Citrus Sinensis ID: 017020

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------38
Protein Sequence
MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYRFRELFLIFRRRLQRSC
Secondary Structure (PSIPRED)
ccccccHHHHHHHHHHccccccEEEEEccccHHHHHHHHHHcccccEEEEEEcccccccccEEEEEEEEccccHHHHHHHHHHHccccccEEEEEccccHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccccEEEEEcccccccccccccEEEEcccccccccccccccccccccccccEEEEEcccHHHHHHHHHHHHccccEEcccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccccccccccccccEEEEEEEccccccccccHHHHHHHHHHcccccccccccEEEEccccEEEEcHHHHHHHHHHHHccccccEEEEEEEEccccHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
HHccccHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEEEEEcccEEEcccEEEEEEEEccHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHccccHHHHcccccHHHHHHHHHHHHccccEEEEEEcHHHccccccccEEEEEEccccccccEEEEccccccccccEEEEEEEcHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHccccccccccccccccccccEEEEEEEccccccccHHHHHHHHHHHccccHccEEEEEEcccccEEEcccccHHHHHHHHHHHHcccEEEEEcHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MLAVGFEEDVELILenlppkrqsmLFSATMPSWVKKLSRkyldnplnidlvgnqDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAlhgdisqhqrertlngfrqgkFTVLVATDVaargldipnvdliihyelpndpetfvhrsgrtgragkegTAILMFTSSQRRTVRslerdvgckfefvsppvveDVLESSAEQVVATLngvhpesvefftPTAQRLIEEKGTDALAAALAQLsgfsrppssrslinheqgWVTLQLTRDSAFSRGFMSARSVMGflsdvyptaadeigkihiiaddrVCIDTVILLYFYASVRLGLFNTKSVIWLTYRFRELFLIFRRRLQRSC
Flexible Loop (DISEMBL)
MLAVGFEEDVELILEnlppkrqsmLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAisttatskrtiLSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRsgrtgragkegtailmftssqrrtvrslerdvgckfefvSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYRFRELFLIFRRRLQRSC
Low Complexity Region (SEG)
MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYrfrelflifrrrlqrSC
Disordered region (IsUnstruct)
*********VELILEN*******MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH************TAILMFTS**RRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALA*************LINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYRFRELFLIFRR******
Disordered Region (DISOPRED)
MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV**LNGVHPESVEFFTPTAQRLIEEKGTDALAAALA************************************MSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVR*******************************
Disordered Region (DISEMBL)
MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYRFRELFLIFRRRLQRSC
Disordered Region (DISPRO)
*LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFS*************GWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYRFRELFLIFRRRLQR*C
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYRFRELFLIFRRRLQRSC
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	379	2.2.26 [Sep-21-2011]
Q8L7S8	748	DEAD-box ATP-dependent RN	no	no	0.878	0.445	0.852	1e-164
Q0DM51	758	DEAD-box ATP-dependent RN	yes	no	0.878	0.439	0.825	1e-162
Q0D8N0	602	DEAD-box ATP-dependent RN	no	no	0.588	0.370	0.64	3e-81
Q9LUW5	616	DEAD-box ATP-dependent RN	no	no	0.577	0.355	0.643	8e-81
Q0ILZ4	628	DEAD-box ATP-dependent RN	no	no	0.554	0.334	0.638	8e-80
Q9LUW6	610	DEAD-box ATP-dependent RN	no	no	0.577	0.359	0.616	5e-79
Q650T9	696	DEAD-box ATP-dependent RN	no	no	0.786	0.428	0.420	4e-58
Q41382	685	DEAD-box ATP-dependent RN	N/A	no	0.849	0.470	0.398	1e-56
Q9BQ39	737	ATP-dependent RNA helicas	yes	no	0.757	0.389	0.433	3e-56
Q39189	671	DEAD-box ATP-dependent RN	no	no	0.810	0.457	0.413	5e-56

>sp|Q8L7S8|RH3_ARATH DEAD-box ATP-dependent RNA helicase 3, chloroplastic OS=Arabidopsis thaliana GN=RH3 PE=1 SV=2

 Score =  577 bits (1488), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 284/333 (85%), Positives = 314/333 (94%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           MLAVGFEE VE ILENLP KRQSMLFSATMP+WVKKL+RKYLDNPLNIDLVG+QDEKLAE
Sbjct: 264 MLAVGFEEAVESILENLPTKRQSMLFSATMPTWVKKLARKYLDNPLNIDLVGDQDEKLAE 323

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAI+TT+TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLAL++ IA+EALHGD
Sbjct: 324 GIKLYAIATTSTSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALSNSIATEALHGD 383

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLN FRQGKFTVLVATDVA+RGLDIPNVDL+IHYELPNDPETFVHRSGRTGR
Sbjct: 384 ISQHQRERTLNAFRQGKFTVLVATDVASRGLDIPNVDLVIHYELPNDPETFVHRSGRTGR 443

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGKEG+AILM TSSQ+RTVRSLERDVGC FEF+SPP V D+LESSA+QVVATLNGVHP+S
Sbjct: 444 AGKEGSAILMHTSSQKRTVRSLERDVGCHFEFISPPTVGDLLESSADQVVATLNGVHPDS 503

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           ++FF+ TAQ+L EEKGTDALAAALA LSGFS+PPSSRSL++HE+GWVTLQL RD   +RG
Sbjct: 504 IKFFSATAQKLYEEKGTDALAAALAHLSGFSQPPSSRSLLSHEKGWVTLQLIRDPTNARG 563

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           F+SARSV GFLSD+Y TAADE+GKI +IADDR+
Sbjct: 564 FLSARSVTGFLSDLYRTAADEVGKIFLIADDRI 596

Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q0DM51|RH3_ORYSJ DEAD-box ATP-dependent RNA helicase 3, chloroplastic OS=Oryza sativa subsp. japonica GN=Os03g0827700 PE=2 SV=2

 Score =  570 bits (1469), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 275/333 (82%), Positives = 303/333 (90%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           MLAVGFEEDVE IL+ LP +RQSMLFSATMP WVKKLSR+YL+NPL IDLVG+QDEKLAE
Sbjct: 264 MLAVGFEEDVETILQQLPAERQSMLFSATMPGWVKKLSRRYLNNPLTIDLVGDQDEKLAE 323

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAI  T+TSKRT+LSDLITVYAKGGKTIVFT+TKRDADEVSLALT+ IASEALHGD
Sbjct: 324 GIKLYAIPLTSTSKRTVLSDLITVYAKGGKTIVFTKTKRDADEVSLALTNSIASEALHGD 383

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR
Sbjct: 384 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 443

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGK GTAILMFT+SQRRTVRSLERDVGC+F+F+SPP +EDVLESSAE V+ATL GVH ES
Sbjct: 444 AGKAGTAILMFTNSQRRTVRSLERDVGCRFDFISPPAIEDVLESSAEHVIATLRGVHTES 503

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           +++F P A+RL EE G +ALA+ALA LSGFS+PPSSRSLI+HEQGWVTLQLTRD  + RG
Sbjct: 504 IQYFIPAAERLQEELGPNALASALAHLSGFSQPPSSRSLISHEQGWVTLQLTRDPGYGRG 563

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           F S RSV GFLSDV   AADE+GKI + AD++V
Sbjct: 564 FFSPRSVTGFLSDVSSAAADEVGKIFLTADEKV 596

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0D8N0|RH53_ORYSJ DEAD-box ATP-dependent RNA helicase 53 OS=Oryza sativa subsp. japonica GN=Os07g0143700 PE=2 SV=2

 Score =  302 bits (773), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 144/225 (64%), Positives = 182/225 (80%), Gaps = 2/225 (0%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           MLAVGF+EDVE+I+ENLP  RQSMLFSATMPSW++K++ KYL +P+ IDLVG++D+KL E
Sbjct: 241 MLAVGFDEDVEVIMENLPQNRQSMLFSATMPSWIRKITSKYLKDPIIIDLVGDEDQKLPE 300

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GI LY+I++    K +IL  LI  +A GGK IVFTQTKR+AD ++ A+    A +ALHGD
Sbjct: 301 GISLYSIASEHYGKPSILGPLIKEHANGGKCIVFTQTKREADRLAYAMGRSYACQALHGD 360

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQ+QRERTL+GFR G+F +LVATDVAARGLDIPNVDL+IHYELPN  E FVHRSGRT R
Sbjct: 361 ISQNQRERTLSGFRDGRFNILVATDVAARGLDIPNVDLVIHYELPNTSELFVHRSGRTAR 420

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESS 225
           AGK+G+AIL++T+ Q R VR +E+D+GCKF  +  P +E   E+S
Sbjct: 421 AGKKGSAILIYTNDQARAVRIIEQDIGCKFTEL--PKIEVADEAS 463

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9LUW5|RH53_ARATH DEAD-box ATP-dependent RNA helicase 53 OS=Arabidopsis thaliana GN=RH53 PE=2 SV=1

 Score =  301 bits (770), Expect = 8e-81,   Method: Compositional matrix adjust.
 Identities = 141/219 (64%), Positives = 174/219 (79%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML VGF EDVE+ILE LP KRQSM+FSATMPSW++ L++KYL+NPL +DLVG+ D+KLA+
Sbjct: 262 MLQVGFAEDVEIILEKLPEKRQSMMFSATMPSWIRSLTKKYLNNPLTVDLVGDSDQKLAD 321

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GI  Y+I   +  + +I+  L+T +AKGGK IVFTQTKRDAD +S AL      EALHGD
Sbjct: 322 GITTYSIIADSYGRASIIGPLVTEHAKGGKCIVFTQTKRDADRLSYALARSFKCEALHGD 381

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQ QRERTL GFR G F +LVATDVAARGLD+PNVDLIIHYELPN+ ETFVHR+GRTGR
Sbjct: 382 ISQSQRERTLAGFRDGHFNILVATDVAARGLDVPNVDLIIHYELPNNTETFVHRTGRTGR 441

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE 219
           AGK+G+AIL+++  Q R V+ +ER+VG +F  +    VE
Sbjct: 442 AGKKGSAILIYSQDQSRAVKIIEREVGSRFTELPSIAVE 480

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0ILZ4|RH9_ORYSJ DEAD-box ATP-dependent RNA helicase 9 OS=Oryza sativa subsp. japonica GN=Os12g0611200 PE=2 SV=1

 Score =  297 bits (761), Expect = 8e-80,   Method: Compositional matrix adjust.
 Identities = 134/210 (63%), Positives = 170/210 (80%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+VGF+EDVE IL+ +PPKRQ+++FSATMP+W+++L++KYL NP+ IDLVG  D+KLAE
Sbjct: 255 MLSVGFDEDVETILDRVPPKRQTLMFSATMPTWIQRLTQKYLKNPVTIDLVGEDDQKLAE 314

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GI LY+I++   +K  +L +LI  +AKGGK IVFTQTKRDAD +S  +      +ALHGD
Sbjct: 315 GISLYSIASEGHAKPAVLGELIKEHAKGGKCIVFTQTKRDADRLSYTMGRSFQCQALHGD 374

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           I+Q QRERTL GFR+G F +L+ATDVAARGLDIPNVDL+IH+ELPN  E FVHRSGRTGR
Sbjct: 375 ITQAQRERTLKGFREGHFNILIATDVAARGLDIPNVDLVIHFELPNSSELFVHRSGRTGR 434

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKF 210
           AGK+G AI+M +  Q R +R +E DVGCKF
Sbjct: 435 AGKKGKAIVMHSYQQSRAIRMVENDVGCKF 464

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9LUW6|RH9_ARATH DEAD-box ATP-dependent RNA helicase 9 OS=Arabidopsis thaliana GN=RH9 PE=2 SV=1

 Score =  295 bits (754), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 135/219 (61%), Positives = 172/219 (78%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML VGF EDVE+IL+ LP KRQSM+FSATMPSW++ L++KYL+NPL IDLVG+ D+KLA+
Sbjct: 274 MLQVGFAEDVEIILQKLPAKRQSMMFSATMPSWIRSLTKKYLNNPLTIDLVGDSDQKLAD 333

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GI +Y+I+  +  + +I+  L+  + KGGK IVFTQTKRDAD ++  L      EALHGD
Sbjct: 334 GITMYSIAADSYGRASIIGPLVKEHGKGGKCIVFTQTKRDADRLAFGLAKSYKCEALHGD 393

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQ QRERTL GFR G F++LVATDVAARGLD+PNVDL+IHYELPN+ ETFVHR+GRTGR
Sbjct: 394 ISQAQRERTLAGFRDGNFSILVATDVAARGLDVPNVDLVIHYELPNNTETFVHRTGRTGR 453

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE 219
           AGK+G+AIL+    Q R V+ +E++VG +F  +    VE
Sbjct: 454 AGKKGSAILIHGQDQTRAVKMIEKEVGSRFNELPSIAVE 492

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q650T9|RH7_ORYSJ DEAD-box ATP-dependent RNA helicase 7 OS=Oryza sativa subsp. japonica GN=Os09g0520700 PE=2 SV=1

 Score =  225 bits (574), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 130/309 (42%), Positives = 188/309 (60%), Gaps = 11/309 (3%)

Query: 1   MLAVGFEEDVELILENLP--PKRQSMLFSATMPSWVKKLSRKYLDN-PLNIDLVGNQDEK 57
           ML +GF +DVELIL  +    K Q++LFSAT+P WVKKLS ++L +    +DLVG++  K
Sbjct: 279 MLNMGFVDDVELILGKVEDVTKVQTLLFSATIPEWVKKLSLRFLKSGKKTVDLVGDEKLK 338

Query: 58  LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL 117
            +  ++  A+     ++  ++ D+I  Y++GG+TI+FT+TK  A ++S     I  S AL
Sbjct: 339 ASASVRHLALPCNRAARAQVIPDIIRCYSRGGRTIIFTETKESASDLS---GLIAGSRAL 395

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           HGD++Q QRE  L GFR GKF VLVAT+VAARGLDI +V LII  E P D E ++HRSGR
Sbjct: 396 HGDVAQAQREVILAGFRSGKFLVLVATNVAARGLDINDVQLIIQCEPPRDVEAYIHRSGR 455

Query: 178 TGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVH 237
           TGRAG  G A+++F    +  V  +ER+ G KFE +S P   DV +S+  +    ++ V 
Sbjct: 456 TGRAGNTGVAVMLFEPRYKFNVNRIERESGVKFEHISAPQPTDVAQSAGTEAAEAISSVS 515

Query: 238 PESVEFFTPTAQRLIEEKG---TDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL-TR 293
              +  F   A++L+   G    D LA ALA+  G++     RSL++      TL L T 
Sbjct: 516 DSVIPVFREQAEQLLNSSGMSAVDLLAKALAKAVGYTD-IKKRSLLSSMDNHTTLLLQTG 574

Query: 294 DSAFSRGFM 302
            S ++ GF+
Sbjct: 575 RSVYAAGFV 583

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q41382|RH7_SPIOL DEAD-box ATP-dependent RNA helicase 7 OS=Spinacia oleracea GN=RH7 PE=2 SV=1

 Score =  220 bits (561), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 134/336 (39%), Positives = 197/336 (58%), Gaps = 14/336 (4%)

Query: 1   MLAVGFEEDVELILENLP--PKRQSMLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQDEK 57
           ML +GF +DVELIL  +    K Q++LFSAT+PSWVK++S ++L +    +DLV +Q  K
Sbjct: 271 MLKMGFVDDVELILGKVDHVSKVQTLLFSATLPSWVKQISTRFLKSAKKTVDLVSDQKMK 330

Query: 58  LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL 117
            +  ++   I  +A+++  ++ D+I  Y  GG++I+FT+TK  A +++  LT    +  L
Sbjct: 331 ASISVRHIVIPCSASARPDLIPDIIRCYGSGGRSIIFTETKESASQLAGLLT---GARPL 387

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           HGDI Q QRE TL GFR GKF  LVAT+VAARGLDI +V LII  E P D E ++HRSGR
Sbjct: 388 HGDIQQTQREVTLKGFRTGKFMTLVATNVAARGLDINDVQLIIQCEPPRDVEDYIHRSGR 447

Query: 178 TGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVH 237
           TGRAG  G A++++   +R +V  +ER+ G KFE +S P   DV ++   +  A +  + 
Sbjct: 448 TGRAGNTGVAVMLY-DPKRSSVTKIERESGVKFEHLSAPQPVDVAKAVGIEAAAAILQIS 506

Query: 238 PESVEFFTPTAQRLIEEKG---TDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRD 294
              +  F   A+ L+   G    D L+ ALA+ +G+S     RSL+   +G+VTL L   
Sbjct: 507 DSVIPAFKDAAEELLSTSGLSAVDILSKALAKAAGYSD-IKERSLLTGMEGYVTLLLDAG 565

Query: 295 SAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIAD 330
             F     +   +  FL     T AD I  + + AD
Sbjct: 566 RPFYGQSFAYTVLKRFLP---ATKADSIMGVALTAD 598

Spinacia oleracea (taxid: 3562)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9BQ39|DDX50_HUMAN ATP-dependent RNA helicase DDX50 OS=Homo sapiens GN=DDX50 PE=1 SV=1

 Score =  219 bits (558), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 131/302 (43%), Positives = 190/302 (62%), Gaps = 15/302 (4%)

Query: 1   MLAVGFEEDVELIL--------ENLPPKRQSMLFSATMPSWVKKLSRKYLDNPL-NIDLV 51
           ML +GF E VE I+        E+ P   Q++LFSAT P WV K+++KY+ +    +DLV
Sbjct: 295 MLDLGFAEQVEDIIHESYKTDSEDNP---QTLLFSATCPQWVYKVAKKYMKSRYEQVDLV 351

Query: 52  GNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALTS 110
           G   +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++    
Sbjct: 352 GKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHI 411

Query: 111 IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 170
              ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E+
Sbjct: 412 KQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVES 471

Query: 171 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 230
           ++HRSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   +
Sbjct: 472 YIHRSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAI 531

Query: 231 ATLNGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVTL 289
            +L  V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT+
Sbjct: 532 RSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGAS-SFEPRSLITSDKGFVTM 590

Query: 290 QL 291
            L
Sbjct: 591 TL 592

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q39189|RH7_ARATH DEAD-box ATP-dependent RNA helicase 7 OS=Arabidopsis thaliana GN=RH7 PE=1 SV=2

 Score =  218 bits (556), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 133/322 (41%), Positives = 186/322 (57%), Gaps = 15/322 (4%)

Query: 1   MLAVGFEEDVELILENL--PPKRQSMLFSATMPSWVKKLSRKYLD-NPLNIDLVGNQDEK 57
           ML +GF EDVELIL  +    K Q++LFSAT+PSWVK +S ++L  +   IDLVGN   K
Sbjct: 260 MLRMGFVEDVELILGKVEDSTKVQTLLFSATLPSWVKNISNRFLKRDQKTIDLVGNDKMK 319

Query: 58  LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL 117
            +  ++  AI     +   ++ D+I+ Y+ GG+TI+F +TK    E+S  L     S AL
Sbjct: 320 ASNSVRHIAIPCNKAAMARLIPDIISCYSSGGQTIIFAETKVQVSELSGLLD---GSRAL 376

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           HG+I Q QRE TL GFR GKF  LVAT+VAARGLDI +V LII  E P + E ++HRSGR
Sbjct: 377 HGEIPQSQREVTLAGFRNGKFATLVATNVAARGLDINDVQLIIQCEPPREVEAYIHRSGR 436

Query: 178 TGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVH 237
           TGRAG  G A+ ++  S++ +V  +E++ G KFE ++ P  +++  S   +    +  V 
Sbjct: 437 TGRAGNTGVAVTLY-DSRKSSVSRIEKEAGIKFEHLAAPQPDEIARSGGMEAAEKVKQVC 495

Query: 238 PESVEFFTPTAQRLIEEKGTDA---LAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRD 294
              V  F   A+ L+E  G  A   LA ALA+ +GF+     RSL+   + +VTL L   
Sbjct: 496 DSVVPAFLEAAKELLETSGLSAEVLLAKALAKTAGFTE-IKKRSLLTSMENYVTLHLEA- 553

Query: 295 SAFSRGFMSARSVMGFLSDVYP 316
               +   S   V G L  V P
Sbjct: 554 ---GKPIYSPSFVYGLLRRVLP 572

Arabidopsis thaliana (taxid: 3702)

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	379
225450401	764	PREDICTED: DEAD-box ATP-dependent RNA he	0.878	0.435	0.900	1e-172
224124522	775	predicted protein [Populus trichocarpa]	0.878	0.429	0.876	1e-169
118489724	481	unknown [Populus trichocarpa x Populus d	0.878	0.692	0.879	1e-169
224124506	735	predicted protein [Populus trichocarpa]	0.878	0.453	0.879	1e-168
255543078	772	dead box ATP-dependent RNA helicase, put	0.878	0.431	0.870	1e-167
343172314	782	DEAD-box ATP-dependent RNA helicase, par	0.878	0.425	0.834	1e-167
343172316	782	DEAD-box ATP-dependent RNA helicase, par	0.878	0.425	0.831	1e-165
356505715	771	PREDICTED: DEAD-box ATP-dependent RNA he	0.875	0.430	0.873	1e-165
356572874	771	PREDICTED: DEAD-box ATP-dependent RNA he	0.875	0.430	0.870	1e-163
357511641	753	DEAD-box ATP-dependent RNA helicase [Med	0.878	0.442	0.876	1e-163

>gi|225450401|ref|XP_002278318.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 3, chloroplastic [Vitis vinifera] gi|296089875|emb|CBI39694.3| unnamed protein product [Vitis vinifera]

 Score =  610 bits (1573), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 300/333 (90%), Positives = 321/333 (96%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           MLAVGFEEDVE+ILE LP +RQSMLFSATMP+WVKKL+RKYLDNPL IDLVG+ DEKLAE
Sbjct: 278 MLAVGFEEDVEVILEKLPSERQSMLFSATMPAWVKKLARKYLDNPLTIDLVGDHDEKLAE 337

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAI TTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS+ALT+ IASEALHGD
Sbjct: 338 GIKLYAIPTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSMALTNSIASEALHGD 397

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR
Sbjct: 398 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 457

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGKEGTAILMFTSSQRRTV+SLERDVGCKFEF+SPP +E+VLESSAEQVVATLNGVHPES
Sbjct: 458 AGKEGTAILMFTSSQRRTVKSLERDVGCKFEFISPPAIEEVLESSAEQVVATLNGVHPES 517

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           VEFFTPTAQ+LIEEKGT ALAAALA LSGFS+PPS RSLI+HEQGWVTLQLTRDS +SRG
Sbjct: 518 VEFFTPTAQKLIEEKGTGALAAALAHLSGFSQPPSFRSLISHEQGWVTLQLTRDSGYSRG 577

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           F+SARSV GFLSDVYPTAADE+GKI+++AD+RV
Sbjct: 578 FLSARSVTGFLSDVYPTAADELGKIYLVADERV 610

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124522|ref|XP_002330044.1| predicted protein [Populus trichocarpa] gi|222871469|gb|EEF08600.1| predicted protein [Populus trichocarpa]

 Score =  599 bits (1545), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 292/333 (87%), Positives = 317/333 (95%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GFEEDVE+ILENLP KRQSMLFSATMP+WVKKL+RKYLDNPL IDLVG+Q+EKLAE
Sbjct: 295 MLSFGFEEDVEVILENLPSKRQSMLFSATMPTWVKKLARKYLDNPLQIDLVGDQEEKLAE 354

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYA+S TA SKRTILSDL+TVYAKGGKTI+FTQTKRDADEVS+ALT+ IASEALHGD
Sbjct: 355 GIKLYALSATAASKRTILSDLVTVYAKGGKTIIFTQTKRDADEVSMALTNTIASEALHGD 414

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDLIIHYELPND ETFVHRSGRTGR
Sbjct: 415 ISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLIIHYELPNDAETFVHRSGRTGR 474

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGKEGTAILMFTSSQRRTVRSLERD GCKFEFVSPP +E+VLESSAEQVVATL+GVHPES
Sbjct: 475 AGKEGTAILMFTSSQRRTVRSLERDAGCKFEFVSPPAIEEVLESSAEQVVATLSGVHPES 534

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           VEFFTPTAQ+LIEE+GT+ALAAALA LSGFS+PPSSRSLI+H QGW TLQLTRD  +SRG
Sbjct: 535 VEFFTPTAQKLIEEQGTNALAAALAHLSGFSQPPSSRSLISHAQGWATLQLTRDPTYSRG 594

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           F+SARSV GFLSDVYP AADE+GKIH+IAD+RV
Sbjct: 595 FLSARSVTGFLSDVYPAAADEVGKIHVIADERV 627

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489724|gb|ABK96663.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  599 bits (1544), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 293/333 (87%), Positives = 318/333 (95%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GFEEDVE+ILENLP KRQSMLFSATMP+WVKKL+RKYLDNPL IDLVG+Q+EKLAE
Sbjct: 1   MLSFGFEEDVEVILENLPSKRQSMLFSATMPTWVKKLARKYLDNPLQIDLVGDQEEKLAE 60

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYA+S TA SKRTILSDL+TVYAKGGKTI+FTQTKRDADEVS+ALT+ IASEALHGD
Sbjct: 61  GIKLYALSATAASKRTILSDLVTVYAKGGKTIIFTQTKRDADEVSMALTNTIASEALHGD 120

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDLIIHYELPND ETFVHRSGRTGR
Sbjct: 121 ISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLIIHYELPNDAETFVHRSGRTGR 180

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGKEGTAILMFTSSQRRTVRSLERD GCKFEFVSPP +E+VLESSAEQVVATL+GVHPES
Sbjct: 181 AGKEGTAILMFTSSQRRTVRSLERDAGCKFEFVSPPAIEEVLESSAEQVVATLSGVHPES 240

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           VEFFTPTAQ+LIEE+GT+ALAAALA LSGFS+PPSSRSLI+HEQGW TLQLTRD  +SRG
Sbjct: 241 VEFFTPTAQKLIEEQGTNALAAALAHLSGFSQPPSSRSLISHEQGWATLQLTRDPTYSRG 300

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           F+SARSV GFLSDVYP AADE+GKIH+IAD+RV
Sbjct: 301 FLSARSVTGFLSDVYPAAADEVGKIHVIADERV 333

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124506|ref|XP_002330040.1| predicted protein [Populus trichocarpa] gi|222871465|gb|EEF08596.1| predicted protein [Populus trichocarpa]

 Score =  597 bits (1539), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 293/333 (87%), Positives = 317/333 (95%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GFEEDVE+ILE+LP KRQSMLFSATMP+WVKKL+RKYLDNPL IDLVG+++EKLAE
Sbjct: 258 MLSFGFEEDVEVILESLPSKRQSMLFSATMPTWVKKLARKYLDNPLQIDLVGDREEKLAE 317

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAISTTATSKRTILSDL+TVYAKG KTI+FT+TKRDADEVS+ALT  IASEALHGD
Sbjct: 318 GIKLYAISTTATSKRTILSDLVTVYAKGEKTIIFTRTKRDADEVSMALTQSIASEALHGD 377

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDLIIHYELPNDPETFVHRSGRTGR
Sbjct: 378 ISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 437

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGKEGTAILMFT+SQRRTVRSLERD GCKFEFVSPP +E++LESS EQVVATLNGVHPES
Sbjct: 438 AGKEGTAILMFTNSQRRTVRSLERDAGCKFEFVSPPAIEELLESSTEQVVATLNGVHPES 497

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           VEFFTPTAQ+LIEE+GT ALAAALA LSGFSRPPSSRSLI+HEQGW TLQLTRD  +SRG
Sbjct: 498 VEFFTPTAQKLIEEQGTSALAAALAHLSGFSRPPSSRSLISHEQGWTTLQLTRDPTYSRG 557

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           F+SARSV GFLSDVYP AADEIGKIH+IAD+RV
Sbjct: 558 FLSARSVTGFLSDVYPAAADEIGKIHLIADERV 590

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255543078|ref|XP_002512602.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223548563|gb|EEF50054.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  593 bits (1530), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 290/333 (87%), Positives = 318/333 (95%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GFEEDVE+ILENLP KRQSMLFSATMP+WVKKL+RKYLDNPL IDLVG+Q+EKLAE
Sbjct: 280 MLSFGFEEDVEVILENLPSKRQSMLFSATMPTWVKKLARKYLDNPLQIDLVGDQEEKLAE 339

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAIST ATSKR+ILSDL+TVYAKGGKTI+FTQTKRDADEVS+ LT+ IASEALHGD
Sbjct: 340 GIKLYAISTNATSKRSILSDLVTVYAKGGKTIIFTQTKRDADEVSMVLTNSIASEALHGD 399

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDL+IHYELPNDPETFVHRSGRTGR
Sbjct: 400 ISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLVIHYELPNDPETFVHRSGRTGR 459

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGKEGTA+LMFTSSQRRTV+SLERDVGC+FEFVSPP  E+VLESSAEQV+ATL+GVHPES
Sbjct: 460 AGKEGTAVLMFTSSQRRTVKSLERDVGCRFEFVSPPGTEEVLESSAEQVIATLSGVHPES 519

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           V FFTPTAQRLIEE+GT ALAAALAQLSGFS+PPSSRSLI+HEQGW TLQLTRD ++SRG
Sbjct: 520 VGFFTPTAQRLIEEQGTSALAAALAQLSGFSQPPSSRSLISHEQGWTTLQLTRDPSYSRG 579

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           F+SARSV GFLSDVY  AADE+GKIHIIAD++V
Sbjct: 580 FLSARSVTGFLSDVYTAAADEVGKIHIIADEKV 612

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|343172314|gb|AEL98861.1| DEAD-box ATP-dependent RNA helicase, partial [Silene latifolia]

 Score =  592 bits (1527), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 278/333 (83%), Positives = 318/333 (95%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           MLAVGFEEDVE+ILE LP +RQSMLFSATMP+W+KKLSRKYLDNPL IDLVG+++EKLAE
Sbjct: 287 MLAVGFEEDVEVILETLPKERQSMLFSATMPTWIKKLSRKYLDNPLTIDLVGDREEKLAE 346

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAIS+TA SKRT+LSD+ITVYAKGGKTIVFTQTKRDADEVSLAL++ I SEALHGD
Sbjct: 347 GIKLYAISSTAASKRTMLSDVITVYAKGGKTIVFTQTKRDADEVSLALSNSIPSEALHGD 406

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKF+VLVATDVA+RGLDIPNVDL++HYE+PNDPETFVHRSGRTGR
Sbjct: 407 ISQHQRERTLNGFRQGKFSVLVATDVASRGLDIPNVDLVVHYEMPNDPETFVHRSGRTGR 466

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGKEGTA+LM+TS+QRRTVRSLERDVGC FE+V  P VE+VLESSA+QVVATL GVHP+S
Sbjct: 467 AGKEGTALLMYTSNQRRTVRSLERDVGCHFEYVGAPSVEEVLESSADQVVATLRGVHPDS 526

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           ++FFTPTAQ+L+EE+GT ALAAA+A LSGFS+PPS++SL++HEQGWVTLQL+RDS FSRG
Sbjct: 527 IKFFTPTAQKLLEEQGTGALAAAIAHLSGFSQPPSAKSLLSHEQGWVTLQLSRDSVFSRG 586

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           +MSARSVMGFLSDVYPTAADE+GKI +IAD+RV
Sbjct: 587 YMSARSVMGFLSDVYPTAADEVGKIQLIADERV 619

Source: Silene latifolia

Species: Silene latifolia

Genus: Silene

Family: Caryophyllaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|343172316|gb|AEL98862.1| DEAD-box ATP-dependent RNA helicase, partial [Silene latifolia]

 Score =  587 bits (1513), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 277/333 (83%), Positives = 316/333 (94%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           MLAVGFEEDVE+ILE LP +RQSMLFSATMP+W+KKLSRKYLDNPL IDLVG+++EKLAE
Sbjct: 287 MLAVGFEEDVEVILEKLPKERQSMLFSATMPTWIKKLSRKYLDNPLTIDLVGDREEKLAE 346

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAIS+TA SKRT+LSD+ITVYAKGGKTIVFTQTKRDADEVSLAL++ I SEALHGD
Sbjct: 347 GIKLYAISSTAASKRTMLSDVITVYAKGGKTIVFTQTKRDADEVSLALSNSIPSEALHGD 406

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKF+VLVATDVA+RGLDIPNVDL++HYE+PNDPETFVHRSGRTGR
Sbjct: 407 ISQHQRERTLNGFRQGKFSVLVATDVASRGLDIPNVDLVVHYEMPNDPETFVHRSGRTGR 466

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGKEGTA+LM+TS+QRRTVRSLERDVGC F +V  P VE+VL SSA+QVVATL GVHPES
Sbjct: 467 AGKEGTALLMYTSNQRRTVRSLERDVGCHFGYVGAPSVEEVLVSSADQVVATLRGVHPES 526

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           ++FFTPTAQ+L+EE+GT ALAAA+A LSGFS+PPS++SL++HEQGWVTLQL+RDS FSRG
Sbjct: 527 IKFFTPTAQKLLEEQGTGALAAAIAHLSGFSQPPSAKSLLSHEQGWVTLQLSRDSVFSRG 586

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           +MSARSVMGFLSDVYPTAADE+GKI +IAD+RV
Sbjct: 587 YMSARSVMGFLSDVYPTAADEVGKIQLIADERV 619

Source: Silene latifolia

Species: Silene latifolia

Genus: Silene

Family: Caryophyllaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505715|ref|XP_003521635.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 3, chloroplastic-like [Glycine max]

 Score =  586 bits (1510), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 291/333 (87%), Positives = 316/333 (94%), Gaps = 1/333 (0%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           MLAVGFEEDVE+ILENLP +RQSMLFSATMPSWVKKL+RKYL+NPL IDLVG+++EKLAE
Sbjct: 272 MLAVGFEEDVEMILENLPAQRQSMLFSATMPSWVKKLARKYLNNPLTIDLVGDEEEKLAE 331

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAI+ TATSKRTILSDL+TVYAKGGKTIVFTQTKRDADEVSL+LT+ I SEALHGD
Sbjct: 332 GIKLYAIAATATSKRTILSDLVTVYAKGGKTIVFTQTKRDADEVSLSLTNSIMSEALHGD 391

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR
Sbjct: 392 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 451

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGK+G AIL++TSSQRRTVRSLERDVGCKFEFVS P +E+VLESSAEQVVATL GVHPES
Sbjct: 452 AGKQGNAILLYTSSQRRTVRSLERDVGCKFEFVSAPAMEEVLESSAEQVVATLGGVHPES 511

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           V+FFTPTAQRLIEE+GT ALAAALAQLSGFSRPPSSRSLI HEQGW+TLQLTRDS  SR 
Sbjct: 512 VQFFTPTAQRLIEEQGTSALAAALAQLSGFSRPPSSRSLITHEQGWITLQLTRDSD-SRR 570

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           + SARS+ GFLSDVYP AADE+GKIH+IAD++V
Sbjct: 571 YFSARSITGFLSDVYPAAADEVGKIHLIADEKV 603

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572874|ref|XP_003554590.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 3, chloroplastic-like [Glycine max]

 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 290/333 (87%), Positives = 315/333 (94%), Gaps = 1/333 (0%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           MLAVGFEEDVE+ILENLP +RQSMLFSATMPSWVKKL+RKYL+NPL IDLVG+++EKLAE
Sbjct: 271 MLAVGFEEDVEMILENLPSQRQSMLFSATMPSWVKKLARKYLNNPLTIDLVGDEEEKLAE 330

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAI+ TATSKRTILSDL+TVYAKGGKTIVFTQTKRDADEVSL+LT+ I SEALHGD
Sbjct: 331 GIKLYAIAATATSKRTILSDLVTVYAKGGKTIVFTQTKRDADEVSLSLTNSIMSEALHGD 390

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR
Sbjct: 391 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 450

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGK+G AIL++TSSQRRTVRSLERDVGCKFEFVS P +E+VLE+SAEQVVATL GVHPES
Sbjct: 451 AGKQGNAILLYTSSQRRTVRSLERDVGCKFEFVSSPAMEEVLEASAEQVVATLCGVHPES 510

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           V+FFTPTAQ+LIEE+GT ALAAALAQLSGFSRPPSSRSLI HEQGW+TLQLTRDS  SR 
Sbjct: 511 VQFFTPTAQKLIEEQGTSALAAALAQLSGFSRPPSSRSLITHEQGWITLQLTRDSD-SRR 569

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           + SARSV GFLSDVY  AADE+GKIH+IAD+RV
Sbjct: 570 YFSARSVTGFLSDVYSAAADEVGKIHLIADERV 602

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357511641|ref|XP_003626109.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula] gi|87240993|gb|ABD32851.1| Helicase, C-terminal; Zinc finger, CCHC-type; GUCT [Medicago truncatula] gi|355501124|gb|AES82327.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula]

 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 292/333 (87%), Positives = 312/333 (93%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           MLAVGFEEDVE+ILE LP KRQSMLFSATMPSWVKKL+RKYL+NPL IDLVG+++EKLAE
Sbjct: 268 MLAVGFEEDVEVILEKLPAKRQSMLFSATMPSWVKKLARKYLNNPLTIDLVGDEEEKLAE 327

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           GIKLYAIS T+TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT+ I SEALHGD
Sbjct: 328 GIKLYAISATSTSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTNSITSEALHGD 387

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           ISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDLIIHYELPNDPETFVHRSGRTGR
Sbjct: 388 ISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 447

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AGK GTAILMFT SQRRTVRSLERDVGCKFEFV+ P VEDVLESSAEQVV TLNGVHPES
Sbjct: 448 AGKLGTAILMFTGSQRRTVRSLERDVGCKFEFVNAPSVEDVLESSAEQVVVTLNGVHPES 507

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
           + FFTPTAQ+LIEEKGT ALAAALAQ+SGFS+PPSSRSLI HEQGWVTLQLTRDS  S+ 
Sbjct: 508 IAFFTPTAQKLIEEKGTTALAAALAQMSGFSQPPSSRSLITHEQGWVTLQLTRDSENSQR 567

Query: 301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
           + SARSV GFLSDVY  AADE+GK+H+IAD+RV
Sbjct: 568 YFSARSVTGFLSDVYSKAADEVGKVHLIADERV 600

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

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	379
TAIR|locus:504955106	748	emb1138 "embryo defective 1138	0.878	0.445	0.852	3e-149
TAIR|locus:2087852	616	PMH2 "putative mitochondrial R	0.577	0.355	0.643	9.6e-73
TAIR|locus:2087832	610	PMH1 "putative mitochondrial R	0.620	0.385	0.595	4.8e-71
ZFIN|ZDB-GENE-031113-10	759	ddx21 "DEAD (Asp-Glu-Ala-Asp)	0.765	0.382	0.441	1.4e-57
UNIPROTKB|E1BW15	693	DDX50 "Uncharacterized protein	0.765	0.418	0.424	2e-56
UNIPROTKB|F1MMK3	737	DDX50 "Uncharacterized protein	0.765	0.393	0.434	3.3e-56
UNIPROTKB|E2QTT0	738	DDX50 "Uncharacterized protein	0.765	0.392	0.431	5.3e-56
UNIPROTKB|E2RPT4	687	DDX50 "Uncharacterized protein	0.765	0.422	0.431	5.3e-56
UNIPROTKB|Q9BQ39	737	DDX50 "ATP-dependent RNA helic	0.765	0.393	0.431	5.3e-56
UNIPROTKB|F1SUG8	737	DDX50 "Uncharacterized protein	0.765	0.393	0.431	5.3e-56

TAIR|locus:504955106 emb1138 "embryo defective 1138" [Arabidopsis thaliana (taxid:3702)]

 Score = 1457 (517.9 bits), Expect = 3.0e-149, P = 3.0e-149
 Identities = 284/333 (85%), Positives = 314/333 (94%)

Query:     1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
             MLAVGFEE VE ILENLP KRQSMLFSATMP+WVKKL+RKYLDNPLNIDLVG+QDEKLAE
Sbjct:   264 MLAVGFEEAVESILENLPTKRQSMLFSATMPTWVKKLARKYLDNPLNIDLVGDQDEKLAE 323

Query:    61 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
             GIKLYAI+TT+TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLAL++ IA+EALHGD
Sbjct:   324 GIKLYAIATTSTSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALSNSIATEALHGD 383

Query:   121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
             ISQHQRERTLN FRQGKFTVLVATDVA+RGLDIPNVDL+IHYELPNDPETFVHRSGRTGR
Sbjct:   384 ISQHQRERTLNAFRQGKFTVLVATDVASRGLDIPNVDLVIHYELPNDPETFVHRSGRTGR 443

Query:   181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
             AGKEG+AILM TSSQ+RTVRSLERDVGC FEF+SPP V D+LESSA+QVVATLNGVHP+S
Sbjct:   444 AGKEGSAILMHTSSQKRTVRSLERDVGCHFEFISPPTVGDLLESSADQVVATLNGVHPDS 503

Query:   241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
             ++FF+ TAQ+L EEKGTDALAAALA LSGFS+PPSSRSL++HE+GWVTLQL RD   +RG
Sbjct:   504 IKFFSATAQKLYEEKGTDALAAALAHLSGFSQPPSSRSLLSHEKGWVTLQLIRDPTNARG 563

Query:   301 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
             F+SARSV GFLSD+Y TAADE+GKI +IADDR+
Sbjct:   564 FLSARSVTGFLSDLYRTAADEVGKIFLIADDRI 596

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

TAIR|locus:2087852 PMH2 "putative mitochondrial RNA helicase 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 735 (263.8 bits), Expect = 9.6e-73, P = 9.6e-73
 Identities = 141/219 (64%), Positives = 174/219 (79%)

Query:     1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
             ML VGF EDVE+ILE LP KRQSM+FSATMPSW++ L++KYL+NPL +DLVG+ D+KLA+
Sbjct:   262 MLQVGFAEDVEIILEKLPEKRQSMMFSATMPSWIRSLTKKYLNNPLTVDLVGDSDQKLAD 321

Query:    61 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
             GI  Y+I   +  + +I+  L+T +AKGGK IVFTQTKRDAD +S AL      EALHGD
Sbjct:   322 GITTYSIIADSYGRASIIGPLVTEHAKGGKCIVFTQTKRDADRLSYALARSFKCEALHGD 381

Query:   121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
             ISQ QRERTL GFR G F +LVATDVAARGLD+PNVDLIIHYELPN+ ETFVHR+GRTGR
Sbjct:   382 ISQSQRERTLAGFRDGHFNILVATDVAARGLDVPNVDLIIHYELPNNTETFVHRTGRTGR 441

Query:   181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE 219
             AGK+G+AIL+++  Q R V+ +ER+VG +F  +    VE
Sbjct:   442 AGKKGSAILIYSQDQSRAVKIIEREVGSRFTELPSIAVE 480

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0000373 "Group II intron splicing" evidence=IMP

GO:0009409 "response to cold" evidence=IEP

GO:0043234 "protein complex" evidence=IDA

TAIR|locus:2087832 PMH1 "putative mitochondrial RNA helicase 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 719 (258.2 bits), Expect = 4.8e-71, P = 4.8e-71
 Identities = 140/235 (59%), Positives = 177/235 (75%)

Query:     1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
             ML VGF EDVE+IL+ LP KRQSM+FSATMPSW++ L++KYL+NPL IDLVG+ D+KLA+
Sbjct:   274 MLQVGFAEDVEIILQKLPAKRQSMMFSATMPSWIRSLTKKYLNNPLTIDLVGDSDQKLAD 333

Query:    61 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
             GI +Y+I+  +  + +I+  L+  + KGGK IVFTQTKRDAD ++  L      EALHGD
Sbjct:   334 GITMYSIAADSYGRASIIGPLVKEHGKGGKCIVFTQTKRDADRLAFGLAKSYKCEALHGD 393

Query:   121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
             ISQ QRERTL GFR G F++LVATDVAARGLD+PNVDL+IHYELPN+ ETFVHR+GRTGR
Sbjct:   394 ISQAQRERTLAGFRDGNFSILVATDVAARGLDVPNVDLVIHYELPNNTETFVHRTGRTGR 453

Query:   181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNG 235
             AGK+G+AIL+    Q R V+ +E++VG +F  +    VE    S  E V A   G
Sbjct:   454 AGKKGSAILIHGQDQTRAVKMIEKEVGSRFNELPSIAVERGSASMFEGVGARSGG 508

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0003677 "DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009651 "response to salt stress" evidence=IMP

GO:0043234 "protein complex" evidence=IDA

ZFIN|ZDB-GENE-031113-10 ddx21 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 21" [Danio rerio (taxid:7955)]

 Score = 592 (213.5 bits), Expect = 1.4e-57, P = 1.4e-57
 Identities = 133/301 (44%), Positives = 197/301 (65%)

Query:     1 MLAVGFEEDVELIL-----ENLPPKRQSMLFSATMPSWVKKLSRKYLDNP-LNIDLVGNQ 54
             ML +GF E VE IL     ++   K Q++LFSAT PSWV  +++KY+ +  +++DL+G +
Sbjct:   324 MLDMGFAEQVEEILSASYKKDAEQKPQTLLFSATCPSWVYDVAKKYMRSQFIHVDLIGKK 383

Query:    55 DEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALTSIIA 113
              +K A  ++  AI+   + + +++ D+I VY+   G+TIVF +TK++A E+SL  TSI  
Sbjct:   384 TQKAATTVEHLAIACHWSQRASVIGDVIQVYSGSHGRTIVFCETKKEATELSLN-TSIKQ 442

Query:   114 S-EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFV 172
             S ++LHGDI Q QRE TL GFR G F VLVAT+VAARGLDIP VDL+I    PND E+++
Sbjct:   443 SAQSLHGDIPQKQREVTLKGFRNGSFEVLVATNVAARGLDIPEVDLVIQSSPPNDVESYI 502

Query:   173 HRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVAT 232
             HRSGRTGRAG+ G  I  +   +   ++ +E+  G  F+ V  P   D+++SS++  V  
Sbjct:   503 HRSGRTGRAGRTGICICFYQRKEESQLKFVEQKAGITFKRVGVPTAYDIIQSSSKDAVRF 562

Query:   233 LNGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL 291
             L+ V   +V +F   AQ LI+++G  +ALAAALA +SG +     RSLIN E G+ ++ L
Sbjct:   563 LDSVPAVAVGYFREAAQELIQQRGAVEALAAALAHISG-ATSLEQRSLINSEPGFSSMIL 621

Query:   292 T 292
             +
Sbjct:   622 S 622

GO:0003677 "DNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|E1BW15 DDX50 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 581 (209.6 bits), Expect = 2.0e-56, P = 2.0e-56
 Identities = 127/299 (42%), Positives = 190/299 (63%)

Query:     1 MLAVGFEEDVELIL-----ENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQ 54
             ML +GF E VE IL     ++     Q++LFSAT P+WV  +++KY+ +    +DL+G +
Sbjct:   271 MLDMGFAEQVEDILRVAYKKDSEDNPQTLLFSATCPNWVYDVAKKYMKSKYEQVDLIGRK 330

Query:    55 DEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALTSIIA 113
              +K A  ++  AI    + +  ++ D+I VY+   G+TIVF +TK+DA+E++L  +    
Sbjct:   331 TQKAATTVEHLAIECHWSQRAAVIGDVIQVYSGSYGRTIVFCETKKDANELALNASIKQD 390

Query:   114 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH 173
              ++LHGDI Q QRE TL GFR G F VLVAT+VAARGLDIP VDL++    P D E+++H
Sbjct:   391 CQSLHGDIPQKQREITLKGFRNGAFKVLVATNVAARGLDIPEVDLVVQSSPPKDVESYIH 450

Query:   174 RSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL 233
             RSGRTGRAG+ G  I  +   +   +R +E   G  F+ V  P   D++++S++  +  L
Sbjct:   451 RSGRTGRAGRTGICICFYQRKEENQLRYVEVKAGITFKRVGVPTATDIIKASSKDAIRCL 510

Query:   234 NGVHPESVEFFTPTAQRLIEEKG-TDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL 291
             + V   ++E+F  +AQ LIEEKG  +ALAAALA +SG +     RSL+N + G+VT+ L
Sbjct:   511 DSVPQTAIEYFKESAQLLIEEKGPVNALAAALAHISG-ATSIEQRSLLNSDVGFVTMVL 568

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0043330 "response to exogenous dsRNA" evidence=IEA

UNIPROTKB|F1MMK3 DDX50 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 579 (208.9 bits), Expect = 3.3e-56, P = 3.3e-56
 Identities = 130/299 (43%), Positives = 188/299 (62%)

Query:     1 MLAVGFEEDVELILE-----NLPPKRQSMLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQ 54
             ML +GF E VE IL      +     Q++LFSAT P WV K+++KY+ +    +DLVG  
Sbjct:   295 MLDLGFAEQVEDILHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKM 354

Query:    55 DEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALTSIIA 113
              +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++       
Sbjct:   355 TQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQN 414

Query:   114 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH 173
             ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E+++H
Sbjct:   415 AQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIH 474

Query:   174 RSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL 233
             RSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   + +L
Sbjct:   475 RSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSL 534

Query:   234 NGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL 291
               V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT+ L
Sbjct:   535 ASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVTMTL 592

GO:0005886 "plasma membrane" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2QTT0 DDX50 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 129/299 (43%), Positives = 188/299 (62%)

Query:     1 MLAVGFEEDVELILE-----NLPPKRQSMLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQ 54
             ML +GF E VE I+      +     Q++LFSAT P WV K+++KY+ +    +DLVG  
Sbjct:   296 MLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKM 355

Query:    55 DEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALTSIIA 113
              +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++       
Sbjct:   356 TQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQN 415

Query:   114 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH 173
             ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E+++H
Sbjct:   416 AQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIH 475

Query:   174 RSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL 233
             RSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   + +L
Sbjct:   476 RSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSL 535

Query:   234 NGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL 291
               V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT+ L
Sbjct:   536 ASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVTMTL 593

GO:0005886 "plasma membrane" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2RPT4 DDX50 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 129/299 (43%), Positives = 188/299 (62%)

Query:     1 MLAVGFEEDVELILE-----NLPPKRQSMLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQ 54
             ML +GF E VE I+      +     Q++LFSAT P WV K+++KY+ +    +DLVG  
Sbjct:   297 MLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKM 356

Query:    55 DEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALTSIIA 113
              +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++       
Sbjct:   357 TQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQN 416

Query:   114 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH 173
             ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E+++H
Sbjct:   417 AQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIH 476

Query:   174 RSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL 233
             RSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   + +L
Sbjct:   477 RSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSL 536

Query:   234 NGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL 291
               V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT+ L
Sbjct:   537 ASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVTMTL 594

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|Q9BQ39 DDX50 "ATP-dependent RNA helicase DDX50" [Homo sapiens (taxid:9606)]

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 129/299 (43%), Positives = 188/299 (62%)

Query:     1 MLAVGFEEDVELILE-----NLPPKRQSMLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQ 54
             ML +GF E VE I+      +     Q++LFSAT P WV K+++KY+ +    +DLVG  
Sbjct:   295 MLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKM 354

Query:    55 DEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALTSIIA 113
              +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++       
Sbjct:   355 TQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQN 414

Query:   114 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH 173
             ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E+++H
Sbjct:   415 AQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIH 474

Query:   174 RSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL 233
             RSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   + +L
Sbjct:   475 RSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSL 534

Query:   234 NGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL 291
               V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT+ L
Sbjct:   535 ASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVTMTL 592

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

UNIPROTKB|F1SUG8 DDX50 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 129/299 (43%), Positives = 188/299 (62%)

Query:     1 MLAVGFEEDVELILE-----NLPPKRQSMLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQ 54
             ML +GF E VE I+      +     Q++LFSAT P WV K+++KY+ +    +DLVG  
Sbjct:   295 MLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKM 354

Query:    55 DEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALTSIIA 113
              +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++       
Sbjct:   355 TQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQN 414

Query:   114 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH 173
             ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E+++H
Sbjct:   415 AQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIH 474

Query:   174 RSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL 233
             RSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   + +L
Sbjct:   475 RSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSL 534

Query:   234 NGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL 291
               V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT+ L
Sbjct:   535 ASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVTMTL 592

GO:0005886 "plasma membrane" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003723 "RNA 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)
Q0DM51	RH3_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8258	0.8786	0.4393	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.824
3rd Layer	3.6.4	0.766

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00022481001	SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (762 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00000559001	SubName- Full=Chromosome chr8 scaffold_106, whole genome shotgun sequence; (169 aa)			•						0.499

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	379
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	8e-64
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-49
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-42
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	7e-41
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-40
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	3e-38
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	3e-35
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-34
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	6e-34
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-28
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	3e-28
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	4e-28
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	1e-25
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	9e-20
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	3e-15
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	1e-14
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	1e-13
cd00268	203	cd00268, DEADc, DEAD-box helicases	4e-13
pfam08152	97	pfam08152, GUCT, GUCT (NUC152) domain	1e-12
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	1e-12
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	5e-11
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	7e-10
cd12938	74	cd12938, GUCT_Hera, RNA-binding GUCT-like domain f	1e-09
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	1e-08
TIGR01587	358	TIGR01587, cas3_core, CRISPR-associated helicase C	6e-08
TIGR00631	655	TIGR00631, uvrb, excinuclease ABC, B subunit	1e-07
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	2e-07
TIGR00580	926	TIGR00580, mfd, transcription-repair coupling fact	3e-07
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	5e-07
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	9e-07
COG1197	1139	COG1197, Mfd, Transcription-repair coupling factor	1e-06
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	4e-06
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	7e-06
COG1205	851	COG1205, COG1205, Distinct helicase family with a	8e-06
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	1e-05
cd09639	353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	1e-05
PRK10689	1147	PRK10689, PRK10689, transcription-repair coupling	1e-05
COG1200	677	COG1200, RecG, RecG-like helicase [DNA replication	2e-05
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	6e-05
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	6e-04
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	7e-04
PRK05580	679	PRK05580, PRK05580, primosome assembly protein Pri	0.001
COG4098	441	COG4098, comFA, Superfamily II DNA/RNA helicase re	0.001
PRK05298	652	PRK05298, PRK05298, excinuclease ABC subunit B; Pr	0.001
PRK10917	681	PRK10917, PRK10917, ATP-dependent DNA helicase Rec	0.002
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	0.003

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

 Score =  211 bits (539), Expect = 8e-64
 Identities = 100/289 (34%), Positives = 157/289 (54%), Gaps = 12/289 (4%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML +GF +D+E IL+ LPP RQ++LFSATMP  +++L+R+YL++P+ I++   + E+  +
Sbjct: 186 MLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLK 245

Query: 61  GIKLYAIST-TATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
            IK + +   +   K  +L  L+    +G + IVF +TKR  +E++ +L        ALH
Sbjct: 246 KIKQFYLEVESEEEKLELLLKLLKDEDEG-RVIVFVRTKRLVEELAESLRKRGFKVAALH 304

Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +R+R L  F+ G+  VLVATDVAARGLDIP+V  +I+Y+LP DPE +VHR GRT
Sbjct: 305 GDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRT 364

Query: 179 GRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFE-FVSPPVVEDVLESSAEQVVATLNGV 236
           GRAG++G AI   T   + + ++ +E+ +  K    V  P+ E       +     L   
Sbjct: 365 GRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLLKTTRPGLEEE 424

Query: 237 HPESVE-------FFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRS 278
              S E                +    +  LA    ++ G     +   
Sbjct: 425 SDISDEIKKLKSSKKALLRGLGVRFTLSKLLANLGKEIPGAGDAVTIDP 473

Length = 513

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

 Score =  173 bits (440), Expect = 1e-49
 Identities = 75/217 (34%), Positives = 124/217 (57%), Gaps = 5/217 (2%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML +GF++ ++ I+   P +RQ++LFSAT P  +  +S+++  +P+ +  V +  +  A 
Sbjct: 159 MLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVK-VESTHDLPA- 216

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHG 119
            I+      +   +   L  L+  + +    +VF  TK++  EV+ AL +   ++ ALHG
Sbjct: 217 -IEQRFYEVSPDERLPALQRLLLHH-QPESCVVFCNTKKECQEVADALNAQGFSALALHG 274

Query: 120 DISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG 179
           D+ Q  R++ L  F     +VLVATDVAARGLDI  ++ +I+YEL  DPE  VHR GRTG
Sbjct: 275 DLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTG 334

Query: 180 RAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP 216
           RAG +G A+ +    + +   ++E  +G K  +   P
Sbjct: 335 RAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLP 371

Length = 460

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

 Score =  153 bits (389), Expect = 2e-42
 Identities = 84/207 (40%), Positives = 121/207 (58%), Gaps = 8/207 (3%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML +GF  D+  +L  LP KRQ++LFSAT    +K L+ K L NPL I++   +    +E
Sbjct: 161 MLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVA--RRNTASE 218

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGG--KTIVFTQTKRDADEVSLALTSI-IASEAL 117
            +  +        KR +LS +I    KG   + +VFT+TK  A+ ++  L    I S A+
Sbjct: 219 QVTQHVHFVDKKRKRELLSQMI---GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAI 275

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           HG+ SQ  R R L  F+ G   VLVATD+AARGLDI  +  +++YELPN PE +VHR GR
Sbjct: 276 HGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGR 335

Query: 178 TGRAGKEGTAILMFTSSQRRTVRSLER 204
           TGRA   G A+ +    + + +R +E+
Sbjct: 336 TGRAAATGEALSLVCVDEHKLLRDIEK 362

Length = 456

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

 Score =  151 bits (382), Expect = 7e-41
 Identities = 75/208 (36%), Positives = 117/208 (56%), Gaps = 6/208 (2%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYL-DNPLNIDLVGNQDEKLA 59
           ML +GFE  +  I+  + P RQ++++SAT P  V+ L+R    + P++++ VG+ D    
Sbjct: 289 MLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVN-VGSLDLTAC 347

Query: 60  EGIKLYAISTTATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL- 117
             IK          KR  L  L+  +   G K ++F +TK+ AD ++  L  +    AL 
Sbjct: 348 HNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKEL-RLDGWPALC 406

Query: 118 -HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 176
            HGD  Q +R   LN F+ GK  +++ATDVA+RGLD+ +V  +I+++ PN  E +VHR G
Sbjct: 407 IHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIG 466

Query: 177 RTGRAGKEGTAILMFTSSQRRTVRSLER 204
           RTGRAG +G +    T  + R  R L +
Sbjct: 467 RTGRAGAKGASYTFLTPDKYRLARDLVK 494

Length = 545

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

 Score =  150 bits (381), Expect = 2e-40
 Identities = 98/304 (32%), Positives = 153/304 (50%), Gaps = 58/304 (19%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML +GF EDVE I+  +P   Q+ LFSATMP  +++++R+++  P  +            
Sbjct: 161 MLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEV------------ 208

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGK--------------TIVFTQTKRDADEVSL 106
                 I ++ T++  I     TV+                    I+F +TK    EV+ 
Sbjct: 209 -----RIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAE 263

Query: 107 ALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 165
           AL  +   S AL+GD++Q  RE+TL   + G+  +L+ATDVAARGLD+  + L+++Y++P
Sbjct: 264 ALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIP 323

Query: 166 NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP--------- 216
            D E++VHR GRTGRAG+ G A+L   + +RR +R++ER +      V  P         
Sbjct: 324 MDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEVELPNAELLGKRR 383

Query: 217 ------VVEDVLESS-AEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSG 269
                  V+  LESS  +Q  A L  + P +            EE   + LAAAL +++ 
Sbjct: 384 LEKFAAKVQQQLESSDLDQYRALLAKIQPTAEG----------EELDLETLAAALLKMAQ 433

Query: 270 FSRP 273
             RP
Sbjct: 434 GERP 437

Length = 629

>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 =  133 bits (337), Expect = 3e-38
 Identities = 59/130 (45%), Positives = 82/130 (63%), Gaps = 1/130 (0%)

Query: 62  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGD 120
           IK Y +         +L  L     KGGK ++F  +K+  DE++  L    I   ALHGD
Sbjct: 2   IKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGD 61

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
            SQ +RE  L  FR+G+  VLVATDV ARG+D+PNV ++I+Y+LP  P +++ R GR GR
Sbjct: 62  GSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGR 121

Query: 181 AGKEGTAILM 190
           AG++GTAIL+
Sbjct: 122 AGQKGTAILL 131

Length = 131

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

 Score =  133 bits (335), Expect = 3e-35
 Identities = 72/209 (34%), Positives = 117/209 (55%), Gaps = 11/209 (5%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GF+  +  + + LPP  Q  LFSATMP+ + +L+ K++ +P  I LV  +DE   E
Sbjct: 182 MLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRI-LV-KKDELTLE 239

Query: 61  GIKLYAISTTATS-KRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASE 115
           GI+ + ++      K   L DL   +T+     + I++  T+R  D ++  +        
Sbjct: 240 GIRQFYVAVEKEEWKFDTLCDLYETLTIT----QAIIYCNTRRKVDYLTKKMHERDFTVS 295

Query: 116 ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS 175
            +HGD+ Q  R+  +  FR G   VL+ TD+ ARG+D+  V L+I+Y+LP  PE ++HR 
Sbjct: 296 CMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRI 355

Query: 176 GRTGRAGKEGTAILMFTSSQRRTVRSLER 204
           GR+GR G++G AI   T      ++ +ER
Sbjct: 356 GRSGRFGRKGVAINFVTPDDIEQLKEIER 384

Length = 401

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

 Score =  131 bits (333), Expect = 1e-34
 Identities = 63/190 (33%), Positives = 111/190 (58%), Gaps = 4/190 (2%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMP-SWVKKLSRKYLDNPLNIDLVGNQDEKLA 59
           ML +GF +D+E I      ++Q++LFSAT+    V+  + + L++P+ ++   ++ E+  
Sbjct: 159 MLDMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRER-K 217

Query: 60  EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           +  + Y  +     K  +L  L+    +  ++IVF +T+    E++  L    I    L 
Sbjct: 218 KIHQWYYRADDLEHKTALLCHLLK-QPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLE 276

Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           G++ Q +R   +     G+  VLVATDVAARG+DI +V  +I++++P   +T++HR GRT
Sbjct: 277 GEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRT 336

Query: 179 GRAGKEGTAI 188
           GRAG++GTAI
Sbjct: 337 GRAGRKGTAI 346

Length = 434

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

 Score =  130 bits (329), Expect = 6e-34
 Identities = 73/219 (33%), Positives = 116/219 (52%), Gaps = 6/219 (2%)

Query: 1   MLAVGFEEDVELILENLPPK--RQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKL 58
           ML +GF   V  I+   P K  RQ++LFSAT    V  L++++  +P  +++    +   
Sbjct: 249 MLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEI--EPENVA 306

Query: 59  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEAL 117
           ++ ++ +  +   + K  +L +L+T      + +VF   K +   +   L    I +  L
Sbjct: 307 SDTVEQHVYAVAGSDKYKLLYNLVT-QNPWERVMVFANRKDEVRRIEERLVKDGINAAQL 365

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
            GD+ QH+R +TL GFR+GK  VLVATDVA RG+ I  +  +I++ LP DP+ +VHR GR
Sbjct: 366 SGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGR 425

Query: 178 TGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP 216
           TGRAG  G +I          +  +E  +G K     PP
Sbjct: 426 TGRAGASGVSISFAGEDDAFQLPEIEELLGRKISCEMPP 464

Length = 475

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

 Score =  115 bits (289), Expect = 1e-28
 Identities = 71/195 (36%), Positives = 109/195 (55%), Gaps = 14/195 (7%)

Query: 1   MLAVGFEEDVELILENLPP--KRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKL 58
           M  +GF +D+  +   +PP  +R +MLFSAT+   V++L+ ++++NP  +++   Q  K 
Sbjct: 169 MFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQ--KT 226

Query: 59  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-- 116
              IK      +   K  +L  LI       + I+F  TK   +E+       +A++   
Sbjct: 227 GHRIKEELFYPSNEEKMRLLQTLIE-EEWPDRAIIFANTKHRCEEI----WGHLAADGHR 281

Query: 117 ---LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH 173
              L GD++Q +R R L  F +G   +LVATDVAARGL IP V  + +Y+LP+D E +VH
Sbjct: 282 VGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVH 341

Query: 174 RSGRTGRAGKEGTAI 188
           R GRTGRAG  G +I
Sbjct: 342 RIGRTGRAGASGHSI 356

Length = 423

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

 Score =  115 bits (290), Expect = 3e-28
 Identities = 71/191 (37%), Positives = 110/191 (57%), Gaps = 6/191 (3%)

Query: 1   MLAVGFEEDVELILENLPPK--RQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKL 58
           M  +GF +D+  +L  +P +  RQ++LFSAT+   V +L+ ++++ P    LV   +   
Sbjct: 171 MFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEK--LVVETETIT 228

Query: 59  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEAL 117
           A  ++          K+T+L  L++  ++G +T+VF  TK   + V+  L         L
Sbjct: 229 AARVRQRIYFPADEEKQTLLLGLLS-RSEGARTMVFVNTKAFVERVARTLERHGYRVGVL 287

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
            GD+ Q +RE  LN F++G+  +LVATDVAARGL I  V  + +Y+LP D E +VHR GR
Sbjct: 288 SGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGR 347

Query: 178 TGRAGKEGTAI 188
           T R G+EG AI
Sbjct: 348 TARLGEEGDAI 358

Length = 572

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

 Score =  104 bits (263), Expect = 4e-28
 Identities = 39/71 (54%), Positives = 52/71 (73%)

Query: 112 IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF 171
           I    LHG +SQ +RE  L  FR GK  VLVATDVA RG+D+P+V+L+I+Y+LP +P ++
Sbjct: 8   IKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASY 67

Query: 172 VHRSGRTGRAG 182
           + R GR GRAG
Sbjct: 68  IQRIGRAGRAG 78

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

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

 Score = 98.4 bits (246), Expect = 1e-25
 Identities = 42/82 (51%), Positives = 55/82 (67%), Gaps = 1/82 (1%)

Query: 102 DEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 160
           +E++  L  + I    LHG +SQ +RE  L+ F  GK  VLVATDVA RGLD+P VDL+I
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 161 HYELPNDPETFVHRSGRTGRAG 182
            Y+LP  P +++ R GR GRAG
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score = 90.2 bits (224), Expect = 9e-20
 Identities = 60/200 (30%), Positives = 103/200 (51%), Gaps = 6/200 (3%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML  GF + V  I + L  + Q +LFSAT+   V+K +     + + I  +GN + +  +
Sbjct: 282 MLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILIS-IGNPN-RPNK 338

Query: 61  GIKLYAISTTATSKRTILSDLITVYAK-GGKTIVFTQTKRDADEVSLALTSIIASEAL-- 117
            +K  AI      K+  L D++          +VF  ++  AD ++ A+T +   +AL  
Sbjct: 339 AVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSI 398

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           HG+ S  +R   +  F  G+  V+VAT V  RG+D+  V  +I +++PN  + ++H+ GR
Sbjct: 399 HGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGR 458

Query: 178 TGRAGKEGTAILMFTSSQRR 197
             R G++GTAI+      R 
Sbjct: 459 ASRMGEKGTAIVFVNEEDRN 478

Length = 518

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

 Score = 77.0 bits (190), Expect = 3e-15
 Identities = 42/120 (35%), Positives = 64/120 (53%), Gaps = 11/120 (9%)

Query: 87  KGGKTIVFTQTKRDADEVSLALTSI--------IASEALHGD--ISQHQRERTLNGFRQG 136
              + IVFT+ +  A+E+   L  I        I   +  GD  +SQ +++  ++ FR+G
Sbjct: 365 GDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKG 424

Query: 137 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR 196
           ++ VLVAT V   GLDIP VDL+I YE        + R GRTGR  ++G  +++ T   R
Sbjct: 425 EYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR-KRKGRVVVLVTEGTR 483

Length = 542

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

 Score = 75.3 bits (186), Expect = 1e-14
 Identities = 47/131 (35%), Positives = 68/131 (51%), Gaps = 22/131 (16%)

Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGD--------ISQHQRERTLNGFRQGK 137
              + IVFTQ +  A+++   L    I +    G         +SQ ++   L+ FR G+
Sbjct: 364 PDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGE 423

Query: 138 FTVLVATDVAARGLDIPNVDLIIHYELPNDPET-FVHRSGRTGRAGKEGTA-ILM----- 190
           F VLV+T VA  GLDIP+VDL+I YE P   E   + R GRTGR  +EG   +L+     
Sbjct: 424 FNVLVSTSVAEEGLDIPSVDLVIFYE-PVPSEIRSIQRKGRTGR-QEEGRVVVLIAKGTR 481

Query: 191 ----FTSSQRR 197
               + SS+R+
Sbjct: 482 DEAYYWSSRRK 492

Length = 773

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

 Score = 71.7 bits (176), Expect = 1e-13
 Identities = 42/165 (25%), Positives = 67/165 (40%), Gaps = 2/165 (1%)

Query: 38  SRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQT 97
            R+Y         +      L    +   I+  +  K   +  L+  +A+G KT++F   
Sbjct: 233 EREYAKESARFRELLRARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASD 292

Query: 98  KRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD 157
              A E++    +    EA+ G+  + +RE  L  FR G   VLV   V   G+DIP+ D
Sbjct: 293 VEHAYEIAKLFLAPGIVEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDAD 352

Query: 158 LIIHYELPNDPETFVHRSGRTGRA--GKEGTAILMFTSSQRRTVR 200
           ++I          F+ R GR  R   GKE T  L ++        
Sbjct: 353 VLIILRPTGSRRLFIQRLGRGLRPAEGKEDTLALDYSLVPDDLGE 397

Length = 442

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

 Score = 67.1 bits (165), Expect = 4e-13
 Identities = 26/48 (54%), Positives = 36/48 (75%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           ML +GFE+ +  IL+ LP  RQ++LFSATMP  V+ L+RK+L NP+ I
Sbjct: 155 MLDMGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI 202

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Length = 203

>gnl|CDD|203861 pfam08152, GUCT, GUCT (NUC152) domain

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 269 GFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHII 328
           G++     RSL+  E+G+VTLQLT          + +S+  FL D      D I  + ++
Sbjct: 1   GYTSI-KQRSLLTSEEGYVTLQLTSGRPIPTPSFAWKSLRRFLPD---EKVDSIKGMTLL 56

Query: 329 ADDR-VCID 336
           AD++    D
Sbjct: 57  ADNQGAVFD 65

This is the C terminal domain found in the RNA helicase II / Gu protein family. Length = 97

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

 Score = 68.9 bits (169), Expect = 1e-12
 Identities = 37/118 (31%), Positives = 62/118 (52%), Gaps = 1/118 (0%)

Query: 86  AKGGKTIVFTQTKRDADEVSLAL-TSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 144
                 I++  T++  +E++  L  + I++ A H  +S  +RER    F   +  V+VAT
Sbjct: 228 QLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVAT 287

Query: 145 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 202
           +    G+D P+V  +IHY+LP   E++   +GR GR G    AIL+++    R  R L
Sbjct: 288 NAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYL 345

Length = 590

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

 Score = 63.6 bits (155), Expect = 5e-11
 Identities = 32/103 (31%), Positives = 56/103 (54%), Gaps = 1/103 (0%)

Query: 92  IVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG 150
           I++  +++  +E++  L S  I++ A H  +S   R      F      V+VAT+    G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287

Query: 151 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS 193
           +D PNV  +IHY++P + E++   +GR GR G    AIL+++ 
Sbjct: 288 IDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSP 330

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 = 60.2 bits (146), Expect = 7e-10
 Identities = 33/117 (28%), Positives = 62/117 (52%), Gaps = 1/117 (0%)

Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           KG   I++  +++ +++V+ +L ++ IA+ A H  +    R+   + F++ +  V+VAT 
Sbjct: 225 KGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATV 284

Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 202
               G++ P+V  +IHY LP   E++   SGR GR G      L +  +    +R L
Sbjct: 285 AFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRL 341

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|240595 cd12938, GUCT_Hera, RNA-binding GUCT-like domain found in Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 25/55 (45%), Positives = 30/55 (54%), Gaps = 5/55 (9%)

Query: 276 SRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIAD 330
            RSL+  E+GW TLQLT          S R  +G LS     AAD +GKI I+AD
Sbjct: 1   PRSLLTGEEGWTTLQLTGSR--LLPPGSVRRAVGLLSRA---AADGVGKIRILAD 50

This subfamily corresponds to the Gu C-terminal (GUCT)-like domain of Hera and similar proteins. Thermus thermophilus Hera is a DEAD box helicase that binds fragments of 23S rRNA and RNase P RNA via its C-terminal domain. It contains a helicase core that harbors two RecA-like domains termed RecA_N and RecA_C, a dimerization domain (DD), and a C-terminal RNA-binding domain (RBD) that reveals a compact, RRM-like fold and shows sequence similarity with GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and plant DEAD-box ATP-dependent RNA helicase 7 (RH7 or PRH75). Length = 74

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

 Score = 56.5 bits (137), Expect = 1e-08
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 2/93 (2%)

Query: 90  KTIVFTQTKRDADEVSLALTSI--IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA 147
            T++FT T+  A+ ++  L  +     E  HG +S+  R       ++G+   +VAT   
Sbjct: 255 TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSL 314

Query: 148 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
             G+DI ++DL+I    P     F+ R GR G 
Sbjct: 315 ELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347

Length = 814

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

 Score = 53.6 bits (129), Expect = 6e-08
 Identities = 42/167 (25%), Positives = 72/167 (43%), Gaps = 11/167 (6%)

Query: 24  MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 83
           +L SAT+P ++K+ + K        + +  ++E+  E  +   I +    + + L  L+ 
Sbjct: 159 LLMSATLPKFLKEYAEKI-GYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLE 217

Query: 84  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEA---LHGDISQHQRER----TLNGFRQG 136
              KGGK  +   T   A E    L      E    LH   ++  R +     L   ++ 
Sbjct: 218 FIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKN 277

Query: 137 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK 183
           +  V+VAT V    LDI + D++I    P D  + + R GR  R G+
Sbjct: 278 EKFVIVATQVIEASLDI-SADVMITELAPID--SLIQRLGRLHRYGR 321

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model [Mobile and extrachromosomal element functions, Other]. Length = 358

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

 Score = 53.1 bits (128), Expect = 1e-07
 Identities = 43/140 (30%), Positives = 70/140 (50%), Gaps = 16/140 (11%)

Query: 77  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 135
           +LS++    A+  + +V T TK+ A++++  L  + I    LH +I   +R   +   R 
Sbjct: 431 LLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRL 490

Query: 136 GKFTVLVATDVAARGLDIPNVDLI-IHYELPNDPETFVHRSGRT-----GRAGK--EGTA 187
           G+F VLV  ++   GLD+P V L+ I   L  D E F+ RS R+     GRA +   G  
Sbjct: 491 GEFDVLVGINLLREGLDLPEVSLVAI---LDADKEGFL-RSERSLIQTIGRAARNVNGKV 546

Query: 188 ILM---FTSSQRRTVRSLER 204
           I+     T S ++ +   ER
Sbjct: 547 IMYADKITDSMQKAIEETER 566

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

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

 Score = 53.0 bits (128), Expect = 2e-07
 Identities = 45/139 (32%), Positives = 69/139 (49%), Gaps = 14/139 (10%)

Query: 77  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 135
           +LS++    AK  + +V T TK+ A++++  L  + I    LH DI   +R   +   R 
Sbjct: 435 LLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRL 494

Query: 136 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAI 188
           G+F VLV  ++   GLD+P V L+    L  D E F+ RS R+     GRA +   G  I
Sbjct: 495 GEFDVLVGINLLREGLDLPEVSLVA--ILDADKEGFL-RSERSLIQTIGRAARNVNGKVI 551

Query: 189 L---MFTSSQRRTVRSLER 204
           L     T S ++ +   ER
Sbjct: 552 LYADKITDSMQKAIDETER 570

Length = 663

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

 Score = 52.4 bits (126), Expect = 3e-07
 Identities = 27/93 (29%), Positives = 49/93 (52%), Gaps = 9/93 (9%)

Query: 117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 172
            HG +++++ E  +  F +G+F VLV T +   G+DIPN + II        + F    +
Sbjct: 692 AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTII----IERADKFGLAQL 747

Query: 173 HR-SGRTGRAGKEGTAILMFTSSQRRTVRSLER 204
           ++  GR GR+ K+  A L++   +  T  + +R
Sbjct: 748 YQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKR 780

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families [DNA metabolism, DNA replication, recombination, and repair]. Length = 926

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

 Score = 48.8 bits (117), Expect = 5e-07
 Identities = 18/37 (48%), Positives = 26/37 (70%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKL 37
           +L +GF +D+E IL  LPP RQ +L SAT+P  ++ L
Sbjct: 133 LLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169

Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Length = 169

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

 Score = 50.6 bits (121), Expect = 9e-07
 Identities = 46/196 (23%), Positives = 74/196 (37%), Gaps = 32/196 (16%)

Query: 83  TVYAKG--GKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFT 139
           T  +KG  G+TIVFT ++R   E++ ALT   + +   H  +   +R+     F   +  
Sbjct: 433 TESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELA 492

Query: 140 VLVATDVAARGLDIPNVDLIIH-YELPND---PETFVHRSGRTGRAG--KEGTAILM--- 190
            +V T   A G+D P   +I     +  +      F    GR GR      G   L+   
Sbjct: 493 AVVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEP 552

Query: 191 ---FTSSQRRTVRSLERDVGCKFEFVSPP---VVEDVLESSAEQVVAT---------LNG 235
              + +S   T    E +V  K    S P   +VE   E   E V+A+         +  
Sbjct: 553 GKKYHASMEET----EDEVAFKL-LESEPEPVIVEYDEEDEEENVLASAGVTNSLSVIER 607

Query: 236 VHPESVEFFTPTAQRL 251
           V+   +       + L
Sbjct: 608 VNSLMLGAAFDPKKAL 623

Length = 830

>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

 Score = 50.0 bits (120), Expect = 1e-06
 Identities = 25/99 (25%), Positives = 43/99 (43%), Gaps = 23/99 (23%)

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS-- 175
           HG + + + E  +  F  G++ VLV T +   G+DIPN + II           + R+  
Sbjct: 836 HGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTII-----------IERADK 884

Query: 176 ----------GRTGRAGKEGTAILMFTSSQRRTVRSLER 204
                     GR GR+ K+  A  ++   +  T  + +R
Sbjct: 885 FGLAQLYQLRGRVGRSNKQAYAYFLYPPQKALTEDAEKR 923

Length = 1139

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

 Score = 48.1 bits (115), Expect = 4e-06
 Identities = 29/112 (25%), Positives = 53/112 (47%), Gaps = 17/112 (15%)

Query: 99  RDADEVSLALTSIIASEA---LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN 155
           + A+ +   L           LHG +   ++E  +  FR+G+  +LVAT V   G+D+PN
Sbjct: 467 KAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN 526

Query: 156 VDLIIHYELPNDPETF----VHR-SGRTGRAGKEGTAILMF-----TSSQRR 197
             +++      D E F    +H+  GR GR   +   +L++      S+++R
Sbjct: 527 ATVMVIE----DAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAKKR 574

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

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

 Score = 45.9 bits (109), Expect = 7e-06
 Identities = 18/49 (36%), Positives = 30/49 (61%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNID 49
           +L  GF + +E +L+ LP   Q +L SAT P  ++ L   +L++P+ ID
Sbjct: 141 LLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFID 189

Length = 201

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

 Score = 47.8 bits (114), Expect = 8e-06
 Identities = 32/132 (24%), Positives = 56/132 (42%), Gaps = 17/132 (12%)

Query: 68  STTATSKRTILSDLITVYAKGG-KTIVFTQTKRDADEVSLALTSIIASEALHGDISQH-- 124
            +   S    L+ L  +  + G +T+VF ++++   +V L   S        G       
Sbjct: 285 ESIRRSALAELATLAALLVRNGIQTLVFFRSRK---QVELLYLSPRRRLVREGGKLLDAV 341

Query: 125 ----------QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET-FVH 173
                     +R R    F++G+   ++AT+    G+DI ++D +I Y  P      F  
Sbjct: 342 STYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQ 401

Query: 174 RSGRTGRAGKEG 185
           R+GR GR G+E 
Sbjct: 402 RAGRAGRRGQES 413

Length = 851

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

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 26/106 (24%), Positives = 54/106 (50%), Gaps = 1/106 (0%)

Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +G   I++  ++   ++ +  L S  I++ A H  +    R      F++    ++VAT 
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATV 294

Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 191
               G++ PNV  ++H+++P + E++   +GR GR G    A+L +
Sbjct: 295 AFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 340

Length = 607

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

 Score = 46.3 bits (110), Expect = 1e-05
 Identities = 43/168 (25%), Positives = 71/168 (42%), Gaps = 16/168 (9%)

Query: 24  MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 83
           +L SAT+P ++K+ + K        + +  +  + A  IK+ +       + + L  L+ 
Sbjct: 158 LLMSATLPKFLKEYAEKI-GYVEENEPLDLKPNERAPFIKIESDKV---GEISSLERLLE 213

Query: 84  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEA---LHGDISQHQRER-----TLNGFRQ 135
              KGG   +   T   A E    L      E    +H   ++  R +      L   + 
Sbjct: 214 FIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKS 273

Query: 136 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK 183
            KF V+VAT V    LDI +VD++I    P D  + + R GR  R G+
Sbjct: 274 EKF-VIVATQVIEASLDI-SVDVMITELAPID--SLIQRLGRLHRYGE 317

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

>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor; Provisional

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 36/108 (33%), Positives = 53/108 (49%), Gaps = 21/108 (19%)

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----HYELPNDPETFV 172
           HG + + + ER +N F   +F VLV T +   G+DIP  + II     H+ L       +
Sbjct: 842 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ-----L 896

Query: 173 HR-SGRTGRAGKEGTAIL-------MFTSSQRR--TVRSLERDVGCKF 210
           H+  GR GR+  +  A L       M T +Q+R   + SLE D+G  F
Sbjct: 897 HQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLE-DLGAGF 943

Length = 1147

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

 Score = 46.1 bits (110), Expect = 2e-05
 Identities = 26/104 (25%), Positives = 51/104 (49%), Gaps = 14/104 (13%)

Query: 99  RDADEVSLALTSIIASEA---LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN 155
           + A+E+   L S +       +HG +   +++  +  F++G+  +LVAT V   G+D+PN
Sbjct: 492 QAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPN 551

Query: 156 VDLIIHYELPNDPETF----VH--RSGRTGRAGKEGTAILMFTS 193
             +++      + E F    +H  R GR GR   +   +L++  
Sbjct: 552 ATVMVIE----NAERFGLAQLHQLR-GRVGRGDLQSYCVLLYKP 590

Length = 677

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

 Score = 44.9 bits (106), Expect = 6e-05
 Identities = 46/163 (28%), Positives = 70/163 (42%), Gaps = 10/163 (6%)

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           HG +S+ QR  T    + G+   +VAT     G+D+  VDL+I    P    + + R GR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367

Query: 178 TGRAGKEGTAILMFTSSQRRTVRS---LERDVGCKFEFVSPPVVEDVLESSAEQVVATLN 234
            G      +  L F  ++R  V S   +E     + E ++PP   + L+  A+Q VA   
Sbjct: 368 AGHQVGGVSKGLFFPRTRRDLVDSAVIVECMFAGRLENLTPP--HNPLDVLAQQTVAAA- 424

Query: 235 GVHPESVEFFTPTAQRLIEEKG--TDALAAALAQLSGFSRPPS 275
            +    V+ +    +R    K        A L  LSG  R PS
Sbjct: 425 AMDALQVDEWYSRVRRAAPWKDLPRRVFDATLDMLSG--RYPS 465

Length = 1490

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

 Score = 41.6 bits (98), Expect = 6e-04
 Identities = 33/145 (22%), Positives = 66/145 (45%), Gaps = 19/145 (13%)

Query: 59  AEGIKLYAISTTATSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEVSLA----LTSIIA 113
             G     +  +A+++   +L+DL+   A+G +T+ F +++R A+ V+      L  +  
Sbjct: 244 LTGENGAPVRRSASAEAADLLADLV---AEGARTLTFVRSRRGAELVAAIARRLLGEVDP 300

Query: 114 SEALH------GDISQHQR--ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 165
             A        G + + +R  ER L   R G+   +  T+    G+DI  +D ++    P
Sbjct: 301 DLAERVAAYRAGYLPEDRRELERAL---RDGELLGVATTNALELGVDISGLDAVVIAGFP 357

Query: 166 NDPETFVHRSGRTGRAGKEGTAILM 190
               +   ++GR GR G+    +L+
Sbjct: 358 GTRASLWQQAGRAGRRGQGALVVLV 382

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

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

 Score = 41.4 bits (97), Expect = 7e-04
 Identities = 26/104 (25%), Positives = 50/104 (48%), Gaps = 1/104 (0%)

Query: 92  IVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVAARG 150
           I++  ++ D ++V+  L       A  HG +   QR      + + +  ++ AT     G
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG 743

Query: 151 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS 194
           ++ P+V  +IH+ LP   E +    GR GR G+  + +L ++ S
Sbjct: 744 INKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYS 787

Length = 1195

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

 Score = 40.9 bits (97), Expect = 0.001
 Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 22/80 (27%)

Query: 127 ERTLNGFRQGKFTVLVATDVAARGLDIPNV--------DLIIHYELPNDP----ETF--- 171
           E+ L  F +G+  +L+ T + A+G D PNV        DL +      D      TF   
Sbjct: 470 EQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFS---PDFRASERTFQLL 526

Query: 172 --VHRSGRTGRAGKEGTAIL 189
             V  +GR GRA K G  ++
Sbjct: 527 TQV--AGRAGRAEKPGEVLI 544

Length = 679

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

 Score = 40.5 bits (95), Expect = 0.001
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 122 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL-IIHYELPN-DPETFVHRSGRTG 179
            QH++E+ +  FR GK T+L+ T +  RG+  PNVD+ ++  E         V  +GR G
Sbjct: 341 DQHRKEK-VEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVG 399

Query: 180 RAGKEGTAILMF 191
           R+ +  T  ++F
Sbjct: 400 RSLERPTGDVLF 411

Length = 441

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

 Score = 40.4 bits (96), Expect = 0.001
 Identities = 43/113 (38%), Positives = 59/113 (52%), Gaps = 13/113 (11%)

Query: 86  AKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVAT 144
           AKG + +V T TKR A++++  L  + I    LH DI   +R   +   R G+F VLV  
Sbjct: 444 AKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGI 503

Query: 145 DVAARGLDIPNVDLI-IHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 189
           ++   GLDIP V L+ I   L  D E F+ RS R+     GRA +   G  IL
Sbjct: 504 NLLREGLDIPEVSLVAI---LDADKEGFL-RSERSLIQTIGRAARNVNGKVIL 552

Length = 652

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

 Score = 39.7 bits (94), Expect = 0.002
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 11/80 (13%)

Query: 117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 172
           LHG +   +++  +  F+ G+  +LVAT V   G+D+PN  +++      + E F    +
Sbjct: 511 LHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIE----NAERFGLAQL 566

Query: 173 H--RSGRTGRAGKEGTAILM 190
           H  R GR GR   +   +L+
Sbjct: 567 HQLR-GRVGRGAAQSYCVLL 585

Length = 681

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

 Score = 39.1 bits (92), Expect = 0.003
 Identities = 32/110 (29%), Positives = 48/110 (43%), Gaps = 6/110 (5%)

Query: 91  TIVFTQTKRDADEVSLALTSIIASEAL-----HGDISQHQRERTLNGFRQGKFTVLVATD 145
           T+VFT T+  A+    AL       AL     HG + + QR         G+   +V T 
Sbjct: 250 TLVFTNTRSQAELWFQALWEANPEFALPIALHHGSLDREQRRWVEAAMAAGRLRAVVCTS 309

Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG-RAGKEGTAILMFTSS 194
               G+D   VDL+I    P      + R+GR+  R G+   A+L+ T+ 
Sbjct: 310 SLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPGEPSRALLVPTNR 359

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	379
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.98
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.97
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.97
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.97
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.96
KOG4284	980	consensus DEAD box protein [Transcription]	99.96
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.96
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.96
PHA02653	675	RNA helicase NPH-II; Provisional	99.96
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.95
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.95
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.94
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.94
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.94
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.94
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.92
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.92
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.92
PRK10689	1147	transcription-repair coupling factor; Provisional	99.92
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.91
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.91
PRK13767	876	ATP-dependent helicase; Provisional	99.91
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.9
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.9
PRK02362	737	ski2-like helicase; Provisional	99.9
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.89
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.89
PRK00254	720	ski2-like helicase; Provisional	99.89
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.88
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.87
PRK04914	956	ATP-dependent helicase HepA; Validated	99.87
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.86
PRK09401	1176	reverse gyrase; Reviewed	99.85
PRK01172	674	ski2-like helicase; Provisional	99.85
PRK14701	1638	reverse gyrase; Provisional	99.83
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.83
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.83
PRK05298	652	excinuclease ABC subunit B; Provisional	99.83
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.82
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.82
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.81
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.81
PHA02558	501	uvsW UvsW helicase; Provisional	99.81
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.8
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.79
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.78
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.77
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.75
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.75
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.74
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.74
COG1202	830	Superfamily II helicase, archaea-specific [General	99.74
PRK13766	773	Hef nuclease; Provisional	99.71
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.7
COG1204	766	Superfamily II helicase [General function predicti	99.69
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.69
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.67
PRK09694	878	helicase Cas3; Provisional	99.67
KOG0354	746	consensus DEAD-box like helicase [General function	99.66
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.63
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.62
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.61
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.61
PRK05580	679	primosome assembly protein PriA; Validated	99.59
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	99.55
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.51
COG1205	851	Distinct helicase family with a unique C-terminal	99.51
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.5
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.48
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.48
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.47
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.46
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.45
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.45
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.43
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.42
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.4
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.37
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.34
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.32
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	99.31
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.3
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.28
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.27
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.19
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.12
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.06
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.01
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	98.92
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.89
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.88
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.85
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.81
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.76
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.71
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.69
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.6
PF08152	97	GUCT: GUCT (NUC152) domain; InterPro: IPR012562 Th	98.58
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.5
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.31
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.26
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.26
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.26
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	98.2
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.15
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.14
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.07
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.96
KOG1123	776	consensus RNA polymerase II transcription initiati	97.91
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	97.87
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.85
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.84
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.82
COG4096	875	HsdR Type I site-specific restriction-modification	97.81
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.73
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.7
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	97.61
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	97.58
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	97.56
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.41
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.37
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.29
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	97.21
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.18
COG4889	1518	Predicted helicase [General function prediction on	96.92
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	96.69
PRK14873	665	primosome assembly protein PriA; Provisional	96.52
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	96.47
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	96.32
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	96.05
PF13871	278	Helicase_C_4: Helicase_C-like	95.83
PRK05580	679	primosome assembly protein PriA; Validated	95.8
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.73
TIGR00595	505	priA primosomal protein N'. All proteins in this f	95.64
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	95.44
KOG2340	698	consensus Uncharacterized conserved protein [Funct	95.17
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	94.78
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	94.76
PRK14873	665	primosome assembly protein PriA; Provisional	94.75
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	94.74
KOG4439	901	consensus RNA polymerase II transcription terminat	94.19
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	94.15
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.12
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	93.98
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	93.96
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	91.93
PRK10689	1147	transcription-repair coupling factor; Provisional	91.93
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	91.53
PRK14701	1638	reverse gyrase; Provisional	89.19
KOG0347	731	consensus RNA helicase [RNA processing and modific	88.77
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	88.2
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	87.78
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	86.16
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	85.49
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	85.23
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	85.08
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	84.83
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	84.28
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	82.85
smart00487	201	DEXDc DEAD-like helicases superfamily.	81.51
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	80.93
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	80.6
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	80.16
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	80.1
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	80.06

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=8.6e-54  Score=446.62  Aligned_cols=352  Identities=28%  Similarity=0.440  Sum_probs=300.6

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      ||+|||.++++.|+..+|..+|+++||||+|+.+..+++.|+.+|..+.+...  ......+.+.++.+....|.+.|..
T Consensus       161 ml~~gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~--~~~~~~i~q~~~~v~~~~k~~~L~~  238 (629)
T PRK11634        161 MLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSS--VTTRPDISQSYWTVWGMRKNEALVR  238 (629)
T ss_pred             HhhcccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCc--cccCCceEEEEEEechhhHHHHHHH
Confidence            78999999999999999999999999999999999999999999988876532  2344567777777777789899998


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ++... ...++||||+|+..++.++..|.. ++.+..+||+|++.+|++++++|++|+++||||||++++|||+|+|++|
T Consensus       239 ~L~~~-~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~V  317 (629)
T PRK11634        239 FLEAE-DFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLV  317 (629)
T ss_pred             HHHhc-CCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEE
Confidence            88765 357999999999999999999985 8999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHHHHHHHHHHHHHHHccc-Cc
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGV-HP  238 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~-~~  238 (379)
                      ||||+|.++++|+||+|||||+|+.|.+++|+++.|...++.+++.++..+++..+|..+++.+.....+.+.+... ..
T Consensus       318 I~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l~~ie~~~~~~i~~~~~p~~~~~~~~~~~~~~~~~~~~~~~  397 (629)
T PRK11634        318 VNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEVELPNAELLGKRRLEKFAAKVQQQLES  397 (629)
T ss_pred             EEeCCCCCHHHHHHHhccccCCCCcceEEEEechHHHHHHHHHHHHhCCCcceecCCcHHHHHHHHHHHHHHHHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999888888887777543 33


Q ss_pred             cchhchHHHHHHHHhh-----hCHHHHHHHHHHHcCCCCC------C-----C---CCc-----------------c--c
Q 017020          239 ESVEFFTPTAQRLIEE-----KGTDALAAALAQLSGFSRP------P-----S---SRS-----------------L--I  280 (379)
Q Consensus       239 ~~~~~~~~~~~~l~~~-----~~~~~~a~al~~~~~~~~~------~-----~---~~~-----------------~--~  280 (379)
                      ..++.|.+.++++.++     .+++.+|+||+.+.....+      +     .   .++                 .  .
T Consensus       398 ~~~~~~~~~~~~l~~~~~~~~~~~~~~a~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  477 (629)
T PRK11634        398 SDLDQYRALLAKIQPTAEGEELDLETLAAALLKMAQGERPLILPPDAPMRPKREFRDRDDRGPRDRNDRGPRGDREDRPR  477 (629)
T ss_pred             hhHHHHHHHHHHHHhhhccccCCHHHHHHHHHHHHcCCCccccccccccccccccccccccccccccccccccccccccc
Confidence            4577788888888754     5789999999988533211      0     0   000                 0  0


Q ss_pred             c---CCCCeEEEEEeeCCcccCCCCChhHHHHHHhhhCCCCCCccccEEeeeCCceeeeecchhhHHHHhhhhcccCcce
Q 017020          281 N---HEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSV  357 (379)
Q Consensus       281 ~---~~~~~~~l~~~~g~~~~~~~~~~~~i~~~~~~~~~~~~~~ig~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  357 (379)
                      .   ..++|++|++++|+   +|++.|++|+++|++++|+++.+||+|+|+++++    .++||..+++.++..+++.++
T Consensus       478 ~~~~~~~~~~~~~~~~g~---~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~~~s----~v~~~~~~~~~~~~~~~~~~~  550 (629)
T PRK11634        478 RERRDVGDMQLYRIEVGR---DDGVEVRHIVGAIANEGDISSRYIGNIKLFASHS----TIELPKGMPGEVLQHFTRTRI  550 (629)
T ss_pred             cccccCCCCEEEEEeccc---ccCCCHHHHHHHHHhhcCCChhhCCcEEEeCCce----EEEcChhhHHHHHHHhccccc
Confidence            0   12269999999999   9999999999999999999999999999999999    666666666666666655555


Q ss_pred             Eeeee
Q 017020          358 IWLTY  362 (379)
Q Consensus       358 ~~~~~  362 (379)
                      .++..
T Consensus       551 ~~~~~  555 (629)
T PRK11634        551 LNKPM  555 (629)
T ss_pred             cCCce
Confidence            55444

