Psyllid ID: psy6093

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350

MAIFFQIWFLQCPSSGLKHLQNKSVFELGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYAHDYCRENFLTNNTLLLLRDMKDQFSRTMHEMNFISSRTWS

cccccEEEEEEcccccccHHHHHHcccccccEEEEEEcccccccccccEEEEEcccccccccccccccccccccccccHHHHHHHcccccccccccEEEcccHHHHHccccccccccccccHHHHHHHHHHcccccHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHHccccccHHHHHHHHHHHccccHHHHHHHHHHccccccccccHHHHHHHHHHccccccccHHHHcccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcccccccccc

ccccHcEEEEEEEHccccHHHHHHHccccccEEEEEEEEEEEEEEEccEEEEEcccccEEccccccccccEEEEccccHHHHHHHcccccccccccEEEEEcHHHHHHHcccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHEEEEEccccccccHHHHHHHHHHHHHHHcccccccccHHHHHHccccccHHHHHHHHHHHcccccHHHHHHHHHHcccccEEccHHHHHHHHHccccccccEEEEEEEcccccEEEccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcEEEEEcccc

MAIFFQIWFlqcpssglkhlqnksvfELGVRKIVLATniaetsitidDIVYVVdcgktkmsnfdvkdniatlkpEWISLANAKqrrgragrvqeGVCYHLYSRareqtfqdyplpeiqrtRLDEVVRTLESKKFKMVSRRFKVMLNTaftpyvwvpkqvldppdpasVQLSLKLLRLIDaldddehltplgyhlaklpldpqigKMLLMASIFSCVDPVFTVAAslgfkdafycpmiGKMLLMASIFSCVDPVFTVAAslgfkdafycpmnmekdvDKQKNILAQGAKSDYVVLINAMQGWEQALEHNyahdycrenfltnNTLLLLRDMKDQFSRTMHEMNfissrtws

MAIFFQIWFLQCPSSGLKHLQNKSVFELGVRKIVLatniaetsitiddiVYVVDCGKTKMSNFDVKDNIATLKPEWISLAnakqrrgragrvQEGVCYHLYSRareqtfqdyplpeiqrtrlDEVVRTleskkfkmvsrrFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYAHDYCRENFLTNNTLLLLRDMKDQFSRTMHEmnfissrtws

**IFFQIWFLQCPSSGLKHLQNKSVFELGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYAHDYCRENFLTNNTLLLLRDMKDQ*****************

***FFQIWFLQCPSSGLKHL*NKSVFELGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVDPVFTVAASLGFKDA****************ILAQGAKSDYVVLINAMQGWEQALEHNYAHDYCRENFLTNNTLLLLRDMKDQFSRTMHEMN*IS*****

MAIFFQIWFLQCPSSGLKHLQNKSVFELGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLAN**********VQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYAHDYCRENFLTNNTLLLLRDMKDQFSRTMHEMNFISSRTWS

*AIFFQIWFLQCPSSGLKHLQNKSVFELGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLAN***********QEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYAHDYCRENFLTNNTLLLLRDMKDQFSRTMHEMNFISSR***

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		350
307204348		976	Probable ATP-dependent RNA helicase DHX3	0.768	0.275	0.481	6e-82
307169079		962	Probable ATP-dependent RNA helicase DHX3	0.765	0.278	0.498	3e-81
380029828		863	PREDICTED: probable ATP-dependent RNA he	0.78	0.316	0.484	2e-80
322798986		933	hypothetical protein SINV_02899 [Solenop	0.768	0.288	0.481	2e-80
110755029		964	PREDICTED: probable ATP-dependent RNA he	0.774	0.281	0.484	5e-80
332028283		958	Putative ATP-dependent RNA helicase DHX3	0.78	0.284	0.490	1e-79
350402556		977	PREDICTED: probable ATP-dependent RNA he	0.768	0.275	0.493	1e-78
340711835		977	PREDICTED: probable ATP-dependent RNA he	0.768	0.275	0.493	1e-78
345483837		985	PREDICTED: probable ATP-dependent RNA he	0.802	0.285	0.447	4e-76
383865235		976	PREDICTED: probable ATP-dependent RNA he	0.768	0.275	0.462	1e-75

>gi\|307204348\|gb\|EFN83103.1\| Probable ATP-dependent RNA helicase DHX36 [Harpegnathos saltator]	Back alignment and taxonomy information

 Score =  310 bits (795), Expect = 6e-82,   Method: Compositional matrix adjust.
 Identities = 153/318 (48%), Positives = 212/318 (66%), Gaps = 49/318 (15%)

Query: 29  GVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGR 88
           G+RKI++AT+IAETSITI+D++YV++CGKTK+  FD+ +NI TL+ EW+SLA+AKQRRGR
Sbjct: 513 GIRKIIIATSIAETSITIEDVIYVINCGKTKLGRFDIHNNIQTLESEWVSLASAKQRRGR 572

Query: 89  AGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTA 148
           AGRVQ G CYHLYS+ARE+TF  YPLPE+ RTRL+EV+  +   K   + +  + + N  
Sbjct: 573 AGRVQSGECYHLYSKAREKTFDQYPLPEMLRTRLEEVILQI---KILQLGKAKEFLAN-- 627

Query: 149 FTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLL 208
                     V+DPPD  ++ LSL LLR ++ALD+DEHLTPLGYHLA LPLDP+ GKM+L
Sbjct: 628 ----------VMDPPDLKAIDLSLDLLRTLNALDNDEHLTPLGYHLAHLPLDPRTGKMIL 677

Query: 209 MASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVDPVFTVAASLGFKDAFYC 268
            A++FSC +P+F +AASL FKDAFY                                  C
Sbjct: 678 WAALFSCAEPIFAIAASLTFKDAFY----------------------------------C 703

Query: 269 PMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYAHDYCRENFLTNNTLLLLR 328
           P++ E++ +++K  L+ G  SD++ L  A+Q +E A +H  A  +CRE FL+ NTL LL 
Sbjct: 704 PLDREEEANEKKLELSLGQYSDHMALAEALQRFEMAYQHGVAGRFCREYFLSYNTLKLLS 763

Query: 329 DMKDQFSRTMHEMNFISS 346
           +MK  F++ ++EM F+ S
Sbjct: 764 EMKTDFAKYLYEMKFLDS 781

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|307169079\|gb\|EFN61923.1\| Probable ATP-dependent RNA helicase DHX36 [Camponotus floridanus]	Back alignment and taxonomy information

>gi\|380029828\|ref\|XP_003698567.1\| PREDICTED: probable ATP-dependent RNA helicase DHX36-like, partial [Apis florea]	Back alignment and taxonomy information

>gi\|322798986\|gb\|EFZ20446.1\| hypothetical protein SINV_02899 [Solenopsis invicta]	Back alignment and taxonomy information

