262 IIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG 321
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
           +DI  V  VINFD P   E Y+HRIGR+GR G+L
Sbjct: 322 IDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHL 355

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 70.1 bits (170), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 51/93 (54%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            ++FV++ +    L   L    +P  +IH    Q+ER    ++F+  +  ILVAT +  R
Sbjct: 34  VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 93
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           G+DI  V    N+D+P D + Y+HR+ R GR G
Sbjct: 94  GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 126

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 51/93 (54%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            ++FV++ +    L   L    +P  +IH    Q+ER    ++F+  +  ILVAT +  R
Sbjct: 253 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 312
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           G+DI  V    N+D+P D + Y+HR+ R GR G
Sbjct: 313 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 345

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 51/93 (54%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            ++FV++ +    L   L    +P  +IH    Q+ER    ++F+  +  ILVAT +  R
Sbjct: 252 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 311
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           G+DI  V    N+D+P D + Y+HR+ R GR G
Sbjct: 312 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 344

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 51/93 (54%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            ++FV++ +    L   L    +P  +IH    Q+ER    ++F+  +  ILVAT +  R
Sbjct: 253 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 312
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           G+DI  V    N+D+P D + Y+HR+ R GR G
Sbjct: 313 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 345

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/92 (25%), Positives = 44/92 (47%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           +++  ++   +     L   G    + H       R +   +F+  +  I+VAT     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXG 299
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           ++ P+V+ V++FD+P ++E Y    GR GR G
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/92 (25%), Positives = 44/92 (47%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           +++  ++   +     L   G    + H       R +   +F+  +  I+VAT     G
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG 299
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           ++ P+V+ V++FD+P ++E Y    GR GR G
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331

>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Length = 658

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           TLV   TKK A+ L D+L   G  V  +H +    ER E +R  R G+  +LV   +   
Sbjct: 448 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 171 GLDIPHVKHVINFDLPSDVEEY-------VHRIGRTGRMGN 204
           GLDIP V  V   D  +D E +       +  IGR  R  N
Sbjct: 508 GLDIPEVSLVAILD--ADKEGFLRSERSLIQTIGRAARNAN 546

>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 = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           TLV   TKK A+ L D+L   G  V  +H +    ER E +R  R G+  +LV   +   
Sbjct: 448 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 171 GLDIPHVKHVINFDLPSDVEEY-------VHRIGRTGRMGN 204
           GLDIP V  V   D  +D E +       +  IGR  R  N
Sbjct: 508 GLDIPEVSLVAILD--ADKEGFLRSERSLIQTIGRAARNAN 546

>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In Complex With Atp Length = 657

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           TLV   TKK A+ L D+L   G  V  +H +    ER E +R  R G+  +LV   +   
Sbjct: 447 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 506
Query: 171 GLDIPHVKHVINFDLPSDVEEY-------VHRIGRTGRMGN 204
           GLDIP V  V   D  +D E +       +  IGR  R  N
Sbjct: 507 GLDIPEVSLVAILD--ADKEGFLRSERSLIQTIGRAARNAN 545

>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 = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           TLV   TKK A+ L D+L   G  V  +H +    ER E +R  R G+  +LV   +   
Sbjct: 448 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 171 GLDIPHVKHVINFDLPSDVEEY-------VHRIGRTGRMGN 204
           GLDIP V  V   D  +D E +       +  IGR  R  N
Sbjct: 508 GLDIPEVSLVAILD--ADKEGFLRSERSLIQTIGRAARNAN 546

>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex Length = 683

Iteration: 1
 Score = 50.8 bits (120), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           TLV   TKK A+ L D+L   G  V  +H +    ER E +R  R G+  +LV   +   
Sbjct: 473 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 532
Query: 171 GLDIPHVKHVINFDLPSDVEEY-------VHRIGRTGRMGN 204
           GLDIP V  V   D  +D E +       +  IGR  R  N
Sbjct: 533 GLDIPEVSLVAILD--ADKEGFLRSERSLIQTIGRAARNAN 571

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 47/183 (25%), Positives = 82/183 (44%), Gaps = 23/183 (12%)
Query: 31  WVDEQDKRSCLL-DLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGD 89
           + +E+DK+  ++ D L  P + +  D  L  +F E  K   +L +   +    +T +   
Sbjct: 330 YNEEKDKKFAVIEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNT 389
Query: 90  RTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFL------------HHH--GYPV 135
             +       QYT    + A  ++F +T++ A  L  ++             HH  G   
Sbjct: 390 IME-------QYTRTE-ESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGH 441
Query: 136 TSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHR 195
           +S     TQ E++E + +FR+G+  +L+AT VA  GLDI     VI + L ++    V  
Sbjct: 442 SSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQA 501
Query: 196 IGR 198
            GR
Sbjct: 502 RGR 504

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/90 (24%), Positives = 46/90 (51%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
           +++  ++K ++Q+   L + G    + H +   +++    R++ + E  ++VAT     G
Sbjct: 271 IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMG 330
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGR 201
           +D P V+ VI+  +   +E Y    GR GR
Sbjct: 331 IDKPDVRFVIHHSMSKSMENYYQESGRAGR 360

>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex Length = 667

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/98 (33%), Positives = 45/98 (45%), Gaps = 9/98 (9%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            LV   TKK ++ L D+L   G  V  +H +    ER E +R  R G+  +LV   +   
Sbjct: 454 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 513
Query: 171 GLDIPHVKHVINFDLPSDVEEY-------VHRIGRTGR 201
           GLDIP V  V   D  +D E +       +  IGR  R
Sbjct: 514 GLDIPEVSLVAILD--ADKEGFLRSERSLIQTIGRAAR 549

>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase Activity Of Uvrb Length = 661

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/98 (33%), Positives = 45/98 (45%), Gaps = 9/98 (9%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            LV   TKK ++ L D+L   G  V  +H +    ER E +R  R G+  +LV   +   
Sbjct: 448 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Query: 171 GLDIPHVKHVINFDLPSDVEEY-------VHRIGRTGR 201
           GLDIP V  V   D  +D E +       +  IGR  R
Sbjct: 508 GLDIPEVSLVAILD--ADKEGFLRSERSLIQTIGRAAR 543

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 52/99 (52%), Gaps = 10/99 (10%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHG------DR--TQKEREEALRRFRSGETPILV 163
           +VF   ++ A ++ + L   G       G      DR  +Q+E++  L  F  GE  +LV
Sbjct: 365 IVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLV 424
Query: 164 ATAVAARGLDIPHVKHVINFD-LPSDVEEYVHRIGRTGR 201
           AT+V   GLD+P V  V+ ++ +PS +   + R GRTGR
Sbjct: 425 ATSVGEEGLDVPEVDLVVFYEPVPSAIRS-IQRRGRTGR 462

>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase Domain Complex With Inhibitor Non-structural Protein V Length = 243

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 75/169 (44%), Gaps = 25/169 (14%)
Query: 31  WVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDR 90
           + DE++K+    ++LS     +  D  L  +F+  KK   +L +   +    +T +    
Sbjct: 84  YNDEKEKK---FEVLSGSGSLDESDIFLXTLFLRNKKILKKLAENPEYENEKLTKL---- 136
Query: 91  TQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFL------------HHH--GYPVT 136
               R    ++   + + A  ++F +T++ A  L  ++             HH  G   +
Sbjct: 137 ----RNTIXEHFTRTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHS 192
Query: 137 SIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL 185
           S     TQ E+ E + +FR+G+  +L+AT VA  GLDI     VI + L
Sbjct: 193 SEFKPXTQNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL 241

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/28 (64%), Positives = 23/28 (82%)
Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRI 29
           LA +FLY YIF+ +GRVGSTS++I Q I
Sbjct: 226 LAADFLYNYIFMTVGRVGSTSDSIKQEI 253

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	237
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	6e-87
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-84
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	6e-81
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	4e-74
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	3e-49
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	6e-49
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	3e-47
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	9e-47
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	3e-46
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	5e-46
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	2e-45
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	6e-45
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-44
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-44
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	5e-44
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	9e-44
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	1e-43
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	2e-43
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	7e-43
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	7e-43
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	1e-42
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-42
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	3e-42
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-41
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	9e-41
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-25
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	5e-16
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	1e-15
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	2e-15
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	7e-15
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	8e-15
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	4e-14
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	1e-10
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	1e-10
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	4e-10
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	2e-09
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	2e-09
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	1e-07
1yks_A	440	Genome polyprotein [contains: flavivirin protease	4e-07
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	5e-07
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	6e-07
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	8e-07
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	3e-05
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	5e-05
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	1e-04

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  262 bits (672), Expect = 6e-87
 Identities = 114/204 (55%), Positives = 132/204 (64%), Gaps = 57/204 (27%)

Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLV 61
           LA++FL  YIFLA+GRVGSTSENITQ++ WV+E DKRS LLDLL        G ++LTLV
Sbjct: 227 LARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLL-----NATGKDSLTLV 281

Query: 62  FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA 121
           FVETKKGAD LEDFL+H GY  TSIHGDR+                              
Sbjct: 282 FVETKKGADSLEDFLYHEGYACTSIHGDRS------------------------------ 311

Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
                                 Q++REEAL +FRSG++PILVATAVAARGLDI +VKHVI
Sbjct: 312 ----------------------QRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVI 349

Query: 182 NFDLPSDVEEYVHRIGRTGRMGNL 205
           NFDLPSD+EEYVHRIGRTGR+GNL
Sbjct: 350 NFDLPSDIEEYVHRIGRTGRVGNL 373

>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 =  256 bits (657), Expect = 2e-84
 Identities = 79/203 (38%), Positives = 108/203 (53%), Gaps = 59/203 (29%)

Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLV 61
           +A EFL  Y+F+AIG VG    ++ Q I  V++  KRS L+++LS            T+V
Sbjct: 253 MAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQ-------ADGTIV 305

Query: 62  FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA 121
           FVETK+GAD L  FL    +P TSIHGDR                               
Sbjct: 306 FVETKRGADFLASFLSEKEFPTTSIHGDRL------------------------------ 335

Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
                                 Q +RE+ALR F++G   +L+AT+VA+RGLDI ++KHVI
Sbjct: 336 ----------------------QSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVI 373

Query: 182 NFDLPSDVEEYVHRIGRTGRMGN 204
           N+D+PS +++YVHRIGRTGR+GN
Sbjct: 374 NYDMPSKIDDYVHRIGRTGRVGN 396

>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 =  239 bits (612), Expect = 6e-81
 Identities = 102/196 (52%), Positives = 119/196 (60%), Gaps = 57/196 (29%)

Query: 10  YIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGA 69
           +    +   GSTSENITQ++ WV+E DKRS LLDLL        G ++LTLVFVETKKGA
Sbjct: 5   HHHENLYFQGSTSENITQKVVWVEESDKRSFLLDLL-----NATGKDSLTLVFVETKKGA 59

Query: 70  DQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLH 129
           D LEDFL+H GY  TSIHGDR+                                      
Sbjct: 60  DSLEDFLYHEGYACTSIHGDRS-------------------------------------- 81

Query: 130 HHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDV 189
                         Q++REEAL +FRSG++PILVATAVAARGLDI +VKHVINFDLPSD+
Sbjct: 82  --------------QRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDI 127

Query: 190 EEYVHRIGRTGRMGNL 205
           EEYVHRIGRTGR+GNL
Sbjct: 128 EEYVHRIGRTGRVGNL 143

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  222 bits (568), Expect = 4e-74
 Identities = 55/207 (26%), Positives = 83/207 (40%), Gaps = 66/207 (31%)

Query: 5   EFLYRYIF-------LAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEA 57
              +           L    +G+ S ++ Q + +V E+ K   LL+ L            
Sbjct: 3   HHHHHSSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQK-------TPP 55

Query: 58  LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVET 117
             L+F E K   D + ++L   G    +IHG +                           
Sbjct: 56  PVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKD-------------------------- 89

Query: 118 KKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV 177
                                     Q+ER +A+  FR G+  +LVAT VA++GLD P +
Sbjct: 90  --------------------------QEERTKAIEAFREGKKDVLVATDVASKGLDFPAI 123

Query: 178 KHVINFDLPSDVEEYVHRIGRTGRMGN 204
           +HVIN+D+P ++E YVHRIGRTG  GN
Sbjct: 124 QHVINYDMPEEIENYVHRIGRTGCSGN 150

>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 =  158 bits (401), Expect = 3e-49
 Identities = 41/94 (43%), Positives = 58/94 (61%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           ++VFV  ++   +L ++L   G     + G+  Q +R EA++R   G   +LVAT VAAR
Sbjct: 33  SIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAAR 92

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           G+DIP V HV NFD+P   + Y+HRIGRT R G 
Sbjct: 93  GIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGR 126

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  157 bits (399), Expect = 6e-49
 Identities = 47/95 (49%), Positives = 61/95 (64%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++F  TK+  +QL D L   GYP   IHG   Q++R + +  F+ GE   LVAT VAA
Sbjct: 37  SCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAA 96

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           RG+DI ++  VIN+DLP + E YVHR GRTGR GN
Sbjct: 97  RGIDIENISLVINYDLPLEKESYVHRTGRTGRAGN 131

>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 =  153 bits (388), Expect = 9e-47
 Identities = 46/98 (46%), Positives = 58/98 (59%)

Query: 107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA 166
                +VF  TK   +++   L   G+P  ++HGD +Q ERE  L  FR GE  +LVAT 
Sbjct: 30  SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD 89

Query: 167 VAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           VAARGLDIP V  V+++ LP   E Y HR GRTGR G 
Sbjct: 90  VAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGR 127

>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 =  156 bits (397), Expect = 3e-46
 Identities = 43/102 (42%), Positives = 63/102 (61%)

Query: 103 LISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPIL 162
           L+   E   LVF +TK+   +L   L   G+   +IHGD +Q +RE+ +R F+  +  IL
Sbjct: 233 LLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRIL 292

Query: 163 VATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           +AT V +RG+D+  +  VIN+ LP + E Y+HRIGRTGR G 
Sbjct: 293 IATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGK 334

>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 =  154 bits (390), Expect = 5e-46
 Identities = 44/95 (46%), Positives = 58/95 (61%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             +VF  TK   +++   L   G+P  ++HGD +Q ERE  +  FR GE  +LVAT VAA
Sbjct: 30  RAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAA 89

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           RGLDIP V  V+++ +P   E Y HR GRTGR G 
Sbjct: 90  RGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGR 124

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  155 bits (393), Expect = 2e-45
 Identities = 37/210 (17%), Positives = 67/210 (31%), Gaps = 74/210 (35%)

Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLV 61
           +        +   +GR+ S + NIT        ++K   LL++               L+
Sbjct: 208 IRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEIF----------RDGILI 257

Query: 62  FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGA 121
           F +T++   +L ++L    + V     +  +                             
Sbjct: 258 FAQTEEEGKELYEYLKRFKFNVGETWSEFEKN---------------------------- 289

Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV----AARGLDIPH- 176
              EDF                           + G+  IL+          RG+D+P  
Sbjct: 290 --FEDF---------------------------KVGKINILIGVQAYYGKLTRGVDLPER 320

Query: 177 VKHVINFDLPS--DVEEYVHRIGRTGRMGN 204
           +K+VI +  PS  DV  Y+   GR+ R+ N
Sbjct: 321 IKYVIFWGTPSGPDVYTYIQASGRSSRILN 350

>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 =  153 bits (390), Expect = 6e-45
 Identities = 38/94 (40%), Positives = 63/94 (67%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++F  T++  ++L   L +  + V++I+ D  Q+ER+  ++ FRSG + IL++T + A
Sbjct: 261 QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLA 320

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           RG+D+  V  VIN+DLP++ E Y+HRIGR GR G
Sbjct: 321 RGIDVQQVSLVINYDLPANKENYIHRIGRGGRFG 354

>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 =  153 bits (389), Expect = 1e-44
 Identities = 41/94 (43%), Positives = 64/94 (68%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++F+ T++  D L + +H   + V+++HGD  QKER+  +R FRSG + +L+ T + A
Sbjct: 282 QAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLA 341

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           RG+D+  V  VIN+DLP++ E Y+HRIGR GR G
Sbjct: 342 RGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFG 375

>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 =  153 bits (388), Expect = 1e-44
 Identities = 44/94 (46%), Positives = 65/94 (69%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++F  TK+  D L + +    + V+S+HGD  QKERE  ++ FRSG + +L++T V A
Sbjct: 278 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA 337

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           RGLD+P V  +IN+DLP++ E Y+HRIGR+GR G
Sbjct: 338 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 371

>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 =  149 bits (380), Expect = 5e-44
 Identities = 42/95 (44%), Positives = 53/95 (55%), Gaps = 4/95 (4%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             +VFV T+    +L             + GD  Q  R   +  FR GE  +L+ T VA+
Sbjct: 222 GVIVFVRTRNRVAKLVRLF----DNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVAS 277

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           RGLDIP V+ VINFD P D+  Y+HRIGRTGRMG 
Sbjct: 278 RGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGR 312

>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 =  144 bits (365), Expect = 9e-44
 Identities = 32/94 (34%), Positives = 51/94 (54%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++FV++ +    L   L    +P  +IH    Q+ER    ++F+  +  ILVAT +  
Sbjct: 33  QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 92

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           RG+DI  V    N+D+P D + Y+HR+ R GR G
Sbjct: 93  RGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 126

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  143 bits (364), Expect = 1e-43
 Identities = 38/94 (40%), Positives = 63/94 (67%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++F  T++  ++L   L +  + V++I+ D  Q+ER+  ++ FRSG + IL++T + A
Sbjct: 32  QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLA 91

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           RG+D+  V  VIN+DLP++ E Y+HRIGR GR G
Sbjct: 92  RGIDVQQVSLVINYDLPANKENYIHRIGRGGRFG 125

>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 =  150 bits (380), Expect = 2e-43
 Identities = 35/96 (36%), Positives = 49/96 (51%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++F  +    + L   +   GY     H    Q+ER +    FR G+   LV + +  
Sbjct: 260 QAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLT 319

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNL 205
           RG+DI  V  VINFD P   E Y+HRIGR+GR G+L
Sbjct: 320 RGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHL 355

>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 =  151 bits (383), Expect = 7e-43
 Identities = 45/206 (21%), Positives = 68/206 (33%), Gaps = 53/206 (25%)

Query: 2   LAKEFLYRYIFLAIGRVG----STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEA 57
           LA   + +   L +  V        E I Q +   ++                +E     
Sbjct: 281 LANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNY 340

Query: 58  LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVET 117
             ++F  T K    L   L +                                       
Sbjct: 341 KAIIFAPTVKFTSFLCSILKNEFKK----------------------------------- 365

Query: 118 KKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV 177
                           P+   HG  TQ +R   ++RF+  E+ ILV T V ARG+D P+V
Sbjct: 366 --------------DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 411

Query: 178 KHVINFDLPSDVEEYVHRIGRTGRMG 203
             V+   +PS++  Y+HRIGRT R G
Sbjct: 412 HEVLQIGVPSELANYIHRIGRTARSG 437

>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 =  148 bits (376), Expect = 7e-43
 Identities = 44/100 (44%), Positives = 62/100 (62%), Gaps = 6/100 (6%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
            +++FV TKK A+ L   L   G+ V+ +HGD   +ER+  +  FR G + +L+ T V A
Sbjct: 245 SSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA 304

Query: 170 RGLDIPHVKHVINFDLP------SDVEEYVHRIGRTGRMG 203
           RG+DIP V  V+N+DLP      +D   Y+HRIGRTGR G
Sbjct: 305 RGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFG 344

>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 =  141 bits (358), Expect = 1e-42
 Identities = 39/100 (39%), Positives = 60/100 (60%), Gaps = 6/100 (6%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++F +T++ A  L   +   G+ V+ + G+ T ++R   ++RFR G+  +L+ T V A
Sbjct: 36  QAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCA 95

Query: 170 RGLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMG 203
           RG+D+  V  V+NFDLP       D E Y+HRIGRTGR G
Sbjct: 96  RGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFG 135

>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 =  149 bits (379), Expect = 3e-42
 Identities = 45/206 (21%), Positives = 68/206 (33%), Gaps = 53/206 (25%)

Query: 2   LAKEFLYRYIFLAIGRVG----STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEA 57
           LA   + +   L +  V        E I Q +   ++                +E     
Sbjct: 230 LANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNY 289

Query: 58  LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVET 117
             ++F  T K    L   L +                                       
Sbjct: 290 KAIIFAPTVKFTSFLCSILKNEFKK----------------------------------- 314

Query: 118 KKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV 177
                           P+   HG  TQ +R   ++RF+  E+ ILV T V ARG+D P+V
Sbjct: 315 --------------DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 360

Query: 178 KHVINFDLPSDVEEYVHRIGRTGRMG 203
             V+   +PS++  Y+HRIGRT R G
Sbjct: 361 HEVLQIGVPSELANYIHRIGRTARSG 386

>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 =  146 bits (371), Expect = 3e-42
 Identities = 32/94 (34%), Positives = 51/94 (54%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++FV++ +    L   L    +P  +IH    Q+ER    ++F+  +  ILVAT +  
Sbjct: 252 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFG 311

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           RG+DI  V    N+D+P D + Y+HR+ R GR G
Sbjct: 312 RGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 345

>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 =  145 bits (368), Expect = 1e-41
 Identities = 42/100 (42%), Positives = 56/100 (56%), Gaps = 6/100 (6%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++F  T+K A  L   L   G+ V  + G+   ++R   + RFR G+  +LV T V A
Sbjct: 268 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 327

Query: 170 RGLDIPHVKHVINFDLP------SDVEEYVHRIGRTGRMG 203
           RG+D+  V  VINFDLP       D E Y+HRIGRTGR G
Sbjct: 328 RGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 367

>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 =  144 bits (365), Expect = 9e-41
 Identities = 42/100 (42%), Positives = 56/100 (56%), Gaps = 6/100 (6%)

Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
             ++F  T+K A  L   L   G+ V  + G+   ++R   + RFR G+  +LV T V A
Sbjct: 335 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA 394

Query: 170 RGLDIPHVKHVINFDLP------SDVEEYVHRIGRTGRMG 203
           RG+D+  V  VINFDLP       D E Y+HRIGRTGR G
Sbjct: 395 RGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG 434

>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 =  102 bits (256), Expect = 2e-25
 Identities = 29/106 (27%), Positives = 47/106 (44%), Gaps = 8/106 (7%)

Query: 107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDR--------TQKEREEALRRFRSGE 158
             +  +VF   ++ A ++ + L   G       G          +Q+E++  L  F  GE
Sbjct: 360 QNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE 419

Query: 159 TPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
             +LVAT+V   GLD+P V  V+ ++        + R GRTGR   
Sbjct: 420 FNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP 465

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 75.7 bits (185), Expect = 5e-16
 Identities = 38/169 (22%), Positives = 68/169 (40%), Gaps = 16/169 (9%)

Query: 51  EELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQ--QYTLISCDE 108
           +    +     F ET++   +  +        V+    +   K R+     Q       E
Sbjct: 330 KAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPE 389

Query: 109 ALTLVFVETKKGADQLEDFLHHH------------GYPVTSIHGDRTQKEREEALRRFR- 155
             T++FV+T+   D L+ ++  +            G   T+     T   ++  L  FR 
Sbjct: 390 TKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRA 449

Query: 156 SGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           SG+  IL+AT+VA  G+DI     VI ++   +V + +   GR GR  +
Sbjct: 450 SGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRARD 497

>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 = 75.0 bits (183), Expect = 1e-15
 Identities = 24/125 (19%), Positives = 47/125 (37%), Gaps = 14/125 (11%)

Query: 93  KEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHH------------GYPVTSIHG 140
           +E             +  TL+F +T+     L+  +  +            G        
Sbjct: 375 EELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTT 434

Query: 141 DRTQKEREEALRRFRSGET-PILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRT 199
             T   ++  L  F++ +   +L+AT+VA  G+DI     V+ ++   +V + +   GR 
Sbjct: 435 GMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR- 493

Query: 200 GRMGN 204
           GR   
Sbjct: 494 GRAAG 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 = 74.2 bits (181), Expect = 2e-15
 Identities = 23/111 (20%), Positives = 45/111 (40%), Gaps = 14/111 (12%)

Query: 107 DEALTLVFVETKKGADQLEDFLHHH------------GYPVTSIHGDRTQKEREEALRRF 154
            +  TL+F +T+     L+  +  +            G          T   ++  L  F
Sbjct: 630 PQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAF 689

Query: 155 RSGET-PILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           ++ +   +L+AT+VA  G+DI     V+ ++   +V + +   GR GR   
Sbjct: 690 KTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAG 739

>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 = 72.3 bits (176), Expect = 7e-15
 Identities = 23/122 (18%), Positives = 45/122 (36%), Gaps = 14/122 (11%)

Query: 96  EEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHH------------GYPVTSIHGDRT 143
                       +  TL+F +T+     L+  +  +            G          T
Sbjct: 619 VCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMT 678

Query: 144 QKEREEALRRFRSGET-PILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRM 202
              ++  L  F++ +   +L+AT+VA  G+DI     V+ ++   +V + +   GR GR 
Sbjct: 679 LPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA 737

Query: 203 GN 204
             
Sbjct: 738 AG 739

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 72.3 bits (176), Expect = 8e-15
 Identities = 35/168 (20%), Positives = 67/168 (39%), Gaps = 15/168 (8%)

Query: 51  EELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQ--QYTLISCDE 108
           ++         F E ++   Q  +        V+    +   K  +     Q       E
Sbjct: 339 KDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPE 398

Query: 109 ALTLVFVETKKGADQLEDFLHHH------------GYPVTSIHGDRTQKEREEALRRFR- 155
            +T++FV+T+   D L++++  +            G   T+ +   T   ++  L  F+ 
Sbjct: 399 TITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKA 458

Query: 156 SGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           SG+  IL+AT+VA  G+DI     VI ++   +V + +   GR    G
Sbjct: 459 SGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARG 506

>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 = 70.1 bits (171), Expect = 4e-14
 Identities = 44/202 (21%), Positives = 71/202 (35%), Gaps = 7/202 (3%)

Query: 8   YRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKK 67
              + + + R G++          V    KR      L  P+Q +     ++ +    K 
Sbjct: 401 QELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQT-AIKVSGIMGARKS 459

Query: 68  GADQLEDFLHHHGYPVTSIHGDRTQKE---REEAQQYTLISCDEALTLVFVETKKGADQL 124
             D+  D L+           + T      R E     L S      LV       A QL
Sbjct: 460 AEDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQL 519

Query: 125 EDFLH-HHGYPVTSIHGDRTQKEREEALRRFRSGETP--ILVATAVAARGLDIPHVKHVI 181
           E  L    G      H   +  ER+ A   F   +T   +L+ + + + G +     H++
Sbjct: 520 EQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMV 579

Query: 182 NFDLPSDVEEYVHRIGRTGRMG 203
            FDLP + +    RIGR  R+G
Sbjct: 580 MFDLPFNPDLLEQRIGRLDRIG 601

>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 = 59.4 bits (145), Expect = 1e-10
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 117 TKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA-ARGLDIP 175
           ++   +     L   G    + H       R +   +F+  +  I+VAT VA   G++ P
Sbjct: 245 SRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVAT-VAFGMGINKP 303

Query: 176 HVKHVINFDLPSDVEEYVHRIGRTGR 201
           +V+ V++FD+P ++E Y    GR GR
Sbjct: 304 NVRFVVHFDIPRNIESYYQETGRAGR 329

>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 = 59.6 bits (144), Expect = 1e-10
 Identities = 28/147 (19%), Positives = 40/147 (27%), Gaps = 30/147 (20%)

Query: 81  YPVTSIHGDRTQKEREEAQQYTLISCDEAL---TLVFVETKKGADQLEDFLHHHGYPVTS 137
            P  +I         E       I  +       L+F  +KK  D+L   L   G    +
Sbjct: 366 VPHPNIEEVALSNTGEIPFYGKAIPIEAIRGGRHLIFCHSKKKCDELAAKLSGLGINAVA 425

Query: 138 IHGDRTQKEREEALRRFRSGETPILVATAVAARGL--DIPHV-------KHVINFDL--- 185
            +                +    ++VAT     G   D   V          ++F L   
Sbjct: 426 YYRGLDVSV-------IPTIGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPT 478

Query: 186 --------PSDVEEYVHRIGRTGRMGN 204
                   P D      R GRTGR   
Sbjct: 479 FTIETTTVPQDAVSRSQRRGRTGRGRR 505

>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 = 57.9 bits (140), Expect = 4e-10
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 7/92 (7%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            ++F    +   ++             I    +++EREE L  FR+G    +V++ V   
Sbjct: 352 IIIFTRHNELVYRISKVFLIPA-----ITHRTSREEREEILEGFRTGRFRAIVSSQVLDE 406

Query: 171 GLDIPHVKHVINFDLPS-DVEEYVHRIGRTGR 201
           G+D+P     +     S    EY+ R+GR  R
Sbjct: 407 GIDVPDANVGV-IMSGSGSAREYIQRLGRILR 437

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score = 55.2 bits (134), Expect = 2e-09
 Identities = 18/28 (64%), Positives = 23/28 (82%)

Query: 2   LAKEFLYRYIFLAIGRVGSTSENITQRI 29
           LA +FLY YIF+ +GRVGSTS++I Q I
Sbjct: 226 LAADFLYNYIFMTVGRVGSTSDSIKQEI 253

>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 = 55.8 bits (135), Expect = 2e-09
 Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 117 TKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA-ARGLDIP 175
           ++K ++Q+   L + G    + H +   +++    R++ + E  ++VAT VA   G+D P
Sbjct: 276 SQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT-VAFGMGIDKP 334

Query: 176 HVKHVINFDLPSDVEEYVHRIGRTGR 201
            V+ VI+  +   +E Y    GR GR
Sbjct: 335 DVRFVIHHSMSKSMENYYQESGRAGR 360

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B* Length = 1054

 Score = 50.8 bits (122), Expect = 1e-07
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 11/81 (13%)

Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA----V 167
           +++  T + A+++ + L +  + +  +        ++    +F  GE   L+ TA     
Sbjct: 279 IIYARTGEEAEEIYESLKN-KFRIGIVT-----ATKKGDYEKFVEGEIDHLIGTAHYYGT 332

Query: 168 AARGLDIPH-VKHVINFDLPS 187
             RGLD+P  ++  +    PS
Sbjct: 333 LVRGLDLPERIRFAVFVGCPS 353

>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 = 49.1 bits (117), Expect = 4e-07
 Identities = 19/110 (17%), Positives = 36/110 (32%), Gaps = 24/110 (21%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           T  F+ + + A+ +   L   G  V  ++     K  E      +  +   ++AT +A  
Sbjct: 180 TAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEM 235

Query: 171 GLDIPHVKHVINFDL-------------------PSDVEEYVHRIGRTGR 201
           G ++  V+ V++                               R GR GR
Sbjct: 236 GANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGR 284

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A Length = 451

 Score = 49.1 bits (117), Expect = 5e-07
 Identities = 30/172 (17%), Positives = 48/172 (27%), Gaps = 35/172 (20%)

Query: 81  YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHG 140
            P+  I  +  ++          I+  +  T+ FV + K  + + + L   G  V  +  
Sbjct: 163 SPIEDIEREIPERSWNTGFD--WITDYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSR 220

Query: 141 DRTQKEREEALRRFRSGETPILVATAVAARGL--DIPHV-------KHVINFDLPSDVEE 191
                E  +     +  +   +V T ++  G       V       K VI  D P  V  
Sbjct: 221 KTFDTEYPKT----KLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVIL 276

