Psyllid ID: psy7792

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------14
Protein Sequence
MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTKAASSIGRRDYLNSNQADY
Secondary Structure (PSIPRED)
ccHHHHHccccccccccEEEEccccccccccccccccccccccccEEEEEEcccccHHHHHHHHHHHHHccccccHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHccccccccEEEEEccccHHHHHHHEEccccccccccEEEEEEEcccccHHHHHHHHHHHHHHHcHccHHHHHHHcccccccccccccccccEccccccccccccHHHHHHHHHHHHcccHHHcccccccc
Coil and Loop (DISEMBL)
mvatdvaskgldfeeikhvinydmpddvenYVHRigrtgrsgktglaTTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDlggdergcaycgglghritacpkLEAVQTKAAssigrrdylnsnqady
Flexible Loop (DISEMBL)
mvatdvaskgldfeeikhvinydmpddVENYVHRIgrtgrsgktglATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTKaassigrrdylnsnqady
Low Complexity Region (SEG)
MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTKAASSIGRRDYLNSNQADY
Disordered region (IsUnstruct)
**********LDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQ********************
Disordered Region (DISOPRED)
MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLA***********************************************************
Disordered Region (DISEMBL)
********KGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTKAASSIGRRDYLNSNQADY
Disordered Region (DISPRO)
MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESE******************GLGHRITACPKLEAVQTKA*****************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTKAASSIGRRDYLNSNQADY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	138	2.2.26 [Sep-21-2011]
Q9V3C0	619	ATP-dependent RNA helicas	yes	N/A	0.992	0.221	0.726	8e-55
Q91VN6	622	Probable ATP-dependent RN	yes	N/A	0.992	0.220	0.710	2e-54
Q9UJV9	622	Probable ATP-dependent RN	yes	N/A	0.992	0.220	0.710	2e-54
Q9LU46	591	DEAD-box ATP-dependent RN	yes	N/A	0.949	0.221	0.669	9e-46
Q9SZB4	542	Putative DEAD-box ATP-dep	no	N/A	0.956	0.243	0.656	2e-45
Q0E3X4	627	DEAD-box ATP-dependent RN	yes	N/A	0.891	0.196	0.672	7e-44
Q5Z6G5	619	DEAD-box ATP-dependent RN	no	N/A	0.942	0.210	0.589	8e-41
Q54KG1	671	Probable ATP-dependent RN	yes	N/A	0.956	0.196	0.526	3e-33
A7TKR8	650	ATP-dependent RNA helicas	N/A	N/A	0.623	0.132	0.505	3e-21
Q75B50	623	ATP-dependent RNA helicas	yes	N/A	0.601	0.133	0.535	3e-21

>sp|Q9V3C0|DDX41_DROME ATP-dependent RNA helicase abstrakt OS=Drosophila melanogaster GN=abs PE=1 SV=1

 Score =  211 bits (538), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 101/139 (72%), Positives = 115/139 (82%), Gaps = 2/139 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF  ++HVINYDMPDD+ENYVHRIGRTGRS   GLATT INK+ ++SVL
Sbjct: 482 LVATDVASKGLDFPNVQHVINYDMPDDIENYVHRIGRTGRSNTKGLATTLINKTTEQSVL 541

Query: 61  LDLKHLLLEARQRIPPFLAELESETE-KFLDLGGDERGCAYCGGLGHRITACPKLEAVQT 119
           LDLKHLL+E +Q +P FL EL  ETE + LDL GD  GC YCGGLGHRIT CPKLEAVQ 
Sbjct: 542 LDLKHLLIEGKQEVPDFLDELAPETEHQHLDL-GDSHGCTYCGGLGHRITECPKLEAVQN 600

Query: 120 KAASSIGRRDYLNSNQADY 138
           K AS+IGRRDYL++  ADY
Sbjct: 601 KQASNIGRRDYLSNTAADY 619

ATP-dependent RNA helicase. Is essential for the directed and fasciculated early outgrowth of the bolwig nerves, as well as for its navigation at later stages. Is required during post-transcriptional gene expression. Plays a role during morphogenetic process, apoptosis and the establishment of cell polarity.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q91VN6|DDX41_MOUSE Probable ATP-dependent RNA helicase DDX41 OS=Mus musculus GN=Ddx41 PE=1 SV=2

 Score =  210 bits (535), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 98/138 (71%), Positives = 116/138 (84%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct: 486 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 545

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           +DLK LLLEA+Q++PP L  L    E  LD+GG ERGCA+CGGLGHRIT CPKLEA+QTK
Sbjct: 546 MDLKALLLEAKQKVPPVLQVLHCGDESMLDIGG-ERGCAFCGGLGHRITDCPKLEAMQTK 604

Query: 121 AASSIGRRDYLNSNQADY 138
             S+IGR+DYL  +  D+
Sbjct: 605 QVSNIGRKDYLAHSSMDF 622

Probable ATP-dependent RNA helicase. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9UJV9|DDX41_HUMAN Probable ATP-dependent RNA helicase DDX41 OS=Homo sapiens GN=DDX41 PE=1 SV=2

 Score =  210 bits (534), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 98/138 (71%), Positives = 116/138 (84%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct: 486 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 545

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           +DLK LLLEA+Q++PP L  L    E  LD+GG ERGCA+CGGLGHRIT CPKLEA+QTK
Sbjct: 546 MDLKALLLEAKQKVPPVLQVLHCGDESMLDIGG-ERGCAFCGGLGHRITDCPKLEAMQTK 604

Query: 121 AASSIGRRDYLNSNQADY 138
             S+IGR+DYL  +  D+
Sbjct: 605 QVSNIGRKDYLAHSSMDF 622

Probable ATP-dependent RNA helicase. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9LU46|RH35_ARATH DEAD-box ATP-dependent RNA helicase 35 OS=Arabidopsis thaliana GN=RH35 PE=2 SV=1

 Score =  181 bits (460), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 91/136 (66%), Positives = 103/136 (75%), Gaps = 5/136 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +I+HVINYDMP ++ENYVHRIGRTGR GKTG+ATTFINK+  E+ L
Sbjct: 451 LVATDVASKGLDFPDIQHVINYDMPAEIENYVHRIGRTGRCGKTGIATTFINKNQSETTL 510

Query: 61  LDLKHLLLEARQRIPPFLAELE---SETEKFLDLGGDERGCAYCGGLGHRITACPKLEAV 117
           LDLKHLL EA+QRIPP LAEL     E E   +  G  +GCAYCGGLGHRI  CPKLE  
Sbjct: 511 LDLKHLLQEAKQRIPPVLAELNDPMEEAETIANASG-VKGCAYCGGLGHRIRDCPKLEH- 568

Query: 118 QTKAASSIGRRDYLNS 133
           Q   A S  R+DY  S
Sbjct: 569 QKSVAISNSRKDYFGS 584

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9SZB4|RH43_ARATH Putative DEAD-box ATP-dependent RNA helicase 43 OS=Arabidopsis thaliana GN=RH43 PE=3 SV=1

 Score =  180 bits (457), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 90/137 (65%), Positives = 105/137 (76%), Gaps = 5/137 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +I+HVINYDMP ++ENYVHRIGRTGR GKTG+ATTFINK+  E  L
Sbjct: 402 LVATDVASKGLDFPDIQHVINYDMPGEIENYVHRIGRTGRCGKTGIATTFINKNQSEITL 461

Query: 61  LDLKHLLLEARQRIPPFLAELE---SETEKFLDLGGDERGCAYCGGLGHRITACPKLEAV 117
           LDLKHLL EA+QRIPP LAEL     ETE   +  G  +GCAYCGGLGHRI  CPK E  
Sbjct: 462 LDLKHLLQEAKQRIPPVLAELNGPMEETETIANASG-VKGCAYCGGLGHRILQCPKFEHQ 520

Query: 118 QTKAASSIGRRDYLNSN 134
           ++ A SS  R+D+  S+
Sbjct: 521 KSVAISS-SRKDHFGSD 536

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0E3X4|RH35A_ORYSJ DEAD-box ATP-dependent RNA helicase 35A OS=Oryza sativa subsp. japonica GN=Os02g0150100 PE=2 SV=2

 Score =  175 bits (444), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 84/125 (67%), Positives = 100/125 (80%), Gaps = 2/125 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +I+HVINYDMP ++ENYVHRIGRTGR GKTG+ATTFINK+  E+ L
Sbjct: 487 LVATDVASKGLDFPDIQHVINYDMPAEIENYVHRIGRTGRCGKTGIATTFINKNQTETTL 546

Query: 61  LDLKHLLLEARQRIPPFLAELES--ETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQ 118
           LDLKHLL EA+QRIPP LAEL    E E+ +      +GCAYCGGLGHR+T CPKLE  +
Sbjct: 547 LDLKHLLKEAKQRIPPVLAELNDPLEDEETMAKESGVKGCAYCGGLGHRVTDCPKLEHQK 606

Query: 119 TKAAS 123
           + A +
Sbjct: 607 SMAIA 611

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5Z6G5|RH35B_ORYSJ DEAD-box ATP-dependent RNA helicase 35B OS=Oryza sativa subsp. japonica GN=Os06g0697200 PE=3 SV=1

 Score =  165 bits (417), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 79/134 (58%), Positives = 99/134 (73%), Gaps = 4/134 (2%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLD  +I+HVINYDMP ++ENYVHRIGRTGR GKTG+ATTFINK+  E+ L
Sbjct: 478 LVATDVASKGLDIPDIQHVINYDMPAEIENYVHRIGRTGRRGKTGVATTFINKNQTETTL 537

Query: 61  LDLKHLLLEARQRIPPFLAELESETEK---FLDLGGDERGCAYCGGLGHRITACPKLEAV 117
           LDLK LL+E++QR+PP LA+L+   E     +      +GCA+CGGLGHRI ACPK + +
Sbjct: 538 LDLKQLLIESKQRLPPILADLDDPQEDDKVAIAQQSGVKGCAFCGGLGHRIEACPK-QQL 596

Query: 118 QTKAASSIGRRDYL 131
           Q     +  R DY 
Sbjct: 597 QNSVTLARARSDYF 610

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q54KG1|DDX41_DICDI Probable ATP-dependent RNA helicase ddx41 OS=Dictyostelium discoideum GN=ddx41 PE=1 SV=1

 Score =  140 bits (352), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 79/150 (52%), Positives = 102/150 (68%), Gaps = 18/150 (12%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF EI+HVIN+DMP ++ENY+HRIGRTGR G  G+ATTFINK+N ES+L
Sbjct: 528 LVATDVASKGLDFPEIQHVINFDMPREIENYIHRIGRTGRRGNKGVATTFINKNNTESLL 587

Query: 61  LDLKHLLLEARQRIPPFLAELESET---EKFLDLGG---------DERGCAYCGGLGHRI 108
           LDLK+LL+EA+Q++PP L E+  +    +K  D  G         D + C YC G GHR+
Sbjct: 588 LDLKYLLIEAKQKVPPALLEIPDDNQYLQKLQDRNGNTGGGADDDDTKPCEYCDGRGHRL 647

Query: 109 TACPKLEAVQTKAASSIGRRDYLNSNQADY 138
             CPKL+    K A    +RD+  S   D+
Sbjct: 648 VNCPKLK----KQAGP--KRDFFGSGGGDW 671

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A7TKR8|DED1_VANPO ATP-dependent RNA helicase DED1 OS=Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294) GN=DED1 PE=3 SV=1

 Score =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 44/87 (50%), Positives = 64/87 (73%), Gaps = 1/87 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT VA++GLD   + HV+NYD+P D+++YVHRIGRTGR+G TG+AT F N+ N  +++
Sbjct: 471 LVATAVAARGLDIPNVTHVVNYDLPSDIDDYVHRIGRTGRAGNTGVATAFFNRGN-RNIV 529

Query: 61  LDLKHLLLEARQRIPPFLAELESETEK 87
             +  LL EA Q IPPFL ++  E+ +
Sbjct: 530 KGMYELLAEANQEIPPFLNDVMRESGR 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.

Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294) (taxid: 436907)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q75B50|DED1_ASHGO ATP-dependent RNA helicase DED1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=DED1 PE=3 SV=2

 Score =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 45/84 (53%), Positives = 64/84 (76%), Gaps = 1/84 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT VA++GLD   + HVINYD+P D+++YVHRIGRTGR+G TGLAT F N+ N ++V+
Sbjct: 456 LVATAVAARGLDIPNVTHVINYDLPSDIDDYVHRIGRTGRAGNTGLATAFFNRGN-KNVV 514

Query: 61  LDLKHLLLEARQRIPPFLAELESE 84
            +L  +L EA Q +P FL+++  E
Sbjct: 515 KELVDILEEANQEVPSFLSQIAKE 538

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.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

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	138
193683780	615	PREDICTED: ATP-dependent RNA helicase ab	0.992	0.222	0.840	8e-64
322784405	626	hypothetical protein SINV_10914 [Solenop	0.992	0.218	0.826	4e-63
332024917	625	ATP-dependent RNA helicase abstrakt [Acr	0.992	0.219	0.818	1e-62
307174080	620	ATP-dependent RNA helicase abstrakt [Cam	0.992	0.220	0.818	1e-62
380024659	621	PREDICTED: ATP-dependent RNA helicase ab	0.992	0.220	0.811	1e-62
328783258	621	PREDICTED: ATP-dependent RNA helicase ab	0.992	0.220	0.811	1e-62
340725455	625	PREDICTED: ATP-dependent RNA helicase ab	0.992	0.219	0.811	1e-62
307203840	624	ATP-dependent RNA helicase abstrakt [Har	0.992	0.219	0.818	1e-62
350415294	625	PREDICTED: ATP-dependent RNA helicase ab	0.992	0.219	0.811	2e-62
383858565	625	PREDICTED: ATP-dependent RNA helicase ab	0.992	0.219	0.811	2e-62

>gi|193683780|ref|XP_001952119.1| PREDICTED: ATP-dependent RNA helicase abstrakt-like [Acyrthosiphon pisum]

 Score =  248 bits (632), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 116/138 (84%), Positives = 129/138 (93%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDFEEI+HVINYDMPDDVENYVHRIGRTGRSGKTG+ATTFINK+NDESVL
Sbjct: 479 LVATDVASKGLDFEEIQHVINYDMPDDVENYVHRIGRTGRSGKTGIATTFINKANDESVL 538

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EARQ +P FL+ELESE EK+L L GDERGC+YCGGLGHRIT CPKLEA+QTK
Sbjct: 539 LDLKHLLIEARQNVPLFLSELESENEKYLQL-GDERGCSYCGGLGHRITDCPKLEAIQTK 597

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL ++ ADY
Sbjct: 598 QASNIGRRDYLATSAADY 615

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322784405|gb|EFZ11376.1| hypothetical protein SINV_10914 [Solenopsis invicta]

 Score =  245 bits (625), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 114/138 (82%), Positives = 128/138 (92%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF E++HVINYDMPDDVENYVHRIGRTGRSG+TG+ATTFINK+NDESVL
Sbjct: 490 LVATDVASKGLDFAEVQHVINYDMPDDVENYVHRIGRTGRSGRTGIATTFINKANDESVL 549

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EA+Q++PPFL EL SE EK+L+L GDERGC+YCGGLGHRIT CPKLEAVQ K
Sbjct: 550 LDLKHLLMEAKQKVPPFLLELCSENEKYLNL-GDERGCSYCGGLGHRITECPKLEAVQNK 608

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL SN ADY
Sbjct: 609 QASNIGRRDYLASNAADY 626

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332024917|gb|EGI65105.1| ATP-dependent RNA helicase abstrakt [Acromyrmex echinatior]

 Score =  244 bits (622), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 113/138 (81%), Positives = 128/138 (92%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +++HVINYDMPDDVENYVHRIGRTGRSG+TG+ATTFINK+NDESVL
Sbjct: 489 LVATDVASKGLDFADVQHVINYDMPDDVENYVHRIGRTGRSGRTGIATTFINKANDESVL 548

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EA+Q++PPFL EL SE EK+L+L GDERGC+YCGGLGHRIT CPKLEAVQ K
Sbjct: 549 LDLKHLLMEAKQKVPPFLLELCSENEKYLNL-GDERGCSYCGGLGHRITECPKLEAVQNK 607

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL SN ADY
Sbjct: 608 QASNIGRRDYLASNAADY 625

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307174080|gb|EFN64767.1| ATP-dependent RNA helicase abstrakt [Camponotus floridanus]

 Score =  244 bits (622), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 113/138 (81%), Positives = 128/138 (92%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +++HVINYDMPDDVENYVHRIGRTGRSG+TG+ATTFINK+NDESVL
Sbjct: 484 LVATDVASKGLDFADVQHVINYDMPDDVENYVHRIGRTGRSGRTGIATTFINKANDESVL 543

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EA+Q++PPFL EL SE EK+L+L GDERGC+YCGGLGHRIT CPKLEAVQ K
Sbjct: 544 LDLKHLLMEAKQKVPPFLLELCSENEKYLNL-GDERGCSYCGGLGHRITECPKLEAVQNK 602

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL SN ADY
Sbjct: 603 QASNIGRRDYLASNAADY 620

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380024659|ref|XP_003696110.1| PREDICTED: ATP-dependent RNA helicase abstrakt-like [Apis florea]

 Score =  244 bits (622), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 112/138 (81%), Positives = 128/138 (92%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +++HVINYDMPDDVENYVHRIGRTGRSG+TG+ATTFINK+NDESVL
Sbjct: 485 LVATDVASKGLDFADVQHVINYDMPDDVENYVHRIGRTGRSGRTGIATTFINKANDESVL 544

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EA+Q++PPFL EL SE EK+L+L GDERGC+YCGGLGHRIT CPKLEA+Q K
Sbjct: 545 LDLKHLLMEAKQKVPPFLLELCSENEKYLNL-GDERGCSYCGGLGHRITECPKLEAIQNK 603

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL SN ADY
Sbjct: 604 QASNIGRRDYLASNAADY 621

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328783258|ref|XP_392069.4| PREDICTED: ATP-dependent RNA helicase abstrakt isoform 1 [Apis mellifera]

 Score =  244 bits (622), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 112/138 (81%), Positives = 128/138 (92%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +++HVINYDMPDDVENYVHRIGRTGRSG+TG+ATTFINK+NDESVL
Sbjct: 485 LVATDVASKGLDFADVQHVINYDMPDDVENYVHRIGRTGRSGRTGIATTFINKANDESVL 544

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EA+Q++PPFL EL SE EK+L+L GDERGC+YCGGLGHRIT CPKLEA+Q K
Sbjct: 545 LDLKHLLMEAKQKVPPFLLELCSENEKYLNL-GDERGCSYCGGLGHRITECPKLEAIQNK 603

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL SN ADY
Sbjct: 604 QASNIGRRDYLASNAADY 621

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340725455|ref|XP_003401085.1| PREDICTED: ATP-dependent RNA helicase abstrakt-like [Bombus terrestris]

 Score =  243 bits (621), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 112/138 (81%), Positives = 128/138 (92%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +++HVINYDMPDDVENYVHRIGRTGRSG+TG+ATTFINK+NDESVL
Sbjct: 489 LVATDVASKGLDFADVQHVINYDMPDDVENYVHRIGRTGRSGRTGIATTFINKANDESVL 548

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EA+Q++PPFL EL SE EK+L+L GDERGC+YCGGLGHRIT CPKLEA+Q K
Sbjct: 549 LDLKHLLMEAKQKVPPFLLELCSENEKYLNL-GDERGCSYCGGLGHRITECPKLEAIQNK 607

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL SN ADY
Sbjct: 608 QASNIGRRDYLASNAADY 625

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307203840|gb|EFN82776.1| ATP-dependent RNA helicase abstrakt [Harpegnathos saltator]

 Score =  243 bits (621), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 113/138 (81%), Positives = 128/138 (92%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +++HVINYDMPDDVENYVHRIGRTGRSG+TG+ATTFINK+NDESVL
Sbjct: 488 LVATDVASKGLDFADVQHVINYDMPDDVENYVHRIGRTGRSGRTGIATTFINKANDESVL 547

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EA+Q++PPFL EL SE EK+L+L GDERGC+YCGGLGHRIT CPKLEAVQ K
Sbjct: 548 LDLKHLLMEAKQKVPPFLLELCSENEKYLNL-GDERGCSYCGGLGHRITECPKLEAVQNK 606

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL SN ADY
Sbjct: 607 QASNIGRRDYLASNAADY 624

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350415294|ref|XP_003490595.1| PREDICTED: ATP-dependent RNA helicase abstrakt-like [Bombus impatiens]

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 112/138 (81%), Positives = 128/138 (92%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +++HVINYDMPDDVENYVHRIGRTGRSG+TG+ATTFINK+NDESVL
Sbjct: 489 LVATDVASKGLDFADVQHVINYDMPDDVENYVHRIGRTGRSGRTGIATTFINKANDESVL 548

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EA+Q++PPFL EL SE EK+L+L GDERGC+YCGGLGHRIT CPKLEA+Q K
Sbjct: 549 LDLKHLLMEAKQKVPPFLLELCSENEKYLNL-GDERGCSYCGGLGHRITECPKLEAIQNK 607

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL SN ADY
Sbjct: 608 QASNIGRRDYLASNAADY 625

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858565|ref|XP_003704771.1| PREDICTED: ATP-dependent RNA helicase abstrakt-like [Megachile rotundata]

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 112/138 (81%), Positives = 128/138 (92%), Gaps = 1/138 (0%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF +++HVINYDMPDDVENYVHRIGRTGRSG+TG+ATTFINK+NDESVL
Sbjct: 489 LVATDVASKGLDFADVQHVINYDMPDDVENYVHRIGRTGRSGRTGIATTFINKANDESVL 548

Query: 61  LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
           LDLKHLL+EA+Q++PPFL EL SE EK+L+L GDERGC+YCGGLGHRIT CPKLEA+Q K
Sbjct: 549 LDLKHLLMEAKQKVPPFLLELCSENEKYLNL-GDERGCSYCGGLGHRITDCPKLEAIQNK 607

Query: 121 AASSIGRRDYLNSNQADY 138
            AS+IGRRDYL SN ADY
Sbjct: 608 QASNIGRRDYLASNAADY 625

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

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	138
FB|FBgn0015331	619	abs "abstrakt" [Drosophila mel	0.992	0.221	0.726	5.1e-51
UNIPROTKB|E2R052	622	DDX41 "Uncharacterized protein	0.992	0.220	0.710	4.6e-50
UNIPROTKB|J9NZF6	649	DDX41 "Uncharacterized protein	0.992	0.211	0.710	4.6e-50
UNIPROTKB|J3KNN5	640	DDX41 "Probable ATP-dependent	0.992	0.214	0.710	4.6e-50
UNIPROTKB|Q9UJV9	622	DDX41 "Probable ATP-dependent	0.992	0.220	0.710	4.6e-50
MGI|MGI:1920185	622	Ddx41 "DEAD (Asp-Glu-Ala-Asp)	0.992	0.220	0.710	4.6e-50
RGD|1311758	622	Ddx41 "DEAD (Asp-Glu-Ala-Asp)	0.992	0.220	0.710	4.6e-50
UNIPROTKB|A3KN07	622	DDX41 "Uncharacterized protein	0.992	0.220	0.702	1.2e-49
ZFIN|ZDB-GENE-030131-1927	473	ddx41 "DEAD (Asp-Glu-Ala-Asp)	0.992	0.289	0.688	1.2e-49
RGD|1559513	621	RGD1559513 "similar to DEAD (A	0.992	0.220	0.695	4.1e-49

FB|FBgn0015331 abs "abstrakt" [Drosophila melanogaster (taxid:7227)]

 Score = 530 (191.6 bits), Expect = 5.1e-51, P = 5.1e-51
 Identities = 101/139 (72%), Positives = 115/139 (82%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  ++HVINYDMPDD+ENYVHRIGRTGRS   GLATT INK+ ++SVL
Sbjct:   482 LVATDVASKGLDFPNVQHVINYDMPDDIENYVHRIGRTGRSNTKGLATTLINKTTEQSVL 541

Query:    61 LDLKHLLLEARQRIPPFLAELESETE-KFLDLGGDERGCAYCGGLGHRITACPKLEAVQT 119
             LDLKHLL+E +Q +P FL EL  ETE + LDLG D  GC YCGGLGHRIT CPKLEAVQ 
Sbjct:   542 LDLKHLLIEGKQEVPDFLDELAPETEHQHLDLG-DSHGCTYCGGLGHRITECPKLEAVQN 600

Query:   120 KAASSIGRRDYLNSNQADY 138
             K AS+IGRRDYL++  ADY
Sbjct:   601 KQASNIGRRDYLSNTAADY 619

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

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

GO:0004386 "helicase activity" evidence=ISS

GO:0030010 "establishment of cell polarity" evidence=NAS

GO:0007399 "nervous system development" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

GO:0009653 "anatomical structure morphogenesis" evidence=NAS

GO:0006915 "apoptotic process" evidence=NAS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

UNIPROTKB|E2R052 DDX41 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 98/138 (71%), Positives = 116/138 (84%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct:   486 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 545

Query:    61 LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
             +DLK LLLEA+Q++PP L  L    E  LD+GG ERGCA+CGGLGHRIT CPKLEA+QTK
Sbjct:   546 MDLKALLLEAKQKVPPVLQVLHCGDESMLDIGG-ERGCAFCGGLGHRITDCPKLEAMQTK 604

Query:   121 AASSIGRRDYLNSNQADY 138
               S+IGR+DYL  +  D+
Sbjct:   605 QVSNIGRKDYLAHSSMDF 622

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

GO:0051607 "defense response to virus" evidence=IEA

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

GO:0035458 "cellular response to interferon-beta" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|J9NZF6 DDX41 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 98/138 (71%), Positives = 116/138 (84%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct:   513 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 572

Query:    61 LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
             +DLK LLLEA+Q++PP L  L    E  LD+GG ERGCA+CGGLGHRIT CPKLEA+QTK
Sbjct:   573 MDLKALLLEAKQKVPPVLQVLHCGDESMLDIGG-ERGCAFCGGLGHRITDCPKLEAMQTK 631

Query:   121 AASSIGRRDYLNSNQADY 138
               S+IGR+DYL  +  D+
Sbjct:   632 QVSNIGRKDYLAHSSMDF 649

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|J3KNN5 DDX41 "Probable ATP-dependent RNA helicase DDX41" [Homo sapiens (taxid:9606)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 98/138 (71%), Positives = 116/138 (84%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct:   504 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 563

Query:    61 LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
             +DLK LLLEA+Q++PP L  L    E  LD+GG ERGCA+CGGLGHRIT CPKLEA+QTK
Sbjct:   564 MDLKALLLEAKQKVPPVLQVLHCGDESMLDIGG-ERGCAFCGGLGHRITDCPKLEAMQTK 622

Query:   121 AASSIGRRDYLNSNQADY 138
               S+IGR+DYL  +  D+
Sbjct:   623 QVSNIGRKDYLAHSSMDF 640

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q9UJV9 DDX41 "Probable ATP-dependent RNA helicase DDX41" [Homo sapiens (taxid:9606)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 98/138 (71%), Positives = 116/138 (84%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct:   486 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 545

Query:    61 LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
             +DLK LLLEA+Q++PP L  L    E  LD+GG ERGCA+CGGLGHRIT CPKLEA+QTK
Sbjct:   546 MDLKALLLEAKQKVPPVLQVLHCGDESMLDIGG-ERGCAFCGGLGHRITDCPKLEAMQTK 604

Query:   121 AASSIGRRDYLNSNQADY 138
               S+IGR+DYL  +  D+
Sbjct:   605 QVSNIGRKDYLAHSSMDF 622

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA

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

GO:0051607 "defense response to virus" evidence=IEA

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

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

GO:0007275 "multicellular organismal development" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:1920185 Ddx41 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Mus musculus (taxid:10090)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 98/138 (71%), Positives = 116/138 (84%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct:   486 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 545

Query:    61 LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
             +DLK LLLEA+Q++PP L  L    E  LD+GG ERGCA+CGGLGHRIT CPKLEA+QTK
Sbjct:   546 MDLKALLLEAKQKVPPVLQVLHCGDESMLDIGG-ERGCAFCGGLGHRITDCPKLEAMQTK 604

Query:   121 AASSIGRRDYLNSNQADY 138
               S+IGR+DYL  +  D+
Sbjct:   605 QVSNIGRKDYLAHSSMDF 622

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IMP

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0051607 "defense response to virus" evidence=IMP

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

RGD|1311758 Ddx41 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Rattus norvegicus (taxid:10116)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 98/138 (71%), Positives = 116/138 (84%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct:   486 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 545

Query:    61 LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
             +DLK LLLEA+Q++PP L  L    E  LD+GG ERGCA+CGGLGHRIT CPKLEA+QTK
Sbjct:   546 MDLKALLLEAKQKVPPVLQVLHCGDESMLDIGG-ERGCAFCGGLGHRITDCPKLEAMQTK 604

Query:   121 AASSIGRRDYLNSNQADY 138
               S+IGR+DYL  +  D+
Sbjct:   605 QVSNIGRKDYLAHSSMDF 622

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005783 "endoplasmic reticulum" evidence=IEA;ISO

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA;ISO

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

GO:0051607 "defense response to virus" evidence=IEA;ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|A3KN07 DDX41 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 517 (187.1 bits), Expect = 1.2e-49, P = 1.2e-49
 Identities = 97/138 (70%), Positives = 116/138 (84%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct:   486 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 545

Query:    61 LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
             +DLK LLLEA+Q++PP L  L    E  L++GG ERGCA+CGGLGHRIT CPKLEA+QTK
Sbjct:   546 MDLKALLLEAKQKVPPVLQVLHCGDESMLEIGG-ERGCAFCGGLGHRITDCPKLEAMQTK 604

Query:   121 AASSIGRRDYLNSNQADY 138
               S+IGR+DYL  +  D+
Sbjct:   605 QVSNIGRKDYLAHSSMDF 622

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0051607 "defense response to virus" evidence=IEA

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

GO:0035458 "cellular response to interferon-beta" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

ZFIN|ZDB-GENE-030131-1927 ddx41 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Danio rerio (taxid:7955)]

 Score = 517 (187.1 bits), Expect = 1.2e-49, P = 1.2e-49
 Identities = 95/138 (68%), Positives = 117/138 (84%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  I+HV+NYDMP+++ENYVHRIGRTGRSGKTG+ATTFINK  DESVL
Sbjct:   337 LVATDVASKGLDFPAIQHVVNYDMPEEIENYVHRIGRTGRSGKTGIATTFINKGCDESVL 396

Query:    61 LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
             +DLK LL+EA+Q++PP L  L +  E  LD+GG ERGC +CGGLGHRIT CPKLEA+QTK
Sbjct:   397 MDLKALLVEAKQKVPPVLQVLHTGDETMLDIGG-ERGCTFCGGLGHRITDCPKLEAMQTK 455

Query:   121 AASSIGRRDYLNSNQADY 138
               ++IGR+DYL ++  D+
Sbjct:   456 QVTNIGRKDYLANSSMDF 473

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

RGD|1559513 RGD1559513 "similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Rattus norvegicus (taxid:10116)]

 Score = 512 (185.3 bits), Expect = 4.1e-49, P = 4.1e-49
 Identities = 96/138 (69%), Positives = 115/138 (83%)

Query:     1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
             +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTGRSG TG+ATTFINK+ DESVL
Sbjct:   485 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVL 544

Query:    61 LDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLEAVQTK 120
             +DLK LLLEA+Q++PP L  L    E  LD+GG E+GCA+CGGLGHRIT CPKLEA+QTK
Sbjct:   545 MDLKALLLEAKQKVPPVLQVLHCGDESMLDIGG-EQGCAFCGGLGHRITDCPKLEAMQTK 603