>gi\|110755029\|ref\|XP_394965.3\| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Apis mellifera]	Back alignment and taxonomy information

>gi\|332028283\|gb\|EGI68330.1\| Putative ATP-dependent RNA helicase DHX36 [Acromyrmex echinatior]	Back alignment and taxonomy information

>gi\|350402556\|ref\|XP_003486528.1\| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Bombus impatiens]	Back alignment and taxonomy information

>gi\|340711835\|ref\|XP_003394474.1\| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Bombus terrestris]	Back alignment and taxonomy information

>gi\|345483837\|ref\|XP_001604337.2\| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Nasonia vitripennis]	Back alignment and taxonomy information

>gi\|383865235\|ref\|XP_003708080.1\| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Megachile rotundata]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		350
ZFIN\|ZDB-GENE-050419-20		1037	si:dkey-119o24.1 "si:dkey-119o	0.631	0.213	0.485	5.4e-53
UNIPROTKB\|E7EWK3		797	DHX36 "Probable ATP-dependent	0.614	0.269	0.506	4.2e-51
UNIPROTKB\|F6V8H1		1122	DHX36 "Uncharacterized protein	0.614	0.191	0.510	5.2e-51
UNIPROTKB\|I3LCY3		987	DHX36 "Uncharacterized protein	0.597	0.211	0.517	5.5e-51
UNIPROTKB\|E2QTL7		988	DHX36 "Uncharacterized protein	0.557	0.197	0.535	7.2e-51
RGD\|1308767		1000	Dhx36 "DEAH (Asp-Glu-Ala-His)	0.614	0.215	0.510	7.5e-51
MGI\|MGI:1919412		1001	Dhx36 "DEAH (Asp-Glu-Ala-His)	0.614	0.214	0.510	9.6e-51
UNIPROTKB\|Q05B79		1010	DHX36 "Uncharacterized protein	0.614	0.212	0.493	1.3e-50
UNIPROTKB\|Q9H2U1		1008	DHX36 "Probable ATP-dependent	0.614	0.213	0.506	1.6e-50
UNIPROTKB\|H7C5F5		188	DHX36 "Probable ATP-dependent	0.277	0.515	0.659	2.3e-50

ZFIN\|ZDB-GENE-050419-20 si:dkey-119o24.1 "si:dkey-119o24.1" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

 Score = 544 (196.6 bits), Expect = 5.4e-53, Sum P(2) = 5.4e-53
 Identities = 118/243 (48%), Positives = 161/243 (66%)

Query:    29 GVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGR 88
             GVRKIV+ATNIAETSITIDD+VYV+D GK K ++FD ++NI T+  EW+S+ANAKQR+GR
Sbjct:   566 GVRKIVIATNIAETSITIDDVVYVIDGGKIKETHFDTQNNIRTMTAEWVSIANAKQRKGR 625

Query:    89 AGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTA 148
             AGRV  G CYHLY+  R     +Y LPEIQRT L+E+   L+ K  K+            
Sbjct:   626 AGRVSPGKCYHLYNGLRASLLDNYQLPEIQRTPLEELC--LQIKVLKL------------ 671

Query:   149 FTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLL 208
               P     ++ +DPP   +++L++  L  ++ALD DE LTPLG+HLA++P++P IGKM+L
Sbjct:   672 -GPIATFLQKTMDPPSDRAIELAITHLVDLNALDRDEKLTPLGFHLARMPVEPHIGKMIL 730

Query:   209 MASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLL------MASIFSCVDPVFTVAASLGF 262
               ++  C+DPV T+AASL FKD F+ P+ GK  +      M S  S  D +  V A LG+
Sbjct:   731 FGALLGCLDPVLTIAASLSFKDPFFIPL-GKEKIADQRRKMFSQNSRSDHLSIVNAFLGW 789

Query:   263 KDA 265
             +DA
Sbjct:   790 EDA 792

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB\|E7EWK3 DHX36 "Probable ATP-dependent RNA helicase DHX36" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F6V8H1 DHX36 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LCY3 DHX36 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QTL7 DHX36 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

RGD\|1308767 Dhx36 "DEAH (Asp-Glu-Ala-His) box polypeptide 36" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

MGI\|MGI:1919412 Dhx36 "DEAH (Asp-Glu-Ala-His) box polypeptide 36" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|Q05B79 DHX36 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9H2U1 DHX36 "Probable ATP-dependent RNA helicase DHX36" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|H7C5F5 DHX36 "Probable ATP-dependent RNA helicase DHX36" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		350
COG1643		845	COG1643, HrpA, HrpA-like helicases [DNA replicatio	9e-64
TIGR01967		1283	TIGR01967, DEAH_box_HrpA, ATP-dependent helicase H	5e-42
PRK11131		1294	PRK11131, PRK11131, ATP-dependent RNA helicase Hrp	1e-36
PRK11664		812	PRK11664, PRK11664, ATP-dependent RNA helicase Hrp	2e-33
TIGR01970		819	TIGR01970, DEAH_box_HrpB, ATP-dependent helicase H	2e-30
pfam04408		91	pfam04408, HA2, Helicase associated domain (HA2)	2e-22
smart00847		82	smart00847, HA2, Helicase associated domain (HA2)	3e-17
smart00490		82	smart00490, HELICc, helicase superfamily c-termina	1e-08
pfam00271		78	pfam00271, Helicase_C, Helicase conserved C-termin	3e-08
cd00079		131	cd00079, HELICc, Helicase superfamily c-terminal d	2e-04
PHA02653		675	PHA02653, PHA02653, RNA helicase NPH-II; Provision	4e-04

>gnl\|CDD\|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

 Score =  216 bits (553), Expect = 9e-64
 Identities = 90/213 (42%), Positives = 121/213 (56%), Gaps = 20/213 (9%)

Query: 21  QNKSVFE---LGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWI 77
           Q + VFE    G RK+VLATNIAETS+TI  I YV+D G  K   +D +  +  L+ E I
Sbjct: 302 QVR-VFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPI 360

Query: 78  SLANAKQRRGRAGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMV 137
           S A+A QR GRAGR   G+CY LYS      F ++ LPEI RT L  +V  L+S      
Sbjct: 361 SKASADQRAGRAGRTGPGICYRLYSEEDFLAFPEFTLPEILRTDLSGLVLQLKS------ 414

Query: 138 SRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKL 197
                +  + A  P+       LDPP  A++Q +L LL+ + ALDD   LTPLG  ++ L
Sbjct: 415 ---LGIGQDIAPFPF-------LDPPPEAAIQAALTLLQELGALDDSGKLTPLGKQMSLL 464

Query: 198 PLDPQIGKMLLMASIFSCVDPVFTVAASLGFKD 230
           PLDP++ +MLL A    C+    T+A+ L  +D
Sbjct: 465 PLDPRLARMLLTAPEGGCLGEAATIASMLSEQD 497