Query: 192 YV----------HRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSSQNSNAPDW 233
                        R GR GR                  Y  S     N  D 
Sbjct: 277 AGPIPVTPASAAQRRGRIGRNP----------AQEDDQYVFSGDPLKNDEDH 318

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 48.7 bits (115), Expect = 6e-07
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 1/92 (1%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT-AVAA 169
             V  +       + D + +    V  + G+   + R        +G+  I+VA+  V +
Sbjct: 350 AFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFS 409

Query: 170 RGLDIPHVKHVINFDLPSDVEEYVHRIGRTGR 201
            G+ + ++ HV+           +  IGR  R
Sbjct: 410 TGISVKNLHHVVLAHGVKSKIIVLQTIGRVLR 441

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A Length = 618

 Score = 48.4 bits (115), Expect = 8e-07
 Identities = 27/142 (19%), Positives = 39/142 (27%), Gaps = 33/142 (23%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           T+ FV + K  + + + L   G  V  +       E  +     +  +   +V T ++  
Sbjct: 358 TVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKT----KLTDWDFVVTTDISEM 413

Query: 171 GL--DIPHV-------KHVINFDLPSDVEEYV----------HRIGRTGRMGNLDFPFSY 211
           G       V       K VI  D P  V               R GR GR          
Sbjct: 414 GANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNP-------- 465

Query: 212 NQPGYGGSYGGSSSQNSNAPDW 233
                   Y  S     N  D 
Sbjct: 466 --AQEDDQYVFSGDPLKNDEDH 485

>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 = 43.7 bits (104), Expect = 3e-05
 Identities = 24/67 (35%), Positives = 33/67 (49%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           TLV V T + A++L  FL  HG     +H +    +R+  +R  R G    LV   +   
Sbjct: 442 TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLRE 501

Query: 171 GLDIPHV 177
           GLDIP V
Sbjct: 502 GLDIPEV 508

>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* Length = 661

 Score = 42.9 bits (102), Expect = 5e-05
 Identities = 25/67 (37%), Positives = 34/67 (50%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            LV   TKK ++ L D+L   G  V  +H +    ER E +R  R G+  +LV   +   
Sbjct: 448 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507

Query: 171 GLDIPHV 177
           GLDIP V
Sbjct: 508 GLDIPEV 514

>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 Length = 780

 Score = 41.8 bits (99), Expect = 1e-04
 Identities = 21/92 (22%), Positives = 41/92 (44%), Gaps = 9/92 (9%)

Query: 89  DRTQKEREEAQQ----YTLISCDEALTLVFVETKKGADQL-EDFLHHHGYPVTSIHGDRT 143
           +  ++E     Q    Y LI   + L +      +  + L ++      + +  +HG  +
Sbjct: 569 EFVRQEVMRGGQAFIVYPLIEESDKLNVKSAV--EMYEYLSKEVFP--EFKLGLMHGRLS 624

Query: 144 QKEREEALRRFRSGETPILVATAVAARGLDIP 175
           Q+E++  +  F  G   ILV+T V   G+D+P
Sbjct: 625 QEEKDRVMLEFAEGRYDILVSTTVIEVGIDVP 656

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	237
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.98
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.97
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.97
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.96
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.96
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.96
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.96
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.95
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.95
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.91
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.94
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.93
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.93
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.92
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.92
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.92
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.92
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.92
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.9
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.9
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.9
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.9
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.9
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.89
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.88
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.86
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.85
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.85
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.84
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.84
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.84
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.83
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.83
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.83
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.83
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.83
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.82
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.82
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.82
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.82
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.81
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.81
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.81
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.81
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.81
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.81
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.81
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.81
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.8
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.8
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.8
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.8
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.79
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.79
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.78
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.78
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.78
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.78
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.76
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.76
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.76
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.76
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.76
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.76
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.75
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.75
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.74
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.73
3h1t_A	590	Type I site-specific restriction-modification syst	99.68
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.25
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.71
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.45
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.24
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	97.56
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	96.19
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	95.97
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	95.31
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	94.48
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	94.34
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	94.25
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	94.17
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	94.16
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	93.83
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	93.58
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	93.55
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	93.45
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	93.2
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	92.35
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	91.56
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	91.89
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	91.31
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	91.23
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	91.04
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	90.19
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	89.29
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	88.64
3jux_A	822	Protein translocase subunit SECA; protein transloc	87.85
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	87.54
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	87.5
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	86.69
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	86.69
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	86.25
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	86.16
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	86.05
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	85.79
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	85.66
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	85.18
3bor_A	237	Human initiation factor 4A-II; translation initiat	84.87
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	84.68
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	84.36
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	83.91
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	83.61
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	83.17
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	83.07
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	82.98
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	82.58
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	82.33
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	82.07
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	82.03
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	81.83
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	81.42
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	80.13
4gl2_A	699	Interferon-induced helicase C domain-containing P;	80.06

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.98  E-value=4.1e-32  Score=210.59  Aligned_cols=155  Identities=35%  Similarity=0.622  Sum_probs=126.8

Q ss_pred             HHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCC
Q psy15610          3 AKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYP   82 (237)
Q Consensus         3 ~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~   82 (237)
                      ..+||.+|+.|.+...+....+|.|.++.+++.+|+..|.++|...                                  
T Consensus         8 ~~~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~~~K~~~L~~~l~~~----------------------------------   53 (191)
T 2p6n_A            8 SSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQKT----------------------------------   53 (191)
T ss_dssp             --------------------CCSEEEEEECCGGGHHHHHHHHHTTS----------------------------------
T ss_pred             cccccCCCEEEEECCCCCCCcCceEEEEEcChHHHHHHHHHHHHhC----------------------------------
Confidence            3679999999999877788899999999999999999999999865                                  


Q ss_pred             ceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEE
Q psy15610         83 VTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPIL  162 (237)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vl  162 (237)
                                               +.++||||++...++.++..|...++.+..+||+|++.+|..+++.|++|..+||
T Consensus        54 -------------------------~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vL  108 (191)
T 2p6n_A           54 -------------------------PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVL  108 (191)
T ss_dssp             -------------------------CSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTSCSEE
T ss_pred             -------------------------CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEE
Confidence                                     4689999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        163 VATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       163 v~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      |||+++++|+|+|++++||++++|+++..|.||+||+||.|++|.+++|+.+.+
T Consensus       109 vaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~  162 (191)
T 2p6n_A          109 VATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKAC  162 (191)
T ss_dssp             EECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTS
T ss_pred             EEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCch
Confidence            999999999999999999999999999999999999999999999999998764

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.97  E-value=4.7e-30  Score=194.15  Aligned_cols=145  Identities=41%  Similarity=0.599  Sum_probs=133.2

Q ss_pred             ccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHH
Q psy15610         18 VGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE   97 (237)
Q Consensus        18 ~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   97 (237)
                      ++....+|.|.|+.+++.+|+..|.++|....                                                
T Consensus         3 ~~~~~~~i~~~~~~~~~~~K~~~L~~ll~~~~------------------------------------------------   34 (163)
T 2hjv_A            3 AGLTTRNIEHAVIQVREENKFSLLKDVLMTEN------------------------------------------------   34 (163)
T ss_dssp             ---CCCCEEEEEEECCGGGHHHHHHHHHHHHC------------------------------------------------
T ss_pred             cccCcccceEEEEECChHHHHHHHHHHHHhcC------------------------------------------------
Confidence            34567789999999999999999999997642                                                


Q ss_pred             HhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC
Q psy15610         98 AQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV  177 (237)
Q Consensus        98 ~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~  177 (237)
                                ..++||||++...++.+++.|...++.+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++
T Consensus        35 ----------~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gld~~~~  104 (163)
T 2hjv_A           35 ----------PDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENI  104 (163)
T ss_dssp             ----------CSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTTTCCCSCC
T ss_pred             ----------CCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCchhcC
Confidence                      5789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCC
Q psy15610        178 KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSY  220 (237)
Q Consensus       178 ~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~  220 (237)
                      ++||++++|+++..|.||+||+||.|++|.+++|+.+.+...+
T Consensus       105 ~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~  147 (163)
T 2hjv_A          105 SLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFL  147 (163)
T ss_dssp             SEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHH
T ss_pred             CEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHH
Confidence            9999999999999999999999999999999999987765443

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=99.97  E-value=9e-30  Score=194.27  Aligned_cols=138  Identities=28%  Similarity=0.499  Sum_probs=128.7

Q ss_pred             CCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         21 TSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        21 ~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +..+|.|+|+.+++.+|+..|.+++....                                                   
T Consensus         2 ~~~~i~q~~~~~~~~~K~~~L~~ll~~~~---------------------------------------------------   30 (172)
T 1t5i_A            2 SLHGLQQYYVKLKDNEKNRKLFDLLDVLE---------------------------------------------------   30 (172)
T ss_dssp             ---CCEEEEEECCGGGHHHHHHHHHHHSC---------------------------------------------------
T ss_pred             ccCCeEEEEEECChHHHHHHHHHHHHhCC---------------------------------------------------
Confidence            35689999999999999999999997652                                                   


Q ss_pred             hhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEE
Q psy15610        101 YTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV  180 (237)
Q Consensus       101 ~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~V  180 (237)
                             ..++||||++...++.++..|...++.+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++++|
T Consensus        31 -------~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~V  103 (172)
T 1t5i_A           31 -------FNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIA  103 (172)
T ss_dssp             -------CSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEE
T ss_pred             -------CCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCchhcCcchhhCCEE
Confidence                   4789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        181 INFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       181 i~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      |++++|+++..|.||+||+||.|+.|.+++|+.+.+
T Consensus       104 i~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~  139 (172)
T 1t5i_A          104 FNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  139 (172)
T ss_dssp             EESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHH
T ss_pred             EEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChh
Confidence            999999999999999999999999999999998753

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=99.96  E-value=2.3e-29  Score=192.49  Aligned_cols=144  Identities=33%  Similarity=0.539  Sum_probs=129.4

Q ss_pred             CCCCCceeEEEEeechh-HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHH
Q psy15610         20 STSENITQRIAWVDEQD-KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        20 ~~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   98 (237)
                      .+..+|.|+|+.++..+ |+..|.+++....                                                 
T Consensus         3 ~~~~~i~q~~~~~~~~~~K~~~L~~ll~~~~-------------------------------------------------   33 (175)
T 2rb4_A            3 LTLNNIRQYYVLCEHRKDKYQALCNIYGSIT-------------------------------------------------   33 (175)
T ss_dssp             CCBCCEEEEEEECSSHHHHHHHHHHHHTTSC-------------------------------------------------
T ss_pred             CccCCceEEEEEcCChHhHHHHHHHHHHhCC-------------------------------------------------
Confidence            45678999999999766 9999999998652                                                 


Q ss_pred             hhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCc
Q psy15610         99 QQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVK  178 (237)
Q Consensus        99 ~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~  178 (237)
                               ..++||||+++..++.++..|...++.+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|.++
T Consensus        34 ---------~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~  104 (175)
T 2rb4_A           34 ---------IGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVT  104 (175)
T ss_dssp             ---------CSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCTTTCCTTEE
T ss_pred             ---------CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhcCCCcccCC
Confidence                     57899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCC------CCHHHHHHhhcccccCCCCCceEEeecCCCCCCCC
Q psy15610        179 HVINFDLP------SDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYG  221 (237)
Q Consensus       179 ~Vi~~~~p------~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  221 (237)
                      +||+++.|      .+...|+||+||+||.|+.|.+++|+.+.+...+.
T Consensus       105 ~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~  153 (175)
T 2rb4_A          105 IVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLM  153 (175)
T ss_dssp             EEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHH
T ss_pred             EEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHH
Confidence            99999999      89999999999999999999999999887754443

>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=99.96  E-value=1e-29  Score=196.13  Aligned_cols=150  Identities=68%  Similarity=1.009  Sum_probs=121.6

Q ss_pred             eeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhH
Q psy15610         16 GRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKER   95 (237)
Q Consensus        16 ~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~   95 (237)
                      ..+.....+|.|.|+.+++.+|+..|.++|....                                              
T Consensus        11 ~~~~~~~~~i~q~~~~v~~~~K~~~L~~ll~~~~----------------------------------------------   44 (185)
T 2jgn_A           11 YFQGSTSENITQKVVWVEESDKRSFLLDLLNATG----------------------------------------------   44 (185)
T ss_dssp             -----CCTTEEEEEEECCGGGHHHHHHHHHHHC-----------------------------------------------
T ss_pred             cccCCCCCCceEEEEEeCcHHHHHHHHHHHHhcC----------------------------------------------
Confidence            3455678899999999999999999999997652                                              


Q ss_pred             HHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCC
Q psy15610         96 EEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP  175 (237)
Q Consensus        96 ~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~  175 (237)
                                 ++.++||||++...++.++..|...++.+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|
T Consensus        45 -----------~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~  113 (185)
T 2jgn_A           45 -----------KDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDIS  113 (185)
T ss_dssp             -----------CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHTSSSEEEEEC------CCC
T ss_pred             -----------CCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcChhhcCCCcc
Confidence                       147899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCC
Q psy15610        176 HVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGG  222 (237)
Q Consensus       176 ~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~  222 (237)
                      ++++||++++|+++..|.||+||+||.|+.|.+++|+.+.+...+..
T Consensus       114 ~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~  160 (185)
T 2jgn_A          114 NVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKD  160 (185)
T ss_dssp             SBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHH
T ss_pred             cCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHH
Confidence            99999999999999999999999999999999999999887665544

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.96  E-value=3.1e-29  Score=190.00  Aligned_cols=141  Identities=36%  Similarity=0.633  Sum_probs=125.5

Q ss_pred             CCceeEEEEeechh-HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhh
Q psy15610         23 ENITQRIAWVDEQD-KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQY  101 (237)
Q Consensus        23 ~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  101 (237)
                      .+|+|+|+.+++.+ |+..|.+++....                                                    
T Consensus         2 ~~i~~~~~~~~~~~~K~~~l~~ll~~~~----------------------------------------------------   29 (165)
T 1fuk_A            2 EGIKQFYVNVEEEEYKYECLTDLYDSIS----------------------------------------------------   29 (165)
T ss_dssp             --CEEEEEEEESGGGHHHHHHHHHHHTT----------------------------------------------------
T ss_pred             CCcEEEEEECCcchhHHHHHHHHHHhCC----------------------------------------------------
Confidence            47899999999887 9999999998652                                                    


Q ss_pred             hhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEE
Q psy15610        102 TLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI  181 (237)
Q Consensus       102 ~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi  181 (237)
                            ..++||||++...++.++..|...++.+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++++||
T Consensus        30 ------~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G~d~~~~~~Vi  103 (165)
T 1fuk_A           30 ------VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVI  103 (165)
T ss_dssp             ------CSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEE
T ss_pred             ------CCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChhhcCCCcccCCEEE
Confidence                  57899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCC
Q psy15610        182 NFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYG  221 (237)
Q Consensus       182 ~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  221 (237)
                      ++++|+++..|.||+||+||.|+.|.+++|+.+.+...+.
T Consensus       104 ~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~  143 (165)
T 1fuk_A          104 NYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMR  143 (165)
T ss_dssp             ESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHH
T ss_pred             EeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHH
Confidence            9999999999999999999999999999999987754443

>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=99.96  E-value=1.1e-28  Score=213.92  Aligned_cols=176  Identities=47%  Similarity=0.785  Sum_probs=156.2

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      +++.|+.+|..+.+........++.+.+..+.+.+|...|.+++...                                 
T Consensus       253 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~---------------------------------  299 (434)
T 2db3_A          253 MAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQ---------------------------------  299 (434)
T ss_dssp             HHHTTCSSCEEEEESSTTCCCTTEEEEEEECCGGGHHHHHHHHHHHC---------------------------------
T ss_pred             HHHHhccCCEEEEeccccccccccceEEEEeCcHHHHHHHHHHHHhC---------------------------------
Confidence            57788999999988777777889999999999999999999888765                                 


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                                ..++||||+++..++.+++.|...++.+..+||++++.+|+.+++.|++|..+|
T Consensus       300 --------------------------~~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~v  353 (434)
T 2db3_A          300 --------------------------ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKV  353 (434)
T ss_dssp             --------------------------CTTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSE
T ss_pred             --------------------------CCCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcE
Confidence                                      245999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCC-----CCCCCCCCCCCccC
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGG-----SSSQNSNAPDWWND  236 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~  236 (237)
                      ||||+++++|+|+|++++||+|++|.+...|+||+||+||.|+.|.+++|+.+.+...+..     ........|+|+.+
T Consensus       354 LvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~~~~~~vp~~l~~  433 (434)
T 2db3_A          354 LIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLRT  433 (434)
T ss_dssp             EEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHHHTTCCCCGGGC-
T ss_pred             EEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            9999999999999999999999999999999999999999999999999999765433322     33356678888764

>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=99.95  E-value=6.2e-28  Score=190.08  Aligned_cols=136  Identities=38%  Similarity=0.545  Sum_probs=125.5

Q ss_pred             CceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhh
Q psy15610         24 NITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTL  103 (237)
Q Consensus        24 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (237)
                      .+.+.++.++..+|+..|.+++....                                                      
T Consensus         5 ~~~~~~~~~~~~~k~~~l~~ll~~~~------------------------------------------------------   30 (212)
T 3eaq_A            5 TYEEEAVPAPVRGRLEVLSDLLYVAS------------------------------------------------------   30 (212)
T ss_dssp             CBCCEEEECCTTSHHHHHHHHHHHHC------------------------------------------------------
T ss_pred             ceeeeEEeCCHHHHHHHHHHHHHhCC------------------------------------------------------
Confidence            35677888888999999999997543                                                      


Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEe
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                          +.++||||+++..++.+++.|...++.+..+||+|++.+|.++++.|++|..+|||||+++++|+|+|++++||++
T Consensus        31 ----~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidi~~v~~Vi~~  106 (212)
T 3eaq_A           31 ----PDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHY  106 (212)
T ss_dssp             ----CSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCSSSCCCBSEEEES
T ss_pred             ----CCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcCCCCccCcEEEEC
Confidence                5799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ++|+++..|.||+||+||.|++|.+++|+++.+.
T Consensus       107 ~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~  140 (212)
T 3eaq_A          107 RLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRER  140 (212)
T ss_dssp             SCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGH
T ss_pred             CCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHH
Confidence            9999999999999999999999999999988763

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.95  E-value=2.2e-27  Score=195.66  Aligned_cols=136  Identities=37%  Similarity=0.540  Sum_probs=124.4

Q ss_pred             CceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhh
Q psy15610         24 NITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTL  103 (237)
Q Consensus        24 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (237)
                      .+.|+++.++.++|+..|.+++....                                                      
T Consensus         2 ~v~~~~i~~~~~~K~~~L~~ll~~~~------------------------------------------------------   27 (300)
T 3i32_A            2 TYEEEAVPAPVRGRLEVLSDLLYVAS------------------------------------------------------   27 (300)
T ss_dssp             CSEEEEEECCSSSHHHHHHHHHHHHC------------------------------------------------------
T ss_pred             ceEEEEEECCHHHHHHHHHHHHHhcC------------------------------------------------------
Confidence            47899999999999999999997653                                                      


Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEe
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                          +.++||||+++..++.+++.|...++.+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++++||++
T Consensus        28 ----~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~~Gidi~~v~~VI~~  103 (300)
T 3i32_A           28 ----PDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHY  103 (300)
T ss_dssp             ----CSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTTCSTTCCCCSEEEES
T ss_pred             ----CCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhhcCccccceeEEEEc
Confidence                5799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +.|+++..|.||+||+||.|++|.|++|+++.+.
T Consensus       104 d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~  137 (300)
T 3i32_A          104 RMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRER  137 (300)
T ss_dssp             SCCSSTTHHHHHHTCCC-----CEEEEEECSSTH
T ss_pred             CCCCCHHHHHHHccCcCcCCCCceEEEEeChHHH
Confidence            9999999999999999999999999999998763

>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=99.91  E-value=2.2e-29  Score=191.73  Aligned_cols=145  Identities=35%  Similarity=0.579  Sum_probs=133.9

Q ss_pred             CCceeEEEEeec-hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhh
Q psy15610         23 ENITQRIAWVDE-QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQY  101 (237)
Q Consensus        23 ~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  101 (237)
                      .+|.|.|+.++. .+|+..|.+++....                                                    
T Consensus         2 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~----------------------------------------------------   29 (170)
T 2yjt_D            2 KKIHQWYYRADDLEHKTALLVHLLKQPE----------------------------------------------------   29 (170)
Confidence            368889998888 889999999987642                                                    


Q ss_pred             hhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEE
Q psy15610        102 TLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI  181 (237)
Q Consensus       102 ~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi  181 (237)
                            +.++||||++...++.+++.|...++.+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++++||
T Consensus        30 ------~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi  103 (170)
T 2yjt_D           30 ------ATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVF  103 (170)
Confidence                  46899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCCC
Q psy15610        182 NFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS  225 (237)
Q Consensus       182 ~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  225 (237)
                      ++++|+++..|.||+||+||.|+.|.+++|+.+.+...+.....
T Consensus       104 ~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  147 (170)
T 2yjt_D          104 NFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGR  147 (170)
Confidence            99999999999999999999999999999999888777666544

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.94  E-value=5.3e-26  Score=195.44  Aligned_cols=176  Identities=66%  Similarity=1.034  Sum_probs=149.6

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGY   81 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~   81 (237)
                      +++.++.+|..+.+........++.+.+..++..+|...+.+++....                                
T Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~--------------------------------  274 (417)
T 2i4i_A          227 LARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATG--------------------------------  274 (417)
T ss_dssp             HHHHHCSSCEEEEEC----CCSSEEEEEEECCGGGHHHHHHHHHHTCC--------------------------------
T ss_pred             HHHHHcCCCEEEEeCCCCCCccCceEEEEEeccHhHHHHHHHHHHhcC--------------------------------
Confidence            456788889888877666778889999999999899999998887652                                


Q ss_pred             CceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCE
Q psy15610         82 PVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI  161 (237)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  161 (237)
                                               .+.++||||++++.++.+++.|...++.+..+||++++++|..+++.|++|..+|
T Consensus       275 -------------------------~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~v  329 (417)
T 2i4i_A          275 -------------------------KDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPI  329 (417)
T ss_dssp             -------------------------TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCE
T ss_pred             -------------------------CCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCE
Confidence                                     1478999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCCC----CCCCCCCCc
Q psy15610        162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS----QNSNAPDWW  234 (237)
Q Consensus       162 lv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~  234 (237)
                      ||||+++++|+|+|++++||++++|++...|.||+||+||.|+.|.+++|+.+.+........+    +....++|+
T Consensus       330 lvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l  406 (417)
T 2i4i_A          330 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWL  406 (417)
T ss_dssp             EEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHH
T ss_pred             EEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHHHHHHhcCcCCHHH
Confidence            9999999999999999999999999999999999999999999999999999877665544322    344455554

>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=99.93  E-value=6.1e-26  Score=194.87  Aligned_cols=158  Identities=35%  Similarity=0.589  Sum_probs=143.2

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechh-HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQD-KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      +++.++.+|..+.+........++.+.+..++..+ |...+.+++....                               
T Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~-------------------------------  275 (410)
T 2j0s_A          227 MTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT-------------------------------  275 (410)
T ss_dssp             TGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHHHHHHHT-------------------------------
T ss_pred             HHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHHHHHhcC-------------------------------
Confidence            46678889988877766677888999888887655 8888888776542                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++||||++.+.++.+++.|...++.+..+||++++.+|..+++.|++|..+
T Consensus       276 ---------------------------~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  328 (410)
T 2j0s_A          276 ---------------------------ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASR  328 (410)
T ss_dssp             ---------------------------SSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSC
T ss_pred             ---------------------------CCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCC
Confidence                                       46899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      |||||+++++|+|+|++++||++++|+++..|.||+||+||.|++|.+++|+.+.+.
T Consensus       329 vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~  385 (410)
T 2j0s_A          329 VLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI  385 (410)
T ss_dssp             EEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGH
T ss_pred             EEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHH
Confidence            999999999999999999999999999999999999999999999999999987764

>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=99.93  E-value=1.1e-24  Score=185.55  Aligned_cols=157  Identities=25%  Similarity=0.458  Sum_probs=139.6

Q ss_pred             hHHHHhhcceeEEEeecc-CCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVG-STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      ++..++.+|..+.+.... .....+.+.+..+...+|...+.+++....                               
T Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~-------------------------------  249 (391)
T 1xti_A          201 VCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLE-------------------------------  249 (391)
T ss_dssp             HHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCGGGHHHHHHHHHHHSC-------------------------------
T ss_pred             HHHHHcCCCeEEEecCccccCcccceEEEEEcCchhHHHHHHHHHHhcC-------------------------------
Confidence            356777888777665443 455678888888888888888888776542                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++||||++.+.++.+++.|...++.+..+||++++.+|..+++.|++|..+
T Consensus       250 ---------------------------~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  302 (391)
T 1xti_A          250 ---------------------------FNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR  302 (391)
T ss_dssp             ---------------------------CSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCS
T ss_pred             ---------------------------CCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCc
Confidence                                       57999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      |||||+++++|+|+|++++||+++.|+++..|.||+||+||.|++|.+++|+.+.+
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            99999999999999999999999999999999999999999999999999998754

>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=99.92  E-value=9.3e-25  Score=186.83  Aligned_cols=158  Identities=30%  Similarity=0.475  Sum_probs=136.9

Q ss_pred             HHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCC
Q psy15610          3 AKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYP   82 (237)
Q Consensus         3 ~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~   82 (237)
                      ...++.+|..+.+. ......++.+++..++...|...+..++....                                 
T Consensus       212 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~---------------------------------  257 (400)
T 1s2m_A          212 MVKHLHKPYEINLM-EELTLKGITQYYAFVEERQKLHCLNTLFSKLQ---------------------------------  257 (400)
T ss_dssp             HHHHCSSCEEESCC-SSCBCTTEEEEEEECCGGGHHHHHHHHHHHSC---------------------------------
T ss_pred             HHHHcCCCeEEEec-cccccCCceeEEEEechhhHHHHHHHHHhhcC---------------------------------
Confidence            34556666666543 33455677777777777778877777776542                                 


Q ss_pred             ceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEE
Q psy15610         83 VTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPIL  162 (237)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vl  162 (237)
                                               ..++||||++.+.++.+++.|...++.+..+||++++.+|..+++.|++|..+||
T Consensus       258 -------------------------~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vL  312 (400)
T 1s2m_A          258 -------------------------INQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTL  312 (400)
T ss_dssp             -------------------------CSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEE
T ss_pred             -------------------------CCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEE
Confidence                                     5789999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCC
Q psy15610        163 VATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGS  219 (237)
Q Consensus       163 v~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~  219 (237)
                      |||+++++|+|+|++++||++++|+++..|.||+||+||.|++|.|++|+.+.+...
T Consensus       313 v~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~  369 (400)
T 1s2m_A          313 VCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFN  369 (400)
T ss_dssp             EESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHH
T ss_pred             EEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHHH
Confidence            999999999999999999999999999999999999999999999999999876543

>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=99.92  E-value=2.6e-25  Score=190.91  Aligned_cols=162  Identities=33%  Similarity=0.564  Sum_probs=130.3

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeechh-HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQD-KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      +++.++.+|..+.+.........+.+.+..++..+ |...+.+++....                               
T Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------------------------------  279 (414)
T 3eiq_A          231 VTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLT-------------------------------  279 (414)
T ss_dssp             HHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHHHHHSSC-------------------------------
T ss_pred             HHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHHHHHhCC-------------------------------
Confidence            35677888888877766777888888888877654 8888888887653                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|..+
T Consensus       280 ---------------------------~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  332 (414)
T 3eiq_A          280 ---------------------------ITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSR  332 (414)
T ss_dssp             ---------------------------CSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---
T ss_pred             ---------------------------CCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCc
Confidence                                       46899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYG  221 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  221 (237)
                      |||||+++++|+|+|++++||+++.|++...|.||+||+||.|++|.+++|+.+.+...+.
T Consensus       333 vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~  393 (414)
T 3eiq_A          333 VLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLR  393 (414)
T ss_dssp             CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHHHHHH
T ss_pred             EEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999987654433

>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=99.92  E-value=1.9e-24  Score=185.20  Aligned_cols=157  Identities=32%  Similarity=0.508  Sum_probs=140.1

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeec-hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDE-QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      +++.++.+|..+.+..+......+.+.+..+.. ..|...+.+++....                               
T Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------------------------------  265 (412)
T 3fht_A          217 FAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAIT-------------------------------  265 (412)
T ss_dssp             HHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHHHHHHHHHHHHHHS-------------------------------
T ss_pred             HHHHhcCCCeEEeeccccccccCceEEEEEcCChHHHHHHHHHHHhhcC-------------------------------
Confidence            466788888888877777778888888877765 457788887776542                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++||||+++..++.+++.|...++.+..+||+|++.+|..+++.|++|..+
T Consensus       266 ---------------------------~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~  318 (412)
T 3fht_A          266 ---------------------------IAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK  318 (412)
T ss_dssp             ---------------------------SSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             ---------------------------CCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCc
Confidence                                       57899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCC------CHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      |||||+++++|+|+|++++||+++.|+      +...|.||+||+||.|+.|.+++|+.+.+
T Consensus       319 vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  380 (412)
T 3fht_A          319 VLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  380 (412)
T ss_dssp             EEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             EEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChh
Confidence            999999999999999999999999994      67899999999999999999999998654

>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=99.92  E-value=3.8e-24  Score=182.15  Aligned_cols=157  Identities=34%  Similarity=0.527  Sum_probs=136.9

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeec-hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDE-QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      +++.++.++..+.+.........+.+.+..+.. ..|...+..++....                               
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------------------------------  242 (395)
T 3pey_A          194 YAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMT-------------------------------  242 (395)
T ss_dssp             HHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHHTTTT-------------------------------
T ss_pred             HHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHHHhcc-------------------------------
Confidence            345666777777766566667777777776654 457777777766542                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++||||+++..++.+++.|...++.+..+||++++.+|..+++.|++|..+
T Consensus       243 ---------------------------~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~  295 (395)
T 3pey_A          243 ---------------------------IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK  295 (395)
T ss_dssp             ---------------------------SSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCC
T ss_pred             ---------------------------CCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCC
Confidence                                       57899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCC------CHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      |||||+++++|+|+|++++||+++.|+      ++..|.||+||+||.|+.|.+++|+...+
T Consensus       296 vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  357 (395)
T 3pey_A          296 VLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN  357 (395)
T ss_dssp             EEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             EEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechH
Confidence            999999999999999999999999998      99999999999999999999999998644

>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=99.92  E-value=7.1e-24  Score=178.80  Aligned_cols=152  Identities=36%  Similarity=0.587  Sum_probs=132.4

Q ss_pred             HHHHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCC
Q psy15610          3 AKEFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYP   82 (237)
Q Consensus         3 ~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~   82 (237)
                      ++.++.++..+..    ....++.+.+..+...+|...+.+++...                                  
T Consensus       196 ~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~l~~~l~~~----------------------------------  237 (367)
T 1hv8_A          196 AKKYMGDYSFIKA----KINANIEQSYVEVNENERFEALCRLLKNK----------------------------------  237 (367)
T ss_dssp             HHHHCCSEEEEEC----CSSSSSEEEEEECCGGGHHHHHHHHHCST----------------------------------
T ss_pred             HHHHcCCCeEEEe----cCCCCceEEEEEeChHHHHHHHHHHHhcC----------------------------------
Confidence            3455555555532    22346777777777777888777777643                                  