Query:   121 AASSIGRRDYLNSNQADY 138
               S+IG +DYL  +  D+
Sbjct:   604 QVSNIGHKDYLAHSSMDF 621

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6CLR3	DED1_KLULA	3, ., 6, ., 4, ., 1, 3	0.5357	0.6014	0.1323	yes	N/A
Q75B50	DED1_ASHGO	3, ., 6, ., 4, ., 1, 3	0.5357	0.6014	0.1332	yes	N/A
Q9LU46	RH35_ARATH	3, ., 6, ., 4, ., 1, 3	0.6691	0.9492	0.2216	yes	N/A
A2QI25	DED1_ASPNC	3, ., 6, ., 4, ., 1, 3	0.5555	0.5797	0.1179	yes	N/A
Q54KG1	DDX41_DICDI	3, ., 6, ., 4, ., 1, 3	0.5266	0.9565	0.1967	yes	N/A
C8V8H4	DED1_EMENI	3, ., 6, ., 4, ., 1, 3	0.5555	0.5797	0.1197	yes	N/A
Q2UGK3	DED1_ASPOR	3, ., 6, ., 4, ., 1, 3	0.5555	0.5797	0.1185	yes	N/A
A3LQ01	DED1_PICST	3, ., 6, ., 4, ., 1, 3	0.5294	0.6086	0.1298	yes	N/A
P24784	DBP1_YEAST	3, ., 6, ., 4, ., 1, 3	0.5238	0.6014	0.1345	yes	N/A
Q0E3X4	RH35A_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.672	0.8913	0.1961	yes	N/A
Q4WP13	DED1_ASPFU	3, ., 6, ., 4, ., 1, 3	0.5555	0.5797	0.1186	yes	N/A
Q91VN6	DDX41_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7101	0.9927	0.2202	yes	N/A
Q9V3C0	DDX41_DROME	3, ., 6, ., 4, ., 1, 3	0.7266	0.9927	0.2213	yes	N/A
Q8TFK8	DED1_CANGA	3, ., 6, ., 4, ., 1, 3	0.5769	0.5579	0.1247	yes	N/A
Q4I7K4	DED1_GIBZE	3, ., 6, ., 4, ., 1, 3	0.5294	0.6086	0.1244	yes	N/A
Q9UJV9	DDX41_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7101	0.9927	0.2202	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	138
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	6e-27
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	5e-26
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	2e-20
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	4e-20
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	8e-20
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	2e-18
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-17
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-17
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-17
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-16
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	1e-15
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	2e-14
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-13
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	7e-13
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	3e-06
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	1e-05
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	4e-05
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	0.003

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

 Score =  103 bits (259), Expect = 6e-27
 Identities = 42/84 (50%), Positives = 62/84 (73%), Gaps = 1/84 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           M+ATDVAS+GLD +++K+VIN+D P+ +E+YVHRIGRTGR+G  G + TF+   +   + 
Sbjct: 431 MIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLT-PDKYRLA 489

Query: 61  LDLKHLLLEARQRIPPFLAELESE 84
            DL  +L EA+Q +PP L +L +E
Sbjct: 490 RDLVKVLREAKQPVPPELEKLSNE 513

Length = 545

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

 Score =  101 bits (253), Expect = 5e-26
 Identities = 37/93 (39%), Positives = 56/93 (60%), Gaps = 3/93 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVA++GLD  ++ HVINYD+P D E+YVHRIGRTGR+G+ G+A +F+ +  +   L
Sbjct: 327 LVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKL 386

Query: 61  LDLKHLL---LEARQRIPPFLAELESETEKFLD 90
             ++  L   L +   +P    E     +    
Sbjct: 387 KRIEKRLERKLPSAVLLPLDEPEDAKLLKTTRP 419

Length = 513

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

 Score = 85.0 bits (211), Expect = 2e-20
 Identities = 29/50 (58%), Positives = 39/50 (78%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF 50
           +VATDVA++GL    + HV NYD+PDD E+YVHRIGRTGR+G +G + + 
Sbjct: 309 LVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358

Length = 423

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

 Score = 84.5 bits (210), Expect = 4e-20
 Identities = 28/52 (53%), Positives = 40/52 (76%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
           +VATDVA++GLD + ++ VINY++  D E +VHRIGRTGR+G  GLA + + 
Sbjct: 296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVA 347

Length = 460

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

 Score = 83.5 bits (207), Expect = 8e-20
 Identities = 27/51 (52%), Positives = 41/51 (80%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFI 51
           +VATDVA++G+D +++ HVIN+DMP   + Y+HRIGRTGR+G+ G A + +
Sbjct: 299 LVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLV 349

Length = 434

>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 = 75.0 bits (185), Expect = 2e-18
 Identities = 23/50 (46%), Positives = 33/50 (66%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF 50
           +VATDV ++G+D   +  VINYD+P    +Y+ RIGR GR+G+ G A   
Sbjct: 82  LVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131

Length = 131

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

 Score = 71.8 bits (177), Expect = 1e-17
 Identities = 22/42 (52%), Positives = 32/42 (76%)

Query: 1  MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG 42
          +VATDVA +G+D  ++  VINYD+P +  +Y+ RIGR GR+G
Sbjct: 37 LVATDVAGRGIDLPDVNLVINYDLPWNPASYIQRIGRAGRAG 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|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 77.2 bits (190), Expect = 1e-17
 Identities = 35/61 (57%), Positives = 45/61 (73%), Gaps = 2/61 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++ATDVA++GLD E I  V+NYD+P D E+YVHRIGRTGR+G+ G A  F+   N E  L
Sbjct: 299 LIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVE--NRERRL 356

Query: 61  L 61
           L
Sbjct: 357 L 357

Length = 629

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

 Score = 76.8 bits (189), Expect = 2e-17
 Identities = 38/76 (50%), Positives = 55/76 (72%), Gaps = 6/76 (7%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATD+A++GLD EE+ HV+NY++P+  E+YVHRIGRTGR+  TG A + +    DE  L
Sbjct: 299 LVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLV--CVDEHKL 356

Query: 61  L-DLKHLLLEARQRIP 75
           L D++ LL   ++ IP
Sbjct: 357 LRDIEKLL---KKEIP 369

Length = 456

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

 Score = 72.3 bits (177), Expect = 9e-16
 Identities = 29/61 (47%), Positives = 45/61 (73%), Gaps = 2/61 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVA +G+  + I HVIN+ +P+D ++YVHRIGRTGR+G +G++ +F     D++  
Sbjct: 389 LVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFA--GEDDAFQ 446

Query: 61  L 61
           L
Sbjct: 447 L 447

Length = 475

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

 Score = 66.9 bits (164), Expect = 1e-15
 Identities = 22/42 (52%), Positives = 29/42 (69%)

Query: 1  MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG 42
          +VATDVA +GLD   +  VI YD+P    +Y+ RIGR GR+G
Sbjct: 41 LVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score = 68.4 bits (167), Expect = 2e-14
 Identities = 38/83 (45%), Positives = 51/83 (61%), Gaps = 6/83 (7%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVA++GL  + +K+V NYD+P D E+YVHRIGRT R G+ G A +F      E   
Sbjct: 311 LVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFAC----ERYA 366

Query: 61  LDLKHLLLEARQRIP--PFLAEL 81
           + L  +     Q+IP  P  AEL
Sbjct: 367 MSLPDIEAYIEQKIPVEPVTAEL 389

Length = 572

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

 Score = 66.0 bits (161), Expect = 1e-13
 Identities = 25/57 (43%), Positives = 41/57 (71%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDE 57
           ++ TD+ ++G+D +++  VINYD+P   ENY+HRIGR+GR G+ G+A  F+   + E
Sbjct: 321 LITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIE 377

Length = 401

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

 Score = 64.0 bits (156), Expect = 7e-13
 Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 1/79 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT V  +G+D   ++ VI +DMP+ ++ Y+H+IGR  R G+ G A  F+N+ +  ++ 
Sbjct: 422 IVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEED-RNLF 480

Query: 61  LDLKHLLLEARQRIPPFLA 79
            +L  LL  +   IP  LA
Sbjct: 481 PELVALLKSSGAAIPRELA 499

Length = 518

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 28/121 (23%), Positives = 46/121 (38%), Gaps = 23/121 (19%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF---------- 50
           MVAT+    G+D  +++ VI+YD+P  +E+Y    GR GR G    A             
Sbjct: 284 MVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQR 343

Query: 51  --INKSNDESVLLDLKHLLLEARQRIPPFLAELESET---EKFLDLGGDER--GCAYCGG 103
             I +S  +               ++   +A  E++T      L   G++    C  C  
Sbjct: 344 YLIEQSKPDEEQKQ------IELAKLRQMIAYCETQTCRRLVLLKYFGEDEPEPCGNCDN 397

Query: 104 L 104
            
Sbjct: 398 C 398

Length = 590

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 19/42 (45%), Positives = 27/42 (64%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG 42
           MVAT+    G+D   ++ VI+YDMP ++E+Y    GR GR G
Sbjct: 278 MVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDG 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|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family

 Score = 41.3 bits (97), Expect = 4e-05
 Identities = 15/41 (36%), Positives = 24/41 (58%)

Query: 2   VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG 42
           VAT     G++  +++ VI+Y +P  +E+Y    GR GR G
Sbjct: 281 VATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDG 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|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 2/42 (4%)

Query: 1   MVATDVASKGLDFEEIKHVINYD-MPDDVENYVHRIGRTGRS 41
           +VAT V  +GLD  E+  VI Y+ +P ++   + R GRTGR 
Sbjct: 429 LVATSVGEEGLDIPEVDLVIFYEPVPSEIR-SIQRKGRTGRK 469

Length = 542

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	138
KOG0341|consensus	610		99.97
KOG0331|consensus	519		99.86
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.86
KOG0328|consensus	400		99.85
KOG0336|consensus	629		99.84
KOG0335|consensus	482		99.83
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.83
PTZ00110	545	helicase; Provisional	99.83
KOG0333|consensus	673		99.83
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.81
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.8
KOG0330|consensus	476		99.8
KOG0342|consensus	543		99.79
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.79
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.79
KOG0340|consensus	442		99.78
KOG0326|consensus	459		99.78
KOG0332|consensus	477		99.75
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.75
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.75
KOG0345|consensus	567		99.74
KOG0344|consensus	593		99.73
KOG0352|consensus	641		99.73
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.71
KOG0348|consensus	708		99.7
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.69
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.69
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.69
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.69
KOG0338|consensus	691		99.68
KOG0351|consensus	941		99.68
KOG0350|consensus	620		99.68
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.68
KOG0343|consensus	758		99.66
PTZ00424	401	helicase 45; Provisional	99.66
KOG0347|consensus	731		99.64
KOG0329|consensus	387		99.63
KOG0339|consensus	731		99.63
KOG0327|consensus	397		99.62
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.6
KOG0334|consensus	997		99.58
KOG0353|consensus	695		99.57
KOG0346|consensus	569		99.52
KOG4284|consensus	980		99.51
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.51
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.48
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.45
PRK04914	956	ATP-dependent helicase HepA; Validated	99.43
PRK13767	876	ATP-dependent helicase; Provisional	99.33
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.32
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.31
PHA02653	675	RNA helicase NPH-II; Provisional	99.29
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.26
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.25
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.24
PRK05298	652	excinuclease ABC subunit B; Provisional	99.24
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.23
KOG0337|consensus	529		99.22
KOG0349|consensus	725		99.22
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.2
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.2
PRK13766	773	Hef nuclease; Provisional	99.2
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.19
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.17
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.16
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.16
PRK10689	1147	transcription-repair coupling factor; Provisional	99.12
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.11
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.05
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.03
PRK02362	737	ski2-like helicase; Provisional	99.01
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.0
KOG0354|consensus	746		98.97
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.94
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.92
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.9
PHA02558	501	uvsW UvsW helicase; Provisional	98.9
PRK00254	720	ski2-like helicase; Provisional	98.83
COG1201	814	Lhr Lhr-like helicases [General function predictio	98.73
PRK01172	674	ski2-like helicase; Provisional	98.7
PRK14701	1638	reverse gyrase; Provisional	98.55
KOG4150|consensus	1034		98.52
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.44
PRK05580	679	primosome assembly protein PriA; Validated	98.42
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.33
PRK09401	1176	reverse gyrase; Reviewed	98.3
PRK09694	878	helicase Cas3; Provisional	98.09
COG1205	851	Distinct helicase family with a unique C-terminal	98.03
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	97.9
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	97.79
KOG0947|consensus	1248		97.63
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	97.5
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	97.49
KOG0953|consensus	700		97.45
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	97.42
KOG0948|consensus	1041		97.41
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	97.4
PRK12904	830	preprotein translocase subunit SecA; Reviewed	97.33
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.17
KOG0390|consensus	776		96.92
KOG0950|consensus	1008		96.91
COG1204	766	Superfamily II helicase [General function predicti	96.88
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	96.81
PRK12326	764	preprotein translocase subunit SecA; Reviewed	96.79
KOG0926|consensus	1172		96.74
PRK13107	908	preprotein translocase subunit SecA; Reviewed	96.74
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	96.74
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	96.36
COG1202	830	Superfamily II helicase, archaea-specific [General	96.35
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	96.33
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	96.32
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	96.23
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	96.23
KOG0387|consensus	923		96.1
KOG0923|consensus	902		96.05
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	96.05
KOG0924|consensus	1042		95.83
KOG0385|consensus	971		95.64
KOG0922|consensus	674		95.55
KOG0384|consensus	1373		95.4
KOG0920|consensus	924		95.31
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	95.15
KOG0949|consensus	1330		94.79
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.68
PF13871	278	Helicase_C_4: Helicase_C-like	94.38
KOG1000|consensus	689		93.89
COG4889	1518	Predicted helicase [General function prediction on	93.76
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	93.55
KOG1015|consensus	1567		93.2
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	91.91
KOG0388|consensus	1185		91.67
KOG0951|consensus	1674		91.56
CHL00122	870	secA preprotein translocase subunit SecA; Validate	91.26
KOG0389|consensus	941		90.94
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	89.62
KOG0701|consensus	1606		89.44
KOG0925|consensus	699		89.2
KOG0952|consensus	1230		88.91
KOG0386|consensus	1157		88.89
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	88.8
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	88.77
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	88.03
KOG0392|consensus	1549		87.46
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	86.0
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	82.93
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	82.31
COG4096	875	HsdR Type I site-specific restriction-modification	81.26

>KOG0341|consensus

Probab=99.97  E-value=9.3e-32  Score=215.04  Aligned_cols=133  Identities=74%  Similarity=1.205  Sum_probs=125.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      |||||+++.|+|+|++.+|||||+|.++++|+||+||+||.|+.|.+.+|++...++..+.+++..+.+.++++|+.|..
T Consensus       475 LVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~~esvLlDLK~LL~EakQ~vP~~L~~  554 (610)
T KOG0341|consen  475 LVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQEESVLLDLKHLLQEAKQEVPPVLAE  554 (610)
T ss_pred             EEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccchHHHHHHHHHHHHHhhccCCHHHHH
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHH--HHHhhCCCCCCCCcCCCCCcccccccchHHHHHHHhhhcCCccccCcC
Q psy7792          81 LESETE--KFLDLGGDERGCAYCGGLGHRITACPKLEAVQTKAASSIGRRDYLNSN  134 (138)
Q Consensus        81 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~crr~~~~~~  134 (138)
                      +....+  .+++. +.+.+|.||+|+||++++|+|++.++.+..++..|++|+.+.
T Consensus       555 L~~~~E~~~~a~~-~~~kGCayCgGLGHRItdCPKle~~~~k~~sn~gRkdy~~~~  609 (610)
T KOG0341|consen  555 LAGPMEEETIADA-GGEKGCAYCGGLGHRITDCPKLEAQQNKQISNIGRKDYLGSG  609 (610)
T ss_pred             hCCCccccccccC-CCccccccccCCCcccccCchhhhhcchhhhhhccccccCCC
Confidence            987666  34443 577899999999999999999999999999999999999875

>KOG0331|consensus

Probab=99.86  E-value=4.9e-22  Score=164.78  Aligned_cols=84  Identities=50%  Similarity=0.827  Sum_probs=78.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      |||||+++||||+|+|++|||||+|.+++.|+||+||+||+|+.|.+++|++.. +......+.+.+.+..+.+|+.+..
T Consensus       395 LVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~-~~~~a~~l~~~l~e~~q~v~~~l~~  473 (519)
T KOG0331|consen  395 LVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSD-NAKLARELIKVLREAGQTVPPDLLE  473 (519)
T ss_pred             EEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHH-HHHHHHHHHHHHHHccCCCChHHHH
Confidence            799999999999999999999999999999999999999999999999999987 8889999999999999999998776


Q ss_pred             HHHHH
Q psy7792          81 LESET   85 (138)
Q Consensus        81 ~~~~~   85 (138)
                      .....
T Consensus       474 ~~~~~  478 (519)
T KOG0331|consen  474 YARVS  478 (519)
T ss_pred             HHhhc
Confidence            65443

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

Probab=99.86  E-value=5.9e-22  Score=166.62  Aligned_cols=60  Identities=33%  Similarity=0.564  Sum_probs=55.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLL   61 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~   61 (138)
                      ||||.+|+||||+|||++|||||+|.++++|+|++|||||+|.++.|++||++. |....+
T Consensus       284 iVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAGRDG~~a~aill~~~~-D~~~~~  343 (590)
T COG0514         284 MVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPE-DIRWQR  343 (590)
T ss_pred             EEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhccCCCCcceEEEeeccc-cHHHHH
Confidence            699999999999999999999999999999999999999999999999999998 444333

>KOG0328|consensus

Probab=99.85  E-value=1.3e-21  Score=151.69  Aligned_cols=79  Identities=37%  Similarity=0.744  Sum_probs=75.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||+||+++||||+|.|++|||||+|.+.+.|+||+||.||.|++|++|.|+... +...++++++++.....++|..+.+
T Consensus       320 LitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~-d~~~lrdieq~yst~i~emp~nvad  398 (400)
T KOG0328|consen  320 LITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSD-DLRILRDIEQYYSTQIDEMPMNVAD  398 (400)
T ss_pred             EEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHH-HHHHHHHHHHHHhhhcccccchhhh
Confidence            689999999999999999999999999999999999999999999999999876 9999999999999999999987654

>KOG0336|consensus

Probab=99.84  E-value=1.2e-20  Score=152.27  Aligned_cols=87  Identities=44%  Similarity=0.761  Sum_probs=83.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      |||||+++||||++||.+|+|||+|.+++.|+||+||+||+|+.|.+++|++.+ |..+...+.+.+....+++|..|-.
T Consensus       519 LvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~-D~~~a~eLI~ILe~aeQevPdeL~~  597 (629)
T KOG0336|consen  519 LVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRN-DWSMAEELIQILERAEQEVPDELVR  597 (629)
T ss_pred             EEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehh-hHHHHHHHHHHHHHhhhhCcHHHHH
Confidence            799999999999999999999999999999999999999999999999999987 9999999999999999999999988


Q ss_pred             HHHHHHHH
Q psy7792          81 LESETEKF   88 (138)
Q Consensus        81 ~~~~~~~~   88 (138)
                      .++.++..
T Consensus       598 mAeryk~~  605 (629)
T KOG0336|consen  598 MAERYKLK  605 (629)
T ss_pred             HHHHHHhh
Confidence            88877654

>KOG0335|consensus

Probab=99.83  E-value=7.2e-21  Score=156.12  Aligned_cols=80  Identities=54%  Similarity=0.953  Sum_probs=76.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||++++||||+|+|++|||||+|.+...|+|||||+||+|..|.+++|++.. +......+.+.+.+.++++|+||.+
T Consensus       391 lVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~-~~~i~~~L~~~l~ea~q~vP~wl~~  469 (482)
T KOG0335|consen  391 LVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEK-NQNIAKALVEILTEANQEVPQWLSE  469 (482)
T ss_pred             EEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccc-cchhHHHHHHHHHHhcccCcHHHHh
Confidence            699999999999999999999999999999999999999999999999999954 8889999999999999999999988


Q ss_pred             H
Q psy7792          81 L   81 (138)
Q Consensus        81 ~   81 (138)
                      +
T Consensus       470 ~  470 (482)
T KOG0335|consen  470 L  470 (482)
T ss_pred             h
Confidence            4

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

Probab=99.83  E-value=3.6e-21  Score=170.46  Aligned_cols=54  Identities=26%  Similarity=0.517  Sum_probs=52.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||++|+||||+|+|++|||||+|.+++.|+||+|||||+|.+|.+|+||+..
T Consensus       734 LVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~  787 (1195)
T PLN03137        734 ICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYS  787 (1195)
T ss_pred             EEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHH
Confidence            699999999999999999999999999999999999999999999999999876

>PTZ00110 helicase; Provisional

Probab=99.83  E-value=1.9e-20  Score=157.82  Aligned_cols=84  Identities=50%  Similarity=0.852  Sum_probs=79.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||++++||||+|+|++|||||+|.++++|+||+||+||+|+.|.+++|+++. +......+.+.+....+.+|++|..
T Consensus       431 LVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~-~~~~~~~l~~~l~~~~q~vp~~l~~  509 (545)
T PTZ00110        431 MIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPD-KYRLARDLVKVLREAKQPVPPELEK  509 (545)
T ss_pred             EEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcc-hHHHHHHHHHHHHHccCCCCHHHHH
Confidence            699999999999999999999999999999999999999999999999999987 8888999999999999999999988


Q ss_pred             HHHHH
Q psy7792          81 LESET   85 (138)
Q Consensus        81 ~~~~~   85 (138)
                      +....
T Consensus       510 ~~~~~  514 (545)
T PTZ00110        510 LSNER  514 (545)
T ss_pred             HHHHh
Confidence            85433

>KOG0333|consensus

Probab=99.83  E-value=6.6e-21  Score=156.99  Aligned_cols=80  Identities=49%  Similarity=0.847  Sum_probs=69.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHH-HhcccCcHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLL-EARQRIPPFLA   79 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~l~   79 (138)
                      |||||+++||||+|+|.+|||||++++++.|+|||||+||+|+.|.+++|+++. +..++.+|+..+. ......|+.+.
T Consensus       571 lVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~-dt~v~ydLkq~l~es~~s~~P~Ela  649 (673)
T KOG0333|consen  571 LVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPA-DTAVFYDLKQALRESVKSHCPPELA  649 (673)
T ss_pred             EEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccc-hhHHHHHHHHHHHHhhhccCChhhc
Confidence            699999999999999999999999999999999999999999999999999998 7777778877766 44555666554


Q ss_pred             HH
Q psy7792          80 EL   81 (138)
Q Consensus        80 ~~   81 (138)
                      ..
T Consensus       650 ~h  651 (673)
T KOG0333|consen  650 NH  651 (673)
T ss_pred             cC
Confidence            43

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

Probab=99.81  E-value=5.7e-20  Score=154.04  Aligned_cols=81  Identities=37%  Similarity=0.689  Sum_probs=76.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||++++||||+|+|++|||||+|.++++|+||+|||||.|..|.+++|+++. +...+..+.+.++..++.+|++|..
T Consensus       422 LVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~-~~~~~~~l~~~l~~~~~~vp~~l~~  500 (518)
T PLN00206        422 IVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEE-DRNLFPELVALLKSSGAAIPRELAN  500 (518)
T ss_pred             EEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchh-HHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            699999999999999999999999999999999999999999999999999876 7788899999999999999998876


Q ss_pred             HH
Q psy7792          81 LE   82 (138)
Q Consensus        81 ~~   82 (138)
                      ..
T Consensus       501 ~~  502 (518)
T PLN00206        501 SR  502 (518)
T ss_pred             Ch
Confidence            53

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.80  E-value=5.2e-20  Score=156.82  Aligned_cols=54  Identities=30%  Similarity=0.608  Sum_probs=52.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||++++||||+|+|++|||||+|.++++|+||+|||||+|.+|.+++|+++.
T Consensus       290 LVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~  343 (607)
T PRK11057        290 VVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPA  343 (607)
T ss_pred             EEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHH
Confidence            699999999999999999999999999999999999999999999999999987

>KOG0330|consensus

Probab=99.80  E-value=1.3e-19  Score=145.17  Aligned_cols=72  Identities=39%  Similarity=0.739  Sum_probs=66.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhccc
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQR   73 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~   73 (138)
                      |||||+++||+|+|+|++|||||+|.+...||||+||+||+|.+|.+|+|++.- |...+..|+..+.+...+
T Consensus       354 Lv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqy-Dve~~qrIE~~~gkkl~~  425 (476)
T KOG0330|consen  354 LVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQY-DVELVQRIEHALGKKLPE  425 (476)
T ss_pred             EEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehh-hhHHHHHHHHHHhcCCCc
Confidence            699999999999999999999999999999999999999999999999999985 788888888888777655

>KOG0342|consensus

Probab=99.79  E-value=1.2e-19  Score=148.28  Aligned_cols=84  Identities=39%  Similarity=0.610  Sum_probs=68.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      |||||+++||+|+|+|++||+||+|++++.||||+||+||.|+.|.+++++.|. +..+++.+++.-.+..+-.+.....
T Consensus       384 L~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~-El~Flr~LK~lpl~~~e~~~~~~~~  462 (543)
T KOG0342|consen  384 LVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPW-ELGFLRYLKKLPLEEFEFPPLKPED  462 (543)
T ss_pred             EEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChh-HHHHHHHHhhCCCcccCCCCCCHHH
Confidence            699999999999999999999999999999999999999999999999999997 7888888875433333333333333


Q ss_pred             HHHHH
Q psy7792          81 LESET   85 (138)
Q Consensus        81 ~~~~~   85 (138)
                      +....
T Consensus       463 v~~~~  467 (543)
T KOG0342|consen  463 VQSQL  467 (543)
T ss_pred             HHHHH
Confidence            33333

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

Probab=99.79  E-value=6.9e-20  Score=153.46  Aligned_cols=70  Identities=49%  Similarity=0.868  Sum_probs=64.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHh
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA   70 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~   70 (138)
                      |||||+++||||+++|++|||||+|.+++.|+||+||+||+|+.|.+++|+++.++...+..+++.....
T Consensus       327 LVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~~~~~~  396 (513)
T COG0513         327 LVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERK  396 (513)
T ss_pred             EEEechhhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Confidence            7999999999999999999999999999999999999999999999999999865788888888876555

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.79  E-value=1.5e-19  Score=149.82  Aligned_cols=60  Identities=30%  Similarity=0.528  Sum_probs=55.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLL   61 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~   61 (138)
                      ||||++++||||+|+|++||||++|.+++.|+||+|||||+|.+|.+++|+++. +...++
T Consensus       280 LVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~-d~~~~~  339 (470)
T TIGR00614       280 VVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPA-DINRLR  339 (470)
T ss_pred             EEEechhhccCCcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechh-HHHHHH
Confidence            699999999999999999999999999999999999999999999999999987 443333

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

>KOG0340|consensus

Probab=99.78  E-value=1.9e-19  Score=142.89  Aligned_cols=74  Identities=35%  Similarity=0.677  Sum_probs=66.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCc
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIP   75 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~   75 (138)
                      |||||+++||+|+|.|.+|||||+|.+|..|+||+||++|+|+.|.+|+++++. |...+..++....+...+.+
T Consensus       308 liaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~r-Dv~l~~aiE~~igkKl~e~~  381 (442)
T KOG0340|consen  308 LIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQR-DVELLQAIEEEIGKKLTEYN  381 (442)
T ss_pred             EEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechh-hHHHHHHHHHHHhccccccc
Confidence            699999999999999999999999999999999999999999999999999977 77777777777666655443

>KOG0326|consensus

Probab=99.78  E-value=2e-19  Score=141.54  Aligned_cols=76  Identities=38%  Similarity=0.681  Sum_probs=70.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPF   77 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~   77 (138)
                      |||||.+.||||+++|++|||||+|+++++|+||+||+||.|..|.||++++.+ |...+..++..+......+|+.
T Consensus       376 LVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLitye-drf~L~~IE~eLGtEI~pip~~  451 (459)
T KOG0326|consen  376 LVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYE-DRFNLYRIEQELGTEIKPIPSN  451 (459)
T ss_pred             eeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehh-hhhhHHHHHHHhccccccCCCc
Confidence            799999999999999999999999999999999999999999999999999997 8888888888888777777764

>KOG0332|consensus

Probab=99.75  E-value=1.5e-18  Score=138.48  Aligned_cols=76  Identities=36%  Similarity=0.743  Sum_probs=67.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC------CHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRI   74 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~------~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~   74 (138)
                      ||+|++++||||++.|+.|||||+|.      ++++|+||+||+||.|+.|.+|+++.......++..|+++++.....+
T Consensus       384 LitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~i~~~  463 (477)
T KOG0332|consen  384 LITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMKIKRL  463 (477)
T ss_pred             EEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhcceec
Confidence            69999999999999999999999994      699999999999999999999999988877788888888886665554


Q ss_pred             cH
Q psy7792          75 PP   76 (138)
Q Consensus        75 ~~   76 (138)
                      .+
T Consensus       464 ~~  465 (477)
T KOG0332|consen  464 DP  465 (477)
T ss_pred             CC
Confidence            44

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.75  E-value=4.2e-19  Score=145.11  Aligned_cols=69  Identities=43%  Similarity=0.761  Sum_probs=61.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHh
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA   70 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~   70 (138)
                      |||||+++||||+|+|++|||||+|.+++.|+||+||+||+|+.|.+|+|+++. +...+..+++.+...
T Consensus       309 LVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~-~~~~~~~i~~~~~~~  377 (423)
T PRK04837        309 LVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEE-YALNLPAIETYIGHS  377 (423)
T ss_pred             EEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHH-HHHHHHHHHHHhCCC
Confidence            699999999999999999999999999999999999999999999999999886 566666666555444

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.75  E-value=2.2e-18  Score=146.26  Aligned_cols=54  Identities=37%  Similarity=0.660  Sum_probs=52.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||++++||||+|+|++|||||+|.++++|+||+|||||+|..+.+++++++.
T Consensus       278 lVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~  331 (591)
T TIGR01389       278 MVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPA  331 (591)
T ss_pred             EEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHH
Confidence            699999999999999999999999999999999999999999999999999876

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.