Length = 845

>gnl\|CDD\|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA	Back alignment and domain information

>gnl\|CDD\|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional	Back alignment and domain information

>gnl\|CDD\|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional	Back alignment and domain information

>gnl\|CDD\|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB	Back alignment and domain information

>gnl\|CDD\|218070 pfam04408, HA2, Helicase associated domain (HA2)	Back alignment and domain information

>gnl\|CDD\|214852 smart00847, HA2, Helicase associated domain (HA2) Add an annotation	Back alignment and domain information

>gnl\|CDD\|197757 smart00490, HELICc, helicase superfamily c-terminal domain	Back alignment and domain information

>gnl\|CDD\|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain	Back alignment and domain information

>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

Back alignment and domain information

>gnl\|CDD\|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		350
KOG0922\|consensus		674		100.0
KOG0924\|consensus		1042		100.0
KOG0923\|consensus		902		100.0
KOG0920\|consensus		924		100.0
KOG0925\|consensus		699		100.0
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	100.0
COG1643		845	HrpA HrpA-like helicases [DNA replication, recombi	100.0
KOG0926\|consensus		1172		100.0
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	100.0
KOG0921\|consensus		1282		100.0
PHA02653		675	RNA helicase NPH-II; Provisional	100.0
PF04408		102	HA2: Helicase associated domain (HA2); InterPro: I	99.77
PRK01172		674	ski2-like helicase; Provisional	99.74
PRK02362		737	ski2-like helicase; Provisional	99.7
smart00847		92	HA2 Helicase associated domain (HA2) Add an annota	99.69
PRK00254		720	ski2-like helicase; Provisional	99.61
KOG0921\|consensus		1282		99.38
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	99.21
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	99.21
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.21
PF00271		78	Helicase_C: Helicase conserved C-terminal domain;	99.2
PTZ00424		401	helicase 45; Provisional	99.19
PTZ00110		545	helicase; Provisional	99.19
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	99.18
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	99.17
KOG0331\|consensus		519		99.16
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	99.15
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.15
COG1204		766	Superfamily II helicase [General function predicti	99.09
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.07
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	99.06
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	99.05
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	99.05
COG1202		830	Superfamily II helicase, archaea-specific [General	99.04
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	99.04
smart00490		82	HELICc helicase superfamily c-terminal domain.	99.01
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	99.01
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	98.97
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	98.96
KOG0333\|consensus		673		98.89
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	98.87
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	98.87
KOG0330\|consensus		476		98.84
PRK10689		1147	transcription-repair coupling factor; Provisional	98.83
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.78
PRK13767		876	ATP-dependent helicase; Provisional	98.76
cd00079		131	HELICc Helicase superfamily c-terminal domain; ass	98.69
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	98.69
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	98.68
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	98.67
KOG0336\|consensus		629		98.66
KOG0328\|consensus		400		98.61
KOG0335\|consensus		482		98.54
KOG0345\|consensus		567		98.54
KOG0348\|consensus		708		98.51
TIGR00631		655	uvrb excinuclease ABC, B subunit. This family is b	98.49
KOG0332\|consensus		477		98.48
PRK13766		773	Hef nuclease; Provisional	98.48
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.47
PRK05298		652	excinuclease ABC subunit B; Provisional	98.43
KOG0354\|consensus		746		98.43
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	98.41
KOG0338\|consensus		691		98.37
KOG0340\|consensus		442		98.37
PRK09200		790	preprotein translocase subunit SecA; Reviewed	98.37
PHA02558		501	uvsW UvsW helicase; Provisional	98.35
KOG0342\|consensus		543		98.34
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	98.34
KOG0951\|consensus		1674		98.28
KOG0344\|consensus		593		98.26
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	98.24
KOG0339\|consensus		731		98.19
KOG0341\|consensus		610		98.19
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	98.18
KOG0351\|consensus		941		98.04
PRK04914		956	ATP-dependent helicase HepA; Validated	98.03
KOG0326\|consensus		459		97.96
KOG0343\|consensus		758		97.95
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	97.94
KOG0350\|consensus		620		97.93
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	97.92
KOG0347\|consensus		731		97.85
PRK09694		878	helicase Cas3; Provisional	97.84
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	97.83
KOG0948\|consensus		1041		97.8
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	97.79
KOG0950\|consensus		1008		97.76
TIGR00595		505	priA primosomal protein N'. All proteins in this f	97.75
KOG0352\|consensus		641		97.75
KOG0947\|consensus		1248		97.73
KOG0952\|consensus		1230		97.71
KOG0349\|consensus		725		97.7
COG1205		851	Distinct helicase family with a unique C-terminal	97.7
PRK05580		679	primosome assembly protein PriA; Validated	97.69
COG1201		814	Lhr Lhr-like helicases [General function predictio	97.68
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	97.65
KOG0327\|consensus		397		97.62
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	97.53
KOG4150\|consensus		1034		97.33
KOG0334\|consensus		997		97.3
KOG0953\|consensus		700		97.3
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	97.1
KOG4284\|consensus		980		97.06
KOG0949\|consensus		1330		96.85
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	96.65
PRK14701		1638	reverse gyrase; Provisional	96.55
KOG0353\|consensus		695		96.53
PRK13107		908	preprotein translocase subunit SecA; Reviewed	96.41
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	96.33
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	96.13
PRK09401		1176	reverse gyrase; Reviewed	95.87
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	95.8
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	95.14
PRK12904		830	preprotein translocase subunit SecA; Reviewed	95.06
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	93.76
KOG0337\|consensus		529		93.29
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	91.44
TIGR02562		1110	cas3_yersinia CRISPR-associated helicase Cas3. The	90.44
KOG0329\|consensus		387		89.69
KOG0385\|consensus		971		88.8
PRK12326		764	preprotein translocase subunit SecA; Reviewed	88.7
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	87.82
KOG0346\|consensus		569		87.37
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	86.21
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	83.7
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	82.9
KOG0391\|consensus		1958		80.25

>KOG0922\|consensus	Back alignment and domain information

Probab=100.00  E-value=4.3e-74  Score=577.64  Aligned_cols=282  Identities=34%  Similarity=0.595  Sum_probs=270.6