Q ss_pred             ceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEE
Q psy15610         83 VTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPIL  162 (237)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vl  162 (237)
                                               +.++||||++.+.++.+++.|...+..+..+||+++..+|..+++.|++|..+||
T Consensus       238 -------------------------~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vl  292 (367)
T 1hv8_A          238 -------------------------EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRIL  292 (367)
T ss_dssp             -------------------------TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEE
T ss_pred             -------------------------CCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEE
Confidence                                     5789999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        163 VATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       163 v~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      |||+++++|+|+|++++||++++|+++..|.||+||+||.|++|.+++++.+.+.
T Consensus       293 v~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  347 (367)
T 1hv8_A          293 IATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREY  347 (367)
T ss_dssp             EECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSH
T ss_pred             EECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHH
Confidence            9999999999999999999999999999999999999999999999999987654

>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=99.90  E-value=1.5e-23  Score=187.74  Aligned_cols=163  Identities=17%  Similarity=0.227  Sum_probs=129.4

Q ss_pred             cccceeEEeecccc--hhhHHHHhhhcCCCce-----------ee-cCCcc-hhhHHHHhhhhhhccCCceEEEEeeccc
Q psy15610         55 DEALTLVFVETKKG--ADQLEDFLHHHGYPVT-----------SI-HGDRT-QKEREEAQQYTLISCDEALTLVFVETKK  119 (237)
Q Consensus        55 ~~~~~i~f~~t~~~--~~~~~~~l~~~~~~~~-----------~~-~~~~~-~~~~~~~~~~~~~~~~~~~~iIF~~t~~  119 (237)
                      ++.+++++++|...  .+++..++........           .+ ..... ......+........++.++||||+|++
T Consensus       199 ~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~~~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~  278 (591)
T 2v1x_A          199 PNASLIGLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQK  278 (591)
T ss_dssp             TTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEECCCCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHH
T ss_pred             CCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEecCCCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHH
Confidence            46789999999877  3566666644321110           00 01000 1111111112212235789999999999


Q ss_pred             chHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhccc
Q psy15610        120 GADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRT  199 (237)
Q Consensus       120 ~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~  199 (237)
                      .++.+++.|...++.+..+||+|++++|..+++.|++|..+|||||+++++|+|+|++++||++++|.|.+.|+|++||+
T Consensus       279 ~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRa  358 (591)
T 2v1x_A          279 DSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRA  358 (591)
T ss_dssp             HHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCceEEeecCCCC
Q psy15610        200 GRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       200 ~R~g~~~~~~~~~~~~~~  217 (237)
                      ||.|.+|.|++|+.+.+.
T Consensus       359 GR~G~~g~~i~l~~~~D~  376 (591)
T 2v1x_A          359 GRDDMKADCILYYGFGDI  376 (591)
T ss_dssp             CTTSSCEEEEEEECHHHH
T ss_pred             CcCCCCceEEEEEChHHH
Confidence            999999999999986654

>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=99.90  E-value=1.1e-23  Score=186.51  Aligned_cols=111  Identities=22%  Similarity=0.449  Sum_probs=106.5

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLP  186 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p  186 (237)
                      .+.++||||+|++.++.+++.|...++.+..+||+|++++|..+++.|++|+.+|||||+++++|+|+|++++||+++.|
T Consensus       235 ~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p  314 (523)
T 1oyw_A          235 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIP  314 (523)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECCC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        187 SDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       187 ~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +|.+.|+||+||+||.|.+|.+++|+.+.+.
T Consensus       315 ~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~  345 (523)
T 1oyw_A          315 RNIESYYQETGRAGRDGLPAEAMLFYDPADM  345 (523)
T ss_dssp             SSHHHHHHHHTTSCTTSSCEEEEEEECHHHH
T ss_pred             CCHHHHHHHhccccCCCCCceEEEEeCHHHH
Confidence            9999999999999999999999999976543

>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=99.90  E-value=2.6e-25  Score=194.90  Aligned_cols=157  Identities=32%  Similarity=0.508  Sum_probs=12.4

Q ss_pred             hHHHHhhcceeEEEeeccCCCCCceeEEEEeec-hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcC
Q psy15610          2 LAKEFLYRYIFLAIGRVGSTSENITQRIAWVDE-QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG   80 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~   80 (237)
                      +++.++.+|..+.+..+......+.+.++.+.. ..|...|..++....                               
T Consensus       284 ~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------------------------------  332 (479)
T 3fmp_B          284 FAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAIT-------------------------------  332 (479)
T ss_dssp             HHHHHSSSEEEEEEC-----------------------------------------------------------------
T ss_pred             HHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHHHHHhhcc-------------------------------
Confidence            567888899988887777777888888877765 457777777666542                               


Q ss_pred             CCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC
Q psy15610         81 YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP  160 (237)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~  160 (237)
                                                 ..++||||+++..++.++..|...++.+..+||++++.+|..+++.|++|..+
T Consensus       333 ---------------------------~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~  385 (479)
T 3fmp_B          333 ---------------------------IAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK  385 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ---------------------------CCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCc
Confidence                                       46899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCccccccCCCCCcEEEEecCCC------CHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        161 ILVATAVAARGLDIPHVKHVINFDLPS------DVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       161 vlv~T~~~~~Gvdl~~~~~Vi~~~~p~------s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      |||||+++++|+|+|++++||++++|.      +...|+||+||+||.|..|.+++|+.+.+
T Consensus       386 iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~  447 (479)
T 3fmp_B          386 VLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  447 (479)
T ss_dssp             --------------------------------------------------------------
T ss_pred             EEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcc
Confidence            999999999999999999999999995      56899999999999999999999998776

>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=99.90  E-value=4.6e-23  Score=184.02  Aligned_cols=116  Identities=32%  Similarity=0.505  Sum_probs=109.1

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhC---CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN  182 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~---~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~  182 (237)
                      ..+.++||||+|+..++.++..|...   ++.+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++++||+
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            56779999999999999999999876   899999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCCC
Q psy15610        183 FDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYG  221 (237)
Q Consensus       183 ~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~  221 (237)
                      +++|.++..|+||+||+||.|..|.+++|+.+.+...+.
T Consensus       417 ~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~  455 (563)
T 3i5x_A          417 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR  455 (563)
T ss_dssp             ESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHH
T ss_pred             ECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHH
Confidence            999999999999999999999999999999987654443

>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=99.90  E-value=4.2e-25  Score=188.30  Aligned_cols=118  Identities=33%  Similarity=0.623  Sum_probs=0.0

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS  187 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~  187 (237)
                      ..++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|..+|||||+++++|+|+|++++||++++|+
T Consensus       259 ~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~  338 (394)
T 1fuu_A          259 VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPA  338 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHhhcccccCCCCCceEEeecCCCCCCCCCCCC
Q psy15610        188 DVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS  225 (237)
Q Consensus       188 s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~~~  225 (237)
                      ++..|.||+||+||.|++|.+++|+.+.+...+.....
T Consensus       339 s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~  376 (394)
T 1fuu_A          339 NKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEK  376 (394)
T ss_dssp             --------------------------------------
T ss_pred             CHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHH
Confidence            99999999999999999999999999888766655444

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.89  E-value=1.3e-22  Score=181.73  Aligned_cols=111  Identities=33%  Similarity=0.551  Sum_probs=106.2

Q ss_pred             CceEEEEeecccchHHHHHHHhhC---CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~---~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      +.++||||+|+..++.+++.|...   ++.+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++++||+++
T Consensus       288 ~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~VI~~~  367 (579)
T 3sqw_A          288 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIG  367 (579)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEES
T ss_pred             CCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCCcccCCEEEEcC
Confidence            578999999999999999999876   89999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        185 LPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       185 ~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      +|.++..|+||+||+||.|+.|.+++|+.+.+..
T Consensus       368 ~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~  401 (579)
T 3sqw_A          368 VPSELANYIHRIGRTARSGKEGSSVLFICKDELP  401 (579)
T ss_dssp             CCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHH
T ss_pred             CCCCHHHhhhhccccccCCCCceEEEEEcccHHH
Confidence            9999999999999999999999999999987643

>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=99.86  E-value=1.6e-21  Score=162.61  Aligned_cols=104  Identities=40%  Similarity=0.691  Sum_probs=99.3

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      ..+.++||||++.+.++.+++.|.    .+..+||+++..+|..+++.|++|..+|||||+++++|+|+|++++||++++
T Consensus       218 ~~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~  293 (337)
T 2z0m_A          218 NKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDA  293 (337)
T ss_dssp             CCCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSC
T ss_pred             CCCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecC
Confidence            346789999999999999999886    6789999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHhhcccccCCCCCceEEeec
Q psy15610        186 PSDVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       186 p~s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      |+|+..|.||+||+||.|++|.+++|+.
T Consensus       294 ~~s~~~~~Q~~GR~gR~g~~g~~~~~~~  321 (337)
T 2z0m_A          294 PQDLRTYIHRIGRTGRMGRKGEAITFIL  321 (337)
T ss_dssp             CSSHHHHHHHHTTBCGGGCCEEEEEEES
T ss_pred             CCCHHHhhHhcCccccCCCCceEEEEEe
Confidence            9999999999999999999999999998

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.85  E-value=1.1e-21  Score=159.68  Aligned_cols=109  Identities=16%  Similarity=0.275  Sum_probs=85.7

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC-CCceEEEeCCCCHHHHHHHHHHhhcC-CCC-EEEEcCccccccCCCCCcEEEEe
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH-GYPVTSIHGDRTQKEREEALRRFRSG-ETP-ILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~r~~~~~~f~~g-~~~-vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      .+.++||||++...++.++..|... |+.+..+||+++..+|..+++.|+++ ... +|++|+++++|+|++.+++||+|
T Consensus       111 ~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~~g~Glnl~~a~~VI~~  190 (271)
T 1z5z_A          111 EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHF  190 (271)
T ss_dssp             TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEEC
T ss_pred             CCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhhhcCCcCcccCCEEEEE
Confidence            4689999999999999999999885 99999999999999999999999998 666 78899999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceE--EeecCC
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPF--SYNQPG  215 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~--~~~~~~  215 (237)
                      |+||++..|.|++||++|.|+.+.+.  .|+..+
T Consensus       191 d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~  224 (271)
T 1z5z_A          191 DRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  224 (271)
T ss_dssp             SCCSCTTTC--------------CCEEEEEEETT
T ss_pred             CCCCChhHHHHHHHhccccCCCCceEEEEEeeCC
Confidence            99999999999999999999887764  444443

>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=99.85  E-value=1.8e-21  Score=169.25  Aligned_cols=109  Identities=28%  Similarity=0.401  Sum_probs=102.0

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeC--------CCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHG--------DRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKH  179 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~--------~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~  179 (237)
                      +.++||||+++..++.+++.|...++.+..+||        +|+..+|..+++.|++|..+|||||+++++|+|+|.+++
T Consensus       361 ~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~  440 (494)
T 1wp9_A          361 NSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDL  440 (494)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCE
T ss_pred             CCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCE
Confidence            689999999999999999999999999999999        999999999999999999999999999999999999999


Q ss_pred             EEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        180 VINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       180 Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||++++|+++..|.||+||+||.|+ |.++.|+.++..
T Consensus       441 Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~  477 (494)
T 1wp9_A          441 VVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTR  477 (494)
T ss_dssp             EEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSH
T ss_pred             EEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCH
Confidence            9999999999999999999999998 999999987653

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.84  E-value=2.9e-21  Score=166.17  Aligned_cols=99  Identities=25%  Similarity=0.482  Sum_probs=92.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceE-EEeCCCCHHHHHHHHHHhhcCCCCEEEE----cCccccccCCCC-CcEEE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVT-SIHGDRTQKEREEALRRFRSGETPILVA----TAVAARGLDIPH-VKHVI  181 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~-~~h~~~~~~~r~~~~~~f~~g~~~vlv~----T~~~~~Gvdl~~-~~~Vi  181 (237)
                      +.++||||+++..++.++..|...++.+. .+||.    +|.  ++.|++|..+||||    |+++++|+|+|+ +++||
T Consensus       252 ~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI  325 (414)
T 3oiy_A          252 RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVI  325 (414)
T ss_dssp             CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECCTTCCCCCCCCCTTTCCEEE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecCcCchhhccCccccccCEEE
Confidence            47899999999999999999999999998 89984    444  99999999999999    999999999999 99999


Q ss_pred             EecCC--CCHHHHHHhhcccccCC----CCCceEEee
Q psy15610        182 NFDLP--SDVEEYVHRIGRTGRMG----NLDFPFSYN  212 (237)
Q Consensus       182 ~~~~p--~s~~~~~Q~~GR~~R~g----~~~~~~~~~  212 (237)
                      +++.|  .++..|+||+||+||.|    ..|.+++|+
T Consensus       326 ~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~  362 (414)
T 3oiy_A          326 FWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE  362 (414)
T ss_dssp             EESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC
T ss_pred             EECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE
Confidence            99999  99999999999999988    478899888

>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=99.84  E-value=3.1e-21  Score=171.38  Aligned_cols=108  Identities=21%  Similarity=0.320  Sum_probs=57.3

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC------------CCceEEEeCCCCHHHHHHHHHHhhc-CCCCEEEEcCccccccC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH------------GYPVTSIHGDRTQKEREEALRRFRS-GETPILVATAVAARGLD  173 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~------------~~~~~~~h~~~~~~~r~~~~~~f~~-g~~~vlv~T~~~~~Gvd  173 (237)
                      ++.++||||+++..++.+++.|...            |.....+||+|++.+|..+++.|++ |.++|||||+++++|+|
T Consensus       389 ~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiD  468 (556)
T 4a2p_A          389 PQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGID  468 (556)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC-------
T ss_pred             CCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCC
Confidence            3689999999999999999999775            5566677889999999999999999 99999999999999999


Q ss_pred             CCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        174 IPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       174 l~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      +|++++||+||+|+|+..|+||+|| ||. .+|.+++|+..++
T Consensus       469 ip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~  509 (556)
T 4a2p_A          469 IVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTE  509 (556)
T ss_dssp             ----CEEEEETCCSCHHHHHHC----------CCEEEEESCHH
T ss_pred             chhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcc
Confidence            9999999999999999999999999 999 7899999987654

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.84  E-value=3.3e-20  Score=174.64  Aligned_cols=109  Identities=21%  Similarity=0.233  Sum_probs=99.9

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCC---------------------------------------ceEEEeCCCCHHHH
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGY---------------------------------------PVTSIHGDRTQKER  147 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~---------------------------------------~~~~~h~~~~~~~r  147 (237)
                      +..++||||+++..|+.++..|...++                                       .+..+||+|++.+|
T Consensus       342 ~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR  421 (1010)
T 2xgj_A          342 KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILK  421 (1010)
T ss_dssp             TCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHH
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHH
Confidence            456899999999999999999876433                                       27899999999999


Q ss_pred             HHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE----ecC----CCCHHHHHHhhcccccCCC--CCceEEeecCC
Q psy15610        148 EEALRRFRSGETPILVATAVAARGLDIPHVKHVIN----FDL----PSDVEEYVHRIGRTGRMGN--LDFPFSYNQPG  215 (237)
Q Consensus       148 ~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~----~~~----p~s~~~~~Q~~GR~~R~g~--~~~~~~~~~~~  215 (237)
                      +.+++.|++|.++|||||+++++|+|+|.+++||+    ||.    |.++..|.||+||+||.|.  .|.|++++.+.
T Consensus       422 ~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~  499 (1010)
T 2xgj_A          422 EVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEK  499 (1010)
T ss_dssp             HHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSC
T ss_pred             HHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCC
Confidence            99999999999999999999999999999999999    998    8899999999999999996  59999999865

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.83  E-value=1.3e-20  Score=172.57  Aligned_cols=161  Identities=20%  Similarity=0.214  Sum_probs=120.7

Q ss_pred             ccceeEEeecccchhhHHHHhhhc-------CCCce--eecCC-------c--c----hh---hHHHHhhhhhhccCCce
Q psy15610         56 EALTLVFVETKKGADQLEDFLHHH-------GYPVT--SIHGD-------R--T----QK---EREEAQQYTLISCDEAL  110 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~~~~~~l~~~-------~~~~~--~~~~~-------~--~----~~---~~~~~~~~~~~~~~~~~  110 (237)
                      +.++|++|+|..+.+++++|+...       .++..  .....       .  .    ..   .........-...++.+
T Consensus       175 ~~~ii~lSATl~n~~~~~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  254 (715)
T 2va8_A          175 RRNLLALSATISNYKQIAKWLGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNGQ  254 (715)
T ss_dssp             TSEEEEEESCCTTHHHHHHHHTCEEEECCCCSSCEEEEEEEECSSTTEEEEEETTSCEEEEESSSHHHHHHHHHHTTTCC
T ss_pred             cCcEEEEcCCCCCHHHHHHHhCCCccCCCCCCCCceEEEEecCCcccceeeecCcchhhhcccchHHHHHHHHHHhcCCC
Confidence            578999999999999999999743       12211  00000       0  0    00   00001111111235789


Q ss_pred             EEEEeecccchHHHHHHHhhCC------------------------------------CceEEEeCCCCHHHHHHHHHHh
Q psy15610        111 TLVFVETKKGADQLEDFLHHHG------------------------------------YPVTSIHGDRTQKEREEALRRF  154 (237)
Q Consensus       111 ~iIF~~t~~~~~~l~~~L~~~~------------------------------------~~~~~~h~~~~~~~r~~~~~~f  154 (237)
                      +||||++++.++.++..|....                                    ..+..+||++++++|..+++.|
T Consensus       255 ~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~~v~~~f  334 (715)
T 2va8_A          255 VLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGF  334 (715)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHH
T ss_pred             EEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHHHHHHHH
Confidence            9999999999999999987531                                    2489999999999999999999


Q ss_pred             hcCCCCEEEEcCccccccCCCCCcEEEE----ec-------CCCCHHHHHHhhcccccCC--CCCceEEeecCCC
Q psy15610        155 RSGETPILVATAVAARGLDIPHVKHVIN----FD-------LPSDVEEYVHRIGRTGRMG--NLDFPFSYNQPGY  216 (237)
Q Consensus       155 ~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~----~~-------~p~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~  216 (237)
                      ++|..+|||||+++++|+|+|++++||+    |+       .|.|...|.||+|||||.|  ..|.|+.++...+
T Consensus       335 ~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  409 (715)
T 2va8_A          335 RQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKE  409 (715)
T ss_dssp             HTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEECSCGG
T ss_pred             HcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCCch
Confidence            9999999999999999999999999998    88       7899999999999999988  4788999987665

>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=99.83  E-value=7e-21  Score=172.87  Aligned_cols=108  Identities=19%  Similarity=0.223  Sum_probs=99.5

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCC--------CCcE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP--------HVKH  179 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~--------~~~~  179 (237)
                      +.++||||+|.+.++.++..|...|+++.++||++.+.+|..+..+++.|  .|+|||+++++|+|++        +..+
T Consensus       432 ~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~  509 (844)
T 1tf5_A          432 GQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLA  509 (844)
T ss_dssp             TCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEE
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcE
Confidence            57899999999999999999999999999999999888887666666654  6999999999999999        7889


Q ss_pred             EEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        180 VINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       180 Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||+++.|.|...|.||+||+||.|.+|.+++|++..+.
T Consensus       510 VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          510 VVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             EEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             EEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            99999999999999999999999999999999998774

>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=99.83  E-value=4.1e-20  Score=175.37  Aligned_cols=111  Identities=20%  Similarity=0.202  Sum_probs=95.3

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCc---------------------------------------eEEEeCCCCHHH
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYP---------------------------------------VTSIHGDRTQKE  146 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~---------------------------------------~~~~h~~~~~~~  146 (237)
                      .+..++||||+++..|+.++..|...++.                                       +..+||+|++.+
T Consensus       439 ~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~  518 (1108)
T 3l9o_A          439 KKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPIL  518 (1108)
T ss_dssp             TTCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHH
T ss_pred             cCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHH
Confidence            45679999999999999999988653222                                       799999999999


Q ss_pred             HHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC--------CCCHHHHHHhhcccccCC--CCCceEEeecCCC
Q psy15610        147 REEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL--------PSDVEEYVHRIGRTGRMG--NLDFPFSYNQPGY  216 (237)
Q Consensus       147 r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~--------p~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~  216 (237)
                      |+.+++.|++|.++|||||+++++|+|+|++++||+++.        |.|+..|+||+||+||.|  ..|.|++++.+..
T Consensus       519 R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~~  598 (1108)
T 3l9o_A          519 KEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKM  598 (1108)
T ss_dssp             HHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCCC
T ss_pred             HHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCCc
Confidence            999999999999999999999999999999999997654        347888999999999999  6788888887663

>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=99.83  E-value=2.6e-20  Score=170.74  Aligned_cols=158  Identities=19%  Similarity=0.221  Sum_probs=123.1

Q ss_pred             ccceeEEeecccchhhHHHHhhhcC-------CCcee--e-cC-----Cc----chhhHHHHhhhhhhccCCceEEEEee
Q psy15610         56 EALTLVFVETKKGADQLEDFLHHHG-------YPVTS--I-HG-----DR----TQKEREEAQQYTLISCDEALTLVFVE  116 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~~~~~~l~~~~-------~~~~~--~-~~-----~~----~~~~~~~~~~~~~~~~~~~~~iIF~~  116 (237)
                      +.++|++|+|..+.+++++|+...-       .+...  . ..     ..    .......+   .-...++.++||||+
T Consensus       169 ~~~ii~lSATl~n~~~~~~~l~~~~~~~~~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~LVF~~  245 (720)
T 2zj8_A          169 KAQIIGLSATIGNPEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELV---YDAIRKKKGALIFVN  245 (720)
T ss_dssp             TBEEEEEECCCSCHHHHHHHTTEEEEECCCCSSEEEEEEEETTEEEETTSCEEECSSTTHHH---HHHHHTTCCEEEECS
T ss_pred             CCeEEEEcCCcCCHHHHHHHhCCcccCCCCCCCcceEEEEeCCeeeccccchhhhhHHHHHH---HHHHhCCCCEEEEec
Confidence            6789999999999999999996421       11110  0 00     00    00000000   111235689999999


Q ss_pred             cccchHHHHHHHhhC---------------------------------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEE
Q psy15610        117 TKKGADQLEDFLHHH---------------------------------GYPVTSIHGDRTQKEREEALRRFRSGETPILV  163 (237)
Q Consensus       117 t~~~~~~l~~~L~~~---------------------------------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv  163 (237)
                      +++.++.++..|...                                 ...+..+||++++++|..+++.|++|.++|||
T Consensus       246 sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlv  325 (720)
T 2zj8_A          246 MRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVV  325 (720)
T ss_dssp             CHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTSSCEEE
T ss_pred             CHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHHHHHHCCCCeEEE
Confidence            999999998888642                                 12489999999999999999999999999999


Q ss_pred             EcCccccccCCCCCcEEEE----ec----CCCCHHHHHHhhcccccCC--CCCceEEeecCCC
Q psy15610        164 ATAVAARGLDIPHVKHVIN----FD----LPSDVEEYVHRIGRTGRMG--NLDFPFSYNQPGY  216 (237)
Q Consensus       164 ~T~~~~~Gvdl~~~~~Vi~----~~----~p~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~  216 (237)
                      ||+++++|+|+|.+++||+    |+    .|.+...|.||+|||||.|  ..|.|++++...+
T Consensus       326 aT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  388 (720)
T 2zj8_A          326 ATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDD  388 (720)
T ss_dssp             ECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSC
T ss_pred             ECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCcc
Confidence            9999999999999999998    66    5889999999999999988  4688999988766

>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=99.83  E-value=9e-21  Score=164.49  Aligned_cols=167  Identities=19%  Similarity=0.258  Sum_probs=114.5

Q ss_pred             EEEeechhHH--------HHHHHhhcCchhhhcccccceeEEeecccc-hhhHHHHhhhcCCCceeecCCcchhhHHHHh
Q psy15610         29 IAWVDEQDKR--------SCLLDLLSSPSQEELGDEALTLVFVETKKG-ADQLEDFLHHHGYPVTSIHGDRTQKEREEAQ   99 (237)
Q Consensus        29 ~~~~~~~~k~--------~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   99 (237)
                      +++++|.+++        ..+..++.       ..+.++++||+|... ...+...    ..+...+............ 
T Consensus       102 ~vViDEah~~~~~~~~~~~~~~~~~~-------~~~~~~l~~SAT~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~-  169 (440)
T 1yks_A          102 VIIMDEAHFLDPASIAARGWAAHRAR-------ANESATILMTATPPGTSDEFPHS----NGEIEDVQTDIPSEPWNTG-  169 (440)
T ss_dssp             EEEETTTTCCSHHHHHHHHHHHHHHH-------TTSCEEEEECSSCTTCCCSSCCC----SSCEEEEECCCCSSCCSSS-
T ss_pred             EEEEECccccCcchHHHHHHHHHHhc-------cCCceEEEEeCCCCchhhhhhhc----CCCeeEeeeccChHHHHHH-
Confidence            5677887775        22222221       246789999999854 3322221    1122121111111100000 


Q ss_pred             hhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcE
Q psy15610        100 QYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKH  179 (237)
Q Consensus       100 ~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~  179 (237)
                       .......+.+++|||++++.++.+++.|...++++..+||    ++|..+++.|++|..+|||||+++++|+|+| +++
T Consensus       170 -~~~l~~~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~  243 (440)
T 1yks_A          170 -HDWILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VER  243 (440)
T ss_dssp             -CHHHHHCCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSE
T ss_pred             -HHHHHhcCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceE
Confidence             1112223679999999999999999999999999999999    4688999999999999999999999999999 999


Q ss_pred             EEE-------------------ecCCCCHHHHHHhhcccccC-CCCCceEEeec
Q psy15610        180 VIN-------------------FDLPSDVEEYVHRIGRTGRM-GNLDFPFSYNQ  213 (237)
Q Consensus       180 Vi~-------------------~~~p~s~~~~~Q~~GR~~R~-g~~~~~~~~~~  213 (237)
                      ||+                   ++.|.+..+|+||+||+||. |..|.|++|+.
T Consensus       244 VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~  297 (440)
T 1yks_A          244 VLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSE  297 (440)
T ss_dssp             EEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             EEeCCccceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEec
Confidence            886                   88899999999999999997 68999999974

>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=99.82  E-value=1.8e-20  Score=163.10  Aligned_cols=173  Identities=17%  Similarity=0.263  Sum_probs=122.1

Q ss_pred             EEEeechhHHH----HHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhh
Q psy15610         29 IAWVDEQDKRS----CLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLI  104 (237)
Q Consensus        29 ~~~~~~~~k~~----~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (237)
                      +++++|.+.+.    .+..++..   ....++.++++||+|...-.  ...+. .+..............  ........
T Consensus       113 ~iViDEah~~~~~~~~~~~~~~~---~~~~~~~~~i~~SAT~~~~~--~~~~~-~~~~~~~~~~~~p~~~--~~~~~~~l  184 (451)
T 2jlq_A          113 LIVMDEAHFTDPCSVAARGYIST---RVEMGEAAAIFMTATPPGST--DPFPQ-SNSPIEDIEREIPERS--WNTGFDWI  184 (451)
T ss_dssp             EEEEETTTCCSHHHHHHHHHHHH---HHHTTSCEEEEECSSCTTCC--CSSCC-CSSCEEEEECCCCSSC--CSSSCHHH
T ss_pred             EEEEeCCccCCcchHHHHHHHHH---hhcCCCceEEEEccCCCccc--hhhhc-CCCceEecCccCCchh--hHHHHHHH
Confidence            66778877642    22222211   11245688999999986511  11111 1111111111111000  00001122


Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      .....++||||++++.++.+++.|...++.+..+|+++.    .++++.|++|..+|||||+++++|+|+|+ ++||+++
T Consensus       185 ~~~~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~  259 (451)
T 2jlq_A          185 TDYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPR  259 (451)
T ss_dssp             HHCCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECC
T ss_pred             HhCCCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECC
Confidence            233668999999999999999999999999999999764    57889999999999999999999999999 9999988


Q ss_pred             --------------------CCCCHHHHHHhhcccccCCC-CCceEEeecC
Q psy15610        185 --------------------LPSDVEEYVHRIGRTGRMGN-LDFPFSYNQP  214 (237)
Q Consensus       185 --------------------~p~s~~~~~Q~~GR~~R~g~-~~~~~~~~~~  214 (237)
                                          .|.+...|+||+||+||.|. .|.+++|...
T Consensus       260 ~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          260 RCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             EEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             CcccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence                                89999999999999999998 7888888643

>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=99.82  E-value=1.2e-20  Score=172.33  Aligned_cols=106  Identities=28%  Similarity=0.456  Sum_probs=90.6

Q ss_pred             CceEEEEeecccchHHHHHHHhhC------CCceEEEeCC--------CCHHHHHHHHHHhhcCCCCEEEEcCccccccC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH------GYPVTSIHGD--------RTQKEREEALRRFRSGETPILVATAVAARGLD  173 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~------~~~~~~~h~~--------~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvd  173 (237)
                      +.++||||+++..++.++++|...      |+.+..+||+        |++.+|..+++.|++|.++|||||+++++|+|
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GID  479 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLD  479 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSC
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCc
Confidence            589999999999999999999987      8999999999        99999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        174 IPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       174 l~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      +|++++||+||+|+|+..|+||+|||||.|  +.++++....
T Consensus       480 ip~v~~VI~~d~p~s~~~~~Qr~GRArr~g--~~~~l~~~~~  519 (699)
T 4gl2_A          480 IKECNIVIRYGLVTNEIAMVQARGRARADE--STYVLVAHSG  519 (699)
T ss_dssp             CCSCCCCEEESCCCCHHHHHHHHTTSCSSS--CEEEEEEESS
T ss_pred             cccCCEEEEeCCCCCHHHHHHHcCCCCCCC--ceEEEEEeCC
Confidence            999999999999999999999999987665  3344443433

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.82  E-value=6.7e-21  Score=169.00  Aligned_cols=108  Identities=29%  Similarity=0.423  Sum_probs=77.0

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC------------CCceEEEeCCCCHHHHHHHHHHhhc-CCCCEEEEcCccccccC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH------------GYPVTSIHGDRTQKEREEALRRFRS-GETPILVATAVAARGLD  173 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~------------~~~~~~~h~~~~~~~r~~~~~~f~~-g~~~vlv~T~~~~~Gvd  173 (237)
                      +..++||||+++..++.++..|...            |.....+||+|++.+|..+++.|++ |.++|||||+++++|+|
T Consensus       388 ~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlD  467 (555)
T 3tbk_A          388 PETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGID  467 (555)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCEE
T ss_pred             CCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCc
Confidence            3589999999999999999999875            3355666779999999999999999 99999999999999999


Q ss_pred             CCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        174 IPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       174 l~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      +|++++||+||+|+|+..|+||+|| ||. ..|.++.|+.+++
T Consensus       468 lp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~  508 (555)
T 3tbk_A          468 IAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSAD  508 (555)
T ss_dssp             TTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHH
T ss_pred             cccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCC
Confidence            9999999999999999999999999 888 7899999987654

>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=99.82  E-value=3.1e-20  Score=169.86  Aligned_cols=160  Identities=20%  Similarity=0.260  Sum_probs=124.6