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.7e-46  Score=374.19  Aligned_cols=206  Identities=45%  Similarity=0.725  Sum_probs=192.0

Q ss_pred             CCCCChHHHHHHHHHhC-CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHH
Q 017020            1 MLAVGFEEDVELILENL-PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~-p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~   79 (379)
                      ||||||.++|+.|+..+ ++.+|+++||||+|.+++.++..||++|..+.+..........++.|....++...|...|.
T Consensus       251 MldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~  330 (519)
T KOG0331|consen  251 MLDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLG  330 (519)
T ss_pred             hhccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHH
Confidence            99999999999999999 56779999999999999999999999999998875545667788999999999889999999


Q ss_pred             HHHHHHc--CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCcc
Q 017020           80 DLITVYA--KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV  156 (379)
Q Consensus        80 ~ll~~~~--~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v  156 (379)
                      .+|..+.  .++++||||+|++.|++++..|.. ++++.+|||+.+|.+|+.+++.|++|+..||||||+|+||||||+|
T Consensus       331 ~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV  410 (519)
T KOG0331|consen  331 KLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDV  410 (519)
T ss_pred             HHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccc
Confidence            9998874  567999999999999999999987 7999999999999999999999999999999999999999999999


Q ss_pred             ceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHh
Q 017020          157 DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  206 (379)
Q Consensus       157 ~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~  206 (379)
                      ++|||||+|.++++|+||+|||||+|++|.+++|++..+......+.+.+
T Consensus       411 ~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~~~l  460 (519)
T KOG0331|consen  411 DLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELIKVL  460 (519)
T ss_pred             cEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999988777776554

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

Probab=100.00  E-value=4.3e-45  Score=374.22  Aligned_cols=220  Identities=43%  Similarity=0.724  Sum_probs=201.2

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCcc-HHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~-k~~~L~   79 (379)
                      ||||||.+|++.|++.+|.++|+++||||||..+.++++.++++|..+.+.......+...+.|+++.++..+ |.++|.
T Consensus       186 mLd~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~  265 (513)
T COG0513         186 MLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLL  265 (513)
T ss_pred             hhcCCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHH
Confidence            8999999999999999999999999999999999999999999999888764444447788999999998766 999999


Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  158 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~  158 (379)
                      .+++... ..++||||+|+..|+.++..|.. ++.+..+||+|+|++|.++++.|++|+.+||||||+++||||||++++
T Consensus       266 ~ll~~~~-~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~  344 (513)
T COG0513         266 KLLKDED-EGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSH  344 (513)
T ss_pred             HHHhcCC-CCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccce
Confidence            9998764 56899999999999999999985 899999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCChhHHHHHHhhccCCCCCceEEEEeChh-hHHHHHHHHHHhCCCce-eeCCCCHHHH
Q 017020          159 IIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFE-FVSPPVVEDV  221 (379)
Q Consensus       159 VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~-e~~~l~~le~~~~~~~~-~~~~p~~~~i  221 (379)
                      |||||+|.++++|+||+|||||+|++|.+++|+++. |...+..+|+..+..++ ...+|..+..
T Consensus       345 VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~~~~~~~~~~~~~~~~~~~  409 (513)
T COG0513         345 VINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPE  409 (513)
T ss_pred             eEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHHHHhccccccccCCcchhh
Confidence            999999999999999999999999999999999986 99999999999887766 4555554433

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=6.8e-44  Score=362.35  Aligned_cols=297  Identities=29%  Similarity=0.473  Sum_probs=257.1

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      |++|||.++++.|++.+|..+|+++||||+|+.+..++..++.+|..+.+....   ....+.++++.++...|.+.+..
T Consensus       159 ~l~~g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~---~~~~i~~~~~~~~~~~k~~~l~~  235 (460)
T PRK11776        159 MLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH---DLPAIEQRFYEVSPDERLPALQR  235 (460)
T ss_pred             HhCcCcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC---CCCCeeEEEEEeCcHHHHHHHHH
Confidence            789999999999999999999999999999999999999999999988765322   23557788888888889999999


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ++... .+.++||||+|+..++.++..|.. ++.+..+||+|++.+|+.+++.|++|+.+||||||+++||+|+|++++|
T Consensus       236 ll~~~-~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~V  314 (460)
T PRK11776        236 LLLHH-QPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAV  314 (460)
T ss_pred             HHHhc-CCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeE
Confidence            98765 467899999999999999999985 8999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHHHHHHHHHHHHHHHcccCcc
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPE  239 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~  239 (379)
                      ||||+|.+.++|+||+|||||+|+.|.|++|+++.|...++.+++..+..+++..+|.....               .  
T Consensus       315 I~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i~~~~~~~~~~~~l~~~~~~---------------~--  377 (460)
T PRK11776        315 INYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLPSLSPL---------------S--  377 (460)
T ss_pred             EEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHHHHHHHHHHHhCCCCceecCCchhhc---------------c--
Confidence            99999999999999999999999999999999999999999999999988887766642210               0  


Q ss_pred             chhchHHHHHHHHhhhCHHHHHHHHHHHcCCCCCCCCCccccCCCCeEEEEEeeCCcccCCCCChhHHHHHHhhhCCCCC
Q 017020          240 SVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAA  319 (379)
Q Consensus       240 ~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~i~~~~~~~~~~~~  319 (379)
                                                     ..+        ....+.++.+..|+   ++++.+++++|++++..++..
T Consensus       378 -------------------------------~~~--------~~~~~~~l~i~~~~---~~~~~~~~~~~~~~~~~~~~~  415 (460)
T PRK11776        378 -------------------------------GVP--------LLPEMVTLCIDGGK---KDKLRPGDILGALTGDAGLDG  415 (460)
T ss_pred             -------------------------------ccc--------CCCCeEEEEEeccc---ccCCCccchHHHhhcccCCCh
Confidence                                           000        12468899999998   889999999999999999999


Q ss_pred             CccccEEeeeCCceeeeecchhhHHHHhhhhcccCcceEeeeehh
Q 017020          320 DEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYRF  364 (379)
Q Consensus       320 ~~ig~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  364 (379)
                      .++|.|++.+.++    ..+++....+.....+++.+++++.+++
T Consensus       416 ~~~g~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~  456 (460)
T PRK11776        416 AQIGKINVTDFHA----YVAVERAVAKKALKKLQNGKIKGKSFRV  456 (460)
T ss_pred             hhcCCcccccccc----eeecchhhHHHHHHHhccCCccCceeEE
Confidence            9999999999998    4455555555555566666666666654

>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.6e-44  Score=329.20  Aligned_cols=213  Identities=35%  Similarity=0.603  Sum_probs=198.7

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCcc-HHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~-k~~~L~   79 (379)
                      ||+-||.+++-.|.+.+|++.|++++|||+|.++.+..++||.+|+.+-+.  ..+.+.+++++||+.+..++ |.+.|.
T Consensus       181 mL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvk--rdeltlEgIKqf~v~ve~EewKfdtLc  258 (400)
T KOG0328|consen  181 MLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVK--RDELTLEGIKQFFVAVEKEEWKFDTLC  258 (400)
T ss_pred             HHHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEe--cCCCchhhhhhheeeechhhhhHhHHH
Confidence            789999999999999999999999999999999999999999999998554  34566788999999887655 999999


Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  158 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~  158 (379)
                      ++.+.+. -.+++|||||++.++.|.+.+.. ++.+..+||+|+|++|++++++||+|+.+||++||+.+||+|+|.|++
T Consensus       259 dLYd~Lt-ItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVsl  337 (400)
T KOG0328|consen  259 DLYDTLT-ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSL  337 (400)
T ss_pred             HHhhhhe-hheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEE
Confidence            9988774 68999999999999999999985 899999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCC
Q 017020          159 IIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  216 (379)
Q Consensus       159 VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p  216 (379)
                      |||||+|.+.+.|+||+||.||.|++|.++-|+...|.+.++.+|++++..+++.+..
T Consensus       338 viNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~lrdieq~yst~i~emp~n  395 (400)
T KOG0328|consen  338 VINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILRDIEQYYSTQIDEMPMN  395 (400)
T ss_pred             EEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHHHHHHHHHHHhhhcccccch
Confidence            9999999999999999999999999999999999999999999999999888876543

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=6.9e-44  Score=337.23  Aligned_cols=213  Identities=36%  Similarity=0.591  Sum_probs=200.4

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      +|||-|.+++..||+.+|.++|++|||||||+.+.++.+..+++|+.|.+.  ....+.++++++|+.++..+|...|..
T Consensus       216 lLd~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s--~ky~tv~~lkQ~ylfv~~k~K~~yLV~  293 (476)
T KOG0330|consen  216 LLDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVS--SKYQTVDHLKQTYLFVPGKDKDTYLVY  293 (476)
T ss_pred             hhhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEecc--chhcchHHhhhheEeccccccchhHHH
Confidence            589999999999999999999999999999999999999999999998764  456677889999999999999999999


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      +++.. .+.++||||+|...++.++-.|.. ++.+..+||+|+|..|...++.|++|...||||||+++||+|+|.|++|
T Consensus       294 ll~e~-~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~V  372 (476)
T KOG0330|consen  294 LLNEL-AGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVV  372 (476)
T ss_pred             HHHhh-cCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEE
Confidence            99977 478999999999999999999986 9999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCC
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  216 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p  216 (379)
                      ||||+|.+..+|+||+|||||+|++|.+|.|++..|.+.+.+||...+.+.+..+.+
T Consensus       373 VNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE~~~gkkl~~~~~~  429 (476)
T KOG0330|consen  373 VNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIEHALGKKLPEYKVD  429 (476)
T ss_pred             EecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHHHHHHHhcCCCccCcc
Confidence            999999999999999999999999999999999999999999999999887654333

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=100.00  E-value=4.9e-43  Score=339.87  Aligned_cols=271  Identities=33%  Similarity=0.491  Sum_probs=221.4

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcC-CCceEEeecccccccccceEEEEEEcCCccHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLD-NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~-~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~   79 (379)
                      +|||||.+||+.|++.+|..+|++|||||+|++|+++++..|+ +|+.|++++.....+.+.+.|-|+.++...+...+.
T Consensus       242 lLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~ll~  321 (543)
T KOG0342|consen  242 LLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSRFSLLY  321 (543)
T ss_pred             hhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccchHHHHH
Confidence            4899999999999999999999999999999999999998887 699999988778888999999888888888888889


Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  158 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~  158 (379)
                      .+|+.+....++||||+|...+..+++.|.. .++|..+||+++|..|..+..+|++.+..|||||||+|||+|+|+|++
T Consensus       322 ~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~  401 (543)
T KOG0342|consen  322 TFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDW  401 (543)
T ss_pred             HHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceE
Confidence            9998875558999999999999999999985 789999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHH-HHHHHHHHHHHHHHcccC
Q 017020          159 IIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE-DVLESSAEQVVATLNGVH  237 (379)
Q Consensus       159 VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~-~i~~~~~~~~~~~l~~~~  237 (379)
                      ||+||+|.++++|+||+|||||.|++|.++++..|.|...++.++   ..++++.+.|+.. +-.+...+.++..--.+.
T Consensus       402 VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK---~lpl~~~e~~~~~~~~v~~~~~~li~~~y~~~  478 (543)
T KOG0342|consen  402 VVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLK---KLPLEEFEFPPLKPEDVQSQLEKLISKNYSLK  478 (543)
T ss_pred             EEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHh---hCCCcccCCCCCCHHHHHHHHHHHHHHHhhHH
Confidence            999999999999999999999999999999999999999999998   4455554444432 233334444443222222


Q ss_pred             ccchhchHHHHHHHHhh-----h--CHHHHHHHHHHHcCCCCCCC
Q 017020          238 PESVEFFTPTAQRLIEE-----K--GTDALAAALAQLSGFSRPPS  275 (379)
Q Consensus       238 ~~~~~~~~~~~~~l~~~-----~--~~~~~a~al~~~~~~~~~~~  275 (379)
                      ....+.|..+..-+-..     +  +.-.++ ++++.+|++.||.
T Consensus       479 ~aak~ay~syl~~y~s~slk~~~~~~~l~La-~~~~s~gf~~pp~  522 (543)
T KOG0342|consen  479 EAAKEAYKSYLGAYNSHSLKDIFNVNLLELA-AVAKSFGFSVPPA  522 (543)
T ss_pred             HHHHHHHHhhhhhccchhhhcccccchhhHH-HHHHHcCCCCCcc
Confidence            22222222222221111     1  123456 8899999987763

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=100.00  E-value=4.4e-43  Score=341.82  Aligned_cols=203  Identities=40%  Similarity=0.640  Sum_probs=185.3

Q ss_pred             CCCCChHHHHHHHHHhCCC---C----------------------CcEEEEeeeCChHHHHHHHHhcCCCceEEeecccc
Q 017020            1 MLAVGFEEDVELILENLPP---K----------------------RQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQD   55 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~---~----------------------~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~   55 (379)
                      |+||||.+|+..||.++|.   .                      +|+++||||||+.+..+++.||.+|+.+.+.  ..
T Consensus       408 miDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig--~~  485 (673)
T KOG0333|consen  408 MIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIG--SA  485 (673)
T ss_pred             hhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEec--cC
Confidence            8999999999999999983   1                      7999999999999999999999999998764  33


Q ss_pred             cccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhccc
Q 017020           56 EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR  134 (379)
Q Consensus        56 ~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~  134 (379)
                      ....+.++|.++.++..+|...|..++..+ ...++|||+|+++.|+.+++.|.+ ++.+..|||+-+|++|+.+++.|+
T Consensus       486 gk~~~rveQ~v~m~~ed~k~kkL~eil~~~-~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr  564 (673)
T KOG0333|consen  486 GKPTPRVEQKVEMVSEDEKRKKLIEILESN-FDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFR  564 (673)
T ss_pred             CCCccchheEEEEecchHHHHHHHHHHHhC-CCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHH
Confidence            455677888888888889999999999876 468999999999999999999986 899999999999999999999999


Q ss_pred             CCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHh
Q 017020          135 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  206 (379)
Q Consensus       135 ~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~  206 (379)
                      +|...||||||+|+||||||+|++|||||++.+.++|+||+|||||+|+.|++++|+++.+...+..|...+
T Consensus       565 ~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~v~ydLkq~l  636 (673)
T KOG0333|consen  565 EGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTAVFYDLKQAL  636 (673)
T ss_pred             hcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999966555554443

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=3.3e-41  Score=325.34  Aligned_cols=219  Identities=34%  Similarity=0.511  Sum_probs=198.7

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      +|||||.++++.||+.+|+++.|-|||||+..++.++++..++||+.|.+.......++..+..+|+.|++..|...|.+
T Consensus       169 LldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~  248 (567)
T KOG0345|consen  169 LLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVH  248 (567)
T ss_pred             HhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999988766555678889999999999999999999


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      +|..+ ..+++|||.+|+..+++.+..+..   ...+..+||.|++.+|.++++.|++....+|+|||++|||||||+|+
T Consensus       249 ~L~~~-~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD  327 (567)
T KOG0345|consen  249 LLNNN-KDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGID  327 (567)
T ss_pred             HHhcc-ccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCce
Confidence            99876 478999999999999999988874   67899999999999999999999998889999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHH
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVED  220 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~  220 (379)
                      +||+||+|.++++|+||+|||||+|+.|.+++|+.+.|..++..+.-.-....++...|....
T Consensus       328 ~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~aYveFl~i~~~v~le~~~~e~~~~  390 (567)
T KOG0345|consen  328 LVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEAYVEFLRIKGKVELERIDTEKASL  390 (567)
T ss_pred             EEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHHHHHHHHhcCccchhhhcccccch
Confidence            999999999999999999999999999999999999999888887655445555555554433

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=1.6e-40  Score=325.32  Aligned_cols=271  Identities=29%  Similarity=0.425  Sum_probs=219.3

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      ||||||.+.++.|++.+|+.+||+|||||.+..+.++++..++||..|.+-......++.+++|+|+.++..+|.++|..
T Consensus       227 ~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~s  306 (758)
T KOG0343|consen  227 MLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWS  306 (758)
T ss_pred             HHHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHHHHHHH
Confidence            79999999999999999999999999999999999999999999999988755567789999999999999999999999


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      ++..+ ...+.|||++|++++..+++.+.+   +++..++||.|+|..|..++.+|-....-||+|||+++||+|+|.|+
T Consensus       307 FI~sh-lk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVd  385 (758)
T KOG0343|consen  307 FIKSH-LKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVD  385 (758)
T ss_pred             HHHhc-cccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccc
Confidence            99887 468999999999999999998864   89999999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh-HHHHHHHHHHhCCCceeeCCCCHHHH--HHHHHHHHHHHHc
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ-RRTVRSLERDVGCKFEFVSPPVVEDV--LESSAEQVVATLN  234 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e-~~~l~~le~~~~~~~~~~~~p~~~~i--~~~~~~~~~~~l~  234 (379)
                      |||++|+|.++++|+||+|||+|.+..|.++++++|.| ..++..|++.. +.++.+.+. .+.+  .+..++.+...-.
T Consensus       386 wViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~k~-I~i~~i~i~-~~k~~~i~~~l~~ll~~~~  463 (758)
T KOG0343|consen  386 WVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQKKK-IPIKEIKID-PEKLTSIRNKLEALLAKDP  463 (758)
T ss_pred             eEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHHcC-CCHHhhccC-HHHhhhHHHHHHHHHhhCH
Confidence            99999999999999999999999999999999999998 66677777653 555543332 1211  2222222222222


Q ss_pred             ccCccchhchHHHHHHHHhhhCHHH------HHHHHHHHcCCCCCC
Q 017020          235 GVHPESVEFFTPTAQRLIEEKGTDA------LAAALAQLSGFSRPP  274 (379)
Q Consensus       235 ~~~~~~~~~~~~~~~~l~~~~~~~~------~a~al~~~~~~~~~~  274 (379)
                      .+..-....|..+++.+....++..      -+.|++..+|.+..|
T Consensus       464 eLk~~aqka~isY~rsi~~~rdK~~f~~~~l~~~afa~s~Gl~~~p  509 (758)
T KOG0343|consen  464 ELKEYAQKAFISYLRSIYLMRDKRVFDVEKLDIEAFADSLGLPGTP  509 (758)
T ss_pred             HHHHHHHHHHHHHHHHHHhhccchhhcchhccHHHHHHhcCCCCCc
Confidence            2222222345555555544333321      156777777765544

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=7.6e-40  Score=311.13  Aligned_cols=203  Identities=37%  Similarity=0.619  Sum_probs=186.5

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      ||||||..+|..||-.+.+++|+++.|||+|+.+.+++..|+++|..+- ++.-.-.....+++..+.....+|.+.+..
T Consensus       379 MLDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~-vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~  457 (629)
T KOG0336|consen  379 MLDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVY-VGSLDLVAVKSVKQNIIVTTDSEKLEIVQF  457 (629)
T ss_pred             hhcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEE-ecccceeeeeeeeeeEEecccHHHHHHHHH
Confidence            8999999999999999999999999999999999999999999998774 343333445567788888888899999999


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ++...++..++||||..+..|+.|...|. .++.+..+||+-+|.+|+..++.|++|+++||||||+++||+|+|+++||
T Consensus       458 f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV  537 (629)
T KOG0336|consen  458 FVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHV  537 (629)
T ss_pred             HHHhcCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhccee
Confidence            99988888999999999999999999887 58999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHH
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  204 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~  204 (379)
                      +|||+|.+.+.|+||+|||||+|++|.+++|++.+++.+...|-+
T Consensus       538 ~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~a~eLI~  582 (629)
T KOG0336|consen  538 YNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEELIQ  582 (629)
T ss_pred             eccCCCccHHHHHHHhcccccCCCCcceEEEEehhhHHHHHHHHH
Confidence            999999999999999999999999999999999999887776643

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.7e-39  Score=312.11  Aligned_cols=213  Identities=35%  Similarity=0.564  Sum_probs=188.4

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC---ccHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA---TSKRTI   77 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~---~~k~~~   77 (379)
                      ||+-||.++|.+|+..+|+++|++||||||+.+|.++++..|++|+.|-+.+  +..+...+.+.|+...+   .++...
T Consensus       339 MLeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~--~~~~a~~LtQEFiRIR~~re~dRea~  416 (691)
T KOG0338|consen  339 MLEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDP--NKDTAPKLTQEFIRIRPKREGDREAM  416 (691)
T ss_pred             HHHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCC--ccccchhhhHHHheeccccccccHHH
Confidence            8999999999999999999999999999999999999999999999996643  34456667776665543   357777


Q ss_pred             HHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCcc
Q 017020           78 LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV  156 (379)
Q Consensus        78 L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v  156 (379)
                      |..++... ...++|||+.|++.|..+.-.|.- ++.+.-+||.|+|.+|-..++.|+++++++|||||+|+||+||++|
T Consensus       417 l~~l~~rt-f~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV  495 (691)
T KOG0338|consen  417 LASLITRT-FQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGV  495 (691)
T ss_pred             HHHHHHHh-cccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccce
Confidence            88887765 368999999999999999988874 8999999999999999999999999999999999999999999999


Q ss_pred             ceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHH---hCCCceeeCCC
Q 017020          157 DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD---VGCKFEFVSPP  216 (379)
Q Consensus       157 ~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~---~~~~~~~~~~p  216 (379)
                      ..||||++|.+.+.|+||+|||+|+|+.|.+++|+...|+..++.+-+.   .+.++....+|
T Consensus       496 ~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~~~~a~~klk~R~i~  558 (691)
T KOG0338|consen  496 QTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKSSTKAGSKLKNRNIP  558 (691)
T ss_pred             eEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhhhhhcccchhhcCCC
Confidence            9999999999999999999999999999999999999999999998766   44555443333

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.2e-38  Score=295.05  Aligned_cols=210  Identities=30%  Similarity=0.540  Sum_probs=198.9

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      ||+.-|.+-++.++..+|+++|++|||||+|-.+..+..++|++|..|.+-   ++.+..++.+||..+.+.+|...|..
T Consensus       239 lLs~~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM---~eLtl~GvtQyYafV~e~qKvhCLnt  315 (459)
T KOG0326|consen  239 LLSVDFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLM---EELTLKGVTQYYAFVEERQKVHCLNT  315 (459)
T ss_pred             hhchhhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehh---hhhhhcchhhheeeechhhhhhhHHH
Confidence            578889999999999999999999999999999999999999999999875   45567889999999999999999998


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      +...+. -.++|||||+...++.+|..+.. ++++.++|+.|-|++|.+++.+|++|..+.|||||.+-||||++.+++|
T Consensus       316 LfskLq-INQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvV  394 (459)
T KOG0326|consen  316 LFSKLQ-INQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVV  394 (459)
T ss_pred             HHHHhc-ccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEE
Confidence            887774 67899999999999999999986 9999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeC
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~  214 (379)
                      ||||+|.+.++|+||+||.||.|.-|.++.+++-.|+..+.++|..+|..+++++
T Consensus       395 INFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~L~~IE~eLGtEI~pip  449 (459)
T KOG0326|consen  395 INFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIEQELGTEIKPIP  449 (459)
T ss_pred             EecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhhHHHHHHHhccccccCC
Confidence            9999999999999999999999999999999999999999999999999988755

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.4e-38  Score=294.23  Aligned_cols=215  Identities=32%  Similarity=0.512  Sum_probs=192.3

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      ||+-+|-++++.|.+.+|..+|+++||||+.+.+.++..--..++............+.+.+.+.|+.++...|...|..
T Consensus       165 vL~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vkdaYLv~  244 (442)
T KOG0340|consen  165 VLAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVKDAYLVH  244 (442)
T ss_pred             hhccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhhHHHHHH
Confidence            68889999999999999999999999999999888876544444222222233455677888999999999899999999


Q ss_pred             HHHHHcC--CCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           81 LITVYAK--GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        81 ll~~~~~--~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      +|..+..  .+.++||+||..+|+.++..|.. .+.+..+||.|+|.+|...+.+|+++..+||||||||+||+|||.|+
T Consensus       245 ~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~  324 (442)
T KOG0340|consen  245 LLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVE  324 (442)
T ss_pred             HHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCcee
Confidence            9987744  67899999999999999999986 89999999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCC
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  215 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~  215 (379)
                      +|||||+|.++.+|+||+|||+|+|+.|.+++++++.+.+.+..||...|.+.++...
T Consensus       325 LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~~igkKl~e~~~  382 (442)
T KOG0340|consen  325 LVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEEEIGKKLTEYNK  382 (442)
T ss_pred             EEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHHHHhcccccccc
Confidence            9999999999999999999999999999999999999999999999999999876443

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=100.00  E-value=1.8e-38  Score=299.97  Aligned_cols=191  Identities=32%  Similarity=0.576  Sum_probs=164.1

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      |+||||.+||..|+..+...+|++|||||||..|..+++..+-+|+.|++- .. ...+-++-+..-.+..+.|.-.|.+
T Consensus       338 miDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVG-RA-GAAsldViQevEyVkqEaKiVylLe  415 (610)
T KOG0341|consen  338 MIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVG-RA-GAASLDVIQEVEYVKQEAKIVYLLE  415 (610)
T ss_pred             HhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecc-cc-cccchhHHHHHHHHHhhhhhhhHHH
Confidence            899999999999999999999999999999999999999999999999864 22 2222222222222333445444444


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      .|.  ....+++|||..+.+++.+.++|- ++..+.++||+-.|++|...++.|+.|+-+||||||+|+.|+|+|++.||
T Consensus       416 CLQ--KT~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHV  493 (610)
T KOG0341|consen  416 CLQ--KTSPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHV  493 (610)
T ss_pred             Hhc--cCCCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhh
Confidence            443  246799999999999999999986 69999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      ||||+|.+.+.|+||+|||||.|++|.+.+|+..+.
T Consensus       494 INyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~  529 (610)
T KOG0341|consen  494 INYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQ  529 (610)
T ss_pred             ccCCChHHHHHHHHHhcccCCCCCcceeeeeecccc
Confidence            999999999999999999999999999999998754

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.9e-36  Score=304.65  Aligned_cols=211  Identities=34%  Similarity=0.554  Sum_probs=188.8

Q ss_pred             CCCCChHHHHHHHHHhCCC--CCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH
Q 017020            1 MLAVGFEEDVELILENLPP--KRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL   78 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~--~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L   78 (379)
                      |+++||..++..|+..+|.  .+|+++||||+|..+..++..++.+|..+.+...  ......+.+.++.+....|...|
T Consensus       169 l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~--~~~~~~i~~~~~~~~~~~k~~~l  246 (423)
T PRK04837        169 MFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPE--QKTGHRIKEELFYPSNEEKMRLL  246 (423)
T ss_pred             HhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCC--CcCCCceeEEEEeCCHHHHHHHH
Confidence            6899999999999999984  6788999999999999999999999988876432  23345666666666667788888


Q ss_pred             HHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           79 SDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        79 ~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      ..++... ...++||||+|+..|+.++..|.. ++.+..+||+|++++|..++++|++|+++||||||+++||||+|+++
T Consensus       247 ~~ll~~~-~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~  325 (423)
T PRK04837        247 QTLIEEE-WPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVT  325 (423)
T ss_pred             HHHHHhc-CCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccC
Confidence            8888764 468999999999999999999975 89999999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeC
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~  214 (379)
                      +|||||+|.+.++|+||+|||||+|+.|.+++|+++.+...+..++++.+..++..+
T Consensus       326 ~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i~~~~~~~~~~~~  382 (423)
T PRK04837        326 HVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAIETYIGHSIPVSK  382 (423)
T ss_pred             EEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHHHHHhCCCCCCcc
Confidence            999999999999999999999999999999999999999999999999988875433

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.1e-36  Score=288.75  Aligned_cols=210  Identities=34%  Similarity=0.605  Sum_probs=197.2

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      ||.-||.|+|..|++.+|++.|++++|||+|+++..+.++|+.+|+.|.+..  ...+...++++|+.+....|.+.|.+
T Consensus       181 mLs~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk--~~ltl~gikq~~i~v~k~~k~~~l~d  258 (397)
T KOG0327|consen  181 MLSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKK--DELTLEGIKQFYINVEKEEKLDTLCD  258 (397)
T ss_pred             hhccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecc--hhhhhhheeeeeeeccccccccHHHH
Confidence            7899999999999999999999999999999999999999999999997653  34567889999999888889999888


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      +.+   .-.+++|||||++.++.+...|.. ++.+.++||+|.|.+|+.++..|+.|+.+|||+||.++||+|+.+++.|
T Consensus       259 l~~---~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slv  335 (397)
T KOG0327|consen  259 LYR---RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLV  335 (397)
T ss_pred             HHH---hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhccee
Confidence            887   357899999999999999999975 7999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCC
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  215 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~  215 (379)
                      |||++|...++|+||+||+||.|++|.++.+++..+...++.+|+.++..+++.+.
T Consensus       336 inydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk~ie~~y~~~i~e~p~  391 (397)
T KOG0327|consen  336 VNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDIEKFYNTPIEELPS  391 (397)
T ss_pred             eeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHHhHHHhcCCcceeccc
Confidence            99999999999999999999999999999999999999999999999999987653

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=4.5e-36  Score=304.61  Aligned_cols=214  Identities=39%  Similarity=0.605  Sum_probs=192.2

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      |+++||..++..|+..+|..+|+++||||+|+++..++.+++.+|..+.+...  ......+.+++..++...+.+++..
T Consensus       161 ll~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~--~~~~~~i~~~~~~~~~~~k~~~l~~  238 (456)
T PRK10590        161 MLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARR--NTASEQVTQHVHFVDKKRKRELLSQ  238 (456)
T ss_pred             HhccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecc--cccccceeEEEEEcCHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999988876432  2334567777777777778888877


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ++... ...++||||+|+..++.++..|.. ++.+..+||+|++.+|..++++|++|+++||||||+++||+|+|++++|
T Consensus       239 l~~~~-~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~V  317 (456)
T PRK10590        239 MIGKG-NWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHV  317 (456)
T ss_pred             HHHcC-CCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEE
Confidence            77653 457999999999999999999975 8999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCC
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPV  217 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~  217 (379)
                      |||++|.++++|+||+|||||+|..|.+++|+...|...++.+|+.++.+++...++.
T Consensus       318 I~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie~~l~~~~~~~~~~~  375 (456)
T PRK10590        318 VNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEIPRIAIPG  375 (456)
T ss_pred             EEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHHHHhcCCCcccccCC
Confidence            9999999999999999999999999999999999999999999999988886655443

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.8e-36  Score=284.21  Aligned_cols=215  Identities=31%  Similarity=0.496  Sum_probs=192.8

Q ss_pred             CChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC-ccHHHHHHHHH
Q 017020            4 VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSDLI   82 (379)
Q Consensus         4 ~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll   82 (379)
                      .||.|+--.|...+|++.|.++||||+...+..++.+..++|..+.+.  .+.....++.++|+.|+. .+|.++|..+.
T Consensus       248 qG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk--~eel~L~~IkQlyv~C~~~~~K~~~l~~ly  325 (477)
T KOG0332|consen  248 QGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILK--REELALDNIKQLYVLCACRDDKYQALVNLY  325 (477)
T ss_pred             ccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeee--hhhccccchhhheeeccchhhHHHHHHHHH
Confidence            499999999999999999999999999999999999999999888664  344556888888887765 57999988876


Q ss_pred             HHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020           83 TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus        83 ~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                      ... .-++.||||.|++.|..++..|.. |+.|..+||+|.-.+|..++++||.|..+|||+|+|++||||++.|++|||
T Consensus       326 g~~-tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvN  404 (477)
T KOG0332|consen  326 GLL-TIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVN  404 (477)
T ss_pred             hhh-hhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEe
Confidence            655 368999999999999999999985 999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC------ChhHHHHHHhhccCCCCCceEEEEeChh-hHHHHHHHHHHhCCCceeeCCCCHHHH
Q 017020          162 YELPN------DPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFVSPPVVEDV  221 (379)
Q Consensus       162 ~~~P~------~~~~yiqR~GRtgR~G~~g~~i~l~~~~-e~~~l~~le~~~~~~~~~~~~p~~~~i  221 (379)
                      ||+|.      +.+.|+||+|||||.|+.|.++.++... ....+..|+++++.++....+.+.+++
T Consensus       405 ydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~i~~~~~~d~~E~  471 (477)
T KOG0332|consen  405 YDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMKIKRLDPDDLDEL  471 (477)
T ss_pred             cCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhcceecCCccHHHH
Confidence            99995      7899999999999999999999999765 567888999999999988777555544

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=7.1e-36  Score=308.64  Aligned_cols=206  Identities=34%  Similarity=0.579  Sum_probs=183.4

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcC-CCceEEeecccccccccceEEEEEEcCCccHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLD-NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~-~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~   79 (379)
                      ||+|||.+++..|+..+++++|+++||||+|.++..+++.++. +|..+.+... ......++.+.+..+....|...|.
T Consensus       289 mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~-~l~~~~~i~q~~~~~~~~~k~~~L~  367 (545)
T PTZ00110        289 MLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSL-DLTACHNIKQEVFVVEEHEKRGKLK  367 (545)
T ss_pred             hhhcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCC-ccccCCCeeEEEEEEechhHHHHHH
Confidence            7899999999999999999999999999999999999999886 5777765322 2233456777777777778888888


Q ss_pred             HHHHHHc-CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           80 DLITVYA-KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        80 ~ll~~~~-~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      .++.... .+.++||||+|++.|+.++..|.. ++.+..+||+|++++|+.++++|++|+.+||||||+++||||+|+|+
T Consensus       368 ~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~  447 (545)
T PTZ00110        368 MLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVK  447 (545)
T ss_pred             HHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCC
Confidence            8887653 567999999999999999999984 89999999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhC
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  207 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~  207 (379)
                      +|||||+|.+.++|+||+|||||+|+.|.|++|+++.+...++.+.+.+.
T Consensus       448 ~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~~~~~l~~~l~  497 (545)
T PTZ00110        448 YVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLR  497 (545)
T ss_pred             EEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999888877766643

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=3.2e-36  Score=296.16  Aligned_cols=202  Identities=41%  Similarity=0.657  Sum_probs=178.3

Q ss_pred             CCC-CChHHHHHHHHHhCCC----CCcEEEEeeeCChHHHHHHHHhcCC-CceEEeecccccccccceEEEEEEcCCccH
Q 017020            1 MLA-VGFEEDVELILENLPP----KRQSMLFSATMPSWVKKLSRKYLDN-PLNIDLVGNQDEKLAEGIKLYAISTTATSK   74 (379)
Q Consensus         1 mL~-~GF~~di~~Il~~~p~----~~Q~llfSAT~p~~i~~l~~~~l~~-p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k   74 (379)
                      ||| |||.++|.+|+.....    ++|++|||||.|+++..++..|+.+ ...+.+.  .......++.+....+...+|
T Consensus       238 MlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~--rvg~~~~ni~q~i~~V~~~~k  315 (482)
T KOG0335|consen  238 MLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVG--RVGSTSENITQKILFVNEMEK  315 (482)
T ss_pred             hhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEe--eeccccccceeEeeeecchhh
Confidence            899 9999999999998854    8999999999999999999999986 5555543  234456888888888888889


Q ss_pred             HHHHHHHHHHHc---CCC-----cEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           75 RTILSDLITVYA---KGG-----KTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        75 ~~~L~~ll~~~~---~~~-----~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ...|.+++....   ..+     +++|||.|++.|+.++..|.. ++++..+||+-+|.+|++.++.|++|+..+||||+
T Consensus       316 r~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~  395 (482)
T KOG0335|consen  316 RSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATN  395 (482)
T ss_pred             HHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEeh
Confidence            888888887542   223     899999999999999999985 89999999999999999999999999999999999


Q ss_pred             ccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHH
Q 017020          146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  204 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~  204 (379)
                      +++||+|+|+|+||||||+|.+..+|+||+|||||+|+.|.+..|++.......+.|-+
T Consensus       396 VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L~~  454 (482)
T KOG0335|consen  396 VAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIAKALVE  454 (482)
T ss_pred             hhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhHHHHHH
Confidence            99999999999999999999999999999999999999999999999766555555433

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2e-35  Score=306.53  Aligned_cols=210  Identities=34%  Similarity=0.539  Sum_probs=188.0

Q ss_pred             CCCCChHHHHHHHHHhCCC--CCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH
Q 017020            1 MLAVGFEEDVELILENLPP--KRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL   78 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~--~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L   78 (379)
                      |+++||.+++..|+..+|.  .+|+++||||++..+..++..++.+|..+.+..  .......+.++++.+...+|...+
T Consensus       171 lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~--~~~~~~~i~q~~~~~~~~~k~~~L  248 (572)
T PRK04537        171 MFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVET--ETITAARVRQRIYFPADEEKQTLL  248 (572)
T ss_pred             HhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEecc--ccccccceeEEEEecCHHHHHHHH
Confidence            6899999999999999997  789999999999999999999999987765432  223445677777777767788887


Q ss_pred             HHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           79 SDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        79 ~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      ..++... .+.++||||+|+..|+.+++.|.. ++.+..+||+|++.+|+.+++.|++|+.+||||||++++|||+|+++
T Consensus       249 ~~ll~~~-~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~  327 (572)
T PRK04537        249 LGLLSRS-EGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVK  327 (572)
T ss_pred             HHHHhcc-cCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCC
Confidence            7777654 467999999999999999999975 89999999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceee
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV  213 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~  213 (379)
                      +|||||+|.+.++|+||+|||||.|+.|.|++|+++.+...+..+++.++.+++..
T Consensus       328 ~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i~~~~~~~~~~~  383 (572)
T PRK04537        328 YVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQKIPVE  383 (572)
T ss_pred             EEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHHHHHHcCCCCcc
Confidence            99999999999999999999999999999999999999999999999988777543

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=1.5e-34  Score=291.67  Aligned_cols=209  Identities=31%  Similarity=0.534  Sum_probs=186.3

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCCh-HHHHHHHHhcCCCceEEeecccccccccceEEEEEEcC-CccHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPS-WVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTT-ATSKRTIL   78 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~-~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~-~~~k~~~L   78 (379)
                      |+++||..+++.|...++...|+++||||++. .+..++..++.+|..+.+...  .....++.+++..+. ...|.+.|
T Consensus       159 ~l~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~--~~~~~~i~~~~~~~~~~~~k~~~l  236 (434)
T PRK11192        159 MLDMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPS--RRERKKIHQWYYRADDLEHKTALL  236 (434)
T ss_pred             HhCCCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCC--cccccCceEEEEEeCCHHHHHHHH
Confidence            78999999999999999999999999999985 588999999999988876532  233456677766654 35688888


Q ss_pred             HHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           79 SDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        79 ~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      ..++... ...++||||+++..++.++..|.. ++.+..+||+|++.+|..+++.|++|+++||||||++++|+|+|+++
T Consensus       237 ~~l~~~~-~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~  315 (434)
T PRK11192        237 CHLLKQP-EVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVS  315 (434)
T ss_pred             HHHHhcC-CCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCC
Confidence            8887653 468999999999999999999985 89999999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCcee
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF  212 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~  212 (379)
                      +|||||+|.+.+.|+||+|||||+|..|.++++++..|...+..+++++...++.
T Consensus       316 ~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i~~~~~~~~~~  370 (434)
T PRK11192        316 HVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIEEPLKA  370 (434)
T ss_pred             EEEEECCCCCHHHHhhcccccccCCCCceEEEEecHHHHHHHHHHHHHHhccccc
Confidence            9999999999999999999999999999999999999999999999988776644

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

Probab=100.00  E-value=2e-34  Score=296.53  Aligned_cols=204  Identities=28%  Similarity=0.452  Sum_probs=179.7

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      |+++||.+++..|+..++ ++|+++||||+|+++..++..++.++..+.+..  .......+.+.++.+....|...+..
T Consensus       282 ml~~gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~--~~~~~~~v~q~~~~~~~~~k~~~l~~  358 (518)
T PLN00206        282 MLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGN--PNRPNKAVKQLAIWVETKQKKQKLFD  358 (518)
T ss_pred             HhhcchHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCC--CCCCCcceeEEEEeccchhHHHHHHH
Confidence            789999999999999986 689999999999999999999999998887642  22334556777777777777777888


Q ss_pred             HHHHHc-CCCcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           81 LITVYA-KGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        81 ll~~~~-~~~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      ++.... ...++||||+|+..++.++..|..  ++.+..+||+|++.+|..++++|++|+.+||||||+++||+|+|+++
T Consensus       359 ~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~  438 (518)
T PLN00206        359 ILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVR  438 (518)
T ss_pred             HHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCC
Confidence            776542 236899999999999999999963  78999999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhC
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  207 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~  207 (379)
                      +|||||+|.+.++|+||+|||||+|..|.+++|+++.+...+..+.+.+.
T Consensus       439 ~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~~~l~  488 (518)
T PLN00206        439 QVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLK  488 (518)
T ss_pred             EEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999998877777766543

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.7e-33  Score=285.75  Aligned_cols=209  Identities=33%  Similarity=0.578  Sum_probs=186.5

Q ss_pred             CCCCChHHHHHHHHHhCCC--CCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH
Q 017020            1 MLAVGFEEDVELILENLPP--KRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL   78 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~--~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L   78 (379)
                      |+++||..++..|+..++.  ++|+++||||++..+.++++.++.+|..+.+...  .....++.+++..+...+|...+
T Consensus       249 l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~--~~~~~~~~~~~~~~~~~~k~~~l  326 (475)
T PRK01297        249 MLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPE--NVASDTVEQHVYAVAGSDKYKLL  326 (475)
T ss_pred             HHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccC--cCCCCcccEEEEEecchhHHHHH
Confidence            4789999999999999975  6799999999999999999999999988766432  22334556666666667888888


Q ss_pred             HHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           79 SDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        79 ~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      ..++... ...++||||++++.++.++..|.. ++.+..+||+|++++|.++++.|++|++++|||||++++|||+|+++
T Consensus       327 ~~ll~~~-~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~  405 (475)
T PRK01297        327 YNLVTQN-PWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGIS  405 (475)
T ss_pred             HHHHHhc-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCC
Confidence            8887654 357999999999999999999975 78999999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCcee
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF  212 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~  212 (379)
                      +||+|++|.+..+|+||+||+||.|+.|.+++|++++|..++..+|+.++.+++.
T Consensus       406 ~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~~~~~~~~~~~~  460 (475)
T PRK01297        406 HVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKISC  460 (475)
T ss_pred             EEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHHHHHHhCCCCcc
Confidence            9999999999999999999999999999999999999999999999999988753

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.3e-33  Score=269.21  Aligned_cols=206  Identities=26%  Similarity=0.477  Sum_probs=188.1

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      ||..||.+|+..|.+.+|+..|.+|+|||+..++..+-+.++++|+.+.+... +...+.++.||++.|..++|..++..
T Consensus       182 llsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~-el~~~dqL~Qy~v~cse~DKflllya  260 (569)
T KOG0346|consen  182 LLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEG-ELPNPDQLTQYQVKCSEEDKFLLLYA  260 (569)
T ss_pred             hhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccc-cCCCcccceEEEEEeccchhHHHHHH
Confidence            68899999999999999999999999999999999999999999999887643 33456889999999999999999999


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc-------------
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-------------  146 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv-------------  146 (379)
                      +++..--.++.|||+||.+.|..+...|+. |+..+.+.|.||.+.|-.++++|..|.++|+||||.             
T Consensus       261 llKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kg  340 (569)
T KOG0346|consen  261 LLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKG  340 (569)
T ss_pred             HHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccc
Confidence            987654468999999999999999999987 899999999999999999999999999999999992             


Q ss_pred             ----------------------cccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHH
Q 017020          147 ----------------------AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  204 (379)
Q Consensus       147 ----------------------~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~  204 (379)
                                            ++||||+.+|.+|+|||+|.++.+|+||+|||+|++++|.+++|+.|.|..-...+|.
T Consensus       341 k~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~  420 (569)
T KOG0346|consen  341 KSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLES  420 (569)
T ss_pred             cccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHhhhhHHHH
Confidence                                  3699999999999999999999999999999999999999999999999876666665


Q ss_pred             HhC
Q 017020          205 DVG  207 (379)
Q Consensus       205 ~~~  207 (379)
                      ...
T Consensus       421 ~~~  423 (569)
T KOG0346|consen  421 ILK  423 (569)
T ss_pred             HHh
Confidence            543

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=4.5e-33  Score=270.85  Aligned_cols=202  Identities=35%  Similarity=0.552  Sum_probs=176.9

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcC-CccHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTT-ATSKRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~-~~~k~~~L~   79 (379)
                      |.+|||..++..|-+++.+++|+|+||||++..|..+++.+|.+|+.+...  .-...+..|.|.+..++ ...|+..|.
T Consensus       382 mfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg--~vgean~dITQ~V~V~~s~~~Kl~wl~  459 (731)
T KOG0339|consen  382 MFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQG--EVGEANEDITQTVSVCPSEEKKLNWLL  459 (731)
T ss_pred             hhccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEe--ehhccccchhheeeeccCcHHHHHHHH
Confidence            899999999999999999999999999999999999999999999987443  22233455655554444 456777766


Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  158 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~  158 (379)
                      .-|......+++|||+..+..+++++..|. +++.+..+||+|.|.+|.+++.+|+.+...||||||+++||+|||++..
T Consensus       460 ~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikT  539 (731)
T KOG0339|consen  460 RHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKT  539 (731)
T ss_pred             HHhhhhccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccce
Confidence            666555557899999999999999999997 5899999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHH
Q 017020          159 IIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  204 (379)
Q Consensus       159 VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~  204 (379)
                      |||||+-.+++.|.||+|||||+|..|.+|+++++++....-.|-+
T Consensus       540 VvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~fAG~LVn  585 (731)
T KOG0339|consen  540 VVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHLVN  585 (731)
T ss_pred             eecccccchhHHHHHHhhhcccccccceeeEEechhhHHHhhHHHH
Confidence            9999999999999999999999999999999999999765554433

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=2.3e-32  Score=272.77  Aligned_cols=213  Identities=32%  Similarity=0.586  Sum_probs=185.4

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC-ccHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~   79 (379)
                      +++.||...+..++..++++.|++++|||+|.++.++...++.+|..+.+...  .....++.+++...+. ..+...+.
T Consensus       182 ~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~  259 (401)
T PTZ00424        182 MLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKD--ELTLEGIRQFYVAVEKEEWKFDTLC  259 (401)
T ss_pred             HHhcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCC--CcccCCceEEEEecChHHHHHHHHH
Confidence            35678999999999999999999999999999999999999999887754322  2234556666666543 34566666


Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  158 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~  158 (379)
                      .++... ...++||||+|++.++.++..|.. ++.+..+||+|++.+|..+++.|++|+++|||||+++++|+|+|++++
T Consensus       260 ~~~~~~-~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~  338 (401)
T PTZ00424        260 DLYETL-TITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSL  338 (401)
T ss_pred             HHHHhc-CCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCE
Confidence            666544 357899999999999999999975 789999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCC
Q 017020          159 IIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  216 (379)
Q Consensus       159 VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p  216 (379)
                      ||+||+|.+..+|+||+||+||.|+.|.|++++++++...++.+|+.....++..+++
T Consensus       339 VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~~~  396 (401)
T PTZ00424        339 VINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPME  396 (401)
T ss_pred             EEEECCCCCHHHEeecccccccCCCCceEEEEEcHHHHHHHHHHHHHHCCcccccCcc
Confidence            9999999999999999999999999999999999999999999999999887765443

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.5e-33  Score=274.26  Aligned_cols=207  Identities=30%  Similarity=0.481  Sum_probs=176.5

Q ss_pred             CCCCChHHHHHHHHHhC-------------CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeeccc-------------
Q 017020            1 MLAVGFEEDVELILENL-------------PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQ-------------   54 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~-------------p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~-------------   54 (379)
                      +||+||.+||+.|++.+             |...|.+|+||||...|.+++...++||+.|......             
T Consensus       299 lleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev  378 (708)
T KOG0348|consen  299 LLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEV  378 (708)
T ss_pred             HHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhc
Confidence            58999999999999887             2358999999999999999999999999999722100             


Q ss_pred             ----------ccccccceEEEEEEcCCccHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhcC----------
Q 017020           55 ----------DEKLAEGIKLYAISTTATSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI----------  111 (379)
Q Consensus        55 ----------~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~~----------  111 (379)
                                ...+++++.+.|..+|+.-++-.|..+|...   ....++|||.++.+.++.=+..+...          
T Consensus       379 ~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~  458 (708)
T KOG0348|consen  379 DDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSG  458 (708)
T ss_pred             CCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccC
Confidence                      0223556678888888888887777777543   23568999999999999777665421          


Q ss_pred             -------------CcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhc
Q 017020          112 -------------IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT  178 (379)
Q Consensus       112 -------------~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRt  178 (379)
                                   ..+.-+||+|+|++|..+++.|+.....||.||||++||+|+|+|++||+||+|.++++|+||+|||
T Consensus       459 ~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRT  538 (708)
T KOG0348|consen  459 APDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRT  538 (708)
T ss_pred             CcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhh
Confidence                         1356799999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCCCCCceEEEEeChhhHHHHHHHHHHhC
Q 017020          179 GRAGKEGTAILMFTSSQRRTVRSLERDVG  207 (379)
Q Consensus       179 gR~G~~g~~i~l~~~~e~~~l~~le~~~~  207 (379)
                      +|+|..|.+++|..|.|.++++.++.+..
T Consensus       539 ARaG~kG~alLfL~P~Eaey~~~l~~~~~  567 (708)
T KOG0348|consen  539 ARAGEKGEALLFLLPSEAEYVNYLKKHHI  567 (708)
T ss_pred             hhccCCCceEEEecccHHHHHHHHHhhcc
Confidence            99999999999999999999999987754

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.98  E-value=1.7e-33  Score=276.19  Aligned_cols=225  Identities=33%  Similarity=0.522  Sum_probs=183.7

Q ss_pred             CCCCChHHHHHHHHHhCC-----CCCcEEEEeeeCChH---------------------HHHHHHH--hcCCCceEEeec
Q 017020            1 MLAVGFEEDVELILENLP-----PKRQSMLFSATMPSW---------------------VKKLSRK--YLDNPLNIDLVG   52 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p-----~~~Q~llfSAT~p~~---------------------i~~l~~~--~l~~p~~i~~~~   52 (379)
                      |++-|+.+++..||..+.     ..+|++.||||++-.                     +..+.+.  +..+|..|++..
T Consensus       352 mvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpkiiD~t~  431 (731)
T KOG0347|consen  352 MVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGKPKIIDLTP  431 (731)
T ss_pred             HhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccCCCeeEecCc
Confidence            789999999999999986     468999999998431                     2222221  224677777653


Q ss_pred             ccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHh
Q 017020           53 NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLN  131 (379)
Q Consensus        53 ~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~  131 (379)
                        ...+...+..-.+.|+..+|.-.|..+|..|  ++++|||||+.+.+..|+-.|.. +++...+|+.|.|.+|.+.++
T Consensus       432 --q~~ta~~l~Es~I~C~~~eKD~ylyYfl~ry--PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLE  507 (731)
T KOG0347|consen  432 --QSATASTLTESLIECPPLEKDLYLYYFLTRY--PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLE  507 (731)
T ss_pred             --chhHHHHHHHHhhcCCccccceeEEEEEeec--CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHH
Confidence              3334444444455566666666666666555  68999999999999999999986 899999999999999999999


Q ss_pred             cccCCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCce
Q 017020          132 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE  211 (379)
Q Consensus       132 ~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~  211 (379)
                      +|++....|||||||||||+|||+|+|||||.+|.+.+.|+||+|||+|++..|.++.++.|.|...+++|.+.+..+.+
T Consensus       508 kF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~KL~ktL~k~~d  587 (731)
T KOG0347|consen  508 KFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKLCKTLKKKED  587 (731)
T ss_pred             HHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHHHHHHHHHhhccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999888877766


Q ss_pred             eeCCCCHHHHHHHHHHHH
Q 017020          212 FVSPPVVEDVLESSAEQV  229 (379)
Q Consensus       212 ~~~~p~~~~i~~~~~~~~  229 (379)
                      .-..|..+.++....+++
T Consensus       588 lpifPv~~~~m~~lkeRv  605 (731)
T KOG0347|consen  588 LPIFPVETDIMDALKERV  605 (731)
T ss_pred             CCceeccHHHHHHHHHHH
Confidence            544666677766554444

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.97  E-value=8.6e-32  Score=281.47  Aligned_cols=204  Identities=36%  Similarity=0.609  Sum_probs=188.7

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcC-CccHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTT-ATSKRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~-~~~k~~~L~   79 (379)
                      |+||||.+.+..|++.+++.+|+++||||+|..+..+++..++.|+.|.+.+  .......+.+.+..++ ...|...|.
T Consensus       527 mfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~--~svV~k~V~q~v~V~~~e~eKf~kL~  604 (997)
T KOG0334|consen  527 MFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGG--RSVVCKEVTQVVRVCAIENEKFLKLL  604 (997)
T ss_pred             hheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEcc--ceeEeccceEEEEEecCchHHHHHHH
Confidence            7899999999999999999999999999999999999999999999876543  3345566777776666 788999999


Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  158 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~  158 (379)
                      .+|..+....++||||.....|+.+...|.+ ++.+..+||+.+|.+|+.+++.|+++.+++||||++++||+|++++.+
T Consensus       605 eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~L  684 (997)
T KOG0334|consen  605 ELLGERYEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELIL  684 (997)
T ss_pred             HHHHHHhhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceE
Confidence            9998887789999999999999999999986 899999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHh
Q 017020          159 IIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  206 (379)
Q Consensus       159 VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~  206 (379)
                      |||||+|...++|+||+|||||+|++|.|++|+++.+..+.-.|.+.+
T Consensus       685 vvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~al  732 (997)
T KOG0334|consen  685 VVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKAL  732 (997)
T ss_pred             EEEcccchhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHHHH
Confidence            999999999999999999999999999999999999888888888877

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

Probab=99.97  E-value=3.2e-30  Score=274.34  Aligned_cols=232  Identities=19%  Similarity=0.271  Sum_probs=176.7

Q ss_pred             ChHHHHHHHHHhC-------CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcC-------
Q 017020            5 GFEEDVELILENL-------PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTT-------   70 (379)
Q Consensus         5 GF~~di~~Il~~~-------p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~-------   70 (379)
                      .|..++..+++.+       +.++|+++||||++.... ++++++.+|..+ +. ... .......+.++..+       
T Consensus       172 ~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~-i~-~~~-~~~~~~~~~~~~p~~~~~~~~  247 (742)
T TIGR03817       172 VFGSHVALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVA-VT-EDG-SPRGARTVALWEPPLTELTGE  247 (742)
T ss_pred             ccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEE-EC-CCC-CCcCceEEEEecCCccccccc
Confidence            3777766666543       567899999999998754 677888877544 22 111 11122222222221       


Q ss_pred             ---------CccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc---------CCcEEEeeCCCCHHHHHHHHhc
Q 017020           71 ---------ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---------IIASEALHGDISQHQRERTLNG  132 (379)
Q Consensus        71 ---------~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~---------~~~v~~lhg~m~~~~R~~~~~~  132 (379)
                               ...+...+..++.   .+.++||||+|++.|+.++..|..         +..+..+||+|++++|.+++++
T Consensus       248 ~~~~~r~~~~~~~~~~l~~l~~---~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~  324 (742)
T TIGR03817       248 NGAPVRRSASAEAADLLADLVA---EGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERA  324 (742)
T ss_pred             cccccccchHHHHHHHHHHHHH---CCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHH
Confidence                     1124444555543   468999999999999999998753         3578899999999999999999


Q ss_pred             ccCCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeC--hhhHHHHHHHHHHhCCCc
Q 017020          133 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT--SSQRRTVRSLERDVGCKF  210 (379)
Q Consensus       133 F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~--~~e~~~l~~le~~~~~~~  210 (379)
                      |++|++++|||||++++|||||++++||||+.|.+.++|+||+|||||.|+.|.++++..  +.|...+..+++.++.++
T Consensus       325 f~~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~~~  404 (742)
T TIGR03817       325 LRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDRPV  404 (742)
T ss_pred             HHcCCceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcCCC
Confidence            999999999999999999999999999999999999999999999999999999999986  567778888898988888


Q ss_pred             eee-CCCCHHHHHHHHHHHHHHHHcccCccchhch
Q 017020          211 EFV-SPPVVEDVLESSAEQVVATLNGVHPESVEFF  244 (379)
Q Consensus       211 ~~~-~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~  244 (379)
                      +.. ..|....++..++..+..++ .+..++.+.|
T Consensus       405 e~~~~~~~n~~il~~hl~~aa~e~-~l~~~~~~~~  438 (742)
T TIGR03817       405 EATVFDPDNPYVLGPHLCCAAAEL-PLTEADLELF  438 (742)
T ss_pred             ccceeCCCcHHHHHHHHHHHHhcC-CCChHHHHhh
Confidence            763 44777778888777766554 3444444444

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.

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=3e-31  Score=253.55  Aligned_cols=212  Identities=33%  Similarity=0.484  Sum_probs=196.4

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      +++|||.+++.+|+..+|..+|+++||||+|....++++..+.+|..|.+.  -+..+.+.++..+..+...+|..+|..
T Consensus       176 lfemgfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRld--vetkise~lk~~f~~~~~a~K~aaLl~  253 (529)
T KOG0337|consen  176 LFEMGFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLD--VETKISELLKVRFFRVRKAEKEAALLS  253 (529)
T ss_pred             HHhhhhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEee--hhhhcchhhhhheeeeccHHHHHHHHH
Confidence            368999999999999999999999999999999999999999999998764  245567788888888888999999999


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ++.....+.+++|||.|+..|+.+...|.. ++.+..++|.|.+..|...+.+|+.++..+||.||+++||+|||-.+.|
T Consensus       254 il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnv  333 (529)
T KOG0337|consen  254 ILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNV  333 (529)
T ss_pred             HHhccccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCcccccc
Confidence            988765567899999999999999999985 8999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeC
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~  214 (379)
                      ||||+|.+...|+||+||+.|+|++|.+|.++.+.+..++-.|.-.++..+....
T Consensus       334 inyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~yl~DL~lflgr~~~~~~  388 (529)
T KOG0337|consen  334 INYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPYLLDLQLFLGRPLIFAI  388 (529)
T ss_pred             ccccCCCCCceEEEEecchhhccccceEEEEEecccchhhhhhhhhcCCceeecc
Confidence            9999999999999999999999999999999999999999999999988776543

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

Probab=99.96  E-value=5.1e-29  Score=266.47  Aligned_cols=199  Identities=19%  Similarity=0.252  Sum_probs=156.4

Q ss_pred             CCCCC--hHHHHHHH--HHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCcc-HH
Q 017020            1 MLAVG--FEEDVELI--LENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KR   75 (379)
Q Consensus         1 mL~~G--F~~di~~I--l~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~-k~   75 (379)
                      |++.|  |+++...+  +....++.|+++||||+++.+.+.+...+.-...+.+... .  ...++.  |...+... ..
T Consensus       593 VSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~S-f--~RpNL~--y~Vv~k~kk~l  667 (1195)
T PLN03137        593 VSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQS-F--NRPNLW--YSVVPKTKKCL  667 (1195)
T ss_pred             hhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeecc-c--CccceE--EEEeccchhHH
Confidence            35667  88888764  4444567899999999999988866666653222222211 1  123332  22222222 23


Q ss_pred             HHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC
Q 017020           76 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP  154 (379)
Q Consensus        76 ~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip  154 (379)
                      ..+..++.....+.++||||+|+++|+.++..|.. ++.+..+||+|++++|..++++|++|+++|||||+++++|||+|
T Consensus       668 e~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkP  747 (1195)
T PLN03137        668 EDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKP  747 (1195)
T ss_pred             HHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCcc
Confidence            44555554433456899999999999999999985 89999999999999999999999999999999999999999999


Q ss_pred             ccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHH
Q 017020          155 NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  204 (379)
Q Consensus       155 ~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~  204 (379)
                      +|++||||++|.++++|+||+|||||.|..|.|++||+..|...++.+..
T Consensus       748 DVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI~  797 (1195)
T PLN03137        748 DVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMIS  797 (1195)
T ss_pred             CCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999988877776653

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.96  E-value=1.5e-29  Score=252.05  Aligned_cols=190  Identities=29%  Similarity=0.509  Sum_probs=170.8

Q ss_pred             CChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCc--------cHH
Q 017020            4 VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT--------SKR   75 (379)
Q Consensus         4 ~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~--------~k~   75 (379)
                      -.|.++|..|+..+|..+|++.||||.|........+||++|..|.....  ....-++++|++..+..        .|.
T Consensus       183 ~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~--d~~L~GikQyv~~~~s~nnsveemrlkl  260 (980)
T KOG4284|consen  183 ESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNAD--DVQLFGIKQYVVAKCSPNNSVEEMRLKL  260 (980)
T ss_pred             hhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccC--CceeechhheeeeccCCcchHHHHHHHH
Confidence            35999999999999999999999999999999999999999999977532  33456788887765542        277


Q ss_pred             HHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC
Q 017020           76 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP  154 (379)
Q Consensus        76 ~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip  154 (379)
                      +.|.++++.+ +..++||||+....|+.++..|.. |+.|.++.|.|+|.+|..+++.+|.-..+|||+||+.+||||-|
T Consensus       261 q~L~~vf~~i-py~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~  339 (980)
T KOG4284|consen  261 QKLTHVFKSI-PYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDAD  339 (980)
T ss_pred             HHHHHHHhhC-chHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCcc
Confidence            7788888776 467999999999999999999985 99999999999999999999999999999999999999999999


Q ss_pred             ccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhH
Q 017020          155 NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  196 (379)
Q Consensus       155 ~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~  196 (379)
                      ++++|||.|+|.+.++|.||+||+||.|..|.+++|+...+.
T Consensus       340 ~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  340 NVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             ccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchh
Confidence            999999999999999999999999999999999999876543

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.96  E-value=1.2e-28  Score=251.26  Aligned_cols=196  Identities=23%  Similarity=0.378  Sum_probs=154.3

Q ss_pred             CCCC--hHHHHHHH---HHhCCCCCcEEEEeeeCChHHHHHHHHhc--CCCceEEeecccccccccceEEEEEEcCCccH
Q 017020            2 LAVG--FEEDVELI---LENLPPKRQSMLFSATMPSWVKKLSRKYL--DNPLNIDLVGNQDEKLAEGIKLYAISTTATSK   74 (379)
Q Consensus         2 L~~G--F~~di~~I---l~~~p~~~Q~llfSAT~p~~i~~l~~~~l--~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k   74 (379)
                      ++.|  |+++...|   .... ++.|++++|||+++.+.......+  .+|..+...   ..  ..++.. .+.......
T Consensus       140 ~~~g~~fr~~~~~l~~l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s---~~--r~nl~~-~v~~~~~~~  212 (470)
T TIGR00614       140 SQWGHDFRPDYKALGSLKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFCTS---FD--RPNLYY-EVRRKTPKI  212 (470)
T ss_pred             CccccccHHHHHHHHHHHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCC---CC--CCCcEE-EEEeCCccH
Confidence            4555  77776654   3444 578999999999998876655554  355544221   11  123322 222222234


Q ss_pred             HHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCC
Q 017020           75 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI  153 (379)
Q Consensus        75 ~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDi  153 (379)
                      .+.+..++....++..+||||+|++.|+.++..|.. ++.+..+||+|++++|..++++|++|+++|||||+++++|||+
T Consensus       213 ~~~l~~~l~~~~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~  292 (470)
T TIGR00614       213 LEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINK  292 (470)
T ss_pred             HHHHHHHHHHhcCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCc
Confidence            444555554333456779999999999999999985 8999999999999999999999999999999999999999999


Q ss_pred             CccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHH
Q 017020          154 PNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  204 (379)
Q Consensus       154 p~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~  204 (379)
                      |+|++||||++|.+.++|+||+|||||.|..|.|++++++.+...++.+..
T Consensus       293 p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~~  343 (470)
T TIGR00614       293 PDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLM  343 (470)
T ss_pred             ccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechhHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999888877754

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

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.96  E-value=3.8e-29  Score=248.18  Aligned_cols=199  Identities=30%  Similarity=0.469  Sum_probs=173.9

Q ss_pred             ChHHHHHHHHHhCC-CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEc-CCccHHHHHHHHH
Q 017020            5 GFEEDVELILENLP-PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAIST-TATSKRTILSDLI   82 (379)
Q Consensus         5 GF~~di~~Il~~~p-~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~-~~~~k~~~L~~ll   82 (379)
                      +|.+++..|++.+. ++..+-+||||+|..++++++..+.++..|.+. ..+. ....+.|..+.+ ....|.-++..++
T Consensus       305 ~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg-~~~s-a~~~V~QelvF~gse~~K~lA~rq~v  382 (593)
T KOG0344|consen  305 FFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVG-LRNS-ANETVDQELVFCGSEKGKLLALRQLV  382 (593)
T ss_pred             hHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEe-cchh-HhhhhhhhheeeecchhHHHHHHHHH
Confidence            89999999999885 466777999999999999999999999888553 2222 244555554444 4457888888888


Q ss_pred             HHHcCCCcEEEEecccccHHHHHHHHh--cCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE
Q 017020           83 TVYAKGGKTIVFTQTKRDADEVSLALT--SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII  160 (379)
Q Consensus        83 ~~~~~~~~~IIF~~t~~~~~~l~~~L~--~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI  160 (379)
                      ..- -..+++||+.+.+.|.+|...|.  .++.+.++||+.++.+|+.++++||.|++++|||||+++||+|+.+++.||
T Consensus       383 ~~g-~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VI  461 (593)
T KOG0344|consen  383 ASG-FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVI  461 (593)
T ss_pred             hcc-CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEE
Confidence            764 46899999999999999999995  488999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHh
Q 017020          161 HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  206 (379)
Q Consensus       161 ~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~  206 (379)
                      |||+|.+.-+|+||+||+||+|+.|.+|+||+..+..+++.++...
T Consensus       462 nyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae~~  507 (593)
T KOG0344|consen  462 NYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAEVM  507 (593)
T ss_pred             ecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHHHH
Confidence            9999999999999999999999999999999999999988886654

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.96  E-value=1.8e-27  Score=248.73  Aligned_cols=235  Identities=16%  Similarity=0.243  Sum_probs=166.9

Q ss_pred             CCCChHHHHHHHHHhCC-CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC---------
Q 017020            2 LAVGFEEDVELILENLP-PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA---------   71 (379)
Q Consensus         2 L~~GF~~di~~Il~~~p-~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~---------   71 (379)
                      +.+|  +.+..++...+ ..+|+++||||+|.++..+ ..|+++|..+.+.+    .+...++++|+....         
T Consensus       304 ~~~~--DllL~llk~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~g----rt~~pV~~~yi~~~~~~~~~~~y~  376 (675)
T PHA02653        304 DQIG--DIIIAVARKHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPG----GTLFPISEVYVKNKYNPKNKRAYI  376 (675)
T ss_pred             ccch--hHHHHHHHHhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCC----CcCCCeEEEEeecCcccccchhhh
Confidence            4455  45666666554 4469999999999998887 57999998887642    233556777764331         


Q ss_pred             -ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcc-cCCceeEEEecc
Q 017020           72 -TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGF-RQGKFTVLVATD  145 (379)
Q Consensus        72 -~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F-~~g~~~iLVaTd  145 (379)
                       ..+..++..+.... ..++++||||+++.+++.+++.|..   ++.+..+||+|++.  ++.+++| ++|+.+||||||
T Consensus       377 ~~~k~~~l~~L~~~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATd  454 (675)
T PHA02653        377 EEEKKNIVTALKKYTPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTP  454 (675)
T ss_pred             HHHHHHHHHHHHHhhcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccC
Confidence             12333333333222 1356899999999999999999985   58899999999985  5677777 789999999999


Q ss_pred             ccccCCCCCccceEEecC---CCC---------ChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceee
Q 017020          146 VAARGLDIPNVDLIIHYE---LPN---------DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV  213 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~---~P~---------~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~  213 (379)
                      +|+||||||+|++||++|   .|.         +.++|+||+|||||. ++|.|+.|+++.+...+              
T Consensus       455 IAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~~pI--------------  519 (675)
T PHA02653        455 YLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLLKPI--------------  519 (675)
T ss_pred             hhhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHhHHH--------------
Confidence            999999999999999999   665         888999999999999 79999999999874222              


Q ss_pred             CCCCHHHHHHHHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcCCC
Q 017020          214 SPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFS  271 (379)
Q Consensus       214 ~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~  271 (379)
                           .++....+..++..++.+.....+.+      +++.++.+.+.+|+..|...+
T Consensus       520 -----~ri~~~~L~~~vL~lk~~g~~~~~~~------~ldpP~~~~l~~A~~~L~~lg  566 (675)
T PHA02653        520 -----KRIDSEFLHNYILYAKYFNLTLPEDL------FVIPSNLDRLRKTEEYIDSFN  566 (675)
T ss_pred             -----HHHhHHHHHHHHHHHHHcCCCCcccc------cCCCCCHHHHHHHHHHHHHcC
Confidence                 22222223444444444433221111      566677777777666664443

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.95  E-value=1.7e-27  Score=249.27  Aligned_cols=189  Identities=20%  Similarity=0.371  Sum_probs=148.7

Q ss_pred             hHHHHHHH---HHhCCCCCcEEEEeeeCChHHHHHHHHhc--CCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            6 FEEDVELI---LENLPPKRQSMLFSATMPSWVKKLSRKYL--DNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         6 F~~di~~I---l~~~p~~~Q~llfSAT~p~~i~~l~~~~l--~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      |++++..|   .+.. ++.|++++|||+++.+.......+  .+|... ...  .  ...++..  .......+...+..
T Consensus       158 fr~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~-~~~--~--~r~nl~~--~v~~~~~~~~~l~~  229 (607)
T PRK11057        158 FRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQ-ISS--F--DRPNIRY--TLVEKFKPLDQLMR  229 (607)
T ss_pred             ccHHHHHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEE-ECC--C--CCCccee--eeeeccchHHHHHH
Confidence            77665444   4444 478999999999988766444443  344432 211  1  1223322  22222334444555


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ++... .+.++||||+|+++|+.++..|.. ++.+..+||+|++++|..+++.|++|+.+|||||+++++|||+|+|++|
T Consensus       230 ~l~~~-~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~V  308 (607)
T PRK11057        230 YVQEQ-RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFV  308 (607)
T ss_pred             HHHhc-CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEE
Confidence            55443 468999999999999999999985 8999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHH
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                      ||||+|.+.++|+||+|||||.|..|.|++|+++.+...++.+.
T Consensus       309 I~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~~~~  352 (607)
T PRK11057        309 VHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  352 (607)
T ss_pred             EEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999987777664

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.95  E-value=8.3e-27  Score=248.90  Aligned_cols=243  Identities=17%  Similarity=0.240  Sum_probs=175.9

Q ss_pred             CCCCChHHH-HHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHH----
Q 017020            1 MLAVGFEED-VELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKR----   75 (379)
Q Consensus         1 mL~~GF~~d-i~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~----   75 (379)
                      ||+.+|.-. +..+.+.++++.|+++||||++...   ...|+.++..|.+.+.     ...++++|...+..++.    
T Consensus       126 ~L~~Dl~L~ll~~i~~~lr~dlqlIlmSATl~~~~---l~~~l~~~~vI~~~gr-----~~pVe~~y~~~~~~~~~~~~v  197 (819)
T TIGR01970       126 SLDADLGLALALDVQSSLREDLKILAMSATLDGER---LSSLLPDAPVVESEGR-----SFPVEIRYLPLRGDQRLEDAV  197 (819)
T ss_pred             hhccchHHHHHHHHHHhcCCCceEEEEeCCCCHHH---HHHHcCCCcEEEecCc-----ceeeeeEEeecchhhhHHHHH
Confidence            355444322 3455666788999999999998754   3568877766765432     12356777665444432    


Q ss_pred             -HHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccC
Q 017020           76 -TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG  150 (379)
Q Consensus        76 -~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rG  150 (379)
                       ..+..++..  ..+++||||+++.+++.++..|..    ++.+..+||+|++++|.++++.|++|..+||||||++++|
T Consensus       198 ~~~l~~~l~~--~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErg  275 (819)
T TIGR01970       198 SRAVEHALAS--ETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETS  275 (819)
T ss_pred             HHHHHHHHHh--cCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhc
Confidence             223333332  357899999999999999999974    5789999999999999999999999999999999999999


Q ss_pred             CCCCccceEEecCCCC------------------ChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCcee
Q 017020          151 LDIPNVDLIIHYELPN------------------DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF  212 (379)
Q Consensus       151 iDip~v~~VI~~~~P~------------------~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~  212 (379)
                      ||||+|++|||+++|.                  +..+|.||+||+||. +.|.||.+++..+...+   ..+       
T Consensus       276 ItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~~~l---~~~-------  344 (819)
T TIGR01970       276 LTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQHQRL---PAQ-------  344 (819)
T ss_pred             ccccCceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHHHhh---hcC-------
Confidence            9999999999999885                  335699999999999 69999999998775433   221       


Q ss_pred             eCCCCHHHHHHHHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcCCCCC
Q 017020          213 VSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRP  273 (379)
Q Consensus       213 ~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~~~  273 (379)
                          ...+|....+..++-.+..+...+...|     .+++.+...++.+|+..|...+..
T Consensus       345 ----~~PEI~r~~L~~~~L~l~~~g~~~~~~~-----~~l~~P~~~~i~~a~~~L~~lgal  396 (819)
T TIGR01970       345 ----DEPEILQADLSGLALELAQWGAKDPSDL-----RWLDAPPSVALAAARQLLQRLGAL  396 (819)
T ss_pred             ----CCcceeccCcHHHHHHHHHcCCCChhhC-----CCCCCcCHHHHHHHHHHHHHCCCC
Confidence                1234455555556666665543333323     356677778888887777554433

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

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

Probab=99.94  E-value=1.4e-26  Score=244.12  Aligned_cols=183  Identities=21%  Similarity=0.289  Sum_probs=141.9

Q ss_pred             CCCChHHHHHHHHHhC--CCC---CcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH
Q 017020            2 LAVGFEEDVELILENL--PPK---RQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT   76 (379)
Q Consensus         2 L~~GF~~di~~Il~~~--p~~---~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~   76 (379)
                      |+|||.++++.|++.+  |+.   +|+++||||+|.++.+++..++.+|..+.+..  ......++.++ +.++...|..
T Consensus       182 Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~--~~l~a~ki~q~-v~v~~e~Kl~  258 (844)
T TIGR02621       182 LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLK--KRLAAKKIVKL-VPPSDEKFLS  258 (844)
T ss_pred             hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeeccc--ccccccceEEE-EecChHHHHH
Confidence            6899999999999975  443   69999999999999999988988887776542  22333455554 3333334443


Q ss_pred             HHHHHH-HHH-cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHH-----HHHhcccC----Cc-------
Q 017020           77 ILSDLI-TVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRE-----RTLNGFRQ----GK-------  137 (379)
Q Consensus        77 ~L~~ll-~~~-~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~-----~~~~~F~~----g~-------  137 (379)
                      .+...+ ... ..++++||||||++.|+.+++.|.. ++  ..+||+|+|.+|+     .++++|++    |+       
T Consensus       259 ~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g  336 (844)
T TIGR02621       259 TMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQG  336 (844)
T ss_pred             HHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhcccccccccccccc
Confidence            322222 111 2457899999999999999999975 44  8999999999999     88999987    44       


Q ss_pred             eeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCC-ceEEEEeC
Q 017020          138 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE-GTAILMFT  192 (379)
Q Consensus       138 ~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~-g~~i~l~~  192 (379)
                      ..||||||++++|+||+. ++||++..|  .++|+||+||+||.|+. +..+.++.
T Consensus       337 ~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~  389 (844)
T TIGR02621       337 TVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVH  389 (844)
T ss_pred             ceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEe
Confidence            689999999999999986 899998776  69999999999999975 34355553

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.94  E-value=1.7e-26  Score=246.93  Aligned_cols=233  Identities=18%  Similarity=0.251  Sum_probs=177.1

Q ss_pred             HHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH-----HHHHHHHHH
Q 017020           11 ELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-----ILSDLITVY   85 (379)
Q Consensus        11 ~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-----~L~~ll~~~   85 (379)
                      ..+++.++++.|+++||||++.+  .+ ..|+.++..|.+.+.     ...++++|+..+..++.+     .+..++.. 
T Consensus       140 ~~i~~~lr~~lqlilmSATl~~~--~l-~~~~~~~~~I~~~gr-----~~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~-  210 (812)
T PRK11664        140 LDVQQGLRDDLKLLIMSATLDND--RL-QQLLPDAPVIVSEGR-----SFPVERRYQPLPAHQRFDEAVARATAELLRQ-  210 (812)
T ss_pred             HHHHHhCCccceEEEEecCCCHH--HH-HHhcCCCCEEEecCc-----cccceEEeccCchhhhHHHHHHHHHHHHHHh-
Confidence            34567788899999999999875  23 467877776755432     123677777665544443     23333322 


Q ss_pred             cCCCcEEEEecccccHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020           86 AKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus        86 ~~~~~~IIF~~t~~~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                       ..+.+||||+++.+++.+++.|..    ++.+..+||+|++.+|.++++.|++|+.+||||||++++|||||+|++|||
T Consensus       211 -~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID  289 (812)
T PRK11664        211 -ESGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVD  289 (812)
T ss_pred             -CCCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEE
Confidence             368999999999999999999974    577999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC------------------ChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHHHHH
Q 017020          162 YELPN------------------DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLE  223 (379)
Q Consensus       162 ~~~P~------------------~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~i~~  223 (379)
                      +++|.                  +.++|.||+||+||. ..|.||.++++.+...+              ......||+.
T Consensus       290 ~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~~~l--------------~~~~~PEI~r  354 (812)
T PRK11664        290 SGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQAERA--------------AAQSEPEILH  354 (812)
T ss_pred             CCCcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHHHHhhC--------------ccCCCCceec
Confidence            88774                  346899999999999 59999999999775321              1222346777


Q ss_pred             HHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcCCCCC
Q 017020          224 SSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRP  273 (379)
Q Consensus       224 ~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~~~  273 (379)
                      ..+..++-.++.+...+...|     .+++.+....+.+|+..|...+..
T Consensus       355 ~dL~~~~L~l~~~g~~~~~~~-----~~ld~P~~~~~~~A~~~L~~lgal  399 (812)
T PRK11664        355 SDLSGLLLELLQWGCHDPAQL-----SWLDQPPAAALAAAKRLLQQLGAL  399 (812)
T ss_pred             cchHHHHHHHHHcCCCCHHhC-----CCCCCCCHHHHHHHHHHHHHCCCC
Confidence            777777777777654433333     467778888888888877554443

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.94  E-value=8.1e-26  Score=236.51  Aligned_cols=189  Identities=23%  Similarity=0.414  Sum_probs=152.5

Q ss_pred             hHHHHHHHH---HhCCCCCcEEEEeeeCChHHHHHHHHhcC--CCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            6 FEEDVELIL---ENLPPKRQSMLFSATMPSWVKKLSRKYLD--NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         6 F~~di~~Il---~~~p~~~Q~llfSAT~p~~i~~l~~~~l~--~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      |+++...|.   ..+| +.+++++|||+|+.+.......+.  ++..+  ... .  ...++.  +.......+...+..
T Consensus       146 frp~y~~l~~l~~~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~--~~~-~--~r~nl~--~~v~~~~~~~~~l~~  217 (591)
T TIGR01389       146 FRPEYQRLGSLAERFP-QVPRIALTATADAETRQDIRELLRLADANEF--ITS-F--DRPNLR--FSVVKKNNKQKFLLD  217 (591)
T ss_pred             cHHHHHHHHHHHHhCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeE--ecC-C--CCCCcE--EEEEeCCCHHHHHHH
Confidence            777665554   4444 456999999999998876666665  33333  211 1  122332  222233456666667


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ++... .+.++||||+|++.|+.+++.|.. ++.+..+||+|++++|+.+++.|.+|+++|||||+++++|||+|++++|
T Consensus       218 ~l~~~-~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~V  296 (591)
T TIGR01389       218 YLKKH-RGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFV  296 (591)
T ss_pred             HHHhc-CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEE
Confidence            76654 367999999999999999999975 8999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHH
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                      |||++|.+.++|+||+||+||.|..|.|++++++.+...++.+.
T Consensus       297 I~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~~~i  340 (591)
T TIGR01389       297 IHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRI  340 (591)
T ss_pred             EEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999988777664

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.

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.94  E-value=2.1e-26  Score=224.44  Aligned_cols=199  Identities=27%  Similarity=0.420  Sum_probs=168.8

Q ss_pred             HHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecc--cccccccceEEEEEEcCCccHHHHHHHHHHHHc
Q 017020            9 DVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGN--QDEKLAEGIKLYAISTTATSKRTILSDLITVYA   86 (379)
Q Consensus         9 di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~--~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~   86 (379)
                      ++...+..+++..+.++||||+...-.++..--++.|....+...  ..-.++..+.++++.+...-|.-.+..++... 
T Consensus       349 e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~~~kpl~~~~lI~~~-  427 (620)
T KOG0350|consen  349 ELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPKFKPLAVYALITSN-  427 (620)
T ss_pred             HHHhhcCCcCchhHhhhcchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeecccccchHhHHHHHHHh-
Confidence            344444445667789999999988777778777888866554421  12345677888888888777888888888876 


Q ss_pred             CCCcEEEEecccccHHHHHHHHh-c----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020           87 KGGKTIVFTQTKRDADEVSLALT-S----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~-~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                      +..++|+|+++.+.+..++..|. .    .+.+..+.|.+++..|.+.+++|+.|.+++|||||+++||+|+.+++.|||
T Consensus       428 k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VIN  507 (620)
T KOG0350|consen  428 KLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVIN  507 (620)
T ss_pred             hcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEee
Confidence            47899999999999999999987 1    467788999999999999999999999999999999999999999999999


Q ss_pred             cCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCC
Q 017020          162 YELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGC  208 (379)
Q Consensus       162 ~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~  208 (379)
                      ||+|.+...|+||+|||||+|+.|.||.+.+..+.+.+.++-+..+.
T Consensus       508 Yd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~~~~  554 (620)
T KOG0350|consen  508 YDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKKTNL  554 (620)
T ss_pred             cCCCchhhHHHHhhcccccccCCceEEEeeccccchHHHHHHHHhcc
Confidence            99999999999999999999999999999999999888887766654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.92  E-value=2.9e-24  Score=231.73  Aligned_cols=191  Identities=18%  Similarity=0.280  Sum_probs=150.8

Q ss_pred             HHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcC
Q 017020            8 EDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAK   87 (379)
Q Consensus         8 ~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~   87 (379)
                      .+....++.++.+.|+++||||+++....++...+.++..|...+.  .  ...+.+++....   ...+...++.....
T Consensus       587 v~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~--~--R~~V~t~v~~~~---~~~i~~~i~~el~~  659 (926)
T TIGR00580       587 VKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPE--D--RLPVRTFVMEYD---PELVREAIRRELLR  659 (926)
T ss_pred             hhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCC--C--ccceEEEEEecC---HHHHHHHHHHHHHc
Confidence            3456677888889999999999888777777667777777754321  1  123455444322   11222233333445


Q ss_pred             CCcEEEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCC
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL  164 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~  164 (379)
                      +++++||||+++.++.+++.|..   ++.+..+||+|++.+|++++++|++|+.+|||||+++++|+|+|++++||+++.
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~~a  739 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERA  739 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEEecC
Confidence            78999999999999999999985   578999999999999999999999999999999999999999999999999998


Q ss_pred             CC-ChhHHHHHHhhccCCCCCceEEEEeCh------hhHHHHHHHHHH
Q 017020          165 PN-DPETFVHRSGRTGRAGKEGTAILMFTS------SQRRTVRSLERD  205 (379)
Q Consensus       165 P~-~~~~yiqR~GRtgR~G~~g~~i~l~~~------~e~~~l~~le~~  205 (379)
                      |. +..+|+||+||+||.|+.|.||+++.+      .....++.+++.
T Consensus       740 ~~~gls~l~Qr~GRvGR~g~~g~aill~~~~~~l~~~~~~RL~~~~~~  787 (926)
T TIGR00580       740 DKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEF  787 (926)
T ss_pred             CCCCHHHHHHHhcCCCCCCCCeEEEEEECCcccCCHHHHHHHHHHHHh
Confidence            75 678999999999999999999999864      345566666554

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.92  E-value=1.6e-24  Score=236.56  Aligned_cols=240  Identities=18%  Similarity=0.339  Sum_probs=174.3

Q ss_pred             CCCCChHHH-HHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCcc---HHH
Q 017020            1 MLAVGFEED-VELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS---KRT   76 (379)
Q Consensus         1 mL~~GF~~d-i~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~---k~~   76 (379)
                      ||+++|... +..++... ++.|+|+||||++.  ..+++.|.+.| .|.+.+..     ..++++|.......   +.+
T Consensus       199 sLn~DfLLg~Lk~lL~~r-pdlKvILmSATid~--e~fs~~F~~ap-vI~V~Gr~-----~pVei~y~p~~~~~~~~~~d  269 (1294)
T PRK11131        199 SLNIDFILGYLKELLPRR-PDLKVIITSATIDP--ERFSRHFNNAP-IIEVSGRT-----YPVEVRYRPIVEEADDTERD  269 (1294)
T ss_pred             ccccchHHHHHHHhhhcC-CCceEEEeeCCCCH--HHHHHHcCCCC-EEEEcCcc-----ccceEEEeecccccchhhHH
Confidence            688999853 44444433 46899999999975  46776665555 46554321     23456665543221   233


Q ss_pred             HHHHHHHH---H--cCCCcEEEEecccccHHHHHHHHhc-CC---cEEEeeCCCCHHHHHHHHhcccCCceeEEEecccc
Q 017020           77 ILSDLITV---Y--AKGGKTIVFTQTKRDADEVSLALTS-II---ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  147 (379)
Q Consensus        77 ~L~~ll~~---~--~~~~~~IIF~~t~~~~~~l~~~L~~-~~---~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~  147 (379)
                      .+..++..   .  ...+.+||||+++.+++.+++.|.. ++   .+.++||+|++++|.++++.  .|..+|+||||++
T Consensus       270 ~l~~ll~~V~~l~~~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIA  347 (1294)
T PRK11131        270 QLQAIFDAVDELGREGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVA  347 (1294)
T ss_pred             HHHHHHHHHHHHhcCCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHH
Confidence            34333322   1  2457899999999999999999985 43   47899999999999999987  4788999999999


Q ss_pred             ccCCCCCccceEEecC---------------CC---CChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCC
Q 017020          148 ARGLDIPNVDLIIHYE---------------LP---NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCK  209 (379)
Q Consensus       148 ~rGiDip~v~~VI~~~---------------~P---~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~  209 (379)
                      ++|||||+|++|||++               +|   .+.++|.||+|||||. .+|.||.+|++.+...+   .      
T Consensus       348 EtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~~~~---~------  417 (1294)
T PRK11131        348 ETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDFLSR---P------  417 (1294)
T ss_pred             hhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHHHhh---h------
Confidence            9999999999999986               34   4568999999999999 69999999998764322   1      


Q ss_pred             ceeeCCCCHHHHHHHHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcCCC
Q 017020          210 FEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFS  271 (379)
Q Consensus       210 ~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~  271 (379)
                           .-+..+|++..+..++..++.+...++..|     .+++.++.+.+..++..|...+
T Consensus       418 -----~~~~PEIlR~~L~~viL~lk~lgl~di~~F-----~fldpP~~~~i~~al~~L~~Lg  469 (1294)
T PRK11131        418 -----EFTDPEILRTNLASVILQMTALGLGDIAAF-----PFVEAPDKRNIQDGVRLLEELG  469 (1294)
T ss_pred             -----cccCCccccCCHHHHHHHHHHcCCCCccee-----eCCCCCCHHHHHHHHHHHHHCC
Confidence                 112346777777788888877765555555     4677888888888877775444

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.92  E-value=1e-23  Score=233.81  Aligned_cols=220  Identities=23%  Similarity=0.336  Sum_probs=154.4

Q ss_pred             hHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcC-CCceEEeecccccccccceEEEEEEcCCccH----------
Q 017020            6 FEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLD-NPLNIDLVGNQDEKLAEGIKLYAISTTATSK----------   74 (379)
Q Consensus         6 F~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~-~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k----------   74 (379)
                      |...++.|...++.+.|+|++|||+++ ..++++.... +|+.|  +.....+ ...+..+ +......+          
T Consensus       145 Lel~LeRL~~l~~~~~QrIgLSATI~n-~eevA~~L~g~~pv~I--v~~~~~r-~~~l~v~-vp~~d~~~~~~~~~~~~~  219 (1490)
T PRK09751        145 LALSLERLDALLHTSAQRIGLSATVRS-ASDVAAFLGGDRPVTV--VNPPAMR-HPQIRIV-VPVANMDDVSSVASGTGE  219 (1490)
T ss_pred             HHHHHHHHHHhCCCCCeEEEEEeeCCC-HHHHHHHhcCCCCEEE--ECCCCCc-ccceEEE-EecCchhhcccccccccc
Confidence            556778888888888999999999987 4666653332 35444  2211111 1223221 22111000          


Q ss_pred             -----------HHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcC--------------------------------
Q 017020           75 -----------RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI--------------------------------  111 (379)
Q Consensus        75 -----------~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~--------------------------------  111 (379)
                                 ..+...++.....+.++||||||++.|+.++..|.+.                                
T Consensus       220 ~~~~~r~~~i~~~v~~~il~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  299 (1490)
T PRK09751        220 DSHAGREGSIWPYIETGILDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSS  299 (1490)
T ss_pred             ccchhhhhhhhHHHHHHHHHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccc
Confidence                       0112334444445689999999999999999988642                                


Q ss_pred             --CcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCC-CCCceEE
Q 017020          112 --IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA-GKEGTAI  188 (379)
Q Consensus       112 --~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~-G~~g~~i  188 (379)
                        +.+.+|||+|++++|..+++.|++|++++||||+++++|||++++++||||+.|.++.+|+||+||+||. |..+.++
T Consensus       300 ~~~ia~~HHGsLSkeeR~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gl  379 (1490)
T PRK09751        300 DVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGL  379 (1490)
T ss_pred             cceeeeeccccCCHHHHHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEE
Confidence              1256899999999999999999999999999999999999999999999999999999999999999996 3345555


Q ss_pred             EEeChhhHHHHH---HHHHHhCCCceeeCCCC-HHHHHHHHHHHHHH
Q 017020          189 LMFTSSQRRTVR---SLERDVGCKFEFVSPPV-VEDVLESSAEQVVA  231 (379)
Q Consensus       189 ~l~~~~e~~~l~---~le~~~~~~~~~~~~p~-~~~i~~~~~~~~~~  231 (379)
                      ++... ....+.   -++.+....+|...+|. .-+++..++-.+..
T Consensus       380 i~p~~-r~dlle~~~~ve~~l~g~iE~~~~p~nplDVLaqqiva~a~  425 (1490)
T PRK09751        380 FFPRT-RRDLVDSAVIVECMFAGRLENLTPPHNPLDVLAQQTVAAAA  425 (1490)
T ss_pred             EEeCc-HHHHHhhHHHHHHHhcCCCCccCCCCChHHHHHHHHHHHHh
Confidence            44333 222232   47888888898866654 44677666555444

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.92  E-value=4.5e-24  Score=234.68  Aligned_cols=194  Identities=16%  Similarity=0.243  Sum_probs=149.8

Q ss_pred             CChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHH
Q 017020            4 VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT   83 (379)
Q Consensus         4 ~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~   83 (379)
                      +|+..  ..+++.++.++|+++||||+++.+..++..++.++..|.....  .  ...++++......   ......++.
T Consensus       734 fG~~~--~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~--~--r~~v~~~~~~~~~---~~~k~~il~  804 (1147)
T PRK10689        734 FGVRH--KERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPA--R--RLAVKTFVREYDS---LVVREAILR  804 (1147)
T ss_pred             cchhH--HHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCC--C--CCCceEEEEecCc---HHHHHHHHH
Confidence            45542  4567888899999999999988888888888889988764321  1  1234444433221   112233343


Q ss_pred             HHcCCCcEEEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE
Q 017020           84 VYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII  160 (379)
Q Consensus        84 ~~~~~~~~IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI  160 (379)
                      ....+++++||||+++.++.+++.|..   +..+..+||+|++.+|++++.+|++|+.+|||||+++++|+|+|++++||
T Consensus       805 el~r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VI  884 (1147)
T PRK10689        805 EILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII  884 (1147)
T ss_pred             HHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEE
Confidence            344578999999999999999999975   46899999999999999999999999999999999999999999999999


Q ss_pred             ecCCC-CChhHHHHHHhhccCCCCCceEEEEeCh------hhHHHHHHHHHHh
Q 017020          161 HYELP-NDPETFVHRSGRTGRAGKEGTAILMFTS------SQRRTVRSLERDV  206 (379)
Q Consensus       161 ~~~~P-~~~~~yiqR~GRtgR~G~~g~~i~l~~~------~e~~~l~~le~~~  206 (379)
                      ..+.+ .+...|+||+||+||.|+.|.|++++.+      .....++.|+...
T Consensus       885 i~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~~~~~~~~~~rl~~~~~~~  937 (1147)
T PRK10689        885 IERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLE  937 (1147)
T ss_pred             EecCCCCCHHHHHHHhhccCCCCCceEEEEEeCCCcccCHHHHHHHHHHHHhc
Confidence            44332 3556799999999999999999999854      3355666666654

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.91  E-value=4e-24  Score=210.46  Aligned_cols=180  Identities=24%  Similarity=0.321  Sum_probs=132.1

Q ss_pred             HHHHHHhCC-CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEE--EcCCccHHHHHHHHHHHHc
Q 017020           10 VELILENLP-PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAI--STTATSKRTILSDLITVYA   86 (379)
Q Consensus        10 i~~Il~~~p-~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~--~~~~~~k~~~L~~ll~~~~   86 (379)
                      +..+++.++ .+.|+++||||+|+.+.++++.+...+....... ...  .....+.+.  ......+...+..++....
T Consensus       144 l~~~l~~l~~~~~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~  220 (358)
T TIGR01587       144 ILAVLEVLKDNDVPILLMSATLPKFLKEYAEKIGYVEFNEPLDL-KEE--RRFERHRFIKIESDKVGEISSLERLLEFIK  220 (358)
T ss_pred             HHHHHHHHHHcCCCEEEEecCchHHHHHHHhcCCCcccccCCCC-ccc--cccccccceeeccccccCHHHHHHHHHHhh
Confidence            555665554 5789999999999888887766544322111110 000  001122221  1222356677777777665


Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-CC--cEEEeeCCCCHHHHHH----HHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-II--ASEALHGDISQHQRER----TLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-~~--~v~~lhg~m~~~~R~~----~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      .++++||||||++.|+.++..|.. +.  .+..+||+|++.+|.+    +++.|++|..++|||||++++|+|++ +++|
T Consensus       221 ~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~v  299 (358)
T TIGR01587       221 KGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVM  299 (358)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEE
Confidence            678999999999999999999975 33  5899999999999976    48999999999999999999999995 8899


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCC----ceEEEEeChhh
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKE----GTAILMFTSSQ  195 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~----g~~i~l~~~~e  195 (379)
                      |++..|  +++|+||+||+||.|+.    |..+++....+
T Consensus       300 i~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~~  337 (358)
T TIGR01587       300 ITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAPE  337 (358)
T ss_pred             EEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecCC
Confidence            998876  78999999999998844    36677765433

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.