Q ss_pred             eeccCCCCCHHHHHHhcc---CCCceEEEecCccccCCCCCCccEEEeCCCcceeeeecCCCccccccccccHhhHHhhh
Q psy6093          10 LQCPSSGLKHLQNKSVFE---LGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRR   86 (350)
Q Consensus        10 ~~~lHs~l~~~~q~~vf~---~g~rkvIlaTniaEtsvtip~v~~VID~G~~k~~~yd~~~~~~~l~~~~iSka~~~QR~   86 (350)
                      +.++||+||.++|.+||.   +|.||||+||||||||+|||||+||||+|++|++.|||+.|++.|..+||||++|.||+
T Consensus       293 ~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRa  372 (674)
T KOG0922|consen  293 ILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRA  372 (674)
T ss_pred             eeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhc
Confidence            456799999999999998   59999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCceEEEcccccccccccCCCCccccccchHHHHHHHhhccCccchhhHhhhhccccCCccccCccCCCCCCHH
Q psy6093          87 GRAGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTAFTPYVWVPKQVLDPPDPA  166 (350)
Q Consensus        87 GRaGR~~~G~c~rLyt~~~~~~~~~~~~pEi~r~~L~~~~L~~k~~~~~~~~~~f~~~l~~~~~p~~~~l~~~~~pP~~~  166 (350)
                      |||||++||+|||||++++|+.|++.+.|||+|.+|..++|++|++|++++ ..|                +|+|||+++
T Consensus       373 GRAGRt~pGkcyRLYte~~~~~~~~~~~PEI~R~~Ls~~vL~Lkalgi~d~-l~F----------------~f~d~P~~~  435 (674)
T KOG0922|consen  373 GRAGRTGPGKCYRLYTESAYDKMPLQTVPEIQRVNLSSAVLQLKALGINDP-LRF----------------PFIDPPPPE  435 (674)
T ss_pred             ccCCCCCCceEEEeeeHHHHhhcccCCCCceeeechHHHHHHHHhcCCCCc-ccC----------------CCCCCCChH
Confidence            999999999999999999999999999999999999999999999999999 889                999999999


Q ss_pred             HHHHHHHHHHHHHccCCCCCCCH-HHhhhccCCCchhHHHHHHHhhhcCChhHHHHHhhhccccccccccccchhhhhhh
Q psy6093         167 SVQLSLKLLRLIDALDDDEHLTP-LGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMAS  245 (350)
Q Consensus       167 ~i~~al~~L~~lgald~~~~LT~-lG~~ls~Lpldp~~ak~ll~~~~~~C~~~~l~iaa~l~~~~~~~~~~~g~~~~~~~  245 (350)
                      ++..|++.|..+||||++|.||. +|+.|+.||++|.++||++.+..+||.+++++|                       
T Consensus       436 ~l~~AL~~L~~lgald~~g~lt~p~G~~ma~~Pl~p~lsk~ll~s~~~gc~~e~l~i-----------------------  492 (674)
T KOG0922|consen  436 ALEEALEELYSLGALDDRGKLTSPLGRQMAELPLEPHLSKMLLKSSELGCSEEILTI-----------------------  492 (674)
T ss_pred             HHHHHHHHHHhcCcccCcCCcCchHHhhhhhcCCCcchhhhhhhccccCCcchhhhh-----------------------
Confidence            99999999999999999999998 999999999999999999999999999999999                       


Q ss_pred             hcccCCccchhcccccCCCccccCCCchHH-HHHHHHHhccCCCChHHHHHHHHHHHHHHHccChhHHHHHHccCCHHHH
Q psy6093         246 IFSCVDPVFTVAASLGFKDAFYCPMNMEKD-VDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYAHDYCRENFLTNNTL  324 (350)
Q Consensus       246 i~s~~~~~~~~aa~ls~~~~f~~p~~~~~~-~~~~r~~f~~~~~sDhltll~~f~~w~~~~~~~~~~~~C~~~~L~~~~l  324 (350)
                                 +|+||++++|+.|.+.+.+ ++..|.+|.. ..|||+|++|+|+.|.+   ++..++||++|++|.+.|
T Consensus       493 -----------~a~Lsv~~~f~~p~~~~~~~a~~~~~kf~~-~eGDh~tlL~vy~~~~~---~~~~~~wC~en~i~~r~l  557 (674)
T KOG0922|consen  493 -----------AAMLSVQSVFSRPKDKKAEDADRKRAKFAN-PEGDHLTLLNVYESWKE---NGTSKKWCKENFINARSL  557 (674)
T ss_pred             -----------eeeeeccceecCccchhhhhhhHHHHhhcC-cccCHHHHHHHHHHHHh---cCChhhHHHHhcccHHHH
Confidence                       7888999999999988776 8889999986 68899999999999985   677899999999999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCCcC
Q psy6093         325 LLLRDMKDQFSRTMHEMNFISS  346 (350)
Q Consensus       325 ~~~~~lr~ql~~~l~~~~~~~~  346 (350)
                      +.+.++|+||.+++.+.++..+
T Consensus       558 ~~a~~ir~QL~~i~~~~~~~~~  579 (674)
T KOG0922|consen  558 KRAKDIRKQLRRILDKFGLPVS  579 (674)
T ss_pred             HHHHHHHHHHHHHHHHcCCCcc
Confidence            9999999999999988887763

>KOG0924\|consensus	Back alignment and domain information

>KOG0923\|consensus	Back alignment and domain information

>KOG0920\|consensus	Back alignment and domain information

>KOG0925\|consensus	Back alignment and domain information

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional	Back alignment and domain information

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA	Back alignment and domain information

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG0926\|consensus	Back alignment and domain information

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB	Back alignment and domain information

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional	Back alignment and domain information

>KOG0921\|consensus	Back alignment and domain information

>PHA02653 RNA helicase NPH-II; Provisional	Back alignment and domain information

>PF04408 HA2: Helicase associated domain (HA2); InterPro: IPR007502 This presumed domain is about 90 amino acid residues in length	Back alignment and domain information

>PRK01172 ski2-like helicase; Provisional	Back alignment and domain information

>PRK02362 ski2-like helicase; Provisional	Back alignment and domain information

>smart00847 HA2 Helicase associated domain (HA2) Add an annotation	Back alignment and domain information

>PRK00254 ski2-like helicase; Provisional	Back alignment and domain information

>KOG0921\|consensus	Back alignment and domain information

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional	Back alignment and domain information

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional	Back alignment and domain information

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family	Back alignment and domain information

>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	Back alignment and domain information

>PTZ00424 helicase 45; Provisional	Back alignment and domain information

>PTZ00110 helicase; Provisional	Back alignment and domain information

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional	Back alignment and domain information

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>KOG0331\|consensus	Back alignment and domain information

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional	Back alignment and domain information

>COG1204 Superfamily II helicase [General function prediction only]	Back alignment and domain information

>TIGR01389 recQ ATP-dependent DNA helicase RecQ	Back alignment and domain information

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional	Back alignment and domain information

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>TIGR00643 recG ATP-dependent DNA helicase RecG	Back alignment and domain information

>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]	Back alignment and domain information

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional	Back alignment and domain information

>smart00490 HELICc helicase superfamily c-terminal domain	Back alignment and domain information

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase	Back alignment and domain information

>PRK10917 ATP-dependent DNA helicase RecG; Provisional	Back alignment and domain information

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional	Back alignment and domain information

>KOG0333\|consensus	Back alignment and domain information

>TIGR00580 mfd transcription-repair coupling factor (mfd)	Back alignment and domain information