Q ss_pred             ccccceeEEeecccchhhHHHHhhhcC-------CCcee--ecCCc---chh---------hHHHHhhhhhhccCCceEE
Q psy15610         54 GDEALTLVFVETKKGADQLEDFLHHHG-------YPVTS--IHGDR---TQK---------EREEAQQYTLISCDEALTL  112 (237)
Q Consensus        54 ~~~~~~i~f~~t~~~~~~~~~~l~~~~-------~~~~~--~~~~~---~~~---------~~~~~~~~~~~~~~~~~~i  112 (237)
                      .++.++|++|+|..+.+++++|+...-       ++...  .....   ...         ....+.   -...++.++|
T Consensus       170 ~~~~~ii~lSATl~n~~~~~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~L  246 (702)
T 2p6r_A          170 NKALRVIGLSATAPNVTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVE---ECVAENGGVL  246 (702)
T ss_dssp             CTTCEEEEEECCCTTHHHHHHHTTCEEEECCCCSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHH---HHHHTTCCEE
T ss_pred             CcCceEEEECCCcCCHHHHHHHhCCCcccCCCCCccceEEEeeCCeeeccCcchhhhhhhhHHHHHH---HHHhcCCCEE
Confidence            456889999999999999999996431       11111  00000   000         111111   1123578999


Q ss_pred             EEeecccchHHHHHHHhhC------------------------------CCceEEEeCCCCHHHHHHHHHHhhcCCCCEE
Q psy15610        113 VFVETKKGADQLEDFLHHH------------------------------GYPVTSIHGDRTQKEREEALRRFRSGETPIL  162 (237)
Q Consensus       113 IF~~t~~~~~~l~~~L~~~------------------------------~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vl  162 (237)
                      |||++++.++.++..|...                              +..+..+||++++++|..+++.|++|.++||
T Consensus       247 VF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vl  326 (702)
T 2p6r_A          247 VFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVV  326 (702)
T ss_dssp             EECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTSCCEE
T ss_pred             EEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHHHCCCCeEE
Confidence            9999999999998888642                              1358899999999999999999999999999


Q ss_pred             EEcCccccccCCCCCcEEEE----ec---CCCCHHHHHHhhcccccCC--CCCceEEeecCCC
Q psy15610        163 VATAVAARGLDIPHVKHVIN----FD---LPSDVEEYVHRIGRTGRMG--NLDFPFSYNQPGY  216 (237)
Q Consensus       163 v~T~~~~~Gvdl~~~~~Vi~----~~---~p~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~  216 (237)
                      |||+++++|+|+|++++||+    ||   .|.+...|.||+|||||.|  ..|.|+.++...+
T Consensus       327 vaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  389 (702)
T 2p6r_A          327 VATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  389 (702)
T ss_dssp             EECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             EECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCcc
Confidence            99999999999999999998    66   6889999999999999988  5788999988765

>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=99.81  E-value=1e-20  Score=165.00  Aligned_cols=173  Identities=17%  Similarity=0.272  Sum_probs=122.0

Q ss_pred             EEEeechhHH----HHHHHhhcCchhhhcccccceeEEeecccch-hhHHHHhhhcCCCceeecCCcchhhHHHHhhhhh
Q psy15610         29 IAWVDEQDKR----SCLLDLLSSPSQEELGDEALTLVFVETKKGA-DQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTL  103 (237)
Q Consensus        29 ~~~~~~~~k~----~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (237)
                      +++++|.+.+    ......+...   ...++.++++||+|.... ..+.    ....+...+..........  ....+
T Consensus       115 ~iViDEaH~~~~~~~~~~~~~~~~---~~~~~~~~il~SAT~~~~~~~~~----~~~~pi~~~~~~~~~~~~~--~~~~~  185 (459)
T 2z83_A          115 LFVMDEAHFTDPASIAARGYIATK---VELGEAAAIFMTATPPGTTDPFP----DSNAPIHDLQDEIPDRAWS--SGYEW  185 (459)
T ss_dssp             EEEESSTTCCSHHHHHHHHHHHHH---HHTTSCEEEEECSSCTTCCCSSC----CCSSCEEEEECCCCSSCCS--SCCHH
T ss_pred             EEEEECCccCCchhhHHHHHHHHH---hccCCccEEEEEcCCCcchhhhc----cCCCCeEEecccCCcchhH--HHHHH
Confidence            6678887763    1122222211   113567899999998752 1111    1122222221111110000  00112


Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE-
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN-  182 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~-  182 (237)
                      ......++||||+++..++.+++.|...++.+..+||+    +|..+++.|++|..+|||||+++++|+|+|+ ++||+ 
T Consensus       186 l~~~~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~  260 (459)
T 2z83_A          186 ITEYAGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDC  260 (459)
T ss_dssp             HHHCCSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEEC
T ss_pred             HHhcCCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEEC
Confidence            22236799999999999999999999999999999995    6888899999999999999999999999999 99998 


Q ss_pred             -------------------ecCCCCHHHHHHhhcccccCCC-CCceEEeecCC
Q psy15610        183 -------------------FDLPSDVEEYVHRIGRTGRMGN-LDFPFSYNQPG  215 (237)
Q Consensus       183 -------------------~~~p~s~~~~~Q~~GR~~R~g~-~~~~~~~~~~~  215 (237)
                                         |+.|.|...|+||+||+||.|. +|.+++|+.+.
T Consensus       261 G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          261 RKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             CEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             CcccccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence                               6799999999999999999997 89999999876

>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=99.81  E-value=6.2e-20  Score=168.78  Aligned_cols=160  Identities=14%  Similarity=0.200  Sum_probs=125.1

Q ss_pred             cccceeEEeecccchhhHHHHhhhcC--------CCceeecCCc-chhhHHHHhh---hhhhccCCceEEEEeecccchH
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHG--------YPVTSIHGDR-TQKEREEAQQ---YTLISCDEALTLVFVETKKGAD  122 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~--------~~~~~~~~~~-~~~~~~~~~~---~~~~~~~~~~~iIF~~t~~~~~  122 (237)
                      ++.+++++|+|. +.+.+++++....        +++....... ..........   ........+++||||+++..++
T Consensus       239 ~~~~iIl~SAT~-~~~~l~~~~~~~~vi~v~gr~~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~  317 (773)
T 2xau_A          239 PDLKIIIMSATL-DAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIE  317 (773)
T ss_dssp             TTCEEEEEESCS-CCHHHHHHTTSCCEEECCCCCCCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHH
T ss_pred             CCceEEEEeccc-cHHHHHHHhcCCCcccccCcccceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHH
Confidence            467899999999 5678888885321        2222211111 1111111111   1112335789999999999999


Q ss_pred             HHHHHHhh-----------CCCceEEEeCCCCHHHHHHHHHHhh-----cCCCCEEEEcCccccccCCCCCcEEEEecC-
Q psy15610        123 QLEDFLHH-----------HGYPVTSIHGDRTQKEREEALRRFR-----SGETPILVATAVAARGLDIPHVKHVINFDL-  185 (237)
Q Consensus       123 ~l~~~L~~-----------~~~~~~~~h~~~~~~~r~~~~~~f~-----~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~-  185 (237)
                      .+++.|..           .++.+..+||++++++|.++++.|.     +|..+|||||+++++|+|+|++++||+++. 
T Consensus       318 ~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~  397 (773)
T 2xau_A          318 DAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFS  397 (773)
T ss_dssp             HHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEE
T ss_pred             HHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCc
Confidence            99999874           5778999999999999999999999     999999999999999999999999999776 


Q ss_pred             -----------------CCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        186 -----------------PSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       186 -----------------p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                                       |.|...|.||+||+||. .+|.|+.|++..+
T Consensus       398 k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~  444 (773)
T 2xau_A          398 KQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEA  444 (773)
T ss_dssp             EEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHH
T ss_pred             cceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHH
Confidence                             88999999999999999 7999999997554

>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=99.81  E-value=2.9e-20  Score=172.24  Aligned_cols=108  Identities=21%  Similarity=0.320  Sum_probs=62.8

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC------------CCceEEEeCCCCHHHHHHHHHHhhc-CCCCEEEEcCccccccC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH------------GYPVTSIHGDRTQKEREEALRRFRS-GETPILVATAVAARGLD  173 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~------------~~~~~~~h~~~~~~~r~~~~~~f~~-g~~~vlv~T~~~~~Gvd  173 (237)
                      ++.++||||+++..++.++++|...            |.....+||+|++.+|..+++.|++ |.++|||||+++++|+|
T Consensus       630 ~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GID  709 (797)
T 4a2q_A          630 PQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGID  709 (797)
T ss_dssp             SSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC------
T ss_pred             CCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCC
Confidence            3689999999999999999999763            5567778999999999999999999 99999999999999999


Q ss_pred             CCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        174 IPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       174 l~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      +|++++||+||+|+|+..|+||+|| ||. .+|.++.|+..++
T Consensus       710 lp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~  750 (797)
T 4a2q_A          710 IVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTE  750 (797)
T ss_dssp             -CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHH
T ss_pred             chhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCc
Confidence            9999999999999999999999999 999 7899999987653

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.81  E-value=3.1e-20  Score=168.10  Aligned_cols=171  Identities=17%  Similarity=0.293  Sum_probs=123.2

Q ss_pred             EEEeechhHHHH----HHHhhcCchhhhcccccceeEEeecccc-hhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhh
Q psy15610         29 IAWVDEQDKRSC----LLDLLSSPSQEELGDEALTLVFVETKKG-ADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTL  103 (237)
Q Consensus        29 ~~~~~~~~k~~~----l~~ll~~~~~~~~~~~~~~i~f~~t~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (237)
                      +++++|.+++..    ....+....   .....++++||+|... +.++..    ...+...+............  ...
T Consensus       335 lvViDEaH~~~~~~~~~~~~l~~~~---~~~~~~vl~~SAT~~~~i~~~~~----~~~~i~~v~~~~~~~~~~~~--l~~  405 (673)
T 2wv9_A          335 LFVMDEAHFTDPASIAARGYIATRV---EAGEAAAIFMTATPPGTSDPFPD----TNSPVHDVSSEIPDRAWSSG--FEW  405 (673)
T ss_dssp             EEEEESTTCCCHHHHHHHHHHHHHH---HTTSCEEEEECSSCTTCCCSSCC----CSSCEEEEECCCCSSCCSSC--CHH
T ss_pred             EEEEeCCcccCccHHHHHHHHHHhc---cccCCcEEEEcCCCChhhhhhcc----cCCceEEEeeecCHHHHHHH--HHH
Confidence            667888776511    112221111   1246789999999864 222111    12222222211111100001  112


Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE-
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN-  182 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~-  182 (237)
                      ....+.++||||++++.++.+++.|...++.+..+||+    +|.++++.|++|..+|||||+++++|+|+| +++||+ 
T Consensus       406 l~~~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~  480 (673)
T 2wv9_A          406 ITDYAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDC  480 (673)
T ss_dssp             HHSCCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEEC
T ss_pred             HHhCCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEEC
Confidence            22357899999999999999999999999999999994    799999999999999999999999999999 999997 


Q ss_pred             -------------------ecCCCCHHHHHHhhcccccC-CCCCceEEeec
Q psy15610        183 -------------------FDLPSDVEEYVHRIGRTGRM-GNLDFPFSYNQ  213 (237)
Q Consensus       183 -------------------~~~p~s~~~~~Q~~GR~~R~-g~~~~~~~~~~  213 (237)
                                         ++.|.+..+|+||+||+||. |+.|.|++|+.
T Consensus       481 g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~  531 (673)
T 2wv9_A          481 RKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGG  531 (673)
T ss_dssp             CEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECS
T ss_pred             CCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEe
Confidence                               56899999999999999998 78999999974

>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=99.81  E-value=4.3e-20  Score=181.00  Aligned_cols=174  Identities=13%  Similarity=0.105  Sum_probs=135.3

Q ss_pred             cccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhh---------------HH-----HHhhhhhhccCCceEE
Q psy15610         53 LGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKE---------------RE-----EAQQYTLISCDEALTL  112 (237)
Q Consensus        53 ~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~---------------~~-----~~~~~~~~~~~~~~~i  112 (237)
                      .+.+.++|.+|+|..+++++++||.........+....+..+               +.     ..........+..++|
T Consensus      1080 ~~~~~riI~lSATl~N~~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~l 1159 (1724)
T 4f92_B         1080 IERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVI 1159 (1724)
T ss_dssp             TSSCCEEEEEESCBTTHHHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHHTTHHHHHHHHHHHCSSSCEE
T ss_pred             cCCCceEEEEeCCCCCHHHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhhhhcchHHHHHHHhcCCCCee
Confidence            456789999999999999999999877655544443332211               10     1111222345678999


Q ss_pred             EEeecccchHHHHHHHhhC----------------------------------CCceEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610        113 VFVETKKGADQLEDFLHHH----------------------------------GYPVTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus       113 IF~~t~~~~~~l~~~L~~~----------------------------------~~~~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                      |||+|+..|+.++..|...                                  ...++++||+|++.+|..+++.|++|.
T Consensus      1160 VF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE~lF~~G~ 1239 (1724)
T 4f92_B         1160 VFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGA 1239 (1724)
T ss_dssp             EEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHHHHHHHTS
T ss_pred             eeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHHHHHHCCC
Confidence            9999999998887655311                                  235899999999999999999999999


Q ss_pred             CCEEEEcCccccccCCCCCcEEEE----ec------CCCCHHHHHHhhcccccCCC--CCceEEeecCCCCCCCCCCCCC
Q psy15610        159 TPILVATAVAARGLDIPHVKHVIN----FD------LPSDVEEYVHRIGRTGRMGN--LDFPFSYNQPGYGGSYGGSSSQ  226 (237)
Q Consensus       159 ~~vlv~T~~~~~Gvdl~~~~~Vi~----~~------~p~s~~~~~Q~~GR~~R~g~--~~~~~~~~~~~~~~~~~~~~~~  226 (237)
                      ++|||||+.+++|+|+|...+||.    |+      .|.+..+|.||+|||||.|.  .|.+++++.+.+...|......
T Consensus      1240 i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~~~~~~~~ll~~ 1319 (1724)
T 4f92_B         1240 IQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYE 1319 (1724)
T ss_dssp             BCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGGGHHHHHHHTTS
T ss_pred             CeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecchHHHHHHHHhCC
Confidence            999999999999999999998883    32      35689999999999999885  6899999998887777665443

>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=99.81  E-value=6.5e-20  Score=179.77  Aligned_cols=179  Identities=16%  Similarity=0.193  Sum_probs=134.2

Q ss_pred             ccccceeEEeecccchhhHHHHhhhcCC-CceeecC---------------Ccchhh-----HHHHhhhhhhccCCceEE
Q psy15610         54 GDEALTLVFVETKKGADQLEDFLHHHGY-PVTSIHG---------------DRTQKE-----REEAQQYTLISCDEALTL  112 (237)
Q Consensus        54 ~~~~~~i~f~~t~~~~~~~~~~l~~~~~-~~~~~~~---------------~~~~~~-----~~~~~~~~~~~~~~~~~i  112 (237)
                      +.+.++|.+|+|.++++++++||..... .+..+..               ......     .............++++|
T Consensus       242 ~~~~riI~LSATl~N~~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~L  321 (1724)
T 4f92_B          242 QEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVL  321 (1724)
T ss_dssp             TCCCEEEEEECSCTTHHHHHHHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHHHHHHHHHHHHHHHTTCCSSCCEE
T ss_pred             CCCCcEEEEecccCCHHHHHHHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhhhhHHHHHHHHHHHHHHhcCCcEE
Confidence            5667899999999999999999975310 0111111               010000     111111223344567899


Q ss_pred             EEeecccchHHHHHHHhhC-------------------------------------CCceEEEeCCCCHHHHHHHHHHhh
Q psy15610        113 VFVETKKGADQLEDFLHHH-------------------------------------GYPVTSIHGDRTQKEREEALRRFR  155 (237)
Q Consensus       113 IF~~t~~~~~~l~~~L~~~-------------------------------------~~~~~~~h~~~~~~~r~~~~~~f~  155 (237)
                      |||+|++.|+.++..|.+.                                     ...++++||+|++++|..+++.|+
T Consensus       322 VF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~~vE~~F~  401 (1724)
T 4f92_B          322 VFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFA  401 (1724)
T ss_dssp             EECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHHHHHHHHH
T ss_pred             EECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHHHHHHHHH
Confidence            9999999999888777421                                     234899999999999999999999


Q ss_pred             cCCCCEEEEcCccccccCCCCCcEEEE----ecC------CCCHHHHHHhhcccccCC--CCCceEEeecCCCCCCCCCC
Q psy15610        156 SGETPILVATAVAARGLDIPHVKHVIN----FDL------PSDVEEYVHRIGRTGRMG--NLDFPFSYNQPGYGGSYGGS  223 (237)
Q Consensus       156 ~g~~~vlv~T~~~~~Gvdl~~~~~Vi~----~~~------p~s~~~~~Q~~GR~~R~g--~~~~~~~~~~~~~~~~~~~~  223 (237)
                      +|.++|||||+.+++|+|+|..++||.    |++      |.++.+|.||+|||||.|  ..|.+++++...+...|...
T Consensus       402 ~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~~~~~~~l  481 (1724)
T 4f92_B          402 DKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSL  481 (1724)
T ss_dssp             TTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTTCCHHHHH
T ss_pred             CCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchhHHHHHHH
Confidence            999999999999999999999999985    443      458999999999999976  56999999999998888776


Q ss_pred             CCCCCCCCC
Q psy15610        224 SSQNSNAPD  232 (237)
Q Consensus       224 ~~~~~~~~~  232 (237)
                      .......++
T Consensus       482 l~~~~pieS  490 (1724)
T 4f92_B          482 LNQQLPIES  490 (1724)
T ss_dssp             TTTCSCCCC
T ss_pred             HcCCCcchh
Confidence            555444433

>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=99.81  E-value=4.9e-20  Score=165.65  Aligned_cols=148  Identities=18%  Similarity=0.300  Sum_probs=112.7

Q ss_pred             cccceeEEeecccch-hhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCC
Q psy15610         55 DEALTLVFVETKKGA-DQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGY  133 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~-~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~  133 (237)
                      .+.++++||+|.... ..+..    .+.....+............  .........++||||+|++.++.+++.|...++
T Consensus       307 ~~~q~il~SAT~~~~~~~~~~----~~~~~~~v~~~~~~~~~~~l--l~~l~~~~~~~LVF~~s~~~a~~l~~~L~~~g~  380 (618)
T 2whx_A          307 GEAAAIFMTATPPGSTDPFPQ----SNSPIEDIEREIPERSWNTG--FDWITDYQGKTVWFVPSIKAGNDIANCLRKSGK  380 (618)
T ss_dssp             TSCEEEEECSSCTTCCCSSCC----CSSCEEEEECCCCSSCCSSS--CHHHHHCCSCEEEECSSHHHHHHHHHHHHHTTC
T ss_pred             cCccEEEEECCCchhhhhhhc----cCCceeeecccCCHHHHHHH--HHHHHhCCCCEEEEECChhHHHHHHHHHHHcCC
Confidence            467899999998653 22211    22222222211111000000  111222467999999999999999999999999


Q ss_pred             ceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEE--------------------EEecCCCCHHHHH
Q psy15610        134 PVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHV--------------------INFDLPSDVEEYV  193 (237)
Q Consensus       134 ~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~V--------------------i~~~~p~s~~~~~  193 (237)
                      .+..+||+    +|.++++.|++|..+|||||+++++|+|+| +++|                    |+++.|.+.+.|+
T Consensus       381 ~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yi  455 (618)
T 2whx_A          381 RVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAA  455 (618)
T ss_dssp             CEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHH
T ss_pred             cEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHH
Confidence            99999984    688899999999999999999999999997 8887                    7788899999999


Q ss_pred             HhhcccccCCC-CCceEEeec
Q psy15610        194 HRIGRTGRMGN-LDFPFSYNQ  213 (237)
Q Consensus       194 Q~~GR~~R~g~-~~~~~~~~~  213 (237)
                      ||+||+||.|. +|.+++|+.
T Consensus       456 QR~GRaGR~g~~~G~ai~l~~  476 (618)
T 2whx_A          456 QRRGRIGRNPAQEDDQYVFSG  476 (618)
T ss_dssp             HHHTTSSCCTTCCCEEEEECS
T ss_pred             HhccccCCCCCCCCeEEEEcc
Confidence            99999999974 899999997

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.81  E-value=2.4e-19  Score=160.15  Aligned_cols=108  Identities=21%  Similarity=0.227  Sum_probs=97.0

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCC--------CCcE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP--------HVKH  179 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~--------~~~~  179 (237)
                      +.++||||+|...++.++..|...|+++.++||+....++..+..+++.|  .|+|||+++++|+|++        ...+
T Consensus       474 gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI~lg~~V~~~Gglh  551 (822)
T 3jux_A          474 GQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDIKLGPGVAELGGLC  551 (822)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCCCCCTTTTTTTSCE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCccCCcchhhcCCCE
Confidence            57899999999999999999999999999999996655555556666655  6999999999999998        5569


Q ss_pred             EEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        180 VINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       180 Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||+++.|.+...|.|+.||+||.|.+|.+++|++..+.
T Consensus       552 VInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~  589 (822)
T 3jux_A          552 IIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDD  589 (822)
T ss_dssp             EEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSH
T ss_pred             EEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHH
Confidence            99999999999999999999999999999999998773

>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=99.80  E-value=6.5e-20  Score=172.50  Aligned_cols=109  Identities=24%  Similarity=0.327  Sum_probs=102.1

Q ss_pred             CCceEEEEeecccchHHHHHHHhh-CCCceEEEeCCCCHHHHHHHHHHhhcCC--CCEEEEcCccccccCCCCCcEEEEe
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH-HGYPVTSIHGDRTQKEREEALRRFRSGE--TPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~-~~~~~~~~h~~~~~~~r~~~~~~f~~g~--~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      ++.++||||++...++.++..|.. .|+++..+||+|++.+|+++++.|++|+  ++|||||+++++|+|+|.+++||++
T Consensus       502 ~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~  581 (968)
T 3dmq_A          502 RSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMF  581 (968)
T ss_dssp             SSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECS
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhhcCCCcccCcEEEEe
Confidence            368999999999999999999985 5999999999999999999999999998  9999999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      ++|+++..|.|++||+||.|+.+.++++....
T Consensus       582 d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~  613 (968)
T 3dmq_A          582 DLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYL  613 (968)
T ss_dssp             SCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEE
T ss_pred             cCCCCHHHHHHHhhccccCCCCceEEEEEecC
Confidence            99999999999999999999999877775443

>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=99.80  E-value=5e-19  Score=160.46  Aligned_cols=109  Identities=28%  Similarity=0.363  Sum_probs=103.4

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC-
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL-  185 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~-  185 (237)
                      .+.++||||+|...++.++++|...|+.+..+||++++.+|..+++.|++|.++|||||+++++|+|+|++++||+++. 
T Consensus       438 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d  517 (664)
T 1c4o_A          438 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD  517 (664)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTT
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCc
Confidence            3579999999999999999999999999999999999999999999999999999999999999999999999999997 


Q ss_pred             ----CCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        186 ----PSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       186 ----p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                          |.+...|+||+||+||.| +|.+++|+++..
T Consensus       518 ~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~  551 (664)
T 1c4o_A          518 KEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVS  551 (664)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCC
T ss_pred             ccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCC
Confidence                889999999999999995 899999987654

>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=99.80  E-value=8e-20  Score=171.52  Aligned_cols=107  Identities=21%  Similarity=0.331  Sum_probs=63.4

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC------------CCceEEEeCCCCHHHHHHHHHHhhc-CCCCEEEEcCccccccC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH------------GYPVTSIHGDRTQKEREEALRRFRS-GETPILVATAVAARGLD  173 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~------------~~~~~~~h~~~~~~~r~~~~~~f~~-g~~~vlv~T~~~~~Gvd  173 (237)
                      ++.++||||+++..++.++++|...            |.....+||+|++.+|..+++.|++ |.++|||||+++++|+|
T Consensus       630 ~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGID  709 (936)
T 4a2w_A          630 PQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGID  709 (936)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC------
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCc
Confidence            3689999999999999999999875            5566777999999999999999999 99999999999999999


Q ss_pred             CCCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        174 IPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       174 l~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      +|++++||+||+|+|+..|+||+|| ||. ..|.+++|+..+
T Consensus       710 lp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~  749 (936)
T 4a2w_A          710 IVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKT  749 (936)
T ss_dssp             CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCH
T ss_pred             chhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCC
Confidence            9999999999999999999999999 998 688899888764

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.80  E-value=2.5e-20  Score=170.10  Aligned_cols=107  Identities=26%  Similarity=0.410  Sum_probs=67.3

Q ss_pred             CceEEEEeecccchHHHHHHHhhCC----CceEEE--------eCCCCHHHHHHHHHHhhc-CCCCEEEEcCccccccCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHG----YPVTSI--------HGDRTQKEREEALRRFRS-GETPILVATAVAARGLDI  174 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~----~~~~~~--------h~~~~~~~r~~~~~~f~~-g~~~vlv~T~~~~~Gvdl  174 (237)
                      +.++||||+++..++.+++.|...+    +.+..+        ||+|++.+|..+++.|++ |..+|||||+++++|+|+
T Consensus       398 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDi  477 (696)
T 2ykg_A          398 ETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDI  477 (696)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC---
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcC
Confidence            5789999999999999999999887    788877        569999999999999998 999999999999999999


Q ss_pred             CCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        175 PHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       175 ~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      |++++||+||+|+++..|+||+|| ||. +.|.+++++..++
T Consensus       478 p~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~  517 (696)
T 2ykg_A          478 AQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAG  517 (696)
T ss_dssp             CCCSEEEEESCC--CCCC-----------CCCEEEEEESCHH
T ss_pred             ccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCC
Confidence            999999999999999999999999 998 6889998887654

>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=99.79  E-value=6.5e-19  Score=159.64  Aligned_cols=109  Identities=29%  Similarity=0.384  Sum_probs=103.8

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC-
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL-  185 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~-  185 (237)
                      .+.++||||+|...++.+++.|...|+++..+||++++.+|..+++.|++|.++|||+|+++++|+|+|++++||+++. 
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d  523 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD  523 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcc
Confidence            3579999999999999999999999999999999999999999999999999999999999999999999999999997 


Q ss_pred             ----CCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        186 ----PSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       186 ----p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                          |.+...|+||+||+||. .+|.+++|+.+.+
T Consensus       524 ~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~  557 (661)
T 2d7d_A          524 KEGFLRSERSLIQTIGRAARN-AEGRVIMYADKIT  557 (661)
T ss_dssp             CCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCC
T ss_pred             cccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCC
Confidence                89999999999999998 6899999998754

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.79  E-value=2.6e-19  Score=154.96  Aligned_cols=172  Identities=15%  Similarity=0.155  Sum_probs=118.5

Q ss_pred             EEEeechhHHH----HHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhh
Q psy15610         29 IAWVDEQDKRS----CLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLI  104 (237)
Q Consensus        29 ~~~~~~~~k~~----~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (237)
                      +++++|.+++.    .....+....   ...+.++++||+|.....   ..+.....+...+............  ..+.
T Consensus        96 ~vViDEaH~~~~~~~~~~~~l~~~~---~~~~~~~l~~SAT~~~~~---~~~~~~~~~i~~~~~~~~~~~~~~~--~~~l  167 (431)
T 2v6i_A           96 LYIMDEAHFLDPASVAARGYIETRV---SMGDAGAIFMTATPPGTT---EAFPPSNSPIIDEETRIPDKAWNSG--YEWI  167 (431)
T ss_dssp             EEEEESTTCCSHHHHHHHHHHHHHH---HTTSCEEEEEESSCTTCC---CSSCCCSSCCEEEECCCCSSCCSSC--CHHH
T ss_pred             EEEEeCCccCCccHHHHHHHHHHHh---hCCCCcEEEEeCCCCcch---hhhcCCCCceeeccccCCHHHHHHH--HHHH
Confidence            66778877652    2222222221   235678999999987621   1111112222222111111100001  1122


Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcE-----
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKH-----  179 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~-----  179 (237)
                      ...+.+++|||++++.++.+++.|...++.+..+||+    +|..+++.|++|..+|||||+++++|+|+| +.+     
T Consensus       168 ~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g  242 (431)
T 2v6i_A          168 TEFDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPR  242 (431)
T ss_dssp             HSCSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECC
T ss_pred             HcCCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecC
Confidence            2346789999999999999999999999999999997    578899999999999999999999999999 544     


Q ss_pred             ------------EEEecCCCCHHHHHHhhcccccCCCCCceEEeec
Q psy15610        180 ------------VINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       180 ------------Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                                  ||+++.|.+..+|+||+||+||.|..+.+++++.
T Consensus       243 ~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          243 KTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             EEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             ccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence                        6788899999999999999999985444444443

>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=99.78  E-value=6.5e-19  Score=159.77  Aligned_cols=108  Identities=19%  Similarity=0.141  Sum_probs=101.0

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC----------
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV----------  177 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~----------  177 (237)
                      +.++||||.|...++.++..|...|+++.++||++...++..+..+|+.|  .|+|||++++||+|++..          
T Consensus       441 gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~  518 (853)
T 2fsf_A          441 GQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAAL  518 (853)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHC
T ss_pred             CCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhc
Confidence            57899999999999999999999999999999999888888888889887  699999999999999974          


Q ss_pred             ---------------------------cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        178 ---------------------------KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       178 ---------------------------~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                                                 .+||+++.|.|...|.|+.||+||.|.+|.+++|++..+.
T Consensus       519 ~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD~  585 (853)
T 2fsf_A          519 ENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDA  585 (853)
T ss_dssp             SSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSG
T ss_pred             ccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccHH
Confidence                                       5899999999999999999999999999999999998764

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.78  E-value=5.7e-19  Score=159.68  Aligned_cols=179  Identities=16%  Similarity=0.135  Sum_probs=125.5

Q ss_pred             EEEEeechhHH------HHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhh
Q psy15610         28 RIAWVDEQDKR------SCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQY  101 (237)
Q Consensus        28 ~~~~~~~~~k~------~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  101 (237)
                      .+++++|.+.+      ..+...+....    ....+++.+++|.+.++.+...... .+.+................ .
T Consensus       241 ~lvVIDEaH~l~d~~~g~~~~~~l~~l~----~~~i~il~~SAT~~~i~~l~~~~~~-~~~v~~~~r~~~l~~~~~~l-~  314 (677)
T 3rc3_A          241 EVAVIDEIQMIRDPARGWAWTRALLGLC----AEEVHLCGEPAAIDLVMELMYTTGE-EVEVRDYKRLTPISVLDHAL-E  314 (677)
T ss_dssp             EEEEECSGGGGGCTTTHHHHHHHHHHCC----EEEEEEEECGGGHHHHHHHHHHHTC-CEEEEECCCSSCEEECSSCC-C
T ss_pred             CEEEEecceecCCccchHHHHHHHHccC----ccceEEEeccchHHHHHHHHHhcCC-ceEEEEeeecchHHHHHHHH-H
Confidence            46678887654      12222222211    2567788999997666666655421 11111110000000000000 0


Q ss_pred             hhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhc--CCCCEEEEcCccccccCCCCCcE
Q psy15610        102 TLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRS--GETPILVATAVAARGLDIPHVKH  179 (237)
Q Consensus       102 ~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~--g~~~vlv~T~~~~~Gvdl~~~~~  179 (237)
                      .+... ....+|||++++.++.+++.|...++.+..+||+|++++|..+++.|++  |..+|||||+++++|+|+ ++++
T Consensus       315 ~l~~~-~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~  392 (677)
T 3rc3_A          315 SLDNL-RPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRR  392 (677)
T ss_dssp             SGGGC-CTTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSE
T ss_pred             HHHhc-CCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccE
Confidence            01111 3445899999999999999999999999999999999999999999999  889999999999999999 8999