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

Probab=99.91  E-value=6.5e-24  Score=215.99  Aligned_cols=192  Identities=26%  Similarity=0.388  Sum_probs=150.7

Q ss_pred             hHHHHHHHH---HhCCCCCcEEEEeeeCChHHHHHHHHhcC--CCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            6 FEEDVELIL---ENLPPKRQSMLFSATMPSWVKKLSRKYLD--NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         6 F~~di~~Il---~~~p~~~Q~llfSAT~p~~i~~l~~~~l~--~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      |++|-..+-   ..+| +.+++.++||.++.+..-+...|.  +|..+...   .  ..+|+........ +.+.... .
T Consensus       150 FRP~Y~~lg~l~~~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~s---f--dRpNi~~~v~~~~-~~~~q~~-f  221 (590)
T COG0514         150 FRPDYRRLGRLRAGLP-NPPVLALTATATPRVRDDIREQLGLQDANIFRGS---F--DRPNLALKVVEKG-EPSDQLA-F  221 (590)
T ss_pred             cCHhHHHHHHHHhhCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcceEEec---C--CCchhhhhhhhcc-cHHHHHH-H
Confidence            777766554   4455 889999999999998887766665  44333221   1  1233332222221 1222222 2


Q ss_pred             HHH-HHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce
Q 017020           81 LIT-VYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  158 (379)
Q Consensus        81 ll~-~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~  158 (379)
                      +.+ .....+..||||.|++.|+.+++.|.. ++.+..+||||+.++|+.+.++|.+++.+|+|||..+++|||-|||.+
T Consensus       222 i~~~~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRf  301 (590)
T COG0514         222 LATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRF  301 (590)
T ss_pred             HHhhccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceE
Confidence            222 123456799999999999999999985 799999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHH
Q 017020          159 IIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  205 (379)
Q Consensus       159 VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~  205 (379)
                      |||||+|.++++|+|-+||+||.|....|++|+++.|....+.+...
T Consensus       302 ViH~~lP~s~EsYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i~~  348 (590)
T COG0514         302 VIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQ  348 (590)
T ss_pred             EEEecCCCCHHHHHHHHhhccCCCCcceEEEeeccccHHHHHHHHHh
Confidence            99999999999999999999999999999999999998877776544

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.91  E-value=4.6e-23  Score=223.56  Aligned_cols=219  Identities=21%  Similarity=0.288  Sum_probs=143.3

Q ss_pred             HHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCC-----CceEEeecccccccccceEEEE-----EEcCCccHHHHHH
Q 017020           10 VELILENLPPKRQSMLFSATMPSWVKKLSRKYLDN-----PLNIDLVGNQDEKLAEGIKLYA-----ISTTATSKRTILS   79 (379)
Q Consensus        10 i~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~-----p~~i~~~~~~~~~~~~~i~~~~-----~~~~~~~k~~~L~   79 (379)
                      ++.+....+...|++++|||+++ ..++++.....     +..+.++...... ...+....     ...........+.
T Consensus       197 L~rL~~l~~~~~q~IglSATl~~-~~~va~~L~~~~~~~~~r~~~iv~~~~~k-~~~i~v~~p~~~l~~~~~~~~~~~l~  274 (876)
T PRK13767        197 LERLEELAGGEFVRIGLSATIEP-LEEVAKFLVGYEDDGEPRDCEIVDARFVK-PFDIKVISPVDDLIHTPAEEISEALY  274 (876)
T ss_pred             HHHHHHhcCCCCeEEEEecccCC-HHHHHHHhcCccccCCCCceEEEccCCCc-cceEEEeccCccccccccchhHHHHH
Confidence            44444555568899999999975 33444332221     2222222111100 01111100     0011111112222


Q ss_pred             H-HHHHHcCCCcEEEEecccccHHHHHHHHhc-------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCC
Q 017020           80 D-LITVYAKGGKTIVFTQTKRDADEVSLALTS-------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  151 (379)
Q Consensus        80 ~-ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGi  151 (379)
                      . +......++++||||||++.|+.++..|..       +..+.++||+|++++|..++++|++|+.++||||+++++||
T Consensus       275 ~~L~~~i~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GI  354 (876)
T PRK13767        275 ETLHELIKEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGI  354 (876)
T ss_pred             HHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcC
Confidence            2 223334468999999999999999999875       25799999999999999999999999999999999999999


Q ss_pred             CCCccceEEecCCCCChhHHHHHHhhccCC-CCCceEEEEeChh-h-HHHHHHHHHHhCCCceeeCCCC-HHHHHHHHHH
Q 017020          152 DIPNVDLIIHYELPNDPETFVHRSGRTGRA-GKEGTAILMFTSS-Q-RRTVRSLERDVGCKFEFVSPPV-VEDVLESSAE  227 (379)
Q Consensus       152 Dip~v~~VI~~~~P~~~~~yiqR~GRtgR~-G~~g~~i~l~~~~-e-~~~l~~le~~~~~~~~~~~~p~-~~~i~~~~~~  227 (379)
                      |+|++++||+|+.|.++.+|+||+||+||. |..+.++++.... | .+....++......++...+|. ..+++..++.
T Consensus       355 Dip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~~~~l~e~~~~~~~~~~~~ie~~~~~~~~~dvl~q~i~  434 (876)
T PRK13767        355 DIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVDRDDLVECAVLLKKAREGKIDRVHIPKNPLDVLAQHIV  434 (876)
T ss_pred             CCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcCchhHHHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHH
Confidence            999999999999999999999999999986 4444555554432 2 2223344566666777755553 3556655544


Q ss_pred             HHH
Q 017020          228 QVV  230 (379)
Q Consensus       228 ~~~  230 (379)
                      .+.
T Consensus       435 ~~~  437 (876)
T PRK13767        435 GMA  437 (876)
T ss_pred             HHH
Confidence            433

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.90  E-value=1.8e-23  Score=216.35  Aligned_cols=168  Identities=18%  Similarity=0.170  Sum_probs=136.4

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHH-cCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVY-AKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~  100 (379)
                      .+..||||.+.+..++.+.|..++..|.....   . .....+.++.+...+|..+|.+++... ..+.++||||+|++.
T Consensus       410 kl~GmTGTa~~~~~El~~~y~l~vv~IPt~kp---~-~r~~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~  485 (656)
T PRK12898        410 RLAGMTGTAREVAGELWSVYGLPVVRIPTNRP---S-QRRHLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGTRSVAA  485 (656)
T ss_pred             HHhcccCcChHHHHHHHHHHCCCeEEeCCCCC---c-cceecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHH
Confidence            45679999999999999999888776654211   1 122334455566678888888888764 335789999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC---ccc-----eEEecCCCCChhHH
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP---NVD-----LIIHYELPNDPETF  171 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip---~v~-----~VI~~~~P~~~~~y  171 (379)
                      ++.++..|.. ++++..+||++++.++  .+..|+.+...|+||||+|+||+||+   +|.     |||||++|.+...|
T Consensus       486 se~L~~~L~~~gi~~~~Lhg~~~~rE~--~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y  563 (656)
T PRK12898        486 SERLSALLREAGLPHQVLNAKQDAEEA--AIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARID  563 (656)
T ss_pred             HHHHHHHHHHCCCCEEEeeCCcHHHHH--HHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHH
Confidence            9999999985 8999999999665554  44555555557999999999999999   676     99999999999999


Q ss_pred             HHHHhhccCCCCCceEEEEeChhh
Q 017020          172 VHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       172 iqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      .||+|||||+|..|.+++|++..|
T Consensus       564 ~hr~GRTGRqG~~G~s~~~is~eD  587 (656)
T PRK12898        564 RQLAGRCGRQGDPGSYEAILSLED  587 (656)
T ss_pred             HHhcccccCCCCCeEEEEEechhH
Confidence            999999999999999999999866

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.90  E-value=5e-23  Score=225.52  Aligned_cols=242  Identities=17%  Similarity=0.292  Sum_probs=174.5

Q ss_pred             CCCCChHHH-HHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC------cc
Q 017020            1 MLAVGFEED-VELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA------TS   73 (379)
Q Consensus         1 mL~~GF~~d-i~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~------~~   73 (379)
                      ||+++|.-. +..++...| +.|+|+||||++.  ..+++.|.+.| .|.+.+..     ..+..+|.....      .+
T Consensus       192 sL~~D~LL~lLk~il~~rp-dLKlIlmSATld~--~~fa~~F~~ap-vI~V~Gr~-----~PVev~Y~~~~~~~~~~~~~  262 (1283)
T TIGR01967       192 SLNIDFLLGYLKQLLPRRP-DLKIIITSATIDP--ERFSRHFNNAP-IIEVSGRT-----YPVEVRYRPLVEEQEDDDLD  262 (1283)
T ss_pred             hccchhHHHHHHHHHhhCC-CCeEEEEeCCcCH--HHHHHHhcCCC-EEEECCCc-----ccceeEEecccccccchhhh
Confidence            578888865 677776654 7899999999974  56776554444 45554321     223444443321      12


Q ss_pred             HHHHHHHHHHHH--cCCCcEEEEecccccHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecccc
Q 017020           74 KRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  147 (379)
Q Consensus        74 k~~~L~~ll~~~--~~~~~~IIF~~t~~~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~  147 (379)
                      +.+.+...+...  ...+.+|||+++..+++.+++.|..    .+.+..+||+|++++|.++++.+.  ..+|+||||++
T Consensus       263 ~~~~i~~~I~~l~~~~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~~--~rkIVLATNIA  340 (1283)
T TIGR01967       263 QLEAILDAVDELFAEGPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPHS--GRRIVLATNVA  340 (1283)
T ss_pred             HHHHHHHHHHHHHhhCCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCCC--CceEEEeccHH
Confidence            333343333322  2358999999999999999999974    345889999999999999987653  36899999999


Q ss_pred             ccCCCCCccceEEecCCC------------------CChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCC
Q 017020          148 ARGLDIPNVDLIIHYELP------------------NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCK  209 (379)
Q Consensus       148 ~rGiDip~v~~VI~~~~P------------------~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~  209 (379)
                      ++|||||+|++||+++++                  .+.++|.||+||+||.| .|.||.+++..+...+.   .     
T Consensus       341 EtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~~~~~---~-----  411 (1283)
T TIGR01967       341 ETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDFNSRP---E-----  411 (1283)
T ss_pred             HhccccCCeeEEEeCCCccccccccccCccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHHHhhh---h-----
Confidence            999999999999999853                  36689999999999998 99999999987753321   1     


Q ss_pred             ceeeCCCCHHHHHHHHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcCCCCC
Q 017020          210 FEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRP  273 (379)
Q Consensus       210 ~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~~~  273 (379)
                            -+..+|++..+..++..+..+...++..|     .+++.++.+.+..|+..|...+..
T Consensus       412 ------~~~PEIlR~~L~~viL~l~~lg~~di~~f-----~fldpP~~~~i~~A~~~L~~LGAl  464 (1283)
T TIGR01967       412 ------FTDPEILRTNLASVILQMLALRLGDIAAF-----PFIEAPDPRAIRDGFRLLEELGAL  464 (1283)
T ss_pred             ------ccCcccccccHHHHHHHHHhcCCCCcccc-----cCCCCCCHHHHHHHHHHHHHCCCC
Confidence                  12346777778888888877655444444     467788888888888777544433

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.

>PRK02362 ski2-like helicase; Provisional

Probab=99.90  E-value=1.2e-22  Score=217.40  Aligned_cols=206  Identities=23%  Similarity=0.319  Sum_probs=142.0

Q ss_pred             CCCCChHHHHHHHHHhC---CCCCcEEEEeeeCChHHHHHHHHhcCC-------CceEEeecccccccccceEEEEEEcC
Q 017020            1 MLAVGFEEDVELILENL---PPKRQSMLFSATMPSWVKKLSRKYLDN-------PLNIDLVGNQDEKLAEGIKLYAISTT   70 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~---p~~~Q~llfSAT~p~~i~~l~~~~l~~-------p~~i~~~~~~~~~~~~~i~~~~~~~~   70 (379)
                      |++.++...++.++..+   +++.|++++|||+|. ..+++.+.-..       |+.+...-.........-.+..+.. 
T Consensus       149 l~d~~rg~~le~il~rl~~~~~~~qii~lSATl~n-~~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~-  226 (737)
T PRK02362        149 IDSANRGPTLEVTLAKLRRLNPDLQVVALSATIGN-ADELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEV-  226 (737)
T ss_pred             cCCCcchHHHHHHHHHHHhcCCCCcEEEEcccCCC-HHHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCC-
Confidence            34667888888887665   568999999999975 45555543211       2111100000000000001111111 


Q ss_pred             CccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcC-------------------------------------Cc
Q 017020           71 ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------------IA  113 (379)
Q Consensus        71 ~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~-------------------------------------~~  113 (379)
                       ..+...+..+++....++++||||+|++.|+.++..|...                                     ..
T Consensus       227 -~~~~~~~~~~~~~~~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~g  305 (737)
T PRK02362        227 -PSKDDTLNLVLDTLEEGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKG  305 (737)
T ss_pred             -ccchHHHHHHHHHHHcCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhC
Confidence             1223344444444446789999999999999988877531                                     36


Q ss_pred             EEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe----cC-----CCCChhHHHHHHhhccCCCC-
Q 017020          114 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE-----LPNDPETFVHRSGRTGRAGK-  183 (379)
Q Consensus       114 v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~----~~-----~P~~~~~yiqR~GRtgR~G~-  183 (379)
                      +.++||+|++.+|..+++.|++|.++|||||+++++|+|+|.+++||+    ||     .|.+..+|+||+|||||+|. 
T Consensus       306 va~hHagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d  385 (737)
T PRK02362        306 AAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLD  385 (737)
T ss_pred             EEeecCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCC
Confidence            889999999999999999999999999999999999999999999997    76     68999999999999999995 


Q ss_pred             -CceEEEEeChhhHHHHHHHHHHhCCCc
Q 017020          184 -EGTAILMFTSSQRRTVRSLERDVGCKF  210 (379)
Q Consensus       184 -~g~~i~l~~~~e~~~l~~le~~~~~~~  210 (379)
                       .|.+++++.+.+. .-+.+++++....
T Consensus       386 ~~G~~ii~~~~~~~-~~~~~~~~l~~~~  412 (737)
T PRK02362        386 PYGEAVLLAKSYDE-LDELFERYIWADP  412 (737)
T ss_pred             CCceEEEEecCchh-HHHHHHHHHhCCC
Confidence             4999999976532 2223445554333

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.89  E-value=4.9e-24  Score=192.78  Aligned_cols=169  Identities=28%  Similarity=0.565  Sum_probs=143.1

Q ss_pred             ChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHH
Q 017020            5 GFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV   84 (379)
Q Consensus         5 GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~   84 (379)
                      ..+.|+++|.+.+|.+.|+++||||++++++.++++||.||..|-+. .....+..++++||+......|...+.++|+.
T Consensus       202 DMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vD-dE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~  280 (387)
T KOG0329|consen  202 DMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVD-DEAKLTLHGLQQYYVKLKENEKNRKLNDLLDV  280 (387)
T ss_pred             HHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhcc-chhhhhhhhHHHHHHhhhhhhhhhhhhhhhhh
Confidence            35789999999999999999999999999999999999999988543 44556678899999999999999999999998


Q ss_pred             HcCCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCC
Q 017020           85 YAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL  164 (379)
Q Consensus        85 ~~~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~  164 (379)
                      +. -.+++||+.+...       |             +          |   ..+ +||||+.+||+||..++.|+|||+
T Consensus       281 Le-FNQVvIFvKsv~R-------l-------------~----------f---~kr-~vat~lfgrgmdiervNi~~NYdm  325 (387)
T KOG0329|consen  281 LE-FNQVVIFVKSVQR-------L-------------S----------F---QKR-LVATDLFGRGMDIERVNIVFNYDM  325 (387)
T ss_pred             hh-hcceeEeeehhhh-------h-------------h----------h---hhh-hHHhhhhccccCcccceeeeccCC
Confidence            84 6799999987653       1             0          3   123 899999999999999999999999


Q ss_pred             CCChhHHHHHHhhccCCCCCceEEEEeChh-hHHHHHHHHHHhCCC
Q 017020          165 PNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCK  209 (379)
Q Consensus       165 P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~-e~~~l~~le~~~~~~  209 (379)
                      |.++++|.||+||+||.|..|.++.|++.. +...+..++......
T Consensus       326 p~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~  371 (387)
T KOG0329|consen  326 PEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVN  371 (387)
T ss_pred             CCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhhhcc
Confidence            999999999999999999999999999865 445555555544433

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.89  E-value=6.6e-22  Score=209.61  Aligned_cols=189  Identities=19%  Similarity=0.294  Sum_probs=135.9

Q ss_pred             HHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCC
Q 017020           10 VELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGG   89 (379)
Q Consensus        10 i~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~   89 (379)
                      ....+...+..+|+++||||..+....+......++..++..  ...  ...+..++..  ...+..++..+......+.
T Consensus       399 qr~~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~~--p~~--r~~i~~~~~~--~~~~~~~~~~i~~~~~~g~  472 (681)
T PRK10917        399 QRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDEL--PPG--RKPITTVVIP--DSRRDEVYERIREEIAKGR  472 (681)
T ss_pred             HHHHHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCceEEEecC--CCC--CCCcEEEEeC--cccHHHHHHHHHHHHHcCC
Confidence            344455556679999999998766555543222233333211  111  1234444332  2333344444444445678


Q ss_pred             cEEEEecccc--------cHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce
Q 017020           90 KTIVFTQTKR--------DADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  158 (379)
Q Consensus        90 ~~IIF~~t~~--------~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~  158 (379)
                      +++|||++.+        .++.+++.|..   ++.+..+||+|++.+|+.++++|++|+.+|||||+++++|+|+|++++
T Consensus       473 q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~v~~  552 (681)
T PRK10917        473 QAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATV  552 (681)
T ss_pred             cEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccCCCcE
Confidence            9999999654        45566777764   367999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCC-ChhHHHHHHhhccCCCCCceEEEEeC-h---hhHHHHHHHHH
Q 017020          159 IIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFT-S---SQRRTVRSLER  204 (379)
Q Consensus       159 VI~~~~P~-~~~~yiqR~GRtgR~G~~g~~i~l~~-~---~e~~~l~~le~  204 (379)
                      ||+++.|. ....|.||+||+||.|..|.|+++++ +   .....++.+++
T Consensus       553 VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~~~~~~~~rl~~~~~  603 (681)
T PRK10917        553 MVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRE  603 (681)
T ss_pred             EEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCCCChhHHHHHHHHHH
Confidence            99999997 57888899999999999999999995 3   24445555554

>PRK00254 ski2-like helicase; Provisional

Probab=99.89  E-value=5e-22  Score=212.23  Aligned_cols=206  Identities=23%  Similarity=0.301  Sum_probs=141.4

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccce-EEEEEEcCCc--cHH-H
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGI-KLYAISTTAT--SKR-T   76 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i-~~~~~~~~~~--~k~-~   76 (379)
                      |.+.++...++.++..++...|++++|||+|. ..+++. ++..+... . ..........+ .+.+......  .+. .
T Consensus       150 l~~~~rg~~le~il~~l~~~~qiI~lSATl~n-~~~la~-wl~~~~~~-~-~~rpv~l~~~~~~~~~~~~~~~~~~~~~~  225 (720)
T PRK00254        150 IGSYDRGATLEMILTHMLGRAQILGLSATVGN-AEELAE-WLNAELVV-S-DWRPVKLRKGVFYQGFLFWEDGKIERFPN  225 (720)
T ss_pred             cCCccchHHHHHHHHhcCcCCcEEEEEccCCC-HHHHHH-HhCCcccc-C-CCCCCcceeeEecCCeeeccCcchhcchH
Confidence            34678889999999999999999999999976 466776 44432211 1 00110110011 0111111111  110 1


Q ss_pred             HH-HHHHHHHcCCCcEEEEecccccHHHHHHHHhc----------------------------------CCcEEEeeCCC
Q 017020           77 IL-SDLITVYAKGGKTIVFTQTKRDADEVSLALTS----------------------------------IIASEALHGDI  121 (379)
Q Consensus        77 ~L-~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~----------------------------------~~~v~~lhg~m  121 (379)
                      .. ..+.+....++++||||+|++.|+.++..|..                                  ...+.++||+|
T Consensus       226 ~~~~~~~~~i~~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl  305 (720)
T PRK00254        226 SWESLVYDAVKKGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGL  305 (720)
T ss_pred             HHHHHHHHHHHhCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCC
Confidence            11 11222233468999999999999887766531                                  12588999999


Q ss_pred             CHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe-------cCCCC-ChhHHHHHHhhccCCC--CCceEEEEe
Q 017020          122 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-------YELPN-DPETFVHRSGRTGRAG--KEGTAILMF  191 (379)
Q Consensus       122 ~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~-------~~~P~-~~~~yiqR~GRtgR~G--~~g~~i~l~  191 (379)
                      ++++|..+++.|++|.++|||||+++++|+|+|.+++||.       ++.|. +..+|+||+||+||.|  ..|.+++++
T Consensus       306 ~~~eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~  385 (720)
T PRK00254        306 GRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVA  385 (720)
T ss_pred             CHHHHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEe
Confidence            9999999999999999999999999999999999999994       55544 5679999999999976  679999999


Q ss_pred             ChhhHHHHHHHHHHhCCCcee
Q 017020          192 TSSQRRTVRSLERDVGCKFEF  212 (379)
Q Consensus       192 ~~~e~~~l~~le~~~~~~~~~  212 (379)
                      .+.+...  .++++....++.
T Consensus       386 ~~~~~~~--~~~~~~~~~pe~  404 (720)
T PRK00254        386 TTEEPSK--LMERYIFGKPEK  404 (720)
T ss_pred             cCcchHH--HHHHHHhCCchh
Confidence            8755222  245555555544

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.88  E-value=2.7e-21  Score=203.54  Aligned_cols=167  Identities=22%  Similarity=0.283  Sum_probs=123.3

Q ss_pred             CCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccc
Q 017020           20 KRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKR   99 (379)
Q Consensus        20 ~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~   99 (379)
                      .+|+++||||+++....+.....-+...++...  ..  ...+..+++.  ...+..++..+......+.+++|||++.+
T Consensus       386 ~~~~l~~SATp~prtl~l~~~~~l~~~~i~~~p--~~--r~~i~~~~~~--~~~~~~~~~~i~~~l~~g~q~~v~~~~i~  459 (630)
T TIGR00643       386 TPHVLVMSATPIPRTLALTVYGDLDTSIIDELP--PG--RKPITTVLIK--HDEKDIVYEFIEEEIAKGRQAYVVYPLIE  459 (630)
T ss_pred             CCCEEEEeCCCCcHHHHHHhcCCcceeeeccCC--CC--CCceEEEEeC--cchHHHHHHHHHHHHHhCCcEEEEEcccc
Confidence            689999999986654444321111222222111  11  1233333332  23344444444444456789999999764


Q ss_pred             --------cHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCCC-C
Q 017020          100 --------DADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-D  167 (379)
Q Consensus       100 --------~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~-~  167 (379)
                              .++.+++.|..   ++.+..+||+|++++|+.++++|++|+.+|||||+++++|+|+|++++||+++.|. +
T Consensus       460 ~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~v~~VIi~~~~r~g  539 (630)
T TIGR00643       460 ESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFG  539 (630)
T ss_pred             ccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccCCCcEEEEeCCCcCC
Confidence                    45567777764   57799999999999999999999999999999999999999999999999999986 6


Q ss_pred             hhHHHHHHhhccCCCCCceEEEEeC
Q 017020          168 PETFVHRSGRTGRAGKEGTAILMFT  192 (379)
Q Consensus       168 ~~~yiqR~GRtgR~G~~g~~i~l~~  192 (379)
                      ...|.||+||+||.|+.|.|++++.
T Consensus       540 ls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       540 LSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             HHHHHHHhhhcccCCCCcEEEEEEC
Confidence            7888999999999999999999993

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=99.87  E-value=6.5e-22  Score=190.19  Aligned_cols=190  Identities=31%  Similarity=0.493  Sum_probs=151.1

Q ss_pred             CCCCChHHHHHHHHHhCCC------CCcEEEEeeeCCh-HHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCc-
Q 017020            1 MLAVGFEEDVELILENLPP------KRQSMLFSATMPS-WVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT-   72 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~------~~Q~llfSAT~p~-~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~-   72 (379)
                      +|..|+-|-|......+|.      ..|.+++|||+.. ++..+.++.|+-|..+++.+.  ...++.+.|....+.+. 
T Consensus       375 lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkge--D~vpetvHhvv~lv~p~~  452 (725)
T KOG0349|consen  375 LLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGE--DLVPETVHHVVKLVCPSV  452 (725)
T ss_pred             hhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccc--cccchhhccceeecCCcc
Confidence            3567888888888888873      5799999999954 688899999999999987643  23344444433322110 


Q ss_pred             c---------------------------------HHHHH-----HHHHHHHcCCCcEEEEecccccHHHHHHHHhc----
Q 017020           73 S---------------------------------KRTIL-----SDLITVYAKGGKTIVFTQTKRDADEVSLALTS----  110 (379)
Q Consensus        73 ~---------------------------------k~~~L-----~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~----  110 (379)
                      +                                 ...+|     ...++.+ ...++||||.|+.+|+.|...+..    
T Consensus       453 d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h-~mdkaiifcrtk~dcDnLer~~~qkgg~  531 (725)
T KOG0349|consen  453 DGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRH-AMDKAIIFCRTKQDCDNLERMMNQKGGK  531 (725)
T ss_pred             CccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhh-ccCceEEEEeccccchHHHHHHHHcCCc
Confidence            0                                 00011     1111222 246999999999999999999973    


Q ss_pred             CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEE
Q 017020          111 IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  190 (379)
Q Consensus       111 ~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l  190 (379)
                      .+++.++||+..+.+|.+.++.|+.+..+.|||||+++||+||.++.++||.-+|.+...|+||+||.||+.+-|.+|.+
T Consensus       532 ~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgraermglaisl  611 (725)
T KOG0349|consen  532 HYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISL  611 (725)
T ss_pred             cceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhhhcceeEEE
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             eCh
Q 017020          191 FTS  193 (379)
Q Consensus       191 ~~~  193 (379)
                      +..
T Consensus       612 vat  614 (725)
T KOG0349|consen  612 VAT  614 (725)
T ss_pred             eec
Confidence            753

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.87  E-value=2.2e-21  Score=209.04  Aligned_cols=163  Identities=17%  Similarity=0.243  Sum_probs=139.8

Q ss_pred             cHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHh-c-CCcEEEeeCCCCHHHHHHHHhcccCC--ceeEEEeccccc
Q 017020           73 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-S-IIASEALHGDISQHQRERTLNGFRQG--KFTVLVATDVAA  148 (379)
Q Consensus        73 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~-~-~~~v~~lhg~m~~~~R~~~~~~F~~g--~~~iLVaTdv~~  148 (379)
                      .|.+.|.++++.. .+.++||||+++..++.+++.|. . ++.+..+||+|++.+|+++++.|+++  ..+|||||++++
T Consensus       479 ~Ki~~L~~~L~~~-~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgs  557 (956)
T PRK04914        479 PRVEWLIDFLKSH-RSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGS  557 (956)
T ss_pred             HHHHHHHHHHHhc-CCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhc
Confidence            4666777777665 36899999999999999999995 3 89999999999999999999999984  599999999999


Q ss_pred             cCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCC--CceeeCCCCHHHHHHHHH
Q 017020          149 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGC--KFEFVSPPVVEDVLESSA  226 (379)
Q Consensus       149 rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~--~~~~~~~p~~~~i~~~~~  226 (379)
                      +|+|++.+++|||||+|++++.|.||+||+||.|+++.+.+++...+......+.+.+..  .+-....|+.+++.+...
T Consensus       558 eGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i~~~~~~~l~ife~~~~~~~~v~~~~~  637 (956)
T PRK04914        558 EGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHEGLNAFEHTCPTGRALYDEFG  637 (956)
T ss_pred             cCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccCCCCHHHHHHHHHhhhcCceeccCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999988777765555556666665544  556788999999999888


Q ss_pred             HHHHHHHccc
Q 017020          227 EQVVATLNGV  236 (379)
Q Consensus       227 ~~~~~~l~~~  236 (379)
                      ..+...+...
T Consensus       638 ~~l~~~l~~~  647 (956)
T PRK04914        638 DELIPYLASP  647 (956)
T ss_pred             HHHHHHHhCC
Confidence            8887777554

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=1.5e-20  Score=198.42  Aligned_cols=169  Identities=18%  Similarity=0.200  Sum_probs=132.9

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHH-HcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~  100 (379)
                      .+..+|.|...+-.++.+.|--+  .+.+ +...........- .+.....+|..++...+.. +..+.++||||+|++.
T Consensus       365 kl~GmTGTa~t~~~e~~~~Y~l~--v~~I-Pt~kp~~r~d~~~-~i~~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~  440 (790)
T PRK09200        365 KLSGMTGTAKTEEKEFFEVYNME--VVQI-PTNRPIIRIDYPD-KVFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQ  440 (790)
T ss_pred             HHhccCCCChHHHHHHHHHhCCc--EEEC-CCCCCcccccCCC-eEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHH
Confidence            45678999876666776666332  2222 2111111111111 2234456788888777754 3457899999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCC---Cccc-----eEEecCCCCChhHH
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI---PNVD-----LIIHYELPNDPETF  171 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDi---p~v~-----~VI~~~~P~~~~~y  171 (379)
                      ++.++..|.. ++++..+||+++++++..+..+++.|  .|+||||+|+||+||   |+|.     |||||++|.+...|
T Consensus       441 se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y  518 (790)
T PRK09200        441 SETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVD  518 (790)
T ss_pred             HHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHH
Confidence            9999999985 89999999999999999999888877  699999999999999   7998     99999999999999


Q ss_pred             HHHHhhccCCCCCceEEEEeChhhH
Q 017020          172 VHRSGRTGRAGKEGTAILMFTSSQR  196 (379)
Q Consensus       172 iqR~GRtgR~G~~g~~i~l~~~~e~  196 (379)
                      .||+|||||.|.+|.++.|++..|.
T Consensus       519 ~qr~GRtGR~G~~G~s~~~is~eD~  543 (790)
T PRK09200        519 LQLRGRSGRQGDPGSSQFFISLEDD  543 (790)
T ss_pred             HHhhccccCCCCCeeEEEEEcchHH
Confidence            9999999999999999999998663

>PRK09401 reverse gyrase; Reviewed

Probab=99.85  E-value=4.6e-21  Score=211.46  Aligned_cols=163  Identities=24%  Similarity=0.307  Sum_probs=133.3

Q ss_pred             CChH-HHHHHHHHhCCC------------------------CCcEEEEeeeCChH-HHHHHHHhcCCCceEEeecccccc
Q 017020            4 VGFE-EDVELILENLPP------------------------KRQSMLFSATMPSW-VKKLSRKYLDNPLNIDLVGNQDEK   57 (379)
Q Consensus         4 ~GF~-~di~~Il~~~p~------------------------~~Q~llfSAT~p~~-i~~l~~~~l~~p~~i~~~~~~~~~   57 (379)
                      |||. ++|+.|++.+|.                        +.|+++||||+++. +..   .++.++..+.+..  ...
T Consensus       227 lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~--~~~  301 (1176)
T PRK09401        227 LGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGS--PVF  301 (1176)
T ss_pred             CCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecC--ccc
Confidence            8995 789999998875                        78999999999875 332   2334555555432  223


Q ss_pred             cccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEeccccc---HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcc
Q 017020           58 LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD---ADEVSLALTS-IIASEALHGDISQHQRERTLNGF  133 (379)
Q Consensus        58 ~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~---~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F  133 (379)
                      ...++.+.|+.++  ++.+.|..++...  +.++||||+|+..   |+.++..|.. ++.+..+||+|     ++.+++|
T Consensus       302 ~~rnI~~~yi~~~--~k~~~L~~ll~~l--~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F  372 (1176)
T PRK09401        302 YLRNIVDSYIVDE--DSVEKLVELVKRL--GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKF  372 (1176)
T ss_pred             ccCCceEEEEEcc--cHHHHHHHHHHhc--CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHH
Confidence            4567888887665  6777888888765  3589999999988   9999999985 89999999999     2345999


Q ss_pred             cCCceeEEEe----ccccccCCCCCc-cceEEecCCCC------ChhHHHHHHhhccC
Q 017020          134 RQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELPN------DPETFVHRSGRTGR  180 (379)
Q Consensus       134 ~~g~~~iLVa----Tdv~~rGiDip~-v~~VI~~~~P~------~~~~yiqR~GRtgR  180 (379)
                      ++|+++||||    ||+++||||+|+ |++|||||+|.      ..+.|.||+||+-.
T Consensus       373 ~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~~  430 (1176)
T PRK09401        373 EEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLLS  430 (1176)
T ss_pred             HCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHHh
Confidence            9999999999    699999999999 89999999998      77899999999953

>PRK01172 ski2-like helicase; Provisional

Probab=99.85  E-value=1.1e-20  Score=200.75  Aligned_cols=188  Identities=23%  Similarity=0.307  Sum_probs=127.7

Q ss_pred             CCCChHHHHHHHHHh---CCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceE---EEEEEcCCccHH
Q 017020            2 LAVGFEEDVELILEN---LPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIK---LYAISTTATSKR   75 (379)
Q Consensus         2 L~~GF~~di~~Il~~---~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~---~~~~~~~~~~k~   75 (379)
                      .|.++...++.++..   .+++.|++++|||++. ..+++++ +..+. +... ....+....+.   ..+.........
T Consensus       148 ~d~~rg~~le~ll~~~~~~~~~~riI~lSATl~n-~~~la~w-l~~~~-~~~~-~r~vpl~~~i~~~~~~~~~~~~~~~~  223 (674)
T PRK01172        148 GDEDRGPTLETVLSSARYVNPDARILALSATVSN-ANELAQW-LNASL-IKSN-FRPVPLKLGILYRKRLILDGYERSQV  223 (674)
T ss_pred             cCCCccHHHHHHHHHHHhcCcCCcEEEEeCccCC-HHHHHHH-hCCCc-cCCC-CCCCCeEEEEEecCeeeecccccccc
Confidence            455666777777654   4568999999999975 5667764 33221 1100 00000000010   011111111111


Q ss_pred             HHHHHHHHH-HcCCCcEEEEecccccHHHHHHHHhcC--------------------------CcEEEeeCCCCHHHHHH
Q 017020           76 TILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTSI--------------------------IASEALHGDISQHQRER  128 (379)
Q Consensus        76 ~~L~~ll~~-~~~~~~~IIF~~t~~~~~~l~~~L~~~--------------------------~~v~~lhg~m~~~~R~~  128 (379)
                      . +..++.. ...++++||||+|++.|+.++..|...                          ..+..+||+|++++|..
T Consensus       224 ~-~~~~i~~~~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~  302 (674)
T PRK01172        224 D-INSLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRF  302 (674)
T ss_pred             c-HHHHHHHHHhCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHH
Confidence            1 2233332 345789999999999999999887531                          24788999999999999


Q ss_pred             HHhcccCCceeEEEeccccccCCCCCccceEEecC---------CCCChhHHHHHHhhccCCC--CCceEEEEeChhh
Q 017020          129 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE---------LPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQ  195 (379)
Q Consensus       129 ~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~---------~P~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~e  195 (379)
                      +++.|++|.++|||||+++++|+|+|+..+|| ++         .|.++.+|.||+|||||.|  ..|.+++++...+
T Consensus       303 ve~~f~~g~i~VLvaT~~la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~  379 (674)
T PRK01172        303 IEEMFRNRYIKVIVATPTLAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPA  379 (674)
T ss_pred             HHHHHHcCCCeEEEecchhhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcc
Confidence            99999999999999999999999999876555 33         3568899999999999998  4677888876543

>PRK14701 reverse gyrase; Provisional

Probab=99.83  E-value=2.9e-20  Score=209.44  Aligned_cols=187  Identities=18%  Similarity=0.246  Sum_probs=144.5

Q ss_pred             CChHHHHHH----HHH----------------------hCCCCCc-EEEEeeeCChHHHHHHHHhcCCCceEEeeccccc
Q 017020            4 VGFEEDVEL----ILE----------------------NLPPKRQ-SMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDE   56 (379)
Q Consensus         4 ~GF~~di~~----Il~----------------------~~p~~~Q-~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~   56 (379)
                      |||.+|+..    |+.                      .+|..+| +++||||+++.-.  ...+++++..+.+..  ..
T Consensus       226 lGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~~--~~~l~~~~l~f~v~~--~~  301 (1638)
T PRK14701        226 LGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGD--RVKLYRELLGFEVGS--GR  301 (1638)
T ss_pred             CCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchhH--HHHHhhcCeEEEecC--CC
Confidence            799999975    543                      3456667 5779999986311  123446666665532  23


Q ss_pred             ccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccH---HHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhc
Q 017020           57 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA---DEVSLALTS-IIASEALHGDISQHQRERTLNG  132 (379)
Q Consensus        57 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~---~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~  132 (379)
                      ....++.+.|+.+....+ ..+.++++..  +..+||||+|++.+   ++++..|.. ++.+..+||+     |..++++
T Consensus       302 ~~lr~i~~~yi~~~~~~k-~~L~~ll~~~--g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~~  373 (1638)
T PRK14701        302 SALRNIVDVYLNPEKIIK-EHVRELLKKL--GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFDL  373 (1638)
T ss_pred             CCCCCcEEEEEECCHHHH-HHHHHHHHhC--CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHHH
Confidence            445678888876654445 5667777665  46899999999875   899999985 8999999996     8999999


Q ss_pred             ccCCceeEEEec----cccccCCCCCc-cceEEecCCCC---ChhHHHHHH-------------hhccCCCCCceEEEEe
Q 017020          133 FRQGKFTVLVAT----DVAARGLDIPN-VDLIIHYELPN---DPETFVHRS-------------GRTGRAGKEGTAILMF  191 (379)
Q Consensus       133 F~~g~~~iLVaT----dv~~rGiDip~-v~~VI~~~~P~---~~~~yiqR~-------------GRtgR~G~~g~~i~l~  191 (379)
                      |++|+.+|||||    |+++||||+|+ |.+|||||+|.   +.+.|.|..             ||+||.|..+.++..+
T Consensus       374 F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~  453 (1638)
T PRK14701        374 FEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLDV  453 (1638)
T ss_pred             HHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhHHHh
Confidence            999999999999    59999999999 99999999999   888777766             9999999888887766


Q ss_pred             ChhhHHHHHHH
Q 017020          192 TSSQRRTVRSL  202 (379)
Q Consensus       192 ~~~e~~~l~~l  202 (379)
                      ...+...++.+
T Consensus       454 ~~~~~~~~~~~  464 (1638)
T PRK14701        454 FPEDVEFLRSI  464 (1638)
T ss_pred             HHHHHHHHHHH
Confidence            66666655554

>TIGR01054 rgy reverse gyrase

Probab=99.83  E-value=1.1e-19  Score=200.79  Aligned_cols=150  Identities=23%  Similarity=0.405  Sum_probs=115.7

Q ss_pred             CChHHH-HHHHH----------------------HhCCCCCc--EEEEeee-CChHHHHHHHHhcCCCceEEeecccccc
Q 017020            4 VGFEED-VELIL----------------------ENLPPKRQ--SMLFSAT-MPSWVKKLSRKYLDNPLNIDLVGNQDEK   57 (379)
Q Consensus         4 ~GF~~d-i~~Il----------------------~~~p~~~Q--~llfSAT-~p~~i~~l~~~~l~~p~~i~~~~~~~~~   57 (379)
                      |||.+| ++.|+                      +.+|..+|  +++|||| +|..+..   .+++++..+++..  ...
T Consensus       225 lGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~r~ll~~~v~~--~~~  299 (1171)
T TIGR01054       225 LGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLFRELLGFEVGG--GSD  299 (1171)
T ss_pred             cCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHcccccceEecC--ccc
Confidence            899875 66654                      34566666  5679999 5765543   3455666666532  233


Q ss_pred             cccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEeccc---ccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcc
Q 017020           58 LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK---RDADEVSLALTS-IIASEALHGDISQHQRERTLNGF  133 (379)
Q Consensus        58 ~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~---~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F  133 (379)
                      ...++.+.++.+..  +...|.+++...  +.++||||+|+   +.|++++..|.. ++.+..+||+|++    .++++|
T Consensus       300 ~~r~I~~~~~~~~~--~~~~L~~ll~~l--~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l~~F  371 (1171)
T TIGR01054       300 TLRNVVDVYVEDED--LKETLLEIVKKL--GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDYEKF  371 (1171)
T ss_pred             cccceEEEEEeccc--HHHHHHHHHHHc--CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHHHHH
Confidence            45678888775543  345667777665  46899999999   999999999985 8999999999973    689999


Q ss_pred             cCCceeEEEe----ccccccCCCCCc-cceEEecCCCC
Q 017020          134 RQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELPN  166 (379)
Q Consensus       134 ~~g~~~iLVa----Tdv~~rGiDip~-v~~VI~~~~P~  166 (379)
                      ++|+++||||    ||+++||||+|+ |++|||||+|.
T Consensus       372 r~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       372 AEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             HcCCCCEEEEeccccCcccccCCCCccccEEEEECCCC
Confidence            9999999999    599999999999 89999999873

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.

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=99.83  E-value=1.4e-19  Score=193.78  Aligned_cols=194  Identities=21%  Similarity=0.324  Sum_probs=154.2

Q ss_pred             hHHHHHHH---HHhCCCCCcEEEEeeeCChHHHHHHHHhcC--CCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            6 FEEDVELI---LENLPPKRQSMLFSATMPSWVKKLSRKYLD--NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         6 F~~di~~I---l~~~p~~~Q~llfSAT~p~~i~~l~~~~l~--~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      |+++-.++   ....| ...+|.++||.+..+.+-+-..|+  +|..+.-   .  ....|+...+......+....+..
T Consensus       404 FRp~Yk~l~~l~~~~~-~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~---s--fnR~NL~yeV~~k~~~~~~~~~~~  477 (941)
T KOG0351|consen  404 FRPSYKRLGLLRIRFP-GVPFIALTATATERVREDVIRSLGLRNPELFKS---S--FNRPNLKYEVSPKTDKDALLDILE  477 (941)
T ss_pred             ccHHHHHHHHHHhhCC-CCCeEEeehhccHHHHHHHHHHhCCCCcceecc---c--CCCCCceEEEEeccCccchHHHHH
Confidence            55554443   34444 489999999999888876655554  6664321   1  223444443333222233333444


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      .+..+.+...+||||.++.+|+.++..|.. ++.+.+||+||+..+|+.+..+|..++++|+|||=++++|||.|+|..|
T Consensus       478 ~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~V  557 (941)
T KOG0351|consen  478 ESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFV  557 (941)
T ss_pred             HhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEE
Confidence            445555788999999999999999999986 8899999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHH
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  205 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~  205 (379)
                      |||.+|.+.+.|.|-+||+||.|....|++|+...+...++.+-..
T Consensus       558 iH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~s  603 (941)
T KOG0351|consen  558 IHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADISELRRLLTS  603 (941)
T ss_pred             EECCCchhHHHHHHhccccCcCCCcceeEEecchhHHHHHHHHHHc
Confidence            9999999999999999999999999999999999988888776543

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.83  E-value=1.8e-19  Score=189.88  Aligned_cols=140  Identities=27%  Similarity=0.385  Sum_probs=120.9

Q ss_pred             HHHHHHHHHH-HHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCC
Q 017020           74 KRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  151 (379)
Q Consensus        74 k~~~L~~ll~-~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGi  151 (379)
                      +.+.+..-+. ....+.++||||+|+..++.++..|.. ++.+..+||++++.+|..+++.|+.|.+.|||||+++++|+
T Consensus       431 q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGf  510 (652)
T PRK05298        431 QVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGL  510 (652)
T ss_pred             cHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCc
Confidence            3444444443 334578999999999999999999986 89999999999999999999999999999999999999999


Q ss_pred             CCCccceEEecCC-----CCChhHHHHHHhhccCCCCCceEEEEeCh---------hhHHHHHHHHHHhCCCceeeC
Q 017020          152 DIPNVDLIIHYEL-----PNDPETFVHRSGRTGRAGKEGTAILMFTS---------SQRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       152 Dip~v~~VI~~~~-----P~~~~~yiqR~GRtgR~G~~g~~i~l~~~---------~e~~~l~~le~~~~~~~~~~~  214 (379)
                      |+|++++||++|.     |.+..+|+||+|||||. ..|.+++|++.         .|...++.++..++.+....+
T Consensus       511 dlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  586 (652)
T PRK05298        511 DIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITP  586 (652)
T ss_pred             cccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCC
Confidence            9999999999885     78999999999999996 78999999984         577788888888877765543

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.82  E-value=3e-19  Score=187.14  Aligned_cols=168  Identities=18%  Similarity=0.184  Sum_probs=130.7

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHH-HcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~  100 (379)
                      .+..||.|...+..++.+-|--+-  +.+. ........... -.+......|..++...+.. +..+.++||||+|++.
T Consensus       361 kl~GmTGTa~~~~~Ef~~iY~l~v--~~IP-t~kp~~r~d~~-d~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~  436 (762)
T TIGR03714       361 KLSGMTGTGKVAEKEFIETYSLSV--VKIP-TNKPIIRIDYP-DKIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEM  436 (762)
T ss_pred             hhcccCCCChhHHHHHHHHhCCCE--EEcC-CCCCeeeeeCC-CeEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHH
Confidence            456788898777777776663222  2222 11111111111 12334445788777776654 3567899999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC---------ccceEEecCCCCChhH
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP---------NVDLIIHYELPNDPET  170 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip---------~v~~VI~~~~P~~~~~  170 (379)
                      ++.++..|.. ++++..+||++.++++..+..+++.|  .|+||||+|+||+|||         ++.+|++|++|....+
T Consensus       437 se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid  514 (762)
T TIGR03714       437 SEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD  514 (762)
T ss_pred             HHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH
Confidence            9999999985 89999999999999999999888888  6999999999999999         9999999999998777


Q ss_pred             HHHHHhhccCCCCCceEEEEeChhhH
Q 017020          171 FVHRSGRTGRAGKEGTAILMFTSSQR  196 (379)
Q Consensus       171 yiqR~GRtgR~G~~g~~i~l~~~~e~  196 (379)
                       .||+|||||+|.+|.++.|++..|.
T Consensus       515 -~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       515 -LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             -HHhhhcccCCCCceeEEEEEccchh
Confidence             9999999999999999999998664

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.82  E-value=2.8e-19  Score=176.12  Aligned_cols=157  Identities=20%  Similarity=0.261  Sum_probs=112.6

Q ss_pred             HHHHhCCCCCcEEEEeeeCChHHHHHHHHh--cCCCceEEeecc--cc---------------cccccceEEEEEEcCCc
Q 017020           12 LILENLPPKRQSMLFSATMPSWVKKLSRKY--LDNPLNIDLVGN--QD---------------EKLAEGIKLYAISTTAT   72 (379)
Q Consensus        12 ~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~--l~~p~~i~~~~~--~~---------------~~~~~~i~~~~~~~~~~   72 (379)
                      .++...+...+++++|||+|+++.+..+..  +..|..+ +.+.  ..               ..+.+.+.+.+.. ...
T Consensus       173 ~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~-v~g~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~  250 (357)
T TIGR03158       173 QLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAP-IDGEKYQFPDNPELEADNKTQSFRPVLPPVELELIP-APD  250 (357)
T ss_pred             HHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeee-ecCcccccCCChhhhccccccccceeccceEEEEEe-CCc
Confidence            444444456799999999999988877654  4444322 1221  00               0111345555554 334


Q ss_pred             cHHHHHHHHHHHH------cCCCcEEEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEe
Q 017020           73 SKRTILSDLITVY------AKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVA  143 (379)
Q Consensus        73 ~k~~~L~~ll~~~------~~~~~~IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVa  143 (379)
                      .+.+.+..+++..      .+++++||||||++.++.++..|..   ++.+..+||.+++.+|++..      +..||||
T Consensus       251 ~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~~------~~~iLVa  324 (357)
T TIGR03158       251 FKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERAM------QFDILLG  324 (357)
T ss_pred             hhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHhc------cCCEEEE
Confidence            4555554444322      2457999999999999999999985   35788999999999997653      6789999


Q ss_pred             ccccccCCCCCccceEEecCCCCChhHHHHHHhhcc
Q 017020          144 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG  179 (379)
Q Consensus       144 Tdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtg  179 (379)
                      ||+++||+|+|.+ +|| ++ |.+.++|+||+||||
T Consensus       325 Tdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       325 TSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             ecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            9999999999987 666 55 899999999999997

subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.81  E-value=2.1e-19  Score=187.41  Aligned_cols=169  Identities=20%  Similarity=0.217  Sum_probs=132.0

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH-HHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD-LITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~-ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+..||.|...+..++.+-|--+-+.|  . ...........-. +.....+|..++.. +...+..+.++||||+|+..
T Consensus       342 kl~GmTGTa~te~~E~~~iY~l~vv~I--P-tnkp~~R~d~~d~-i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~  417 (745)
T TIGR00963       342 KLSGMTGTAKTEEEEFEKIYNLEVVVV--P-TNRPVIRKDLSDL-VYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEK  417 (745)
T ss_pred             hhhccCCCcHHHHHHHHHHhCCCEEEe--C-CCCCeeeeeCCCe-EEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHH
Confidence            455689999877777777774432222  2 1111111111111 22233456665544 44555678999999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCc-------cceEEecCCCCChhHHH
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN-------VDLIIHYELPNDPETFV  172 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~-------v~~VI~~~~P~~~~~yi  172 (379)
                      ++.++..|.. ++++..+||+  +.+|+..+..|+.+...|+||||+|+||+||+.       ..|||+++.|.+...|.
T Consensus       418 se~ls~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~  495 (745)
T TIGR00963       418 SELLSNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDN  495 (745)
T ss_pred             HHHHHHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHH
Confidence            9999999985 8999999999  899999999999999999999999999999998       55999999999999999


Q ss_pred             HHHhhccCCCCCceEEEEeChhhH
Q 017020          173 HRSGRTGRAGKEGTAILMFTSSQR  196 (379)
Q Consensus       173 qR~GRtgR~G~~g~~i~l~~~~e~  196 (379)
                      ||.|||||.|.+|.+..|++..|.
T Consensus       496 q~~GRtGRqG~~G~s~~~ls~eD~  519 (745)
T TIGR00963       496 QLRGRSGRQGDPGSSRFFLSLEDN  519 (745)
T ss_pred             HHhccccCCCCCcceEEEEeccHH
Confidence            999999999999999999998764

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.81  E-value=5.9e-19  Score=185.18  Aligned_cols=132  Identities=24%  Similarity=0.388  Sum_probs=114.9

Q ss_pred             cHHHHHHHHH-HHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccC
Q 017020           73 SKRTILSDLI-TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG  150 (379)
Q Consensus        73 ~k~~~L~~ll-~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rG  150 (379)
                      .+.+.|..-+ .....+.++||||+|++.++.++..|.. ++.+..+||++++.+|.++++.|+.|++.|||||+++++|
T Consensus       426 ~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rG  505 (655)
T TIGR00631       426 GQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREG  505 (655)
T ss_pred             chHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCC
Confidence            3444444444 3345678999999999999999999986 8999999999999999999999999999999999999999


Q ss_pred             CCCCccceEEecC-----CCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHH
Q 017020          151 LDIPNVDLIIHYE-----LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  205 (379)
Q Consensus       151 iDip~v~~VI~~~-----~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~  205 (379)
                      +|+|++++||++|     .|.+..+|+||+|||||. ..|.++++++..+..+.+.++..
T Consensus       506 fDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~ai~~~  564 (655)
T TIGR00631       506 LDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSMQKAIEET  564 (655)
T ss_pred             eeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHHHHHHH
Confidence            9999999999988     799999999999999998 58999999998776666655443

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

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.81  E-value=9e-19  Score=179.92  Aligned_cols=113  Identities=18%  Similarity=0.216  Sum_probs=98.3

Q ss_pred             HHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEec-cccccC
Q 017020           74 KRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT-DVAARG  150 (379)
Q Consensus        74 k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaT-dv~~rG  150 (379)
                      +...+..++... ..+.+++|||++.+.++.+++.|.. +..+..+||+|++++|..+++.|++|+..+|||| +++++|
T Consensus       329 Rn~~I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG  408 (501)
T PHA02558        329 RNKWIANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTG  408 (501)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccc
Confidence            444444444332 3467899999999999999999985 8899999999999999999999999999999998 999999


Q ss_pred             CCCCccceEEecCCCCChhHHHHHHhhccCCCCCce
Q 017020          151 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGT  186 (379)
Q Consensus       151 iDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~  186 (379)
                      +|+|++++||++.+|.+...|+||+||++|.+..+.
T Consensus       409 ~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K~  444 (501)
T PHA02558        409 ISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKS  444 (501)
T ss_pred             cccccccEEEEecCCcchhhhhhhhhccccCCCCCc
Confidence            999999999999999999999999999999875543

>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=99.80  E-value=5.1e-19  Score=147.89  Aligned_cols=127  Identities=46%  Similarity=0.772  Sum_probs=112.3

Q ss_pred             EEEEEEcCCccHHHHHHHHHHHHc-CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeE
Q 017020           63 KLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTV  140 (379)
Q Consensus        63 ~~~~~~~~~~~k~~~L~~ll~~~~-~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~i  140 (379)
                      .+++...+ ..|...+..++.... .++++||||++...++.++..|.. ...+..+||++++.+|..+++.|+++...+
T Consensus         3 ~~~~~~~~-~~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~i   81 (131)
T cd00079           3 KQYVLPVE-DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVV   81 (131)
T ss_pred             EEEEEECC-HHHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcE
Confidence            34444433 267777777776553 468999999999999999999975 788999999999999999999999999999


Q ss_pred             EEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEE
Q 017020          141 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  190 (379)
Q Consensus       141 LVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l  190 (379)
                      |++|+++++|+|+|++++||.+++|.+...|.|++||++|.|..|.++++
T Consensus        82 li~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          82 LVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             EEEcChhhcCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            99999999999999999999999999999999999999999998888764

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=2e-18  Score=181.40  Aligned_cols=168  Identities=22%  Similarity=0.243  Sum_probs=130.8

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHH-HHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT-VYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~-~~~~~~~~IIF~~t~~~  100 (379)
                      .+..||.|...+..++.+-|--+  .+.+. ........... -.+......|..++...+. .+..+.|+||||+|+..
T Consensus       377 kl~GmTGTa~~e~~Ef~~iY~l~--vv~IP-tnkp~~r~d~~-d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~  452 (796)
T PRK12906        377 KLSGMTGTAKTEEEEFREIYNME--VITIP-TNRPVIRKDSP-DLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIES  452 (796)
T ss_pred             hhhccCCCCHHHHHHHHHHhCCC--EEEcC-CCCCeeeeeCC-CeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHH
Confidence            45568899877777777666433  22222 11111111111 1122334567777766664 34567899999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCC---Cccc-----eEEecCCCCChhHH
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI---PNVD-----LIIHYELPNDPETF  171 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDi---p~v~-----~VI~~~~P~~~~~y  171 (379)
                      ++.++..|.. ++++..+||++.+.+++.+.++++.|.  |+||||+|+||+||   ++|.     |||+++.|.+...|
T Consensus       453 se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~  530 (796)
T PRK12906        453 SERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRID  530 (796)
T ss_pred             HHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHH
Confidence            9999999985 899999999999999999998888886  99999999999999   5899     99999999999999


Q ss_pred             HHHHhhccCCCCCceEEEEeChhh
Q 017020          172 VHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       172 iqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      .|+.|||||.|.+|.+..|++.+|
T Consensus       531 ~Ql~GRtGRqG~~G~s~~~~sleD  554 (796)
T PRK12906        531 NQLRGRSGRQGDPGSSRFYLSLED  554 (796)
T ss_pred             HHHhhhhccCCCCcceEEEEeccc
Confidence            999999999999999999998875

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

Probab=99.78  E-value=3.9e-17  Score=172.14  Aligned_cols=201  Identities=22%  Similarity=0.334  Sum_probs=141.2

Q ss_pred             HHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCC--CceEEeecccccccccceEEEEEEcCCc------cHHHHHHHH
Q 017020           10 VELILENLPPKRQSMLFSATMPSWVKKLSRKYLDN--PLNIDLVGNQDEKLAEGIKLYAISTTAT------SKRTILSDL   81 (379)
Q Consensus        10 i~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~--p~~i~~~~~~~~~~~~~i~~~~~~~~~~------~k~~~L~~l   81 (379)
                      ++.+....+ +.|.|.+|||..+ ...+++.....  +..|--+  ...   ...+...+.+...      .-..++..+
T Consensus       174 LeRL~~l~~-~~qRIGLSATV~~-~~~varfL~g~~~~~~Iv~~--~~~---k~~~i~v~~p~~~~~~~~~~~~~~~~~i  246 (814)
T COG1201         174 LERLRELAG-DFQRIGLSATVGP-PEEVAKFLVGFGDPCEIVDV--SAA---KKLEIKVISPVEDLIYDEELWAALYERI  246 (814)
T ss_pred             HHHHHhhCc-ccEEEeehhccCC-HHHHHHHhcCCCCceEEEEc--ccC---CcceEEEEecCCccccccchhHHHHHHH
Confidence            344444555 8999999999953 34445433333  3333211  111   1122222222111      112233333


Q ss_pred             HHHHcCCCcEEEEecccccHHHHHHHHhcC--CcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           82 ITVYAKGGKTIVFTQTKRDADEVSLALTSI--IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        82 l~~~~~~~~~IIF~~t~~~~~~l~~~L~~~--~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      .+.......+|||+||+..++.++..|...  ..+..+||.++.++|..+.++|++|+.+++|||+.++-|||+.+++.|
T Consensus       247 ~~~v~~~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdlV  326 (814)
T COG1201         247 AELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLV  326 (814)
T ss_pred             HHHHhhcCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCceEE
Confidence            333344568999999999999999999863  689999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccC-CCCCceEEEEeChhh--HHHHHHHHHHhCCCceeeCCCC
Q 017020          160 IHYELPNDPETFVHRSGRTGR-AGKEGTAILMFTSSQ--RRTVRSLERDVGCKFEFVSPPV  217 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR-~G~~g~~i~l~~~~e--~~~l~~le~~~~~~~~~~~~p~  217 (379)
                      |||+.|.++...+||+||+|+ .|....++++....+  ..-..-........++...+|.
T Consensus       327 Iq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~r~dllE~~vi~~~a~~g~le~~~i~~  387 (814)
T COG1201         327 IQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAEDRDDLLECLVLADLALEGKLERIKIPK  387 (814)
T ss_pred             EEeCCcHHHHHHhHhccccccccCCcccEEEEecCHHHHHHHHHHHHHHHhCCcccCCCCC
Confidence            999999999999999999996 455677777777632  1223334556666777555543

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

Probab=99.77  E-value=1.8e-18  Score=170.16  Aligned_cols=123  Identities=33%  Similarity=0.555  Sum_probs=107.2

Q ss_pred             ccHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-CCcE--EEe-------eCCCCHHHHHHHHhcccCCce
Q 017020           72 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIAS--EAL-------HGDISQHQRERTLNGFRQGKF  138 (379)
Q Consensus        72 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v--~~l-------hg~m~~~~R~~~~~~F~~g~~  138 (379)
                      ..|++.+.+++...   ..+.++|||++.+++++.+...|.. +..+  .++       ..||+|.++.+++++|++|++
T Consensus       347 HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~  426 (542)
T COG1111         347 HPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEY  426 (542)
T ss_pred             CccHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCc
Confidence            35777777777654   3457999999999999999999986 4433  222       257999999999999999999


Q ss_pred             eEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          139 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       139 ~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      ++||||++++.|+|||+++.||.|++-.|+--++||.|||||. +.|.++++++...
T Consensus       427 nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gt  482 (542)
T COG1111         427 NVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGT  482 (542)
T ss_pred             eEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCc
Confidence            9999999999999999999999999999999999999999997 7999999998763

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.75  E-value=1.2e-17  Score=176.95  Aligned_cols=168  Identities=21%  Similarity=0.231  Sum_probs=130.4

Q ss_pred             EEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHH-HcCCCcEEEEecccccH
Q 017020           23 SMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDA  101 (379)
Q Consensus        23 ~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~~  101 (379)
                      +-.||.|...+-.++.+-|--+-+.|   +...........- .+......|..++...+.. +..+.++||||+|+..+
T Consensus       536 LaGMTGTA~te~~Ef~~iY~L~Vv~I---PTnrP~~R~D~~d-~vy~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~s  611 (1025)
T PRK12900        536 LAGMTGTAETEASEFFEIYKLDVVVI---PTNKPIVRKDMDD-LVYKTRREKYNAIVLKVEELQKKGQPVLVGTASVEVS  611 (1025)
T ss_pred             hcccCCCChhHHHHHHHHhCCcEEEC---CCCCCcceecCCC-eEecCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHH
Confidence            44578888777777776664332222   1111111111111 2233445688888777754 34578999999999999


Q ss_pred             HHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC---ccc-----eEEecCCCCChhHHH
Q 017020          102 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP---NVD-----LIIHYELPNDPETFV  172 (379)
Q Consensus       102 ~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip---~v~-----~VI~~~~P~~~~~yi  172 (379)
                      +.++..|.. ++++..||+  .|.+|+..+..|+.+...|+||||+|+||+||+   +|.     +||+++.|.+...|.
T Consensus       612 E~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~  689 (1025)
T PRK12900        612 ETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDR  689 (1025)
T ss_pred             HHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHH
Confidence            999999985 899999997  599999999999999999999999999999998   554     459999999999999


Q ss_pred             HHHhhccCCCCCceEEEEeChhhH
Q 017020          173 HRSGRTGRAGKEGTAILMFTSSQR  196 (379)
Q Consensus       173 qR~GRtgR~G~~g~~i~l~~~~e~  196 (379)
                      ||+|||||+|.+|.+++|++..|.
T Consensus       690 Ql~GRtGRqGdpGsS~ffvSleD~  713 (1025)
T PRK12900        690 QLRGRAGRQGDPGESVFYVSLEDE  713 (1025)
T ss_pred             HHhhhhhcCCCCcceEEEechhHH
Confidence            999999999999999999998764

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

Probab=99.75  E-value=2.3e-17  Score=174.93  Aligned_cols=236  Identities=19%  Similarity=0.313  Sum_probs=179.7

Q ss_pred             HHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC-cc-HHHHHHHHHHHH--c
Q 017020           11 ELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TS-KRTILSDLITVY--A   86 (379)
Q Consensus        11 ~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~-k~~~L~~ll~~~--~   86 (379)
                      ..++...+++-.+|++|||+.  .+++++ |+.++..+.+.+..     -.++.+|..... .. -.+.+...+..+  .
T Consensus       186 k~~~~~rr~DLKiIimSATld--~~rfs~-~f~~apvi~i~GR~-----fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~  257 (845)
T COG1643         186 KDLLARRRDDLKLIIMSATLD--AERFSA-YFGNAPVIEIEGRT-----YPVEIRYLPEAEADYILLDAIVAAVDIHLRE  257 (845)
T ss_pred             HHHHhhcCCCceEEEEecccC--HHHHHH-HcCCCCEEEecCCc-----cceEEEecCCCCcchhHHHHHHHHHHHhccC
Confidence            345677777899999999995  445554 66766667665432     334555543332 23 334444555443  3


Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                      ..+.+|||.+..++.+.+++.|.+     ...+.++||.|+.+++.++++.-..|..+|++||++|+.+|.||+|.+||+
T Consensus       258 ~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VID  337 (845)
T COG1643         258 GSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVID  337 (845)
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEec
Confidence            468999999999999999999975     366899999999999999999999898889999999999999999999997


Q ss_pred             cCC------------------CCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHHHHH
Q 017020          162 YEL------------------PNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLE  223 (379)
Q Consensus       162 ~~~------------------P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~i~~  223 (379)
                      -+.                  |.+..+..||.||+||.+ +|.||-+|+..+..              ..+.-+..||+.
T Consensus       338 sG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~-pGicyRLyse~~~~--------------~~~~~t~PEIlr  402 (845)
T COG1643         338 SGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTG-PGICYRLYSEEDFL--------------AFPEFTLPEILR  402 (845)
T ss_pred             CCcccccccccccCceeeeEEEechhhhhhhccccccCC-CceEEEecCHHHHH--------------hcccCCChhhhh
Confidence            553                  557889999999999996 99999999996642              112334568999


Q ss_pred             HHHHHHHHHHcccCcc-chhchHHHHHHHHhhhCHHHHHHHHHHHcCCCCCC
Q 017020          224 SSAEQVVATLNGVHPE-SVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPP  274 (379)
Q Consensus       224 ~~~~~~~~~l~~~~~~-~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~~~~  274 (379)
                      ..+..++..++++... +...|     .+++.++..++.+|+..+...+...
T Consensus       403 tdLs~~vL~l~~~G~~~d~~~f-----~fld~P~~~~i~~A~~~L~~LGAld  449 (845)
T COG1643         403 TDLSGLVLQLKSLGIGQDIAPF-----PFLDPPPEAAIQAALTLLQELGALD  449 (845)
T ss_pred             cchHHHHHHHHhcCCCCCcccC-----ccCCCCChHHHHHHHHHHHHcCCcC
Confidence            9999999999998763 55555     5677888888888887776554443

>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=99.74  E-value=3.4e-18  Score=131.20  Aligned_cols=76  Identities=39%  Similarity=0.768  Sum_probs=72.6

Q ss_pred             HHh-cCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCC
Q 017020          107 ALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  182 (379)
Q Consensus       107 ~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G  182 (379)
                      .|+ .++.+..+||++++.+|+.+++.|+++...+||||+++++|+|+|++++||++++|.++..|.|++||+||.|
T Consensus         2 ~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    2 FLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             HHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             ChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            354 3899999999999999999999999999999999999999999999999999999999999999999999986

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 ....

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=99.74  E-value=4.2e-18  Score=163.92  Aligned_cols=180  Identities=22%  Similarity=0.349  Sum_probs=141.1

Q ss_pred             CCCcEEEEeeeCChHHHHHHH--HhcCCCceEEeecccccccccceEEEEEE-c--CCccHHHHHHHHHHH-Hc------
Q 017020           19 PKRQSMLFSATMPSWVKKLSR--KYLDNPLNIDLVGNQDEKLAEGIKLYAIS-T--TATSKRTILSDLITV-YA------   86 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~i~~l~~--~~l~~p~~i~~~~~~~~~~~~~i~~~~~~-~--~~~~k~~~L~~ll~~-~~------   86 (379)
                      ++...+.++||.++++++-+-  ..+++|+.+--.+.    -..|+  +|-. .  .-++-...|.++... ++      
T Consensus       175 ~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~----FR~NL--FYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~~  248 (641)
T KOG0352|consen  175 PGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPT----FRDNL--FYDNHMKSFITDCLTVLADFSSSNLGKHEKAS  248 (641)
T ss_pred             CCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcc----hhhhh--hHHHHHHHHhhhHhHhHHHHHHHhcCChhhhh
Confidence            478899999999998887443  44568876622111    01111  1100 0  012333344443321 11      


Q ss_pred             -----CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE
Q 017020           87 -----KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII  160 (379)
Q Consensus        87 -----~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI  160 (379)
                           ..+-.||||.|+++|+.++-.|.. |+++.++|.|+...+|..+.++|-+++..|++||..+++|+|-|+|..||
T Consensus       249 ~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFVi  328 (641)
T KOG0352|consen  249 QNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVI  328 (641)
T ss_pred             cCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEE
Confidence                 124679999999999999999985 99999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHH
Q 017020          161 HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  204 (379)
Q Consensus       161 ~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~  204 (379)
                      |+++|.+...|.|.+||+||.|+...|-++|+.++...+..|-+
T Consensus       329 HW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FLi~  372 (641)
T KOG0352|consen  329 HWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFLVS  372 (641)
T ss_pred             ecCchhhhHHHHHhccccccCCCccceeeeecccchHHHHHHHh
Confidence            99999999999999999999999999999999999888877643

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

Probab=99.74  E-value=1.9e-17  Score=164.46  Aligned_cols=175  Identities=23%  Similarity=0.343  Sum_probs=135.2

Q ss_pred             HHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHH-------c
Q 017020           14 LENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVY-------A   86 (379)
Q Consensus        14 l~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~-------~   86 (379)
                      |+.+-++.|+|.+|||+.. -.++++++--+++..  .    .+..+--.|..++....+|.+.+..+.+..       +
T Consensus       366 Lr~l~~~AQ~i~LSATVgN-p~elA~~l~a~lV~y--~----~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg  438 (830)
T COG1202         366 LRYLFPGAQFIYLSATVGN-PEELAKKLGAKLVLY--D----ERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKG  438 (830)
T ss_pred             HHHhCCCCeEEEEEeecCC-hHHHHHHhCCeeEee--c----CCCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccC
Confidence            3444568999999999943 356676654444332  1    111122244555555778999988888653       2


Q ss_pred             CCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe---c
Q 017020           87 KGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH---Y  162 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~---~  162 (379)
                      -.+++|||++|++.|++++..|. +++.+.++|+||+..+|..+...|.++++.++|+|-.++.|+|+|.-.+|..   .
T Consensus       439 ~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaM  518 (830)
T COG1202         439 YRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAM  518 (830)
T ss_pred             cCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHHHHHc
Confidence            24799999999999999999998 4999999999999999999999999999999999999999999997664431   2


Q ss_pred             CCC-CChhHHHHHHhhccCCC--CCceEEEEeChhh
Q 017020          163 ELP-NDPETFVHRSGRTGRAG--KEGTAILMFTSSQ  195 (379)
Q Consensus       163 ~~P-~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~e  195 (379)
                      +.- -++.+|.|+.||+||.+  ..|.+|+++.+..
T Consensus       519 G~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg~  554 (830)
T COG1202         519 GIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGK  554 (830)
T ss_pred             ccccCCHHHHHHHhcccCCCCcccCceEEEEecCCh
Confidence            222 38999999999999988  5699999987743

>PRK13766 Hef nuclease; Provisional

Probab=99.71  E-value=5.4e-17  Score=175.15  Aligned_cols=122  Identities=35%  Similarity=0.558  Sum_probs=109.8

Q ss_pred             ccHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCC--------CCHHHHHHHHhcccCCcee
Q 017020           72 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGD--------ISQHQRERTLNGFRQGKFT  139 (379)
Q Consensus        72 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~--------m~~~~R~~~~~~F~~g~~~  139 (379)
                      ..|.+.|.+++...   .++.++||||++++.|+.++..|.. ++.+..+||.        |++.+|..++++|++|+.+
T Consensus       346 ~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~  425 (773)
T PRK13766        346 HPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFN  425 (773)
T ss_pred             ChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCC
Confidence            45778888888654   3568999999999999999999964 7888899886        9999999999999999999


Q ss_pred             EEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChh
Q 017020          140 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS  194 (379)
Q Consensus       140 iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~  194 (379)
                      +||||+++++|+|+|++++||+||+|.++..|+||+||+||.| .|.+++++...
T Consensus       426 vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~-~~~v~~l~~~~  479 (773)
T PRK13766        426 VLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQE-EGRVVVLIAKG  479 (773)
T ss_pred             EEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCC-CCEEEEEEeCC
Confidence            9999999999999999999999999999999999999999987 58888888653

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=99.70  E-value=3.3e-16  Score=158.65  Aligned_cols=231  Identities=20%  Similarity=0.344  Sum_probs=173.6

Q ss_pred             HHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH-HHHHHHHHH--cCCC
Q 017020           13 ILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-ILSDLITVY--AKGG   89 (379)
Q Consensus        13 Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-~L~~ll~~~--~~~~   89 (379)
                      |++.- ++-.+|++|||+.  ...+ +.|+.+...+.+.+.     .-.++.+|...+..+-.+ .+.-+++.+  .+++
T Consensus       189 i~~~R-~~LklIimSATld--a~kf-S~yF~~a~i~~i~GR-----~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~G  259 (674)
T KOG0922|consen  189 ILKKR-PDLKLIIMSATLD--AEKF-SEYFNNAPILTIPGR-----TFPVEILYLKEPTADYVDAALITVIQIHLTEPPG  259 (674)
T ss_pred             HHhcC-CCceEEEEeeeec--HHHH-HHHhcCCceEeecCC-----CCceeEEeccCCchhhHHHHHHHHHHHHccCCCC
Confidence            34433 3578999999995  3344 457777666666543     234566666655555443 333333333  4567


Q ss_pred             cEEEEecccccHHHHHHHHhcC---C------cEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE
Q 017020           90 KTIVFTQTKRDADEVSLALTSI---I------ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII  160 (379)
Q Consensus        90 ~~IIF~~t~~~~~~l~~~L~~~---~------~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI  160 (379)
                      -+|||.+..++.+.+++.|.+.   .      -+.++||.||.+++.++++.-..|..+|++||++|+..+.||++.+||
T Consensus       260 DILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVV  339 (674)
T KOG0922|consen  260 DILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVV  339 (674)
T ss_pred             CEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEE
Confidence            9999999999999999998741   1      246899999999999999999999999999999999999999999999


Q ss_pred             ecC------------------CCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHHHH
Q 017020          161 HYE------------------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVL  222 (379)
Q Consensus       161 ~~~------------------~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~i~  222 (379)
                      +.+                  .|-|..+-.||.||+||.| .|.||-+|+..+.              +.....+..+|.
T Consensus       340 DsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRLYte~~~--------------~~~~~~~~PEI~  404 (674)
T KOG0922|consen  340 DSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRTG-PGKCYRLYTESAY--------------DKMPLQTVPEIQ  404 (674)
T ss_pred             cCCceEEEeeccccCccceeEEechHHHHhhhcccCCCCC-CceEEEeeeHHHH--------------hhcccCCCCcee
Confidence            655                  3668889999999999997 9999999999774              222344456777


Q ss_pred             HHHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcCCCC
Q 017020          223 ESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSR  272 (379)
Q Consensus       223 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~~  272 (379)
                      ...+..++..++.+..+++-.|     .+++.+.++.+.+||..+.....
T Consensus       405 R~~Ls~~vL~Lkalgi~d~l~F-----~f~d~P~~~~l~~AL~~L~~lga  449 (674)
T KOG0922|consen  405 RVNLSSAVLQLKALGINDPLRF-----PFIDPPPPEALEEALEELYSLGA  449 (674)
T ss_pred             eechHHHHHHHHhcCCCCcccC-----CCCCCCChHHHHHHHHHHHhcCc
Confidence            7888888888888776655555     56778888999999988864443

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.69  E-value=3e-16  Score=166.74  Aligned_cols=182  Identities=23%  Similarity=0.379  Sum_probs=130.8

Q ss_pred             HHHHHHhCC---CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCc-------cHHHHHH
Q 017020           10 VELILENLP---PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT-------SKRTILS   79 (379)
Q Consensus        10 i~~Il~~~p---~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~-------~k~~~L~   79 (379)
                      ++.|+..+.   ...|++.+|||+|. ..+++.+.-.++..-..-..+........... +.....       .....+.
T Consensus       167 lE~iv~r~~~~~~~~rivgLSATlpN-~~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~-~~~~~~~k~~~~~~~~~~~~  244 (766)
T COG1204         167 LESIVARMRRLNELIRIVGLSATLPN-AEEVADWLNAKLVESDWRPVPLRRGVPYVGAF-LGADGKKKTWPLLIDNLALE  244 (766)
T ss_pred             ehhHHHHHHhhCcceEEEEEeeecCC-HHHHHHHhCCcccccCCCCcccccCCccceEE-EEecCccccccccchHHHHH
Confidence            344555443   34799999999976 67778765545542222111111111111222 222211       2345556


Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHhc---C-C----------------------------------cEEEeeCCC
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALTS---I-I----------------------------------ASEALHGDI  121 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~---~-~----------------------------------~v~~lhg~m  121 (379)
                      .++.....++++||||+|++.+...+..+..   + +                                  .+..+|++|
T Consensus       245 ~v~~~~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL  324 (766)
T COG1204         245 LVLESLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGL  324 (766)
T ss_pred             HHHHHHhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCC
Confidence            6666777789999999999999999988872   1 0                                  356799999


Q ss_pred             CHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE----ecC-----CCCChhHHHHHHhhccCCC--CCceEEEE
Q 017020          122 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII----HYE-----LPNDPETFVHRSGRTGRAG--KEGTAILM  190 (379)
Q Consensus       122 ~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI----~~~-----~P~~~~~yiqR~GRtgR~G--~~g~~i~l  190 (379)
                      +.++|..+.+.|+.|.++|||||+.+|+|+|.|.-.+||    -|+     .+.++-+|+|+.|||||.|  ..|.++++
T Consensus       325 ~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~  404 (766)
T COG1204         325 PREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIIL  404 (766)
T ss_pred             CHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEE
Confidence            999999999999999999999999999999999888877    466     5678999999999999999  56788887


Q ss_pred             eCh
Q 017020          191 FTS  193 (379)
Q Consensus       191 ~~~  193 (379)
                      .+.
T Consensus       405 ~~~  407 (766)
T COG1204         405 ATS  407 (766)
T ss_pred             ecC
Confidence            743

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.69  E-value=1.2e-16  Score=167.49  Aligned_cols=120  Identities=23%  Similarity=0.344  Sum_probs=103.6

Q ss_pred             cHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCC-ceeEEEeccccccC
Q 017020           73 SKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQG-KFTVLVATDVAARG  150 (379)
Q Consensus        73 ~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g-~~~iLVaTdv~~rG  150 (379)
                      .|..++..++..+ ..+.++||||++...++.++..|    .+..+||++++.+|++++++|++| .+++||+|+++.+|
T Consensus       480 ~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L----~~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgdeG  555 (732)
T TIGR00603       480 NKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKL----GKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTS  555 (732)
T ss_pred             HHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHc----CCceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccc
Confidence            4666777777665 35689999999999988888877    356799999999999999999875 88999999999999


Q ss_pred             CCCCccceEEecCCC-CChhHHHHHHhhccCCCCCceE-------EEEeChhhH
Q 017020          151 LDIPNVDLIIHYELP-NDPETFVHRSGRTGRAGKEGTA-------ILMFTSSQR  196 (379)
Q Consensus       151 iDip~v~~VI~~~~P-~~~~~yiqR~GRtgR~G~~g~~-------i~l~~~~e~  196 (379)
                      +|+|++++||+++.| .+...|+||+||++|.+..|.+       |.|+++...
T Consensus       556 IDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~  609 (732)
T TIGR00603       556 IDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQ  609 (732)
T ss_pred             cCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCch
Confidence            999999999999998 4999999999999999877665       778876543

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).

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.67  E-value=4.5e-16  Score=156.69  Aligned_cols=231  Identities=19%  Similarity=0.306  Sum_probs=174.9

Q ss_pred             CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH-HHHHHHH--cCCCcEEEEe
Q 017020           19 PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVY--AKGGKTIVFT   95 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L-~~ll~~~--~~~~~~IIF~   95 (379)
                      ++-..++.||||.  .+++.. |+.+...+.+.+.     .-.+..+|-..+..+-.++. ..+++.+  .+.+-+|||.
T Consensus       409 pdLKllIsSAT~D--AekFS~-fFDdapIF~iPGR-----RyPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFl  480 (902)
T KOG0923|consen  409 PDLKLLISSATMD--AEKFSA-FFDDAPIFRIPGR-----RYPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFL  480 (902)
T ss_pred             CcceEEeeccccC--HHHHHH-hccCCcEEeccCc-----ccceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEe
Confidence            6789999999995  345554 6666555555433     23456677777776666543 3344333  4568899999


Q ss_pred             cccccHHHHHHHHhc----------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecC--
Q 017020           96 QTKRDADEVSLALTS----------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE--  163 (379)
Q Consensus        96 ~t~~~~~~l~~~L~~----------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~--  163 (379)
                      ...++.+...+.|..          .+-++++|+.||+..+.++++.--.|..+|++||++|+..+.|++|.+||+-+  
T Consensus       481 tGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~  560 (902)
T KOG0923|consen  481 TGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFV  560 (902)
T ss_pred             ccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccc
Confidence            998888877766642          24688999999999999999999999999999999999999999999999644  


Q ss_pred             ----------------CCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHHHHHHHHH
Q 017020          164 ----------------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAE  227 (379)
Q Consensus       164 ----------------~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~i~~~~~~  227 (379)
                                      .|.+..+-.||.||+||.| +|.|+-+|+...  +.+.+|..        .   ..+|.+..+.
T Consensus       561 K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt~~a--Y~~eLE~~--------t---~PEIqRtnL~  626 (902)
T KOG0923|consen  561 KQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYTAWA--YEHELEEM--------T---VPEIQRTNLG  626 (902)
T ss_pred             cccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeechhh--hhhhhccC--------C---Ccceeeccch
Confidence                            3668888999999999998 999999999733  33444322        2   2345666677


Q ss_pred             HHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcCCCCCCCC
Q 017020          228 QVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSS  276 (379)
Q Consensus       228 ~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~~~~~~  276 (379)
                      .++..++++...++-.|     .+++.++.+.+..||..|.+++.....
T Consensus       627 nvVL~LkSLGI~Dl~~F-----dFmDpPp~etL~~aLE~LyaLGALn~~  670 (902)
T KOG0923|consen  627 NVVLLLKSLGIHDLIHF-----DFLDPPPTETLLKALEQLYALGALNHL  670 (902)
T ss_pred             hHHHHHHhcCcchhccc-----ccCCCCChHHHHHHHHHHHHhhccccc
Confidence            78888888877776666     678888999999999999877766543

>PRK09694 helicase Cas3; Provisional

Probab=99.67  E-value=1.3e-15  Score=163.64  Aligned_cols=106  Identities=25%  Similarity=0.452  Sum_probs=90.8

Q ss_pred             HHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcC----CcEEEeeCCCCHHHH----HHHHhcc-cCCc---eeEEE
Q 017020           75 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI----IASEALHGDISQHQR----ERTLNGF-RQGK---FTVLV  142 (379)
Q Consensus        75 ~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~----~~v~~lhg~m~~~~R----~~~~~~F-~~g~---~~iLV  142 (379)
                      ..++..+++....+++++|||||++.|+++++.|...    ..+..+||.+++.+|    +++++.| ++|+   ..|||
T Consensus       547 ~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILV  626 (878)
T PRK09694        547 LTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILV  626 (878)
T ss_pred             HHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEE
Confidence            4556666666556789999999999999999999852    579999999999999    4678888 6665   47999


Q ss_pred             eccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCC
Q 017020          143 ATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  183 (379)
Q Consensus       143 aTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~  183 (379)
                      ||+++++|+|| +++++|....|  .+.|+||+||+||.++
T Consensus       627 aTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        627 ATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             ECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            99999999999 68999998888  6899999999999885

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=99.66  E-value=6.6e-16  Score=159.81  Aligned_cols=125  Identities=32%  Similarity=0.519  Sum_probs=106.8

Q ss_pred             ccHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc----CCcEEEee--------CCCCHHHHHHHHhcccCC
Q 017020           72 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS----IIASEALH--------GDISQHQRERTLNGFRQG  136 (379)
Q Consensus        72 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~----~~~v~~lh--------g~m~~~~R~~~~~~F~~g  136 (379)
                      ..|.+.+.+++..+   .+..++||||.++..|..+..+|..    ++.+..+-        .+|+|.++.+++++|++|
T Consensus       394 npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G  473 (746)
T KOG0354|consen  394 NPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDG  473 (746)
T ss_pred             ChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCC
Confidence            56788777777544   4567999999999999999999873    33333333        389999999999999999


Q ss_pred             ceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHH
Q 017020          137 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT  198 (379)
Q Consensus       137 ~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~  198 (379)
                      ++++||||+++++|+||+++++||-||.-.++-..+||.|| ||+ +.|.++++++..+...
T Consensus       474 ~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa-~ns~~vll~t~~~~~~  533 (746)
T KOG0354|consen  474 EINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRA-RNSKCVLLTTGSEVIE  533 (746)
T ss_pred             CccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-ccc-cCCeEEEEEcchhHHH
Confidence            99999999999999999999999999999999999999999 998 5899999998655433

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=99.63  E-value=3.2e-15  Score=142.32  Aligned_cols=191  Identities=21%  Similarity=0.323  Sum_probs=150.0

Q ss_pred             hHHHHH--HHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHH
Q 017020            6 FEEDVE--LILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT   83 (379)
Q Consensus         6 F~~di~--~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~   83 (379)
                      |+.|-.  .||+.--++..++.++||.+..+.+-++..+.-...+.+..   .-..+++.+.... .+..-.+.+.++.+
T Consensus       234 fr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~a---~fnr~nl~yev~q-kp~n~dd~~edi~k  309 (695)
T KOG0353|consen  234 FRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFRA---GFNRPNLKYEVRQ-KPGNEDDCIEDIAK  309 (695)
T ss_pred             cCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheeec---ccCCCCceeEeee-CCCChHHHHHHHHH
Confidence            444433  46666667899999999999998888877765333333321   1112444433333 33344445555554


Q ss_pred             HH---cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           84 VY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        84 ~~---~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ..   -.+...||||-+.++++.++..|.+ ++.+..+|..|.+.+|..+-+.|-.|++.|+|||-..+.|||-|+|++|
T Consensus       310 ~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfv  389 (695)
T KOG0353|consen  310 LIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFV  389 (695)
T ss_pred             HhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEE
Confidence            43   2366889999999999999999986 8999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHH-------------------------------------------HHhhccCCCCCceEEEEeChhhH
Q 017020          160 IHYELPNDPETFVH-------------------------------------------RSGRTGRAGKEGTAILMFTSSQR  196 (379)
Q Consensus       160 I~~~~P~~~~~yiq-------------------------------------------R~GRtgR~G~~g~~i~l~~~~e~  196 (379)
                      ||..+|.+.+.|.|                                           ..||+||.+.+..|+++|.-.+.
T Consensus       390 ihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~di  469 (695)
T KOG0353|consen  390 IHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFADI  469 (695)
T ss_pred             EecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEechHHH
Confidence            99999999999999                                           78999999999999999987665


Q ss_pred             HHHH
Q 017020          197 RTVR  200 (379)
Q Consensus       197 ~~l~  200 (379)
                      ....
T Consensus       470 fk~s  473 (695)
T KOG0353|consen  470 FKIS  473 (695)
T ss_pred             HhHH
Confidence            4443

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

Probab=99.62  E-value=1.8e-14  Score=147.43  Aligned_cols=170  Identities=19%  Similarity=0.268  Sum_probs=130.5

Q ss_pred             CCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccc
Q 017020           20 KRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKR   99 (379)
Q Consensus        20 ~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~   99 (379)
                      .+-.++||||.-+....+..-.--+-..|+-    ...-...|.-+.+  +.+.+.+++..+-.....+.++.+.|+-.+
T Consensus       411 ~Ph~LvMTATPIPRTLAlt~fgDldvS~IdE----lP~GRkpI~T~~i--~~~~~~~v~e~i~~ei~~GrQaY~VcPLIe  484 (677)
T COG1200         411 NPHVLVMTATPIPRTLALTAFGDLDVSIIDE----LPPGRKPITTVVI--PHERRPEVYERIREEIAKGRQAYVVCPLIE  484 (677)
T ss_pred             CCcEEEEeCCCchHHHHHHHhccccchhhcc----CCCCCCceEEEEe--ccccHHHHHHHHHHHHHcCCEEEEEecccc
Confidence            6789999999866665555322112222321    1111233444444  346677777777777777899999998665


Q ss_pred             cH--------HHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCC-CC
Q 017020          100 DA--------DEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP-ND  167 (379)
Q Consensus       100 ~~--------~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P-~~  167 (379)
                      +.        .++++.|..   ++.+..+||.|++.+++++|++|++|+++|||||.|.+.|||+|+.++.|..+.- ..
T Consensus       485 ESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFG  564 (677)
T COG1200         485 ESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFG  564 (677)
T ss_pred             ccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEechhhhh
Confidence            44        456666664   4679999999999999999999999999999999999999999999998877754 36


Q ss_pred             hhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          168 PETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       168 ~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      .....|-.||.||.+..+.|++++.+..
T Consensus       565 LaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         565 LAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             HHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            8899999999999999999999998876

>TIGR00595 priA primosomal protein N'

Probab=99.61  E-value=1.5e-14  Score=148.34  Aligned_cols=95  Identities=26%  Similarity=0.430  Sum_probs=79.0

Q ss_pred             HHHHHHHHhc---CCcEEEeeCCCCHHHH--HHHHhcccCCceeEEEeccccccCCCCCccceEE--ecCC----CC---
Q 017020          101 ADEVSLALTS---IIASEALHGDISQHQR--ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII--HYEL----PN---  166 (379)
Q Consensus       101 ~~~l~~~L~~---~~~v~~lhg~m~~~~R--~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI--~~~~----P~---  166 (379)
                      ++.+.+.|.+   +.++..+|+++++..+  +.++++|++|+.+|||+|+++++|+|+|+|++|+  ++|.    |.   
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra  350 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRA  350 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccch
Confidence            5777777775   4678999999988766  8999999999999999999999999999999875  6664    32   


Q ss_pred             ---ChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          167 ---DPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       167 ---~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                         ....|+|++||+||.++.|.+++.....+
T Consensus       351 ~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~  382 (505)
T TIGR00595       351 AERGFQLLTQVAGRAGRAEDPGQVIIQTYNPN  382 (505)
T ss_pred             HHHHHHHHHHHHhccCCCCCCCEEEEEeCCCC
Confidence               24678999999999999999986554433

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).