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

>KOG0330\|consensus	Back alignment and domain information

>PRK10689 transcription-repair coupling factor; Provisional	Back alignment and domain information

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK13767 ATP-dependent helicase; Provisional	Back alignment and domain information

>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

Back alignment and domain information

>TIGR01587 cas3_core CRISPR-associated helicase Cas3	Back alignment and domain information

>PRK09751 putative ATP-dependent helicase Lhr; Provisional	Back alignment and domain information

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG0336\|consensus	Back alignment and domain information

>KOG0328\|consensus	Back alignment and domain information

>KOG0335\|consensus	Back alignment and domain information

>KOG0345\|consensus	Back alignment and domain information

>KOG0348\|consensus	Back alignment and domain information

>TIGR00631 uvrb excinuclease ABC, B subunit	Back alignment and domain information

>KOG0332\|consensus	Back alignment and domain information

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype	Back alignment and domain information

>PRK05298 excinuclease ABC subunit B; Provisional	Back alignment and domain information

>KOG0354\|consensus	Back alignment and domain information

>PRK12898 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0338\|consensus	Back alignment and domain information

>KOG0340\|consensus	Back alignment and domain information

>PRK09200 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PHA02558 uvsW UvsW helicase; Provisional	Back alignment and domain information

>KOG0342\|consensus	Back alignment and domain information

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

>KOG0951\|consensus	Back alignment and domain information

>KOG0344\|consensus	Back alignment and domain information

>TIGR03714 secA2 accessory Sec system translocase SecA2	Back alignment and domain information

>KOG0339\|consensus	Back alignment and domain information

>KOG0341\|consensus	Back alignment and domain information

>TIGR00603 rad25 DNA repair helicase rad25	Back alignment and domain information

>KOG0351\|consensus	Back alignment and domain information

>PRK04914 ATP-dependent helicase HepA; Validated	Back alignment and domain information

>KOG0326\|consensus	Back alignment and domain information

>KOG0343\|consensus	Back alignment and domain information

>PRK12906 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0350\|consensus	Back alignment and domain information

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type	Back alignment and domain information

>KOG0347\|consensus	Back alignment and domain information

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

>TIGR00963 secA preprotein translocase, SecA subunit	Back alignment and domain information

>KOG0948\|consensus	Back alignment and domain information

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

>KOG0950\|consensus	Back alignment and domain information

>TIGR00595 priA primosomal protein N'	Back alignment and domain information

>KOG0352\|consensus	Back alignment and domain information

>KOG0947\|consensus	Back alignment and domain information

>KOG0952\|consensus	Back alignment and domain information

>KOG0349\|consensus	Back alignment and domain information

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

>PRK05580 primosome assembly protein PriA; Validated	Back alignment and domain information

>COG1201 Lhr Lhr-like helicases [General function prediction only]	Back alignment and domain information

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

>KOG0327\|consensus	Back alignment and domain information

>PRK12900 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG4150\|consensus	Back alignment and domain information

>KOG0334\|consensus	Back alignment and domain information

>KOG0953\|consensus	Back alignment and domain information

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG4284\|consensus	Back alignment and domain information

>KOG0949\|consensus	Back alignment and domain information

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]	Back alignment and domain information

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

>KOG0353\|consensus	Back alignment and domain information

>PRK13107 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PRK13104 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional	Back alignment and domain information

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

>PRK12904 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional	Back alignment and domain information

>KOG0337\|consensus	Back alignment and domain information

>PRK12903 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3	Back alignment and domain information

>KOG0329\|consensus	Back alignment and domain information

>KOG0385\|consensus	Back alignment and domain information

>PRK12326 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PRK12901 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0346\|consensus	Back alignment and domain information

>PRK13103 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

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

>PRK12899 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0391\|consensus	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		350
3kx2_B		767	Crystal Structure Of Prp43p In Complex With Adp Len		8e-32
2xau_A		773	Crystal Structure Of The Prp43p Deah-Box Rna Helica		8e-32
3i4u_A		270	Crystal Structure Analysis Of A Helicase Associated		1e-07

>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp Length = 767

Back alignment and structure

Iteration: 1

Score = 134 bits (337), Expect = 8e-32, Method: Compositional matrix adjust. Identities = 96/318 (30%), Positives = 145/318 (45%), Gaps = 60/318 (18%) Query: 31 RKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAG 90 RK+V++TNIAETS+TID IVYVVD G +K ++ + + +L IS A+A+QR GRAG Sbjct: 370 RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAG 429 Query: 91 RVQEGVCYHLYSRAREQTFQ----DYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLN 146 R + G C+ LY+ E+ FQ + PEI R+ L V LE KK + Sbjct: 430 RTRPGKCFRLYT---EEAFQKELIEQSYPEILRSNLSSTV--LELKKLGIDD-------- 476 Query: 147 TAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKM 206 V +DPP P ++ +L+ L + LDD+ +LTPLG ++ PLDP + M Sbjct: 477 -------LVHFDFMDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVM 529 Query: 207 LLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVDPVFTVAASLGFKDAF 266 L+ + F C + T+ A L + F P K Sbjct: 530 LIGSFEFQCSQEILTIVAMLSVPNVFIRPTKDK--------------------------- 562 Query: 267 YCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYA-HDYCRENFXXXXXXX 325 K D KNI A D++ L+N ++ + Y H +CR+++ Sbjct: 563 -------KRADDAKNIFAH-PDGDHITLLNVYHAFKSDEAYEYGIHKWCRDHYLNYRSLS 614 Query: 326 XXRDMKDQFSRTMHEMNF 343 +++ Q R M+ N Sbjct: 615 AADNIRSQLERLMNRYNL 632

PyMOL of 3kx2

>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In Complex With Adp Length = 773

Back alignment and structure

>pdb|3I4U|A Chain A, Crystal Structure Analysis Of A Helicase Associated Domain Length = 270

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		350
2xau_A		773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	3e-68
2v6i_A		431	RNA helicase; membrane, hydrolase, transmembrane,	1e-28
2jlq_A		451	Serine protease subunit NS3; ribonucleoprotein, nu	8e-28
2whx_A		618	Serine protease/ntpase/helicase NS3; transcription	1e-27
3o8b_A		666	HCV NS3 protease/helicase; ntpase, RNA, translocat	1e-26
3i4u_A		270	ATP-dependent RNA helicase DHX8; splicing, ATP-bin	4e-25
1yks_A		440	Genome polyprotein [contains: flavivirin protease	2e-24
2wv9_A		673	Flavivirin protease NS2B regulatory subunit, FLAV	3e-24
2z83_A		459	Helicase/nucleoside triphosphatase; hydrolase, mem	5e-24
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06

>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* Length = 773	Back alignment and structure

 Score =  227 bits (580), Expect = 3e-68
 Identities = 97/335 (28%), Positives = 153/335 (45%), Gaps = 63/335 (18%)