>KOG0345|consensus

Probab=99.74  E-value=1.6e-18  Score=141.47  Aligned_cols=62  Identities=42%  Similarity=0.725  Sum_probs=56.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDL   63 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l   63 (138)
                      |+|||+++||||+|+|++||+||+|.++++|+||+||+||.|+.|.||+|+.+. ++.++..+
T Consensus       311 l~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~-E~aYveFl  372 (567)
T KOG0345|consen  311 LFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPR-EEAYVEFL  372 (567)
T ss_pred             EEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEeccc-HHHHHHHH
Confidence            689999999999999999999999999999999999999999999999999996 55444433

>KOG0344|consensus

Probab=99.73  E-value=5.4e-18  Score=140.88  Aligned_cols=83  Identities=33%  Similarity=0.667  Sum_probs=77.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||++++||||+.+|+.|||||+|.+.-+|+||+||+||+|+.|.||+||+.. +-...+.+...+...+.++|.++..
T Consensus       442 LicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~-d~~~ir~iae~~~~sG~evpe~~m~  520 (593)
T KOG0344|consen  442 LICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQ-DMPRIRSIAEVMEQSGCEVPEKIMG  520 (593)
T ss_pred             EEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccc-cchhhhhHHHHHHHcCCcchHHHHh
Confidence            699999999999999999999999999999999999999999999999999986 8888999999999999999999877


Q ss_pred             HHHH
Q psy7792          81 LESE   84 (138)
Q Consensus        81 ~~~~   84 (138)
                      +..-
T Consensus       521 ~~k~  524 (593)
T KOG0344|consen  521 IKKL  524 (593)
T ss_pred             hhhh
Confidence            7653

>KOG0352|consensus

Probab=99.73  E-value=8.7e-18  Score=136.40  Aligned_cols=63  Identities=25%  Similarity=0.464  Sum_probs=57.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLK   64 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~   64 (138)
                      ++||..|+||+|+|+|++|||||+|.|+..|+|+.|||||+|.++++-+||+.+ |...+..+.
T Consensus       309 I~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~-D~~~i~FLi  371 (641)
T KOG0352|consen  309 IAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQ-DKNALNFLV  371 (641)
T ss_pred             EEEEeccccccCCcceeEEEecCchhhhHHHHHhccccccCCCccceeeeeccc-chHHHHHHH
Confidence            589999999999999999999999999999999999999999999999999987 555554443

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.71  E-value=8.4e-18  Score=138.88  Aligned_cols=69  Identities=48%  Similarity=0.858  Sum_probs=62.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHh
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA   70 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~   70 (138)
                      ||||++++||||+|+|++|||||+|.++++|+||+||+||+|..|.+++|+... +...+..+++.+...
T Consensus       299 LVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~-d~~~~~~ie~~l~~~  367 (456)
T PRK10590        299 LVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVD-EHKLLRDIEKLLKKE  367 (456)
T ss_pred             EEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecHH-HHHHHHHHHHHhcCC
Confidence            699999999999999999999999999999999999999999999999999886 777777777765544

>KOG0348|consensus

Probab=99.70  E-value=2.1e-17  Score=136.79  Aligned_cols=66  Identities=38%  Similarity=0.644  Sum_probs=60.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLL   67 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~   67 (138)
                      |+|||+++||||+|+|.+||+||.|.+++.|+||+||++|+|..|.+++|+.|. +..++..+++..
T Consensus       501 LLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~-Eaey~~~l~~~~  566 (708)
T KOG0348|consen  501 LLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPS-EAEYVNYLKKHH  566 (708)
T ss_pred             EEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEEeccc-HHHHHHHHHhhc
Confidence            689999999999999999999999999999999999999999999999999999 555666666543

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.69  E-value=2.3e-17  Score=135.06  Aligned_cols=67  Identities=43%  Similarity=0.870  Sum_probs=60.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLL   68 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~   68 (138)
                      ||||++++||||+|+|++|||||+|.+.+.|+||+||+||+|..|.+++|++.. +...+..++.++.
T Consensus       299 LVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~-d~~~~~~i~~~~~  365 (434)
T PRK11192        299 LVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAH-DHLLLGKIERYIE  365 (434)
T ss_pred             EEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecHH-HHHHHHHHHHHHh
Confidence            699999999999999999999999999999999999999999999999999876 6666666665544

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.69  E-value=2.5e-17  Score=135.96  Aligned_cols=67  Identities=43%  Similarity=0.696  Sum_probs=60.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLL   68 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~   68 (138)
                      ||||+++++|||+|+|++|||||+|.++++|+||+||+||+|+.|.+++|+++. +...+..+++.+.
T Consensus       296 LVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~-e~~~~~~i~~~~~  362 (460)
T PRK11776        296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPE-EMQRANAIEDYLG  362 (460)
T ss_pred             EEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchh-HHHHHHHHHHHhC
Confidence            699999999999999999999999999999999999999999999999999887 5666666666554

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.69  E-value=3.2e-17  Score=135.94  Aligned_cols=70  Identities=44%  Similarity=0.826  Sum_probs=63.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhc
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEAR   71 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~   71 (138)
                      ||||+++++|||+++|++|||||+|.++.+|+||+||+||.|+.|.+++|++.. |...+..+++.+....
T Consensus       389 LvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~-d~~~~~~~~~~~~~~~  458 (475)
T PRK01297        389 LVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGED-DAFQLPEIEELLGRKI  458 (475)
T ss_pred             EEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHH-HHHHHHHHHHHhCCCC
Confidence            699999999999999999999999999999999999999999999999999876 6777777777765543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.69  E-value=3.4e-17  Score=140.11  Aligned_cols=67  Identities=48%  Similarity=0.872  Sum_probs=60.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLL   68 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~   68 (138)
                      ||||+++++|||+|+|++|||||+|.++++|+||+||+||+|+.|.+++|+++. +...+..+++.++
T Consensus       299 LVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~-e~~~l~~ie~~~~  365 (629)
T PRK11634        299 LIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENR-ERRLLRNIERTMK  365 (629)
T ss_pred             EEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechH-HHHHHHHHHHHhC
Confidence            699999999999999999999999999999999999999999999999999876 5666666665543

>KOG0338|consensus

Probab=99.68  E-value=4.6e-17  Score=134.23  Aligned_cols=65  Identities=46%  Similarity=0.870  Sum_probs=60.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHL   66 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~   66 (138)
                      |||||+++|||||+.|..||||++|.+.+.|+||+||++|+|+.|.+|+|+... +..+++.+.+.
T Consensus       480 LiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~-dRkllK~iik~  544 (691)
T KOG0338|consen  480 LIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGES-DRKLLKEIIKS  544 (691)
T ss_pred             EEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccc-cHHHHHHHHhh
Confidence            799999999999999999999999999999999999999999999999999887 77777777665

>KOG0351|consensus

Probab=99.68  E-value=4e-17  Score=143.75  Aligned_cols=55  Identities=29%  Similarity=0.558  Sum_probs=53.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      +|||.+|+||||+|||+.||||.+|++++.|+|++|||||+|..+.+++|+...+
T Consensus       539 ivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D  593 (941)
T KOG0351|consen  539 IVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYAD  593 (941)
T ss_pred             EEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEecchhH
Confidence            5899999999999999999999999999999999999999999999999999873

>KOG0350|consensus

Probab=99.68  E-value=3e-17  Score=134.88  Aligned_cols=68  Identities=37%  Similarity=0.663  Sum_probs=61.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLL   68 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~   68 (138)
                      |||||+++||||+.+|..|||||+|.+..+|+||+||++|+|+.|.|+++.+..+...+.+.+++...
T Consensus       487 LIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~~~~  554 (620)
T KOG0350|consen  487 LICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKKTNL  554 (620)
T ss_pred             EEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHHHHHHHHhcc
Confidence            79999999999999999999999999999999999999999999999999999866666665555444

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.68  E-value=4e-17  Score=138.44  Aligned_cols=68  Identities=46%  Similarity=0.720  Sum_probs=60.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLE   69 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~   69 (138)
                      ||||+++++|||+++|++|||||+|.+++.|+||+||+||.|+.|.+|+|+++. +...+..+++.+..
T Consensus       311 LVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~-~~~~l~~i~~~~~~  378 (572)
T PRK04537        311 LVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACER-YAMSLPDIEAYIEQ  378 (572)
T ss_pred             EEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHH-HHHHHHHHHHHHcC
Confidence            799999999999999999999999999999999999999999999999999876 55566666665543

>KOG0343|consensus

Probab=99.66  E-value=1.3e-16  Score=132.53  Aligned_cols=89  Identities=34%  Similarity=0.602  Sum_probs=70.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHH--HHhcccCcHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLL--LEARQRIPPFL   78 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~l   78 (138)
                      |+|||+++||||+|.|+|||++|-|.++++||||+||++|.+..|.++++++|++++.++..+.+..  ......-|..+
T Consensus       369 LF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~k~I~i~~i~i~~~k~  448 (758)
T KOG0343|consen  369 LFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQKKKIPIKEIKIDPEKL  448 (758)
T ss_pred             EEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHHcCCCHHhhccCHHHh
Confidence            6899999999999999999999999999999999999999999999999999997677777776641  11122224445


Q ss_pred             HHHHHHHHHHH
Q psy7792          79 AELESETEKFL   89 (138)
Q Consensus        79 ~~~~~~~~~~~   89 (138)
                      ..+....+.++
T Consensus       449 ~~i~~~l~~ll  459 (758)
T KOG0343|consen  449 TSIRNKLEALL  459 (758)
T ss_pred             hhHHHHHHHHH
Confidence            55555554443

>PTZ00424 helicase 45; Provisional

Probab=99.66  E-value=5.3e-17  Score=131.09  Aligned_cols=75  Identities=36%  Similarity=0.740  Sum_probs=65.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPP   76 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~   76 (138)
                      ||||+++++|||+|+|++|||||+|.++..|+||+||+||.|+.|.+++|+++. +...+..+++.+....++.++
T Consensus       321 LvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~-~~~~~~~~e~~~~~~~~~~~~  395 (401)
T PTZ00424        321 LITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPD-DIEQLKEIERHYNTQIEEMPM  395 (401)
T ss_pred             EEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHH-HHHHHHHHHHHHCCcccccCc
Confidence            699999999999999999999999999999999999999999999999999876 666677777666655555443

>KOG0347|consensus

Probab=99.64  E-value=8e-17  Score=133.72  Aligned_cols=69  Identities=38%  Similarity=0.639  Sum_probs=61.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHh
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA   70 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~   70 (138)
                      |||||+++||||||.|.+||||-+|.+.+-|+||.||++|++..|..++++.|. +...+..+-+.++..
T Consensus       517 LiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~-e~~~~~KL~ktL~k~  585 (731)
T KOG0347|consen  517 LIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQ-EVGPLKKLCKTLKKK  585 (731)
T ss_pred             EEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChH-HhHHHHHHHHHHhhc
Confidence            699999999999999999999999999999999999999999999999999998 455555555555544

>KOG0329|consensus

Probab=99.63  E-value=1.1e-16  Score=123.15  Aligned_cols=77  Identities=39%  Similarity=0.729  Sum_probs=67.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPF   77 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~   77 (138)
                      ||||++|+||+|+..|+.|||||+|.++.+|+||+|||||.|.+|.+|+|++..++..++..+.........++|..
T Consensus       302 ~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~i~eLpde  378 (387)
T KOG0329|consen  302 LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVNIKELPDE  378 (387)
T ss_pred             hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhhhccHhhcCcc
Confidence            68999999999999999999999999999999999999999999999999998888777777766665555555553

>KOG0339|consensus

Probab=99.63  E-value=8e-16  Score=127.03  Aligned_cols=87  Identities=43%  Similarity=0.670  Sum_probs=83.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      |||||+++||+|+++++.|||||+-.+++.|.||+||+||+|..|.+++|++.. |..+...|.+.+....+.+|+.|.+
T Consensus       522 lvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeK-Da~fAG~LVnnLe~agQnVP~~l~d  600 (731)
T KOG0339|consen  522 LVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEK-DAEFAGHLVNNLEGAGQNVPDELMD  600 (731)
T ss_pred             EEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechh-hHHHhhHHHHHHhhccccCChHHHH
Confidence            699999999999999999999999999999999999999999999999999998 7889999999999999999999999


Q ss_pred             HHHHHHHH
Q psy7792          81 LESETEKF   88 (138)
Q Consensus        81 ~~~~~~~~   88 (138)
                      +......|
T Consensus       601 lamk~s~f  608 (731)
T KOG0339|consen  601 LAMKSSWF  608 (731)
T ss_pred             HHhhhhhh
Confidence            99888655

>KOG0327|consensus

Probab=99.62  E-value=2e-16  Score=126.27  Aligned_cols=79  Identities=35%  Similarity=0.751  Sum_probs=74.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||+|+.++||||+.++..|||||+|.+.++|+||+||+||.|++|.++.+++.. +...++++++++....+++|....+
T Consensus       317 lIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~-d~~~lk~ie~~y~~~i~e~p~~~~~  395 (397)
T KOG0327|consen  317 LITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEE-DVRDLKDIEKFYNTPIEELPSNFAD  395 (397)
T ss_pred             EeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHh-hHHHHHhHHHhcCCcceecccchhh
Confidence            699999999999999999999999999999999999999999999999999887 8999999999999998888876544

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

Probab=99.60  E-value=7.2e-16  Score=134.09  Aligned_cols=69  Identities=19%  Similarity=0.317  Sum_probs=58.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC-CcHHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS-NDESVLLDLKHLLLE   69 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~-~~~~~~~~l~~~~~~   69 (138)
                      |||||++++|||+++|++|||||+|.++++|+||+|||||.|+.|.++++.+.. .|...+...++.++.
T Consensus       333 LVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~  402 (742)
T TIGR03817       333 VATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDR  402 (742)
T ss_pred             EEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcC
Confidence            699999999999999999999999999999999999999999999999998643 244455555555443

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.

>KOG0334|consensus

Probab=99.58  E-value=5.6e-15  Score=129.23  Aligned_cols=91  Identities=41%  Similarity=0.662  Sum_probs=82.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||++++||+|++++.+|||||+|...+.|+||+||+||+|++|.|++|+++. +..+..+|.+.+...++.+|..+..
T Consensus       667 LvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~-q~~~a~dl~~al~~~~~~~P~~l~~  745 (997)
T KOG0334|consen  667 LVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPD-QLKYAGDLCKALELSKQPVPKLLQA  745 (997)
T ss_pred             EEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChH-HhhhHHHHHHHHHhccCCCchHHHH
Confidence            699999999999999999999999999999999999999999999999999994 8888999999999999999988888


Q ss_pred             HHHHHHHHHhhC
Q psy7792          81 LESETEKFLDLG   92 (138)
Q Consensus        81 ~~~~~~~~~~~~   92 (138)
                      +..........+
T Consensus       746 l~~~f~~~~~~~  757 (997)
T KOG0334|consen  746 LSERFKAKQKAG  757 (997)
T ss_pred             HHHHHHhhhhcc
Confidence            877776554444

>KOG0353|consensus

Probab=99.57  E-value=1.1e-15  Score=123.09  Aligned_cols=78  Identities=22%  Similarity=0.353  Sum_probs=66.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHH-------------------------------------------Hhhc
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVH-------------------------------------------RIGR   37 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~q-------------------------------------------r~GR   37 (138)
                      +|||-+|+||||.|+|++|||..+|++++.|+|                                           +.||
T Consensus       371 ivatvafgmgidkpdvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgr  450 (695)
T KOG0353|consen  371 IVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGR  450 (695)
T ss_pred             EEEEeeecccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccc
Confidence            589999999999999999999999999999999                                           8999


Q ss_pred             cccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHH
Q psy7792          38 TGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLA   79 (138)
Q Consensus        38 agR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~   79 (138)
                      |||++.++.+|+||.-. |......+..+.+...+.+-.++.
T Consensus       451 agrd~~~a~cilyy~~~-difk~ssmv~~e~~g~q~ly~mv~  491 (695)
T KOG0353|consen  451 AGRDDMKADCILYYGFA-DIFKISSMVQMENTGIQKLYEMVR  491 (695)
T ss_pred             cccCCCcccEEEEechH-HHHhHHHHHHHHhhhHHHHHHHHH
Confidence            99999999999999776 666666677776666666555433

>KOG0346|consensus

Probab=99.52  E-value=1.4e-14  Score=117.94  Aligned_cols=63  Identities=35%  Similarity=0.719  Sum_probs=53.9

Q ss_pred             cccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHH
Q psy7792           6 VASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLE   69 (138)
Q Consensus         6 ~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~   69 (138)
                      -.+||||+.+|..|||||+|.++.+||||+||++|++++|.+++|+.|. +......++..+..
T Consensus       362 GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~-e~~g~~~le~~~~d  424 (569)
T KOG0346|consen  362 GVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPK-EEFGKESLESILKD  424 (569)
T ss_pred             chhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecch-HHhhhhHHHHHHhh
Confidence            3579999999999999999999999999999999999999999999998 44434555555444

>KOG4284|consensus

Probab=99.51  E-value=1.9e-14  Score=121.72  Aligned_cols=63  Identities=37%  Similarity=0.697  Sum_probs=56.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDL   63 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l   63 (138)
                      ||+||+.+||||-++|++|||.|+|.+-++|+||||||||.|..|.+|+|+....+..-+..|
T Consensus       326 LVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e~~~f~~m  388 (980)
T KOG4284|consen  326 LVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERELKGFTAM  388 (980)
T ss_pred             EEecchhhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchhhhhhHHH
Confidence            799999999999999999999999999999999999999999999999999877553444444

>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=99.51  E-value=1.4e-14  Score=92.03  Aligned_cols=42  Identities=48%  Similarity=0.884  Sum_probs=40.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG   42 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g   42 (138)
                      ||||+++++|||+|++++||++++|+++..|+|++||++|.|
T Consensus        37 li~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen   37 LIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             EEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             EEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            689999999999999999999999999999999999999986

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 ....

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.48  E-value=5.3e-14  Score=120.42  Aligned_cols=54  Identities=30%  Similarity=0.439  Sum_probs=51.7

Q ss_pred             CeecccccccCCCC---Ccc-----EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFE---EIK-----HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~---~V~-----~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      |||||+++||+|++   +|.     +|||||+|.+...|+||+||+||.|.+|.+++|++..
T Consensus       525 lVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~e  586 (656)
T PRK12898        525 TVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLE  586 (656)
T ss_pred             EEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechh
Confidence            59999999999999   777     9999999999999999999999999999999999986

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.45  E-value=3.4e-13  Score=117.54  Aligned_cols=55  Identities=31%  Similarity=0.488  Sum_probs=52.4

Q ss_pred             CeecccccccCCC---CCcc-----EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDF---EEIK-----HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~---~~V~-----~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      +||||+++||+|+   ++|.     +|||||+|.+...|.||+||+||.|.+|.+++|++..+
T Consensus       480 lIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD  542 (790)
T PRK09200        480 TVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLED  542 (790)
T ss_pred             EEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchH
Confidence            5999999999999   6999     99999999999999999999999999999999998863

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.43  E-value=1.9e-13  Score=121.23  Aligned_cols=68  Identities=21%  Similarity=0.355  Sum_probs=54.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLE   69 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~   69 (138)
                      ||||+++++|+|++.+++|||||+|+||+.|.||+||++|.|+++.+..++-.. .......+...+..
T Consensus       550 LIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~-~~t~~e~i~~~~~~  617 (956)
T PRK04914        550 LLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYL-EGTAQERLFRWYHE  617 (956)
T ss_pred             EEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccC-CCCHHHHHHHHHhh
Confidence            699999999999999999999999999999999999999999988765555333 33344444444444

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.33  E-value=2.4e-12  Score=114.01  Aligned_cols=54  Identities=24%  Similarity=0.439  Sum_probs=46.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccC-CCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRS-GKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~-g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|+|++||+|+.|.++.+|+||+||+||. |..+..+.+....
T Consensus       344 LVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~~  398 (876)
T PRK13767        344 VVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVDR  398 (876)
T ss_pred             EEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcCc
Confidence            69999999999999999999999999999999999999976 4445555555443

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.32  E-value=1.1e-11  Score=106.49  Aligned_cols=52  Identities=21%  Similarity=0.291  Sum_probs=49.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC-CHHHHHHHhhccccCCCcceEEEeee
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD-DVENYVHRIGRTGRSGKTGLATTFIN   52 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~-~~~~y~qr~GRagR~g~~g~~i~~~~   52 (138)
                      ||||+++++|||+|++++||+++.|. +.+.|.||+||+||.|++|.|++++.
T Consensus       512 LVaT~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       512 LVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             EEECceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            69999999999999999999999997 68888999999999999999999983

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.31  E-value=4.3e-12  Score=109.78  Aligned_cols=53  Identities=19%  Similarity=0.288  Sum_probs=49.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC-CHHHHHHHhhccccCCCcceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD-DVENYVHRIGRTGRSGKTGLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~-~~~~y~qr~GRagR~g~~g~~i~~~~~   53 (138)
                      ||||+++++|+|+|++++||++++|. ..+.|.|++||+||.|.+|.|+++++.
T Consensus       535 LVaT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~  588 (681)
T PRK10917        535 LVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKD  588 (681)
T ss_pred             EEECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECC
Confidence            69999999999999999999999997 578888999999999999999999953

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.29  E-value=2e-12  Score=111.48  Aligned_cols=54  Identities=20%  Similarity=0.353  Sum_probs=49.9

Q ss_pred             CeecccccccCCCCCccEEEEcC---CCC---------CHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD---MPD---------DVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d---lP~---------~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      |||||++++|||+++|++||++|   .|.         +.++|+||+|||||. ++|.++.|++..+
T Consensus       450 LVATdIAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~  515 (675)
T PHA02653        450 IISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDL  515 (675)
T ss_pred             EeccChhhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHH
Confidence            69999999999999999999999   676         888999999999999 7899999998763

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.26  E-value=2.5e-11  Score=105.43  Aligned_cols=54  Identities=26%  Similarity=0.449  Sum_probs=50.7

Q ss_pred             CeecccccccCCCC---------CccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFE---------EIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~---------~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      +||||+++||+|++         .+.+|++|++|..... .||+||+||.|.+|.+++|++..+
T Consensus       476 lIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD  538 (762)
T TIGR03714       476 TVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLED  538 (762)
T ss_pred             EEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccch
Confidence            59999999999999         9999999999998876 999999999999999999998863

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

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

Probab=99.25  E-value=1.6e-11  Score=101.54  Aligned_cols=53  Identities=34%  Similarity=0.559  Sum_probs=50.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|+|+.||.|++-+|+-.++||.||+||. +.|.++++++..
T Consensus       429 LVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~g  481 (542)
T COG1111         429 LVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEG  481 (542)
T ss_pred             EEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecC
Confidence            79999999999999999999999999999999999999996 778999988766

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.24  E-value=3.6e-11  Score=104.13  Aligned_cols=55  Identities=25%  Similarity=0.360  Sum_probs=51.9

Q ss_pred             CeecccccccCCCCC-------ccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEE-------IKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~-------V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      +||||.++||+|++.       .-+||++++|.+...|.|++||+||.|.+|.+++|++..+
T Consensus       457 tIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD  518 (745)
T TIGR00963       457 TIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLED  518 (745)
T ss_pred             EEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccH
Confidence            589999999999998       4499999999999999999999999999999999999873

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.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.24  E-value=2e-11  Score=105.24  Aligned_cols=77  Identities=19%  Similarity=0.323  Sum_probs=63.7

Q ss_pred             CeecccccccCCCCCccEEEEcCC-----CCCHHHHHHHhhccccCCCcceEEEeeeCC--------CcHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDM-----PDDVENYVHRIGRTGRSGKTGLATTFINKS--------NDESVLLDLKHLL   67 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dl-----P~~~~~y~qr~GRagR~g~~g~~i~~~~~~--------~~~~~~~~l~~~~   67 (138)
                      ||||+++++|+|+|++++||++|.     |.+.++|+||+||+||. ..|.+++|++..        .+....+.+...+
T Consensus       500 lV~t~~L~rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~  578 (652)
T PRK05298        500 LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAY  578 (652)
T ss_pred             EEEeCHHhCCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHh
Confidence            488999999999999999999985     78999999999999996 789999999843        2455566666677


Q ss_pred             HHhcccCcHHH
Q psy7792          68 LEARQRIPPFL   78 (138)
Q Consensus        68 ~~~~~~~~~~l   78 (138)
                      +.....+|...
T Consensus       579 ~~~~~~~~~~~  589 (652)
T PRK05298        579 NEEHGITPKTI  589 (652)
T ss_pred             hhccCCCChhH
Confidence            77777777643

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.23  E-value=1.1e-11  Score=110.01  Aligned_cols=54  Identities=22%  Similarity=0.331  Sum_probs=50.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC-CHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD-DVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~-~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|+|++||+++.|. +...|+||+||+||.|+.|.|++++.+.
T Consensus       716 LVaT~iie~GIDIp~v~~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       716 LVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             EEECChhhcccccccCCEEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            69999999999999999999999975 6889999999999999999999998653

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.

>KOG0337|consensus

Probab=99.22  E-value=2.4e-12  Score=104.53  Aligned_cols=64  Identities=47%  Similarity=0.835  Sum_probs=56.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKH   65 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~   65 (138)
                      ||.||+++||+|+|-...|||||+|.+..-|+||+||+.|+|+.|++++++.+. +...+-++..
T Consensus       315 lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~-~~~yl~DL~l  378 (529)
T KOG0337|consen  315 LVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVAST-DDPYLLDLQL  378 (529)
T ss_pred             EEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecc-cchhhhhhhh
Confidence            689999999999999999999999999999999999999999999999999887 4444444443

>KOG0349|consensus

Probab=99.22  E-value=5e-12  Score=103.48  Aligned_cols=61  Identities=44%  Similarity=0.795  Sum_probs=55.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLD   62 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~   62 (138)
                      |||||+++||||+..+.++||..+|.+...|+||+||+||+.+-|.+|+++... .+..+..
T Consensus       562 lictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgraermglaislvat~-~ekvwyh  622 (725)
T KOG0349|consen  562 LICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVATV-PEKVWYH  622 (725)
T ss_pred             EEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhhhcceeEEEeecc-chheeeh
Confidence            699999999999999999999999999999999999999999999999999765 4554443

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.20  E-value=3e-11  Score=104.09  Aligned_cols=61  Identities=23%  Similarity=0.419  Sum_probs=52.7

Q ss_pred             CeecccccccCCCCCccEEEEcC-----CCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD-----MPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDL   63 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d-----lP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l   63 (138)
                      ||||+++++|+|+|+|++||++|     .|.+..+|+||+|||||. ..|.+++|++.. ...+...+
T Consensus       496 LV~t~~L~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~-~~~~~~ai  561 (655)
T TIGR00631       496 LVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKI-TDSMQKAI  561 (655)
T ss_pred             EEEcChhcCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCC-CHHHHHHH
Confidence            58899999999999999999999     899999999999999998 679999999865 44443333

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

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.20  E-value=1.4e-11  Score=107.36  Aligned_cols=55  Identities=25%  Similarity=0.447  Sum_probs=52.3

Q ss_pred             CeecccccccCCCC---Ccc-----EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFE---EIK-----HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~---~V~-----~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      +|||+.++||+||+   +|.     +||++++|.+...|.|+.||+||.|.+|.+..|++..+
T Consensus       492 tIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD  554 (796)
T PRK12906        492 TIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLED  554 (796)
T ss_pred             EEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccc
Confidence            58999999999994   899     99999999999999999999999999999999999874

>PRK13766 Hef nuclease; Provisional

Probab=99.20  E-value=3.5e-11  Score=105.02  Aligned_cols=53  Identities=36%  Similarity=0.540  Sum_probs=47.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|. |.++.++...
T Consensus       427 LvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~  479 (773)
T PRK13766        427 LVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKG  479 (773)
T ss_pred             EEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCC
Confidence            6999999999999999999999999999999999999999876 6677776543

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.19  E-value=1e-11  Score=99.12  Aligned_cols=42  Identities=31%  Similarity=0.541  Sum_probs=37.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcc
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTG   45 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g   45 (138)
                      ||||+++++|||++ +++||+++.|  +++|+||+||+||.|+..
T Consensus       282 lvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR~g~~~  323 (358)
T TIGR01587       282 IVATQVIEASLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRKN  323 (358)
T ss_pred             EEECcchhceeccC-CCEEEEcCCC--HHHHHHHhccccCCCCCC
Confidence            69999999999995 8999999877  789999999999998653

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.17  E-value=3.1e-11  Score=110.78  Aligned_cols=52  Identities=31%  Similarity=0.449  Sum_probs=45.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccC-CCcceEEEeee
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRS-GKTGLATTFIN   52 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~-g~~g~~i~~~~   52 (138)
                      ||||+.+++|||+++|++||||+.|.++.+|+||+||+||. |..+.++.+..
T Consensus       331 LVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~  383 (1490)
T PRK09751        331 VVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPR  383 (1490)
T ss_pred             EEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeC
Confidence            69999999999999999999999999999999999999985 34455554433

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.16  E-value=2.2e-11  Score=76.53  Aligned_cols=42  Identities=52%  Similarity=0.919  Sum_probs=40.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG   42 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g   42 (138)
                      ||+|+++++|+|++++++||.+++|+++..|.|++||++|.|
T Consensus        41 li~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~g   82 (82)
T smart00490       41 LVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG   82 (82)
T ss_pred             EEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccCC
Confidence            589999999999999999999999999999999999999975

>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=99.16  E-value=2.1e-11  Score=83.10  Aligned_cols=50  Identities=46%  Similarity=0.856  Sum_probs=46.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEe
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF   50 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~   50 (138)
                      |++|.++++|+|+|.+++||.+++|+++..|+|++||++|.|+.|.++.|
T Consensus        82 li~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          82 LVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             EEEcChhhcCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            58999999999999999999999999999999999999999988877653

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.12  E-value=2.7e-11  Score=109.57  Aligned_cols=53  Identities=21%  Similarity=0.265  Sum_probs=44.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCC-CCHHHHHHHhhccccCCCcceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP-DDVENYVHRIGRTGRSGKTGLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP-~~~~~y~qr~GRagR~g~~g~~i~~~~~   53 (138)
                      ||||+++++|||+|+|++||..+.. .++..|+||+||+||.|+.|.+++++..
T Consensus       865 LVaTdIierGIDIP~v~~VIi~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~  918 (1147)
T PRK10689        865 LVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPH  918 (1147)
T ss_pred             EEECchhhcccccccCCEEEEecCCCCCHHHHHHHhhccCCCCCceEEEEEeCC
Confidence            6999999999999999999933221 1345699999999999999999998754

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.11  E-value=3.4e-11  Score=105.86  Aligned_cols=53  Identities=26%  Similarity=0.447  Sum_probs=48.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCC------------------HHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDD------------------VENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~------------------~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      |||||++++|||+++|++||++++|..                  -++|.||+|||||. .+|.|+.+++..
T Consensus       266 lVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~  336 (819)
T TIGR01970       266 VLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEE  336 (819)
T ss_pred             EEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHH
Confidence            699999999999999999999999963                  34689999999999 799999999865

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.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.05  E-value=5.5e-10  Score=98.84  Aligned_cols=55  Identities=20%  Similarity=0.437  Sum_probs=50.4

Q ss_pred             CeecccccccCCCC---CccE-----EEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFE---EIKH-----VINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~---~V~~-----VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      +||||.++||+||+   .|..     ||+++.|.+...|.|++||+||.|.+|.+++|++..+
T Consensus       650 tIATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD  712 (1025)
T PRK12900        650 TIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLED  712 (1025)
T ss_pred             EEeccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhH
Confidence            59999999999999   6654     5999999999999999999999999999999999863

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.03  E-value=1.2e-10  Score=102.45  Aligned_cols=53  Identities=26%  Similarity=0.488  Sum_probs=47.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCH------------------HHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDV------------------ENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~------------------~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      |||||++++|||+++|++||++++|...                  ++|+||+|||||. .+|.|+.+++..
T Consensus       269 lvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~  339 (812)
T PRK11664        269 VLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKE  339 (812)
T ss_pred             EEecchHHhcccccCceEEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHH
Confidence            6999999999999999999998888643                  5899999999998 689999999865

>PRK02362 ski2-like helicase; Provisional

Probab=99.01  E-value=4.1e-10  Score=98.20  Aligned_cols=54  Identities=30%  Similarity=0.481  Sum_probs=48.8

Q ss_pred             CeecccccccCCCCCccEEEE----cC-----CCCCHHHHHHHhhccccCCCc--ceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----YD-----MPDDVENYVHRIGRTGRSGKT--GLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----~d-----lP~~~~~y~qr~GRagR~g~~--g~~i~~~~~~   54 (138)
                      ||||+++++|+|+|++++||+    ||     .|-+..+|.||+|||||.|..  |.++++....
T Consensus       333 LvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~  397 (737)
T PRK02362        333 ISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSY  397 (737)
T ss_pred             EEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCc
Confidence            699999999999999999998    77     689999999999999999864  8899988654

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.00  E-value=2.4e-10  Score=103.83  Aligned_cols=53  Identities=30%  Similarity=0.450  Sum_probs=47.4

Q ss_pred             CeecccccccCCCCCccEEEEcC---------------CCC---CHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD---------------MPD---DVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d---------------lP~---~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      |||||++++|||+|+|++||+++               +|.   +.++|.||+|||||. .+|.|+.+|+..
T Consensus       341 IVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~  411 (1294)
T PRK11131        341 VLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSED  411 (1294)
T ss_pred             EEeccHHhhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHH
Confidence            69999999999999999999986               453   458999999999999 689999999865

>KOG0354|consensus

Probab=98.97  E-value=1.1e-09  Score=94.46  Aligned_cols=52  Identities=38%  Similarity=0.532  Sum_probs=47.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+++|+.||-||...++-..+||.|| ||.. .|.++++++..
T Consensus       478 LVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa~-ns~~vll~t~~  529 (746)
T KOG0354|consen  478 LVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRAR-NSKCVLLTTGS  529 (746)
T ss_pred             EEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-cccc-CCeEEEEEcch
Confidence            7999999999999999999999999999999999999 8974 47888888744

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.94  E-value=5.7e-10  Score=101.48  Aligned_cols=53  Identities=26%  Similarity=0.398  Sum_probs=48.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC------------------CHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD------------------DVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~------------------~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      |||||++++|||+|+|++||++++|.                  |.++|.||+||+||.+ +|.|+.+|+..
T Consensus       334 VLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~  404 (1283)
T TIGR01967       334 VLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEE  404 (1283)
T ss_pred             EEeccHHHhccccCCeeEEEeCCCccccccccccCccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHH
Confidence            68999999999999999999999653                  5689999999999998 89999999865

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.92  E-value=3e-09  Score=92.46  Aligned_cols=55  Identities=20%  Similarity=0.306  Sum_probs=48.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCC-CCHHHHHHHhhccccCCCcceE-------EEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP-DDVENYVHRIGRTGRSGKTGLA-------TTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP-~~~~~y~qr~GRagR~g~~g~~-------i~~~~~~~   55 (138)
                      ||+|+++.+|||+|++++||+++.| .+...|+||+||++|.+..+.+       +.|+++..
T Consensus       546 Lv~SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT  608 (732)
T TIGR00603       546 IFLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDT  608 (732)
T ss_pred             EEEecccccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCc
Confidence            6899999999999999999999998 5999999999999998865554       78887664

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).