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.61  E-value=1.9e-15  Score=115.67  Aligned_cols=80  Identities=53%  Similarity=0.867  Sum_probs=74.6

Q ss_pred             HHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCC
Q 017020          103 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  181 (379)
Q Consensus       103 ~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~  181 (379)
                      .++..|.. ++.+..+||+|++.+|..+++.|+++...+||+|+++++|+|+|++++||.+++|.+...|.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            35566654 78899999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 017020          182 G  182 (379)
Q Consensus       182 G  182 (379)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            6

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.59  E-value=4e-14  Score=150.12  Aligned_cols=103  Identities=23%  Similarity=0.377  Sum_probs=83.3

Q ss_pred             cHHHHHHHHhc---CCcEEEeeCCCCH--HHHHHHHhcccCCceeEEEeccccccCCCCCccceEE--ecCCCCCh----
Q 017020          100 DADEVSLALTS---IIASEALHGDISQ--HQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII--HYELPNDP----  168 (379)
Q Consensus       100 ~~~~l~~~L~~---~~~v~~lhg~m~~--~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI--~~~~P~~~----  168 (379)
                      .++.+++.|..   +.++..+|+++++  .++++++++|++|+.+|||+|+++++|+|+|++++|+  +.|.+.+.    
T Consensus       438 G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfr  517 (679)
T PRK05580        438 GTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFR  517 (679)
T ss_pred             cHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccc
Confidence            45567777765   5678999999975  5789999999999999999999999999999999985  55555433    


Q ss_pred             ------hHHHHHHhhccCCCCCceEEEEeChhhHHHHHHH
Q 017020          169 ------ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  202 (379)
Q Consensus       169 ------~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~l  202 (379)
                            ..|+|++||+||.++.|.+++.....+...++.+
T Consensus       518 a~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~~~~~~~~  557 (679)
T PRK05580        518 ASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQAL  557 (679)
T ss_pred             hHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCCCHHHHHH
Confidence                  5789999999999999999987665554444433

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.55  E-value=3.8e-14  Score=143.29  Aligned_cols=228  Identities=19%  Similarity=0.289  Sum_probs=165.5

Q ss_pred             CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH-HHHHHHHHH--cCCCcEEEEe
Q 017020           19 PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-ILSDLITVY--AKGGKTIVFT   95 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-~L~~ll~~~--~~~~~~IIF~   95 (379)
                      .+..+|..||||  +..+++. |+.+...+.+.+..     -.++..|...+.++-.+ ++...+..+  ...+.+|||.
T Consensus       499 rdlKliVtSATm--~a~kf~n-fFgn~p~f~IpGRT-----yPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfm  570 (1042)
T KOG0924|consen  499 RDLKLIVTSATM--DAQKFSN-FFGNCPQFTIPGRT-----YPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFM  570 (1042)
T ss_pred             ccceEEEeeccc--cHHHHHH-HhCCCceeeecCCc-----cceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEec
Confidence            477899999999  4556665 55555445554321     23455555555555443 334444333  3457899999


Q ss_pred             cccccHHHHHHHHhc-----------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecC-
Q 017020           96 QTKRDADEVSLALTS-----------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE-  163 (379)
Q Consensus        96 ~t~~~~~~l~~~L~~-----------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~-  163 (379)
                      ...+.++-.+..+..           .+.+.++++.||+.-+.++++.--.|..+++|||++|+..+.||++.+||+.+ 
T Consensus       571 tGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy  650 (1042)
T KOG0924|consen  571 TGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGY  650 (1042)
T ss_pred             CCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCc
Confidence            998887766555431           35789999999999999999999999999999999999999999999999755 


Q ss_pred             -----------------CCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHHHHHHHH
Q 017020          164 -----------------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSA  226 (379)
Q Consensus       164 -----------------~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~i~~~~~  226 (379)
                                       .|.+...-.||.||+||.| .|.||-+|+....             ....-+.+..+|.+...
T Consensus       651 ~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe~ay-------------~~eml~stvPEIqRTNl  716 (1042)
T KOG0924|consen  651 CKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTEDAY-------------KNEMLPSTVPEIQRTNL  716 (1042)
T ss_pred             eeeeecccccccceeEEEechhccchhhccccCCCC-CcceeeehhhhHH-------------HhhcccCCCchhhhcch
Confidence                             3667788899999999997 9999999998542             11122344567888888


Q ss_pred             HHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcCCCCC
Q 017020          227 EQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRP  273 (379)
Q Consensus       227 ~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~~~  273 (379)
                      .++...++++..+++..|     .+++.+..+.+.+++-.|.-++..
T Consensus       717 ~nvVLlLkslgV~dll~F-----dFmD~Pped~~~~sly~Lw~LGAl  758 (1042)
T KOG0924|consen  717 SNVVLLLKSLGVDDLLKF-----DFMDPPPEDNLLNSLYQLWTLGAL  758 (1042)
T ss_pred             hhHHHHHHhcChhhhhCC-----CcCCCCHHHHHHHHHHHHHHhhcc
Confidence            888888888877665555     455566667788888777544433

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.51  E-value=3.8e-13  Score=142.81  Aligned_cols=168  Identities=18%  Similarity=0.159  Sum_probs=126.0

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH-HHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD-LITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~-ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+-.||.|...+..++.+-|--+-+.|   +...........-. +......|..++.. +...+..+.|+||||+|++.
T Consensus       381 kLsGMTGTa~te~~Ef~~iY~l~Vv~I---Ptnkp~~R~d~~d~-v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~  456 (896)
T PRK13104        381 KLSGMTGTADTEAYEFQQIYNLEVVVI---PTNRSMIRKDEADL-VYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEA  456 (896)
T ss_pred             hhccCCCCChhHHHHHHHHhCCCEEEC---CCCCCcceecCCCe-EEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHH
Confidence            345688898877777777774332222   21111111111111 22333456655544 44555678999999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCc------------------------
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN------------------------  155 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~------------------------  155 (379)
                      ++.++..|.. ++++..|||++.+.+++.+.++|+.|.  |+||||+|+||+||.=                        
T Consensus       457 sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~  534 (896)
T PRK13104        457 SEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVK  534 (896)
T ss_pred             HHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCCc--EEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHH
Confidence            9999999985 899999999999999999999999995  9999999999999841                        


Q ss_pred             --------------cceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          156 --------------VDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       156 --------------v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                                    -=|||--..+.+..-=-|-.||+||.|.+|.+-.|++-.|
T Consensus       535 ~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD  588 (896)
T PRK13104        535 KEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  588 (896)
T ss_pred             HHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCc
Confidence                          1268877788888888899999999999999999988655

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

Probab=99.51  E-value=3.9e-13  Score=144.92  Aligned_cols=189  Identities=20%  Similarity=0.354  Sum_probs=140.1

Q ss_pred             HhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcC---------CccHHHHHHHHHHHH
Q 017020           15 ENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTT---------ATSKRTILSDLITVY   85 (379)
Q Consensus        15 ~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~---------~~~k~~~L~~ll~~~   85 (379)
                      ...+.+.|+|..|||+.. ..++++.+.+.+....+.   ....+....++....+         ..++...+..+....
T Consensus       227 ~~~~~~~q~i~~SAT~~n-p~e~~~~l~~~~f~~~v~---~~g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~~~~~  302 (851)
T COG1205         227 RRYGSPLQIICTSATLAN-PGEFAEELFGRDFEVPVD---EDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAALL  302 (851)
T ss_pred             hccCCCceEEEEeccccC-hHHHHHHhcCCcceeecc---CCCCCCCceEEEEeCCcchhhhhhcccchHHHHHHHHHHH
Confidence            334568999999999954 456677777655544332   2223344444544444         124444455555433


Q ss_pred             -cCCCcEEEEecccccHHHHHHHH----h-cC----CcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCc
Q 017020           86 -AKGGKTIVFTQTKRDADEVSLAL----T-SI----IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN  155 (379)
Q Consensus        86 -~~~~~~IIF~~t~~~~~~l~~~L----~-~~----~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~  155 (379)
                       ..+-++|+|+.++..++.++...    . .+    ..+..+||+|...+|.++...|++|+..++++|+.+.-|+||.+
T Consensus       303 ~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~  382 (851)
T COG1205         303 VRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGS  382 (851)
T ss_pred             HHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehh
Confidence             35779999999999999986332    2 23    46889999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCC-ChhHHHHHHhhccCCCCCceEEEEeCh--hhHHHHHHHHHHhC
Q 017020          156 VDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTS--SQRRTVRSLERDVG  207 (379)
Q Consensus       156 v~~VI~~~~P~-~~~~yiqR~GRtgR~G~~g~~i~l~~~--~e~~~l~~le~~~~  207 (379)
                      ++.||+++.|. +..+++||.||+||.++.+..+.++..  -+..++..-+....
T Consensus       383 ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~d~yy~~~p~~~~~  437 (851)
T COG1205         383 LDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPLDSYYLRHPEELLE  437 (851)
T ss_pred             hhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCccchhhhhCcHhhhh
Confidence            99999999999 899999999999999977777776653  34555555555554

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.50  E-value=2.2e-13  Score=144.22  Aligned_cols=168  Identities=20%  Similarity=0.173  Sum_probs=129.5

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHH-HcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~  100 (379)
                      .+..||.|...+..++.+-|--+-+.|   +...........- .+.....+|..++...+.. +..+.|+||||+|+..
T Consensus       367 kl~GmTGTa~te~~E~~~iY~l~vv~I---Ptnkp~~r~d~~d-~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~  442 (830)
T PRK12904        367 KLAGMTGTADTEAEEFREIYNLDVVVI---PTNRPMIRIDHPD-LIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEK  442 (830)
T ss_pred             hhcccCCCcHHHHHHHHHHhCCCEEEc---CCCCCeeeeeCCC-eEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHH
Confidence            455689999887777777774332222   1111111111111 2223445688887777754 3467899999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCcc-----------------------
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV-----------------------  156 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v-----------------------  156 (379)
                      ++.++..|.. ++++..+||.  +.+|+..+.+|+.+...|+||||+|+||+||+--                       
T Consensus       443 se~Ls~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~  520 (830)
T PRK12904        443 SELLSKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIK  520 (830)
T ss_pred             HHHHHHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHH
Confidence            9999999985 8999999996  8899999999999999999999999999999642                       


Q ss_pred             ---------------ceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          157 ---------------DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       157 ---------------~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                                     =|||--..|.+..---|-.||+||.|.+|.+-.|++-.|
T Consensus       521 ~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~lSleD  574 (830)
T PRK12904        521 AEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLED  574 (830)
T ss_pred             HHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEEEEcCc
Confidence                           278888899999999999999999999999999988655

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=99.48  E-value=3.4e-13  Score=141.29  Aligned_cols=116  Identities=29%  Similarity=0.499  Sum_probs=98.4

Q ss_pred             CCCcEEEEecccccHHHHHHHHhcCC---------------------------------------cEEEeeCCCCHHHHH
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTSII---------------------------------------ASEALHGDISQHQRE  127 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~~~---------------------------------------~v~~lhg~m~~~~R~  127 (379)
                      .+.++||||++++.|+.++..+...+                                       .+.++|+|++.++|+
T Consensus       459 e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER~  538 (1008)
T KOG0950|consen  459 EGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEERE  538 (1008)
T ss_pred             cCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchHH
Confidence            34579999999999999886654211                                       467899999999999


Q ss_pred             HHHhcccCCceeEEEeccccccCCCCCccceEEec---CC-CCChhHHHHHHhhccCCC--CCceEEEEeChhhHHHHHH
Q 017020          128 RTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY---EL-PNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRS  201 (379)
Q Consensus       128 ~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~---~~-P~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~e~~~l~~  201 (379)
                      .+...|++|.+.|++||+.++.|++.|...++|-.   +. +.+.-.|.||+|||||+|  ..|.+++++.+.|......
T Consensus       539 ~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e~~~~~~  618 (1008)
T KOG0950|consen  539 IIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSEKKRVRE  618 (1008)
T ss_pred             HHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccchhHHHH
Confidence            99999999999999999999999999999988843   33 347789999999999998  5699999999999766654


Q ss_pred             H
Q 017020          202 L  202 (379)
Q Consensus       202 l  202 (379)
                      +
T Consensus       619 l  619 (1008)
T KOG0950|consen  619 L  619 (1008)
T ss_pred             H
Confidence            4

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.48  E-value=1.1e-12  Score=139.04  Aligned_cols=169  Identities=18%  Similarity=0.213  Sum_probs=126.1

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH-HHHHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L-~~ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+-.||.|...+..++.+-|--+-+.|  . ...........-..+ .....|..++ ..+...+..+.++||||+|...
T Consensus       386 kL~GMTGTa~te~~Ef~~iY~l~Vv~I--P-Tnkp~~R~d~~d~iy-~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~  461 (908)
T PRK13107        386 KLAGMTGTADTEAFEFQHIYGLDTVVV--P-TNRPMVRKDMADLVY-LTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQ  461 (908)
T ss_pred             HhhcccCCChHHHHHHHHHhCCCEEEC--C-CCCCccceeCCCcEE-eCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHH
Confidence            345688888777777777664332222  1 111111111111122 2224555444 4455556678999999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC-------------------------
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP-------------------------  154 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip-------------------------  154 (379)
                      ++.++..|.. ++++..+|+++++.+++.+.+.|+.|.  |+||||+|+||+||.                         
T Consensus       462 se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~  539 (908)
T PRK13107        462 SELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKA  539 (908)
T ss_pred             HHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHH
Confidence            9999999985 899999999999999999999999998  999999999999985                         


Q ss_pred             ------------ccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhH
Q 017020          155 ------------NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  196 (379)
Q Consensus       155 ------------~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~  196 (379)
                                  +-=|||--..|.|..-=-|-.||+||.|.+|.+-.|++-.|.
T Consensus       540 ~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        540 DWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             HHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCcH
Confidence                        112788888888888888999999999999999999987653

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

Probab=99.47  E-value=1.8e-12  Score=122.61  Aligned_cols=179  Identities=19%  Similarity=0.287  Sum_probs=125.3

Q ss_pred             CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH------HHHHHHHH-HcCCCc
Q 017020           18 PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT------ILSDLITV-YAKGGK   90 (379)
Q Consensus        18 p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~------~L~~ll~~-~~~~~~   90 (379)
                      .++.-+|.+|||.|++.++-+...  +-..+.+. ...+..+-.+..+....++..+..      .|...|+. ...+.+
T Consensus       231 k~~g~~IylTATp~k~l~r~~~~g--~~~~~klp-~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P  307 (441)
T COG4098         231 KKEGATIYLTATPTKKLERKILKG--NLRILKLP-ARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRP  307 (441)
T ss_pred             cccCceEEEecCChHHHHHHhhhC--CeeEeecc-hhhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCc
Confidence            356789999999988766544322  22223322 223333333444444444433331      34455544 345789


Q ss_pred             EEEEecccccHHHHHHHHhcC---CcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE-ecCCC-
Q 017020           91 TIVFTQTKRDADEVSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-HYELP-  165 (379)
Q Consensus        91 ~IIF~~t~~~~~~l~~~L~~~---~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI-~~~~P-  165 (379)
                      ++||+++....+.++..|...   ......|+.  ...|.+-.++||+|++++||+|.+++||+.+|+|+++| ...-+ 
T Consensus       308 ~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~v  385 (441)
T COG4098         308 VLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRV  385 (441)
T ss_pred             EEEEecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEecCCccc
Confidence            999999999999999999653   356788887  56788999999999999999999999999999999755 33322 


Q ss_pred             CChhHHHHHHhhccCCC--CCceEEEEeChhhHHHHHH
Q 017020          166 NDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRS  201 (379)
Q Consensus       166 ~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~e~~~l~~  201 (379)
                      .+.++.+|.+||+||.-  .+|..+.|-......+.+.
T Consensus       386 fTesaLVQIaGRvGRs~~~PtGdv~FFH~G~skaM~~A  423 (441)
T COG4098         386 FTESALVQIAGRVGRSLERPTGDVLFFHYGKSKAMKQA  423 (441)
T ss_pred             ccHHHHHHHhhhccCCCcCCCCcEEEEeccchHHHHHH
Confidence            57899999999999965  4688888766655554443

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=99.46  E-value=2e-12  Score=137.58  Aligned_cols=233  Identities=18%  Similarity=0.262  Sum_probs=165.2

Q ss_pred             CCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeeccccccc--------------ccceEEEE-----------E-EcC
Q 017020           17 LPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKL--------------AEGIKLYA-----------I-STT   70 (379)
Q Consensus        17 ~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~--------------~~~i~~~~-----------~-~~~   70 (379)
                      ..++-++||||||+.   .+..+.|+.....+.+.+......              .....++.           + ...
T Consensus       316 ~~p~LkvILMSAT~d---ae~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  392 (924)
T KOG0920|consen  316 RNPDLKVILMSATLD---AELFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWE  392 (924)
T ss_pred             hCCCceEEEeeeecc---hHHHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhcc
Confidence            346899999999996   345556777666665543221100              00001110           0 000


Q ss_pred             CccHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc--------CCcEEEeeCCCCHHHHHHHHhcccCCcee
Q 017020           71 ATSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS--------IIASEALHGDISQHQRERTLNGFRQGKFT  139 (379)
Q Consensus        71 ~~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~--------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~  139 (379)
                      .+-..+++..++...   ...+.+|||.++..+...+.+.|..        .+-+.++|+.|+..+++.++..--.|..+
T Consensus       393 ~~id~~Li~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RK  472 (924)
T KOG0920|consen  393 PEIDYDLIEDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRK  472 (924)
T ss_pred             ccccHHHHHHHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcch
Confidence            112345566666554   3367899999999999999999862        25678899999999999999999999999


Q ss_pred             EEEeccccccCCCCCccceEEecC--------CCC----------ChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHH
Q 017020          140 VLVATDVAARGLDIPNVDLIIHYE--------LPN----------DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS  201 (379)
Q Consensus       140 iLVaTdv~~rGiDip~v~~VI~~~--------~P~----------~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~  201 (379)
                      |++||++|+.+|.|++|-+||+.+        +-.          +...-.||.||+||. .+|.||-+|+......+- 
T Consensus       473 IIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~~~~~-  550 (924)
T KOG0920|consen  473 IILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRYEKLM-  550 (924)
T ss_pred             hhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhhhhcc-
Confidence            999999999999999999999644        322          445568999999998 599999999986542221 


Q ss_pred             HHHHhCCCceeeCCCCHHHHHHHHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcC
Q 017020          202 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSG  269 (379)
Q Consensus       202 le~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~  269 (379)
                                  ..-+..|+++..++++.-.++-+....+.   +...++++.+...++..|+..+..
T Consensus       551 ------------~~~q~PEilR~pL~~l~L~iK~l~~~~~~---~fLskaldpP~~~~v~~a~~~L~~  603 (924)
T KOG0920|consen  551 ------------LAYQLPEILRTPLEELCLHIKVLEQGSIK---AFLSKALDPPPADAVDLAIERLKQ  603 (924)
T ss_pred             ------------cccCChHHHhChHHHhhheeeeccCCCHH---HHHHHhcCCCChHHHHHHHHHHHH
Confidence                        11234578888888888888866655555   555578888888888777776643

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

Probab=99.45  E-value=2.5e-12  Score=127.67  Aligned_cols=170  Identities=25%  Similarity=0.342  Sum_probs=130.3

Q ss_pred             CCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccc
Q 017020           20 KRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKR   99 (379)
Q Consensus        20 ~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~   99 (379)
                      ..|++.+|||..++-.+.+.    + ..++-+-.+.....+.+   .+.....+-.+++.++-.....+.+++|-+=|++
T Consensus       386 ~~q~i~VSATPg~~E~e~s~----~-~vveQiIRPTGLlDP~i---evRp~~~QvdDL~~EI~~r~~~~eRvLVTtLTKk  457 (663)
T COG0556         386 IPQTIYVSATPGDYELEQSG----G-NVVEQIIRPTGLLDPEI---EVRPTKGQVDDLLSEIRKRVAKNERVLVTTLTKK  457 (663)
T ss_pred             cCCEEEEECCCChHHHHhcc----C-ceeEEeecCCCCCCCce---eeecCCCcHHHHHHHHHHHHhcCCeEEEEeehHH
Confidence            46999999998765444332    1 12221111111112222   2233344556666676665667899999999999


Q ss_pred             cHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecC-----CCCChhHHHH
Q 017020          100 DADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE-----LPNDPETFVH  173 (379)
Q Consensus       100 ~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~-----~P~~~~~yiq  173 (379)
                      .|+.|.++|.. ++.+..+|+++..-+|.+++.++|.|.++|||.-+.+-.|+|+|.|++|...|     +..+..+.+|
T Consensus       458 mAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQ  537 (663)
T COG0556         458 MAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQ  537 (663)
T ss_pred             HHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHH
Confidence            99999999985 99999999999999999999999999999999999999999999999998777     4568999999


Q ss_pred             HHhhccCCCCCceEEEEeChhhHHH
Q 017020          174 RSGRTGRAGKEGTAILMFTSSQRRT  198 (379)
Q Consensus       174 R~GRtgR~G~~g~~i~l~~~~e~~~  198 (379)
                      -+||++|- -.|.++++.+.-...+
T Consensus       538 tIGRAARN-~~GkvIlYAD~iT~sM  561 (663)
T COG0556         538 TIGRAARN-VNGKVILYADKITDSM  561 (663)
T ss_pred             HHHHHhhc-cCCeEEEEchhhhHHH
Confidence            99999996 4899999877544333

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=99.45  E-value=1.4e-12  Score=136.29  Aligned_cols=106  Identities=28%  Similarity=0.399  Sum_probs=91.3

Q ss_pred             CcEEEEecccccHHHHHHHHhc-CC---------------------------------------cEEEeeCCCCHHHHHH
Q 017020           89 GKTIVFTQTKRDADEVSLALTS-II---------------------------------------ASEALHGDISQHQRER  128 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~~-~~---------------------------------------~v~~lhg~m~~~~R~~  128 (379)
                      -|+||||=+++.|++.++.|.. .+                                       .++++|||+-+--++-
T Consensus       568 LP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~  647 (1248)
T KOG0947|consen  568 LPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEV  647 (1248)
T ss_pred             CceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHH
Confidence            4899999999999999999874 21                                       3678999999999999


Q ss_pred             HHhcccCCceeEEEeccccccCCCCCccceEEecC--------CCCChhHHHHHHhhccCCC--CCceEEEEeChh
Q 017020          129 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE--------LPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  194 (379)
Q Consensus       129 ~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~--------~P~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~  194 (379)
                      +..-|..|-++||+||..+|+|+|.|.-.+|+.-=        .--.+.+|.|++||+||-|  .+|+++++....
T Consensus       648 VE~LFqrGlVKVLFATETFAMGVNMPARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~  723 (1248)
T KOG0947|consen  648 VELLFQRGLVKVLFATETFAMGVNMPARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDS  723 (1248)
T ss_pred             HHHHHhcCceEEEeehhhhhhhcCCCceeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecCC
Confidence            99999999999999999999999999888887321        1236889999999999998  779998887654

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

Probab=99.43  E-value=1.6e-12  Score=139.83  Aligned_cols=186  Identities=18%  Similarity=0.280  Sum_probs=142.0

Q ss_pred             HHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcE
Q 017020           12 LILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKT   91 (379)
Q Consensus        12 ~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~   91 (379)
                      +-|+.+..+.-++-+|||.-+....++-..+++-..|...+.  .  .-.++-|+...   +..-+=..++..+..++++
T Consensus       734 EkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~--~--R~pV~T~V~~~---d~~~ireAI~REl~RgGQv  806 (1139)
T COG1197         734 EKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPE--D--RLPVKTFVSEY---DDLLIREAILRELLRGGQV  806 (1139)
T ss_pred             HHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCC--C--CcceEEEEecC---ChHHHHHHHHHHHhcCCEE
Confidence            445666678899999999877888888777777776654321  1  12233333322   2222223444555678999


Q ss_pred             EEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCC-CCC
Q 017020           92 IVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL-PND  167 (379)
Q Consensus        92 IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~-P~~  167 (379)
                      -.-+|..+..+.++..|+.   ...+...||.|+..+-+.+|.+|-+|+.+|||||.+.+.|||||+++.+|..+. -..
T Consensus       807 fYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fG  886 (1139)
T COG1197         807 FYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFG  886 (1139)
T ss_pred             EEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEecccccc
Confidence            8889999999999999986   456899999999999999999999999999999999999999999998774443 246


Q ss_pred             hhHHHHHHhhccCCCCCceEEEEeChhh------HHHHHHHHH
Q 017020          168 PETFVHRSGRTGRAGKEGTAILMFTSSQ------RRTVRSLER  204 (379)
Q Consensus       168 ~~~yiqR~GRtgR~G~~g~~i~l~~~~e------~~~l~~le~  204 (379)
                      .+...|-.||.||..+.+.||+++.+..      .+.++.|+.
T Consensus       887 LsQLyQLRGRVGRS~~~AYAYfl~p~~k~lT~~A~kRL~aI~~  929 (1139)
T COG1197         887 LAQLYQLRGRVGRSNKQAYAYFLYPPQKALTEDAEKRLEAIAS  929 (1139)
T ss_pred             HHHHHHhccccCCccceEEEEEeecCccccCHHHHHHHHHHHh
Confidence            8899999999999999999999998532      345555544

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.42  E-value=1.3e-12  Score=139.90  Aligned_cols=174  Identities=22%  Similarity=0.273  Sum_probs=122.1

Q ss_pred             CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeeccccccc-ccceEEEEEEcCCccH--HHHHHHHHHHHcCCCcEEEEe
Q 017020           19 PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKL-AEGIKLYAISTTATSK--RTILSDLITVYAKGGKTIVFT   95 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~-~~~i~~~~~~~~~~~k--~~~L~~ll~~~~~~~~~IIF~   95 (379)
                      .+..++++|||+|+...+....++.+...+.......... ...+.... .....+.  .............+.+++|-|
T Consensus       369 ~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~kvlvI~  447 (733)
T COG1203         369 AGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKE-RVDVEDGPQEELIELISEEVKEGKKVLVIV  447 (733)
T ss_pred             CCCCEEEEecCCCHHHHHHHHHHHhcccceecccccccccccccccccc-chhhhhhhhHhhhhcchhhhccCCcEEEEE
Confidence            3789999999999999998888877655443221100000 01111110 0111111  123333444455678999999


Q ss_pred             cccccHHHHHHHHhcCC-cEEEeeCCCCHHHHHHHHhccc----CCceeEEEeccccccCCCCCccceEEecCCCCChhH
Q 017020           96 QTKRDADEVSLALTSII-ASEALHGDISQHQRERTLNGFR----QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET  170 (379)
Q Consensus        96 ~t~~~~~~l~~~L~~~~-~v~~lhg~m~~~~R~~~~~~F~----~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~  170 (379)
                      ||...|.+++..|+... .+..+||.+...+|.+.++.+.    .+...|+|||++.+.|+|+. .+++|-=  +..+++
T Consensus       448 NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-fd~mITe--~aPidS  524 (733)
T COG1203         448 NTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-FDVLITE--LAPIDS  524 (733)
T ss_pred             ecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-cCeeeec--CCCHHH
Confidence            99999999999998744 5999999999999988887544    46778999999999999994 6665532  456899


Q ss_pred             HHHHHhhccCCC--CCceEEEEeChhhH
Q 017020          171 FVHRSGRTGRAG--KEGTAILMFTSSQR  196 (379)
Q Consensus       171 yiqR~GRtgR~G--~~g~~i~l~~~~e~  196 (379)
                      .+||.||++|.|  ..|..+++......
T Consensus       525 LIQR~GRv~R~g~~~~~~~~v~~~~~~~  552 (733)
T COG1203         525 LIQRAGRVNRHGKKENGKIYVYNDEERG  552 (733)
T ss_pred             HHHHHHHHhhcccccCCceeEeecccCC
Confidence            999999999999  56788877665443

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=99.40  E-value=5.5e-12  Score=134.72  Aligned_cols=179  Identities=21%  Similarity=0.334  Sum_probs=127.7

Q ss_pred             CCCcEEEEeeeCChHHHHHHHHhcC-CCceEEeecccccccccceEEEEEEcCCcc--H-HH-----HHHHHHHHHcCCC
Q 017020           19 PKRQSMLFSATMPSWVKKLSRKYLD-NPLNIDLVGNQDEKLAEGIKLYAISTTATS--K-RT-----ILSDLITVYAKGG   89 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~i~~l~~~~l~-~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~--k-~~-----~L~~ll~~~~~~~   89 (379)
                      .....+.+|||+|.- .+.+. |++ +|..+-.-+.+-  .+..+.|.++-+....  + ..     ....++...+ ..
T Consensus       473 e~~RlVGLSATLPNy-~DV~~-Fl~v~~~glf~fd~sy--RpvPL~qq~Igi~ek~~~~~~qamNe~~yeKVm~~ag-k~  547 (1674)
T KOG0951|consen  473 EGSRLVGLSATLPNY-EDVAS-FLRVDPEGLFYFDSSY--RPVPLKQQYIGITEKKPLKRFQAMNEACYEKVLEHAG-KN  547 (1674)
T ss_pred             cCceeeeecccCCch-hhhHH-HhccCcccccccCccc--CcCCccceEeccccCCchHHHHHHHHHHHHHHHHhCC-CC
Confidence            467899999999973 33333 333 443332222222  2344566666554432  2 22     2234444444 48


Q ss_pred             cEEEEecccccHHHHHHHHhcC--------------------------------------CcEEEeeCCCCHHHHHHHHh
Q 017020           90 KTIVFTQTKRDADEVSLALTSI--------------------------------------IASEALHGDISQHQRERTLN  131 (379)
Q Consensus        90 ~~IIF~~t~~~~~~l~~~L~~~--------------------------------------~~v~~lhg~m~~~~R~~~~~  131 (379)
                      ++|||+.+++++-+.|..++..                                      +..+.+|+||+..+|+.+.+
T Consensus       548 qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R~dR~~~Ed  627 (1674)
T KOG0951|consen  548 QVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNRKDRELVED  627 (1674)
T ss_pred             cEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCcchHHHHHH
Confidence            9999999999998888776510                                      14677999999999999999


Q ss_pred             cccCCceeEEEeccccccCCCCCccceEE----ecCC------CCChhHHHHHHhhccCCC--CCceEEEEeChhhHHHH
Q 017020          132 GFRQGKFTVLVATDVAARGLDIPNVDLII----HYEL------PNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTV  199 (379)
Q Consensus       132 ~F~~g~~~iLVaTdv~~rGiDip~v~~VI----~~~~------P~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~e~~~l  199 (379)
                      .|++|.+++||+|-.+|+|+|+|.-+++|    -||+      +.++.+-.||.||+||.+  ..|..++.-...|..+.
T Consensus       628 Lf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~~se~qyy  707 (1674)
T KOG0951|consen  628 LFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSELQYY  707 (1674)
T ss_pred             HHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeeccCchHhhhh
Confidence            99999999999999999999999988888    3553      458899999999999987  55777777777776655


Q ss_pred             HHH
Q 017020          200 RSL  202 (379)
Q Consensus       200 ~~l  202 (379)
                      ..+
T Consensus       708 ls~  710 (1674)
T KOG0951|consen  708 LSL  710 (1674)
T ss_pred             HHh
Confidence            544

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=99.37  E-value=2.3e-11  Score=128.51  Aligned_cols=180  Identities=19%  Similarity=0.292  Sum_probs=125.1

Q ss_pred             CCCcEEEEeeeCChHHHHHHHHhcCCCc-e-EEeecccccccccceEEEEEEcCCc---cHHH-----HHHHHHHHHcCC
Q 017020           19 PKRQSMLFSATMPSWVKKLSRKYLDNPL-N-IDLVGNQDEKLAEGIKLYAISTTAT---SKRT-----ILSDLITVYAKG   88 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~i~~l~~~~l~~p~-~-i~~~~~~~~~~~~~i~~~~~~~~~~---~k~~-----~L~~ll~~~~~~   88 (379)
                      ...+++.+|||+|. +.+++.+.--||. . ..+.. ...  +-.+.+.++-.+..   ....     ....+++....+
T Consensus       274 s~IRivgLSATlPN-~eDvA~fL~vn~~~glfsFd~-~yR--PvpL~~~~iG~k~~~~~~~~~~~d~~~~~kv~e~~~~g  349 (1230)
T KOG0952|consen  274 SMIRIVGLSATLPN-YEDVARFLRVNPYAGLFSFDQ-RYR--PVPLTQGFIGIKGKKNRQQKKNIDEVCYDKVVEFLQEG  349 (1230)
T ss_pred             hheEEEEeeccCCC-HHHHHHHhcCCCccceeeecc-ccc--ccceeeeEEeeecccchhhhhhHHHHHHHHHHHHHHcC
Confidence            46789999999986 6787874433532 2 22221 111  22334444333322   1111     223445555678


Q ss_pred             CcEEEEecccccHHHHHHHHhc-----CC-------------------cEEEeeCCCCHHHHHHHHhcccCCceeEEEec
Q 017020           89 GKTIVFTQTKRDADEVSLALTS-----II-------------------ASEALHGDISQHQRERTLNGFRQGKFTVLVAT  144 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~~-----~~-------------------~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaT  144 (379)
                      .+++|||.++..+-..|+.|..     +.                   ....+|+||..++|..+.+.|..|.++||+||
T Consensus       350 ~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~cT  429 (1230)
T KOG0952|consen  350 HQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIKVLCCT  429 (1230)
T ss_pred             CeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCceEEEec
Confidence            9999999999999999988852     11                   35678999999999999999999999999999


Q ss_pred             cccccCCCCCccceEE----ecCCC------CChhHHHHHHhhccCCC--CCceEEEEeChhhHHHHHHH
Q 017020          145 DVAARGLDIPNVDLII----HYELP------NDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRSL  202 (379)
Q Consensus       145 dv~~rGiDip~v~~VI----~~~~P------~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~e~~~l~~l  202 (379)
                      ..+++|+++|+--++|    -||.-      ...-+.+|..||+||.+  ..|.++++.+.+.......+
T Consensus       430 aTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~Y~sL  499 (1230)
T KOG0952|consen  430 ATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDHYESL  499 (1230)
T ss_pred             ceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHHHHHH
Confidence            9999999999654444    23322      25677899999999976  77999998887665554444

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.34  E-value=6.4e-11  Score=116.44  Aligned_cols=221  Identities=18%  Similarity=0.334  Sum_probs=158.8

Q ss_pred             HHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH-HHHHHHH--cCCCc
Q 017020           14 LENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVY--AKGGK   90 (379)
Q Consensus        14 l~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L-~~ll~~~--~~~~~   90 (379)
                      +..-| +-.++.+|||+..   .-.+.|+.|+-.+.+.+      ...++.+|...+..+..++. ..+++.+  ...+-
T Consensus       186 ~~~rp-dLk~vvmSatl~a---~Kfq~yf~n~Pll~vpg------~~PvEi~Yt~e~erDylEaairtV~qih~~ee~GD  255 (699)
T KOG0925|consen  186 VRNRP-DLKLVVMSATLDA---EKFQRYFGNAPLLAVPG------THPVEIFYTPEPERDYLEAAIRTVLQIHMCEEPGD  255 (699)
T ss_pred             HhhCC-CceEEEeecccch---HHHHHHhCCCCeeecCC------CCceEEEecCCCChhHHHHHHHHHHHHHhccCCCC
Confidence            44444 8899999999832   23456888888777643      13345566666656666544 4444443  34689


Q ss_pred             EEEEecccccHHHHHHHHhc----------CCcEEEeeCCCCHHHHHHHHhcccC---C--ceeEEEeccccccCCCCCc
Q 017020           91 TIVFTQTKRDADEVSLALTS----------IIASEALHGDISQHQRERTLNGFRQ---G--KFTVLVATDVAARGLDIPN  155 (379)
Q Consensus        91 ~IIF~~t~~~~~~l~~~L~~----------~~~v~~lhg~m~~~~R~~~~~~F~~---g--~~~iLVaTdv~~rGiDip~  155 (379)
                      ++||....++.+..++.+..          .+.+.++|    +++..++++.-..   |  ..+|+|+|++++..+.+++
T Consensus       256 ilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidg  331 (699)
T KOG0925|consen  256 ILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDG  331 (699)
T ss_pred             EEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEecchheeeeecc
Confidence            99999999999988888762          14688888    4455555554432   2  3579999999999999999


Q ss_pred             cceEEecCC------------------CCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCC
Q 017020          156 VDLIIHYEL------------------PNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPV  217 (379)
Q Consensus       156 v~~VI~~~~------------------P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~  217 (379)
                      |.+||+-++                  |.+..+-.||.||+||. +.|.|+.+|+..-.          +.   ...+.+
T Consensus       332 iv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~~~----------~~---em~~~t  397 (699)
T KOG0925|consen  332 IVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF----------EK---EMQPQT  397 (699)
T ss_pred             EEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHHhh----------hh---cCCCCC
Confidence            999997553                  66888899999999997 69999999997431          11   123445


Q ss_pred             HHHHHHHHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHH
Q 017020          218 VEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQL  267 (379)
Q Consensus       218 ~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~  267 (379)
                      ..+++++.+..+...++.+..+++.+|     .+++.+.++.++.||-.+
T Consensus       398 ypeilrsNL~s~VL~LKklgI~dlvhf-----dfmDpPAPEtLMrALE~L  442 (699)
T KOG0925|consen  398 YPEILRSNLSSTVLQLKKLGIDDLVHF-----DFMDPPAPETLMRALEVL  442 (699)
T ss_pred             cHHHHHHhhHHHHHHHHhcCcccccCC-----cCCCCCChHHHHHHHHHh
Confidence            678999999999999998877766666     566677778777776554

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=99.32  E-value=6.1e-12  Score=128.74  Aligned_cols=174  Identities=20%  Similarity=0.352  Sum_probs=125.8

Q ss_pred             hCCCCCcEEEEeeeCChHHHHHHHHhc---CCCceEEeecccccccccceEEEEEE---------cCCcc--HHHH----
Q 017020           16 NLPPKRQSMLFSATMPSWVKKLSRKYL---DNPLNIDLVGNQDEKLAEGIKLYAIS---------TTATS--KRTI----   77 (379)
Q Consensus        16 ~~p~~~Q~llfSAT~p~~i~~l~~~~l---~~p~~i~~~~~~~~~~~~~i~~~~~~---------~~~~~--k~~~----   77 (379)
                      .+|++...+++|||+|.. .++++|..   +.|.+|-.....    +..++||.+.         +....  +.+-    
T Consensus       262 llP~~vr~VFLSATiPNA-~qFAeWI~~ihkQPcHVVYTdyR----PTPLQHyifP~ggdGlylvVDek~~FrednF~~a  336 (1041)
T KOG0948|consen  262 LLPDNVRFVFLSATIPNA-RQFAEWICHIHKQPCHVVYTDYR----PTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKA  336 (1041)
T ss_pred             eccccceEEEEeccCCCH-HHHHHHHHHHhcCCceEEeecCC----CCcceeeeecCCCCeeEEEEecccccchHHHHHH
Confidence            478999999999999873 45565543   467777554322    3345665433         21111  1111    


Q ss_pred             ----------------------------------HHHHHHHH--cCCCcEEEEecccccHHHHHHHHhc-CC--------
Q 017020           78 ----------------------------------LSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-II--------  112 (379)
Q Consensus        78 ----------------------------------L~~ll~~~--~~~~~~IIF~~t~~~~~~l~~~L~~-~~--------  112 (379)
                                                        +..+++..  ....++|||+=++++|+.+|..+.+ .+        
T Consensus       337 m~~l~~~~~~~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~  416 (1041)
T KOG0948|consen  337 MSVLRKAGESDGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKEL  416 (1041)
T ss_pred             HHHhhccCCCccccccccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHH
Confidence                                              11222221  2345899999999999999988864 11        


Q ss_pred             -------------------------------cEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020          113 -------------------------------ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus       113 -------------------------------~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                                                     .+..+|||+-+--++-+.--|.+|-+++|.||..++.|+|.|.-++|.-
T Consensus       417 V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT  496 (1041)
T KOG0948|consen  417 VETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFT  496 (1041)
T ss_pred             HHHHHHHHHHhcChhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEe
Confidence                                           3567899999999999999999999999999999999999999887772


Q ss_pred             ----cCCC----CChhHHHHHHhhccCCC--CCceEEEEeChh
Q 017020          162 ----YELP----NDPETFVHRSGRTGRAG--KEGTAILMFTSS  194 (379)
Q Consensus       162 ----~~~P----~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~  194 (379)
                          ||--    .+.-.|+|++||+||-|  ..|.||++++..
T Consensus       497 ~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDek  539 (1041)
T KOG0948|consen  497 AVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEK  539 (1041)
T ss_pred             eccccCCcceeeecccceEEecccccccCCCCCceEEEEecCc
Confidence                3322    26788999999999999  558999988753

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=99.31  E-value=5.2e-13  Score=101.62  Aligned_cols=72  Identities=19%  Similarity=0.198  Sum_probs=52.3

Q ss_pred             EEEEEeeCCcccCCCCChhHHHHHHhhhCCCCCCccccEEeeeCCceeeeecchhhHHHHhhhhcccCcceEeeeehhh
Q 017020          287 VTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYRFR  365 (379)
Q Consensus       287 ~~l~~~~g~~~~~~~~~~~~i~~~~~~~~~~~~~~ig~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  365 (379)
                      +||+++.|+   +|+++|++|+++|++.+|+++++||+|+|+++++    .|+||+..++.++..+++.++++++.+++
T Consensus         1 vrl~in~Gr---~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~~S----~vev~~~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    1 VRLFINVGR---KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDNFS----FVEVPEEVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             -EEEES-SG---GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-E----EEEE-TT-HHHHHHHHTT--SSS----EE
T ss_pred             CEEEEEccc---ccCCCHHHHHHHHHhccCCCHHhEEEEEEeeeEE----EEEECHHHHHHHHHHhcCCCCCCeeEEEE
Confidence            689999999   9999999999999999999999999999999999    77888888888888888888888777765

; PDB: 2G0C_A 3MOJ_B.

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.30  E-value=2e-11  Score=125.69  Aligned_cols=135  Identities=24%  Similarity=0.365  Sum_probs=98.3

Q ss_pred             EEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCC--------C----------ChhHHHHHH
Q 017020          114 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP--------N----------DPETFVHRS  175 (379)
Q Consensus       114 v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P--------~----------~~~~yiqR~  175 (379)
                      |.+|++-++.+.+.++++.--.|..-++|||+||+..+.||+|.+||+.+.-        .          +..+--||+
T Consensus       607 vLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRA  686 (1172)
T KOG0926|consen  607 VLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRA  686 (1172)
T ss_pred             EeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhc
Confidence            5567888999999999999999999999999999999999999999976532        2          344557999


Q ss_pred             hhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHHHHHHHHHHHHHHHcccCccchhchHHHHHHHHhhh
Q 017020          176 GRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEK  255 (379)
Q Consensus       176 GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~  255 (379)
                      ||+||.| .|+||-+|+..=.          ...|+..+   ..+|++.-++.++..++..+-..+..|     .+-..+
T Consensus       687 GRAGRtg-pGHcYRLYSSAVf----------~~~Fe~fS---~PEIlk~Pve~lvLqMKsMnI~kVvnF-----PFPtpP  747 (1172)
T KOG0926|consen  687 GRAGRTG-PGHCYRLYSSAVF----------SNDFEEFS---LPEILKKPVESLVLQMKSMNIDKVVNF-----PFPTPP  747 (1172)
T ss_pred             cccCCCC-CCceeehhhhHHh----------hcchhhhc---cHHHhhCcHHHHHHHHHhcCccceecC-----CCCCCc
Confidence            9999998 9999999987432          11233333   347888888888888888765544433     122234


Q ss_pred             CHHHHHHHHHHH
Q 017020          256 GTDALAAALAQL  267 (379)
Q Consensus       256 ~~~~~a~al~~~  267 (379)
                      +..++-+|.-.|
T Consensus       748 d~~~L~~Aer~L  759 (1172)
T KOG0926|consen  748 DRSALEKAERRL  759 (1172)
T ss_pred             cHHHHHHHHHHH
Confidence            445554444444

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.28  E-value=1.9e-11  Score=133.22  Aligned_cols=134  Identities=18%  Similarity=0.363  Sum_probs=110.9

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccCC---ceeEEEeccc
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQG---KFTVLVATDV  146 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g---~~~iLVaTdv  146 (379)
                      ..|..+|..++... ..+.++|||+......+.|...|. .++....+||+++..+|+.+++.|.+.   ..-+|++|.+
T Consensus       470 SgKl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrA  549 (1033)
T PLN03142        470 SGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRA  549 (1033)
T ss_pred             hhHHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccc
Confidence            46888888888665 346799999999999999999887 489999999999999999999999753   3467899999


Q ss_pred             cccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceE--EEEeChh--hHHHHHHHHHH
Q 017020          147 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA--ILMFTSS--QRRTVRSLERD  205 (379)
Q Consensus       147 ~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~--i~l~~~~--e~~~l~~le~~  205 (379)
                      ++.|||+..+++||+||+|+++..+.|++||+.|.|++..+  |.|++..  |...+....+.
T Consensus       550 GGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIEEkIlera~~K  612 (1033)
T PLN03142        550 GGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKK  612 (1033)
T ss_pred             cccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999976544  4455543  44455444333

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

Probab=99.27  E-value=2.7e-11  Score=122.69  Aligned_cols=103  Identities=32%  Similarity=0.524  Sum_probs=92.5

Q ss_pred             HHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCc
Q 017020           77 ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN  155 (379)
Q Consensus        77 ~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~  155 (379)
                      .+..++..+..+.+++|||.+..+++.++..+.. +. +..+.|+.++.+|+.+++.|+.|.+++||++.++..|+|+|+
T Consensus       272 ~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~  350 (442)
T COG1061         272 AVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPD  350 (442)
T ss_pred             HHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCC
Confidence            3344444332367999999999999999999975 45 899999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCCChhHHHHHHhhccC
Q 017020          156 VDLIIHYELPNDPETFVHRSGRTGR  180 (379)
Q Consensus       156 v~~VI~~~~P~~~~~yiqR~GRtgR  180 (379)
                      ++++|......+...|+||+||.-|
T Consensus       351 ~~~~i~~~~t~S~~~~~Q~lGR~LR  375 (442)
T COG1061         351 ADVLIILRPTGSRRLFIQRLGRGLR  375 (442)
T ss_pred             CcEEEEeCCCCcHHHHHHHhhhhcc
Confidence            9999999999999999999999999

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.19  E-value=1.4e-09  Score=108.77  Aligned_cols=211  Identities=18%  Similarity=0.214  Sum_probs=144.8

Q ss_pred             CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC---cc------HHHHHHHHH-HHHcCC
Q 017020           19 PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA---TS------KRTILSDLI-TVYAKG   88 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~---~~------k~~~L~~ll-~~~~~~   88 (379)
                      .+.|++-.|||+...++-....+--+.  ++++.....  +..-+++.++.++   .+      +..-...++ +....+
T Consensus       450 ~~~~~~~~~~~~K~~~~~~~~~~~~~E--~~Li~~DGS--Ps~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~~  525 (1034)
T KOG4150|consen  450 INMGVYDGDTPYKDRTRLRSELANLSE--LELVTIDGS--PSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEMVQHG  525 (1034)
T ss_pred             cCcceEeCCCCcCCHHHHHHHhcCCcc--eEEEEecCC--CCccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHHHHcC
Confidence            578999999999777665554333233  333322222  3344666665442   11      111122222 222346


Q ss_pred             CcEEEEecccccHHHHHHHHhcC---------CcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           89 GKTIVFTQTKRDADEVSLALTSI---------IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~~~---------~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      -++|-||.+++-|+.+....++-         -.+..+.||.+.++|.++....-.|+..-+|||+.++-||||.+.+.|
T Consensus       526 ~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LDAV  605 (1034)
T KOG4150|consen  526 LRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLDAV  605 (1034)
T ss_pred             CcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccceeE
Confidence            79999999999998776554321         135678899999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEe--ChhhHHHHHHHHHHhCCCceeeCC-CCHHHHHHHHHHHHHHHH
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMF--TSSQRRTVRSLERDVGCKFEFVSP-PVVEDVLESSAEQVVATL  233 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~--~~~e~~~l~~le~~~~~~~~~~~~-p~~~~i~~~~~~~~~~~l  233 (379)
                      ++.++|.+...+.|..||+||-.+...++.++  .|-+..+++.-+...+..-.+..+ -+.+-++...++-+.-++
T Consensus       606 l~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y~~HP~~l~~~pN~EL~LD~~N~~iL~~HlQCAA~EL  682 (1034)
T KOG4150|consen  606 LHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYYMSHPDKLFGSPNEELHLDSQNKHVLMQHLQCAALEL  682 (1034)
T ss_pred             EEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHhhcCcHHHhCCCcceeEEecccHHHHHHHHhHHhhcC
Confidence            99999999999999999999998887766554  466777777766666544333222 233445555555544443

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

Probab=99.12  E-value=2.7e-10  Score=126.09  Aligned_cols=93  Identities=23%  Similarity=0.429  Sum_probs=81.9

Q ss_pred             CCcEEEEecccccHHHHHHHHhcC-------C---cEEEeeCCCCHHHHHHHHhcccCCce-eEEEeccccccCCCCCcc
Q 017020           88 GGKTIVFTQTKRDADEVSLALTSI-------I---ASEALHGDISQHQRERTLNGFRQGKF-TVLVATDVAARGLDIPNV  156 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~~-------~---~v~~lhg~m~~~~R~~~~~~F~~g~~-~iLVaTdv~~rGiDip~v  156 (379)
                      ++++||||.+++.|+.++..|...       +   .+..+||+++  ++..++++|+++.. +|+|++|++.+|+|+|.+
T Consensus       698 ~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v  775 (1123)
T PRK11448        698 EGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSI  775 (1123)
T ss_pred             CCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccc
Confidence            479999999999999988887531       1   4567999986  46789999999886 699999999999999999


Q ss_pred             ceEEecCCCCChhHHHHHHhhccCCC
Q 017020          157 DLIIHYELPNDPETFVHRSGRTGRAG  182 (379)
Q Consensus       157 ~~VI~~~~P~~~~~yiqR~GRtgR~G  182 (379)
                      ++||.+.+|.|...|+||+||+.|.-
T Consensus       776 ~~vVf~rpvkS~~lf~QmIGRgtR~~  801 (1123)
T PRK11448        776 CNLVFLRRVRSRILYEQMLGRATRLC  801 (1123)
T ss_pred             cEEEEecCCCCHHHHHHHHhhhccCC
Confidence            99999999999999999999999953

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

Probab=99.06  E-value=2.2e-09  Score=115.81  Aligned_cols=106  Identities=25%  Similarity=0.402  Sum_probs=88.2

Q ss_pred             CCcEEEEecccccHHHHHHHHhc----------C-------------------C-------------cEEEeeCCCCHHH
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS----------I-------------------I-------------ASEALHGDISQHQ  125 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~----------~-------------------~-------------~v~~lhg~m~~~~  125 (379)
                      .-++|+|+=+++.|+..+..+..          .                   +             ...++|++|-+..
T Consensus       379 ~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~  458 (1041)
T COG4581         379 LLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAI  458 (1041)
T ss_pred             CCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHH
Confidence            35899999999999988877651          1                   0             1346899999999


Q ss_pred             HHHHHhcccCCceeEEEeccccccCCCCCccceEE----ecC----CCCChhHHHHHHhhccCCC--CCceEEEEeCh
Q 017020          126 RERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII----HYE----LPNDPETFVHRSGRTGRAG--KEGTAILMFTS  193 (379)
Q Consensus       126 R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI----~~~----~P~~~~~yiqR~GRtgR~G--~~g~~i~l~~~  193 (379)
                      +..+...|..|-.+|++||.+++.|+|.|.-++|+    .+|    .+-++..|.|+.||+||.|  ..|.+++.-.+
T Consensus       459 K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~  536 (1041)
T COG4581         459 KELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPP  536 (1041)
T ss_pred             HHHHHHHHhccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCC
Confidence            99999999999999999999999999999888776    233    3558999999999999999  56888887443

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.01  E-value=1e-08  Score=108.53  Aligned_cols=167  Identities=19%  Similarity=0.210  Sum_probs=115.1

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHH-HHHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILS-DLITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~-~ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+-.||.|...+-.++.+-|--+-+.|   +...........-. +......|..++. ++...+..+.|+||.|.|.+.
T Consensus       363 kLsGMTGTA~te~~Ef~~iY~l~Vv~I---PTnkP~~R~D~~d~-iy~t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~  438 (925)
T PRK12903        363 KLSGMTGTAKTEEQEFIDIYNMRVNVV---PTNKPVIRKDEPDS-IFGTKHAKWKAVVKEVKRVHKKGQPILIGTAQVED  438 (925)
T ss_pred             hhhccCCCCHHHHHHHHHHhCCCEEEC---CCCCCeeeeeCCCc-EEEcHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHH
Confidence            345688888777777776664332222   11111111111111 2223345555444 455556678999999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCC-ceeEEEeccccccCCCCCccc--------eEEecCCCCChhH
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFTVLVATDVAARGLDIPNVD--------LIIHYELPNDPET  170 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g-~~~iLVaTdv~~rGiDip~v~--------~VI~~~~P~~~~~  170 (379)
                      ++.++..|.. +++...+++.  +.+++.-+-. ..| .-.|.|||++|+||.||.--.        |||....|.+..-
T Consensus       439 SE~ls~~L~~~gi~h~vLNAk--~~e~EA~IIa-~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRI  515 (925)
T PRK12903        439 SETLHELLLEANIPHTVLNAK--QNAREAEIIA-KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRI  515 (925)
T ss_pred             HHHHHHHHHHCCCCceeeccc--chhhHHHHHH-hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHH
Confidence            9999999985 8999999987  3344433333 223 456999999999999995222        8999999999988


Q ss_pred             HHHHHhhccCCCCCceEEEEeChhh
Q 017020          171 FVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       171 yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      --|-.||+||.|.+|.+-.|++-.|
T Consensus       516 DnQLrGRaGRQGDpGss~f~lSLeD  540 (925)
T PRK12903        516 DNQLRGRSGRQGDVGESRFFISLDD  540 (925)
T ss_pred             HHHHhcccccCCCCCcceEEEecch
Confidence            8899999999999999999888655

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=98.92  E-value=3.3e-09  Score=106.11  Aligned_cols=119  Identities=24%  Similarity=0.347  Sum_probs=91.6

Q ss_pred             CCcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCCHHHHHHHHhcccC--CceeEEEeccccccCCCCCccceEEecC
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQ--GKFTVLVATDVAARGLDIPNVDLIIHYE  163 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~~~~R~~~~~~F~~--g~~~iLVaTdv~~rGiDip~v~~VI~~~  163 (379)
                      ++-|||-. +++..-.+...++.  +..+++++|++|++.|.+--..|.+  ++.+||||||..++|+|+ +++-||.|+
T Consensus       357 ~GDCvV~F-Skk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~s  434 (700)
T KOG0953|consen  357 PGDCVVAF-SKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYS  434 (700)
T ss_pred             CCCeEEEe-ehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEee
Confidence            46666654 56678888888875  4559999999999999999999988  899999999999999999 788898877


Q ss_pred             C---------CCChhHHHHHHhhccCCC---CCceEEEEeChhhHHHHHHHHHHhCCCcee
Q 017020          164 L---------PNDPETFVHRSGRTGRAG---KEGTAILMFTSSQRRTVRSLERDVGCKFEF  212 (379)
Q Consensus       164 ~---------P~~~~~yiqR~GRtgR~G---~~g~~i~l~~~~e~~~l~~le~~~~~~~~~  212 (379)
                      +         |.+.....|-+||+||.|   ..|.+.++..    +.+..+.+.+..++++
T Consensus       435 l~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~----eDL~~L~~~l~~p~ep  491 (700)
T KOG0953|consen  435 LIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHS----EDLKLLKRILKRPVEP  491 (700)
T ss_pred             cccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeH----hhHHHHHHHHhCCchH
Confidence            5         457788999999999987   3355555443    3444555555545443

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.89  E-value=2.3e-08  Score=104.52  Aligned_cols=168  Identities=18%  Similarity=0.181  Sum_probs=117.8

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH-HHHHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L-~~ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+-.||.|...+..++.+-|--+  .+.+ +..............+ .....|..++ .++...+..+.|+||.|.|.+.
T Consensus       364 kLsGMTGTa~t~~~Ef~~iY~l~--Vv~I-Ptnkp~~R~d~~d~iy-~t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~  439 (764)
T PRK12326        364 TVCGMTGTAVAAGEQLRQFYDLG--VSVI-PPNKPNIREDEADRVY-ATAAEKNDAIVEHIAEVHETGQPVLVGTHDVAE  439 (764)
T ss_pred             hheeecCCChhHHHHHHHHhCCc--EEEC-CCCCCceeecCCCceE-eCHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHH
Confidence            45678999988888877767433  2222 2211111111111222 2233455544 4455566778999999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC---------------ccceEEecCC
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP---------------NVDLIIHYEL  164 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip---------------~v~~VI~~~~  164 (379)
                      .+.++..|.. +++...|++.-...+-+.+-+.=+.|  .|-|||+.|+||.||.               +==|||--..
T Consensus       440 SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa~AG~~g--aVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTer  517 (764)
T PRK12326        440 SEELAERLRAAGVPAVVLNAKNDAEEARIIAEAGKYG--AVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGR  517 (764)
T ss_pred             HHHHHHHHHhCCCcceeeccCchHhHHHHHHhcCCCC--cEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccC
Confidence            9999999985 89999998874444433333333333  5899999999999985               2237999999


Q ss_pred             CCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          165 PNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       165 P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      |.+..---|-.||+||.|.+|.+-.|++-.|
T Consensus       518 heSrRID~QLrGRaGRQGDpGss~f~lSleD  548 (764)
T PRK12326        518 HRSERLDNQLRGRAGRQGDPGSSVFFVSLED  548 (764)
T ss_pred             CchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            9999999999999999999999999988655

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.88  E-value=1.2e-07  Score=100.88  Aligned_cols=131  Identities=24%  Similarity=0.361  Sum_probs=93.8

Q ss_pred             CCCcEEEEeeeCChH-H-HHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEec
Q 017020           19 PKRQSMLFSATMPSW-V-KKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQ   96 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~-i-~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~   96 (379)
                      +..+.+..|||..+. . ..+.+..++    +++.  .......|+...|+..   .-.+.+..+++.++  .-.|||++
T Consensus       275 k~g~LvvsSATg~~rg~R~~LfReLlg----FevG--~~~~~LRNIvD~y~~~---~~~e~~~elvk~lG--~GgLIfV~  343 (1187)
T COG1110         275 KLGILVVSSATGKPRGSRLKLFRELLG----FEVG--SGGEGLRNIVDIYVES---ESLEKVVELVKKLG--DGGLIFVP  343 (1187)
T ss_pred             CCceEEEeeccCCCCCchHHHHHHHhC----CccC--ccchhhhheeeeeccC---ccHHHHHHHHHHhC--CCeEEEEE
Confidence            456889999998432 2 234444443    1111  1222345666666654   33445566777764  46799999


Q ss_pred             c---cccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEec----cccccCCCCCcc-ceEEecCCC
Q 017020           97 T---KRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT----DVAARGLDIPNV-DLIIHYELP  165 (379)
Q Consensus        97 t---~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaT----dv~~rGiDip~v-~~VI~~~~P  165 (379)
                      .   ++.+++++++|.. |+.+..+|+.     .++.++.|..|++++||..    .++.||+|+|.. .++|.|++|
T Consensus       344 ~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvP  416 (1187)
T COG1110         344 IDYGREKAEELAEYLRSHGINAELIHAE-----KEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVP  416 (1187)
T ss_pred             cHHhHHHHHHHHHHHHhcCceEEEeecc-----chhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCC
Confidence            9   9999999999986 8999999985     3778999999999999875    489999999965 578877766

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

Probab=98.85  E-value=1.2e-07  Score=100.22  Aligned_cols=194  Identities=18%  Similarity=0.314  Sum_probs=120.7

Q ss_pred             HHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccH-----HHHHHHH
Q 017020            7 EEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSK-----RTILSDL   81 (379)
Q Consensus         7 ~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k-----~~~L~~l   81 (379)
                      ..||.-..++. .+.+++|-|||.+=  +.....--+....+.+...........+............     ..++..+
T Consensus       337 ARdvA~~Ra~~-~~~pvvLgSATPSL--ES~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i  413 (730)
T COG1198         337 ARDVAVLRAKK-ENAPVVLGSATPSL--ESYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAI  413 (730)
T ss_pred             HHHHHHHHHHH-hCCCEEEecCCCCH--HHHHhhhcCceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHH
Confidence            44555555544 58899999999754  4444332222344444433332223333322222111111     3344455


Q ss_pred             HHHHcCCCcEEEEecccc------------------------------------------------------------cH
Q 017020           82 ITVYAKGGKTIVFTQTKR------------------------------------------------------------DA  101 (379)
Q Consensus        82 l~~~~~~~~~IIF~~t~~------------------------------------------------------------~~  101 (379)
                      -+....+.++|+|.|.+-                                                            -+
T Consensus       414 ~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~Gt  493 (730)
T COG1198         414 RKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGT  493 (730)
T ss_pred             HHHHhcCCeEEEEEccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCeeEEecccH
Confidence            455567889999977654                                                            23


Q ss_pred             HHHHHHHhc---CCcEEEeeCCCCHHH--HHHHHhcccCCceeEEEeccccccCCCCCccceEEecCC------CC----
Q 017020          102 DEVSLALTS---IIASEALHGDISQHQ--RERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL------PN----  166 (379)
Q Consensus       102 ~~l~~~L~~---~~~v~~lhg~m~~~~--R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~------P~----  166 (379)
                      +.+.+.|..   +..+..+-+|.+...  -+..++.|.+|+.+|||.|.+++.|.|+|++++|.-.|.      |.    
T Consensus       494 erieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~  573 (730)
T COG1198         494 ERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRAS  573 (730)
T ss_pred             HHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchH
Confidence            344444432   234556666655433  467899999999999999999999999999998663332      21    


Q ss_pred             --ChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHH
Q 017020          167 --DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       167 --~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                        ....+.|-.||+||+++.|.+++-....+...++.+.
T Consensus       574 Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~~  612 (730)
T COG1198         574 ERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAIQALK  612 (730)
T ss_pred             HHHHHHHHHHHhhhccCCCCCeEEEEeCCCCcHHHHHHH
Confidence              3455789999999999999998877766666665553

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.81  E-value=9.9e-08  Score=102.14  Aligned_cols=168  Identities=17%  Similarity=0.146  Sum_probs=116.0

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHH-HHHHHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTI-LSDLITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~-L~~ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+..||.|.-.+-.++.+-|--+  .+.+. ............. +......|..+ +.++...+..+.|+||-|.|...
T Consensus       505 kl~GmTGTa~~e~~Ef~~iY~l~--v~~iP-t~kp~~r~d~~d~-iy~t~~~k~~ai~~ei~~~~~~grPvLigt~si~~  580 (970)
T PRK12899        505 KLAGMTGTAITESREFKEIYNLY--VLQVP-TFKPCLRIDHNDE-FYMTEREKYHAIVAEIASIHRKGNPILIGTESVEV  580 (970)
T ss_pred             hhcccCCCCHHHHHHHHHHhCCC--EEECC-CCCCceeeeCCCc-EecCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHH
Confidence            55678899877777776666432  22222 1111111111111 22233455544 45556666778899999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC---c-----cceEEecCCCCChhHH
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP---N-----VDLIIHYELPNDPETF  171 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip---~-----v~~VI~~~~P~~~~~y  171 (379)
                      .+.++..|.. +++...++..-...+-+-+-+.=+.  -.|.|||+.|+||.||.   .     -=|||.-..|.+..--
T Consensus       581 se~ls~~L~~~gi~h~vLNak~~~~Ea~iia~AG~~--g~VTIATNmAGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid  658 (970)
T PRK12899        581 SEKLSRILRQNRIEHTVLNAKNHAQEAEIIAGAGKL--GAVTVATNMAGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRID  658 (970)
T ss_pred             HHHHHHHHHHcCCcceecccchhhhHHHHHHhcCCC--CcEEEeeccccCCcccccCchHHhcCCcEEEeeccCchHHHH
Confidence            9999999985 8888888887433333333333333  46899999999999983   2     2379999999999999


Q ss_pred             HHHHhhccCCCCCceEEEEeChhh
Q 017020          172 VHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       172 iqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      -|-.||+||.|.+|.+..|++-.|
T Consensus       659 ~Ql~GRagRQGdpGss~f~lSlED  682 (970)
T PRK12899        659 RQLRGRCARLGDPGAAKFFLSFED  682 (970)
T ss_pred             HHHhcccccCCCCCceeEEEEcch
Confidence            999999999999999999988765

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.76  E-value=1.8e-07  Score=100.66  Aligned_cols=167  Identities=20%  Similarity=0.190  Sum_probs=117.5

Q ss_pred             EEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHH-HHHHHHHHcCCCcEEEEecccccH
Q 017020           23 SMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTI-LSDLITVYAKGGKTIVFTQTKRDA  101 (379)
Q Consensus        23 ~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~-L~~ll~~~~~~~~~IIF~~t~~~~  101 (379)
                      +-.||.|...+-.++..-|--+-+.|   +...........-.. ......|..+ +.++...+..+.|+||-|.|.+..
T Consensus       566 LsGMTGTA~tea~Ef~~IY~L~Vv~I---PTnrP~~R~D~~D~v-y~t~~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~S  641 (1112)
T PRK12901        566 LAGMTGTAETEAGEFWDIYKLDVVVI---PTNRPIARKDKEDLV-YKTKREKYNAVIEEITELSEAGRPVLVGTTSVEIS  641 (1112)
T ss_pred             hcccCCCCHHHHHHHHHHhCCCEEEC---CCCCCcceecCCCeE-ecCHHHHHHHHHHHHHHHHHCCCCEEEEeCcHHHH
Confidence            34578888777777777664332222   111111111111122 2223455544 455556667789999999999999


Q ss_pred             HHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC--------ccceEEecCCCCChhHHH
Q 017020          102 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP--------NVDLIIHYELPNDPETFV  172 (379)
Q Consensus       102 ~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip--------~v~~VI~~~~P~~~~~yi  172 (379)
                      +.++..|.. +++...|++.....+-+-+-++=+.|  .|-|||+.|+||.||.        +-=|||--..|.|..---
T Consensus       642 E~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~G--aVTIATNMAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~  719 (1112)
T PRK12901        642 ELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQPG--TVTIATNMAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDR  719 (1112)
T ss_pred             HHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCCC--cEEEeccCcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHH
Confidence            999999985 88888888875555555444544444  5889999999999995        334899999999999999


Q ss_pred             HHHhhccCCCCCceEEEEeChhh
Q 017020          173 HRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       173 qR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      |-.||+||.|.+|.+-.|++-.|
T Consensus       720 QLrGRaGRQGDPGsS~f~lSLED  742 (1112)
T PRK12901        720 QLRGRAGRQGDPGSSQFYVSLED  742 (1112)
T ss_pred             HHhcccccCCCCCcceEEEEccc
Confidence            99999999999999999988655

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.71  E-value=2.4e-07  Score=99.08  Aligned_cols=168  Identities=20%  Similarity=0.174  Sum_probs=115.4

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH-HHHHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L-~~ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+-.||.|...+..++.+-|--+-+.|   +...........-.. ......|..++ .++...+..+.|+||-|.|.+.
T Consensus       386 kLsGMTGTa~te~~Ef~~iY~l~Vv~I---PTnkP~~R~D~~d~v-y~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~  461 (913)
T PRK13103        386 KLSGMTGTADTEAFEFRQIYGLDVVVI---PPNKPLARKDFNDLV-YLTAEEKYAAIITDIKECMALGRPVLVGTATIET  461 (913)
T ss_pred             hhccCCCCCHHHHHHHHHHhCCCEEEC---CCCCCcccccCCCeE-EcCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHH
Confidence            345688898777777777664332222   211111111111122 22334565544 4455556678999999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC-------------------------
Q 017020          101 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP-------------------------  154 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip-------------------------  154 (379)
                      .+.++..|.. +++...|+..-...+-+-+-+.=+.  -.|-|||+.|+||.||.                         
T Consensus       462 SE~ls~~L~~~gi~h~VLNAk~~~~EA~IIa~AG~~--GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~  539 (913)
T PRK13103        462 SEHMSNLLKKEGIEHKVLNAKYHEKEAEIIAQAGRP--GALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKA  539 (913)
T ss_pred             HHHHHHHHHHcCCcHHHhccccchhHHHHHHcCCCC--CcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHH
Confidence            9999999985 7887778776444443434433333  45899999999999993                         


Q ss_pred             ------------ccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          155 ------------NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       155 ------------~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                                  +==|||--..|.|..-=-|-.||+||.|.+|.+-.|++-.|
T Consensus       540 ~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED  592 (913)
T PRK13103        540 DWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  592 (913)
T ss_pred             HHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCc
Confidence                        12278888889998888999999999999999999988755

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

Probab=98.69  E-value=1.3e-07  Score=103.29  Aligned_cols=106  Identities=21%  Similarity=0.276  Sum_probs=76.5

Q ss_pred             CCCcEEEEecccccHHHHHHHHhcC---CcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc--eEEe
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD--LIIH  161 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~~---~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~--~VI~  161 (379)
                      .++++|||++|.+..+.++..|...   .....+..+.. ..|.+++++|++++..||++|+.+++|||+|+..  +||.
T Consensus       673 ~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI  751 (850)
T TIGR01407       673 TSPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVI  751 (850)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHhhhccccCceEEecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEE
Confidence            3579999999999999999998641   12223333333 5789999999999999999999999999999887  4565


Q ss_pred             cCCCCC----h--------------------------hHHHHHHhhccCCCCCceEEEEeCh
Q 017020          162 YELPND----P--------------------------ETFVHRSGRTGRAGKEGTAILMFTS  193 (379)
Q Consensus       162 ~~~P~~----~--------------------------~~yiqR~GRtgR~G~~g~~i~l~~~  193 (379)
                      ..+|..    +                          ..+.|-+||.=|.....-+++++++
T Consensus       752 ~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~  813 (850)
T TIGR01407       752 PRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDR  813 (850)
T ss_pred             eCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEEcc
Confidence            665531    1                          2236778888887644334444444

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.

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=98.60  E-value=3.3e-06  Score=84.64  Aligned_cols=181  Identities=17%  Similarity=0.217  Sum_probs=135.2

Q ss_pred             CcEEEEeeeCChHHHHHHHHhcCCCc-eEEeecccc-----cccccceEEEEEEcCCcc-------HHH-----HHHHHH
Q 017020           21 RQSMLFSATMPSWVKKLSRKYLDNPL-NIDLVGNQD-----EKLAEGIKLYAISTTATS-------KRT-----ILSDLI   82 (379)
Q Consensus        21 ~Q~llfSAT~p~~i~~l~~~~l~~p~-~i~~~~~~~-----~~~~~~i~~~~~~~~~~~-------k~~-----~L~~ll   82 (379)
                      +|+|+||+...+++..+...++.|.. .+.+.....     ......++|.+...+..+       +.+     +|..+.
T Consensus       216 RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~~~iLP~l~  295 (442)
T PF06862_consen  216 RQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSSPADDPDARFKYFTKKILPQLK  295 (442)
T ss_pred             eEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCCcchhhhHHHHHHHHHHHHHhh
Confidence            79999999999999999999877643 343332222     234456677776544322       222     233333


Q ss_pred             HHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc--cccCCCCCccceE
Q 017020           83 TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV--AARGLDIPNVDLI  159 (379)
Q Consensus        83 ~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv--~~rGiDip~v~~V  159 (379)
                      . -...+.+|||+++--+=-.+..+|.. .+....+|--.++.+-.+.-..|.+|+.++|+.|.=  .-+-..|.++.+|
T Consensus       296 ~-~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~irGi~~v  374 (442)
T PF06862_consen  296 R-DSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIRGIRHV  374 (442)
T ss_pred             h-ccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceecCCcEE
Confidence            2 12457899999999888888888875 788999999999999999999999999999999973  3455667889999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCC------CceEEEEeChhhHHHHHHH
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGK------EGTAILMFTSSQRRTVRSL  202 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~------~g~~i~l~~~~e~~~l~~l  202 (379)
                      |.|++|..+.-|-..++-.+....      ...|.++++..|.-.|++|
T Consensus       375 iFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErI  423 (442)
T PF06862_consen  375 IFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERI  423 (442)
T ss_pred             EEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHH
Confidence            999999999999888876555432      5789999999887655544

; GO: 0005634 nucleus

>PF08152 GUCT: GUCT (NUC152) domain; InterPro: IPR012562 This is the C-terminal domain found in the RNA helicase II / Gu protein family []

Probab=98.58  E-value=6.9e-08  Score=77.15  Aligned_cols=81  Identities=23%  Similarity=0.272  Sum_probs=51.8

Q ss_pred             CCCCCCCCCccccCCCCeEEEEEeeCCcccCCCCChhHHHHHHhhhCC-CCCCccccEEeeeCCceeeeecchhhHHHHh
Q 017020          269 GFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYP-TAADEIGKIHIIADDRVCIDTVILLYFYASV  347 (379)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~i~~~~~~~~~-~~~~~ig~i~i~~~~~~~~~~~~~~~~~~~~  347 (379)
                      |+.+ ++.||++++.+|++|+.+..+.    ..-++.+.|+.|.+..+ ...++||+|.+.+|.+  |+|||||+..++.
T Consensus         1 G~t~-~~~RSLLt~~~g~vTl~l~~~~----~i~~~~y~~~~L~~~L~e~~~~~v~~m~l~~d~~--GavFDvP~~~~~~   73 (97)
T PF08152_consen    1 GYTE-IKQRSLLTSEEGFVTLQLTCSR----EIRSPGYAWRILRRQLSEEIADKVKGMTLLKDKM--GAVFDVPSEIAEE   73 (97)
T ss_dssp             S-S--------------EEEEEEE-SS------SSTHHHHHHHHHHS-HHHHTT-EEEEE-TTSS--EEEEEEEHHHHHH
T ss_pred             CCCC-CCccccccCCCCCEEEEEEcCC----cCCCchhHHHHHHHhcCHHHHHhhCcEEEecCCC--EEEEEChHHHHHH
Confidence            4455 6789999999999999998875    45679999999998877 4677999999999998  9999999999999


Q ss_pred             hhhcccCcc
Q 017020          348 RLGLFNTKS  356 (379)
Q Consensus       348 ~~~~~~~~~  356 (379)
                      ++...+...
T Consensus        74 ~~~~~~~~~   82 (97)
T PF08152_consen   74 FLAKWEDSR   82 (97)
T ss_dssp             HHHH--SS-
T ss_pred             HHHhCcccC
Confidence            998877764

; GO: 0003723 RNA binding, 0004386 helicase activity, 0005524 ATP binding, 0005634 nucleus; PDB: 2E29_A.

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.50  E-value=3.8e-06  Score=89.66  Aligned_cols=126  Identities=18%  Similarity=0.182  Sum_probs=79.4

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH-HHHHHHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-ILSDLITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-~L~~ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+..||.|...+-.++.+-|--+-  +.+. ...........- .+......|.. ++.++...+..+.|+||-|.|.+.
T Consensus       361 kL~GMTGTa~te~~Ef~~iY~l~v--v~IP-tnkp~~R~d~~d-~v~~t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~  436 (870)
T CHL00122        361 KLSGMTGTAKTEELEFEKIYNLEV--VCIP-THRPMLRKDLPD-LIYKDELSKWRAIADECLQMHQTGRPILIGTTTIEK  436 (870)
T ss_pred             hhcccCCCCHHHHHHHHHHhCCCE--EECC-CCCCccceeCCC-eEEeCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHH
Confidence            456688888777667766664332  2222 111111111111 12223334554 445566667778999999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCC--HHHHHHHHhcccCCceeEEEeccccccCCCC
Q 017020          101 ADEVSLALTS-IIASEALHGDIS--QHQRERTLNGFRQGKFTVLVATDVAARGLDI  153 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~--~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDi  153 (379)
                      .+.++..|.. +++...+++.-.  ..+-+-+-++=+  .-.|-|||+.|+||.||
T Consensus       437 SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIA~AG~--~G~VTIATNMAGRGTDI  490 (870)
T CHL00122        437 SELLSQLLKEYRLPHQLLNAKPENVRRESEIVAQAGR--KGSITIATNMAGRGTDI  490 (870)
T ss_pred             HHHHHHHHHHcCCccceeeCCCccchhHHHHHHhcCC--CCcEEEeccccCCCcCe
Confidence            9999999985 899999998632  333333333323  34689999999999998

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.31  E-value=1.4e-05  Score=85.54  Aligned_cols=126  Identities=18%  Similarity=0.154  Sum_probs=79.4

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH-HHHHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L-~~ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+-.||.|.-.+-.++.+-|--+-+.|  . ...........-. +......|..++ .++...+..+.|+||-|.|.+.
T Consensus       376 kLsGMTGTa~te~~Ef~~iY~l~Vv~I--P-TnkP~~R~d~~d~-vy~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~  451 (939)
T PRK12902        376 KLAGMTGTAKTEEVEFEKTYKLEVTVI--P-TNRPRRRQDWPDQ-VYKTEIAKWRAVANETAEMHKQGRPVLVGTTSVEK  451 (939)
T ss_pred             hhcccCCCCHHHHHHHHHHhCCcEEEc--C-CCCCeeeecCCCe-EEcCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHH
Confidence            455688898777777777664332222  1 1111111111111 222334555544 4555666778999999999999


Q ss_pred             HHHHHHHHhc-CCcEEEeeCCCCH--HHHHHHHhcccCCceeEEEeccccccCCCC
Q 017020          101 ADEVSLALTS-IIASEALHGDISQ--HQRERTLNGFRQGKFTVLVATDVAARGLDI  153 (379)
Q Consensus       101 ~~~l~~~L~~-~~~v~~lhg~m~~--~~R~~~~~~F~~g~~~iLVaTdv~~rGiDi  153 (379)
                      .+.++..|.. +++...++..-.+  .+-+-+-++=+  .-.|-|||++|+||.||
T Consensus       452 SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIa~AG~--~GaVTIATNMAGRGTDI  505 (939)
T PRK12902        452 SELLSALLQEQGIPHNLLNAKPENVEREAEIVAQAGR--KGAVTIATNMAGRGTDI  505 (939)
T ss_pred             HHHHHHHHHHcCCchheeeCCCcchHhHHHHHHhcCC--CCcEEEeccCCCCCcCE
Confidence            9999999985 8998899986322  23333333333  34588999999999998

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=98.26  E-value=7.4e-06  Score=86.68  Aligned_cols=117  Identities=19%  Similarity=0.267  Sum_probs=90.0

Q ss_pred             ccHHHHHHHHHHHHcCCCcEEEEe---cccccHHHHHHHHh--cCCcEEEeeCCCCHHHHHHHHhcccCCc---eeEEEe
Q 017020           72 TSKRTILSDLITVYAKGGKTIVFT---QTKRDADEVSLALT--SIIASEALHGDISQHQRERTLNGFRQGK---FTVLVA  143 (379)
Q Consensus        72 ~~k~~~L~~ll~~~~~~~~~IIF~---~t~~~~~~l~~~L~--~~~~v~~lhg~m~~~~R~~~~~~F~~g~---~~iLVa  143 (379)
                      ..|...|..++...  ..++++|+   ....+..++.+.+.  .|+.+..+||.|+..+|+.+++.|.+..   .-.|.+
T Consensus       577 s~kl~~L~~ll~~~--~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlS  654 (776)
T KOG0390|consen  577 SGKLLVLVFLLEVI--REKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLS  654 (776)
T ss_pred             hhHHHHHHHHHHHH--hhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEe
Confidence            34666666666443  34444444   33344444444443  3899999999999999999999998743   336678


Q ss_pred             ccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEE
Q 017020          144 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  190 (379)
Q Consensus       144 Tdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l  190 (379)
                      |-+.+.||++-+.+.||.||++++|+.=.|-++|+-|.|++-.|+++
T Consensus       655 sKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iY  701 (776)
T KOG0390|consen  655 SKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIY  701 (776)
T ss_pred             cccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEE
Confidence            88999999999999999999999999999999999999977666553

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=98.26  E-value=3.8e-06  Score=91.00  Aligned_cols=128  Identities=19%  Similarity=0.363  Sum_probs=107.7

Q ss_pred             HHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccC---CceeEEEeccccc
Q 017020           74 KRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQ---GKFTVLVATDVAA  148 (379)
Q Consensus        74 k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~---g~~~iLVaTdv~~  148 (379)
                      |+-+|..||..+ ..+.++|||..-....+-|+++|. ++|+..-|-|.+..+.|+..++.|..   ..+-.|.||-+.+
T Consensus       684 KlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGG  763 (1373)
T KOG0384|consen  684 KLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGG  763 (1373)
T ss_pred             cEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCc
Confidence            444455555544 346899999999999999999998 59999999999999999999999986   3567999999999


Q ss_pred             cCCCCCccceEEecCCCCChhHHHHHHhhccCCCCC--ceEEEEeChh--hHHHHHH
Q 017020          149 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE--GTAILMFTSS--QRRTVRS  201 (379)
Q Consensus       149 rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~--g~~i~l~~~~--e~~~l~~  201 (379)
                      -|||+...+.||.||--++|..=+|---||.|-|++  -.+|-|++.+  |..++.+
T Consensus       764 LGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEilER  820 (1373)
T KOG0384|consen  764 LGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEILER  820 (1373)
T ss_pred             ccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHHHHHHH
Confidence            999999999999999999999999999999999955  4567788865  4445544

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=98.26  E-value=7.7e-06  Score=85.10  Aligned_cols=124  Identities=21%  Similarity=0.347  Sum_probs=106.1

Q ss_pred             CccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccCCc---eeEEEecc
Q 017020           71 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK---FTVLVATD  145 (379)
Q Consensus        71 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g~---~~iLVaTd  145 (379)
                      ...|..+|..+|..+ ..+.++|||..-....+-+-.++. ++|..+-+.|.++.++|...++.|....   .-.|++|-
T Consensus       469 nSGKm~vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTR  548 (971)
T KOG0385|consen  469 NSGKMLVLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTR  548 (971)
T ss_pred             cCcceehHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEecc
Confidence            356888888888665 557899999988877777777765 5899999999999999999999998643   55789999


Q ss_pred             ccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCC--ceEEEEeChh
Q 017020          146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE--GTAILMFTSS  194 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~--g~~i~l~~~~  194 (379)
                      +.+-|||+-..+.||.||-.++|..=.|-.-|+.|-|++  -.+|-|++.+
T Consensus       549 AGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLiten  599 (971)
T KOG0385|consen  549 AGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITEN  599 (971)
T ss_pred             ccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccc
Confidence            999999999999999999999999999999999999955  4556667765

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=98.20  E-value=2.6e-06  Score=90.44  Aligned_cols=83  Identities=28%  Similarity=0.456  Sum_probs=71.9

Q ss_pred             cEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecC-CCCChhHHHHHHhhccCCC--CCceEEE
Q 017020          113 ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE-LPNDPETFVHRSGRTGRAG--KEGTAIL  189 (379)
Q Consensus       113 ~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~-~P~~~~~yiqR~GRtgR~G--~~g~~i~  189 (379)
                      ....+|++|....|..+.--||.|...||+||..++-|||.|--++|.--| +--++-.|.|++||+||-|  ..|.++.
T Consensus       964 GiG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~F 1043 (1330)
T KOG0949|consen  964 GIGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVF 1043 (1330)
T ss_pred             cccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEE
Confidence            356799999999999999999999999999999999999999888777665 4458899999999999988  5588777


Q ss_pred             EeChhh
Q 017020          190 MFTSSQ  195 (379)
Q Consensus       190 l~~~~e  195 (379)
                      +--|..
T Consensus      1044 mgiP~~ 1049 (1330)
T KOG0949|consen 1044 MGIPRQ 1049 (1330)
T ss_pred             EeCcHH
Confidence            766643

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

Probab=98.15  E-value=1.9e-05  Score=87.23  Aligned_cols=80  Identities=21%  Similarity=0.252  Sum_probs=61.7

Q ss_pred             CCCcEEEEecccccHHHHHHHHhcCCc---EEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCcc--ceEEe
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTSIIA---SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV--DLIIH  161 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~~~~---v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v--~~VI~  161 (379)
                      .+++++||++|.+..+.++..|.....   ...+.=+++...|.++++.|++++-.||++|..+.+|||+|+-  ++||.
T Consensus       751 ~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI  830 (928)
T PRK08074        751 TKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVI  830 (928)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEE
Confidence            467999999999999999999864211   2222223444568899999999888999999999999999975  67887


Q ss_pred             cCCCC
Q 017020          162 YELPN  166 (379)
Q Consensus       162 ~~~P~  166 (379)
                      ..+|.
T Consensus       831 ~kLPF  835 (928)
T PRK08074        831 VRLPF  835 (928)
T ss_pred             ecCCC
Confidence            66553

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=98.14  E-value=9.6e-06  Score=84.68  Aligned_cols=122  Identities=19%  Similarity=0.342  Sum_probs=106.5

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHh--cCCcEEEeeCCCCHHHHHHHHhcccCCce--eEEEeccc
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT--SIIASEALHGDISQHQRERTLNGFRQGKF--TVLVATDV  146 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~--~~~~v~~lhg~m~~~~R~~~~~~F~~g~~--~iLVaTdv  146 (379)
                      ..|..++..++... ..+.++|+|..|+...+-+-..|.  ++|...-+.|..+-..|...+++|.++..  -.|++|-|
T Consensus       529 sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTrv  608 (923)
T KOG0387|consen  529 SGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTRV  608 (923)
T ss_pred             cchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEecc
Confidence            46888999988765 457799999999999999999998  48999999999999999999999997653  36789999


Q ss_pred             cccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCc--eEEEEeCh
Q 017020          147 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG--TAILMFTS  193 (379)
Q Consensus       147 ~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g--~~i~l~~~  193 (379)
                      .+-|+|+-..+-||.||+-++|..=.|-.-|+-|.|++-  .+|-|++.
T Consensus       609 GGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~  657 (923)
T KOG0387|consen  609 GGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTA  657 (923)
T ss_pred             cccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecC
Confidence            999999999999999999999999999999999999553  34555654

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.07  E-value=2.2e-05  Score=85.18  Aligned_cols=123  Identities=21%  Similarity=0.329  Sum_probs=102.0

Q ss_pred             ccHHHHHHHHHHHHc---------------CCCcEEEEecccccHHHHHHHHhcC--CcE--EEeeCCCCHHHHHHHHhc
Q 017020           72 TSKRTILSDLITVYA---------------KGGKTIVFTQTKRDADEVSLALTSI--IAS--EALHGDISQHQRERTLNG  132 (379)
Q Consensus        72 ~~k~~~L~~ll~~~~---------------~~~~~IIF~~t~~~~~~l~~~L~~~--~~v--~~lhg~m~~~~R~~~~~~  132 (379)
                      .-|..+|.++|...+               .+.+++|||.-+...+-+.+.|.+.  ..+  ..+.|..++.+|.++.++
T Consensus      1309 spKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~ 1388 (1549)
T KOG0392|consen 1309 SPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVER 1388 (1549)
T ss_pred             chhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHH
Confidence            458889999887642               2358999999999999999888652  233  478999999999999999


Q ss_pred             ccCC-ceeEE-EeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCce--EEEEeChh
Q 017020          133 FRQG-KFTVL-VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGT--AILMFTSS  194 (379)
Q Consensus       133 F~~g-~~~iL-VaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~--~i~l~~~~  194 (379)
                      |.++ .+++| .+|.|.+-|+|+.+.+.||.++-.++|..=+|-..|+.|-|++-.  +|-+++..
T Consensus      1389 FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlItrG 1454 (1549)
T KOG0392|consen 1389 FNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLITRG 1454 (1549)
T ss_pred             hcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCceeeeeeeehhcc
Confidence            9998 78877 578999999999999999999999999999999999999996644  44455543

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

Probab=97.96  E-value=0.00021  Score=76.21  Aligned_cols=77  Identities=22%  Similarity=0.274  Sum_probs=60.2

Q ss_pred             CCCcEEEEecccccHHHHHHHHhcCCc--EEEeeCCCCHHHHHHHHhcccCCce-eEEEeccccccCCCCCcc--ceEEe
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTSIIA--SEALHGDISQHQRERTLNGFRQGKF-TVLVATDVAARGLDIPNV--DLIIH  161 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~~~~--v~~lhg~m~~~~R~~~~~~F~~g~~-~iLVaTdv~~rGiDip~v--~~VI~  161 (379)
                      .+++++||++|.+..+.+++.+.....  ....+|.-+   +...++.|+.+.- .++|+|..+++|+|+|+-  ..||.
T Consensus       478 ~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~---~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI  554 (654)
T COG1199         478 SPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDE---REELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVI  554 (654)
T ss_pred             cCCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCc---HHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEE
Confidence            356999999999999999999986432  455566544   4578888887655 899999999999999866  56777


Q ss_pred             cCCCC
Q 017020          162 YELPN  166 (379)
Q Consensus       162 ~~~P~  166 (379)
                      ..+|.
T Consensus       555 ~~lPf  559 (654)
T COG1199         555 VGLPF  559 (654)
T ss_pred             EecCC
Confidence            77664

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=97.91  E-value=7e-05  Score=74.89  Aligned_cols=108  Identities=24%  Similarity=0.343  Sum_probs=88.6

Q ss_pred             CccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccC-CceeEEEeccccc
Q 017020           71 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQ-GKFTVLVATDVAA  148 (379)
Q Consensus        71 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~-g~~~iLVaTdv~~  148 (379)
                      ...|..+..-+++.+ ..+.++|||....-...+.+..|.    --+++|..+|.+|.++++.|+- ..++-+.-+.|..
T Consensus       525 NP~KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~----KpfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVgD  600 (776)
T KOG1123|consen  525 NPNKFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLG----KPFIYGPTSQNERMKILQNFQTNPKVNTIFLSKVGD  600 (776)
T ss_pred             CcchhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHcC----CceEECCCchhHHHHHHHhcccCCccceEEEeeccC
Confidence            356888888888876 346799999988777777776664    4578999999999999999985 4678888899999


Q ss_pred             cCCCCCccceEEecCCCC-ChhHHHHHHhhccCCC
Q 017020          149 RGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAG  182 (379)
Q Consensus       149 rGiDip~v~~VI~~~~P~-~~~~yiqR~GRtgR~G  182 (379)
                      ..+|+|..++.|+..-.. +...=-||.||.-|+.
T Consensus       601 tSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAK  635 (776)
T KOG1123|consen  601 TSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAK  635 (776)
T ss_pred             ccccCCcccEEEEEcccccchHHHHHHHHHHHHHh
Confidence            999999999999876543 5566789999998875

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

Probab=97.87  E-value=8.2e-05  Score=81.32  Aligned_cols=122  Identities=20%  Similarity=0.305  Sum_probs=102.8

Q ss_pred             cHHHHHHHHH-HH-HcCCC--cEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCC--ceeEEEecc
Q 017020           73 SKRTILSDLI-TV-YAKGG--KTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG--KFTVLVATD  145 (379)
Q Consensus        73 ~k~~~L~~ll-~~-~~~~~--~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g--~~~iLVaTd  145 (379)
                      .|...+.+++ .. ...+.  +++||+......+-+...+.. ++....++|.++.+.|...++.|.++  ..-++++|.
T Consensus       692 ~k~~~l~~ll~~~~~~~~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~k  771 (866)
T COG0553         692 GKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLK  771 (866)
T ss_pred             hHHHHHHHHHHHHHHhhcccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEec
Confidence            6788888888 33 33455  899999999999999999986 56899999999999999999999986  455777888


Q ss_pred             ccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceE--EEEeChh
Q 017020          146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA--ILMFTSS  194 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~--i~l~~~~  194 (379)
                      +.+.|+|....++||+||+.+++....|...|+.|.|++..+  +-+++..
T Consensus       772 agg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~  822 (866)
T COG0553         772 AGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRG  822 (866)
T ss_pred             ccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEEeecCC
Confidence            999999999999999999999999999999999999866544  4444443

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

Probab=97.85  E-value=0.00017  Score=77.07  Aligned_cols=93  Identities=18%  Similarity=0.217  Sum_probs=73.1

Q ss_pred             CCcEEEEecccccHHHHHHHHhcC------CcEEEeeCCCCHH---------------------HHHHHHhcccC-Ccee
Q 017020           88 GGKTIVFTQTKRDADEVSLALTSI------IASEALHGDISQH---------------------QRERTLNGFRQ-GKFT  139 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~~------~~v~~lhg~m~~~---------------------~R~~~~~~F~~-g~~~  139 (379)
                      +++++|||.++..|..++..|...      ..+..+++..+..                     ..+.++++|++ +..+
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            489999999999999999887532      3455666654332                     23478889976 6889


Q ss_pred             EEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCC
Q 017020          140 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  181 (379)
Q Consensus       140 iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~  181 (379)
                      |||++|.+..|.|.|.++.++..-+-.+ -.++|.+||+-|.
T Consensus       594 ilIVvdmllTGFDaP~l~tLyldKplk~-h~LlQai~R~nR~  634 (667)
T TIGR00348       594 LLIVVDMLLTGFDAPILNTLYLDKPLKY-HGLLQAIARTNRI  634 (667)
T ss_pred             EEEEEcccccccCCCccceEEEeccccc-cHHHHHHHHhccc
Confidence            9999999999999999998776665454 4589999999993

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

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

Probab=97.84  E-value=6.6e-05  Score=81.79  Aligned_cols=77  Identities=16%  Similarity=0.153  Sum_probs=58.4

Q ss_pred             cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCc--cceEEec
Q 017020           86 AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN--VDLIIHY  162 (379)
Q Consensus        86 ~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~--v~~VI~~  162 (379)
                      ..+++++|+++|.+..+.++..|.. .+.+ ...|.-.  .+.+++++|++++..||++|+.+.+|+|+|+  ...||..
T Consensus       645 ~~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~  721 (820)
T PRK07246        645 QLQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVIT  721 (820)
T ss_pred             hcCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEe
Confidence            3468999999999999999998864 3344 4445322  2566899999988899999999999999973  4555655


Q ss_pred             CCC
Q 017020          163 ELP  165 (379)
Q Consensus       163 ~~P  165 (379)
                      .+|
T Consensus       722 kLP  724 (820)
T PRK07246        722 RLP  724 (820)
T ss_pred             cCC
Confidence            554

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.82  E-value=0.00061  Score=73.15  Aligned_cols=77  Identities=26%  Similarity=0.403  Sum_probs=58.3

Q ss_pred             CCCcEEEEecccccHHHHHHHHhcCC-cEEEeeCCCCHHHHHHHHhccc----CCceeEEEeccccccCCCCCc--cceE
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTSII-ASEALHGDISQHQRERTLNGFR----QGKFTVLVATDVAARGLDIPN--VDLI  159 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~~~-~v~~lhg~m~~~~R~~~~~~F~----~g~~~iLVaTdv~~rGiDip~--v~~V  159 (379)
                      .++.++||++|.+..+.++..|.... .....+|..   .|.++++.|+    .++..||++|..+..|||+|+  +++|
T Consensus       533 ~~gg~LVlFtSy~~l~~v~~~l~~~~~~~ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~v  609 (697)
T PRK11747        533 KHKGSLVLFASRRQMQKVADLLPRDLRLMLLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQV  609 (697)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHhcCCcEEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEE
Confidence            35568999999999999999886421 233446653   4677786665    467789999999999999986  6788


Q ss_pred             EecCCCC
Q 017020          160 IHYELPN  166 (379)
Q Consensus       160 I~~~~P~  166 (379)
                      |...+|.
T Consensus       610 II~kLPF  616 (697)
T PRK11747        610 IITKIPF  616 (697)
T ss_pred             EEEcCCC
Confidence            8777664

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

Probab=97.81  E-value=4.6e-05  Score=80.42  Aligned_cols=92  Identities=25%  Similarity=0.360  Sum_probs=76.4

Q ss_pred             CCcEEEEecccccHHHHHHHHhcC------CcEEEeeCCCCHHHHHHHHhcccC--CceeEEEeccccccCCCCCccceE
Q 017020           88 GGKTIVFTQTKRDADEVSLALTSI------IASEALHGDISQHQRERTLNGFRQ--GKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~~------~~v~~lhg~m~~~~R~~~~~~F~~--g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      .+++||||.+...|+.+...|...      --+..+.|+-.+.+  ..++.|..  .-.+|.|+.|++..|+|+|.|.++
T Consensus       426 ~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~~~~q--~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nl  503 (875)
T COG4096         426 IGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAEQAQ--ALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNL  503 (875)
T ss_pred             cCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccchhhH--HHHHHHHhcCCCCceEEehhhhhcCCCchheeee
Confidence            469999999999999999999742      34778888865554  34555543  456799999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCC
Q 017020          160 IHYELPNDPETFVHRSGRTGRA  181 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~  181 (379)
                      |.+..-.|...|.|++||.-|.
T Consensus       504 VF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         504 VFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             eehhhhhhHHHHHHHhcCcccc
Confidence            9999999999999999998883

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

Probab=97.73  E-value=8e-05  Score=65.58  Aligned_cols=105  Identities=23%  Similarity=0.379  Sum_probs=69.9

Q ss_pred             CCCcEEEEecccccHHHHHHHHhcCC---cEEEeeCCCCHHHHHHHHhcccCCceeEEEecc--ccccCCCCCc--cceE
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTSII---ASEALHGDISQHQRERTLNGFRQGKFTVLVATD--VAARGLDIPN--VDLI  159 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~~~---~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd--v~~rGiDip~--v~~V  159 (379)
                      .++.+|||++|.+..+.+...+....   ....+.-  ....+..+++.|+++.-.||+|+.  ..+.|+|+|+  ++.|
T Consensus         8 ~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~v   85 (167)
T PF13307_consen    8 VPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAV   85 (167)
T ss_dssp             CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhhee
Confidence            35899999999999999999887522   1222222  255788999999999999999999  9999999986  6689


Q ss_pred             EecCCCCC----h--------------------------hHHHHHHhhccCCCCCceEEEEeCh
Q 017020          160 IHYELPND----P--------------------------ETFVHRSGRTGRAGKEGTAILMFTS  193 (379)
Q Consensus       160 I~~~~P~~----~--------------------------~~yiqR~GRtgR~G~~g~~i~l~~~  193 (379)
                      |..++|..    +                          ....|-+||.=|....--+++++++
T Consensus        86 ii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~  149 (167)
T PF13307_consen   86 IIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDS  149 (167)
T ss_dssp             EEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESG
T ss_pred             eecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcC
Confidence            98888742    1                          1115778999887654444445544

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.70  E-value=0.00012  Score=78.17  Aligned_cols=206  Identities=17%  Similarity=0.171  Sum_probs=118.2

Q ss_pred             EEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHH-HHHHHHHHHHcCCCcEEEEecccccHHH
Q 017020           25 LFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKR-TILSDLITVYAKGGKTIVFTQTKRDADE  103 (379)
Q Consensus        25 lfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~-~~L~~ll~~~~~~~~~IIF~~t~~~~~~  103 (379)
                      .++.|.-.+..++..-|..+-+.|..   .............+ .....|. .++.++...+..++|+||-+.+.+..+.
T Consensus       369 gmTGTa~te~~EF~~iY~l~vv~iPT---nrp~~R~D~~D~vy-~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~  444 (822)
T COG0653         369 GMTGTADTEEEEFDVIYGLDVVVIPT---NRPIIRLDEPDLVY-KTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSEL  444 (822)
T ss_pred             CCCCcchhhhhhhhhccCCceeeccC---CCcccCCCCccccc-cchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchh
Confidence            35666666666666655443322211   11111111111111 1223444 4455566667778999999999999999


Q ss_pred             HHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc-----------eEEecCCCCChhHH
Q 017020          104 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD-----------LIIHYELPNDPETF  171 (379)
Q Consensus       104 l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~-----------~VI~~~~P~~~~~y  171 (379)
                      ++..|.+ +++...+...-..  |+.-+-......--+-|||+.|+||.||.--.           +||--.--.+..-=
T Consensus       445 ls~~L~~~~i~h~VLNAk~h~--~EA~Iia~AG~~gaVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRID  522 (822)
T COG0653         445 LSKLLRKAGIPHNVLNAKNHA--REAEIIAQAGQPGAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRID  522 (822)
T ss_pred             HHHHHHhcCCCceeeccccHH--HHHHHHhhcCCCCccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHH
Confidence            9999985 8888888777554  44434343333335789999999999983222           34443333344444


Q ss_pred             HHHHhhccCCCCCceEEEEeChhhHHHHHHHHH-HhCCCceee----CCCCHHHHHHHHHHHHHHHHcccC
Q 017020          172 VHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER-DVGCKFEFV----SPPVVEDVLESSAEQVVATLNGVH  237 (379)
Q Consensus       172 iqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~-~~~~~~~~~----~~p~~~~i~~~~~~~~~~~l~~~~  237 (379)
                      -|-.||+||.|-.|.+-.+++-.+. .++.+.. .+...+...    ..|.........+++.....++.+
T Consensus       523 nQLRGRsGRQGDpG~S~F~lSleD~-L~r~F~~d~~~~~~~~l~~~~~e~i~~~~~~~~ie~aQk~vE~~n  592 (822)
T COG0653         523 NQLRGRAGRQGDPGSSRFYLSLEDD-LMRRFASDRLPALMDKLGLKEGEAIESKMVTRAVERAQRKVEGRN  592 (822)
T ss_pred             HHhhcccccCCCcchhhhhhhhHHH-HHHHhcchhhHHHHHhhcCCccCccccHHHHHHHHHHHHHHHhcC
Confidence            5888999999999988877775442 2222111 000111111    113344566666777777666644