Q ss_pred             EEEecC--------------CCCHHHHHHhhcccccCCCC---CceEEeecC
Q psy15610        180 VINFDL--------------PSDVEEYVHRIGRTGRMGNL---DFPFSYNQP  214 (237)
Q Consensus       180 Vi~~~~--------------p~s~~~~~Q~~GR~~R~g~~---~~~~~~~~~  214 (237)
                      ||+++.              |.+..+|.||+||+||.|..   |.|+.++..
T Consensus       393 VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~~~  444 (677)
T 3rc3_A          393 IIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNHE  444 (677)
T ss_dssp             EEESCSBC-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESSTT
T ss_pred             EEECCccccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEecc
Confidence            999998              78999999999999999954   666666543

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.78  E-value=2.4e-18  Score=161.91  Aligned_cols=106  Identities=25%  Similarity=0.338  Sum_probs=91.7

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCC---------------------------------------ceEEEeCCCCHHH
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGY---------------------------------------PVTSIHGDRTQKE  146 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~---------------------------------------~~~~~h~~~~~~~  146 (237)
                      .+..++||||++++.|+.++..|...++                                       .+..+||+|++.+
T Consensus       334 ~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl~~~~  413 (997)
T 4a4z_A          334 RELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIV  413 (997)
T ss_dssp             TTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEECTTSCHHH
T ss_pred             CCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeecCCCCHHH
Confidence            3457899999999999999999977554                                       5799999999999


Q ss_pred             HHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC---------CHHHHHHhhcccccCC--CCCceEEee
Q psy15610        147 REEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS---------DVEEYVHRIGRTGRMG--NLDFPFSYN  212 (237)
Q Consensus       147 r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~---------s~~~~~Q~~GR~~R~g--~~~~~~~~~  212 (237)
                      |+.+++.|++|.++|||||+++++|+|+|+ ..||+++.|.         |+..|+||+|||||.|  ..|.+++++
T Consensus       414 R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~  489 (997)
T 4a4z_A          414 KELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMA  489 (997)
T ss_dssp             HHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEEC
T ss_pred             HHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEec
Confidence            999999999999999999999999999999 5555544443         9999999999999998  456666666

>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=99.78  E-value=3.3e-19  Score=168.87  Aligned_cols=107  Identities=19%  Similarity=0.336  Sum_probs=90.0

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEE----cCccccccCCCCC-cEEEE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVA----TAVAARGLDIPHV-KHVIN  182 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~----T~~~~~Gvdl~~~-~~Vi~  182 (237)
                      +.++||||+++..++.+++.|... +.+..+||++     ..+++.|++|..+||||    |+++++|+|+|++ ++||+
T Consensus       275 ~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~-----~~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~  348 (1054)
T 1gku_B          275 GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATK-----KGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVF  348 (1054)
T ss_dssp             CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSS-----SHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEE
T ss_pred             CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccH-----HHHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEEE
Confidence            468999999999999999999988 9999999998     37789999999999999    8999999999995 99999


Q ss_pred             ecCC-----------------------------------------------------------------------CCHHH
Q psy15610        183 FDLP-----------------------------------------------------------------------SDVEE  191 (237)
Q Consensus       183 ~~~p-----------------------------------------------------------------------~s~~~  191 (237)
                      ++.|                                                                       .+...
T Consensus       349 ~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  428 (1054)
T 1gku_B          349 VGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLRT  428 (1054)
T ss_dssp             ESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTEEEEECHHH
T ss_pred             eCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecceecCcHHH
Confidence            9999                                                                       78999


Q ss_pred             HHHhhcccccCCCCC--ceEEeecCCCCCCC
Q psy15610        192 YVHRIGRTGRMGNLD--FPFSYNQPGYGGSY  220 (237)
Q Consensus       192 ~~Q~~GR~~R~g~~~--~~~~~~~~~~~~~~  220 (237)
                      |+||+||+||.|..|  .++.|+...+...+
T Consensus       429 yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~  459 (1054)
T 1gku_B          429 YIQGSGRTSRLFAGGLTKGASFLLEDDSELL  459 (1054)
T ss_dssp             HHHHHHTTCCEETTEECCEEEEEECSCHHHH
T ss_pred             HhhhhchhhhccCCCCceEEEEEEecCHHHH
Confidence            999999999987664  47777776655433

>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=99.76  E-value=4.1e-18  Score=162.50  Aligned_cols=109  Identities=17%  Similarity=0.248  Sum_probs=102.7

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      .+.+++|||++.+.++.+++.|...  +..+..+||+|++.+|+++++.|++|..+|||||+++++|+|+|++++||.++
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            3689999999999999999999887  78999999999999999999999999999999999999999999999999998


Q ss_pred             C-CCCHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        185 L-PSDVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       185 ~-p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      . ++++..|.||+||+||.|+.|.|++++.+.
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            8 569999999999999999999999998764

>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=99.76  E-value=3.1e-18  Score=155.02  Aligned_cols=105  Identities=16%  Similarity=0.307  Sum_probs=97.9

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC---EEEEcCccccccCCCCCcEEEEe
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP---ILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~---vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      .+.++||||++...++.++.+|...++.+..+||+++..+|..+++.|+++...   +|++|+++++|+|++.+++||++
T Consensus       415 ~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~  494 (644)
T 1z3i_X          415 TSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMF  494 (644)
T ss_dssp             CCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEEC
T ss_pred             CCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEE
Confidence            368999999999999999999999999999999999999999999999998754   88999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEe
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSY  211 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~  211 (237)
                      |+||++..+.|++||++|.|+...+.++
T Consensus       495 d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~  522 (644)
T 1z3i_X          495 DPDWNPANDEQAMARVWRDGQKKTCYIY  522 (644)
T ss_dssp             SCCSSHHHHHHHHTTSSSTTCCSCEEEE
T ss_pred             CCCCCccHHHHHHHhhhhcCCCCceEEE
Confidence            9999999999999999999988765443

>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=99.76  E-value=3.1e-18  Score=155.76  Aligned_cols=108  Identities=20%  Similarity=0.167  Sum_probs=99.8

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC----------
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV----------  177 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~----------  177 (237)
                      +.++||||.|.+.++.++..|.+.|+++.++||++...++..+.++|+.|  .|+|||++++||+|++..          
T Consensus       460 gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~  537 (922)
T 1nkt_A          460 GQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQR  537 (922)
T ss_dssp             TCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHH
Confidence            47899999999999999999999999999999998877777777888877  699999999999999975          


Q ss_pred             ------------------------------------------cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        178 ------------------------------------------KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       178 ------------------------------------------~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                                                                .+||+++.|.|...|.|+.||+||.|.+|.+++|++..
T Consensus       538 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSle  617 (922)
T 1nkt_A          538 LRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLG  617 (922)
T ss_dssp             HHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETT
T ss_pred             HhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechh
Confidence                                                      48999999999999999999999999999999999987


Q ss_pred             CC
Q psy15610        216 YG  217 (237)
Q Consensus       216 ~~  217 (237)
                      +.
T Consensus       618 D~  619 (922)
T 1nkt_A          618 DE  619 (922)
T ss_dssp             SH
T ss_pred             HH
Confidence            64

>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=99.76  E-value=1.4e-18  Score=152.98  Aligned_cols=109  Identities=16%  Similarity=0.275  Sum_probs=94.5

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC-CCceEEEeCCCCHHHHHHHHHHhhcC-CCC-EEEEcCccccccCCCCCcEEEEe
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH-GYPVTSIHGDRTQKEREEALRRFRSG-ETP-ILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~r~~~~~~f~~g-~~~-vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      .+.++||||++...++.++..|... ++.+..+||+++..+|..+++.|+++ ... +|++|+++++|+|+|.+++||++
T Consensus       340 ~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi~~  419 (500)
T 1z63_A          340 EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHF  419 (500)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEEES
T ss_pred             cCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhCCEEEEe
Confidence            4679999999999999999999875 89999999999999999999999998 454 78999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceE--EeecCC
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPF--SYNQPG  215 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~--~~~~~~  215 (237)
                      ++||++..|.|++||++|.|+.+.+.  .|+..+
T Consensus       420 d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~  453 (500)
T 1z63_A          420 DRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  453 (500)
T ss_dssp             SCCSCC---CHHHHTTTTTTTTSCEEEEEEEETT
T ss_pred             CCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCC
Confidence            99999999999999999999887764  344443

>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=99.76  E-value=3e-19  Score=156.10  Aligned_cols=108  Identities=21%  Similarity=0.373  Sum_probs=94.3

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS  187 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~  187 (237)
                      +.++||||++.+.++.+++.|.     +..+||+++..+|+.+++.|++|..+|||||+++++|+|+|++++||+++.|+
T Consensus       349 ~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~  423 (472)
T 2fwr_A          349 KDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSG  423 (472)
T ss_dssp             SSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSS
T ss_pred             CCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCC
Confidence            6799999999999999999883     56799999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHhhcccccCCCC-Cc--eEEeecCCCCCCC
Q psy15610        188 DVEEYVHRIGRTGRMGNL-DF--PFSYNQPGYGGSY  220 (237)
Q Consensus       188 s~~~~~Q~~GR~~R~g~~-~~--~~~~~~~~~~~~~  220 (237)
                      ++..|.|++||+||.|+. +.  ++.|+..+..+.+
T Consensus       424 s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~t~ee~  459 (472)
T 2fwr_A          424 SAREYIQRLGRILRPSKGKKEAVLYELISRGTGEVN  459 (472)
T ss_dssp             CCHHHHHHHHHSBCCCTTTCCEEEEEEEECSCC---
T ss_pred             CHHHHHHHHhhccCCCCCCceEEEEEEEeCCCchHH
Confidence            999999999999999854 33  4445665555444

>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=99.76  E-value=8.3e-19  Score=157.39  Aligned_cols=104  Identities=26%  Similarity=0.352  Sum_probs=93.4

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEE----
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI----  181 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi----  181 (237)
                      .+..++||||++++.++.+++.|.+.++.+..+||++++++       |.++..+|||||+++++|+|++ +++||    
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            35789999999999999999999999999999999999875       4556669999999999999997 99988    


Q ss_pred             ------Eec-----------CCCCHHHHHHhhcccccCCCCCceEEeecCCCCCC
Q psy15610        182 ------NFD-----------LPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGS  219 (237)
Q Consensus       182 ------~~~-----------~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~  219 (237)
                            +||           .|.+.+.|+||+||+|| |.+|. +.|+.+.+.+.
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 88999 99998877665

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.75  E-value=1.7e-18  Score=164.29  Aligned_cols=74  Identities=26%  Similarity=0.491  Sum_probs=69.7

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceE-EEeCCCCHHHHHHHHHHhhcCCCCEEEE----cCccccccCCCC-CcEEE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVT-SIHGDRTQKEREEALRRFRSGETPILVA----TAVAARGLDIPH-VKHVI  181 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~-~~h~~~~~~~r~~~~~~f~~g~~~vlv~----T~~~~~Gvdl~~-~~~Vi  181 (237)
                      +.++||||+++..++.++..|...++.+. .+||     +|.+ ++.|++|..+||||    |+++++|+|+|+ +++||
T Consensus       309 ~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg-----~rr~-l~~F~~G~~~VLVatas~TdvlarGIDip~~V~~VI  382 (1104)
T 4ddu_A          309 RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSE-----FEKN-FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVI  382 (1104)
T ss_dssp             CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSS-----HHHH-HHHHHHTSCSEEEEETTTHHHHCCSCCCTTTCCEEE
T ss_pred             CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecC-----cHHH-HHHHHCCCCCEEEEecCCCCeeEecCcCCCCCCEEE
Confidence            47899999999999999999999999998 9999     2555 99999999999999    999999999999 99999


Q ss_pred             EecCCC
Q psy15610        182 NFDLPS  187 (237)
Q Consensus       182 ~~~~p~  187 (237)
                      +||+|.
T Consensus       383 ~~d~P~  388 (1104)
T 4ddu_A          383 FWGTPS  388 (1104)
T ss_dssp             EESCCE
T ss_pred             EECCCC
Confidence            999998

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.75  E-value=3.8e-18  Score=157.98  Aligned_cols=104  Identities=20%  Similarity=0.372  Sum_probs=97.2

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCC---CEEEEcCccccccCCCCCcEEEEec
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGET---PILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~---~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      +.++||||.....++.++++|...|+++..+||+++..+|..+++.|+++..   .+|++|.+++.|+|++.+++||++|
T Consensus       572 g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~agg~GlNL~~a~~VI~~D  651 (800)
T 3mwy_W          572 GHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFD  651 (800)
T ss_dssp             TCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHHTTTCCCTTCCEEEESS
T ss_pred             CCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecccccCCCCccccceEEEec
Confidence            6799999999999999999999999999999999999999999999998654   4899999999999999999999999


Q ss_pred             CCCCHHHHHHhhcccccCCCCCceEEe
Q psy15610        185 LPSDVEEYVHRIGRTGRMGNLDFPFSY  211 (237)
Q Consensus       185 ~p~s~~~~~Q~~GR~~R~g~~~~~~~~  211 (237)
                      +|||+..+.|+.||++|.|+...+.++
T Consensus       652 ~~wnp~~~~Qa~gR~~RiGQ~k~V~Vy  678 (800)
T 3mwy_W          652 SDWNPQADLQAMARAHRIGQKNHVMVY  678 (800)
T ss_dssp             CCSCSHHHHHHHTTTSCSSCCSCEEEE
T ss_pred             CCCChhhHHHHHHHHHhcCCCceEEEE
Confidence            999999999999999999988665443

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.74  E-value=1.8e-18  Score=152.48  Aligned_cols=105  Identities=17%  Similarity=0.171  Sum_probs=95.5

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEc-CccccccCCCCCcEEEEecCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT-AVAARGLDIPHVKHVINFDLP  186 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T-~~~~~Gvdl~~~~~Vi~~~~p  186 (237)
                      +.+.+|||. .+.++.+++.|...+.++..+||+++..+|+.+++.|++|..+||||| +++++|+|+|++++||+++.|
T Consensus       348 ~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~~  426 (510)
T 2oca_A          348 ENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGV  426 (510)
T ss_dssp             CEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEESSCC
T ss_pred             CCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEeCCC
Confidence            456667776 888889999999988899999999999999999999999999999999 999999999999999999999


Q ss_pred             CCHHHHHHhhcccccCCCCCceEEeec
Q psy15610        187 SDVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       187 ~s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      +++..|.|++||+||.|+.+.+++++.
T Consensus       427 ~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          427 KSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             CSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             CCHHHHHHHHhcccccCCCCceEEEEE
Confidence            999999999999999998874445544

>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=99.73  E-value=3.4e-18  Score=156.80  Aligned_cols=109  Identities=20%  Similarity=0.352  Sum_probs=96.9

Q ss_pred             cCCceEEEEeeccc--------chHHHHHHHhh---CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCC
Q psy15610        106 CDEALTLVFVETKK--------GADQLEDFLHH---HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDI  174 (237)
Q Consensus       106 ~~~~~~iIF~~t~~--------~~~~l~~~L~~---~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl  174 (237)
                      ..+.+++|||++.+        .++.+++.|..   .++.+..+||+|++.+|+.+++.|++|..+|||||+++++|+|+
T Consensus       576 ~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDi  655 (780)
T 1gm5_A          576 MRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDV  655 (780)
T ss_dssp             TTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCC
T ss_pred             hcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccccC
Confidence            45678999999664        46778888877   47889999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEecCCC-CHHHHHHhhcccccCCCCCceEEeecC
Q psy15610        175 PHVKHVINFDLPS-DVEEYVHRIGRTGRMGNLDFPFSYNQP  214 (237)
Q Consensus       175 ~~~~~Vi~~~~p~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~  214 (237)
                      |++++||+++.|. +...+.||+||+||.|..|.|++++.+
T Consensus       656 P~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~  696 (780)
T 1gm5_A          656 PRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD  696 (780)
T ss_dssp             TTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             CCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECC
Confidence            9999999999996 789999999999999999999999873

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.68  E-value=1e-16  Score=143.84  Aligned_cols=98  Identities=24%  Similarity=0.367  Sum_probs=87.2

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCC--------ceEEEeCCCCHHHHHHHHHHhhcCCCC---EEEEcCccccccCC
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGY--------PVTSIHGDRTQKEREEALRRFRSGETP---ILVATAVAARGLDI  174 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~--------~~~~~h~~~~~~~r~~~~~~f~~g~~~---vlv~T~~~~~Gvdl  174 (237)
                      ....++||||+++.+++.+++.|...+.        .+..+||+++. +|+.+++.|+++..+   |++||+++++|+|+
T Consensus       437 ~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDi  515 (590)
T 3h1t_A          437 DRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQELETSTPVILTTSQLLTTGVDA  515 (590)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCTTCCCCCEEEESSTTTTTCCC
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCCCCCCCEEEEECChhhcCccc
Confidence            4468999999999999999999976543        26788998764 799999999998765   88999999999999


Q ss_pred             CCCcEEEEecCCCCHHHHHHhhcccccCCC
Q psy15610        175 PHVKHVINFDLPSDVEEYVHRIGRTGRMGN  204 (237)
Q Consensus       175 ~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~  204 (237)
                      |.+++||++++|+|+..|.||+||+||.|.
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

>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=99.25  E-value=2.6e-11  Score=114.22  Aligned_cols=106  Identities=10%  Similarity=0.149  Sum_probs=85.3

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCC------------CceE-EEeCC----------C----------CHH--------
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHG------------YPVT-SIHGD----------R----------TQK--------  145 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~------------~~~~-~~h~~----------~----------~~~--------  145 (237)
                      .+.+++|||+++..|..+++.|.+.+            ..+. ++|++          +          ++.        
T Consensus       536 ~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~  615 (1038)
T 2w00_A          536 KGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAA  615 (1038)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHH
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHH
Confidence            34689999999999999999987643            4454 45542          2          221        


Q ss_pred             ---------------------HHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCCCHHHHHHhhcccccCCC
Q psy15610        146 ---------------------EREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN  204 (237)
Q Consensus       146 ---------------------~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~  204 (237)
                                           .|..+.++|++|.+++||+|+.+.+|+|+|.+ .++++|.|.+...|+|++||++|.+.
T Consensus       616 I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~  694 (1038)
T 2w00_A          616 IREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYD  694 (1038)
T ss_dssp             HHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCC
T ss_pred             HHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCC
Confidence                                 47788999999999999999999999999999 67889999999999999999999875


Q ss_pred             C----CceEEeec
Q psy15610        205 L----DFPFSYNQ  213 (237)
Q Consensus       205 ~----~~~~~~~~  213 (237)
                      .    |.++.|+.
T Consensus       695 ~~K~~G~IVdf~~  707 (1038)
T 2w00_A          695 ATKTFGNIVTFRD  707 (1038)
T ss_dssp             TTCCSEEEEESSC
T ss_pred             CCCCcEEEEEccc
Confidence            3    44555553

>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=98.71  E-value=3.1e-08  Score=81.36  Aligned_cols=104  Identities=12%  Similarity=0.053  Sum_probs=75.3

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccC-----CCCCcEEE
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLD-----IPHVKHVI  181 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvd-----l~~~~~Vi  181 (237)
                      .+.+++||++..+..+.+++++...++.+..+.|.....+ .+.    .+....+.+.|..++-|+|     +..++.||
T Consensus       124 ~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~-~k~----~~~~~~i~Lltsag~~gin~~~~nl~~aD~VI  198 (328)
T 3hgt_A          124 YETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSA-AAA----NDFSCTVHLFSSEGINFTKYPIKSKARFDMLI  198 (328)
T ss_dssp             SCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCCCTTTSCCCCCSCCSEEE
T ss_pred             CCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhh-hhc----ccCCceEEEEECCCCCCcCcccccCCCCCEEE
Confidence            3689999999999999999999999999999999855432 221    2344455566777777776     68899999


Q ss_pred             EecCCCCHHHH-HHhhcccccCC--C--CCceEEeecCC
Q psy15610        182 NFDLPSDVEEY-VHRIGRTGRMG--N--LDFPFSYNQPG  215 (237)
Q Consensus       182 ~~~~p~s~~~~-~Q~~GR~~R~g--~--~~~~~~~~~~~  215 (237)
                      .||+.|++..- +|++-|++|.|  +  .-.+|-++..+
T Consensus       199 ~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~  237 (328)
T 3hgt_A          199 CLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAIN  237 (328)
T ss_dssp             ECSTTCCTTSHHHHHHHCCC---------CCEEEEEETT
T ss_pred             EECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCC
Confidence            99999999885 89999999984  3  33455555544

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.45  E-value=1.7e-06  Score=79.45  Aligned_cols=39  Identities=18%  Similarity=0.088  Sum_probs=35.7

Q ss_pred             EEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        179 HVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       179 ~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +||....+.|...--|-.||+||.|.+|...+|++-.+.
T Consensus       662 hVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeDd  700 (997)
T 2ipc_A          662 FIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDDD  700 (997)
T ss_dssp             CEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSSH
T ss_pred             EEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECChH
Confidence            789999999999999999999999999999999987753

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.24  E-value=1.9e-06  Score=76.30  Aligned_cols=104  Identities=18%  Similarity=0.223  Sum_probs=66.8

Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEE--EcCccccccCCCC----Cc
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILV--ATAVAARGLDIPH----VK  178 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv--~T~~~~~Gvdl~~----~~  178 (237)
                      ....+.++||++|...++.+.+.+..  .+ ...++..  .++..+++.|+++. .|++  +|+.+.+|+|+|+    +.
T Consensus       381 ~~~~g~~lvff~S~~~~~~v~~~l~~--~~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~  454 (540)
T 2vl7_A          381 ENSSKSVLVFFPSYEMLESVRIHLSG--IP-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFE  454 (540)
T ss_dssp             HTCSSEEEEEESCHHHHHHHHTTCTT--SC-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEE
T ss_pred             HhCCCCEEEEeCCHHHHHHHHHHhcc--Cc-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCccccc
Confidence            34567899999999999999988864  23 4555554  46888999998864 6776  7899999999997    78


Q ss_pred             EEEEecCCC----CH--------------------------HHHHHhhcccccCCCCCceEEeecC
Q psy15610        179 HVINFDLPS----DV--------------------------EEYVHRIGRTGRMGNLDFPFSYNQP  214 (237)
Q Consensus       179 ~Vi~~~~p~----s~--------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~  214 (237)
                      +||.++.|.    ++                          ..+.|.+||+-|......++++++.
T Consensus       455 ~Vii~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD~  520 (540)
T 2vl7_A          455 SLVLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDS  520 (540)
T ss_dssp             EEEEESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEESG
T ss_pred             EEEEECCCCCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEcc
Confidence            899998874    22                          2356899999997655455555553

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=97.56  E-value=0.00021  Score=64.28  Aligned_cols=155  Identities=18%  Similarity=0.159  Sum_probs=92.9

Q ss_pred             ceeEEeecccchhhHHHHhhhc--------CCCc----eeecCCcchh--hH-----HHHhh--hhhhccCCceEEEEee
Q psy15610         58 LTLVFVETKKGADQLEDFLHHH--------GYPV----TSIHGDRTQK--ER-----EEAQQ--YTLISCDEALTLVFVE  116 (237)
Q Consensus        58 ~~i~f~~t~~~~~~~~~~l~~~--------~~~~----~~~~~~~~~~--~~-----~~~~~--~~~~~~~~~~~iIF~~  116 (237)
                      .+|++|+|....+.+.+.++-.        .|+.    ..+...+...  .+     .....  ..+....++.++||++
T Consensus       377 ~~il~SaTL~p~~~~~~~lGl~~~~~~~~spf~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~~~g~~lvlF~  456 (620)
T 4a15_A          377 KTIHMSGTLDPFDFYSDITGFEIPFKKIGEIFPPENRYIAYYDGVSSKYDTLDEKELDRMATVIEDIILKVKKNTIVYFP  456 (620)
T ss_dssp             EEEEEESSCCSHHHHHHHHCCCCCEEECCCCSCGGGEEEEEECCC-------CHHHHHHHHHHHHHHHHHHCSCEEEEES
T ss_pred             eEEEEccCCCcHHHHHHHhCCCceeeecCCCCCHHHeEEEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEeC
Confidence            4899999999988888877542        1111    1111111110  01     11111  1222233566999999


Q ss_pred             cccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEc--CccccccCCCC--CcEEEEecCCC---CH
Q psy15610        117 TKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT--AVAARGLDIPH--VKHVINFDLPS---DV  189 (237)
Q Consensus       117 t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T--~~~~~Gvdl~~--~~~Vi~~~~p~---s~  189 (237)
                      |...++.+.+.+..  .... ..-+++..++..+++.|+ +.-.||+++  ..+.+|+|+|+  ...||....|.   ++
T Consensus       457 Sy~~l~~v~~~l~~--~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~lPfp~~~p  532 (620)
T 4a15_A          457 SYSLMDRVENRVSF--EHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFPRPDA  532 (620)
T ss_dssp             CHHHHHHHTSSCCS--CCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESSCCCCCCCH
T ss_pred             CHHHHHHHHHHHHh--cchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEcCCCCCCCH
Confidence            99999999888862  2222 445566678999999999 888899997  49999999987  55788877653   11


Q ss_pred             --------------------------HHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        190 --------------------------EEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       190 --------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                                                ..+.|.+||+-|.-.+..++++++..-
T Consensus       533 ~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R~  585 (620)
T 4a15_A          533 INRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKRA  585 (620)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECGGG
T ss_pred             HHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEccch
Confidence                                      123589999999877766677766543

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=96.19  E-value=0.018  Score=50.83  Aligned_cols=104  Identities=16%  Similarity=0.134  Sum_probs=69.9

Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEc--CccccccCCC-----CC
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT--AVAARGLDIP-----HV  177 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T--~~~~~Gvdl~-----~~  177 (237)
                      ...++.++||.++...++.+.+.   .+.++..-..+++.   ...++.|+...-.||+++  ..+.+|+|+|     .+
T Consensus       390 ~~~~g~~lvlF~Sy~~l~~v~~~---~~~~v~~q~~~~~~---~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l  463 (551)
T 3crv_A          390 FQAKANVLVVFPSYEIMDRVMSR---ISLPKYVESEDSSV---EDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLI  463 (551)
T ss_dssp             HHCSSEEEEEESCHHHHHHHHTT---CCSSEEECCSSCCH---HHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESE
T ss_pred             HhCCCCEEEEecCHHHHHHHHHh---cCCcEEEcCCCCCH---HHHHHHHHhcCCeEEEEEecceecccccccccCCcce
Confidence            34467899999999998888863   34444433334554   446677754444799998  6999999999     36


Q ss_pred             cEEEEecCCC---CH---------------------------HHHHHhhcccccCCCCCceEEeecC
Q psy15610        178 KHVINFDLPS---DV---------------------------EEYVHRIGRTGRMGNLDFPFSYNQP  214 (237)
Q Consensus       178 ~~Vi~~~~p~---s~---------------------------~~~~Q~~GR~~R~g~~~~~~~~~~~  214 (237)
                      ..||....|.   ++                           ..+.|.+||+-|..++..++++++.
T Consensus       464 ~~viI~~lPfp~~dp~~~ar~~~~~~~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~  530 (551)
T 3crv_A          464 SDVVIVGIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDK  530 (551)
T ss_dssp             EEEEEESCCCCCCSHHHHHHHHHTTCCSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEESG
T ss_pred             eEEEEEcCCCCCCCHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEeeh
Confidence            7788766543   11                           1234888999887666556666653

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=95.97  E-value=0.017  Score=53.28  Aligned_cols=76  Identities=20%  Similarity=0.157  Sum_probs=63.1

Q ss_pred             CCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-cccccCCCCCcEEE
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-AARGLDIPHVKHVI  181 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~~~Gvdl~~~~~Vi  181 (237)
                      .+.+++|.+||+.-+.++.+.+.+    .++++..+||+++..++....+.+.+|..+|+|+|.. +...+.+.++.+||
T Consensus       416 ~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVV  495 (780)
T 1gm5_A          416 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVI  495 (780)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEE
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEE
Confidence            357899999999988877766653    4789999999999999999999999999999999965 34456778888776


Q ss_pred             E
Q psy15610        182 N  182 (237)
Q Consensus       182 ~  182 (237)
                      .
T Consensus       496 I  496 (780)
T 1gm5_A          496 I  496 (780)
T ss_dssp             E
T ss_pred             e
Confidence            5

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=95.31  E-value=0.043  Score=46.29  Aligned_cols=77  Identities=14%  Similarity=0.113  Sum_probs=62.9

Q ss_pred             cCCceEEEEeecccchHHHHHHHhh---CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccc----cccCCCCCc
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHH---HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA----RGLDIPHVK  178 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~---~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~----~Gvdl~~~~  178 (237)
                      .++.+++|.+|++.-+.++.+.+..   .++.+..++|+.+..++....+.+.++..+|+|+|+..-    .-+++..++
T Consensus        62 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~  141 (414)
T 3oiy_A           62 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFD  141 (414)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhcccccc
Confidence            3567899999999999999988887   578999999999999998889999999999999995321    124555677


Q ss_pred             EEEE
Q psy15610        179 HVIN  182 (237)
Q Consensus       179 ~Vi~  182 (237)
                      +||.
T Consensus       142 ~iVi  145 (414)
T 3oiy_A          142 FVFV  145 (414)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7664

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=94.48  E-value=0.018  Score=42.18  Aligned_cols=58  Identities=29%  Similarity=0.406  Sum_probs=46.9

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+.+..++.-.....         +|+||+++..++.+++.|...++.+..+|+.+.+..|.....
T Consensus        22 K~~~L~~ll~~~~~~~---------~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~   79 (163)
T 2hjv_A           22 KFSLLKDVLMTENPDS---------CIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMN   79 (163)
T ss_dssp             HHHHHHHHHHHHCCSS---------EEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCc---------EEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHH
Confidence            4455545555555545         899999999999999999999999999999999988876643

>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=94.34  E-value=0.019  Score=42.57  Aligned_cols=58  Identities=17%  Similarity=0.269  Sum_probs=47.0

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +-+.+..+++-....+         +|+||+++..++.++..|...++.+..+|+.+.+..|.....
T Consensus        21 K~~~L~~ll~~~~~~~---------~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~   78 (175)
T 2rb4_A           21 KYQALCNIYGSITIGQ---------AIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQ   78 (175)
T ss_dssp             HHHHHHHHHTTSCCSE---------EEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCC---------EEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHH
Confidence            3344555555555545         899999999999999999999999999999999998877644

>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=94.25  E-value=0.018  Score=42.61  Aligned_cols=58  Identities=28%  Similarity=0.385  Sum_probs=47.8

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+.+..+++-....+         +|+||+++..++.+++.|...++.+..+|+.+.+..|.....
T Consensus        18 K~~~L~~ll~~~~~~~---------~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~   75 (172)
T 1t5i_A           18 KNRKLFDLLDVLEFNQ---------VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQ   75 (172)
T ss_dssp             HHHHHHHHHHHSCCSS---------EEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCc---------EEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHH
Confidence            4455555555556555         899999999999999999999999999999999988877644

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=94.17  E-value=0.024  Score=41.53  Aligned_cols=58  Identities=22%  Similarity=0.390  Sum_probs=47.5

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+.+..+++-.....         +|+|++++..++.++..|...++.+..+|+.+.+..|.....
T Consensus        17 K~~~l~~ll~~~~~~~---------~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~   74 (165)
T 1fuk_A           17 KYECLTDLYDSISVTQ---------AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMK   74 (165)
T ss_dssp             HHHHHHHHHHHTTCSC---------EEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCC---------EEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHH
Confidence            4455555555555555         899999999999999999999999999999999988876644

>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=94.16  E-value=0.23  Score=47.79  Aligned_cols=77  Identities=21%  Similarity=0.187  Sum_probs=62.8