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

Probab=98.90  E-value=1.1e-09  Score=96.21  Aligned_cols=50  Identities=22%  Similarity=0.410  Sum_probs=42.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCc-ceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKT-GLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~-g~~i~~~~~   53 (138)
                      ||||+++++|||++. ++||++..|  .++|+||+||+||.|+. +.+++++..
T Consensus       340 LVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~~  390 (844)
T TIGR02621       340 LVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVHL  390 (844)
T ss_pred             EeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEee
Confidence            699999999999987 899998777  68999999999999985 444666644

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=98.90  E-value=1.3e-09  Score=91.33  Aligned_cols=52  Identities=25%  Similarity=0.296  Sum_probs=45.0

Q ss_pred             Ceec-ccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeee
Q psy7792           1 MVAT-DVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN   52 (138)
Q Consensus         1 LvaT-~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~   52 (138)
                      |||| +++++|+|+|++++||++++|++...|+||+||++|.+.......+++
T Consensus       398 LvaT~~~l~eG~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K~~~~i~D  450 (501)
T PHA02558        398 IVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKSIATVWD  450 (501)
T ss_pred             EEEEcceeccccccccccEEEEecCCcchhhhhhhhhccccCCCCCceEEEEE
Confidence            5788 899999999999999999999999999999999999876554444443

>PRK00254 ski2-like helicase; Provisional

Probab=98.83  E-value=6.6e-09  Score=90.52  Aligned_cols=54  Identities=24%  Similarity=0.417  Sum_probs=46.4

Q ss_pred             CeecccccccCCCCCccEEEE-------cCCCC-CHHHHHHHhhccccCC--CcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN-------YDMPD-DVENYVHRIGRTGRSG--KTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~-------~dlP~-~~~~y~qr~GRagR~g--~~g~~i~~~~~~   54 (138)
                      ||||+++++|+|+|.+++||+       ++.|. ....|.||+|||||.|  ..|.++++..+.
T Consensus       325 LvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~  388 (720)
T PRK00254        325 ITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTE  388 (720)
T ss_pred             EEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCc
Confidence            699999999999999999994       66665 4679999999999965  679999998764

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

Probab=98.73  E-value=1.2e-08  Score=89.50  Aligned_cols=54  Identities=31%  Similarity=0.560  Sum_probs=50.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccc-cCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTG-RSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRag-R~g~~g~~i~~~~~~   54 (138)
                      +|||+.++.|||+.+|+.||||.-|.+++..+||+||+| |.+..+..+.+....
T Consensus       308 vV~TSSLELGIDiG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~r  362 (814)
T COG1201         308 VVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAEDR  362 (814)
T ss_pred             EEEccchhhccccCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecCH
Confidence            599999999999999999999999999999999999999 788888888887664

>PRK01172 ski2-like helicase; Provisional

Probab=98.70  E-value=2.1e-08  Score=86.69  Aligned_cols=53  Identities=26%  Similarity=0.360  Sum_probs=42.5

Q ss_pred             CeecccccccCCCCCccEEEEcCC---------CCCHHHHHHHhhccccCCC--cceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDM---------PDDVENYVHRIGRTGRSGK--TGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dl---------P~~~~~y~qr~GRagR~g~--~g~~i~~~~~~   54 (138)
                      ||||+++++|+|+|... ||.+|.         |-++.+|.||+|||||.|.  .|.++.+....
T Consensus       315 LvaT~~la~Gvnipa~~-VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~  378 (674)
T PRK01172        315 IVATPTLAAGVNLPARL-VIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASP  378 (674)
T ss_pred             EEecchhhccCCCcceE-EEEcCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCc
Confidence            69999999999999864 555554         4578899999999999984  56787776544

>PRK14701 reverse gyrase; Provisional

Probab=98.55  E-value=2e-08  Score=93.71  Aligned_cols=52  Identities=19%  Similarity=0.268  Sum_probs=45.5

Q ss_pred             Ceec----ccccccCCCCC-ccEEEEcCCCC---CHHHHHHHh-------------hccccCCCcceEEEeee
Q psy7792           1 MVAT----DVASKGLDFEE-IKHVINYDMPD---DVENYVHRI-------------GRTGRSGKTGLATTFIN   52 (138)
Q Consensus         1 LvaT----~~~~~GiD~~~-V~~VI~~dlP~---~~~~y~qr~-------------GRagR~g~~g~~i~~~~   52 (138)
                      ||||    ++++||||+|+ |++|||||+|+   +++.|.|..             ||+||+|.++.+++.+.
T Consensus       382 LVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~  454 (1638)
T PRK14701        382 LIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLDVF  454 (1638)
T ss_pred             EEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhHHHhH
Confidence            6999    58999999998 99999999999   999999987             99999998777764443

>KOG4150|consensus

Probab=98.52  E-value=1.3e-07  Score=80.22  Aligned_cols=65  Identities=23%  Similarity=0.406  Sum_probs=54.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC-cHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN-DESVLLDLKH   65 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~-~~~~~~~l~~   65 (138)
                      +|||++++.|||+...+.|++.++|-++..+.|..|||||..+++.++.++.... |..++..-..
T Consensus       587 iIaTNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y~~HP~~  652 (1034)
T KOG4150|consen  587 IIATNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYYMSHPDK  652 (1034)
T ss_pred             EEecchhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHhhcCcHH
Confidence            5899999999999999999999999999999999999999999999888775443 3333333333

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.44  E-value=4.2e-07  Score=81.87  Aligned_cols=47  Identities=19%  Similarity=0.259  Sum_probs=44.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceE
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLA   47 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~   47 (138)
                      |++|.+++.|||+..+++||+||+||||..+.|++||+-|.|+...+
T Consensus       544 LLSTrAGGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V  590 (1033)
T PLN03142        544 LLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEV  590 (1033)
T ss_pred             EEeccccccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceE
Confidence            68999999999999999999999999999999999999999986444

>PRK05580 primosome assembly protein PriA; Validated

Probab=98.42  E-value=3.8e-07  Score=79.28  Aligned_cols=51  Identities=25%  Similarity=0.387  Sum_probs=43.0

Q ss_pred             CeecccccccCCCCCccEE--EEcCCCCC----------HHHHHHHhhccccCCCcceEEEee
Q psy7792           1 MVATDVASKGLDFEEIKHV--INYDMPDD----------VENYVHRIGRTGRSGKTGLATTFI   51 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~V--I~~dlP~~----------~~~y~qr~GRagR~g~~g~~i~~~   51 (138)
                      ||+|+++++|+|+|+|.+|  ++.|.+-+          ...|+|++||+||.++.|.++..-
T Consensus       484 LVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra~Er~~~~l~q~~GRagR~~~~g~viiqT  546 (679)
T PRK05580        484 LIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQT  546 (679)
T ss_pred             EEEChhhccCCCCCCcCEEEEEcCchhccCCccchHHHHHHHHHHHHhhccCCCCCCEEEEEe
Confidence            6999999999999999998  45565543          367999999999999999988654

>TIGR00595 priA primosomal protein N'

Probab=98.33  E-value=1.1e-06  Score=74.15  Aligned_cols=54  Identities=26%  Similarity=0.474  Sum_probs=43.9

Q ss_pred             CeecccccccCCCCCccEE--EEcCC----CC------CHHHHHHHhhccccCCCcceEEEe-eeCC
Q psy7792           1 MVATDVASKGLDFEEIKHV--INYDM----PD------DVENYVHRIGRTGRSGKTGLATTF-INKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~V--I~~dl----P~------~~~~y~qr~GRagR~g~~g~~i~~-~~~~   54 (138)
                      ||+|+.+++|+|+|+|.+|  +++|.    |+      ....|+|++||+||.++.|.++.. +++.
T Consensus       316 LVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~  382 (505)
T TIGR00595       316 LIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPN  382 (505)
T ss_pred             EEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEEEEeCCCC
Confidence            6999999999999999987  57775    43      257799999999999999988843 3443

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).

>PRK09401 reverse gyrase; Reviewed

Probab=98.30  E-value=1.1e-06  Score=80.42  Aligned_cols=39  Identities=26%  Similarity=0.335  Sum_probs=36.1

Q ss_pred             Cee----cccccccCCCCC-ccEEEEcCCCC------CHHHHHHHhhccc
Q psy7792           1 MVA----TDVASKGLDFEE-IKHVINYDMPD------DVENYVHRIGRTG   39 (138)
Q Consensus         1 Lva----T~~~~~GiD~~~-V~~VI~~dlP~------~~~~y~qr~GRag   39 (138)
                      ||+    ||+++||||+|+ |++|||||+|.      ..+.|.||+||+-
T Consensus       380 LVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~  429 (1176)
T PRK09401        380 LVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLL  429 (1176)
T ss_pred             EEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHH
Confidence            578    799999999999 89999999999      7789999999995

>PRK09694 helicase Cas3; Provisional

Probab=98.09  E-value=1.4e-05  Score=71.27  Aligned_cols=40  Identities=33%  Similarity=0.545  Sum_probs=36.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGK   43 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~   43 (138)
                      ||||+++++|||+ +++++|....|  +++|+||+||++|.+.
T Consensus       625 LVaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        625 LVATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             EEECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            6999999999999 68999998888  6799999999999876

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

Probab=98.03  E-value=2.3e-06  Score=76.06  Aligned_cols=54  Identities=30%  Similarity=0.596  Sum_probs=49.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC-CHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD-DVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~-~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      +++|+++.-|||+.++..||++..|. +..++.||.||+||.++.+..+.++..+
T Consensus       368 ~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~  422 (851)
T COG1205         368 VIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSD  422 (851)
T ss_pred             EecchhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCC
Confidence            58999999999999999999999999 8999999999999999877777777633

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

Probab=97.90  E-value=1.4e-05  Score=72.92  Aligned_cols=41  Identities=22%  Similarity=0.334  Sum_probs=39.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRS   41 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~   41 (138)
                      ||+++.+..|+|+|.|.+||.+++|.|...|+|++||+.|.
T Consensus       760 lVsvdmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR~  800 (1123)
T PRK11448        760 VVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQMLGRATRL  800 (1123)
T ss_pred             EEEecccccCCCcccccEEEEecCCCCHHHHHHHHhhhccC
Confidence            58899999999999999999999999999999999999995

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

Probab=97.79  E-value=3.4e-05  Score=64.06  Aligned_cols=40  Identities=23%  Similarity=0.409  Sum_probs=38.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhcccc
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGR   40 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR   40 (138)
                      ||++.++.+|+|+|+++.+|......++..|+||+||.=|
T Consensus       336 lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR  375 (442)
T COG1061         336 LVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLR  375 (442)
T ss_pred             EEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhcc
Confidence            5788999999999999999999999999999999999999

>KOG0947|consensus

Probab=97.63  E-value=7.1e-05  Score=66.74  Aligned_cols=53  Identities=25%  Similarity=0.433  Sum_probs=41.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC---------CHHHHHHHhhccccCC--CcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD---------DVENYVHRIGRTGRSG--KTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~---------~~~~y~qr~GRagR~g--~~g~~i~~~~~~   54 (138)
                      |+||..|+||++-|. ++||.-.+-+         .|..|+|..|||||.|  ..|.+|.+....
T Consensus       660 LFATETFAMGVNMPA-RtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~  723 (1248)
T KOG0947|consen  660 LFATETFAMGVNMPA-RTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDS  723 (1248)
T ss_pred             EeehhhhhhhcCCCc-eeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecCC
Confidence            689999999999998 5555445554         4889999999999988  467777766544

>TIGR01054 rgy reverse gyrase

Probab=97.50  E-value=0.0001  Score=67.68  Aligned_cols=27  Identities=19%  Similarity=0.427  Sum_probs=24.9

Q ss_pred             Cee----cccccccCCCCC-ccEEEEcCCCCC
Q psy7792           1 MVA----TDVASKGLDFEE-IKHVINYDMPDD   27 (138)
Q Consensus         1 Lva----T~~~~~GiD~~~-V~~VI~~dlP~~   27 (138)
                      |||    ||+++||||+|+ |++|||||+|+.
T Consensus       379 LVata~~tdv~aRGIDip~~V~~vI~~~~P~~  410 (1171)
T TIGR01054       379 LIGVASYYGTLVRGLDLPERVRYAVFLGVPKF  410 (1171)
T ss_pred             EEEeccccCcccccCCCCccccEEEEECCCCE
Confidence            578    599999999999 899999999986

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.

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

Probab=97.49  E-value=0.00022  Score=61.64  Aligned_cols=106  Identities=20%  Similarity=0.165  Sum_probs=71.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCC-CCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhccc--CcHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP-DDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQR--IPPF   77 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP-~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~--~~~~   77 (138)
                      ||||.+.+-|||+|+...+|..|.= -..+...|=.||+||.+.++.|++++.+......-..+.-+ ....+.  +.+ 
T Consensus       537 LVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~~~~a~~RL~im-~~t~DGF~IAE-  614 (677)
T COG1200         537 LVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPLSEVAKQRLKIM-RETTDGFVIAE-  614 (677)
T ss_pred             EEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCCChhHHHHHHHH-HhcCCcceehh-
Confidence            7999999999999999998888754 36888999999999999999999999887423222222222 222211  111 


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCCcCCCCCcccccccchH
Q psy7792          78 LAELESETEKFLDLGGDERGCAYCGGLGHRITACPKLE  115 (138)
Q Consensus        78 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (138)
                            .. --+.-.||-.+-+..+..+.+..+..+-.
T Consensus       615 ------~D-LklRGpGe~lG~rQSG~~~f~~Adl~~D~  645 (677)
T COG1200         615 ------ED-LKLRGPGELLGTRQSGLPEFRVADLVRDY  645 (677)
T ss_pred             ------hh-HhccCCccccCCcccCCcceEEeeHHhhH
Confidence                  00 01222366667777777777776664433

>KOG0953|consensus

Probab=97.45  E-value=0.00017  Score=61.22  Aligned_cols=52  Identities=33%  Similarity=0.530  Sum_probs=41.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCC---------CCHHHHHHHhhccccCCC---cceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP---------DDVENYVHRIGRTGRSGK---TGLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP---------~~~~~y~qr~GRagR~g~---~g~~i~~~~~   53 (138)
                      |||||+.+||+++ +++.||-|++-         -....-.|=.|||||.|.   .|.+.++...
T Consensus       413 lVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~e  476 (700)
T KOG0953|consen  413 LVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHSE  476 (700)
T ss_pred             EEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeHh
Confidence            6999999999997 77888888764         346778899999999885   4777776543

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=97.42  E-value=0.0011  Score=59.14  Aligned_cols=54  Identities=30%  Similarity=0.439  Sum_probs=48.1

Q ss_pred             eecccccccCCCCCcc--------EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           2 VATDVASKGLDFEEIK--------HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         2 vaT~~~~~GiD~~~V~--------~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      |||+.+|||.||.--.        +||....|.|..-=-|-.||+||-|.+|.+..|++-.+
T Consensus       479 IATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD  540 (925)
T PRK12903        479 IATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDD  540 (925)
T ss_pred             EecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecch
Confidence            8999999999997333        89999999998777899999999999999999998763

>KOG0948|consensus

Probab=97.41  E-value=9e-05  Score=64.78  Aligned_cols=58  Identities=26%  Similarity=0.471  Sum_probs=42.5

Q ss_pred             CeecccccccCCCCCccEEEE----cCCCC----CHHHHHHHhhccccCCC--cceEEEeeeCCCcHH
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----YDMPD----DVENYVHRIGRTGRSGK--TGLATTFINKSNDES   58 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----~dlP~----~~~~y~qr~GRagR~g~--~g~~i~~~~~~~~~~   58 (138)
                      |+||..|++|++-|.-..|+-    ||=-.    +--.|||..|||||.|.  .|.+|+.++..-+..
T Consensus       476 LFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDekm~~~  543 (1041)
T KOG0948|consen  476 LFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEKMEPQ  543 (1041)
T ss_pred             HHhhhhhhhccCCcceeEEEeeccccCCcceeeecccceEEecccccccCCCCCceEEEEecCcCCHH
Confidence            679999999999998554442    22111    45689999999999884  688999887554333

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

Probab=97.40  E-value=0.0002  Score=65.00  Aligned_cols=54  Identities=22%  Similarity=0.296  Sum_probs=47.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCC-CCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP-DDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP-~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||-..+-|||+|+++.+|-.+.= -.++..+|=.||+||..+.+.|++++.+.
T Consensus       859 Lv~TTIIEtGIDIPnANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~  913 (1139)
T COG1197         859 LVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQ  913 (1139)
T ss_pred             EEEeeeeecCcCCCCCceEEEeccccccHHHHHHhccccCCccceEEEEEeecCc
Confidence            6999999999999999998776543 35889999999999999999999998753

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=97.33  E-value=0.0012  Score=58.72  Aligned_cols=55  Identities=25%  Similarity=0.398  Sum_probs=48.9

Q ss_pred             CeecccccccCCCCCc--------------------------------------cEEEEcCCCCCHHHHHHHhhccccCC
Q psy7792           1 MVATDVASKGLDFEEI--------------------------------------KHVINYDMPDDVENYVHRIGRTGRSG   42 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V--------------------------------------~~VI~~dlP~~~~~y~qr~GRagR~g   42 (138)
                      +||||+++||+|++-=                                      =+||--..|.|..-=-|=.||+||-|
T Consensus       482 tIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQG  561 (830)
T PRK12904        482 TIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQG  561 (830)
T ss_pred             EEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCC
Confidence            5999999999999742                                      27898889999888899999999999


Q ss_pred             CcceEEEeeeCCC
Q psy7792          43 KTGLATTFINKSN   55 (138)
Q Consensus        43 ~~g~~i~~~~~~~   55 (138)
                      .+|.+..|++-++
T Consensus       562 dpGss~f~lSleD  574 (830)
T PRK12904        562 DPGSSRFYLSLED  574 (830)
T ss_pred             CCCceeEEEEcCc
Confidence            9999999999874

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

Probab=97.17  E-value=0.00072  Score=57.36  Aligned_cols=53  Identities=25%  Similarity=0.444  Sum_probs=44.2

Q ss_pred             CeecccccccCCCCCccEEEEcC-----CCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD-----MPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d-----lP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||--+.+-+|||+|.|.+|..+|     +..+-.+.||-+|||+|. -.|.+|+|...-
T Consensus       500 LVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN-~~GkvIlYAD~i  557 (663)
T COG0556         500 LVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKI  557 (663)
T ss_pred             EEeehhhhccCCCcceeEEEEeecCccccccccchHHHHHHHHhhc-cCCeEEEEchhh
Confidence            35557788999999999999987     556889999999999996 458999997643

>KOG0390|consensus

Probab=96.92  E-value=0.00097  Score=58.75  Aligned_cols=50  Identities=14%  Similarity=0.248  Sum_probs=45.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEe
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF   50 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~   50 (138)
                      |.+|-|.+.||++-..+.||.||++|||+.=.|.++||-|+|++-.++.|
T Consensus       652 LlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iY  701 (776)
T KOG0390|consen  652 LLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIY  701 (776)
T ss_pred             EEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEE
Confidence            46788999999999999999999999999999999999999987655554

>KOG0950|consensus

Probab=96.91  E-value=0.0014  Score=58.48  Aligned_cols=60  Identities=23%  Similarity=0.347  Sum_probs=47.7

Q ss_pred             CeecccccccCCCCCccEEEEcCC----CCCHHHHHHHhhccccCCC--cceEEEeeeCCCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDM----PDDVENYVHRIGRTGRSGK--TGLATTFINKSNDESVLL   61 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dl----P~~~~~y~qr~GRagR~g~--~g~~i~~~~~~~~~~~~~   61 (138)
                      ++||+.++-|++.|..+++|-.-.    +.+--.|.|++|||||.|-  .|.+|+++.+. +...+.
T Consensus       552 l~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~-e~~~~~  617 (1008)
T KOG0950|consen  552 LVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSS-EKKRVR  617 (1008)
T ss_pred             EEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeecc-chhHHH
Confidence            579999999999999998887521    2356789999999999984  68899999887 443333

>COG1204 Superfamily II helicase [General function prediction only]

Probab=96.88  E-value=0.0012  Score=58.53  Aligned_cols=54  Identities=26%  Similarity=0.438  Sum_probs=42.8

Q ss_pred             CeecccccccCCCCCccEEEE----cC-----CCCCHHHHHHHhhccccCC--CcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----YD-----MPDDVENYVHRIGRTGRSG--KTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----~d-----lP~~~~~y~qr~GRagR~g--~~g~~i~~~~~~   54 (138)
                      ||||+.++.|+++|.=+.||-    ||     .+-++-.|+|..|||||.|  ..|.++.+.+..
T Consensus       344 lv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~~~~  408 (766)
T COG1204         344 LVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSH  408 (766)
T ss_pred             EEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEEecCc
Confidence            689999999999998665553    66     5667889999999999988  456677666444

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=96.81  E-value=0.011  Score=53.32  Aligned_cols=54  Identities=30%  Similarity=0.358  Sum_probs=48.5

Q ss_pred             eecccccccCCCC---Ccc-----EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           2 VATDVASKGLDFE---EIK-----HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         2 vaT~~~~~GiD~~---~V~-----~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      |||+.++||.||.   .|.     +||--..|.|..---|=.||+||-|.+|.+..|++-.+
T Consensus       621 IATNmAGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlED  682 (970)
T PRK12899        621 VATNMAGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFED  682 (970)
T ss_pred             EeeccccCCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            8999999999985   233     79999999999999999999999999999999998864

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=96.79  E-value=0.0014  Score=57.43  Aligned_cols=54  Identities=28%  Similarity=0.422  Sum_probs=48.1

Q ss_pred             eecccccccCCCCC----------cc-----EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           2 VATDVASKGLDFEE----------IK-----HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         2 vaT~~~~~GiD~~~----------V~-----~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      |||+.++||.||.-          |.     +||--..|.|..-=-|=.||+||-|.+|.+..|++-++
T Consensus       480 IATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleD  548 (764)
T PRK12326        480 VSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLED  548 (764)
T ss_pred             EEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            89999999999962          22     79999999999888999999999999999999998763

>KOG0926|consensus

Probab=96.74  E-value=0.00057  Score=60.40  Aligned_cols=53  Identities=32%  Similarity=0.516  Sum_probs=42.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCC--------CCHHHH----------HHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP--------DDVENY----------VHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP--------~~~~~y----------~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      +|||++++--|-||+|++||..+--        ..+++|          -||.|||||.| +|+|+=+|+..
T Consensus       634 VVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg-pGHcYRLYSSA  704 (1172)
T KOG0926|consen  634 VVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG-PGHCYRLYSSA  704 (1172)
T ss_pred             EEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC-CCceeehhhhH
Confidence            5899999999999999999975433        333333          69999999986 58999988754

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=96.74  E-value=0.0041  Score=55.71  Aligned_cols=55  Identities=22%  Similarity=0.421  Sum_probs=47.4

Q ss_pred             CeecccccccCCCCC--------------------------------cc-----EEEEcCCCCCHHHHHHHhhccccCCC
Q psy7792           1 MVATDVASKGLDFEE--------------------------------IK-----HVINYDMPDDVENYVHRIGRTGRSGK   43 (138)
Q Consensus         1 LvaT~~~~~GiD~~~--------------------------------V~-----~VI~~dlP~~~~~y~qr~GRagR~g~   43 (138)
                      +|||+.++||+|+.=                                |.     +||--..|.|..-=-|=.||+||-|.
T Consensus       501 tIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGD  580 (908)
T PRK13107        501 TIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGD  580 (908)
T ss_pred             EEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCC
Confidence            599999999999962                                21     68888888887777899999999999


Q ss_pred             cceEEEeeeCCC
Q psy7792          44 TGLATTFINKSN   55 (138)
Q Consensus        44 ~g~~i~~~~~~~   55 (138)
                      +|.+..|++-++
T Consensus       581 PGss~f~lSlED  592 (908)
T PRK13107        581 AGSSRFYLSMED  592 (908)
T ss_pred             CCceeEEEEeCc
Confidence            999999999864

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=96.74  E-value=0.0044  Score=55.51  Aligned_cols=55  Identities=22%  Similarity=0.385  Sum_probs=46.5

Q ss_pred             CeecccccccCCCCC---------------------------------cc-----EEEEcCCCCCHHHHHHHhhccccCC
Q psy7792           1 MVATDVASKGLDFEE---------------------------------IK-----HVINYDMPDDVENYVHRIGRTGRSG   42 (138)
Q Consensus         1 LvaT~~~~~GiD~~~---------------------------------V~-----~VI~~dlP~~~~~y~qr~GRagR~g   42 (138)
                      +||||+++||+|+.=                                 |.     +||--..+.|..-=-|=.||+||-|
T Consensus       496 tIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQG  575 (896)
T PRK13104        496 TIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQG  575 (896)
T ss_pred             EEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCC
Confidence            599999999999962                                 11     6777778888777788999999999


Q ss_pred             CcceEEEeeeCCC
Q psy7792          43 KTGLATTFINKSN   55 (138)
Q Consensus        43 ~~g~~i~~~~~~~   55 (138)
                      .+|.+-.|++-++
T Consensus       576 DPGss~f~lSleD  588 (896)
T PRK13104        576 DPGSSRFYLSLED  588 (896)
T ss_pred             CCCceEEEEEcCc
Confidence            9999999998764

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

Probab=96.36  E-value=0.0035  Score=56.89  Aligned_cols=54  Identities=20%  Similarity=0.326  Sum_probs=41.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCC---------CCHHHHHHHhhccccCCC--cceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP---------DDVENYVHRIGRTGRSGK--TGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP---------~~~~~y~qr~GRagR~g~--~g~~i~~~~~~~   55 (138)
                      |+||.++++||+.|. +.|+...+-         -++..|+|..|||||.|.  .|.+|+...+..
T Consensus       474 vFaTeT~s~GiNmPa-rtvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~~~  538 (1041)
T COG4581         474 VFATETFAIGINMPA-RTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPPFE  538 (1041)
T ss_pred             EeehhhhhhhcCCcc-cceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCCCC
Confidence            579999999999997 444444433         368899999999999885  588888755443

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

Probab=96.35  E-value=0.0015  Score=56.07  Aligned_cols=54  Identities=20%  Similarity=0.425  Sum_probs=42.3

Q ss_pred             CeecccccccCCCCCccEEEE---cCCCC-CHHHHHHHhhccccCC--CcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN---YDMPD-DVENYVHRIGRTGRSG--KTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~---~dlP~-~~~~y~qr~GRagR~g--~~g~~i~~~~~~   54 (138)
                      +|+|-+++-|+|+|.-..|+-   .+.-| ++..|.|..|||||.+  ..|.+++++.+.
T Consensus       494 VVTTAAL~AGVDFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         494 VVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             EeehhhhhcCCCCchHHHHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCC
Confidence            488999999999998664432   23333 7899999999999988  468888888764

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=96.33  E-value=0.0046  Score=54.53  Aligned_cols=50  Identities=26%  Similarity=0.517  Sum_probs=40.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCC--CcceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG--KTGLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g--~~g~~i~~~~~   53 (138)
                      +|||.+.+-|+|+. .+++|-  =|..+.+.+||.||.+|.|  ..|.++.+...
T Consensus       498 vVaTQVIEagvDid-fd~mIT--e~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~  549 (733)
T COG1203         498 VVATQVIEAGVDID-FDVLIT--ELAPIDSLIQRAGRVNRHGKKENGKIYVYNDE  549 (733)
T ss_pred             EEEeeEEEEEeccc-cCeeee--cCCCHHHHHHHHHHHhhcccccCCceeEeecc
Confidence            58999999999985 677665  4677889999999999999  56777776543

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=96.32  E-value=0.007  Score=54.99  Aligned_cols=54  Identities=26%  Similarity=0.487  Sum_probs=48.4

Q ss_pred             eecccccccCCCC---Ccc-----EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           2 VATDVASKGLDFE---EIK-----HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         2 vaT~~~~~GiD~~---~V~-----~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      |||+.+|||-||.   .|.     +||--..|.|..---|=.||+||-|.+|.+..|++-.+
T Consensus       681 IATNMAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLED  742 (1112)
T PRK12901        681 IATNMAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLED  742 (1112)
T ss_pred             EeccCcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEccc
Confidence            8999999999996   332     78998999999999999999999999999999998764

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=96.23  E-value=0.024  Score=50.94  Aligned_cols=54  Identities=26%  Similarity=0.449  Sum_probs=47.0

Q ss_pred             eecccccccCCCC--------------------------------Ccc-----EEEEcCCCCCHHHHHHHhhccccCCCc
Q psy7792           2 VATDVASKGLDFE--------------------------------EIK-----HVINYDMPDDVENYVHRIGRTGRSGKT   44 (138)
Q Consensus         2 vaT~~~~~GiD~~--------------------------------~V~-----~VI~~dlP~~~~~y~qr~GRagR~g~~   44 (138)
                      |||+.+|||-||.                                .|.     +||--..|.|..-=-|=.||+||-|.+
T Consensus       502 IATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDP  581 (913)
T PRK13103        502 IATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDP  581 (913)
T ss_pred             EeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCC
Confidence            8999999999994                                122     688888999988888999999999999


Q ss_pred             ceEEEeeeCCC
Q psy7792          45 GLATTFINKSN   55 (138)
Q Consensus        45 g~~i~~~~~~~   55 (138)
                      |.+-.|++-++
T Consensus       582 GsS~f~lSlED  592 (913)
T PRK13103        582 GSSRFYLSLED  592 (913)
T ss_pred             CceEEEEEcCc
Confidence            99999999864

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

Probab=96.23  E-value=0.018  Score=46.83  Aligned_cols=54  Identities=19%  Similarity=0.309  Sum_probs=39.1

Q ss_pred             CeecccccccCCCCCccEE-EEcCCC-CCHHHHHHHhhccccCCC-cceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHV-INYDMP-DDVENYVHRIGRTGRSGK-TGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~V-I~~dlP-~~~~~y~qr~GRagR~g~-~g~~i~~~~~~   54 (138)
                      ||+|.+++||+-+|+|+.+ +.-.-+ -+-++.+|-.||+||.-. +.--+.|+...
T Consensus       359 LiTTTILERGVTfp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~G  415 (441)
T COG4098         359 LITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYG  415 (441)
T ss_pred             EEEeehhhcccccccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEecc
Confidence            6899999999999999974 444433 467889999999998543 33334444443

>KOG0387|consensus

Probab=96.10  E-value=0.0045  Score=54.63  Aligned_cols=50  Identities=20%  Similarity=0.243  Sum_probs=45.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEe
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF   50 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~   50 (138)
                      |++|-|.+.|+++-..+-||.||+-|||++=.|..-||-|.|++-.+++|
T Consensus       603 LLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VY  652 (923)
T KOG0387|consen  603 LLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVY  652 (923)
T ss_pred             EEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEE
Confidence            67899999999999999999999999999999999999999987555554

>KOG0923|consensus

Probab=96.05  E-value=0.0046  Score=53.82  Aligned_cols=51  Identities=29%  Similarity=0.470  Sum_probs=42.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC------------------CHHHHHHHhhccccCCCcceEEEeee
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD------------------DVENYVHRIGRTGRSGKTGLATTFIN   52 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~------------------~~~~y~qr~GRagR~g~~g~~i~~~~   52 (138)
                      ++||++++--|-|++|.+||.=++.+                  +-++=.||.|||||.| +|.|+=+|+
T Consensus       536 VLATNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt  604 (902)
T KOG0923|consen  536 VLATNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYT  604 (902)
T ss_pred             EEeecchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeec
Confidence            47999999999999999999654433                  4556689999999986 589999987

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

Probab=96.05  E-value=0.0041  Score=55.54  Aligned_cols=53  Identities=26%  Similarity=0.470  Sum_probs=44.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCC------------------CCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP------------------DDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP------------------~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ++||++++-+|-|++|++||.-++-                  -+-++-.||.|||||-+ +|.|+=+|+..
T Consensus       317 VlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~-pGicyRLyse~  387 (845)
T COG1643         317 VLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTG-PGICYRLYSEE  387 (845)
T ss_pred             EEEccccccceeeCCeEEEecCCcccccccccccCceeeeEEEechhhhhhhccccccCC-CceEEEecCHH
Confidence            5899999999999999999976543                  34677899999999974 69999999753

>KOG0924|consensus

Probab=95.83  E-value=0.0045  Score=54.13  Aligned_cols=52  Identities=33%  Similarity=0.523  Sum_probs=43.6

Q ss_pred             CeecccccccCCCCCccEEEEcC------------------CCCCHHHHHHHhhccccCCCcceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD------------------MPDDVENYVHRIGRTGRSGKTGLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d------------------lP~~~~~y~qr~GRagR~g~~g~~i~~~~~   53 (138)
                      +|||++++--|-++.+.+||..+                  .|-+-++=-||.|||||.| +|.|+-+|+.
T Consensus       627 IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe  696 (1042)
T KOG0924|consen  627 IVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTE  696 (1042)
T ss_pred             EEeccchhhceeecceEEEEecCceeeeecccccccceeEEEechhccchhhccccCCCC-Ccceeeehhh
Confidence            58999999999999999999865                  3445566689999999976 5899998875