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=97.61  E-value=0.00041  Score=75.30  Aligned_cols=123  Identities=20%  Similarity=0.334  Sum_probs=96.3

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCc--eeEEEecccc
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK--FTVLVATDVA  147 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~--~~iLVaTdv~  147 (379)
                      ..|++.|.-||..+ ..+.++|||+.-.+..+-|..+|.- ++.-.-|.|...-++|+..+++|....  +..+.+|-.-
T Consensus      1259 cGKLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSg 1338 (1958)
T KOG0391|consen 1259 CGKLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSG 1338 (1958)
T ss_pred             cchHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCC
Confidence            46777777777654 4578999999999999988888874 777888999999999999999998653  4567789999


Q ss_pred             ccCCCCCccceEEecCCCCChhHHHHHHhhccCCC--CCceEEEEeChh
Q 017020          148 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  194 (379)
Q Consensus       148 ~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~  194 (379)
                      +.|||+-+.+.||.||--+++.---|---|+.|.|  +.-+.|-|++..
T Consensus      1339 gvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIYRLISe~ 1387 (1958)
T KOG0391|consen 1339 GVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIYRLISER 1387 (1958)
T ss_pred             ccccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEEEeeccc
Confidence            99999999999999998887654444333333333  345677788764

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=97.58  E-value=0.00011  Score=73.54  Aligned_cols=115  Identities=19%  Similarity=0.351  Sum_probs=93.3

Q ss_pred             cHHHHHHHHHHH-----HcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCc-eeE-EEec
Q 017020           73 SKRTILSDLITV-----YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK-FTV-LVAT  144 (379)
Q Consensus        73 ~k~~~L~~ll~~-----~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~-~~i-LVaT  144 (379)
                      .|...+.+.|..     ..++.+.+|||......+.+...+.+ +++..-+.|..+...|....+.|+..+ ..| +++-
T Consensus       472 aK~~av~eyi~~~~~l~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsI  551 (689)
T KOG1000|consen  472 AKAAAVCEYILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSI  551 (689)
T ss_pred             cccHHHHHHHHhCcccccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEE
Confidence            455555444433     13467999999999999999999975 899999999999999999999998653 333 3455


Q ss_pred             cccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceE
Q 017020          145 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA  187 (379)
Q Consensus       145 dv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~  187 (379)
                      ..++.|+++...+.|+...+|+++.-.+|--.|+.|.|++..+
T Consensus       552 tA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQkssV  594 (689)
T KOG1000|consen  552 TAAGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSSV  594 (689)
T ss_pred             eecccceeeeccceEEEEEecCCCceEEechhhhhhcccccee
Confidence            6889999999999999999999999999988888888866443

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=97.56  E-value=0.00038  Score=73.05  Aligned_cols=124  Identities=21%  Similarity=0.333  Sum_probs=103.5

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCc--eeEEEecccc
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK--FTVLVATDVA  147 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~--~~iLVaTdv~  147 (379)
                      ..|...|..+|... ..+.+++||..-....+-|-..|.. ++.-.-+.|...-..|+.+++.|...+  .-+|.+|-+.
T Consensus       760 SgK~r~L~~LLp~~k~~G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAG  839 (941)
T KOG0389|consen  760 SGKCRKLKELLPKIKKKGDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAG  839 (941)
T ss_pred             hhhHhHHHHHHHHHhhcCCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccC
Confidence            35778888888765 3468999999888777777777764 888999999999999999999998753  4477899999


Q ss_pred             ccCCCCCccceEEecCCCCChhHHHHHHhhccCCCC--CceEEEEeChhh
Q 017020          148 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK--EGTAILMFTSSQ  195 (379)
Q Consensus       148 ~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~--~g~~i~l~~~~e  195 (379)
                      +-|||+-..++||.||+..+|-+=.|---|+.|.|+  +-+++.+++...
T Consensus       840 G~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~T  889 (941)
T KOG0389|consen  840 GFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKST  889 (941)
T ss_pred             cceecccccceEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEEecCc
Confidence            999999999999999999998888888889999884  466777787654

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=97.41  E-value=0.0023  Score=67.45  Aligned_cols=78  Identities=21%  Similarity=0.199  Sum_probs=61.1

Q ss_pred             CCCcEEEEecccccHHHHHHHHhcCC-cEEEeeCCCCHHHHHHHHhcccC----CceeEEEeccccccCCCC--------
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTSII-ASEALHGDISQHQRERTLNGFRQ----GKFTVLVATDVAARGLDI--------  153 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~~~-~v~~lhg~m~~~~R~~~~~~F~~----g~~~iLVaTdv~~rGiDi--------  153 (379)
                      .++.++|-+.|....+.++..|...+ ....++|+.+  .+...+++|+.    |...||++|+.+..|+|+        
T Consensus       469 ~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~p~  546 (636)
T TIGR03117       469 AQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSPD  546 (636)
T ss_pred             cCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCCCC
Confidence            46799999999999999999997644 3445667653  34567888886    478999999999999999        


Q ss_pred             --CccceEEecCCCC
Q 017020          154 --PNVDLIIHYELPN  166 (379)
Q Consensus       154 --p~v~~VI~~~~P~  166 (379)
                        +.+++||...+|.
T Consensus       547 ~G~~Ls~ViI~kLPF  561 (636)
T TIGR03117       547 KDNLLTDLIITCAPF  561 (636)
T ss_pred             CCCcccEEEEEeCCC
Confidence              3478898777764

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.37  E-value=0.0056  Score=66.00  Aligned_cols=78  Identities=15%  Similarity=0.240  Sum_probs=57.7

Q ss_pred             CCcEEEEecccccHHHHHHHHhc-CC-------cEEEeeCCCCHHHHHHHHhcccC----CceeEEEec--cccccCCCC
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS-II-------ASEALHGDISQHQRERTLNGFRQ----GKFTVLVAT--DVAARGLDI  153 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~-~~-------~v~~lhg~m~~~~R~~~~~~F~~----g~~~iLVaT--dv~~rGiDi  153 (379)
                      ++.+|||++|....+.+...+.. +.       .....-+. ...+++.+++.|+.    |.-.||+|+  ..+++|||+
T Consensus       522 pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~-~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGIDf  600 (705)
T TIGR00604       522 PDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETK-DAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGIDF  600 (705)
T ss_pred             CCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCC-CcchHHHHHHHHHHHHhcCCceEEEEecCCcccCcccc
Confidence            68899999999999988887753 11       12222222 12577889999964    455699998  889999999


Q ss_pred             Cc--cceEEecCCCC
Q 017020          154 PN--VDLIIHYELPN  166 (379)
Q Consensus       154 p~--v~~VI~~~~P~  166 (379)
                      ++  .+.||..++|.
T Consensus       601 ~~~~~r~ViivGlPf  615 (705)
T TIGR00604       601 CDDLGRAVIMVGIPY  615 (705)
T ss_pred             CCCCCcEEEEEccCC
Confidence            87  57898898886

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

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.29  E-value=0.0007  Score=73.28  Aligned_cols=39  Identities=21%  Similarity=0.335  Sum_probs=29.5

Q ss_pred             ccHHHHHHHHHHHH----------cCCCcEEEEecccccHHHHHHHHhc
Q 017020           72 TSKRTILSDLITVY----------AKGGKTIVFTQTKRDADEVSLALTS  110 (379)
Q Consensus        72 ~~k~~~L~~ll~~~----------~~~~~~IIF~~t~~~~~~l~~~L~~  110 (379)
                      .-|...|.++|+..          ..++++||||+..++|..|.+.|..
T Consensus       269 ~PKw~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       269 NPKWEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             CCCHHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHh
Confidence            45777777776542          1346899999999999999998854

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

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=97.21  E-value=0.0012  Score=68.67  Aligned_cols=122  Identities=19%  Similarity=0.312  Sum_probs=104.2

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccCCce-eEEEeccccc
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKF-TVLVATDVAA  148 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g~~-~iLVaTdv~~  148 (379)
                      ..|+..|..+|..+ ..+.++|+|..-.+..+.+.++|. +++.-.-+.|...-.+|..++.+|...++ -.|.+|-..+
T Consensus      1027 SgKL~~LDeLL~kLkaegHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGG 1106 (1185)
T KOG0388|consen 1027 SGKLVVLDELLPKLKAEGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGG 1106 (1185)
T ss_pred             ccceeeHHHHHHHhhcCCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCc
Confidence            45777788887665 457899999999999999999997 58999999999999999999999998554 4678999999


Q ss_pred             cCCCCCccceEEecCCCCChhHHHHHHhhccCCCCC--ceEEEEeCh
Q 017020          149 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE--GTAILMFTS  193 (379)
Q Consensus       149 rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~--g~~i~l~~~  193 (379)
                      -||++...+.||.||-.+++..-.|-..|+.|-|++  -++|-+++.
T Consensus      1107 LGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~r 1153 (1185)
T KOG0388|consen 1107 LGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITR 1153 (1185)
T ss_pred             ccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeeccc
Confidence            999999999999999999999999999999999955  445555554

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=97.18  E-value=0.0021  Score=64.45  Aligned_cols=123  Identities=18%  Similarity=0.242  Sum_probs=97.3

Q ss_pred             ccHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCC-cee-EEEecc
Q 017020           72 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFT-VLVATD  145 (379)
Q Consensus        72 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g-~~~-iLVaTd  145 (379)
                      ..|.++|.+-|...   ...-+.|||..-....+.+.-.|.+ |+.+.-+-|+|++..|...++.|.+. .++ .||+-.
T Consensus       619 STKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLk  698 (791)
T KOG1002|consen  619 STKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLK  698 (791)
T ss_pred             hhHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEec
Confidence            35777776554433   2235889999988888888888876 99999999999999999999999975 344 456667


Q ss_pred             ccccCCCCCccceEEecCCCCChhHHHHHHhhccCCC--CCceEEEEeChh
Q 017020          146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  194 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~  194 (379)
                      ..+..+|+-..++|...|+-+++.--+|--.|..|.|  ++-.++.|+-.+
T Consensus       699 AGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEn  749 (791)
T KOG1002|consen  699 AGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIEN  749 (791)
T ss_pred             cCceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehhc
Confidence            7778889999999999999999988888777777777  456667776554

>COG4889 Predicted helicase [General function prediction only]

Probab=96.92  E-value=0.00045  Score=73.27  Aligned_cols=102  Identities=20%  Similarity=0.394  Sum_probs=79.6

Q ss_pred             CcEEEEecccccHHHHHHHHhc--------------CC--cEEEeeCCCCHHHHHHHHh---cccCCceeEEEecccccc
Q 017020           89 GKTIVFTQTKRDADEVSLALTS--------------II--ASEALHGDISQHQRERTLN---GFRQGKFTVLVATDVAAR  149 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~~--------------~~--~v~~lhg~m~~~~R~~~~~---~F~~g~~~iLVaTdv~~r  149 (379)
                      .++|-||.+.++...+++.+..              ++  .+....|.|.-.+|...+.   .|...+++||--.-++++
T Consensus       461 ~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSE  540 (1518)
T COG4889         461 QRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSE  540 (1518)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhhhc
Confidence            4778999998888877766531              12  3444568899999865554   456778899988889999


Q ss_pred             CCCCCccceEEecCCCCChhHHHHHHhhccCCC---CCceEEEE
Q 017020          150 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG---KEGTAILM  190 (379)
Q Consensus       150 GiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G---~~g~~i~l  190 (379)
                      |+|+|.++.||.+++-.+..+.+|-+||.-|-.   +-|..|+-
T Consensus       541 GVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILP  584 (1518)
T COG4889         541 GVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILP  584 (1518)
T ss_pred             CCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEE
Confidence            999999999999999999999999999999943   23555543

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=96.69  E-value=0.0062  Score=65.71  Aligned_cols=119  Identities=21%  Similarity=0.333  Sum_probs=102.1

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccCCc---eeEEEeccc
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK---FTVLVATDV  146 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g~---~~iLVaTdv  146 (379)
                      ..|.++|.+++..+ ..+++++.||.-..-.+-+..+|. +.+.-.-+.|.....+|-..++.|....   ..+|.+|-.
T Consensus       709 sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~Fllstra  788 (1157)
T KOG0386|consen  709 SGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRA  788 (1157)
T ss_pred             ccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeecc
Confidence            57899999998766 457899999998888888888887 4788888999999999999999998754   457889999


Q ss_pred             cccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEE
Q 017020          147 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  190 (379)
Q Consensus       147 ~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l  190 (379)
                      .+.|+|+.-.+.||.||.-+++-...|+--|+.|.|..-.+-++
T Consensus       789 gglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~  832 (1157)
T KOG0386|consen  789 GGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVL  832 (1157)
T ss_pred             cccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeee
Confidence            99999999999999999999999999999999999955444333

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.52  E-value=0.11  Score=55.51  Aligned_cols=69  Identities=12%  Similarity=0.161  Sum_probs=47.0

Q ss_pred             HHHHhcccCCceeEEEecc----ccccCCCCCccceEEecC------CCC------ChhHHHHHHhhccCCCCCceEEEE
Q 017020          127 ERTLNGFRQGKFTVLVATD----VAARGLDIPNVDLIIHYE------LPN------DPETFVHRSGRTGRAGKEGTAILM  190 (379)
Q Consensus       127 ~~~~~~F~~g~~~iLVaTd----v~~rGiDip~v~~VI~~~------~P~------~~~~yiqR~GRtgR~G~~g~~i~l  190 (379)
                      +.+++.|. ++.+|||+|.    +++     ++++.|+..|      .|.      ....+.|-+||+||.++.|.+++.
T Consensus       462 d~~l~~~~-~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfRA~Er~~qll~qvagragr~~~~G~V~iq  535 (665)
T PRK14873        462 DQVVDTVD-AGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVV  535 (665)
T ss_pred             HHHHHhhc-cCCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcChHHHHHHHHHHHHHhhcCCCCCCEEEEE
Confidence            45778886 5899999998    555     3566665444      232      234457899999999999999988


Q ss_pred             eChhhHHHHHHH
Q 017020          191 FTSSQRRTVRSL  202 (379)
Q Consensus       191 ~~~~e~~~l~~l  202 (379)
                      ..+ +...++.+
T Consensus       536 ~~p-~~~~~~~l  546 (665)
T PRK14873        536 AES-SLPTVQAL  546 (665)
T ss_pred             eCC-CCHHHHHH
Confidence            644 43444443

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=96.47  E-value=0.012  Score=63.26  Aligned_cols=119  Identities=18%  Similarity=0.238  Sum_probs=98.2

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc----C--C-----------------cEEEeeCCCCHHHHH
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS----I--I-----------------ASEALHGDISQHQRE  127 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~----~--~-----------------~v~~lhg~m~~~~R~  127 (379)
                      ..|.-+|.++|... .-+.+.|||..+....+.+-.+|..    +  +                 .-.-|.|..+..+|+
T Consensus      1125 SgKmiLLleIL~mceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~ 1204 (1567)
T KOG1015|consen 1125 SGKMILLLEILRMCEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRK 1204 (1567)
T ss_pred             CcceehHHHHHHHHHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHH
Confidence            45777788888754 3478999999999999988888862    1  1                 134578899999999


Q ss_pred             HHHhcccCCc----eeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEE
Q 017020          128 RTLNGFRQGK----FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  190 (379)
Q Consensus       128 ~~~~~F~~g~----~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l  190 (379)
                      ++.+.|.+-.    .-.||+|-+.+-|||+-..+-||.||..++|..=.|-+=|+-|.|+.--||++
T Consensus      1205 k~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiY 1271 (1567)
T KOG1015|consen 1205 KWAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIY 1271 (1567)
T ss_pred             HHHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeeh
Confidence            9999998742    34899999999999999999999999999999999999999999977666654

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=96.32  E-value=0.015  Score=63.90  Aligned_cols=105  Identities=16%  Similarity=0.161  Sum_probs=73.3

Q ss_pred             EEEecccccHHHHHHHHhc-----C--CcEEEeeCCCCHHHHHHHHhcc----------------------cC----Cce
Q 017020           92 IVFTQTKRDADEVSLALTS-----I--IASEALHGDISQHQRERTLNGF----------------------RQ----GKF  138 (379)
Q Consensus        92 IIF~~t~~~~~~l~~~L~~-----~--~~v~~lhg~m~~~~R~~~~~~F----------------------~~----g~~  138 (379)
                      +|=.++.+.+-.++..|..     +  +..+++|+..+...|..+.+..                      ++    +..
T Consensus       760 liR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~  839 (1110)
T TIGR02562       760 LIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHL  839 (1110)
T ss_pred             EEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCCC
Confidence            6777888888888887752     2  4578899999887776655442                      11    456


Q ss_pred             eEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCC--ceEEEEeChhhHHHH
Q 017020          139 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE--GTAILMFTSSQRRTV  199 (379)
Q Consensus       139 ~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~--g~~i~l~~~~e~~~l  199 (379)
                      .|+|+|.+.+.|+|+ +.+++|  --|.+..+.+||.||+.|.|..  +..-+++-....+.+
T Consensus       840 ~i~v~Tqv~E~g~D~-dfd~~~--~~~~~~~sliQ~aGR~~R~~~~~~~~~N~~i~~~N~r~l  899 (1110)
T TIGR02562       840 FIVLATPVEEVGRDH-DYDWAI--ADPSSMRSIIQLAGRVNRHRLEKVQQPNIVILQWNYRYL  899 (1110)
T ss_pred             eEEEEeeeEEEEecc-cCCeee--eccCcHHHHHHHhhcccccccCCCCCCcEEEeHhHHHHh
Confidence            799999999999998 455554  3467899999999999998733  233333334444444

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.

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=96.05  E-value=0.15  Score=56.74  Aligned_cols=118  Identities=17%  Similarity=0.293  Sum_probs=86.6

Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHhc-----------------------CCcEEEeeCCCCHHHHHHHHhcccCC
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-----------------------IIASEALHGDISQHQRERTLNGFRQG  136 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----------------------~~~v~~lhg~m~~~~R~~~~~~F~~g  136 (379)
                      .+......+++++||+++++.|..++..+-.                       .++...=|-+|+.....-+-.-|..|
T Consensus      1351 ai~~~a~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g 1430 (1674)
T KOG0951|consen 1351 AIVRHAGNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAG 1430 (1674)
T ss_pred             HHHHHhcCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcC
Confidence            3334345578999999999999887754421                       01222238899999999999999999


Q ss_pred             ceeEEEeccccccCCCCCccceEE-----ecC------CCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHH
Q 017020          137 KFTVLVATDVAARGLDIPNVDLII-----HYE------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  202 (379)
Q Consensus       137 ~~~iLVaTdv~~rGiDip~v~~VI-----~~~------~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~l  202 (379)
                      .+.++|...- -.|+-... +.||     -||      .+.+.....|+.|++.|   .|.|+++.....+.++++.
T Consensus      1431 ~i~v~v~s~~-~~~~~~~~-~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~vi~~~~~~k~yykkf 1502 (1674)
T KOG0951|consen 1431 AIQVCVMSRD-CYGTKLKA-HLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AGKCVIMCHTPKKEYYKKF 1502 (1674)
T ss_pred             cEEEEEEEcc-cccccccc-eEEEEecceeecccccccccCchhHHHHHhhhhcC---CccEEEEecCchHHHHHHh
Confidence            9999987755 66665532 3343     233      46678999999999988   5789999999888887754

>PF13871 Helicase_C_4: Helicase_C-like

Probab=95.83  E-value=0.035  Score=52.70  Aligned_cols=78  Identities=21%  Similarity=0.370  Sum_probs=58.9

Q ss_pred             HHHhcccCCceeEEEeccccccCCCCCc--------cceEEecCCCCChhHHHHHHhhccCCCCC-ceEEEEeC---hhh
Q 017020          128 RTLNGFRQGKFTVLVATDVAARGLDIPN--------VDLIIHYELPNDPETFVHRSGRTGRAGKE-GTAILMFT---SSQ  195 (379)
Q Consensus       128 ~~~~~F~~g~~~iLVaTdv~~rGiDip~--------v~~VI~~~~P~~~~~yiqR~GRtgR~G~~-g~~i~l~~---~~e  195 (379)
                      ...+.|.+|+..|+|.|+.++.|+.+..        -.+-|...+|++.+..+|..||+.|.|+. .-.|.++.   +.|
T Consensus        52 ~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE  131 (278)
T PF13871_consen   52 AEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGE  131 (278)
T ss_pred             HHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHH
Confidence            4566899999999999999999998742        23456788999999999999999999853 44455443   346


Q ss_pred             HHHHHHHHHH
Q 017020          196 RRTVRSLERD  205 (379)
Q Consensus       196 ~~~l~~le~~  205 (379)
                      ++....+.+.
T Consensus       132 ~Rfas~va~r  141 (278)
T PF13871_consen  132 RRFASTVARR  141 (278)
T ss_pred             HHHHHHHHHH
Confidence            6655555544

>PRK05580 primosome assembly protein PriA; Validated

Probab=95.80  E-value=0.055  Score=58.11  Aligned_cols=91  Identities=21%  Similarity=0.269  Sum_probs=72.0

Q ss_pred             ccHHHHHHHHHH-HHcCCCcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccc
Q 017020           72 TSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  148 (379)
Q Consensus        72 ~~k~~~L~~ll~-~~~~~~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~  148 (379)
                      ..|..+...++. ....+.++||.+++++-+.++.+.+..  +..+..+||+++..+|.+...+..+|..+|+|+|..+.
T Consensus       173 SGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal  252 (679)
T PRK05580        173 SGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSAL  252 (679)
T ss_pred             ChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHh
Confidence            457666544443 334467899999999999999999975  56789999999999999999999999999999997543


Q ss_pred             cCCCCCccceEEecC
Q 017020          149 RGLDIPNVDLIIHYE  163 (379)
Q Consensus       149 rGiDip~v~~VI~~~  163 (379)
                      . +.+.++.+||--+
T Consensus       253 ~-~p~~~l~liVvDE  266 (679)
T PRK05580        253 F-LPFKNLGLIIVDE  266 (679)
T ss_pred             c-ccccCCCEEEEEC
Confidence            2 5677888877443

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.73  E-value=0.031  Score=60.05  Aligned_cols=90  Identities=17%  Similarity=0.268  Sum_probs=71.3

Q ss_pred             ccHHHH-HHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           72 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        72 ~~k~~~-L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ..|..+ +..++.....+.+++|.++|+.-|.+.+..+..     ++.+..+||+++..+|..+++...+|..+|+|+|.
T Consensus       293 SGKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~  372 (681)
T PRK10917        293 SGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTH  372 (681)
T ss_pred             CcHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchH
Confidence            455543 233344444577999999999999988887763     47899999999999999999999999999999997


Q ss_pred             c-cccCCCCCccceEEe
Q 017020          146 V-AARGLDIPNVDLIIH  161 (379)
Q Consensus       146 v-~~rGiDip~v~~VI~  161 (379)
                      . +...+.+.++.+||-
T Consensus       373 ~ll~~~v~~~~l~lvVI  389 (681)
T PRK10917        373 ALIQDDVEFHNLGLVII  389 (681)
T ss_pred             HHhcccchhcccceEEE
Confidence            4 444577888998873

>TIGR00595 priA primosomal protein N'

Probab=95.64  E-value=0.052  Score=56.22  Aligned_cols=89  Identities=20%  Similarity=0.259  Sum_probs=71.0

Q ss_pred             ccHHHHHHHHHH-HHcCCCcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccc
Q 017020           72 TSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  148 (379)
Q Consensus        72 ~~k~~~L~~ll~-~~~~~~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~  148 (379)
                      ..|.++...++. ....++++||.+++..-+.+++..|..  +..+..+||+++..+|.+...+..+|+.+|+|+|..+.
T Consensus         8 sGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsal   87 (505)
T TIGR00595         8 SGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSAL   87 (505)
T ss_pred             CCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHH
Confidence            456666554443 334567899999999999999999975  46788999999999999999999999999999997644


Q ss_pred             cCCCCCccceEEe
Q 017020          149 RGLDIPNVDLIIH  161 (379)
Q Consensus       149 rGiDip~v~~VI~  161 (379)
                      . ..++++.+||-
T Consensus        88 f-~p~~~l~lIIV   99 (505)
T TIGR00595        88 F-LPFKNLGLIIV   99 (505)
T ss_pred             c-CcccCCCEEEE
Confidence            3 45778887773

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).

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=95.44  E-value=0.039  Score=59.27  Aligned_cols=115  Identities=17%  Similarity=0.301  Sum_probs=91.8

Q ss_pred             CCcEEEEecccccHHHHHHHHhc--------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS--------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~--------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      .+.+++|.+.-...-.|...|..        .+....+|+.++..+..++.+....|..++++.|.++...+.+.++.+|
T Consensus       643 ~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~v  722 (1282)
T KOG0921|consen  643 DGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVYV  722 (1282)
T ss_pred             ccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeEE
Confidence            56889999998888888777642        3678899999999999999999999999999999999999999998888


Q ss_pred             EecCC------------------CCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHh
Q 017020          160 IHYEL------------------PNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  206 (379)
Q Consensus       160 I~~~~------------------P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~  206 (379)
                      |..+.                  -.+....+||.||+||. +.|.|..+++..   .+..+++..
T Consensus       723 id~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~lcs~a---rF~~l~~~~  783 (1282)
T KOG0921|consen  723 IDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFHLCSRA---RFEALEDHG  783 (1282)
T ss_pred             EeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccccccHHH---HHHHHHhcC
Confidence            75442                  12556679999999997 688998887764   344444443

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.17  E-value=0.056  Score=55.05  Aligned_cols=181  Identities=19%  Similarity=0.254  Sum_probs=114.9

Q ss_pred             CcEEEEeeeCChHHHHHHHHhcCCCc-eEEeecccc----cccccceEEEE--EEcCC-----ccHHHHHH-HHHHHHc-
Q 017020           21 RQSMLFSATMPSWVKKLSRKYLDNPL-NIDLVGNQD----EKLAEGIKLYA--ISTTA-----TSKRTILS-DLITVYA-   86 (379)
Q Consensus        21 ~Q~llfSAT~p~~i~~l~~~~l~~p~-~i~~~~~~~----~~~~~~i~~~~--~~~~~-----~~k~~~L~-~ll~~~~-   86 (379)
                      +|+++||+--.+.+..+...++.|-. .+.......    ......+.|.+  +.+..     ..+..... .++-.+. 
T Consensus       470 rQtl~Fs~y~~~~~nS~fn~~c~N~~Gkv~~~~~~~~gsi~~v~~~l~Qvf~ri~~~si~~~~D~RFkyFv~~ImPq~~k  549 (698)
T KOG2340|consen  470 RQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQSGGSISNVGIPLCQVFQRIEVKSIIETPDARFKYFVDKIMPQLIK  549 (698)
T ss_pred             HHHHHHHhhccHHHHHHHHHhhhhhcceeeeccccCCCchhhccchhhhhhhheeccCcccCchHHHHHHHHhhchhhcc
Confidence            69999999999999999988887642 222111000    11111122211  11111     12222211 1121121 


Q ss_pred             -CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecccc--ccCCCCCccceEEec
Q 017020           87 -KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA--ARGLDIPNVDLIIHY  162 (379)
Q Consensus        87 -~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~--~rGiDip~v~~VI~~  162 (379)
                       ...-++||.++--+--.+..++.. .+....+|---++..-.+.-+-|-.|...+|+-|.=+  -|--+|.+|..||.|
T Consensus       550 ~t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfY  629 (698)
T KOG2340|consen  550 RTESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFY  629 (698)
T ss_pred             cccCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEe
Confidence             124679999998888888888874 5555556655556666667777889999999999754  577889999999999


Q ss_pred             CCCCChhHH---HHHHhhccCCC----CCceEEEEeChhhHHHHHH
Q 017020          163 ELPNDPETF---VHRSGRTGRAG----KEGTAILMFTSSQRRTVRS  201 (379)
Q Consensus       163 ~~P~~~~~y---iqR~GRtgR~G----~~g~~i~l~~~~e~~~l~~  201 (379)
                      .+|..|.-|   +.+.+|+.-.|    ..-.|.++|+..+.-.|..
T Consensus       630 qpP~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~  675 (698)
T KOG2340|consen  630 QPPNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLEN  675 (698)
T ss_pred             cCCCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHH
Confidence            999998665   66777765433    3457888999887654443

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=94.78  E-value=0.92  Score=49.01  Aligned_cols=113  Identities=19%  Similarity=0.222  Sum_probs=77.3

Q ss_pred             HHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCC
Q 017020           74 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  152 (379)
Q Consensus        74 k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiD  152 (379)
                      .......++..+..+.++-||++|...++.+++.... ...+..++|.-+..+-    +.|  ++.+|++=|++...|++
T Consensus       268 ~~tF~~~L~~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv----~~W--~~~~VviYT~~itvG~S  341 (824)
T PF02399_consen  268 ETTFFSELLARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDV----ESW--KKYDVVIYTPVITVGLS  341 (824)
T ss_pred             hhhHHHHHHHHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCcccc----ccc--cceeEEEEeceEEEEec
Confidence            3345556666666678888999999999988888775 5677888887655522    223  56899999999999999


Q ss_pred             CCccc--eEEecCCC----CChhHHHHHHhhccCCCCCceEEEEeCh
Q 017020          153 IPNVD--LIIHYELP----NDPETFVHRSGRTGRAGKEGTAILMFTS  193 (379)
Q Consensus       153 ip~v~--~VI~~~~P----~~~~~yiqR~GRtgR~G~~g~~i~l~~~  193 (379)
                      +....  -+.-|=-|    .+..+..|++||.-.-. ....++.+++
T Consensus       342 f~~~HF~~~f~yvk~~~~gpd~~s~~Q~lgRvR~l~-~~ei~v~~d~  387 (824)
T PF02399_consen  342 FEEKHFDSMFAYVKPMSYGPDMVSVYQMLGRVRSLL-DNEIYVYIDA  387 (824)
T ss_pred             cchhhceEEEEEecCCCCCCcHHHHHHHHHHHHhhc-cCeEEEEEec
Confidence            96443  23333112    35567899999976554 4555555544

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=94.76  E-value=0.089  Score=56.06  Aligned_cols=89  Identities=17%  Similarity=0.282  Sum_probs=70.6

Q ss_pred             ccHHHH-HHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           72 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        72 ~~k~~~-L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ..|..+ +..++.....+.+++|-++|+.-|.+.+..+..     ++.+..+||+++..+|...++...+|+.+|+|+|.
T Consensus       267 SGKT~va~l~il~~~~~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~  346 (630)
T TIGR00643       267 SGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTH  346 (630)
T ss_pred             CcHHHHHHHHHHHHHHcCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecH
Confidence            455543 334444445577999999999999988877753     57899999999999999999999999999999997


Q ss_pred             cc-ccCCCCCccceEE
Q 017020          146 VA-ARGLDIPNVDLII  160 (379)
Q Consensus       146 v~-~rGiDip~v~~VI  160 (379)
                      .. ...+++.++.+||
T Consensus       347 ~ll~~~~~~~~l~lvV  362 (630)
T TIGR00643       347 ALIQEKVEFKRLALVI  362 (630)
T ss_pred             HHHhccccccccceEE
Confidence            54 3457778888877

>PRK14873 primosome assembly protein PriA; Provisional

Probab=94.75  E-value=0.11  Score=55.62  Aligned_cols=92  Identities=18%  Similarity=0.242  Sum_probs=74.4

Q ss_pred             CccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhcC---CcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc
Q 017020           71 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  146 (379)
Q Consensus        71 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~~---~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv  146 (379)
                      .+.|.++..+++... ..++++||-++....+..+...|...   ..+..+|+++++.+|.+...+..+|+.+|+|.|-.
T Consensus       170 GSGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRS  249 (665)
T PRK14873        170 GEDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRS  249 (665)
T ss_pred             CCcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcce
Confidence            346777777777543 45789999999999999999999863   45899999999999999999999999999999975


Q ss_pred             cccCCCCCccceEEecC
Q 017020          147 AARGLDIPNVDLIIHYE  163 (379)
Q Consensus       147 ~~rGiDip~v~~VI~~~  163 (379)
                      +. =.-+++..+||-.+
T Consensus       250 Av-FaP~~~LgLIIvdE  265 (665)
T PRK14873        250 AV-FAPVEDLGLVAIWD  265 (665)
T ss_pred             eE-EeccCCCCEEEEEc
Confidence            42 34566777777444

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=94.74  E-value=0.16  Score=43.36  Aligned_cols=46  Identities=22%  Similarity=0.302  Sum_probs=35.4

Q ss_pred             CCHHHHHHHHhcccCCc-eeEEEeccccccCCCCCcc--ceEEecCCCC
Q 017020          121 ISQHQRERTLNGFRQGK-FTVLVATDVAARGLDIPNV--DLIIHYELPN  166 (379)
Q Consensus       121 m~~~~R~~~~~~F~~g~-~~iLVaTdv~~rGiDip~v--~~VI~~~~P~  166 (379)
                      ....+...+++.|++.. ..||++|.-.++|+|+|+-  +.||..++|.
T Consensus        31 ~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492       31 EDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             CChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCC
Confidence            44445788888888654 3799999889999999874  5788777774

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=94.19  E-value=0.25  Score=52.08  Aligned_cols=118  Identities=16%  Similarity=0.266  Sum_probs=85.0

Q ss_pred             ccHHHHHHHHHHHH--cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccC--CceeE-EEecc
Q 017020           72 TSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ--GKFTV-LVATD  145 (379)
Q Consensus        72 ~~k~~~L~~ll~~~--~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~--g~~~i-LVaTd  145 (379)
                      .-|...+...+...  ....+++|...=.....-+...|.. +.....+||.....+|+.+++.|..  |..+| |++=.
T Consensus       728 S~Ki~~~l~~le~i~~~skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLt  807 (901)
T KOG4439|consen  728 SCKIAMVLEILETILTSSKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLT  807 (901)
T ss_pred             hhHHHHHHHHHHHHhhcccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEc
Confidence            34544444444332  2345555544333333444556654 6778899999999999999999964  43444 45556


Q ss_pred             ccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEE
Q 017020          146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL  189 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~  189 (379)
                      .-+.|+|+-+.+|+|..|+-+++.-=.|-+.|.-|.|++..+++
T Consensus       808 AGGVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V~I  851 (901)
T KOG4439|consen  808 AGGVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDVFI  851 (901)
T ss_pred             cCcceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCceEE
Confidence            77889999999999999999999999999999999997665544

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=94.15  E-value=0.18  Score=43.07  Aligned_cols=42  Identities=21%  Similarity=0.373  Sum_probs=31.3

Q ss_pred             HHHHHHhcccCCce---eEEEeccc--cccCCCCCc--cceEEecCCCC
Q 017020          125 QRERTLNGFRQGKF---TVLVATDV--AARGLDIPN--VDLIIHYELPN  166 (379)
Q Consensus       125 ~R~~~~~~F~~g~~---~iLVaTdv--~~rGiDip~--v~~VI~~~~P~  166 (379)
                      +...+++.|++...   .||+++.-  .++|||+|+  ++.||..++|.
T Consensus        32 ~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPf   80 (142)
T smart00491       32 ETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPF   80 (142)
T ss_pred             hHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCC
Confidence            34667777776433   58888876  999999987  46788888774

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

Probab=94.12  E-value=0.14  Score=54.89  Aligned_cols=91  Identities=23%  Similarity=0.283  Sum_probs=75.0

Q ss_pred             cCCccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           69 TTATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        69 ~~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      +..+.|.++...++... ..++++||-++....+..+...+..  +..+..+|+++++.+|.....+.++|+.+|+|.|-
T Consensus       225 vTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtR  304 (730)
T COG1198         225 VTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTR  304 (730)
T ss_pred             CCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEec
Confidence            44567888887777643 5678999999999999999999875  67899999999999999999999999999999996


Q ss_pred             ccccCCCCCccceEE
Q 017020          146 VAARGLDIPNVDLII  160 (379)
Q Consensus       146 v~~rGiDip~v~~VI  160 (379)
                      .| --.-+++..+||
T Consensus       305 SA-lF~Pf~~LGLII  318 (730)
T COG1198         305 SA-LFLPFKNLGLII  318 (730)
T ss_pred             hh-hcCchhhccEEE
Confidence            53 234456777666

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=93.98  E-value=0.025  Score=64.73  Aligned_cols=94  Identities=21%  Similarity=0.379  Sum_probs=77.5

Q ss_pred             CcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCC-----------HHHHHHHHhcccCCceeEEEeccccccCCCCCc
Q 017020           89 GKTIVFTQTKRDADEVSLALTS--IIASEALHGDIS-----------QHQRERTLNGFRQGKFTVLVATDVAARGLDIPN  155 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~-----------~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~  155 (379)
                      -..|+||+-+..+..+.+.+..  ...+..+-|.+.           +..++.++..|+....++|++|.++..|+|++.
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~  372 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPK  372 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhh
Confidence            3569999999999888888764  334444544432           223678999999999999999999999999999


Q ss_pred             cceEEecCCCCChhHHHHHHhhccCCC
Q 017020          156 VDLIIHYELPNDPETFVHRSGRTGRAG  182 (379)
Q Consensus       156 v~~VI~~~~P~~~~~yiqR~GRtgR~G  182 (379)
                      ++.|+.++.|....+|+|+.||+-+++
T Consensus       373 ~~~~~~~~~~~~~~~~vq~~~r~~~~~  399 (1606)
T KOG0701|consen  373 CNLVVLFDAPTYYRSYVQKKGRARAAD  399 (1606)
T ss_pred             hhhheeccCcchHHHHHHhhcccccch
Confidence            999999999999999999999977654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=93.96  E-value=0.15  Score=56.55  Aligned_cols=90  Identities=17%  Similarity=0.225  Sum_probs=70.3

Q ss_pred             ccHHHHHH-HHHHHHcCCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           72 TSKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        72 ~~k~~~L~-~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ..|..+.. .++.....+.+++|.++|+.-|.+.+..+..     ++.+..++|..+..++.++++.+++|+.+|+|+|.
T Consensus       483 sGKT~val~a~l~al~~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp  562 (926)
T TIGR00580       483 FGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTH  562 (926)
T ss_pred             ccHHHHHHHHHHHHHHhCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchH
Confidence            45665432 3334444568999999999999998887763     35678899999999999999999999999999997


Q ss_pred             -ccccCCCCCccceEEe
Q 017020          146 -VAARGLDIPNVDLIIH  161 (379)
Q Consensus       146 -v~~rGiDip~v~~VI~  161 (379)
                       .+...+.+.++.+||-
T Consensus       563 ~ll~~~v~f~~L~llVI  579 (926)
T TIGR00580       563 KLLQKDVKFKDLGLLII  579 (926)
T ss_pred             HHhhCCCCcccCCEEEe
Confidence             4455678888888773

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.

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=91.93  E-value=0.23  Score=54.45  Aligned_cols=61  Identities=20%  Similarity=0.327  Sum_probs=51.7

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-----C-CcEEE-eeCCCCHHHHHHHHhcccCCceeEEEecccc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-----I-IASEA-LHGDISQHQRERTLNGFRQGKFTVLVATDVA  147 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-----~-~~v~~-lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~  147 (379)
                      .++++++.++|..-+.+.++.|..     + +.+.. +||.|+.++++..+++|.+|..+|||+|...
T Consensus       124 kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~F  191 (1187)
T COG1110         124 KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQF  191 (1187)
T ss_pred             cCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHH
Confidence            468999999999999988888863     2 33333 9999999999999999999999999999753

>PRK10689 transcription-repair coupling factor; Provisional

Probab=91.93  E-value=0.44  Score=54.11  Aligned_cols=89  Identities=16%  Similarity=0.164  Sum_probs=68.1

Q ss_pred             ccHHHHHHH-HHHHHcCCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           72 TSKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        72 ~~k~~~L~~-ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ..|..+... .......+.+++|-++|+.-|.+.+..+..     ++.+..++|..+..++..+++..++|..+|+|+|.
T Consensus       632 sGKT~val~aa~~~~~~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp  711 (1147)
T PRK10689        632 FGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTH  711 (1147)
T ss_pred             cCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECH
Confidence            467653321 122223578999999999999999888763     35678899999999999999999999999999996


Q ss_pred             -ccccCCCCCccceEE
Q 017020          146 -VAARGLDIPNVDLII  160 (379)
Q Consensus       146 -v~~rGiDip~v~~VI  160 (379)
                       .+...+++.++.++|
T Consensus       712 ~lL~~~v~~~~L~lLV  727 (1147)
T PRK10689        712 KLLQSDVKWKDLGLLI  727 (1147)
T ss_pred             HHHhCCCCHhhCCEEE
Confidence             444456777888776

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

Probab=91.53  E-value=0.65  Score=48.29  Aligned_cols=66  Identities=23%  Similarity=0.422  Sum_probs=54.3

Q ss_pred             EEEEecccccHHHHHHHHhc------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc-----ccccC-CCCCccce
Q 017020           91 TIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNVDL  158 (379)
Q Consensus        91 ~IIF~~t~~~~~~l~~~L~~------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd-----v~~rG-iDip~v~~  158 (379)
                      +||.++|++-|.++++.+..      ++.+..++|+++...+...++.   | .+|+|||+     .+.+| +|+..+.+
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~---~-~~ivVaTPGRllD~i~~~~l~l~~v~~  177 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKR---G-VDIVVATPGRLLDLIKRGKLDLSGVET  177 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhc---C-CCEEEECccHHHHHHHcCCcchhhcCE
Confidence            99999999999999888762      4668999999998777655554   6 89999997     46666 88889998


Q ss_pred             EE
Q 017020          159 II  160 (379)
Q Consensus       159 VI  160 (379)
                      +|
T Consensus       178 lV  179 (513)
T COG0513         178 LV  179 (513)
T ss_pred             EE
Confidence            77

>PRK14701 reverse gyrase; Provisional

Probab=89.19  E-value=1.5  Score=51.71  Aligned_cols=60  Identities=22%  Similarity=0.316  Sum_probs=52.4

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  146 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv  146 (379)
                      ++.++||.++|+.-+.+++..+..       +..+..+||+++..++..+++.+++|..+|||+|+-
T Consensus       121 ~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        121 KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            456899999999999988888763       346788999999999999999999999999999984

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=88.77  E-value=0.57  Score=48.20  Aligned_cols=52  Identities=27%  Similarity=0.387  Sum_probs=46.5

Q ss_pred             cEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           90 KTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        90 ~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      -+|||++|++-|..+...|..     ++.+..+.|||+...+++++++    ...|+|||+
T Consensus       265 ~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATP  321 (731)
T KOG0347|consen  265 IALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATP  321 (731)
T ss_pred             eeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc----CCCEEEecc
Confidence            489999999999999998862     6889999999999999999987    457999998

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases

Probab=88.20  E-value=3.9  Score=38.11  Aligned_cols=104  Identities=14%  Similarity=0.201  Sum_probs=74.3

Q ss_pred             ecccccHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCc----eeEEEeccccccCCCCCccceEEecCCCC
Q 017020           95 TQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGK----FTVLVATDVAARGLDIPNVDLIIHYELPN  166 (379)
Q Consensus        95 ~~t~~~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~----~~iLVaTdv~~rGiDip~v~~VI~~~~P~  166 (379)
                      +.....-+++...|..    ++.+..++|+.+...     -.+.++.    ..|+|.=+.++||+.+++........-|.
T Consensus        90 ~~~~~s~~ei~~~l~~~~~~~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~  164 (239)
T PF10593_consen   90 DPDPPSWEEIKPELPKAISDGIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSK  164 (239)
T ss_pred             cCCCcCHHHHHHHHHHHHhcCceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCc
Confidence            3444555566665542    378888887765433     3455443    88999999999999999999988888899


Q ss_pred             ChhHHHHHHhhcc-CCCCCceEEEEeChhhHHHHHHHH
Q 017020          167 DPETFVHRSGRTG-RAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       167 ~~~~yiqR~GRtg-R~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                      ..+++.||.=--| |.|-.+.|-++.++.-...+..+.
T Consensus       165 ~~DTL~QmgRwFGYR~gY~dl~Ri~~~~~l~~~f~~i~  202 (239)
T PF10593_consen  165 QYDTLMQMGRWFGYRPGYEDLCRIYMPEELYDWFRHIA  202 (239)
T ss_pred             hHHHHHHHhhcccCCcccccceEEecCHHHHHHHHHHH
Confidence            9999999954444 455567788888776665555553

This domain is found associated with a helicase domain of superfamily type II [].

>TIGR01054 rgy reverse gyrase

Probab=87.78  E-value=2.1  Score=48.94  Aligned_cols=60  Identities=18%  Similarity=0.343  Sum_probs=50.4

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-----CCc---EEEeeCCCCHHHHHHHHhcccCCceeEEEeccc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-----IIA---SEALHGDISQHQRERTLNGFRQGKFTVLVATDV  146 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-----~~~---v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv  146 (379)
                      .+.+++|.++|+.-|.+++..+..     ++.   +..+||+++..++...++.+.+|..+|+|+|+-
T Consensus       120 ~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~  187 (1171)
T TIGR01054       120 KGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTM  187 (1171)
T ss_pred             cCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHH
Confidence            367899999999999998887763     233   335899999999999999999999999999984

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.

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=86.16  E-value=3.6  Score=42.57  Aligned_cols=89  Identities=20%  Similarity=0.333  Sum_probs=67.6

Q ss_pred             CCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc-----ccccC-CCCCcc
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNV  156 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd-----v~~rG-iDip~v  156 (379)
                      +..+||-++|++-|..+......     .+.+.+++|+.+...+..-++   +| +.|+|||+     .+..| +|+..+
T Consensus       165 ~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~---~g-vdiviaTPGRl~d~le~g~~~l~~v  240 (519)
T KOG0331|consen  165 GPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLE---RG-VDVVIATPGRLIDLLEEGSLNLSRV  240 (519)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHh---cC-CcEEEeCChHHHHHHHcCCccccce
Confidence            45699999999999988877652     355899999999877665554   23 68999996     45666 688899


Q ss_pred             ceEE--------ecCCCCChhHHHHHHhhccC
Q 017020          157 DLII--------HYELPNDPETFVHRSGRTGR  180 (379)
Q Consensus       157 ~~VI--------~~~~P~~~~~yiqR~GRtgR  180 (379)
                      +++|        ..++-.++...++.++|+-|
T Consensus       241 ~ylVLDEADrMldmGFe~qI~~Il~~i~~~~r  272 (519)
T KOG0331|consen  241 TYLVLDEADRMLDMGFEPQIRKILSQIPRPDR  272 (519)
T ss_pred             eEEEeccHHhhhccccHHHHHHHHHhcCCCcc
Confidence            9888        34455577888888888777

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=85.49  E-value=6.2  Score=40.57  Aligned_cols=67  Identities=16%  Similarity=0.245  Sum_probs=51.3

Q ss_pred             cEEEEecccccHHHHHHHHh---c--CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc------ccccCCCCCccce
Q 017020           90 KTIVFTQTKRDADEVSLALT---S--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVDL  158 (379)
Q Consensus        90 ~~IIF~~t~~~~~~l~~~L~---~--~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd------v~~rGiDip~v~~  158 (379)
                      -.+|.|+|++-|..+...-.   +  ++.+.++||+++.-++..-++    -...++|||+      +--.++|+..+++
T Consensus       298 i~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTPgRlid~VkmKatn~~rvS~  373 (731)
T KOG0339|consen  298 IGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK----EGAEIVVATPGRLIDMVKMKATNLSRVSY  373 (731)
T ss_pred             eEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh----cCCeEEEechHHHHHHHHhhcccceeeeE
Confidence            45777899988877765443   3  578999999999988877776    3357999998      4456888999987


Q ss_pred             EE
Q 017020          159 II  160 (379)
Q Consensus       159 VI  160 (379)
                      .|
T Consensus       374 LV  375 (731)
T KOG0339|consen  374 LV  375 (731)
T ss_pred             EE
Confidence            66

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=85.23  E-value=3.1  Score=42.39  Aligned_cols=69  Identities=19%  Similarity=0.253  Sum_probs=52.4

Q ss_pred             CcEEEEecccccHHHHHHHHhc------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc-----ccc-cCCCCCcc
Q 017020           89 GKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAA-RGLDIPNV  156 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~~------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd-----v~~-rGiDip~v  156 (379)
                      .++||.|+|++-+.++++.+..      ++.+..++|+.+...+...+.    ...+|+|+|+     .+. ..+++.++
T Consensus        73 ~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~----~~~~IvV~Tp~rl~~~l~~~~~~l~~l  148 (460)
T PRK11776         73 VQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE----HGAHIIVGTPGRILDHLRKGTLDLDAL  148 (460)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc----CCCCEEEEChHHHHHHHHcCCccHHHC
Confidence            4799999999999988877652      467888999998876655444    4578999995     333 35788888


Q ss_pred             ceEEe
Q 017020          157 DLIIH  161 (379)
Q Consensus       157 ~~VI~  161 (379)
                      ++||.
T Consensus       149 ~~lVi  153 (460)
T PRK11776        149 NTLVL  153 (460)
T ss_pred             CEEEE
Confidence            88873

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

Probab=85.08  E-value=3.5  Score=43.72  Aligned_cols=85  Identities=19%  Similarity=0.294  Sum_probs=68.5

Q ss_pred             HHHHHHHHHcCCCcEEEEecccccHHHHHHHHh----c-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc-cccC
Q 017020           77 ILSDLITVYAKGGKTIVFTQTKRDADEVSLALT----S-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-AARG  150 (379)
Q Consensus        77 ~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~----~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv-~~rG  150 (379)
                      ++...+..+..+.++..-.+|---|+.-+..+.    . ++.+..+.|.+...+|.+++++..+|+++++|.|-. +-..
T Consensus       300 A~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~  379 (677)
T COG1200         300 ALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDK  379 (677)
T ss_pred             HHHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcc
Confidence            344455556668899999999766665555544    3 688999999999999999999999999999999975 5667


Q ss_pred             CCCCccceEEe
Q 017020          151 LDIPNVDLIIH  161 (379)
Q Consensus       151 iDip~v~~VI~  161 (379)
                      +++.+.-+||-
T Consensus       380 V~F~~LgLVIi  390 (677)
T COG1200         380 VEFHNLGLVII  390 (677)
T ss_pred             eeecceeEEEE
Confidence            88888888774

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=84.83  E-value=2.5  Score=43.33  Aligned_cols=60  Identities=23%  Similarity=0.321  Sum_probs=52.9

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  146 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv  146 (379)
                      .++.+||.+++++-+......|.. ++.+..++|+.+..++..++.....|..+++++|+-
T Consensus        50 ~~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe  110 (470)
T TIGR00614        50 SDGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPE  110 (470)
T ss_pred             cCCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHH
Confidence            467899999999988877777764 889999999999999999999999999999999974

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

>cd00268 DEADc DEAD-box helicases

Probab=84.28  E-value=5.3  Score=35.40  Aligned_cols=69  Identities=22%  Similarity=0.325  Sum_probs=49.4

Q ss_pred             CCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc-----cccC-CCCCcc
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----AARG-LDIPNV  156 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv-----~~rG-iDip~v  156 (379)
                      +.++||.|+++.-+.+.+..+..     +..+..+||+.+..+....+.    +...|+|+|.-     +..+ .+++++
T Consensus        69 ~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~iiv~T~~~l~~~l~~~~~~~~~l  144 (203)
T cd00268          69 GPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK----RGPHIVVATPGRLLDLLERGKLDLSKV  144 (203)
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhc----CCCCEEEEChHHHHHHHHcCCCChhhC
Confidence            45899999999998887776642     467788999998876654443    56789999952     2222 456677


Q ss_pred             ceEE
Q 017020          157 DLII  160 (379)
Q Consensus       157 ~~VI  160 (379)
                      +++|
T Consensus       145 ~~lI  148 (203)
T cd00268         145 KYLV  148 (203)
T ss_pred             CEEE
Confidence            7766

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=82.85  E-value=3.9  Score=43.70  Aligned_cols=69  Identities=25%  Similarity=0.290  Sum_probs=51.4

Q ss_pred             CCcEEEEecccccHHHHHHHHhc------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc-----ccccC-CCCCc
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPN  155 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd-----v~~rG-iDip~  155 (379)
                      ..++||.|+|++-|.+++..+..      ++.+..+||+.+...+...+.    ....|+|+|+     .+.++ +++.+
T Consensus        74 ~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~----~~~~IVVgTPgrl~d~l~r~~l~l~~  149 (629)
T PRK11634         74 APQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALR----QGPQIVVGTPGRLLDHLKRGTLDLSK  149 (629)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhc----CCCCEEEECHHHHHHHHHcCCcchhh
Confidence            45799999999999988877652      567889999988766554442    3468999995     33444 67888


Q ss_pred             cceEE
Q 017020          156 VDLII  160 (379)
Q Consensus       156 v~~VI  160 (379)
                      +.+||
T Consensus       150 l~~lV  154 (629)
T PRK11634        150 LSGLV  154 (629)
T ss_pred             ceEEE
Confidence            88777

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=81.51  E-value=3  Score=35.84  Aligned_cols=46  Identities=37%  Similarity=0.636  Sum_probs=40.0

Q ss_pred             ChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEe
Q 017020            5 GFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL   50 (379)
Q Consensus         5 GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~   50 (379)
                      .+.+.+..++..++...+.+++|||.++.....+..++.+...+..
T Consensus       145 ~~~~~~~~~~~~~~~~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~  190 (201)
T smart00487      145 GFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDV  190 (201)
T ss_pred             CcHHHHHHHHHhCCccceEEEEecCCchhHHHHHHHhcCCCEEEeC
Confidence            6778889999999889999999999999999999999887766654

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=80.93  E-value=6  Score=41.81  Aligned_cols=60  Identities=15%  Similarity=0.183  Sum_probs=52.1

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  146 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv  146 (379)
                      .++.++|.++++.-+......|.. ++.+..+||+++..++..++.....|..+++++|+-
T Consensus        52 ~~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe  112 (591)
T TIGR01389        52 LKGLTVVISPLISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPE  112 (591)
T ss_pred             cCCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChh
Confidence            357899999999888777777764 889999999999999999999999999999998864

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.

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=80.60  E-value=5.6  Score=42.87  Aligned_cols=103  Identities=21%  Similarity=0.327  Sum_probs=81.3

Q ss_pred             CCcEEEEecccccHHHHHHHHhc-CC------------------cEEEeeCCCCHHHHHHHHhcccCC---ceeEEEecc
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS-II------------------ASEALHGDISQHQRERTLNGFRQG---KFTVLVATD  145 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~-~~------------------~v~~lhg~m~~~~R~~~~~~F~~g---~~~iLVaTd  145 (379)
                      +.++|||.......+.+.+.|.. .+                  .-.-+.|-.+..+|++.+++|.+.   ..-+|++|-
T Consensus       719 g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllstr  798 (1387)
T KOG1016|consen  719 GEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLSTR  798 (1387)
T ss_pred             CceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehhc
Confidence            56888998888777777777653 11                  123467888899999999999863   235788899


Q ss_pred             ccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEE
Q 017020          146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  190 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l  190 (379)
                      ...-||++-..+-+|.||.-+++.--.|.+-|.-|.|+...|+++
T Consensus       799 ag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvY  843 (1387)
T KOG1016|consen  799 AGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVY  843 (1387)
T ss_pred             cccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEE
Confidence            999999998888888899888888888888899999977777665

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=80.16  E-value=4.9  Score=40.58  Aligned_cols=69  Identities=16%  Similarity=0.232  Sum_probs=51.9

Q ss_pred             CcEEEEecccccHHHHHHHHh---c--CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc------cccCCCCCccc
Q 017020           89 GKTIVFTQTKRDADEVSLALT---S--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV------AARGLDIPNVD  157 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~---~--~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv------~~rGiDip~v~  157 (379)
                      .++||.++|++-+..+++.+.   .  ++.+..++|+.+...+...+.    +..+|+|+|+-      ....++..+++
T Consensus        74 ~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~----~~~~IlV~Tp~rl~~~~~~~~~~~~~v~  149 (434)
T PRK11192         74 PRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFS----ENQDIVVATPGRLLQYIKEENFDCRAVE  149 (434)
T ss_pred             ceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhc----CCCCEEEEChHHHHHHHHcCCcCcccCC
Confidence            579999999998888777654   2  578899999998877765553    45689999972      23456778888


Q ss_pred             eEEe
Q 017020          158 LIIH  161 (379)
Q Consensus       158 ~VI~  161 (379)
                      +||.
T Consensus       150 ~lVi  153 (434)
T PRK11192        150 TLIL  153 (434)
T ss_pred             EEEE
Confidence            7773

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=80.10  E-value=12  Score=37.26  Aligned_cols=131  Identities=17%  Similarity=0.212  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecccc--
Q 017020           75 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA--  147 (379)
Q Consensus        75 ~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~--  147 (379)
                      +.+|..++... ....++|.++|++-|..+++.++.     ++.+..+-|||.-...  .+..++  +..|||||+-.  
T Consensus       117 LPIl~~LL~~p-~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q--~~~L~k--kPhilVaTPGrL~  191 (476)
T KOG0330|consen  117 LPILQRLLQEP-KLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQ--ANQLSK--KPHILVATPGRLW  191 (476)
T ss_pred             HHHHHHHHcCC-CCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHH--HHHhhc--CCCEEEeCcHHHH
Confidence            34556666532 346899999999999998887762     5789999999875543  344443  45689999842  


Q ss_pred             -----ccCCCCCccceEE--------ecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeC
Q 017020          148 -----ARGLDIPNVDLII--------HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       148 -----~rGiDip~v~~VI--------~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~  214 (379)
                           ..|..+..+.+.|        +-|+-... +|+-++=..+      .-.++++..--..+++|++..-..+..+.
T Consensus       192 dhl~~Tkgf~le~lk~LVlDEADrlLd~dF~~~l-d~ILk~ip~e------rqt~LfsATMt~kv~kL~rasl~~p~~v~  264 (476)
T KOG0330|consen  192 DHLENTKGFSLEQLKFLVLDEADRLLDMDFEEEL-DYILKVIPRE------RQTFLFSATMTKKVRKLQRASLDNPVKVA  264 (476)
T ss_pred             HHHHhccCccHHHhHHHhhchHHhhhhhhhHHHH-HHHHHhcCcc------ceEEEEEeecchhhHHHHhhccCCCeEEe
Confidence                 5777877777665        23332222 3333332322      22333443334455666655544454444


Q ss_pred             CCC
Q 017020          215 PPV  217 (379)
Q Consensus       215 ~p~  217 (379)
                      .+.
T Consensus       265 ~s~  267 (476)
T KOG0330|consen  265 VSS  267 (476)
T ss_pred             ccc
Confidence            444

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=80.06  E-value=4  Score=43.08  Aligned_cols=68  Identities=10%  Similarity=0.199  Sum_probs=51.0

Q ss_pred             CcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc-----cccc--CCCCCcc
Q 017020           89 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR--GLDIPNV  156 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd-----v~~r--GiDip~v  156 (379)
                      .++||.++|++-|.+++..+..     ++.+..+||+.+...+...+.    +..+|+|+|+     .+..  .+++..+
T Consensus        85 ~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~----~~~dIiV~TP~rL~~~l~~~~~~~l~~v  160 (572)
T PRK04537         85 PRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQ----QGVDVIIATPGRLIDYVKQHKVVSLHAC  160 (572)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHh----CCCCEEEECHHHHHHHHHhccccchhhe
Confidence            5899999999999988887653     467899999998877665553    3568999996     2322  3667777


Q ss_pred             ceEE
Q 017020          157 DLII  160 (379)
Q Consensus       157 ~~VI  160 (379)
                      ++||
T Consensus       161 ~~lV  164 (572)
T PRK04537        161 EICV  164 (572)
T ss_pred             eeeE
Confidence            7666

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	379
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		6e-37
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		4e-34
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-33
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		5e-32
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		7e-32
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-31
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-31
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-31
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-31
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		6e-31
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		8e-30
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		7e-26
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		9e-25
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-24
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		5e-24
2jgn_A	185	Ddx3 Helicase Domain Length = 185		7e-24
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		1e-23
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		1e-23
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		2e-23
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		1e-22
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-21
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		4e-21
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		3e-20
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		3e-20
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		4e-20
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		8e-20
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-19
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-19
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-19
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-19
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		2e-19
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		3e-19
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		3e-18
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		3e-18
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		4e-18
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		1e-17
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		7e-16
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		9e-16
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		2e-15
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		2e-15
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		2e-15
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		3e-15
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		4e-13
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		2e-12
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		2e-12
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		9e-12
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		4e-09
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		2e-08
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		3e-08
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		5e-08
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		9e-07
2eyq_A	1151	Crystal Structure Of Escherichia Coli Transcription		5e-06
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		6e-06
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		9e-06
2fwr_A	472	Structure Of Archaeoglobus Fulgidis Xpb Length = 47		1e-05
2fzl_A	219	Structure Of C-Terminal Domain Of Archaeoglobus Ful		1e-05
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		4e-05
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		5e-05
1d9z_A	657	Crystal Structure Of The Dna Repair Protein Uvrb In		1e-04
1d9x_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Le		1e-04
2fdc_A	658	Structural Basis Of Dna Damage Recognition And Proc		1e-04
4i1s_A	243	Melanoma Differentiation Associated Protein-5 Helic		1e-04
1t5l_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Po		2e-04
3v4r_A	667	Crystal Structure Of A Uvrb Dimer-Dna Complex Lengt		2e-04
2d7d_A	661	Structural Insights Into The Cryptic Dna Dependent		2e-04
3uwx_B	683	Crystal Structure Of Uvra-Uvrb Complex Length = 683		2e-04
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		3e-04
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		3e-04
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-04
2p6r_A	702	Crystal Structure Of Superfamily 2 Helicase Hel308		4e-04
1d2m_A	665	Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleot		4e-04
1c4o_A	664	Crystal Structure Of The Dna Nucleotide Excision Re		4e-04
3ly5_A	262	Ddx18 Dead-Domain Length = 262		4e-04

>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 =  151 bits (382), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 112/281 (39%), Positives = 162/281 (57%), Gaps = 16/281 (5%)
Query: 66  AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 124
           A+      +  +LSDL+ V A   + +VFT+TK + +E++  L  +   ++ALHGD+SQ 
Sbjct: 7   AVPAPVRGRLEVLSDLLYV-ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQG 65
Query: 125 QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 184
           +RER +  FRQG+  VLVATDVAARGLDIP VDL++HY +P+  E + HRSGRTGRAG+ 
Sbjct: 66  ERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRG 125
Query: 185 GTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFF 244
           G  +L++   +RR V +LER VG +F+ V+PP  E+VLE+    ++A L  V  +    +
Sbjct: 126 GRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLY 185
Query: 245 TPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVT-------LQLTRDSAF 297
              A RL  E   + +AA LA L G +   + RSL+  E+GW T       L L R  A 
Sbjct: 186 QDFAGRLFAEGRVEVVAALLALLLGGAP--AERSLLTGEEGWRTYKATGPRLSLPRLVAL 243
Query: 298 SRG-----FMSARSVMGFLSDVYPTAADEIGKIHIIADDRV 333
            +G        A +  GF  D+ P A  E+  + +    RV
Sbjct: 244 LKGQGLEVGKVAEAEGGFYVDLRPEARPEVAGLRLEPARRV 284

>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 =  142 bits (357), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 87/190 (45%), Positives = 123/190 (64%), Gaps = 2/190 (1%)
Query: 66  AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 124
           A+      +  +LSDL+ V A   + +VFT+TK + +E++  L  +   ++ALHGD+SQ 
Sbjct: 10  AVPAPVRGRLEVLSDLLYV-ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQG 68
Query: 125 QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 184
           +RER L  FRQG+  VLVATDVAARGLDIP VDL++HY LP+  E + HRSGRTGRAG+ 
Sbjct: 69  ERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRG 128
Query: 185 GTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFF 244
           G  +L++   +RR V +LER VG +F+ V+PP  E+VLE+    ++A L  V  +    +
Sbjct: 129 GRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLY 188
Query: 245 TPTAQRLIEE 254
              A RL  E
Sbjct: 189 QDFAGRLFAE 198

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

Iteration: 1
 Score =  139 bits (350), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 82/199 (41%), Positives = 115/199 (57%), Gaps = 11/199 (5%)
Query: 1   MLAVGFEEDVELILEN--LPPK--RQSMLFSATMPSWVKKLSRKYLDNP--LNIDLVGNQ 54
           ML +GFE  +  I+E   +PPK  R +M+FSAT P  ++ L+R +LD    L +  VG+ 
Sbjct: 187 MLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGST 246
Query: 55  DEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIA 113
            E + + +    +    + KR+ L DL+    K   T+VF +TK+ AD +         A
Sbjct: 247 SENITQKV----VWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYA 302
Query: 114 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH 173
             ++HGD SQ  RE  L+ FR GK  +LVAT VAARGLDI NV  +I+++LP+D E +VH
Sbjct: 303 CTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVH 362
Query: 174 RSGRTGRAGKEGTAILMFT 192
           R GRTGR G  G A   F 
Sbjct: 363 RIGRTGRVGNLGLATSFFN 381

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

Iteration: 1
 Score =  135 bits (339), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 77/225 (34%), Positives = 126/225 (56%), Gaps = 5/225 (2%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML  GF+E +  +   LPP  Q +L SAT+P  + +++ K++ +P+ I  +  +DE   E
Sbjct: 170 MLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLE 227
Query: 61  GIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GIK + ++      K   L DL        + ++F  TKR  D ++  +        ++H
Sbjct: 228 GIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMH 286
Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+
Sbjct: 287 GDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 346
Query: 179 GRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLE 223
           GR G++G AI    +   R +R +E+    + + +   V + +LE
Sbjct: 347 GRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE 391

>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 =  134 bits (338), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 77/225 (34%), Positives = 126/225 (56%), Gaps = 5/225 (2%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML  GF+E +  +   LPP  Q +L SAT+P  + +++ K++ +P+ I  +  +DE   E
Sbjct: 192 MLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLE 249
Query: 61  GIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GIK + ++      K   L DL        + ++F  TKR  D ++  +        ++H
Sbjct: 250 GIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMH 308
Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+
Sbjct: 309 GDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 368
Query: 179 GRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLE 223
           GR G++G AI    +   R +R +E+    + + +   V + +LE
Sbjct: 369 GRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE 413

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

Iteration: 1
 Score =  134 bits (336), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 74/206 (35%), Positives = 118/206 (57%), Gaps = 5/206 (2%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML  GF+E +  +   LPP  Q +L SAT+P  V +++ K++ +P+ I  +  +DE   E
Sbjct: 155 MLNKGFKEQIYDVYRYLPPATQVVLISATLPHEVLEMTNKFMTDPIRI--LVKRDELTLE 212
Query: 61  GIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GIK + ++      K   L DL        + ++F  TKR  D ++  +        ++H
Sbjct: 213 GIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMH 271
Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+
Sbjct: 272 GDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 331
Query: 179 GRAGKEGTAILMFTSSQRRTVRSLER 204
           GR G++G A+    +   R +R +E+
Sbjct: 332 GRYGRKGVAVNFVKNDDIRVLRDIEQ 357

>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 =  134 bits (336), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 74/206 (35%), Positives = 118/206 (57%), Gaps = 5/206 (2%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML  GF+E +  +   LPP  Q +L SAT+P  + +++ K++ +P+ I  +  +DE   E
Sbjct: 192 MLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLE 249
Query: 61  GIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GIK + ++      K   L DL        + ++F  TKR  D ++  +        ++H
Sbjct: 250 GIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMH 308
Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+
Sbjct: 309 GDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 368
Query: 179 GRAGKEGTAILMFTSSQRRTVRSLER 204
           GR G++G AI    +   R +R +E+
Sbjct: 369 GRYGRKGVAINFVKNDDIRILRDIEQ 394

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

Iteration: 1
 Score =  134 bits (336), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 73/206 (35%), Positives = 118/206 (57%), Gaps = 5/206 (2%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML  GF+E +  +   LPP  Q +L SAT+P  + +++ K++ +P+ I  +  +DE   E
Sbjct: 155 MLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLE 212
Query: 61  GIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GIK + ++      K   L DL        + ++F  TKR  D ++  +        ++H
Sbjct: 213 GIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMH 271
Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+
Sbjct: 272 GDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 331
Query: 179 GRAGKEGTAILMFTSSQRRTVRSLER 204
           GR G++G A+    +   R +R +E+
Sbjct: 332 GRYGRKGVAVNFVKNDDIRVLRDIEQ 357

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

Iteration: 1
 Score =  133 bits (335), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 74/206 (35%), Positives = 118/206 (57%), Gaps = 5/206 (2%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML  GF+E +  +   LPP  Q +L SAT+P  + +++ K++ +P+ I  +  +DE   E
Sbjct: 191 MLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLE 248
Query: 61  GIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GIK + ++      K   L DL        + ++F  TKR  D ++  +        ++H
Sbjct: 249 GIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMH 307
Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+
Sbjct: 308 GDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 367
Query: 179 GRAGKEGTAILMFTSSQRRTVRSLER 204
           GR G++G AI    +   R +R +E+
Sbjct: 368 GRYGRKGVAINFVKNDDIRILRDIEQ 393

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

Iteration: 1
 Score =  131 bits (329), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 74/204 (36%), Positives = 116/204 (56%), Gaps = 9/204 (4%)
Query: 2   LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEG 61
           L  GF +DVE IL      ++ +LFSAT P  +  L++KY  +   I        K+   
Sbjct: 160 LNXGFIKDVEKILNACNKDKRILLFSATXPREILNLAKKYXGDYSFIK------AKINAN 213
Query: 62  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGD 120
           I+   +      +   L  L+    K    +VF +TKRD  E++  L  I   + A+HGD
Sbjct: 214 IEQSYVEVNENERFEALCRLLK--NKEFYGLVFCKTKRDTKELASXLRDIGFKAGAIHGD 271
Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           +SQ QRE+ +  F+Q K  +L+ATDV +RG+D+ +++ +I+Y LP +PE++ HR GRTGR
Sbjct: 272 LSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGR 331
Query: 181 AGKEGTAILMFTSSQRRTVRSLER 204
           AGK+G AI +    + + +R +ER
Sbjct: 332 AGKKGKAISIINRREYKKLRYIER 355

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

Iteration: 1
 Score =  127 bits (320), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 75/204 (36%), Positives = 123/204 (60%), Gaps = 11/204 (5%)
Query: 1   MLAVGFEEDVELILEN--LPPKRQSMLFSATMPSWVKKLSRKYLDNPL--NIDLVGNQDE 56
           ML +GF ED+  I+ +  + P+ Q+++FSAT P  +++++ ++L N +   I +VG    
Sbjct: 215 MLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACS 274
Query: 57  KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASE 115
            + + I  Y ++  A  KR+ L ++++  A G  TIVF +TKR AD ++  L+     + 
Sbjct: 275 DVKQTI--YEVNKYA--KRSKLIEILSEQADG--TIVFVETKRGADFLASFLSEKEFPTT 328
Query: 116 ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS 175
           ++HGD  Q QRE+ L  F+ G   VL+AT VA+RGLDI N+  +I+Y++P+  + +VHR 
Sbjct: 329 SIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRI 388
Query: 176 GRTGRAGKEGTAILMFTSSQRRTV 199
           GRTGR G  G A   F   + R +
Sbjct: 389 GRTGRVGNNGRATSFFDPEKDRAI 412

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

Iteration: 1
 Score =  114 bits (286), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 69/210 (32%), Positives = 115/210 (54%), Gaps = 9/210 (4%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+  F+  +E IL  LPP  QS+LFSAT P  VK+   K+L  P  I+L+   +E   +
Sbjct: 175 MLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM---EELTLK 231
Query: 61  GIKLYAISTTATSKRTILSDLITVYAKG--GKTIVFTQTKRDADEVSLALTSI-IASEAL 117
           GI  Y        +R  L  L T+++K    + I+F  +    + ++  +T +  +    
Sbjct: 232 GITQYY---AFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYS 288
Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           H  + Q +R +  + FRQGK   LV +D+  RG+DI  V+++I+++ P   ET++HR GR
Sbjct: 289 HARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGR 348
Query: 178 TGRAGKEGTAILMFTSSQRRTVRSLERDVG 207
           +GR G  G AI +   + R  +  +E+++G
Sbjct: 349 SGRFGHLGLAINLINWNDRFNLYKIEQELG 378

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

Iteration: 1
 Score =  110 bits (276), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 68/184 (36%), Positives = 104/184 (56%), Gaps = 19/184 (10%)
Query: 17  LPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIK-LYAISTTATSKR 75
           LP   Q +LFSAT    V++ ++K + N   ++L  N  E   + IK LY        K 
Sbjct: 174 LPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTN--EVNVDAIKQLYMDCKNEADKF 231
Query: 76  TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-----LHGDISQHQRERTL 130
            +L++L  V   G  +I+F  TK+ A+     L   + SE      LHGD+   +R+R +
Sbjct: 232 DVLTELYGVMTIGS-SIIFVATKKTAN----VLYGKLKSEGHEVSILHGDLQTQERDRLI 286
Query: 131 NGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKE 184
           + FR+G+  VL+ T+V ARG+DIP V ++++Y+LP       DP T++HR GRTGR G++
Sbjct: 287 DDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRK 346
Query: 185 GTAI 188
           G AI
Sbjct: 347 GVAI 350

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

Iteration: 1
 Score =  109 bits (273), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 67/184 (36%), Positives = 104/184 (56%), Gaps = 19/184 (10%)
Query: 17  LPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIK-LYAISTTATSKR 75
           LP   Q +LFSAT    V++ ++K + N   ++L  N  E   + IK LY        K 
Sbjct: 174 LPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTN--EVNVDAIKQLYMDCKNEADKF 231
Query: 76  TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-----LHGDISQHQRERTL 130
            +L++L  +   G  +I+F  TK+ A+     L   + SE      LHGD+   +R+R +
Sbjct: 232 DVLTELYGLMTIGS-SIIFVATKKTAN----VLYGKLKSEGHEVSILHGDLQTQERDRLI 286
Query: 131 NGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKE 184
           + FR+G+  VL+ T+V ARG+DIP V ++++Y+LP       DP T++HR GRTGR G++
Sbjct: 287 DDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRK 346
Query: 185 GTAI 188
           G AI
Sbjct: 347 GVAI 350

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

Iteration: 1
 Score =  108 bits (270), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 122/216 (56%), Gaps = 11/216 (5%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GF+E +  I   LPP  Q +L SATMP+ V +++ K++ NP+ I  +  +DE   E
Sbjct: 175 MLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRI--LVKKDELTLE 232
Query: 61  GIKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL-TSIIASE 115
           GIK + ++      +    T L D I+V     + ++F  T+R  +E++  L        
Sbjct: 233 GIKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLRNDKFTVS 288
Query: 116 ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS 175
           A++ D+ Q +R+  +  FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR 
Sbjct: 289 AIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRI 348
Query: 176 GRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 211
           GR GR G++G AI   T+     +R LE+    + E
Sbjct: 349 GRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIE 384

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

Iteration: 1
 Score =  108 bits (269), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 60/145 (41%), Positives = 80/145 (55%), Gaps = 1/145 (0%)
Query: 59  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEAL 117
           +E I    +    + KR+ L DL+    K   T+VF +TK+ AD +         A  ++
Sbjct: 17  SENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSI 76
Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           HGD SQ  RE  L+ FR GK  +LVAT VAARGLDI NV  +I+++LP+D E +VHR GR
Sbjct: 77  HGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGR 136
Query: 178 TGRAGKEGTAILMFTSSQRRTVRSL 202
           TGR G  G A   F        + L
Sbjct: 137 TGRVGNLGLATSFFNERNINITKDL 161

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

Iteration: 1
 Score =  107 bits (267), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 71/205 (34%), Positives = 119/205 (58%), Gaps = 5/205 (2%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GF++ +  I + L    Q +L SATMPS V ++++K++ +P+ I  +  ++E   E
Sbjct: 169 MLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRI--LVKKEELTLE 226
Query: 61  GIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GI+ + I+      K   L DL        + ++F  T+R  D ++  + +      A+H
Sbjct: 227 GIRQFYINVEREEWKLDTLCDLYETLTIT-QAVIFINTRRKVDWLTEKMHARDFTVSAMH 285
Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +R+  +  FR G   VL+ TD+ ARG+D+  V L+I+Y+LP + E ++HR GR 
Sbjct: 286 GDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRG 345
Query: 179 GRAGKEGTAILMFTSSQRRTVRSLE 203
           GR G++G AI M T   +RT+R +E
Sbjct: 346 GRFGRKGVAINMVTEEDKRTLRDIE 370

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

Iteration: 1
 Score =  107 bits (266), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 71/205 (34%), Positives = 119/205 (58%), Gaps = 5/205 (2%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GF++ +  I + L    Q +L SATMPS V ++++K++ +P+ I  +  ++E   E
Sbjct: 195 MLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRI--LVKKEELTLE 252
Query: 61  GIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALH 118
           GI+ + I+      K   L DL        + ++F  T+R  D ++  + +      A+H
Sbjct: 253 GIRQFYINVEREEWKLDTLCDLYETLTIT-QAVIFINTRRKVDWLTEKMHARDFTVSAMH 311
Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +R+  +  FR G   VL+ TD+ ARG+D+  V L+I+Y+LP + E ++HR GR 
Sbjct: 312 GDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRG 371
Query: 179 GRAGKEGTAILMFTSSQRRTVRSLE 203
           GR G++G AI M T   +RT+R +E
Sbjct: 372 GRFGRKGVAINMVTEEDKRTLRDIE 396

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

Iteration: 1
 Score =  106 bits (264), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 66/192 (34%), Positives = 107/192 (55%), Gaps = 19/192 (9%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL---VGNQDEK 57
           M  +GF +D+++IL     ++ + LFSAT+P  ++K+ + ++ N   I+    + N + K
Sbjct: 141 MFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEACIGLANVEHK 200
Query: 58  LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK-RDADEVSLALTSIIASEA 116
                    +     SK   L +      K    IVF +T+ R A  V L   +I     
Sbjct: 201 FVH------VKDDWRSKVQALRE-----NKDKGVIVFVRTRNRVAKLVRLFDNAI----E 245
Query: 117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 176
           L GD+ Q  R R ++ FR+G++ +L+ TDVA+RGLDIP V+ +I+++ P D  T++HR G
Sbjct: 246 LRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIG 305
Query: 177 RTGRAGKEGTAI 188
           RTGR G++G AI
Sbjct: 306 RTGRMGRKGEAI 317

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

Iteration: 1
 Score =  103 bits (257), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 52/142 (36%), Positives = 88/142 (61%), Gaps = 2/142 (1%)
Query: 67  ISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQ 125
           I     +K ++L D++         I+F +TK   ++++  L  +    + +HG + Q  
Sbjct: 15  IQVREENKFSLLKDVLMT-ENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQED 73
Query: 126 RERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG 185
           R   +N F++G++  LVATDVAARG+DI N+ L+I+Y+LP + E++VHR+GRTGRAG +G
Sbjct: 74  RFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKG 133
Query: 186 TAILMFTSSQRRTVRSLERDVG 207
            AI   T+ ++R +  +E  +G
Sbjct: 134 KAISFVTAFEKRFLADIEEYIG 155

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

Iteration: 1
 Score =  100 bits (248), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 71/215 (33%), Positives = 117/215 (54%), Gaps = 11/215 (5%)
Query: 2   LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEG 61
           L+ GF+E +  I   LPP  Q +L SAT P+ V +++ K+  NP+ I  +  +DE   EG
Sbjct: 175 LSSGFKEQIYQIFTLLPPTTQVVLLSATXPNDVLEVTTKFXRNPVRI--LVKKDELTLEG 232
Query: 62  IKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL-TSIIASEA 116
           IK + ++      +    T L D I+V     + ++F  T+R  +E++  L        A
Sbjct: 233 IKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLRNDKFTVSA 288
Query: 117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 176
           ++ D+ Q +R+     FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR G
Sbjct: 289 IYSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIG 348
Query: 177 RTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 211
           R GR G++G AI   T+      R LE+    + E
Sbjct: 349 RGGRFGRKGVAINFVTNEDVGAXRELEKFYSTQIE 383

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

Iteration: 1
 Score = 96.3 bits (238), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 92/180 (51%), Gaps = 1/180 (0%)
Query: 9   DVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAIS 68
           DV+ I    P ++Q M+FSAT+   ++ + RK++ +P+ I  V ++ +    G++ Y + 
Sbjct: 173 DVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEI-FVDDETKLTLHGLQQYYVK 231
Query: 69  TTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRER 128
                K   L DL+ V       I     +R      L +     + A+H  + Q +R  
Sbjct: 232 LKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLS 291
Query: 129 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 188
               F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R GR G +G AI
Sbjct: 292 RYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAI 351

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

Iteration: 1
 Score = 95.9 bits (237), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 92/180 (51%), Gaps = 1/180 (0%)
Query: 9   DVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAIS 68
           DV+ I    P ++Q M+FSAT+   ++ + RK++ +P+ I  V ++ +    G++ Y + 
Sbjct: 173 DVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEI-FVDDETKLTLHGLQQYYVK 231
Query: 69  TTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRER 128
                K   L DL+ V       I     +R      L +     + A+H  + Q +R  
Sbjct: 232 LKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLS 291
Query: 129 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 188
               F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R GR G +G AI
Sbjct: 292 RYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAI 351

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

Iteration: 1
 Score = 95.9 bits (237), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 92/180 (51%), Gaps = 1/180 (0%)
Query: 9   DVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAIS 68
           DV+ I    P ++Q M+FSAT+   ++ + RK++ +P+ I  V ++ +    G++ Y + 
Sbjct: 172 DVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEI-FVDDETKLTLHGLQQYYVK 230
Query: 69  TTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRER 128
                K   L DL+ V       I     +R      L +     + A+H  + Q +R  
Sbjct: 231 LKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLS 290
Query: 129 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 188
               F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R GR G +G AI
Sbjct: 291 RYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAI 350

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

Iteration: 1
 Score = 94.7 bits (234), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 53/158 (33%), Positives = 87/158 (55%), Gaps = 30/158 (18%)
Query: 44  NPLNIDLVG-------NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQ 96
           N +N+D +        N+ +K     +LY + T  +S       +I V  K    +++ +
Sbjct: 2   NEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSS-------IIFVATKKTANVLYGK 54
Query: 97  TKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV 156
            K +  EVS+          LHGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V
Sbjct: 55  LKSEGHEVSI----------LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTV 104
Query: 157 DLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 188
            ++++Y+LP       DP T++HR GRTGR G++G AI
Sbjct: 105 SMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 142

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

Iteration: 1
 Score = 94.0 bits (232), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 65/210 (30%), Positives = 111/210 (52%), Gaps = 16/210 (7%)
Query: 1   MLAVGFEEDVELILENLPPKR-QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLA 59
           M+A    +D  + ++ + P+  Q +LFSAT    V K ++K + +P N+  +  ++E L 
Sbjct: 196 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-NVIKLKREEETLD 254
Query: 60  EGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA 116
              + Y + ++   K   L +L   IT+     + ++F  T++ A  ++  L+      A
Sbjct: 255 TIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAAELSKEGHQVA 310
Query: 117 L-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP------NDPE 169
           L  G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I+++LP       D E
Sbjct: 311 LLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE 370
Query: 170 TFVHRSGRTGRAGKEGTAILMFTSSQRRTV 199
           T++HR GRTGR GK G A+ M  S     +
Sbjct: 371 TYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 400

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 65/210 (30%), Positives = 111/210 (52%), Gaps = 16/210 (7%)
Query: 1   MLAVGFEEDVELILENLPPKR-QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLA 59
           M+A    +D  + ++ + P+  Q +LFSAT    V K ++K + +P N+  +  ++E L 
Sbjct: 180 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-NVIKLKREEETLD 238
Query: 60  EGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA 116
              + Y + ++   K   L +L   IT+     + ++F  T++ A  ++  L+      A
Sbjct: 239 TIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAAELSKEGHQVA 294
Query: 117 L-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP------NDPE 169
           L  G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I+++LP       D E
Sbjct: 295 LLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE 354
Query: 170 TFVHRSGRTGRAGKEGTAILMFTSSQRRTV 199
           T++HR GRTGR GK G A+ M  S     +
Sbjct: 355 TYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 384

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 65/210 (30%), Positives = 111/210 (52%), Gaps = 16/210 (7%)
Query: 1   MLAVGFEEDVELILENLPPKR-QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLA 59
           M+A    +D  + ++ + P+  Q +LFSAT    V K ++K + +P N+  +  ++E L 
Sbjct: 217 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-NVIKLKREEETLD 275
Query: 60  EGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA 116
              + Y + ++   K   L +L   IT+     + ++F  T++ A  ++  L+      A
Sbjct: 276 TIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAAELSKEGHQVA 331
Query: 117 L-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP------NDPE 169
           L  G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I+++LP       D E
Sbjct: 332 LLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE 391
Query: 170 TFVHRSGRTGRAGKEGTAILMFTSSQRRTV 199
           T++HR GRTGR GK G A+ M  S     +
Sbjct: 392 TYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 421

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 65/210 (30%), Positives = 111/210 (52%), Gaps = 16/210 (7%)
Query: 1   MLAVGFEEDVELILENLPPKR-QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLA 59
           M+A    +D  + ++ + P+  Q +LFSAT    V K ++K + +P N+  +  ++E L 
Sbjct: 247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-NVIKLKREEETLD 305
Query: 60  EGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA 116
              + Y + ++   K   L +L   IT+     + ++F  T++ A  ++  L+      A
Sbjct: 306 TIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAAELSKEGHQVA 361
Query: 117 L-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP------NDPE 169
           L  G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I+++LP       D E
Sbjct: 362 LLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNE 421
Query: 170 TFVHRSGRTGRAGKEGTAILMFTSSQRRTV 199
           T++HR GRTGR GK G A+ M  S     +
Sbjct: 422 TYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 451

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

Iteration: 1
 Score = 93.2 bits (230), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/158 (33%), Positives = 86/158 (54%), Gaps = 30/158 (18%)
Query: 44  NPLNIDLVG-------NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQ 96
           N +N+D +        N+ +K     +LY + T  +S       +I V  K    +++ +
Sbjct: 3   NEVNVDAIKQLYXDCKNEADKFDVLTELYGVXTIGSS-------IIFVATKKTANVLYGK 55
Query: 97  TKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV 156
            K +  EVS+          LHGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V
Sbjct: 56  LKSEGHEVSI----------LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTV 105
Query: 157 DLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 188
             +++Y+LP       DP T++HR GRTGR G++G AI
Sbjct: 106 SXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 143

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

Iteration: 1
 Score = 92.8 bits (229), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 53/158 (33%), Positives = 86/158 (54%), Gaps = 30/158 (18%)
Query: 44  NPLNIDLVG-------NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQ 96
           N +N+D +        N+ +K     +LY + T  +S       +I V  K    +++ +
Sbjct: 4   NEVNVDAIKQLYXDCKNEADKFDVLTELYGLXTIGSS-------IIFVATKKTANVLYGK 56
Query: 97  TKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV 156
            K +  EVS+          LHGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V
Sbjct: 57  LKSEGHEVSI----------LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTV 106
Query: 157 DLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 188
             +++Y+LP       DP T++HR GRTGR G++G AI
Sbjct: 107 SXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 144

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

Iteration: 1
 Score = 89.7 bits (221), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 112/227 (49%), Gaps = 30/227 (13%)
Query: 1   MLAVGFEEDVELILENLPPKR-------QSMLFSATMPSWVKKLSRKYLDNP--LNIDLV 51
           +L +GF +D+E I   L  K        +++LFSAT+   V+KL+   ++    L +D V
Sbjct: 238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTV 297
Query: 52  GNQDEKLAEGI-------KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEV 104
              + +  E I       + +A S  A  +   +   I       K I+F  T +     
Sbjct: 298 DKNEPEAHERIDQSVVISEKFANSIFAAVEH--IKKQIKERDSNYKAIIFAPTVK----F 351
Query: 105 SLALTSIIASE--------ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV 156
           +  L SI+ +E          HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV
Sbjct: 352 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 411
Query: 157 DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 203
             ++   +P++   ++HR GRT R+GKEG+++L     +   VR LE
Sbjct: 412 HEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELE 458

>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 = 89.4 bits (220), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 112/227 (49%), Gaps = 30/227 (13%)
Query: 1   MLAVGFEEDVELILENLPPKR-------QSMLFSATMPSWVKKLSRKYLDNP--LNIDLV 51
           +L +GF +D+E I   L  K        +++LFSAT+   V+KL+   ++    L +D V
Sbjct: 187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTV 246
Query: 52  GNQDEKLAEGI-------KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEV 104
              + +  E I       + +A S  A  +   +   I       K I+F  T +     
Sbjct: 247 DKNEPEAHERIDQSVVISEKFANSIFAAVEH--IKKQIKERDSNYKAIIFAPTVK----F 300
Query: 105 SLALTSIIASE--------ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV 156
           +  L SI+ +E          HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV
Sbjct: 301 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 360
Query: 157 DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 203
             ++   +P++   ++HR GRT R+GKEG+++L     +   VR LE
Sbjct: 361 HEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELE 407

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

Iteration: 1
 Score = 89.0 bits (219), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 112/227 (49%), Gaps = 30/227 (13%)
Query: 1   MLAVGFEEDVELILENLPPKR-------QSMLFSATMPSWVKKLSRKYLDNP--LNIDLV 51
           +L +GF +D+E I   L  K        +++LFSAT+   V+KL+   ++    L +D V
Sbjct: 187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTV 246
Query: 52  GNQDEKLAEGI-------KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEV 104
              + +  E I       + +A S  A  +   +   I       K I+F  T +     
Sbjct: 247 DKNEPEAHERIDQSVVISEKFANSIFAAVEH--IKKQIKERDSNYKAIIFAPTVK----F 300
Query: 105 SLALTSIIASE--------ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV 156
           +  L SI+ +E          HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV
Sbjct: 301 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 360
Query: 157 DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 203
             ++   +P++   ++HR GRT R+GKEG+++L     +   VR LE
Sbjct: 361 HEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELE 407

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

Iteration: 1
 Score = 87.4 bits (215), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 1/110 (0%)
Query: 91  TIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR 149
            ++F + K D D +    L   + + A+HG   Q +R + +  FR+GK  VLVATDVA++
Sbjct: 57  VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 150 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTV 199
           GLD P +  +I+Y++P + E +VHR GRTG +G  G A      +   +V
Sbjct: 117 GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESV 166

>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 = 81.6 bits (200), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 87/165 (52%), Gaps = 5/165 (3%)
Query: 44  NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE 103
           +P  I+L+   +E   +G+  Y    T   K   L+ L +   +  ++I+F  + +  + 
Sbjct: 4   DPYEINLM---EELTLKGVTQYYAYVTERQKVHCLNTLFSR-LQINQSIIFCNSSQRVEL 59
Query: 104 VSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY 162
           ++  ++ +  +   +H  + Q  R R  + FR G    LV TD+  RG+DI  V+++I++
Sbjct: 60  LAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINF 119
Query: 163 ELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG 207
           + P   ET++HR GR+GR G  G AI + T   R  ++S+E  +G
Sbjct: 120 DFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLG 164

>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 = 81.3 bits (199), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 40/100 (40%), Positives = 65/100 (65%), Gaps = 1/100 (1%)
Query: 90  KTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA 148
           ++IVF + +    E++  L    I +  L G++ Q +R   +    +G+  VLVATDVAA
Sbjct: 32  RSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAA 91
Query: 149 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 188
           RG+DIP+V  + ++++P   +T++HR GRT RAG++GTAI
Sbjct: 92  RGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAI 131

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 176
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 177 RTGRAGKEGTAILMFTSSQRRTVRSLE 203
           RT R+GKEG+++L     +   VR LE
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE 152

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 176
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 177 RTGRAGKEGTAILMFTSSQRRTVRSLE 203
           RT R+GKEG+++L     +   VR LE
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE 152

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 176
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 177 RTGRAGKEGTAILMFTSSQRRTVRSLE 203
           RT R+GKEG+++L     +   VR LE
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE 152

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 67/110 (60%), Gaps = 7/110 (6%)
Query: 89  GKTIVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVA 147
           G+ I+F QT+R+A  +++ +       +L  G+++  QR   +  FR GK  VL+ T+V 
Sbjct: 35  GQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVC 94
Query: 148 ARGLDIPNVDLIIHYELP------NDPETFVHRSGRTGRAGKEGTAILMF 191
           ARG+D+  V ++++++LP       D ET++HR GRTGR GK+G A  M 
Sbjct: 95  ARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMI 144

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 49/150 (32%), Positives = 84/150 (56%), Gaps = 9/150 (6%)
Query: 60  EGIKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL-TSIIAS 114
           EGIK + ++      +    T L D I+V     + ++F  T+R  +E++  L       
Sbjct: 2   EGIKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLRNDKFTV 57
Query: 115 EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHR 174
            A++ D+ Q +R+  +  FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR
Sbjct: 58  SAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 117
Query: 175 SGRTGRAGKEGTAILMFTSSQRRTVRSLER 204
            GR GR G++G AI   T+     +R LE+
Sbjct: 118 IGRGGRFGRKGVAINFVTNEDVGAMRELEK 147

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 42/51 (82%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLV 51
           ML++GFEE+VE +L   PP RQ++LFSAT+PSW K+L+ +Y+ NP+ I+++
Sbjct: 156 MLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVI 206

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 42/51 (82%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLV 51
           ML++GFEE+VE +L   PP RQ++LFSAT+PSW K+L+ +Y+ NP+ I+++
Sbjct: 156 MLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVI 206

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 71/151 (47%), Gaps = 3/151 (1%)
Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
           G++ Y +      K   L DL+ V       I     +R      L +     + A+H  
Sbjct: 5   GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 64
Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R GR
Sbjct: 65  MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 124
Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFE 211
            G +G AI  F S +      +  DV  +FE
Sbjct: 125 FGTKGLAI-TFVSDENDA--KILNDVQDRFE 152

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 37/113 (32%), Positives = 55/113 (48%), Gaps = 9/113 (7%)
Query: 87  KGGKTIVFTQTKRDADEV-------SLALTSIIASEALHGD--ISQHQRERTLNGFRQGK 137
           +  K IVFT  +  A ++        +     +   +   D  +SQ +++  L+ F +G+
Sbjct: 360 QNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE 419
Query: 138 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM 190
           F VLVAT V   GLD+P VDL++ YE        + R GRTGR       ILM
Sbjct: 420 FNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILM 472

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/112 (25%), Positives = 57/112 (50%), Gaps = 1/112 (0%)
Query: 81  LITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFT 139
           LI    KG   I++  +++D+++V+++L ++ I + A H ++    +      +   +  
Sbjct: 260 LINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQ 319
Query: 140 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 191
           V+VAT     G+D P+V  +IH+ +    E +   SGR GR   +   IL +
Sbjct: 320 VVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYY 371

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/106 (24%), Positives = 55/106 (51%), Gaps = 1/106 (0%)
Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +G   I++  ++   ++ +  L S  I++ A H  +  + R      F++    ++VAT 
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV 294
Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 191
               G++ PNV  ++H+++P + E++   +GR GR G    A+L +
Sbjct: 295 AFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 340

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/106 (24%), Positives = 54/106 (50%), Gaps = 1/106 (0%)
Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +G   I++  ++   ++ +  L S  I++ A H  +  + R      F++    ++VAT 
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV 294
Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 191
               G++ PNV  ++H+++P + E++   +GR GR G    A L +
Sbjct: 295 AFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFY 340

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 47/79 (59%), Gaps = 9/79 (11%)
Query: 117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 172
           +HG +SQ +++R +  F +G++ +LV+T V   G+D+P  ++++      +PE F    +
Sbjct: 619 MHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMV----IENPERFGLAQL 674
Query: 173 HR-SGRTGRAGKEGTAILM 190
           H+  GR GR G+E    L+
Sbjct: 675 HQLRGRVGRGGQEAYCFLV 693

>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair Coupling Factor Length = 1151

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 21/112 (18%)
Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----HYELPNDPETFV 172
           HG + + + ER +N F   +F VLV T +   G+DIP  + II     H+ L       +
Sbjct: 845 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ-----L 899
Query: 173 HR-SGRTGRAGKEGTAIL-------MFTSSQRR--TVRSLERDVGCKFEFVS 214
           H+  GR GR+  +  A L       M T +Q+R   + SLE D+G  F   +
Sbjct: 900 HQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLE-DLGAGFALAT 950

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 41/147 (27%), Positives = 71/147 (48%), Gaps = 21/147 (14%)
Query: 72  TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-----SIIASEALH-------- 118
           T  R  + +  T   +  + I+FT+T++ A  +S  +T     + +  +A H        
Sbjct: 384 TKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSS 443
Query: 119 --GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 176
               ++Q++++  ++ FR GK  +L+AT VA  GLDI   +++I Y L  +    V   G
Sbjct: 444 EFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARG 503
Query: 177 RTGRAGKEGTAILMFTSS----QRRTV 199
           R  RA  E T +L+  S     +R TV
Sbjct: 504 R-ARAD-ESTYVLVAHSGSGVIERETV 528

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 48.1 bits (113), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 31/45 (68%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNP 45
           +L +GF + +  ++ENLP KRQ++LFSAT    VK L+R  L NP
Sbjct: 183 ILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNP 227

>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb Length = 472

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 35/156 (22%), Positives = 72/156 (46%), Gaps = 9/156 (5%)
Query: 47  NIDLVGNQDEKLAEGIKLYA----ISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDAD 102
            I +    DE+  E ++ +     I+  + +K   L +++  + K  K I+FT+     +
Sbjct: 305 KIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKD-KIIIFTRH----N 359
Query: 103 EVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY 162
           E+   ++ +    A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +  
Sbjct: 360 ELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIM 419
Query: 163 ELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT 198
                   ++ R GR  R  K     +++    R T
Sbjct: 420 SGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGT 455

>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus Xpb Length = 219

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 33/149 (22%), Positives = 70/149 (46%), Gaps = 9/149 (6%)
Query: 47  NIDLVGNQDEKLAEGIKLYA----ISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDAD 102
            I +    DE+  E ++ +     I+  + +K   L +++  + K  K I+FT+     +
Sbjct: 70  KIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKD-KIIIFTRH----N 124
Query: 103 EVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY 162
           E+   ++ +    A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +  
Sbjct: 125 ELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIM 184
Query: 163 ELPNDPETFVHRSGRTGRAGKEGTAILMF 191
                   ++ R GR  R  K     +++
Sbjct: 185 SGSGSAREYIQRLGRILRPSKGKKEAVLY 213

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 32/48 (66%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           ML+ GF+E +  I   LPP  Q +L SATMP+ V +++ K++ NP+ I
Sbjct: 174 MLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRI 221

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 32/48 (66%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           ML+ GF+E +  I   LPP  Q +L SATMP+ V +++ K++ NP+ I
Sbjct: 167 MLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRI 214

>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In Complex With Atp Length = 657

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 443 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 502
Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 194
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 503 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 554

>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Length = 658

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 194
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555

>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX Length = 658

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 194
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555

>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase Domain Complex With Inhibitor Non-structural Protein V Length = 243

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 40/158 (25%), Positives = 72/158 (45%), Gaps = 34/158 (21%)
Query: 22  QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL 81
           +S +F  T+    KK+ +K  +NP        ++EKL             T  R  + + 
Sbjct: 103 ESDIFLXTLFLRNKKILKKLAENP------EYENEKL-------------TKLRNTIXEH 143
Query: 82  ITVYAKGGKTIVFTQTKRDADEVSLALT-----SIIASEALH----------GDISQHQR 126
            T   +  + I+FT+T++ A  +S  +T     + +  +A H             +Q+++
Sbjct: 144 FTRTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSSEFKPXTQNEQ 203
Query: 127 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL 164
              ++ FR GK  +L+AT VA  GLDI   +++I Y L
Sbjct: 204 REVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL 241

>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point Mutant Y96a Revealing A Novel Fold For Domain 2 Length = 658

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 194
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555

>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex Length = 667

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 11/111 (9%)
Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +  + +V T TK+ +++++  L  I I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 450 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 509
Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 189
           +   GLDIP V L+    L  D E F+ RS R+     GRA +  EG  I+
Sbjct: 510 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNAEGRVIM 557

>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase Activity Of Uvrb Length = 661

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 11/111 (9%)
Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +  + +V T TK+ +++++  L  I I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 189
           +   GLDIP V L+    L  D E F+ RS R+     GRA +  EG  I+
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNAEGRVIM 551

>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex Length = 683

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 87  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 145
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 469 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 528
Query: 146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 194
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 529 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 580

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 31/47 (65%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLN 47
           +L + FE +V+ IL+ +P  R++ LFSATM   V+KL R  L NP+ 
Sbjct: 198 ILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVK 244

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 35/50 (70%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL 50
           ML +GFE  +  I++ + P RQ++++SAT P  V++L+  +L + ++I++
Sbjct: 202 MLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINI 251

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 35/50 (70%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL 50
           ML +GFE  +  I++ + P RQ++++SAT P  V++L+  +L + ++I++
Sbjct: 188 MLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINI 237

>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In Complex With Unwound Dna Length = 702

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 40/167 (23%), Positives = 68/167 (40%), Gaps = 41/167 (24%)
Query: 71  ATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSIIA----SEAL-------- 117
           +TS+R    +L+    A+ G  +VF  T+R A++ ++ L++I A    +E L        
Sbjct: 224 STSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEEN 283
Query: 118 -------------------HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL 158
                              H  +   QR    + FR+G   V+VAT   A G+++P   +
Sbjct: 284 EGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRV 343
Query: 159 IIH-------YELPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQR 196
           I+        Y        +   +GR GR G  + G AI++     R
Sbjct: 344 IVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR 390

>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide Excision Repair Enzyme Length = 665

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 86  AKGGKTIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 144
           A+G +T+V   T R A+E+ S  +   I +  LH ++   +R+  +   R G +  LV  
Sbjct: 438 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI 497
Query: 145 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK 183
           ++   GLDIP V L+    L  D E F+ RS R+     GRA +
Sbjct: 498 NLLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAAR 538

>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair Enzyme Uvrb From Thermus Thermophilus Length = 664

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 86  AKGGKTIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 144
           A+G +T+V   T R A+E+ S  +   I +  LH ++   +R+  +   R G +  LV  
Sbjct: 437 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI 496
Query: 145 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK 183
           ++   GLDIP V L+    L  D E F+ RS R+     GRA +
Sbjct: 497 NLLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAAR 537

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/39 (51%), Positives = 30/39 (76%)
Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSR 39
           +L VGFEE+++ I++ LP +RQ+MLFSAT    V+ L+R
Sbjct: 213 ILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLAR 251

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	379
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	1e-93
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	3e-83
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	8e-80
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-77
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-77
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-76
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	5e-73
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	8e-73
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	3e-72
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	3e-72
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-71
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	7e-67
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	9e-66
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-65
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	2e-65
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	3e-65
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-63
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	2e-54
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	7e-52
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	9e-50
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	7e-47
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	2e-44
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	5e-44
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	8e-41
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	1e-40
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	5e-22
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	2e-17
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	3e-17
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	7e-17
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-15
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	2e-15
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	3e-15
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-15
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	3e-15
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-14
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	1e-14
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	4e-14
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	5e-14
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-13
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	3e-13
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	4e-13
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	9e-13
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	9e-13
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	2e-12
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	6e-12
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	8e-11
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	2e-10
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	1e-09
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	2e-09
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	8e-09
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	2e-08
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	6e-06
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	7e-06
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	1e-05
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	5e-05
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	6e-05
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	1e-04
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	5e-04
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	7e-04

>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 =  281 bits (720), Expect = 1e-93
 Identities = 107/285 (37%), Positives = 159/285 (55%), Gaps = 16/285 (5%)

Query: 62  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGD 120
            +  A+      +  +LSDL+ V     + +VFT+TK + +E++  L  +   ++ALHGD
Sbjct: 3   YEEEAVPAPVRGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGD 61

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           +SQ +RER +  FRQG+  VLVATDVAARGLDIP VDL++HY +P+  E + HRSGRTGR
Sbjct: 62  MSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGR 121

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AG+ G  +L++   +RR V +LER VG +F+ V+PP  E+VLE+    ++A L  V  + 
Sbjct: 122 AGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKD 181

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRG 300
              +   A RL  E   + +AA LA L G    P+ RSL+  E+GW T + T        
Sbjct: 182 YRLYQDFAGRLFAEGRVEVVAALLALLLGG--APAERSLLTGEEGWRTYKATGPRLSLPR 239

Query: 301 FMSA------------RSVMGFLSDVYPTAADEIGKIHIIADDRV 333
            ++              +  GF  D+ P A  E+  + +    RV
Sbjct: 240 LVALLKGQGLEVGKVAEAEGGFYVDLRPEARPEVAGLRLEPARRV 284

>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 =  251 bits (644), Expect = 3e-83
 Identities = 91/207 (43%), Positives = 130/207 (62%), Gaps = 2/207 (0%)

Query: 62  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGD 120
            +  A+      +  +LSDL+ V     + +VFT+TK + +E++  L  +   ++ALHGD
Sbjct: 6   YEEEAVPAPVRGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGD 64

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           +SQ +RER L  FRQG+  VLVATDVAARGLDIP VDL++HY LP+  E + HRSGRTGR
Sbjct: 65  LSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGR 124

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPES 240
           AG+ G  +L++   +RR V +LER VG +F+ V+PP  E+VLE+    ++A L  V  + 
Sbjct: 125 AGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKD 184

Query: 241 VEFFTPTAQRLIEEKGTDALAAALAQL 267
              +   A RL  E   + +AA LA L
Sbjct: 185 YRLYQDFAGRLFAEGRVEVVAALLALL 211

>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 =  248 bits (635), Expect = 8e-80
 Identities = 77/212 (36%), Positives = 123/212 (58%), Gaps = 9/212 (4%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML +GF +DVE IL      ++ +LFSATMP  +  L++KY+ +   I    N       
Sbjct: 159 MLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKIN------A 212

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHG 119
            I+   +      +   L  L+      G  +VF +TKRD  E++  L  I   + A+HG
Sbjct: 213 NIEQSYVEVNENERFEALCRLLKNKEFYG--LVFCKTKRDTKELASMLRDIGFKAGAIHG 270

Query: 120 DISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG 179
           D+SQ QRE+ +  F+Q K  +L+ATDV +RG+D+ +++ +I+Y LP +PE+++HR GRTG
Sbjct: 271 DLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTG 330

Query: 180 RAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 211
           RAGK+G AI +    + + +R +ER +  K +
Sbjct: 331 RAGKKGKAISIINRREYKKLRYIERAMKLKIK 362

>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 =  247 bits (632), Expect = 3e-77
 Identities = 63/297 (21%), Positives = 120/297 (40%), Gaps = 25/297 (8%)

Query: 1   MLAVGFEEDVELILENLPPKR-------QSMLFSATMPSWVKKLSRKYLDNP--LNIDLV 51
           +L +GF +D+E I   L  K        +++LFSAT+   V+KL+   ++    L +D V
Sbjct: 238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTV 297

Query: 52  GNQDEKLAEGIKLYAISTTATSKRT------ILSDLITVYAKGGKTIVFTQTKRDADEVS 105
              + +  E I    + +   +         I   +        K I+F  T +    + 
Sbjct: 298 DKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERD-SNYKAIIFAPTVKFTSFLC 356

Query: 106 LALTSI----IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH 161
             L +     +     HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++ 
Sbjct: 357 SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQ 416

Query: 162 YELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDV 221
             +P++   ++HR GRT R+GKEG+++L     +   VR LE                + 
Sbjct: 417 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEE 476

Query: 222 ----LESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPP 274
               +  +  +    ++ +    +  +    +     +    L    +        P
Sbjct: 477 IKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSE-RRILPEIASTYGVLLNDP 532

>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 =  246 bits (630), Expect = 1e-76
 Identities = 68/296 (22%), Positives = 123/296 (41%), Gaps = 23/296 (7%)

Query: 1   MLAVGFEEDVELILENLPPKR-------QSMLFSATMPSWVKKLSRKYLDNP--LNIDLV 51
           +L +GF +D+E I   L  K        +++LFSAT+   V+KL+   ++    L +D V
Sbjct: 187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTV 246

Query: 52  GNQDEKLAEGIKLYAISTTATSKRT------ILSDLITVYAKGGKTIVFTQTKRDADEVS 105
              + +  E I    + +   +         I   +    +   K I+F  T +    + 
Sbjct: 247 DKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNY-KAIIFAPTVKFTSFLC 305

Query: 106 LALTSI----IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH 161
             L +     +     HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++ 
Sbjct: 306 SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQ 365

Query: 162 YELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDV 221
             +P++   ++HR GRT R+GKEG+++L     +   VR LE                + 
Sbjct: 366 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEE 425

Query: 222 LESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKG---TDALAAALAQLSGFSRPP 274
           ++S   + V        + V     + +  I+E        L    +        P
Sbjct: 426 IKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDP 481

>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 =  232 bits (594), Expect = 5e-73
 Identities = 73/223 (32%), Positives = 122/223 (54%), Gaps = 5/223 (2%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GF++ +  I + L    Q +L SATMPS V ++++K++ +P+ I +   ++E   E
Sbjct: 195 MLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK--KEELTLE 252

Query: 61  GIK-LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GI+  Y        K   L DL        + ++F  T+R  D ++  + +      A+H
Sbjct: 253 GIRQFYINVEREEWKLDTLCDLYETLTIT-QAVIFINTRRKVDWLTEKMHARDFTVSAMH 311

Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +R+  +  FR G   VL+ TD+ ARG+D+  V L+I+Y+LP + E ++HR GR 
Sbjct: 312 GDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRG 371

Query: 179 GRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDV 221
           GR G++G AI M T   +RT+R +E       E +   V + +
Sbjct: 372 GRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI 414

>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 =  231 bits (592), Expect = 8e-73
 Identities = 75/223 (33%), Positives = 121/223 (54%), Gaps = 5/223 (2%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML  GF+E +  +   LPP  Q +L SAT+P  + +++ K++ +P+ I +   +DE   E
Sbjct: 191 MLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVK--RDELTLE 248

Query: 61  GIK-LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GIK  +        K   L DL          ++F  TKR  D ++  +        ++H
Sbjct: 249 GIKQFFVAVEREEWKFDTLCDLYDTLTITQ-AVIFCNTKRKVDWLTEKMREANFTVSSMH 307

Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
           GD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+
Sbjct: 308 GDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRS 367

Query: 179 GRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDV 221
           GR G++G AI    +   R +R +E+    + + +   V + +
Sbjct: 368 GRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 410

>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 =  228 bits (583), Expect = 3e-72
 Identities = 57/204 (27%), Positives = 107/204 (52%), Gaps = 12/204 (5%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           M  +GF +D+++IL     ++ + LFSAT+P  ++K+ + ++ N   I+           
Sbjct: 141 MFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEA-----CIGLA 195

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 120
            ++   +              +      G  IVF +T+    ++     +   +  L GD
Sbjct: 196 NVEHKFVHVK--DDWRSKVQALRENKDKG-VIVFVRTRNRVAKLVRLFDN---AIELRGD 249

Query: 121 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
           + Q  R R ++ FR+G++ +L+ TDVA+RGLDIP V+ +I+++ P D  T++HR GRTGR
Sbjct: 250 LPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGR 309

Query: 181 AGKEGTAILMFTSSQRRTVRSLER 204
            G++G AI  F  ++    + +++
Sbjct: 310 MGRKGEAIT-FILNEYWLEKEVKK 332

>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 =  229 bits (587), Expect = 3e-72
 Identities = 73/223 (32%), Positives = 122/223 (54%), Gaps = 5/223 (2%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+ GF+E +  I   LPP  Q +L SATMP+ V +++ K++ NP+ I +   +DE   E
Sbjct: 174 MLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVK--KDELTLE 231

Query: 61  GIK-LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
           GIK  Y        K   L+DL    +     ++F  T+R  +E++  L +      A++
Sbjct: 232 GIKQFYVNVEEEEYKYECLTDLYDSISVTQ-AVIFCNTRRKVEELTTKLRNDKFTVSAIY 290

Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
            D+ Q +R+  +  FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR GR 
Sbjct: 291 SDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRG 350

Query: 179 GRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDV 221
           GR G++G AI   T+     +R LE+    + E +   +   +
Sbjct: 351 GRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 393

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score =  228 bits (584), Expect = 1e-71
 Identities = 69/223 (30%), Positives = 116/223 (52%), Gaps = 6/223 (2%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
           ML+  F+  +E IL  LPP  QS+LFSAT P  VK+   K+L  P  I+L    +E   +
Sbjct: 175 MLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL---MEELTLK 231

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHG 119
           GI  Y        K   L+ L +      + I+F  +    + ++  +T +  +    H 
Sbjct: 232 GITQYYAFVEERQKLHCLNTLFSKLQIN-QAIIFCNSTNRVELLAKKITDLGYSCYYSHA 290

Query: 120 DISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG 179
            + Q +R +  + FRQGK   LV +D+  RG+DI  V+++I+++ P   ET++HR GR+G
Sbjct: 291 RMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSG 350

Query: 180 RAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVL 222
           R G  G AI +   + R  +  +E+++G +   + P  ++  L
Sbjct: 351 RFGHLGLAINLINWNDRFNLYKIEQELGTEIAAI-PATIDKSL 392

>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 =  216 bits (552), Expect = 7e-67
 Identities = 68/233 (29%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 1   MLAV-GFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLA 59
           M+A  G ++    I   LP   Q +LFSAT    V K ++K + +P  I L   ++E+  
Sbjct: 180 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLK--REEETL 237

Query: 60  EGIK-LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEAL 117
           + IK  Y + ++   K   L +L        + ++F  T++ A  ++  L+        L
Sbjct: 238 DTIKQYYVLCSSRDEKFQALCNLYGAITIA-QAMIFCHTRKTASWLAAELSKEGHQVALL 296

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP------ETF 171
            G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I+++LP D       ET+
Sbjct: 297 SGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETY 356

Query: 172 VHRSGRTGRAGKEGTAILMFTSSQR-RTVRSLERDVGCKFEFVSPPVVEDVLE 223
           +HR GRTGR GK G A+ M  S      +  ++     K E +    ++++ +
Sbjct: 357 LHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLDEIEK 409

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

 Score =  213 bits (545), Expect = 9e-66
 Identities = 84/207 (40%), Positives = 116/207 (56%), Gaps = 7/207 (3%)

Query: 1   MLAVGFEEDVELILE--NLPPK--RQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDE 56
           ML +GFE  +  I+E   +PPK  R +M+FSAT P  ++ L+R +LD  + +  VG    
Sbjct: 187 MLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLA-VGRVG- 244

Query: 57  KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASE 115
             +E I    +    + KR+ L DL+    K   T+VF +TK+ AD +   L     A  
Sbjct: 245 STSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACT 304

Query: 116 ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS 175
           ++HGD SQ  RE  L+ FR GK  +LVAT VAARGLDI NV  +I+++LP+D E +VHR 
Sbjct: 305 SIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRI 364

Query: 176 GRTGRAGKEGTAILMFTSSQRRTVRSL 202
           GRTGR G  G A   F        + L
Sbjct: 365 GRTGRVGNLGLATSFFNERNINITKDL 391

>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 =  212 bits (542), Expect = 1e-65
 Identities = 53/207 (25%), Positives = 104/207 (50%), Gaps = 5/207 (2%)

Query: 1   MLA-VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLA 59
           ML  +    DV+ I    P ++Q M+FSAT+   ++ + RK++ +P+ I  V ++ +   
Sbjct: 164 MLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEI-FVDDETKLTL 222

Query: 60  EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
            G++ Y +      K   L DL+ V       ++F ++ +    ++  L      + A+H
Sbjct: 223 HGLQQYYVKLKDNEKNRKLFDLLDVLEFNQ-VVIFVKSVQRCIALAQLLVEQNFPAIAIH 281

Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
             + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R 
Sbjct: 282 RGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARA 341

Query: 179 GRAGKEGTAILMFTSSQ-RRTVRSLER 204
           GR G +G AI   +     + +  ++ 
Sbjct: 342 GRFGTKGLAITFVSDENDAKILNDVQD 368

>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 =  212 bits (542), Expect = 2e-65
 Identities = 68/214 (31%), Positives = 113/214 (52%), Gaps = 13/214 (6%)

Query: 1   MLA-VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLA 59
           ML   G  +    +   LP   Q +LFSAT    V++ ++K + N   ++L    +E   
Sbjct: 157 MLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQ--TNEVNV 214

Query: 60  EGIK-LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEAL 117
           + IK LY        K  +L++L  +   G  +I+F  TK+ A+ +   L S       L
Sbjct: 215 DAIKQLYMDCKNEADKFDVLTELYGLMTIGS-SIIFVATKKTANVLYGKLKSEGHEVSIL 273

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETF 171
           HGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V ++++Y+LP       DP T+
Sbjct: 274 HGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATY 333

Query: 172 VHRSGRTGRAGKEGTAILMFTSSQR-RTVRSLER 204
           +HR GRTGR G++G AI           + ++++
Sbjct: 334 IHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQK 367

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score =  213 bits (545), Expect = 3e-65
 Identities = 68/233 (29%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 1   MLAV-GFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLA 59
           M+A  G ++    I   LP   Q +LFSAT    V K ++K + +P  I L   ++E+  
Sbjct: 247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLK--REEETL 304

Query: 60  EGIK-LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEAL 117
           + IK  Y + ++   K   L +L        + ++F  T++ A  ++  L+        L
Sbjct: 305 DTIKQYYVLCSSRDEKFQALCNLYGAITIA-QAMIFCHTRKTASWLAAELSKEGHQVALL 363

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP------ETF 171
            G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I+++LP D       ET+
Sbjct: 364 SGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETY 423

Query: 172 VHRSGRTGRAGKEGTAILMFTSSQR-RTVRSLERDVGCKFEFVSPPVVEDVLE 223
           +HR GRTGR GK G A+ M  S      +  ++     K E +    ++++ +
Sbjct: 424 LHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLDEIEK 476

>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 =  208 bits (531), Expect = 2e-63
 Identities = 70/206 (33%), Positives = 117/206 (56%), Gaps = 8/206 (3%)

Query: 1   MLAVGFEEDVELILEN--LPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKL 58
           ML +GF ED+  I+ +  + P+ Q+++FSAT P  +++++ ++L N + +  +G      
Sbjct: 215 MLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVA-IGIVG-GA 272

Query: 59  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEAL 117
              +K         +KR+ L ++++   +   TIVF +TKR AD ++  L+     + ++
Sbjct: 273 CSDVKQTIYEVNKYAKRSKLIEILS--EQADGTIVFVETKRGADFLASFLSEKEFPTTSI 330

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           HGD  Q QRE+ L  F+ G   VL+AT VA+RGLDI N+  +I+Y++P+  + +VHR GR
Sbjct: 331 HGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGR 390

Query: 178 TGRAGKEGTAILMFTSSQ-RRTVRSL 202
           TGR G  G A   F   + R     L
Sbjct: 391 TGRVGNNGRATSFFDPEKDRAIAADL 416

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

 Score =  176 bits (448), Expect = 2e-54
 Identities = 53/154 (34%), Positives = 92/154 (59%), Gaps = 2/154 (1%)

Query: 59  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEAL 117
              I+   I     +K ++L D++         I+F +TK   ++++  L  +    + +
Sbjct: 7   TRNIEHAVIQVREENKFSLLKDVLMTE-NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKI 65

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           HG + Q  R   +N F++G++  LVATDVAARG+DI N+ L+I+Y+LP + E++VHR+GR
Sbjct: 66  HGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGR 125

Query: 178 TGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 211
           TGRAG +G AI   T+ ++R +  +E  +G + +
Sbjct: 126 TGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQ 159

>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 =  169 bits (431), Expect = 7e-52
 Identities = 44/147 (29%), Positives = 79/147 (53%), Gaps = 2/147 (1%)

Query: 74  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNG 132
           K  +L  L+    +  ++IVF + +    E++  L    I +  L G++ Q +R   +  
Sbjct: 17  KTALLVHLLKQ-PEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKR 75

Query: 133 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT 192
             +G+  VLVATDVAARG+DIP+V  + ++++P   +T++HR GRT RAG++GTAI +  
Sbjct: 76  LTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVE 135

Query: 193 SSQRRTVRSLERDVGCKFEFVSPPVVE 219
           +     +  + R +    +      + 
Sbjct: 136 AHDHLLLGKVGRYIEEPIKARVIDELR 162

>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 =  164 bits (418), Expect = 9e-50
 Identities = 59/130 (45%), Positives = 76/130 (58%), Gaps = 1/130 (0%)

Query: 74  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNG 132
           KR+ L DL+    K   T+VF +TK+ AD +   L     A  ++HGD SQ  RE  L+ 
Sbjct: 32  KRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQ 91

Query: 133 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT 192
           FR GK  +LVAT VAARGLDI NV  +I+++LP+D E +VHR GRTGR G  G A   F 
Sbjct: 92  FRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFN 151

Query: 193 SSQRRTVRSL 202
                  + L
Sbjct: 152 ERNINITKDL 161

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

 Score =  157 bits (399), Expect = 7e-47
 Identities = 43/131 (32%), Positives = 68/131 (51%), Gaps = 4/131 (3%)

Query: 74  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNG 132
           K   L + +         ++F + K D D +   L    + + A+HG   Q +R + +  
Sbjct: 42  KMVYLLECLQ--KTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEA 99

Query: 133 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT 192
           FR+GK  VLVATDVA++GLD P +  +I+Y++P + E +VHR GRTG +G  G A     
Sbjct: 100 FREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFIN 159

Query: 193 SSQ-RRTVRSL 202
            +     +  L
Sbjct: 160 KACDESVLMDL 170

>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 =  150 bits (381), Expect = 2e-44
 Identities = 45/170 (26%), Positives = 86/170 (50%), Gaps = 9/170 (5%)

Query: 60  EGIK-LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEAL 117
             I+  Y +      K   L ++      G + I+F QT+R+A  +++ +         L
Sbjct: 6   NNIRQYYVLCEHRKDKYQALCNIYGSITIG-QAIIFCQTRRNAKWLTVEMIQDGHQVSLL 64

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETF 171
            G+++  QR   +  FR GK  VL+ T+V ARG+D+  V ++++++LP       D ET+
Sbjct: 65  SGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETY 124

Query: 172 VHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDV 221
           +HR GRTGR GK+G A  M    +  ++  ++       + ++   ++++
Sbjct: 125 LHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMDEI 174

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

 Score =  156 bits (396), Expect = 5e-44
 Identities = 40/257 (15%), Positives = 82/257 (31%), Gaps = 37/257 (14%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKL-- 58
           +L      D  L++  +P +     FS      + +  +      L +     +   +  
Sbjct: 151 VLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRP 210

Query: 59  -----------------AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA 101
                            A  I    IS+ +  K   L ++          ++F QT+ + 
Sbjct: 211 LLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEIF-----RDGILIFAQTEEEG 265

Query: 102 DEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV----AARGLDIPN-V 156
            E+   L         +   +  + E+    F+ GK  +L+          RG+D+P  +
Sbjct: 266 KELYEYL----KRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGVDLPERI 321

Query: 157 DLIIHYELPN--DPETFVHRSGRTGRAGKEG--TAILMFTSSQRRTVRSLERDVGCKFEF 212
             +I +  P+  D  T++  SGR+ R         + +          SL+  +    E 
Sbjct: 322 KYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAEE 381

Query: 213 VSPPVVEDVLESSAEQV 229
                 E   +    +V
Sbjct: 382 EIIEEAEANWKELVHEV 398

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score =  141 bits (357), Expect = 8e-41
 Identities = 36/147 (24%), Positives = 72/147 (48%), Gaps = 3/147 (2%)

Query: 60  EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALH 118
            G++ Y +      K   L DL+ V     + ++F ++ +    ++  L      + A+H
Sbjct: 4   HGLQQYYVKLKDNEKNRKLFDLLDVLEFN-QVVIFVKSVQRCIALAQLLVEQNFPAIAIH 62

Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
             + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R 
Sbjct: 63  RGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARA 122

Query: 179 GRAGKEGTAILMFTSSQ-RRTVRSLER 204
           GR G +G AI   +     + +  ++ 
Sbjct: 123 GRFGTKGLAITFVSDENDAKILNDVQD 149

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

 Score =  140 bits (354), Expect = 1e-40
 Identities = 52/165 (31%), Positives = 89/165 (53%), Gaps = 4/165 (2%)

Query: 60  EGIK-LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEAL 117
           EGIK  Y        K   L+DL    +   + ++F  T+R  +E++  L +      A+
Sbjct: 2   EGIKQFYVNVEEEEYKYECLTDLYDSISVT-QAVIFCNTRRKVEELTTKLRNDKFTVSAI 60

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 177
           + D+ Q +R+  +  FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR GR
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 120

Query: 178 TGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVL 222
            GR G++G AI   T+     +R LE+    + E + P  +  +L
Sbjct: 121 GGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEEL-PSDIATLL 164

>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 = 96.4 bits (239), Expect = 5e-22
 Identities = 43/170 (25%), Positives = 68/170 (40%), Gaps = 13/170 (7%)

Query: 39  RKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVY---AKGGKTIVFT 95
           +              + +K    +           K   L ++I       +  K IVFT
Sbjct: 309 KAGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFT 368

Query: 96  QTKRDADEVSLALTSI-IASEALHGD--------ISQHQRERTLNGFRQGKFTVLVATDV 146
             +  A ++   L    I ++   G         +SQ +++  L+ F +G+F VLVAT V
Sbjct: 369 NYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSV 428

Query: 147 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR 196
              GLD+P VDL++ YE        + R GRTGR    G  I++     R
Sbjct: 429 GEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH-MPGRVIILMAKGTR 477

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 79.5 bits (197), Expect = 2e-17
 Identities = 19/56 (33%), Positives = 33/56 (58%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDE 56
           ML +GF  DV+ I   +P   Q ++FSAT+P  +K   +KY++NP  + ++ +   
Sbjct: 162 MLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLEHHHH 217

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score = 78.3 bits (194), Expect = 3e-17
 Identities = 27/48 (56%), Positives = 39/48 (81%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           ML++GFEE+VE +L   PP RQ++LFSAT+PSW K+L+ +Y+ NP+ I
Sbjct: 156 MLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLI 203

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 77.6 bits (192), Expect = 7e-17
 Identities = 18/49 (36%), Positives = 29/49 (59%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNID 49
           +L+  F + +E I+  LP  RQ +L+SAT P  V+K    +L+ P  I+
Sbjct: 158 LLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEIN 206

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score = 74.6 bits (184), Expect = 1e-15
 Identities = 17/48 (35%), Positives = 32/48 (66%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           ML+ GF++ +  I + L    Q +L SATMP+ V ++++K++ +P+ I
Sbjct: 185 MLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRI 232

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score = 73.7 bits (182), Expect = 2e-15
 Identities = 21/48 (43%), Positives = 32/48 (66%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           ML+ GF+E +  I   LPP  Q +L SATMP+ V +++ K++ NP+ I
Sbjct: 167 MLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRI 214

>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 = 76.5 bits (187), Expect = 3e-15
 Identities = 37/174 (21%), Positives = 64/174 (36%), Gaps = 19/174 (10%)

Query: 49  DLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVS 105
            L     EK  E I L    T    K   L  ++          +T++F +T+     + 
Sbjct: 589 HLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALK 648

Query: 106 LALTSI-----IASEALHG--------DISQHQRERTLNGFRQGKF-TVLVATDVAARGL 151
             +        I    L G         ++   ++  L+ F+  K   +L+AT VA  G+
Sbjct: 649 KCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI 708

Query: 152 DIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD 205
           DI   +L++ YE   +    +   GR GRA      IL+ + ++        R 
Sbjct: 709 DIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENEKCNRY 760

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score = 73.4 bits (181), Expect = 3e-15
 Identities = 22/50 (44%), Positives = 33/50 (66%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL 50
           +L +GF + +  ++ENLP KRQ++LFSAT    VK L+R  L NP  + +
Sbjct: 183 ILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWV 232

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score = 73.5 bits (181), Expect = 3e-15
 Identities = 21/48 (43%), Positives = 31/48 (64%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           +L + FE +V+ IL+ +P  R++ LFSATM   V+KL R  L NP+  
Sbjct: 198 ILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKC 245

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score = 71.5 bits (176), Expect = 1e-14
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 1   MLA-VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           ML  +    DV+ I    P ++Q M+FSAT+   ++ + RK++ +P+ I
Sbjct: 170 MLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEI 218

>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 = 74.6 bits (182), Expect = 1e-14
 Identities = 38/184 (20%), Positives = 66/184 (35%), Gaps = 19/184 (10%)

Query: 39  RKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVY---AKGGKTIVFT 95
           +      L   L     EK  E I L    T    K   L  ++          +T++F 
Sbjct: 579 KNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFA 638

Query: 96  QTKRDADEVSLALTSI-----IASEALHG--------DISQHQRERTLNGFRQGKF-TVL 141
           +T+     +   +        I    L G         ++   ++  L+ F+  K   +L
Sbjct: 639 KTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLL 698

Query: 142 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 201
           +AT VA  G+DI   +L++ YE   +    +   GR GRA      IL+ + ++      
Sbjct: 699 IATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENEK 756

Query: 202 LERD 205
             R 
Sbjct: 757 CNRY 760

>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 = 72.7 bits (177), Expect = 4e-14
 Identities = 37/174 (21%), Positives = 64/174 (36%), Gaps = 19/174 (10%)

Query: 49  DLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVS 105
            L     EK  E I L    T    K   L  ++          +T++F +T+     + 
Sbjct: 348 HLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALK 407

Query: 106 LALTSI-----IASEALHG--------DISQHQRERTLNGFRQGKF-TVLVATDVAARGL 151
             +        I    L G         ++   ++  L+ F+  K   +L+AT VA  G+
Sbjct: 408 KCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI 467

Query: 152 DIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD 205
           DI   +L++ YE   +    +   GR GRA      IL+ + ++        R 
Sbjct: 468 DIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENEKCNRY 519

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score = 69.6 bits (171), Expect = 5e-14
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 1   MLAVG-FEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL 50
           +L  G F+E +  I  +LP  +Q +  SAT P ++     KY+ +P  + L
Sbjct: 178 LLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 228

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score = 68.7 bits (169), Expect = 1e-13
 Identities = 18/48 (37%), Positives = 31/48 (64%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           ML + FE  +  IL ++ P RQ+++ SAT P  V++L+  YL +P+ +
Sbjct: 179 MLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIV 226

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score = 67.6 bits (166), Expect = 3e-13
 Identities = 18/55 (32%), Positives = 37/55 (67%), Gaps = 1/55 (1%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQD 55
           ML +GFE  +  I++ + P RQ++++SAT P  V++L+  +L + ++I+ +G  +
Sbjct: 188 MLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHIN-IGALE 241

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score = 67.7 bits (166), Expect = 4e-13
 Identities = 21/45 (46%), Positives = 31/45 (68%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNP 45
           +L VGFEE+++ I++ LP +RQ+MLFSAT    V+ L+R  L   
Sbjct: 213 ILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKE 257

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score = 67.0 bits (164), Expect = 9e-13
 Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 1   MLAV-GFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL 50
           M+A  G ++    I   LP   Q +LFSAT    V K ++K + +P  I L
Sbjct: 247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 297

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

 Score = 68.4 bits (166), Expect = 9e-13
 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 3/86 (3%)

Query: 113 ASEALHGDISQHQRERTLNGFRQ-GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF 171
                   ++   ++  L  FR  G   +L+AT VA  G+DI   +L+I YE   +    
Sbjct: 427 GRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKM 486

Query: 172 VHRSGRTGRAGKEGTAILMFTSSQRR 197
           +   GR GRA ++    L+ +S+   
Sbjct: 487 IQTRGR-GRA-RDSKCFLLTSSADVI 510

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

 Score = 67.7 bits (164), Expect = 2e-12
 Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 113 ASEALHGDISQHQRERTLNGFRQ-GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF 171
                +  ++   ++  L+ F+  G   +L+AT VA  G+DI   +L+I YE   +    
Sbjct: 436 GKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKM 495

Query: 172 VHRSGRTGRAGKEGTAILMFTSSQR 196
           +   GR GRA +     L+ +++  
Sbjct: 496 IQTRGR-GRA-RGSKCFLLTSNAGV 518

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Length = 472

 Score = 65.6 bits (160), Expect = 6e-12
 Identities = 25/106 (23%), Positives = 50/106 (47%), Gaps = 5/106 (4%)

Query: 55  DEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIAS 114
            E L    +   I+  + +K   L +++  + +  K I+FT+       +S         
Sbjct: 317 YEALRAWEEARRIAFNSKNKIRKLREILERH-RKDKIIIFTRHNELVYRISKVFLI---- 371

Query: 115 EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 160
            A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +
Sbjct: 372 PAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGV 417

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score = 60.7 bits (148), Expect = 8e-11
 Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 5   GFEEDVELILENL-PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQD 55
           GF + +  I       K +  +FSAT    V++  +  LDN +++  +G ++
Sbjct: 194 GFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVS-IGARN 244

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A* Length = 591

 Score = 61.5 bits (150), Expect = 2e-10
 Identities = 32/127 (25%), Positives = 63/127 (49%), Gaps = 3/127 (2%)

Query: 78  LSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQG 136
           +  LI    KG   I++  +++D+++V+++L ++ I + A H ++    +      +   
Sbjct: 257 IVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSAN 316

Query: 137 KFTVLVATDVA-ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ 195
           +  V+VAT VA   G+D P+V  +IH+ +    E +   SGR GR   +   IL +    
Sbjct: 317 EIQVVVAT-VAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGD 375

Query: 196 RRTVRSL 202
              + S+
Sbjct: 376 IFRISSM 382

>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 = 59.3 bits (143), Expect = 1e-09
 Identities = 42/281 (14%), Positives = 78/281 (27%), Gaps = 31/281 (11%)

Query: 19  PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKL------AEGIKLYAISTTAT 72
           PKR+       +P+  +   +                + L       E     A      
Sbjct: 429 PKRELHTIKLPLPTQYQTAIKVSGIMGARKSAEDRARDMLYPERIYQEFEGDNATWWNFD 488

Query: 73  SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI--IASEALHGDISQHQRERTL 130
            +   L   +T   +  K +V       A ++   L     I +   H  +S  +R+R  
Sbjct: 489 PRVEWLMGYLT-SHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAA 547

Query: 131 NGFRQ--GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 188
             F +      VL+ +++ + G +      ++ ++LP +P+    R GR  R G      
Sbjct: 548 AWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIG------ 601

Query: 189 LMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTA 248
                 Q   ++                  + VL     + +       P     +    
Sbjct: 602 ------QAHDIQI--------HVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRTIYDSVY 647

Query: 249 QRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTL 289
             LI    +         L    R          EQG   L
Sbjct: 648 NDLINYLASPDQTEGFDDLIKNCREQHEALKAQLEQGRDRL 688

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score = 56.8 bits (138), Expect = 2e-09
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 4/52 (7%)

Query: 1   MLAVGFEEDVELILENLPP----KRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           ML +GFE  +  I+E         RQ+++FSAT P  ++KL+  +L N + +
Sbjct: 186 MLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFM 237

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A* Length = 523

 Score = 56.0 bits (136), Expect = 8e-09
 Identities = 28/113 (24%), Positives = 58/113 (51%), Gaps = 3/113 (2%)

Query: 92  IVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA-AR 149
           I++  ++   ++ +  L S  I++ A H  +  + R      F++    ++VAT VA   
Sbjct: 240 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVAT-VAFGM 298

Query: 150 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 202
           G++ PNV  ++H+++P + E++   +GR GR G    A+L +  +    +R  
Sbjct: 299 GINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRC 351

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 54.9 bits (132), Expect = 2e-08
 Identities = 67/387 (17%), Positives = 118/387 (30%), Gaps = 92/387 (23%)

Query: 10  VELILENLPPKRQSMLFSATMP------SWVKKLSRKYLDNPLNIDLVGNQD--EKLAEG 61
           +E+IL ++  K Q +  SAT+        W            LN +L+ +     KL  G
Sbjct: 159 LEVILAHMLGKAQIIGLSATIGNPEELAEW------------LNAELIVSDWRPVKLRRG 206

Query: 62  IKLYAISTTATSK----RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL 117
           +      T          +    +     K    ++F   +R A+ V+L L+  + S   
Sbjct: 207 VFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLT 266

Query: 118 ----------------------------------HGDISQHQRERTLNGFRQGKFTVLVA 143
                                             H  + + +R      FR+G    +VA
Sbjct: 267 KPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVA 326

Query: 144 TDVAARGLDIPNVDLIIHYELPNDPETFVHRS--------GRTGRAG--KEGTAILMFTS 193
           T   + G++ P   +II                       GR GR    + G  I++ TS
Sbjct: 327 TPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTS 386

Query: 194 SQRRTVRSLERDVGCKFEFVSPPV-----VEDVLESSAEQVVATLNGVHPES-VEFFTPT 247
              R V +               +      E  L S    ++AT      E  ++F + T
Sbjct: 387 DDPREVMNH------YIFGKPEKLFSQLSNESNLRSQVLALIATFGYSTVEEILKFISNT 440

Query: 248 ---AQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSA 304
               QR       + +   L  L       +    I+ E     L L      ++ ++  
Sbjct: 441 FYAYQRKDTYSLEEKIRNILYFLL-----ENEFIEISLEDKIRPLSLGI--RTAKLYIDP 493

Query: 305 RSVMGFLSDVYPTA--ADEIGKIHIIA 329
            +   F   +       + IG  H+I+
Sbjct: 494 YTAKMFKDKMEEVVKDPNPIGIFHLIS 520

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Length = 702

 Score = 49.4 bits (118), Expect = 1e-06
 Identities = 49/225 (21%), Positives = 81/225 (36%), Gaps = 62/225 (27%)

Query: 27  SATMP------SWVKKLSRKYLDN-----PLNIDLVGNQDEKLAEGIKLYAISTTATSKR 75
           SAT P       W   L   Y  +     PL   ++     +L +G         +TS+R
Sbjct: 179 SATAPNVTEIAEW---LDADYYVSDWRPVPLVEGVLCEGTLELFDGAF-------STSRR 228

Query: 76  TILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSIIASEA------------------ 116
               +L+    A+ G  +VF  T+R A++ ++ L++I A                     
Sbjct: 229 VKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMS 288

Query: 117 -------------LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-- 161
                         H  +   QR    + FR+G   V+VAT   A G+++P   +I+   
Sbjct: 289 RKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSL 348

Query: 162 -----YELPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTV 199
                Y        +   +GR GR G  + G AI++     R   
Sbjct: 349 YRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIA 393

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

 Score = 47.9 bits (113), Expect = 4e-06
 Identities = 60/401 (14%), Positives = 119/401 (29%), Gaps = 99/401 (24%)

Query: 2   LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEG 61
           L +      E +LE L    Q  L     P+W  +      +  L I  +  +  +L + 
Sbjct: 187 LNLKNCNSPETVLEML----QK-LLYQIDPNWTSRSDHSS-NIKLRIHSIQAELRRLLKS 240

Query: 62  IKLYAISTTATSKRT--ILSD-----LITVYAKGGKTIVFTQTKRDADEVSLALTSIIAS 114
            K Y        +    +L +         +    K ++ T+ K+  D +S A T+ I+ 
Sbjct: 241 -KPY--------ENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISL 291

Query: 115 EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI-PNVDLIIHYELPNDPETFVH 173
           +  H  ++    E   +     K+      D+    L   P    II   + +   T   
Sbjct: 292 D--HHSMTLTPDE-VKSLLL--KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT--- 343

Query: 174 RSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL 233
                            + + +      L   +      + P     + +  +       
Sbjct: 344 -----------------WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS------- 379

Query: 234 NGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTR 293
             V P S    T     +  +     +   + +L          SL+            +
Sbjct: 380 --VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKL-------HKYSLVE-----------K 419

Query: 294 DSAFSRGFMSARSVMGFLSDVYPTAADEIGKIH--IIADDRV----CIDTVILL----YF 343
                    S  S+     ++     +E   +H  I+    +      D +I      YF
Sbjct: 420 QPK-----ESTISIPSIYLELKVKLENEY-ALHRSIVDHYNIPKTFDSDDLIPPYLDQYF 473

Query: 344 YASVRLG--LFNTKSVIWLTYRFRELFLIFR---RRLQRSC 379
           Y+   +G  L N +        FR +FL FR   ++++   
Sbjct: 474 YS--HIGHHLKNIEH-PERMTLFRMVFLDFRFLEQKIRHDS 511

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

 Score = 44.1 bits (103), Expect = 6e-05
 Identities = 56/438 (12%), Positives = 119/438 (27%), Gaps = 134/438 (30%)

Query: 7   EEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYA 66
           +E+++ I+ +      ++    T+ S  +++ +K+++  L I+      + L   IK   
Sbjct: 48  KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY-----KFLMSPIKTEQ 102

Query: 67  ISTTA-----TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASE--ALHG 119
              +        +R  L +   V+AK           +   ++  AL  +  ++   + G
Sbjct: 103 RQPSMMTRMYIEQRDRLYNDNQVFAKY-----NVSRLQPYLKLRQALLELRPAKNVLIDG 157

Query: 120 DISQHQRERTLNGFRQGKFTVLVATDVAARGL----------------DIPNVDLII--- 160
            +          G   GK T +      +  +                + P   L +   
Sbjct: 158 VL----------GS--GK-TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK 204

Query: 161 -HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE--RDV----------- 206
             Y++  +  +    S           A L      +     L    +V           
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNL 264

Query: 207 GCK----------FEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFF----TPTAQRLI 252
            CK           +F+S      +   S +    TL     E             Q L 
Sbjct: 265 SCKILLTTRFKQVTDFLSAATTTHI---SLDHHSMTLT--PDEVKSLLLKYLDCRPQDLP 319

Query: 253 EE-KGTDALAAAL--AQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMG 309
            E   T+    ++    +         R  +     W    +  D        +      
Sbjct: 320 REVLTTNPRRLSIIAESI---------RDGLATWDNW--KHVNCDK-----LTTIIES-- 361

Query: 310 FLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLF--NTK------SVIWLT 361
            L+ + P    E  K                  F     L +F  +        S+IW  
Sbjct: 362 SLNVLEP---AEYRK-----------------MFDR---LSVFPPSAHIPTILLSLIWFD 398

Query: 362 YRFRELFLIFRRRLQRSC 379
               ++ ++  +  + S 
Sbjct: 399 VIKSDVMVVVNKLHKYSL 416

>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 Length = 1151

 Score = 47.3 bits (113), Expect = 6e-06
 Identities = 26/99 (26%), Positives = 42/99 (42%), Gaps = 23/99 (23%)

Query: 118 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS-- 175
           HG + + + ER +N F   +F VLV T +   G+DIP  + II           + R+  
Sbjct: 845 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII-----------IERADH 893

Query: 176 ----------GRTGRAGKEGTAILMFTSSQRRTVRSLER 204
                     GR GR+  +  A L+    +  T  + +R
Sbjct: 894 FGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKR 932

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B* Length = 661

 Score = 47.2 bits (113), Expect = 7e-06
 Identities = 41/131 (31%), Positives = 63/131 (48%), Gaps = 16/131 (12%)

Query: 86  AKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVAT 144
            +  + +V T TK+ +++++  L  I I    LH +I   +R   +   R GK+ VLV  
Sbjct: 443 ERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGI 502

Query: 145 DVAARGLDIPNVDLI-IHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL---MFTS 193
           ++   GLDIP V L+ I   L  D E F+ RS R+     GRA +  EG  I+     T 
Sbjct: 503 NLLREGLDIPEVSLVAI---LDADKEGFL-RSERSLIQTIGRAARNAEGRVIMYADKITK 558

Query: 194 SQRRTVRSLER 204
           S    +   +R
Sbjct: 559 SMEIAINETKR 569

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A* Length = 664

 Score = 46.4 bits (111), Expect = 1e-05
 Identities = 39/131 (29%), Positives = 62/131 (47%), Gaps = 16/131 (12%)

Query: 86  AKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVAT 144
           A+G +T+V   T R A+E++  L    I +  LH ++   +R+  +   R G +  LV  
Sbjct: 437 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI 496

Query: 145 DVAARGLDIPNVDLI-IHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL---MFTS 193
           ++   GLDIP V L+ I   L  D E F+ RS R+     GRA +   G   L     + 
Sbjct: 497 NLLREGLDIPEVSLVAI---LDADKEGFL-RSERSLIQTIGRAARNARGEVWLYADRVSE 552

Query: 194 SQRRTVRSLER 204
           + +R +    R
Sbjct: 553 AMQRAIEETNR 563

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B* Length = 1054

 Score = 44.3 bits (105), Expect = 5e-05
 Identities = 31/168 (18%), Positives = 63/168 (37%), Gaps = 26/168 (15%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLF--SATMPSWVKKLSRKYLDNPLNIDLVGNQDEKL 58
           +  +GF    +L  ++   + +  L   +AT     K    + L   LN D +G+    +
Sbjct: 198 LHLLGFHY--DLKTKSWVGEARGCLMVSTATAKKGKKAELFRQL---LNFD-IGSSRITV 251

Query: 59  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALH 118
                +           + LS ++     GG  I++ +T  +A+E+  +L +      + 
Sbjct: 252 RNVEDVA----VNDESISTLSSILEKLGTGG--IIYARTGEEAEEIYESLKNKFRIGIVT 305

Query: 119 GDISQHQRERTLNGFRQGKFTVLVAT----DVAARGLDIPNVDLIIHY 162
                  ++     F +G+   L+ T        RGLD+P     I +
Sbjct: 306 AT-----KKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPER---IRF 345

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

 Score = 43.8 bits (103), Expect = 6e-05
 Identities = 29/130 (22%), Positives = 47/130 (36%), Gaps = 27/130 (20%)

Query: 87  KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV 146
           +GG+ ++F  +K+  DE++  L        L  +   + R   ++        V+VATD 
Sbjct: 395 RGGRHLIFCHSKKKCDELAAKL------SGLGINAVAYYRGLDVSVIPTIGDVVVVATDA 448

Query: 147 AARGL--DI-----------PNVD-------LIIHYELPNDPETFVHRSGRTGRAGKEGT 186
              G   D              VD        I    +P D  +   R GRTGR G+ G 
Sbjct: 449 LMTGYTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI 507

Query: 187 AILMFTSSQR 196
              +    + 
Sbjct: 508 YRFVTPGERP 517

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 43.0 bits (100), Expect = 1e-04
 Identities = 17/119 (14%), Positives = 36/119 (30%), Gaps = 4/119 (3%)

Query: 75  RTILSDLITVYAKGGKTIVFTQTKRDADEVSLAL-TSIIASEALHGDISQHQRERTLNGF 133
           + I    I +  K     V  +       +   +         + G++    R       
Sbjct: 334 KWIAKLAIKLAQKDENAFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLA 393

Query: 134 RQGKFTVLVAT-DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR--AGKEGTAIL 189
             GK  ++VA+  V + G+ + N+  ++           +   GR  R    K    + 
Sbjct: 394 ENGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVW 452

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

 Score = 41.1 bits (96), Expect = 5e-04
 Identities = 20/129 (15%), Positives = 35/129 (27%), Gaps = 27/129 (20%)

Query: 88  GGKTIVFTQTKRDADEVSLALTSIIAS-EALHGDISQHQRERTLNGFRQGKFTVLVATDV 146
            GKT+ F  + +  ++++  L         L       +  +T           +V TD+
Sbjct: 355 QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWD----FVVTTDI 410

Query: 147 AARGLDIPNVDLII------HYELPNDPETFV--------------HRSGRTGRAGKEGT 186
           +  G +      +I         +  D    V               R GR GR      
Sbjct: 411 SEMGANF-RAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGR-NPAQE 468

Query: 187 AILMFTSSQ 195
                 S  
Sbjct: 469 DDQYVFSGD 477

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 40.5 bits (95), Expect = 7e-04
 Identities = 42/232 (18%), Positives = 80/232 (34%), Gaps = 65/232 (28%)

Query: 27  SATMP------SWVKKLSRKYLDN-----PLNIDLVG-NQDEKLAEGIKLYAISTTATSK 74
           SAT+        W   L  + +       PL   ++   + +K    I     +      
Sbjct: 182 SATISNYKQIAKW---LGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGD 238

Query: 75  RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL----------------- 117
             I++  +   +K G+ +VF  +++ A+  +L + + +   +L                 
Sbjct: 239 DAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEE 298

Query: 118 --------------------HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD 157
                               H  +S+  R+    GFRQ K  V+VAT   A G+++P   
Sbjct: 299 GGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPART 358

Query: 158 LIIHYELPNDPETFVHR-----------SGRTGRAGK--EGTAILMFTSSQR 196
           +II      + +   +            SGR GR G    G +I++    + 
Sbjct: 359 VIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKED 410

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	379
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.98
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.97
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.97
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.97
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.97
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.97
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.97
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.97
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.97
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.97
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.96
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.96
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.96
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.96
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.92
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.95
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.95
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.94
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.93
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.92
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.92
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.91
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.91
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.91
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.9
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.9
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.9
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.9
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.9
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.9
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.9
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.89
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.89
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.89
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.89
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.89
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.89
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.88
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.88
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.88
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.88
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.88
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.88
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.87
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.86
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.86
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.85
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.85
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.84
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.84
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.84
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.81
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.81
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.81
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.8
3h1t_A	590	Type I site-specific restriction-modification syst	99.77
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.67
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.64
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.6
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.53
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	99.12
2e29_A	92	ATP-dependent RNA helicase DDX50; ATP binding, hyd	98.78
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.67
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.2
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	97.92
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	97.79
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	97.39
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	96.95
3i31_A	88	Heat resistant RNA dependent ATPase; RNA helicase,	95.53
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	94.74
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	93.52
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	90.57
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	90.35
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	86.33
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	85.12
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	85.02
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	83.9
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	82.6
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	81.84
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	80.98
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	80.86
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	80.06

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

Probab=100.00  E-value=4.9e-45  Score=349.32  Aligned_cols=269  Identities=39%  Similarity=0.602  Sum_probs=245.9

Q ss_pred             ceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCcee
Q 017020           61 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  139 (379)
Q Consensus        61 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~  139 (379)
                      .+.|+++.++..+|.++|.+++.... ++++||||+|++.++.++..|.. ++.+..+||+|++.+|+.+++.|++|..+
T Consensus         2 ~v~~~~i~~~~~~K~~~L~~ll~~~~-~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~   80 (300)
T 3i32_A            2 TYEEEAVPAPVRGRLEVLSDLLYVAS-PDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVR   80 (300)
T ss_dssp             CSEEEEEECCSSSHHHHHHHHHHHHC-CSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCC
T ss_pred             ceEEEEEECCHHHHHHHHHHHHHhcC-CCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCce
Confidence            35788999999999999999998875 78999999999999999999975 89999999999999999999999999999


Q ss_pred             EEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHH
Q 017020          140 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE  219 (379)
Q Consensus       140 iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~  219 (379)
                      ||||||++++|+|+|++++|||||+|.+.++|+||+|||||.|+.|.|++|+++.+...++.+++..+.+++...+|+.+
T Consensus        81 vLVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie~~~~~~~~~~~~~~~~  160 (300)
T 3i32_A           81 VLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPE  160 (300)
T ss_dssp             EEEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHHHHHHHHHTCCCEECCCCCHH
T ss_pred             EEEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHHHHhCCcceEeCCCCHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHcCCCCCCCCCccccCCCCeEEEEEeeCCcccC
Q 017020          220 DVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSR  299 (379)
Q Consensus       220 ~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~  299 (379)
                      ++.+.....+...+..+..+....|.+.++++++++.++.+++||+.+.+...  +++++.++.++|++++++.|+   .
T Consensus       161 ei~~~~~~~~~~~l~~~~~~~~~~f~~~~~~l~~~~~~e~laaal~~l~~~~~--~~~~l~~~~~~~~~~~~~~g~---~  235 (300)
T 3i32_A          161 EVLEAKWRHLLARLARVPEKDYRLYQDFAGRLFAEGRVEVVAALLALLLGGAP--AERSLLTGEEGWRTYKATGPR---L  235 (300)
T ss_dssp             HHHHHHHHHHHHHHTTSCHHHHHTTHHHHHHHHHHTCHHHHHHHHHHHHTCCC--CCBCTTTCCBSCBCEEEECTT---C
T ss_pred             HHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhcCcHHHHHHHHHHHhcCCc--CccccccCCCCcEEEEEecCC---C
Confidence            99999999999999988878889999999999999999999999999998776  567888888999999999999   5


Q ss_pred             CCCChhHHHHHHhhhCCCCCCccccEEeeeCCceeeeecchhhHHHH
Q 017020          300 GFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYAS  346 (379)
Q Consensus       300 ~~~~~~~i~~~~~~~~~~~~~~ig~i~i~~~~~~~~~~~~~~~~~~~  346 (379)
                      ++  |++++ +|++. |+   +||+|++.++++    +||||...++
T Consensus       236 ~~--~~~~~-~i~~~-~~---~ig~i~~~~~~~----~~dvp~~~~~  271 (300)
T 3i32_A          236 SL--PRLVA-LLKGQ-GL---EVGKVAEAEGGF----YVDLRPEARP  271 (300)
T ss_dssp             CH--HHHHH-HHHHT-TC---CCCCEEEETTEE----EECBCSSCCC
T ss_pred             CC--cHHHH-HHHhc-CC---eECcEEEeCCEE----EEEeCHHHcC
Confidence            55  99997 77764 65   999999988887    9999987776

>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=100.00  E-value=2e-36  Score=275.70  Aligned_cols=206  Identities=44%  Similarity=0.704  Sum_probs=192.5

Q ss_pred             eEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeE
Q 017020           62 IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTV  140 (379)
Q Consensus        62 i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~i  140 (379)
                      +.+.++.++...|.+.|.+++... +++++||||+++..++.++..|.. ++.+..+||+|++.+|+.+++.|++|..+|
T Consensus         6 ~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~v   84 (212)
T 3eaq_A            6 YEEEAVPAPVRGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRV   84 (212)
T ss_dssp             BCCEEEECCTTSHHHHHHHHHHHH-CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCE
T ss_pred             eeeeEEeCCHHHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeE
Confidence            456677788889999999999876 478999999999999999999975 899999999999999999999999999999


Q ss_pred             EEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCCCHHH
Q 017020          141 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVED  220 (379)
Q Consensus       141 LVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p~~~~  220 (379)
                      ||||+++++|+|+|++++|||||+|.++.+|+||+|||||.|+.|.|++|+++.+...++.+++..+.+++...+|..++
T Consensus        85 lvaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~e  164 (212)
T 3eaq_A           85 LVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEE  164 (212)
T ss_dssp             EEECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHHHHSSCCEECCCCCHHH
T ss_pred             EEecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHHHhcCcCeecCCCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcccCccchhchHHHHHHHHhhhCHHHHHHHHHHHc
Q 017020          221 VLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLS  268 (379)
Q Consensus       221 i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~a~al~~~~  268 (379)
                      +.+.....+...+..........|.+.+++++++++++++++||+++.
T Consensus       165 i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~l~~al~~ll  212 (212)
T 3eaq_A          165 VLEAKWRHLLARLARVPEKDYRLYQDFAGRLFAEGRVEVVAALLALLL  212 (212)
T ss_dssp             HHHHHHHHHHHHHTTSCHHHHTTTHHHHHHHHHHTCHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCHHHHHHHHHhhC
Confidence            999999999999999877666899999999999999999999999873

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

Probab=100.00  E-value=2.2e-35  Score=296.20  Aligned_cols=203  Identities=34%  Similarity=0.586  Sum_probs=180.3

Q ss_pred             CCCCChHHHHHHHHHhC--CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH
Q 017020            1 MLAVGFEEDVELILENL--PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL   78 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~--p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L   78 (379)
                      |+++||.+++..|+..+  ++++|+++||||+|+++.+++..++.+|..+.+..  ......++.+.+..+....|...|
T Consensus       215 ~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~--~~~~~~~i~~~~~~~~~~~k~~~l  292 (434)
T 2db3_A          215 MLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGI--VGGACSDVKQTIYEVNKYAKRSKL  292 (434)
T ss_dssp             HTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESS--TTCCCTTEEEEEEECCGGGHHHHH
T ss_pred             hhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEecc--ccccccccceEEEEeCcHHHHHHH
Confidence            68999999999999985  67899999999999999999999999998886542  233456788888888888899888


Q ss_pred             HHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           79 SDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        79 ~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                      .+++....  .++||||+|++.|+.++..|.. ++.+..+||+|++.+|+.++++|++|+.+||||||++++|+|+|+++
T Consensus       293 ~~~l~~~~--~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~  370 (434)
T 2db3_A          293 IEILSEQA--DGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIK  370 (434)
T ss_dssp             HHHHHHCC--TTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCC
T ss_pred             HHHHHhCC--CCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCC
Confidence            88887653  4599999999999999999985 89999999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChh-hHHHHHHHHHHhC
Q 017020          158 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVG  207 (379)
Q Consensus       158 ~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~-e~~~l~~le~~~~  207 (379)
                      +|||||+|.+.++|+||+|||||+|+.|.|++|+++. +...++.+.+.+.
T Consensus       371 ~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~  421 (434)
T 2db3_A          371 HVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILE  421 (434)
T ss_dssp             EEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHH
T ss_pred             EEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999954 5556666655543

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

Probab=100.00  E-value=1.1e-33  Score=293.47  Aligned_cols=214  Identities=27%  Similarity=0.418  Sum_probs=180.1

Q ss_pred             CCCCChHHHHHHHHHhCC-------CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeec--ccccccccceEEEEEEcCC
Q 017020            1 MLAVGFEEDVELILENLP-------PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVG--NQDEKLAEGIKLYAISTTA   71 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p-------~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~--~~~~~~~~~i~~~~~~~~~   71 (379)
                      |+++||.++++.|+..++       .+.|+++||||+|+.+..++..++.+|..+.+..  .........+.+.+.....
T Consensus       187 l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  266 (579)
T 3sqw_A          187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK  266 (579)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESS
T ss_pred             hhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecc
Confidence            579999999999998764       3779999999999999999999999887665432  2223334556666555543


Q ss_pred             c-c-HHHHHHHHHH---HHcCCCcEEEEecccccHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEE
Q 017020           72 T-S-KRTILSDLIT---VYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  142 (379)
Q Consensus        72 ~-~-k~~~L~~ll~---~~~~~~~~IIF~~t~~~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLV  142 (379)
                      . . +...+..+..   ...++.++||||+|+..|+.++..|..    ++.+..+||+|++.+|..++++|++|+.+|||
T Consensus       267 ~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLV  346 (579)
T 3sqw_A          267 FANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV  346 (579)
T ss_dssp             TTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEE
T ss_pred             hhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEE
Confidence            2 2 2333333333   224567999999999999999999974    78999999999999999999999999999999


Q ss_pred             eccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeC
Q 017020          143 ATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       143 aTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~  214 (379)
                      ||+++++|+|+|++++||+|++|.+++.|+||+|||||+|+.|.|++++++.|...++.+++..+..++...
T Consensus       347 aT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~~~  418 (579)
T 3sqw_A          347 CTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQE  418 (579)
T ss_dssp             ECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCEEE
T ss_pred             EcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHHHhCCCccccc
Confidence            999999999999999999999999999999999999999999999999999999999999999988887643

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=100.00  E-value=1.2e-33  Score=279.56  Aligned_cols=213  Identities=35%  Similarity=0.601  Sum_probs=192.0

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCcc-HHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~-k~~~L~   79 (379)
                      |+++||.+.+..++..++++.|++++|||+|.++.+++..++.+|..+.+..  ......++.+++..+.... |...+.
T Consensus       191 ~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~k~~~l~  268 (410)
T 2j0s_A          191 MLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKR--DELTLEGIKQFFVAVEREEWKFDTLC  268 (410)
T ss_dssp             HTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCG--GGCSCTTEEEEEEEESSTTHHHHHHH
T ss_pred             HHhhhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecC--ccccCCCceEEEEEeCcHHhHHHHHH
Confidence            5789999999999999999999999999999999999999999998775432  2334566777777665544 888888


Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  158 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~  158 (379)
                      .++.... .+++||||++++.++.++..|.. ++.+..+||+|++.+|+.+++.|++|+.+|||||+++++|+|+|++++
T Consensus       269 ~~~~~~~-~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~  347 (410)
T 2j0s_A          269 DLYDTLT-ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSL  347 (410)
T ss_dssp             HHHHHHT-SSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEE
T ss_pred             HHHHhcC-CCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCE
Confidence            8887763 67999999999999999999975 889999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCC
Q 017020          159 IIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  216 (379)
Q Consensus       159 VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p  216 (379)
                      ||+||+|.+...|+||+||+||.|+.|.|++|+++.+...++.++++++..+++.+.+
T Consensus       348 Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~  405 (410)
T 2j0s_A          348 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN  405 (410)
T ss_dssp             EEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSC
T ss_pred             EEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHHHHHHHHHHHhCCCceecccc
Confidence            9999999999999999999999999999999999999999999999999999887654

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=100.00  E-value=4.8e-33  Score=287.13  Aligned_cols=214  Identities=27%  Similarity=0.421  Sum_probs=179.1

Q ss_pred             CCCCChHHHHHHHHHhCC-------CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeec--ccccccccceEEEEEEcCC
Q 017020            1 MLAVGFEEDVELILENLP-------PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVG--NQDEKLAEGIKLYAISTTA   71 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p-------~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~--~~~~~~~~~i~~~~~~~~~   71 (379)
                      |+++||.++++.|+..++       ++.|+++||||+|+.+.+++..++.+|..+.+..  .........+.+.+.....
T Consensus       238 l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  317 (563)
T 3i5x_A          238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK  317 (563)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESS
T ss_pred             HhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECch
Confidence            578999999999998763       3779999999999999999999999887665432  2222334556665555443


Q ss_pred             c-cH-HHHHHHHHH---HHcCCCcEEEEecccccHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEE
Q 017020           72 T-SK-RTILSDLIT---VYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  142 (379)
Q Consensus        72 ~-~k-~~~L~~ll~---~~~~~~~~IIF~~t~~~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLV  142 (379)
                      . .+ ...+..+..   ....+.++||||+|+..|+.++..|..    ++.+..+||+|++.+|..+++.|++|+.+|||
T Consensus       318 ~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLv  397 (563)
T 3i5x_A          318 FANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV  397 (563)
T ss_dssp             TTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEE
T ss_pred             hHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEE
Confidence            2 22 223333332   224578999999999999999999974    78999999999999999999999999999999


Q ss_pred             eccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeC
Q 017020          143 ATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       143 aTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~  214 (379)
                      ||+++++|+|+|++++||+|++|.++.+|+||+|||||+|+.|.|++++++.|...++.+++..+..++...
T Consensus       398 aT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~~~  469 (563)
T 3i5x_A          398 CTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQE  469 (563)
T ss_dssp             ECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCEEE
T ss_pred             EcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHHhCCCccccc
Confidence            999999999999999999999999999999999999999999999999999999999999999988887643

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

Probab=100.00  E-value=1.1e-32  Score=272.78  Aligned_cols=205  Identities=40%  Similarity=0.605  Sum_probs=180.4

Q ss_pred             CCCCChHHHHHHHHHh--CCC--CCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH
Q 017020            1 MLAVGFEEDVELILEN--LPP--KRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT   76 (379)
Q Consensus         1 mL~~GF~~di~~Il~~--~p~--~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~   76 (379)
                      |+++||..++..++..  ++.  ..|++++|||+|+.+..++..++.+|..+.+..  ......++.+.+..++...|..
T Consensus       187 ~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~i~~~~~~~~~~~~~~  264 (417)
T 2i4i_A          187 MLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGR--VGSTSENITQKVVWVEESDKRS  264 (417)
T ss_dssp             HHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC------CCSSEEEEEEECCGGGHHH
T ss_pred             hhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCC--CCCCccCceEEEEEeccHhHHH
Confidence            3568999999999985  443  689999999999999999999999988776532  2334567788888888888999


Q ss_pred             HHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCc
Q 017020           77 ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN  155 (379)
Q Consensus        77 ~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~  155 (379)
                      .+.+++.....++++||||++++.++.++..|.. ++.+..+||+|++++|..+++.|++|+.+|||||+++++|+|+|+
T Consensus       265 ~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~  344 (417)
T 2i4i_A          265 FLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISN  344 (417)
T ss_dssp             HHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCC
T ss_pred             HHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCccc
Confidence            9999988776678999999999999999999975 899999999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhC
Q 017020          156 VDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  207 (379)
Q Consensus       156 v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~  207 (379)
                      +++||+|++|.+..+|+||+||+||.|+.|.|++|+++.+...++.+.+.+.
T Consensus       345 v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~~~~  396 (417)
T 2i4i_A          345 VKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLV  396 (417)
T ss_dssp             EEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHHHHH
T ss_pred             CCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999888888877664

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=100.00  E-value=7.3e-32  Score=265.99  Aligned_cols=215  Identities=31%  Similarity=0.482  Sum_probs=185.1

Q ss_pred             CChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC-ccHHHHHHHHH
Q 017020            4 VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSDLI   82 (379)
Q Consensus         4 ~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll   82 (379)
                      .||...+..++..++.+.|++++|||+|..+..++..++.+|..+.+..  .......+.+++..+.. ..+...+..++
T Consensus       184 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  261 (412)
T 3fht_A          184 QGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR--EEETLDTIKQYYVLCSSRDEKFQALCNLY  261 (412)
T ss_dssp             TTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCG--GGSSCTTEEEEEEECSSHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeecc--ccccccCceEEEEEcCChHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999999998876543  23345666777666654 46777788877


Q ss_pred             HHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020           83 TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus        83 ~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                      ... .++++||||++++.++.++..|.. ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||+
T Consensus       262 ~~~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~  340 (412)
T 3fht_A          262 GAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN  340 (412)
T ss_dssp             HHH-SSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEE
T ss_pred             hhc-CCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEE
Confidence            766 468999999999999999999985 889999999999999999999999999999999999999999999999999


Q ss_pred             cCCC------CChhHHHHHHhhccCCCCCceEEEEeChhh-HHHHHHHHHHhCCCceeeCCCCHHHH
Q 017020          162 YELP------NDPETFVHRSGRTGRAGKEGTAILMFTSSQ-RRTVRSLERDVGCKFEFVSPPVVEDV  221 (379)
Q Consensus       162 ~~~P------~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e-~~~l~~le~~~~~~~~~~~~p~~~~i  221 (379)
                      ||+|      .+..+|+||+||+||.|+.|.|++++++.+ ...++.+++.++..++....+..+++
T Consensus       341 ~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  407 (412)
T 3fht_A          341 FDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLDEI  407 (412)
T ss_dssp             SSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC--------
T ss_pred             ECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccCCCccHHHH
Confidence            9999      467899999999999999999999998664 88999999999999998877665544

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=100.00  E-value=6.4e-32  Score=266.13  Aligned_cols=211  Identities=31%  Similarity=0.530  Sum_probs=191.5

Q ss_pred             CCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHH
Q 017020            2 LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL   81 (379)
Q Consensus         2 L~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~l   81 (379)
                      ++.+|...+..++..+++..|++++|||+|..+.++...++.+|..+.+..   .....++.+++.......|...+..+
T Consensus       176 ~~~~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~k~~~l~~~  252 (400)
T 1s2m_A          176 LSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME---ELTLKGITQYYAFVEERQKLHCLNTL  252 (400)
T ss_dssp             SSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCS---SCBCTTEEEEEEECCGGGHHHHHHHH
T ss_pred             hhhchHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEecc---ccccCCceeEEEEechhhHHHHHHHH
Confidence            456789999999999999999999999999999999999999988775542   23456677888888878888888888


Q ss_pred             HHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE
Q 017020           82 ITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII  160 (379)
Q Consensus        82 l~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI  160 (379)
                      +... ..+++||||++++.++.++..|.. ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||
T Consensus       253 ~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi  331 (400)
T 1s2m_A          253 FSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVI  331 (400)
T ss_dssp             HHHS-CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEE
T ss_pred             Hhhc-CCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEE
Confidence            8775 468999999999999999999985 89999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCC
Q 017020          161 HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  216 (379)
Q Consensus       161 ~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p  216 (379)
                      +|++|.+..+|+||+||+||.|+.|.|++++++.|...++.+++.++.+++..+..
T Consensus       332 ~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~  387 (400)
T 1s2m_A          332 NFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPAT  387 (400)
T ss_dssp             ESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSS
T ss_pred             EeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHHHHHHHHHHhCCCccccccc
Confidence            99999999999999999999999999999999999999999999999999876543

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=100.00  E-value=1.5e-32  Score=271.43  Aligned_cols=212  Identities=33%  Similarity=0.574  Sum_probs=174.3

Q ss_pred             CCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC-ccHHHHHHH
Q 017020            2 LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSD   80 (379)
Q Consensus         2 L~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~   80 (379)
                      ++.||...+..++..++++.|++++|||+|..+..+...++.+|..+.+..  .......+.+++..... ..+...+..
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~  273 (414)
T 3eiq_A          196 LSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKK--EELTLEGIRQFYINVEREEWKLDTLCD  273 (414)
T ss_dssp             HHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCC--CCCCTTSCCEEEEECSSSTTHHHHHHH
T ss_pred             hccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecC--CccCCCCceEEEEEeChHHhHHHHHHH
Confidence            567899999999999999999999999999999999999999998775532  23334556666666554 448888888


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ++... ..+++||||++++.++.++..|.. ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++|
T Consensus       274 ~~~~~-~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~V  352 (414)
T 3eiq_A          274 LYETL-TITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLV  352 (414)
T ss_dssp             HHHSS-CCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCE
T ss_pred             HHHhC-CCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEE
Confidence            88765 467999999999999999999986 8999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCC
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  216 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p  216 (379)
                      |+|++|.+..+|+||+||+||.|+.|.|++++++.+...++.+++.++..++..+..
T Consensus       353 i~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (414)
T 3eiq_A          353 INYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLN  409 (414)
T ss_dssp             EESSCCSSTHHHHHHSCCC-------CEEEEECSTHHHHHHHHHHHTTCCCEECCC-
T ss_pred             EEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHHHHHHHHcCCccccChh
Confidence            999999999999999999999999999999999999999999999999998886543

>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=99.98  E-value=3.2e-31  Score=259.82  Aligned_cols=210  Identities=24%  Similarity=0.465  Sum_probs=188.7

Q ss_pred             CChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHH
Q 017020            4 VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT   83 (379)
Q Consensus         4 ~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~   83 (379)
                      ++|...+..++...+...|++++|||+|+.+..++..++.+|..+.+.. ........+.+++...+...|...+..++.
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~  246 (391)
T 1xti_A          168 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDD-ETKLTLHGLQQYYVKLKDNEKNRKLFDLLD  246 (391)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCC-CCCCCCTTCEEEEEECCGGGHHHHHHHHHH
T ss_pred             cchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecC-ccccCcccceEEEEEcCchhHHHHHHHHHH
Confidence            5889999999999999999999999999999999999999998876543 222334567788888888889998988888


Q ss_pred             HHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEec
Q 017020           84 VYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY  162 (379)
Q Consensus        84 ~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~  162 (379)
                      .. .++++||||++++.++.++..|.. ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||+|
T Consensus       247 ~~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~  325 (391)
T 1xti_A          247 VL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY  325 (391)
T ss_dssp             HS-CCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEES
T ss_pred             hc-CCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEe
Confidence            76 578999999999999999999985 8899999999999999999999999999999999999999999999999999


Q ss_pred             CCCCChhHHHHHHhhccCCCCCceEEEEeChh-hHHHHHHHHHHhCCCceeeCC
Q 017020          163 ELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFVSP  215 (379)
Q Consensus       163 ~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~-e~~~l~~le~~~~~~~~~~~~  215 (379)
                      ++|.+..+|+||+||+||.|+.|.|++++++. +...++.+++.++..++..+.
T Consensus       326 ~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  379 (391)
T 1xti_A          326 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPD  379 (391)
T ss_dssp             SCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCS
T ss_pred             CCCCCHHHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCChhhCCc
Confidence            99999999999999999999999999999876 567889999999988887554

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

Probab=99.97  E-value=3.2e-31  Score=231.23  Aligned_cols=155  Identities=34%  Similarity=0.613  Sum_probs=146.9

Q ss_pred             cccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCC
Q 017020           58 LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG  136 (379)
Q Consensus        58 ~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g  136 (379)
                      ...++.|+++.++..+|...|..++... .++++||||+++..++.++..|.. ++.+..+||+|++.+|..++++|++|
T Consensus         6 ~~~~i~~~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g   84 (163)
T 2hjv_A            6 TTRNIEHAVIQVREENKFSLLKDVLMTE-NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRG   84 (163)
T ss_dssp             CCCCEEEEEEECCGGGHHHHHHHHHHHH-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CcccceEEEEECChHHHHHHHHHHHHhc-CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence            4567899999999999999999999876 468999999999999999999985 89999999999999999999999999


Q ss_pred             ceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceee
Q 017020          137 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV  213 (379)
Q Consensus       137 ~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~  213 (379)
                      +.+|||||+++++|+|+|++++||+||+|.++.+|+||+||+||.|+.|.+++|+++.+...++.+++.++.++++.
T Consensus        85 ~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~  161 (163)
T 2hjv_A           85 EYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKI  161 (163)
T ss_dssp             SCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHHHHHTSCCEEC
T ss_pred             CCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHHHHHHHHHCCCcCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999888764

>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=99.97  E-value=9.5e-31  Score=256.03  Aligned_cols=216  Identities=31%  Similarity=0.538  Sum_probs=187.3

Q ss_pred             CChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC-ccHHHHHHHHH
Q 017020            4 VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSDLI   82 (379)
Q Consensus         4 ~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll   82 (379)
                      .||...+..+...++.+.|++++|||+|+.+..++..++.++..+....  .......+.+.+..... ..+...+..++
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  238 (395)
T 3pey_A          161 QGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQT--NEVNVDAIKQLYMDCKNEADKFDVLTELY  238 (395)
T ss_dssp             TTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCG--GGCSCTTEEEEEEECSSHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccc--cccccccccEEEEEcCchHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999999888776543  22334556666665543 45677777776


Q ss_pred             HHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020           83 TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus        83 ~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                      ... .++++||||++++.++.++..|.. ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||+
T Consensus       239 ~~~-~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~  317 (395)
T 3pey_A          239 GLM-TIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVN  317 (395)
T ss_dssp             TTT-TSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEE
T ss_pred             Hhc-cCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEE
Confidence            654 468999999999999999999985 789999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC------ChhHHHHHHhhccCCCCCceEEEEeCh-hhHHHHHHHHHHhC-CCceeeCCCCHHHHH
Q 017020          162 YELPN------DPETFVHRSGRTGRAGKEGTAILMFTS-SQRRTVRSLERDVG-CKFEFVSPPVVEDVL  222 (379)
Q Consensus       162 ~~~P~------~~~~yiqR~GRtgR~G~~g~~i~l~~~-~e~~~l~~le~~~~-~~~~~~~~p~~~~i~  222 (379)
                      ||+|.      ++.+|+||+||+||.|+.|.|++++++ ++...++.+++..+ ..+...+.+..+++.
T Consensus       318 ~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~  386 (395)
T 3pey_A          318 YDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVE  386 (395)
T ss_dssp             SSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTTSCCCEECCSSCHHHHH
T ss_pred             cCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhCCceeecCChHHHHHHH
Confidence            99998      999999999999999999999999985 56778899999998 778877777665544

>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=99.97  E-value=2.3e-31  Score=234.71  Aligned_cols=161  Identities=28%  Similarity=0.502  Sum_probs=145.7

Q ss_pred             cccceEEEEEEcCCcc-HHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccC
Q 017020           58 LAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ  135 (379)
Q Consensus        58 ~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~  135 (379)
                      ++.++.|+++.++..+ |...|..++... +++++||||+++..++.++..|.. ++.+..+||+|++.+|..+++.|++
T Consensus         4 ~~~~i~q~~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~   82 (175)
T 2rb4_A            4 TLNNIRQYYVLCEHRKDKYQALCNIYGSI-TIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRD   82 (175)
T ss_dssp             CBCCEEEEEEECSSHHHHHHHHHHHHTTS-CCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHT
T ss_pred             ccCCceEEEEEcCChHhHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHc
Confidence            4578899999888755 999999888765 468999999999999999999985 8999999999999999999999999


Q ss_pred             CceeEEEeccccccCCCCCccceEEecCCC------CChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCC
Q 017020          136 GKFTVLVATDVAARGLDIPNVDLIIHYELP------NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCK  209 (379)
Q Consensus       136 g~~~iLVaTdv~~rGiDip~v~~VI~~~~P------~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~  209 (379)
                      |+.+|||||+++++|+|+|++++||+||+|      .+..+|+||+||+||.|+.|.+++|+++.+...++.+++.++.+
T Consensus        83 g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~  162 (175)
T 2rb4_A           83 GKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSS  162 (175)
T ss_dssp             TSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHHHHHHTCC
T ss_pred             CCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHHHHHhcCc
Confidence            999999999999999999999999999999      99999999999999999999999999999999999999999999


Q ss_pred             ceeeCCCCHH
Q 017020          210 FEFVSPPVVE  219 (379)
Q Consensus       210 ~~~~~~p~~~  219 (379)
                      +++.+++..+
T Consensus       163 ~~~~~~~~~~  172 (175)
T 2rb4_A          163 IKQLNAEDMD  172 (175)
T ss_dssp             CEEECSSCCC
T ss_pred             ccccCCchhc
Confidence            9988777644

>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=99.97  E-value=5.6e-31  Score=255.17  Aligned_cols=205  Identities=36%  Similarity=0.599  Sum_probs=185.6

Q ss_pred             CCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHH
Q 017020            2 LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL   81 (379)
Q Consensus         2 L~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~l   81 (379)
                      ++.||...+..++..+++..|++++|||+|.++.++...++.++..+...      ...++.+.+.......+.+.+..+
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~l~~~  233 (367)
T 1hv8_A          160 LNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAK------INANIEQSYVEVNENERFEALCRL  233 (367)
T ss_dssp             HTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECC------SSSSSEEEEEECCGGGHHHHHHHH
T ss_pred             hhhchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEec------CCCCceEEEEEeChHHHHHHHHHH
Confidence            46789999999999999999999999999999999999999887766432      124566777777778888888777


Q ss_pred             HHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE
Q 017020           82 ITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII  160 (379)
Q Consensus        82 l~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI  160 (379)
                      +.  ..+.++||||++++.++.++..|.. ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||
T Consensus       234 l~--~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi  311 (367)
T 1hv8_A          234 LK--NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVI  311 (367)
T ss_dssp             HC--STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEE
T ss_pred             Hh--cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEE
Confidence            76  3567999999999999999999985 88999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeC
Q 017020          161 HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       161 ~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~  214 (379)
                      ++++|.++.+|+||+||+||.|+.|.+++++++.|...++.+++..+.+++...
T Consensus       312 ~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  365 (367)
T 1hv8_A          312 NYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKLK  365 (367)
T ss_dssp             ESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCCCBC
T ss_pred             EecCCCCHHHhhhcccccccCCCccEEEEEEcHHHHHHHHHHHHHhCCCCceec
Confidence            999999999999999999999999999999999999999999999999887653

>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=99.97  E-value=6.9e-33  Score=280.67  Aligned_cols=214  Identities=31%  Similarity=0.475  Sum_probs=44.8

Q ss_pred             CChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCC-ccHHHHHHHHH
Q 017020            4 VGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSDLI   82 (379)
Q Consensus         4 ~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll   82 (379)
                      .||...+..|+..++.+.|+++||||+|.++..++..++.+|..+.+...  ......+.++++.++. ..+...+..++
T Consensus       251 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~~  328 (479)
T 3fmp_B          251 QGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE--EETLDTIKQYYVLCSSRDEKFQALCNLY  328 (479)
T ss_dssp             TTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC--------------------------------
T ss_pred             CCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEecccc--ccCcCCceEEEEEeCCHHHHHHHHHHHH
Confidence            69999999999999999999999999999999999999999988876532  2334556666665543 45777777776


Q ss_pred             HHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020           83 TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus        83 ~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                      ... ...++||||+++..++.++..|.. ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++|||
T Consensus       329 ~~~-~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~  407 (479)
T 3fmp_B          329 GAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN  407 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhc-cCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEE
Confidence            654 467999999999999999999985 789999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC------ChhHHHHHHhhccCCCCCceEEEEeChhh-HHHHHHHHHHhCCCceeeCCCCHHH
Q 017020          162 YELPN------DPETFVHRSGRTGRAGKEGTAILMFTSSQ-RRTVRSLERDVGCKFEFVSPPVVED  220 (379)
Q Consensus       162 ~~~P~------~~~~yiqR~GRtgR~G~~g~~i~l~~~~e-~~~l~~le~~~~~~~~~~~~p~~~~  220 (379)
                      ||+|.      +..+|+||+|||||.|+.|.|++|+++.+ ...++.+++.++..++....+..++
T Consensus       408 ~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~  473 (479)
T 3fmp_B          408 FDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLDE  473 (479)
T ss_dssp             ------------------------------------------------------------------
T ss_pred             ecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceECCCccHHH
Confidence            99994      66899999999999999999999998765 7889999999888887765554443

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=99.97  E-value=1e-30  Score=230.17  Aligned_cols=155  Identities=23%  Similarity=0.455  Sum_probs=143.9

Q ss_pred             ccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCc
Q 017020           59 AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK  137 (379)
Q Consensus        59 ~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~  137 (379)
                      +.++.|+++.++..+|...|.+++... +++++||||+++..++.++..|.. ++.+..+||+|++.+|+.+++.|++|+
T Consensus         3 ~~~i~q~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~   81 (172)
T 1t5i_A            3 LHGLQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQ   81 (172)
T ss_dssp             --CCEEEEEECCGGGHHHHHHHHHHHS-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             cCCeEEEEEECChHHHHHHHHHHHHhC-CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCC
Confidence            467889999999999999999999876 468999999999999999999975 899999999999999999999999999


Q ss_pred             eeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChh-hHHHHHHHHHHhCCCceeeC
Q 017020          138 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       138 ~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~-e~~~l~~le~~~~~~~~~~~  214 (379)
                      .+|||||+++++|+|+|++++||+||+|.++.+|+||+||+||.|+.|.+++|+++. +...++.+++.++..++..+
T Consensus        82 ~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  159 (172)
T 1t5i_A           82 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELP  159 (172)
T ss_dssp             CSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC
T ss_pred             CcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCC
Confidence            999999999999999999999999999999999999999999999999999999875 67889999999999888754

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

Probab=99.97  E-value=5.3e-31  Score=236.14  Aligned_cols=167  Identities=27%  Similarity=0.397  Sum_probs=133.0

Q ss_pred             HHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEE
Q 017020           38 SRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEA  116 (379)
Q Consensus        38 ~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~  116 (379)
                      ...||++|..|.+..  ......++.++++.++...|...|.+++...  ++++||||+++..++.++..|.. ++.+..
T Consensus         8 ~~~~~~~p~~i~v~~--~~~~~~~i~q~~~~~~~~~K~~~L~~~l~~~--~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~   83 (191)
T 2p6n_A            8 SSGVDLGTENLYFQS--MGAASLDVIQEVEYVKEEAKMVYLLECLQKT--PPPVLIFAEKKADVDAIHEYLLLKGVEAVA   83 (191)
T ss_dssp             ----------------------CCSEEEEEECCGGGHHHHHHHHHTTS--CSCEEEECSCHHHHHHHHHHHHHHTCCEEE
T ss_pred             cccccCCCEEEEECC--CCCCCcCceEEEEEcChHHHHHHHHHHHHhC--CCCEEEEECCHHHHHHHHHHHHHcCCcEEE
Confidence            457899999887643  3345678999999998889999998888653  56899999999999999999975 899999


Q ss_pred             eeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChh-h
Q 017020          117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-Q  195 (379)
Q Consensus       117 lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~-e  195 (379)
                      +||+|++.+|+.+++.|++|+.+|||||+++++|+|+|++++||+||+|.++++|+||+||+||.|+.|.+++|+++. +
T Consensus        84 lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~  163 (191)
T 2p6n_A           84 IHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACD  163 (191)
T ss_dssp             ECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSC
T ss_pred             EeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999976 6


Q ss_pred             HHHHHHHHHHhCC
Q 017020          196 RRTVRSLERDVGC  208 (379)
Q Consensus       196 ~~~l~~le~~~~~  208 (379)
                      ...++.+++.+..
T Consensus       164 ~~~~~~l~~~l~~  176 (191)
T 2p6n_A          164 ESVLMDLKALLLE  176 (191)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            7788888776543

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

Probab=99.97  E-value=1.7e-30  Score=226.85  Aligned_cols=156  Identities=31%  Similarity=0.584  Sum_probs=139.8

Q ss_pred             cceEEEEEEcCCcc-HHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCc
Q 017020           60 EGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK  137 (379)
Q Consensus        60 ~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~  137 (379)
                      .++.|+++.++..+ |.+.|..++... +++++||||++++.++.++..|.. ++.+..+||+|++.+|..+++.|++|+
T Consensus         2 ~~i~~~~~~~~~~~~K~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   80 (165)
T 1fuk_A            2 EGIKQFYVNVEEEEYKYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGS   80 (165)
T ss_dssp             --CEEEEEEEESGGGHHHHHHHHHHHT-TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CCcEEEEEECCcchhHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCC
Confidence            35778888887777 999999999876 468999999999999999999985 899999999999999999999999999


Q ss_pred             eeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCC
Q 017020          138 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  216 (379)
Q Consensus       138 ~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p  216 (379)
                      .+|||||+++++|+|+|++++||+||+|.++.+|+||+||+||.|+.|.|++++++.+...++.+++.++..++..+.+
T Consensus        81 ~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (165)
T 1fuk_A           81 SRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSD  159 (165)
T ss_dssp             CSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSC
T ss_pred             CEEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHHHHHHHHccCccccCcc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999998876654

>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=99.97  E-value=6.8e-32  Score=264.64  Aligned_cols=211  Identities=34%  Similarity=0.589  Sum_probs=45.5

Q ss_pred             CCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCc-cHHHHHHH
Q 017020            2 LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT-SKRTILSD   80 (379)
Q Consensus         2 L~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~-~k~~~L~~   80 (379)
                      ++.||...+..++..+++..|++++|||+|+.+.++...++.+|..+.+..  ......++.+++..+... .+...+..
T Consensus       175 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~  252 (394)
T 1fuu_A          175 LSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKK--DELTLEGIKQFYVNVEEEEYKYECLTD  252 (394)
T ss_dssp             HHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC-----------------------------
T ss_pred             hCCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecC--ccccCCCceEEEEEcCchhhHHHHHHH
Confidence            457899999999999999999999999999999999999999998876542  222334555555554443 37777777


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      ++... ..+++||||++++.++.++..|.. ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++|
T Consensus       253 ~~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~V  331 (394)
T 1fuu_A          253 LYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLV  331 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhcC-CCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEE
Confidence            77665 467999999999999999999985 7899999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCC
Q 017020          160 IHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  215 (379)
Q Consensus       160 I~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~  215 (379)
                      |+|++|.++.+|+||+||+||.|+.|.|++++++.+...++.+++.++..++..+.
T Consensus       332 i~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  387 (394)
T 1fuu_A          332 INYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPS  387 (394)
T ss_dssp             --------------------------------------------------------
T ss_pred             EEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHHHhCCcccccCc
Confidence            99999999999999999999999999999999999999999999998888876544

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=99.96  E-value=3.7e-30  Score=229.46  Aligned_cols=153  Identities=40%  Similarity=0.564  Sum_probs=128.3

Q ss_pred             ccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccC
Q 017020           57 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ  135 (379)
Q Consensus        57 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~  135 (379)
                      .++.++.++++.++..+|...|.+++....++.++||||+++..++.++..|.. ++.+..+||+|++.+|+.+++.|++
T Consensus        15 ~~~~~i~q~~~~v~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~   94 (185)
T 2jgn_A           15 STSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRS   94 (185)
T ss_dssp             -CCTTEEEEEEECCGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHH
T ss_pred             CCCCCceEEEEEeCcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHc
Confidence            356789999999999999999999998875678999999999999999999985 8999999999999999999999999


Q ss_pred             CceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCC
Q 017020          136 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCK  209 (379)
Q Consensus       136 g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~  209 (379)
                      |+.+|||||+++++|+|+|++++||+||+|.++.+|+||+||+||.|+.|.|++|+++.+...++.+++.++..
T Consensus        95 g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~l~~~  168 (185)
T 2jgn_A           95 GKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEA  168 (185)
T ss_dssp             TSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHHHHHHT
T ss_pred             CCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999888877544

>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=99.96  E-value=4.4e-29  Score=259.44  Aligned_cols=199  Identities=20%  Similarity=0.324  Sum_probs=159.5

Q ss_pred             CCCCC--hHHHHHH--HHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH
Q 017020            1 MLAVG--FEEDVEL--ILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT   76 (379)
Q Consensus         1 mL~~G--F~~di~~--Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~   76 (379)
                      |+++|  |.+++..  ++....++.|+++||||+|+.+.+.+..++..+..+.+...   ....++.+.... ....+..
T Consensus       177 is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~~---~~r~nl~~~v~~-~~~~~~~  252 (591)
T 2v1x_A          177 CSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTAS---FNRPNLYYEVRQ-KPSNTED  252 (591)
T ss_dssp             GSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEECC---CCCTTEEEEEEE-CCSSHHH
T ss_pred             ccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEecC---CCCcccEEEEEe-CCCcHHH
Confidence            35667  8777765  45455568999999999999998888888876654433321   122344433332 2223333


Q ss_pred             HHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCC
Q 017020           77 ILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  152 (379)
Q Consensus        77 ~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiD  152 (379)
                      .+..+++..   .++.++||||+|++.++.++..|.. ++.+..+||+|++.+|..++++|++|+.+|||||+++++|||
T Consensus       253 ~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID  332 (591)
T 2v1x_A          253 FIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGID  332 (591)
T ss_dssp             HHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCC
T ss_pred             HHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCC
Confidence            444444333   2468999999999999999999985 899999999999999999999999999999999999999999


Q ss_pred             CCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHH
Q 017020          153 IPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       153 ip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                      +|+|++||||++|.+.++|+||+||+||.|+.|.|++++++.|...++.+.
T Consensus       333 ~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~~~  383 (591)
T 2v1x_A          333 KPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMV  383 (591)
T ss_dssp             CSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHT
T ss_pred             cccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999887776653

>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=99.96  E-value=8.3e-29  Score=237.38  Aligned_cols=194  Identities=28%  Similarity=0.540  Sum_probs=164.1

Q ss_pred             CCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHH
Q 017020            2 LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL   81 (379)
Q Consensus         2 L~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~l   81 (379)
                      .+.||..++..++...+...|++++|||+|..+.+....++.++..+...     ....++.+.++......+.. + ..
T Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~-~-~~  214 (337)
T 2z0m_A          142 FEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC-----IGLANVEHKFVHVKDDWRSK-V-QA  214 (337)
T ss_dssp             HHTTCHHHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS-----GGGGGEEEEEEECSSSSHHH-H-HH
T ss_pred             hccccHHHHHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc-----cccCCceEEEEEeChHHHHH-H-HH
Confidence            45789999999999999999999999999999999999999888776432     22345666666665544332 2 33


Q ss_pred             HHHHcCCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020           82 ITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus        82 l~~~~~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                      +.. ..++++||||++++.++.++..|.   .+..+||+|++.+|.+++++|++|+.+|||||+++++|+|+|++++||+
T Consensus       215 ~~~-~~~~~~lvf~~~~~~~~~l~~~l~---~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~  290 (337)
T 2z0m_A          215 LRE-NKDKGVIVFVRTRNRVAKLVRLFD---NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVIN  290 (337)
T ss_dssp             HHT-CCCSSEEEECSCHHHHHHHHTTCT---TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEE
T ss_pred             HHh-CCCCcEEEEEcCHHHHHHHHHHhh---hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEE
Confidence            333 356899999999999999988876   5889999999999999999999999999999999999999999999999


Q ss_pred             cCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhC
Q 017020          162 YELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  207 (379)
Q Consensus       162 ~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~  207 (379)
                      |++|.++.+|+||+||+||.|+.|.|++++. .|...++.+++.++
T Consensus       291 ~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~~~~~~~i~~~~~  335 (337)
T 2z0m_A          291 FDAPQDLRTYIHRIGRTGRMGRKGEAITFIL-NEYWLEKEVKKVSQ  335 (337)
T ss_dssp             SSCCSSHHHHHHHHTTBCGGGCCEEEEEEES-SCHHHHHHHC----
T ss_pred             ecCCCCHHHhhHhcCccccCCCCceEEEEEe-CcHHHHHHHHHHhc
Confidence            9999999999999999999999999999999 88888888887654

>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=99.92  E-value=1.7e-30  Score=228.10  Aligned_cols=156  Identities=29%  Similarity=0.492  Sum_probs=142.2

Q ss_pred             cceEEEEEEcCC-ccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCc
Q 017020           60 EGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK  137 (379)
Q Consensus        60 ~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~  137 (379)
                      .++.|+++.++. ..|...|..++... .++++||||+++..++.++..|.. ++.+..+||+|++.+|..+++.|++|+
T Consensus         2 ~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~   80 (170)
T 2yjt_D            2 KKIHQWYYRADDLEHKTALLVHLLKQP-EATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGR   80 (170)
Confidence            356777777776 78999999888764 468999999999999999999985 789999999999999999999999999


Q ss_pred             eeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCC
Q 017020          138 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  216 (379)
Q Consensus       138 ~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p  216 (379)
                      .+|||||+++++|+|+|++++||+||+|.++.+|+||+||+||.|+.|.+++++++.+...++.+++.++..+++..++
T Consensus        81 ~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (170)
T 2yjt_D           81 VNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARVID  159 (170)
Confidence            9999999999999999999999999999999999999999999999999999999999999999999888877664443

>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=99.95  E-value=4e-27  Score=241.62  Aligned_cols=194  Identities=20%  Similarity=0.366  Sum_probs=155.9

Q ss_pred             CCCC--hHHHHHH---HHHhCCCCCcEEEEeeeCChHHHHHHHHhc--CCCceEEeecccccccccceEEEEEEcCCccH
Q 017020            2 LAVG--FEEDVEL---ILENLPPKRQSMLFSATMPSWVKKLSRKYL--DNPLNIDLVGNQDEKLAEGIKLYAISTTATSK   74 (379)
Q Consensus         2 L~~G--F~~di~~---Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l--~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k   74 (379)
                      .+.|  |..+...   +....| +.|++++|||+++.+..-....+  .+|..+ ....    ...++....  .+...+
T Consensus       152 ~~~g~~fr~~~~~l~~l~~~~~-~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~-~~~~----~r~~l~~~v--~~~~~~  223 (523)
T 1oyw_A          152 SQWGHDFRPEYAALGQLRQRFP-TLPFMALTATADDTTRQDIVRLLGLNDPLIQ-ISSF----DRPNIRYML--MEKFKP  223 (523)
T ss_dssp             CTTSSCCCHHHHGGGGHHHHCT-TSCEEEEESCCCHHHHHHHHHHHTCCSCEEE-ECCC----CCTTEEEEE--EECSSH
T ss_pred             CcCCCccHHHHHHHHHHHHhCC-CCCEEEEeCCCCHHHHHHHHHHhCCCCCeEE-eCCC----CCCceEEEE--EeCCCH
Confidence            4556  7666554   455554 68999999999988765444333  345433 2211    123443332  233566


Q ss_pred             HHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCC
Q 017020           75 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI  153 (379)
Q Consensus        75 ~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDi  153 (379)
                      ...+..++... ++.++||||+|++.++.++..|.. ++.+..+||+|++++|+.+++.|++|+.+|||||+++++|+|+
T Consensus       224 ~~~l~~~l~~~-~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~  302 (523)
T 1oyw_A          224 LDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINK  302 (523)
T ss_dssp             HHHHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCC
T ss_pred             HHHHHHHHHhc-CCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCc
Confidence            77777777654 567999999999999999999985 8999999999999999999999999999999999999999999


Q ss_pred             CccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHH
Q 017020          154 PNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  204 (379)
Q Consensus       154 p~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~  204 (379)
                      |++++||||++|.+.++|+||+||+||.|..|.|++++++.+...++.+..
T Consensus       303 p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~~~~~  353 (523)
T 1oyw_A          303 PNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLE  353 (523)
T ss_dssp             TTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHH
T ss_pred             cCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999888777654

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

Probab=99.95  E-value=3.9e-28  Score=241.07  Aligned_cols=193  Identities=22%  Similarity=0.383  Sum_probs=156.7

Q ss_pred             CCC-CChHHH-HHHHHHhCC-----------CCCcEEEEeee-CChHHH-HHHHHhcCCCceEEeecccccccccceEEE
Q 017020            1 MLA-VGFEED-VELILENLP-----------PKRQSMLFSAT-MPSWVK-KLSRKYLDNPLNIDLVGNQDEKLAEGIKLY   65 (379)
Q Consensus         1 mL~-~GF~~d-i~~Il~~~p-----------~~~Q~llfSAT-~p~~i~-~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~   65 (379)
                      ||+ +||.++ +..+++.+|           .+.|+++|||| .|..+. .+...++.    +.+.  .......++.+.
T Consensus       161 ~l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~--~~~~~~~~i~~~  234 (414)
T 3oiy_A          161 LLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVG--RLVSVARNITHV  234 (414)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSS--CCCCCCCSEEEE
T ss_pred             HHhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcC--ccccccccchhe
Confidence            456 999999 999999887           88999999999 676655 33443433    2111  122344667777


Q ss_pred             EEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEE-EeeCCCCHHHHHHHHhcccCCceeEEEe
Q 017020           66 AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASE-ALHGDISQHQRERTLNGFRQGKFTVLVA  143 (379)
Q Consensus        66 ~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~-~lhg~m~~~~R~~~~~~F~~g~~~iLVa  143 (379)
                      +...   ++.+.+..++...  ++++||||+++..|+.++..|.. ++.+. .+||+    +|+  +++|++|+.+||||
T Consensus       235 ~~~~---~~~~~l~~~l~~~--~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLva  303 (414)
T 3oiy_A          235 RISS---RSKEKLVELLEIF--RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIG  303 (414)
T ss_dssp             EESS---CCHHHHHHHHHHH--CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEE
T ss_pred             eecc---CHHHHHHHHHHHc--CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEE
Confidence            6654   4666677777764  58999999999999999999985 88998 99995    444  99999999999999


Q ss_pred             ----ccccccCCCCCc-cceEEecCCC--CChhHHHHHHhhccCCC----CCceEEEEeChhhHHHHHHHHHHhC--CCc
Q 017020          144 ----TDVAARGLDIPN-VDLIIHYELP--NDPETFVHRSGRTGRAG----KEGTAILMFTSSQRRTVRSLERDVG--CKF  210 (379)
Q Consensus       144 ----Tdv~~rGiDip~-v~~VI~~~~P--~~~~~yiqR~GRtgR~G----~~g~~i~l~~~~e~~~l~~le~~~~--~~~  210 (379)
                          |+++++|+|+|+ +++||+||+|  .+..+|+||+||+||.|    +.|.+++++  .+...++.+++.++  ..+
T Consensus       304 t~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l~~~~~~~~~~  381 (414)
T 3oiy_A          304 VQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLLLIAEE  381 (414)
T ss_dssp             ECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC--CCHHHHHHHHHHHHHHHCC
T ss_pred             ecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE--ccHHHHHHHHHHhcccccc
Confidence                999999999999 9999999999  99999999999999988    589999999  67778888888877  555


Q ss_pred             ee
Q 017020          211 EF  212 (379)
Q Consensus       211 ~~  212 (379)
                      +.
T Consensus       382 ~~  383 (414)
T 3oiy_A          382 EI  383 (414)
T ss_dssp             CE
T ss_pred             cc
Confidence            44

>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=99.94  E-value=5.6e-28  Score=254.76  Aligned_cols=126  Identities=21%  Similarity=0.260  Sum_probs=112.6

Q ss_pred             EcCCccHHHHHHHHHHH-HcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           68 STTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        68 ~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      .+...+|..++...+.. +..+.++||||+|++.++.++..|.. ++++..+||++.+.+|+.+.++|+.|  .|+||||
T Consensus       411 ~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATd  488 (844)
T 1tf5_A          411 YRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATN  488 (844)
T ss_dssp             ESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEET
T ss_pred             EeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCC
Confidence            34456788888777754 34578999999999999999999985 89999999999999998888888877  5999999


Q ss_pred             ccccCCCCC--------ccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          146 VAARGLDIP--------NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       146 v~~rGiDip--------~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      +|+||+||+        ++.|||||++|.+.+.|+||+|||||+|.+|.+++|++..|
T Consensus       489 mAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD  546 (844)
T 1tf5_A          489 MAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  546 (844)
T ss_dssp             TSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             ccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHH
Confidence            999999999        88899999999999999999999999999999999998776

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

Probab=99.93  E-value=9.4e-26  Score=248.65  Aligned_cols=204  Identities=20%  Similarity=0.350  Sum_probs=158.0

Q ss_pred             CCC-CChHHH-HHHHHHhCC-----------CCCcEEEEeee-CChHHHH-HHHHhcCCCceEEeecccccccccceEEE
Q 017020            1 MLA-VGFEED-VELILENLP-----------PKRQSMLFSAT-MPSWVKK-LSRKYLDNPLNIDLVGNQDEKLAEGIKLY   65 (379)
Q Consensus         1 mL~-~GF~~d-i~~Il~~~p-----------~~~Q~llfSAT-~p~~i~~-l~~~~l~~p~~i~~~~~~~~~~~~~i~~~   65 (379)
                      ||+ +||.++ ++.|++.+|           .+.|+++|||| .|..+.. +...++.    +.+..  ......++.+.
T Consensus       218 ~L~~~gf~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~--~~~~~~~i~~~  291 (1104)
T 4ddu_A          218 LLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGR--LVSVARNITHV  291 (1104)
T ss_dssp             HHHTSSCCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCB--CCCCCCCEEEE
T ss_pred             hhHhcCCCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEecc--CCCCcCCceeE
Confidence            466 999999 999999888           89999999999 6766553 3333332    32221  23345667777


Q ss_pred             EEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEE-EeeCCCCHHHHHHHHhcccCCceeEEEe
Q 017020           66 AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASE-ALHGDISQHQRERTLNGFRQGKFTVLVA  143 (379)
Q Consensus        66 ~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~-~lhg~m~~~~R~~~~~~F~~g~~~iLVa  143 (379)
                      ++.+   ++...|..++...  ++++||||++++.++.++..|.. ++.+. .+||+     |.+ +++|++|+.+||||
T Consensus       292 ~~~~---~k~~~L~~ll~~~--~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~~VLVa  360 (1104)
T 4ddu_A          292 RISS---RSKEKLVELLEIF--RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKINILIG  360 (1104)
T ss_dssp             EESC---CCHHHHHHHHHHH--CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSCSEEEE
T ss_pred             EEec---CHHHHHHHHHHhc--CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCCCEEEE
Confidence            7655   4666777777764  48999999999999999999985 88998 99993     555 99999999999999


Q ss_pred             ----ccccccCCCCCc-cceEEecCCCC----------------------------------------------------
Q 017020          144 ----TDVAARGLDIPN-VDLIIHYELPN----------------------------------------------------  166 (379)
Q Consensus       144 ----Tdv~~rGiDip~-v~~VI~~~~P~----------------------------------------------------  166 (379)
                          ||+++||+|+|+ |++|||||+|.                                                    
T Consensus       361 tas~TdvlarGIDip~~V~~VI~~d~P~~~~Sle~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~  440 (1104)
T 4ddu_A          361 VQAYYGKLTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEK  440 (1104)
T ss_dssp             ETTTHHHHCCSCCCTTTCCEEEEESCCEEEEECSSSSCCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_pred             ecCCCCeeEecCcCCCCCCEEEEECCCCCCCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHH
Confidence                999999999999 99999999998                                                    


Q ss_pred             --------------------ChhHHHHHHhhccCCCC----CceEEEEeChhhHHHHHHHHHHhC----CCceeeCCCCH
Q 017020          167 --------------------DPETFVHRSGRTGRAGK----EGTAILMFTSSQRRTVRSLERDVG----CKFEFVSPPVV  218 (379)
Q Consensus       167 --------------------~~~~yiqR~GRtgR~G~----~g~~i~l~~~~e~~~l~~le~~~~----~~~~~~~~p~~  218 (379)
                                          ++.+|+||+|||||.|.    .|.+++++  +|...++.|++.++    ..+.+....+.
T Consensus       441 i~~~~~~l~~~~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~--~d~~~~~~l~~~~~~~~~~~~~~~~~~~~  518 (1104)
T 4ddu_A          441 VKEMFRGVVVKDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLLLIAEEEIIEEAEANW  518 (1104)
T ss_dssp             HHHHCCSSEEETTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEEC--CCHHHHHHHHHHHHHHTCCCEEEGGGCCH
T ss_pred             HhhccceEEecCCeeEEEecChhhhhcccCchhcccCCCcccceEEEEE--ecHHHHHHHHHHHhhhcccccccccccCH
Confidence                                88899999999999653    45666666  66777778777764    33434444445


Q ss_pred             HHHHH
Q 017020          219 EDVLE  223 (379)
Q Consensus       219 ~~i~~  223 (379)
                      +++++
T Consensus       519 ~~~~~  523 (1104)
T 4ddu_A          519 KELVH  523 (1104)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55554

>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=99.92  E-value=4.2e-25  Score=235.89  Aligned_cols=177  Identities=16%  Similarity=0.368  Sum_probs=140.1

Q ss_pred             HHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH-HHHHHHHHH--c
Q 017020           10 VELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-ILSDLITVY--A   86 (379)
Q Consensus        10 i~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-~L~~ll~~~--~   86 (379)
                      +..|+... ++.|+++||||++.  ..++ .++.++..+.+.+.     ...+.++|...+..++.+ .+..++..+  .
T Consensus       231 l~~l~~~~-~~~~iIl~SAT~~~--~~l~-~~~~~~~vi~v~gr-----~~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~  301 (773)
T 2xau_A          231 LKQVVKRR-PDLKIIIMSATLDA--EKFQ-RYFNDAPLLAVPGR-----TYPVELYYTPEFQRDYLDSAIRTVLQIHATE  301 (773)
T ss_dssp             HHHHHHHC-TTCEEEEEESCSCC--HHHH-HHTTSCCEEECCCC-----CCCEEEECCSSCCSCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHhC-CCceEEEEeccccH--HHHH-HHhcCCCcccccCc-----ccceEEEEecCCchhHHHHHHHHHHHHHHhc
Confidence            34444444 47899999999965  3444 45665555654332     134666666655555443 333333332  2


Q ss_pred             CCCcEEEEecccccHHHHHHHHh------------cCCcEEEeeCCCCHHHHHHHHhccc-----CCceeEEEecccccc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALT------------SIIASEALHGDISQHQRERTLNGFR-----QGKFTVLVATDVAAR  149 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~------------~~~~v~~lhg~m~~~~R~~~~~~F~-----~g~~~iLVaTdv~~r  149 (379)
                      .++++||||+++++++.++..|.            .++.+..+||+|++++|.++++.|+     +|..+|||||+++++
T Consensus       302 ~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~  381 (773)
T 2xau_A          302 EAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAET  381 (773)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHH
T ss_pred             CCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHh
Confidence            47899999999999999999886            2577999999999999999999999     999999999999999


Q ss_pred             CCCCCccceEEecCC------------------CCChhHHHHHHhhccCCCCCceEEEEeChhhH
Q 017020          150 GLDIPNVDLIIHYEL------------------PNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  196 (379)
Q Consensus       150 GiDip~v~~VI~~~~------------------P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~  196 (379)
                      |||+|++++||++++                  |.+..+|+||+|||||. +.|.|+.|+++.+.
T Consensus       382 GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          382 SLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             TCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             CcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHHh
Confidence            999999999999888                  89999999999999999 79999999988764

>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=99.92  E-value=5e-26  Score=237.46  Aligned_cols=179  Identities=15%  Similarity=0.175  Sum_probs=143.3

Q ss_pred             CCCChHHHHHHHHHhCC-CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHH
Q 017020            2 LAVGFEEDVELILENLP-PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD   80 (379)
Q Consensus         2 L~~GF~~di~~Il~~~p-~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~   80 (379)
                      ++++|..++..|+..++ +++|+++||||+|..+..++.   .++..+.+....               +.......+..
T Consensus       289 ~~~~~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~~~~---------------~~~~~~~ll~~  350 (618)
T 2whx_A          289 TDPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIEREI---------------PERSWNTGFDW  350 (618)
T ss_dssp             CSHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEEECCC---------------CSSCCSSSCHH
T ss_pred             CCccHHHHHHHHHHHhcccCccEEEEECCCchhhhhhhc---cCCceeeecccC---------------CHHHHHHHHHH
Confidence            47889999999999886 689999999999887554332   244444433110               10111112222


Q ss_pred             HHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceE
Q 017020           81 LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI  159 (379)
Q Consensus        81 ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~V  159 (379)
                      +. .  .++++||||+|++.|+.+++.|.. ++.+..+||+    +|++++++|++|+.+||||||++++|+|+| +++|
T Consensus       351 l~-~--~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~V  422 (618)
T 2whx_A          351 IT-D--YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRV  422 (618)
T ss_dssp             HH-H--CCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEE
T ss_pred             HH-h--CCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEE
Confidence            22 2  367999999999999999999985 8899999995    688899999999999999999999999997 9988


Q ss_pred             --------------------EecCCCCChhHHHHHHhhccCCC-CCceEEEEeC---hhhHHHHHHHHHHh
Q 017020          160 --------------------IHYELPNDPETFVHRSGRTGRAG-KEGTAILMFT---SSQRRTVRSLERDV  206 (379)
Q Consensus       160 --------------------I~~~~P~~~~~yiqR~GRtgR~G-~~g~~i~l~~---~~e~~~l~~le~~~  206 (379)
                                          |||+.|.+.++|+||+|||||.| +.|.|++|++   +.|...++.+|+.+
T Consensus       423 Id~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i  493 (618)
T 2whx_A          423 IDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKM  493 (618)
T ss_dssp             EECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHH
T ss_pred             EECcceecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHh
Confidence                                78888999999999999999997 4899999998   78888888888865

>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=99.91  E-value=4e-24  Score=235.74  Aligned_cols=198  Identities=22%  Similarity=0.313  Sum_probs=147.8

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChH--HHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCc------
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSW--VKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT------   72 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~--i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~------   72 (379)
                      |+++||...++.++..+|++.|+++||||+|..  +.++...+..+|..+......    +..++++++.....      
T Consensus       302 l~d~~rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~r----p~pl~~~~~~~~~~~~~~~v  377 (1108)
T 3l9o_A          302 MRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR----PTPLQHYLFPAHGDGIYLVV  377 (1108)
T ss_dssp             TTSHHHHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCC----SSCEEEEEEETTSSCCEEEE
T ss_pred             ccccchHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCC----cccceEEEeecCCcceeeee
Confidence            577899999999999999999999999999874  456666666677665433211    22234433321100      


Q ss_pred             -------------------------------------------cH---HHHHHHHHHHH--cCCCcEEEEecccccHHHH
Q 017020           73 -------------------------------------------SK---RTILSDLITVY--AKGGKTIVFTQTKRDADEV  104 (379)
Q Consensus        73 -------------------------------------------~k---~~~L~~ll~~~--~~~~~~IIF~~t~~~~~~l  104 (379)
                                                                 .+   ...+..++..+  ....++||||++++.|+.+
T Consensus       378 d~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~l  457 (1108)
T 3l9o_A          378 DEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEEL  457 (1108)
T ss_dssp             ETTTEECHHHHHHHHTTC-----------------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHH
T ss_pred             ccccchhhhhHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHH
Confidence                                                       00   22333344332  2356999999999999999


Q ss_pred             HHHHhc-CC---------------------------------------cEEEeeCCCCHHHHHHHHhcccCCceeEEEec
Q 017020          105 SLALTS-II---------------------------------------ASEALHGDISQHQRERTLNGFRQGKFTVLVAT  144 (379)
Q Consensus       105 ~~~L~~-~~---------------------------------------~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaT  144 (379)
                      +..|.. ++                                       .+..+||+|++.+|+.+++.|++|.++|||||
T Consensus       458 a~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT  537 (1108)
T 3l9o_A          458 ALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFAT  537 (1108)
T ss_dssp             HHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEEEE
T ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEEEC
Confidence            998753 11                                       17899999999999999999999999999999


Q ss_pred             cccccCCCCCccceEEecCCC--------CChhHHHHHHhhccCCC--CCceEEEEeChh-hHHHHHHH
Q 017020          145 DVAARGLDIPNVDLIIHYELP--------NDPETFVHRSGRTGRAG--KEGTAILMFTSS-QRRTVRSL  202 (379)
Q Consensus       145 dv~~rGiDip~v~~VI~~~~P--------~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~-e~~~l~~l  202 (379)
                      +++++|||+|++++||+++.|        .++.+|+||+|||||.|  ..|.|++++++. +...++.+
T Consensus       538 ~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~~~~~~~~~l  606 (1108)
T 3l9o_A          538 ETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGM  606 (1108)
T ss_dssp             SCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCCCCHHHHHHH
T ss_pred             cHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCCcCHHHHHHH
Confidence            999999999999999988764        46778999999999999  789999998875 44444444

>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=99.91  E-value=3.3e-25  Score=233.28  Aligned_cols=127  Identities=25%  Similarity=0.252  Sum_probs=114.2

Q ss_pred             EEcCCccHHHHHHHHHHH-HcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEec
Q 017020           67 ISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT  144 (379)
Q Consensus        67 ~~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaT  144 (379)
                      +.+...+|..++...+.. +..+.++||||+|+..++.++..|.. ++++.++||++.+.+++.+.++|+.|  .|+|||
T Consensus       419 v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIAT  496 (853)
T 2fsf_A          419 VYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIAT  496 (853)
T ss_dssp             EESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEE
T ss_pred             EEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEec
Confidence            344556788888887754 34578999999999999999999985 89999999999999999999999998  699999


Q ss_pred             cccccCCCCCc--------------------------------c-----ceEEecCCCCChhHHHHHHhhccCCCCCceE
Q 017020          145 DVAARGLDIPN--------------------------------V-----DLIIHYELPNDPETFVHRSGRTGRAGKEGTA  187 (379)
Q Consensus       145 dv~~rGiDip~--------------------------------v-----~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~  187 (379)
                      |+|+||+||+.                                |     .|||||+.|.+...|.||+|||||+|.+|.+
T Consensus       497 nmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s  576 (853)
T 2fsf_A          497 NMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSS  576 (853)
T ss_dssp             SCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEE
T ss_pred             ccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeE
Confidence            99999999987                                3     6999999999999999999999999999999


Q ss_pred             EEEeChhh
Q 017020          188 ILMFTSSQ  195 (379)
Q Consensus       188 i~l~~~~e  195 (379)
                      ++|++..|
T Consensus       577 ~~fls~eD  584 (853)
T 2fsf_A          577 RFYLSMED  584 (853)
T ss_dssp             EEEEETTS
T ss_pred             EEEecccH
Confidence            99999876

>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=99.91  E-value=4.2e-25  Score=243.05  Aligned_cols=206  Identities=18%  Similarity=0.280  Sum_probs=158.1

Q ss_pred             hHHHHHHHHHhC-----------CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccH
Q 017020            6 FEEDVELILENL-----------PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSK   74 (379)
Q Consensus         6 F~~di~~Il~~~-----------p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k   74 (379)
                      |..+++.++..+           +..+|+++||||+|.. ..++..++.++..+.+..  ......++.++++   ..++
T Consensus       190 ~~~~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~--~~~~~~~i~~~~~---~~~k  263 (1054)
T 1gku_B          190 ASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGS--SRITVRNVEDVAV---NDES  263 (1054)
T ss_dssp             STHHHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSC--CEECCCCEEEEEE---SCCC
T ss_pred             ccccHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccC--cccCcCCceEEEe---chhH
Confidence            456777777776           4678999999999988 666666666665554332  2233456677666   2456


Q ss_pred             HHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEe----ccccccC
Q 017020           75 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA----TDVAARG  150 (379)
Q Consensus        75 ~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVa----Tdv~~rG  150 (379)
                      ...|..++...  ++++||||+|++.|+.++..|...+.+..+||+|     +.++++|++|+.+||||    ||++++|
T Consensus       264 ~~~L~~ll~~~--~~~~LVF~~t~~~a~~l~~~L~~~~~v~~lhg~~-----~~~l~~F~~G~~~VLVaTas~Tdv~~rG  336 (1054)
T 1gku_B          264 ISTLSSILEKL--GTGGIIYARTGEEAEEIYESLKNKFRIGIVTATK-----KGDYEKFVEGEIDHLIGTAHYYGTLVRG  336 (1054)
T ss_dssp             TTTTHHHHTTS--CSCEEEEESSHHHHHHHHHTTTTSSCEEECTTSS-----SHHHHHHHHTSCSEEEEECC------CC
T ss_pred             HHHHHHHHhhc--CCCEEEEEcCHHHHHHHHHHHhhccCeeEEeccH-----HHHHHHHHcCCCcEEEEecCCCCeeEec
Confidence            66677777654  5789999999999999999998668999999998     37889999999999999    9999999


Q ss_pred             CCCCcc-ceEEecCCC----------------------------------------------------------------
Q 017020          151 LDIPNV-DLIIHYELP----------------------------------------------------------------  165 (379)
Q Consensus       151 iDip~v-~~VI~~~~P----------------------------------------------------------------  165 (379)
                      +|+|+| ++|||||+|                                                                
T Consensus       337 IDip~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  416 (1054)
T 1gku_B          337 LDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVV  416 (1054)
T ss_dssp             SCCTTTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEE
T ss_pred             cccCCcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeE
Confidence            999995 999999999                                                                


Q ss_pred             -------CChhHHHHHHhhccCCCCCc--eEEEEeChhhHHHHHHHHHHhC---CCceeeCCCCHHHHHHH
Q 017020          166 -------NDPETFVHRSGRTGRAGKEG--TAILMFTSSQRRTVRSLERDVG---CKFEFVSPPVVEDVLES  224 (379)
Q Consensus       166 -------~~~~~yiqR~GRtgR~G~~g--~~i~l~~~~e~~~l~~le~~~~---~~~~~~~~p~~~~i~~~  224 (379)
                             .+..+|+||+|||||.|..|  .+++++...+...++.+++.++   ..+.....++.+++++.
T Consensus       417 ~~~~~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~  487 (1054)
T 1gku_B          417 REGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFIERAKLYDIEFKSIDEVDFEKLSRE  487 (1054)
T ss_dssp             ETTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECSCHHHHHHHHHHHHTTSSCCCBCSCCCHHHHHHH
T ss_pred             eecceecCcHHHHhhhhchhhhccCCCCceEEEEEEecCHHHHHHHHHHHhhccCccccCCcCCHHHHHHh
Confidence                   78999999999999987765  4787777778888888888876   35555666666666654

>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=99.90  E-value=2.3e-25  Score=223.95  Aligned_cols=176  Identities=19%  Similarity=0.204  Sum_probs=124.4

Q ss_pred             ChHHHHHHHHHhC-CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHH
Q 017020            5 GFEEDVELILENL-PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT   83 (379)
Q Consensus         5 GF~~di~~Il~~~-p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~   83 (379)
                      +|..++..+.... +.+.|+++||||+|+.+..++.    .+..+...              ....+...+...+..+.+
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~~~~~----~~~~~~~~--------------~~~~~~~~~~~~~~~l~~  175 (440)
T 1yks_A          114 ASIAARGWAAHRARANESATILMTATPPGTSDEFPH----SNGEIEDV--------------QTDIPSEPWNTGHDWILA  175 (440)
T ss_dssp             HHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCC----CSSCEEEE--------------ECCCCSSCCSSSCHHHHH
T ss_pred             chHHHHHHHHHHhccCCceEEEEeCCCCchhhhhhh----cCCCeeEe--------------eeccChHHHHHHHHHHHh
Confidence            3444444444443 3689999999999887543332    11111111              001111111222222222


Q ss_pred             HHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe-
Q 017020           84 VYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-  161 (379)
Q Consensus        84 ~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~-  161 (379)
                         .++++||||++++.++.+++.|.. ++.+..+||    ++|++++++|++|+.+|||||+++++|+|+| +++||| 
T Consensus       176 ---~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~  247 (440)
T 1yks_A          176 ---DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDC  247 (440)
T ss_dssp             ---CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEEC
T ss_pred             ---cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeC
Confidence               368999999999999999999985 889999999    4688999999999999999999999999999 999996 


Q ss_pred             ------------------cCCCCChhHHHHHHhhccCC-CCCceEEEEe---ChhhHHHHHHHHHHh
Q 017020          162 ------------------YELPNDPETFVHRSGRTGRA-GKEGTAILMF---TSSQRRTVRSLERDV  206 (379)
Q Consensus       162 ------------------~~~P~~~~~yiqR~GRtgR~-G~~g~~i~l~---~~~e~~~l~~le~~~  206 (379)
                                        |+.|.+.++|+||+||+||. |+.|.|++|+   ++.+...++.++...
T Consensus       248 g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~  314 (440)
T 1yks_A          248 RTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASM  314 (440)
T ss_dssp             CEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHH
T ss_pred             CccceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhhhhhhhhHHh
Confidence                              89999999999999999998 6899999996   677888888888765

>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=99.90  E-value=9.7e-25  Score=227.48  Aligned_cols=187  Identities=22%  Similarity=0.296  Sum_probs=141.5

Q ss_pred             CCCCChHHHHHHHHHhCCCCCc--EEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH
Q 017020            1 MLAVGFEEDVELILENLPPKRQ--SMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL   78 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q--~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L   78 (379)
                      |++++|..++..|++.++..+|  ++++|||+|..+.      ...|....+....    ...+..+    .....    
T Consensus       329 ~l~~~~~~~l~~Il~~l~~~~~~llil~SAT~~~~i~------~~~p~i~~v~~~~----~~~i~~~----~~~~~----  390 (666)
T 3o8b_A          329 STDSTTILGIGTVLDQAETAGARLVVLATATPPGSVT------VPHPNIEEVALSN----TGEIPFY----GKAIP----  390 (666)
T ss_dssp             CCSHHHHHHHHHHHHHTTTTTCSEEEEEESSCTTCCC------CCCTTEEEEECBS----CSSEEET----TEEEC----
T ss_pred             hcCccHHHHHHHHHHhhhhcCCceEEEECCCCCcccc------cCCcceEEEeecc----cchhHHH----Hhhhh----
Confidence            6899999999999999998888  6777999988421      1233322221100    1111111    00000    


Q ss_pred             HHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccc
Q 017020           79 SDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  157 (379)
Q Consensus        79 ~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~  157 (379)
                         +.. ..++++||||+|++.++.+++.|.. ++.+..+||+|++++       |+++..+||||||+++||||+| ++
T Consensus       391 ---l~~-~~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~  458 (666)
T 3o8b_A          391 ---IEA-IRGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FD  458 (666)
T ss_dssp             ---GGG-SSSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BS
T ss_pred             ---hhh-ccCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-Cc
Confidence               111 2478999999999999999999985 899999999999875       4556669999999999999997 99


Q ss_pred             eEE----------ecC-----------CCCChhHHHHHHhhccCCCCCceEEEEeChhhHHH--H--HHHHHHhCCCcee
Q 017020          158 LII----------HYE-----------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT--V--RSLERDVGCKFEF  212 (379)
Q Consensus       158 ~VI----------~~~-----------~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~--l--~~le~~~~~~~~~  212 (379)
                      +||          |||           .|.+.++|+||+||||| |+.|. +.|+++.|...  +  +.+++..+..+++
T Consensus       459 ~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~~~l~~~~i~~~~~~~~~~  536 (666)
T 3o8b_A          459 SVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGERPSGMFDSSVLCECYDAGCAW  536 (666)
T ss_dssp             EEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCCBCSSBCCHHHHHHHHHHHHHT
T ss_pred             EEEecCcccccccccccccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecchhhcccccHHHHHHHhcCCccc
Confidence            988          677           89999999999999999 99999 99999887665  4  7788877777777


Q ss_pred             eCCCCHH
Q 017020          213 VSPPVVE  219 (379)
Q Consensus       213 ~~~p~~~  219 (379)
                      ..+|..+
T Consensus       537 ~~l~~~~  543 (666)
T 3o8b_A          537 YELTPAE  543 (666)
T ss_dssp             SCCCHHH
T ss_pred             ccCCchH
Confidence            6666543

>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=99.90  E-value=5.1e-24  Score=224.70  Aligned_cols=127  Identities=24%  Similarity=0.280  Sum_probs=112.4

Q ss_pred             EcCCccHHHHHHHHHHH-HcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           68 STTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        68 ~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ......|..++...+.. +..+.++||||+|++.++.++..|.. ++++..|||++.+.++..+.++|+.|  .|+||||
T Consensus       439 ~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATn  516 (922)
T 1nkt_A          439 YKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATN  516 (922)
T ss_dssp             ESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEET
T ss_pred             EeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecc
Confidence            34445688777776654 34567999999999999999999985 89999999999888888899999988  6999999


Q ss_pred             ccccCCCCCcc----------------------------------------------------ceEEecCCCCChhHHHH
Q 017020          146 VAARGLDIPNV----------------------------------------------------DLIIHYELPNDPETFVH  173 (379)
Q Consensus       146 v~~rGiDip~v----------------------------------------------------~~VI~~~~P~~~~~yiq  173 (379)
                      +|+||+||+.+                                                    .|||||+.|.+...|.|
T Consensus       517 mAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~q  596 (922)
T 1nkt_A          517 MAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQ  596 (922)
T ss_dssp             TCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHH
T ss_pred             hhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHH
Confidence            99999999975                                                    59999999999999999


Q ss_pred             HHhhccCCCCCceEEEEeChhhH
Q 017020          174 RSGRTGRAGKEGTAILMFTSSQR  196 (379)
Q Consensus       174 R~GRtgR~G~~g~~i~l~~~~e~  196 (379)
                      |+|||||+|.+|.+++|++..|.
T Consensus       597 r~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          597 LRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             HHHTSSGGGCCEEEEEEEETTSH
T ss_pred             HhcccccCCCCeeEEEEechhHH
Confidence            99999999999999999998764

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

Probab=99.90  E-value=6.7e-23  Score=224.20  Aligned_cols=197  Identities=22%  Similarity=0.319  Sum_probs=148.3

Q ss_pred             CCCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHH---hcCCCceEEeecccccccccceEEEEEEcC-------
Q 017020            1 MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRK---YLDNPLNIDLVGNQDEKLAEGIKLYAISTT-------   70 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~---~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~-------   70 (379)
                      |.++++...++.++..+|.+.|++++|||+|.. .+++.+   ...+|..+......    +..+.++++..+       
T Consensus       204 l~d~~rg~~~e~il~~l~~~~~il~LSATi~n~-~e~a~~l~~~~~~~~~vi~~~~r----p~pl~~~~~~~~~~~~~~~  278 (1010)
T 2xgj_A          204 MRDKERGVVWEETIILLPDKVRYVFLSATIPNA-MEFAEWICKIHSQPCHIVYTNFR----PTPLQHYLFPAHGDGIYLV  278 (1010)
T ss_dssp             GGCTTTHHHHHHHHHHSCTTCEEEEEECCCTTH-HHHHHHHHHHHTSCEEEEEECCC----SSCEEEEEEETTSSCCEEE
T ss_pred             hcccchhHHHHHHHHhcCCCCeEEEEcCCCCCH-HHHHHHHHhhcCCCeEEEecCCC----cccceEEEEecCCcceeee
Confidence            457788888999999999999999999999864 334433   33556555333211    223444443311       


Q ss_pred             --Ccc-----------------------------------H--------HHHHHHHHHHH--cCCCcEEEEecccccHHH
Q 017020           71 --ATS-----------------------------------K--------RTILSDLITVY--AKGGKTIVFTQTKRDADE  103 (379)
Q Consensus        71 --~~~-----------------------------------k--------~~~L~~ll~~~--~~~~~~IIF~~t~~~~~~  103 (379)
                        ...                                   |        ...+..++...  ....++||||+|+..|+.
T Consensus       279 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~  358 (1010)
T 2xgj_A          279 VDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEE  358 (1010)
T ss_dssp             ECTTCCBCHHHHHHHHHTCC------------------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHH
T ss_pred             eccccccchHHHHHHHHHHhhhhcccccccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHH
Confidence              000                                   1        12223333332  134699999999999999


Q ss_pred             HHHHHhc-CC---------------------------------------cEEEeeCCCCHHHHHHHHhcccCCceeEEEe
Q 017020          104 VSLALTS-II---------------------------------------ASEALHGDISQHQRERTLNGFRQGKFTVLVA  143 (379)
Q Consensus       104 l~~~L~~-~~---------------------------------------~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVa  143 (379)
                      ++..|.. ++                                       .+..+||+|++.+|+.+++.|++|.++||||
T Consensus       359 la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVA  438 (1010)
T 2xgj_A          359 LALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFA  438 (1010)
T ss_dssp             HHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEEE
Confidence            9988864 22                                       2788999999999999999999999999999


Q ss_pred             ccccccCCCCCccceEEe----cCC----CCChhHHHHHHhhccCCCC--CceEEEEeChh-hHHHHHHH
Q 017020          144 TDVAARGLDIPNVDLIIH----YEL----PNDPETFVHRSGRTGRAGK--EGTAILMFTSS-QRRTVRSL  202 (379)
Q Consensus       144 Tdv~~rGiDip~v~~VI~----~~~----P~~~~~yiqR~GRtgR~G~--~g~~i~l~~~~-e~~~l~~l  202 (379)
                      |+++++|+|+|++++||+    ||.    |.++.+|+||+||+||.|.  .|.|++++++. +...++.+
T Consensus       439 T~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e~~~~~~l  508 (1010)
T 2xgj_A          439 TETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGM  508 (1010)
T ss_dssp             EGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCCHHHHHHH
T ss_pred             ehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCCHHHHHHH
Confidence            999999999999999999    999    8999999999999999996  59999999865 55555555

>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=99.90  E-value=2.8e-23  Score=220.04  Aligned_cols=198  Identities=22%  Similarity=0.329  Sum_probs=144.6

Q ss_pred             CCCChHHHHHHHHHhC---CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEE-------EEcCC
Q 017020            2 LAVGFEEDVELILENL---PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYA-------ISTTA   71 (379)
Q Consensus         2 L~~GF~~di~~Il~~~---p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~-------~~~~~   71 (379)
                      .+.++...++.++..+   +++.|++++|||+|. ..+++++ +..+ .+.....   .  ..+...+       +....
T Consensus       151 ~~~~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~~-l~~~-~~~~~~r---~--~~l~~~~~~~~~~~~~~~~  222 (702)
T 2p6r_A          151 DSEKRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEW-LDAD-YYVSDWR---P--VPLVEGVLCEGTLELFDGA  222 (702)
T ss_dssp             GCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHHH-TTCE-EEECCCC---S--SCEEEEEECSSEEEEEETT
T ss_pred             CCCCcccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHHH-hCCC-cccCCCC---C--ccceEEEeeCCeeeccCcc
Confidence            3557778888887766   578999999999986 5666664 4422 2221110   0  1111111       11100


Q ss_pred             ------ccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcC-------------------------------CcE
Q 017020           72 ------TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------IAS  114 (379)
Q Consensus        72 ------~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~-------------------------------~~v  114 (379)
                            ..+...+.+.+   .+++++||||+++++++.++..|...                               ..+
T Consensus       223 ~~~~~~~~~~~~~~~~~---~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v  299 (702)
T 2p6r_A          223 FSTSRRVKFEELVEECV---AENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGA  299 (702)
T ss_dssp             EEEEEECCHHHHHHHHH---HTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTC
T ss_pred             hhhhhhhhHHHHHHHHH---hcCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCe
Confidence                  01444444443   45789999999999999999888631                               358


Q ss_pred             EEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe----cC---CCCChhHHHHHHhhccCCC--CCc
Q 017020          115 EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE---LPNDPETFVHRSGRTGRAG--KEG  185 (379)
Q Consensus       115 ~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~----~~---~P~~~~~yiqR~GRtgR~G--~~g  185 (379)
                      ..+||+|++++|..+++.|++|..+|||||+++++|+|+|++++||+    ||   .|.+..+|+||+||+||.|  ..|
T Consensus       300 ~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G  379 (702)
T 2p6r_A          300 AFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERG  379 (702)
T ss_dssp             CEECTTSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCE
T ss_pred             EEecCCCCHHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCc
Confidence            89999999999999999999999999999999999999999999999    76   7899999999999999998  589


Q ss_pred             eEEEEeChhhHHHHHHHHHHhCCCcee
Q 017020          186 TAILMFTSSQRRTVRSLERDVGCKFEF  212 (379)
Q Consensus       186 ~~i~l~~~~e~~~l~~le~~~~~~~~~  212 (379)
                      .|++++++.+..  ..+++++....+.
T Consensus       380 ~~~~l~~~~~~~--~~~~~~l~~~~e~  404 (702)
T 2p6r_A          380 EAIIIVGKRDRE--IAVKRYIFGEPER  404 (702)
T ss_dssp             EEEEECCGGGHH--HHHHTTTSSCCCC
T ss_pred             eEEEEecCccHH--HHHHHHhcCCCCC
Confidence            999999988732  2233444444443

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

Probab=99.90  E-value=3.5e-23  Score=211.79  Aligned_cols=124  Identities=20%  Similarity=0.330  Sum_probs=67.3

Q ss_pred             cHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-------------CCcEEEeeCCCCHHHHHHHHhcccC-
Q 017020           73 SKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-------------IIASEALHGDISQHQRERTLNGFRQ-  135 (379)
Q Consensus        73 ~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-------------~~~v~~lhg~m~~~~R~~~~~~F~~-  135 (379)
                      .|...|..++...   .++.++||||+++..++.++..|..             +.....+||+|++.+|..++++|++ 
T Consensus       372 ~K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~  451 (556)
T 4a2p_A          372 PKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTS  451 (556)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC----------------------------
T ss_pred             hHHHHHHHHHHHHhcCCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhccc
Confidence            4666666666543   4578999999999999999999964             2344567888999999999999999 


Q ss_pred             CceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHH
Q 017020          136 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT  198 (379)
Q Consensus       136 g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~  198 (379)
                      |+++|||||+++++|+|+|++++|||||+|+++..|+||+|| ||. +.|.+++|+++.+...
T Consensus       452 g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~  512 (556)
T 4a2p_A          452 KDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVE  512 (556)
T ss_dssp             --CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHHHHH
T ss_pred             CceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcchHH
Confidence            999999999999999999999999999999999999999999 999 7999999999876543

>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=99.90  E-value=6.7e-23  Score=215.58  Aligned_cols=175  Identities=19%  Similarity=0.314  Sum_probs=132.6

Q ss_pred             CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEeccc
Q 017020           19 PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK   98 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~   98 (379)
                      ..+|+++||||+++.....+    ...  +......... ...  ...+.........++..+......+.++||||+|+
T Consensus       385 ~~~q~i~~SAT~~~~~~~~~----~~~--~~~~~r~~~l-~~p--~i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~  455 (661)
T 2d7d_A          385 HMHNIVYVSATPGPYEIEHT----DEM--VEQIIRPTGL-LDP--LIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTK  455 (661)
T ss_dssp             TCSEEEEECSSCCHHHHHHC----SSC--EEECCCTTCC-CCC--EEEEECSTTHHHHHHHHHHHHHTTTCEEEEECSSH
T ss_pred             cCCCEEEEecCCChhHHHhh----hCe--eeeeecccCC-CCC--eEEEecccchHHHHHHHHHHHHhcCCeEEEEECCH
Confidence            47899999999987543321    111  2211111111 111  12222222233344444444444578999999999


Q ss_pred             ccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCC-----CCChhHHH
Q 017020           99 RDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL-----PNDPETFV  172 (379)
Q Consensus        99 ~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~-----P~~~~~yi  172 (379)
                      ..++.++..|.. ++.+..+||+|++.+|..++++|++|+++|||||+++++|+|+|++++||++|.     |.+..+|+
T Consensus       456 ~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~i  535 (661)
T 2d7d_A          456 KMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLI  535 (661)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHH
T ss_pred             HHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHH
Confidence            999999999985 899999999999999999999999999999999999999999999999999997     99999999


Q ss_pred             HHHhhccCCCCCceEEEEeChhhHHHHHHHH
Q 017020          173 HRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       173 qR~GRtgR~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                      ||+|||||. ..|.|++++++.+..+.+.++
T Consensus       536 Qr~GRagR~-~~G~~i~~~~~~~~~~~~~i~  565 (661)
T 2d7d_A          536 QTIGRAARN-AEGRVIMYADKITKSMEIAIN  565 (661)
T ss_dssp             HHHHTTTTS-TTCEEEEECSSCCHHHHHHHH
T ss_pred             HHhCcccCC-CCCEEEEEEeCCCHHHHHHHH
Confidence            999999998 689999999987665544443

>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=99.89  E-value=2.9e-23  Score=220.50  Aligned_cols=199  Identities=22%  Similarity=0.238  Sum_probs=148.0

Q ss_pred             CCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEE------EcC-----
Q 017020            2 LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAI------STT-----   70 (379)
Q Consensus         2 L~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~------~~~-----   70 (379)
                      .+.++...++.++..++.+.|++++|||+|. ..+++++ +..+ .+...   ...  ..+...+.      ...     
T Consensus       151 ~~~~r~~~~~~ll~~l~~~~~ii~lSATl~n-~~~~~~~-l~~~-~~~~~---~rp--~~l~~~~~~~~~~~~~~~~~~~  222 (720)
T 2zj8_A          151 GSRDRGATLEVILAHMLGKAQIIGLSATIGN-PEELAEW-LNAE-LIVSD---WRP--VKLRRGVFYQGFVTWEDGSIDR  222 (720)
T ss_dssp             GCTTTHHHHHHHHHHHBTTBEEEEEECCCSC-HHHHHHH-TTEE-EEECC---CCS--SEEEEEEEETTEEEETTSCEEE
T ss_pred             CCCcccHHHHHHHHHhhcCCeEEEEcCCcCC-HHHHHHH-hCCc-ccCCC---CCC--CcceEEEEeCCeeeccccchhh
Confidence            3557889999999998878999999999986 4666654 4321 12111   001  11111111      111     


Q ss_pred             CccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcC----------------------------------CcEEE
Q 017020           71 ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI----------------------------------IASEA  116 (379)
Q Consensus        71 ~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~----------------------------------~~v~~  116 (379)
                      ...+...+.+.+   .+++++||||+|++.++.++..|...                                  ..+..
T Consensus       223 ~~~~~~~~~~~~---~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~  299 (720)
T 2zj8_A          223 FSSWEELVYDAI---RKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAF  299 (720)
T ss_dssp             CSSTTHHHHHHH---HTTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEE
T ss_pred             hhHHHHHHHHHH---hCCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeee
Confidence            123344444433   35789999999999999999888631                                  24899


Q ss_pred             eeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe----cC----CCCChhHHHHHHhhccCCC--CCce
Q 017020          117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE----LPNDPETFVHRSGRTGRAG--KEGT  186 (379)
Q Consensus       117 lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~----~~----~P~~~~~yiqR~GRtgR~G--~~g~  186 (379)
                      +||+|++.+|..+++.|++|.++|||||+++++|+|+|++++||+    ||    .|.+..+|+||+||+||.|  ..|.
T Consensus       300 ~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~  379 (720)
T 2zj8_A          300 HHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGE  379 (720)
T ss_dssp             ECTTSCHHHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEE
T ss_pred             ecCCCCHHHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCce
Confidence            999999999999999999999999999999999999999999999    77    6899999999999999998  5799


Q ss_pred             EEEEeChhhHHHHHHHHHHhCCCceee
Q 017020          187 AILMFTSSQRRTVRSLERDVGCKFEFV  213 (379)
Q Consensus       187 ~i~l~~~~e~~~l~~le~~~~~~~~~~  213 (379)
                      |++++++.+.  ...+++.+...++..
T Consensus       380 ~~~l~~~~~~--~~~~~~~~~~~~~~i  404 (720)
T 2zj8_A          380 GIIVSTSDDP--REVMNHYIFGKPEKL  404 (720)
T ss_dssp             EEEECSSSCH--HHHHHHHTTSCCCCC
T ss_pred             EEEEecCccH--HHHHHHHhcCCCCCc
Confidence            9999998773  233455665555543

>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=99.89  E-value=8.4e-23  Score=211.55  Aligned_cols=204  Identities=19%  Similarity=0.189  Sum_probs=149.5

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEE-EEEEcCCccHHHHHHHHHHHH-cCCCcEEEEecccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKL-YAISTTATSKRTILSDLITVY-AKGGKTIVFTQTKR   99 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~-~~~~~~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~   99 (379)
                      .+..||+|+..+..++.+.|--  ..+.+. ..  .....+.+ ..+.....+|..++...+... ..+.++||||+|+.
T Consensus       411 kL~GMTGTa~te~~Ef~~iY~l--~vv~IP-tn--kp~~R~d~~d~vy~t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e  485 (822)
T 3jux_A          411 KLAGMTGTAKTEESEFVQVYGM--EVVVIP-TH--KPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIE  485 (822)
T ss_dssp             EEEEEESSCGGGHHHHHHHSCC--CEEECC-CS--SCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESSHH
T ss_pred             HHeEECCCCchHHHHHHHHhCC--eEEEEC-CC--CCcceeecCcEEEecHHHHHHHHHHHHHHHhhCCCCEEEEECCHH
Confidence            5778999999998888887743  333332 11  11122222 234455567888887777643 45789999999999


Q ss_pred             cHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCC--------ccceEEecCCCCChhH
Q 017020          100 DADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP--------NVDLIIHYELPNDPET  170 (379)
Q Consensus       100 ~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip--------~v~~VI~~~~P~~~~~  170 (379)
                      .++.++..|.. ++++..+||++.+.++..+..+++.|  .|+||||+|+||+||+        +..+|||+++|.+...
T Consensus       486 ~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~  563 (822)
T 3jux_A          486 KSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRI  563 (822)
T ss_dssp             HHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHH
T ss_pred             HHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHH
Confidence            99999999986 89999999996666666666777776  5999999999999998        6679999999999999


Q ss_pred             HHHHHhhccCCCCCceEEEEeChhhH-------HHHHHHHHHhCCCceeeCCCCHHHHHHHHHHHHHHHHcc
Q 017020          171 FVHRSGRTGRAGKEGTAILMFTSSQR-------RTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNG  235 (379)
Q Consensus       171 yiqR~GRtgR~G~~g~~i~l~~~~e~-------~~l~~le~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~  235 (379)
                      |+||+|||||+|.+|.+++|++..|.       ..++.+.+.++.+-   ..|.....+...++.+...++.
T Consensus       564 y~qriGRTGRqG~~G~a~~fvsleD~l~r~fg~~~~~~~m~~~~~~~---~~~i~~~~v~~~ie~AQkkvE~  632 (822)
T 3jux_A          564 DNQLRGRAGRQGDPGESIFFLSLEDDLLRIFGSEQIGKVMNILKIEE---GQPIQHPMLSKLIENIQKKVEG  632 (822)
T ss_dssp             HHHHHTTSSCSSCCCEEEEEEETTSHHHHHTTHHHHHHHHHHSSCCS---SSCBCCHHHHHHHHHHHHHHHH
T ss_pred             HHHhhCccccCCCCeeEEEEechhHHHHHhhhHHHHHHHHHHcCCCC---CceeccHHHHHHHHHHHHHHHH
Confidence            99999999999999999999998773       23444444444321   1122334555555555555544

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

Probab=99.89  E-value=8.3e-23  Score=216.73  Aligned_cols=198  Identities=21%  Similarity=0.271  Sum_probs=140.8

Q ss_pred             CCCChHHHHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEE------------EEEc
Q 017020            2 LAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLY------------AIST   69 (379)
Q Consensus         2 L~~GF~~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~------------~~~~   69 (379)
                      .+.+|...++.++..++ +.|++++|||+|. ..++++++ ..+ .+.....   .  ..+...            ....
T Consensus       158 ~~~~~~~~l~~i~~~~~-~~~ii~lSATl~n-~~~~~~~l-~~~-~~~~~~r---~--~~l~~~~~~~~~~~~~~~~~~~  228 (715)
T 2va8_A          158 NDPERGPVVESVTIRAK-RRNLLALSATISN-YKQIAKWL-GAE-PVATNWR---P--VPLIEGVIYPERKKKEYNVIFK  228 (715)
T ss_dssp             GCTTTHHHHHHHHHHHH-TSEEEEEESCCTT-HHHHHHHH-TCE-EEECCCC---S--SCEEEEEEEECSSTTEEEEEET
T ss_pred             CCcccchHHHHHHHhcc-cCcEEEEcCCCCC-HHHHHHHh-CCC-ccCCCCC---C--CCceEEEEecCCcccceeeecC
Confidence            35578888999998887 8999999999975 46666644 322 1211100   0  001111            1111


Q ss_pred             C--------CccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcC------------------------------
Q 017020           70 T--------ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI------------------------------  111 (379)
Q Consensus        70 ~--------~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~------------------------------  111 (379)
                      .        ...+..   .+.+...+++++||||+++++++.++..|...                              
T Consensus       229 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  305 (715)
T 2va8_A          229 DNTTKKVHGDDAIIA---YTLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKE  305 (715)
T ss_dssp             TSCEEEEESSSHHHH---HHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHH
T ss_pred             cchhhhcccchHHHH---HHHHHHhcCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccH
Confidence            1        122333   33333456789999999999999999998742                              


Q ss_pred             -------CcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe----cC-------CCCChhHHHH
Q 017020          112 -------IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE-------LPNDPETFVH  173 (379)
Q Consensus       112 -------~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~----~~-------~P~~~~~yiq  173 (379)
                             ..+..+||+|++.+|..+++.|++|..+|||||+++++|+|+|++++||+    ||       .|.+..+|+|
T Consensus       306 ~l~~~~~~~v~~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Q  385 (715)
T 2va8_A          306 LLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQ  385 (715)
T ss_dssp             HHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHH
T ss_pred             HHHHHHhcCEEEECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHH
Confidence                   24899999999999999999999999999999999999999999999999    99       8999999999


Q ss_pred             HHhhccCCC--CCceEEEEeChhhHHHHHHHHHHhCCCcee
Q 017020          174 RSGRTGRAG--KEGTAILMFTSSQRRTVRSLERDVGCKFEF  212 (379)
Q Consensus       174 R~GRtgR~G--~~g~~i~l~~~~e~~~l~~le~~~~~~~~~  212 (379)
                      |+||+||.|  ..|.|++++++.+. ....+++++...++.
T Consensus       386 r~GRaGR~g~~~~G~~~~l~~~~~~-~~~~~~~~l~~~~e~  425 (715)
T 2va8_A          386 MSGRAGRPGFDQIGESIVVVRDKED-VDRVFKKYVLSDVEP  425 (715)
T ss_dssp             HHTTBCCTTTCSCEEEEEECSCGGG-HHHHHHHTTSSCCCC
T ss_pred             HhhhcCCCCCCCCceEEEEeCCchH-HHHHHHHHHcCCCCC
Confidence            999999998  57999999987663 222344444444443

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

Probab=99.89  E-value=1e-24  Score=230.19  Aligned_cols=129  Identities=22%  Similarity=0.364  Sum_probs=82.7

Q ss_pred             ccHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-C----CcEEEe--------eCCCCHHHHHHHHhcccC
Q 017020           72 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-I----IASEAL--------HGDISQHQRERTLNGFRQ  135 (379)
Q Consensus        72 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-~----~~v~~l--------hg~m~~~~R~~~~~~F~~  135 (379)
                      ..|...|..++...   .++.++||||+++..++.++..|.. +    +.+..+        ||+|++++|.+++++|++
T Consensus       379 ~~k~~~L~~ll~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~  458 (696)
T 2ykg_A          379 NPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKA  458 (696)
T ss_dssp             CHHHHHHHHHHHHHHTTCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC---------------------------
T ss_pred             CHHHHHHHHHHHHHhccCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHh
Confidence            46778888888765   3467999999999999999999985 4    788888        559999999999999998


Q ss_pred             -CceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHH
Q 017020          136 -GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  202 (379)
Q Consensus       136 -g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~l  202 (379)
                       |+.+|||||+++++|||+|++++||+||+|.++++|+||+|| ||. +.|.+++++++.+......+
T Consensus       459 ~g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~~~~~  524 (696)
T 2ykg_A          459 SGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIEKEQI  524 (696)
T ss_dssp             --CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC-----------CCCEEEEEESCHHHHHHHHH
T ss_pred             cCCccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHHHHHHH
Confidence             999999999999999999999999999999999999999999 998 78999999998877555544

>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=99.89  E-value=1.6e-22  Score=212.79  Aligned_cols=174  Identities=21%  Similarity=0.316  Sum_probs=132.2

Q ss_pred             CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHH-HHHHHHHHHcCCCcEEEEecc
Q 017020           19 PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-ILSDLITVYAKGGKTIVFTQT   97 (379)
Q Consensus        19 ~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-~L~~ll~~~~~~~~~IIF~~t   97 (379)
                      ...|+++||||++......    .  ...+........ ....  ...+. +...+.. ++..+......+.++||||+|
T Consensus       379 ~~~q~i~~SAT~~~~~~~~----~--~~~~~~~~r~~~-l~~p--~i~v~-~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t  448 (664)
T 1c4o_A          379 RVSQVVFVSATPGPFELAH----S--GRVVEQIIRPTG-LLDP--LVRVK-PTENQILDLMEGIRERAARGERTLVTVLT  448 (664)
T ss_dssp             TCSEEEEEESSCCHHHHHH----C--SEEEEECSCTTC-CCCC--EEEEE-CSTTHHHHHHHHHHHHHHTTCEEEEECSS
T ss_pred             hcCCEEEEecCCCHHHHHh----h--hCeeeeeeccCC-CCCC--eEEEe-cccchHHHHHHHHHHHHhcCCEEEEEECC
Confidence            4679999999998754222    1  112222111111 1111  11222 2233443 344444444457899999999


Q ss_pred             cccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCC-----CCChhHH
Q 017020           98 KRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL-----PNDPETF  171 (379)
Q Consensus        98 ~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~-----P~~~~~y  171 (379)
                      +..++.++..|.. ++.+..+||+|++.+|..++++|++|+++|||||+++++|+|+|++++||++|.     |.+..+|
T Consensus       449 ~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s~~~~  528 (664)
T 1c4o_A          449 VRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSL  528 (664)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHH
T ss_pred             HHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCcccCCCCCHHHH
Confidence            9999999999985 889999999999999999999999999999999999999999999999999997     8999999


Q ss_pred             HHHHhhccCCCCCceEEEEeChhhHHHHHHHH
Q 017020          172 VHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       172 iqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                      +||+|||||.| .|.+++++++.+....+.++
T Consensus       529 iQr~GRagR~~-~G~~i~~~~~~~~~~~~~i~  559 (664)
T 1c4o_A          529 IQTIGRAARNA-RGEVWLYADRVSEAMQRAIE  559 (664)
T ss_dssp             HHHHGGGTTST-TCEEEEECSSCCHHHHHHHH
T ss_pred             HHHHCccCcCC-CCEEEEEEcCCCHHHHHHHH
Confidence            99999999995 89999999987765555544

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

Probab=99.89  E-value=4.5e-24  Score=224.44  Aligned_cols=175  Identities=14%  Similarity=0.182  Sum_probs=131.4

Q ss_pred             hHHHHHHHHHhCC-CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHH
Q 017020            6 FEEDVELILENLP-PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV   84 (379)
Q Consensus         6 F~~di~~Il~~~p-~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~   84 (379)
                      +..++..+...++ .+.|+++||||+|+.+..+...   ++....+..               ..+.......+..+.  
T Consensus       348 ~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~---~~~i~~v~~---------------~~~~~~~~~~l~~l~--  407 (673)
T 2wv9_A          348 SIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT---NSPVHDVSS---------------EIPDRAWSSGFEWIT--  407 (673)
T ss_dssp             HHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC---SSCEEEEEC---------------CCCSSCCSSCCHHHH--
T ss_pred             HHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc---CCceEEEee---------------ecCHHHHHHHHHHHH--
Confidence            3344555555543 6899999999998765433211   111111110               011111112222222  


Q ss_pred             HcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe--
Q 017020           85 YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH--  161 (379)
Q Consensus        85 ~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~--  161 (379)
                       ..++++||||++++.++.++..|.. ++.+..+||+    +|+++++.|++|+.+|||||+++++|+|+| +++|||  
T Consensus       408 -~~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g  481 (673)
T 2wv9_A          408 -DYAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCR  481 (673)
T ss_dssp             -SCCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECC
T ss_pred             -hCCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECC
Confidence             2468999999999999999999986 7899999994    799999999999999999999999999999 999998  


Q ss_pred             ------------------cCCCCChhHHHHHHhhccCC-CCCceEEEEe---ChhhHHHHHHHHHHh
Q 017020          162 ------------------YELPNDPETFVHRSGRTGRA-GKEGTAILMF---TSSQRRTVRSLERDV  206 (379)
Q Consensus       162 ------------------~~~P~~~~~yiqR~GRtgR~-G~~g~~i~l~---~~~e~~~l~~le~~~  206 (379)
                                        |++|.+.++|+||+||+||. |+.|.|++|+   ++.+...++.+|...
T Consensus       482 ~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~  548 (673)
T 2wv9_A          482 KSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKI  548 (673)
T ss_dssp             EECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHH
T ss_pred             CcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHH
Confidence                              67899999999999999999 7899999996   577777777777654

>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=99.88  E-value=3.2e-23  Score=208.86  Aligned_cols=164  Identities=18%  Similarity=0.217  Sum_probs=123.1

Q ss_pred             CChHHHHHHHHHh-CCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHH
Q 017020            4 VGFEEDVELILEN-LPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI   82 (379)
Q Consensus         4 ~GF~~di~~Il~~-~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll   82 (379)
                      +++...+..+... .+++.|+++||||+|..+..+   +..++..+.....    .+.  ..+      ...    ...+
T Consensus       124 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~---~~~~~~~~~~~~~----~p~--~~~------~~~----~~~l  184 (451)
T 2jlq_A          124 PCSVAARGYISTRVEMGEAAAIFMTATPPGSTDPF---PQSNSPIEDIERE----IPE--RSW------NTG----FDWI  184 (451)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSS---CCCSSCEEEEECC----CCS--SCC------SSS----CHHH
T ss_pred             cchHHHHHHHHHhhcCCCceEEEEccCCCccchhh---hcCCCceEecCcc----CCc--hhh------HHH----HHHH
Confidence            3444444444432 356899999999998865432   2344554443211    010  000      111    1223


Q ss_pred             HHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe
Q 017020           83 TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH  161 (379)
Q Consensus        83 ~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  161 (379)
                      ..  ..+++||||+|++.++.++..|.. ++.+..+||++.    +++++.|++|+.+||||||++++|+|+|+ ++|||
T Consensus       185 ~~--~~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~  257 (451)
T 2jlq_A          185 TD--YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVID  257 (451)
T ss_dssp             HH--CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEE
T ss_pred             Hh--CCCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEE
Confidence            22  357999999999999999999985 889999999864    57999999999999999999999999999 99999


Q ss_pred             cC--------------------CCCChhHHHHHHhhccCCCC-CceEEEEeCh
Q 017020          162 YE--------------------LPNDPETFVHRSGRTGRAGK-EGTAILMFTS  193 (379)
Q Consensus       162 ~~--------------------~P~~~~~yiqR~GRtgR~G~-~g~~i~l~~~  193 (379)
                      ||                    .|.+.++|+||+|||||.|+ .|.|++++..
T Consensus       258 ~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          258 PRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             CCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             CCCcccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence            99                    99999999999999999997 8999888754

>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=99.88  E-value=1.9e-22  Score=201.01  Aligned_cols=123  Identities=33%  Similarity=0.545  Sum_probs=110.0

Q ss_pred             ccHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeC--------CCCHHHHHHHHhcccCCcee
Q 017020           72 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHG--------DISQHQRERTLNGFRQGKFT  139 (379)
Q Consensus        72 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg--------~m~~~~R~~~~~~F~~g~~~  139 (379)
                      ..|...|.+++...   .++.++||||+++..++.++..|.. ++.+..+||        +|++.+|..++++|++|..+
T Consensus       342 ~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~  421 (494)
T 1wp9_A          342 HPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFN  421 (494)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCS
T ss_pred             ChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCce
Confidence            34666677777654   4578999999999999999999985 899999999        99999999999999999999


Q ss_pred             EEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          140 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       140 iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      |||||+++++|+|+|++++||+||+|+++..|+||+||+||.|. |.++.++++.+
T Consensus       422 vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t  476 (494)
T 1wp9_A          422 VLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGT  476 (494)
T ss_dssp             EEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTS
T ss_pred             EEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCC
Confidence            99999999999999999999999999999999999999999997 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=99.88  E-value=2.5e-24  Score=217.42  Aligned_cols=151  Identities=18%  Similarity=0.294  Sum_probs=114.4

Q ss_pred             CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecc
Q 017020           18 PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQT   97 (379)
Q Consensus        18 p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t   97 (379)
                      +++.|+++||||+|..+..+...  ..|... +..    ..+.        .......    .++..  .++++||||+|
T Consensus       141 ~~~~~~il~SAT~~~~~~~~~~~--~~pi~~-~~~----~~~~--------~~~~~~~----~~l~~--~~~~~LVF~~s  199 (459)
T 2z83_A          141 LGEAAAIFMTATPPGTTDPFPDS--NAPIHD-LQD----EIPD--------RAWSSGY----EWITE--YAGKTVWFVAS  199 (459)
T ss_dssp             TTSCEEEEECSSCTTCCCSSCCC--SSCEEE-EEC----CCCS--------SCCSSCC----HHHHH--CCSCEEEECSC
T ss_pred             cCCccEEEEEcCCCcchhhhccC--CCCeEE-ecc----cCCc--------chhHHHH----HHHHh--cCCCEEEEeCC
Confidence            36899999999999765433211  223221 110    0000        0001111    22332  36899999999


Q ss_pred             cccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe---------------
Q 017020           98 KRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH---------------  161 (379)
Q Consensus        98 ~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~---------------  161 (379)
                      ++.++.++..|.. ++.+..+||+    +|+.+++.|++|+.+||||||++++|+|+|+ ++|||               
T Consensus       200 ~~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~  274 (459)
T 2z83_A          200 VKMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEG  274 (459)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSC
T ss_pred             hHHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCccccccccccccc
Confidence            9999999999985 8999999995    6889999999999999999999999999999 99999               


Q ss_pred             -----cCCCCChhHHHHHHhhccCCCC-CceEEEEeChh
Q 017020          162 -----YELPNDPETFVHRSGRTGRAGK-EGTAILMFTSS  194 (379)
Q Consensus       162 -----~~~P~~~~~yiqR~GRtgR~G~-~g~~i~l~~~~  194 (379)
                           |+.|.+.++|+||+|||||.|+ .|.|++|+++.
T Consensus       275 ~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          275 RVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             EEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             ccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence                 7799999999999999999997 99999999875

>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=99.88  E-value=4.3e-22  Score=220.63  Aligned_cols=179  Identities=17%  Similarity=0.234  Sum_probs=146.0

Q ss_pred             HHHHHHHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCC
Q 017020            9 DVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKG   88 (379)
Q Consensus         9 di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~   88 (379)
                      +...++..++.+.|+++||||+++....++...+.++..+...   . .....+..++...   .+......++.....+
T Consensus       740 ~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~---~-~~r~~i~~~~~~~---~~~~i~~~il~~l~~g  812 (1151)
T 2eyq_A          740 RHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATP---P-ARRLAVKTFVREY---DSMVVREAILREILRG  812 (1151)
T ss_dssp             HHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCC---C-CBCBCEEEEEEEC---CHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecC---C-CCccccEEEEecC---CHHHHHHHHHHHHhcC
Confidence            4566777777889999999999888877776666655444221   1 1122344443332   3445555666666668


Q ss_pred             CcEEEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCC-
Q 017020           89 GKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL-  164 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~-  164 (379)
                      ++++||||+++.++.++..|..   +..+..+||+|++.+|++++++|++|+.+|||||+++++|+|+|++++||+++. 
T Consensus       813 ~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~~~~  892 (1151)
T 2eyq_A          813 GQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERAD  892 (1151)
T ss_dssp             CEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTTT
T ss_pred             CeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEeCCC
Confidence            9999999999999999999975   578999999999999999999999999999999999999999999999999988 


Q ss_pred             CCChhHHHHHHhhccCCCCCceEEEEeChh
Q 017020          165 PNDPETFVHRSGRTGRAGKEGTAILMFTSS  194 (379)
Q Consensus       165 P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~  194 (379)
                      +.+...|+||+||+||.|+.|.|++++.+.
T Consensus       893 ~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          893 HFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             SSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             CCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            568999999999999999999999999764

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

Probab=99.88  E-value=6e-23  Score=209.57  Aligned_cols=128  Identities=24%  Similarity=0.357  Sum_probs=90.1

Q ss_pred             cHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-C----Cc--------EEEeeCCCCHHHHHHHHhcccC-
Q 017020           73 SKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-I----IA--------SEALHGDISQHQRERTLNGFRQ-  135 (379)
Q Consensus        73 ~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-~----~~--------v~~lhg~m~~~~R~~~~~~F~~-  135 (379)
                      .|...|..++...   .++.++||||+++..++.++..|.. +    +.        ...+||+|++.+|.+++++|++ 
T Consensus       371 ~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~  450 (555)
T 3tbk_A          371 PKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRAS  450 (555)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-------------------------
T ss_pred             HHHHHHHHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcC
Confidence            4566666666543   3468999999999999999999974 2    33        4455679999999999999999 


Q ss_pred             CceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHH
Q 017020          136 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  202 (379)
Q Consensus       136 g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~l  202 (379)
                      |+++|||||+++++|+|+|++++|||||+|+++..|+||+|| ||. +.|.+++|+++.+......+
T Consensus       451 g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~~~~  515 (555)
T 3tbk_A          451 GDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIEKEKA  515 (555)
T ss_dssp             -CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHHHHHHHH
T ss_pred             CCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCHHHHHHH
Confidence            999999999999999999999999999999999999999999 999 89999999998876555444

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

Probab=99.88  E-value=7.3e-22  Score=215.92  Aligned_cols=127  Identities=24%  Similarity=0.302  Sum_probs=102.4

Q ss_pred             HHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CC---------------------------------------cE
Q 017020           75 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-II---------------------------------------AS  114 (379)
Q Consensus        75 ~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~---------------------------------------~v  114 (379)
                      ...+...+... ...++||||+|++.|+.++..|.. ++                                       .+
T Consensus       324 ~~~li~~l~~~-~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi  402 (997)
T 4a4z_A          324 WPEIVNYLRKR-ELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGI  402 (997)
T ss_dssp             HHHHHHHHHHT-TCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTE
T ss_pred             HHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCe
Confidence            44444455443 357999999999999999998864 33                                       47


Q ss_pred             EEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE--------ecCCCCChhHHHHHHhhccCCC--CC
Q 017020          115 EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII--------HYELPNDPETFVHRSGRTGRAG--KE  184 (379)
Q Consensus       115 ~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI--------~~~~P~~~~~yiqR~GRtgR~G--~~  184 (379)
                      ..+||+|++.+|+.+++.|++|.++|||||+++++|+|+|++.+|+        +++.|.++.+|+||+|||||.|  ..
T Consensus       403 ~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~  482 (997)
T 4a4z_A          403 AVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDST  482 (997)
T ss_dssp             EEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCCSEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSS
T ss_pred             eeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCCceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcc
Confidence            8999999999999999999999999999999999999999955555        2334449999999999999998  67


Q ss_pred             ceEEEEeC--hhhHHHHHHH
Q 017020          185 GTAILMFT--SSQRRTVRSL  202 (379)
Q Consensus       185 g~~i~l~~--~~e~~~l~~l  202 (379)
                      |.|++++.  +.+...++.+
T Consensus       483 G~vi~l~~~~~~~~~~~~~~  502 (997)
T 4a4z_A          483 GTVIVMAYNSPLSIATFKEV  502 (997)
T ss_dssp             EEEEEECCSSCCCHHHHHHH
T ss_pred             eEEEEecCCCcchHHHHHHH
Confidence            88888883  3455555555

>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=99.87  E-value=2.5e-21  Score=207.84  Aligned_cols=123  Identities=20%  Similarity=0.333  Sum_probs=72.4

Q ss_pred             cHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-------------CCcEEEeeCCCCHHHHHHHHhcccC-
Q 017020           73 SKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-------------IIASEALHGDISQHQRERTLNGFRQ-  135 (379)
Q Consensus        73 ~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-------------~~~v~~lhg~m~~~~R~~~~~~F~~-  135 (379)
                      .|...|..++...   .++.++||||++++.++.++..|..             +..+..+||+|++.+|..++++|++ 
T Consensus       613 ~K~~~L~~lL~~~~~~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~  692 (797)
T 4a2q_A          613 PKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTS  692 (797)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC---------------------------
T ss_pred             hHHHHHHHHHHHHhccCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhcc
Confidence            3556666666542   4568999999999999999999964             2355677999999999999999999 


Q ss_pred             CceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHH
Q 017020          136 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRR  197 (379)
Q Consensus       136 g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~  197 (379)
                      |.++|||||+++++|||+|++++||+||+|.++..|+||+|| ||. +.|.+++|+++.+..
T Consensus       693 g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~e  752 (797)
T 4a2q_A          693 KDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (797)
T ss_dssp             -CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHHHH
T ss_pred             CCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcHH
Confidence            999999999999999999999999999999999999999999 999 799999999987653

>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=99.86  E-value=3.1e-21  Score=210.76  Aligned_cols=166  Identities=17%  Similarity=0.252  Sum_probs=144.1

Q ss_pred             CCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCCHHHHHHHHhcccCCc--eeEEEecc
Q 017020           70 TATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGK--FTVLVATD  145 (379)
Q Consensus        70 ~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~~~~R~~~~~~F~~g~--~~iLVaTd  145 (379)
                      ....|...|..++... ++.++||||+++..++.++..|..  ++.+..+||+|++.+|+.++++|++|+  ++|||||+
T Consensus       486 ~~~~K~~~L~~ll~~~-~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~  564 (968)
T 3dmq_A          486 NFDPRVEWLMGYLTSH-RSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSE  564 (968)
T ss_dssp             TTSHHHHHHHHHHHHT-SSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSC
T ss_pred             CccHHHHHHHHHHHhC-CCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecc
Confidence            3456888999988874 578999999999999999999983  899999999999999999999999998  99999999


Q ss_pred             ccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHh--CCCceeeCCCCHHHHHH
Q 017020          146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV--GCKFEFVSPPVVEDVLE  223 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~--~~~~~~~~~p~~~~i~~  223 (379)
                      ++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++++...+....+.+.+..  +.++.....|..+++.+
T Consensus       565 v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~ee~i~~~~~~k~~~~~~~~~~~~~i~~  644 (968)
T 3dmq_A          565 IGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRTIYD  644 (968)
T ss_dssp             CTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSHHHHHHHHHHHTTCCSSSCCSSHHHHHH
T ss_pred             hhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEecCCChHHHHHHHHHHhCCCceecCCCCHHHHHH
Confidence            9999999999999999999999999999999999999999777775544444445555555  56666678899999999


Q ss_pred             HHHHHHHHHHccc
Q 017020          224 SSAEQVVATLNGV  236 (379)
Q Consensus       224 ~~~~~~~~~l~~~  236 (379)
                      ...+.+...+...
T Consensus       645 ~~~~~l~~~l~~~  657 (968)
T 3dmq_A          645 SVYNDLINYLASP  657 (968)
T ss_dssp             HHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHhcc
Confidence            8888888877654

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

Probab=99.86  E-value=2.7e-21  Score=203.07  Aligned_cols=191  Identities=17%  Similarity=0.164  Sum_probs=142.3

Q ss_pred             CCCCChHHHHHHHHHhCC-CCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHH
Q 017020            1 MLAVGFEEDVELILENLP-PKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILS   79 (379)
Q Consensus         1 mL~~GF~~di~~Il~~~p-~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~   79 (379)
                      |++++|..+++.++..++ .+.|++++|||. +.+..++... ..+..+...   ...  .....   ....      + 
T Consensus       251 l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~-~~i~~l~~~~-~~~~~v~~~---~r~--~~l~~---~~~~------l-  313 (677)
T 3rc3_A          251 IRDPARGWAWTRALLGLCAEEVHLCGEPAAI-DLVMELMYTT-GEEVEVRDY---KRL--TPISV---LDHA------L-  313 (677)
T ss_dssp             GGCTTTHHHHHHHHHHCCEEEEEEEECGGGH-HHHHHHHHHH-TCCEEEEEC---CCS--SCEEE---CSSC------C-
T ss_pred             cCCccchHHHHHHHHccCccceEEEeccchH-HHHHHHHHhc-CCceEEEEe---eec--chHHH---HHHH------H-
Confidence            578899999999999998 788999999995 3456665543 333333211   000  11110   0000      0 


Q ss_pred             HHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccC--CceeEEEeccccccCCCCCcc
Q 017020           80 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ--GKFTVLVATDVAARGLDIPNV  156 (379)
Q Consensus        80 ~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~--g~~~iLVaTdv~~rGiDip~v  156 (379)
                      ..+..  .....||||+|+++++.++..|.. ++.+..+||+|++++|+.+++.|++  |..+|||||+++++|+|+ ++
T Consensus       314 ~~l~~--~~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v  390 (677)
T 3rc3_A          314 ESLDN--LRPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SI  390 (677)
T ss_dssp             CSGGG--CCTTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CB
T ss_pred             HHHHh--cCCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-Cc
Confidence            01111  134568999999999999999985 7899999999999999999999999  889999999999999999 89


Q ss_pred             ceEEecCC--------------CCChhHHHHHHhhccCCCCC---ceEEEEeChhhHHHHHHHHHHhCCCcee
Q 017020          157 DLIIHYEL--------------PNDPETFVHRSGRTGRAGKE---GTAILMFTSSQRRTVRSLERDVGCKFEF  212 (379)
Q Consensus       157 ~~VI~~~~--------------P~~~~~yiqR~GRtgR~G~~---g~~i~l~~~~e~~~l~~le~~~~~~~~~  212 (379)
                      ++||++++              |.+..+|+||+|||||.|..   |.|+.++. .+...++.+.......++.
T Consensus       391 ~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~~-~d~~~~~~~~~~~~~~i~~  462 (677)
T 3rc3_A          391 RRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNH-EDLSLLKEILKRPVDPIRA  462 (677)
T ss_dssp             SEEEESCSBC-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESST-THHHHHHHHHHSCCCCCCC
T ss_pred             cEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEec-chHHHHHHHHhcCcchhhh
Confidence            99999999              88999999999999999964   66666554 4555666666655555544

>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=99.85  E-value=1.3e-21  Score=206.42  Aligned_cols=103  Identities=28%  Similarity=0.518  Sum_probs=89.0

Q ss_pred             CCcEEEEecccccHHHHHHHHhc-------CCcEEEeeCC--------CCHHHHHHHHhcccCCceeEEEeccccccCCC
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS-------IIASEALHGD--------ISQHQRERTLNGFRQGKFTVLVATDVAARGLD  152 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~-------~~~v~~lhg~--------m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiD  152 (379)
                      +.++||||++++.++.++..|..       ++.+..+||+        |++.+|.+++++|++|+.+|||||+++++|||
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GID  479 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLD  479 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSC
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCc
Confidence            68999999999999999999985       5889999999        99999999999999999999999999999999


Q ss_pred             CCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeCh
Q 017020          153 IPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS  193 (379)
Q Consensus       153 ip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~  193 (379)
                      +|++++|||||+|.++.+|+||+||+||.|   .+++++.+
T Consensus       480 ip~v~~VI~~d~p~s~~~~~Qr~GRArr~g---~~~~l~~~  517 (699)
T 4gl2_A          480 IKECNIVIRYGLVTNEIAMVQARGRARADE---STYVLVAH  517 (699)
T ss_dssp             CCSCCCCEEESCCCCHHHHHHHHTTSCSSS---CEEEEEEE
T ss_pred             cccCCEEEEeCCCCCHHHHHHHcCCCCCCC---ceEEEEEe
Confidence            999999999999999999999999976654   45555443

>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=99.85  E-value=8.6e-22  Score=209.76  Aligned_cols=179  Identities=17%  Similarity=0.299  Sum_probs=129.1

Q ss_pred             CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecc
Q 017020           18 PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQT   97 (379)
Q Consensus        18 p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t   97 (379)
                      ..+.|+++||||+++....+.  +..+.. +.+..... .....+..++  .+......++..+.+....+.+++|||++
T Consensus       514 ~~~~~vL~mSATp~p~tl~~~--~~g~~~-~s~i~~~p-~~r~~i~~~~--~~~~~~~~l~~~i~~~l~~g~qvlVf~~~  587 (780)
T 1gm5_A          514 GKMVDTLVMSATPIPRSMALA--FYGDLD-VTVIDEMP-PGRKEVQTML--VPMDRVNEVYEFVRQEVMRGGQAFIVYPL  587 (780)
T ss_dssp             SSCCCEEEEESSCCCHHHHHH--HTCCSS-CEEECCCC-SSCCCCEECC--CCSSTHHHHHHHHHHHTTTSCCBCCBCCC
T ss_pred             CCCCCEEEEeCCCCHHHHHHH--HhCCcc-eeeeeccC-CCCcceEEEE--eccchHHHHHHHHHHHHhcCCcEEEEecc
Confidence            357899999999877655544  333322 11111111 1112233222  22233444444444455567899999997


Q ss_pred             cc--------cHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCC
Q 017020           98 KR--------DADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP  165 (379)
Q Consensus        98 ~~--------~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P  165 (379)
                      .+        .++.+++.|..    ++.+..+||+|++.+|+.++++|++|+.+|||||+++++|+|+|++++||+++.|
T Consensus       588 ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDiP~v~~VIi~d~~  667 (780)
T 1gm5_A          588 IEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPE  667 (780)
T ss_dssp             C--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCS
T ss_pred             hhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccccCCCCCEEEEeCCC
Confidence            64        46778888876    4679999999999999999999999999999999999999999999999999999


Q ss_pred             C-ChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHH
Q 017020          166 N-DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  202 (379)
Q Consensus       166 ~-~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~l  202 (379)
                      . +...|.||+||+||.|+.|.|++++++.+....+.+
T Consensus       668 r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~~~~~~~rl  705 (780)
T 1gm5_A          668 RFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERL  705 (780)
T ss_dssp             SSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHH
T ss_pred             CCCHHHHHHHhcccCcCCCCCEEEEEECCCChHHHHHH
Confidence            6 788999999999999999999999985443333333

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

Probab=99.84  E-value=1.4e-21  Score=195.81  Aligned_cols=162  Identities=17%  Similarity=0.190  Sum_probs=116.8

Q ss_pred             CChHHHHHHHHHhC-CCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHHHHHH
Q 017020            4 VGFEEDVELILENL-PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI   82 (379)
Q Consensus         4 ~GF~~di~~Il~~~-p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll   82 (379)
                      ++|......+.... +.+.|+++||||+|+.+..+..   .++..+.+..               ..+... ...+...+
T Consensus       107 ~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~~---~~~~i~~~~~---------------~~~~~~-~~~~~~~l  167 (431)
T 2v6i_A          107 PASVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPP---SNSPIIDEET---------------RIPDKA-WNSGYEWI  167 (431)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSCC---CSSCCEEEEC---------------CCCSSC-CSSCCHHH
T ss_pred             ccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhcC---CCCceeeccc---------------cCCHHH-HHHHHHHH
Confidence            34555555555543 5689999999999875332221   0111111110               011111 11112233


Q ss_pred             HHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccce---
Q 017020           83 TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL---  158 (379)
Q Consensus        83 ~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~---  158 (379)
                      ..  .++++||||++++.++.+++.|.. ++.+..+||+    +|++++++|++|+.+|||||+++++|+|+| +.+   
T Consensus       168 ~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~  240 (431)
T 2v6i_A          168 TE--FDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVID  240 (431)
T ss_dssp             HS--CSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEE
T ss_pred             Hc--CCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEe
Confidence            32  357999999999999999999985 7899999998    578899999999999999999999999999 654   


Q ss_pred             --------------EEecCCCCChhHHHHHHhhccCCCC-CceEEEEe
Q 017020          159 --------------IIHYELPNDPETFVHRSGRTGRAGK-EGTAILMF  191 (379)
Q Consensus       159 --------------VI~~~~P~~~~~yiqR~GRtgR~G~-~g~~i~l~  191 (379)
                                    ||+++.|.+.++|+||+||+||.|. .|.++++.
T Consensus       241 ~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          241 PRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             CCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             cCccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence                          6788999999999999999999984 55656655

>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=99.84  E-value=2.4e-20  Score=203.29  Aligned_cols=123  Identities=20%  Similarity=0.333  Sum_probs=72.4

Q ss_pred             cHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-------------CCcEEEeeCCCCHHHHHHHHhcccC-
Q 017020           73 SKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-------------IIASEALHGDISQHQRERTLNGFRQ-  135 (379)
Q Consensus        73 ~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-------------~~~v~~lhg~m~~~~R~~~~~~F~~-  135 (379)
                      .|...|..++...   .++.++||||++++.++.++..|..             +..+..+||+|++.+|..++++|++ 
T Consensus       613 ~K~~~L~~lL~~~~~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~  692 (936)
T 4a2w_A          613 PKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTS  692 (936)
T ss_dssp             HHHHHHHHHHHHTTTSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC---------------------------
T ss_pred             HHHHHHHHHHHHHhccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhcc
Confidence            3555555666543   3468999999999999999999974             2345567999999999999999999 


Q ss_pred             CceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHH
Q 017020          136 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRR  197 (379)
Q Consensus       136 g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~  197 (379)
                      |+++|||||+++++|||+|++++||+||+|.++..|+||+|| ||. +.|.++++++..+..
T Consensus       693 g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~e  752 (936)
T 4a2w_A          693 KDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (936)
T ss_dssp             -CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHHHH
T ss_pred             CCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCHH
Confidence            999999999999999999999999999999999999999999 999 789999999886543

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.84  E-value=3.1e-20  Score=211.88  Aligned_cols=186  Identities=14%  Similarity=0.164  Sum_probs=139.1

Q ss_pred             HHhCCCCCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHH-------HHHHHHHHHHc
Q 017020           14 LENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKR-------TILSDLITVYA   86 (379)
Q Consensus        14 l~~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~-------~~L~~ll~~~~   86 (379)
                      ...++++.|++++|||+|. ..+++++.-.++..+.......  .+..++.+....+.....       ..+...+..+.
T Consensus      1077 ~~~~~~~~riI~lSATl~N-~~dla~WL~~~~~~~~~~~~~~--RPvpL~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~ 1153 (1724)
T 4f92_B         1077 SSQIERPIRIVALSSSLSN-AKDVAHWLGCSATSTFNFHPNV--RPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHS 1153 (1724)
T ss_dssp             HHTTSSCCEEEEEESCBTT-HHHHHHHHTCCSTTEEECCGGG--CSSCEEEEEEEECCCSHHHHHHTTHHHHHHHHHHHC
T ss_pred             HhhcCCCceEEEEeCCCCC-HHHHHHHhCCCCCCeEEeCCCC--CCCCeEEEEEeccCCCchhhhhhhcchHHHHHHHhc
Confidence            3456789999999999985 6778876654443332222111  123344443333322221       12334455556


Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-----------------------------------CCcEEEeeCCCCHHHHHHHHh
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-----------------------------------IIASEALHGDISQHQRERTLN  131 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-----------------------------------~~~v~~lhg~m~~~~R~~~~~  131 (379)
                      +++++||||+|++.|+.++..|..                                   ...+.++||+|++.+|..+.+
T Consensus      1154 ~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE~ 1233 (1724)
T 4f92_B         1154 PKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQ 1233 (1724)
T ss_dssp             SSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHHH
T ss_pred             CCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHHH
Confidence            678999999999999988876531                                   125789999999999999999


Q ss_pred             cccCCceeEEEeccccccCCCCCccceEEe----------cCCCCChhHHHHHHhhccCCCC--CceEEEEeChhhHHHH
Q 017020          132 GFRQGKFTVLVATDVAARGLDIPNVDLIIH----------YELPNDPETFVHRSGRTGRAGK--EGTAILMFTSSQRRTV  199 (379)
Q Consensus       132 ~F~~g~~~iLVaTdv~~rGiDip~v~~VI~----------~~~P~~~~~yiqR~GRtgR~G~--~g~~i~l~~~~e~~~l  199 (379)
                      .|++|.++|||||+++++|+|+|...+||.          ...|.++.+|+||+|||||+|.  .|.|++++.+.+...+
T Consensus      1234 lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~~~~~~ 1313 (1724)
T 4f92_B         1234 LFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFF 1313 (1724)
T ss_dssp             HHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGGGHHHH
T ss_pred             HHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecchHHHHH
Confidence            999999999999999999999999999993          3357899999999999999995  7999999999888777


Q ss_pred             HHH
Q 017020          200 RSL  202 (379)
Q Consensus       200 ~~l  202 (379)
                      +.+
T Consensus      1314 ~~l 1316 (1724)
T 4f92_B         1314 KKF 1316 (1724)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            655

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.81  E-value=7.7e-20  Score=208.59  Aligned_cols=184  Identities=19%  Similarity=0.262  Sum_probs=134.7

Q ss_pred             hCCCCCcEEEEeeeCChHHHHHHHHhcCCCc-eEEeecccccccccceEEEEEEcCCccH---HHHHH----HHHHHHcC
Q 017020           16 NLPPKRQSMLFSATMPSWVKKLSRKYLDNPL-NIDLVGNQDEKLAEGIKLYAISTTATSK---RTILS----DLITVYAK   87 (379)
Q Consensus        16 ~~p~~~Q~llfSAT~p~~i~~l~~~~l~~p~-~i~~~~~~~~~~~~~i~~~~~~~~~~~k---~~~L~----~ll~~~~~   87 (379)
                      .++++.|++++|||+|+ ..+++++.-.++. .+.+.....  .+..++++++.......   ...+.    ..+.....
T Consensus       240 ~~~~~~riI~LSATl~N-~~dvA~wL~~~~~~~~~~~~~~~--RPvpL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~  316 (1724)
T 4f92_B          240 MTQEDVRLIGLSATLPN-YEDVATFLRVDPAKGLFYFDNSF--RPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAG  316 (1724)
T ss_dssp             HHTCCCEEEEEECSCTT-HHHHHHHTTCCHHHHEEECCGGG--CSSCEEEECCEECCCCHHHHHHHHHHHHHHHHTTCCS
T ss_pred             hCCCCCcEEEEecccCC-HHHHHHHhCCCCCCCeEEECCCC--ccCccEEEEeccCCcchhhhhHHHHHHHHHHHHHHhc
Confidence            45788999999999985 6777765433332 222222111  12345555544443322   22222    22222234


Q ss_pred             CCcEEEEecccccHHHHHHHHhc--------------------------------------CCcEEEeeCCCCHHHHHHH
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS--------------------------------------IIASEALHGDISQHQRERT  129 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~--------------------------------------~~~v~~lhg~m~~~~R~~~  129 (379)
                      ++++||||+|++.|+.++..|..                                      ...+.++||+|++.+|..+
T Consensus       317 ~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~~v  396 (1724)
T 4f92_B          317 KNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLV  396 (1724)
T ss_dssp             SCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHHHH
T ss_pred             CCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHHHH
Confidence            67999999999999999887742                                      0247899999999999999


Q ss_pred             HhcccCCceeEEEeccccccCCCCCccceEEe----cC------CCCChhHHHHHHhhccCCC--CCceEEEEeChhhHH
Q 017020          130 LNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE------LPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRR  197 (379)
Q Consensus       130 ~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~----~~------~P~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~e~~  197 (379)
                      .+.|++|.++|||||+++++|||+|.+++||.    |+      .|.++.+|.||+|||||+|  ..|.++++.++.+..
T Consensus       397 E~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~~~  476 (1724)
T 4f92_B          397 EDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQ  476 (1724)
T ss_dssp             HHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTTCC
T ss_pred             HHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchhHH
Confidence            99999999999999999999999999999995    44      3568999999999999988  579999999888766


Q ss_pred             HHHHH
Q 017020          198 TVRSL  202 (379)
Q Consensus       198 ~l~~l  202 (379)
                      ....+
T Consensus       477 ~~~~l  481 (1724)
T 4f92_B          477 YYLSL  481 (1724)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55554

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

Probab=99.81  E-value=3.8e-20  Score=188.44  Aligned_cols=184  Identities=11%  Similarity=0.107  Sum_probs=129.7

Q ss_pred             HHHHHHHHhCCCCCcEEEEeeeCChHHHHHHH-HhcCCCceEEeeccc----ccccccceEEEEEEcC------------
Q 017020            8 EDVELILENLPPKRQSMLFSATMPSWVKKLSR-KYLDNPLNIDLVGNQ----DEKLAEGIKLYAISTT------------   70 (379)
Q Consensus         8 ~di~~Il~~~p~~~Q~llfSAT~p~~i~~l~~-~~l~~p~~i~~~~~~----~~~~~~~i~~~~~~~~------------   70 (379)
                      +++..+++.++...+++++|||+|.....+.. ..+.++..+.+....    ....+..+....+..+            
T Consensus       240 ~~~~~il~~~~~~~~~l~lSATp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  319 (510)
T 2oca_A          240 KSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTY  319 (510)
T ss_dssp             HHHHHHGGGCTTCCEEEEEESCGGGCSSCHHHHHHHHCSEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCH
T ss_pred             ccHHHHHHhcccCcEEEEEEeCCCCCcccHHHhHHhhCCeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccch
Confidence            56788889998899999999999766433221 122334333221100    0000111111111111            


Q ss_pred             ---------CccHHHHHHHHHHHH-cC-CCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCce
Q 017020           71 ---------ATSKRTILSDLITVY-AK-GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF  138 (379)
Q Consensus        71 ---------~~~k~~~L~~ll~~~-~~-~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~  138 (379)
                               ...+...+..++... .. +.++||||+ .+.++.+++.|.. +..+..+||+|++.+|+++++.|++|+.
T Consensus       320 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~  398 (510)
T 2oca_A          320 QEEIKIITGLSKRNKWIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKG  398 (510)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCS
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCC
Confidence                     112333445555443 22 345666666 7888889999986 5789999999999999999999999999


Q ss_pred             eEEEec-cccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeC
Q 017020          139 TVLVAT-DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT  192 (379)
Q Consensus       139 ~iLVaT-dv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~  192 (379)
                      +||||| +++++|+|+|++++||++++|.++..|+||+||+||.|..|.++++++
T Consensus       399 ~vLv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          399 IIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             CEEEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             CEEEEEcChhhcccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            999999 999999999999999999999999999999999999998775555554

>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=99.81  E-value=4.5e-21  Score=193.43  Aligned_cols=118  Identities=24%  Similarity=0.433  Sum_probs=103.7

Q ss_pred             CccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccC
Q 017020           71 ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG  150 (379)
Q Consensus        71 ~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rG  150 (379)
                      ...|...+.+++... .+.++||||++++.++.++..|    .+..+||++++.+|++++++|++|+.+|||||+++++|
T Consensus       333 ~~~k~~~l~~~l~~~-~~~k~lvF~~~~~~~~~l~~~l----~~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~G  407 (472)
T 2fwr_A          333 SKNKIRKLREILERH-RKDKIIIFTRHNELVYRISKVF----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEG  407 (472)
T ss_dssp             CSHHHHHHHHHHHHT-SSSCBCCBCSCHHHHHHHHHHT----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSS
T ss_pred             ChHHHHHHHHHHHhC-CCCcEEEEECCHHHHHHHHHHh----CcceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcC
Confidence            345777888888774 5789999999999999999887    36789999999999999999999999999999999999


Q ss_pred             CCCCccceEEecCCCCChhHHHHHHhhccCCCCC-ceEE--EEeCh
Q 017020          151 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE-GTAI--LMFTS  193 (379)
Q Consensus       151 iDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~-g~~i--~l~~~  193 (379)
                      +|+|++++||+++.|.++..|+||+||+||.|.. +.++  .+++.
T Consensus       408 ldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~  453 (472)
T 2fwr_A          408 IDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISR  453 (472)
T ss_dssp             SCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEEC
T ss_pred             cccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeC
Confidence            9999999999999999999999999999999844 3444  45543

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

Probab=99.80  E-value=1e-19  Score=171.34  Aligned_cols=125  Identities=15%  Similarity=0.272  Sum_probs=98.0

Q ss_pred             CCccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCCHHHHHHHHhcccCC-cee-EEEec
Q 017020           70 TATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQG-KFT-VLVAT  144 (379)
Q Consensus        70 ~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~~~~R~~~~~~F~~g-~~~-iLVaT  144 (379)
                      ....|...|.+++... ..+.++||||+++..++.+...|..  ++.+..+||++++.+|+.++++|+++ ..+ +|++|
T Consensus        93 ~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st  172 (271)
T 1z5z_A           93 RRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSV  172 (271)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEEC
T ss_pred             ccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEeh
Confidence            3467999999888765 3578999999999999999999974  88999999999999999999999998 677 78999


Q ss_pred             cccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceE--EEEeChh
Q 017020          145 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA--ILMFTSS  194 (379)
Q Consensus       145 dv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~--i~l~~~~  194 (379)
                      +++++|+|++++++||+||+|+++..|.||+||++|.|+++.+  +.+++..
T Consensus       173 ~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~  224 (271)
T 1z5z_A          173 KAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  224 (271)
T ss_dssp             CTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             hhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCC
Confidence            9999999999999999999999999999999999999977655  4555543

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

Probab=99.77  E-value=1.3e-18  Score=180.50  Aligned_cols=101  Identities=21%  Similarity=0.280  Sum_probs=88.8

Q ss_pred             HHHHcCCCcEEEEecccccHHHHHHHHhc-C--------CcEEEeeCCCCHHHHHHHHhcccCCcee---EEEecccccc
Q 017020           82 ITVYAKGGKTIVFTQTKRDADEVSLALTS-I--------IASEALHGDISQHQRERTLNGFRQGKFT---VLVATDVAAR  149 (379)
Q Consensus        82 l~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~--------~~v~~lhg~m~~~~R~~~~~~F~~g~~~---iLVaTdv~~r  149 (379)
                      +....+.+++||||++++.|+.++..|.. +        -.+..+||++++ +|+.++++|++|+.+   |||||+++++
T Consensus       433 l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~  511 (590)
T 3h1t_A          433 MKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQELETSTPVILTTSQLLTT  511 (590)
T ss_dssp             HHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCTTCCCCCEEEESSTTTT
T ss_pred             HHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCCCCCCCEEEEECChhhc
Confidence            33334568999999999999999999964 2        127889999864 799999999998876   8999999999


Q ss_pred             CCCCCccceEEecCCCCChhHHHHHHhhccCCCC
Q 017020          150 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  183 (379)
Q Consensus       150 GiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~  183 (379)
                      |+|+|++++||++++|.++..|+||+||+||.|.
T Consensus       512 GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          512 GVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             TCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             CccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            9999999999999999999999999999999774

>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=99.67  E-value=1e-16  Score=162.61  Aligned_cols=123  Identities=15%  Similarity=0.278  Sum_probs=103.6

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCCHHHHHHHHhcccCC-cee-EEEeccc
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQG-KFT-VLVATDV  146 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~~~~R~~~~~~F~~g-~~~-iLVaTdv  146 (379)
                      ..|...+.+++... ..+.++||||+++..++.++..|..  ++.+..+||++++.+|++++++|++| ..+ +|++|++
T Consensus       324 s~K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~  403 (500)
T 1z63_A          324 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKA  403 (500)
T ss_dssp             CHHHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCC
T ss_pred             chhHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEeccc
Confidence            46777777777654 4578999999999999999999974  78999999999999999999999988 555 8999999


Q ss_pred             cccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceE--EEEeChh
Q 017020          147 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA--ILMFTSS  194 (379)
Q Consensus       147 ~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~--i~l~~~~  194 (379)
                      +++|+|+|++++||+||+|+++..|.||+||++|.|+.+.+  +.++...
T Consensus       404 ~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~  453 (500)
T 1z63_A          404 GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  453 (500)
T ss_dssp             C-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETT
T ss_pred             ccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCC
Confidence            99999999999999999999999999999999999977655  4455543

>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=99.64  E-value=1.2e-15  Score=160.00  Aligned_cols=134  Identities=12%  Similarity=0.244  Sum_probs=113.0

Q ss_pred             ccHHHHHHHHHHHH--cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCcee---EEEecc
Q 017020           72 TSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT---VLVATD  145 (379)
Q Consensus        72 ~~k~~~L~~ll~~~--~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~---iLVaTd  145 (379)
                      ..|...+..++...  ..+.++||||+++..++.+...|.. ++.+..+||++++.+|++++++|++|...   +|++|+
T Consensus       398 s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~  477 (644)
T 1z3i_X          398 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK  477 (644)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG
T ss_pred             ChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecc
Confidence            45777888887765  2478999999999999999999975 89999999999999999999999998754   899999


Q ss_pred             ccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCce--EEEEeChh--hHHHHHHHHHH
Q 017020          146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGT--AILMFTSS--QRRTVRSLERD  205 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~--~i~l~~~~--e~~~l~~le~~  205 (379)
                      ++++|+|++++++||+||+|+++..|.|++||++|.|++..  +|.+++..  |...+...++.
T Consensus       478 a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~tiEe~i~~~~~~K  541 (644)
T 1z3i_X          478 AGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQRQAHK  541 (644)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHHHHHHHHHH
T ss_pred             cccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEEECCCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999996654  44455544  44444444443

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

Probab=99.60  E-value=5.7e-15  Score=158.54  Aligned_cols=136  Identities=18%  Similarity=0.323  Sum_probs=116.9

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCce---eEEEeccc
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF---TVLVATDV  146 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~---~iLVaTdv  146 (379)
                      ..|..+|..++..+ ..+.++||||.....++.+...|.. ++.+..+||++++.+|+.++++|+++..   .+|++|++
T Consensus       555 s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~a  634 (800)
T 3mwy_W          555 SGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRA  634 (800)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHH
T ss_pred             ChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEeccc
Confidence            45788888888776 3467999999999999999999974 8999999999999999999999998655   49999999


Q ss_pred             cccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCce--EEEEeChh--hHHHHHHHHHHhC
Q 017020          147 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGT--AILMFTSS--QRRTVRSLERDVG  207 (379)
Q Consensus       147 ~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~--~i~l~~~~--e~~~l~~le~~~~  207 (379)
                      ++.|+|++.+++||+||+|+++..+.||+||++|.|++..  ++.|++..  |...+...++...
T Consensus       635 gg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe~i~~~~~~K~~  699 (800)
T 3mwy_W          635 GGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMI  699 (800)
T ss_dssp             HTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHHHHHHHHHHHTT
T ss_pred             ccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999996544  45556554  6667777666653

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=99.53  E-value=4e-14  Score=154.70  Aligned_cols=120  Identities=11%  Similarity=0.111  Sum_probs=95.4

Q ss_pred             CCcEEEEecccccHHHHHHHHhc-C------------CcE-EEeeCC----------C----------CHH---------
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS-I------------IAS-EALHGD----------I----------SQH---------  124 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~-~------------~~v-~~lhg~----------m----------~~~---------  124 (379)
                      +.++||||+|+..|..++..|.. +            +.+ ..+||+          +          ++.         
T Consensus       537 g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I  616 (1038)
T 2w00_A          537 GFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAI  616 (1038)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHH
Confidence            45899999999999999998864 2            344 455642          2          332         


Q ss_pred             --------------------HHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCC
Q 017020          125 --------------------QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE  184 (379)
Q Consensus       125 --------------------~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~  184 (379)
                                          +|..++++|++|+++|||+||++.+|+|+|.+ +|+++|.|.+...|+|++||++|.+..
T Consensus       617 ~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~  695 (1038)
T 2w00_A          617 REYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDA  695 (1038)
T ss_dssp             HHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCT
T ss_pred             HHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCC
Confidence                                48889999999999999999999999999999 789999999999999999999998753


Q ss_pred             ----ceEEEEeChhhHHHHHHHHHHhCCC
Q 017020          185 ----GTAILMFTSSQRRTVRSLERDVGCK  209 (379)
Q Consensus       185 ----g~~i~l~~~~e~~~l~~le~~~~~~  209 (379)
                          |.++.|+.. .......+..+.+..
T Consensus       696 ~K~~G~IVdf~~~-~~~l~~Al~~y~~~~  723 (1038)
T 2w00_A          696 TKTFGNIVTFRDL-ERSTIDAITLFGDKN  723 (1038)
T ss_dssp             TCCSEEEEESSCC-HHHHHHHHHHTSCSS
T ss_pred             CCCcEEEEEcccc-HHHHHHHHHHHhCCC
Confidence                666666654 445556666665544

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=99.12  E-value=1.8e-11  Score=92.54  Aligned_cols=72  Identities=18%  Similarity=0.227  Sum_probs=53.4

Q ss_pred             EEEEEeeCCcccCCCCChhHHHHHHhhhCCCCCCccccEEeeeCCceeeeecchhhHHHHhhhhcccCcceEeeeehhh
Q 017020          287 VTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFNTKSVIWLTYRFR  365 (379)
Q Consensus       287 ~~l~~~~g~~~~~~~~~~~~i~~~~~~~~~~~~~~ig~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  365 (379)
                      +||+++.|+   +|++.|++|+++|++++|+++++||+|+|+++++    .+++|+..++.++..+++.+++++..+++
T Consensus         1 ~~~~i~~Gr---k~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~~s----~v~v~~~~~~~~~~~l~~~~i~g~~~~v~   72 (76)
T 2g0c_A            1 MKLYFNGGK---KKKIRAVDFVGTIAKIDGVSADDIGIITIMDNAS----YVEILNGKGPHVLKVMKNTTVKGKQLKVN   72 (76)
T ss_dssp             CEEEESCCC---C----CHHHHHHHHTSTTCCGGGEEEEEECSSCE----EEEECTTCHHHHHHHHTTCCC---CCCEE
T ss_pred             CEEEEeCCC---ccCCCHHHHHHHHHHccCCChhhccEEEEeCCcE----EEEECHHHHHHHHHHhccccCcCceEEEE
Confidence            379999999   9999999999999999999999999999999999    55666666666666666666666655543

>2e29_A ATP-dependent RNA helicase DDX50; ATP binding, hydrolase, nuclear protein, nucleotide-binding, RNA-binding, GUCT domain, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.5

Probab=98.78  E-value=9.6e-09  Score=79.92  Aligned_cols=83  Identities=17%  Similarity=0.141  Sum_probs=71.1

Q ss_pred             HcCCCCCCCCCccccCCCCeEEEEEeeCCcccCCCCChhHHHHHHhhhCC-CCCCccccEEeeeCCceeeeecchhhHHH
Q 017020          267 LSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYP-TAADEIGKIHIIADDRVCIDTVILLYFYA  345 (379)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~i~~~~~~~~~-~~~~~ig~i~i~~~~~~~~~~~~~~~~~~  345 (379)
                      ++|+.+ +++||++++.+|++|+.+..++    ..-+|+++|++|++..+ ...++|++|++.+|.+  |+|||||+..+
T Consensus         2 ~SG~te-~~~RSLLt~~eG~~Tl~l~~~~----~i~~~~y~w~~L~~~l~e~~~~~v~~m~l~~d~~--GavFDvP~e~~   74 (92)
T 2e29_A            2 SSGSSG-FEPRSLITSDKGFVTMTLESLE----EIQDVSCAWKELNRKLSSNAVSQITRMCLLKGNM--GVCFDVPTTES   74 (92)
T ss_dssp             CCSCSC-CCCCCCCCCCCCEEEEEEECSS----CCSSTHHHHHHHHHHSCHHHHTTCEEEEECTTSS--EEEEEEEHHHH
T ss_pred             CCCcCC-CCCcccccCCCCCEEEEEecCC----cccchHHHHHHHHHhcCHHHHhhhCeEEEecCCC--EEEEECcHHHH
Confidence            467777 4569999999999999998876    46789999999999666 4556899999999999  99999999999


Q ss_pred             HhhhhcccCcc
Q 017020          346 SVRLGLFNTKS  356 (379)
Q Consensus       346 ~~~~~~~~~~~  356 (379)
                      +.+++...+..
T Consensus        75 ~~~~~~~~~~~   85 (92)
T 2e29_A           75 ERLQAEWHDSD   85 (92)
T ss_dssp             HHHHHHCCSSS
T ss_pred             HHHHhhCCCCc
Confidence            99998776655

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.67  E-value=6.7e-07  Score=95.00  Aligned_cols=205  Identities=19%  Similarity=0.222  Sum_probs=130.4

Q ss_pred             cEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEEEEEcCCccHHHHH-HHHHHHHcCCCcEEEEeccccc
Q 017020           22 QSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVYAKGGKTIVFTQTKRD  100 (379)
Q Consensus        22 Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~L-~~ll~~~~~~~~~IIF~~t~~~  100 (379)
                      .+..||.|...+..++.+.|--+  .+.+ +........... -.+......|..++ .++...+..+.|+||+|.|.+.
T Consensus       380 kLsGMTGTA~tE~~Ef~~iY~l~--Vv~I-PTn~p~~R~D~~-d~vy~t~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~  455 (997)
T 2ipc_A          380 KRAGMTGTAKTEEKEFQEIYGMD--VVVV-PTNRPVIRKDFP-DVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEK  455 (997)
T ss_dssp             EEEEEESSCGGGHHHHHHHHCCC--EEEC-CCSSCCCCEEEE-EEEESSHHHHHHHHHHHHHHHHHHTCCEEEECSSHHH
T ss_pred             HheecCCCchHHHHHHHHHhCCC--EEEc-CCCCCcccccCC-CeEEcCHHHHHHHHHHHHHHHHHCCCCEEEEeCCHHH
Confidence            56679999988888888877544  2322 222111111111 22233345566554 4555566678999999999999


Q ss_pred             HHHHHHHHh-----------------------------------------------------------------------
Q 017020          101 ADEVSLALT-----------------------------------------------------------------------  109 (379)
Q Consensus       101 ~~~l~~~L~-----------------------------------------------------------------------  109 (379)
                      .+.++..|.                                                                       
T Consensus       456 SE~LS~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~  535 (997)
T 2ipc_A          456 SERLSQMLKEPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVH  535 (997)
T ss_dssp             HHHHHHHHHCGGGGHHHHHHHHHHHHHHHTTCCSHHHHHHHHHTSSSTTCSHHHHSGGGGGCCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhccccchhhhhhhhhhhhhhhhccccchhhhhhhhhccccccccccccccccccccccccccccccchhhh
Confidence            999998887                                                                       


Q ss_pred             -----c-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCcc-------------------c-------
Q 017020          110 -----S-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV-------------------D-------  157 (379)
Q Consensus       110 -----~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v-------------------~-------  157 (379)
                           . +++..+|.+.-...+-+-+-+.=+.|  .|-|||+.|+||.||.--                   +       
T Consensus       536 ~~~~~~~gI~H~VLNAK~he~EAeIIAqAG~~G--aVTIATNMAGRGTDIkLggn~e~~~~~~~~~~~~~~~~~~~~~~~  613 (997)
T 2ipc_A          536 TLAVLRQGIPHQVLNAKHHAREAEIVAQAGRSK--TVTIATNMAGRGTDIKLGGNPEYLAAALLEKEGFDRYEWKVELFI  613 (997)
T ss_dssp             HHHHHHHCCCCCEECSSSHHHHHHHHHTTTSTT--CEEEECSSTTTTSCCCSSCCHHHHHHHTTSSSCSSTTHHHHHHHH
T ss_pred             hhHHHHcCCCeeeccccchHHHHHHHHhcCCCC--eEEEEecccCCCcCeecCCCHHHHHHHHHHhhccccccccccccc
Confidence                 2 45556666664333333333433444  588999999999998321                   1       


Q ss_pred             ------------------------------------------------eEEecCCCCChhHHHHHHhhccCCCCCceEEE
Q 017020          158 ------------------------------------------------LIIHYELPNDPETFVHRSGRTGRAGKEGTAIL  189 (379)
Q Consensus       158 ------------------------------------------------~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~  189 (379)
                                                                      |||--..+.|..-=.|-.||+||.|.+|.+..
T Consensus       614 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~V~e~GGLhVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF  693 (997)
T 2ipc_A          614 KKMVAGKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRF  693 (997)
T ss_dssp             HHHHHTCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTCCCCEEESSCCSSHHHHHHHHHTSSCSSCCCEEEE
T ss_pred             ccccccchhhccccchhhhhhhhHHHHHHHhhhhhhhhhhHHHhcCCeEEEeccCCchHHHHHHHhcccccCCCCCCeEE
Confidence                                                            78888889999999999999999999999988


Q ss_pred             EeChhhH-------HHHHHHHHHhCCCceeeCCCCHHHHHHHHHHHHHHHHcc
Q 017020          190 MFTSSQR-------RTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNG  235 (379)
Q Consensus       190 l~~~~e~-------~~l~~le~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~  235 (379)
                      |++-.|.       ..+..+...++.+-   ..|....++...++.+...++.
T Consensus       694 ~LSLeDdLmr~fg~~~~~~~m~~l~~~~---~~~Ie~~~v~~~ie~AQkkvE~  743 (997)
T 2ipc_A          694 YVSFDDDLMRLFASDRVIAMLDRMGFDD---SEPIEHPMVTRSIERAQKRVED  743 (997)
T ss_dssp             EEESSSHHHHHSSCTTHHHHHHHTCCCS---SSCBCCHHHHHHHHHHHHHHHH
T ss_pred             EEECChHHHHhhchHHHHHHHHHcCCCC---CCcccchHHHHHHHHHHHHHHH
Confidence            8876542       12334444444321   1233334555555555555443

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.20  E-value=1.7e-06  Score=88.54  Aligned_cols=75  Identities=16%  Similarity=0.287  Sum_probs=49.7

Q ss_pred             CCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCCceeEEE--eccccccCCCCCc----cceEE
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLV--ATDVAARGLDIPN----VDLII  160 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLV--aTdv~~rGiDip~----v~~VI  160 (379)
                      .++.+|||++|....+.++..|.. .. ...+|..  .+|+++++.|+++. .||+  +|+.+++|||+|+    +++||
T Consensus       383 ~~g~~lvff~S~~~~~~v~~~l~~-~~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~Vi  457 (540)
T 2vl7_A          383 SSKSVLVFFPSYEMLESVRIHLSG-IP-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFESLV  457 (540)
T ss_dssp             CSSEEEEEESCHHHHHHHHTTCTT-SC-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHhcc-Cc-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccEEE
Confidence            467899999999999999887754 33 4556654  46889999999864 5666  8999999999998    89999


Q ss_pred             ecCCCC
Q 017020          161 HYELPN  166 (379)
Q Consensus       161 ~~~~P~  166 (379)
                      ++++|.
T Consensus       458 i~~lPf  463 (540)
T 2vl7_A          458 LAGLPY  463 (540)
T ss_dssp             EESCCC
T ss_pred             EECCCC
Confidence            999985

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=97.92  E-value=8.4e-05  Score=77.28  Aligned_cols=76  Identities=22%  Similarity=0.294  Sum_probs=53.7

Q ss_pred             CCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc--ccccCCCCCc--cceEEecC
Q 017020           88 GGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATD--VAARGLDIPN--VDLIIHYE  163 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd--v~~rGiDip~--v~~VI~~~  163 (379)
                      ++.++||++|....+.+++.|. .+... ..-+++..++..++++|+ +...||++|.  .+++|||+|+  ..+||..+
T Consensus       448 ~g~~lvlF~Sy~~l~~v~~~l~-~~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~  524 (620)
T 4a15_A          448 KKNTIVYFPSYSLMDRVENRVS-FEHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAG  524 (620)
T ss_dssp             CSCEEEEESCHHHHHHHTSSCC-SCCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHH-hcchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEc
Confidence            6789999999999988888775 22222 445566678999999999 8888999975  9999999986  45899888


Q ss_pred             CCC
Q 017020          164 LPN  166 (379)
Q Consensus       164 ~P~  166 (379)
                      +|.
T Consensus       525 lPf  527 (620)
T 4a15_A          525 LPF  527 (620)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            775

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=97.79  E-value=1.5e-05  Score=72.92  Aligned_cols=63  Identities=33%  Similarity=0.566  Sum_probs=45.2

Q ss_pred             CCCCChHHHHHHHHHh--CCC--CCcEEEEeeeCChHHHHHHHHhcCCCceEEeecccccccccceEEE
Q 017020            1 MLAVGFEEDVELILEN--LPP--KRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLY   65 (379)
Q Consensus         1 mL~~GF~~di~~Il~~--~p~--~~Q~llfSAT~p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~   65 (379)
                      |+++||.+++..|+..  .+.  ++|+++||||+|+++.++++.++.+|..|.+..  ......+++|+
T Consensus       186 ~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~--~~~~~~~i~q~  252 (253)
T 1wrb_A          186 MLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGR--VGSTSDSIKQE  252 (253)
T ss_dssp             HHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC--------------
T ss_pred             HHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECC--CCCCcCCceec
Confidence            4678999999999995  454  789999999999999999999999999887642  22334555543

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=97.39  E-value=0.0028  Score=64.73  Aligned_cols=75  Identities=12%  Similarity=0.119  Sum_probs=53.1

Q ss_pred             CCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEec--cccccCCCCC-----ccceE
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT--DVAARGLDIP-----NVDLI  159 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaT--dv~~rGiDip-----~v~~V  159 (379)
                      .++.++||++|....+.+++.  .+..+..=..+++.   ...++.|+.....||+||  .....|||+|     .+++|
T Consensus       392 ~~g~~lvlF~Sy~~l~~v~~~--~~~~v~~q~~~~~~---~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~v  466 (551)
T 3crv_A          392 AKANVLVVFPSYEIMDRVMSR--ISLPKYVESEDSSV---EDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDV  466 (551)
T ss_dssp             CSSEEEEEESCHHHHHHHHTT--CCSSEEECCSSCCH---HHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEEE
T ss_pred             CCCCEEEEecCHHHHHHHHHh--cCCcEEEcCCCCCH---HHHHHHHHhcCCeEEEEEecceecccccccccCCcceeEE
Confidence            367999999999988888863  23333333335554   446667743334799998  6999999999     36788


Q ss_pred             EecCCCC
Q 017020          160 IHYELPN  166 (379)
Q Consensus       160 I~~~~P~  166 (379)
                      |..++|.
T Consensus       467 iI~~lPf  473 (551)
T 3crv_A          467 VIVGIPY  473 (551)
T ss_dssp             EEESCCC
T ss_pred             EEEcCCC
Confidence            8877764

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=96.95  E-value=0.0069  Score=57.59  Aligned_cols=121  Identities=13%  Similarity=0.119  Sum_probs=85.0

Q ss_pred             CccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHh-cCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccc
Q 017020           71 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  148 (379)
Q Consensus        71 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~-~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~  148 (379)
                      .+.|..+|.+++... ..+.+++||++..+..+-+..++. +++...-+.|.....+ .+.    .+....+.+.|...+
T Consensus       107 ~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~-~k~----~~~~~~i~Lltsag~  181 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSA-AAA----NDFSCTVHLFSSEGI  181 (328)
T ss_dssp             TCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCC
T ss_pred             cCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhh-hhc----ccCCceEEEEECCCC
Confidence            468999999999876 346799999999999999988887 4888889998855432 221    234555555566666


Q ss_pred             cCCC-----CCccceEEecCCCCChhH-HHHHHhhccCCC----CCceEEEEeChhhH
Q 017020          149 RGLD-----IPNVDLIIHYELPNDPET-FVHRSGRTGRAG----KEGTAILMFTSSQR  196 (379)
Q Consensus       149 rGiD-----ip~v~~VI~~~~P~~~~~-yiqR~GRtgR~G----~~g~~i~l~~~~e~  196 (379)
                      -|+|     ....+.||-||.-+++.. .+|..-|+.|.|    +.-.+|.+++....
T Consensus       182 ~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~Ti  239 (328)
T 3hgt_A          182 NFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSI  239 (328)
T ss_dssp             CTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSH
T ss_pred             CCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCH
Confidence            6675     678899999999998876 488777777752    45677878876543

>3i31_A Heat resistant RNA dependent ATPase; RNA helicase, RNA recognition motif, ATP-binding, helicase, nucleotide-binding; 1.80A {Thermus thermophilus}

Probab=95.53  E-value=0.016  Score=43.20  Aligned_cols=56  Identities=27%  Similarity=0.277  Sum_probs=44.0

Q ss_pred             CCCccccCCCCeEEEEEeeCCcccCCCCChhHHHHHHhhhCCCCCCccccEEeeeCCceeeeecchhhHH
Q 017020          275 SSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVCIDTVILLYFY  344 (379)
Q Consensus       275 ~~~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~i~~~~~~~~~~~~~~ig~i~i~~~~~~~~~~~~~~~~~  344 (379)
                      +++|++++++||+|+.++.-      .++..-+|.+|.+.+-    +||+|..-+...    +.|++...
T Consensus         2 ~~~SLLTGEEGw~Tlkl~G~------rLS~~R~VAlLk~aG~----~iGkI~~~~~ga----yaDlr~e~   57 (88)
T 3i31_A            2 AERSLLTGEEGWRTYKATGP------RLSLPRLVALLKGQGL----EVGKVAEAEGGF----YVDLRPEA   57 (88)
T ss_dssp             CCBCTTTCCBSCEEEEEECT------TCCHHHHHHHHHHTTC----CEEEEEEETTEE----EEEECTTC
T ss_pred             CcccccccCcceEEEEEecc------cccHHHHHHHHHHccc----ccccEEecccee----EEecChHH
Confidence            35799999999999999654      4888899998887665    999999766555    77776544

>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=94.74  E-value=0.057  Score=57.44  Aligned_cols=90  Identities=20%  Similarity=0.286  Sum_probs=70.4

Q ss_pred             ccHHHH-HHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           72 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        72 ~~k~~~-L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ..|..+ +..++.....+.+++|.++|+.-+.+.+..+..     ++.+..+||+++..+|...++.+.+|..+|+|+|.
T Consensus       400 SGKTlvall~il~~l~~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~  479 (780)
T 1gm5_A          400 SGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTH  479 (780)
T ss_dssp             SSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECT
T ss_pred             CCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            455543 333344444578999999999988888877652     57899999999999999999999999999999996


Q ss_pred             c-cccCCCCCccceEEe
Q 017020          146 V-AARGLDIPNVDLIIH  161 (379)
Q Consensus       146 v-~~rGiDip~v~~VI~  161 (379)
                      . +...+++.++.+||-
T Consensus       480 ~ll~~~~~~~~l~lVVI  496 (780)
T 1gm5_A          480 ALIQEDVHFKNLGLVII  496 (780)
T ss_dssp             THHHHCCCCSCCCEEEE
T ss_pred             HHHhhhhhccCCceEEe
Confidence            4 445678888888874

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

Probab=93.52  E-value=0.1  Score=50.58  Aligned_cols=79  Identities=14%  Similarity=0.206  Sum_probs=63.5

Q ss_pred             HHHHcCCCcEEEEecccccHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccc----cCCCC
Q 017020           82 ITVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA----RGLDI  153 (379)
Q Consensus        82 l~~~~~~~~~IIF~~t~~~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~----rGiDi  153 (379)
                      +.....+.++||.++|+.-+.+++..+..    ++.+..+||+.+..++....+.+..|..+|+|+|+-.-    .-++.
T Consensus        58 ~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~  137 (414)
T 3oiy_A           58 LWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQ  137 (414)
T ss_dssp             HHHHTTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTT
T ss_pred             HHHhcCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhcc
Confidence            33334578999999999999999988875    67899999999999998888999889899999997432    12455


Q ss_pred             CccceEE
Q 017020          154 PNVDLII  160 (379)
Q Consensus       154 p~v~~VI  160 (379)
                      .++++||
T Consensus       138 ~~~~~iV  144 (414)
T 3oiy_A          138 KRFDFVF  144 (414)
T ss_dssp             CCCSEEE
T ss_pred             ccccEEE
Confidence            6777777

>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=90.57  E-value=0.58  Score=51.90  Aligned_cols=89  Identities=15%  Similarity=0.178  Sum_probs=69.6

Q ss_pred             ccHHHHHH-HHHHHHcCCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           72 TSKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        72 ~~k~~~L~-~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ..|..+.. ..+.....+.+++|.|+|+.-+.+.++.+..     ++.+..++|..+..++...++.+.+|..+|+|+|.
T Consensus       635 sGKT~val~aa~~~~~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~  714 (1151)
T 2eyq_A          635 FGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTH  714 (1151)
T ss_dssp             TTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECT
T ss_pred             CCHHHHHHHHHHHHHHhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            45654332 2233334567999999999999888888763     36788999999999999999999999999999995


Q ss_pred             -ccccCCCCCccceEE
Q 017020          146 -VAARGLDIPNVDLII  160 (379)
Q Consensus       146 -v~~rGiDip~v~~VI  160 (379)
                       .+...+.+.++.+||
T Consensus       715 ~ll~~~~~~~~l~lvI  730 (1151)
T 2eyq_A          715 KLLQSDVKFKDLGLLI  730 (1151)
T ss_dssp             HHHHSCCCCSSEEEEE
T ss_pred             HHHhCCccccccceEE
Confidence             555568888888877

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

Probab=90.35  E-value=0.34  Score=53.44  Aligned_cols=90  Identities=14%  Similarity=0.182  Sum_probs=68.4

Q ss_pred             ccHHHHH-HHHHHHHcCCCcEEEEecccccHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc
Q 017020           72 TSKRTIL-SDLITVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  146 (379)
Q Consensus        72 ~~k~~~L-~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv  146 (379)
                      ..|..+. ..++.....+.++||.++|+.-+.+++..+..    ++.+..+||+++..+|...++.+.+|..+|+|+|+-
T Consensus       104 SGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~  183 (1104)
T 4ddu_A          104 VGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQ  183 (1104)
T ss_dssp             CCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHH
T ss_pred             CcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHH
Confidence            4565533 22333334578999999999999999999876    468999999999988888999999999999999973


Q ss_pred             cc-c---CCCCCccceEEe
Q 017020          147 AA-R---GLDIPNVDLIIH  161 (379)
Q Consensus       147 ~~-r---GiDip~v~~VI~  161 (379)
                      .- .   -++..++++||-
T Consensus       184 rL~~~l~~l~~~~l~~lVi  202 (1104)
T 4ddu_A          184 FVSKNREKLSQKRFDFVFV  202 (1104)
T ss_dssp             HHHHSHHHHHTSCCSEEEE
T ss_pred             HHHHHHHhhcccCcCEEEE
Confidence            22 1   145567887773

>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=86.33  E-value=1.3  Score=45.46  Aligned_cols=60  Identities=13%  Similarity=0.172  Sum_probs=53.0

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcc--cCCceeEEEeccc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGF--RQGKFTVLVATDV  146 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F--~~g~~~iLVaTdv  146 (379)
                      ..+.+||.++++.-++.....|.. ++.+..+||+++..++..++..+  ..+..+|+++|+-
T Consensus        83 ~~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe  145 (591)
T 2v1x_A           83 SDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPE  145 (591)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHH
T ss_pred             cCCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChh
Confidence            467999999999999988888875 89999999999999999888888  5788999999983

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=85.12  E-value=2  Score=38.06  Aligned_cols=69  Identities=16%  Similarity=0.225  Sum_probs=50.3

Q ss_pred             CCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc-----cc-cCCCCCcc
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----AA-RGLDIPNV  156 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv-----~~-rGiDip~v  156 (379)
                      +.++||.|+|+.-+.+++..+..     ++.+..++|+.+.......+..    ..+|+|+|+-     +. ..+++.++
T Consensus       102 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~~~~  177 (242)
T 3fe2_A          102 GPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLECGKTNLRRT  177 (242)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHTSCCCTTC
T ss_pred             CCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCCcccc
Confidence            56799999999999888777653     6789999999988776655542    3689999962     22 23456666


Q ss_pred             ceEE
Q 017020          157 DLII  160 (379)
Q Consensus       157 ~~VI  160 (379)
                      ++||
T Consensus       178 ~~lV  181 (242)
T 3fe2_A          178 TYLV  181 (242)
T ss_dssp             CEEE
T ss_pred             cEEE
Confidence            6665

>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=85.02  E-value=1.8  Score=43.44  Aligned_cols=74  Identities=19%  Similarity=0.188  Sum_probs=59.6

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccc------cCCCCCccceE
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA------RGLDIPNVDLI  159 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~------rGiDip~v~~V  159 (379)
                      ..+.+||.++++.-++.....|.. ++.+..+||+.+..++..+...+..|..+++++|+---      ..++..++++|
T Consensus        64 ~~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~v  143 (523)
T 1oyw_A           64 LNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLL  143 (523)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEE
T ss_pred             hCCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEE
Confidence            357899999999999988888875 78999999999999999999999999999999996321      12333456665


Q ss_pred             E
Q 017020          160 I  160 (379)
Q Consensus       160 I  160 (379)
                      |
T Consensus       144 V  144 (523)
T 1oyw_A          144 A  144 (523)
T ss_dssp             E
T ss_pred             E
Confidence            5

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=83.90  E-value=2.6  Score=36.44  Aligned_cols=69  Identities=17%  Similarity=0.250  Sum_probs=49.6

Q ss_pred             CcEEEEecccccHHHHHHHHhc------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecccc------ccCCCCCcc
Q 017020           89 GKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA------ARGLDIPNV  156 (379)
Q Consensus        89 ~~~IIF~~t~~~~~~l~~~L~~------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~------~rGiDip~v  156 (379)
                      .++||.|+|+.-++++++.+..      +..+..+||+.+...+...+.   ++..+|+|+|.-.      ...+++.++
T Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~---~~~~~i~v~T~~~l~~~~~~~~~~~~~~  159 (220)
T 1t6n_A           83 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK---KNCPHIVVGTPGRILALARNKSLNLKHI  159 (220)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHH---HSCCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             EEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHh---cCCCCEEEeCHHHHHHHHHhCCCCcccC
Confidence            4899999999999888877653      577899999998776654443   3556899999631      223455666


Q ss_pred             ceEE
Q 017020          157 DLII  160 (379)
Q Consensus       157 ~~VI  160 (379)
                      ++||
T Consensus       160 ~~lV  163 (220)
T 1t6n_A          160 KHFI  163 (220)
T ss_dssp             CEEE
T ss_pred             CEEE
Confidence            6655

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=82.60  E-value=2.5  Score=35.97  Aligned_cols=70  Identities=23%  Similarity=0.252  Sum_probs=48.9

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc-----cc-cCCCCCccc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----AA-RGLDIPNVD  157 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv-----~~-rGiDip~v~  157 (379)
                      .+.++||.|+++.-+.++++.+..   .+.+..+||+.+.......+.    ...+|+|+|+-     .. ..+++.+++
T Consensus        71 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~~  146 (207)
T 2gxq_A           71 RKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL----RGADAVVATPGRALDYLRQGVLDLSRVE  146 (207)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH----HCCSEEEECHHHHHHHHHHTSSCCTTCS
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh----CCCCEEEECHHHHHHHHHcCCcchhhce
Confidence            356899999999999999888874   467888999887655443332    24679999962     12 234556666


Q ss_pred             eEE
Q 017020          158 LII  160 (379)
Q Consensus       158 ~VI  160 (379)
                      +||
T Consensus       147 ~iV  149 (207)
T 2gxq_A          147 VAV  149 (207)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            665

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=81.84  E-value=4.6  Score=35.95  Aligned_cols=69  Identities=19%  Similarity=0.268  Sum_probs=49.5

Q ss_pred             CCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecccc-----c--cCCCCCc
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA-----A--RGLDIPN  155 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~-----~--rGiDip~  155 (379)
                      +.++||.++|+.-+.++++.+..     ++.+..++|+.+...+...+.    +..+|+|+|+--     .  .++++.+
T Consensus       111 ~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~I~v~Tp~~l~~~l~~~~~~~l~~  186 (249)
T 3ber_A          111 RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALA----KKPHIIIATPGRLIDHLENTKGFNLRA  186 (249)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHH----TCCSEEEECHHHHHHHHHHSTTCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhc----CCCCEEEECHHHHHHHHHcCCCcCccc
Confidence            45799999999999888877652     578899999988766554442    357899999631     1  3456666


Q ss_pred             cceEE
Q 017020          156 VDLII  160 (379)
Q Consensus       156 v~~VI  160 (379)
                      +++||
T Consensus       187 ~~~lV  191 (249)
T 3ber_A          187 LKYLV  191 (249)
T ss_dssp             CCEEE
T ss_pred             cCEEE
Confidence            66665

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=80.98  E-value=3  Score=36.49  Aligned_cols=84  Identities=15%  Similarity=0.186  Sum_probs=55.8

Q ss_pred             ccHHHH-HHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc------CCcEEEeeCCCCHHHHHHHHhcccCCceeEE
Q 017020           72 TSKRTI-LSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVL  141 (379)
Q Consensus        72 ~~k~~~-L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iL  141 (379)
                      ..|..+ +..++...   ..+.++||.|+|+.-+.++++.+..      ++.+..++|+.+..++...+.     ..+|+
T Consensus        72 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~Ii  146 (230)
T 2oxc_A           72 TGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-----KCHIA  146 (230)
T ss_dssp             SSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTT-----SCSEE
T ss_pred             CcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhcc-----CCCEE
Confidence            456644 33334332   2346899999999999988887763      467889999998877655542     46899


Q ss_pred             Eecccc------ccCCCCCccceEE
Q 017020          142 VATDVA------ARGLDIPNVDLII  160 (379)
Q Consensus       142 VaTdv~------~rGiDip~v~~VI  160 (379)
                      |+|+-.      ...++..++++||
T Consensus       147 v~Tp~~l~~~~~~~~~~~~~~~~lV  171 (230)
T 2oxc_A          147 VGSPGRIKQLIELDYLNPGSIRLFI  171 (230)
T ss_dssp             EECHHHHHHHHHTTSSCGGGCCEEE
T ss_pred             EECHHHHHHHHhcCCcccccCCEEE
Confidence            999732      1234555555555

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=80.86  E-value=4.1  Score=34.64  Aligned_cols=69  Identities=19%  Similarity=0.153  Sum_probs=47.7

Q ss_pred             CCcEEEEecccccHHHHHHHHhc------CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc-----ccc-CCCCCc
Q 017020           88 GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----AAR-GLDIPN  155 (379)
Q Consensus        88 ~~~~IIF~~t~~~~~~l~~~L~~------~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv-----~~r-GiDip~  155 (379)
                      +.++||.|+|+.-+.++++.+..      +..+..++|+.+..+....+    .+..+|+|+|+-     ..+ ..++.+
T Consensus        71 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~i~v~T~~~l~~~~~~~~~~~~~  146 (206)
T 1vec_A           71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL----DDTVHVVIATPGRILDLIKKGVAKVDH  146 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT----TSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhc----CCCCCEEEeCHHHHHHHHHcCCcCccc
Confidence            45799999999999888887753      46788899998876544333    245789999972     122 234555


Q ss_pred             cceEE
Q 017020          156 VDLII  160 (379)
Q Consensus       156 v~~VI  160 (379)
                      +++||
T Consensus       147 ~~~lV  151 (206)
T 1vec_A          147 VQMIV  151 (206)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            66555

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=80.06  E-value=2.5  Score=36.80  Aligned_cols=70  Identities=14%  Similarity=0.236  Sum_probs=44.4

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecccc------ccCCCCCcc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA------ARGLDIPNV  156 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~------~rGiDip~v  156 (379)
                      .+.++||.++|+.-+.++++.+..    ++.+..++|+.+...+...+.    ...+|+|+|+-.      ...+++.++
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDIS----KGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHHH----SCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHhc----CCCCEEEECHHHHHHHHHcCCcCcccc
Confidence            456899999999999998888764    577888999877655443332    236899999621      223455566


Q ss_pred             ceEE
Q 017020          157 DLII  160 (379)
Q Consensus       157 ~~VI  160 (379)
                      ++||
T Consensus       169 ~~lV  172 (228)
T 3iuy_A          169 TYLV  172 (228)
T ss_dssp             CEEE
T ss_pred             eEEE
Confidence            6555

---

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	379
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	3e-34
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	2e-27
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	1e-24
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	2e-23
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	2e-22
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	2e-22
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-21
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	5e-19
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	9e-18
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-17
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	4e-16
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	1e-15
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	7e-15
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	7e-15
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	8e-15
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	9e-15
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	1e-14
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	5e-14
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-13
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	1e-13
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	2e-13
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	2e-13
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	3e-13
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-12
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	2e-12
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	2e-11
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	8e-08
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	3e-07
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	4e-06
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	2e-04
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	0.004

>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 =  126 bits (318), Expect = 3e-34
 Identities = 37/180 (20%), Positives = 62/180 (34%), Gaps = 21/180 (11%)

Query: 62  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGD 120
           I+  A+STT          +     KGG+ ++F  +K+  DE++  L ++ I + A +  
Sbjct: 11  IEEVALSTTG-EIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRG 69

Query: 121 ISQHQR----------ERTLNGFRQGKFTVLVATDVAARG---LDIPNVDLIIHYELPND 167
           +                  L     G F  ++  +          +     I    LP D
Sbjct: 70  LDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQD 129

Query: 168 PETFVHRSGRTGRAGKEGTAILMFTSSQRR-TVRSLE----RDVGCKFEFVSPPVVEDVL 222
             +   R GRTGR GK G    +    +      S       D GC +  ++P      L
Sbjct: 130 AVSRTQRRGRTGR-GKPGIYRFVAPGERPSGMFDSSVLCECYDAGCAWYELTPAETTVRL 188

>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 =  106 bits (265), Expect = 2e-27
 Identities = 33/203 (16%), Positives = 64/203 (31%), Gaps = 21/203 (10%)

Query: 74  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGF 133
             + LS ++     G   I++ +T  +A+E+  +L            I    ++     F
Sbjct: 13  SISTLSSILE--KLGTGGIIYARTGEEAEEIYESL-----KNKFRIGIVTATKKGDYEKF 65

Query: 134 RQGKFTVLVAT----DVAARGLDIP-NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 188
            +G+   L+ T        RGLD+P  +   +    P+    F            +   +
Sbjct: 66  VEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKL 121

Query: 189 LMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTA 248
           L +       +  L   V    +      V ++L+    +       V     E   P  
Sbjct: 122 LAYLYRNVDEIERLLPAVERHID-----EVREILKKVMGKERPQAKDVVVREGEVIFPDL 176

Query: 249 QRLIEEKGTDALAAALAQLSGFS 271
           +  I+  G  +   A     G S
Sbjct: 177 RTYIQGSGRTSRLFAGGLTKGAS 199

>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 = 96.5 bits (239), Expect = 1e-24
 Identities = 47/150 (31%), Positives = 83/150 (55%), Gaps = 3/150 (2%)

Query: 74  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNG 132
           K   L+DL        + ++F  T+R  +E++  L +      A++ D+ Q +R+  +  
Sbjct: 14  KYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKE 72

Query: 133 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT 192
           FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR GR GR G++G AI   T
Sbjct: 73  FRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVT 132

Query: 193 SSQRRTVRSLERDVGCKFEFVSPPVVEDVL 222
           +     +R LE+    + E + P  +  +L
Sbjct: 133 NEDVGAMRELEKFYSTQIEEL-PSDIATLL 161

>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 = 96.5 bits (239), Expect = 2e-23
 Identities = 41/136 (30%), Positives = 61/136 (44%), Gaps = 13/136 (9%)

Query: 73  SKRTILSDLITVY---AKGGKTIVFTQTKRDADE-VSLALTSIIASEALHGDISQHQR-- 126
            K   L ++I       +  K IVFT  +  A + V+  +   I ++   G  S+     
Sbjct: 143 PKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRG 202

Query: 127 ------ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
                 +  L+ F +G+F VLVAT V   GLD+P VDL++ YE        + R GRTGR
Sbjct: 203 LSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 262

Query: 181 AGKEGTAILMFTSSQR 196
               G  I++     R
Sbjct: 263 HMP-GRVIILMAKGTR 277

>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 = 91.2 bits (225), Expect = 2e-22
 Identities = 60/170 (35%), Positives = 95/170 (55%), Gaps = 4/170 (2%)

Query: 55  DEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIA 113
           DE   EGIK + ++      K   L DL        + ++F  TKR  D ++  +     
Sbjct: 1   DELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANF 59

Query: 114 SEA-LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFV 172
           + + +HGD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++
Sbjct: 60  TVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYI 119

Query: 173 HRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVL 222
           HR GR+GR G++G AI    +   R +R +E+    + + + P  V D++
Sbjct: 120 HRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEM-PMNVADLI 168

>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 = 90.4 bits (223), Expect = 2e-22
 Identities = 51/151 (33%), Positives = 84/151 (55%), Gaps = 3/151 (1%)

Query: 62  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDI 121
           I+   +      +   L  L+    K    +VF +TKRD  E++  L  I          
Sbjct: 4   IEQSYVEVNENERFEALCRLLK--NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGD 61

Query: 122 S-QHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 180
             Q QRE+ +  F+Q K  +L+ATDV +RG+D+ +++ +I+Y LP +PE+++HR GRTGR
Sbjct: 62  LSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGR 121

Query: 181 AGKEGTAILMFTSSQRRTVRSLERDVGCKFE 211
           AGK+G AI +    + + +R +ER +  K +
Sbjct: 122 AGKKGKAISIINRREYKKLRYIERAMKLKIK 152

>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 = 89.6 bits (221), Expect = 1e-21
 Identities = 30/137 (21%), Positives = 61/137 (44%), Gaps = 5/137 (3%)

Query: 56  EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASE 115
           E L    +   I+  + +K   L +++  + +  K I+FT+       +S     +    
Sbjct: 62  EALRAWEEARRIAFNSKNKIRKLREILERH-RKDKIIIFTRHNELVYRIS----KVFLIP 116

Query: 116 ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS 175
           A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +          ++ R 
Sbjct: 117 AITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRL 176

Query: 176 GRTGRAGKEGTAILMFT 192
           GR  R  K     +++ 
Sbjct: 177 GRILRPSKGKKEAVLYE 193

>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 = 80.5 bits (198), Expect = 5e-19
 Identities = 36/138 (26%), Positives = 55/138 (39%), Gaps = 12/138 (8%)

Query: 62  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDI 121
           I+  A+STT        +  + V  KGG+ ++F  +K+  DE++  L       AL  + 
Sbjct: 10  IEEVALSTTGEIPFYGKAIPLEVI-KGGRHLIFCHSKKKCDELAAKL------VALGINA 62

Query: 122 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN---VDLIIHYELPNDPETFVHRSGRT 178
             + R   ++        V+VATD    G        +D       P D  +   R GRT
Sbjct: 63  VAYYRGLDVSVIPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRT 122

Query: 179 GRAGKEGTAILMFTSSQR 196
           GR GK G         +R
Sbjct: 123 GR-GKPGI-YRFVAPGER 138

>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 = 80.7 bits (198), Expect = 1e-17
 Identities = 23/213 (10%), Positives = 50/213 (23%), Gaps = 45/213 (21%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAE 60
                      +       +   +  +AT P       +           +  +      
Sbjct: 112 TDPASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPIMDEEREIPERSWNSG- 170

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHG 119
                                  V    GKT+ F  + +  ++++  L         L  
Sbjct: 171 --------------------HEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSR 210

Query: 120 DISQHQRERTLNGFRQGKFTVLVATDVAARGLDI-------------------PNVDLII 160
                +  +     R   +  +V TD++  G +                        +I+
Sbjct: 211 KTFDSEYIK----TRTNDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVIL 266

Query: 161 HYELPNDPETFVHRSGRTGRAGKEGTAILMFTS 193
              +P    +   R GR GR  K      ++  
Sbjct: 267 AGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMG 299

>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 = 73.7 bits (180), Expect = 4e-16
 Identities = 30/118 (25%), Positives = 54/118 (45%), Gaps = 3/118 (2%)

Query: 77  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 135
           ++ ++     +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R 
Sbjct: 20  LIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRL 79

Query: 136 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS--GRTGRAGKEGTAILMF 191
           GK+ VLV  ++   GLDIP V L+   +   +      RS     GRA +     ++ 
Sbjct: 80  GKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM 137

>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 = 72.6 bits (177), Expect = 1e-15
 Identities = 38/169 (22%), Positives = 63/169 (37%), Gaps = 41/169 (24%)

Query: 72  TSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-------------- 116
           TS+R    +L+    A+ G  +VF  T+R A++ ++ L++I A                 
Sbjct: 23  TSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENE 82

Query: 117 -----------------LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI 159
                             H  +   QR    + FR+G   V+VAT   A G+++P   +I
Sbjct: 83  GEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVI 142

Query: 160 IH-------YELPNDPETFVHRSGRTGRAGK--EGTAILMFTSSQRRTV 199
           +        Y        +   +GR GR G    G AI++     R   
Sbjct: 143 VRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIA 191

>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 = 69.7 bits (170), Expect = 7e-15
 Identities = 31/136 (22%), Positives = 58/136 (42%), Gaps = 8/136 (5%)

Query: 77  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 135
           ++  +    A+G +T+V   T R A+E++  L    I +  LH ++   +R+  +   R 
Sbjct: 20  LMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRL 79

Query: 136 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS--GRTGRAGKEGTAILMF-- 191
           G +  LV  ++   GLDIP V L+   +   +      RS     GRA +     +    
Sbjct: 80  GHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYA 139

Query: 192 ---TSSQRRTVRSLER 204
              + + +R +    R
Sbjct: 140 DRVSEAMQRAIEETNR 155

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.0 bits (173), Expect = 7e-15
 Identities = 15/46 (32%), Positives = 29/46 (63%)

Query: 5   GFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL 50
           GF+E +  +   LPP  Q +L SAT+P  + +++ K++ +P+ I +
Sbjct: 175 GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV 220

>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 = 69.7 bits (169), Expect = 8e-15
 Identities = 44/167 (26%), Positives = 76/167 (45%), Gaps = 1/167 (0%)

Query: 59  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALH 118
            +GI  Y        K   L+ L +        I    T R             +    H
Sbjct: 4   LKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSH 63

Query: 119 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT 178
             + Q +R +  + FRQGK   LV +D+  RG+DI  V+++I+++ P   ET++HR GR+
Sbjct: 64  ARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRS 123

Query: 179 GRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESS 225
           GR G  G AI +   + R  +  +E+++G +   + P  ++  L  +
Sbjct: 124 GRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAI-PATIDKSLYVA 169

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 70.2 bits (171), Expect = 9e-15
 Identities = 19/44 (43%), Positives = 29/44 (65%)

Query: 5   GFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
           GF+E +  I   LPP  Q +L SATMP+ V +++ K++ NP+ I
Sbjct: 167 GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRI 210

>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 = 69.7 bits (169), Expect = 1e-14
 Identities = 28/129 (21%), Positives = 60/129 (46%), Gaps = 2/129 (1%)

Query: 73  SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLN 131
                L   +    +G   I++  ++   ++ +  L S  I++ A H  +  + R     
Sbjct: 16  KPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQE 74

Query: 132 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 191
            F++    ++VAT     G++ PNV  ++H+++P + E++   +GR GR G    A+L +
Sbjct: 75  KFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 134

Query: 192 TSSQRRTVR 200
             +    +R
Sbjct: 135 DPADMAWLR 143

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.3 bits (166), Expect = 5e-14
 Identities = 16/46 (34%), Positives = 30/46 (65%)

Query: 5   GFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL 50
           GF++ +  I + L    Q +L SATMPS V ++++K++ +P+ I +
Sbjct: 171 GFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILV 216

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.2 bits (163), Expect = 1e-13
 Identities = 14/44 (31%), Positives = 26/44 (59%)

Query: 5   GFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNI 48
               DV+ I    P ++Q M+FSAT+   ++ + RK++ +P+ I
Sbjct: 162 DMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEI 205

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.3 bits (163), Expect = 1e-13
 Identities = 17/44 (38%), Positives = 26/44 (59%)

Query: 6   FEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNID 49
           F + +E I+  LP  RQ +L+SAT P  V+K    +L+ P  I+
Sbjct: 163 FVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEIN 206

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 66.5 bits (161), Expect = 2e-13
 Identities = 22/45 (48%), Positives = 28/45 (62%)

Query: 6   FEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL 50
           F+  +E IL  LPP  QS+LFSAT P  VK+   K+L  P  I+L
Sbjct: 160 FKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL 204

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 66.6 bits (161), Expect = 2e-13
 Identities = 16/46 (34%), Positives = 28/46 (60%)

Query: 6   FEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLV 51
           F  DV+ I   +P   Q ++FSAT+P  +K   +KY++NP  + ++
Sbjct: 164 FITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVL 209

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 66.2 bits (161), Expect = 3e-13
 Identities = 20/50 (40%), Positives = 30/50 (60%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDL 50
           ML +GF +DVE IL      ++ +LFSATMP  +  L++KY+ +   I  
Sbjct: 157 MLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA 206

>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 = 63.6 bits (153), Expect = 1e-12
 Identities = 37/166 (22%), Positives = 79/166 (47%), Gaps = 4/166 (2%)

Query: 61  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEALHG 119
           G++ Y +      K   L DL+ V  +  + ++F ++ +    ++ L +     + A+H 
Sbjct: 1   GLQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHR 59

Query: 120 DISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG 179
            + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R G
Sbjct: 60  GMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAG 119

Query: 180 RAGKEGTAILMFTSSQ-RRTVRSLERDVGCKFEFVSPPV-VEDVLE 223
           R G +G AI   +     + +  ++         +   + +   +E
Sbjct: 120 RFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 165

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 211

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]

 Score = 63.5 bits (154), Expect = 2e-12
 Identities = 34/149 (22%), Positives = 59/149 (39%), Gaps = 15/149 (10%)

Query: 115 EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFV-H 173
              HG + + + ER +N F   +F VLV T +   G+DIP  + II     +     +  
Sbjct: 61  AIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQ 120

Query: 174 RSGRTGRAGKEGTAILMFTSSQRRTVRSLER--------DVGCKFEFVSPPVVEDVLESS 225
             GR GR+  +  A L+    +  T  + +R        D+G  F   +     D+    
Sbjct: 121 LRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALAT----HDLEIRG 176

Query: 226 AEQVVATLNGVHPESVEFFTPTAQRLIEE 254
           A +++        E++ F       L+E 
Sbjct: 177 AGELLGEEQSGSMETIGF--SLYMELLEN 203

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 61.1 bits (147), Expect = 2e-11
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 5/51 (9%)

Query: 6   FEEDVELILENL----PPKRQSMLFSATMPSWVKKLSRKYLDNPLNIDLVG 52
           FE  +  I+E         RQ+++FSAT P  ++KL+  +L N + +  VG
Sbjct: 189 FEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMT-VG 238

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 50.2 bits (119), Expect = 8e-08
 Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 1/97 (1%)

Query: 117 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET-FVHRS 175
           +HG +SQ +++R +  F +G++ +LV+T V   G+D+P  ++++                
Sbjct: 70  MHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLR 129

Query: 176 GRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF 212
           GR GR G+E    L+        +  L         F
Sbjct: 130 GRVGRGGQEAYCFLVVGDVGEEAMERLRFFTLNTDGF 166

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 48.7 bits (115), Expect = 3e-07
 Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 3/49 (6%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPLNID 49
           +  +GF  D++        +   M+ +AT     K    + L   LN D
Sbjct: 185 LHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQL---LNFD 230

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

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

 Score = 45.7 bits (108), Expect = 4e-06
 Identities = 20/125 (16%), Positives = 39/125 (31%), Gaps = 23/125 (18%)

Query: 88  GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV 146
              T  F  + R A+ ++ +L     +   L+    + +        +Q K   ++ATD+
Sbjct: 36  KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPT----IKQKKPDFILATDI 91

Query: 147 AARGLDIPNV------------------DLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 188
           A  G ++                      + I   L     +   R GR GR        
Sbjct: 92  AEMGANLCVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDS 151

Query: 189 LMFTS 193
             ++ 
Sbjct: 152 YYYSE 156

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 39.6 bits (91), Expect = 2e-04
 Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 2/36 (5%)

Query: 13  ILENLPPKRQSMLFSATMPSWVKK--LSRKYLDNPL 46
            L    P    M  +AT     ++  +    L++PL
Sbjct: 167 QLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPL 202

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 35.9 bits (81), Expect = 0.004
 Identities = 5/64 (7%), Positives = 19/64 (29%), Gaps = 1/64 (1%)

Query: 1   MLAVGFEEDVELILENLPPKRQSMLFSATMPSWVKKLSRKYLDNPL-NIDLVGNQDEKLA 59
            +       +    +        +  +A+  S  +K+     +  + +I+        + 
Sbjct: 137 AVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVR 196

Query: 60  EGIK 63
             +K
Sbjct: 197 PYVK 200

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	379
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	100.0
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.98
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.97
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.95
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.95
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.92
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.87
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.85
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.84
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.83
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.8
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.79
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.76
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.67
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.47
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.47
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.46
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.31
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.62
d2e29a1	85	ATP-dependent RNA helicase DDX50 {Human (Homo sapi	98.35
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.69
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.18
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	86.37

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.3e-34  Score=252.49  Aligned_cols=158  Identities=35%  Similarity=0.588  Sum_probs=147.5

Q ss_pred             ccccceEEEEEEcCCc-cHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhccc
Q 017020           57 KLAEGIKLYAISTTAT-SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR  134 (379)
Q Consensus        57 ~~~~~i~~~~~~~~~~-~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~  134 (379)
                      .+..+++|+|+.++.. .|.+.|.++++.. ++.++||||++++.|+.++..|.. ++.+..+||+|++.+|..+++.|+
T Consensus         3 ~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~-~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk   81 (168)
T d2j0sa2           3 LTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFR   81 (168)
T ss_dssp             CSCTTEEEEEEEESSTTHHHHHHHHHHHHH-TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCCCcEEEEEEecChHHHHHHHHHHHHhC-CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHh
Confidence            3568899999888764 5999999999876 468999999999999999999985 899999999999999999999999


Q ss_pred             CCceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeC
Q 017020          135 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  214 (379)
Q Consensus       135 ~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~  214 (379)
                      +|+.++|||||+++||+|+|++++|||||+|.+++.|+||+|||||.|+.|.+++|+++.|...++.+++.++..++..+
T Consensus        82 ~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i~~~~~~~i~e~p  161 (168)
T d2j0sa2          82 SGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMP  161 (168)
T ss_dssp             HTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECC
T ss_pred             cCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHHHHHHHcCcCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998888764


Q ss_pred             C
Q 017020          215 P  215 (379)
Q Consensus       215 ~  215 (379)
                      .
T Consensus       162 ~  162 (168)
T d2j0sa2         162 M  162 (168)
T ss_dssp             S
T ss_pred             c
Confidence            3

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.6e-34  Score=251.19  Aligned_cols=158  Identities=27%  Similarity=0.496  Sum_probs=149.7

Q ss_pred             cccceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCC
Q 017020           58 LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG  136 (379)
Q Consensus        58 ~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g  136 (379)
                      +..+++|+|+.++..+|...|.++++.. +..++||||+|++.++.++..|.. ++.+..+||+|++++|..++++|++|
T Consensus         3 tl~~i~q~yi~v~~~~K~~~L~~ll~~~-~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~   81 (171)
T d1s2ma2           3 TLKGITQYYAFVEERQKLHCLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQG   81 (171)
T ss_dssp             BCTTEEEEEEECCGGGHHHHHHHHHHHS-CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CccceEEEEEEcCHHHHHHHHHHHHHhC-CCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccC
Confidence            4678999999999999999999999876 578999999999999999999986 89999999999999999999999999


Q ss_pred             ceeEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCCC
Q 017020          137 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  216 (379)
Q Consensus       137 ~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~p  216 (379)
                      ..++|||||++++|+|+|++++|||||+|.++++|+||+||+||.|+.|.|++|+++.|...++.+++.++.+++.++..
T Consensus        82 ~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~~~l~~~~~~~p~~  161 (171)
T d1s2ma2          82 KVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPAT  161 (171)
T ss_dssp             SSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSS
T ss_pred             ccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHHHHHCCCCCCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998876543

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.1e-34  Score=251.42  Aligned_cols=153  Identities=31%  Similarity=0.570  Sum_probs=137.8

Q ss_pred             eEEEEEEcCC-ccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCcee
Q 017020           62 IKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  139 (379)
Q Consensus        62 i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~  139 (379)
                      |+|+|+.+.. +.|.+.|..+++.. +..++||||+|+..++.++..|.. ++.+..+||+|++.+|..+++.|+.|+.+
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~~-~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~   79 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSR   79 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHHT-TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHhC-CCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccc
Confidence            4677777754 56999999999876 468999999999999999999985 89999999999999999999999999999


Q ss_pred             EEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceeeCC
Q 017020          140 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  215 (379)
Q Consensus       140 iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~~~  215 (379)
                      +|||||+++||+|+|++++|||||+|.+++.|+||+|||||.|+.|.|++++++.|...++.+++..+.+++.++.
T Consensus        80 iLv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~~~~ip~  155 (162)
T d1fuka_          80 ILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPS  155 (162)
T ss_dssp             EEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCS
T ss_pred             eeeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHHHHHHHHcCcCCCCCh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999887644

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=8.9e-34  Score=243.84  Aligned_cols=152  Identities=36%  Similarity=0.616  Sum_probs=143.8

Q ss_pred             cceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCce
Q 017020           60 EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF  138 (379)
Q Consensus        60 ~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~  138 (379)
                      .+++|+|+.++..+|.+.|.++++.  .+.++||||+|++.|+.++..|.. ++.+..+||++++.+|..++++|++|+.
T Consensus         2 ~nI~~~~i~v~~~~K~~~L~~ll~~--~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~   79 (155)
T d1hv8a2           2 ANIEQSYVEVNENERFEALCRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI   79 (155)
T ss_dssp             SSSEEEEEECCGGGHHHHHHHHHCS--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSS
T ss_pred             CCeEEEEEEeChHHHHHHHHHHHcc--CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccc
Confidence            5789999999999999999999875  357899999999999999999985 8999999999999999999999999999


Q ss_pred             eEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHHHhCCCceee
Q 017020          139 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV  213 (379)
Q Consensus       139 ~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~~~~~~~~~~  213 (379)
                      ++|||||++++|+|+|++++|||||+|.++.+|+||+||+||.|+.|.+++++++.|...++.+++.++.+++++
T Consensus        80 ~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~i~~l  154 (155)
T d1hv8a2          80 RILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKL  154 (155)
T ss_dssp             SEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCCCB
T ss_pred             eeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHHHHHHHHHHCCCcccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999887653

>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=99.98  E-value=4.7e-32  Score=236.13  Aligned_cols=152  Identities=24%  Similarity=0.465  Sum_probs=142.3

Q ss_pred             ceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCcee
Q 017020           61 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  139 (379)
Q Consensus        61 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~  139 (379)
                      +++|||+.+..++|.+.|.++++.. ...++||||++++.++.++..|.. ++.+..+||+|++++|..++++|++|+.+
T Consensus         1 ~l~q~~v~~~~~~K~~~L~~ll~~~-~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~   79 (168)
T d1t5ia_           1 GLQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR   79 (168)
T ss_dssp             CCEEEEEECCGGGHHHHHHHHHHHS-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             CcEEEEEEeChHHHHHHHHHHHHhC-CCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccce
Confidence            4689999999999999999999887 468999999999999999999985 89999999999999999999999999999


Q ss_pred             EEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChh-hHHHHHHHHHHhCCCceee
Q 017020          140 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFV  213 (379)
Q Consensus       140 iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~-e~~~l~~le~~~~~~~~~~  213 (379)
                      +||||+++++|+|+|++++||+||+|.+++.|+||+||+||.|++|.|++|+++. +...+..+++.++..++.+
T Consensus        80 iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~~~i~~~~~~~~~el  154 (168)
T d1t5ia_          80 ILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISEL  154 (168)
T ss_dssp             EEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEEC
T ss_pred             eeeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchHHHHHHHHHHHHHcCCcccC
Confidence            9999999999999999999999999999999999999999999999999999875 6778889999998887764

>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=99.97  E-value=8.7e-31  Score=234.14  Aligned_cols=141  Identities=21%  Similarity=0.431  Sum_probs=127.8

Q ss_pred             cceEEEEEEcCCccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCce
Q 017020           60 EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF  138 (379)
Q Consensus        60 ~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~  138 (379)
                      +|+.+  ...+..+|.+.|..++... ++.++||||+|+..++.++..|.. ++.+..+||+|++++|.++++.|++|+.
T Consensus         5 pNi~y--~v~~~~~k~~~L~~~l~~~-~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~   81 (200)
T d1oywa3           5 PNIRY--MLMEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDL   81 (200)
T ss_dssp             TTEEE--EEEECSSHHHHHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCcEE--EEEcCCcHHHHHHHHHHhc-CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccc
Confidence            44543  3344567888888888776 467999999999999999999985 8999999999999999999999999999


Q ss_pred             eEEEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHH
Q 017020          139 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       139 ~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                      +||||||++++|||+|+|++|||||+|.++++|+||+|||||+|+.|.|++|+++.|...++++.
T Consensus        82 ~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~i  146 (200)
T d1oywa3          82 QIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  146 (200)
T ss_dssp             SEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHH
T ss_pred             eEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999999999988887653

>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=99.95  E-value=8.5e-28  Score=211.03  Aligned_cols=123  Identities=24%  Similarity=0.429  Sum_probs=106.3

Q ss_pred             HHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCC
Q 017020           75 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI  153 (379)
Q Consensus        75 ~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDi  153 (379)
                      .++|..+.+....+.++||||+++..++.++..|.. ++.+..+||+|++.+|.+++++|++|+++||||||+++||+|+
T Consensus        18 d~ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDi   97 (181)
T d1t5la2          18 DDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDI   97 (181)
T ss_dssp             HHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCC
T ss_pred             HHHHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCC
Confidence            445566555555678999999999999999999986 8999999999999999999999999999999999999999999


Q ss_pred             CccceEEecCCCC-----ChhHHHHHHhhccCCCCCceEEEEeChhhHHH
Q 017020          154 PNVDLIIHYELPN-----DPETFVHRSGRTGRAGKEGTAILMFTSSQRRT  198 (379)
Q Consensus       154 p~v~~VI~~~~P~-----~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~  198 (379)
                      |+|++|||||+|.     +...|+||+|||||.|. |.+++++.......
T Consensus        98 p~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~-~~~~~~~~~~~~~~  146 (181)
T d1t5la2          98 PEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIMYADTITKSM  146 (181)
T ss_dssp             TTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSCCHHH
T ss_pred             CCCCEEEEecCCcccccccHHHHHHHHHhhccccC-ceeEeecchhhHHH
Confidence            9999999999996     68899999999999984 55555555444333

>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=99.95  E-value=1.2e-27  Score=207.81  Aligned_cols=129  Identities=24%  Similarity=0.404  Sum_probs=112.2

Q ss_pred             HHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCC
Q 017020           74 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  152 (379)
Q Consensus        74 k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiD  152 (379)
                      ..+++..+.+....+.++||||+|++.|+.++..|.. ++.+..+||+|++.+|++++++|++|+++|||||+++++|+|
T Consensus        17 v~dll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiD   96 (174)
T d1c4oa2          17 ILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLD   96 (174)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCC
T ss_pred             HHHHHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeecc
Confidence            3456666666556788999999999999999999985 899999999999999999999999999999999999999999


Q ss_pred             CCccceEEecCCCC-----ChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHH
Q 017020          153 IPNVDLIIHYELPN-----DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       153 ip~v~~VI~~~~P~-----~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                      +|+|++||||++|.     +.++|+||+||+||.| .|.+++++...+..+.+.++
T Consensus        97 ip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~-~g~~~~~~~~~~~~~~~~i~  151 (174)
T d1c4oa2          97 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSEAMQRAIE  151 (174)
T ss_dssp             CTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCHHHHHHHH
T ss_pred             CCCCcEEEEeccccccccchhHHHHHHhhhhhhcC-CCeeEEeecCCCHHHHHHHH
Confidence            99999999999765     5688999999999987 58888888776655444443

>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=99.92  E-value=7e-26  Score=190.16  Aligned_cols=99  Identities=29%  Similarity=0.469  Sum_probs=90.7

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecC--
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE--  163 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~--  163 (379)
                      .++++||||+|++.|+.+++.|.. ++.+..+||+|++       +.|++|+.++|||||+++||+| |++++||||+  
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~-------~~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~  105 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDV-------SVIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTS  105 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCS-------CCCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEE
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchh-------hhhhhhhcceeehhHHHHhccc-cccceEEEEEec
Confidence            478999999999999999999975 8999999999985       5688999999999999999999 9999999855  


Q ss_pred             --CCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          164 --LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       164 --~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                        +|.++++|+||+||||| |++|. ++|+++.|
T Consensus       106 ~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         106 DGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             TTEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             CCCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence              69999999999999999 99995 77888876

>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=99.87  E-value=8.1e-23  Score=191.46  Aligned_cols=122  Identities=34%  Similarity=0.550  Sum_probs=105.4

Q ss_pred             cHHHHHHHHHHHH---cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeC--------CCCHHHHHHHHhcccCCceeE
Q 017020           73 SKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHG--------DISQHQRERTLNGFRQGKFTV  140 (379)
Q Consensus        73 ~k~~~L~~ll~~~---~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg--------~m~~~~R~~~~~~F~~g~~~i  140 (379)
                      .|.+.|.+++...   .++.++||||+++..++.++..|.. ++++..+||        +|++.+|..+++.|++|+++|
T Consensus       143 pK~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~v  222 (286)
T d1wp9a2         143 PKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNV  222 (286)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSE
T ss_pred             cHHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcE
Confidence            4777777776543   4567999999999999999999975 788877765        577778999999999999999


Q ss_pred             EEeccccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          141 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       141 LVaTdv~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      ||||+++++|+|+|++++||+||+|+++..|+||+|||||.+ +|.++.|+++..
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            999999999999999999999999999999999999999975 788999888754

>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=99.85  E-value=6.4e-22  Score=176.30  Aligned_cols=120  Identities=27%  Similarity=0.529  Sum_probs=103.3

Q ss_pred             HHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcC-------------------------------CcEEEeeCCCCH
Q 017020           75 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------IASEALHGDISQ  123 (379)
Q Consensus        75 ~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~-------------------------------~~v~~lhg~m~~  123 (379)
                      .+++.+++.   .++++||||+|++.|+.++..|...                               ..+.++||+|++
T Consensus        30 ~~l~~~~i~---~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          30 EELVEECVA---ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHHH---TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHH---cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            344444443   5789999999999999888877531                               137889999999


Q ss_pred             HHHHHHHhcccCCceeEEEeccccccCCCCCccceEEe-------cCCCCChhHHHHHHhhccCCC--CCceEEEEeChh
Q 017020          124 HQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-------YELPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  194 (379)
Q Consensus       124 ~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~-------~~~P~~~~~yiqR~GRtgR~G--~~g~~i~l~~~~  194 (379)
                      .+|..+.+.|++|.++|||||+++++|+|+|..++||+       ++.|.+..+|+||+|||||.|  ..|.+++++.+.
T Consensus       107 ~~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~  186 (201)
T d2p6ra4         107 GQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKR  186 (201)
T ss_dssp             HHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGG
T ss_pred             hhHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCC
Confidence            99999999999999999999999999999999999996       778899999999999999998  479999998887


Q ss_pred             hHH
Q 017020          195 QRR  197 (379)
Q Consensus       195 e~~  197 (379)
                      +..
T Consensus       187 ~~~  189 (201)
T d2p6ra4         187 DRE  189 (201)
T ss_dssp             GHH
T ss_pred             ChH
Confidence            654

>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=99.84  E-value=4.8e-24  Score=196.12  Aligned_cols=123  Identities=18%  Similarity=0.317  Sum_probs=105.9

Q ss_pred             CccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEec----cc
Q 017020           71 ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT----DV  146 (379)
Q Consensus        71 ~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaT----dv  146 (379)
                      .++|.+.|..++..+  +.++||||+|++.|+.++..|...     +||+|++.+|.+++++|++|+++|||||    |+
T Consensus        10 ~~~~~~~l~~~l~~~--~~~~iif~~~~~~~~~l~~~l~~~-----~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v   82 (248)
T d1gkub2          10 NDESISTLSSILEKL--GTGGIIYARTGEEAEEIYESLKNK-----FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGT   82 (248)
T ss_dssp             SCCCTTTTHHHHTTS--CSCEEEEESSHHHHHHHHHTTTTS-----SCEEECTTSSSHHHHHHHHTSCSEEEEECC----
T ss_pred             CchHHHHHHHHHHHh--CCCEEEEECCHHHHHHHHHHHHHh-----ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccch
Confidence            356788888888765  468999999999999999999753     7999999999999999999999999999    89


Q ss_pred             cccCCCCCc-cceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHHH
Q 017020          147 AARGLDIPN-VDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  204 (379)
Q Consensus       147 ~~rGiDip~-v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le~  204 (379)
                      ++||||+|+ |++|||||+|+    |.||+||+||+|+.|.+++++.+.+...+..+..
T Consensus        83 ~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~~  137 (248)
T d1gkub2          83 LVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLP  137 (248)
T ss_dssp             --CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCT
T ss_pred             hhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHHHHHHHH
Confidence            999999996 99999999994    8899999999999999999998888776665543

>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=99.83  E-value=5.8e-22  Score=176.56  Aligned_cols=128  Identities=20%  Similarity=0.410  Sum_probs=99.9

Q ss_pred             HHHHHHHHHHcCCCcEEEEecccccHHH--------HHHHHhc----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEe
Q 017020           76 TILSDLITVYAKGGKTIVFTQTKRDADE--------VSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVA  143 (379)
Q Consensus        76 ~~L~~ll~~~~~~~~~IIF~~t~~~~~~--------l~~~L~~----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVa  143 (379)
                      .+...+......++++-+.||..++.+.        ..+.|.+    ++.+..+||+|++++|++++++|++|+++||||
T Consensus        17 ~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVa   96 (206)
T d1gm5a4          17 EVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVS   96 (206)
T ss_dssp             HHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCC
T ss_pred             HHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEE
Confidence            3444444555677888888987665543        3333332    457889999999999999999999999999999


Q ss_pred             ccccccCCCCCccceEEecCCCC-ChhHHHHHHhhccCCCCCceEEEEeChhhHHHHHHHH
Q 017020          144 TDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  203 (379)
Q Consensus       144 Tdv~~rGiDip~v~~VI~~~~P~-~~~~yiqR~GRtgR~G~~g~~i~l~~~~e~~~l~~le  203 (379)
                      |+++++|||+|++++||+++.|. ..+.|.|..||+||.|.+|.|++++++......++++
T Consensus        97 TtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~rl~  157 (206)
T d1gm5a4          97 TTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERLR  157 (206)
T ss_dssp             SSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHHH
T ss_pred             ehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchhhhh
Confidence            99999999999999999999997 5777777799999999999999999876655555544

>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=99.80  E-value=6.1e-21  Score=176.34  Aligned_cols=105  Identities=25%  Similarity=0.372  Sum_probs=92.5

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHH----------HHHHhcccCCceeEEEecccccc---CCC
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQR----------ERTLNGFRQGKFTVLVATDVAAR---GLD  152 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R----------~~~~~~F~~g~~~iLVaTdv~~r---GiD  152 (379)
                      .++++||||+|++.|++++..|.. ++.+..+||+|+++.|          ..+++.|++|+.+++|+|+++++   |+|
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giD  114 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFS  114 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCC
Confidence            368999999999999999999985 8999999999999887          46788999999999999999999   667


Q ss_pred             CCccceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeC
Q 017020          153 IPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT  192 (379)
Q Consensus       153 ip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~  192 (379)
                      ++.+.+||+|++|.++++|+||+||||| |+.|....+..
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~  153 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAP  153 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCS
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEec
Confidence            7778899999999999999999999999 89998776544

>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=99.79  E-value=1.4e-20  Score=166.97  Aligned_cols=108  Identities=25%  Similarity=0.449  Sum_probs=98.9

Q ss_pred             ccHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhcCCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCC
Q 017020           72 TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  151 (379)
Q Consensus        72 ~~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGi  151 (379)
                      ..|.+.|.++++.+ ++.++||||++...++.+++.|    .+..+||++++.+|+.++++|++|+.+|||||+++++|+
T Consensus        78 ~~K~~~l~~ll~~~-~~~k~lvf~~~~~~~~~l~~~l----~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gi  152 (200)
T d2fwra1          78 KNKIRKLREILERH-RKDKIIIFTRHNELVYRISKVF----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGI  152 (200)
T ss_dssp             SHHHHHHHHHHHHT-SSSCBCCBCSCHHHHHHHHHHT----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSS
T ss_pred             HHHHHHHHHHHHhC-CCCcEEEEeCcHHHHHHHHhhc----CcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhccc
Confidence            46888889998876 4689999999999888887766    566789999999999999999999999999999999999


Q ss_pred             CCCccceEEecCCCCChhHHHHHHhhccCCCCC
Q 017020          152 DIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE  184 (379)
Q Consensus       152 Dip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~  184 (379)
                      |+|.+++||++++|+++..|+||+||++|.|..
T Consensus       153 dl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~  185 (200)
T d2fwra1         153 DVPDANVGVIMSGSGSAREYIQRLGRILRPSKG  185 (200)
T ss_dssp             CSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTT
T ss_pred             CCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCC
Confidence            999999999999999999999999999999854

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.76  E-value=7.5e-18  Score=148.94  Aligned_cols=122  Identities=21%  Similarity=0.365  Sum_probs=110.1

Q ss_pred             cHHHHHHHHHHHHcCCCcEEEEecccccHHHHHHHHhc---CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecccccc
Q 017020           73 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR  149 (379)
Q Consensus        73 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~---~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~r  149 (379)
                      ++..+...+......++++-+.||..++.+.++..+.+   .+.+..+||.|+++++++++.+|++|+++|||||.+.+.
T Consensus        16 ~~~~i~~~I~~El~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEv   95 (211)
T d2eyqa5          16 DSMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIET   95 (211)
T ss_dssp             CHHHHHHHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGG
T ss_pred             CHHHHHHHHHHHHHcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhh
Confidence            44455566666777899999999999999999999875   678999999999999999999999999999999999999


Q ss_pred             CCCCCccceEEecCCCC-ChhHHHHHHhhccCCCCCceEEEEeChh
Q 017020          150 GLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTSS  194 (379)
Q Consensus       150 GiDip~v~~VI~~~~P~-~~~~yiqR~GRtgR~G~~g~~i~l~~~~  194 (379)
                      |||+|+++++|..+.+. ....+.|..||+||.+..|.||+++.+.
T Consensus        96 GiDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5          96 GIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             GSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             ccCCCCCcEEEEecchhccccccccccceeeecCccceEEEEecCC
Confidence            99999999999888875 8899999999999999999999998653

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.67  E-value=4.3e-17  Score=152.04  Aligned_cols=103  Identities=18%  Similarity=0.291  Sum_probs=87.5

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEE-----
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----  160 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI-----  160 (379)
                      .++++||||+++++++.++..|.. ++.+..+||++++..    ...|++|..+++|||+++++|+|++ +++||     
T Consensus       177 ~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~  251 (305)
T d2bmfa2         177 FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRC  251 (305)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEE
T ss_pred             hCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCc
Confidence            468999999999999999999985 889999999997654    4578899999999999999999994 55554     


Q ss_pred             -----ecCC----------CCChhHHHHHHhhccCCCCCceEEEEeChh
Q 017020          161 -----HYEL----------PNDPETFVHRSGRTGRAGKEGTAILMFTSS  194 (379)
Q Consensus       161 -----~~~~----------P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~  194 (379)
                           +|+.          |.+..+|+||+||+||.|+.+...++|...
T Consensus       252 ~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~  300 (305)
T d2bmfa2         252 MKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGE  300 (305)
T ss_dssp             EEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECSC
T ss_pred             eeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECCC
Confidence                 4443          568899999999999999888888777653

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.47  E-value=1.4e-13  Score=131.28  Aligned_cols=133  Identities=12%  Similarity=0.247  Sum_probs=110.4

Q ss_pred             ccHHHHHHHHHHHH--cCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCcee---EEEecc
Q 017020           72 TSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT---VLVATD  145 (379)
Q Consensus        72 ~~k~~~L~~ll~~~--~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~---iLVaTd  145 (379)
                      ..|..+|..++...  .++.++|||++.....+.+...|.. ++....+||+++..+|..+++.|+++...   +|++|.
T Consensus       100 S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~  179 (346)
T d1z3ix1         100 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK  179 (346)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG
T ss_pred             CHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecch
Confidence            46888888888654  4578999999999999999999975 89999999999999999999999987543   778899


Q ss_pred             ccccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCceEE--EEeChh--hHHHHHHHHH
Q 017020          146 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI--LMFTSS--QRRTVRSLER  204 (379)
Q Consensus       146 v~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i--~l~~~~--e~~~l~~le~  204 (379)
                      +++.|+|++.+++||.||+++++..+.|++||+.|.|++..+.  .|+...  |...++.+.+
T Consensus       180 agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~TiEe~i~~~~~~  242 (346)
T d1z3ix1         180 AGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQRQAH  242 (346)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHHHHHHHHH
T ss_pred             hhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCCCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999765554  344432  3344444433

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.47  E-value=1e-13  Score=125.82  Aligned_cols=131  Identities=16%  Similarity=0.269  Sum_probs=94.4

Q ss_pred             ccHHHHHHHHHHHH-cCCCcEEEEecccccHHHHHHHHhc--CCcEEEeeCCCCHHHHHHHHhcccCC-ceeEEE-eccc
Q 017020           72 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQG-KFTVLV-ATDV  146 (379)
Q Consensus        72 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~~~~l~~~L~~--~~~v~~lhg~m~~~~R~~~~~~F~~g-~~~iLV-aTdv  146 (379)
                      ..|...+.+++... ..+.++||||+.....+.+...+..  +..+..+||++++.+|+.++++|.++ ...+++ +|.+
T Consensus        68 S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~  147 (244)
T d1z5za1          68 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKA  147 (244)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCT
T ss_pred             hhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccc
Confidence            46888888888653 4578999999999999998888863  78888999999999999999999866 456665 5589


Q ss_pred             cccCCCCCccceEEecCCCCChhHHHHHHhhccCCCCCc--eEEEEeChh--hHHHHHHH
Q 017020          147 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG--TAILMFTSS--QRRTVRSL  202 (379)
Q Consensus       147 ~~rGiDip~v~~VI~~~~P~~~~~yiqR~GRtgR~G~~g--~~i~l~~~~--e~~~l~~l  202 (379)
                      ++.|+|++.+++||+|++|+++..+.|+.||+.|.|+..  .++.++...  |...++.+
T Consensus       148 ~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~Tiee~i~~~~  207 (244)
T d1z5za1         148 GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLL  207 (244)
T ss_dssp             TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSHHHHHHHHH
T ss_pred             cccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999543  444455543  33334433

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

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

Probab=99.46  E-value=4.5e-14  Score=131.82  Aligned_cols=101  Identities=19%  Similarity=0.253  Sum_probs=80.8

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccccCCCCCccceEEecCC-
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL-  164 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~-  164 (379)
                      .+++++|||++..++++++..|.. +..+..+||.++..+++    +|++|+.++|||||+++.|+|+ ++.+||+++. 
T Consensus        35 ~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~  109 (299)
T d1yksa2          35 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTA  109 (299)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCce
Confidence            368999999999999999999985 88999999999988765    5788999999999999999999 5999997664 


Q ss_pred             ------------------CCChhHHHHHHhhccCCCCCceEEEEeC
Q 017020          165 ------------------PNDPETFVHRSGRTGRAGKEGTAILMFT  192 (379)
Q Consensus       165 ------------------P~~~~~yiqR~GRtgR~G~~g~~i~l~~  192 (379)
                                        |.+..+-.||.||+||.+....++.+|.
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         110 FKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             eceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                              3477888999999999875555655654

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=99.31  E-value=1.6e-11  Score=104.61  Aligned_cols=124  Identities=22%  Similarity=0.284  Sum_probs=98.9

Q ss_pred             CCccHHHHHHHHH-HHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecccc
Q 017020           70 TATSKRTILSDLI-TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  147 (379)
Q Consensus        70 ~~~~k~~~L~~ll-~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~  147 (379)
                      ....|..++..-+ ..+..+.|+||+|.|.+.++.++..|.. +++...++......+-+-+-+.-..|  .|.|||++|
T Consensus        15 T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~Ag~~g--~VtIATNmA   92 (175)
T d1tf5a4          15 TMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMA   92 (175)
T ss_dssp             SHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTS
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhccCCC--ceeehhhHH
Confidence            3456766554444 5556789999999999999999999986 88999999986544444444444434  699999999


Q ss_pred             ccCCCCC---cc-----ceEEecCCCCChhHHHHHHhhccCCCCCceEEEEeChhh
Q 017020          148 ARGLDIP---NV-----DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       148 ~rGiDip---~v-----~~VI~~~~P~~~~~yiqR~GRtgR~G~~g~~i~l~~~~e  195 (379)
                      +||.||.   .|     -|||.-..|.+..-..|-.||+||.|.+|.+.+|++-.|
T Consensus        93 GRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          93 GRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             STTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             HcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            9999984   22     379999999999999999999999999999999987654

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.62  E-value=9.5e-08  Score=82.59  Aligned_cols=123  Identities=23%  Similarity=0.260  Sum_probs=94.7

Q ss_pred             CccHHHHHH-HHHHHHcCCCcEEEEecccccHHHHHHHHhc-CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccccc
Q 017020           71 ATSKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  148 (379)
Q Consensus        71 ~~~k~~~L~-~ll~~~~~~~~~IIF~~t~~~~~~l~~~L~~-~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv~~  148 (379)
                      ...|..++. ++...+..+.|+||.+.|.+..+.++..|.. +++...|++.-...+-+-+-++=+  .-.|-|||++|+
T Consensus        16 ~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAeIIAqAG~--~GaVTIATNMAG   93 (219)
T d1nkta4          16 EEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGR--RGGVTVATNMAG   93 (219)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTS--TTCEEEEETTCS
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHHHHHhccc--CCcEEeeccccC
Confidence            346665554 4455567789999999999999999999985 899999999844333333333333  345899999999


Q ss_pred             cCCCCCc----------------------------------------------------cceEEecCCCCChhHHHHHHh
Q 017020          149 RGLDIPN----------------------------------------------------VDLIIHYELPNDPETFVHRSG  176 (379)
Q Consensus       149 rGiDip~----------------------------------------------------v~~VI~~~~P~~~~~yiqR~G  176 (379)
                      ||.||-=                                                    ==|||--....+..-=-|-.|
T Consensus        94 RGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRG  173 (219)
T d1nkta4          94 RGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRG  173 (219)
T ss_dssp             TTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHH
T ss_pred             CCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccccccccc
Confidence            9999921                                                    126777777778877889999


Q ss_pred             hccCCCCCceEEEEeChhh
Q 017020          177 RTGRAGKEGTAILMFTSSQ  195 (379)
Q Consensus       177 RtgR~G~~g~~i~l~~~~e  195 (379)
                      |+||.|.+|.+..|++-.|
T Consensus       174 RsGRQGDPGsSrFflSLeD  192 (219)
T d1nkta4         174 RSGRQGDPGESRFYLSLGD  192 (219)
T ss_dssp             TSSGGGCCEEEEEEEETTS
T ss_pred             cccccCCCccceeEEeccH
Confidence            9999999999999998765

>d2e29a1 d.58.7.5 (A:8-92) ATP-dependent RNA helicase DDX50 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: GUCT domain
domain: ATP-dependent RNA helicase DDX50
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.35  E-value=4.1e-07  Score=67.17  Aligned_cols=78  Identities=15%  Similarity=0.155  Sum_probs=69.3

Q ss_pred             CCCccccCCCCeEEEEEeeCCcccCCCCChhHHHHHHhhhCCC-CCCccccEEeeeCCceeeeecchhhHHHHhhhhccc
Q 017020          275 SSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPT-AADEIGKIHIIADDRVCIDTVILLYFYASVRLGLFN  353 (379)
Q Consensus       275 ~~~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~i~~~~~~~~~~-~~~~ig~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~  353 (379)
                      ++||++++.+|++|+.+..++    ..-+|+++++.|.+..+- ..+.|..+.+..+.+  |+|||||+.-.+.+.+..+
T Consensus         2 k~RSLLts~~g~~T~~l~~~~----~i~~~~y~w~~Lr~~L~e~~~~~I~~M~l~kd~~--GavFDVpse~~~~i~~~W~   75 (85)
T d2e29a1           2 EPRSLITSDKGFVTMTLESLE----EIQDVSCAWKELNRKLSSNAVSQITRMCLLKGNM--GVCFDVPTTESERLQAEWH   75 (85)
T ss_dssp             CCCCCCCCCCCEEEEEEECSS----CCSSTHHHHHHHHHHSCHHHHTTCEEEEECTTSS--EEEEEEEHHHHHHHHHHCC
T ss_pred             ccccccccCCCcEEEEEecCc----cccccHHHHHHHHHHccHHHHHhhheeEEecCCC--EEEEeccHHHHHHHHHHhc
Confidence            468999999999999998876    467899999999999883 366899999999999  9999999999999999998


Q ss_pred             CcceE
Q 017020          354 TKSVI  358 (379)
Q Consensus       354 ~~~~~  358 (379)
                      .++-+
T Consensus        76 dsr~~   80 (85)
T d2e29a1          76 DSDWI   80 (85)
T ss_dssp             SSSCE
T ss_pred             ccceE
Confidence            87644

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.69  E-value=0.0016  Score=58.03  Aligned_cols=103  Identities=19%  Similarity=0.236  Sum_probs=74.7

Q ss_pred             ccHHHHHHHH-HHHHcCCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           72 TSKRTILSDL-ITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        72 ~~k~~~L~~l-l~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ..|..+.... ......+.++++-++|.--+.+.+..+..     ++.+..+||+++..+|..++.+.++|+.+|+|+|-
T Consensus       115 SGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGTh  194 (264)
T d1gm5a3         115 SGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTH  194 (264)
T ss_dssp             SSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECT
T ss_pred             ccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeeh
Confidence            4566544333 33445678999999999888887777653     57899999999999999999999999999999996


Q ss_pred             cc-ccCCCCCccceEEecCCCCChhHHHHHHh
Q 017020          146 VA-ARGLDIPNVDLIIHYELPNDPETFVHRSG  176 (379)
Q Consensus       146 v~-~rGiDip~v~~VI~~~~P~~~~~yiqR~G  176 (379)
                      .+ ...+.+.++.+||-=.  ...-.|-||-+
T Consensus       195 sl~~~~~~f~~LglviiDE--qH~fgv~Qr~~  224 (264)
T d1gm5a3         195 ALIQEDVHFKNLGLVIIDE--QHRFGVKQREA  224 (264)
T ss_dssp             THHHHCCCCSCCCEEEEES--CCCC-----CC
T ss_pred             HHhcCCCCccccceeeecc--ccccchhhHHH
Confidence            55 4468888888877433  23335666643

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.18  E-value=0.0067  Score=52.87  Aligned_cols=102  Identities=15%  Similarity=0.127  Sum_probs=78.6

Q ss_pred             ccHHHHHHHHH-HHHcCCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEecc
Q 017020           72 TSKRTILSDLI-TVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  145 (379)
Q Consensus        72 ~~k~~~L~~ll-~~~~~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTd  145 (379)
                      ..|.++....+ .....+.++++-++|..-+...+..+..     +..+..+||.++..+|..+++.+.+|+.+|+|.|-
T Consensus        87 sGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGth  166 (233)
T d2eyqa3          87 FGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTH  166 (233)
T ss_dssp             TTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECT
T ss_pred             CCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeeh
Confidence            46766554443 4456688999999999999999888874     45788999999999999999999999999999997


Q ss_pred             ccc-cCCCCCccceEEecCCCCChhHHHHHH
Q 017020          146 VAA-RGLDIPNVDLIIHYELPNDPETFVHRS  175 (379)
Q Consensus       146 v~~-rGiDip~v~~VI~~~~P~~~~~yiqR~  175 (379)
                      .+- ..+.++++.+||-=.-  .-..|-||.
T Consensus       167 s~l~~~~~f~~LgLiIiDEe--H~fg~kQ~~  195 (233)
T d2eyqa3         167 KLLQSDVKFKDLGLLIVDEE--HRFGVRHKE  195 (233)
T ss_dssp             HHHHSCCCCSSEEEEEEESG--GGSCHHHHH
T ss_pred             hhhccCCccccccceeeech--hhhhhHHHH
Confidence            554 4688889888774321  223455554

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=86.37  E-value=0.82  Score=37.83  Aligned_cols=69  Identities=22%  Similarity=0.261  Sum_probs=51.1

Q ss_pred             CCCcEEEEecccccHHHHHHHHhc-----CCcEEEeeCCCCHHHHHHHHhcccCCceeEEEeccc-----c-ccCCCCCc
Q 017020           87 KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----A-ARGLDIPN  155 (379)
Q Consensus        87 ~~~~~IIF~~t~~~~~~l~~~L~~-----~~~v~~lhg~m~~~~R~~~~~~F~~g~~~iLVaTdv-----~-~rGiDip~  155 (379)
                      .+.++||.|+|++-|.++...+..     +..+..++|+.+..+..+.++     ..+|+|+|+-     + ...+++.+
T Consensus        71 ~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-----~~~IlV~TP~~l~~~l~~~~~~~~~  145 (208)
T d1hv8a1          71 NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLKN  145 (208)
T ss_dssp             SSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTTS
T ss_pred             cCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-----CCCEEEEChHHHHHHHHcCCCCccc
Confidence            355899999999999998777653     467889999988777665553     2579999962     2 33457777


Q ss_pred             cceEE
Q 017020          156 VDLII  160 (379)
Q Consensus       156 v~~VI  160 (379)
                      +.++|
T Consensus       146 l~~lV  150 (208)
T d1hv8a1         146 VKYFI  150 (208)
T ss_dssp             CCEEE
T ss_pred             CcEEE
Confidence            77766