Q ss_pred             cCCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-cccccCCCCCcEE
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-AARGLDIPHVKHV  180 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~~~Gvdl~~~~~V  180 (237)
                      ..+.+++|.|||+.-+.++.+.+.+    .++.+..+++..+..++...++.+.+|..+|+|+|.. +...+.+.+..+|
T Consensus       650 ~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lv  729 (1151)
T 2eyq_A          650 DNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLL  729 (1151)
T ss_dssp             TTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEE
T ss_pred             HhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceE
Confidence            3467999999999988888777753    3678899999999999999999999999999999954 4445677777776


Q ss_pred             EE
Q psy15610        181 IN  182 (237)
Q Consensus       181 i~  182 (237)
                      |.
T Consensus       730 Ii  731 (1151)
T 2eyq_A          730 IV  731 (1151)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

>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=93.83  E-value=0.075  Score=46.78  Aligned_cols=97  Identities=19%  Similarity=0.255  Sum_probs=62.3

Q ss_pred             HHHHhhcceeEEEeec----cCCCCCceeEEEEeech-hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhh
Q psy15610          3 AKEFLYRYIFLAIGRV----GSTSENITQRIAWVDEQ-DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLH   77 (237)
Q Consensus         3 ~~~~l~~~~~i~~~~~----~~~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~   77 (237)
                      ++.++.+|..+.+...    ......+.+.+...+.. .+...+...+.... .......++|+||+|+..++.+++.|.
T Consensus       282 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~iVF~~s~~~~~~l~~~L~  360 (563)
T 3i5x_A          282 ANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSFLCSILK  360 (563)
T ss_dssp             TTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHH-HHTTTCCEEEEECSCHHHHHHHHHHHH
T ss_pred             HHHhcCCCceEEEeccCCCCccccccCceEEEECchhHhhHHHHHHHHHHHH-hhcCCCCcEEEEcCcHHHHHHHHHHHH
Confidence            4456666655544321    13345566666666542 33333332222211 111345689999999999999999998


Q ss_pred             hc---CCCceeecCCcchhhHHHHhh
Q psy15610         78 HH---GYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        78 ~~---~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      ..   ++.+..+|+.+.+..|..+..
T Consensus       361 ~~~~~~~~v~~~h~~~~~~~R~~~~~  386 (563)
T 3i5x_A          361 NEFKKDLPILEFHGKITQNKRTSLVK  386 (563)
T ss_dssp             HHHTTTSCEEEESTTSCHHHHHHHHH
T ss_pred             HhccCCceEEEecCCCCHHHHHHHHH
Confidence            87   899999999999999887754

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=93.58  E-value=0.13  Score=49.20  Aligned_cols=77  Identities=14%  Similarity=0.113  Sum_probs=63.2

Q ss_pred             cCCceEEEEeecccchHHHHHHHhh---CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccc----cccCCCCCc
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHH---HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA----RGLDIPHVK  178 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~---~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~----~Gvdl~~~~  178 (237)
                      .++.+++|.+||+.-+.++.+.+..   .++.+..+||+++..++....+.+.+|..+|+|+|+-.-    .-+++..+.
T Consensus       119 ~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~  198 (1104)
T 4ddu_A          119 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFD  198 (1104)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCS
T ss_pred             hcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcC
Confidence            4567899999999999999999987   467899999999998888899999999999999995311    114556777


Q ss_pred             EEEE
Q psy15610        179 HVIN  182 (237)
Q Consensus       179 ~Vi~  182 (237)
                      ++|.
T Consensus       199 ~lVi  202 (1104)
T 4ddu_A          199 FVFV  202 (1104)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7765

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=93.55  E-value=0.018  Score=43.49  Aligned_cols=57  Identities=28%  Similarity=0.437  Sum_probs=46.5

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+.+..++.-....          +|+||+++..++.++..|...++.+..+++.+.+..|.....
T Consensus        42 K~~~L~~~l~~~~~~----------~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~   98 (191)
T 2p6n_A           42 KMVYLLECLQKTPPP----------VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIE   98 (191)
T ss_dssp             HHHHHHHHHTTSCSC----------EEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCC----------EEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHH
Confidence            344454444445567          899999999999999999999999999999999988877644

>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=93.45  E-value=0.053  Score=41.57  Aligned_cols=56  Identities=32%  Similarity=0.431  Sum_probs=45.6

Q ss_pred             hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         36 DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        36 ~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+..+++......         +|+||+++..++.+++.|...++.+..+|+.+.+..|..+..
T Consensus        20 ~~l~~ll~~~~~~~---------~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~   75 (212)
T 3eaq_A           20 EVLSDLLYVASPDR---------AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLG   75 (212)
T ss_dssp             HHHHHHHHHHCCSC---------EEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCe---------EEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHH
Confidence            34444444554445         899999999999999999999999999999999998877744

>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=93.20  E-value=0.025  Score=42.42  Aligned_cols=58  Identities=59%  Similarity=0.816  Sum_probs=38.8

Q ss_pred             chhHHHHHHHhh-cCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLL-SSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll-~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+.+..+++-. ....         +|+||+++..++.+++.|...++.+..+++.+.+..|.....
T Consensus        32 K~~~L~~ll~~~~~~~k---------~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~   90 (185)
T 2jgn_A           32 KRSFLLDLLNATGKDSL---------TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALH   90 (185)
T ss_dssp             HHHHHHHHHHHC-CCSC---------EEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHH
T ss_pred             HHHHHHHHHHhcCCCCe---------EEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHH
Confidence            445555555555 3342         899999999999999999999999999999998887766543

>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=92.35  E-value=0.4  Score=36.35  Aligned_cols=72  Identities=26%  Similarity=0.333  Sum_probs=52.7

Q ss_pred             CceEEEEeecccchHHHHHHHhhC-----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----c-ccccCCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH-----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----A-ARGLDIPH  176 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~-~~Gvdl~~  176 (237)
                      ..+++|.++++..+.++.+.+...     +..+..++|+.+..+...   .+.++..+|+|+|..     + ...+++..
T Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~---~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~  158 (220)
T 1t6n_A           82 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE---VLKKNCPHIVVGTPGRILALARNKSLNLKH  158 (220)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHH---HHHHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHH---HHhcCCCCEEEeCHHHHHHHHHhCCCCccc
Confidence            348999999999999888777653     678999999988766543   345567799999952     1 22356677


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      ++++|.
T Consensus       159 ~~~lVi  164 (220)
T 1t6n_A          159 IKHFIL  164 (220)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            777665

>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=91.56  E-value=0.024  Score=41.75  Aligned_cols=40  Identities=28%  Similarity=0.528  Sum_probs=37.0

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHH
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   98 (237)
                      +|+||+++..++.+++.|...++.+..+|+.+.+..|...
T Consensus        33 ~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~   72 (170)
T 2yjt_D           33 SIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEA   72 (170)
Confidence            8999999999999999999999999999999988887765

>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=91.89  E-value=0.41  Score=41.88  Aligned_cols=59  Identities=19%  Similarity=0.286  Sum_probs=54.3

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA  166 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~  166 (237)
                      .+.++|.+|++.-+....+.+...++.+..++++.+..++......+..+..+++++|+
T Consensus        65 ~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tp  123 (523)
T 1oyw_A           65 NGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAP  123 (523)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECH
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            46799999999999999999999999999999999999999999999999999999985

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=91.31  E-value=0.12  Score=42.00  Aligned_cols=42  Identities=33%  Similarity=0.541  Sum_probs=39.4

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +|+||+|+..++.+++.|...++.+..+|+.+.+..+..+..
T Consensus        31 ~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~   72 (300)
T 3i32_A           31 AMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMG   72 (300)
T ss_dssp             EEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHH
T ss_pred             EEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHH
Confidence            899999999999999999999999999999999999887755

>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=91.23  E-value=0.42  Score=42.58  Aligned_cols=59  Identities=14%  Similarity=0.182  Sum_probs=53.2

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHh--hcCCCCEEEEcC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRF--RSGETPILVATA  166 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f--~~g~~~vlv~T~  166 (237)
                      .+.+||.+|++.-+....+.|...|+.+..++|+++..++..+...+  ..+..+|+++|+
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            46899999999999999999988899999999999999998888888  567899999996

>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=91.04  E-value=0.76  Score=35.48  Aligned_cols=71  Identities=18%  Similarity=0.201  Sum_probs=51.6

Q ss_pred             CceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----cc-cccCCCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----AA-RGLDIPHV  177 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~-~Gvdl~~~  177 (237)
                      +.+++|.+++++-+.++.+.+..    .++.+..++|+.+.......+..    ..+|+|+|+.     +. ..+++..+
T Consensus       102 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~~~~  177 (242)
T 3fe2_A          102 GPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLECGKTNLRRT  177 (242)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHTSCCCTTC
T ss_pred             CCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCCcccc
Confidence            56799999999988888776654    47889999999988766544432    4789999952     22 23467777


Q ss_pred             cEEEE
Q psy15610        178 KHVIN  182 (237)
Q Consensus       178 ~~Vi~  182 (237)
                      .++|.
T Consensus       178 ~~lVi  182 (242)
T 3fe2_A          178 TYLVL  182 (242)
T ss_dssp             CEEEE
T ss_pred             cEEEE
Confidence            77664

>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=90.19  E-value=0.11  Score=44.23  Aligned_cols=57  Identities=47%  Similarity=0.696  Sum_probs=47.2

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +..++..++.-....          +|+||+|+..++.+++.|...++.+..+|+++.+..|..+..
T Consensus       288 k~~~l~~~l~~~~~~----------~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~  344 (434)
T 2db3_A          288 KRSKLIEILSEQADG----------TIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALR  344 (434)
T ss_dssp             HHHHHHHHHHHCCTT----------EEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCC----------EEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHH
Confidence            445555555555566          799999999999999999999999999999999998887644

>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=89.29  E-value=1.2  Score=34.60  Aligned_cols=72  Identities=21%  Similarity=0.290  Sum_probs=51.4

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----cc--cccCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----AA--RGLDIP  175 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~--~Gvdl~  175 (237)
                      ...+++|.++++..+.++.+.+...    ++.+..++|+.+..+....+    .+..+|+|+|..     +.  .++++.
T Consensus       110 ~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~I~v~Tp~~l~~~l~~~~~~~l~  185 (249)
T 3ber_A          110 QRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL----AKKPHIIIATPGRLIDHLENTKGFNLR  185 (249)
T ss_dssp             CSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH----HTCCSEEEECHHHHHHHHHHSTTCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh----cCCCCEEEECHHHHHHHHHcCCCcCcc
Confidence            3457999999999888887776553    78889999998876544332    246789999942     11  345677


Q ss_pred             CCcEEEE
Q psy15610        176 HVKHVIN  182 (237)
Q Consensus       176 ~~~~Vi~  182 (237)
                      .++++|.
T Consensus       186 ~~~~lVi  192 (249)
T 3ber_A          186 ALKYLVM  192 (249)
T ss_dssp             TCCEEEE
T ss_pred             ccCEEEE
Confidence            7777665

>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=88.64  E-value=0.5  Score=43.53  Aligned_cols=89  Identities=8%  Similarity=0.061  Sum_probs=57.0

Q ss_pred             HHhhcceeEEEeeccCCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhh------
Q psy15610          5 EFLYRYIFLAIGRVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHH------   78 (237)
Q Consensus         5 ~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~------   78 (237)
                      +|+.++..+.+.   .....++++|...+..++....+..+.....  .....++|+|+++...++.+++.|..      
T Consensus       257 ~~~~~~~vi~v~---gr~~pv~~~~~~~~~~~~~~~~l~~l~~~~~--~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~  331 (773)
T 2xau_A          257 RYFNDAPLLAVP---GRTYPVELYYTPEFQRDYLDSAIRTVLQIHA--TEEAGDILLFLTGEDEIEDAVRKISLEGDQLV  331 (773)
T ss_dssp             HHTTSCCEEECC---CCCCCEEEECCSSCCSCHHHHHHHHHHHHHH--HSCSCEEEEECSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcCCCccccc---CcccceEEEEecCCchhHHHHHHHHHHHHHH--hcCCCCEEEECCCHHHHHHHHHHHHHHHHhhc
Confidence            455554445443   2224566666655555544333333222111  12356899999999999999999975      


Q ss_pred             -----cCCCceeecCCcchhhHHHH
Q psy15610         79 -----HGYPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        79 -----~~~~~~~~~~~~~~~~~~~~   98 (237)
                           .++.+..+|+.+.+..+..+
T Consensus       332 ~~~~~~~~~v~~lhg~l~~~eR~~v  356 (773)
T 2xau_A          332 REEGCGPLSVYPLYGSLPPHQQQRI  356 (773)
T ss_dssp             HHHCCCCEEEEEECTTCCHHHHGGG
T ss_pred             ccccCCCeEEEEeCCCCCHHHHHHH
Confidence                 56778999999998888766

>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=87.85  E-value=1.3  Score=40.60  Aligned_cols=131  Identities=15%  Similarity=0.189  Sum_probs=85.2

Q ss_pred             eccCCCCCcee-EEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhH
Q psy15610         17 RVGSTSENITQ-RIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKER   95 (237)
Q Consensus        17 ~~~~~~~~i~~-~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~   95 (237)
                      +.+.+...+.+ .++...+.+|...+.+.+....    ....++|+|++|+..++.+++.|...|++...+|+...+..+
T Consensus       438 Ptnkp~~R~d~~d~vy~t~~eK~~al~~~I~~~~----~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~  513 (822)
T 3jux_A          438 PTHKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRY----KKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEA  513 (822)
T ss_dssp             CCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHH----HHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHH
T ss_pred             CCCCCcceeecCcEEEecHHHHHHHHHHHHHHHh----hCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHH
Confidence            34444455555 3556677889999998887542    134689999999999999999999999999999998544444


Q ss_pred             HHHhhhhhhccCCceEEEEeecccchHHHHHHH----hhCCCceEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610         96 EEAQQYTLISCDEALTLVFVETKKGADQLEDFL----HHHGYPVTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus        96 ~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L----~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                      ..+.    .......  |.+.|.-.++.+.--|    .+.| ...+++..++...|.-+...=++|+
T Consensus       514 ~ii~----~ag~~g~--VtVATdmAgRGtDI~lg~~V~~~G-glhVInte~Pes~r~y~qriGRTGR  573 (822)
T 3jux_A          514 EIVA----KAGQKGM--VTIATNMAGRGTDIKLGPGVAELG-GLCIIGTERHESRRIDNQLRGRAGR  573 (822)
T ss_dssp             HHHH----HHHSTTC--EEEEETTTTTTCCCCCCTTTTTTT-SCEEEESSCCSSHHHHHHHHTTSSC
T ss_pred             HHHH----hCCCCCe--EEEEcchhhCCcCccCCcchhhcC-CCEEEecCCCCCHHHHHHhhCcccc
Confidence            3332    1222334  4445544333322111    1112 1268888888888877777777654

>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=87.54  E-value=1.4  Score=40.74  Aligned_cols=119  Identities=14%  Similarity=0.184  Sum_probs=80.9

Q ss_pred             EEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCC
Q psy15610         29 IAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDE  108 (237)
Q Consensus        29 ~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (237)
                      ++.+.+.+|...|.+++....    ....++|+||+|+..++.++..|...|+++..+|++..+..+..+.    .....
T Consensus       409 ~v~~~~~~K~~al~~~i~~~~----~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~----~ag~~  480 (844)
T 1tf5_A          409 LIYRTMEGKFKAVAEDVAQRY----MTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIE----EAGQK  480 (844)
T ss_dssp             EEESSHHHHHHHHHHHHHHHH----HHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHT----TTTST
T ss_pred             EEEeCHHHHHHHHHHHHHHHH----hcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHH----HcCCC
Confidence            455667889999998886431    1345799999999999999999999999999999998777765442    22223


Q ss_pred             ceEEEEeecccchHHHHHHH----hhCCCceEEEeCCCCHHHHHHHHHHhhcCC
Q psy15610        109 ALTLVFVETKKGADQLEDFL----HHHGYPVTSIHGDRTQKEREEALRRFRSGE  158 (237)
Q Consensus       109 ~~~iIF~~t~~~~~~l~~~L----~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~  158 (237)
                      ..  |.+.|.-.++.+.--+    .+.| ...+++-+++.+.+.-+...=++|+
T Consensus       481 g~--VlIATdmAgRG~DI~l~~~V~~~g-gl~VIn~d~p~s~r~y~hr~GRTGR  531 (844)
T 1tf5_A          481 GA--VTIATNMAGRGTDIKLGEGVKELG-GLAVVGTERHESRRIDNQLRGRSGR  531 (844)
T ss_dssp             TC--EEEEETTSSTTCCCCCCTTSGGGT-SEEEEESSCCSSHHHHHHHHTTSSG
T ss_pred             Ce--EEEeCCccccCcCccccchhhhcC-CcEEEEecCCCCHHHHHhhcCcccc
Confidence            34  4455544444332211    1111 2367888888888877777777664

>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=87.50  E-value=1.2  Score=33.91  Aligned_cols=72  Identities=18%  Similarity=0.212  Sum_probs=47.1

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC---CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc------cccccCCCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV------AARGLDIPHV  177 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~---~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~~Gvdl~~~  177 (237)
                      .+.+++|.++++.-+.++.+.+...   +..+..++|+.+.......   +. ...+|+|+|..      ....+++..+
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIED---IS-KGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHH---HH-SCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHH---hc-CCCCEEEECHHHHHHHHHcCCcCcccc
Confidence            4567999999999999998888763   6788888888776544332   22 34789999952      1224566777


Q ss_pred             cEEEE
Q psy15610        178 KHVIN  182 (237)
Q Consensus       178 ~~Vi~  182 (237)
                      +++|.
T Consensus       169 ~~lVi  173 (228)
T 3iuy_A          169 TYLVI  173 (228)
T ss_dssp             CEEEE
T ss_pred             eEEEE
Confidence            77665

>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=86.69  E-value=0.47  Score=39.46  Aligned_cols=42  Identities=24%  Similarity=0.380  Sum_probs=39.0

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +|+||++...++.+++.|...++.+..+|+.+.+..|.....
T Consensus       269 ~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~  310 (412)
T 3fht_A          269 AMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIE  310 (412)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHH
T ss_pred             EEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHH
Confidence            899999999999999999999999999999999988877644

>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=86.69  E-value=1.9  Score=31.99  Aligned_cols=71  Identities=24%  Similarity=0.201  Sum_probs=49.8

Q ss_pred             CceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----cc-cccCCCCCcE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----AA-RGLDIPHVKH  179 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~-~Gvdl~~~~~  179 (237)
                      +.+++|.++++..+.++.+.+...  ...+..++|+.+.......+.    ...+|+|+|..     +. ..+++...++
T Consensus        72 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~~~  147 (207)
T 2gxq_A           72 KPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL----RGADAVVATPGRALDYLRQGVLDLSRVEV  147 (207)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH----HCCSEEEECHHHHHHHHHHTSSCCTTCSE
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh----CCCCEEEECHHHHHHHHHcCCcchhhceE
Confidence            567999999999999998888765  467888898887654433322    25789999952     22 2345667777


Q ss_pred             EEE
Q psy15610        180 VIN  182 (237)
Q Consensus       180 Vi~  182 (237)
                      +|.
T Consensus       148 iVi  150 (207)
T 2gxq_A          148 AVL  150 (207)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            665

>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=86.25  E-value=1.4  Score=33.59  Aligned_cols=71  Identities=15%  Similarity=0.141  Sum_probs=50.8

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC-----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----c-ccccCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH-----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----A-ARGLDIP  175 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~-~~Gvdl~  175 (237)
                      .+.+++|.++++.-+.++.+.+...     ++.+..++|+.+..++....     ...+|+|+|..     + ...+++.
T Consensus        91 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~~l~~~~~~~~~~~~  165 (230)
T 2oxc_A           91 LSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPGRIKQLIELDYLNPG  165 (230)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHHHHHHHHHTTSSCGG
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHHHHHHHHhcCCcccc
Confidence            3568999999999999888877653     67889999998876654432     25789999953     1 1234566


Q ss_pred             CCcEEEE
Q psy15610        176 HVKHVIN  182 (237)
Q Consensus       176 ~~~~Vi~  182 (237)
                      .++++|.
T Consensus       166 ~~~~lVi  172 (230)
T 2oxc_A          166 SIRLFIL  172 (230)
T ss_dssp             GCCEEEE
T ss_pred             cCCEEEe
Confidence            6666664

>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=86.16  E-value=0.57  Score=38.59  Aligned_cols=56  Identities=34%  Similarity=0.463  Sum_probs=46.0

Q ss_pred             hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         36 DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        36 ~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+..+........         +|+|++++..++.+++.|...++.+..+|+.+.+..|.....
T Consensus       232 ~~l~~~~~~~~~~~---------~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~  287 (395)
T 3pey_A          232 DVLTELYGLMTIGS---------SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLID  287 (395)
T ss_dssp             HHHHHHHTTTTSSE---------EEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHhccCCC---------EEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHH
Confidence            44445555555555         899999999999999999999999999999999988877644

>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=86.05  E-value=0.4  Score=39.98  Aligned_cols=56  Identities=29%  Similarity=0.538  Sum_probs=42.8

Q ss_pred             hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         36 DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        36 ~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+..+..-.....         +|+|+++...++.+++.|...++.+..+|+.+.+..|..+..
T Consensus       269 ~~l~~~~~~~~~~~---------~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~  324 (414)
T 3eiq_A          269 DTLCDLYETLTITQ---------AVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMR  324 (414)
T ss_dssp             HHHHHHHHSSCCSS---------CEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCc---------EEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHH
Confidence            44545555555445         899999999999999999999999999999999988877643

>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=85.79  E-value=0.45  Score=39.74  Aligned_cols=42  Identities=36%  Similarity=0.617  Sum_probs=38.8

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +|+||+++..++.+++.|...++.+..+|+.+.+..|.....
T Consensus       279 ~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~  320 (410)
T 2j0s_A          279 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMK  320 (410)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHH
T ss_pred             EEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHH
Confidence            899999999999999999999999999999999988876644

>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=85.66  E-value=2  Score=33.28  Aligned_cols=71  Identities=14%  Similarity=0.102  Sum_probs=48.7

Q ss_pred             CceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----cc-cccCCCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----AA-RGLDIPHV  177 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~-~Gvdl~~~  177 (237)
                      +.+++|.+++++.+.++.+.+..    .+..+..++|+.+.......+    ....+|+|+|..     +. ..+++..+
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~  175 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV----QMGCHLLVATPGRLVDFIEKNKISLEFC  175 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHH----SSCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh----CCCCCEEEECHHHHHHHHHcCCCChhhC
Confidence            35899999999998888777654    356788889888765443222    246789999952     11 23466677


Q ss_pred             cEEEE
Q psy15610        178 KHVIN  182 (237)
Q Consensus       178 ~~Vi~  182 (237)
                      +++|.
T Consensus       176 ~~lVi  180 (253)
T 1wrb_A          176 KYIVL  180 (253)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            77664

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=85.18  E-value=1.4  Score=33.70  Aligned_cols=71  Identities=20%  Similarity=0.231  Sum_probs=48.0

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----ccc--ccCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----AAR--GLDIP  175 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~~--Gvdl~  175 (237)
                      ++.+++|.+|++..+.++.+.+...    +..+..++|+.+........     +..+|+|+|..     +..  .+++.
T Consensus        96 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~~~  170 (236)
T 2pl3_A           96 DGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFHAT  170 (236)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCcccc
Confidence            3568999999999998888877654    47888999987765443322     36789999952     222  35566


Q ss_pred             CCcEEEE
Q psy15610        176 HVKHVIN  182 (237)
Q Consensus       176 ~~~~Vi~  182 (237)
                      .++++|.
T Consensus       171 ~~~~lVi  177 (236)
T 2pl3_A          171 DLQMLVL  177 (236)
T ss_dssp             TCCEEEE
T ss_pred             cccEEEE
Confidence            6766664

>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=84.87  E-value=1.5  Score=33.61  Aligned_cols=73  Identities=19%  Similarity=0.295  Sum_probs=44.0

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC-----cccc-ccCCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATA-----VAAR-GLDIPH  176 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~-Gvdl~~  176 (237)
                      .+.+++|.++++..+.++.+.+...    +..+..++|+.+....   ...+..+..+|+|+|.     .+.. .+++..
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~  173 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNE---MQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKW  173 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSCSTT
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHH---HHHHhcCCCCEEEECHHHHHHHHHhCCcCccc
Confidence            4568999999999999888887653    5677778887654332   2345566789999994     2223 345666


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      ++++|.
T Consensus       174 ~~~lVi  179 (237)
T 3bor_A          174 IKMFVL  179 (237)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            776664

>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=84.68  E-value=0.65  Score=38.31  Aligned_cols=58  Identities=28%  Similarity=0.385  Sum_probs=47.8

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+.+..++.......         +|+|+++...++.+++.|...++.+..+|+.+.+..|.....
T Consensus       237 ~~~~l~~~l~~~~~~~---------~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~  294 (391)
T 1xti_A          237 KNRKLFDLLDVLEFNQ---------VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQ  294 (391)
T ss_dssp             HHHHHHHHHHHSCCSE---------EEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCc---------EEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHH
Confidence            3455555666666656         899999999999999999999999999999999888876644

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=84.36  E-value=0.63  Score=37.92  Aligned_cols=42  Identities=36%  Similarity=0.637  Sum_probs=38.3

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +|+||++...++.+++.|...++.+..+|+.+.+..|.....
T Consensus       241 ~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~  282 (367)
T 1hv8_A          241 GLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIR  282 (367)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHH
T ss_pred             EEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHH
Confidence            799999999999999999999999999999999888876644

>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=83.91  E-value=3.5  Score=32.19  Aligned_cols=72  Identities=19%  Similarity=0.218  Sum_probs=50.7

Q ss_pred             CCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC-----ccc--cccCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA-----VAA--RGLDIP  175 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~--~Gvdl~  175 (237)
                      .+.+++|.+|++.-+.++.+.+..    .+..+..+.|+.+.......   +..+ .+|+|+|+     .+.  .++++.
T Consensus       125 ~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~-~~Iiv~Tp~~l~~~~~~~~~~~~~  200 (262)
T 3ly5_A          125 NGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQK---LGNG-INIIVATPGRLLDHMQNTPGFMYK  200 (262)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHH---HHHC-CSEEEECHHHHHHHHHHCTTCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHH---hcCC-CCEEEEcHHHHHHHHHccCCcccc
Confidence            467799999999999888777765    36678888998876654433   3333 78999994     121  245677


Q ss_pred             CCcEEEE
Q psy15610        176 HVKHVIN  182 (237)
Q Consensus       176 ~~~~Vi~  182 (237)
                      .+.++|.
T Consensus       201 ~l~~lVi  207 (262)
T 3ly5_A          201 NLQCLVI  207 (262)
T ss_dssp             TCCEEEE
T ss_pred             cCCEEEE
Confidence            7777664

>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=83.61  E-value=0.68  Score=41.79  Aligned_cols=40  Identities=20%  Similarity=0.193  Sum_probs=37.1

Q ss_pred             cccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhh
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKE   94 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~   94 (237)
                      ...++|+|++|+..++.+++.|...++.+..+|+.+.+..
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e  434 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV  434 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH
Confidence            4568999999999999999999999999999999998875

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=83.17  E-value=0.42  Score=42.25  Aligned_cols=98  Identities=19%  Similarity=0.266  Sum_probs=63.5

Q ss_pred             hHHHHhhcceeEEEeec----cCCCCCceeEEEEeech-hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHh
Q psy15610          2 LAKEFLYRYIFLAIGRV----GSTSENITQRIAWVDEQ-DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFL   76 (237)
Q Consensus         2 ~~~~~l~~~~~i~~~~~----~~~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l   76 (237)
                      +++.++.+|..+.+...    ......+.+.+...+.. .+...+...+.... .......++|+||+|+..++.+++.|
T Consensus       230 ~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~iVF~~t~~~~~~l~~~L  308 (579)
T 3sqw_A          230 LANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQI-KERDSNYKAIIFAPTVKFTSFLCSIL  308 (579)
T ss_dssp             HTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHH-HHTTTCCEEEEECSSHHHHHHHHHHH
T ss_pred             HHHHHcCCCceEEEeecCccccccccccceEEEEecchhhhHHHHHHHHHHHH-hhcCCCCcEEEECCcHHHHHHHHHHH
Confidence            34566676655554321    13345666666666542 23322222222211 11134568999999999999999999


Q ss_pred             hhc---CCCceeecCCcchhhHHHHhh
Q psy15610         77 HHH---GYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        77 ~~~---~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      ...   ++.+..+|+.+.+..|.....
T Consensus       309 ~~~~~~~~~v~~~hg~~~~~~R~~~~~  335 (579)
T 3sqw_A          309 KNEFKKDLPILEFHGKITQNKRTSLVK  335 (579)
T ss_dssp             HHHHTTTSCEEEESTTSCHHHHHHHHH
T ss_pred             HHhhcCCCcEEEecCCCCHHHHHHHHH
Confidence            887   899999999999998887755

>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=83.07  E-value=2.6  Score=31.25  Aligned_cols=71  Identities=17%  Similarity=0.226  Sum_probs=49.3

Q ss_pred             CceEEEEeecccchHHHHHHHhhC-----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----ccc-ccCCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH-----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----AAR-GLDIPH  176 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~~-Gvdl~~  176 (237)
                      +.+++|.++++..+.++.+.+...     +..+..++|+.+..+....   + .+..+|+|+|..     +.. ..++..
T Consensus        71 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~i~v~T~~~l~~~~~~~~~~~~~  146 (206)
T 1vec_A           71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR---L-DDTVHVVIATPGRILDLIKKGVAKVDH  146 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH---T-TSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHh---c-CCCCCEEEeCHHHHHHHHHcCCcCccc
Confidence            457999999999988887777543     5778889999887654322   2 346789999952     222 335666


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      ++++|.
T Consensus       147 ~~~lVi  152 (206)
T 1vec_A          147 VQMIVL  152 (206)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            777664

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=82.98  E-value=0.69  Score=38.38  Aligned_cols=57  Identities=18%  Similarity=0.274  Sum_probs=46.4

Q ss_pred             hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         35 QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        35 ~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      ...+..+++......         +|+||++...++.+++.|...++.+..+|+.+.+..|.....
T Consensus       246 ~~~l~~~~~~~~~~~---------~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~  302 (400)
T 1s2m_A          246 LHCLNTLFSKLQINQ---------AIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFH  302 (400)
T ss_dssp             HHHHHHHHHHSCCSE---------EEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHhhcCCCc---------EEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHH
Confidence            344555555555545         899999999999999999999999999999999888876644

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=82.58  E-value=0.66  Score=38.69  Aligned_cols=42  Identities=76%  Similarity=1.134  Sum_probs=38.8

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +|+|+++...++.+++.|...++.+..+|+.+.+..|.....
T Consensus       279 ~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~  320 (417)
T 2i4i_A          279 TLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALH  320 (417)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             EEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHH
Confidence            899999999999999999999999999999999988876644

>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=82.33  E-value=0.26  Score=42.35  Aligned_cols=40  Identities=25%  Similarity=0.400  Sum_probs=0.0

Q ss_pred             eeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHH
Q psy15610         59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        59 ~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   98 (237)
                      +|+||+++..++.+++.|...++.+..+|+.+.+..|..+
T Consensus       336 ~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~  375 (479)
T 3fmp_B          336 AMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAV  375 (479)
T ss_dssp             ----------------------------------------
T ss_pred             eEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHH
Confidence            7999999999999999999999999999999998888665