Query: 19  HLQNKSVFE--------LGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIA 70
           H Q + +FE           RK+V++TNIAETS+TID IVYVVD G +K   ++ +  + 
Sbjct: 351 HQQQR-IFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVE 409

Query: 71  TLKPEWISLANAKQRRGRAGRVQEGVCYHLYS-RAREQTFQDYPLPEIQRTRLDEVVRTL 129
           +L    IS A+A+QR GRAGR + G C+ LY+  A ++   +   PEI R+ L   V  L
Sbjct: 410 SLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLEL 469

Query: 130 ESKKFKMVSRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTP 189
           +      +   F          +       +DPP P ++  +L+ L  +  LDD+ +LTP
Sbjct: 470 KKLGIDDL-VHF---------DF-------MDPPAPETMMRALEELNYLACLDDEGNLTP 512

Query: 190 LGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSC 249
           LG   ++ PLDP +  ML+ +  F C   + T+ A               ML   S+ + 
Sbjct: 513 LGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVA---------------ML---SVPNV 554

Query: 250 VDPVFTVAASLGFKDAFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQA-LEHN 308
                           F  P   +K  D  KNI A     D++ L+N    ++       
Sbjct: 555 ----------------FIRPTKDKKRADDAKNIFAH-PDGDHITLLNVYHAFKSDEAYEY 597

Query: 309 YAHDYCRENFLTNNTLLLLRDMKDQFSRTMHEMNF 343
             H +CR+++L   +L    +++ Q  R M+  N 
Sbjct: 598 GIHKWCRDHYLNYRSLSAADNIRSQLERLMNRYNL 632

PyMOL of 2xau

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431	Back alignment and structure

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A Length = 451	Back alignment and structure

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A Length = 618	Back alignment and structure

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666	Back alignment and structure

>3i4u_A ATP-dependent RNA helicase DHX8; splicing, ATP-binding, hydrolase, mRNA processing, splicing, nucleotide-binding, nucleus, phosphoprotein, SPLI; 2.10A {Homo sapiens} Length = 270	Back alignment and structure

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A* Length = 440	Back alignment and structure

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus} Length = 673	Back alignment and structure

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A Length = 459	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		350
2xau_A		773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	100.0
3i4u_A		270	ATP-dependent RNA helicase DHX8; splicing, ATP-bin	100.0
2va8_A		715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.96
2p6r_A		702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.95
2zj8_A		720	DNA helicase, putative SKI2-type helicase; RECA fo	99.92
3eaq_A		212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.81
3i32_A		300	Heat resistant RNA dependent ATPase; RNA helicase,	99.79
3rc3_A		677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.73
2z83_A		459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.5
3o8b_A		666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.46
4f92_B		1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.44
2jlq_A		451	Serine protease subunit NS3; ribonucleoprotein, nu	99.44
4f92_B		1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.39
1fuk_A		165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.36
2hjv_A		163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.36
1yks_A		440	Genome polyprotein [contains: flavivirin protease	99.34
2rb4_A		175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.33
2whx_A		618	Serine protease/ntpase/helicase NS3; transcription	99.33
2ykg_A		696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.32
3eiq_A		414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.32
3pey_A		395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.31
4a4z_A		997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.31
3fht_A		412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.29
2i4i_A		417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.28
1hv8_A		367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.28
1s2m_A		400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.28
2jgn_A		185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.26
2v6i_A		431	RNA helicase; membrane, hydrolase, transmembrane,	99.25
2v1x_A		591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.25
2p6n_A		191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.25
2wv9_A		673	Flavivirin protease NS2B regulatory subunit, FLAV	99.24
3l9o_A		1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.23
2db3_A		434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.23
2j0s_A		410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.22
1t5i_A		172	C_terminal domain of A probable ATP-dependent RNA	99.21
2yjt_D		170	ATP-dependent RNA helicase SRMB, regulator of ribo	98.84
1oyw_A		523	RECQ helicase, ATP-dependent DNA helicase; winged	99.2
1xti_A		391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.18
3i5x_A		563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.17
2xgj_A		1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.17
3fmp_B		479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.13
1fuu_A		394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.13
4a2p_A		556	RIG-I, retinoic acid inducible protein I; hydrolas	99.12
3sqw_A		579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.12
3tbk_A		555	RIG-I helicase domain; DECH helicase, ATP binding,	99.11
2z0m_A		337	337AA long hypothetical ATP-dependent RNA helicase	99.1
3fho_A		508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.04
1wp9_A		494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.03
1c4o_A		664	DNA nucleotide excision repair enzyme UVRB; uvrabc	98.98
4a2q_A		797	RIG-I, retinoic acid inducible protein I; hydrolas	98.96
1gm5_A		780	RECG; helicase, replication restart; HET: DNA ADP;	98.95
2d7d_A		661	Uvrabc system protein B; helicase, protein-DNA-ADP	98.95
4gl2_A		699	Interferon-induced helicase C domain-containing P;	98.93
4a2w_A		936	RIG-I, retinoic acid inducible protein I; hydrolas	98.91
2eyq_A		1151	TRCF, transcription-repair coupling factor; MFD, S	98.8
3oiy_A		414	Reverse gyrase helicase domain; topoisomerase, DNA	98.72
2fwr_A		472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.71
2oca_A		510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	98.65
1gku_B		1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	98.49
1tf5_A		844	Preprotein translocase SECA subunit; ATPase, helic	98.47
3jux_A		822	Protein translocase subunit SECA; protein transloc	98.29
1z5z_A		271	Helicase of the SNF2/RAD54 family; hydrolase, reco	98.27
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.24
4ddu_A		1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	98.19
2fsf_A		853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.12
3h1t_A		590	Type I site-specific restriction-modification syst	98.07
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.03
1nkt_A		922	Preprotein translocase SECA 1 subunit; preprotein	97.93
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	97.78
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	97.62
2w00_A		1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	95.47

>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*	Back alignment and structure

Probab=100.00  E-value=1.2e-58  Score=492.52  Aligned_cols=289  Identities=33%  Similarity=0.542  Sum_probs=269.7

Q ss_pred             cceeeeccCCCCCHHHHHHhcc--------CCCceEEEecCccccCCCCCCccEEEeCCCcceeeeecCCCccccccccc
Q psy6093           6 QIWFLQCPSSGLKHLQNKSVFE--------LGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWI   77 (350)
Q Consensus         6 ~~~~~~~lHs~l~~~~q~~vf~--------~g~rkvIlaTniaEtsvtip~v~~VID~G~~k~~~yd~~~~~~~l~~~~i   77 (350)
                      .++.+.++||+|++++|+++|+        +|.+|||||||+||+|||||+|++|||+|+.|.+.||+..|++.|.+.|+
T Consensus       337 ~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~  416 (773)
T 2xau_A          337 GPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPI  416 (773)
T ss_dssp             CCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEEC
T ss_pred             CCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccC
Confidence            4677888999999999999976        47899999999999999999999999999999999999999999999999