>KOG0385|consensus

Probab=95.64  E-value=0.03  Score=49.58  Aligned_cols=50  Identities=18%  Similarity=0.323  Sum_probs=45.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEe
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF   50 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~   50 (138)
                      |++|=|.|-||++...+.||.||--|||..=+|..-||-|.|+...+++|
T Consensus       544 lLSTRAGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~  593 (971)
T KOG0385|consen  544 LLSTRAGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVY  593 (971)
T ss_pred             EEeccccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEE
Confidence            58999999999999999999999999999999999999999987665554

>KOG0922|consensus

Probab=95.55  E-value=0.0091  Score=51.69  Aligned_cols=53  Identities=26%  Similarity=0.503  Sum_probs=44.7

Q ss_pred             CeecccccccCCCCCccEEEEcC------------------CCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD------------------MPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d------------------lP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ++||++++--|-|+.|.+||.-+                  .|-|-++=.||.|||||.| +|.++=+|+.+
T Consensus       320 IlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRLYte~  390 (674)
T KOG0922|consen  320 ILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRTG-PGKCYRLYTES  390 (674)
T ss_pred             EEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCCC-CceEEEeeeHH
Confidence            58999999999999999998654                  2456778899999999975 59999999865

>KOG0384|consensus

Probab=95.40  E-value=0.017  Score=53.18  Aligned_cols=49  Identities=18%  Similarity=0.298  Sum_probs=44.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEE
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATT   49 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~   49 (138)
                      |++|=|.|.||++...+.||.||--|||..=+|...||-|.|++..+-+
T Consensus       756 LLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnV  804 (1373)
T KOG0384|consen  756 LLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNV  804 (1373)
T ss_pred             EEecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEE
Confidence            6899999999999999999999999999999999999999998654433

>KOG0920|consensus

Probab=95.31  E-value=0.012  Score=53.02  Aligned_cols=53  Identities=25%  Similarity=0.455  Sum_probs=42.6

Q ss_pred             CeecccccccCCCCCccEEEEcC--------CCCC----------HHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD--------MPDD----------VENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d--------lP~~----------~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ++||+.++-.|-|+||-+||...        +-.+          -..=.||.|||||. .+|.|+-+|+..
T Consensus       474 IlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~  544 (924)
T KOG0920|consen  474 ILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRS  544 (924)
T ss_pred             hhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechh
Confidence            57999999999999999999754        3322          33447999999997 569999999765

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

Probab=95.15  E-value=0.04  Score=48.47  Aligned_cols=49  Identities=18%  Similarity=0.224  Sum_probs=43.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEE
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATT   49 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~   49 (138)
                      |++|-+.+.|++....++||+||+.|++....|...|+-|.|++..+-.
T Consensus       767 lls~kagg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v  815 (866)
T COG0553         767 LLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKV  815 (866)
T ss_pred             EEEecccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEE
Confidence            4678899999999999999999999999999999999999987644333

>KOG0949|consensus

Probab=94.79  E-value=0.055  Score=49.21  Aligned_cols=67  Identities=28%  Similarity=0.283  Sum_probs=43.8

Q ss_pred             CeecccccccCCCCCccEEEEcC-CCCCHHHHHHHhhccccCCC--cceEEEeeeCCCcHHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD-MPDDVENYVHRIGRTGRSGK--TGLATTFINKSNDESVLLDLKHLLLE   69 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d-lP~~~~~y~qr~GRagR~g~--~g~~i~~~~~~~~~~~~~~l~~~~~~   69 (138)
                      |+||..++.||+-|--..|+--| +--++-.|-|..|||||.|-  .|.++.+=-|  ...+.+-+...+..
T Consensus       992 lfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~FmgiP--~~kv~rLlts~L~d 1061 (1330)
T KOG0949|consen  992 LFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVFMGIP--RQKVQRLLTSLLPD 1061 (1330)
T ss_pred             EEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEEEeCc--HHHHHHHHHHhhhc
Confidence            58999999999987544444444 44578999999999999884  3554444323  33444444444433

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

Probab=94.68  E-value=0.067  Score=47.32  Aligned_cols=50  Identities=32%  Similarity=0.527  Sum_probs=38.8

Q ss_pred             CeecccccccCCCCCccEEEEcC------CCC------CHHHHHHHhhccccCCCcceEEEe
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD------MPD------DVENYVHRIGRTGRSGKTGLATTF   50 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d------lP~------~~~~y~qr~GRagR~g~~g~~i~~   50 (138)
                      ||-|...+.|.|+|+|..|.-.|      .|+      ...-+.|=.|||||.+++|.++.-
T Consensus       538 LiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll~QvaGRAgR~~~~G~VvIQ  599 (730)
T COG1198         538 LIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAGRAGRAGKPGEVVIQ  599 (730)
T ss_pred             eecchhhhcCCCcccceEEEEEechhhhcCCCcchHHHHHHHHHHHHhhhccCCCCCeEEEE
Confidence            57899999999999999865444      222      255678999999999888777664

>PF13871 Helicase_C_4: Helicase_C-like

Probab=94.38  E-value=0.14  Score=40.40  Aligned_cols=69  Identities=17%  Similarity=0.331  Sum_probs=47.1

Q ss_pred             CeecccccccCCCCC--------ccEEEEcCCCCCHHHHHHHhhccccCCCcce-EEEeeeCC--CcHHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEE--------IKHVINYDMPDDVENYVHRIGRTGRSGKTGL-ATTFINKS--NDESVLLDLKHLLLE   69 (138)
Q Consensus         1 LvaT~~~~~GiD~~~--------V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~-~i~~~~~~--~~~~~~~~l~~~~~~   69 (138)
                      +|.|++++-||-+.+        -+.-|...+||+...-+|-.||+-|.++..- .+.++...  .+..+...+.+.+..
T Consensus        65 ~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE~Rfas~va~rL~s  144 (278)
T PF13871_consen   65 AIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGERRFASTVARRLES  144 (278)
T ss_pred             EEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHHHHHHHHHHHHHhh
Confidence            367888998987763        2355678999999999999999999997433 23333322  144555555555544

>KOG1000|consensus

Probab=93.89  E-value=0.054  Score=46.08  Aligned_cols=69  Identities=14%  Similarity=0.157  Sum_probs=50.7

Q ss_pred             eecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceE-EEe--eeCCCcHHHHHHHHHHHHHh
Q psy7792           2 VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLA-TTF--INKSNDESVLLDLKHLLLEA   70 (138)
Q Consensus         2 vaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~-i~~--~~~~~~~~~~~~l~~~~~~~   70 (138)
                      ++-.++++||++...+.|+...+||||.-.+|.=-|+-|.|+++.+ |.|  .....|+.++..+.+.+...
T Consensus       549 lsItA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQkssV~v~ylvAKgT~Ddy~Wp~l~~KL~vl  620 (689)
T KOG1000|consen  549 LSITAAGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSSVFVQYLVAKGTADDYMWPMLQQKLDVL  620 (689)
T ss_pred             EEEeecccceeeeccceEEEEEecCCCceEEechhhhhhccccceeeEEEEEecCchHHHHHHHHHHHHHHH
Confidence            3445789999999999999999999999999988888888865433 333  33444667777666655443

>COG4889 Predicted helicase [General function prediction only]

Probab=93.76  E-value=0.078  Score=48.03  Aligned_cols=46  Identities=28%  Similarity=0.409  Sum_probs=38.8

Q ss_pred             ccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCC---CcceEEEeee
Q psy7792           7 ASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG---KTGLATTFIN   52 (138)
Q Consensus         7 ~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g---~~g~~i~~~~   52 (138)
                      +++|+|+|..+.||.||+-.++-..+|.+||+-|-.   +-|..|+-+.
T Consensus       538 LSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILPIa  586 (1518)
T COG4889         538 LSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILPIA  586 (1518)
T ss_pred             hhcCCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEEec
Confidence            678999999999999999999999999999998733   3477776553

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

Probab=93.55  E-value=0.06  Score=48.32  Aligned_cols=54  Identities=15%  Similarity=0.200  Sum_probs=38.1

Q ss_pred             CeecccccccCCCCCcc--EEEEcCCCC----CH--------------------------HHHHHHhhccccCCCcceEE
Q psy7792           1 MVATDVASKGLDFEEIK--HVINYDMPD----DV--------------------------ENYVHRIGRTGRSGKTGLAT   48 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~--~VI~~dlP~----~~--------------------------~~y~qr~GRagR~g~~g~~i   48 (138)
                      |++|+.+.+|||+++..  .||-..+|-    ++                          ..+.|-+||.-|..+..-++
T Consensus       729 Llgt~sf~EGVD~~g~~l~~viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v  808 (850)
T TIGR01407       729 LLGTSSFWEGVDFPGNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSI  808 (850)
T ss_pred             EEEcceeecccccCCCceEEEEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEE
Confidence            68999999999999766  566667663    11                          22467889998877655566


Q ss_pred             EeeeCC
Q psy7792          49 TFINKS   54 (138)
Q Consensus        49 ~~~~~~   54 (138)
                      .+++..
T Consensus       809 ~ilD~R  814 (850)
T TIGR01407       809 VILDRR  814 (850)
T ss_pred             EEEccc
Confidence            666554

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.

>KOG1015|consensus

Probab=93.20  E-value=0.049  Score=49.56  Aligned_cols=49  Identities=22%  Similarity=0.238  Sum_probs=44.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEE
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATT   49 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~   49 (138)
                      ||+|-+.+.||++-..+.||.||..|||.-=+|.+=|+-|.|+.--++.
T Consensus      1222 LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyi 1270 (1567)
T KOG1015|consen 1222 LISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYI 1270 (1567)
T ss_pred             EEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceee
Confidence            6899999999999999999999999999999999999999997654444

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=91.91  E-value=0.3  Score=43.84  Aligned_cols=47  Identities=13%  Similarity=0.070  Sum_probs=33.4

Q ss_pred             eecccccccCCCCC----------------------c----------cEEEEcCCCCCHHHHHH--HhhccccCCCcceE
Q psy7792           2 VATDVASKGLDFEE----------------------I----------KHVINYDMPDDVENYVH--RIGRTGRSGKTGLA   47 (138)
Q Consensus         2 vaT~~~~~GiD~~~----------------------V----------~~VI~~dlP~~~~~y~q--r~GRagR~g~~g~~   47 (138)
                      |+|.+...|+|++.                      +          ++||.|++=.+.-.-+|  |.||.||.   +.+
T Consensus       431 ~~~~~~~e~~d~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~L~e~~P~~VImYEP~~sfIR~IEvyra~r~~r~---~rV  507 (814)
T TIGR00596       431 FEIIDEENDIDIYSGAEFDNLPQHITHFLWGERDEYVLRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLRP---LRV  507 (814)
T ss_pred             ccccccccccccchhhccccccceeeeecccccchhhHHHHHhhhCCCEEEEECCChHHHHHHHHHHccCCCCC---cEE
Confidence            56888889999997                      6          89999996555555555  66666665   445


Q ss_pred             EEee
Q psy7792          48 TTFI   51 (138)
Q Consensus        48 i~~~   51 (138)
                      +.++
T Consensus       508 yfL~  511 (814)
T TIGR00596       508 YFLY  511 (814)
T ss_pred             EEEE
Confidence            4444

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

>KOG0388|consensus

Probab=91.67  E-value=0.16  Score=45.08  Aligned_cols=47  Identities=21%  Similarity=0.288  Sum_probs=42.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceE
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLA   47 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~   47 (138)
                      |++|-+.+.||++...+.||.||--|+|..=.|...||-|-|+.-.+
T Consensus      1099 LLSTRAGGLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdv 1145 (1185)
T KOG0388|consen 1099 LLSTRAGGLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDV 1145 (1185)
T ss_pred             EEecccCcccccccccceEEEecCCCCcchhhHHHHHHHhccCccce
Confidence            57899999999999999999999999999999999999999975443

>KOG0951|consensus

Probab=91.56  E-value=0.19  Score=46.99  Aligned_cols=52  Identities=21%  Similarity=0.362  Sum_probs=38.8

Q ss_pred             CeecccccccCCCCCccEEEE----cCCC------CCHHHHHHHhhccccCC--CcceEEEeee
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----YDMP------DDVENYVHRIGRTGRSG--KTGLATTFIN   52 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----~dlP------~~~~~y~qr~GRagR~g--~~g~~i~~~~   52 (138)
                      ||+|-.++.|+++|.-..+|-    ||+-      -++-.-+|+.|||||.+  ..|..|..-.
T Consensus       637 lvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~  700 (1674)
T KOG0951|consen  637 LVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITD  700 (1674)
T ss_pred             EEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeeccC
Confidence            689999999999999666663    5543      35889999999999866  3455555433

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=91.26  E-value=1.4  Score=39.86  Aligned_cols=24  Identities=29%  Similarity=0.545  Sum_probs=20.6

Q ss_pred             HHHhhccccCCCcceEEEeeeCCC
Q psy7792          32 VHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus        32 ~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      -|=.||+||-|.+|.+-.|++-++
T Consensus       609 nQLrGRaGRQGDPG~s~f~lSLED  632 (870)
T CHL00122        609 NQLRGRAGRQGDPGSSRFFLSLED  632 (870)
T ss_pred             HHHhccccCCCCCCcceEEEEecc
Confidence            356789999999999999998764

>KOG0389|consensus

Probab=90.94  E-value=0.41  Score=42.81  Aligned_cols=54  Identities=20%  Similarity=0.214  Sum_probs=42.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCC--cceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGK--TGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~--~g~~i~~~~~~   54 (138)
                      |++|-+.|-||++-..+.||.||+.-||-.=.|.--|+-|.|+  +-.++-+++..
T Consensus       833 LLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~  888 (941)
T KOG0389|consen  833 LLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKS  888 (941)
T ss_pred             EEeeccCcceecccccceEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEEecC
Confidence            5789999999999999999999999887666666666666664  34455567665

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=89.62  E-value=0.29  Score=45.02  Aligned_cols=40  Identities=25%  Similarity=0.386  Sum_probs=33.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGK   43 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~   43 (138)
                      +|+|.+.+-|+|+ |.+++|-  -|..+.+.+|+.||..|.|.
T Consensus       842 ~v~Tqv~E~g~D~-dfd~~~~--~~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       842 VLATPVEEVGRDH-DYDWAIA--DPSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             EEEeeeEEEEecc-cCCeeee--ccCcHHHHHHHhhccccccc
Confidence            5899999999997 4566654  47899999999999998775

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.

>KOG0701|consensus

Probab=89.44  E-value=0.12  Score=49.11  Aligned_cols=42  Identities=29%  Similarity=0.546  Sum_probs=38.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG   42 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g   42 (138)
                      |++|.++..|+|++.++.|+.++.|....+|+|+.||+-..+
T Consensus       358 L~~~~~~~e~~d~~~~~~~~~~~~~~~~~~~vq~~~r~~~~~  399 (1606)
T KOG0701|consen  358 LIATSVLEEGVDVPKCNLVVLFDAPTYYRSYVQKKGRARAAD  399 (1606)
T ss_pred             HHHHHHHHhhcchhhhhhheeccCcchHHHHHHhhcccccch
Confidence            578999999999999999999999999999999999995543

>KOG0925|consensus

Probab=89.20  E-value=0.32  Score=41.48  Aligned_cols=53  Identities=26%  Similarity=0.457  Sum_probs=42.8

Q ss_pred             CeecccccccCCCCCccEEEEcCC------------------CCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDM------------------PDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dl------------------P~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      +|+|+.++--+-++.|.+||.-++                  |-+-.+=.||.|||||. ++|.+.-+|+.+
T Consensus       317 Vvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~  387 (699)
T KOG0925|consen  317 VVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEE  387 (699)
T ss_pred             EEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHH
Confidence            478999999999999999997654                  44566778999999885 678999998754

>KOG0952|consensus

Probab=88.91  E-value=2.6  Score=39.02  Aligned_cols=52  Identities=17%  Similarity=0.305  Sum_probs=38.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCC-----C------CHHHHHHHhhccccCC--CcceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP-----D------DVENYVHRIGRTGRSG--KTGLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP-----~------~~~~y~qr~GRagR~g--~~g~~i~~~~~   53 (138)
                      |+||..++=|+++|+ .+||..+-+     +      ..-.-+|-.|||||.+  ..|.+|.+-+.
T Consensus       426 L~cTaTLAwGVNLPA-~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~  490 (1230)
T KOG0952|consen  426 LCCTATLAWGVNLPA-YAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTR  490 (1230)
T ss_pred             EEecceeeeccCCcc-eEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecc
Confidence            689999999999998 455554433     2      2456799999999965  56777766543

>KOG0386|consensus

Probab=88.89  E-value=0.76  Score=42.08  Aligned_cols=51  Identities=18%  Similarity=0.261  Sum_probs=45.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEee
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFI   51 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~   51 (138)
                      |.+|-+.+.|++++..+.||.||--|+|....|+--||-|.|+.-.+-++.
T Consensus       783 llstragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~r  833 (1157)
T KOG0386|consen  783 LLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLR  833 (1157)
T ss_pred             eeeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeee
Confidence            568899999999999999999999999999999999999999765555544

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

Probab=88.80  E-value=1.1  Score=39.41  Aligned_cols=40  Identities=18%  Similarity=0.208  Sum_probs=33.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRS   41 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~   41 (138)
                      ||+++.+..|.|.|.++.++-.-+-.+. .++|.+||+-|.
T Consensus       595 lIVvdmllTGFDaP~l~tLyldKplk~h-~LlQai~R~nR~  634 (667)
T TIGR00348       595 LIVVDMLLTGFDAPILNTLYLDKPLKYH-GLLQAIARTNRI  634 (667)
T ss_pred             EEEEcccccccCCCccceEEEecccccc-HHHHHHHHhccc
Confidence            5788999999999999988876655554 689999999993

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

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

Probab=88.77  E-value=0.74  Score=33.09  Aligned_cols=54  Identities=24%  Similarity=0.321  Sum_probs=32.1

Q ss_pred             Ceecc--cccccCCCCC--ccEEEEcCCCC-CHH--------H---------------------HHHHhhccccCCCcce
Q psy7792           1 MVATD--VASKGLDFEE--IKHVINYDMPD-DVE--------N---------------------YVHRIGRTGRSGKTGL   46 (138)
Q Consensus         1 LvaT~--~~~~GiD~~~--V~~VI~~dlP~-~~~--------~---------------------y~qr~GRagR~g~~g~   46 (138)
                      |+++.  .+.+|||+++  ++.||-..+|- ++.        .                     ..|-+||+-|..+.--
T Consensus        63 l~~v~~g~~~EGiD~~~~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g  142 (167)
T PF13307_consen   63 LLAVAGGSFSEGIDFPGDLLRAVIIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYG  142 (167)
T ss_dssp             EEEETTSCCGSSS--ECESEEEEEEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EE
T ss_pred             EEEEecccEEEeecCCCchhheeeecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcE
Confidence            45666  7899999994  78899999883 211        1                     1467999988887766


Q ss_pred             EEEeeeCC
Q psy7792          47 ATTFINKS   54 (138)
Q Consensus        47 ~i~~~~~~   54 (138)
                      ++.++++.
T Consensus       143 ~i~llD~R  150 (167)
T PF13307_consen  143 VIILLDSR  150 (167)
T ss_dssp             EEEEESGG
T ss_pred             EEEEEcCc
Confidence            66666554

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=88.03  E-value=1.3  Score=31.27  Aligned_cols=26  Identities=35%  Similarity=0.508  Sum_probs=20.9

Q ss_pred             CeecccccccCCCCC--ccEEEEcCCCC
Q psy7792           1 MVATDVASKGLDFEE--IKHVINYDMPD   26 (138)
Q Consensus         1 LvaT~~~~~GiD~~~--V~~VI~~dlP~   26 (138)
                      |++|.-+.+|||+++  ++.||-..+|-
T Consensus        52 L~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492       52 LLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             EEEccceecceecCCCCeeEEEEEecCC
Confidence            467777999999985  57898888883

>KOG0392|consensus

Probab=87.46  E-value=0.63  Score=43.54  Aligned_cols=50  Identities=16%  Similarity=0.236  Sum_probs=44.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEee
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFI   51 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~   51 (138)
                      |.+|-+.|-|+++-..+.||.++--|||..=.|.+-||-|.|++ ..+++|
T Consensus      1399 lLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQK-rvVNVy 1448 (1549)
T KOG0392|consen 1399 LLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQK-RVVNVY 1448 (1549)
T ss_pred             EEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCc-eeeeee
Confidence            47899999999999999999999999999999999999999986 344443

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=86.00  E-value=1.9  Score=30.40  Aligned_cols=24  Identities=33%  Similarity=0.553  Sum_probs=19.2

Q ss_pred             eeccc--ccccCCCCC--ccEEEEcCCC
Q psy7792           2 VATDV--ASKGLDFEE--IKHVINYDMP   25 (138)
Q Consensus         2 vaT~~--~~~GiD~~~--V~~VI~~dlP   25 (138)
                      +++.-  +.+|||+++  ++.||-..+|
T Consensus        52 ~~v~~G~~~EGiD~~g~~~r~vii~glP   79 (142)
T smart00491       52 LAVARGKVSEGIDFPDDLGRAVIIVGIP   79 (142)
T ss_pred             EEEeCCeeecceecCCCccEEEEEEecC
Confidence            45555  899999985  6789998888

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

Probab=82.93  E-value=2.3  Score=36.92  Aligned_cols=54  Identities=22%  Similarity=0.315  Sum_probs=39.5

Q ss_pred             CeecccccccCCCC--CccEEEEcCCCCC------------------------------HHHHHHHhhccccCCCcceEE
Q psy7792           1 MVATDVASKGLDFE--EIKHVINYDMPDD------------------------------VENYVHRIGRTGRSGKTGLAT   48 (138)
Q Consensus         1 LvaT~~~~~GiD~~--~V~~VI~~dlP~~------------------------------~~~y~qr~GRagR~g~~g~~i   48 (138)
                      +|+|..+.+|+|++  ..+.||...+|--                              +....|-+||+=|.-...-++
T Consensus       532 lv~~gsf~EGVD~~g~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~i  611 (654)
T COG1199         532 LVGGGSFWEGVDFPGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVI  611 (654)
T ss_pred             EEeeccccCcccCCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEE
Confidence            58999999999998  5578888887742                              334578899998866555555


Q ss_pred             EeeeCC
Q psy7792          49 TFINKS   54 (138)
Q Consensus        49 ~~~~~~   54 (138)
                      .++...
T Consensus       612 vllD~R  617 (654)
T COG1199         612 VLLDKR  617 (654)
T ss_pred             EEeccc
Confidence            555543

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

Probab=82.31  E-value=4.4  Score=37.05  Aligned_cols=54  Identities=13%  Similarity=0.223  Sum_probs=36.8

Q ss_pred             CeecccccccCCCCC--ccEEEEcCCCC-CH-----------------------------HHHHHHhhccccCCCcceEE
Q psy7792           1 MVATDVASKGLDFEE--IKHVINYDMPD-DV-----------------------------ENYVHRIGRTGRSGKTGLAT   48 (138)
Q Consensus         1 LvaT~~~~~GiD~~~--V~~VI~~dlP~-~~-----------------------------~~y~qr~GRagR~g~~g~~i   48 (138)
                      |++|..|.+|||+|.  ++.||-..+|- +|                             -.+.|-+||.=|....--++
T Consensus       808 LlG~~sFwEGVD~pg~~l~~viI~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v  887 (928)
T PRK08074        808 LLGTSSFWEGIDIPGDELSCLVIVRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTV  887 (928)
T ss_pred             EEecCcccCccccCCCceEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEE
Confidence            578899999999994  57888877764 11                             11256678887777554456


Q ss_pred             EeeeCC
Q psy7792          49 TFINKS   54 (138)
Q Consensus        49 ~~~~~~   54 (138)
                      .++++.
T Consensus       888 ~ilD~R  893 (928)
T PRK08074        888 FVLDRR  893 (928)
T ss_pred             EEecCc
Confidence            666554

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

Probab=81.26  E-value=1  Score=40.45  Aligned_cols=39  Identities=18%  Similarity=0.377  Sum_probs=35.3

Q ss_pred             eecccccccCCCCCccEEEEcCCCCCHHHHHHHhhcccc
Q psy7792           2 VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGR   40 (138)
Q Consensus         2 vaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR   40 (138)
                      |+.+.+.-|||+|.|..++-+-.-.|...|-|.+||.=|
T Consensus       486 itvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTR  524 (875)
T COG4096         486 ITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTR  524 (875)
T ss_pred             EehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCccc
Confidence            556788889999999999999999999999999999866

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	138
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		4e-32
2jgn_A	185	Ddx3 Helicase Domain Length = 185		4e-21
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		6e-21
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-19
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-13
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-13
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		6e-13
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		6e-13
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		6e-13
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		6e-13
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		6e-13
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		6e-13
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		6e-13
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		7e-13
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		8e-13
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		1e-12
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		4e-12
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		1e-11
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		6e-11
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		6e-11
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		6e-11
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		7e-11
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		7e-11
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		7e-11
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		7e-11
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		9e-11
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		9e-11
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		9e-11
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		3e-10
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		3e-10
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		4e-10
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		8e-10
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		1e-09
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		1e-09
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		1e-09
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		2e-09
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		3e-09
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		2e-05
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		2e-05
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		2e-05
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-05
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-05
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		4e-05
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		2e-04
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		5e-04
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		7e-04

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score =  132 bits (333), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 61/81 (75%), Positives = 72/81 (88%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTG SG TG+ATTFINK+ DESVL
Sbjct: 108 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVL 167
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
           +DLK LLLEA+Q++PP L  L
Sbjct: 168 MDLKALLLEAKQKVPPVLQVL 188

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 96.7 bits (239), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 45/84 (53%), Positives = 61/84 (72%), Gaps = 1/84 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT VA++GLD   +KHVIN+D+P D+E YVHRIGRTGR G  GLAT+F N+ N  ++ 
Sbjct: 100 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNI-NIT 158
Query: 61  LDLKHLLLEARQRIPPFLAELESE 84
            DL  LL+EA+Q +P +L  +  E
Sbjct: 159 KDLLDLLVEAKQEVPSWLENMAYE 182

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 95.9 bits (237), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 45/84 (53%), Positives = 61/84 (72%), Gaps = 1/84 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT VA++GLD   +KHVIN+D+P D+E YVHRIGRTGR G  GLAT+F N+ N  ++ 
Sbjct: 330 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNI-NIT 388
Query: 61  LDLKHLLLEARQRIPPFLAELESE 84
            DL  LL+EA+Q +P +L  +  E
Sbjct: 389 KDLLDLLVEAKQEVPSWLENMAYE 412

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 55/78 (70%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++AT VAS+GLD + IKHVINYDMP  +++YVHRIGRTGR G  G AT+F +   D ++ 
Sbjct: 354 LIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIA 413
Query: 61  LDLKHLLLEARQRIPPFL 78
            DL  +L  + Q +P FL
Sbjct: 414 ADLVKILEGSGQTVPDFL 431

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 32/81 (39%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TDV ++GLD  ++  +INYD+P++ E Y+HRIGR+GR G+ G+A  F+ K++D  VL
Sbjct: 294 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFV-KNDDIRVL 352
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            D++         +P  +A+L
Sbjct: 353 RDIEQYYSTQIDEMPMNVADL 373

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 32/81 (39%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TDV ++GLD  ++  +INYD+P++ E Y+HRIGR+GR G+ G+A  F+ K++D  VL
Sbjct: 294 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFV-KNDDIRVL 352
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            D++         +P  +A+L
Sbjct: 353 RDIEQYYSTQIDEMPMNVADL 373

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TDV ++GLD  ++  +INYD+P++ E Y+HRIGR+GR G+ G+A  F+ K++D  +L
Sbjct: 330 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFV-KNDDIRIL 388
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            D++         +P  +A+L
Sbjct: 389 RDIEQYYSTQIDEMPMNVADL 409

>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 = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TDV ++GLD  ++  +INYD+P++ E Y+HRIGR+GR G+ G+A  F+ K++D  +L
Sbjct: 331 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFV-KNDDIRIL 389
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            D++         +P  +A+L
Sbjct: 390 RDIEQYYSTQIDEMPMNVADL 410

>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 = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TDV ++GLD  ++  +INYD+P++ E Y+HRIGR+GR G+ G+A  F+ K++D  +L
Sbjct: 331 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFV-KNDDIRIL 389
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            D++         +P  +A+L
Sbjct: 390 RDIEQYYSTQIDEMPMNVADL 410

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 43/64 (67%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT++  +G+D E +    NYDMP+D + Y+HR+ R GR G  GLA TF++  ND  +L
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 363
Query: 61  LDLK 64
            D++
Sbjct: 364 NDVQ 367

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TDV ++GLD  ++  +INYD+P++ E Y+HRIGR+GR G+ G+A  F+ K++D  +L
Sbjct: 309 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFV-KNDDIRIL 367
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            D++         +P  +A+L
Sbjct: 368 RDIEQYYSTQIDEMPMNVADL 388

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 43/64 (67%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT++  +G+D E +    NYDMP+D + Y+HR+ R GR G  GLA TF++  ND  +L
Sbjct: 303 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 362
Query: 61  LDLK 64
            D++
Sbjct: 363 NDVQ 366

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 43/64 (67%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT++  +G+D E +    NYDMP+D + Y+HR+ R GR G  GLA TF++  ND  +L
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 363
Query: 61  LDLK 64
            D++
Sbjct: 364 NDVQ 367

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 69.3 bits (168), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 43/64 (67%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT++  +G+D E +    NYDMP+D + Y+HR+ R GR G  GLA TF++  ND  +L
Sbjct: 85  LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 144
Query: 61  LDLK 64
            D++
Sbjct: 145 NDVQ 148

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 68.9 bits (167), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 29/51 (56%), Positives = 38/51 (74%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFI 51
           ++ TDVAS+GLD   ++ VIN+D P D+  Y+HRIGRTGR G+ G A TFI
Sbjct: 270 LITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFI 320

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 40/51 (78%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFI 51
           +VATDVA++G+D E I  VINYD+P + E+YVHR GRTGR+G  G A +F+
Sbjct: 89  LVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFV 139

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 40/53 (75%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINK 53
           ++ATDV S+G+D  ++  VINY +P + E+Y HRIGRTGR+GK G A + IN+
Sbjct: 292 LIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINR 344

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 38/51 (74%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFI 51
           +VATDVA++G+D  ++ HV N+DMP   + Y+HRIGRT R+G+ G A + +
Sbjct: 84  LVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLV 134

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 53/87 (60%), Gaps = 3/87 (3%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESV- 59
           +V TDV ++G+DF  +  V+   +P ++ NY+HRIGRT RSGK G +  FI K     V 
Sbjct: 90  LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR 149
Query: 60  -LLDLKHLLLEARQRIPPFLAELESET 85
            L D K++++  +++  P   E++SE 
Sbjct: 150 ELEDAKNIVIAKQEKYEP-SEEIKSEV 175

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 53/87 (60%), Gaps = 3/87 (3%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESV- 59
           +V TDV ++G+DF  +  V+   +P ++ NY+HRIGRT RSGK G +  FI K     V 
Sbjct: 90  LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR 149
Query: 60  -LLDLKHLLLEARQRIPPFLAELESET 85
            L D K++++  +++  P   E++SE 
Sbjct: 150 ELEDAKNIVIAKQEKYEP-SEEIKSEV 175

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 53/87 (60%), Gaps = 3/87 (3%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESV- 59
           +V TDV ++G+DF  +  V+   +P ++ NY+HRIGRT RSGK G +  FI K     V 
Sbjct: 90  LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR 149
Query: 60  -LLDLKHLLLEARQRIPPFLAELESET 85
            L D K++++  +++  P   E++SE 
Sbjct: 150 ELEDAKNIVIAKQEKYEP-SEEIKSEV 175

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 6/66 (9%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKS 54
           +V T+V ++G+D E++  VIN+D+P       D E Y+HRIGRTGR GK GLA   ++  
Sbjct: 387 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSK 446
Query: 55  NDESVL 60
           +  ++L
Sbjct: 447 HSMNIL 452

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 6/66 (9%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKS 54
           +V T+V ++G+D E++  VIN+D+P       D E Y+HRIGRTGR GK GLA   ++  
Sbjct: 336 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSK 395
Query: 55  NDESVL 60
           +  ++L
Sbjct: 396 HSMNIL 401