>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=82.07  E-value=0.89  Score=41.07  Aligned_cols=62  Identities=23%  Similarity=0.277  Sum_probs=48.2

Q ss_pred             hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         35 QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        35 ~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      ..+...+...|....    ..+.++|+||+|+..++.+++.|...++.+..+|+++.+..|..+..
T Consensus       422 ~~~~~~Ll~~l~~~~----~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~  483 (664)
T 1c4o_A          422 ENQILDLMEGIRERA----ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIR  483 (664)
T ss_dssp             TTHHHHHHHHHHHHH----HTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHH----hcCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHH
Confidence            345555554443321    23468999999999999999999999999999999999998877754

>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=82.03  E-value=1.8  Score=41.25  Aligned_cols=74  Identities=16%  Similarity=0.261  Sum_probs=55.4

Q ss_pred             CCceEEEEeecccchHHHHHHHhh----CCC----ceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-ccccc-CCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH----HGY----PVTSIHGDRTQKEREEALRRFRSGETPILVATAV-AARGL-DIPH  176 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~----~~~----~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~~~Gv-dl~~  176 (237)
                      .+.+++|.+||+.-+.++.+.+..    .++    .+..++|+.+..++....+.+++  .+|+|+|+- +..-+ ++..
T Consensus        98 ~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~L~~  175 (1054)
T 1gku_B           98 KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRELGH  175 (1054)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTTSCC
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHHhcc
Confidence            467899999999998888777754    356    78999999999988888888877  899999952 11111 1556


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      ++++|.
T Consensus       176 l~~lVi  181 (1054)
T 1gku_B          176 FDFIFV  181 (1054)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            666664

>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=81.83  E-value=1.5  Score=33.06  Aligned_cols=71  Identities=21%  Similarity=0.251  Sum_probs=43.4

Q ss_pred             CCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCcc------ccccCCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA------ARGLDIPH  176 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~------~~Gvdl~~  176 (237)
                      .+.+++|.++++..+.++.+.+..    .+..+..++|+.+..+....   +.  ..+|+|+|...      ....++..
T Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~--~~~iiv~Tp~~l~~~~~~~~~~~~~  155 (224)
T 1qde_A           81 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG---LR--DAQIVVGTPGRVFDNIQRRRFRTDK  155 (224)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-------------CT--TCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhc---CC--CCCEEEECHHHHHHHHHhCCcchhh
Confidence            356899999999998888777654    36788889998766544322   22  27899999521      23445666


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      ++++|.
T Consensus       156 ~~~iVi  161 (224)
T 1qde_A          156 IKMFIL  161 (224)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            776664

>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=81.42  E-value=0.75  Score=41.51  Aligned_cols=62  Identities=24%  Similarity=0.312  Sum_probs=47.6

Q ss_pred             hhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         35 QDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        35 ~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      ..+...+...|...    ...+.++|+||+|+..++.+++.|...++++..+|+++.+..|..+..
T Consensus       428 ~~~~~~Ll~~l~~~----~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~  489 (661)
T 2d7d_A          428 EGQIDDLIGEIQAR----IERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIR  489 (661)
T ss_dssp             TTHHHHHHHHHHHH----HTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHH
T ss_pred             cchHHHHHHHHHHH----HhcCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHH
Confidence            34444454444332    123458999999999999999999999999999999999988877754

>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=80.13  E-value=2.2  Score=39.40  Aligned_cols=66  Identities=11%  Similarity=0.165  Sum_probs=53.4

Q ss_pred             EEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHH
Q psy15610         29 IAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA   98 (237)
Q Consensus        29 ~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   98 (237)
                      ++.+.+.+|...+.+++....    ....++|+||+|+...+.+++.|...|++...++++..+..+..+
T Consensus       418 ~v~~~~~~K~~al~~~i~~~~----~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~ii  483 (853)
T 2fsf_A          418 LVYMTEAEKIQAIIEDIKERT----AKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIV  483 (853)
T ss_dssp             EEESSHHHHHHHHHHHHHHHH----TTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHH
T ss_pred             EEEeCHHHHHHHHHHHHHHHh----cCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHH
Confidence            355677889999998885431    134579999999999999999999999999999999766665544

>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=80.06  E-value=0.54  Score=42.41  Aligned_cols=45  Identities=24%  Similarity=0.421  Sum_probs=38.2

Q ss_pred             ccceeEEeecccchhhHHHHhhhc------CCCceeecCC--------cchhhHHHHhh
Q psy15610         56 EALTLVFVETKKGADQLEDFLHHH------GYPVTSIHGD--------RTQKEREEAQQ  100 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~~~~~~l~~~------~~~~~~~~~~--------~~~~~~~~~~~  100 (237)
                      +.++|+|++++..++.++++|...      |+.+..+|+.        +.+..|..+..
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~  458 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVIS  458 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHH
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHH
Confidence            688999999999999999999987      8999999999        88888887755

---

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	237
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	2e-35
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	7e-25
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	8e-25
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	2e-17
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	7e-17
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	7e-17
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-16
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-16
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	2e-13
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	5e-13
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	8e-13
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	4e-12
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	5e-12
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	9e-10
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	1e-09
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	2e-08
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	1e-06
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	3e-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 =  125 bits (316), Expect = 2e-35
 Identities = 20/104 (19%), Positives = 32/104 (30%), Gaps = 13/104 (12%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKER----------EEALRRFRSGETP 160
            L+F  +KK  D+L   L   G    + +                   +AL    +G+  
Sbjct: 39  HLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFD 98

Query: 161 ILVATAVAARG---LDIPHVKHVINFDLPSDVEEYVHRIGRTGR 201
            ++             +     +    LP D      R GRTGR
Sbjct: 99  SVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGR 142

>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 = 97.3 bits (241), Expect = 7e-25
 Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 8/102 (7%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQ--------KEREEALRRFRSGETPIL 162
            +VF   ++ A ++ + L   G       G  ++        +E++  L  F  GE  +L
Sbjct: 164 IIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVL 223

Query: 163 VATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           VAT+V   GLD+P V  V+ ++        + R GRTGR   
Sbjct: 224 VATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP 265

>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 = 96.4 bits (239), Expect = 8e-25
 Identities = 16/98 (16%), Positives = 35/98 (35%), Gaps = 15/98 (15%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA---- 166
            +++  T + A+++ + L +                ++    +F  GE   L+ TA    
Sbjct: 28  GIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYG 81

Query: 167 VAARGLDIPH-VKHVINFDLPSDVEEYVHRIGRTGRMG 203
              RGLD+P  ++  +    P     +   I     + 
Sbjct: 82  TLVRGLDLPERIRFAVFVGCP----SFRVTIEDIDSLS 115

>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 = 75.2 bits (184), Expect = 2e-17
 Identities = 30/93 (32%), Positives = 39/93 (41%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           TLV   TKK A+ L D+L   G  V  +H +    ER E +R  R G+  +LV   +   
Sbjct: 34  TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 93

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
           GLDIP V  V   D   +      R        
Sbjct: 94  GLDIPEVSLVAILDADKEGFLRSERSLIQTIGR 126

>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 = 74.2 bits (181), Expect = 7e-17
 Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 5/94 (5%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            ++F    +   +         + + +I    +++EREE L  FR+G    +V++ V   
Sbjct: 96  IIIFTRHNELVYR-----ISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDE 150

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           G+D+P     +         EY+ R+GR  R   
Sbjct: 151 GIDVPDANVGVIMSGSGSAREYIQRLGRILRPSK 184

>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 = 72.4 bits (177), Expect = 7e-17
 Identities = 20/94 (21%), Positives = 30/94 (31%), Gaps = 10/94 (10%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            L+F  +KK  D+L   L   G    + +                +    ++VAT     
Sbjct: 38  HLIFCHSKKKCDELAAKLVALGINAVAYYRGLDV-------SVIPTNGDVVVVATDALMT 90

Query: 171 GLDIPH---VKHVINFDLPSDVEEYVHRIGRTGR 201
           G        +    +   P D      R GRTGR
Sbjct: 91  GFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR 124

>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 = 75.0 bits (183), Expect = 2e-16
 Identities = 24/151 (15%), Positives = 47/151 (31%), Gaps = 25/151 (16%)

Query: 73  EDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHG 132
            D       P+     +  ++      ++  ++  +  T+ FV + K  + +   L  +G
Sbjct: 145 RDPFPQSNAPIMDEEREIPERSWNSGHEW--VTDFKGKTVWFVPSIKAGNDIAACLRKNG 202

Query: 133 YPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP---------HVKHVINF 183
             V  +       E      + R+ +   +V T ++  G +            +K VI  
Sbjct: 203 KKVIQLSRKTFDSEYI----KTRTNDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILT 258

Query: 184 DLPSDVE----------EYVHRIGRTGRMGN 204
           D    V               R GR GR   
Sbjct: 259 DGEERVILAGPMPVTHSSAAQRRGRVGRNPK 289

>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 = 71.1 bits (173), Expect = 4e-16
 Identities = 38/94 (40%), Positives = 63/94 (67%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            ++F  T++  ++L   L +  + V++I+ D  Q+ER+  ++ FRSG + IL++T + AR
Sbjct: 30  AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLAR 89

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           G+D+  V  VIN+DLP++ E Y+HRIGR GR G 
Sbjct: 90  GIDVQQVSLVINYDLPANKENYIHRIGRGGRFGR 123

>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 = 63.8 bits (154), Expect = 2e-13
 Identities = 43/104 (41%), Positives = 63/104 (60%)

Query: 101 YTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP 160
             L+   E   LVF +TK+   +L   L   G+   +IHGD +Q +RE+ +R F+  +  
Sbjct: 21  CRLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIR 80

Query: 161 ILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
           IL+AT V +RG+D+  +  VIN+ LP + E Y+HRIGRTGR G 
Sbjct: 81  ILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGK 124

>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 = 62.8 bits (152), Expect = 5e-13
 Identities = 30/99 (30%), Positives = 40/99 (40%), Gaps = 5/99 (5%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
           TLV V T + A++L  FL  HG     +H +    +R+  +R  R G    LV   +   
Sbjct: 34  TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLRE 93

Query: 171 GLDIPHVKHVINFDL-----PSDVEEYVHRIGRTGRMGN 204
           GLDIP V  V   D             +  IGR  R   
Sbjct: 94  GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR 132

>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 = 63.1 bits (152), Expect = 8e-13
 Identities = 22/92 (23%), Positives = 43/92 (46%)

Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
            +++  ++   +     L   G    + H       R +   +F+  +  I+VAT     
Sbjct: 33  GIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGM 92

Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRM 202
           G++ P+V+ V++FD+P ++E Y    GR GR 
Sbjct: 93  GINKPNVRFVVHFDIPRNIESYYQETGRAGRD 124

>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 = 61.1 bits (147), Expect = 4e-12
 Identities = 33/195 (16%), Positives = 60/195 (30%), Gaps = 33/195 (16%)

Query: 17  RVGSTSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFL 76
             G   E   +         +R    +L+    +E + +    LVF  T++GA++    L
Sbjct: 5   VEGVLCEGTLELFDGAFSTSRRVKFEELV----EECVAENGGVLVFESTRRGAEKTAVKL 60

Query: 77  HHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVT 136
                          +    E  +  ++  +E             +              
Sbjct: 61  SAITA----------KYVENEGLEKAILEENEG------------EMSRKLAECVRKGAA 98

Query: 137 SIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI-------NFDLPSDV 189
             H      +R      FR G   ++VAT   A G+++P  + ++        +     V
Sbjct: 99  FHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKV 158

Query: 190 EEYVHRIGRTGRMGN 204
            EY    GR GR G 
Sbjct: 159 SEYKQMAGRAGRPGM 173

>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 = 60.0 bits (144), Expect = 5e-12
 Identities = 52/115 (45%), Positives = 75/115 (65%), Gaps = 4/115 (3%)

Query: 94  EREEAQQYTLISCDEALT----LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
           EREE +  TL    + LT    ++F  TK+  D L + +    + V+S+HGD  QKERE 
Sbjct: 16  EREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 75

Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
            ++ FRSG + +L++T V ARGLD+P V  +IN+DLP++ E Y+HRIGR+GR G 
Sbjct: 76  IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGR 130

>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 = 55.0 bits (132), Expect = 1e-09
 Identities = 17/117 (14%), Positives = 39/117 (33%), Gaps = 7/117 (5%)

Query: 81  YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHG 140
             +  +  D   +       +  I  D+  T  F+ + + A+ +   L   G  V  ++ 
Sbjct: 11  GEIEDVQTDIPSEPWNTG--HDWILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR 68

Query: 141 DRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIG 197
               K  E      +  +   ++AT +A  G ++  V+ V++               
Sbjct: 69  ----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRK 120

>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 = 51.0 bits (121), Expect = 2e-08
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 129 HHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSD 188
               + +  +HG  +Q+E++  +  F  G   ILV+T V   G+D+P    ++  +    
Sbjct: 61  VFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERF 120

Query: 189 VEEYVHR-IGRTGRM 202
               +H+  GR GR 
Sbjct: 121 GLAQLHQLRGRVGRG 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 = 44.9 bits (106), Expect = 1e-06
 Identities = 26/132 (19%), Positives = 48/132 (36%), Gaps = 12/132 (9%)

Query: 90  RTQKEREEAQQYTLISCDEAL--TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKER 147
           RT + + +A    +          LV     + ++ +   L + G P   ++    ++E 
Sbjct: 14  RTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREA 73

Query: 148 EEALRRFRSGETPILVATAVAARGLDI---PHVK-----HVINFDLPSDVEEYVHRIGRT 199
           +      + G   + +AT +A RG DI     VK      V+  +            GR+
Sbjct: 74  QIIEEAGQKGA--VTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRS 131

Query: 200 GRMGNLDFPFSY 211
           GR G+      Y
Sbjct: 132 GRQGDPGITQFY 143

>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 = 38.1 bits (87), Expect = 3e-04
 Identities = 44/184 (23%), Positives = 61/184 (33%), Gaps = 58/184 (31%)

Query: 21  TSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHG 80
           T + ITQ  A+V+E+ K  CL  L S     +       ++F  +    + L   +   G
Sbjct: 3   TLKGITQYYAFVEERQKLHCLNTLFSKLQINQ------AIIFCNSTNRVELLAKKITDLG 56

Query: 81  YPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHG 140
           Y     H    Q+ER +                                  G   T +  
Sbjct: 57  YSCYYSHARMKQQERNKVFHE---------------------------FRQGKVRTLVCS 89

Query: 141 DRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTG 200
           D                            RG+DI  V  VINFD P   E Y+HRIGR+G
Sbjct: 90  DL-------------------------LTRGIDIQAVNVVINFDFPKTAETYLHRIGRSG 124

Query: 201 RMGN 204
           R G+
Sbjct: 125 RFGH 128

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	237
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	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
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.98
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.97
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.97
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.96
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.93
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.93
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.9
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.88
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.86
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.83
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.83
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.79
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.79
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.79
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.73
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.69
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.56
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.55
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.44
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.88
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.74
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.48
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	97.06
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	95.82
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	95.79
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	95.77
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	95.72
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	95.5
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.41
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	95.3
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	94.76
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	94.22
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	92.5
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	92.25
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	90.61
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	89.04
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	88.64
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	84.38
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	81.34
d1urha2	120	3-mercaptopyruvate sulfurtransferase {Escherichia	80.58

>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=4.1e-33  Score=209.70  Aligned_cols=143  Identities=37%  Similarity=0.586  Sum_probs=134.0

Q ss_pred             ccCCCCCceeEEEEeech-hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHH
Q psy15610         18 VGSTSENITQRIAWVDEQ-DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKERE   96 (237)
Q Consensus        18 ~~~~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   96 (237)
                      |+.++++|+|+|+.+++. +|+..|.++++...                                               
T Consensus         1 ~~~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~-----------------------------------------------   33 (168)
T d2j0sa2           1 DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT-----------------------------------------------   33 (168)
T ss_dssp             GGCSCTTEEEEEEEESSTTHHHHHHHHHHHHHT-----------------------------------------------
T ss_pred             CCCCCCCcEEEEEEecChHHHHHHHHHHHHhCC-----------------------------------------------
Confidence            356789999999999875 59999999997653                                               


Q ss_pred             HHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCC
Q psy15610         97 EAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPH  176 (237)
Q Consensus        97 ~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~  176 (237)
                                 ..++||||+++..++.++..|...++.+..+||+++..+|..+++.|++|..++||||+++++|+|+|+
T Consensus        34 -----------~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~~rGiDi~~  102 (168)
T d2j0sa2          34 -----------ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQ  102 (168)
T ss_dssp             -----------SSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTT
T ss_pred             -----------CCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchhcccccccC
Confidence                       579999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        177 VKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       177 ~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      +++||+||+|+++..|+||+||+||.|+.|.+++|+.+.+..
T Consensus       103 v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~  144 (168)
T d2j0sa2         103 VSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIR  144 (168)
T ss_dssp             EEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHH
T ss_pred             cceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHH
Confidence            999999999999999999999999999999999999887653

>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=6.3e-33  Score=209.61  Aligned_cols=143  Identities=33%  Similarity=0.538  Sum_probs=134.9

Q ss_pred             CCCCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHh
Q psy15610         20 STSENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQ   99 (237)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   99 (237)
                      .++.+|+|+|+.+++++|+..|.++|+...                                                  
T Consensus         2 ~tl~~i~q~yi~v~~~~K~~~L~~ll~~~~--------------------------------------------------   31 (171)
T d1s2ma2           2 LTLKGITQYYAFVEERQKLHCLNTLFSKLQ--------------------------------------------------   31 (171)
T ss_dssp             CBCTTEEEEEEECCGGGHHHHHHHHHHHSC--------------------------------------------------
T ss_pred             CCccceEEEEEEcCHHHHHHHHHHHHHhCC--------------------------------------------------
Confidence            467889999999999999999999998653                                                  


Q ss_pred             hhhhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcE
Q psy15610        100 QYTLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKH  179 (237)
Q Consensus       100 ~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~  179 (237)
                              ..++||||++++.++.++.+|...|+.+..+||+++..+|.++++.|++|..++||||+++++|+|+|++++
T Consensus        32 --------~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~~~Gid~~~v~~  103 (171)
T d1s2ma2          32 --------INQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNV  103 (171)
T ss_dssp             --------CSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEE
T ss_pred             --------CCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccchhHhhhccccceeEE
Confidence                    579999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCCCC
Q psy15610        180 VINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSY  220 (237)
Q Consensus       180 Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~~~  220 (237)
                      ||+||+|+++..|+||+||+||.|+.|.++.|+.+.+...+
T Consensus       104 VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~  144 (171)
T d1s2ma2         104 VINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNL  144 (171)
T ss_dssp             EEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHH
T ss_pred             EEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHH
Confidence            99999999999999999999999999999999998765443

>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=1.3e-32  Score=204.61  Aligned_cols=137  Identities=37%  Similarity=0.592  Sum_probs=130.7

Q ss_pred             CCCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhh
Q psy15610         22 SENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQY  101 (237)
Q Consensus        22 ~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  101 (237)
                      +.+|+|+|+.+++.+|+..|.++|+..                                                     
T Consensus         1 n~nI~~~~i~v~~~~K~~~L~~ll~~~-----------------------------------------------------   27 (155)
T d1hv8a2           1 NANIEQSYVEVNENERFEALCRLLKNK-----------------------------------------------------   27 (155)
T ss_dssp             SSSSEEEEEECCGGGHHHHHHHHHCST-----------------------------------------------------
T ss_pred             CCCeEEEEEEeChHHHHHHHHHHHccC-----------------------------------------------------
Confidence            368999999999999999999999875                                                     


Q ss_pred             hhhccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEE
Q psy15610        102 TLISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI  181 (237)
Q Consensus       102 ~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi  181 (237)
                            +.++||||++++.++.++..|...++.+..+||++++.+|..+++.|++|..++||||+++++|+|+|.+++||
T Consensus        28 ------~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~~~Gid~~~v~~Vi  101 (155)
T d1hv8a2          28 ------EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVI  101 (155)
T ss_dssp             ------TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEE
T ss_pred             ------CCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccceeeeehhHHhhhhhhccCcEEE
Confidence                  46899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        182 NFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       182 ~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      +|++|+|+..|+||+||+||.|++|.+++|+.+.+.
T Consensus       102 ~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~  137 (155)
T d1hv8a2         102 NYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREY  137 (155)
T ss_dssp             ESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSH
T ss_pred             EecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHH
Confidence            999999999999999999999999999999987654

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.98  E-value=2.5e-32  Score=204.25  Aligned_cols=136  Identities=37%  Similarity=0.646  Sum_probs=123.0

Q ss_pred             ceeEEEEeechh-HHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhh
Q psy15610         25 ITQRIAWVDEQD-KRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTL  103 (237)
Q Consensus        25 i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (237)
                      |+|+|+.+++.+ |+..|.++++...                                                      
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~~~------------------------------------------------------   26 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDSIS------------------------------------------------------   26 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHHTT------------------------------------------------------
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHhCC------------------------------------------------------
Confidence            689999998655 9999999997653                                                      


Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEe
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                          ..++||||+++..++.++..|...++.+..+||+++..+|..+++.|++|..++||||+++++|+|+|++++||+|
T Consensus        27 ----~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~rGiDi~~v~~VI~~  102 (162)
T d1fuka_          27 ----VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINY  102 (162)
T ss_dssp             ----CSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEEES
T ss_pred             ----CCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeeccccccccccCCCceEEEEe
Confidence                5789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      |+|++++.|+||+||+||.|+.|.++.|+.+.+..
T Consensus       103 d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~  137 (162)
T d1fuka_         103 DLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVG  137 (162)
T ss_dssp             SCCSSGGGGGGSSCSCC-----CEEEEEEETTTHH
T ss_pred             ccchhHHHHHhhccccccCCCccEEEEEcCHHHHH
Confidence            99999999999999999999999999999877643

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.2e-31  Score=200.35  Aligned_cols=134  Identities=28%  Similarity=0.518  Sum_probs=128.0

Q ss_pred             CceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhh
Q psy15610         24 NITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTL  103 (237)
Q Consensus        24 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (237)
                      +|+|+|+.+.+++|+..|.++|....                                                      
T Consensus         1 ~l~q~~v~~~~~~K~~~L~~ll~~~~------------------------------------------------------   26 (168)
T d1t5ia_           1 GLQQYYVKLKDNEKNRKLFDLLDVLE------------------------------------------------------   26 (168)
T ss_dssp             CCEEEEEECCGGGHHHHHHHHHHHSC------------------------------------------------------
T ss_pred             CcEEEEEEeChHHHHHHHHHHHHhCC------------------------------------------------------
Confidence            47899999999999999999997663                                                      


Q ss_pred             hccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEe
Q psy15610        104 ISCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       104 ~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~  183 (237)
                          ..++||||++++.++.+.+.|...++.+..+||+|++.+|.++++.|++|..++||||+++++|+|+|.+++||+|
T Consensus        27 ----~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~~~Gid~~~~~~vi~~  102 (168)
T d1t5ia_          27 ----FNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY  102 (168)
T ss_dssp             ----CSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEEES
T ss_pred             ----CCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeeccccccchhhcccchhhhhh
Confidence                5789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      ++|+++..|+||+||+||.|++|.+++|+.+.
T Consensus       103 ~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~  134 (168)
T d1t5ia_         103 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDE  134 (168)
T ss_dssp             SCCSSHHHHHHHHHHHTGGGCCCEEEEEECSH
T ss_pred             hcccchhhHhhhhhhcccCCCccEEEEEECch
Confidence            99999999999999999999999999998764

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.96  E-value=1.7e-29  Score=194.62  Aligned_cols=110  Identities=22%  Similarity=0.454  Sum_probs=106.3

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS  187 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~  187 (237)
                      ..++||||+|+..++.++..|...++.+..+||+++..+|.++++.|++|+.+|||||+++++|+|+|++++||+|++|.
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~  109 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPR  109 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCS
T ss_pred             CCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhccCCCCCCEEEECCCcc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        188 DVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       188 s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ++..|+||+||+||.|.+|.+++|+.+.+.
T Consensus       110 ~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~  139 (200)
T d1oywa3         110 NIESYYQETGRAGRDGLPAEAMLFYDPADM  139 (200)
T ss_dssp             SHHHHHHHHTTSCTTSSCEEEEEEECHHHH
T ss_pred             chHHHHHHhhhhhcCCCCceEEEecCHHHH
Confidence            999999999999999999999999987543

>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=99.93  E-value=8.6e-26  Score=168.50  Aligned_cols=106  Identities=29%  Similarity=0.406  Sum_probs=98.7

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLP  186 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p  186 (237)
                      ++.++||||+|.++++.++..|...|+.+..+||+|+..+|+++++.|++|+++|||+|+++++|+|+|++++||++++|
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~~  109 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD  109 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTT
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEeccc
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999977


Q ss_pred             C-----CHHHHHHhhcccccCCCCCceEEeec
Q psy15610        187 S-----DVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       187 ~-----s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      .     +...|+|++||+||.|. |.+++++.
T Consensus       110 ~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~  140 (174)
T d1c4oa2         110 KEGFLRSERSLIQTIGRAARNAR-GEVWLYAD  140 (174)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTSTT-CEEEEECS
T ss_pred             cccccchhHHHHHHhhhhhhcCC-CeeEEeec
Confidence            5     56889999999999874 66666654

>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=99.93  E-value=1.4e-25  Score=169.54  Aligned_cols=98  Identities=35%  Similarity=0.475  Sum_probs=94.1

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPS  187 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p~  187 (237)
                      +.++||||++...++.++..|...|+++..+||+|++++|.++++.|++|+++|||||+++++|+|+|++++||+||+|.
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p~  110 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADK  110 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEEETTTTS
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEEEecCCc
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999995


Q ss_pred             -----CHHHHHHhhcccccCCCC
Q psy15610        188 -----DVEEYVHRIGRTGRMGNL  205 (237)
Q Consensus       188 -----s~~~~~Q~~GR~~R~g~~  205 (237)
                           +...|+||+||+||.|..
T Consensus       111 ~~~~~s~~~yi~R~GRagR~g~~  133 (181)
T d1t5la2         111 EGFLRSERSLIQTIGRAARNANG  133 (181)
T ss_dssp             CSGGGSHHHHHHHHGGGTTSTTC
T ss_pred             ccccccHHHHHHHHHhhccccCc
Confidence                 688999999999998854

>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=99.90  E-value=9.5e-25  Score=157.85  Aligned_cols=99  Identities=25%  Similarity=0.377  Sum_probs=90.6

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec---
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD---  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~---  184 (237)
                      ..++||||+|++.|+.+++.|...|+.+..+|++|+.       +.|++|..++||||+++++|+| |+++.||+++   
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~-------~~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~~  106 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDV-------SVIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTSD  106 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCS-------CCCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEET
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchh-------hhhhhhhcceeehhHHHHhccc-cccceEEEEEecC
Confidence            5789999999999999999999999999999999985       4578999999999999999999 9999999855   


Q ss_pred             -CCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        185 -LPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       185 -~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                       +|.+.+.|+||+||+|| |++|. +.|+.+++
T Consensus       107 ~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         107 GKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             TEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             CCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence             69999999999999999 98985 77887765

>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=99.88  E-value=3.4e-23  Score=168.16  Aligned_cols=110  Identities=27%  Similarity=0.391  Sum_probs=98.8

Q ss_pred             cCCceEEEEeecccchHHHHHHHhhCCCceEEEeC--------CCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC
Q psy15610        106 CDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHG--------DRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV  177 (237)
Q Consensus       106 ~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~--------~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~  177 (237)
                      .++.++||||+++..++.+++.|.+.++++..+||        +++..+|..+++.|++|+++|||||+++++|+|+|++
T Consensus       159 ~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~~~~Gld~~~~  238 (286)
T d1wp9a2         159 KQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEV  238 (286)
T ss_dssp             CTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTC
T ss_pred             CCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccceeccccCCCC
Confidence            44679999999999999999999999998888866        4666689999999999999999999999999999999


Q ss_pred             cEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCC
Q psy15610        178 KHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGY  216 (237)
Q Consensus       178 ~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~  216 (237)
                      ++||+||+|+++..|+||+||+||.+ +|.++.|+.++.
T Consensus       239 ~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~  276 (286)
T d1wp9a2         239 DLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGT  276 (286)
T ss_dssp             CEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTS
T ss_pred             CEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCC
Confidence            99999999999999999999999965 788888888764

>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=99.86  E-value=1.2e-22  Score=156.39  Aligned_cols=110  Identities=24%  Similarity=0.302  Sum_probs=95.3

Q ss_pred             CceEEEEeecccchHHHHHHHhhC------------------------------CCceEEEeCCCCHHHHHHHHHHhhcC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH------------------------------GYPVTSIHGDRTQKEREEALRRFRSG  157 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~------------------------------~~~~~~~h~~~~~~~r~~~~~~f~~g  157 (237)
                      +.++||||+|++.|+.++..|...                              ...++++||+|++++|..+++.|++|
T Consensus        40 ~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g  119 (201)
T d2p6ra4          40 NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRG  119 (201)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCC
Confidence            578999999999998887776531                              12388999999999999999999999


Q ss_pred             CCCEEEEcCccccccCCCCCcEEEE-------ecCCCCHHHHHHhhcccccCCC--CCceEEeecCCCC
Q psy15610        158 ETPILVATAVAARGLDIPHVKHVIN-------FDLPSDVEEYVHRIGRTGRMGN--LDFPFSYNQPGYG  217 (237)
Q Consensus       158 ~~~vlv~T~~~~~Gvdl~~~~~Vi~-------~~~p~s~~~~~Q~~GR~~R~g~--~~~~~~~~~~~~~  217 (237)
                      .++|||||+.+++|+|+|..++||.       ++.|.+..+|+||+|||||.|.  .|.+++++.+.+.
T Consensus       120 ~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~~  188 (201)
T d2p6ra4         120 NIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR  188 (201)
T ss_dssp             SCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGH
T ss_pred             CceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCCCh
Confidence            9999999999999999999998886       5667899999999999999884  6778887776544

>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=99.83  E-value=1e-21  Score=151.28  Aligned_cols=95  Identities=22%  Similarity=0.409  Sum_probs=87.6

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLP  186 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~p  186 (237)
                      .+.++||||++...++.+++.|.     +..+||+++..+|+.+++.|++|+++|||+|+++++|+|+|.+++||++++|
T Consensus        92 ~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gidl~~~~~vi~~~~~  166 (200)
T d2fwra1          92 RKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGS  166 (200)
T ss_dssp             SSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCS
T ss_pred             CCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccCCCCCCEEEEeCCC
Confidence            35789999999999999988773     4458999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHhhcccccCCCCC
Q psy15610        187 SDVEEYVHRIGRTGRMGNLD  206 (237)
Q Consensus       187 ~s~~~~~Q~~GR~~R~g~~~  206 (237)
                      +|+..|.||+||++|.|+.+
T Consensus       167 ~s~~~~~Q~iGR~~R~~~~k  186 (200)
T d2fwra1         167 GSAREYIQRLGRILRPSKGK  186 (200)
T ss_dssp             SCCHHHHHHHHHSBCCCTTT
T ss_pred             CCHHHHHHHHHhcCCCCCCC
Confidence            99999999999999998654

>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=99.83  E-value=1e-22  Score=161.97  Aligned_cols=101  Identities=16%  Similarity=0.245  Sum_probs=88.9

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEc----CccccccCCCC-CcEEEE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT----AVAARGLDIPH-VKHVIN  182 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T----~~~~~Gvdl~~-~~~Vi~  182 (237)
                      +.++||||+|++.++.++++|...      +||++++++|.++++.|++|+++|||||    +++++|+|+|+ +++||+
T Consensus        25 ~~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~~rGlDip~~v~~VI~   98 (248)
T d1gkub2          25 GTGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVF   98 (248)
T ss_dssp             CSCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchhhhccCccccccEEEE
Confidence            468999999999999999999753      7999999999999999999999999999    77999999996 999999


Q ss_pred             ecCCCCHHHHHHhhcccccCCCCCceEEeecCCCCC
Q psy15610        183 FDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGG  218 (237)
Q Consensus       183 ~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~~  218 (237)
                      ||+|+    |.|++||+||.|..+.+++++...+..
T Consensus        99 ~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~  130 (248)
T d1gkub2          99 VGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVD  130 (248)
T ss_dssp             ESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHH
T ss_pred             eCCCc----chhhhhhhhccCcceEeeeeccHhhHH
Confidence            99995    889999999999999998888766543

>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=99.79  E-value=1.3e-20  Score=144.31  Aligned_cols=108  Identities=19%  Similarity=0.345  Sum_probs=88.1

Q ss_pred             CceEEEEeecccch--------HHHHHHHhhC---CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCC
Q psy15610        108 EALTLVFVETKKGA--------DQLEDFLHHH---GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPH  176 (237)
Q Consensus       108 ~~~~iIF~~t~~~~--------~~l~~~L~~~---~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~  176 (237)
                      +.++-+.||..+..        ....+.|.+.   +.++..+||.|++++|++++..|++|+++|||||++.++|+|+|+
T Consensus        29 g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtViE~GIDip~  108 (206)
T d1gm5a4          29 GGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPR  108 (206)
T ss_dssp             SCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTT
T ss_pred             CCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehhhhccccccC
Confidence            45665666654332        2333444332   677889999999999999999999999999999999999999999


Q ss_pred             CcEEEEecCCC-CHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        177 VKHVINFDLPS-DVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       177 ~~~Vi~~~~p~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      ++++|+++.|. ..+++.|..||+||.|..|.|++++++.
T Consensus       109 a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~  148 (206)
T d1gm5a4         109 ANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDV  148 (206)
T ss_dssp             CCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSC
T ss_pred             CcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccc
Confidence            99999999986 8999999999999999999999998764

>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=99.79  E-value=3.8e-20  Score=146.97  Aligned_cols=105  Identities=20%  Similarity=0.207  Sum_probs=91.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHH----------HHHHHHhhcCCCCEEEEcCcccc---ccCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKER----------EEALRRFRSGETPILVATAVAAR---GLDI  174 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r----------~~~~~~f~~g~~~vlv~T~~~~~---Gvdl  174 (237)
                      +.++||||+|++.++.++..|.+.|+++..+|++++.+.|          ...++.|.+|+.+++|+|+++.+   |+|+
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giDi  115 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSL  115 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECCC
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCCC
Confidence            6899999999999999999999999999999999999876          45678888999999999999888   6678


Q ss_pred             CCCcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeec
Q psy15610        175 PHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQ  213 (237)
Q Consensus       175 ~~~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~  213 (237)
                      +.+.+|++++.|.|.+.|+||+||+|| |.+|...++..
T Consensus       116 d~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~  153 (299)
T d1a1va2         116 DPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAP  153 (299)
T ss_dssp             SSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCS
T ss_pred             CcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEec
Confidence            888899999999999999999999999 87876544433

>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=99.79  E-value=1.2e-18  Score=132.50  Aligned_cols=108  Identities=17%  Similarity=0.260  Sum_probs=101.1

Q ss_pred             CceEEEEeecccchHHHHHHHhhC--CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL  185 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~  185 (237)
                      ++++-+.||..+..+.++..+.+.  +.++.++||.|+++++++++..|.+|+++|||||.+.+.|+|+|+++++|..+.
T Consensus        31 GgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~iiI~~a  110 (211)
T d2eyqa5          31 GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERA  110 (211)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTT
T ss_pred             CCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcEEEEecc
Confidence            689999999999999998888764  789999999999999999999999999999999999999999999999999998


Q ss_pred             CC-CHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        186 PS-DVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       186 p~-s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                      +. ..+++.|..||+||.+..+.|++++++.
T Consensus       111 ~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5         111 DHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             TSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             hhccccccccccceeeecCccceEEEEecCC
Confidence            75 8999999999999999999999998764

>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=99.73  E-value=1.3e-17  Score=137.90  Aligned_cols=105  Identities=16%  Similarity=0.307  Sum_probs=96.9

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCC---EEEEcCccccccCCCCCcEEEEec
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETP---ILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~---vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      +.++|||++.....+.++.+|...++.+..++|+++..+|..+++.|+++...   +|++|.+++.|+|++.++.||++|
T Consensus       118 g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~agg~GlnL~~a~~vi~~d  197 (346)
T d1z3ix1         118 SDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFD  197 (346)
T ss_dssp             CCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECS
T ss_pred             CCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecchhhhhccccccceEEEEec
Confidence            67999999999999999999999999999999999999999999999987543   677889999999999999999999


Q ss_pred             CCCCHHHHHHhhcccccCCCCCceEEee
Q psy15610        185 LPSDVEEYVHRIGRTGRMGNLDFPFSYN  212 (237)
Q Consensus       185 ~p~s~~~~~Q~~GR~~R~g~~~~~~~~~  212 (237)
                      ++|++..+.|++||+.|.|+...+.++.
T Consensus       198 ~~wnp~~~~Qa~~R~~R~GQ~~~V~v~r  225 (346)
T d1z3ix1         198 PDWNPANDEQAMARVWRDGQKKTCYIYR  225 (346)
T ss_dssp             CCSSHHHHHHHHTTSSSTTCCSCEEEEE
T ss_pred             CCCccchHhHhhhcccccCCCCceEEEE
Confidence            9999999999999999999987765544

>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=99.69  E-value=2.4e-17  Score=130.27  Aligned_cols=105  Identities=15%  Similarity=0.257  Sum_probs=80.2

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC-CCceEEEeCCCCHHHHHHHHHHhhcCC-CCEEEE-cCccccccCCCCCcEEEEe
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH-GYPVTSIHGDRTQKEREEALRRFRSGE-TPILVA-TAVAARGLDIPHVKHVINF  183 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~r~~~~~~f~~g~-~~vlv~-T~~~~~Gvdl~~~~~Vi~~  183 (237)
                      ++.++||||......+.+..++... +..+..+||+++..+|..+++.|+++. ..++++ |.+++.|+|++.+++||++
T Consensus        84 ~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~~g~Glnl~~a~~vi~~  163 (244)
T d1z5za1          84 EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHF  163 (244)
T ss_dssp             TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEEC
T ss_pred             cccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccccccccccchhhhhhhc
Confidence            4779999999999999999988754 888999999999999999999998774 566655 5899999999999999999


Q ss_pred             cCCCCHHHHHHhhcccccCCCCCceEEe
Q psy15610        184 DLPSDVEEYVHRIGRTGRMGNLDFPFSY  211 (237)
Q Consensus       184 ~~p~s~~~~~Q~~GR~~R~g~~~~~~~~  211 (237)
                      ++|||+..+.|+.||++|.|+...+.++
T Consensus       164 ~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~  191 (244)
T d1z5za1         164 DRWWNPAVEDQATDRVYRIGQTRNVIVH  191 (244)
T ss_dssp             SCCSCTTTC--------------CCEEE
T ss_pred             CchhhhHHHhhhcceeeecCCCCceEEE
Confidence            9999999999999999999987655543

>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=99.56  E-value=4.3e-15  Score=120.32  Aligned_cols=154  Identities=17%  Similarity=0.208  Sum_probs=107.0

Q ss_pred             ccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeecccchHHHHHHHhhCCC
Q psy15610         54 GDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGADQLEDFLHHHGY  133 (237)
Q Consensus        54 ~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~~~~~l~~~L~~~~~  133 (237)
                      .++.+.+.+++|.......   +.....+.............  ............+++|||++++.++.++..|.+.++
T Consensus       129 ~~~~~~v~~SAT~~~~~~~---~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~  203 (305)
T d2bmfa2         129 MGEAAGIFMTATPPGSRDP---FPQSNAPIMDEEREIPERSW--NSGHEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGK  203 (305)
T ss_dssp             HTSCEEEEECSSCTTCCCS---SCCCSSCEEEEECCCCCSCC--SSCCHHHHSSCSCEEEECSCHHHHHHHHHHHHHHTC
T ss_pred             cccceEEEeecCCCcceee---ecccCCcceEEEEeccHHHH--HHHHHHHHhhCCCEEEEeccHHHHHHHHHHHHhCCC
Confidence            3567889999998663321   11111222111111111110  011222334568899999999999999999999999


Q ss_pred             ceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEE----------ec----------CCCCHHHHH
Q psy15610        134 PVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN----------FD----------LPSDVEEYV  193 (237)
Q Consensus       134 ~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~----------~~----------~p~s~~~~~  193 (237)
                      .+..+||++.+..+    ..|+++..+++++|+++++|+|++ ++.||.          ++          .|.|..+|+
T Consensus       204 ~~~~l~~~~~~~~~----~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~  278 (305)
T d2bmfa2         204 KVIQLSRKTFDSEY----IKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAA  278 (305)
T ss_dssp             CCEECCTTCHHHHG----GGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHH
T ss_pred             CEEEeCCcChHHHH----hhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHh
Confidence            99999999876544    468899999999999999999994 555442          22          356899999


Q ss_pred             HhhcccccCCCCCceEEeecCCCC
Q psy15610        194 HRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       194 Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||+||+||.|+.+...+++.....
T Consensus       279 Qr~GR~GR~~~~~~~~~~~~~~~~  302 (305)
T d2bmfa2         279 QRRGRVGRNPKNENDQYIYMGEPL  302 (305)
T ss_dssp             HHHTTSSCSSSCCCEEEEECSCCC
T ss_pred             hhhcCcCcCCCCceEEEEECCCCC
Confidence            999999999988877777665543

>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=99.55  E-value=1.1e-14  Score=117.07  Aligned_cols=103  Identities=20%  Similarity=0.276  Sum_probs=82.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEecC--
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL--  185 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~~--  185 (237)
                      +++++|||++...++.++..|.+.|..+..+||.+...+..    .|++++.+++|||+++++|+++ ++.+||..+.  
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~  110 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTAF  110 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCcee
Confidence            68899999999999999999999999999999999987765    4678999999999999999999 5998885432  


Q ss_pred             -----------------CCCHHHHHHhhcccccCCCCCceEEeecCC
Q psy15610        186 -----------------PSDVEEYVHRIGRTGRMGNLDFPFSYNQPG  215 (237)
Q Consensus       186 -----------------p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~  215 (237)
                                       |.|..+..||.||+||.+....++.++...
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~~~  157 (299)
T d1yksa2         111 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEP  157 (299)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             ceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeCCC
Confidence                             358889999999999987555566665543

>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=99.44  E-value=5.5e-13  Score=97.83  Aligned_cols=108  Identities=19%  Similarity=0.194  Sum_probs=90.4

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCC--------cE
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV--------KH  179 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~--------~~  179 (237)
                      +.++||+|.|.+..+.++.+|.+.+++..+++......+-+.+.++-  ..-.|.|+|..+++|.|+.--        -+
T Consensus        34 grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~Ag--~~g~VtIATNmAGRGtDikl~~~v~~~GGLh  111 (175)
T d1tf5a4          34 GQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAG--QKGAVTIATNMAGRGTDIKLGEGVKELGGLA  111 (175)
T ss_dssp             TCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTT--STTCEEEEETTSSTTCCCCCCTTSGGGTSEE
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhcc--CCCceeehhhHHHcCCCccchHHHHhCCCcE
Confidence            68999999999999999999999999999999876544444333222  234699999999999988532        37


Q ss_pred             EEEecCCCCHHHHHHhhcccccCCCCCceEEeecCCCC
Q psy15610        180 VINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYG  217 (237)
Q Consensus       180 Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~~~~  217 (237)
                      ||....|.|.....|..||+||.|.+|...+|++..+.
T Consensus       112 VI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD~  149 (175)
T d1tf5a4         112 VVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  149 (175)
T ss_dssp             EEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             EEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCHH
Confidence            99999999999999999999999999999999987663

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.88  E-value=8.4e-09  Score=76.81  Aligned_cols=107  Identities=20%  Similarity=0.174  Sum_probs=88.7

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCC-CCEEEEcCccccccCCCC----------
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGE-TPILVATAVAARGLDIPH----------  176 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~~Gvdl~~----------  176 (237)
                      ++++||.+.|.+..+.++.+|.+.+++..++++..-..+-+.+.+   .|. -.|-|+|.++++|.|+.-          
T Consensus        34 GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAeIIAq---AG~~GaVTIATNMAGRGTDI~LGgn~~~~~~~  110 (219)
T d1nkta4          34 GQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAV---AGRRGGVTVATNMAGRGTDIVLGGNVDFLTDQ  110 (219)
T ss_dssp             TCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHT---TTSTTCEEEEETTCSTTCCCCTTCCHHHHHHH
T ss_pred             CCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHHHHHh---cccCCcEEeeccccCCCCceeecCchhhhhHH
Confidence            789999999999999999999999999999999754333332222   344 458899999999999933          


Q ss_pred             ------------------------------------------CcEEEEecCCCCHHHHHHhhcccccCCCCCceEEeecC
Q psy15610        177 ------------------------------------------VKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQP  214 (237)
Q Consensus       177 ------------------------------------------~~~Vi~~~~p~s~~~~~Q~~GR~~R~g~~~~~~~~~~~  214 (237)
                                                                =-+||......|...--|-.||+||.|.+|...+|++-
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRGRsGRQGDPGsSrFflSL  190 (219)
T d1nkta4         111 RLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSL  190 (219)
T ss_dssp             HHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEET
T ss_pred             HhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccccccccccccccCCCccceeEEec
Confidence                                                      13688888899999999999999999999999999987


Q ss_pred             CCC
Q psy15610        215 GYG  217 (237)
Q Consensus       215 ~~~  217 (237)
                      .+.
T Consensus       191 eDd  193 (219)
T d1nkta4         191 GDE  193 (219)
T ss_dssp             TSH
T ss_pred             cHH
Confidence            654

>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=97.74  E-value=0.00011  Score=56.81  Aligned_cols=127  Identities=16%  Similarity=0.044  Sum_probs=87.7

Q ss_pred             hhhHHHHhhhcCCCceeecCCcchhhHHHHhhhh-hhccCCceEEEEeecccchHHHHHHH----hhCCCceEEEeCCCC
Q psy15610         69 ADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYT-LISCDEALTLVFVETKKGADQLEDFL----HHHGYPVTSIHGDRT  143 (237)
Q Consensus        69 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~iIF~~t~~~~~~l~~~L----~~~~~~~~~~h~~~~  143 (237)
                      ++++.+.+.....-...+.|+.-...-....... .....+.++++.+||..-+.+....+    ...++.+..+||+++
T Consensus        92 i~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~  171 (264)
T d1gm5a3          92 HQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATT  171 (264)
T ss_dssp             HHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSC
T ss_pred             HHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccc
Confidence            5566666666666667777777555544444322 23455789999999988777765554    445889999999999


Q ss_pred             HHHHHHHHHHhhcCCCCEEEEcCccc-cccCCCCCcEEEEecCCCCHHHHHHhhc
Q psy15610        144 QKEREEALRRFRSGETPILVATAVAA-RGLDIPHVKHVINFDLPSDVEEYVHRIG  197 (237)
Q Consensus       144 ~~~r~~~~~~f~~g~~~vlv~T~~~~-~Gvdl~~~~~Vi~~~~p~s~~~~~Q~~G  197 (237)
                      ..+|..++...++|+++|+|+|.++- ..+.+.+.-+||.=...  --.|.||.+
T Consensus       172 ~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~LglviiDEqH--~fgv~Qr~~  224 (264)
T d1gm5a3         172 PSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQH--RFGVKQREA  224 (264)
T ss_dssp             HHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEESCC--CC-----CC
T ss_pred             hHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceeeecccc--ccchhhHHH
Confidence            99999999999999999999997654 46777777766642222  224556654

>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=97.48  E-value=0.00088  Score=50.68  Aligned_cols=114  Identities=18%  Similarity=0.118  Sum_probs=87.9

Q ss_pred             hhhHHHHhhhcCCCceeecCCcchhhHHHHhhhh-hhccCCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCC
Q psy15610         69 ADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYT-LISCDEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRT  143 (237)
Q Consensus        69 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~  143 (237)
                      .+++...+....+....++++.-...-....... .....+.++++.+|+..-+.++...+.+    .+..+..+||.++
T Consensus        64 ~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~  143 (233)
T d2eyqa3          64 INAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRS  143 (233)
T ss_dssp             HHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSC
T ss_pred             HHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCccc
Confidence            4566666777777777888877655544444433 3345678999999999988888777764    4778999999999


Q ss_pred             HHHHHHHHHHhhcCCCCEEEEcCcccc-ccCCCCCcEEEE
Q psy15610        144 QKEREEALRRFRSGETPILVATAVAAR-GLDIPHVKHVIN  182 (237)
Q Consensus       144 ~~~r~~~~~~f~~g~~~vlv~T~~~~~-Gvdl~~~~~Vi~  182 (237)
                      ..+|..+...+.+|..+|+|.|.++-. .+.+++.-.||.
T Consensus       144 ~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiIi  183 (233)
T d2eyqa3         144 AKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIV  183 (233)
T ss_dssp             HHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEE
T ss_pred             chhHHHHHHHHhCCCCCEEEeehhhhccCCccccccceee
Confidence            999999999999999999999986544 677777766554

>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=97.06  E-value=0.00018  Score=52.04  Aligned_cols=46  Identities=28%  Similarity=0.327  Sum_probs=42.8

Q ss_pred             cccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         55 DEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        55 ~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      .+.++|+||.|+..+++++..|...|+.+..+|+.+.+..|.....
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~   75 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIR   75 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHH
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHH
Confidence            4567999999999999999999999999999999999999998855

>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=95.82  E-value=0.0026  Score=44.75  Aligned_cols=103  Identities=22%  Similarity=0.272  Sum_probs=64.5

Q ss_pred             hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEe
Q psy15610         36 DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFV  115 (237)
Q Consensus        36 ~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~  115 (237)
                      +.+..+++-....          .|+||+|+..++.++.+|...++.+..+++.+.+..+.....    .+..+..-|.+
T Consensus        18 ~~L~~ll~~~~~k----------~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~----~f~~~~~~ilv   83 (155)
T d1hv8a2          18 EALCRLLKNKEFY----------GLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIR----LFKQKKIRILI   83 (155)
T ss_dssp             HHHHHHHCSTTCC----------EEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHH----HHHTTSSSEEE
T ss_pred             HHHHHHHccCCCC----------EEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhh----hhhcccceeee
Confidence            4444455555666          799999999999999999999999999999999988876633    22223323444


Q ss_pred             ecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcC
Q psy15610        116 ETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSG  157 (237)
Q Consensus       116 ~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g  157 (237)
                      .|....+.    +.-.+.. .++|-++|..-..-+.+.-+.|
T Consensus        84 ~T~~~~~G----id~~~v~-~Vi~~d~p~~~~~y~qr~GR~g  120 (155)
T d1hv8a2          84 ATDVMSRG----IDVNDLN-CVINYHLPQNPESYMHRIGRTG  120 (155)
T ss_dssp             ECTTHHHH----CCCSCCS-EEEESSCCSCHHHHHHHSTTTC
T ss_pred             ehhHHhhh----hhhccCc-EEEEecCCCCHHHHHHHHHhcC
Confidence            44433322    2212222 4556666654444444443443

>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=95.79  E-value=0.0011  Score=48.19  Aligned_cols=60  Identities=30%  Similarity=0.281  Sum_probs=48.4

Q ss_pred             ccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhhhhhhccCCceEEEEeeccc
Q psy15610         56 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKK  119 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iIF~~t~~  119 (237)
                      +.++|+||+++..++.++..|...|+++..+|+.+.+..|..+..    .+..++.=|.+.|..
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~----~Fr~g~~~vLVaTdv   90 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIR----DLRLGKYDVLVGINL   90 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHH----HHHHTSCSEEEESCC
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHH----HHHCCCCCEEEehhH
Confidence            457999999999999999999999999999999999999987743    333344445555544

>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=95.77  E-value=0.0021  Score=45.65  Aligned_cols=56  Identities=23%  Similarity=0.406  Sum_probs=46.4

Q ss_pred             hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         36 DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        36 ~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+..|++-+...+         +|+||+|+..++++++.|...++.+..+|+.+.+..|.....
T Consensus        16 ~~L~~ll~~~~~~k---------~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~   71 (162)
T d1fuka_          16 ECLTDLYDSISVTQ---------AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMK   71 (162)
T ss_dssp             HHHHHHHHHTTCSC---------EEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCc---------EEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHH
Confidence            44444445555455         899999999999999999999999999999999999988754

>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=95.72  E-value=0.0029  Score=45.20  Aligned_cols=59  Identities=27%  Similarity=0.394  Sum_probs=50.0

Q ss_pred             echhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         33 DEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        33 ~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      ++.+.+..+++.....+         +|+||+++..++.++++|...++.+..+|+++.+..|.....
T Consensus        13 ~K~~~L~~ll~~~~~~k---------~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~   71 (168)
T d1t5ia_          13 EKNRKLFDLLDVLEFNQ---------VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQ   71 (168)
T ss_dssp             GHHHHHHHHHHHSCCSS---------EEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCe---------EEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhh
Confidence            34466666777777666         899999999999999999999999999999999998887643

>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=95.41  E-value=0.0019  Score=46.30  Aligned_cols=58  Identities=17%  Similarity=0.276  Sum_probs=48.1

Q ss_pred             chhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         34 EQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        34 ~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +-..+..+++-....+         +|+||+|+..++.++.+|...++.+..+|+++.+..|.....
T Consensus        19 K~~~L~~ll~~~~~~k---------~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~   76 (171)
T d1s2ma2          19 KLHCLNTLFSKLQINQ---------AIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFH   76 (171)
T ss_dssp             HHHHHHHHHHHSCCSE---------EEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCc---------eEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhh
Confidence            3455555555566556         899999999999999999999999999999999999887743

>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=95.30  E-value=0.0034  Score=43.32  Aligned_cols=41  Identities=20%  Similarity=0.157  Sum_probs=36.9

Q ss_pred             ccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHH
Q psy15610         56 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKERE   96 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   96 (237)
                      ..+.|+||+|+..++.+++.|...++.+..+|+.+.+..+.
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~~~   75 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIP   75 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCCCT
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhhhh
Confidence            45799999999999999999999999999999999877543

>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=94.76  E-value=0.0061  Score=44.78  Aligned_cols=67  Identities=10%  Similarity=0.238  Sum_probs=58.2

Q ss_pred             EEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         28 RIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        28 ~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      .|..+++.+|++.|.++|...      ...++|+|++|+..++.++..|...++.+..+|+.+.+..|.....
T Consensus         8 ~y~v~~~~~k~~~L~~~l~~~------~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~   74 (200)
T d1oywa3           8 RYMLMEKFKPLDQLMRYVQEQ------RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQE   74 (200)
T ss_dssp             EEEEEECSSHHHHHHHHHHHT------TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             EEEEEcCCcHHHHHHHHHHhc------CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHH
Confidence            466778888999999998754      2456999999999999999999999999999999999998887754

>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=94.22  E-value=0.0066  Score=43.23  Aligned_cols=56  Identities=34%  Similarity=0.528  Sum_probs=46.4

Q ss_pred             hHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         36 DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        36 ~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      +.+..+++-....+         +|+||+++..++.++..|...++.+..+|+++.+..|.....
T Consensus        23 ~~L~~ll~~~~~~k---------~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~   78 (168)
T d2j0sa2          23 DTLCDLYDTLTITQ---------AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMK   78 (168)
T ss_dssp             HHHHHHHHHHTSSE---------EEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCc---------eEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHH
Confidence            44544555555555         899999999999999999999999999999999999877643

>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=92.50  E-value=0.11  Score=34.16  Aligned_cols=65  Identities=11%  Similarity=0.050  Sum_probs=50.3

Q ss_pred             CceEEEEeecccchHHHHHHHhhCCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCccccccCCCCCcEEEEec
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFD  184 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gvdl~~~~~Vi~~~  184 (237)
                      ..++|+.|.+.-..+.+.+.|...++.+..+.+.          ..+.++  .+.++...+..|+-+|+..++|..+
T Consensus        34 ~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~~----------~~~~~~--~~~i~~~~l~~GF~~~~~~l~vItE   98 (117)
T d2eyqa2          34 DGPVVFSVESEGRREALGELLARIKIAPQRIMRL----------DEASDR--GRYLMIGAAEHGFVDTVRNLALICE   98 (117)
T ss_dssp             CSCCCEEESSHHHHHHHHHHHGGGTCCCEECSSG----------GGCCTT--CCEEEECCCCSCEEETTTTEEEEEH
T ss_pred             CCeEEEEECCccHHHHHHHHHHHcCCCceEecCh----------hhhcCc--eEEEEEecCccccccCCCCEEEEEc
Confidence            4678888889999999999999999988776542          234333  3566667899999999999888754

>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=92.25  E-value=0.035  Score=42.85  Aligned_cols=40  Identities=20%  Similarity=0.165  Sum_probs=36.6

Q ss_pred             ccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhH
Q psy15610         56 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKER   95 (237)
Q Consensus        56 ~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~   95 (237)
                      ..+.|+||+|+..+++++..|...|+++..+|+.+.+..+
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R   75 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVI   75 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGS
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHH
Confidence            4469999999999999999999999999999999888765

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=90.61  E-value=0.44  Score=34.36  Aligned_cols=71  Identities=21%  Similarity=0.268  Sum_probs=52.6

Q ss_pred             CCceEEEEeecccchHHHHHHHhh----CCCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----c-ccccCCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHH----HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----A-ARGLDIPH  176 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~-~~Gvdl~~  176 (237)
                      .+.+++|.|+|++.+.++.+.+..    .+..+...+|+.+..+..+.++     ..+|+|+|+.     + ...+++..
T Consensus        71 ~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-----~~~IlV~TP~~l~~~l~~~~~~~~~  145 (208)
T d1hv8a1          71 NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLKN  145 (208)
T ss_dssp             SSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTTS
T ss_pred             cCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-----CCCEEEEChHHHHHHHHcCCCCccc
Confidence            356899999999999998777755    3678889999988776654442     3689999952     2 33567888


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      +.++|.
T Consensus       146 l~~lVi  151 (208)
T d1hv8a1         146 VKYFIL  151 (208)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            887765

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.04  E-value=0.83  Score=33.29  Aligned_cols=72  Identities=18%  Similarity=0.188  Sum_probs=52.8

Q ss_pred             CCceEEEEeecccchHHHHHHHhhC----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcC------ccccccCCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHH----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATA------VAARGLDIPH  176 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gvdl~~  176 (237)
                      ...+++|+++|++.+.++.+.+...    ++.+..+.|+.+..+....++   . ..+|+|+|+      .....+++..
T Consensus        84 ~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~---~-~~~Ilv~TPgrl~~~~~~~~~~~~~  159 (222)
T d2j0sa1          84 RETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD---Y-GQHVVAGTPGRVFDMIRRRSLRTRA  159 (222)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH---H-CCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             cCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhc---c-CCeEEeCCCCcHHhccccccccccc
Confidence            3467999999999999998877653    567888889988766554442   2 358999994      2245567778


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      +.++|.
T Consensus       160 l~~lVl  165 (222)
T d2j0sa1         160 IKMLVL  165 (222)
T ss_dssp             CCEEEE
T ss_pred             ceeeee
Confidence            888765

>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=88.64  E-value=0.56  Score=31.06  Aligned_cols=39  Identities=18%  Similarity=0.236  Sum_probs=33.9

Q ss_pred             ccCCceEEEEeecccchHHHHHHHhhCCCceEEEeCCCC
Q psy15610        105 SCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRT  143 (237)
Q Consensus       105 ~~~~~~~iIF~~t~~~~~~l~~~L~~~~~~~~~~h~~~~  143 (237)
                      ..+..++++||.+-..+...+..|.+.|+.+..+.|++.
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            345678999999988899999999999999999999874

>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=84.38  E-value=1.6  Score=31.14  Aligned_cols=72  Identities=25%  Similarity=0.318  Sum_probs=51.2

Q ss_pred             CceEEEEeecccchHHHHHHHhhC-----CCceEEEeCCCCHHHHHHHHHHhhcCCCCEEEEcCc-----c-ccccCCCC
Q psy15610        108 EALTLVFVETKKGADQLEDFLHHH-----GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV-----A-ARGLDIPH  176 (237)
Q Consensus       108 ~~~~iIF~~t~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~-~~Gvdl~~  176 (237)
                      ..+++|.++|++.+.++.+.+...     ......++|+.+.....   +.+.+...+|+|+|+-     + ...+++.+
T Consensus        69 ~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~  145 (207)
T d1t6na_          69 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE---EVLKKNCPHIVVGTPGRILALARNKSLNLKH  145 (207)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHH---HHHHHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHH---HHHHhcCCCEEEeCcchhhhhccCCceeccc
Confidence            457999999999999988888653     24567778887766544   3334466899999952     2 23557788


Q ss_pred             CcEEEE
Q psy15610        177 VKHVIN  182 (237)
Q Consensus       177 ~~~Vi~  182 (237)
                      +.++|.
T Consensus       146 l~~lVl  151 (207)
T d1t6na_         146 IKHFIL  151 (207)
T ss_dssp             CCEEEE
T ss_pred             cceeeh
Confidence            887775

>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=81.34  E-value=0.16  Score=37.96  Aligned_cols=62  Identities=11%  Similarity=0.177  Sum_probs=48.2

Q ss_pred             CCceeEEEEeechhHHHHHHHhhcCchhhhcccccceeEEeecccchhhHHHHhhhcCCCceeecCCcchhhHHHHhh
Q psy15610         23 ENITQRIAWVDEQDKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQ  100 (237)
Q Consensus        23 ~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~~~~~~i~f~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  100 (237)
                      .||...+   .+++|+..|..+|+...       ...|+||+|+..+++++++|...      +|+.+.+..|..+..
T Consensus         2 r~v~d~~---~~~~~~~~l~~~l~~~~-------~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~   63 (248)
T d1gkub2           2 RNVEDVA---VNDESISTLSSILEKLG-------TGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYE   63 (248)
T ss_dssp             CCEEEEE---ESCCCTTTTHHHHTTSC-------SCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHH
T ss_pred             CCEEEEe---cCchHHHHHHHHHHHhC-------CCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHH
Confidence            3455555   46789999999998652       35899999999999999999753      788888887765544

>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=80.58  E-value=2.5  Score=26.94  Aligned_cols=37  Identities=14%  Similarity=-0.029  Sum_probs=31.3

Q ss_pred             CCceEEEEeecccchHHHHHHHhhCCC-ceEEEeCCCC
Q psy15610        107 DEALTLVFVETKKGADQLEDFLHHHGY-PVTSIHGDRT  143 (237)
Q Consensus       107 ~~~~~iIF~~t~~~~~~l~~~L~~~~~-~~~~~h~~~~  143 (237)
                      +..++|+||.+-..+....-.|...|+ ++..|.|++.
T Consensus        81 ~~~~ii~yC~sG~~A~~~~~~L~~lG~~~v~~y~Gs~~  118 (120)
T d1urha2          81 YDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWS  118 (120)
T ss_dssp             SSSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCC
T ss_pred             ccCceEEEccchhHHHHHHHHHHHcCCCCceEcCCChh
Confidence            356899999999888888888888888 5888999875