Q ss_pred             cHhhHHhhhccCCCCCCceEEEccccccc-ccccCCCCccccccchHHHHHHHhhccCccchhhHhhhhccccCCccccC
Q psy6093          78 SLANAKQRRGRAGRVQEGVCYHLYSRARE-QTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTAFTPYVWVP  156 (350)
Q Consensus        78 Ska~~~QR~GRaGR~~~G~c~rLyt~~~~-~~~~~~~~pEi~r~~L~~~~L~~k~~~~~~~~~~f~~~l~~~~~p~~~~l  156 (350)
                      |++++.||+|||||.++|.||+||++..+ +.+.+++.|||++.+|.+++|++|.+|++++ ..|               
T Consensus       417 S~~s~~QR~GRaGR~~~G~~~~l~~~~~~~~~l~~~~~pEi~r~~L~~~~L~l~~~gi~~~-~~f---------------  480 (773)
T 2xau_A          417 SKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDL-VHF---------------  480 (773)
T ss_dssp             CHHHHHHHHHGGGSSSSEEEEESSCHHHHHHTSCSSCCCGGGGSCCHHHHHHHHHTTCCCG-GGC---------------
T ss_pred             CHHHHHhhccccCCCCCCEEEEEecHHHhcccccccCCCccccCcHHHHHHHHHHcCCCCh-hhc---------------
Confidence            99999999999999999999999999888 7799999999999999999999999999988 778               


Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHHccCCCCCCCHHHhhhccCCCchhHHHHHHHhhhcCChhHHHHHhhhccccccccccc
Q psy6093         157 KQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPM  236 (350)
Q Consensus       157 ~~~~~pP~~~~i~~al~~L~~lgald~~~~LT~lG~~ls~Lpldp~~ak~ll~~~~~~C~~~~l~iaa~l~~~~~~~~~~  236 (350)
                       ++++||+.+++..|++.|..+|+||++|+||++|+.|++||+||++||||+.|..++|.+++++|              
T Consensus       481 -~~~~~p~~~~i~~a~~~L~~lgald~~~~lT~lG~~~a~~pl~p~~~~~l~~~~~~~c~~~~l~i--------------  545 (773)
T 2xau_A          481 -DFMDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTI--------------  545 (773)
T ss_dssp             -CCSSCCCHHHHHHHHHHHHHTTSBCTTSCBCHHHHHHTTSSSCHHHHHHHHHGGGGTCHHHHHHH--------------
T ss_pred             -cccCCCcHHHHHHHHHHHHHcCCcccCCCcChhhhhhccccCCHHHHHHHHhhcccCchhHHHHH--------------
Confidence             88999999999999999999999999999999999999999999999999999999999999999              


Q ss_pred             cchhhhhhhhcccCCccchhcccccCCCccccCCCchHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHccChh-HHHHH
Q psy6093         237 IGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYA-HDYCR  315 (350)
Q Consensus       237 ~g~~~~~~~i~s~~~~~~~~aa~ls~~~~f~~p~~~~~~~~~~r~~f~~~~~sDhltll~~f~~w~~~~~~~~~-~~~C~  315 (350)
                                          +|+|+.+++|+.|.+.+++++..|+.|.. ..|||++++|+|++|.+....+.. ..||+
T Consensus       546 --------------------~a~ls~~~~f~~~~~~~~~~~~~~~~f~~-~~~D~~~~l~~~~~~~~~~~~~~~~~~~c~  604 (773)
T 2xau_A          546 --------------------VAMLSVPNVFIRPTKDKKRADDAKNIFAH-PDGDHITLLNVYHAFKSDEAYEYGIHKWCR  604 (773)
T ss_dssp             --------------------HHHHTSCCCBCCCTTCHHHHHHHHHTTCC-TTBHHHHHHHHHHHHTSHHHHHHCHHHHHH
T ss_pred             --------------------HHhcccCCcccCChHHHHHHHHHHHhccC-CCCcHHHHHHHHHHHHHhccccchHHHHHH
Confidence                                67778889999999999999999999975 679999999999999754322233 78999


Q ss_pred             HccCCHHHHHHHHHHHHHHHHHHHHCCCCcC
Q psy6093         316 ENFLTNNTLLLLRDMKDQFSRTMHEMNFISS  346 (350)
Q Consensus       316 ~~~L~~~~l~~~~~lr~ql~~~l~~~~~~~~  346 (350)
                      +||||+++|+++.++|+||.++|.+.|+...
T Consensus       605 ~~~l~~~~l~~~~~~~~ql~~~~~~~~~~~~  635 (773)
T 2xau_A          605 DHYLNYRSLSAADNIRSQLERLMNRYNLELN  635 (773)
T ss_dssp             HTTBCHHHHHHHHHHHHHHHHHHHHTTCCCC
T ss_pred             HhCCCHHHHHHHHHHHHHHHHHHHhcCCCcC
Confidence            9999999999999999999999999988653

PyMOL of 2xau

>3i4u_A ATP-dependent RNA helicase DHX8; splicing, ATP-binding, hydrolase, mRNA processing, splicing, nucleotide-binding, nucleus, phosphoprotein, SPLI; 2.10A {Homo sapiens}	Back alignment and structure

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}	Back alignment and structure

>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	Back alignment and structure

>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*	Back alignment and structure

>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	Back alignment and structure

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}	Back alignment and structure

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A	Back alignment and structure

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A	Back alignment and structure

>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 ...	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19	Back alignment and structure

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

>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*	Back alignment and structure

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}	Back alignment and structure

>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	Back alignment and structure

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*	Back alignment and structure

>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}	Back alignment and structure

>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*	Back alignment and structure

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A	Back alignment and structure

>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	Back alignment and structure

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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}	Back alignment and structure

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A	Back alignment and structure

>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*	Back alignment and structure

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

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}	Back alignment and structure

>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}	Back alignment and structure

>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}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}	Back alignment and structure

>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*	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}	Back alignment and structure

>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}	Back alignment and structure

>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*	Back alignment and structure

>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*	Back alignment and structure

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}	Back alignment and structure

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}	Back alignment and structure

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}	Back alignment and structure

>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	Back alignment and structure

>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*	Back alignment and structure

>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}	Back alignment and structure

>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	Back alignment and structure

>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*	Back alignment and structure

>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}	Back alignment and structure

>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}	Back alignment and structure

>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	Back alignment and structure

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*	Back alignment and structure

>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*	Back alignment and structure

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}	Back alignment and structure

>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*	Back alignment and structure

>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	Back alignment and structure

>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*	Back alignment and structure

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19	Back alignment and structure

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}	Back alignment and structure

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A	Back alignment and structure

>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*	Back alignment and structure

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}	Back alignment and structure