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 6/66 (9%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKS 54
           +V T+V ++G+D E++  VIN+D+P       D E Y+HRIGRTGR GK GLA   ++  
Sbjct: 320 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSK 379
Query: 55  NDESVL 60
           +  ++L
Sbjct: 380 HSMNIL 385

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 6/66 (9%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKS 54
           +V T+V ++G+D E++  VIN+D+P       D E Y+HRIGRTGR GK GLA   ++  
Sbjct: 357 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSK 416
Query: 55  NDESVL 60
           +  ++L
Sbjct: 417 HSMNIL 422

>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 = 62.0 bits (149), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 53/87 (60%), Gaps = 3/87 (3%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESV- 59
           +V TDV ++G+DF  +  V+   +P ++ NY+HRIGRT RSGK G +  FI K     V 
Sbjct: 345 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR 404
Query: 60  -LLDLKHLLLEARQRIPPFLAELESET 85
            L D K++++  +++  P   E++SE 
Sbjct: 405 ELEDAKNIVIAKQEKYEP-SEEIKSEV 430

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 62.0 bits (149), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 53/87 (60%), Gaps = 3/87 (3%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESV- 59
           +V TDV ++G+DF  +  V+   +P ++ NY+HRIGRT RSGK G +  FI K     V 
Sbjct: 345 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR 404
Query: 60  -LLDLKHLLLEARQRIPPFLAELESET 85
            L D K++++  +++  P   E++SE 
Sbjct: 405 ELEDAKNIVIAKQEKYEP-SEEIKSEV 430

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 62.0 bits (149), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 53/87 (60%), Gaps = 3/87 (3%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESV- 59
           +V TDV ++G+DF  +  V+   +P ++ NY+HRIGRT RSGK G +  FI K     V 
Sbjct: 396 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR 455
Query: 60  -LLDLKHLLLEARQRIPPFLAELESET 85
            L D K++++  +++  P   E++SE 
Sbjct: 456 ELEDAKNIVIAKQEKYEP-SEEIKSEV 481

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 6/66 (9%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKS 54
           ++ T+V ++G+D   +  V+NYD+P       D   Y+HRIGRTGR G+ G+A +F++  
Sbjct: 297 LITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK 356
Query: 55  NDESVL 60
           N  ++L
Sbjct: 357 NSFNIL 362

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 6/66 (9%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKS 54
           ++ T+V ++G+D   +  V+NYD+P       D   Y+HRIGRTGR G+ G+A +F++  
Sbjct: 297 LITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK 356
Query: 55  NDESVL 60
           N  ++L
Sbjct: 357 NSFNIL 362

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 60.1 bits (144), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 35/52 (67%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
           +V +D+ ++G+D + +  VIN+D P   E Y+HRIGR+GR G  GLA   IN
Sbjct: 312 LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLIN 363

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 6/66 (9%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKS 54
           ++ T+V ++G+D   +  V+NYD+P       D   Y+HRIGRTGR G+ G+A +F++  
Sbjct: 89  LITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK 148
Query: 55  NDESVL 60
           N  ++L
Sbjct: 149 NSFNIL 154

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 6/66 (9%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKS 54
           ++ T+V ++G+D   +  V+NYD+P       D   Y+HRIGRTGR G+ G+A +F++  
Sbjct: 91  LITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK 150
Query: 55  NDESVL 60
           N  ++L
Sbjct: 151 NSFNIL 156

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 6/66 (9%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKS 54
           ++ T+V ++G+D   +  V+NYD+P       D   Y+HRIGRTGR G+ G+A +F++  
Sbjct: 90  LITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDK 149
Query: 55  NDESVL 60
           N  ++L
Sbjct: 150 NSFNIL 155

>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 = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 34/51 (66%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFI 51
           +V TD+ ++G+D + +  VIN+D P   E Y+HRIGR+GR G  GLA   I
Sbjct: 98  LVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLI 148

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 38/57 (66%), Gaps = 6/57 (10%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFI 51
           ++ T+V ++G+D +++  V+N+D+P       D E Y+HRIGRTGR GK GLA   I
Sbjct: 88  LITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMI 144

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TD+ ++G+D +++  VINYD+P + ENY+HRIGR GR G+ G+A  F+  + D   +
Sbjct: 84  LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVT-NEDVGAM 142
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            +L+       + +P  +A L
Sbjct: 143 RELEKFYSTQIEELPSDIATL 163

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 53/81 (65%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++ TD+ ++G+D +++  VINYD+P + ENY+HRIGR GR G+ G+A   + +  D+  L
Sbjct: 334 LITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTE-EDKRTL 392
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            D++     + + +P  +A+L
Sbjct: 393 RDIETFYNTSIEEMPLNVADL 413

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 53/81 (65%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++ TD+ ++G+D +++  VINYD+P + ENY+HRIGR GR G+ G+A   + +  D+  L
Sbjct: 308 LITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEE-DKRTL 366
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            D++     + + +P  +A+L
Sbjct: 367 RDIETFYNTSIEEMPLNVADL 387

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 1/81 (1%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TD+ ++G+D +++  VINYD+P + ENY+HRIGR GR G+ G+A  F+  + D   +
Sbjct: 314 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVT-NEDVGAM 372
Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            +L+       + +P  +A L
Sbjct: 373 RELEKFYSTQIEELPSDIATL 393

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 41/55 (74%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN 55
           +++TD+ ++G+D +++  VINYD+P + ENY+HRIGR GR G+ G+A  F+   +
Sbjct: 313 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNED 367

>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 = 43.5 bits (101), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 24/33 (72%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVH 33
           +VATDVA++GLD  ++  V++Y MPD  E Y H
Sbjct: 82  LVATDVAARGLDIPQVDLVVHYRMPDRAEAYQH 114

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVH 33
           +VATDVA++GLD  ++  V++Y +PD  E Y H
Sbjct: 85  LVATDVAARGLDIPQVDLVVHYRLPDRAEAYQH 117

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN 55
           +VAT     G++   ++ V+++D+P ++E+Y    GR GR G    A  F + ++
Sbjct: 290 VVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPAD 344

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 39.3 bits (90), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN 55
           +VAT     G++   ++ V+++D+P ++E+Y    GR GR G    A  F + ++
Sbjct: 290 VVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD 344

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	138
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	3e-50
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	3e-47
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	7e-45
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-43
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	9e-29
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	9e-29
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-28
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-28
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	1e-28
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	3e-28
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	6e-28
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	6e-28
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-27
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-27
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	3e-27
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	6e-27
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	3e-26
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	4e-26
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	4e-26
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	4e-25
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	8e-25
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	5e-24
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	7e-24
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-23
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	5e-17
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	5e-12
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	3e-06
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	8e-06
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	8e-06
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	2e-05
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	2e-05
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	3e-05

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  157 bits (400), Expect = 3e-50
 Identities = 61/83 (73%), Positives = 72/83 (86%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VATDVASKGLDF  I+HVINYDMP+++ENYVHRIGRTG SG TG+ATTFINK+ DESVL
Sbjct: 108 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVL 167

Query: 61  LDLKHLLLEARQRIPPFLAELES 83
           +DLK LLLEA+Q++PP L  L  
Sbjct: 168 MDLKALLLEAKQKVPPVLQVLHC 190

>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 =  149 bits (379), Expect = 3e-47
 Identities = 44/84 (52%), Positives = 61/84 (72%), Gaps = 1/84 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT VA++GLD   +KHVIN+D+P D+E YVHRIGRTGR G  GLAT+F N+  + ++ 
Sbjct: 100 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNE-RNINIT 158

Query: 61  LDLKHLLLEARQRIPPFLAELESE 84
            DL  LL+EA+Q +P +L  +  E
Sbjct: 159 KDLLDLLVEAKQEVPSWLENMAYE 182

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  149 bits (380), Expect = 7e-45
 Identities = 44/84 (52%), Positives = 61/84 (72%), Gaps = 1/84 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT VA++GLD   +KHVIN+D+P D+E YVHRIGRTGR G  GLAT+F N+  + ++ 
Sbjct: 330 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNE-RNINIT 388

Query: 61  LDLKHLLLEARQRIPPFLAELESE 84
            DL  LL+EA+Q +P +L  +  E
Sbjct: 389 KDLLDLLVEAKQEVPSWLENMAYE 412

>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 =  146 bits (372), Expect = 2e-43
 Identities = 41/78 (52%), Positives = 55/78 (70%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++AT VAS+GLD + IKHVINYDMP  +++YVHRIGRTGR G  G AT+F +   D ++ 
Sbjct: 354 LIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIA 413

Query: 61  LDLKHLLLEARQRIPPFL 78
            DL  +L  + Q +P FL
Sbjct: 414 ADLVKILEGSGQTVPDFL 431

>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 =  103 bits (259), Expect = 9e-29
 Identities = 24/52 (46%), Positives = 34/52 (65%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
           +VATDVA++GLD  ++  V++Y +PD  E Y HR GRTGR+G+ G       
Sbjct: 85  LVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYG 136

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  101 bits (255), Expect = 9e-29
 Identities = 33/75 (44%), Positives = 47/75 (62%), Gaps = 4/75 (5%)

Query: 2   VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLL 61
           VATDVA++G+D E I  VINYD+P + E+YVHR GRTGR+G  G A +F+  + ++  L 
Sbjct: 90  VATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFV-TAFEKRFLA 148

Query: 62  DLKHLLLEARQRIPP 76
           D++         I  
Sbjct: 149 DIEEY---IGFEIQK 160

>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 =  106 bits (268), Expect = 1e-28
 Identities = 30/85 (35%), Positives = 48/85 (56%), Gaps = 3/85 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT++  +G+D E +    NYDMP+D + Y+HR+ R GR G  GLA TF++  ND  +L
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 363

Query: 61  LDLKHLLLEARQRIPPFLAELESET 85
            D++         I     E++  +
Sbjct: 364 NDVQDRF---EVNISELPDEIDISS 385

>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 =  106 bits (267), Expect = 1e-28
 Identities = 28/52 (53%), Positives = 40/52 (76%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
           ++ATDV S+G+D  ++  VINY +P + E+Y+HRIGRTGR+GK G A + IN
Sbjct: 292 LIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIIN 343

>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 =  101 bits (255), Expect = 1e-28
 Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 5/82 (6%)

Query: 2   VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLL 61
           VATDVA++G+D  ++ HV N+DMP   + Y+HRIGRT R+G+ G A + +  ++D  +L 
Sbjct: 85  VATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVE-AHDHLLLG 143

Query: 62  DLKHLLLEARQRIPP-FLAELE 82
            +   +    + I    + EL 
Sbjct: 144 KVGRYI---EEPIKARVIDELR 162

>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 =  100 bits (252), Expect = 3e-28
 Identities = 30/85 (35%), Positives = 48/85 (56%), Gaps = 3/85 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT++  +G+D E +    NYDMP+D + Y+HR+ R GR G  GLA TF++  ND  +L
Sbjct: 85  LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 144

Query: 61  LDLKHLLLEARQRIPPFLAELESET 85
            D++         I     E++  +
Sbjct: 145 NDVQDRF---EVNISELPDEIDISS 166

>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 =  106 bits (266), Expect = 6e-28
 Identities = 31/92 (33%), Positives = 52/92 (56%), Gaps = 3/92 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +V TDV ++G+DF  +  V+   +P ++ NY+HRIGRT RSGK G +  FI K  +   +
Sbjct: 396 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKD-ELPFV 454

Query: 61  LDLKHLL--LEARQRIPPFLAELESETEKFLD 90
            +L+     + A+Q       E++SE  + + 
Sbjct: 455 RELEDAKNIVIAKQEKYEPSEEIKSEVLEAVT 486

>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 =  103 bits (258), Expect = 6e-28
 Identities = 25/51 (49%), Positives = 33/51 (64%)

Query: 2   VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
           VATDVA++GLD  ++  V++Y MPD  E Y HR GRTGR+G+ G       
Sbjct: 83  VATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYG 133

>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 =  105 bits (263), Expect = 1e-27
 Identities = 31/92 (33%), Positives = 53/92 (57%), Gaps = 3/92 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +V TDV ++G+DF  +  V+   +P ++ NY+HRIGRT RSGK G +  FI K  +   +
Sbjct: 345 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKD-ELPFV 403

Query: 61  LDLKHL--LLEARQRIPPFLAELESETEKFLD 90
            +L+    ++ A+Q       E++SE  + + 
Sbjct: 404 RELEDAKNIVIAKQEKYEPSEEIKSEVLEAVT 435

>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 =  102 bits (256), Expect = 3e-27
 Identities = 31/66 (46%), Positives = 45/66 (68%), Gaps = 2/66 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++ TDVAS+GLD   ++ VIN+D P D+  Y+HRIGRTGR G+ G A TFI   N+  + 
Sbjct: 270 LITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFI--LNEYWLE 327

Query: 61  LDLKHL 66
            ++K +
Sbjct: 328 KEVKKV 333

>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 =  102 bits (256), Expect = 6e-27
 Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 1/87 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +V +D+ ++G+D + +  VIN+D P   E Y+HRIGR+GR G  GLA   I   ND   L
Sbjct: 312 LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLI-NWNDRFNL 370

Query: 61  LDLKHLLLEARQRIPPFLAELESETEK 87
             ++  L      IP  + +     E 
Sbjct: 371 YKIEQELGTEIAAIPATIDKSLYVAEN 397

>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 =  100 bits (252), Expect = 3e-26
 Identities = 29/75 (38%), Positives = 50/75 (66%), Gaps = 4/75 (5%)

Query: 2   VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLL 61
           ++TDV ++GLD  ++  +INYD+P++ E Y+HRIGR+GR G+ G+A  F+ K++D  +L 
Sbjct: 331 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFV-KNDDIRILR 389

Query: 62  DLKHLLLEARQRIPP 76
           D++        +I  
Sbjct: 390 DIEQYY---STQIDE 401

>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 =  100 bits (251), Expect = 4e-26
 Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 4/76 (5%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++ TD+ ++G+D +++  VINYD+P + ENY+HRIGR GR G+ G+A   +    D+  L
Sbjct: 334 LITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMV-TEEDKRTL 392

Query: 61  LDLKHLLLEARQRIPP 76
            D++         I  
Sbjct: 393 RDIETFY---NTSIEE 405

>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 =   99 bits (250), Expect = 4e-26
 Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 1/81 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TD+ ++G+D +++  VINYD+P + ENY+HRIGR GR G+ G+A  F+  + D   +
Sbjct: 313 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFV-TNEDVGAM 371

Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            +L+       + +P  +A L
Sbjct: 372 RELEKFYSTQIEELPSDIATL 392

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 92.6 bits (231), Expect = 4e-25
 Identities = 29/83 (34%), Positives = 53/83 (63%), Gaps = 1/83 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TD+ ++G+D +++  VINYD+P + ENY+HRIGR GR G+ G+A  F+  + D   +
Sbjct: 84  LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFV-TNEDVGAM 142

Query: 61  LDLKHLLLEARQRIPPFLAELES 83
            +L+       + +P  +A L +
Sbjct: 143 RELEKFYSTQIEELPSDIATLLN 165

>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 = 96.5 bits (241), Expect = 8e-25
 Identities = 29/93 (31%), Positives = 50/93 (53%), Gaps = 7/93 (7%)

Query: 2   VATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKSN 55
           + T+V ++G+D   +  V+NYD+P       D   Y+HRIGRTGR G+ G+A +F++  N
Sbjct: 298 ITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 357

Query: 56  DESVLLDL-KHLLLEARQRIPPFLAELESETEK 87
             ++L  + K+       R+P    +   +  K
Sbjct: 358 SFNILSAIQKYFGDIEMTRVPTDDWDEVEKIVK 390

>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 = 94.5 bits (236), Expect = 5e-24
 Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 13/91 (14%)

Query: 2   VATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKSN 55
           V T+V ++G+D E++  VIN+D+P       D E Y+HRIGRTGR GK GLA   ++  +
Sbjct: 321 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 380

Query: 56  DESVLLDLKHLLLEARQRI----PPFLAELE 82
             ++L  ++       ++I       L E+E
Sbjct: 381 SMNILNRIQEHF---NKKIERLDTDDLDEIE 408

>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 = 90.0 bits (224), Expect = 7e-24
 Identities = 30/89 (33%), Positives = 50/89 (56%), Gaps = 8/89 (8%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKS 54
           ++ T+V ++G+D +++  V+N+D+P       D E Y+HRIGRTGR GK GLA   I   
Sbjct: 88  LITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEV- 146

Query: 55  NDESVLLDL-KHLLLEARQRIPPFLAELE 82
           ++   L+ +  H     +Q     + E+E
Sbjct: 147 DELPSLMKIQDHFNSSIKQLNAEDMDEIE 175

>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 = 93.9 bits (234), Expect = 1e-23
 Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 13/91 (14%)

Query: 2   VATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKSN 55
           V T+V ++G+D E++  VIN+D+P       D E Y+HRIGRTGR GK GLA   ++  +
Sbjct: 388 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 447

Query: 56  DESVLLDLKHLLLEARQRI----PPFLAELE 82
             ++L  ++       ++I       L E+E
Sbjct: 448 SMNILNRIQEHF---NKKIERLDTDDLDEIE 475

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 75.1 bits (185), Expect = 5e-17
 Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 9/99 (9%)

Query: 1   MVATDV----ASKGLDF-EEIKHVINYDMP--DDVENYVHRIGRTGRSGKTGL--ATTFI 51
           ++         ++G+D  E IK+VI +  P   DV  Y+   GR+ R     L    + I
Sbjct: 301 LIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVI 360

Query: 52  NKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLD 90
            + ++E        LLL A + I         E    ++
Sbjct: 361 FEEDEEIFESLKTRLLLIAEEEIIEEAEANWKELVHEVE 399

>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 = 61.0 bits (147), Expect = 5e-12
 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT V  +GLD  E+  V+ Y+        + R GRTGR    G     + K   +   
Sbjct: 423 LVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH-MPGRVIILMAKGTRDEAY 481

Query: 61  LDLKH 65
                
Sbjct: 482 YWSSR 486

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 44.2 bits (103), Expect = 3e-06
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRT-GRSGKTGLATTFINKSNDESV 59
           ++AT VA +G+D  +   VI Y+   +V   +   GR   R  K  L T+       E +
Sbjct: 465 LIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQI 524

Query: 60  LLDLKHLLLEARQRIPPFLAELESE 84
            +  + ++ ++  R+  +   +  E
Sbjct: 525 NMYKEKMMNDSILRLQTWDEAVFRE 549

>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 = 43.0 bits (100), Expect = 8e-06
 Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 8/93 (8%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++AT VA +G+D  +   V+ Y+   +V   +   GR GR+          +K+      
Sbjct: 698 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENE 755

Query: 61  L------DLKHLLLEARQRIPPFLAELESETEK 87
                  ++ +  +E  Q+        +    +
Sbjct: 756 KCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQ 788

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 43.0 bits (100), Expect = 8e-06
 Identities = 21/102 (20%), Positives = 40/102 (39%), Gaps = 13/102 (12%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++AT VA +G+D  +   V+ Y+   +V   +   GR GR+          +K+      
Sbjct: 457 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENE 514

Query: 61  LDLKHL------LLEARQRIPPFLAELESETEKFLDLGGDER 96
              ++        +E  Q+        E+  +K  +L   ER
Sbjct: 515 KCNRYKEEMMNKAVEKIQKWDE-----ETFAKKIHNLQMKER 551

>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 = 42.0 bits (98), Expect = 2e-05
 Identities = 20/103 (19%), Positives = 43/103 (41%), Gaps = 6/103 (5%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG--KTGLATTFINKSNDES 58
           ++ +++ S+G +F+   H++ +D+P + +    RIGR  R G            +   +S
Sbjct: 560 LLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQS 619

Query: 59  VLLDLKHLLLEARQRI----PPFLAELESETEKFLDLGGDERG 97
           VL+   H  L+A +            + ++   +L       G
Sbjct: 620 VLVRWYHEGLDAFEHTCPTGRTIYDSVYNDLINYLASPDQTEG 662

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 42.2 bits (98), Expect = 2e-05
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDES 58
           ++AT VA +G+D  E   VI Y+   +V   +   GR GR+ +        + ++   
Sbjct: 456 LIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIE 511

>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 = 41.5 bits (96), Expect = 3e-05
 Identities = 21/102 (20%), Positives = 40/102 (39%), Gaps = 13/102 (12%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++AT VA +G+D  +   V+ Y+   +V   +   GR GR+          +K+      
Sbjct: 698 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENE 755

Query: 61  LDLKHL------LLEARQRIPPFLAELESETEKFLDLGGDER 96
              ++        +E  Q+        E+  +K  +L   ER
Sbjct: 756 KCNRYKEEMMNKAVEKIQKWDE-----ETFAKKIHNLQMKER 792

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	138
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.83
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.82
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.82
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.79
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.78
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.77
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.77
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.75
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.75
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.74
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.73
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.72
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.54
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.69
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.69
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.67
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.67
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.66
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.65
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.65
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.64
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.63
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.62
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.6
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.6
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.6
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.57
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.55
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.54
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.53
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.53
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.52
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.5
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.48
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.47
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.46
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.45
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.44
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.43
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.42
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.42
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.42
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.4
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.39
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.38
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.38
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.38
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.36
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.34
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.31
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.3
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.28
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.27
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.26
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.25
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.25
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.22
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.2
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.18
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.17
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.14
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.1
3h1t_A	590	Type I site-specific restriction-modification syst	99.08
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.07
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.06
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.03
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.85
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.76
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.58
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.45
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	96.53
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	95.25

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.83  E-value=5.6e-21  Score=140.14  Aligned_cols=81  Identities=75%  Similarity=1.168  Sum_probs=73.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||+++++|+|+|++++||+||+|++++.|+||+||+||.|+.|.+++|+++.++......+++.+....+.+|++|.+
T Consensus       108 LvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~~l~~~l~~~~~~~p~~l~~  187 (191)
T 2p6n_A          108 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQV  187 (191)
T ss_dssp             EEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHHHHHHHHHHHHTTCCCCHHHHS
T ss_pred             EEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHHHHHHHHHHHHccCcCCHHHHh
Confidence            69999999999999999999999999999999999999999999999999998778888999999999999999998765


Q ss_pred             H
Q psy7792          81 L   81 (138)
Q Consensus        81 ~   81 (138)
                      +
T Consensus       188 ~  188 (191)
T 2p6n_A          188 L  188 (191)
T ss_dssp             T
T ss_pred             h
Confidence            4

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.82  E-value=9.2e-21  Score=153.50  Aligned_cols=80  Identities=51%  Similarity=0.908  Sum_probs=75.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||+++++|||+|+|++|||||+|.++++|+||+||+||.|+.|.+++|+++.++......+.+.+....+++|++|.+
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            69999999999999999999999999999999999999999999999999998778888999999999999999998754

>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=99.82  E-value=3e-20  Score=135.43  Aligned_cols=81  Identities=53%  Similarity=0.951  Sum_probs=69.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|+++. +...+..+.+.+....+.+|+++..
T Consensus       100 LvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~l~~~l~~~~~~~~~~l~~  178 (185)
T 2jgn_A          100 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNER-NINITKDLLDLLVEAKQEVPSWLEN  178 (185)
T ss_dssp             EEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGG-GGGGHHHHHHHHHHTTCCCCHHHHH
T ss_pred             EEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchh-hHHHHHHHHHHHHhccCCCCHHHHH
Confidence            699999999999999999999999999999999999999999999999999887 7778888999999999999998877


Q ss_pred             HH
Q psy7792          81 LE   82 (138)
Q Consensus        81 ~~   82 (138)
                      +.
T Consensus       179 ~a  180 (185)
T 2jgn_A          179 MA  180 (185)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>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=99.79  E-value=3.4e-20  Score=133.50  Aligned_cols=78  Identities=37%  Similarity=0.724  Sum_probs=68.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFL   78 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l   78 (138)
                      ||||+++++|+|+|++++|||||+|++++.|+||+||+||.|+.|.+++|+++.++...+..+++.+.....++|..+
T Consensus        85 LvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  162 (172)
T 1t5i_A           85 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  162 (172)
T ss_dssp             EEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             EEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCChhh
Confidence            699999999999999999999999999999999999999999999999999887566777888877776666776653

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.78  E-value=2.8e-19  Score=127.37  Aligned_cols=67  Identities=48%  Similarity=0.831  Sum_probs=60.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLL   68 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~   68 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|+++. +...+..+++.+.
T Consensus        89 lv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~i~~~~~  155 (163)
T 2hjv_A           89 LVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAF-EKRFLADIEEYIG  155 (163)
T ss_dssp             EEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGG-GHHHHHHHHHHHT
T ss_pred             EEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHH-HHHHHHHHHHHHC
Confidence            699999999999999999999999999999999999999999999999999887 6666666666553

>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=99.77  E-value=2.4e-19  Score=148.86  Aligned_cols=54  Identities=30%  Similarity=0.608  Sum_probs=52.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||++++||||+|+|++|||||+|+++++|+||+||+||+|.+|.+++|+++.
T Consensus       290 lVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~  343 (523)
T 1oyw_A          290 VVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPA  343 (523)
T ss_dssp             EEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHH
T ss_pred             EEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHH
Confidence            699999999999999999999999999999999999999999999999999876

>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=99.77  E-value=3.2e-19  Score=132.39  Aligned_cols=72  Identities=36%  Similarity=0.626  Sum_probs=62.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhccc
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQR   73 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~   73 (138)
                      ||||+++++|||+|+|++|||||+|++++.|+||+||+||.|+.|.+++|+++. +...+..+++.+......
T Consensus        85 lvaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~-~~~~~~~i~~~~~~~~~~  156 (212)
T 3eaq_A           85 LVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPR-ERRDVEALERAVGRRFKR  156 (212)
T ss_dssp             EEECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGG-GHHHHHHHHHHHSSCCEE
T ss_pred             EEecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchh-HHHHHHHHHHHhcCcCee
Confidence            699999999999999999999999999999999999999999999999999987 677777777766554443

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.75  E-value=4.1e-19  Score=126.62  Aligned_cols=75  Identities=36%  Similarity=0.790  Sum_probs=60.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPP   76 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~   76 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|+++. +...+..+++.+....+.+|.
T Consensus        84 lv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  158 (165)
T 1fuk_A           84 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE-DVGAMRELEKFYSTQIEELPS  158 (165)
T ss_dssp             EEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETT-THHHHHHHHHHSSCCCEECCS
T ss_pred             EEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcch-HHHHHHHHHHHHccCccccCc
Confidence            699999999999999999999999999999999999999999999999999987 666666676666555555544

>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=99.75  E-value=8.2e-19  Score=126.11  Aligned_cols=70  Identities=37%  Similarity=0.738  Sum_probs=56.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCC------CCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhc
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEAR   71 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP------~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~   71 (138)
                      ||||+++++|+|+|++++|||||+|      .++..|+||+||+||.|+.|.+++|+++. +...+..+.+.+....
T Consensus        88 LvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~-~~~~~~~i~~~~~~~~  163 (175)
T 2rb4_A           88 LITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVD-ELPSLMKIQDHFNSSI  163 (175)
T ss_dssp             EEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGG-GHHHHHHHHHHHTCCC
T ss_pred             EEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccc-hHHHHHHHHHHhcCcc
Confidence            6999999999999999999999999      99999999999999999999999999887 5555666655554333

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.74  E-value=1.8e-18  Score=137.32  Aligned_cols=81  Identities=53%  Similarity=0.951  Sum_probs=73.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||+++++|+|+|+|++||+||+|.++..|+||+||+||.|+.|.+++|+++. +......+.+.+....+.+|.++..
T Consensus       330 lvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~l~~  408 (417)
T 2i4i_A          330 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNER-NINITKDLLDLLVEAKQEVPSWLEN  408 (417)
T ss_dssp             EEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGG-GGGGHHHHHHHHHHTTCCCCHHHHH
T ss_pred             EEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccc-cHHHHHHHHHHHHHhcCcCCHHHHH
Confidence            699999999999999999999999999999999999999999999999999887 7788888999999999999998877


Q ss_pred             HH
Q psy7792          81 LE   82 (138)
Q Consensus        81 ~~   82 (138)
                      +.
T Consensus       409 ~~  410 (417)
T 2i4i_A          409 MA  410 (417)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.73  E-value=3e-18  Score=133.86  Aligned_cols=69  Identities=38%  Similarity=0.646  Sum_probs=56.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHh
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA   70 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~   70 (138)
                      ||||+++++|||+|+|++|||||+|+++++|+||+||+||.|+.|.+++|+++. +...+..+++.....
T Consensus        82 LVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~-e~~~~~~ie~~~~~~  150 (300)
T 3i32_A           82 LVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPR-ERRDVEALERAVGRR  150 (300)
T ss_dssp             EEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSS-THHHHHHHHHHHTCC
T ss_pred             EEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChH-HHHHHHHHHHHhCCc
Confidence            699999999999999999999999999999999999999999999999999987 666666666655443

>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=99.72  E-value=1.5e-18  Score=146.17  Aligned_cols=54  Identities=28%  Similarity=0.434  Sum_probs=52.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||++++||||+|+|++|||||+|.++++|+||+|||||+|++|.+++|+++.
T Consensus       321 lVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~  374 (591)
T 2v1x_A          321 VVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFG  374 (591)
T ss_dssp             EEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHH
T ss_pred             EEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChH
Confidence            699999999999999999999999999999999999999999999999999876

>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=99.54  E-value=1e-18  Score=125.26  Aligned_cols=69  Identities=41%  Similarity=0.772  Sum_probs=61.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHh
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA   70 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~   70 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++++++. +...+..+++.+...
T Consensus        84 LvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~  152 (170)
T 2yjt_D           84 LVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAH-DHLLLGKVGRYIEEP  152 (170)
Confidence            699999999999999999999999999999999999999999999999999876 566666666654433

>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=99.69  E-value=8e-18  Score=133.24  Aligned_cols=80  Identities=36%  Similarity=0.754  Sum_probs=61.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      ||||+++++|+|+|+|++||+||+|.++..|+||+||+||.|+.|.+++|+++. +...+..+++++.....++|..+.+
T Consensus       334 lv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  412 (414)
T 3eiq_A          334 LITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEE-DKRTLRDIETFYNTSIEEMPLNVAD  412 (414)
T ss_dssp             EEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECST-HHHHHHHHHHHTTCCCEECCC----
T ss_pred             EEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHH-HHHHHHHHHHHHcCCccccChhhhh
Confidence            699999999999999999999999999999999999999999999999999887 7788888888888888888776554


Q ss_pred             H
Q psy7792          81 L   81 (138)
Q Consensus        81 ~   81 (138)
                      +
T Consensus       413 l  413 (414)
T 3eiq_A          413 L  413 (414)
T ss_dssp             -
T ss_pred             c
Confidence            3

>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=99.69  E-value=1.8e-17  Score=131.61  Aligned_cols=75  Identities=37%  Similarity=0.771  Sum_probs=68.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPP   76 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~   76 (138)
                      ||||+++++|+|+|+|++||+||+|+++..|+||+||+||.|+.|.+++|+++. +...+..+++++.....++|.
T Consensus       330 lv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~-~~~~~~~i~~~~~~~~~~~~~  404 (410)
T 2j0s_A          330 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND-DIRILRDIEQYYSTQIDEMPM  404 (410)
T ss_dssp             EEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGG-GHHHHHHHHHHTTCCCEECCS
T ss_pred             EEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHH-HHHHHHHHHHHhCCCceeccc
Confidence            699999999999999999999999999999999999999999999999999987 777888888877766666654

>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=99.67  E-value=7.1e-17  Score=133.59  Aligned_cols=66  Identities=39%  Similarity=0.759  Sum_probs=60.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLL   67 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~   67 (138)
                      ||||+++++|||+|+|++|||||+|.++++|+||+||+||.|+.|.+++|+++. +...++.++...
T Consensus       396 LvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~-e~~~~~~l~~~~  461 (563)
T 3i5x_A          396 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKD-ELPFVRELEDAK  461 (563)
T ss_dssp             EEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGG-GHHHHHHHHHHH
T ss_pred             EEEcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchh-HHHHHHHHHHHh
Confidence            699999999999999999999999999999999999999999999999999987 666666665543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.67  E-value=7.8e-17  Score=134.46  Aligned_cols=65  Identities=40%  Similarity=0.781  Sum_probs=60.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHL   66 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~   66 (138)
                      ||||+++++|||+|+|++|||||+|.+++.|+||+||+||+|+.|.+++|+++. +..++..++..
T Consensus       345 LVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~-e~~~~~~l~~~  409 (579)
T 3sqw_A          345 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKD-ELPFVRELEDA  409 (579)
T ss_dssp             EEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGG-GHHHHHHHHHH
T ss_pred             EEEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEccc-HHHHHHHHHHH
Confidence            699999999999999999999999999999999999999999999999999987 66666666554

>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=99.66  E-value=4.8e-17  Score=127.88  Aligned_cols=76  Identities=38%  Similarity=0.748  Sum_probs=66.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPP   76 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~   76 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|+++.++..++..+++.+....+++|.
T Consensus       304 lv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  379 (391)
T 1xti_A          304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPD  379 (391)
T ss_dssp             EEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCS
T ss_pred             EEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCChhhCCc
Confidence            6999999999999999999999999999999999999999999999999999876667777777766555555554

>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=99.65  E-value=9.1e-17  Score=125.88  Aligned_cols=68  Identities=37%  Similarity=0.782  Sum_probs=61.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC------CHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLL   68 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~------~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~   68 (138)
                      ||||+++++|+|+|++++||+||+|+      ++..|+||+||+||.|+.|.+++|+++.++......+.+.+.
T Consensus       297 lv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~  370 (395)
T 3pey_A          297 LITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFG  370 (395)
T ss_dssp             EEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTT
T ss_pred             EEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhC
Confidence            69999999999999999999999999      999999999999999999999999988766666666666554

>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=99.65  E-value=9.7e-17  Score=126.81  Aligned_cols=75  Identities=39%  Similarity=0.703  Sum_probs=64.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPP   76 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~   76 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|+++. +...+..+++.+....+.+|.
T Consensus       312 Lv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~-~~~~~~~i~~~~~~~~~~~~~  386 (400)
T 1s2m_A          312 LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWN-DRFNLYKIEQELGTEIAAIPA  386 (400)
T ss_dssp             EEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGG-GHHHHHHHHHHHTCCCEECCS
T ss_pred             EEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccc-hHHHHHHHHHHhCCCcccccc
Confidence            699999999999999999999999999999999999999999999999999887 666666666665554444444

>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=99.64  E-value=1.1e-16  Score=126.36  Aligned_cols=76  Identities=38%  Similarity=0.724  Sum_probs=65.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC------CHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRI   74 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~------~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~   74 (138)
                      ||||+++++|+|+|++++||+||+|+      +...|+||+||+||.|+.|.+++++++.++...+..+++.+......+
T Consensus       320 lv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  399 (412)
T 3fht_A          320 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL  399 (412)
T ss_dssp             EEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC
T ss_pred             EEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccC
Confidence            69999999999999999999999994      678999999999999999999999988766777777777776655555


Q ss_pred             cH
Q psy7792          75 PP   76 (138)
Q Consensus        75 ~~   76 (138)
                      +.
T Consensus       400 ~~  401 (412)
T 3fht_A          400 DT  401 (412)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>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=99.63  E-value=2.9e-16  Score=121.88  Aligned_cols=69  Identities=42%  Similarity=0.756  Sum_probs=61.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHh
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA   70 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~   70 (138)
                      ||||+++++|+|+|++++||++++|+++.+|+||+||+||.|++|.+++++++. +...+..+++.++..
T Consensus       292 lv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~-~~~~~~~i~~~~~~~  360 (367)
T 1hv8_A          292 LIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRR-EYKKLRYIERAMKLK  360 (367)
T ss_dssp             EEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTT-SHHHHHHHHHHHTCC
T ss_pred             EEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHH-HHHHHHHHHHHhCCC
Confidence            689999999999999999999999999999999999999999999999999887 666666666655443

>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=99.62  E-value=2.6e-16  Score=121.02  Aligned_cols=66  Identities=45%  Similarity=0.779  Sum_probs=57.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLL   68 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~   68 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|+. . +......+++.++
T Consensus       270 lv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~-~~~~~~~i~~~~~  335 (337)
T 2z0m_A          270 LITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL-N-EYWLEKEVKKVSQ  335 (337)
T ss_dssp             EEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES-S-CHHHHHHHC----
T ss_pred             EEEcCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe-C-cHHHHHHHHHHhc
Confidence            6899999999999999999999999999999999999999999999999998 4 6666766665543

>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=99.60  E-value=5.6e-17  Score=127.43  Aligned_cols=77  Identities=35%  Similarity=0.762  Sum_probs=0.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFL   78 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l   78 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|+++. +...+..+++++......+|..+
T Consensus       313 lv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~  389 (394)
T 1fuu_A          313 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE-DVGAMRELEKFYSTQIEELPSDI  389 (394)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             EEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchh-HHHHHHHHHHHhCCcccccCcch
Confidence            699999999999999999999999999999999999999999999999999887 66677777777776666666543

>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=99.60  E-value=5.9e-17  Score=131.86  Aligned_cols=76  Identities=38%  Similarity=0.724  Sum_probs=0.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC------CHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRI   74 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~------~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~   74 (138)
                      ||||+++++|||+|+|++|||||+|.      +...|+||+||+||.|+.|.+++|+++.++...+..+.+.+......+
T Consensus       387 Lv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l  466 (479)
T 3fmp_B          387 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERL  466 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceEC
Confidence            79999999999999999999999995      568999999999999999999999998766777777777776655554


Q ss_pred             cH
Q psy7792          75 PP   76 (138)
Q Consensus        75 ~~   76 (138)
                      +.
T Consensus       467 ~~  468 (479)
T 3fmp_B          467 DT  468 (479)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.60  E-value=9.7e-16  Score=122.31  Aligned_cols=65  Identities=34%  Similarity=0.553  Sum_probs=58.8

Q ss_pred             Cee----cccccccCCCCC-ccEEEEcCCC--CCHHHHHHHhhccccCC----CcceEEEeeeCCCcHHHHHHHHHHHH
Q psy7792           1 MVA----TDVASKGLDFEE-IKHVINYDMP--DDVENYVHRIGRTGRSG----KTGLATTFINKSNDESVLLDLKHLLL   68 (138)
Q Consensus         1 Lva----T~~~~~GiD~~~-V~~VI~~dlP--~~~~~y~qr~GRagR~g----~~g~~i~~~~~~~~~~~~~~l~~~~~   68 (138)
                      |||    |+++++|||+|+ |++|||||+|  .++.+|+||+||+||.|    +.|.+++|+   ++...+..+++.+.
T Consensus       301 Lvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~---~~~~~~~~l~~~~~  376 (414)
T 3oiy_A          301 LIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE---EDEEIFESLKTRLL  376 (414)
T ss_dssp             EEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC---CCHHHHHHHHHHHH
T ss_pred             EEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE---ccHHHHHHHHHHhc
Confidence            588    999999999999 9999999999  99999999999999988    589999999   36777777777776

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.57  E-value=2.5e-15  Score=126.96  Aligned_cols=52  Identities=27%  Similarity=0.491  Sum_probs=35.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|+|++|||||+|+++++|+||+|| ||. +.|.++.+++..
T Consensus       465 LVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~  516 (696)
T 2ykg_A          465 LIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNA  516 (696)
T ss_dssp             SEEEESSCCC---CCCSEEEEESCC--CCCC-----------CCCEEEEEESCH
T ss_pred             EEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCC
Confidence            7999999999999999999999999999999999999 998 778998888765

>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=99.55  E-value=9.5e-15  Score=123.46  Aligned_cols=50  Identities=28%  Similarity=0.427  Sum_probs=43.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~   53 (138)
                      ||||+++++|||+|+|++|||||+|+|++.|+||+|||||.|   .+++++.+
T Consensus       468 LVaT~~~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRArr~g---~~~~l~~~  517 (699)
T 4gl2_A          468 LIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADE---STYVLVAH  517 (699)
T ss_dssp             SEEECSCCTTSCCCSCCCCEEESCCCCHHHHHHHHTTSCSSS---CEEEEEEE
T ss_pred             EEEccccccCCccccCCEEEEeCCCCCHHHHHHHcCCCCCCC---ceEEEEEe
Confidence            799999999999999999999999999999999999987765   44444443

>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=99.54  E-value=3.7e-15  Score=129.24  Aligned_cols=56  Identities=21%  Similarity=0.405  Sum_probs=53.2

Q ss_pred             CeecccccccCCCC--------CccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCc
Q psy7792           1 MVATDVASKGLDFE--------EIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSND   56 (138)
Q Consensus         1 LvaT~~~~~GiD~~--------~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~   56 (138)
                      |||||+++||+|++        ++.+|||||+|.+.+.|+||+||+||.|.+|.+++|++..++
T Consensus       484 lIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          484 TIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             EEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             EEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            59999999999999        788999999999999999999999999999999999998753

>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=99.53  E-value=4.5e-15  Score=121.44  Aligned_cols=53  Identities=26%  Similarity=0.485  Sum_probs=31.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      ||||+++++|||+|+|++|||||+|+++..|+||+|| ||. +.|.++.|+++.+
T Consensus       457 LvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~  509 (556)
T 4a2p_A          457 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTE  509 (556)
T ss_dssp             EEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHH
T ss_pred             EEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcc
Confidence            6999999999999999999999999999999999999 998 8899999998763

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.52  E-value=1.9e-15  Score=123.24  Aligned_cols=52  Identities=29%  Similarity=0.505  Sum_probs=49.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|+|++|||||+|+++..|+||+|| ||. +.|.++.|+++.
T Consensus       456 LvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~  507 (555)
T 3tbk_A          456 LIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSA  507 (555)
T ss_dssp             EEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCH
T ss_pred             EEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCC
Confidence            6999999999999999999999999999999999999 998 889999999876

>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=99.50  E-value=1.4e-14  Score=117.77  Aligned_cols=73  Identities=21%  Similarity=0.333  Sum_probs=59.6

Q ss_pred             CeecccccccCCCCCccEEEE-------------------cCCCCCHHHHHHHhhccccC-CCcceEEEeee--CCCcHH
Q psy7792           1 MVATDVASKGLDFEEIKHVIN-------------------YDMPDDVENYVHRIGRTGRS-GKTGLATTFIN--KSNDES   58 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~-------------------~dlP~~~~~y~qr~GRagR~-g~~g~~i~~~~--~~~~~~   58 (138)
                      ||||+++++|||+| |++|||                   |++|.++++|+||+||+||. |++|.+++|++  ...+..
T Consensus       227 LVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~  305 (440)
T 1yks_A          227 ILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAH  305 (440)
T ss_dssp             EEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTT
T ss_pred             EEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhh
Confidence            69999999999999 999996                   99999999999999999998 68999999973  333666


Q ss_pred             HHHHHHHHHHHhcccC
Q psy7792          59 VLLDLKHLLLEARQRI   74 (138)
Q Consensus        59 ~~~~l~~~~~~~~~~~   74 (138)
                      .+..++..+......+
T Consensus       306 ~l~~l~~~~~~~~~~l  321 (440)
T 1yks_A          306 HVCWLEASMLLDNMEV  321 (440)
T ss_dssp             BHHHHHHHHHHTTSCC
T ss_pred             hhhhhhHHhccccccc
Confidence            6666766654444433

>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=99.48  E-value=2.7e-14  Score=122.62  Aligned_cols=55  Identities=24%  Similarity=0.364  Sum_probs=51.8

Q ss_pred             CeecccccccCCCC--------CccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFE--------EIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~--------~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      +||||+++||+|++        .+.+|||+++|.+...|+||+||+||.|.+|.+++|++..+
T Consensus       526 tVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD  588 (822)
T 3jux_A          526 TIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLED  588 (822)
T ss_dssp             EEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTS
T ss_pred             EEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhH
Confidence            59999999999998        55699999999999999999999999999999999999874

>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=99.47  E-value=2.6e-14  Score=120.97  Aligned_cols=67  Identities=25%  Similarity=0.312  Sum_probs=57.2

Q ss_pred             CeecccccccCCCCCccEE--------------------EEcCCCCCHHHHHHHhhccccCCC-cceEEEeee---CCCc
Q psy7792           1 MVATDVASKGLDFEEIKHV--------------------INYDMPDDVENYVHRIGRTGRSGK-TGLATTFIN---KSND   56 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~V--------------------I~~dlP~~~~~y~qr~GRagR~g~-~g~~i~~~~---~~~~   56 (138)
                      |||||++++|||++ |++|                    ||||+|.++++|+||+||+||.|. +|.+++|++   +. +
T Consensus       405 LVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~-d  482 (618)
T 2whx_A          405 VVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKN-D  482 (618)
T ss_dssp             EEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCC-C
T ss_pred             EEECcHHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchh-h
Confidence            69999999999997 9888                    888889999999999999999975 899999997   44 6


Q ss_pred             HHHHHHHHHHHHH
Q psy7792          57 ESVLLDLKHLLLE   69 (138)
Q Consensus        57 ~~~~~~l~~~~~~   69 (138)
                      ...+..+++.+..
T Consensus       483 ~~~l~~le~~i~l  495 (618)
T 2whx_A          483 EDHAHWTEAKMLL  495 (618)
T ss_dssp             TTCHHHHHHHHHH
T ss_pred             HHHHHHHHhHhcc
Confidence            6666777766544

>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=99.46  E-value=5.7e-14  Score=111.56  Aligned_cols=54  Identities=33%  Similarity=0.503  Sum_probs=51.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      ||||+++++|||+|++++||+||+|+++..|+||+||+||.|+ |.++.|+++..
T Consensus       423 Lv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t  476 (494)
T 1wp9_A          423 LVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGT  476 (494)
T ss_dssp             EEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTS
T ss_pred             EEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCC
Confidence            6999999999999999999999999999999999999999998 99999998764

>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=99.45  E-value=6.3e-14  Score=114.47  Aligned_cols=53  Identities=25%  Similarity=0.419  Sum_probs=47.2

Q ss_pred             CeecccccccCCCCCccEEEE--------------------cCCCCCHHHHHHHhhccccCCC-cceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN--------------------YDMPDDVENYVHRIGRTGRSGK-TGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~--------------------~dlP~~~~~y~qr~GRagR~g~-~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|+ ++|||                    ||+|.++++|+||+||+||.|. +|.++.|+++.
T Consensus       240 LVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          240 VITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             EEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             EEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence            699999999999999 99999                    8899999999999999999997 89999999875

>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=99.44  E-value=5e-14  Score=121.61  Aligned_cols=52  Identities=27%  Similarity=0.488  Sum_probs=36.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|+|++|||||+|+|+..|+||+|| ||. +.|.++.|+++.
T Consensus       698 LVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~  749 (797)
T 4a2q_A          698 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKT  749 (797)
T ss_dssp             EEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCH
T ss_pred             EEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCC
Confidence            6999999999999999999999999999999999999 998 889999999775

>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=99.43  E-value=1.1e-13  Score=121.79  Aligned_cols=53  Identities=26%  Similarity=0.485  Sum_probs=37.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      ||||+++++|||+|+|++|||||+|+|+..|+||+|| ||. +.|.++.|++...
T Consensus       698 LVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t  750 (936)
T 4a2w_A          698 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTE  750 (936)
T ss_dssp             EEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHH
T ss_pred             EEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCC
Confidence            6999999999999999999999999999999999999 998 7789999987653

>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=99.42  E-value=7.6e-14  Score=118.98  Aligned_cols=52  Identities=35%  Similarity=0.643  Sum_probs=48.1

Q ss_pred             CeecccccccCCCCCccEEE----------EcC-----------CCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVI----------NYD-----------MPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI----------~~d-----------lP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      |||||+++||||++ |++||          |||           +|.+.++|+||+||+|| |++|. +.|+++.+
T Consensus       443 LVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e  515 (666)
T 3o8b_A          443 VVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGE  515 (666)
T ss_dssp             EEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCC
T ss_pred             EEECChHHccCCCC-CcEEEecCcccccccccccccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecch
Confidence            69999999999996 99988          788           99999999999999999 99999 99998764

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.42  E-value=1.3e-13  Score=117.68  Aligned_cols=66  Identities=20%  Similarity=0.298  Sum_probs=55.3

Q ss_pred             CeecccccccCCCCCccEEEE--------------------cCCCCCHHHHHHHhhccccC-CCcceEEEeee--CCCcH
Q psy7792           1 MVATDVASKGLDFEEIKHVIN--------------------YDMPDDVENYVHRIGRTGRS-GKTGLATTFIN--KSNDE   57 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~--------------------~dlP~~~~~y~qr~GRagR~-g~~g~~i~~~~--~~~~~   57 (138)
                      ||||+++++|||+| |++|||                    ||+|.++++|+||+||+||. |+.|.+++|+.  ...+.
T Consensus       460 LVaTdv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~  538 (673)
T 2wv9_A          460 VITTDISEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDT  538 (673)
T ss_dssp             EEECGGGGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCT
T ss_pred             EEECchhhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHH
Confidence            69999999999999 999998                    67999999999999999999 78999999973  23355


Q ss_pred             HHHHHHHHHH
Q psy7792          58 SVLLDLKHLL   67 (138)
Q Consensus        58 ~~~~~l~~~~   67 (138)
                      ..+..++..+
T Consensus       539 ~~l~~ie~~~  548 (673)
T 2wv9_A          539 MLAHWTEAKI  548 (673)
T ss_dssp             TBHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5555555544

>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=99.42  E-value=1.1e-13  Score=112.74  Aligned_cols=52  Identities=27%  Similarity=0.418  Sum_probs=48.4

Q ss_pred             CeecccccccCCCCCccEEEEcC--------------------CCCCHHHHHHHhhccccCCC-cceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD--------------------MPDDVENYVHRIGRTGRSGK-TGLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d--------------------lP~~~~~y~qr~GRagR~g~-~g~~i~~~~~   53 (138)
                      ||||+++++|||+|+ ++|||||                    +|.++++|+||+||+||.|. .|.+++|+..
T Consensus       238 LVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          238 VVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             EEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             EEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence            699999999999999 9999999                    99999999999999999998 8888888643

>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=99.40  E-value=4.1e-13  Score=114.35  Aligned_cols=59  Identities=24%  Similarity=0.416  Sum_probs=53.0

Q ss_pred             CeecccccccCCCCCccEEEEcCC-----CCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDM-----PDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLL   61 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dl-----P~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~   61 (138)
                      ||||+++++|+|+|+|++||++|.     |.+.++|+||+||+||. ..|.+++|+++. +..+..
T Consensus       499 LVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~-~~~~~~  562 (661)
T 2d7d_A          499 LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-AEGRVIMYADKI-TKSMEI  562 (661)
T ss_dssp             EEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSC-CHHHHH
T ss_pred             EEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCC-CHHHHH
Confidence            689999999999999999999997     99999999999999998 789999999886 444433

>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=99.39  E-value=2.5e-13  Score=117.78  Aligned_cols=55  Identities=24%  Similarity=0.431  Sum_probs=51.8

Q ss_pred             CeecccccccCCCCC--------------------------------c-----cEEEEcCCCCCHHHHHHHhhccccCCC
Q psy7792           1 MVATDVASKGLDFEE--------------------------------I-----KHVINYDMPDDVENYVHRIGRTGRSGK   43 (138)
Q Consensus         1 LvaT~~~~~GiD~~~--------------------------------V-----~~VI~~dlP~~~~~y~qr~GRagR~g~   43 (138)
                      +||||+++||+||+.                                |     .+||||++|.+...|.||+||+||.|.
T Consensus       493 tIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd  572 (853)
T 2fsf_A          493 TIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGD  572 (853)
T ss_dssp             EEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGC
T ss_pred             EEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCC
Confidence            599999999999997                                4     599999999999999999999999999


Q ss_pred             cceEEEeeeCCC
Q psy7792          44 TGLATTFINKSN   55 (138)
Q Consensus        44 ~g~~i~~~~~~~   55 (138)
                      +|.+++|++..+
T Consensus       573 ~G~s~~fls~eD  584 (853)
T 2fsf_A          573 AGSSRFYLSMED  584 (853)
T ss_dssp             CEEEEEEEETTS
T ss_pred             CeeEEEEecccH
Confidence            999999999774

>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=99.38  E-value=5.2e-13  Score=113.76  Aligned_cols=61  Identities=21%  Similarity=0.389  Sum_probs=53.2

Q ss_pred             CeecccccccCCCCCccEEEEcCC-----CCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDM-----PDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDL   63 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dl-----P~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l   63 (138)
                      ||||+++++|+|+|+|++||++|.     |.+..+|+||+||+||.+ .|.+++|+++. +..+...+
T Consensus       493 LvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~-~~~~~~~i  558 (664)
T 1c4o_A          493 LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADRV-SEAMQRAI  558 (664)
T ss_dssp             EEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSC-CHHHHHHH
T ss_pred             EEccChhhcCccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCC-CHHHHHHH
Confidence            689999999999999999999998     999999999999999995 79999999876 44443333

>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=99.38  E-value=4.1e-13  Score=119.35  Aligned_cols=68  Identities=22%  Similarity=0.363  Sum_probs=53.6

Q ss_pred             Cee----cccccccCCCCCc-cEEEEcCCC--------------------------------------------------
Q psy7792           1 MVA----TDVASKGLDFEEI-KHVINYDMP--------------------------------------------------   25 (138)
Q Consensus         1 Lva----T~~~~~GiD~~~V-~~VI~~dlP--------------------------------------------------   25 (138)
                      |||    |+++++|||+|+| ++|||||+|                                                  
T Consensus       323 LVaTas~Tdv~~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (1054)
T 1gku_B          323 LIGTAHYYGTLVRGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKK  402 (1054)
T ss_dssp             EEEECC------CCSCCTTTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHH
T ss_pred             EEEecCCCCeeEeccccCCcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            588    9999999999996 999999999                                                  


Q ss_pred             ---------------------CCHHHHHHHhhccccCCCcc--eEEEeeeCCCcHHHHHHHHHHHHH
Q psy7792          26 ---------------------DDVENYVHRIGRTGRSGKTG--LATTFINKSNDESVLLDLKHLLLE   69 (138)
Q Consensus        26 ---------------------~~~~~y~qr~GRagR~g~~g--~~i~~~~~~~~~~~~~~l~~~~~~   69 (138)
                                           .++.+|+||+||+||.|..|  .+++|+... +...+..+++.+..
T Consensus       403 ~l~~~~~~~~~~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~-d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          403 VMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLED-DSELLSAFIERAKL  468 (1054)
T ss_dssp             HHTTSCCSCSSSEEETTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECS-CHHHHHHHHHHHHT
T ss_pred             HhccccccccceeEeecceecCcHHHHhhhhchhhhccCCCCceEEEEEEec-CHHHHHHHHHHHhh
Confidence                                 79999999999999988775  478887776 67777777777664

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.38  E-value=7.2e-13  Score=118.31  Aligned_cols=66  Identities=33%  Similarity=0.549  Sum_probs=56.1

Q ss_pred             Cee----cccccccCCCCC-ccEEEEcCCCC-------------------------------------------------
Q psy7792           1 MVA----TDVASKGLDFEE-IKHVINYDMPD-------------------------------------------------   26 (138)
Q Consensus         1 Lva----T~~~~~GiD~~~-V~~VI~~dlP~-------------------------------------------------   26 (138)
                      |||    |++++||||+|+ |++|||||+|.                                                 
T Consensus       358 LVatas~TdvlarGIDip~~V~~VI~~d~P~~~~Sle~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~  437 (1104)
T 4ddu_A          358 LIGVQAYYGKLTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEF  437 (1104)
T ss_dssp             EEEETTTHHHHCCSCCCTTTCCEEEEESCCEEEEECSSSSCCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHCCCHHHH
T ss_pred             EEEecCCCCeeEecCcCCCCCCEEEEECCCCCCCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHH
Confidence            688    999999999999 99999999999                                                 


Q ss_pred             -----------------------CHHHHHHHhhccccCCC----cceEEEeeeCCCcHHHHHHHHHHHHH
Q psy7792          27 -----------------------DVENYVHRIGRTGRSGK----TGLATTFINKSNDESVLLDLKHLLLE   69 (138)
Q Consensus        27 -----------------------~~~~y~qr~GRagR~g~----~g~~i~~~~~~~~~~~~~~l~~~~~~   69 (138)
                                             ++.+|+||+|||||.|.    .|.+++++   +|...+..+++.+..
T Consensus       438 ~~~i~~~~~~l~~~~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~---~d~~~~~~l~~~~~~  504 (1104)
T 4ddu_A          438 VEKVKEMFRGVVVKDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFE---EDEEIFESLKTRLLL  504 (1104)
T ss_dssp             HHHHHHHCCSSEEETTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEEC---CCHHHHHHHHHHHHH
T ss_pred             HHHHhhccceEEecCCeeEEEecChhhhhcccCchhcccCCCcccceEEEEE---ecHHHHHHHHHHHhh
Confidence                                   88899999999999654    45666665   377888888887763

>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=99.36  E-value=1e-12  Score=114.43  Aligned_cols=39  Identities=18%  Similarity=0.292  Sum_probs=37.3

Q ss_pred             cEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792          17 KHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus        17 ~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      .+||||++|.+...|.||+||+||.|.+|.+++|++..+
T Consensus       580 lhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD  618 (922)
T 1nkt_A          580 LYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGD  618 (922)
T ss_dssp             EEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTS
T ss_pred             cEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhH
Confidence            499999999999999999999999999999999999874

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.34  E-value=3.7e-13  Score=103.41  Aligned_cols=54  Identities=17%  Similarity=0.199  Sum_probs=34.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceE--EEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLA--TTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~--i~~~~~~   54 (138)
                      |++|+++++|||++.+++||+||+|||+..|.||+||++|.|+.+.+  +.|++..
T Consensus       169 L~st~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~  224 (271)
T 1z5z_A          169 VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  224 (271)
T ss_dssp             EEECCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             EEehhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCC
Confidence            58999999999999999999999999999999999999999987654  4455543

>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=99.31  E-value=3.6e-12  Score=112.49  Aligned_cols=51  Identities=24%  Similarity=0.505  Sum_probs=47.5

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEee
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFI   51 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~   51 (138)
                      ||||+++++|||+|++++||+||+|+++..|+||+||+||.|+.+.++++.
T Consensus       560 LvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~  610 (968)
T 3dmq_A          560 LLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHV  610 (968)
T ss_dssp             EECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEE
T ss_pred             EEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEE
Confidence            699999999999999999999999999999999999999999988666554

>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=99.30  E-value=2.4e-12  Score=111.56  Aligned_cols=54  Identities=19%  Similarity=0.310  Sum_probs=50.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC-CHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD-DVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~-~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|+|++||++|+|. +.+.|.||+||+||.|++|.+++++++.
T Consensus       643 LVaT~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~  697 (780)
T 1gm5_A          643 LVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDV  697 (780)
T ss_dssp             CCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSC
T ss_pred             EEECCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECCC
Confidence            79999999999999999999999996 7889999999999999999999999853

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.28  E-value=3.2e-12  Score=113.28  Aligned_cols=60  Identities=27%  Similarity=0.410  Sum_probs=53.5

Q ss_pred             CeecccccccCCCCCccEEEE----cCC----CCCHHHHHHHhhccccCCC--cceEEEeeeCCCcHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----YDM----PDDVENYVHRIGRTGRSGK--TGLATTFINKSNDESVL   60 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----~dl----P~~~~~y~qr~GRagR~g~--~g~~i~~~~~~~~~~~~   60 (138)
                      ||||+++++|||+|++++||+    ||.    |.++..|+||+|||||.|.  .|.+++++++..+...+
T Consensus       436 LVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e~~~~  505 (1010)
T 2xgj_A          436 LFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVA  505 (1010)
T ss_dssp             EEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCCHHHH
T ss_pred             EEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCCHHHH
Confidence            699999999999999999999    999    9999999999999999996  59999999876444333

>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=99.27  E-value=3.1e-12  Score=114.28  Aligned_cols=60  Identities=25%  Similarity=0.383  Sum_probs=48.9

Q ss_pred             CeecccccccCCCCCccEEEEcCCC--------CCHHHHHHHhhccccCC--CcceEEEeeeCCCcHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP--------DDVENYVHRIGRTGRSG--KTGLATTFINKSNDESVL   60 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP--------~~~~~y~qr~GRagR~g--~~g~~i~~~~~~~~~~~~   60 (138)
                      ||||+++++|||+|+|++||+++.|        -++.+|+||+|||||.|  ..|.+++++++..+...+
T Consensus       534 LVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~~~~~~~  603 (1108)
T 3l9o_A          534 LFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVA  603 (1108)
T ss_dssp             EEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCCCCHHHH
T ss_pred             EEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCCcCHHHH
Confidence            6999999999999999999988764        36778999999999999  689999998876444433

>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=99.26  E-value=5.6e-12  Score=102.13  Aligned_cols=54  Identities=20%  Similarity=0.412  Sum_probs=47.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCc---ceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKT---GLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~---g~~i~~~~~~   54 (138)
                      ||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.   ...+.|++..
T Consensus       398 Lv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          398 IVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             CBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             EEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCC
Confidence            79999999999999999999999999999999999999999954   3444456543

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.25  E-value=4.6e-12  Score=108.28  Aligned_cols=50  Identities=34%  Similarity=0.549  Sum_probs=44.9

Q ss_pred             CeecccccccCCCCCccEEEEcCC--------------CCCHHHHHHHhhccccCCCc---ceEEEee
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDM--------------PDDVENYVHRIGRTGRSGKT---GLATTFI   51 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dl--------------P~~~~~y~qr~GRagR~g~~---g~~i~~~   51 (138)
                      ||||+++++|||+ +|++||++++              |.+.++|+||+|||||.|..   |.++.+.
T Consensus       376 LVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~  442 (677)
T 3rc3_A          376 LVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMN  442 (677)
T ss_dssp             EEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESS
T ss_pred             EEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEe
Confidence            6999999999999 9999999999              88999999999999999964   6666554

>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=99.25  E-value=1.7e-12  Score=112.30  Aligned_cols=53  Identities=23%  Similarity=0.436  Sum_probs=50.0

Q ss_pred             CeecccccccCCCCCccEEEEcCC------------------CCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDM------------------PDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dl------------------P~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|+|++||++++                  |.+.++|+||+|||||. .+|.++.|+++.
T Consensus       373 lVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~  443 (773)
T 2xau_A          373 VISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEE  443 (773)
T ss_dssp             EEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHH
T ss_pred             EEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHH
Confidence            699999999999999999999888                  99999999999999999 889999999754

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.22  E-value=6.5e-12  Score=101.79  Aligned_cols=50  Identities=20%  Similarity=0.359  Sum_probs=42.9

Q ss_pred             CeecccccccCCCCCccE-----------------EEEcCCCCCHHHHHHHhhccccCCC-cceEEEee
Q psy7792           1 MVATDVASKGLDFEEIKH-----------------VINYDMPDDVENYVHRIGRTGRSGK-TGLATTFI   51 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~-----------------VI~~dlP~~~~~y~qr~GRagR~g~-~g~~i~~~   51 (138)
                      ||||+++++|||+| +.+                 ||+++.|.++++|+||+||+||.|. .+.+++|.
T Consensus       221 LVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          221 VITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             EEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             EEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence            69999999999999 654                 6889999999999999999999985 45555554

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.20  E-value=3.4e-12  Score=104.33  Aligned_cols=52  Identities=23%  Similarity=0.270  Sum_probs=47.7

Q ss_pred             Ceec-ccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeee
Q psy7792           1 MVAT-DVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN   52 (138)
Q Consensus         1 LvaT-~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~   52 (138)
                      |||| +++++|+|+|+|++||++++|+++..|+|++||+||.|+.+..+.+++
T Consensus       401 Lv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          401 IVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             EEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             EEEEcChhhcccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            6899 999999999999999999999999999999999999998775566555

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.18  E-value=1.2e-11  Score=105.27  Aligned_cols=55  Identities=22%  Similarity=0.428  Sum_probs=46.3

Q ss_pred             CeecccccccCCCCCccEEEE----cC-------CCCCHHHHHHHhhccccCC--CcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----YD-------MPDDVENYVHRIGRTGRSG--KTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----~d-------lP~~~~~y~qr~GRagR~g--~~g~~i~~~~~~~   55 (138)
                      ||||+++++|||+|++++||+    ||       .|.+..+|.||+|||||.|  ..|.++.+++..+
T Consensus       342 lvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  409 (715)
T 2va8_A          342 IVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKE  409 (715)
T ss_dssp             EEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEECSCGG
T ss_pred             EEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCCch
Confidence            699999999999999999999    99       8999999999999999988  4799999987753

>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=99.17  E-value=1.8e-11  Score=104.51  Aligned_cols=55  Identities=22%  Similarity=0.351  Sum_probs=50.7

Q ss_pred             CeecccccccCCCCCccEEEE----cC----CCCCHHHHHHHhhccccCC--CcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----YD----MPDDVENYVHRIGRTGRSG--KTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----~d----lP~~~~~y~qr~GRagR~g--~~g~~i~~~~~~~   55 (138)
                      ||||+++++|||+|++++||+    ||    .|.++.+|+||+|||||.|  ..|.++.+++..+
T Consensus       324 lvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  388 (720)
T 2zj8_A          324 VVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDD  388 (720)
T ss_dssp             EEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSC
T ss_pred             EEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCcc
Confidence            699999999999999999999    87    6999999999999999988  5799999998764

>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=99.14  E-value=2.2e-11  Score=103.70  Aligned_cols=54  Identities=28%  Similarity=0.512  Sum_probs=50.2

Q ss_pred             CeecccccccCCCCCccEEEE----cC---CCCCHHHHHHHhhccccCC--CcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----YD---MPDDVENYVHRIGRTGRSG--KTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----~d---lP~~~~~y~qr~GRagR~g--~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|++++||+    ||   .|.++.+|+||+|||||.|  ..|.++.+++..
T Consensus       326 lvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~  388 (702)
T 2p6r_A          326 VVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKR  388 (702)
T ss_dssp             EEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGG
T ss_pred             EEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCc
Confidence            699999999999999999999    77   7999999999999999998  579999998876

>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=99.10  E-value=4.1e-11  Score=97.66  Aligned_cols=54  Identities=17%  Similarity=0.199  Sum_probs=43.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceE--EEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLA--TTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~--i~~~~~~   54 (138)
                      ||+|+++++|+|++.+++||+||+|+++..|.|++||++|.|+...+  +.|+...
T Consensus       398 l~st~~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~  453 (500)
T 1z63_A          398 VLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  453 (500)
T ss_dssp             EEECCCC-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETT
T ss_pred             EEecccccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCC
Confidence            57999999999999999999999999999999999999999976554  3444443

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.08  E-value=5.7e-11  Score=99.04  Aligned_cols=43  Identities=16%  Similarity=0.349  Sum_probs=40.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGK   43 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~   43 (138)
                      ||+|+++++|+|+|+|++||++++|+++..|+||+||+||.+.
T Consensus       503 lvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          503 LTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             EEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             EEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            4788999999999999999999999999999999999999774

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.07  E-value=1.2e-10  Score=103.18  Aligned_cols=51  Identities=25%  Similarity=0.445  Sum_probs=44.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC---------CHHHHHHHhhccccCC--CcceEEEeee
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD---------DVENYVHRIGRTGRSG--KTGLATTFIN   52 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~---------~~~~y~qr~GRagR~g--~~g~~i~~~~   52 (138)
                      ||||+++++|||+|+ ..||++++|+         ++.+|+||+|||||.|  ..|.++.++.
T Consensus       429 LvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~~  490 (997)
T 4a4z_A          429 LFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAY  490 (997)
T ss_dssp             EEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEECC
T ss_pred             EEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEecC
Confidence            699999999999999 6666666766         9999999999999998  5677887773

>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=99.06  E-value=1.1e-10  Score=104.76  Aligned_cols=54  Identities=20%  Similarity=0.260  Sum_probs=50.3

Q ss_pred             CeecccccccCCCCCccEEEEcCC-CCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDM-PDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dl-P~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|++++||+++. +.++..|+||+||+||.|+.|.+++++.+.
T Consensus       868 LVaT~v~e~GiDip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          868 LVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             EEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             EEECCcceeeecccCCcEEEEeCCCCCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            699999999999999999999998 579999999999999999999999998654

>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=99.03  E-value=5.6e-10  Score=94.61  Aligned_cols=54  Identities=15%  Similarity=0.258  Sum_probs=47.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcce--EEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGL--ATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~--~i~~~~~~   54 (138)
                      ||+|.++++|||++.+++||+||+|||+..|.|++||++|.|+...  ++.|++..
T Consensus       473 L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~  528 (644)
T 1z3i_X          473 MLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTG  528 (644)
T ss_dssp             EEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETT
T ss_pred             EEecccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEEECC
Confidence            5899999999999999999999999999999999999999997654  44455543

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.85  E-value=2.4e-09  Score=92.70  Aligned_cols=54  Identities=15%  Similarity=0.307  Sum_probs=46.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceE--EEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLA--TTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~--i~~~~~~   54 (138)
                      |++|.+++.|||++.+++||+||+|+|+..++|++||+.|.|+...+  +-|++..
T Consensus       629 LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~  684 (800)
T 3mwy_W          629 LLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKD  684 (800)
T ss_dssp             EEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETT
T ss_pred             EEecccccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCC
Confidence            68999999999999999999999999999999999999999976444  3345443

>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=98.76  E-value=4.3e-09  Score=97.54  Aligned_cols=54  Identities=15%  Similarity=0.178  Sum_probs=47.8

Q ss_pred             CeecccccccCCCCCccEEEE----------cCCCCCHHHHHHHhhccccCCC--cceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----------YDMPDDVENYVHRIGRTGRSGK--TGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----------~dlP~~~~~y~qr~GRagR~g~--~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|++.+||.          ...|-++.+|.|++|||||.|.  .|.++++..+.
T Consensus      1243 LvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~ 1308 (1724)
T 4f92_B         1243 VVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGS 1308 (1724)
T ss_dssp             EEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGG
T ss_pred             EEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecch
Confidence            699999999999999999993          3357789999999999999996  79999998776

>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=98.58  E-value=2e-08  Score=93.09  Aligned_cols=55  Identities=18%  Similarity=0.332  Sum_probs=47.9

Q ss_pred             CeecccccccCCCCCccEEEE----cCC------CCCHHHHHHHhhccccCC--CcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN----YDM------PDDVENYVHRIGRTGRSG--KTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~----~dl------P~~~~~y~qr~GRagR~g--~~g~~i~~~~~~~   55 (138)
                      ||||+++++|||+|.+++||+    ||.      |-++.+|.|++|||||.|  ..|.++.+.++.+
T Consensus       408 lvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~  474 (1724)
T 4f92_B          408 LVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGE  474 (1724)
T ss_dssp             EEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTT
T ss_pred             EEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchh
Confidence            699999999999999999996    553      568999999999999987  4789999888764

>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=98.45  E-value=1e-07  Score=84.81  Aligned_cols=52  Identities=17%  Similarity=0.229  Sum_probs=46.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCc----ceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKT----GLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~----g~~i~~~~~   53 (138)
                      ||+|+.+.+|+|+|.+ .|+++|.|.+...|+|++||++|.+..    |.++.|+..
T Consensus       653 LIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~~  708 (1038)
T 2w00_A          653 LIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRDL  708 (1038)
T ss_dssp             EEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSCC
T ss_pred             EEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEcccc
Confidence            6999999999999999 789999999999999999999998754    778887753

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=96.53  E-value=0.0017  Score=53.73  Aligned_cols=52  Identities=21%  Similarity=0.290  Sum_probs=26.6

Q ss_pred             eecccccccCCCCC----ccEEEEcCCCCC-H-----------------------------HHHHHHhhccccCCCcceE
Q psy7792           2 VATDVASKGLDFEE----IKHVINYDMPDD-V-----------------------------ENYVHRIGRTGRSGKTGLA   47 (138)
Q Consensus         2 vaT~~~~~GiD~~~----V~~VI~~dlP~~-~-----------------------------~~y~qr~GRagR~g~~g~~   47 (138)
                      |+|..+.+|||+|+    +++||++++|.. +                             ....|.+||+-|....--+
T Consensus       435 V~~~~~~EGiD~~~~~~~~~~Vii~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~  514 (540)
T 2vl7_A          435 VMRAKESEGVEFREKENLFESLVLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVK  514 (540)
T ss_dssp             EC---------------CEEEEEEESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCE
T ss_pred             EecCceecceecCCCcccccEEEEECCCCCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEE
Confidence            48999999999996    899999999932 2                             1235788888886554445


Q ss_pred             EEeeeC
Q psy7792          48 TTFINK   53 (138)
Q Consensus        48 i~~~~~   53 (138)
                      |.++.+
T Consensus       515 v~llD~  520 (540)
T 2vl7_A          515 IYLCDS  520 (540)
T ss_dssp             EEEESG
T ss_pred             EEEEcc
Confidence            555544

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=95.25  E-value=0.029  Score=49.69  Aligned_cols=38  Identities=18%  Similarity=0.315  Sum_probs=34.4

Q ss_pred             EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792          18 HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus        18 ~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      +||--..+.|..-=-|=.||+||-|.+|.+..|++-.+
T Consensus       662 hVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeD  699 (997)
T 2ipc_A          662 FIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDD  699 (997)
T ss_dssp             CEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSS
T ss_pred             EEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECCh
Confidence            78998899998888899999999999999999998763

---

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	138
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	8e-18
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	4e-15
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	8e-15
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	6e-14
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	1e-13
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	5e-11
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	2e-10
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	3e-10
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	5e-10
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	8e-09
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	2e-08
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	6e-08
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-07
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	5e-06
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	3e-05
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	4e-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 = 75.3 bits (185), Expect = 8e-18
 Identities = 11/63 (17%), Positives = 20/63 (31%), Gaps = 4/63 (6%)

Query: 1   MVATDVASKG---LDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDE 57
           ++  +           +    +    +P D  +   R GRTGR GK G+           
Sbjct: 100 VIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPGERPS 158

Query: 58  SVL 60
            + 
Sbjct: 159 GMF 161

>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 = 65.7 bits (159), Expect = 4e-15
 Identities = 30/75 (40%), Positives = 49/75 (65%), Gaps = 4/75 (5%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           ++ATDV S+G+D  ++  VINY +P + E+Y+HRIGRTGR+GK G A + IN+  +   L
Sbjct: 82  LIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINR-REYKKL 140

Query: 61  LDLKHLLLEARQRIP 75
             ++  +   + +I 
Sbjct: 141 RYIERAM---KLKIK 152

>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 = 66.8 bits (162), Expect = 8e-15
 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDE 57
           +VAT V  +GLD  E+  V+ Y+        + R GRTGR    G     + K   +
Sbjct: 223 LVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRD 278

>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 = 62.6 bits (151), Expect = 6e-14
 Identities = 29/81 (35%), Positives = 51/81 (62%), Gaps = 1/81 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TD+ ++G+D +++  VINYD+P + ENY+HRIGR GR G+ G+A  F+    D   +
Sbjct: 81  LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE-DVGAM 139

Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            +L+       + +P  +A L
Sbjct: 140 RELEKFYSTQIEELPSDIATL 160

>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 = 62.3 bits (150), Expect = 1e-13
 Identities = 30/81 (37%), Positives = 53/81 (65%), Gaps = 1/81 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +++TDV ++GLD  ++  +INYD+P++ E Y+HRIGR+GR G+ G+A  F+   +D  +L
Sbjct: 88  LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN-DDIRIL 146

Query: 61  LDLKHLLLEARQRIPPFLAEL 81
            D++         +P  +A+L
Sbjct: 147 RDIEQYYSTQIDEMPMNVADL 167

>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 = 55.9 bits (134), Expect = 5e-11
 Identities = 18/137 (13%), Positives = 41/137 (29%), Gaps = 13/137 (9%)

Query: 1   MVAT----DVASKGLDF-EEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN 55
           ++ T        +GLD  E I+  +    P    ++   I          +        N
Sbjct: 73  LIGTAHYYGTLVRGLDLPERIRFAVFVGCP----SFRVTIEDIDSLSPQMVKLLAYLYRN 128

Query: 56  ---DESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITACP 112
               E +L  ++  + E R+ +   + +   + +  +   G+         +        
Sbjct: 129 VDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLRTYI-QGSGRTS 187

Query: 113 KLEAVQTKAASSIGRRD 129
           +L A      +S    D
Sbjct: 188 RLFAGGLTKGASFLLED 204

>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 = 53.5 bits (127), Expect = 2e-10
 Identities = 31/86 (36%), Positives = 46/86 (53%), Gaps = 1/86 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +V +D+ ++G+D + +  VIN+D P   E Y+HRIGR+GR G  GLA   IN  ND   L
Sbjct: 86  LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINW-NDRFNL 144

Query: 61  LDLKHLLLEARQRIPPFLAELESETE 86
             ++  L      IP  + +     E
Sbjct: 145 YKIEQELGTEIAAIPATIDKSLYVAE 170

>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 = 52.4 bits (125), Expect = 3e-10
 Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 1   MVATDVASKGLDFEE---IKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF 50
           +VATD    G   +    I    +   P D  +   R GRTGR GK G+    
Sbjct: 82  VVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR-GKPGIYRFV 133

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 53.0 bits (126), Expect = 5e-10
 Identities = 7/41 (17%), Positives = 11/41 (26%)

Query: 12  DFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
           D  +    +          Y+ R+GR  R  K         
Sbjct: 153 DVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYE 193

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (116), Expect = 8e-09
 Identities = 31/87 (35%), Positives = 51/87 (58%), Gaps = 1/87 (1%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
           +VAT++  +G+D E +    NYDMP+D + Y+HR+ R GR G  GLA TF++  ND  +L
Sbjct: 81  LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 140

Query: 61  LDLKHLLLEARQRIPPFLAELESETEK 87
            D++         +P  + ++ S  E+
Sbjct: 141 NDVQDRFEVNISELPDEI-DISSYIEQ 166

>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 = 47.1 bits (111), Expect = 6e-08
 Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 2/58 (3%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHR--IGRTGRSGKTGLATTFINKSND 56
           +V  ++  +GLD  E+  V   D   +      R  I   GR+ +       +     
Sbjct: 85  LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTI 142

>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 = 45.7 bits (107), Expect = 3e-07
 Identities = 18/76 (23%), Positives = 26/76 (34%), Gaps = 19/76 (25%)

Query: 1   MVATDVASKGLDFE---------EIKHVINYD----------MPDDVENYVHRIGRTGRS 41
           +V TD++  G +F+          +K VI  D          MP    +   R GR GR+
Sbjct: 228 VVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRN 287

Query: 42  GKTGLATTFINKSNDE 57
            K             E
Sbjct: 288 PKNENDQYIYMGEPLE 303

>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 = 41.8 bits (97), Expect = 5e-06
 Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 9/69 (13%)

Query: 1   MVATDVASKGLDFEEIKHVI-------NYDMPDDVENYVHRIGRTGRSGK--TGLATTFI 51
           +VAT   + G++    + ++        Y     V  Y    GR GR G    G A   +
Sbjct: 124 VVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIV 183

Query: 52  NKSNDESVL 60
            K + E  +
Sbjct: 184 GKRDREIAV 192

>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 = 39.6 bits (91), Expect = 3e-05
 Identities = 16/52 (30%), Positives = 29/52 (55%)

Query: 1   MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
           +VAT     G++   ++ V+++D+P ++E+Y    GR GR G    A  F +
Sbjct: 84  VVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYD 135

>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 = 36.2 bits (83), Expect = 4e-04
 Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 11/78 (14%)

Query: 1   MVATDVASKGLDFEEIKHVINYDM-----PDDVENYVHRIGRTGRSGKTGLATTFINKSN 55
           +V  ++  +GLD  E+  V   D           + +  IGR  R+ +  +       S 
Sbjct: 85  LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSE 144

Query: 56  DESVLLDLKHLLLEARQR 73
                  ++  + E  +R
Sbjct: 145 ------AMQRAIEETNRR 156

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	138
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.9
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.88
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.88
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.85
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.84
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.83
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.81
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.7
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.69
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.65
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.63
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.5
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.4
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.32
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.32
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.26
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	98.91
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	98.77
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.61
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	98.43
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.41
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	98.27
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	96.14
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	90.66

>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=99.90  E-value=1.3e-24  Score=159.51  Aligned_cols=54  Identities=30%  Similarity=0.608  Sum_probs=52.8

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||++++||||+|+|++|||||+|+++++|+||+||+||+|++|.+++|+++.
T Consensus        84 lvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~  137 (200)
T d1oywa3          84 VVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPA  137 (200)
T ss_dssp             EEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHH
T ss_pred             EEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHH
Confidence            699999999999999999999999999999999999999999999999999886

>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=99.88  E-value=1.6e-24  Score=154.09  Aligned_cols=79  Identities=35%  Similarity=0.752  Sum_probs=67.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAE   80 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~   80 (138)
                      |||||+++||||+|+|++|||||+|++++.|+||+||+||.|+.|.+++++++. +...+..+++.++...+++|..+.+
T Consensus        81 Lv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~-d~~~~~~i~~~~~~~~~~ip~~~~~  159 (162)
T d1fuka_          81 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE-DVGAMRELEKFYSTQIEELPSDIAT  159 (162)
T ss_dssp             EEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETT-THHHHHHHHHHSSCCCEECCSCCTT
T ss_pred             eeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHH-HHHHHHHHHHHHcCcCCCCChHHHH
Confidence            699999999999999999999999999999999999999999999999999987 7888888888888888888875543

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=4.4e-24  Score=152.66  Aligned_cols=76  Identities=37%  Similarity=0.747  Sum_probs=68.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPF   77 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~   77 (138)
                      |||||+++||||+|+|++|||||+|++++.|+||+||+||.|+.|.+++|+++. +...++.+++.++...+++|..
T Consensus        88 Lv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~-d~~~~~~i~~~~~~~i~e~p~~  163 (168)
T d2j0sa2          88 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND-DIRILRDIEQYYSTQIDEMPMN  163 (168)
T ss_dssp             EEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGG-GHHHHHHHHHHTTCCCEECCSC
T ss_pred             EeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHH-HHHHHHHHHHHHcCcCCCCCcC
Confidence            699999999999999999999999999999999999999999999999999987 7777777777776666666654

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=1e-22  Score=145.48  Aligned_cols=77  Identities=38%  Similarity=0.687  Sum_probs=69.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFL   78 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l   78 (138)
                      ||||++++||||+|+|++|||||+|+++++|+||+||+||.|+.|.+++|+++. +...+..+++.+.....++|..+
T Consensus        86 lv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~-e~~~~~~i~~~l~~~~~~~p~~~  162 (171)
T d1s2ma2          86 LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWN-DRFNLYKIEQELGTEIAAIPATI  162 (171)
T ss_dssp             EEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGG-GHHHHHHHHHHHTCCCEECCSSC
T ss_pred             ccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHH-HHHHHHHHHHHHCCCCCCCCccc
Confidence            689999999999999999999999999999999999999999999999999987 77788888877776666677643

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.84  E-value=6.4e-22  Score=139.13  Aligned_cols=68  Identities=43%  Similarity=0.769  Sum_probs=61.3

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLE   69 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~   69 (138)
                      ||||+++++|||+|+|++|||||+|+++.+|+||+||+||.|+.|.+++++++. +...+..+++.++.
T Consensus        82 lv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-d~~~~~~i~~~~~~  149 (155)
T d1hv8a2          82 LIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRR-EYKKLRYIERAMKL  149 (155)
T ss_dssp             EEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTT-SHHHHHHHHHHHTC
T ss_pred             eeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchH-HHHHHHHHHHHHCC
Confidence            699999999999999999999999999999999999999999999999999887 66666766655543

>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=99.81  E-value=4.3e-21  Score=136.77  Aligned_cols=78  Identities=37%  Similarity=0.724  Sum_probs=68.6

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcHHHHHHHHHHHHHhcccCcHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFL   78 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l   78 (138)
                      ||||+++++|+|+|.+++|||||+|++++.|+||+||+||.|+.|.+|+|+++.++..++..+++.++....++|..+
T Consensus        81 Lv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~~~i~~~~~~~~~elp~~~  158 (168)
T d1t5ia_          81 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  158 (168)
T ss_dssp             EEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             eeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchHHHHHHHHHHHHHcCCcccCCchh
Confidence            699999999999999999999999999999999999999999999999999887667777878877777777777654

>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=99.70  E-value=3.8e-18  Score=118.13  Aligned_cols=51  Identities=37%  Similarity=0.653  Sum_probs=46.5

Q ss_pred             CeecccccccCCCCCccEEEEcC----CCCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYD----MPDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~d----lP~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      |||||+++|||| ++|++|||||    +|.++++|+||+||+|| |++|. ++|+++.
T Consensus        82 lvaTd~~~~GiD-~~v~~Vi~~~~~~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~  136 (138)
T d1jr6a_          82 VVATDALMTGFT-GDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPG  136 (138)
T ss_dssp             EEESSSSCSSSC-CCBSEEEECSEETTEECCHHHHHHHHTTBCS-SSCEE-EEECCSS
T ss_pred             eehhHHHHhccc-cccceEEEEEecCCCCCCHHHHHhHhccccC-CCCcE-EEEEcCC
Confidence            699999999999 9999999965    69999999999999999 99995 7788776

>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=99.69  E-value=1.4e-17  Score=120.00  Aligned_cols=46  Identities=24%  Similarity=0.442  Sum_probs=42.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC-----CHHHHHHHhhccccCCCcce
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD-----DVENYVHRIGRTGRSGKTGL   46 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~-----~~~~y~qr~GRagR~g~~g~   46 (138)
                      ||||++++||||+|+|++|||||+|.     +...|+||+||+||.|....
T Consensus        85 LVaTdv~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~  135 (181)
T d1t5la2          85 LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHV  135 (181)
T ss_dssp             EEESCCCSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEE
T ss_pred             EEehhHHHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccCcee
Confidence            79999999999999999999999996     68999999999999987433

>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=99.65  E-value=4.5e-17  Score=123.44  Aligned_cols=54  Identities=33%  Similarity=0.508  Sum_probs=50.1

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      ||||+++++|||+|+|++||+||+|+++..|+||+||+||.+ +|.++.|+++..
T Consensus       223 Lv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~  276 (286)
T d1wp9a2         223 LVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGT  276 (286)
T ss_dssp             EEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTS
T ss_pred             EEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCC
Confidence            699999999999999999999999999999999999999965 688888888764

>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=99.63  E-value=2.4e-16  Score=112.79  Aligned_cols=53  Identities=23%  Similarity=0.446  Sum_probs=46.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC-----CHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD-----DVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~-----~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||++++||||+|+|++|||||+|.     +.++|+||+||+||.|+ |.++++....
T Consensus        85 LVaT~v~~~GiDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~  142 (174)
T d1c4oa2          85 LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRV  142 (174)
T ss_dssp             EEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSC
T ss_pred             EEeeeeeeeeccCCCCcEEEEeccccccccchhHHHHHHhhhhhhcCC-CeeEEeecCC
Confidence            69999999999999999999999776     55889999999999876 6777766554

>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=99.50  E-value=1.3e-14  Score=106.17  Aligned_cols=54  Identities=19%  Similarity=0.310  Sum_probs=50.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC-CHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD-DVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~-~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|++++||+++.|. ..+.|+|..||+||.|.+|.|++++++.
T Consensus        94 LVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~  148 (206)
T d1gm5a4          94 LVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDV  148 (206)
T ss_dssp             CCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSC
T ss_pred             EEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccc
Confidence            79999999999999999999999997 6888888899999999999999999775

>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=99.40  E-value=8.5e-16  Score=114.51  Aligned_cols=51  Identities=18%  Similarity=0.227  Sum_probs=43.3

Q ss_pred             Ceec----ccccccCCCCC-ccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVAT----DVASKGLDFEE-IKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT----~~~~~GiD~~~-V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      ||||    ++++||||+|+ |++|||||+|+    |+||+||+||+|+.|.+++++...+
T Consensus        73 LVaT~a~~~v~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~  128 (248)
T d1gkub2          73 LIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRN  128 (248)
T ss_dssp             EEEECC------CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSC
T ss_pred             EEEeccccchhhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhh
Confidence            6899    78899999996 99999999995    9999999999999999999888763

>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=99.32  E-value=2.6e-13  Score=98.44  Aligned_cols=54  Identities=28%  Similarity=0.487  Sum_probs=49.1

Q ss_pred             CeecccccccCCCCCccEEEE-------cCCCCCHHHHHHHhhccccCCC--cceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHVIN-------YDMPDDVENYVHRIGRTGRSGK--TGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~-------~dlP~~~~~y~qr~GRagR~g~--~g~~i~~~~~~   54 (138)
                      ||||+++++|||+|.++.||+       ++.|.++..|+|++|||||.|.  .|.+++++.+.
T Consensus       124 lvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~  186 (201)
T d2p6ra4         124 VVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKR  186 (201)
T ss_dssp             EEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGG
T ss_pred             EEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCC
Confidence            699999999999999999997       7889999999999999999984  78888887665

>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=99.32  E-value=6.5e-13  Score=95.49  Aligned_cols=53  Identities=21%  Similarity=0.417  Sum_probs=46.2

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCc---ceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKT---GLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~---g~~i~~~~~   53 (138)
                      ||+|+++++|||+|.+++||++|+|+++..|+||+||++|.|+.   ...+.|++.
T Consensus       142 Lv~~~~~~~Gidl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k~~~~i~~~v~~  197 (200)
T d2fwra1         142 IVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISR  197 (200)
T ss_dssp             CBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEEC
T ss_pred             eeecchhhcccCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCCcEEEEEEEecC
Confidence            78999999999999999999999999999999999999999863   344445543

>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=99.26  E-value=3.5e-13  Score=102.92  Aligned_cols=56  Identities=20%  Similarity=0.366  Sum_probs=47.8

Q ss_pred             Ceecccccc---cCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCCcH
Q psy7792           1 MVATDVASK---GLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDE   57 (138)
Q Consensus         1 LvaT~~~~~---GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~~~   57 (138)
                      ||+|+++.+   |+|++.|.+|||||+|.++++|+||+||+|| |++|....++....+.
T Consensus       100 VVaT~~~a~g~~giDid~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~t~p~  158 (299)
T d1a1va2         100 VIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPGERPS  158 (299)
T ss_dssp             EEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSCCBCS
T ss_pred             EEEEeehhccCCCCCCCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecCCCHH
Confidence            589999888   6777888899999999999999999999999 9999887766544433

>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=98.91  E-value=5.2e-10  Score=83.34  Aligned_cols=53  Identities=28%  Similarity=0.368  Sum_probs=42.6

Q ss_pred             CeecccccccCCCCCccEE----------EEcCC----------CCCHHHHHHHhhccccCCCcceEEEeeeCC
Q psy7792           1 MVATDVASKGLDFEEIKHV----------INYDM----------PDDVENYVHRIGRTGRSGKTGLATTFINKS   54 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~V----------I~~dl----------P~~~~~y~qr~GRagR~g~~g~~i~~~~~~   54 (138)
                      ||||+++++|+|++ ++.|          ++||.          |-++++|+||+||+||.|+.+..+.++...
T Consensus       228 lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~  300 (305)
T d2bmfa2         228 VVTTDISEMGANFK-AERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGE  300 (305)
T ss_dssp             EEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECSC
T ss_pred             hhhhHHHHhcCCCC-ccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECCC
Confidence            58999999999994 4444          34554          568999999999999999998888877654

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=98.77  E-value=3.5e-09  Score=77.02  Aligned_cols=53  Identities=21%  Similarity=0.295  Sum_probs=49.7

Q ss_pred             CeecccccccCCCCCccEEEEcCCCC-CHHHHHHHhhccccCCCcceEEEeeeC
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPD-DVENYVHRIGRTGRSGKTGLATTFINK   53 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~-~~~~y~qr~GRagR~g~~g~~i~~~~~   53 (138)
                      ||||.+.+.|||+|+++++|..+.+. .++.+.|-.||+||.+..|.|++++.+
T Consensus        87 Lv~TtvIEvGiDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~  140 (211)
T d2eyqa5          87 LVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPH  140 (211)
T ss_dssp             EEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECC
T ss_pred             EEEehhhhhccCCCCCcEEEEecchhccccccccccceeeecCccceEEEEecC
Confidence            79999999999999999999999885 899999999999999999999999864

>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=98.61  E-value=3.5e-08  Score=76.33  Aligned_cols=65  Identities=17%  Similarity=0.287  Sum_probs=50.4

Q ss_pred             CeecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcceEE--EeeeCC-CcHHHHHHHHH
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLAT--TFINKS-NDESVLLDLKH   65 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i--~~~~~~-~~~~~~~~l~~   65 (138)
                      |++|.+++.|||++.+++||+||+|||+..+.|++||+-|.|+...+.  -|+... -++.++..+..
T Consensus       175 Lls~~agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~TiEe~i~~~~~~  242 (346)
T d1z3ix1         175 MLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQRQAH  242 (346)
T ss_dssp             EEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHHHHHHHHH
T ss_pred             eecchhhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCCCHHHHHHHHHHH
Confidence            578999999999999999999999999999999999999999864433  333433 24444443333

>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=98.43  E-value=9.5e-08  Score=72.62  Aligned_cols=51  Identities=22%  Similarity=0.384  Sum_probs=41.0

Q ss_pred             CeecccccccCCCCCccEEEEcCCC-------------------CCHHHHHHHhhccccCCCcceEEEeee
Q psy7792           1 MVATDVASKGLDFEEIKHVINYDMP-------------------DDVENYVHRIGRTGRSGKTGLATTFIN   52 (138)
Q Consensus         1 LvaT~~~~~GiD~~~V~~VI~~dlP-------------------~~~~~y~qr~GRagR~g~~g~~i~~~~   52 (138)
                      ||||+++++|||+ +|.+||...++                   -+.++-.||.||+||.+....++.++.
T Consensus        86 ~~~t~~~~~~~~~-~~~~vid~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2          86 ILATDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEESSSTTCCTTC-CCSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             EEEechhhhceec-CceEEEecCceeceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence            6999999999999 69999976653                   356777999999999876655655554

>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=98.41  E-value=9.2e-08  Score=69.90  Aligned_cols=66  Identities=17%  Similarity=0.165  Sum_probs=37.8

Q ss_pred             eecccccccCCCCCccEEEEcCCCCCHHHHHHHhhccccCCCcc--eEEEeeeCC-CcHHHHHHHHHHH
Q psy7792           2 VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTG--LATTFINKS-NDESVLLDLKHLL   67 (138)
Q Consensus         2 vaT~~~~~GiD~~~V~~VI~~dlP~~~~~y~qr~GRagR~g~~g--~~i~~~~~~-~~~~~~~~l~~~~   67 (138)
                      ++|.+.+.|+|++.+++||+||+|||+..+.|++||+-|.|+..  .++.|+... -|+.+...+....
T Consensus       143 ~~~~~~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~Tiee~i~~~~~~K~  211 (244)
T d1z5za1         143 LSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKR  211 (244)
T ss_dssp             EECCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSHHHHHHHHHHHCH
T ss_pred             ccccccccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCCCHHHHHHHHHHHHH
Confidence            56789999999999999999999999999999999999999643  333344443 3455555444433

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=98.27  E-value=1.9e-06  Score=60.57  Aligned_cols=55  Identities=24%  Similarity=0.474  Sum_probs=49.5

Q ss_pred             CeecccccccCCCC---Ccc-----EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792           1 MVATDVASKGLDFE---EIK-----HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus         1 LvaT~~~~~GiD~~---~V~-----~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      .|||+.++||.|+.   .|.     +||.-..|.+..-..|-.||+||-|.+|.+..|++-.+
T Consensus        86 tIATNmAGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          86 TIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             EEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             eehhhHHHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            38999999999985   343     79999999999999999999999999999999998764

>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=96.14  E-value=0.0089  Score=42.50  Aligned_cols=38  Identities=18%  Similarity=0.318  Sum_probs=30.7

Q ss_pred             EEEEcCCCCCHHHHHHHhhccccCCCcceEEEeeeCCC
Q psy7792          18 HVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus        18 ~VI~~dlP~~~~~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      +||--.--.|..-=-|=.||+||-|.+|.+..|++-.+
T Consensus       155 ~VIGTErHeSrRIDnQLRGRsGRQGDPGsSrFflSLeD  192 (219)
T d1nkta4         155 YVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGD  192 (219)
T ss_dssp             EEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTS
T ss_pred             EEEeccccccccccccccccccccCCCccceeEEeccH
Confidence            57766666666555677899999999999999998874

>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=90.66  E-value=0.11  Score=35.41  Aligned_cols=26  Identities=12%  Similarity=0.162  Sum_probs=22.9

Q ss_pred             HHHHHhhccccCCCcceEEEeeeCCC
Q psy7792          30 NYVHRIGRTGRSGKTGLATTFINKSN   55 (138)
Q Consensus        30 ~y~qr~GRagR~g~~g~~i~~~~~~~   55 (138)
                      ++.|.+||+||+|+.|.+..++....
T Consensus       116 s~~~yi~R~GRagR~g~~~~~~~~~~  141 (181)
T d1t5la2         116 SERSLIQTIGRAARNANGHVIMYADT  141 (181)
T ss_dssp             SHHHHHHHHGGGTTSTTCEEEEECSS
T ss_pred             cHHHHHHHHHhhccccCceeEeecch
Confidence            57889999999999999999987654