>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*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		350
d1yksa2		299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	1e-26
d2bmfa2		305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-13
d1a1va2		299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	2e-04

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score =  104 bits (261), Expect = 1e-26
 Identities = 35/180 (19%), Positives = 61/180 (33%), Gaps = 20/180 (11%)

Query: 31  RKIVLATNIAETSITIDDIVYVVDCGKT-KMSNFDVKDNIATLKPEWISLANAKQRRGRA 89
              +LAT+IAE    +  +  V+DC    K    D    +A   P  IS ++A QRRGR 
Sbjct: 83  PDFILATDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRI 141

Query: 90  GRVQEGV-CYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTA 148
           GR        + YS   E T ++     +       ++  +E  +  MV+  +   +   
Sbjct: 142 GRNPNRDGDSYYYS---EPTSEN-NAHHVCWLEASMLLDNMEV-RGGMVAPLY--GVEGT 194

Query: 149 FTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLL 208
                                   +     + + + +    L + +AK  L     K   
Sbjct: 195 K----------TPVSPGEMRLRDDQRKVFRELVRNCDLPVWLSWQVAKAGLKTNDRKWCF 244

PyMOL of d1yksa2

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305	Back information, alignment and structure

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		350
d1yksa2		299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.94
d2rb4a1		168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.33
d2bmfa2		305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.32
d1fuka_		162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.3
d2j0sa2		168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.29
d1t5la2		181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.28
d1c4oa2		174	Nucleotide excision repair enzyme UvrB {Thermus th	99.28
d1oywa3		200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.28
d1hv8a2		155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.28
d1s2ma2		171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.27
d2p6ra4		201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.22
d1gm5a4		206	RecG helicase domain {Thermotoga maritima [TaxId:	99.22
d1t5ia_		168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.19
d1jr6a_		138	HCV helicase domain {Human hepatitis C virus (HCV)	99.16
d1wp9a2		286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.08
d2eyqa5		211	Transcription-repair coupling factor, TRCF {Escher	98.9
d1a1va2		299	HCV helicase domain {Human hepatitis C virus (HCV)	98.54
d2fwra1		200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.52
d1gkub2		248	Helicase-like "domain" of reverse gyrase {Archaeon	98.19
d1z5za1		244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	96.51
d1z3ix1		346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	96.33
d1tf5a4		175	Translocation ATPase SecA, nucleotide-binding doma	95.15
d2p6ra1		85	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	94.17
d1nkta4		219	Translocation ATPase SecA, nucleotide-binding doma	90.81

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.94  E-value=6e-31  Score=248.17  Aligned_cols=176  Identities=18%  Similarity=0.077  Sum_probs=131.1

Q ss_pred             ceeeeccCCCCCHHHHHHhccCCCceEEEecCccccCCCCCCccEEEeCCCc-ceeeeecCCCccccccccccHhhHHhh
Q psy6093           7 IWFLQCPSSGLKHLQNKSVFELGVRKIVLATNIAETSITIDDIVYVVDCGKT-KMSNFDVKDNIATLKPEWISLANAKQR   85 (350)
Q Consensus         7 ~~~~~~lHs~l~~~~q~~vf~~g~rkvIlaTniaEtsvtip~v~~VID~G~~-k~~~yd~~~~~~~l~~~~iSka~~~QR   85 (350)
                      ++.|.++||.++.++++++ +++.++|||||||||+|+|| ||+||||+|+. |...||+..++..+...|||++++.||
T Consensus        60 g~~V~~l~~~~~~~e~~~~-~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~qr  137 (299)
T d1yksa2          60 GKSVVVLNRKTFEREYPTI-KQKKPDFILATDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQR  137 (299)
T ss_dssp             TCCEEECCSSSCC---------CCCSEEEESSSTTCCTTC-CCSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHH
T ss_pred             CCeEEEEcCcCcHhHHhhh-hcCCcCEEEEechhhhceec-CceEEEecCceeceeeecCCCCeeEEeeeecCHHHHHHh
Confidence            5678889999999988764 56788999999999999999 69999999995 888999999999999999999999999


Q ss_pred             hccCCCCCCc-eEEEcccccccccccCCCCccccccc----hHHHHHHHhhccCccchhhHhhhhccccCCccccCccCC
Q psy6093          86 RGRAGRVQEG-VCYHLYSRAREQTFQDYPLPEIQRTR----LDEVVRTLESKKFKMVSRRFKVMLNTAFTPYVWVPKQVL  160 (350)
Q Consensus        86 ~GRaGR~~~G-~c~rLyt~~~~~~~~~~~~pEi~r~~----L~~~~L~~k~~~~~~~~~~f~~~l~~~~~p~~~~l~~~~  160 (350)
                      +||+||..++ .||.+|+...    .+...++++++.    |.++.+.++.++..+. .+|                +++
T Consensus       138 ~gr~gr~~~~~~~~~~y~~~~----~~d~~~~~~~te~~i~l~~i~l~~~~~g~~~~-~e~----------------~~~  196 (299)
T d1yksa2         138 RGRIGRNPNRDGDSYYYSEPT----SENNAHHVCWLEASMLLDNMEVRGGMVAPLYG-VEG----------------TKT  196 (299)
T ss_dssp             HTTSSCCTTCCCEEEEECSCC----CCCCTTBHHHHHHHHHHTTSCCGGGCCCCCST-THH----------------HHS
T ss_pred             cccccccCCCceEEEEeCCCC----CCcccchhhhhhHHHHhhCcccccccccccch-hhh----------------ccc
Confidence            9999998543 2555666432    223334444433    3333456666776666 666                567


Q ss_pred             CCCCHHHHHHHHHHHHHHHccCCCCCCCHHHhhhccCCCchhHHH
Q psy6093         161 DPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGK  205 (350)
Q Consensus       161 ~pP~~~~i~~al~~L~~lgald~~~~LT~lG~~ls~Lpldp~~ak  205 (350)
                      ++|+.+....++..+..+|+|+..+..|++|+.++.+++.+...+
T Consensus       197 ~~p~g~~~L~~~~~l~~l~aL~~~d~p~~La~~va~~~~~~~~~~  241 (299)
T d1yksa2         197 PVSPGEMRLRDDQRKVFRELVRNCDLPVWLSWQVAKAGLKTNDRK  241 (299)
T ss_dssp             SSCTTTTCCCHHHHHHHHHHHHTTCCCHHHHHHHHHTTCCTTCCG
T ss_pred             cCCCchhhhhHhHHHHHHHHHhhcCCCcchHHHHHhccccccccc
Confidence            788777777788999999999887777888888877777665444

PyMOL of d1yksa2

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}	Back information, alignment and structure

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}	Back information, alignment and structure

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}	Back information, alignment and structure

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}	Back information, alignment and structure

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}	Back information, alignment and structure

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d2p6ra1 a.4.5.43 (A:404-488) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure