Citrus Sinensis ID: 012133

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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-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470
Protein Sequence
MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN
Secondary Structure (PSIPRED)
cEEEccccHHHHHHHHHHcccccEEEEEEcccccccccEEEEEEEEccccHHHHHHHHHHcccccccEEEEccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccccEEEcccccccccccccccEEEccccccccccccccccccccccccccEEEEEcccHHHHHHHHHHHHccccEEcccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccccccccccccccccEEEEEccccccccccccHHHHHHHHHccccccccccEEEEEcccccEEEEEccHHHHHHHHHHccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHccccEEEEEEcccEEEcccEEEEEEEEccHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHccccHHHHcccccHHHHHHHHHHHHccccEEEEEEcHHHccccccccEEEEEcccccccccEEEEccccccccccEEEEEEEcHHHHHHHHHHHHHHcccEEEcccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHccccccccccccccccccccEEEEEccccccccccHHHHHHHHHHHcccccHHccEEEEEcccEEEEEEEEccHHHHHHHHHHHccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccccccccccccccccccEEcccccccccccccc
Coil and Loop (DISEMBL)
mlfsatmpsWVKKLSRKyldnplnidlvgnqDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAlhgdisqhqrertlngfrqgkFTVLVATDVaargldipnvdliihyelpndpetfvhrsgrtgragkegTAILMFTSSQRRTVRslerdvgckfefvsppvveDVLESSAEQVVATLngvhpesvefftPTAQRLIEEKGTDALAAALAQLsgfsrppssrslinheqgWVTLQLTRDSAFSRGFMSARSVMGflsdvyptaadeigKIHIiaddrvqgavfDLPEEIAKELLnkqippgntiskitklpalqddgpssdnygrfssrdrfsrgggsrfsrggarggargggsmdrrgfrssrswgsddedgfsssrggrsfrsgnnrgsrfstssdddwliggsrssrsssrdsrsfggacfncgksghrasecpn
Flexible Loop (DISEMBL)
mlfsatmpsWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAisttatskrtiLSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRsgrtgragkegtailmftssqrrtvrslerdvgckfefvSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKEllnkqippgntISKItklpalqddgpssdnygrfssrdrfsrgggsrfsrggarggargggsmdrrgfrssrswgsddedgfsssrggrsfrsgnnrgsrfstssdddwliggsrssrsssrdsrsfggacfncgksghrasecpn
Low Complexity Region (SEG)
MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYgrfssrdrfsrgggsrfsrggarggargggsmdrrgfrssrswgsddEDgfsssrggrsfrsgnnrgsrfstssDDDWLIggsrssrsssrdsrsfggACFNCGKSGHRASECPN
Disordered region (IsUnstruct)
*********WVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH************TAILMFTS**RRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALA*************LINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNK**********************************************************************************************************************************************
Disordered Region (DISOPRED)
MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAAL******************************SAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISK**********************************************************************************************************************NCGKSG********
Disordered Region (DISEMBL)
********SWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRD******************************************************SGNNRGSRFSTSSDDDWLI***************FGGACFNCGK**********
Disordered Region (DISPRO)
MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFS*************GWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPAL*****************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN
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	470	2.2.26 [Sep-21-2011]
Q8L7S8	748	DEAD-box ATP-dependent RN	yes	no	0.774	0.486	0.848	1e-180
Q0DM51	758	DEAD-box ATP-dependent RN	yes	no	0.770	0.477	0.817	1e-176
Q0D8N0	602	DEAD-box ATP-dependent RN	no	no	0.425	0.332	0.623	6e-70
Q9LUW5	616	DEAD-box ATP-dependent RN	no	no	0.417	0.318	0.627	1e-69
Q0ILZ4	628	DEAD-box ATP-dependent RN	no	no	0.397	0.297	0.631	2e-68
Q9LUW6	610	DEAD-box ATP-dependent RN	no	no	0.417	0.321	0.602	1e-67
Q650T9	696	DEAD-box ATP-dependent RN	no	no	0.710	0.479	0.398	7e-57
Q9JIK5	851	Nucleolar RNA helicase 2	yes	no	0.808	0.446	0.354	1e-55
Q9NR30	783	Nucleolar RNA helicase 2	yes	no	0.825	0.495	0.359	1e-54
Q9BQ39	737	ATP-dependent RNA helicas	no	no	0.740	0.472	0.381	1e-54

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

 Score =  632 bits (1629), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 309/364 (84%), Positives = 342/364 (93%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP+WVKKL+RKYLDNPLNIDLVG+QDEKLAEGIKLYAI+TT+TSKRTILSDLIT
Sbjct: 287 MLFSATMPTWVKKLARKYLDNPLNIDLVGDQDEKLAEGIKLYAIATTSTSKRTILSDLIT 346

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTIVFTQTKRDADEVSLAL++ IA+EALHGDISQHQRERTLN FRQGKFTVLVA
Sbjct: 347 VYAKGGKTIVFTQTKRDADEVSLALSNSIATEALHGDISQHQRERTLNAFRQGKFTVLVA 406

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVA+RGLDIPNVDL+IHYELPNDPETFVHRSGRTGRAGKEG+AILM TSSQ+RTVRSLE
Sbjct: 407 TDVASRGLDIPNVDLVIHYELPNDPETFVHRSGRTGRAGKEGSAILMHTSSQKRTVRSLE 466

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RDVGC FEF+SPP V D+LESSA+QVVATLNGVHP+S++FF+ TAQ+L EEKGTDALAAA
Sbjct: 467 RDVGCHFEFISPPTVGDLLESSADQVVATLNGVHPDSIKFFSATAQKLYEEKGTDALAAA 526

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LA LSGFS+PPSSRSL++HE+GWVTLQL RD   +RGF+SARSV GFLSD+Y TAADE+G
Sbjct: 527 LAHLSGFSQPPSSRSLLSHEKGWVTLQLIRDPTNARGFLSARSVTGFLSDLYRTAADEVG 586

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KI +IADDR+QGAVFDLPEEIAKELL K +P GN++S ITKLP LQDDGPSSDNYGRFSS
Sbjct: 587 KIFLIADDRIQGAVFDLPEEIAKELLEKDVPEGNSLSMITKLPPLQDDGPSSDNYGRFSS 646

Query: 361 RDRF 364
           RDR 
Sbjct: 647 RDRM 650

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 =  620 bits (1598), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 296/362 (81%), Positives = 333/362 (91%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP WVKKLSR+YL+NPL IDLVG+QDEKLAEGIKLYAI  T+TSKRT+LSDLIT
Sbjct: 287 MLFSATMPGWVKKLSRRYLNNPLTIDLVGDQDEKLAEGIKLYAIPLTSTSKRTVLSDLIT 346

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTIVFT+TKRDADEVSLALT+ IASEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 347 VYAKGGKTIVFTKTKRDADEVSLALTNSIASEALHGDISQHQRERTLNGFRQGKFTVLVA 406

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK GTAILMFT+SQRRTVRSLE
Sbjct: 407 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKAGTAILMFTNSQRRTVRSLE 466

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RDVGC+F+F+SPP +EDVLESSAE V+ATL GVH ES+++F P A+RL EE G +ALA+A
Sbjct: 467 RDVGCRFDFISPPAIEDVLESSAEHVIATLRGVHTESIQYFIPAAERLQEELGPNALASA 526

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LA LSGFS+PPSSRSLI+HEQGWVTLQLTRD  + RGF S RSV GFLSDV   AADE+G
Sbjct: 527 LAHLSGFSQPPSSRSLISHEQGWVTLQLTRDPGYGRGFFSPRSVTGFLSDVSSAAADEVG 586

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KI + AD++VQGAVFDLPEEIA++LL+ ++PPGNTI+K+TKLPALQDDGP++D+YGRFS+
Sbjct: 587 KIFLTADEKVQGAVFDLPEEIARDLLSMELPPGNTITKVTKLPALQDDGPATDSYGRFSN 646

Query: 361 RD 362
            D
Sbjct: 647 SD 648

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 =  265 bits (677), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 126/202 (62%), Positives = 161/202 (79%), Gaps = 2/202 (0%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMPSW++K++ KYL +P+ IDLVG++D+KL EGI LY+I++    K +IL  LI 
Sbjct: 264 MLFSATMPSWIRKITSKYLKDPIIIDLVGDEDQKLPEGISLYSIASEHYGKPSILGPLIK 323

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
            +A GGK IVFTQTKR+AD ++ A+    A +ALHGDISQ+QRERTL+GFR G+F +LVA
Sbjct: 324 EHANGGKCIVFTQTKREADRLAYAMGRSYACQALHGDISQNQRERTLSGFRDGRFNILVA 383

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVAARGLDIPNVDL+IHYELPN  E FVHRSGRT RAGK+G+AIL++T+ Q R VR +E
Sbjct: 384 TDVAARGLDIPNVDLVIHYELPNTSELFVHRSGRTARAGKKGSAILIYTNDQARAVRIIE 443

Query: 181 RDVGCKFEFVSPPVVEDVLESS 202
           +D+GCKF  +  P +E   E+S
Sbjct: 444 QDIGCKFTEL--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 =  264 bits (674), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 123/196 (62%), Positives = 155/196 (79%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           M+FSATMPSW++ L++KYL+NPL +DLVG+ D+KLA+GI  Y+I   +  + +I+  L+T
Sbjct: 285 MMFSATMPSWIRSLTKKYLNNPLTVDLVGDSDQKLADGITTYSIIADSYGRASIIGPLVT 344

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
            +AKGGK IVFTQTKRDAD +S AL      EALHGDISQ QRERTL GFR G F +LVA
Sbjct: 345 EHAKGGKCIVFTQTKRDADRLSYALARSFKCEALHGDISQSQRERTLAGFRDGHFNILVA 404

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVAARGLD+PNVDLIIHYELPN+ ETFVHR+GRTGRAGK+G+AIL+++  Q R V+ +E
Sbjct: 405 TDVAARGLDVPNVDLIIHYELPNNTETFVHRTGRTGRAGKKGSAILIYSQDQSRAVKIIE 464

Query: 181 RDVGCKFEFVSPPVVE 196
           R+VG +F  +    VE
Sbjct: 465 REVGSRFTELPSIAVE 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 =  260 bits (664), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 118/187 (63%), Positives = 149/187 (79%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           ++FSATMP+W+++L++KYL NP+ IDLVG  D+KLAEGI LY+I++   +K  +L +LI 
Sbjct: 278 LMFSATMPTWIQRLTQKYLKNPVTIDLVGEDDQKLAEGISLYSIASEGHAKPAVLGELIK 337

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
            +AKGGK IVFTQTKRDAD +S  +      +ALHGDI+Q QRERTL GFR+G F +L+A
Sbjct: 338 EHAKGGKCIVFTQTKRDADRLSYTMGRSFQCQALHGDITQAQRERTLKGFREGHFNILIA 397

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVAARGLDIPNVDL+IH+ELPN  E FVHRSGRTGRAGK+G AI+M +  Q R +R +E
Sbjct: 398 TDVAARGLDIPNVDLVIHFELPNSSELFVHRSGRTGRAGKKGKAIVMHSYQQSRAIRMVE 457

Query: 181 RDVGCKF 187
            DVGCKF
Sbjct: 458 NDVGCKF 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 =  257 bits (657), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 118/196 (60%), Positives = 153/196 (78%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           M+FSATMPSW++ L++KYL+NPL IDLVG+ D+KLA+GI +Y+I+  +  + +I+  L+ 
Sbjct: 297 MMFSATMPSWIRSLTKKYLNNPLTIDLVGDSDQKLADGITMYSIAADSYGRASIIGPLVK 356

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
            + KGGK IVFTQTKRDAD ++  L      EALHGDISQ QRERTL GFR G F++LVA
Sbjct: 357 EHGKGGKCIVFTQTKRDADRLAFGLAKSYKCEALHGDISQAQRERTLAGFRDGNFSILVA 416

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVAARGLD+PNVDL+IHYELPN+ ETFVHR+GRTGRAGK+G+AIL+    Q R V+ +E
Sbjct: 417 TDVAARGLDVPNVDLVIHYELPNNTETFVHRTGRTGRAGKKGSAILIHGQDQTRAVKMIE 476

Query: 181 RDVGCKFEFVSPPVVE 196
           ++VG +F  +    VE
Sbjct: 477 KEVGSRFNELPSIAVE 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 =  221 bits (564), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 142/356 (39%), Positives = 205/356 (57%), Gaps = 22/356 (6%)

Query: 1   MLFSATMPSWVKKLSRKYLDN-PLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
           +LFSAT+P WVKKLS ++L +    +DLVG++  K +  ++  A+     ++  ++ D+I
Sbjct: 304 LLFSATIPEWVKKLSLRFLKSGKKTVDLVGDEKLKASASVRHLALPCNRAARAQVIPDII 363

Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSIIA-SEALHGDISQHQRERTLNGFRQGKFTVL 118
             Y++GG+TI+FT+TK  A +    L+ +IA S ALHGD++Q QRE  L GFR GKF VL
Sbjct: 364 RCYSRGGRTIIFTETKESASD----LSGLIAGSRALHGDVAQAQREVILAGFRSGKFLVL 419

Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           VAT+VAARGLDI +V LII  E P D E ++HRSGRTGRAG  G A+++F    +  V  
Sbjct: 420 VATNVAARGLDINDVQLIIQCEPPRDVEAYIHRSGRTGRAGNTGVAVMLFEPRYKFNVNR 479

Query: 179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKG---TD 235
           +ER+ G KFE +S P   DV +S+  +    ++ V    +  F   A++L+   G    D
Sbjct: 480 IERESGVKFEHISAPQPTDVAQSAGTEAAEAISSVSDSVIPVFREQAEQLLNSSGMSAVD 539

Query: 236 ALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL-TRDSAFSRGFMSARSVMGFLSDVYPT 294
            LA ALA+  G++     RSL++      TL L T  S ++ GF     V+  L    P 
Sbjct: 540 LLAKALAKAVGYTD-IKKRSLLSSMDNHTTLLLQTGRSVYAAGF-----VLSTLKRFMPE 593

Query: 295 A--ADEIGKIHIIADDRVQGAVFDLPE-EIAKELLNKQIPPGNTISKITKLPALQD 347
              AD  G I I AD    GAVFD+P  E+   +   Q     T+ ++ +LP LQ+
Sbjct: 594 ERLADVKG-ITITADG--TGAVFDVPSAEVEDYIQGAQNAAMVTVEEVKQLPPLQE 646

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9JIK5|DDX21_MOUSE Nucleolar RNA helicase 2 OS=Mus musculus GN=Ddx21 PE=1 SV=3

 Score =  218 bits (554), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 151/426 (35%), Positives = 231/426 (54%), Gaps = 46/426 (10%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPL-NIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
           +LFSAT P WV  +++KY+ +    +DL+G + +K A  ++  AI    T +  ++ D+I
Sbjct: 444 LLFSATCPHWVFNVAKKYMKSTYEQVDLIGKKTQKAAITVEHLAIKCHWTERAAVIGDVI 503

Query: 60  TVYA-KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVL 118
            VY+   G+TI+F +TK+DA E+S        +++LHGDI Q QRE TL GFR G F VL
Sbjct: 504 RVYSGHQGRTIIFCETKKDAQELSQNTCIKQDAQSLHGDIPQKQREITLKGFRNGNFGVL 563

Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           VAT+VAARGLDIP VDL++    P D E+++HRSGRTGRAG+ G  I  + + +   +  
Sbjct: 564 VATNVAARGLDIPEVDLVVQSCPPKDVESYIHRSGRTGRAGRTGVCICFYQNKEEYQLAQ 623

Query: 179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKG-TDAL 237
           +E+  G KF+ +  P   +++++S++  +  L+ V P ++  F  +A++LIEEKG  +AL
Sbjct: 624 VEQKAGIKFKRIGVPSATEIIKASSKDAIRLLDSVPPTAISHFKQSAEKLIEEKGAVEAL 683

Query: 238 AAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD 297
           AAALA +SG +     RSLIN + G+VT+            +     M  +S  +    +
Sbjct: 684 AAALAHISGATS-VDQRSLINSQAGFVTM-----------ILRCSIEMPNISYAWKELKE 731

Query: 298 EIGKIHIIADDRVQGAV---------FDLPEEIAKELLNKQIPPGN-TISKITKLPALQD 347
           ++G+     D +V+G V         FD+  E   E+  K        ++  T+ P L  
Sbjct: 732 QLGE---SIDAKVKGMVFLKGKLGVCFDVRTEAVTEIQEKWHDSRRWQLTVATEQPEL-- 786

Query: 348 DGPSSDNYGRFSSRD------RFSRGGGSRFSRGGARGGAR--------GGGSMDRRGFR 393
           +GP     GR   RD      R  RGG   F   G RGG+R        GG    +R F 
Sbjct: 787 EGPPDGYRGRMGQRDGSRGAFRGQRGGSRNFRGQGQRGGSRNFRGQRPGGGNRGQKRSF- 845

Query: 394 SSRSWG 399
            S+++G
Sbjct: 846 -SKAFG 850

Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase). Functions as cofactor for JUN-activated transcription.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9NR30|DDX21_HUMAN Nucleolar RNA helicase 2 OS=Homo sapiens GN=DDX21 PE=1 SV=5

 Score =  214 bits (545), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 156/434 (35%), Positives = 235/434 (54%), Gaps = 46/434 (10%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPL-NIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
           +LFSAT P WV  +++KY+ +    +DL+G + +K A  ++  AI    T +  ++ D+I
Sbjct: 372 LLFSATCPHWVFNVAKKYMKSTYEQVDLIGKKTQKTAITVEHLAIKCHWTQRAAVIGDVI 431

Query: 60  TVYA-KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVL 118
            VY+   G+TI+F +TK++A E+S        +++LHGDI Q QRE TL GFR G F VL
Sbjct: 432 RVYSGHQGRTIIFCETKKEAQELSQNSAIKQDAQSLHGDIPQKQREITLKGFRNGSFGVL 491

Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           VAT+VAARGLDIP VDL+I    P D E+++HRSGRTGRAG+ G  I  +   +   +  
Sbjct: 492 VATNVAARGLDIPEVDLVIQSSPPKDVESYIHRSGRTGRAGRTGVCICFYQHKEEYQLVQ 551

Query: 179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKG-TDAL 237
           +E+  G KF+ +  P   +++++S++  +  L+ V P ++  F  +A++LIEEKG  +AL
Sbjct: 552 VEQKAGIKFKRIGVPSATEIIKASSKDAIRLLDSVPPTAISHFKQSAEKLIEEKGAVEAL 611

Query: 238 AAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD 297
           AAALA +SG +     RSLIN   G+VT+            +     M  +S  +    +
Sbjct: 612 AAALAHISGATS-VDQRSLINSNVGFVTM-----------ILQCSIEMPNISYAWKELKE 659

Query: 298 EIGKIHIIADDRVQGAV---------FDLPEEIAKELLNKQIPPGN-TISKITKLPALQD 347
           ++G+     D +V+G V         FD+P     E+  K        +S  T+ P L  
Sbjct: 660 QLGE---EIDSKVKGMVFLKGKLGVCFDVPTASVTEIQEKWHDSRRWQLSVATEQPEL-- 714

Query: 348 DGPSSDNYGRFSSRDRFSRG------GGSRF--SRGGARG--GARGGGSMDRRGFRSSRS 397
           +GP  + YG F  +   SRG      G  RF   R G+RG  G R GG     G +S+RS
Sbjct: 715 EGP-REGYGGFRGQREGSRGFRGQRDGNRRFRGQREGSRGPRGQRSGG-----GNKSNRS 768

Query: 398 WGSDDEDGFSSSRG 411
                +  FS + G
Sbjct: 769 QNKGQKRSFSKAFG 782

Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase). Functions as cofactor for JUN-activated transcription. Involved in rRNA processing.

Homo sapiens (taxid: 9606)

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 =  214 bits (544), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 137/359 (38%), Positives = 210/359 (58%), Gaps = 11/359 (3%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPL-NIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
           +LFSAT P WV K+++KY+ +    +DLVG   +K A  ++  AI    + +  ++ D++
Sbjct: 323 LLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVL 382

Query: 60  TVYA-KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVL 118
            VY+   G+ I+F +TK++  E+++       ++ LHGDI+Q QRE TL GFR+G F VL
Sbjct: 383 QVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVL 442

Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           VAT+VAARGLDIP VDL+I    P D E+++HRSGRTGRAG+ G  I  +   +R  +R 
Sbjct: 443 VATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICFYQPRERGQLRY 502

Query: 179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKG-TDAL 237
           +E+  G  F+ V  P   D+++S +   + +L  V   +V+FF P+AQRLIEEKG  DAL
Sbjct: 503 VEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDAL 562

Query: 238 AAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD 297
           AAALA +SG S     RSLI  ++G+VT+ L           + + +   LS     A  
Sbjct: 563 AAALAHISGAS-SFEPRSLITSDKGFVTMTLESLEEIQDVSCAWKELNRKLSS---NAVS 618

Query: 298 EIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQD--DGPSSDN 354
           +I ++ ++  +   G  FD+P   ++ L  +       +S   KLP +++  DG +S N
Sbjct: 619 QITRMCLLKGN--MGVCFDVPTTESERLQAEWHDSDWILSVPAKLPEIEEYYDGNTSSN 675

Homo sapiens (taxid: 9606)

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	470
225450401	764	PREDICTED: DEAD-box ATP-dependent RNA he	0.972	0.598	0.801	0.0
224124522	775	predicted protein [Populus trichocarpa]	0.965	0.585	0.793	0.0
118489724	481	unknown [Populus trichocarpa x Populus d	0.965	0.943	0.795	0.0
224124506	735	predicted protein [Populus trichocarpa]	0.968	0.619	0.808	0.0
356505715	771	PREDICTED: DEAD-box ATP-dependent RNA he	0.989	0.603	0.791	0.0
356534927	736	PREDICTED: DEAD-box ATP-dependent RNA he	0.955	0.610	0.771	0.0
357511641	753	DEAD-box ATP-dependent RNA helicase [Med	0.963	0.601	0.786	0.0
255543078	772	dead box ATP-dependent RNA helicase, put	0.955	0.581	0.755	0.0
356574052	736	PREDICTED: DEAD-box ATP-dependent RNA he	0.951	0.607	0.769	0.0
343172316	782	DEAD-box ATP-dependent RNA helicase, par	0.961	0.578	0.735	0.0

>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 =  726 bits (1873), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/473 (80%), Positives = 408/473 (86%), Gaps = 16/473 (3%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP+WVKKL+RKYLDNPL IDLVG+ DEKLAEGIKLYAI TTATSKRTILSDLIT
Sbjct: 301 MLFSATMPAWVKKLARKYLDNPLTIDLVGDHDEKLAEGIKLYAIPTTATSKRTILSDLIT 360

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTIVFTQTKRDADEVS+ALT+ IASEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 361 VYAKGGKTIVFTQTKRDADEVSMALTNSIASEALHGDISQHQRERTLNGFRQGKFTVLVA 420

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTV+SLE
Sbjct: 421 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVKSLE 480

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RDVGCKFEF+SPP +E+VLESSAEQVVATLNGVHPESVEFFTPTAQ+LIEEKGT ALAAA
Sbjct: 481 RDVGCKFEFISPPAIEEVLESSAEQVVATLNGVHPESVEFFTPTAQKLIEEKGTGALAAA 540

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LA LSGFS+PPS RSLI+HEQGWVTLQLTRDS +SRGF+SARSV GFLSDVYPTAADE+G
Sbjct: 541 LAHLSGFSQPPSFRSLISHEQGWVTLQLTRDSGYSRGFLSARSVTGFLSDVYPTAADELG 600

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KI+++AD+RVQGAVFDLPEEIAKELLNKQ+PPGNTISKITKLPALQDDGP+ D YGRFS+
Sbjct: 601 KIYLVADERVQGAVFDLPEEIAKELLNKQMPPGNTISKITKLPALQDDGPAGDYYGRFSN 660

Query: 361 RDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNN 420
           RDR S            RGG+R          R S     DD     + RGGRSFRS NN
Sbjct: 661 RDRSS------------RGGSRERRGSRISRGRGSSWGSDDDGGDDLNRRGGRSFRSNNN 708

Query: 421 RGSRFSTSSDDDWLI---GGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN 470
             SR   +S+DDWLI     +RSS S     RSFGG+CF CG+SGHRASECPN
Sbjct: 709 -WSRNLRTSEDDWLIGGRRSNRSSSSFGSRERSFGGSCFTCGRSGHRASECPN 760

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 =  724 bits (1868), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/470 (79%), Positives = 402/470 (85%), Gaps = 16/470 (3%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP+WVKKL+RKYLDNPL IDLVG+Q+EKLAEGIKLYA+S TA SKRTILSDL+T
Sbjct: 318 MLFSATMPTWVKKLARKYLDNPLQIDLVGDQEEKLAEGIKLYALSATAASKRTILSDLVT 377

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTI+FTQTKRDADEVS+ALT+ IASEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 378 VYAKGGKTIIFTQTKRDADEVSMALTNTIASEALHGDISQHQRERTLNGFRQGKFTVLVA 437

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVA+RGLDIPNVDLIIHYELPND ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE
Sbjct: 438 TDVASRGLDIPNVDLIIHYELPNDAETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 497

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RD GCKFEFVSPP +E+VLESSAEQVVATL+GVHPESVEFFTPTAQ+LIEE+GT+ALAAA
Sbjct: 498 RDAGCKFEFVSPPAIEEVLESSAEQVVATLSGVHPESVEFFTPTAQKLIEEQGTNALAAA 557

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LA LSGFS+PPSSRSLI+H QGW TLQLTRD  +SRGF+SARSV GFLSDVYP AADE+G
Sbjct: 558 LAHLSGFSQPPSSRSLISHAQGWATLQLTRDPTYSRGFLSARSVTGFLSDVYPAAADEVG 617

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KIH+IAD+RVQGAVFDLPEEIAKELLNKQIPPGNTI+KITKLPALQDDGP  D YGRFSS
Sbjct: 618 KIHVIADERVQGAVFDLPEEIAKELLNKQIPPGNTIAKITKLPALQDDGPPGDFYGRFSS 677

Query: 361 RDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNN 420
           RDR                     G          R  G D +DG +  RGGRS  S  N
Sbjct: 678 RDR--------------PARGGPRGQRGGFRSSRGRGSGRDSDDGGTYRRGGRS-NSNEN 722

Query: 421 RGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN 470
             S+ S SS DDWLIGG RSSR  SRD RSFGG+CFNCG+SGHRASECPN
Sbjct: 723 SWSQMSRSSGDDWLIGGRRSSRPPSRD-RSFGGSCFNCGRSGHRASECPN 771

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 =  722 bits (1864), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/470 (79%), Positives = 403/470 (85%), Gaps = 16/470 (3%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP+WVKKL+RKYLDNPL IDLVG+Q+EKLAEGIKLYA+S TA SKRTILSDL+T
Sbjct: 24  MLFSATMPTWVKKLARKYLDNPLQIDLVGDQEEKLAEGIKLYALSATAASKRTILSDLVT 83

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTI+FTQTKRDADEVS+ALT+ IASEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 84  VYAKGGKTIIFTQTKRDADEVSMALTNTIASEALHGDISQHQRERTLNGFRQGKFTVLVA 143

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVA+RGLDIPNVDLIIHYELPND ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE
Sbjct: 144 TDVASRGLDIPNVDLIIHYELPNDAETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 203

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RD GCKFEFVSPP +E+VLESSAEQVVATL+GVHPESVEFFTPTAQ+LIEE+GT+ALAAA
Sbjct: 204 RDAGCKFEFVSPPAIEEVLESSAEQVVATLSGVHPESVEFFTPTAQKLIEEQGTNALAAA 263

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LA LSGFS+PPSSRSLI+HEQGW TLQLTRD  +SRGF+SARSV GFLSDVYP AADE+G
Sbjct: 264 LAHLSGFSQPPSSRSLISHEQGWATLQLTRDPTYSRGFLSARSVTGFLSDVYPAAADEVG 323

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KIH+IAD+RVQGAVFDLPEEIAKELLNKQIPPGNTI+KITKLPALQDDGP  D YGRFSS
Sbjct: 324 KIHVIADERVQGAVFDLPEEIAKELLNKQIPPGNTIAKITKLPALQDDGPPGDFYGRFSS 383

Query: 361 RDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNN 420
           RDR                     G          R  G D +DG +  RGGRS  S  N
Sbjct: 384 RDR--------------PARGGPRGQRGGFRSSRGRGSGRDSDDGGTYRRGGRS-NSNEN 428

Query: 421 RGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN 470
             S+ S SS DDWLIGG RSSR  SRD RSFGG+CFNCG+SGHRASECPN
Sbjct: 429 SWSQMSRSSGDDWLIGGRRSSRPPSRD-RSFGGSCFNCGRSGHRASECPN 477

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 =  720 bits (1859), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/470 (80%), Positives = 410/470 (87%), Gaps = 15/470 (3%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP+WVKKL+RKYLDNPL IDLVG+++EKLAEGIKLYAISTTATSKRTILSDL+T
Sbjct: 281 MLFSATMPTWVKKLARKYLDNPLQIDLVGDREEKLAEGIKLYAISTTATSKRTILSDLVT 340

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKG KTI+FT+TKRDADEVS+ALT  IASEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 341 VYAKGEKTIIFTRTKRDADEVSMALTQSIASEALHGDISQHQRERTLNGFRQGKFTVLVA 400

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVA+RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT+SQRRTVRSLE
Sbjct: 401 TDVASRGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTNSQRRTVRSLE 460

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RD GCKFEFVSPP +E++LESS EQVVATLNGVHPESVEFFTPTAQ+LIEE+GT ALAAA
Sbjct: 461 RDAGCKFEFVSPPAIEELLESSTEQVVATLNGVHPESVEFFTPTAQKLIEEQGTSALAAA 520

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LA LSGFSRPPSSRSLI+HEQGW TLQLTRD  +SRGF+SARSV GFLSDVYP AADEIG
Sbjct: 521 LAHLSGFSRPPSSRSLISHEQGWTTLQLTRDPTYSRGFLSARSVTGFLSDVYPAAADEIG 580

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KIH+IAD+RVQGAVFDLPEEIAKELLNKQ+PPGNTI KITKLPALQDDGP SD YGRFSS
Sbjct: 581 KIHLIADERVQGAVFDLPEEIAKELLNKQLPPGNTIEKITKLPALQDDGPPSDFYGRFSS 640

Query: 361 RDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNN 420
           RDR +RGG      G      +G G              SDDE   ++ RGGRS  + N 
Sbjct: 641 RDRPARGGPRGQRGGFRSSRGQGSGRY------------SDDEG--TNRRGGRSNSNENT 686

Query: 421 RGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN 470
           R S  S SS DDWL+GG RSSR SSRDSRSFGG+CFNCG+SGHRASECPN
Sbjct: 687 R-SWMSRSSGDDWLVGGRRSSRPSSRDSRSFGGSCFNCGRSGHRASECPN 735

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  711 bits (1836), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/474 (79%), Positives = 412/474 (86%), Gaps = 9/474 (1%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMPSWVKKL+RKYL+NPL IDLVG+++EKLAEGIKLYAI+ TATSKRTILSDL+T
Sbjct: 295 MLFSATMPSWVKKLARKYLNNPLTIDLVGDEEEKLAEGIKLYAIAATATSKRTILSDLVT 354

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTIVFTQTKRDADEVSL+LT+ I SEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 355 VYAKGGKTIVFTQTKRDADEVSLSLTNSIMSEALHGDISQHQRERTLNGFRQGKFTVLVA 414

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK+G AIL++TSSQRRTVRSLE
Sbjct: 415 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKQGNAILLYTSSQRRTVRSLE 474

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RDVGCKFEFVS P +E+VLESSAEQVVATL GVHPESV+FFTPTAQRLIEE+GT ALAAA
Sbjct: 475 RDVGCKFEFVSAPAMEEVLESSAEQVVATLGGVHPESVQFFTPTAQRLIEEQGTSALAAA 534

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LAQLSGFSRPPSSRSLI HEQGW+TLQLTRDS  SR + SARS+ GFLSDVYP AADE+G
Sbjct: 535 LAQLSGFSRPPSSRSLITHEQGWITLQLTRDSD-SRRYFSARSITGFLSDVYPAAADEVG 593

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KIH+IAD++VQGAVFDLPEEIAKELLN+ IPPGNT+SKITKLP+LQDDGP SD YGRFS 
Sbjct: 594 KIHLIADEKVQGAVFDLPEEIAKELLNRDIPPGNTVSKITKLPSLQDDGPPSDFYGRFSD 653

Query: 361 RDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDE-DGF---SSSRGGRSFR 416
           RDR SR G +      +RGG+    S DRRGF+SSR W  +D  D F   SS RGGR+F+
Sbjct: 654 RDRSSRRGSTSRGGFSSRGGS---ASRDRRGFKSSRGWDVEDSGDDFGDQSSRRGGRNFK 710

Query: 417 SGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN 470
           +GN+       SS DDWLIGG R S   S   R FGG CFNCG+SGHRAS+CPN
Sbjct: 711 TGNSWSRAAGKSSGDDWLIGGGRRSSRPSSSDR-FGGTCFNCGESGHRASDCPN 763

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356534927|ref|XP_003536002.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 3, chloroplastic-like [Glycine max]

 Score =  694 bits (1791), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/472 (77%), Positives = 392/472 (83%), Gaps = 23/472 (4%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP WVKKLSRKYL+NPL IDLVG Q+EKLAEGIKLYA+  TATSKRT+LSDLIT
Sbjct: 276 MLFSATMPGWVKKLSRKYLNNPLTIDLVGEQEEKLAEGIKLYALLATATSKRTVLSDLIT 335

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTIVFTQTK+DADEVS+ALTS IASEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 336 VYAKGGKTIVFTQTKKDADEVSMALTSSIASEALHGDISQHQRERTLNGFRQGKFTVLVA 395

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVAARGLDIPNVDL+IHYELPND ETFVHRSGRTGRAGKEGTAILM+TSSQRRTVRSLE
Sbjct: 396 TDVAARGLDIPNVDLVIHYELPNDAETFVHRSGRTGRAGKEGTAILMYTSSQRRTVRSLE 455

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RDVG KFEFVSPP VE++LESSAEQVVATLN VHPESVEFFT TAQ+L+EE+G  ALAAA
Sbjct: 456 RDVGSKFEFVSPPAVEEILESSAEQVVATLNRVHPESVEFFTATAQKLVEEQGARALAAA 515

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LAQ+SGFS+PPS RSLINHEQGW TLQLTRDS  S  + SARSV GFLSDVY  AADE+G
Sbjct: 516 LAQMSGFSQPPSCRSLINHEQGWTTLQLTRDSDTSGRYFSARSVTGFLSDVYSQAADEVG 575

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KIH+IAD+RVQGAVFDLPEEIAKELLNK +P GNTISKITKLP LQD+ P+SD YG+FS 
Sbjct: 576 KIHLIADERVQGAVFDLPEEIAKELLNKDMPSGNTISKITKLPPLQDNEPASDFYGKFSD 635

Query: 361 RDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSS--RSWGSDDEDGFSSSRGGRSFRSG 418
           RDR                 +   GS D+RGFRSS  R  G D  D F   RGGRSFRSG
Sbjct: 636 RDR-----------------SNPRGSRDQRGFRSSRGREGGQDSNDEF--GRGGRSFRSG 676

Query: 419 NNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRS--FGGACFNCGKSGHRASEC 468
           NNR      SS +DWLIGGS  S   S  +R    GGACFNCGK GHRAS+C
Sbjct: 677 NNRSRTTGKSSGNDWLIGGSSRSSRFSSSNRDGGHGGACFNCGKPGHRASDC 728

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 =  693 bits (1788), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/474 (78%), Positives = 407/474 (85%), Gaps = 21/474 (4%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMPSWVKKL+RKYL+NPL IDLVG+++EKLAEGIKLYAIS T+TSKRTILSDLIT
Sbjct: 291 MLFSATMPSWVKKLARKYLNNPLTIDLVGDEEEKLAEGIKLYAISATSTSKRTILSDLIT 350

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTIVFTQTKRDADEVSLALT+ I SEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 351 VYAKGGKTIVFTQTKRDADEVSLALTNSITSEALHGDISQHQRERTLNGFRQGKFTVLVA 410

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVA+RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK GTAILMFT SQRRTVRSLE
Sbjct: 411 TDVASRGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKLGTAILMFTGSQRRTVRSLE 470

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RDVGCKFEFV+ P VEDVLESSAEQVV TLNGVHPES+ FFTPTAQ+LIEEKGT ALAAA
Sbjct: 471 RDVGCKFEFVNAPSVEDVLESSAEQVVVTLNGVHPESIAFFTPTAQKLIEEKGTTALAAA 530

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LAQ+SGFS+PPSSRSLI HEQGWVTLQLTRDS  S+ + SARSV GFLSDVY  AADE+G
Sbjct: 531 LAQMSGFSQPPSSRSLITHEQGWVTLQLTRDSENSQRYFSARSVTGFLSDVYSKAADEVG 590

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           K+H+IAD+RVQGAVFDLPE+IAKELL+K IP GNTISK+TKLP LQDDGP SD YG+FS 
Sbjct: 591 KVHLIADERVQGAVFDLPEDIAKELLDKDIPAGNTISKVTKLPPLQDDGPPSDFYGKFSD 650

Query: 361 RDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSW----GSDDEDGFSSSRGGRSFR 416
           R+R +R GGSR  RG                  SSR W    GSDD+ G SS RGGRS++
Sbjct: 651 RERNNRRGGSRDGRGFR----------------SSRGWDGGRGSDDDFGDSSRRGGRSYK 694

Query: 417 SGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN 470
           SGN+  S+   SS DDWLIGG +SSRSSS  +RSF G CF CG+SGHRAS+CPN
Sbjct: 695 SGNS-WSKPERSSRDDWLIGGRQSSRSSSSPNRSFAGTCFTCGESGHRASDCPN 747

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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 =  692 bits (1786), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/487 (75%), Positives = 402/487 (82%), Gaps = 38/487 (7%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP+WVKKL+RKYLDNPL IDLVG+Q+EKLAEGIKLYAIST ATSKR+ILSDL+T
Sbjct: 303 MLFSATMPTWVKKLARKYLDNPLQIDLVGDQEEKLAEGIKLYAISTNATSKRSILSDLVT 362

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTI+FTQTKRDADEVS+ LT+ IASEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 363 VYAKGGKTIIFTQTKRDADEVSMVLTNSIASEALHGDISQHQRERTLNGFRQGKFTVLVA 422

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVA+RGLDIPNVDL+IHYELPNDPETFVHRSGRTGRAGKEGTA+LMFTSSQRRTV+SLE
Sbjct: 423 TDVASRGLDIPNVDLVIHYELPNDPETFVHRSGRTGRAGKEGTAVLMFTSSQRRTVKSLE 482

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RDVGC+FEFVSPP  E+VLESSAEQV+ATL+GVHPESV FFTPTAQRLIEE+GT ALAAA
Sbjct: 483 RDVGCRFEFVSPPGTEEVLESSAEQVIATLSGVHPESVGFFTPTAQRLIEEQGTSALAAA 542

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LAQLSGFS+PPSSRSLI+HEQGW TLQLTRD ++SRGF+SARSV GFLSDVY  AADE+G
Sbjct: 543 LAQLSGFSQPPSSRSLISHEQGWTTLQLTRDPSYSRGFLSARSVTGFLSDVYTAAADEVG 602

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KIHIIAD++VQGAVFDLPEEIAKELLNKQ+PPGNTISKITKLP+LQDDGP SD YGRFSS
Sbjct: 603 KIHIIADEKVQGAVFDLPEEIAKELLNKQLPPGNTISKITKLPSLQDDGPPSDFYGRFSS 662

Query: 361 RDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNN 420
           RDR  RGGG       +  G                   SDD+D            +   
Sbjct: 663 RDRPPRGGGRGQRGSRSSQGWG----------GGRGGRNSDDDDD-----------TFRR 701

Query: 421 RGSRFSTSSDDDWLIGGSRSS------RSSSRD-----------SRSFGGACFNCGKSGH 463
            G  FS SS DDWLIGG RSS      RSS RD            RSFGG+CFNCG+SGH
Sbjct: 702 GGRSFSRSSSDDWLIGGGRSSRPSPRGRSSPRDWSSPRDRSSPRDRSFGGSCFNCGRSGH 761

Query: 464 RASECPN 470
           RAS+CPN
Sbjct: 762 RASDCPN 768

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356574052|ref|XP_003555166.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 3, chloroplastic-like [Glycine max]

 Score =  689 bits (1778), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/472 (76%), Positives = 394/472 (83%), Gaps = 25/472 (5%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP WVKKLSRKYL+NPL IDLVG Q+EKLAEGIKLYA+S TA+SKRT+LSDLIT
Sbjct: 278 MLFSATMPGWVKKLSRKYLNNPLTIDLVGEQEEKLAEGIKLYALSATASSKRTVLSDLIT 337

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTIVFTQTK+DADEVS+ALTS IASEALHGDISQHQRERTLNGFRQGKFTVLVA
Sbjct: 338 VYAKGGKTIVFTQTKKDADEVSMALTSSIASEALHGDISQHQRERTLNGFRQGKFTVLVA 397

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVAARGLDIPNVDL+IHYELPND ETFVHRSGRTGRAGKEGTAILM+TSSQRRTVRSLE
Sbjct: 398 TDVAARGLDIPNVDLVIHYELPNDAETFVHRSGRTGRAGKEGTAILMYTSSQRRTVRSLE 457

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RDVGCKFEFVSPP +E++LESSAEQVVATLN VHPESV+FF  TAQ+L+EE+G  ALAAA
Sbjct: 458 RDVGCKFEFVSPPAMEEILESSAEQVVATLNRVHPESVDFFIATAQKLVEEQGARALAAA 517

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           LAQ+SGFS+PPS RSLINHEQGW TLQLTRD   S  + SARSV GFLSDVY  AADE+G
Sbjct: 518 LAQMSGFSQPPSCRSLINHEQGWTTLQLTRDPDTSARYFSARSVTGFLSDVYSPAADEVG 577

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KIH+IAD+RVQGAVFDLPEEIAKELL K +P GNTISKITKLP LQDD P+SD YG+FS 
Sbjct: 578 KIHLIADERVQGAVFDLPEEIAKELLTKDLPSGNTISKITKLPPLQDDEPASDFYGKFSD 637

Query: 361 RDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSW--GSDDEDGFSSSRGGRSFRSG 418
           RDR +R                  GS D+RGFRSSR W  G D +D F   +GGRSFRSG
Sbjct: 638 RDRSNR-----------------RGSRDQRGFRSSRGWEGGQDSDDEF--GQGGRSFRSG 678

Query: 419 NNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRS--FGGACFNCGKSGHRASEC 468
           N    R   SS DDWLIGGS  S   S  +RS   GGACFNCGK GHRAS+C
Sbjct: 679 NK--FRMGKSSGDDWLIGGSSRSSRFSSSNRSGGHGGACFNCGKPGHRASDC 728

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  684 bits (1765), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/487 (73%), Positives = 401/487 (82%), Gaps = 35/487 (7%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSATMP+W+KKLSRKYLDNPL IDLVG+++EKLAEGIKLYAIS+TA SKRT+LSD+IT
Sbjct: 310 MLFSATMPTWIKKLSRKYLDNPLTIDLVGDREEKLAEGIKLYAISSTAASKRTMLSDVIT 369

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           VYAKGGKTIVFTQTKRDADEVSLAL++ I SEALHGDISQHQRERTLNGFRQGKF+VLVA
Sbjct: 370 VYAKGGKTIVFTQTKRDADEVSLALSNSIPSEALHGDISQHQRERTLNGFRQGKFSVLVA 429

Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
           TDVA+RGLDIPNVDL++HYE+PNDPETFVHRSGRTGRAGKEGTA+LM+TS+QRRTVRSLE
Sbjct: 430 TDVASRGLDIPNVDLVVHYEMPNDPETFVHRSGRTGRAGKEGTALLMYTSNQRRTVRSLE 489

Query: 181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
           RDVGC F +V  P VE+VL SSA+QVVATL GVHPES++FFTPTAQ+L+EE+GT ALAAA
Sbjct: 490 RDVGCHFGYVGAPSVEEVLVSSADQVVATLRGVHPESIKFFTPTAQKLLEEQGTGALAAA 549

Query: 241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
           +A LSGFS+PPS++SL++HEQGWVTLQL+RDS FSRG+MSARSVMGFLSDVYPTAADE+G
Sbjct: 550 IAHLSGFSQPPSAKSLLSHEQGWVTLQLSRDSVFSRGYMSARSVMGFLSDVYPTAADEVG 609

Query: 301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSS 360
           KI +IAD+RVQGAVFDLPEEIAKELL K++PPGNT+SKI+KLPALQDD P SDNYGRFS 
Sbjct: 610 KIQLIADERVQGAVFDLPEEIAKELLKKELPPGNTLSKISKLPALQDDAPPSDNYGRFSG 669

Query: 361 R---------DRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSS-- 409
           R         DR   GGGSR SRG                    RS  SD EDG S S  
Sbjct: 670 RGRGSRGGMSDRRGSGGGSRTSRGWG------------------RSQDSDFEDGGSDSFR 711

Query: 410 RGGRSFRSGNNR--GSRFSTSSDDDWLI----GGSRSSRSSSRDSRSFGGACFNCGKSGH 463
           RGGRS R   NR      S+SS DDWLI      SRSS    R    F GACFNCGKSGH
Sbjct: 712 RGGRSPRPSTNRWSSGSSSSSSGDDWLIGGGRSSSRSSPMGGRRDGQFSGACFNCGKSGH 771

Query: 464 RASECPN 470
           RA+ECP 
Sbjct: 772 RATECPT 778

Source: Silene latifolia

Species: Silene latifolia

Genus: Silene

Family: Caryophyllaceae

Order: Caryophyllales

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	470
TAIR|locus:504955106	748	emb1138 "embryo defective 1138	0.755	0.474	0.847	1.3e-167
TAIR|locus:2087852	616	PMH2 "putative mitochondrial R	0.417	0.318	0.627	1.6e-63
TAIR|locus:2087832	610	PMH1 "putative mitochondrial R	0.451	0.347	0.580	3.8e-62
ZFIN|ZDB-GENE-031113-10	759	ddx21 "DEAD (Asp-Glu-Ala-Asp)	0.734	0.454	0.396	1.2e-56
UNIPROTKB|F1MMK3	737	DDX50 "Uncharacterized protein	0.740	0.472	0.381	5.3e-56
UNIPROTKB|E2QTT0	738	DDX50 "Uncharacterized protein	0.740	0.471	0.381	5.3e-56
UNIPROTKB|E2RPT4	687	DDX50 "Uncharacterized protein	0.740	0.506	0.381	5.3e-56
UNIPROTKB|Q9BQ39	737	DDX50 "ATP-dependent RNA helic	0.740	0.472	0.381	1.1e-55
MGI|MGI:2182303	734	Ddx50 "DEAD (Asp-Glu-Ala-Asp)	0.740	0.474	0.376	1.1e-55
UNIPROTKB|F1SUG8	737	DDX50 "Uncharacterized protein	0.740	0.472	0.373	2.6e-54

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

 Score = 1560 (554.2 bits), Expect = 1.3e-167, Sum P(2) = 1.3e-167
 Identities = 301/355 (84%), Positives = 334/355 (94%)

Query:     1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
             MLFSATMP+WVKKL+RKYLDNPLNIDLVG+QDEKLAEGIKLYAI+TT+TSKRTILSDLIT
Sbjct:   287 MLFSATMPTWVKKLARKYLDNPLNIDLVGDQDEKLAEGIKLYAIATTSTSKRTILSDLIT 346

Query:    61 VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
             VYAKGGKTIVFTQTKRDADEVSLAL++ IA+EALHGDISQHQRERTLN FRQGKFTVLVA
Sbjct:   347 VYAKGGKTIVFTQTKRDADEVSLALSNSIATEALHGDISQHQRERTLNAFRQGKFTVLVA 406

Query:   121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
             TDVA+RGLDIPNVDL+IHYELPNDPETFVHRSGRTGRAGKEG+AILM TSSQ+RTVRSLE
Sbjct:   407 TDVASRGLDIPNVDLVIHYELPNDPETFVHRSGRTGRAGKEGSAILMHTSSQKRTVRSLE 466

Query:   181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAA 240
             RDVGC FEF+SPP V D+LESSA+QVVATLNGVHP+S++FF+ TAQ+L EEKGTDALAAA
Sbjct:   467 RDVGCHFEFISPPTVGDLLESSADQVVATLNGVHPDSIKFFSATAQKLYEEKGTDALAAA 526

Query:   241 LAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIG 300
             LA LSGFS+PPSSRSL++HE+GWVTLQL RD   +RGF+SARSV GFLSD+Y TAADE+G
Sbjct:   527 LAHLSGFSQPPSSRSLLSHEKGWVTLQLIRDPTNARGFLSARSVTGFLSDLYRTAADEVG 586

Query:   301 KIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNY 355
             KI +IADDR+QGAVFDLPEEIAKELL K +P GN++S ITKLP LQDDGPSSDNY
Sbjct:   587 KIFLIADDRIQGAVFDLPEEIAKELLEKDVPEGNSLSMITKLPPLQDDGPSSDNY 641

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 = 648 (233.2 bits), Expect = 1.6e-63, P = 1.6e-63
 Identities = 123/196 (62%), Positives = 155/196 (79%)

Query:     1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
             M+FSATMPSW++ L++KYL+NPL +DLVG+ D+KLA+GI  Y+I   +  + +I+  L+T
Sbjct:   285 MMFSATMPSWIRSLTKKYLNNPLTVDLVGDSDQKLADGITTYSIIADSYGRASIIGPLVT 344

Query:    61 VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
              +AKGGK IVFTQTKRDAD +S AL      EALHGDISQ QRERTL GFR G F +LVA
Sbjct:   345 EHAKGGKCIVFTQTKRDADRLSYALARSFKCEALHGDISQSQRERTLAGFRDGHFNILVA 404

Query:   121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
             TDVAARGLD+PNVDLIIHYELPN+ ETFVHR+GRTGRAGK+G+AIL+++  Q R V+ +E
Sbjct:   405 TDVAARGLDVPNVDLIIHYELPNNTETFVHRTGRTGRAGKKGSAILIYSQDQSRAVKIIE 464

Query:   181 RDVGCKFEFVSPPVVE 196
             R+VG +F  +    VE
Sbjct:   465 REVGSRFTELPSIAVE 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 = 635 (228.6 bits), Expect = 3.8e-62, P = 3.8e-62
 Identities = 123/212 (58%), Positives = 158/212 (74%)

Query:     1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
             M+FSATMPSW++ L++KYL+NPL IDLVG+ D+KLA+GI +Y+I+  +  + +I+  L+ 
Sbjct:   297 MMFSATMPSWIRSLTKKYLNNPLTIDLVGDSDQKLADGITMYSIAADSYGRASIIGPLVK 356

Query:    61 VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
              + KGGK IVFTQTKRDAD ++  L      EALHGDISQ QRERTL GFR G F++LVA
Sbjct:   357 EHGKGGKCIVFTQTKRDADRLAFGLAKSYKCEALHGDISQAQRERTLAGFRDGNFSILVA 416

Query:   121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 180
             TDVAARGLD+PNVDL+IHYELPN+ ETFVHR+GRTGRAGK+G+AIL+    Q R V+ +E
Sbjct:   417 TDVAARGLDVPNVDLVIHYELPNNTETFVHRTGRTGRAGKKGSAILIHGQDQTRAVKMIE 476

Query:   181 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNG 212
             ++VG +F  +    VE    S  E V A   G
Sbjct:   477 KEVGSRFNELPSIAVERGSASMFEGVGARSGG 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 = 583 (210.3 bits), Expect = 1.2e-56, P = 1.2e-56
 Identities = 142/358 (39%), Positives = 214/358 (59%)

Query:     1 MLFSATMPSWVKKLSRKYLDNP-LNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
             +LFSAT PSWV  +++KY+ +  +++DL+G + +K A  ++  AI+   + + +++ D+I
Sbjct:   352 LLFSATCPSWVYDVAKKYMRSQFIHVDLIGKKTQKAATTVEHLAIACHWSQRASVIGDVI 411

Query:    60 TVYAKG-GKTIVFTQTKRDADEVSLALTSIIAS-EALHGDISQHQRERTLNGFRQGKFTV 117
              VY+   G+TIVF +TK++A E+SL  TSI  S ++LHGDI Q QRE TL GFR G F V
Sbjct:   412 QVYSGSHGRTIVFCETKKEATELSLN-TSIKQSAQSLHGDIPQKQREVTLKGFRNGSFEV 470

Query:   118 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVR 177
             LVAT+VAARGLDIP VDL+I    PND E+++HRSGRTGRAG+ G  I  +   +   ++
Sbjct:   471 LVATNVAARGLDIPEVDLVIQSSPPNDVESYIHRSGRTGRAGRTGICICFYQRKEESQLK 530

Query:   178 SLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGT-DA 236
              +E+  G  F+ V  P   D+++SS++  V  L+ V   +V +F   AQ LI+++G  +A
Sbjct:   531 FVEQKAGITFKRVGVPTAYDIIQSSSKDAVRFLDSVPAVAVGYFREAAQELIQQRGAVEA 590

Query:   237 LAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAA 296
             LAAALA +SG +     RSLIN E G+ ++ L+          + R +   L +      
Sbjct:   591 LAAALAHISG-ATSLEQRSLINSEPGFSSMILSCSQEMHSISFAWRGLKEQLGEEID--- 646

Query:   297 DEIGKIHIIADDRVQGAVFDLPEEIAKELLNK-QIPPGNTISKITKLPALQDD-GPSS 352
               I   H++     +G  FD+P    KE+  K Q     T+S  T+LP L+    P+S
Sbjct:   647 QHIS--HMVFIKGKKGVCFDVPVSKLKEVQEKWQDSRRWTLSTATQLPELEQSLRPNS 702

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

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 137/359 (38%), Positives = 210/359 (58%)

Query:     1 MLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
             +LFSAT P WV K+++KY+ +    +DLVG   +K A  ++  AI    + +  ++ D++
Sbjct:   323 LLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVL 382

Query:    60 TVYAKG-GKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVL 118
              VY+   G+ I+F +TK++  E+++       ++ LHGDI+Q QRE TL GFR+G F VL
Sbjct:   383 QVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVL 442

Query:   119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
             VAT+VAARGLDIP VDL+I    P D E+++HRSGRTGRAG+ G  I  +   +R  +R 
Sbjct:   443 VATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICFYQPRERGQLRY 502

Query:   179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGT-DAL 237
             +E+  G  F+ V  P   D+++S +   + +L  V   +V+FF P+AQRLIEEKG  DAL
Sbjct:   503 VEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDAL 562

Query:   238 AAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD 297
             AAALA +SG S     RSLI  ++G+VT+ L           + + +   LS     A  
Sbjct:   563 AAALAHISGASSF-EPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSS---NAVS 618

Query:   298 EIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQD--DGPSSDN 354
             +I ++ ++  +   G  FD+P   ++ L  +       +S   KLP +++  DG +S N
Sbjct:   619 QITRMCLLKGN--MGVCFDVPTTESERLQAEWHDSDWILSVPAKLPEIEEYYDGNTSSN 675

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 = 137/359 (38%), Positives = 210/359 (58%)

Query:     1 MLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
             +LFSAT P WV K+++KY+ +    +DLVG   +K A  ++  AI    + +  ++ D++
Sbjct:   324 LLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVL 383

Query:    60 TVYAKG-GKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVL 118
              VY+   G+ I+F +TK++  E+++       ++ LHGDI+Q QRE TL GFR+G F VL
Sbjct:   384 QVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVL 443

Query:   119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
             VAT+VAARGLDIP VDL+I    P D E+++HRSGRTGRAG+ G  I  +   +R  +R 
Sbjct:   444 VATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICFYQPRERGQLRY 503

Query:   179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGT-DAL 237
             +E+  G  F+ V  P   D+++S +   + +L  V   +V+FF P+AQRLIEEKG  DAL
Sbjct:   504 VEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDAL 563

Query:   238 AAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD 297
             AAALA +SG S     RSLI  ++G+VT+ L           + + +   LS     A  
Sbjct:   564 AAALAHISGASSF-EPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSS---NAVS 619

Query:   298 EIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQD--DGPSSDN 354
             +I ++ ++  +   G  FD+P   ++ L  +       +S   KLP +++  DG +S N
Sbjct:   620 QITRMCLLKGN--MGVCFDVPTTESERLQAEWHDSDWILSLPAKLPEIEEYYDGNTSSN 676

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 = 137/359 (38%), Positives = 210/359 (58%)

Query:     1 MLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
             +LFSAT P WV K+++KY+ +    +DLVG   +K A  ++  AI    + +  ++ D++
Sbjct:   325 LLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVL 384

Query:    60 TVYAKG-GKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVL 118
              VY+   G+ I+F +TK++  E+++       ++ LHGDI+Q QRE TL GFR+G F VL
Sbjct:   385 QVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVL 444

Query:   119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
             VAT+VAARGLDIP VDL+I    P D E+++HRSGRTGRAG+ G  I  +   +R  +R 
Sbjct:   445 VATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICFYQPRERGQLRY 504

Query:   179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGT-DAL 237
             +E+  G  F+ V  P   D+++S +   + +L  V   +V+FF P+AQRLIEEKG  DAL
Sbjct:   505 VEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDAL 564

Query:   238 AAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD 297
             AAALA +SG S     RSLI  ++G+VT+ L           + + +   LS     A  
Sbjct:   565 AAALAHISGASSF-EPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSS---NAVS 620

Query:   298 EIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQD--DGPSSDN 354
             +I ++ ++  +   G  FD+P   ++ L  +       +S   KLP +++  DG +S N
Sbjct:   621 QITRMCLLKGN--MGVCFDVPTTESERLQAEWHDSDWILSLPAKLPEIEEYYDGNTSSN 677

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 = 574 (207.1 bits), Expect = 1.1e-55, P = 1.1e-55
 Identities = 137/359 (38%), Positives = 210/359 (58%)

Query:     1 MLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
             +LFSAT P WV K+++KY+ +    +DLVG   +K A  ++  AI    + +  ++ D++
Sbjct:   323 LLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVL 382

Query:    60 TVYAKG-GKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVL 118
              VY+   G+ I+F +TK++  E+++       ++ LHGDI+Q QRE TL GFR+G F VL
Sbjct:   383 QVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVL 442

Query:   119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
             VAT+VAARGLDIP VDL+I    P D E+++HRSGRTGRAG+ G  I  +   +R  +R 
Sbjct:   443 VATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICFYQPRERGQLRY 502

Query:   179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGT-DAL 237
             +E+  G  F+ V  P   D+++S +   + +L  V   +V+FF P+AQRLIEEKG  DAL
Sbjct:   503 VEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDAL 562

Query:   238 AAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD 297
             AAALA +SG S     RSLI  ++G+VT+ L           + + +   LS     A  
Sbjct:   563 AAALAHISGASSF-EPRSLITSDKGFVTMTLESLEEIQDVSCAWKELNRKLSS---NAVS 618

Query:   298 EIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQD--DGPSSDN 354
             +I ++ ++  +   G  FD+P   ++ L  +       +S   KLP +++  DG +S N
Sbjct:   619 QITRMCLLKGN--MGVCFDVPTTESERLQAEWHDSDWILSVPAKLPEIEEYYDGNTSSN 675

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

MGI|MGI:2182303 Ddx50 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 50" [Mus musculus (taxid:10090)]

 Score = 574 (207.1 bits), Expect = 1.1e-55, P = 1.1e-55
 Identities = 135/359 (37%), Positives = 209/359 (58%)

Query:     1 MLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
             +LFSAT P WV K+++KY+ +    +DLVG   +K A  ++  AI    + +  ++ D++
Sbjct:   320 LLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVL 379

Query:    60 TVYAKG-GKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVL 118
              VY+   G+ I+F +TK++  E+++       ++ LHGDI+Q QRE TL GFR+G F VL
Sbjct:   380 QVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVL 439

Query:   119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
             VAT+VAARGLDIP VDL+I    P D E+++HRSGRTGRAG+ G  +  +   +R  +R 
Sbjct:   440 VATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRY 499

Query:   179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGT-DAL 237
             +E+  G  F+ V  P   D+++S +   + +L  V   +V+FF P+AQRLIEEKG  DAL
Sbjct:   500 VEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDAL 559

Query:   238 AAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD 297
             AAALA +SG S     RSLI  ++G+VT+ L           + + +   LS     A  
Sbjct:   560 AAALAHISGASSF-EPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSS---NAVS 615

Query:   298 EIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQD--DGPSSDN 354
              + ++ ++  +   G  FD+P   ++ L  +       +S   KLP +++  DG +S N
Sbjct:   616 HVTRMCLLKGN--MGVCFDVPTSESERLQAEWHDSDWILSVPAKLPEIEEYYDGNTSSN 672

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

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

 Score = 561 (202.5 bits), Expect = 2.6e-54, P = 2.6e-54
 Identities = 134/359 (37%), Positives = 208/359 (57%)

Query:     1 MLFSATMPSWVKKLSRKYLDNPLN-IDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
             +LFSAT P WV K+++KY+ +    +DLVG   +K A  ++  AI    + +  ++ D++
Sbjct:   323 LLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVL 382

Query:    60 TVYAKG-GKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVL 118
              VY+   G+ I+F +TK++  E+++       ++ LHGDI+Q QRE TL GFR+G F VL
Sbjct:   383 QVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVL 442

Query:   119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
             VAT+VAARGLDIP VDL+I    P D E+++HRSGRTGRAG+ G  I  +   +R  +R 
Sbjct:   443 VATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICFYQPRERGQLRY 502

Query:   179 LERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGT-DAL 237
             +E+  G  F+ V  P   D+++S +   + +L  V   +V+FF P+AQRLIEEKG  DAL
Sbjct:   503 VEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDAL 562

Query:   238 AAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD 297
             AAALA +SG S     RSLI  ++G+VT+ L           + + +   LS        
Sbjct:   563 AAALAHISGASSF-EPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNKKLSS---NVLS 618

Query:   298 EIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQD--DGPSSDN 354
             +I ++ ++  +   G  FD+    ++ L  +       +S   KLP +++  DG ++ N
Sbjct:   619 QITRMCLLKGN--MGVCFDVSTAESERLQAEWHDSDWILSVPAKLPEIEEHYDGNTASN 675

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	0.8176	0.7702	0.4775	yes	no
Q8L7S8	RH3_ARATH	3, ., 6, ., 4, ., 1, 3	0.8489	0.7744	0.4866	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	0.914
3rd Layer	3.6.4	0.921

---

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	470
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	4e-54
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	7e-40
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	4e-39
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-32
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	4e-31
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	4e-30
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	5e-30
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	9e-30
pfam08152	97	pfam08152, GUCT, GUCT (NUC152) domain	9e-29
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-28
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	2e-27
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	2e-25
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	4e-25
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-21
cd12938	74	cd12938, GUCT_Hera, RNA-binding GUCT-like domain f	4e-19
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-16
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	7e-16
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	4e-15
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	3e-14
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	9e-10
cd12937	86	cd12937, GUCT_RH7_like, RNA-binding GUCT domain fo	5e-09
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	7e-09
TIGR01587	358	TIGR01587, cas3_core, CRISPR-associated helicase C	9e-09
TIGR00631	655	TIGR00631, uvrb, excinuclease ABC, B subunit	5e-08
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	6e-08
TIGR00580	926	TIGR00580, mfd, transcription-repair coupling fact	1e-07
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	6e-07
COG1197	1139	COG1197, Mfd, Transcription-repair coupling factor	6e-07
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	1e-06
cd09639	353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	1e-06
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	2e-06
smart00343	17	smart00343, ZnF_C2HC, zinc finger	4e-06
COG1205	851	COG1205, COG1205, Distinct helicase family with a	5e-06
COG1200	677	COG1200, RecG, RecG-like helicase [DNA replication	6e-06
PRK10689	1147	PRK10689, PRK10689, transcription-repair coupling	1e-05
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	1e-05
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	2e-04
PRK05580	679	PRK05580, PRK05580, primosome assembly protein Pri	5e-04
COG4098	441	COG4098, comFA, Superfamily II DNA/RNA helicase re	6e-04
cd00268	203	cd00268, DEADc, DEAD-box helicases	7e-04
PRK05298	652	PRK05298, PRK05298, excinuclease ABC subunit B; Pr	7e-04
PRK10917	681	PRK10917, PRK10917, ATP-dependent DNA helicase Rec	9e-04
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	0.001
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	0.001
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	0.002
pfam06682	317	pfam06682, DUF1183, Protein of unknown function (D	0.002
PRK00254	720	PRK00254, PRK00254, ski2-like helicase; Provisiona	0.003
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 =  188 bits (480), Expect = 4e-54
 Identities = 87/266 (32%), Positives = 139/266 (52%), Gaps = 12/266 (4%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAIST-TATSKRTILSDLI 59
           +LFSATMP  +++L+R+YL++P+ I++   + E+  + IK + +   +   K  +L  L+
Sbjct: 209 LLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLL 268

Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
               +G + IVF +TKR  +E++ +L        ALHGD+ Q +R+R L  F+ G+  VL
Sbjct: 269 KDEDEG-RVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVL 327

Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVR 177
           VATDVAARGLDIP+V  +I+Y+LP DPE +VHR GRTGRAG++G AI   T   + + ++
Sbjct: 328 VATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLK 387

Query: 178 SLERDVGCKFE-FVSPPVVEDVLESSAEQVVATLNGVHPESVE-------FFTPTAQRLI 229
            +E+ +  K    V  P+ E       +     L      S E                +
Sbjct: 388 RIEKRLERKLPSAVLLPLDEPEDAKLLKTTRPGLEEESDISDEIKKLKSSKKALLRGLGV 447

Query: 230 EEKGTDALAAALAQLSGFSRPPSSRS 255
               +  LA    ++ G     +   
Sbjct: 448 RFTLSKLLANLGKEIPGAGDAVTIDP 473

Length = 513

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

 Score =  149 bits (378), Expect = 7e-40
 Identities = 67/194 (34%), Positives = 108/194 (55%), Gaps = 5/194 (2%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +LFSAT P  +  +S+++  +P+ +  V +  +  A  I+      +   +   L  L+ 
Sbjct: 182 LLFSATYPEGIAAISQRFQRDPVEVK-VESTHDLPA--IEQRFYEVSPDERLPALQRLLL 238

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLV 119
            + +    +VF  TK++  EV+ AL +   ++ ALHGD+ Q  R++ L  F     +VLV
Sbjct: 239 HH-QPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLV 297

Query: 120 ATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 179
           ATDVAARGLDI  ++ +I+YEL  DPE  VHR GRTGRAG +G A+ +    + +   ++
Sbjct: 298 ATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAI 357

Query: 180 ERDVGCKFEFVSPP 193
           E  +G K  +   P
Sbjct: 358 EDYLGRKLNWEPLP 371

Length = 460

>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 =  137 bits (348), Expect = 4e-39
 Identities = 57/119 (47%), Positives = 81/119 (68%), Gaps = 2/119 (1%)

Query: 51  KRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLN 108
           K   L +L+  +  KGGK ++F  +K+  DE++  L    I   ALHGD SQ +RE  L 
Sbjct: 13  KLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLK 72

Query: 109 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM 167
            FR+G+  VLVATDV ARG+D+PNV ++I+Y+LP  P +++ R GR GRAG++GTAIL+
Sbjct: 73  DFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131

Length = 131

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

 Score =  127 bits (322), Expect = 5e-32
 Identities = 64/184 (34%), Positives = 102/184 (55%), Gaps = 4/184 (2%)

Query: 1   MLFSATMPSWVKKLSRKYL-DNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
           +++SAT P  V+ L+R    + P++++ VG+ D      IK          KR  L  L+
Sbjct: 312 LMWSATWPKEVQSLARDLCKEEPVHVN-VGSLDLTACHNIKQEVFVVEEHEKRGKLKMLL 370

Query: 60  T-VYAKGGKTIVFTQTKRDADEVSLAL-TSIIASEALHGDISQHQRERTLNGFRQGKFTV 117
             +   G K ++F +TK+ AD ++  L      +  +HGD  Q +R   LN F+ GK  +
Sbjct: 371 QRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPI 430

Query: 118 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVR 177
           ++ATDVA+RGLD+ +V  +I+++ PN  E +VHR GRTGRAG +G +    T  + R  R
Sbjct: 431 MIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLAR 490

Query: 178 SLER 181
            L +
Sbjct: 491 DLVK 494

Length = 545

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

 Score =  124 bits (313), Expect = 4e-31
 Identities = 73/184 (39%), Positives = 106/184 (57%), Gaps = 8/184 (4%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +LFSAT    +K L+ K L NPL I++   +    +E +  +        KR +LS +I 
Sbjct: 184 LLFSATFSDDIKALAEKLLHNPLEIEVA--RRNTASEQVTQHVHFVDKKRKRELLSQMI- 240

Query: 61  VYAKGG--KTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTV 117
              KG   + +VFT+TK  A+ ++  L    I S A+HG+ SQ  R R L  F+ G   V
Sbjct: 241 --GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRV 298

Query: 118 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVR 177
           LVATD+AARGLDI  +  +++YELPN PE +VHR GRTGRA   G A+ +    + + +R
Sbjct: 299 LVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLR 358

Query: 178 SLER 181
            +E+
Sbjct: 359 DIEK 362

Length = 456

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

 Score =  123 bits (310), Expect = 4e-30
 Identities = 87/280 (31%), Positives = 138/280 (49%), Gaps = 58/280 (20%)

Query: 2   LFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV 61
           LFSATMP  +++++R+++  P  +                  I ++ T++  I     TV
Sbjct: 185 LFSATMPEAIRRITRRFMKEPQEV-----------------RIQSSVTTRPDISQSYWTV 227

Query: 62  YAKGGK--------------TIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERT 106
           +                    I+F +TK    EV+ AL  +   S AL+GD++Q  RE+T
Sbjct: 228 WGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQT 287

Query: 107 LNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL 166
           L   + G+  +L+ATDVAARGLD+  + L+++Y++P D E++VHR GRTGRAG+ G A+L
Sbjct: 288 LERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALL 347

Query: 167 MFTSSQRRTVRSLERDVGCKFEFVSPP---------------VVEDVLESS-AEQVVATL 210
              + +RR +R++ER +      V  P                V+  LESS  +Q  A L
Sbjct: 348 FVENRERRLLRNIERTMKLTIPEVELPNAELLGKRRLEKFAAKVQQQLESSDLDQYRALL 407

Query: 211 NGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRP 250
             + P +            EE   + LAAAL +++   RP
Sbjct: 408 AKIQPTAEG----------EELDLETLAAALLKMAQGERP 437

Length = 629

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

 Score =  120 bits (303), Expect = 5e-30
 Identities = 64/185 (34%), Positives = 104/185 (56%), Gaps = 11/185 (5%)

Query: 2   LFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDL-- 58
           LFSATMP+ + +L+ K++ +P  I LV  +DE   EGI+ + ++      K   L DL  
Sbjct: 206 LFSATMPNEILELTTKFMRDPKRI-LV-KKDELTLEGIRQFYVAVEKEEWKFDTLCDLYE 263

Query: 59  -ITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT 116
            +T+     + I++  T+R  D ++  +         +HGD+ Q  R+  +  FR G   
Sbjct: 264 TLTIT----QAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTR 319

Query: 117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTV 176
           VL+ TD+ ARG+D+  V L+I+Y+LP  PE ++HR GR+GR G++G AI   T      +
Sbjct: 320 VLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQL 379

Query: 177 RSLER 181
           + +ER
Sbjct: 380 KEIER 384

Length = 401

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

 Score =  120 bits (303), Expect = 9e-30
 Identities = 55/167 (32%), Positives = 97/167 (58%), Gaps = 4/167 (2%)

Query: 1   MLFSATMP-SWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI 59
           +LFSAT+    V+  + + L++P+ ++   ++ E+  +  + Y  +     K  +L  L+
Sbjct: 182 LLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRER-KKIHQWYYRADDLEHKTALLCHLL 240

Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
               +  ++IVF +T+    E++  L    I    L G++ Q +R   +     G+  VL
Sbjct: 241 K-QPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVL 299

Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
           VATDVAARG+DI +V  +I++++P   +T++HR GRTGRAG++GTAI
Sbjct: 300 VATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAI 346

Length = 434

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

 Score =  108 bits (272), Expect = 9e-29
 Identities = 39/103 (37%), Positives = 56/103 (54%), Gaps = 7/103 (6%)

Query: 246 GFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHII 305
           G++     RSL+  E+G+VTLQLT          + +S+  FL D      D I  + ++
Sbjct: 1   GYTSI-KQRSLLTSEEGYVTLQLTSGRPIPTPSFAWKSLRRFLPD---EKVDSIKGMTLL 56

Query: 306 ADDRVQGAVFDLPEEIAKELLNKQIPP-GNTISKITKLPALQD 347
           AD+  QGAVFD+PEE A+E L    P  G  +   T+LP LQ+
Sbjct: 57  ADN--QGAVFDVPEEDAEEFLAGWQPAAGVQLEVATELPPLQE 97

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

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

 Score =  115 bits (288), Expect = 9e-28
 Identities = 63/194 (32%), Positives = 103/194 (53%), Gaps = 4/194 (2%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +LFSAT    V  L++++  +P  +++    +   ++ ++ +  +   + K  +L +L+T
Sbjct: 274 LLFSATFTDDVMNLAKQWTTDPAIVEI--EPENVASDTVEQHVYAVAGSDKYKLLYNLVT 331

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLV 119
                 + +VF   K +   +   L    I +  L GD+ QH+R +TL GFR+GK  VLV
Sbjct: 332 -QNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLV 390

Query: 120 ATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 179
           ATDVA RG+ I  +  +I++ LP DP+ +VHR GRTGRAG  G +I          +  +
Sbjct: 391 ATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEI 450

Query: 180 ERDVGCKFEFVSPP 193
           E  +G K     PP
Sbjct: 451 EELLGRKISCEMPP 464

Length = 475

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

 Score =  104 bits (261), Expect = 2e-27
 Identities = 39/71 (54%), Positives = 52/71 (73%)

Query: 89  IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF 148
           I    LHG +SQ +RE  L  FR GK  VLVATDVA RG+D+P+V+L+I+Y+LP +P ++
Sbjct: 8   IKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASY 67

Query: 149 VHRSGRTGRAG 159
           + 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 = 99.2 bits (248), Expect = 2e-25
 Identities = 42/82 (51%), Positives = 55/82 (67%), Gaps = 1/82 (1%)

Query: 79  DEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 137
           +E++  L  + I    LHG +SQ +RE  L+ F  GK  VLVATDVA RGLD+P VDL+I
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 138 HYELPNDPETFVHRSGRTGRAG 159
            Y+LP  P +++ R GR GRAG
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score =  106 bits (267), Expect = 4e-25
 Identities = 64/170 (37%), Positives = 95/170 (55%), Gaps = 12/170 (7%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           MLFSAT+   V++L+ ++++NP  +++   Q  K    IK      +   K  +L  LI 
Sbjct: 194 MLFSATLSYRVRELAFEHMNNPEYVEVEPEQ--KTGHRIKEELFYPSNEEKMRLLQTLIE 251

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-----LHGDISQHQRERTLNGFRQGKF 115
                 + I+F  TK   +E+       +A++      L GD++Q +R R L  F +G  
Sbjct: 252 -EEWPDRAIIFANTKHRCEEI----WGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDL 306

Query: 116 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
            +LVATDVAARGL IP V  + +Y+LP+D E +VHR GRTGRAG  G +I
Sbjct: 307 DILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSI 356

Length = 423

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

 Score = 97.3 bits (242), Expect = 1e-21
 Identities = 63/166 (37%), Positives = 95/166 (57%), Gaps = 4/166 (2%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +LFSAT+   V +L+ ++++ P    LV   +   A  ++          K+T+L  L++
Sbjct: 196 LLFSATLSHRVLELAYEHMNEPEK--LVVETETITAARVRQRIYFPADEEKQTLLLGLLS 253

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLV 119
             ++G +T+VF  TK   + V+  L         L GD+ Q +RE  LN F++G+  +LV
Sbjct: 254 -RSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILV 312

Query: 120 ATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
           ATDVAARGL I  V  + +Y+LP D E +VHR GRT R G+EG AI
Sbjct: 313 ATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAI 358

Length = 572

>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 = 81.2 bits (201), Expect = 4e-19
 Identities = 42/81 (51%), Positives = 47/81 (58%), Gaps = 7/81 (8%)

Query: 253 SRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQG 312
            RSL+  E+GW TLQLT          S R  +G LS     AAD +GKI I+AD    G
Sbjct: 1   PRSLLTGEEGWTTLQLTGSR--LLPPGSVRRAVGLLSRA---AADGVGKIRILAD--AGG 53

Query: 313 AVFDLPEEIAKELLNKQIPPG 333
           AVFDLPEEIAKELL K    G
Sbjct: 54  AVFDLPEEIAKELLAKSDLDG 74

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

 Score = 81.8 bits (202), Expect = 1e-16
 Identities = 52/177 (29%), Positives = 92/177 (51%), Gaps = 5/177 (2%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +LFSAT+   V+K +     + + I  +GN + +  + +K  AI      K+  L D++ 
Sbjct: 304 LLFSATVSPEVEKFASSLAKDIILIS-IGNPN-RPNKAVKQLAIWVETKQKKQKLFDILK 361

Query: 61  VYAK-GGKTIVFTQTKRDADEVSLALTSIIASEAL--HGDISQHQRERTLNGFRQGKFTV 117
                    +VF  ++  AD ++ A+T +   +AL  HG+ S  +R   +  F  G+  V
Sbjct: 362 SKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPV 421

Query: 118 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRR 174
           +VAT V  RG+D+  V  +I +++PN  + ++H+ GR  R G++GTAI+      R 
Sbjct: 422 IVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRN 478

Length = 518

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

 Score = 79.7 bits (197), Expect = 7e-16
 Identities = 42/120 (35%), Positives = 64/120 (53%), Gaps = 11/120 (9%)

Query: 64  KGGKTIVFTQTKRDADEVSLALTSI--------IASEALHGD--ISQHQRERTLNGFRQG 113
              + IVFT+ +  A+E+   L  I        I   +  GD  +SQ +++  ++ FR+G
Sbjct: 365 GDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKG 424

Query: 114 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR 173
           ++ 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 = 77.6 bits (192), Expect = 4e-15
 Identities = 49/132 (37%), Positives = 69/132 (52%), Gaps = 24/132 (18%)

Query: 64  KGGKTIVFTQTKRD-ADEVSLALTSI-IASEALHGD--------ISQHQRERTLNGFRQG 113
              + IVFTQ  RD A+++   L    I +    G         +SQ ++   L+ FR G
Sbjct: 364 PDSRIIVFTQY-RDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAG 422

Query: 114 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPET-FVHRSGRTGRAGKEGTA-ILM---- 167
           +F VLV+T VA  GLDIP+VDL+I YE P   E   + R GRTGR  +EG   +L+    
Sbjct: 423 EFNVLVSTSVAEEGLDIPSVDLVIFYE-PVPSEIRSIQRKGRTGR-QEEGRVVVLIAKGT 480

Query: 168 -----FTSSQRR 174
                + SS+R+
Sbjct: 481 RDEAYYWSSRRK 492

Length = 773

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

 Score = 74.4 bits (183), Expect = 3e-14
 Identities = 42/165 (25%), Positives = 67/165 (40%), Gaps = 2/165 (1%)

Query: 15  SRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQT 74
            R+Y         +      L    +   I+  +  K   +  L+  +A+G KT++F   
Sbjct: 233 EREYAKESARFRELLRARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASD 292

Query: 75  KRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD 134
              A E++    +    EA+ G+  + +RE  L  FR G   VLV   V   G+DIP+ D
Sbjct: 293 VEHAYEIAKLFLAPGIVEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDAD 352

Query: 135 LIIHYELPNDPETFVHRSGRTGRA--GKEGTAILMFTSSQRRTVR 177
           ++I          F+ R GR  R   GKE T  L ++        
Sbjct: 353 VLIILRPTGSRRLFIQRLGRGLRPAEGKEDTLALDYSLVPDDLGE 397

Length = 442

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

 Score = 70.0 bits (172), Expect = 1e-12
 Identities = 37/118 (31%), Positives = 62/118 (52%), Gaps = 1/118 (0%)

Query: 63  AKGGKTIVFTQTKRDADEVSLAL-TSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 121
                 I++  T++  +E++  L  + I++ A H  +S  +RER    F   +  V+VAT
Sbjct: 228 QLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVAT 287

Query: 122 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 179
           +    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 = 64.3 bits (157), Expect = 5e-11
 Identities = 32/103 (31%), Positives = 56/103 (54%), Gaps = 1/103 (0%)

Query: 69  IVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG 127
           I++  +++  +E++  L S  I++ A H  +S   R      F      V+VAT+    G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287

Query: 128 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS 170
           +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 = 9e-10
 Identities = 33/117 (28%), Positives = 62/117 (52%), Gaps = 1/117 (0%)

Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           KG   I++  +++ +++V+ +L ++ IA+ A H  +    R+   + F++ +  V+VAT 
Sbjct: 225 KGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATV 284

Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 179
               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|240594 cd12937, GUCT_RH7_like, RNA-binding GUCT domain found in plant DEAD-box ATP-dependent RNA helicase 7 (RH7) and similar proteins

 Score = 52.6 bits (127), Expect = 5e-09
 Identities = 28/92 (30%), Positives = 43/92 (46%), Gaps = 8/92 (8%)

Query: 254 RSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYP-TAADEIGKIHIIADDRVQG 312
           RSL+   +G+ TL L      +    S   V   L    P    + I  + + AD +  G
Sbjct: 1   RSLLTSHEGYTTLLLK----SNTPIRSPGYVWNALRRYLPEDIVESIKGMTLTADGK--G 54

Query: 313 AVFDLPEEIAKELLNKQIP-PGNTISKITKLP 343
           AVFD+P E+ +E L+  +   G T+   T+LP
Sbjct: 55  AVFDVPSELIEEFLSAWVDKRGVTLEVATELP 86

This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH7 and similar proteins. RH7, also termed plant RNA helicase 75 (PRH75), is a new nucleus-localized member of the DEAD-box protein family from higher plants. It displays a weak ATPase activity which is barely stimulated by RNA ligands. RH7 contains an N-terminal KDES domain rich in lysine, glutamic acid, aspartic acid, and serine residues, seven highly conserved helicase motifs in the central region, a GUCT domain, and a C-terminal GYR domain harboring a large number of glycine residues interrupted by either arginines or tyrosines. RH7 is RNA specific and harbors two possible RNA-binding motifs, the helicase motif VI (HRIGRTGR) and the C-terminal glycine-rich GYR domain. Length = 86

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

 Score = 58.0 bits (141), Expect = 7e-09
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 2/93 (2%)

Query: 67  KTIVFTQTKRDADEVSLALTSI--IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA 124
            T++FT T+  A+ ++  L  +     E  HG +S+  R       ++G+   +VAT   
Sbjct: 255 TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSL 314

Query: 125 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 157
             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 = 56.7 bits (137), Expect = 9e-09
 Identities = 42/167 (25%), Positives = 72/167 (43%), Gaps = 11/167 (6%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +L SAT+P ++K+ + K        + +  ++E+  E  +   I +    + + L  L+ 
Sbjct: 159 LLMSATLPKFLKEYAEKI-GYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLE 217

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEA---LHGDISQHQRER----TLNGFRQG 113
              KGGK  +   T   A E    L      E    LH   ++  R +     L   ++ 
Sbjct: 218 FIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKN 277

Query: 114 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK 160
           +  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 = 55.0 bits (133), Expect = 5e-08
 Identities = 43/140 (30%), Positives = 70/140 (50%), Gaps = 16/140 (11%)

Query: 54  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 112
           +LS++    A+  + +V T TK+ A++++  L  + I    LH +I   +R   +   R 
Sbjct: 431 LLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRL 490

Query: 113 GKFTVLVATDVAARGLDIPNVDLI-IHYELPNDPETFVHRSGRT-----GRAGK--EGTA 164
           G+F VLV  ++   GLD+P V L+ I   L  D E F+ RS R+     GRA +   G  
Sbjct: 491 GEFDVLVGINLLREGLDLPEVSLVAI---LDADKEGFL-RSERSLIQTIGRAARNVNGKV 546

Query: 165 ILM---FTSSQRRTVRSLER 181
           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 = 54.5 bits (132), Expect = 6e-08
 Identities = 45/139 (32%), Positives = 69/139 (49%), Gaps = 14/139 (10%)

Query: 54  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 112
           +LS++    AK  + +V T TK+ A++++  L  + I    LH DI   +R   +   R 
Sbjct: 435 LLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRL 494

Query: 113 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAI 165
           G+F VLV  ++   GLD+P V L+    L  D E F+ RS R+     GRA +   G  I
Sbjct: 495 GEFDVLVGINLLREGLDLPEVSLVA--ILDADKEGFL-RSERSLIQTIGRAARNVNGKVI 551

Query: 166 L---MFTSSQRRTVRSLER 181
           L     T S ++ +   ER
Sbjct: 552 LYADKITDSMQKAIDETER 570

Length = 663

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

 Score = 53.9 bits (130), Expect = 1e-07
 Identities = 27/93 (29%), Positives = 49/93 (52%), Gaps = 9/93 (9%)

Query: 94  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 149
            HG +++++ E  +  F +G+F VLV T +   G+DIPN + II        + F    +
Sbjct: 692 AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTII----IERADKFGLAQL 747

Query: 150 HR-SGRTGRAGKEGTAILMFTSSQRRTVRSLER 181
           ++  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|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General function prediction only]

 Score = 51.7 bits (124), Expect = 6e-07
 Identities = 49/203 (24%), Positives = 78/203 (38%), Gaps = 34/203 (16%)

Query: 60  TVYAKG--GKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFT 116
           T  +KG  G+TIVFT ++R   E++ ALT   + +   H  +   +R+     F   +  
Sbjct: 433 TESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELA 492

Query: 117 VLVATDVAARGLDIPNVDLIIH-YELPND---PETFVHRSGRTGRAG--KEGTAILM--- 167
            +V T   A G+D P   +I     +  +      F    GR GR      G   L+   
Sbjct: 493 AVVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEP 552

Query: 168 ---FTSSQRRTVRSLERDVGCKFEFVSPP---VVEDVLESSAEQVVAT---------LNG 212
              + +S   T    E +V  K    S P   +VE   E   E V+A+         +  
Sbjct: 553 GKKYHASMEET----EDEVAFKL-LESEPEPVIVEYDEEDEEENVLASAGVTNSLSVIER 607

Query: 213 VHPESVEFFTPTAQRL--IEEKG 233
           V+   +       + L  +EE G
Sbjct: 608 VNSLMLGAAFDPKKALSKLEEYG 630

Length = 830

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

 Score = 51.9 bits (125), Expect = 6e-07
 Identities = 25/99 (25%), Positives = 43/99 (43%), Gaps = 23/99 (23%)

Query: 95  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS-- 152
           HG + + + E  +  F  G++ VLV T +   G+DIPN + II           + R+  
Sbjct: 836 HGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTII-----------IERADK 884

Query: 153 ----------GRTGRAGKEGTAILMFTSSQRRTVRSLER 181
                     GR GR+ K+  A  ++   +  T  + +R
Sbjct: 885 FGLAQLYQLRGRVGRSNKQAYAYFLYPPQKALTEDAEKR 923

Length = 1139

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

 Score = 50.4 bits (121), Expect = 1e-06
 Identities = 29/112 (25%), Positives = 53/112 (47%), Gaps = 17/112 (15%)

Query: 76  RDADEVSLALTSIIASEA---LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN 132
           + A+ +   L           LHG +   ++E  +  FR+G+  +LVAT V   G+D+PN
Sbjct: 467 KAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN 526

Query: 133 VDLIIHYELPNDPETF----VHR-SGRTGRAGKEGTAILMF-----TSSQRR 174
             +++      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|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3

 Score = 49.7 bits (119), Expect = 1e-06
 Identities = 43/168 (25%), Positives = 71/168 (42%), Gaps = 16/168 (9%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +L SAT+P ++K+ + K        + +  +  + A  IK+ +       + + L  L+ 
Sbjct: 158 LLMSATLPKFLKEYAEKI-GYVEENEPLDLKPNERAPFIKIESDKV---GEISSLERLLE 213

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEA---LHGDISQHQRER-----TLNGFRQ 112
              KGG   +   T   A E    L      E    +H   ++  R +      L   + 
Sbjct: 214 FIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKS 273

Query: 113 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK 160
            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|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 44.0 bits (105), Expect = 2e-06
 Identities = 10/18 (55%), Positives = 12/18 (66%)

Query: 453 GACFNCGKSGHRASECPN 470
             C+NCGK GH A +CP 
Sbjct: 1   RKCYNCGKEGHLARDCPE 18

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Length = 18

>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger

 Score = 42.8 bits (102), Expect = 4e-06
 Identities = 10/16 (62%), Positives = 13/16 (81%)

Query: 455 CFNCGKSGHRASECPN 470
           C+NCGK GH A +CP+
Sbjct: 2   CYNCGKEGHIARDCPS 17

Length = 17

>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 = 48.6 bits (116), Expect = 5e-06
 Identities = 39/170 (22%), Positives = 69/170 (40%), Gaps = 19/170 (11%)

Query: 45  STTATSKRTILSDLITVYAKGG-KTIVFTQTKRDADEVSLALTSIIASEALHGDISQH-- 101
            +   S    L+ L  +  + G +T+VF ++++   +V L   S        G       
Sbjct: 285 ESIRRSALAELATLAALLVRNGIQTLVFFRSRK---QVELLYLSPRRRLVREGGKLLDAV 341

Query: 102 ----------QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET-FVH 150
                     +R R    F++G+   ++AT+    G+DI ++D +I Y  P      F  
Sbjct: 342 STYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQ 401

Query: 151 RSGRTGRAGKEGTAILMFTSS--QRRTVRSLERDVGCKFEFVSPPVVEDV 198
           R+GR GR G+E   +++  S       +R  E  +   F  V    V+D 
Sbjct: 402 RAGRAGRRGQESLVLVVLRSDPLDSYYLRHPEELLETGFGPVESVRVDDN 451

Length = 851

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

 Score = 48.4 bits (116), Expect = 6e-06
 Identities = 26/104 (25%), Positives = 51/104 (49%), Gaps = 14/104 (13%)

Query: 76  RDADEVSLALTSIIASEA---LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN 132
           + A+E+   L S +       +HG +   +++  +  F++G+  +LVAT V   G+D+PN
Sbjct: 492 QAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPN 551

Query: 133 VDLIIHYELPNDPETF----VH--RSGRTGRAGKEGTAILMFTS 170
             +++      + E F    +H  R GR GR   +   +L++  
Sbjct: 552 ATVMVIE----NAERFGLAQLHQLR-GRVGRGDLQSYCVLLYKP 590

Length = 677

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

 Score = 47.8 bits (114), Expect = 1e-05
 Identities = 36/108 (33%), Positives = 53/108 (49%), Gaps = 21/108 (19%)

Query: 95  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----HYELPNDPETFV 149
           HG + + + ER +N F   +F VLV T +   G+DIP  + II     H+ L       +
Sbjct: 842 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ-----L 896

Query: 150 HR-SGRTGRAGKEGTAIL-------MFTSSQRR--TVRSLERDVGCKF 187
           H+  GR GR+  +  A L       M T +Q+R   + SLE D+G  F
Sbjct: 897 HQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLE-DLGAGF 943

Length = 1147

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

 Score = 47.4 bits (113), Expect = 1e-05
 Identities = 26/106 (24%), Positives = 54/106 (50%), Gaps = 1/106 (0%)

Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +G   I++  ++   ++ +  L S  I++ A H  +    R      F++    ++VAT 
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATV 294

Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 168
               G++ PNV  ++H+++P + E++   +GR GR G    A+L +
Sbjct: 295 AFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 340

Length = 607

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

 Score = 44.1 bits (104), Expect = 2e-04
 Identities = 37/136 (27%), Positives = 61/136 (44%), Gaps = 6/136 (4%)

Query: 95  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 154
           HG +S+ QR  T    + G+   +VAT     G+D+  VDL+I    P    + + R GR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367

Query: 155 TGRAGKEGTAILMFTSSQRRTVRS---LERDVGCKFEFVSPPVVEDVLESSAEQVVATLN 211
            G      +  L F  ++R  V S   +E     + E ++PP   + L+  A+Q VA   
Sbjct: 368 AGHQVGGVSKGLFFPRTRRDLVDSAVIVECMFAGRLENLTPP--HNPLDVLAQQTVAAA- 424

Query: 212 GVHPESVEFFTPTAQR 227
            +    V+ +    +R
Sbjct: 425 AMDALQVDEWYSRVRR 440

Length = 1490

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

 Score = 42.1 bits (100), Expect = 5e-04
 Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 22/80 (27%)

Query: 104 ERTLNGFRQGKFTVLVATDVAARGLDIPNV--------DLIIHYELPNDP----ETF--- 148
           E+ L  F +G+  +L+ T + A+G D PNV        DL +      D      TF   
Sbjct: 470 EQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFS---PDFRASERTFQLL 526

Query: 149 --VHRSGRTGRAGKEGTAIL 166
             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 = 42.1 bits (99), Expect = 6e-04
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 99  SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL-IIHYELPN-DPETFVHRSGRTG 156
            QH++E+ +  FR GK T+L+ T +  RG+  PNVD+ ++  E         V  +GR G
Sbjct: 341 DQHRKEK-VEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVG 399

Query: 157 RAGKEGTAILMF 168
           R+ +  T  ++F
Sbjct: 400 RSLERPTGDVLF 411

Length = 441

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

 Score = 40.5 bits (96), Expect = 7e-04
 Identities = 15/25 (60%), Positives = 20/25 (80%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNI 25
           +LFSATMP  V+ L+RK+L NP+ I
Sbjct: 178 LLFSATMPKEVRDLARKFLRNPVRI 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|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional

 Score = 41.6 bits (99), Expect = 7e-04
 Identities = 43/113 (38%), Positives = 59/113 (52%), Gaps = 13/113 (11%)

Query: 63  AKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVAT 121
           AKG + +V T TKR A++++  L  + I    LH DI   +R   +   R G+F VLV  
Sbjct: 444 AKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGI 503

Query: 122 DVAARGLDIPNVDLI-IHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 166
           ++   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 = 41.7 bits (99), Expect = 9e-04
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 11/80 (13%)

Query: 94  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 149
           LHG +   +++  +  F+ G+  +LVAT V   G+D+PN  +++      + E F    +
Sbjct: 511 LHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIE----NAERFGLAQL 566

Query: 150 H--RSGRTGRAGKEGTAILM 167
           H  R GR GR   +   +L+
Sbjct: 567 HQLR-GRVGRGAAQSYCVLL 585

Length = 681

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 5/31 (16%)

Query: 445 SRD---SRSFGG--ACFNCGKSGHRASECPN 470
           SR+   +    G  +C+NCGK+GH + ECP 
Sbjct: 40  SRECPSAPGGRGERSCYNCGKTGHLSRECPE 70

Length = 148

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

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 33/145 (22%), Positives = 66/145 (45%), Gaps = 19/145 (13%)

Query: 36  AEGIKLYAISTTATSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEVSLA----LTSIIA 90
             G     +  +A+++   +L+DL+   A+G +T+ F +++R A+ V+      L  +  
Sbjct: 244 LTGENGAPVRRSASAEAADLLADLV---AEGARTLTFVRSRRGAELVAAIARRLLGEVDP 300

Query: 91  SEALH------GDISQHQR--ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 142
             A        G + + +R  ER L   R G+   +  T+    G+DI  +D ++    P
Sbjct: 301 DLAERVAAYRAGYLPEDRRELERAL---RDGELLGVATTNALELGVDISGLDAVVIAGFP 357

Query: 143 NDPETFVHRSGRTGRAGKEGTAILM 167
               +   ++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 = 40.6 bits (95), Expect = 0.002
 Identities = 26/104 (25%), Positives = 50/104 (48%), Gaps = 1/104 (0%)

Query: 69  IVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVAARG 127
           I++  ++ D ++V+  L       A  HG +   QR      + + +  ++ AT     G
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG 743

Query: 128 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS 171
           ++ P+V  +IH+ LP   E +    GR GR G+  + +L ++ S
Sbjct: 744 INKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYS 787

Length = 1195

>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183)

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 29/113 (25%), Positives = 36/113 (31%), Gaps = 10/113 (8%)

Query: 346 QDDGPSSDNY-GRFSSRDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDED 404
              G         F S      G G+  S G   GG R G      GF +    G     
Sbjct: 206 GGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYGSGGTRSGQGGWGPGFWTGLGAG----- 260

Query: 405 GFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSS----RDSRSFGG 453
           G      G    + ++ G  + + S        S SS SSS    R S  FGG
Sbjct: 261 GALGYLFGSRRNNNSSYGRSYGSGSPSYSPSSSSNSSSSSSSSSTRTSSGFGG 313

This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown. Length = 317

>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional

 Score = 39.8 bits (93), Expect = 0.003
 Identities = 47/207 (22%), Positives = 79/207 (38%), Gaps = 48/207 (23%)

Query: 64  KGGKTIVFTQTKRDADEVSLALTSIIAS---------------------------EALHG 96
           KG   +VF  T+R A++ +L L   I                             +AL G
Sbjct: 237 KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRG 296

Query: 97  DISQH-----QRERTL--NGFRQGKFTVLVATDVAARGLDIPNVDLII-------HYELP 142
            ++ H     + ER L  + FR+G   V+ AT   + G+++P   +II       ++   
Sbjct: 297 GVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWE 356

Query: 143 NDPETFVHRS-GRTGRA--GKEGTAILMFTSSQRRTVRSLERDVGCKFE-FVSPPVVEDV 198
           + P   + +  GR GR    + G AI++ T+ +   +  +ER +  K E   S    E  
Sbjct: 357 DIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKL--MERYIFGKPEKLFSMLSNESA 414

Query: 199 LESSAEQVVATLN-GVHPESVEFFTPT 224
             S    ++         E V F   T
Sbjct: 415 FRSQVLALITNFGVSNFKELVNFLERT 441

Length = 720

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

 Score = 39.5 bits (93), Expect = 0.003
 Identities = 32/110 (29%), Positives = 48/110 (43%), Gaps = 6/110 (5%)

Query: 68  TIVFTQTKRDADEVSLALTSIIASEAL-----HGDISQHQRERTLNGFRQGKFTVLVATD 122
           T+VFT T+  A+    AL       AL     HG + + QR         G+   +V T 
Sbjct: 250 TLVFTNTRSQAELWFQALWEANPEFALPIALHHGSLDREQRRWVEAAMAAGRLRAVVCTS 309

Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG-RAGKEGTAILMFTSS 171
               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	470
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	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
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0345	567	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
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.98
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.97
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.97
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.97
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	99.97
PTZ00110	545	helicase; Provisional	99.97
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.97
KOG0327	397	consensus Translation initiation factor 4F, helica	99.97
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.96
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.96
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.96
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.96
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.96
PTZ00424	401	helicase 45; Provisional	99.96
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.95
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.95
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.95
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.95
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.95
PHA02653	675	RNA helicase NPH-II; Provisional	99.94
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.94
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.94
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.94
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.94
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.93
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.93
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.92
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.92
KOG4284	980	consensus DEAD box protein [Transcription]	99.92
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.91
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.91
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.9
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.89
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.88
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.88
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.87
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.87
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.87
PRK04914	956	ATP-dependent helicase HepA; Validated	99.87
PRK10689	1147	transcription-repair coupling factor; Provisional	99.87
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.87
PRK13767	876	ATP-dependent helicase; Provisional	99.86
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.84
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.83
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.82
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.82
PRK02362	737	ski2-like helicase; Provisional	99.81
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.81
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.8
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.79
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.79
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.78
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.78
PRK05298	652	excinuclease ABC subunit B; Provisional	99.78
PRK00254	720	ski2-like helicase; Provisional	99.77
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.77
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.77
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.77
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.76
PRK01172	674	ski2-like helicase; Provisional	99.75
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.74
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.74
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	99.73
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	99.72
PHA02558	501	uvsW UvsW helicase; Provisional	99.72
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.71
PRK09401	1176	reverse gyrase; Reviewed	99.71
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.7
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.69
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.69
PRK09694	878	helicase Cas3; Provisional	99.69
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.68
PRK14701	1638	reverse gyrase; Provisional	99.68
PRK13766	773	Hef nuclease; Provisional	99.68
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.67
KOG0354	746	consensus DEAD-box like helicase [General function	99.67
COG1202	830	Superfamily II helicase, archaea-specific [General	99.65
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.64
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.64
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.62
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.59
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.58
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.54
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.53
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.51
COG1204	766	Superfamily II helicase [General function predicti	99.51
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.5
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.49
PRK05580	679	primosome assembly protein PriA; Validated	99.48
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.47
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.47
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.44
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.41
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.35
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.34
PF08152	97	GUCT: GUCT (NUC152) domain; InterPro: IPR012562 Th	99.3
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.3
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.29
COG1205	851	Distinct helicase family with a unique C-terminal	99.29
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.25
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.24
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.23
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.22
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.16
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.97
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	98.89
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.88
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.78
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.77
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.76
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.75
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.74
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.69
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.67
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.66
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.64
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.61
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.54
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.52
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	98.51
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.48
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.39
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	98.36
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.36
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.32
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	98.19
KOG1123	776	consensus RNA polymerase II transcription initiati	98.19
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	98.1
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	98.09
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.06
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	98.06
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.06
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	98.03
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	98.01
COG4096	875	HsdR Type I site-specific restriction-modification	97.99
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.97
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	97.94
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.92
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.91
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.88
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.79
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.76
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.75
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	97.72
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	97.69
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	97.64
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	97.59
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.4
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	97.34
PF13696	32	zf-CCHC_2: Zinc knuckle	97.31
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.29
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.26
COG4889	1518	Predicted helicase [General function prediction on	97.17
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	97.14
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	97.02
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	96.99
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	96.84
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	96.75
PRK14873	665	primosome assembly protein PriA; Provisional	96.64
KOG4439	901	consensus RNA polymerase II transcription terminat	96.59
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.56
PRK05580	679	primosome assembly protein PriA; Validated	96.55
PF13917	42	zf-CCHC_3: Zinc knuckle	96.53
PF13871	278	Helicase_C_4: Helicase_C-like	96.53
smart00343	26	ZnF_C2HC zinc finger.	96.53
TIGR00595	505	priA primosomal protein N'. All proteins in this f	96.53
PTZ00368	148	universal minicircle sequence binding protein (UMS	96.43
PTZ00368	148	universal minicircle sequence binding protein (UMS	96.41
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.38
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	96.31
PRK14873	665	primosome assembly protein PriA; Provisional	96.28
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	96.18
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	96.05
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	95.87
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	95.86
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	95.82
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	95.34
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	95.25
COG1198	730	PriA Primosomal protein N' (replication factor Y)	95.0
PRK10689	1147	transcription-repair coupling factor; Provisional	94.92
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	94.86
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	94.61
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	94.6
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	94.56
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	94.51
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	94.51
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	94.28
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	94.15
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	93.89
PRK14701	1638	reverse gyrase; Provisional	93.83
KOG0334	997	consensus RNA helicase [RNA processing and modific	93.82
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	93.77
KOG2340	698	consensus Uncharacterized conserved protein [Funct	93.72
KOG0347	731	consensus RNA helicase [RNA processing and modific	93.37
PF15288	40	zf-CCHC_6: Zinc knuckle	92.57
PTZ00110	545	helicase; Provisional	92.4
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	92.37
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	92.31
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	92.3
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	92.26
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	92.13
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	91.67
PF14392	49	zf-CCHC_4: Zinc knuckle	91.38
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	91.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	90.99
KOG1001	674	consensus Helicase-like transcription factor HLTF/	90.67
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	90.21
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	90.08
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	88.83
COG5222	427	Uncharacterized conserved protein, contains RING Z	88.62
PRK13766	773	Hef nuclease; Provisional	88.18
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	88.13
PRK09401	1176	reverse gyrase; Reviewed	87.88
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	87.88
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	87.56
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	87.18
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	86.85
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	86.22
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	85.97
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	85.77
KOG0343	758	consensus RNA Helicase [RNA processing and modific	84.77
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	84.42
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	84.11
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	83.78
PRK13767	876	ATP-dependent helicase; Provisional	83.68
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	83.43
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	83.16
KOG4284	980	consensus DEAD box protein [Transcription]	81.35
KOG0298	1394	consensus DEAD box-containing helicase-like transc	80.81
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	80.37
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	80.3

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=9.1e-47  Score=402.31  Aligned_cols=321  Identities=27%  Similarity=0.448  Sum_probs=276.2

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ||||||||+.+..++++|+.+|..|.+..  .......+.+.|+.+....|.+.|..+|... ...++||||+|+..+++
T Consensus       184 llfSAT~p~~i~~i~~~~l~~~~~i~i~~--~~~~~~~i~q~~~~v~~~~k~~~L~~~L~~~-~~~~~IVF~~tk~~a~~  260 (629)
T PRK11634        184 ALFSATMPEAIRRITRRFMKEPQEVRIQS--SVTTRPDISQSYWTVWGMRKNEALVRFLEAE-DFDAAIIFVRTKNATLE  260 (629)
T ss_pred             EEEEccCChhHHHHHHHHcCCCeEEEccC--ccccCCceEEEEEEechhhHHHHHHHHHHhc-CCCCEEEEeccHHHHHH
Confidence            58999999999999999999999887753  2334567888888888888989998888765 45799999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      |++.|.. ++.+..+|++|++.+|++++++|++++++||||||++++|||+|+|++|||||+|.++++|+||+|||||+|
T Consensus       261 l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaG  340 (629)
T PRK11634        261 VAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAG  340 (629)
T ss_pred             HHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCC
Confidence            9999985 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHHccc-CccchhhhHHHHHHHHHh-----hC
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGV-HPESVEFFTPTAQRLIEE-----KG  233 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~~~a~~l~~~-----~~  233 (470)
                      +.|.+++|+++.+...++.|++.++..++.+.+|..+++.+.....+...+... ....++.|.+.++++++.     .+
T Consensus       341 r~G~ai~~v~~~e~~~l~~ie~~~~~~i~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  420 (629)
T PRK11634        341 RAGRALLFVENRERRLLRNIERTMKLTIPEVELPNAELLGKRRLEKFAAKVQQQLESSDLDQYRALLAKIQPTAEGEELD  420 (629)
T ss_pred             CcceEEEEechHHHHHHHHHHHHhCCCcceecCCcHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhhccccCC
Confidence            999999999999999999999999999999999999888888887777766543 234577788888888864     67


Q ss_pred             HHHHHHHHHHHcCCCCC------C-----C---Ccc-----------------c--cc---CCCCeEEEEEeeCCccccC
Q 012133          234 TDALAAALAQLSGFSRP------P-----S---SRS-----------------L--IN---HEQGWVTLQLTRDSAFSRG  277 (470)
Q Consensus       234 ~~~l~~al~~l~~~~~~------~-----~---~r~-----------------l--~~---~~~~~~~~~~~~~~~~~~~  277 (470)
                      ++.++++|+.+..-..+      +     .   .+.                 .  ..   ...+|++++++.++   ++
T Consensus       421 ~~~~a~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~---~~  497 (629)
T PRK11634        421 LETLAAALLKMAQGERPLILPPDAPMRPKREFRDRDDRGPRDRNDRGPRGDREDRPRRERRDVGDMQLYRIEVGR---DD  497 (629)
T ss_pred             HHHHHHHHHHHHcCCCccccccccccccccccccccccccccccccccccccccccccccccCCCCEEEEEeccc---cc
Confidence            89999999988632211      0     0   000                 0  00   12268999999999   89


Q ss_pred             CcchhhHHhHhhhhcCcCcCccccEEEeecCccceeEeecCHHHHHHHHhhcCC
Q 012133          278 FMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIP  331 (470)
Q Consensus       278 ~~~~~~v~~~l~~~~~~~~~~Ig~I~i~~~~~~~ga~fdv~~~~a~~i~~~~~~  331 (470)
                      .+.|++|+++|++...+...+||+|+|++++    ++||||++.++++++....
T Consensus       498 ~~~~~~~~~~i~~~~~~~~~~ig~i~i~~~~----s~v~~~~~~~~~~~~~~~~  547 (629)
T PRK11634        498 GVEVRHIVGAIANEGDISSRYIGNIKLFASH----STIELPKGMPGEVLQHFTR  547 (629)
T ss_pred             CCCHHHHHHHHHhhcCCChhhCCcEEEeCCc----eEEEcChhhHHHHHHHhcc
Confidence            9999999999999999999999999999998    7999999999999987643

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

Probab=100.00  E-value=5.6e-38  Score=317.60  Aligned_cols=183  Identities=45%  Similarity=0.714  Sum_probs=169.9

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHc--CCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYA--KGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~--~~~~~lVF~~t~~~~   78 (470)
                      ||||||+|.||+.+++.||.+|..|++....+.....+|.|....+++..|...|..+|..+.  ..+|+||||+|++.|
T Consensus       275 lm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~  354 (519)
T KOG0331|consen  275 LMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGKLLEDISSDSEGKVIIFCETKRTC  354 (519)
T ss_pred             EEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHHHHHHHhccCCCcEEEEecchhhH
Confidence            689999999999999999999999998766566778899999999999999999999998874  567999999999999


Q ss_pred             HHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           79 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      ++|+..|.. .+.+.+|||+++|.+|+.+|+.|++|+..||||||||+||||||+|++|||||+|.++++|+||+|||||
T Consensus       355 ~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGR  434 (519)
T KOG0331|consen  355 DELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGR  434 (519)
T ss_pred             HHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCcccc
Confidence            999999996 6999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHHHHh
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLERDV  183 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~~~~  183 (470)
                      +++.|.+++|++..+......+.+.+
T Consensus       435 a~~~G~A~tfft~~~~~~a~~l~~~l  460 (519)
T KOG0331|consen  435 AGKKGTAITFFTSDNAKLARELIKVL  460 (519)
T ss_pred             CCCCceEEEEEeHHHHHHHHHHHHHH
Confidence            99999999999998877666665544

>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=8.9e-37  Score=280.06  Aligned_cols=190  Identities=34%  Similarity=0.598  Sum_probs=175.9

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCccc-HHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      +|+|||+|.+|.+..++||.||+.|-+.  .++.+...|++||+.+..++ |.+.|.+|.+.+. -.+++|||||+..++
T Consensus       204 v~~SATlp~eilemt~kfmtdpvrilvk--rdeltlEgIKqf~v~ve~EewKfdtLcdLYd~Lt-ItQavIFcnTk~kVd  280 (400)
T KOG0328|consen  204 VLVSATLPHEILEMTEKFMTDPVRILVK--RDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLT-ITQAVIFCNTKRKVD  280 (400)
T ss_pred             EEEeccCcHHHHHHHHHhcCCceeEEEe--cCCCchhhhhhheeeechhhhhHhHHHHHhhhhe-hheEEEEecccchhh
Confidence            5899999999999999999999998653  56677788999999987764 9999999988763 479999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .|.+.+.. .+.+..+||+|+|++|++++..||+++.+|||+|||.+||||+|.|++|||||+|.+.+.|+||+||.||.
T Consensus       281 wLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRF  360 (400)
T KOG0328|consen  281 WLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF  360 (400)
T ss_pred             HHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhcccccc
Confidence            99999985 78999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCC
Q 012133          159 GKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      |++|.+|.|+...+.+.++.|++++...+..++..
T Consensus       361 GRkGvainFVk~~d~~~lrdieq~yst~i~emp~n  395 (400)
T KOG0328|consen  361 GRKGVAINFVKSDDLRILRDIEQYYSTQIDEMPMN  395 (400)
T ss_pred             CCcceEEEEecHHHHHHHHHHHHHHhhhcccccch
Confidence            99999999999999999999999999888876554

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

Probab=100.00  E-value=4.5e-36  Score=286.56  Aligned_cols=190  Identities=36%  Similarity=0.564  Sum_probs=176.9

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      +|||||||+.|.+|.+.-+++|+.|.+.  ....+.++++++|+.++..+|...|..||+.. ....+||||+|...++.
T Consensus       239 ~LfsATMt~kv~kL~rasl~~p~~v~~s--~ky~tv~~lkQ~ylfv~~k~K~~yLV~ll~e~-~g~s~iVF~~t~~tt~~  315 (476)
T KOG0330|consen  239 FLFSATMTKKVRKLQRASLDNPVKVAVS--SKYQTVDHLKQTYLFVPGKDKDTYLVYLLNEL-AGNSVIVFCNTCNTTRF  315 (476)
T ss_pred             EEEEeecchhhHHHHhhccCCCeEEecc--chhcchHHhhhheEeccccccchhHHHHHHhh-cCCcEEEEEeccchHHH
Confidence            5899999999999999999999999764  45567788999999999999999999999876 55899999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      ++-.|.. ++.+.+|||+|+|..|.-.+++|+++...|||||||++||+|||.|++|||||+|.+..+||||+|||+|+|
T Consensus       316 la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaG  395 (476)
T KOG0330|consen  316 LALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAG  395 (476)
T ss_pred             HHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccC
Confidence            9999986 899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCccccCCC
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      ++|++|.|++..|.+.+.+||..++.+.+..+.+
T Consensus       396 rsG~~ItlVtqyDve~~qrIE~~~gkkl~~~~~~  429 (476)
T KOG0330|consen  396 RSGKAITLVTQYDVELVQRIEHALGKKLPEYKVD  429 (476)
T ss_pred             CCcceEEEEehhhhHHHHHHHHHHhcCCCccCcc
Confidence            9999999999999999999999999887654433

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

Probab=100.00  E-value=2.8e-35  Score=288.89  Aligned_cols=247  Identities=31%  Similarity=0.442  Sum_probs=201.8

Q ss_pred             CEEeecCCHHHHHHHHHHcC-CCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLD-NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~-~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      +|||||+|++|+++++--|+ +|+.|++.......+.+.+++-|+.++...++.+|..+|+.+-...++||||+|...+.
T Consensus       265 ~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~ll~~~LKk~~~~~KiiVF~sT~~~vk  344 (543)
T KOG0342|consen  265 LLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSRFSLLYTFLKKNIKRYKIIVFFSTCMSVK  344 (543)
T ss_pred             eEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccchHHHHHHHHHHhcCCceEEEEechhhHHH
Confidence            68999999999999998776 69999999888888999999999999888888888889887756689999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .+++.|.. .++|..|||.++|..|..+...|++.+.-|||||||++||+|+|+|++||+||+|.++++||||+|||||.
T Consensus       345 ~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~  424 (543)
T KOG0342|consen  345 FHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTARE  424 (543)
T ss_pred             HHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhcccccc
Confidence            99999985 78999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCH-HHHHHHHHHHHHHHHcccCccchhhhHHHHHHHH-------H
Q 012133          159 GKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVV-EDVLESSAEQVVATLNGVHPESVEFFTPTAQRLI-------E  230 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~l~-------~  230 (470)
                      |++|.+++++.+.|..+++.|+   .+.++..+.|+. .+.++...+.++..-........+.|..+...+-       .
T Consensus       425 gk~G~alL~l~p~El~Flr~LK---~lpl~~~e~~~~~~~~v~~~~~~li~~~y~~~~aak~ay~syl~~y~s~slk~~~  501 (543)
T KOG0342|consen  425 GKEGKALLLLAPWELGFLRYLK---KLPLEEFEFPPLKPEDVQSQLEKLISKNYSLKEAAKEAYKSYLGAYNSHSLKDIF  501 (543)
T ss_pred             CCCceEEEEeChhHHHHHHHHh---hCCCcccCCCCCCHHHHHHHHHHHHHHHhhHHHHHHHHHHhhhhhccchhhhccc
Confidence            9999999999999999999998   445555554443 3444555555554332233333333333322221       1


Q ss_pred             hhCHHHHHHHHHHHcCCCCCC
Q 012133          231 EKGTDALAAALAQLSGFSRPP  251 (470)
Q Consensus       231 ~~~~~~l~~al~~l~~~~~~~  251 (470)
                      ....-.|+ ++++.+|++.||
T Consensus       502 ~~~~l~La-~~~~s~gf~~pp  521 (543)
T KOG0342|consen  502 NVNLLELA-AVAKSFGFSVPP  521 (543)
T ss_pred             ccchhhHH-HHHHHcCCCCCc
Confidence            12233556 888888888765

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

Probab=100.00  E-value=3e-35  Score=308.23  Aligned_cols=195  Identities=42%  Similarity=0.703  Sum_probs=176.3

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCccc-HHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      +|||||||+.|.++++.|+++|..|.+.......+...|.|+++.++..+ |.++|..+++.. ...++||||+|+..++
T Consensus       209 llfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~-~~~~~IVF~~tk~~~~  287 (513)
T COG0513         209 LLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDE-DEGRVIVFVRTKRLVE  287 (513)
T ss_pred             EEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHHhcC-CCCeEEEEeCcHHHHH
Confidence            58999999999999999999999998864444447889999999999876 999999999876 3458999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .|+..|.. ++.+..|||+|+|++|.++++.|++++.+|||||||++||||||+|++|||||+|.+++.|+||+|||||+
T Consensus       288 ~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRa  367 (513)
T COG0513         288 ELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRA  367 (513)
T ss_pred             HHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccC
Confidence            99999985 79999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChh-hHHHHHHHHHHhCCCcc-ccCCCCHH
Q 012133          159 GKEGTAILMFTSS-QRRTVRSLERDVGCKFE-FVSPPVVE  196 (470)
Q Consensus       159 g~~g~~i~l~~~~-~~~~~~~i~~~~~~~~~-~~~~p~~~  196 (470)
                      |++|.+++|+++. |...+..|++.+...++ ...+|...
T Consensus       368 G~~G~ai~fv~~~~e~~~l~~ie~~~~~~~~~~~~~~~~~  407 (513)
T COG0513         368 GRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDE  407 (513)
T ss_pred             CCCCeEEEEeCcHHHHHHHHHHHHHHhccccccccCCcch
Confidence            9999999999986 89999999999877655 44444433

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

Probab=100.00  E-value=3.4e-35  Score=289.52  Aligned_cols=181  Identities=38%  Similarity=0.591  Sum_probs=164.6

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ++||||||+.|..|++.||.+|+.|.+-  ......+-++|.++.+..+.|...|..+|... ...++|||+|+++.|+.
T Consensus       456 ~mftatm~p~verlar~ylr~pv~vtig--~~gk~~~rveQ~v~m~~ed~k~kkL~eil~~~-~~ppiIIFvN~kk~~d~  532 (673)
T KOG0333|consen  456 VMFTATMPPAVERLARSYLRRPVVVTIG--SAGKPTPRVEQKVEMVSEDEKRKKLIEILESN-FDPPIIIFVNTKKGADA  532 (673)
T ss_pred             EEEecCCChHHHHHHHHHhhCCeEEEec--cCCCCccchheEEEEecchHHHHHHHHHHHhC-CCCCEEEEEechhhHHH
Confidence            5899999999999999999999999764  34455677888888888888999999998776 56899999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      |++.|.+ ++.+..|||+-+|++|+.+|+.|+++...|||||||++||||||+|.+|||||+++++++|+||+|||||+|
T Consensus       533 lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAG  612 (673)
T KOG0333|consen  533 LAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAG  612 (673)
T ss_pred             HHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccc
Confidence            9999996 899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhC
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVG  184 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~  184 (470)
                      +.|+++.|+++.+...+..|.+.+.
T Consensus       613 k~GtaiSflt~~dt~v~ydLkq~l~  637 (673)
T KOG0333|consen  613 KSGTAISFLTPADTAVFYDLKQALR  637 (673)
T ss_pred             cCceeEEEeccchhHHHHHHHHHHH
Confidence            9999999999988666666555443

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=1.2e-33  Score=294.74  Aligned_cols=261  Identities=30%  Similarity=0.470  Sum_probs=221.8

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+|+.+..+++.++.+|..|.+...   .....++++++.++...|.+.|..++... ...++||||+|++.++.
T Consensus       182 ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~---~~~~~i~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lVF~~t~~~~~~  257 (460)
T PRK11776        182 LLFSATYPEGIAAISQRFQRDPVEVKVEST---HDLPAIEQRFYEVSPDERLPALQRLLLHH-QPESCVVFCNTKKECQE  257 (460)
T ss_pred             EEEEecCcHHHHHHHHHhcCCCEEEEECcC---CCCCCeeEEEEEeCcHHHHHHHHHHHHhc-CCCceEEEECCHHHHHH
Confidence            589999999999999999999998877432   23455888888888888999999988765 45789999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +++.|.. ++.+..+||+|++.+|+.+++.|+++.++|||||+++++|||+|++++||||++|.++++|+||+|||||+|
T Consensus       258 l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g  337 (460)
T PRK11776        258 VADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAG  337 (460)
T ss_pred             HHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCC
Confidence            9999985 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHHcccCccchhhhHHHHHHHHHhhCHHHHHH
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAA  239 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~l~~~~~~~~l~~  239 (470)
                      +.|.+++|+.+.+...++.|++.++..+++.++|......                                        
T Consensus       338 ~~G~ai~l~~~~e~~~~~~i~~~~~~~~~~~~l~~~~~~~----------------------------------------  377 (460)
T PRK11776        338 SKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLPSLSPLS----------------------------------------  377 (460)
T ss_pred             CcceEEEEEchhHHHHHHHHHHHhCCCCceecCCchhhcc----------------------------------------
Confidence            9999999999999999999999988887776655322100                                        


Q ss_pred             HHHHHcCCCCCCCCcccccCCCCeEEEEEeeCCccccCCcchhhHHhHhhhhcCcCcCccccEEEeecCccceeEeecCH
Q 012133          240 ALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPE  319 (470)
Q Consensus       240 al~~l~~~~~~~~~r~l~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~Ig~I~i~~~~~~~ga~fdv~~  319 (470)
                              ..        .....+.++.+..++   ...+.+.++++.++........++|.|.+.+.+    ++++++.
T Consensus       378 --------~~--------~~~~~~~~l~i~~~~---~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~----~~~~~~~  434 (460)
T PRK11776        378 --------GV--------PLLPEMVTLCIDGGK---KDKLRPGDILGALTGDAGLDGAQIGKINVTDFH----AYVAVER  434 (460)
T ss_pred             --------cc--------cCCCCeEEEEEeccc---ccCCCccchHHHhhcccCCChhhcCCccccccc----ceeecch
Confidence                    00        011246778877776   556778889998888777777889999988776    6899999


Q ss_pred             HHHHHHHhh
Q 012133          320 EIAKELLNK  328 (470)
Q Consensus       320 ~~a~~i~~~  328 (470)
                      +.++.++..
T Consensus       435 ~~~~~~~~~  443 (460)
T PRK11776        435 AVAKKALKK  443 (460)
T ss_pred             hhHHHHHHH
Confidence            988888754

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

Probab=100.00  E-value=7.2e-33  Score=270.26  Aligned_cols=194  Identities=34%  Similarity=0.497  Sum_probs=174.3

Q ss_pred             EEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            2 LFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         2 lfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      |||||+..++.+|++..++||+.|.+.......++..+..+|+.|+...|...|.++|... ..+++|||.+|...++..
T Consensus       193 LFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~~L~~~-~~kK~iVFF~TCasVeYf  271 (567)
T KOG0345|consen  193 LFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNNN-KDKKCIVFFPTCASVEYF  271 (567)
T ss_pred             cccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHHHHHHHHHHhcc-ccccEEEEecCcchHHHH
Confidence            7999999999999999999999999876555557888999999999999999999999875 668999999999999999


Q ss_pred             HHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           82 SLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        82 ~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      +..|..   ...+..+||.|++.+|..+++.|++..-.+|+||||++||||||+|++||+||+|.++..|+||+|||+|+
T Consensus       272 ~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~  351 (567)
T KOG0345|consen  272 GKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARA  351 (567)
T ss_pred             HHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhc
Confidence            998874   57899999999999999999999998889999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHH
Q 012133          159 GKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE  196 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~  196 (470)
                      |+.|.+++|+.+.|..+++.+.-.-....+.+..|...
T Consensus       352 gr~G~Aivfl~p~E~aYveFl~i~~~v~le~~~~e~~~  389 (567)
T KOG0345|consen  352 GREGNAIVFLNPREEAYVEFLRIKGKVELERIDTEKAS  389 (567)
T ss_pred             cCccceEEEecccHHHHHHHHHhcCccchhhhcccccc
Confidence            99999999999988888887765555566655555443

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

Probab=100.00  E-value=2.3e-33  Score=261.59  Aligned_cols=189  Identities=29%  Similarity=0.525  Sum_probs=178.1

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ||||||.|-.|+.+..++|++|..|++   .++.++..+.+||..+.+.+|...|..|+..+ .-.+.|||||+...++.
T Consensus       262 llySATFP~tVk~Fm~~~l~kPy~INL---M~eLtl~GvtQyYafV~e~qKvhCLntLfskL-qINQsIIFCNS~~rVEL  337 (459)
T KOG0326|consen  262 LLYSATFPLTVKGFMDRHLKKPYEINL---MEELTLKGVTQYYAFVEERQKVHCLNTLFSKL-QINQSIIFCNSTNRVEL  337 (459)
T ss_pred             eEEecccchhHHHHHHHhccCcceeeh---hhhhhhcchhhheeeechhhhhhhHHHHHHHh-cccceEEEeccchHhHH
Confidence            689999999999999999999999998   46677889999999999999999999988776 34689999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      ||+.+.+ ++.|..+|+.|-|++|.+++..|++|.++.|||||.+.||||+++|++|||+|+|++.++|+||+||.||.|
T Consensus       338 LAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFG  417 (459)
T KOG0326|consen  338 LAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFG  417 (459)
T ss_pred             HHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCC
Confidence            9999986 899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCccccCCC
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      ..|.+|.|++..++..+..||+.++..+++++..
T Consensus       418 hlGlAInLityedrf~L~~IE~eLGtEI~pip~~  451 (459)
T KOG0326|consen  418 HLGLAINLITYEDRFNLYRIEQELGTEIKPIPSN  451 (459)
T ss_pred             CcceEEEEEehhhhhhHHHHHHHhccccccCCCc
Confidence            9999999999999999999999999999877643

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

Probab=100.00  E-value=6.9e-32  Score=255.19  Aligned_cols=194  Identities=30%  Similarity=0.508  Sum_probs=171.3

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcC--CCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAK--GGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~--~~~~lVF~~t~~~~   78 (470)
                      +||||||.+.++++..--...+....+.......+...+.+.|+.++...|...|..+|..+..  ...++||++|..+|
T Consensus       188 LlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vkdaYLv~~Lr~~~~~~~~simIFvnttr~c  267 (442)
T KOG0340|consen  188 LLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVKDAYLVHLLRDFENKENGSIMIFVNTTREC  267 (442)
T ss_pred             EEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhhHHHHHHHHhhhhhccCceEEEEeehhHHH
Confidence            6899999999887664333332233333335566778899999999999999999999987754  67999999999999


Q ss_pred             HHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           79 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +.|+..|.. .+.+..+|+.|+|++|...+.+|+++.++||||||||+||+|||.|++|||||+|.++.+|+||+|||+|
T Consensus       268 Q~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtAR  347 (442)
T KOG0340|consen  268 QLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTAR  347 (442)
T ss_pred             HHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhc
Confidence            999999986 7899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCC
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPV  194 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~  194 (470)
                      +|+.|.++.++++.+.+.+..||+..+.++.+.....
T Consensus       348 AGR~G~aiSivt~rDv~l~~aiE~~igkKl~e~~~~~  384 (442)
T KOG0340|consen  348 AGRKGMAISIVTQRDVELLQAIEEEIGKKLTEYNKVQ  384 (442)
T ss_pred             ccCCcceEEEechhhHHHHHHHHHHHhcccccccccc
Confidence            9999999999999999999999999999988764443

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=7.1e-32  Score=267.33  Aligned_cols=250  Identities=26%  Similarity=0.360  Sum_probs=196.2

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ||||||....|++|++..++||..|.+-......++.+++++|+.++..+|+.+|..+|+.+ ...++|||+.|.+++..
T Consensus       250 LLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~sh-lk~K~iVF~SscKqvkf  328 (758)
T KOG0343|consen  250 LLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIKSH-LKKKSIVFLSSCKQVKF  328 (758)
T ss_pred             eeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHHHHHHHHHHhc-cccceEEEEehhhHHHH
Confidence            69999999999999999999999999875666778899999999999999999999999887 45899999999999999


Q ss_pred             HHHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           81 VSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        81 l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +++.+.+   ++++..|||.|+|..|..++.+|-..+.-||+|||+++||+|+|.|++||++|.|.++++||||+|||+|
T Consensus       329 ~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR  408 (758)
T KOG0343|consen  329 LYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTAR  408 (758)
T ss_pred             HHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhc
Confidence            9998874   7899999999999999999999999899999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhh-HHHHHHHHHHhCCCccccCCCCH-HHHHHHHHHHHHHHHcccCccchhhhHHHHHHHHHhhCHH
Q 012133          158 AGKEGTAILMFTSSQ-RRTVRSLERDVGCKFEFVSPPVV-EDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTD  235 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~-~~~~~~i~~~~~~~~~~~~~p~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~l~~~~~~~  235 (470)
                      ....|.++++++|.+ ..++..|++.. +.+..+.+.+. -.-+...++.++..-..+..-....|..+++.+....+..
T Consensus       409 ~~~~G~sll~L~psEeE~~l~~Lq~k~-I~i~~i~i~~~k~~~i~~~l~~ll~~~~eLk~~aqka~isY~rsi~~~rdK~  487 (758)
T KOG0343|consen  409 YKERGESLLMLTPSEEEAMLKKLQKKK-IPIKEIKIDPEKLTSIRNKLEALLAKDPELKEYAQKAFISYLRSIYLMRDKR  487 (758)
T ss_pred             ccCCCceEEEEcchhHHHHHHHHHHcC-CCHHhhccCHHHhhhHHHHHHHHHhhCHHHHHHHHHHHHHHHHHHHhhccch
Confidence            999999999999988 56666776654 55554433311 1111222222222222222222345555555554432222


Q ss_pred             H------HHHHHHHHcCCCCCCC
Q 012133          236 A------LAAALAQLSGFSRPPS  252 (470)
Q Consensus       236 ~------l~~al~~l~~~~~~~~  252 (470)
                      .      -..|++..+|++..|+
T Consensus       488 ~f~~~~l~~~afa~s~Gl~~~p~  510 (758)
T KOG0343|consen  488 VFDVEKLDIEAFADSLGLPGTPR  510 (758)
T ss_pred             hhcchhccHHHHHHhcCCCCCch
Confidence            1      1456666677665444

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

Probab=99.98  E-value=4e-32  Score=260.53  Aligned_cols=182  Identities=35%  Similarity=0.584  Sum_probs=165.3

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      +|.|||+|+.|++|+..|+++|..+-+ +.-+-.....+++..+...+++|++++..++..+....++||||..+..|+.
T Consensus       402 vmTSATWP~~VrrLa~sY~Kep~~v~v-GsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~  480 (629)
T KOG0336|consen  402 VMTSATWPEGVRRLAQSYLKEPMIVYV-GSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMADH  480 (629)
T ss_pred             eeecccCchHHHHHHHHhhhCceEEEe-cccceeeeeeeeeeEEecccHHHHHHHHHHHHhcCCCceEEEEEechhhhhh
Confidence            478999999999999999999987743 4444445567888888888889999999999999889999999999999999


Q ss_pred             HHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      |...|. +++.+..|||+-+|.+|+..++.|++|.++||||||+++||||+|+|+||+|||+|.+++.|+||+|||||+|
T Consensus       481 LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaG  560 (629)
T KOG0336|consen  481 LSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAG  560 (629)
T ss_pred             ccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCC
Confidence            998887 6899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHh
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDV  183 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~  183 (470)
                      ++|+++.|++..+..+.+.|-+.+
T Consensus       561 r~G~sis~lt~~D~~~a~eLI~IL  584 (629)
T KOG0336|consen  561 RTGTSISFLTRNDWSMAEELIQIL  584 (629)
T ss_pred             CCcceEEEEehhhHHHHHHHHHHH
Confidence            999999999999988777665443

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

Probab=99.97  E-value=2.1e-31  Score=253.31  Aligned_cols=194  Identities=31%  Similarity=0.489  Sum_probs=173.8

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcc-cHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT-SKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      ||||||....+.+++.+.+++|..+.+.  .+.....+|+++|+.|+.+ +|.++|.+|.... .-++.||||.|++.|.
T Consensus       268 lLFSATf~e~V~~Fa~kivpn~n~i~Lk--~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~-tigqsiIFc~tk~ta~  344 (477)
T KOG0332|consen  268 LLFSATFVEKVAAFALKIVPNANVIILK--REELALDNIKQLYVLCACRDDKYQALVNLYGLL-TIGQSIIFCHTKATAM  344 (477)
T ss_pred             EeeechhHHHHHHHHHHhcCCCceeeee--hhhccccchhhheeeccchhhHHHHHHHHHhhh-hhhheEEEEeehhhHH
Confidence            6899999999999999999999988774  4566678999999998764 8899998876555 3489999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC------ChhHHHHHh
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRS  152 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~------~~~~y~qr~  152 (470)
                      .|+..|.. ++.|..|||+|.-++|..+++.||.|+.+|||+|+|.+||||++.|++|||||+|.      |.++|+||+
T Consensus       345 ~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRi  424 (477)
T KOG0332|consen  345 WLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRI  424 (477)
T ss_pred             HHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHh
Confidence            99999984 89999999999999999999999999999999999999999999999999999995      899999999


Q ss_pred             cccCCCCCCCeEEEeeChh-hHHHHHHHHHHhCCCccccCCCCHHH
Q 012133          153 GRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFVSPPVVED  197 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~-~~~~~~~i~~~~~~~~~~~~~p~~~~  197 (470)
                      |||||.|+.|.+|.|+... ....+..|+++.+.++..+.+...+|
T Consensus       425 GRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~i~~~~~~d~~E  470 (477)
T KOG0332|consen  425 GRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMKIKRLDPDDLDE  470 (477)
T ss_pred             cccccccccceEEEeecccCcHHHHHHHHHHHhhcceecCCccHHH
Confidence            9999999999999998864 56788899999998888877744443

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=1.1e-30  Score=269.67  Aligned_cols=187  Identities=35%  Similarity=0.524  Sum_probs=167.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ++||||+|..+..++..++.+|..+.+...  ......+.+.++.+....|...|..+++.. ...++||||++++.|+.
T Consensus       194 ~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~--~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lVF~~t~~~~~~  270 (423)
T PRK04837        194 MLFSATLSYRVRELAFEHMNNPEYVEVEPE--QKTGHRIKEELFYPSNEEKMRLLQTLIEEE-WPDRAIIFANTKHRCEE  270 (423)
T ss_pred             EEEeccCCHHHHHHHHHHCCCCEEEEEcCC--CcCCCceeEEEEeCCHHHHHHHHHHHHHhc-CCCeEEEEECCHHHHHH
Confidence            589999999999999999999988876432  334456777777777778888888888654 45799999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +++.|.. ++.+..+||+|++++|.++++.|++|+++||||||++++|||+|+|++|||||+|.+.++|+||+||+||.|
T Consensus       271 l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G  350 (423)
T PRK04837        271 IWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAG  350 (423)
T ss_pred             HHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCC
Confidence            9999984 799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCcccc
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEFV  190 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~  190 (470)
                      +.|.+++|+++.+...+..|++.+...++..
T Consensus       351 ~~G~ai~~~~~~~~~~~~~i~~~~~~~~~~~  381 (423)
T PRK04837        351 ASGHSISLACEEYALNLPAIETYIGHSIPVS  381 (423)
T ss_pred             CCeeEEEEeCHHHHHHHHHHHHHhCCCCCCc
Confidence            9999999999999999999998887776543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.97  E-value=2.4e-30  Score=269.21  Aligned_cols=186  Identities=38%  Similarity=0.580  Sum_probs=166.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+++++..++.+++.+|..+.+..  .......+.+++..++...+.++|..++... ...++||||++++.++.
T Consensus       184 l~~SAT~~~~~~~l~~~~~~~~~~i~~~~--~~~~~~~i~~~~~~~~~~~k~~~l~~l~~~~-~~~~~lVF~~t~~~~~~  260 (456)
T PRK10590        184 LLFSATFSDDIKALAEKLLHNPLEIEVAR--RNTASEQVTQHVHFVDKKRKRELLSQMIGKG-NWQQVLVFTRTKHGANH  260 (456)
T ss_pred             EEEeCCCcHHHHHHHHHHcCCCeEEEEec--ccccccceeEEEEEcCHHHHHHHHHHHHHcC-CCCcEEEEcCcHHHHHH
Confidence            58999999999999999999998887643  2334566778887777778888887777543 45799999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      |++.|.+ .+.+..+||+|++++|.++++.|++++++|||||+++++|||+|+|++||||++|.++++|+||+|||||++
T Consensus       261 l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g  340 (456)
T PRK10590        261 LAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAA  340 (456)
T ss_pred             HHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCC
Confidence            9999985 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCccc
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEF  189 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~  189 (470)
                      ..|.+++|+...+...++.|++.+..+++.
T Consensus       341 ~~G~ai~l~~~~d~~~~~~ie~~l~~~~~~  370 (456)
T PRK10590        341 ATGEALSLVCVDEHKLLRDIEKLLKKEIPR  370 (456)
T ss_pred             CCeeEEEEecHHHHHHHHHHHHHhcCCCcc
Confidence            999999999999999999999888766543

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

Probab=99.97  E-value=6.5e-31  Score=258.44  Aligned_cols=179  Identities=35%  Similarity=0.565  Sum_probs=161.2

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCc---ccHHHHHHHHHHHHcCCCeEEEEeCchHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA---TSKRTILSDLITVYAKGGKTIVFTQTKRD   77 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~---~~k~~~l~~ll~~~~~~~~~lVF~~t~~~   77 (470)
                      |||||||..+|++|++-.|++|+.|-+.  ....++..+.+.++.+.+   .++..+|..|+... ...++|||+.|++.
T Consensus       362 mLFSATMteeVkdL~slSL~kPvrifvd--~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rt-f~~~~ivFv~tKk~  438 (691)
T KOG0338|consen  362 MLFSATMTEEVKDLASLSLNKPVRIFVD--PNKDTAPKLTQEFIRIRPKREGDREAMLASLITRT-FQDRTIVFVRTKKQ  438 (691)
T ss_pred             eeehhhhHHHHHHHHHhhcCCCeEEEeC--CccccchhhhHHHheeccccccccHHHHHHHHHHh-cccceEEEEehHHH
Confidence            6999999999999999999999999874  445566777777776543   36778888888765 35899999999999


Q ss_pred             HHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccC
Q 012133           78 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG  156 (470)
Q Consensus        78 ~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~g  156 (470)
                      |..+.-+|-- ++.+.-|||.|+|.+|...+++|++.+++||||||+++|||||+.|..||||++|.+.+.|+||+|||+
T Consensus       439 AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTA  518 (691)
T KOG0338|consen  439 AHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTA  518 (691)
T ss_pred             HHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhh
Confidence            9999888763 789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCeEEEeeChhhHHHHHHHHHH
Q 012133          157 RAGKEGTAILMFTSSQRRTVRSLERD  182 (470)
Q Consensus       157 R~g~~g~~i~l~~~~~~~~~~~i~~~  182 (470)
                      |+|+.|.+++|+...++..++.|-+.
T Consensus       519 RAGRaGrsVtlvgE~dRkllK~iik~  544 (691)
T KOG0338|consen  519 RAGRAGRSVTLVGESDRKLLKEIIKS  544 (691)
T ss_pred             hcccCcceEEEeccccHHHHHHHHhh
Confidence            99999999999999999999988766

>PTZ00110 helicase; Provisional

Probab=99.97  E-value=4.9e-30  Score=271.28  Aligned_cols=184  Identities=34%  Similarity=0.545  Sum_probs=161.1

Q ss_pred             CEEeecCCHHHHHHHHHHcC-CCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHc-CCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLD-NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~-~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~-~~~~~lVF~~t~~~~   78 (470)
                      |+||||+|++++.+++.++. +|..+.+... .......+++.++.+....|...|..++.... ...++||||+|++.|
T Consensus       312 l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~-~l~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a  390 (545)
T PTZ00110        312 LMWSATWPKEVQSLARDLCKEEPVHVNVGSL-DLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGA  390 (545)
T ss_pred             EEEEeCCCHHHHHHHHHHhccCCEEEEECCC-ccccCCCeeEEEEEEechhHHHHHHHHHHHhcccCCeEEEEecChHHH
Confidence            58999999999999999886 5777765322 22344667777777777788888888887654 567999999999999


Q ss_pred             HHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           79 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +.|++.|.. ++.+..+||+|++++|+.+++.|++++++||||||++++|||||+|++|||||+|.++++|+||+|||||
T Consensus       391 ~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR  470 (545)
T PTZ00110        391 DFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGR  470 (545)
T ss_pred             HHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhccccc
Confidence            999999984 7899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHHHHhCC
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLERDVGC  185 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~~~~~~  185 (470)
                      +|+.|.+++|+++.+...++.|.+.+..
T Consensus       471 ~G~~G~ai~~~~~~~~~~~~~l~~~l~~  498 (545)
T PTZ00110        471 AGAKGASYTFLTPDKYRLARDLVKVLRE  498 (545)
T ss_pred             CCCCceEEEEECcchHHHHHHHHHHHHH
Confidence            9999999999999888777777666543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=6.1e-30  Score=271.56  Aligned_cols=185  Identities=34%  Similarity=0.513  Sum_probs=164.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||++..+..++..++.+|..+.+..  .......+.++++.+...+|..+|..++... ...++||||+|++.++.
T Consensus       196 ll~SATl~~~v~~l~~~~l~~p~~i~v~~--~~~~~~~i~q~~~~~~~~~k~~~L~~ll~~~-~~~k~LVF~nt~~~ae~  272 (572)
T PRK04537        196 LLFSATLSHRVLELAYEHMNEPEKLVVET--ETITAARVRQRIYFPADEEKQTLLLGLLSRS-EGARTMVFVNTKAFVER  272 (572)
T ss_pred             EEEeCCccHHHHHHHHHHhcCCcEEEecc--ccccccceeEEEEecCHHHHHHHHHHHHhcc-cCCcEEEEeCCHHHHHH
Confidence            58999999999999999999987775532  2234556777777777778888887777653 56799999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      |++.|.+ ++.+..||++|++.+|+++++.|++++++||||||++++|||+|+|++|||||+|.++++|+||+||+||.|
T Consensus       273 l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G  352 (572)
T PRK04537        273 VARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLG  352 (572)
T ss_pred             HHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCC
Confidence            9999985 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCcc
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFE  188 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~  188 (470)
                      +.|.+++|+.+.+...+..|++.+..+++
T Consensus       353 ~~G~ai~~~~~~~~~~l~~i~~~~~~~~~  381 (572)
T PRK04537        353 EEGDAISFACERYAMSLPDIEAYIEQKIP  381 (572)
T ss_pred             CCceEEEEecHHHHHHHHHHHHHHcCCCC
Confidence            99999999999988888888888776654

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

Probab=99.97  E-value=1.1e-29  Score=243.42  Aligned_cols=187  Identities=34%  Similarity=0.608  Sum_probs=174.5

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      +|||||+|.|+..+.++|+.+|..|.+.  .+..+.+.++++|+.+..+.|+..|.++.+   .-.+.+|||||++.++.
T Consensus       204 ~l~SAT~p~~vl~vt~~f~~~pv~i~vk--k~~ltl~gikq~~i~v~k~~k~~~l~dl~~---~~~q~~if~nt~r~v~~  278 (397)
T KOG0327|consen  204 VLLSATMPSDVLEVTKKFMREPVRILVK--KDELTLEGIKQFYINVEKEEKLDTLCDLYR---RVTQAVIFCNTRRKVDN  278 (397)
T ss_pred             eeecccCcHHHHHHHHHhccCceEEEec--chhhhhhheeeeeeeccccccccHHHHHHH---hhhcceEEecchhhHHH
Confidence            5899999999999999999999999875  344668899999999988889999888887   34789999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      |...|.. .+.+.++|++|.+.+|..+++.|+.|..+|||+|+.++||||+.++++||||++|...++|+||+||+||.|
T Consensus       279 l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~g  358 (397)
T KOG0327|consen  279 LTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFG  358 (397)
T ss_pred             HHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccC
Confidence            9999974 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCccccCC
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  192 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~  192 (470)
                      ++|.++.+++..+...++++++++...++.++.
T Consensus       359 rkg~~in~v~~~d~~~lk~ie~~y~~~i~e~p~  391 (397)
T KOG0327|consen  359 RKGVAINFVTEEDVRDLKDIEKFYNTPIEELPS  391 (397)
T ss_pred             CCceeeeeehHhhHHHHHhHHHhcCCcceeccc
Confidence            999999999999999999999999998887654

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

Probab=99.96  E-value=2.1e-29  Score=251.30  Aligned_cols=179  Identities=41%  Similarity=0.651  Sum_probs=156.3

Q ss_pred             CEEeecCCHHHHHHHHHHcCC-CcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHc---CCC-----eEEEE
Q 012133            1 MLFSATMPSWVKKLSRKYLDN-PLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYA---KGG-----KTIVF   71 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~-p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~---~~~-----~~lVF   71 (470)
                      +|||||.|+++..++..|+.+ ...+.+.  ..-....++.+..+.+...+|...|.++|....   ...     +++||
T Consensus       266 ~mFSAtfp~~iq~l~~~fl~~~yi~laV~--rvg~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvF  343 (482)
T KOG0335|consen  266 LLFSATFPKEIQRLAADFLKDNYIFLAVG--RVGSTSENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVF  343 (482)
T ss_pred             EEEeccCChhhhhhHHHHhhccceEEEEe--eeccccccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEE
Confidence            589999999999999999986 5555543  334557888888888988888888888886443   233     89999


Q ss_pred             eCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHH
Q 012133           72 TQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH  150 (470)
Q Consensus        72 ~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~q  150 (470)
                      |.|++.|.+|+..|.. .+++..+|++.+|.+|.++++.|+++++.|||||+|++||||||+|+||||||+|.+..+|+|
T Consensus       344 vEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvH  423 (482)
T KOG0335|consen  344 VETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVH  423 (482)
T ss_pred             eeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHH
Confidence            9999999999999985 899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcccCCCCCCCeEEEeeChhhHHHHHHHHH
Q 012133          151 RSGRTGRAGKEGTAILMFTSSQRRTVRSLER  181 (470)
Q Consensus       151 r~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~  181 (470)
                      |+|||||+|..|.++.|+........+.|.+
T Consensus       424 RIGRTGR~Gn~G~atsf~n~~~~~i~~~L~~  454 (482)
T KOG0335|consen  424 RIGRTGRVGNGGRATSFFNEKNQNIAKALVE  454 (482)
T ss_pred             hccccccCCCCceeEEEeccccchhHHHHHH
Confidence            9999999999999999999655444444433

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

Probab=99.96  E-value=6.8e-29  Score=261.71  Aligned_cols=183  Identities=27%  Similarity=0.435  Sum_probs=160.4

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHc-CCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~-~~~~~lVF~~t~~~~~   79 (470)
                      |+||||+|++++.+++.++.++..|.+..  .......+.+..+.+....|...|.+++.... ...++||||+++..++
T Consensus       304 l~~SATl~~~v~~l~~~~~~~~~~i~~~~--~~~~~~~v~q~~~~~~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~  381 (518)
T PLN00206        304 LLFSATVSPEVEKFASSLAKDIILISIGN--PNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGAD  381 (518)
T ss_pred             EEEEeeCCHHHHHHHHHhCCCCEEEEeCC--CCCCCcceeEEEEeccchhHHHHHHHHHHhhcccCCCEEEEcCCchhHH
Confidence            58999999999999999999998887643  23345567777777877778777777776542 2368999999999999


Q ss_pred             HHHHHHhc--CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           80 EVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        80 ~l~~~l~~--~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      .|++.|..  .+.+..+||+|++++|..+++.|++|+++|||||+++++|||+|+|++|||||+|.++++|+||+|||||
T Consensus       382 ~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR  461 (518)
T PLN00206        382 LLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASR  461 (518)
T ss_pred             HHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhcccccc
Confidence            99999973  6889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHHHHhCC
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLERDVGC  185 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~~~~~~  185 (470)
                      .|+.|.+++|+++.+...+..|.+.+..
T Consensus       462 ~g~~G~ai~f~~~~~~~~~~~l~~~l~~  489 (518)
T PLN00206        462 MGEKGTAIVFVNEEDRNLFPELVALLKS  489 (518)
T ss_pred             CCCCeEEEEEEchhHHHHHHHHHHHHHH
Confidence            9999999999999888777777766543

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

Probab=99.96  E-value=4e-30  Score=245.32  Aligned_cols=168  Identities=32%  Similarity=0.554  Sum_probs=140.7

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ||||||||..|+.+++.-+-.|+.|++-. . -..+-++.+..-.+..+.|+-.|..+|..  ...++||||..+.+++.
T Consensus       361 LLFSATMP~KIQ~FAkSALVKPvtvNVGR-A-GAAsldViQevEyVkqEaKiVylLeCLQK--T~PpVLIFaEkK~DVD~  436 (610)
T KOG0341|consen  361 LLFSATMPKKIQNFAKSALVKPVTVNVGR-A-GAASLDVIQEVEYVKQEAKIVYLLECLQK--TSPPVLIFAEKKADVDD  436 (610)
T ss_pred             eeeeccccHHHHHHHHhhcccceEEeccc-c-cccchhHHHHHHHHHhhhhhhhHHHHhcc--CCCceEEEeccccChHH
Confidence            69999999999999999999999998742 1 12222222222223344555444444432  35799999999999999


Q ss_pred             HHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +.++|- +++.+..+||+-+|++|...++.|+.|+-+|||||||++.|+|+|++.||||||+|.++++|+||+|||||.|
T Consensus       437 IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg  516 (610)
T KOG0341|consen  437 IHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSG  516 (610)
T ss_pred             HHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCCC
Confidence            999987 7899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhh
Q 012133          160 KEGTAILMFTSSQ  172 (470)
Q Consensus       160 ~~g~~i~l~~~~~  172 (470)
                      ++|.+.+|+....
T Consensus       517 ~~GiATTfINK~~  529 (610)
T KOG0341|consen  517 KTGIATTFINKNQ  529 (610)
T ss_pred             Ccceeeeeecccc
Confidence            9999999988743

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.96  E-value=1.9e-28  Score=254.00  Aligned_cols=185  Identities=30%  Similarity=0.535  Sum_probs=161.7

Q ss_pred             CEEeecCCH-HHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCc-ccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPS-WVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~-~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |+||||++. .+..+++.++.+|..+.+...  ......+.++++.+.. ..|.++|..+++.. ...++||||++++.+
T Consensus       182 ~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~--~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~-~~~~~lVF~~s~~~~  258 (434)
T PRK11192        182 LLFSATLEGDAVQDFAERLLNDPVEVEAEPS--RRERKKIHQWYYRADDLEHKTALLCHLLKQP-EVTRSIVFVRTRERV  258 (434)
T ss_pred             EEEEeecCHHHHHHHHHHHccCCEEEEecCC--cccccCceEEEEEeCCHHHHHHHHHHHHhcC-CCCeEEEEeCChHHH
Confidence            589999985 588899999999988876432  3334567777766653 57888888887643 457999999999999


Q ss_pred             HHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           79 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +.+++.|.. ++.+..+||+|++.+|..+++.|++|+++||||||++++|||+|+|++|||||+|.+.+.|+||+|||||
T Consensus       259 ~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR  338 (434)
T PRK11192        259 HELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGR  338 (434)
T ss_pred             HHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhccccccc
Confidence            999999985 7899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHHHHhCCCcc
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLERDVGCKFE  188 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~  188 (470)
                      +|..|.+++|++..+...+..+++++...+.
T Consensus       339 ~g~~g~ai~l~~~~d~~~~~~i~~~~~~~~~  369 (434)
T PRK11192        339 AGRKGTAISLVEAHDHLLLGKIERYIEEPLK  369 (434)
T ss_pred             CCCCceEEEEecHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999999999887765543

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=3.3e-28  Score=254.68  Aligned_cols=185  Identities=33%  Similarity=0.570  Sum_probs=165.2

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||++..+.++++.++.+|..+.+...  ......+.++.+.+...+|..+|..++... ...++||||++++.++.
T Consensus       274 i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~--~~~~~~~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~IVF~~s~~~~~~  350 (475)
T PRK01297        274 LLFSATFTDDVMNLAKQWTTDPAIVEIEPE--NVASDTVEQHVYAVAGSDKYKLLYNLVTQN-PWERVMVFANRKDEVRR  350 (475)
T ss_pred             EEEEeecCHHHHHHHHHhccCCEEEEeccC--cCCCCcccEEEEEecchhHHHHHHHHHHhc-CCCeEEEEeCCHHHHHH
Confidence            579999999999999999999988876432  333455666667777778888888887653 45799999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +++.|.+ ++.+..+||+|++++|.++++.|++|+++|||||+++++|||||+|++||+|++|.+..+|+||+||+||.|
T Consensus       351 l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g  430 (475)
T PRK01297        351 IEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAG  430 (475)
T ss_pred             HHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCC
Confidence            9999985 788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCcc
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFE  188 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~  188 (470)
                      +.|.+++|+...+...+..+++.++.+++
T Consensus       431 ~~g~~i~~~~~~d~~~~~~~~~~~~~~~~  459 (475)
T PRK01297        431 ASGVSISFAGEDDAFQLPEIEELLGRKIS  459 (475)
T ss_pred             CCceEEEEecHHHHHHHHHHHHHhCCCCc
Confidence            99999999999998999999999887764

>PTZ00424 helicase 45; Provisional

Probab=99.96  E-value=1.1e-27  Score=245.91  Aligned_cols=190  Identities=33%  Similarity=0.582  Sum_probs=164.7

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCc-ccHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      |+||||+|.++..+...|+.+|..+.+..  .......+.++++.+.. ..+...+..++... ...++||||+|++.++
T Consensus       205 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~ivF~~t~~~~~  281 (401)
T PTZ00424        205 ALFSATMPNEILELTTKFMRDPKRILVKK--DELTLEGIRQFYVAVEKEEWKFDTLCDLYETL-TITQAIIYCNTRRKVD  281 (401)
T ss_pred             EEEEecCCHHHHHHHHHHcCCCEEEEeCC--CCcccCCceEEEEecChHHHHHHHHHHHHHhc-CCCeEEEEecCcHHHH
Confidence            57999999999999999999988776532  22334567777776654 34566666666544 4578999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .+++.|.. .+.+..+||+|++++|..++++|++|+++|||||+++++|||+|++++||+|++|.+..+|+||+||+||.
T Consensus       282 ~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~  361 (401)
T PTZ00424        282 YLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRF  361 (401)
T ss_pred             HHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccC
Confidence            99999985 68899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCC
Q 012133          159 GKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      |+.|.|++|+++.+...++.+++.+...++..++.
T Consensus       362 g~~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~~~  396 (401)
T PTZ00424        362 GRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPME  396 (401)
T ss_pred             CCCceEEEEEcHHHHHHHHHHHHHHCCcccccCcc
Confidence            99999999999999999999999998877765443

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.95  E-value=1.6e-27  Score=231.02  Aligned_cols=182  Identities=25%  Similarity=0.459  Sum_probs=164.6

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      +|||||+.+.|..+.+.++++|+.+.+...+ -..+..+.||++.|..++|..+|..+++..--.+++|||+||.+.|..
T Consensus       205 ~LmSATl~dDv~~LKkL~l~nPviLkl~e~e-l~~~dqL~Qy~v~cse~DKflllyallKL~LI~gKsliFVNtIdr~Yr  283 (569)
T KOG0346|consen  205 FLMSATLSDDVQALKKLFLHNPVILKLTEGE-LPNPDQLTQYQVKCSEEDKFLLLYALLKLRLIRGKSLIFVNTIDRCYR  283 (569)
T ss_pred             eeehhhhhhHHHHHHHHhccCCeEEEecccc-CCCcccceEEEEEeccchhHHHHHHHHHHHHhcCceEEEEechhhhHH
Confidence            5899999999999999999999999886443 335688999999999999999999888765567999999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----------------------------------cc
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----------------------------------VA  124 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----------------------------------v~  124 (470)
                      |.-.|+. +++..+|.+.||..-|..++++|..|.++||||||                                   -+
T Consensus       284 LkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GV  363 (569)
T KOG0346|consen  284 LKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGV  363 (569)
T ss_pred             HHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCccccccccCchhch
Confidence            9999986 79999999999999999999999999999999999                                   24


Q ss_pred             cccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHh
Q 012133          125 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  183 (470)
Q Consensus       125 ~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~  183 (470)
                      +||||+.+|..|||+|+|.++.+||||+|||+|++++|.++.|+.+.+..-...|++.+
T Consensus       364 sRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~~~  422 (569)
T KOG0346|consen  364 SRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLESIL  422 (569)
T ss_pred             hccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHhhhhHHHHHH
Confidence            69999999999999999999999999999999999999999999999887555555544

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.95  E-value=1.8e-28  Score=243.32  Aligned_cols=183  Identities=34%  Similarity=0.520  Sum_probs=152.8

Q ss_pred             CCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCC
Q 012133           20 DNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDI   98 (470)
Q Consensus        20 ~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~   98 (470)
                      .+|..|++.  ....+...+..-.+.|+..+|.-.|..+|..|  ++++|||||+.+.+..|+-+|.. .+...+||+.|
T Consensus       422 ~kpkiiD~t--~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~ry--PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M  497 (731)
T KOG0347|consen  422 GKPKIIDLT--PQSATASTLTESLIECPPLEKDLYLYYFLTRY--PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASM  497 (731)
T ss_pred             CCCeeEecC--cchhHHHHHHHHhhcCCccccceeEEEEEeec--CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHH
Confidence            467778775  33445555655666676666665555666554  68999999999999999999986 78999999999


Q ss_pred             CHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHH
Q 012133           99 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS  178 (470)
Q Consensus        99 ~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~  178 (470)
                      .|++|.+.+++|++....||||||||+||||||.|+|||||.+|.+.+.|+||+|||+|++..|..++|+.|.+...+++
T Consensus       498 ~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~K  577 (731)
T KOG0347|consen  498 IQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKK  577 (731)
T ss_pred             HHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCccccCCCCHHHHHHHHHHHH
Q 012133          179 LERDVGCKFEFVSPPVVEDVLESSAEQV  206 (470)
Q Consensus       179 i~~~~~~~~~~~~~p~~~~~~~~~~~~~  206 (470)
                      |.+.+..+...-..|....++....+++
T Consensus       578 L~ktL~k~~dlpifPv~~~~m~~lkeRv  605 (731)
T KOG0347|consen  578 LCKTLKKKEDLPIFPVETDIMDALKERV  605 (731)
T ss_pred             HHHHHhhccCCCceeccHHHHHHHHHHH
Confidence            9888876655444555555555554444

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

Probab=99.95  E-value=3.9e-27  Score=233.13  Aligned_cols=184  Identities=29%  Similarity=0.445  Sum_probs=156.8

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeeccc-----------------------ccccccceEEEEEEcCcccHHHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQ-----------------------DEKLAEGIKLYAISTTATSKRTILSD   57 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~-----------------------~~~~~~~i~~~~~~~~~~~k~~~l~~   57 (470)
                      ||+||||.+-|.+|+.--|+||+.|.+....                       .-.++..+.+.|+.+|..-++-.|..
T Consensus       335 mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa  414 (708)
T KOG0348|consen  335 MLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAA  414 (708)
T ss_pred             HhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHH
Confidence            5899999999999999999999999821100                       02234566788999998888777777


Q ss_pred             HHHHH---cCCCeEEEEeCchHHHHHHHHHHhcC-----------------------CcEEEEeCCCCHHHHHHHHcccc
Q 012133           58 LITVY---AKGGKTIVFTQTKRDADEVSLALTSI-----------------------IASEALHGDISQHQRERTLNGFR  111 (470)
Q Consensus        58 ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~~-----------------------~~~~~lhg~~~~~~R~~~~~~f~  111 (470)
                      +|...   .+..++|||+.+.+.++.-+..|...                       ..+.-|||.|+|++|..+++.|+
T Consensus       415 ~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs  494 (708)
T KOG0348|consen  415 LLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFS  494 (708)
T ss_pred             HHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhc
Confidence            76433   24468999999999999888777531                       35788999999999999999999


Q ss_pred             cCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhC
Q 012133          112 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  184 (470)
Q Consensus       112 ~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~  184 (470)
                      .....||+||||++||||+|+|.+||+||+|.++++|+||+|||+|+|..|.+++|+.|.|.++++.|+.+..
T Consensus       495 ~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~Eaey~~~l~~~~~  567 (708)
T KOG0348|consen  495 HSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSEAEYVNYLKKHHI  567 (708)
T ss_pred             cccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEEecccHHHHHHHHHhhcc
Confidence            9888999999999999999999999999999999999999999999999999999999999998888877653

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

Probab=99.95  E-value=2e-26  Score=250.84  Aligned_cols=213  Identities=19%  Similarity=0.271  Sum_probs=158.3

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcC----------------cccHHHHHHHHHHHHcC
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTT----------------ATSKRTILSDLITVYAK   64 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~----------------~~~k~~~l~~ll~~~~~   64 (470)
                      |+||||+++..+ ++++++..|..+ +..  +........+..+..+                ...+..+|..+++   .
T Consensus       198 i~~SATi~n~~~-~~~~l~g~~~~~-i~~--~~~~~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~l~~l~~---~  270 (742)
T TIGR03817       198 VLASATTADPAA-AASRLIGAPVVA-VTE--DGSPRGARTVALWEPPLTELTGENGAPVRRSASAEAADLLADLVA---E  270 (742)
T ss_pred             EEEecCCCCHHH-HHHHHcCCCeEE-ECC--CCCCcCceEEEEecCCccccccccccccccchHHHHHHHHHHHHH---C
Confidence            589999998865 677788877544 221  1111222222222221                1123444444443   4


Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc---------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccE
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS---------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  135 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~---------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~  135 (470)
                      ..++||||+|++.++.++..|.+         ...+..+||+|++++|.+++++|++|++++|||||++++|||||+|++
T Consensus       271 ~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd~lerGIDI~~vd~  350 (742)
T TIGR03817       271 GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDA  350 (742)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECchHhccCCcccccE
Confidence            57999999999999999998764         256889999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCChhHHHHHhcccCCCCCCCeEEEeeC--hhhHHHHHHHHHHhCCCcccc-CCCCHHHHHHHHHHHHHHHHcc
Q 012133          136 IIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT--SSQRRTVRSLERDVGCKFEFV-SPPVVEDVLESSAEQVVATLNG  212 (470)
Q Consensus       136 VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~--~~~~~~~~~i~~~~~~~~~~~-~~p~~~~~~~~~~~~~~~~l~~  212 (470)
                      ||||++|.+.++|+||+|||||.|+.|.++++..  +.+...+..+++.++..++.. ..|..+.++...+..+...+ .
T Consensus       351 VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~~~e~~~~~~~n~~il~~hl~~aa~e~-~  429 (742)
T TIGR03817       351 VVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDRPVEATVFDPDNPYVLGPHLCCAAAEL-P  429 (742)
T ss_pred             EEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcCCCccceeCCCcHHHHHHHHHHHHhcC-C
Confidence            9999999999999999999999999999999986  456677788888888777653 33556667776665555433 3


Q ss_pred             cCccchhhh
Q 012133          213 VHPESVEFF  221 (470)
Q Consensus       213 ~~~~~~~~~  221 (470)
                      +..++.+.|
T Consensus       430 l~~~~~~~~  438 (742)
T TIGR03817       430 LTEADLELF  438 (742)
T ss_pred             CChHHHHhh
Confidence            333334444

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.

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

Probab=99.95  E-value=5.5e-27  Score=230.60  Aligned_cols=177  Identities=34%  Similarity=0.536  Sum_probs=152.7

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEc-CcccHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAIST-TATSKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~-~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      ||||||++..|+.+++.+|.+|+.|....  -......|.+....+ ....|+..|..-|......+++|||+.-+..++
T Consensus       405 llFsaTf~~kIe~lard~L~dpVrvVqg~--vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e  482 (731)
T KOG0339|consen  405 LLFSATFKKKIEKLARDILSDPVRVVQGE--VGEANEDITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKADAE  482 (731)
T ss_pred             EEeeccchHHHHHHHHHHhcCCeeEEEee--hhccccchhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccCCHH
Confidence            69999999999999999999999875432  222344555544444 445778777776666667799999999999999


Q ss_pred             HHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      +|+..|. +.+.|..+||+|.|.+|.++|.+|+.....|||+||+++||+|||++..|||||+-.+++.|.||+|||||+
T Consensus       483 ~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRa  562 (731)
T KOG0339|consen  483 EIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRA  562 (731)
T ss_pred             HHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccc
Confidence            9999998 689999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHH
Q 012133          159 GKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i  179 (470)
                      |..|++++|+++.+..+.-.|
T Consensus       563 g~kGvayTlvTeKDa~fAG~L  583 (731)
T KOG0339|consen  563 GEKGVAYTLVTEKDAEFAGHL  583 (731)
T ss_pred             cccceeeEEechhhHHHhhHH
Confidence            999999999999886544333

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.94  E-value=5.4e-26  Score=242.29  Aligned_cols=216  Identities=17%  Similarity=0.268  Sum_probs=161.1

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCc----------ccHHHHHHHHHHHH-cCCCeEE
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA----------TSKRTILSDLITVY-AKGGKTI   69 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~----------~~k~~~l~~ll~~~-~~~~~~l   69 (470)
                      ||||||+|++++.+ +.|+.+|..|.+.+    .+...|+++|+....          ..+..++..+.+.. ...+++|
T Consensus       325 ILmSATl~~dv~~l-~~~~~~p~~I~I~g----rt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~~~~g~iL  399 (675)
T PHA02653        325 FLMTATLEDDRDRI-KEFFPNPAFVHIPG----GTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTPPKGSSGI  399 (675)
T ss_pred             EEEccCCcHhHHHH-HHHhcCCcEEEeCC----CcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhcccCCcEE
Confidence            68999999998877 57899999888742    234567788775431          12333333333222 2346899


Q ss_pred             EEeCchHHHHHHHHHHhc---CCcEEEEeCCCCHHHHHHHHccc-ccCCeeEEEecccccccCCCCCccEEEEec---CC
Q 012133           70 VFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGF-RQGKFTVLVATDVAARGLDIPNVDLIIHYE---LP  142 (470)
Q Consensus        70 VF~~t~~~~~~l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f-~~g~~~iLVaTdv~~~Gidip~v~~VI~~~---~p  142 (470)
                      ||++++.+++.+++.|.+   .+.+.+|||+|++.  ++++++| ++++.+||||||+|++|||||+|++||+++   .|
T Consensus       400 VFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p  477 (675)
T PHA02653        400 VFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDTGRVYVP  477 (675)
T ss_pred             EEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEECCCccCC
Confidence            999999999999999985   47899999999985  4667777 689999999999999999999999999998   56


Q ss_pred             C---------ChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHHccc
Q 012133          143 N---------DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGV  213 (470)
Q Consensus       143 ~---------~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~~  213 (470)
                      .         |.++|+||+|||||. ++|.|+.|+++.+..                  | ..++....+..++..++..
T Consensus       478 ~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~~------------------p-I~ri~~~~L~~~vL~lk~~  537 (675)
T PHA02653        478 EPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLLK------------------P-IKRIDSEFLHNYILYAKYF  537 (675)
T ss_pred             CcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHhH------------------H-HHHHhHHHHHHHHHHHHHc
Confidence            4         888999999999999 899999999987631                  1 2233333345555555555


Q ss_pred             CccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCC
Q 012133          214 HPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSR  249 (470)
Q Consensus       214 ~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~  249 (470)
                      .....+.+      +++.++++.+.+|+..|..+..
T Consensus       538 g~~~~~~~------~ldpP~~~~l~~A~~~L~~lga  567 (675)
T PHA02653        538 NLTLPEDL------FVIPSNLDRLRKTEEYIDSFNI  567 (675)
T ss_pred             CCCCcccc------cCCCCCHHHHHHHHHHHHHcCC
Confidence            44333222      6778888999998888876654

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.94  E-value=1.6e-26  Score=251.74  Aligned_cols=238  Identities=18%  Similarity=0.264  Sum_probs=178.4

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHH-----HHHHHHHHHHcCCCeEEEEeCch
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKR-----TILSDLITVYAKGGKTIVFTQTK   75 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~-----~~l~~ll~~~~~~~~~lVF~~t~   75 (470)
                      |+||||++...   ...|+.++..|.+.+.     ...++++|+.....++.     ..+..+++.  ..+++|||++++
T Consensus       150 IlmSATl~~~~---l~~~l~~~~vI~~~gr-----~~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~--~~g~iLVFlpg~  219 (819)
T TIGR01970       150 LAMSATLDGER---LSSLLPDAPVVESEGR-----SFPVEIRYLPLRGDQRLEDAVSRAVEHALAS--ETGSILVFLPGQ  219 (819)
T ss_pred             EEEeCCCCHHH---HHHHcCCCcEEEecCc-----ceeeeeEEeecchhhhHHHHHHHHHHHHHHh--cCCcEEEEECCH
Confidence            68999999764   4568877777765432     23467778776554442     223333322  358999999999


Q ss_pred             HHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC--------
Q 012133           76 RDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN--------  143 (470)
Q Consensus        76 ~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~--------  143 (470)
                      .+++.+++.|.+    .+.+.+|||+|++++|.++++.|++|+.+||||||++++|||||+|++|||+++|.        
T Consensus       220 ~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~  299 (819)
T TIGR01970       220 AEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKT  299 (819)
T ss_pred             HHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCccccccccccc
Confidence            999999999975    57899999999999999999999999999999999999999999999999999885        


Q ss_pred             ----------ChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHHccc
Q 012133          144 ----------DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGV  213 (470)
Q Consensus       144 ----------~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~~  213 (470)
                                |..+|+||+||+||. ++|.||.|++..+...+   ..+           ..+||....+..++..+...
T Consensus       300 g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~~~l---~~~-----------~~PEI~r~~L~~~~L~l~~~  364 (819)
T TIGR01970       300 GITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQHQRL---PAQ-----------DEPEILQADLSGLALELAQW  364 (819)
T ss_pred             CCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHHHhh---hcC-----------CCcceeccCcHHHHHHHHHc
Confidence                      234689999999999 89999999998764332   211           23455555666666666665


Q ss_pred             CccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCcccccCCCCeEEEEE
Q 012133          214 HPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL  268 (470)
Q Consensus       214 ~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r~l~~~~~~~~~~~~  268 (470)
                      ...+...|     .+++.++.+.+.+|+..|..+.+......++.....|..+++
T Consensus       365 g~~~~~~~-----~~l~~P~~~~i~~a~~~L~~lgald~~~~lT~~G~~~~~lp~  414 (819)
T TIGR01970       365 GAKDPSDL-----RWLDAPPSVALAAARQLLQRLGALDAQGRLTAHGKAMAALGC  414 (819)
T ss_pred             CCCChhhC-----CCCCCcCHHHHHHHHHHHHHCCCCCCCCCcCHHHHHHHhcCC
Confidence            54444444     567788889999999988877776655566665555555544

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.

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

Probab=99.94  E-value=2.2e-26  Score=231.34  Aligned_cols=180  Identities=31%  Similarity=0.486  Sum_probs=158.3

Q ss_pred             EEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcC-cccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            2 LFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTT-ATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         2 lfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      +||||+|..|+++++..+.++..|.+-.  .+.....|+|..+.+. ...|+.++.+++..- -..++|||+.+.+.|.+
T Consensus       326 ~FSat~~~~VEE~~~~i~~~~~~vivg~--~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~  402 (593)
T KOG0344|consen  326 LFSATISVYVEEWAELIKSDLKRVIVGL--RNSANETVDQELVFCGSEKGKLLALRQLVASG-FKPPVLIFVQSKERAKQ  402 (593)
T ss_pred             hhhccccHHHHHHHHHhhccceeEEEec--chhHhhhhhhhheeeecchhHHHHHHHHHhcc-CCCCeEEEEecHHHHHH
Confidence            6999999999999999999998886642  2233556666655554 457888888888664 45799999999999999


Q ss_pred             HHHHHh--cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           81 VSLALT--SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        81 l~~~l~--~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      |.+.|.  ..+.+.++||..++.+|++++++||.|+++|||||++++||||+.+|++|||||+|.+..+|+||+||+||+
T Consensus       403 L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRa  482 (593)
T KOG0344|consen  403 LFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRA  482 (593)
T ss_pred             HHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCC
Confidence            999994  478999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHHHhC
Q 012133          159 GKEGTAILMFTSSQRRTVRSLERDVG  184 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~~~~  184 (470)
                      |+.|.+|+||+.++..+++.+++...
T Consensus       483 g~~g~Aitfytd~d~~~ir~iae~~~  508 (593)
T KOG0344|consen  483 GRSGKAITFYTDQDMPRIRSIAEVME  508 (593)
T ss_pred             CCCcceEEEeccccchhhhhHHHHHH
Confidence            99999999999999888888876653

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.94  E-value=2.8e-26  Score=250.37  Aligned_cols=238  Identities=18%  Similarity=0.239  Sum_probs=181.9

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHH-----HHHHHHHHHcCCCeEEEEeCch
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-----ILSDLITVYAKGGKTIVFTQTK   75 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-----~l~~ll~~~~~~~~~lVF~~t~   75 (470)
                      |+||||++.+.   ...|+.++..|.+.+.     ...++++|+..+..++.+     .|..+++  ...+++|||++++
T Consensus       153 ilmSATl~~~~---l~~~~~~~~~I~~~gr-----~~pV~~~y~~~~~~~~~~~~v~~~l~~~l~--~~~g~iLVFlpg~  222 (812)
T PRK11664        153 LIMSATLDNDR---LQQLLPDAPVIVSEGR-----SFPVERRYQPLPAHQRFDEAVARATAELLR--QESGSLLLFLPGV  222 (812)
T ss_pred             EEEecCCCHHH---HHHhcCCCCEEEecCc-----cccceEEeccCchhhhHHHHHHHHHHHHHH--hCCCCEEEEcCCH
Confidence            68999999752   3568877777765432     234777887766555543     2333332  2358999999999


Q ss_pred             HHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC--------
Q 012133           76 RDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN--------  143 (470)
Q Consensus        76 ~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~--------  143 (470)
                      .+++.+++.|.+    .+.+.++||+|++++|.++++.|++|+.+||||||++++|||||+|++|||+++|.        
T Consensus       223 ~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~  302 (812)
T PRK11664        223 GEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKT  302 (812)
T ss_pred             HHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccC
Confidence            999999999984    57799999999999999999999999999999999999999999999999988764        


Q ss_pred             ----------ChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHHccc
Q 012133          144 ----------DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGV  213 (470)
Q Consensus       144 ----------~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~~  213 (470)
                                |..+|+||+||+||. .+|.||.|+++.+...              +..-..+||+...+..++..+...
T Consensus       303 g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~~~--------------l~~~~~PEI~r~dL~~~~L~l~~~  367 (812)
T PRK11664        303 GLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQAER--------------AAAQSEPEILHSDLSGLLLELLQW  367 (812)
T ss_pred             CcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHHHHhh--------------CccCCCCceeccchHHHHHHHHHc
Confidence                      346899999999999 7999999999876422              122334577777888888877776


Q ss_pred             CccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCcccccCCCCeEEEEE
Q 012133          214 HPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL  268 (470)
Q Consensus       214 ~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r~l~~~~~~~~~~~~  268 (470)
                      ...++..|     .+++.++++.+.+|+..|..+.+......++..+..|..+++
T Consensus       368 g~~~~~~~-----~~ld~P~~~~~~~A~~~L~~lgald~~g~lT~~G~~m~~lp~  417 (812)
T PRK11664        368 GCHDPAQL-----SWLDQPPAAALAAAKRLLQQLGALDGQGRLTARGRKMAALGN  417 (812)
T ss_pred             CCCCHHhC-----CCCCCCCHHHHHHHHHHHHHCCCCCCCCCcCHHHHHHHhcCC
Confidence            54444444     577888889999999998877776655566655555555443

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.94  E-value=4.2e-25  Score=230.68  Aligned_cols=175  Identities=25%  Similarity=0.395  Sum_probs=140.3

Q ss_pred             CEEeecCCHHHHHHHHHHc--CCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYL--DNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l--~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |+||||+++.+...+...+  .+|..+.....     ..++. +.+........+.+..++....+..++||||+|++.+
T Consensus       166 l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~~-----r~nl~-~~v~~~~~~~~~~l~~~l~~~~~~~~~IIF~~s~~~~  239 (470)
T TIGR00614       166 MALTATASPSVREDILRQLNLKNPQIFCTSFD-----RPNLY-YEVRRKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKS  239 (470)
T ss_pred             EEEecCCCHHHHHHHHHHcCCCCCcEEeCCCC-----CCCcE-EEEEeCCccHHHHHHHHHHHhcCCCceEEEECcHHHH
Confidence            5799999998876555554  35555433211     12332 2222222234444555554333556779999999999


Q ss_pred             HHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           79 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +.+++.|.. ++.+..+|++|++++|.++++.|++++++|||||+++++|||+|+|++||+|++|.+++.|+||+||+||
T Consensus       240 e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR  319 (470)
T TIGR00614       240 EQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGR  319 (470)
T ss_pred             HHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHHhhhcCcCC
Confidence            999999985 7899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHHH
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLER  181 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~~  181 (470)
                      .|.++.|++|+++.+...++.+..
T Consensus       320 ~G~~~~~~~~~~~~d~~~~~~~~~  343 (470)
T TIGR00614       320 DGLPSECHLFYAPADINRLRRLLM  343 (470)
T ss_pred             CCCCceEEEEechhHHHHHHHHHh
Confidence            999999999999988877777654

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

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

Probab=99.93  E-value=5.9e-25  Score=239.34  Aligned_cols=176  Identities=19%  Similarity=0.251  Sum_probs=138.9

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcc-cHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT-SKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      |+||||+++.+++.+...+.-...+.+...   ....++.  |..++.. .....|..++.......+.||||+|++.++
T Consensus       620 lALTATAT~~V~eDI~~~L~l~~~~vfr~S---f~RpNL~--y~Vv~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~E  694 (1195)
T PLN03137        620 LALTATATASVKEDVVQALGLVNCVVFRQS---FNRPNLW--YSVVPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCE  694 (1195)
T ss_pred             EEEEecCCHHHHHHHHHHcCCCCcEEeecc---cCccceE--EEEeccchhHHHHHHHHHHhcccCCCceeEeCchhHHH
Confidence            579999999988866655542222212111   1123332  2222222 223445555544334568999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .+++.|.. ++.+.++|++|++++|..++++|++++++|||||+++++|||+|+|++||||++|.+++.|+||+|||||.
T Consensus       695 ~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRD  774 (1195)
T PLN03137        695 KVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRD  774 (1195)
T ss_pred             HHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCC
Confidence            99999985 89999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHH
Q 012133          159 GKEGTAILMFTSSQRRTVRSLER  181 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~  181 (470)
                      |.++.|++||...+...++.+..
T Consensus       775 G~~g~cILlys~~D~~~~~~lI~  797 (1195)
T PLN03137        775 GQRSSCVLYYSYSDYIRVKHMIS  797 (1195)
T ss_pred             CCCceEEEEecHHHHHHHHHHHh
Confidence            99999999999988777666654

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.93  E-value=5.2e-25  Score=234.28  Aligned_cols=181  Identities=34%  Similarity=0.563  Sum_probs=166.6

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcC-cccHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTT-ATSKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      +|||||+|..+..++++.++.|+.|.+-  ....+...|++....++ ...|+..|..||..+....++||||...+.|+
T Consensus       550 vlfSatfpr~m~~la~~vl~~Pveiiv~--~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d  627 (997)
T KOG0334|consen  550 VLFSATFPRSMEALARKVLKKPVEIIVG--GRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKAD  627 (997)
T ss_pred             hhhhhhhhHHHHHHHHHhhcCCeeEEEc--cceeEeccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHH
Confidence            5899999999999999999999887654  34556778888888887 77899999999988777899999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .|.+.|.+ ++.|..|||+.+|.+|..+++.|+++.+.+||||+++++|+|++++.+|||||+|...+.|+||+|||||+
T Consensus       628 ~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgra  707 (997)
T KOG0334|consen  628 ALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRA  707 (997)
T ss_pred             HHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccC
Confidence            99999986 78888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHHHh
Q 012133          159 GKEGTAILMFTSSQRRTVRSLERDV  183 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~~~  183 (470)
                      |++|.+++|+++.+..+.-.|.+.+
T Consensus       708 grkg~AvtFi~p~q~~~a~dl~~al  732 (997)
T KOG0334|consen  708 GRKGAAVTFITPDQLKYAGDLCKAL  732 (997)
T ss_pred             CccceeEEEeChHHhhhHHHHHHHH
Confidence            9999999999998888888888887

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.92  E-value=4.6e-24  Score=228.84  Aligned_cols=172  Identities=20%  Similarity=0.382  Sum_probs=137.1

Q ss_pred             CEEeecCCHHHHHHHHHHc--CCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYL--DNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l--~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |+||||+++.+...+...+  .+|... +...    ..+++.+  ..+....+...|..++... ...++||||+|+++|
T Consensus       178 v~lTAT~~~~~~~di~~~l~l~~~~~~-~~~~----~r~nl~~--~v~~~~~~~~~l~~~l~~~-~~~~~IIFc~tr~~~  249 (607)
T PRK11057        178 MALTATADDTTRQDIVRLLGLNDPLIQ-ISSF----DRPNIRY--TLVEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKV  249 (607)
T ss_pred             EEEecCCChhHHHHHHHHhCCCCeEEE-ECCC----CCCccee--eeeeccchHHHHHHHHHhc-CCCCEEEEECcHHHH
Confidence            5799999998766444433  355433 2111    1123322  2222233444455555443 557999999999999


Q ss_pred             HHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           79 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +.+++.|.. ++.+..+|++|++++|.++++.|+.++++|||||+++++|||+|+|++||||++|.+.++|+||+||+||
T Consensus       250 e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRaGR  329 (607)
T PRK11057        250 EDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGR  329 (607)
T ss_pred             HHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHhhhccC
Confidence            999999985 7899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHH
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLE  180 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~  180 (470)
                      .|.++.|++|+++.+...++.+.
T Consensus       330 ~G~~~~~ill~~~~d~~~~~~~~  352 (607)
T PRK11057        330 DGLPAEAMLFYDPADMAWLRRCL  352 (607)
T ss_pred             CCCCceEEEEeCHHHHHHHHHHH
Confidence            99999999999998877776654

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

Probab=99.92  E-value=6.5e-25  Score=216.07  Aligned_cols=184  Identities=28%  Similarity=0.440  Sum_probs=159.6

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeec--ccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVG--NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~--~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |+||||+...-.++...-+..|..+-+..  ...-.++..+.|+++.+....|.-.+..+|+.. +-.++|+|+++.+.+
T Consensus       364 L~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~~~kpl~~~~lI~~~-k~~r~lcf~~S~~sa  442 (620)
T KOG0350|consen  364 LVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPKFKPLAVYALITSN-KLNRTLCFVNSVSSA  442 (620)
T ss_pred             hhcchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeecccccchHhHHHHHHHh-hcceEEEEecchHHH
Confidence            57999998777777777788886655442  122346778889999888878888888888776 558999999999999


Q ss_pred             HHHHHHHh-c----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhc
Q 012133           79 DEVSLALT-S----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG  153 (470)
Q Consensus        79 ~~l~~~l~-~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~G  153 (470)
                      ..|+..|. .    .+.+..+.|.++++.|.+.+++|+.|.++||||||+++||||+.+|+.|||||+|.+..+|+||+|
T Consensus       443 ~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~G  522 (620)
T KOG0350|consen  443 NRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAG  522 (620)
T ss_pred             HHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhc
Confidence            99999987 2    356778999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCCeEEEeeChhhHHHHHHHHHHhCC
Q 012133          154 RTGRAGKEGTAILMFTSSQRRTVRSLERDVGC  185 (470)
Q Consensus       154 R~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~  185 (470)
                      ||+|+|+.|.||++++..+...+.++.+....
T Consensus       523 RTARAgq~G~a~tll~~~~~r~F~klL~~~~~  554 (620)
T KOG0350|consen  523 RTARAGQDGYAITLLDKHEKRLFSKLLKKTNL  554 (620)
T ss_pred             ccccccCCceEEEeeccccchHHHHHHHHhcc
Confidence            99999999999999999998888888777654

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.92  E-value=1.4e-24  Score=218.86  Aligned_cols=170  Identities=29%  Similarity=0.484  Sum_probs=150.4

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcc--------cHHHHHHHHHHHHcCCCeEEEEe
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT--------SKRTILSDLITVYAKGGKTIVFT   72 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~--------~k~~~l~~ll~~~~~~~~~lVF~   72 (470)
                      +.||||.|..+.++..+||++|..|....  .......|++|++.++..        .|++.|.++++.+ +-.++||||
T Consensus       203 ~a~SATYp~nLdn~Lsk~mrdp~lVr~n~--~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~i-py~QAlVF~  279 (980)
T KOG4284|consen  203 AAFSATYPRNLDNLLSKFMRDPALVRFNA--DDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSI-PYVQALVFC  279 (980)
T ss_pred             eEEeccCchhHHHHHHHHhcccceeeccc--CCceeechhheeeeccCCcchHHHHHHHHHHHHHHHhhC-chHHHHhhh
Confidence            46999999999999999999999998753  334456788888776543        3666777777665 457899999


Q ss_pred             CchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHH
Q 012133           73 QTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHR  151 (470)
Q Consensus        73 ~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr  151 (470)
                      +....|+.++.+|. .++.|.+|.|.|+|++|..+++.++.-.++|||+||+.+||||-++|++|||.|+|.+.++|.||
T Consensus       280 ~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HR  359 (980)
T KOG4284|consen  280 DQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHR  359 (980)
T ss_pred             hhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecCCCcchHHHHHH
Confidence            99999999999998 58999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccCCCCCCCeEEEeeChhhH
Q 012133          152 SGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       152 ~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                      +||+||.|..|.+++|+...+.
T Consensus       360 IGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  360 IGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             hhhcccccccceeEEEeccchh
Confidence            9999999999999998876543

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

Probab=99.91  E-value=6.9e-25  Score=211.91  Aligned_cols=188  Identities=32%  Similarity=0.453  Sum_probs=174.2

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      +|||||+|..+.++++.-+.+|..|.+.  -+.++.+.+++.+..+...+|...|..++...-.+.++|||+.|+..++.
T Consensus       199 llfSatlp~~lv~fakaGl~~p~lVRld--vetkise~lk~~f~~~~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~  276 (529)
T KOG0337|consen  199 LLFSATLPRDLVDFAKAGLVPPVLVRLD--VETKISELLKVRFFRVRKAEKEAALLSILGGRIKDKQTIVFVATKHHVEY  276 (529)
T ss_pred             EEEeccCchhhHHHHHccCCCCceEEee--hhhhcchhhhhheeeeccHHHHHHHHHHHhccccccceeEEecccchHHH
Confidence            5899999999999999999999999864  45667788888999999999999999999777667899999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +...|.. ++.+..+++.|++..|..-+.+|+.++..+||.||+++||+|||-.+.|||||+|.+...|+||+||+.|+|
T Consensus       277 ~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~arag  356 (529)
T KOG0337|consen  277 VRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAG  356 (529)
T ss_pred             HHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccccccccCCCCCceEEEEecchhhcc
Confidence            9999985 899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCcccc
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEFV  190 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~  190 (470)
                      +.|.+|.++.+++..++-.|...++..+...
T Consensus       357 rtg~aYs~V~~~~~~yl~DL~lflgr~~~~~  387 (529)
T KOG0337|consen  357 RTGRAYSLVASTDDPYLLDLQLFLGRPLIFA  387 (529)
T ss_pred             ccceEEEEEecccchhhhhhhhhcCCceeec
Confidence            9999999999999999999999888776543

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.91  E-value=2.9e-23  Score=222.83  Aligned_cols=173  Identities=23%  Similarity=0.406  Sum_probs=141.4

Q ss_pred             CEEeecCCHHHHHHHHHHcC--CCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLD--NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~--~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |+||||+++.+...+...+.  ++..+..  ..   ..+++.  +.......+...|.+++... ...++||||+|++.+
T Consensus       166 i~lTAT~~~~~~~~i~~~l~~~~~~~~~~--~~---~r~nl~--~~v~~~~~~~~~l~~~l~~~-~~~~~IIf~~sr~~~  237 (591)
T TIGR01389       166 IALTATADAETRQDIRELLRLADANEFIT--SF---DRPNLR--FSVVKKNNKQKFLLDYLKKH-RGQSGIIYASSRKKV  237 (591)
T ss_pred             EEEEeCCCHHHHHHHHHHcCCCCCCeEec--CC---CCCCcE--EEEEeCCCHHHHHHHHHHhc-CCCCEEEEECcHHHH
Confidence            57999999998876666664  4433321  11   112332  22223345666667777654 357999999999999


Q ss_pred             HHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           79 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +.+++.|.. ++.+..+|++|++++|..+++.|++++++|||||+++++|||+|+|++||+|++|.+.+.|+||+||+||
T Consensus       238 e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR  317 (591)
T TIGR01389       238 EELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGR  317 (591)
T ss_pred             HHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccccC
Confidence            999999974 7899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHHH
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLER  181 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~~  181 (470)
                      .|+++.|+++|++.+...++.+.+
T Consensus       318 ~G~~~~~il~~~~~d~~~~~~~i~  341 (591)
T TIGR01389       318 DGLPAEAILLYSPADIALLKRRIE  341 (591)
T ss_pred             CCCCceEEEecCHHHHHHHHHHHh
Confidence            999999999999988777666543

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.90  E-value=1.3e-23  Score=233.62  Aligned_cols=221  Identities=18%  Similarity=0.325  Sum_probs=164.6

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCccc---HHHHHHHHHH---HH--cCCCeEEEEe
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS---KRTILSDLIT---VY--AKGGKTIVFT   72 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~---k~~~l~~ll~---~~--~~~~~~lVF~   72 (470)
                      |+||||++.+  .+++.|.+.| .|.+.+..     ..++++|.......   +.+.+..++.   .+  ...+++|||+
T Consensus       222 ILmSATid~e--~fs~~F~~ap-vI~V~Gr~-----~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFL  293 (1294)
T PRK11131        222 IITSATIDPE--RFSRHFNNAP-IIEVSGRT-----YPVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFM  293 (1294)
T ss_pred             EEeeCCCCHH--HHHHHcCCCC-EEEEcCcc-----ccceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEc
Confidence            6899999854  5666555444 56664321     23566776654321   2333333332   21  3457899999


Q ss_pred             CchHHHHHHHHHHhc-CC---cEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEec--------
Q 012133           73 QTKRDADEVSLALTS-II---ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE--------  140 (470)
Q Consensus        73 ~t~~~~~~l~~~l~~-~~---~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~--------  140 (470)
                      +++.+++.+++.|.+ .+   .+.+|||+|++++|.++++.  .+..+||||||++++|||||+|++||+++        
T Consensus       294 pg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd  371 (1294)
T PRK11131        294 SGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYS  371 (1294)
T ss_pred             CCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEECCCccccccc
Confidence            999999999999985 33   47899999999999999987  46789999999999999999999999986        


Q ss_pred             -------CC---CChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHH
Q 012133          141 -------LP---NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL  210 (470)
Q Consensus       141 -------~p---~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l  210 (470)
                             +|   .|.++|+||+|||||. .+|.||.||+..+...+   .           .-+.+||+...+..++..+
T Consensus       372 ~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~~~~---~-----------~~~~PEIlR~~L~~viL~l  436 (1294)
T PRK11131        372 YRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDFLSR---P-----------EFTDPEILRTNLASVILQM  436 (1294)
T ss_pred             cccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHHHhh---h-----------cccCCccccCCHHHHHHHH
Confidence                   34   4668999999999999 79999999998664322   1           1234567777778888888


Q ss_pred             cccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCC
Q 012133          211 NGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPP  251 (470)
Q Consensus       211 ~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~  251 (470)
                      +.+...++..|     .+++.++++.+..++..|..+.+..
T Consensus       437 k~lgl~di~~F-----~fldpP~~~~i~~al~~L~~LgAld  472 (1294)
T PRK11131        437 TALGLGDIAAF-----PFVEAPDKRNIQDGVRLLEELGAIT  472 (1294)
T ss_pred             HHcCCCCccee-----eCCCCCCHHHHHHHHHHHHHCCCCC
Confidence            77766666666     5788888999999999887666553

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.89  E-value=3.9e-22  Score=209.90  Aligned_cols=165  Identities=19%  Similarity=0.179  Sum_probs=134.9

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||||++....++.+.|..+++.|.....    ......+.++.++..+|...|.+++... ....++||||+|++.++.|
T Consensus       414 mTGTa~~~~~El~~~y~l~vv~IPt~kp----~~r~~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~L  489 (656)
T PRK12898        414 MTGTAREVAGELWSVYGLPVVRIPTNRP----SQRRHLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGTRSVAASERL  489 (656)
T ss_pred             ccCcChHHHHHHHHHHCCCeEEeCCCCC----ccceecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHH
Confidence            8999999988999999888877754221    1222334456666778888888888654 3457899999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC---Ccc-----EEEEecCCCChhHHHHHh
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP---NVD-----LIIHYELPNDPETFVHRS  152 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip---~v~-----~VI~~~~p~~~~~y~qr~  152 (470)
                      ++.|.+ ++++..||+++++.+  ..+..|+.+...|+||||+++||+||+   +|.     +||+|++|.+...|+||+
T Consensus       490 ~~~L~~~gi~~~~Lhg~~~~rE--~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~  567 (656)
T PRK12898        490 SALLREAGLPHQVLNAKQDAEE--AAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLA  567 (656)
T ss_pred             HHHHHHCCCCEEEeeCCcHHHH--HHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhc
Confidence            999985 899999999966554  444455555567999999999999999   676     999999999999999999


Q ss_pred             cccCCCCCCCeEEEeeChhhH
Q 012133          153 GRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~~~  173 (470)
                      |||||.|.+|.+++|++..|.
T Consensus       568 GRTGRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        568 GRCGRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             ccccCCCCCeEEEEEechhHH
Confidence            999999999999999998663

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.88  E-value=2.9e-22  Score=223.74  Aligned_cols=238  Identities=16%  Similarity=0.279  Sum_probs=170.7

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCc------ccHHHHHHHHHHHH--cCCCeEEEEe
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA------TSKRTILSDLITVY--AKGGKTIVFT   72 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~------~~k~~~l~~ll~~~--~~~~~~lVF~   72 (470)
                      |+||||++.  ..+++.|...| .|.+.+..     ..++.+|.....      .++.+.+..++..+  ...+++|||+
T Consensus       215 IlmSATld~--~~fa~~F~~ap-vI~V~Gr~-----~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFL  286 (1283)
T TIGR01967       215 IITSATIDP--ERFSRHFNNAP-IIEVSGRT-----YPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFL  286 (1283)
T ss_pred             EEEeCCcCH--HHHHHHhcCCC-EEEECCCc-----ccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeC
Confidence            689999985  45666554444 56654321     234455554322      12334444444322  2458999999


Q ss_pred             CchHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCC------
Q 012133           73 QTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP------  142 (470)
Q Consensus        73 ~t~~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p------  142 (470)
                      +++.+++.+++.|.+    .+.+.+|||.|++++|.++++.+.  ..+||||||++++|||||+|++||+++++      
T Consensus       287 pg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~~--~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd  364 (1283)
T TIGR01967       287 PGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPHS--GRRIVLATNVAETSLTVPGIHYVIDTGTARISRYS  364 (1283)
T ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCCC--CceEEEeccHHHhccccCCeeEEEeCCCccccccc
Confidence            999999999999984    245889999999999999988753  46999999999999999999999998843      


Q ss_pred             ------------CChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHH
Q 012133          143 ------------NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL  210 (470)
Q Consensus       143 ------------~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l  210 (470)
                                  .|.++|+||+||+||.+ +|.||.||+..+...+.   .           -+.+||+...+..++..+
T Consensus       365 ~~~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~~~~~---~-----------~~~PEIlR~~L~~viL~l  429 (1283)
T TIGR01967       365 YRTKVQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDFNSRP---E-----------FTDPEILRTNLASVILQM  429 (1283)
T ss_pred             cccCccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHHHhhh---h-----------ccCcccccccHHHHHHHH
Confidence                        36689999999999996 99999999987643221   1           123467777777888888


Q ss_pred             cccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCc---ccccCCCCeEEEEE
Q 012133          211 NGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSR---SLINHEQGWVTLQL  268 (470)
Q Consensus       211 ~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r---~l~~~~~~~~~~~~  268 (470)
                      +.....++..|     .+++.++.+.+..++..|..+.+.....   .++..+..+..+++
T Consensus       430 ~~lg~~di~~f-----~fldpP~~~~i~~A~~~L~~LGAld~~~~~~~LT~lGr~ma~LPl  485 (1283)
T TIGR01967       430 LALRLGDIAAF-----PFIEAPDPRAIRDGFRLLEELGALDDDEAEPQLTPIGRQLAQLPV  485 (1283)
T ss_pred             HhcCCCCcccc-----cCCCCCCHHHHHHHHHHHHHCCCCCCCCCCccccHHHHHHhhcCC
Confidence            77655555555     5778888899999999887766654443   45555544544444

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.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.88  E-value=1.1e-21  Score=216.18  Aligned_cols=175  Identities=18%  Similarity=0.304  Sum_probs=137.3

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+++....++...+.++..|.....  .  ...+++++....   ...+...++..+...++++|||++++.++.
T Consensus       603 L~~SATpiprtl~~~l~g~~d~s~I~~~p~--~--R~~V~t~v~~~~---~~~i~~~i~~el~~g~qv~if~n~i~~~e~  675 (926)
T TIGR00580       603 LTLSATPIPRTLHMSMSGIRDLSIIATPPE--D--RLPVRTFVMEYD---PELVREAIRRELLRGGQVFYVHNRIESIEK  675 (926)
T ss_pred             EEEecCCCHHHHHHHHhcCCCcEEEecCCC--C--ccceEEEEEecC---HHHHHHHHHHHHHcCCeEEEEECCcHHHHH
Confidence            589999888777777667778877764321  1  223555544322   122222334444567899999999999999


Q ss_pred             HHHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC-ChhHHHHHhcccC
Q 012133           81 VSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTG  156 (470)
Q Consensus        81 l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~g  156 (470)
                      +++.|.+   .+.+..+||+|++++|++++++|++|+++|||||+++++|||+|++++||+++.|. +..+|+||+||+|
T Consensus       676 l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~~a~~~gls~l~Qr~GRvG  755 (926)
T TIGR00580       676 LATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVG  755 (926)
T ss_pred             HHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEEecCCCCCHHHHHHHhcCCC
Confidence            9999986   47899999999999999999999999999999999999999999999999999875 6789999999999


Q ss_pred             CCCCCCeEEEeeChh------hHHHHHHHHHH
Q 012133          157 RAGKEGTAILMFTSS------QRRTVRSLERD  182 (470)
Q Consensus       157 R~g~~g~~i~l~~~~------~~~~~~~i~~~  182 (470)
                      |.++.|.||+++.+.      ....++.|++.
T Consensus       756 R~g~~g~aill~~~~~~l~~~~~~RL~~~~~~  787 (926)
T TIGR00580       756 RSKKKAYAYLLYPHQKALTEDAQKRLEAIQEF  787 (926)
T ss_pred             CCCCCeEEEEEECCcccCCHHHHHHHHHHHHh
Confidence            999999999998643      34445555443

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.

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

Probab=99.87  E-value=9.8e-22  Score=211.26  Aligned_cols=161  Identities=20%  Similarity=0.244  Sum_probs=123.2

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHH-HHH-cCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLI-TVY-AKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll-~~~-~~~~~~lVF~~t~~~~   78 (470)
                      ||||||+|.++.++++.++.++..+.+..  .......+.++ +.++.+.|+..+...+ ..+ ...+++||||||++.|
T Consensus       209 LLFSAT~p~ei~~l~~~~~~~p~~i~V~~--~~l~a~ki~q~-v~v~~e~Kl~~lv~~L~~ll~e~g~~vLVF~NTv~~A  285 (844)
T TIGR02621       209 VELTATSRTDGPDRTTLLSAEDYKHPVLK--KRLAAKKIVKL-VPPSDEKFLSTMVKELNLLMKDSGGAILVFCRTVKHV  285 (844)
T ss_pred             EEEecCCCccHHHHHHHHccCCceeeccc--ccccccceEEE-EecChHHHHHHHHHHHHHHHhhCCCcEEEEECCHHHH
Confidence            58999999999999999998888777642  23344556654 3444444543333222 222 3457899999999999


Q ss_pred             HHHHHHHhcCCcEEEEeCCCCHHHHH-----HHHccccc----CC-------eeEEEecccccccCCCCCccEEEEecCC
Q 012133           79 DEVSLALTSIIASEALHGDISQHQRE-----RTLNGFRQ----GK-------FTVLVATDVAARGLDIPNVDLIIHYELP  142 (470)
Q Consensus        79 ~~l~~~l~~~~~~~~lhg~~~~~~R~-----~~~~~f~~----g~-------~~iLVaTdv~~~Gidip~v~~VI~~~~p  142 (470)
                      +.+++.|.+.. ...|||+|++.+|+     +++++|++    ++       .+|||||+++++||||+. ++||++..|
T Consensus       286 q~L~~~L~~~g-~~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP  363 (844)
T TIGR02621       286 RKVFAKLPKEK-FELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP  363 (844)
T ss_pred             HHHHHHHHhcC-CeEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC
Confidence            99999998532 28999999999999     88999987    43       689999999999999986 888887766


Q ss_pred             CChhHHHHHhcccCCCCCCC-eEEEee
Q 012133          143 NDPETFVHRSGRTGRAGKEG-TAILMF  168 (470)
Q Consensus       143 ~~~~~y~qr~GR~gR~g~~g-~~i~l~  168 (470)
                        .++|+||+||++|.|+.+ ..++++
T Consensus       364 --~esyIQRiGRtgR~G~~~~~~i~vv  388 (844)
T TIGR02621       364 --FESMQQRFGRVNRFGELQACQIAVV  388 (844)
T ss_pred             --HHHHHHHhcccCCCCCCCCceEEEE
Confidence              689999999999999753 335554

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.87  E-value=1e-21  Score=198.67  Aligned_cols=165  Identities=24%  Similarity=0.328  Sum_probs=121.8

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEE--EcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAI--STTATSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~--~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |+||||+|+.+.++++.+...+..........   .....+.+.  ......+...+..+++....+.++||||+|++.+
T Consensus       159 i~~SATlp~~l~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~~~~  235 (358)
T TIGR01587       159 LLMSATLPKFLKEYAEKIGYVEFNEPLDLKEE---RRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRA  235 (358)
T ss_pred             EEEecCchHHHHHHHhcCCCcccccCCCCccc---cccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCHHHH
Confidence            58999999888877776544322211110000   001112221  2222356677777777666678999999999999


Q ss_pred             HHHHHHHhc-CC--cEEEEeCCCCHHHHHH----HHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHH
Q 012133           79 DEVSLALTS-II--ASEALHGDISQHQRER----TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHR  151 (470)
Q Consensus        79 ~~l~~~l~~-~~--~~~~lhg~~~~~~R~~----~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr  151 (470)
                      +.+++.|.+ ..  .+..+||.|++.+|.+    +++.|++++.+|||||+++++||||+ +++||++..|  +++|+||
T Consensus       236 ~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iqr  312 (358)
T TIGR01587       236 QEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQR  312 (358)
T ss_pred             HHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEEEEcCCC--HHHHHHH
Confidence            999999975 33  4999999999999976    48999999999999999999999996 8899998766  7899999


Q ss_pred             hcccCCCCCC----CeEEEeeChh
Q 012133          152 SGRTGRAGKE----GTAILMFTSS  171 (470)
Q Consensus       152 ~GR~gR~g~~----g~~i~l~~~~  171 (470)
                      +||+||.|+.    +.++++....
T Consensus       313 ~GR~gR~g~~~~~~~~~~v~~~~~  336 (358)
T TIGR01587       313 LGRLHRYGRKNGENFEVYIITIAP  336 (358)
T ss_pred             hccccCCCCCCCCCCeEEEEeecC
Confidence            9999998844    3666666543

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

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.87  E-value=6.6e-21  Score=215.75  Aligned_cols=185  Identities=25%  Similarity=0.378  Sum_probs=129.4

Q ss_pred             HHHHHHcCCCeEEEEeCchHHHHHHHHHHhcC----------------------------------CcEEEEeCCCCHHH
Q 012133           57 DLITVYAKGGKTIVFTQTKRDADEVSLALTSI----------------------------------IASEALHGDISQHQ  102 (470)
Q Consensus        57 ~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~~----------------------------------~~~~~lhg~~~~~~  102 (470)
                      .++..+....++||||||+..|+.++..|.+.                                  +.+.++||+|++++
T Consensus       236 ~il~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkee  315 (1490)
T PRK09751        236 GILDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQ  315 (1490)
T ss_pred             HHHHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHH
Confidence            44544445689999999999999999988642                                  12568999999999


Q ss_pred             HHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC-CCCCeEEEeeChhhHHHHH---H
Q 012133          103 RERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA-GKEGTAILMFTSSQRRTVR---S  178 (470)
Q Consensus       103 R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~-g~~g~~i~l~~~~~~~~~~---~  178 (470)
                      |..+++.|++|++++||||+.+++||||++|++||||+.|.++.+|+||+||+||. +..+.++++... ....++   .
T Consensus       316 R~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~~-r~dlle~~~~  394 (1490)
T PRK09751        316 RAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPRT-RRDLVDSAVI  394 (1490)
T ss_pred             HHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeCc-HHHHHhhHHH
Confidence            99999999999999999999999999999999999999999999999999999996 333455544332 222222   3


Q ss_pred             HHHHhCCCccccCCCCHH-HHHHHHHHHHHHHHcccCccchhhhHHHHHHH--HHhhCHHHHHHHHHHHcC
Q 012133          179 LERDVGCKFEFVSPPVVE-DVLESSAEQVVATLNGVHPESVEFFTPTAQRL--IEEKGTDALAAALAQLSG  246 (470)
Q Consensus       179 i~~~~~~~~~~~~~p~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~l--~~~~~~~~l~~al~~l~~  246 (470)
                      ++..+...++.+.+|... +++...+-.++.   . ..-..+...+.+...  ...++.+.+...|..|.+
T Consensus       395 ve~~l~g~iE~~~~p~nplDVLaqqiva~a~---~-~~~~~d~l~~~vrra~pf~~L~~~~f~~vl~~L~~  461 (1490)
T PRK09751        395 VECMFAGRLENLTPPHNPLDVLAQQTVAAAA---M-DALQVDEWYSRVRRAAPWKDLPRRVFDATLDMLSG  461 (1490)
T ss_pred             HHHHhcCCCCccCCCCChHHHHHHHHHHHHh---c-CCCCHHHHHHHhhccCCcccCCHHHHHHHHHHHhc
Confidence            667777777776666443 455444433322   2 111222222222221  123456677777776664

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.87  E-value=3.7e-21  Score=211.37  Aligned_cols=163  Identities=17%  Similarity=0.243  Sum_probs=141.1

Q ss_pred             cHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHh-c-CCcEEEEeCCCCHHHHHHHHcccccC--CeeEEEeccccc
Q 012133           50 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-S-IIASEALHGDISQHQRERTLNGFRQG--KFTVLVATDVAA  125 (470)
Q Consensus        50 ~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~-~-~~~~~~lhg~~~~~~R~~~~~~f~~g--~~~iLVaTdv~~  125 (470)
                      .|.+.|.++|+.. ...|+||||++++.+..|++.|. . ++.+..+||+|++.+|.++++.|+++  ..+|||||++++
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 46899999999999999999995 3 78999999999999999999999974  599999999999


Q ss_pred             ccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCC--CccccCCCCHHHHHHHHH
Q 012133          126 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGC--KFEFVSPPVVEDVLESSA  203 (470)
Q Consensus       126 ~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~--~~~~~~~p~~~~~~~~~~  203 (470)
                      +|+|++.+++|||||+||+++.|+||+||++|.|+++.+.+++...+....+.|.+.+..  ++....+|+..++.+...
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            999999999999999999999999999999999999988887776666666777776655  556678889999999888


Q ss_pred             HHHHHHHccc
Q 012133          204 EQVVATLNGV  213 (470)
Q Consensus       204 ~~~~~~l~~~  213 (470)
                      +++...+...
T Consensus       638 ~~l~~~l~~~  647 (956)
T PRK04914        638 DELIPYLASP  647 (956)
T ss_pred             HHHHHHHhCC
Confidence            8888877554

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.87  E-value=4.2e-21  Score=215.88  Aligned_cols=176  Identities=17%  Similarity=0.256  Sum_probs=138.1

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+++.+..++..++.++..|......    ...++++......   ..+...++..+...++++||||+++.++.
T Consensus       752 Ll~SATpiprtl~l~~~gl~d~~~I~~~p~~----r~~v~~~~~~~~~---~~~k~~il~el~r~gqv~vf~n~i~~ie~  824 (1147)
T PRK10689        752 LTLTATPIPRTLNMAMSGMRDLSIIATPPAR----RLAVKTFVREYDS---LVVREAILREILRGGQVYYLYNDVENIQK  824 (1147)
T ss_pred             EEEcCCCCHHHHHHHHhhCCCcEEEecCCCC----CCCceEEEEecCc---HHHHHHHHHHHhcCCeEEEEECCHHHHHH
Confidence            6899999888888888888999888653221    1234444433221   12223344444466899999999999999


Q ss_pred             HHHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCC-CChhHHHHHhcccC
Q 012133           81 VSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP-NDPETFVHRSGRTG  156 (470)
Q Consensus        81 l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p-~~~~~y~qr~GR~g  156 (470)
                      +++.|.+   .+.+..+||+|++++|++++++|++|+++|||||+++++|||+|+|++||.++.. .+...|+||+||+|
T Consensus       825 la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~ad~fglaq~~Qr~GRvG  904 (1147)
T PRK10689        825 AAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVG  904 (1147)
T ss_pred             HHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEecCCCCCHHHHHHHhhccC
Confidence            9999985   4679999999999999999999999999999999999999999999999965443 36678999999999


Q ss_pred             CCCCCCeEEEeeCh------hhHHHHHHHHHHh
Q 012133          157 RAGKEGTAILMFTS------SQRRTVRSLERDV  183 (470)
Q Consensus       157 R~g~~g~~i~l~~~------~~~~~~~~i~~~~  183 (470)
                      |.++.|.|++++..      .....++.|++..
T Consensus       905 R~g~~g~a~ll~~~~~~~~~~~~~rl~~~~~~~  937 (1147)
T PRK10689        905 RSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLE  937 (1147)
T ss_pred             CCCCceEEEEEeCCCcccCHHHHHHHHHHHHhc
Confidence            99999999999854      3355666666553

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

Probab=99.87  E-value=4.3e-21  Score=198.50  Aligned_cols=174  Identities=25%  Similarity=0.413  Sum_probs=138.1

Q ss_pred             CEEeecCCHHHHHHHHHHcC--CCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHH--HHcCCCeEEEEeCchH
Q 012133            1 MLFSATMPSWVKKLSRKYLD--NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT--VYAKGGKTIVFTQTKR   76 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~--~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~--~~~~~~~~lVF~~t~~   76 (470)
                      |.+|||.++.+++-+...|.  ++..+...-+     .++|.+..+... +.+.+.+  .|.  .....+..||||.|++
T Consensus       170 ~AlTATA~~~v~~DI~~~L~l~~~~~~~~sfd-----RpNi~~~v~~~~-~~~~q~~--fi~~~~~~~~~~GIIYc~sRk  241 (590)
T COG0514         170 LALTATATPRVRDDIREQLGLQDANIFRGSFD-----RPNLALKVVEKG-EPSDQLA--FLATVLPQLSKSGIIYCLTRK  241 (590)
T ss_pred             EEEeCCCChHHHHHHHHHhcCCCcceEEecCC-----Cchhhhhhhhcc-cHHHHHH--HHHhhccccCCCeEEEEeeHH
Confidence            46899999998886666554  4444432212     233332222222 2222222  232  1334567899999999


Q ss_pred             HHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhccc
Q 012133           77 DADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT  155 (470)
Q Consensus        77 ~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~  155 (470)
                      .++.+++.|.. ++.+..+|++|+.++|+.+.++|..++++|+|||.+...|||-|||.+||||++|.++++|.|.+||+
T Consensus       242 ~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRA  321 (590)
T COG0514         242 KVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRA  321 (590)
T ss_pred             hHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhc
Confidence            99999999995 79999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCeEEEeeChhhHHHHHHHHHH
Q 012133          156 GRAGKEGTAILMFTSSQRRTVRSLERD  182 (470)
Q Consensus       156 gR~g~~g~~i~l~~~~~~~~~~~i~~~  182 (470)
                      ||.|.+..|++||.+.+....+.+.+.
T Consensus       322 GRDG~~a~aill~~~~D~~~~~~~i~~  348 (590)
T COG0514         322 GRDGLPAEAILLYSPEDIRWQRYLIEQ  348 (590)
T ss_pred             cCCCCcceEEEeeccccHHHHHHHHHh
Confidence            999999999999999998777766554

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.86  E-value=1.2e-20  Score=209.61  Aligned_cols=143  Identities=22%  Similarity=0.344  Sum_probs=110.2

Q ss_pred             HHHcCCCeEEEEeCchHHHHHHHHHHhcC-------CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCC
Q 012133           60 TVYAKGGKTIVFTQTKRDADEVSLALTSI-------IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN  132 (470)
Q Consensus        60 ~~~~~~~~~lVF~~t~~~~~~l~~~l~~~-------~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~  132 (470)
                      +......++||||||+..|+.++..|.+.       ..+.++||+|++++|..+++.|++|+++|||||+++++|||+|+
T Consensus       279 ~~i~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~  358 (876)
T PRK13767        279 ELIKEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGY  358 (876)
T ss_pred             HHHhcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCC
Confidence            33445689999999999999999999752       56999999999999999999999999999999999999999999


Q ss_pred             ccEEEEecCCCChhHHHHHhcccCCC-CCCCeEEEeeChh-h-HHHHHHHHHHhCCCccccCCCC-HHHHHHHH
Q 012133          133 VDLIIHYELPNDPETFVHRSGRTGRA-GKEGTAILMFTSS-Q-RRTVRSLERDVGCKFEFVSPPV-VEDVLESS  202 (470)
Q Consensus       133 v~~VI~~~~p~~~~~y~qr~GR~gR~-g~~g~~i~l~~~~-~-~~~~~~i~~~~~~~~~~~~~p~-~~~~~~~~  202 (470)
                      |++||+|+.|.++.+|+||+||+||. +.....+++.... + .+....++......++.+.+|. ..+++...
T Consensus       359 Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~~~~l~e~~~~~~~~~~~~ie~~~~~~~~~dvl~q~  432 (876)
T PRK13767        359 IDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVDRDDLVECAVLLKKAREGKIDRVHIPKNPLDVLAQH  432 (876)
T ss_pred             CcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcCchhHHHHHHHHHHHHhCCCCCCCCCCCcHHHHHHH
Confidence            99999999999999999999999986 3434444444332 2 2222233444455555554443 33444433

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.84  E-value=7.7e-20  Score=198.45  Aligned_cols=163  Identities=20%  Similarity=0.305  Sum_probs=122.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCch-----
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK-----   75 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~-----   75 (470)
                      |+||||+.+....+......++..|+..    +.....+..+++.  ...+..++..+.+......+++|||++.     
T Consensus       413 L~~SATp~prtl~~~~~g~~~~s~i~~~----p~~r~~i~~~~~~--~~~~~~~~~~i~~~~~~g~q~~v~~~~ie~s~~  486 (681)
T PRK10917        413 LVMTATPIPRTLAMTAYGDLDVSVIDEL----PPGRKPITTVVIP--DSRRDEVYERIREEIAKGRQAYVVCPLIEESEK  486 (681)
T ss_pred             EEEeCCCCHHHHHHHHcCCCceEEEecC----CCCCCCcEEEEeC--cccHHHHHHHHHHHHHcCCcEEEEEcccccccc
Confidence            5899998766554443222233333321    1112234444433  2334444444545555678999999964     


Q ss_pred             ---HHHHHHHHHHhcC---CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC-ChhHH
Q 012133           76 ---RDADEVSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-DPETF  148 (470)
Q Consensus        76 ---~~~~~l~~~l~~~---~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~y  148 (470)
                         ..++++++.|.+.   +.+..+||+|++++|++++++|++|+++|||||+++++|||+|++++||+++.|. ....|
T Consensus       487 l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~v~~VIi~~~~r~gls~l  566 (681)
T PRK10917        487 LDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQL  566 (681)
T ss_pred             hhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccCCCcEEEEeCCCCCCHHHH
Confidence               3456677777753   5799999999999999999999999999999999999999999999999999997 57888


Q ss_pred             HHHhcccCCCCCCCeEEEeeC
Q 012133          149 VHRSGRTGRAGKEGTAILMFT  169 (470)
Q Consensus       149 ~qr~GR~gR~g~~g~~i~l~~  169 (470)
                      +||+||+||.+.+|.|++++.
T Consensus       567 hQ~~GRvGR~g~~g~~ill~~  587 (681)
T PRK10917        567 HQLRGRVGRGAAQSYCVLLYK  587 (681)
T ss_pred             HHHhhcccCCCCceEEEEEEC
Confidence            999999999999999999995

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.83  E-value=1.4e-19  Score=195.00  Aligned_cols=163  Identities=22%  Similarity=0.291  Sum_probs=120.1

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCch-----
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK-----   75 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~-----   75 (470)
                      |+||||+++....+.....-+...++..    +.....+..+++.  ...+..++..+.+......+++|||++.     
T Consensus       390 l~~SATp~prtl~l~~~~~l~~~~i~~~----p~~r~~i~~~~~~--~~~~~~~~~~i~~~l~~g~q~~v~~~~i~~s~~  463 (630)
T TIGR00643       390 LVMSATPIPRTLALTVYGDLDTSIIDEL----PPGRKPITTVLIK--HDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEK  463 (630)
T ss_pred             EEEeCCCCcHHHHHHhcCCcceeeeccC----CCCCCceEEEEeC--cchHHHHHHHHHHHHHhCCcEEEEEcccccccc
Confidence            5899997665443332111122222211    1111234444332  2344444555555555678999999876     


Q ss_pred             ---HHHHHHHHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC-ChhHH
Q 012133           76 ---RDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-DPETF  148 (470)
Q Consensus        76 ---~~~~~l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~y  148 (470)
                         ..++++++.|.+   .+.+..+||+|++++|.+++++|++|+.+|||||+++++|||+|++++||+++.|. ....|
T Consensus       464 ~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~v~~VIi~~~~r~gls~l  543 (630)
T TIGR00643       464 LDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQL  543 (630)
T ss_pred             chHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccCCCcEEEEeCCCcCCHHHH
Confidence               456677777764   46799999999999999999999999999999999999999999999999999987 67889


Q ss_pred             HHHhcccCCCCCCCeEEEeeC
Q 012133          149 VHRSGRTGRAGKEGTAILMFT  169 (470)
Q Consensus       149 ~qr~GR~gR~g~~g~~i~l~~  169 (470)
                      .||+||+||.+++|.|++++.
T Consensus       544 hQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       544 HQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             HHHhhhcccCCCCcEEEEEEC
Confidence            999999999999999999983

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.82  E-value=4e-19  Score=191.08  Aligned_cols=165  Identities=19%  Similarity=0.222  Sum_probs=129.1

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHH-HcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~-~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|.-.+-.++.+.|--+  ++.+... .+....... -.+.+...+|..+|.+.+.. +....++||||+|++.++.|
T Consensus       369 mTGTa~t~~~e~~~~Y~l~--v~~IPt~-kp~~r~d~~-~~i~~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l  444 (790)
T PRK09200        369 MTGTAKTEEKEFFEVYNME--VVQIPTN-RPIIRIDYP-DKVFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETF  444 (790)
T ss_pred             cCCCChHHHHHHHHHhCCc--EEECCCC-CCcccccCC-CeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHH
Confidence            6788766555665555333  2333211 111111111 12334556788888777754 45678999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCC---CCcc-----EEEEecCCCChhHHHHHh
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI---PNVD-----LIIHYELPNDPETFVHRS  152 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidi---p~v~-----~VI~~~~p~~~~~y~qr~  152 (470)
                      +..|.+ ++++..||+++++.++..+.+.++.+  +|+||||+++||+||   |+|.     +||+|++|.+...|+||+
T Consensus       445 ~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~  522 (790)
T PRK09200        445 SKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLR  522 (790)
T ss_pred             HHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhh
Confidence            999985 89999999999999998888888765  799999999999999   7998     999999999999999999


Q ss_pred             cccCCCCCCCeEEEeeChhhH
Q 012133          153 GRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~~~  173 (470)
                      |||||.|++|.+++|++..+.
T Consensus       523 GRtGR~G~~G~s~~~is~eD~  543 (790)
T PRK09200        523 GRSGRQGDPGSSQFFISLEDD  543 (790)
T ss_pred             ccccCCCCCeeEEEEEcchHH
Confidence            999999999999999998653

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=99.82  E-value=1.2e-19  Score=185.77  Aligned_cols=240  Identities=18%  Similarity=0.289  Sum_probs=184.7

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHH-HHHHHHHH--cCCCeEEEEeCchHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTI-LSDLITVY--AKGGKTIVFTQTKRD   77 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~-l~~ll~~~--~~~~~~lVF~~t~~~   77 (470)
                      |+||||+..+   ..+.|+.+...+.+.+.     ...|+.+|...+..+..+. +..+++.+  .+.+.+|||.+..++
T Consensus       199 IimSATlda~---kfS~yF~~a~i~~i~GR-----~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeE  270 (674)
T KOG0922|consen  199 IIMSATLDAE---KFSEYFNNAPILTIPGR-----TFPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEE  270 (674)
T ss_pred             EEEeeeecHH---HHHHHhcCCceEeecCC-----CCceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHH
Confidence            6899999854   45567777667777543     2456778877666666543 33344433  466899999999999


Q ss_pred             HHHHHHHHhcC---C------cEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEec--------
Q 012133           78 ADEVSLALTSI---I------ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE--------  140 (470)
Q Consensus        78 ~~~l~~~l~~~---~------~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~--------  140 (470)
                      ++.+++.|.+.   .      .+.++|+.||.+++.++++.-..|..+|++||++++..|.||.|.+||+.+        
T Consensus       271 Ie~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~  350 (674)
T KOG0922|consen  271 IEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYN  350 (674)
T ss_pred             HHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeec
Confidence            99999998742   1      257899999999999999999999999999999999999999999999533        


Q ss_pred             ----------CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHH
Q 012133          141 ----------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATL  210 (470)
Q Consensus       141 ----------~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l  210 (470)
                                .|.|..+-.||+||+||. .+|+||.+|+..+.              +.++..+.+|+....+..++..|
T Consensus       351 p~~g~~~L~v~~ISkasA~QRaGRAGRt-~pGkcyRLYte~~~--------------~~~~~~~~PEI~R~~Ls~~vL~L  415 (674)
T KOG0922|consen  351 PRTGLDSLIVVPISKASANQRAGRAGRT-GPGKCYRLYTESAY--------------DKMPLQTVPEIQRVNLSSAVLQL  415 (674)
T ss_pred             cccCccceeEEechHHHHhhhcccCCCC-CCceEEEeeeHHHH--------------hhcccCCCCceeeechHHHHHHH
Confidence                      356888899999999999 59999999998764              22344556677888888888899


Q ss_pred             cccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCccccc-CCCCeEEEEE
Q 012133          211 NGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLIN-HEQGWVTLQL  268 (470)
Q Consensus       211 ~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r~l~~-~~~~~~~~~~  268 (470)
                      +.+...++-.|     ++++.++++.+.+||..|..+.+..+...++. ....|..+++
T Consensus       416 kalgi~d~l~F-----~f~d~P~~~~l~~AL~~L~~lgald~~g~lt~p~G~~ma~~Pl  469 (674)
T KOG0922|consen  416 KALGINDPLRF-----PFIDPPPPEALEEALEELYSLGALDDRGKLTSPLGRQMAELPL  469 (674)
T ss_pred             HhcCCCCcccC-----CCCCCCChHHHHHHHHHHHhcCcccCcCCcCchHHhhhhhcCC
Confidence            98887777777     78889999999999999987666654444444 3334444443

>PRK02362 ski2-like helicase; Provisional

Probab=99.81  E-value=5.6e-19  Score=194.12  Aligned_cols=119  Identities=28%  Similarity=0.474  Sum_probs=102.4

Q ss_pred             HHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhcC-------------------------------------CcEEEEe
Q 012133           53 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------------IASEALH   95 (470)
Q Consensus        53 ~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~~-------------------------------------~~~~~lh   95 (470)
                      ..+..+++.+...+++||||+|++.|+.++..|...                                     ..+..+|
T Consensus       231 ~~~~~~~~~~~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hH  310 (737)
T PRK02362        231 DTLNLVLDTLEEGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHH  310 (737)
T ss_pred             HHHHHHHHHHHcCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeec
Confidence            334444444556789999999999999988877531                                     2578999


Q ss_pred             CCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEE----ec-----CCCChhHHHHHhcccCCCCC--CCeE
Q 012133           96 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE-----LPNDPETFVHRSGRTGRAGK--EGTA  164 (470)
Q Consensus        96 g~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~----~~-----~p~~~~~y~qr~GR~gR~g~--~g~~  164 (470)
                      ++|++.+|..+++.|++|.++|||||+++++|||+|.+.+||+    ||     .|.+..+|+||+|||||.|.  .|.+
T Consensus       311 agl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~  390 (737)
T PRK02362        311 AGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEA  390 (737)
T ss_pred             CCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceE
Confidence            9999999999999999999999999999999999999999997    76     68899999999999999985  4999


Q ss_pred             EEeeChh
Q 012133          165 ILMFTSS  171 (470)
Q Consensus       165 i~l~~~~  171 (470)
                      ++++...
T Consensus       391 ii~~~~~  397 (737)
T PRK02362        391 VLLAKSY  397 (737)
T ss_pred             EEEecCc
Confidence            9998764

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

Probab=99.81  E-value=3e-19  Score=192.58  Aligned_cols=238  Identities=19%  Similarity=0.274  Sum_probs=183.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcc-c-HHHHHHHHHHHH--cCCCeEEEEeCchH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT-S-KRTILSDLITVY--AKGGKTIVFTQTKR   76 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~-~-k~~~l~~ll~~~--~~~~~~lVF~~t~~   76 (470)
                      |+||||+..+   -++.|+.+...|.+.+..     ..|+.+|...... . -.+.+...+..+  ...+.+|||.+...
T Consensus       199 IimSATld~~---rfs~~f~~apvi~i~GR~-----fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~  270 (845)
T COG1643         199 IIMSATLDAE---RFSAYFGNAPVIEIEGRT-----YPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQR  270 (845)
T ss_pred             EEEecccCHH---HHHHHcCCCCEEEecCCc-----cceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHH
Confidence            6899999865   345577777778775432     3456666544433 3 344555555444  34689999999999


Q ss_pred             HHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEec-----------
Q 012133           77 DADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE-----------  140 (470)
Q Consensus        77 ~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~-----------  140 (470)
                      +++.+++.|.+     .+.+.+||+.|+.+++.++++.-..++.+|++||+||+.+|.||+|.+||+.+           
T Consensus       271 EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~  350 (845)
T COG1643         271 EIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRT  350 (845)
T ss_pred             HHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCccccccccccc
Confidence            99999999985     35689999999999999999999998888999999999999999999999544           


Q ss_pred             -------CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHHccc
Q 012133          141 -------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGV  213 (470)
Q Consensus       141 -------~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~~  213 (470)
                             .|.|..+..||.||+||. .+|.||-+|+..+..              ..+.-+.+||+...+..++..++..
T Consensus       351 g~~~L~~~~ISqAsA~QRaGRAGR~-~pGicyRLyse~~~~--------------~~~~~t~PEIlrtdLs~~vL~l~~~  415 (845)
T COG1643         351 GLTRLETEPISKASADQRAGRAGRT-GPGICYRLYSEEDFL--------------AFPEFTLPEILRTDLSGLVLQLKSL  415 (845)
T ss_pred             CceeeeEEEechhhhhhhccccccC-CCceEEEecCHHHHH--------------hcccCCChhhhhcchHHHHHHHHhc
Confidence                   245788889999999999 599999999985532              2233456799999999999999988


Q ss_pred             Ccc-chhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCcccccCCCCeEEE
Q 012133          214 HPE-SVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTL  266 (470)
Q Consensus       214 ~~~-~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r~l~~~~~~~~~~  266 (470)
                      ... ++..|     .+++.++...+.+|+..|..+.+......|+.....|.++
T Consensus       416 G~~~d~~~f-----~fld~P~~~~i~~A~~~L~~LGAld~~g~LT~lG~~ms~l  464 (845)
T COG1643         416 GIGQDIAPF-----PFLDPPPEAAIQAALTLLQELGALDDSGKLTPLGKQMSLL  464 (845)
T ss_pred             CCCCCcccC-----ccCCCCChHHHHHHHHHHHHcCCcCCCCCCCHHHHHHHhC
Confidence            774 66666     7788888899999999888776665555555444444433

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

Probab=99.80  E-value=3.6e-19  Score=172.76  Aligned_cols=167  Identities=31%  Similarity=0.489  Sum_probs=132.0

Q ss_pred             CEEeecCCH-HHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcc-c-HHHHH----------------------
Q 012133            1 MLFSATMPS-WVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT-S-KRTIL----------------------   55 (470)
Q Consensus         1 llfSATlp~-~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~-~-k~~~l----------------------   55 (470)
                      +++|||+.. +|+.+.++.|.=|..|++.+.  ..++.++.|+...+..+ + -..-|                      
T Consensus       404 ~vCsatlh~feVkk~~ervmhfptwVdLkge--D~vpetvHhvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Sp  481 (725)
T KOG0349|consen  404 PVCSATLHIFEVKKVGERVMHFPTWVDLKGE--DLVPETVHHVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSP  481 (725)
T ss_pred             ceeeeEEeEEEeeehhhhhccCceeEecccc--cccchhhccceeecCCccCccHHHHhhhhccCCcccccccccccCCC
Confidence            478999864 578889999999999988643  34445554443332211 0 00001                      


Q ss_pred             ------HHHH---------HHHcCCCeEEEEeCchHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCee
Q 012133           56 ------SDLI---------TVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        56 ------~~ll---------~~~~~~~~~lVF~~t~~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                            ..|+         +.+ .-.++||||.|+.+|+.|.+.+.+    ++.|.++|++..+.+|.+.++.|+....+
T Consensus       482 e~~s~a~kilkgEy~v~ai~~h-~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvk  560 (725)
T KOG0349|consen  482 ENPSSATKILKGEYGVVAIRRH-AMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVK  560 (725)
T ss_pred             CChhhhhHHhcCchhhhhhhhh-ccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeE
Confidence                  1111         111 236899999999999999999973    58999999999999999999999999999


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                      .||||||++|||||..+.++||.-+|.+...|+||+||+||+-+-|.+|.|+..
T Consensus       561 flictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgraermglaislvat  614 (725)
T KOG0349|consen  561 FLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVAT  614 (725)
T ss_pred             EEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhhhcceeEEEeec
Confidence            999999999999999999999999999999999999999999988988887643

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

Probab=99.79  E-value=3.1e-20  Score=169.10  Aligned_cols=152  Identities=28%  Similarity=0.581  Sum_probs=126.8

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ++||||++++|+.++++||+||..|-+. +....+...+++||+......|...|.+||+.+ +-.+++||+.+...   
T Consensus       221 mmfsatlskeiRpvC~kFmQdPmEi~vD-dE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~L-eFNQVvIFvKsv~R---  295 (387)
T KOG0329|consen  221 MMFSATLSKEIRPVCHKFMQDPMEIFVD-DEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVL-EFNQVVIFVKSVQR---  295 (387)
T ss_pred             eeeeeecchhhHHHHHhhhcCchhhhcc-chhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhh-hhcceeEeeehhhh---
Confidence            5899999999999999999999998653 445667889999999999999999999999887 44799999988764   


Q ss_pred             HHHHHhcCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCC
Q 012133           81 VSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  160 (470)
Q Consensus        81 l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~  160 (470)
                          |             +          |   ..+ ||||++..||+||..|++|+|||+|.+.++|+||++|+||.|.
T Consensus       296 ----l-------------~----------f---~kr-~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGt  344 (387)
T KOG0329|consen  296 ----L-------------S----------F---QKR-LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGT  344 (387)
T ss_pred             ----h-------------h----------h---hhh-hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhcccc
Confidence                1             0          2   123 8999999999999999999999999999999999999999999


Q ss_pred             CCeEEEeeChh-hHHHHHHHHHHhCCCcc
Q 012133          161 EGTAILMFTSS-QRRTVRSLERDVGCKFE  188 (470)
Q Consensus       161 ~g~~i~l~~~~-~~~~~~~i~~~~~~~~~  188 (470)
                      .|.+|+|++.. +...+..+......++.
T Consensus       345 kglaitfvs~e~da~iLn~vqdRf~v~i~  373 (387)
T KOG0329|consen  345 KGLAITFVSDENDAKILNPVQDRFEVNIK  373 (387)
T ss_pred             ccceeehhcchhhHHHhchhhHhhhccHh
Confidence            99999999864 44555555555544443

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.79  E-value=4.6e-19  Score=179.91  Aligned_cols=241  Identities=17%  Similarity=0.274  Sum_probs=188.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHH-HHHHHHHH--cCCCeEEEEeCchHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTI-LSDLITVY--AKGGKTIVFTQTKRD   77 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~-l~~ll~~~--~~~~~~lVF~~t~~~   77 (470)
                      |+.||||..+   -.+.|+.+...+.+.+..     -.|..+|-..+.-+.+++ +..+++.+  .+.+.+|||....++
T Consensus       414 lIsSAT~DAe---kFS~fFDdapIF~iPGRR-----yPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeE  485 (902)
T KOG0923|consen  414 LISSATMDAE---KFSAFFDDAPIFRIPGRR-----YPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEE  485 (902)
T ss_pred             EeeccccCHH---HHHHhccCCcEEeccCcc-----cceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHH
Confidence            5789999865   345577776666664332     345667777777666654 44444433  356899999999998


Q ss_pred             HHHHHHHHhc----------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEec-------
Q 012133           78 ADEVSLALTS----------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE-------  140 (470)
Q Consensus        78 ~~~l~~~l~~----------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~-------  140 (470)
                      ++...+.|..          .+.+.+||+.||...+.++++.-..|..+|++||++|+..|.|++|.+||+-+       
T Consensus       486 IEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsy  565 (902)
T KOG0923|consen  486 IETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSY  565 (902)
T ss_pred             HHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCc
Confidence            8877777753          15689999999999999999999999999999999999999999999999433       


Q ss_pred             -----------CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHH
Q 012133          141 -----------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVAT  209 (470)
Q Consensus       141 -----------~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~  209 (470)
                                 .|.+..+-.||+||+||.| +|+|+.||+...+  ...++           ..+.++|....+..++..
T Consensus       566 nprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt~~aY--~~eLE-----------~~t~PEIqRtnL~nvVL~  631 (902)
T KOG0923|consen  566 NPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYTAWAY--EHELE-----------EMTVPEIQRTNLGNVVLL  631 (902)
T ss_pred             CCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeechhhh--hhhhc-----------cCCCcceeeccchhHHHH
Confidence                       3557788899999999996 9999999997442  22222           223356777788888999


Q ss_pred             HcccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCcccccCCCCeEEEEE
Q 012133          210 LNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL  268 (470)
Q Consensus       210 l~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r~l~~~~~~~~~~~~  268 (470)
                      |+++...++-.|     ++++.++.+.|..+|..|..+.+......|+...+.|..+++
T Consensus       632 LkSLGI~Dl~~F-----dFmDpPp~etL~~aLE~LyaLGALn~~GeLTk~GrrMaEfP~  685 (902)
T KOG0923|consen  632 LKSLGIHDLIHF-----DFLDPPPTETLLKALEQLYALGALNHLGELTKLGRRMAEFPV  685 (902)
T ss_pred             HHhcCcchhccc-----ccCCCCChHHHHHHHHHHHHhhccccccchhhhhhhhhhcCC
Confidence            999888777777     888999999999999999988888877788877777776665

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

Probab=99.78  E-value=1.6e-18  Score=172.47  Aligned_cols=122  Identities=33%  Similarity=0.555  Sum_probs=107.0

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc-CCcEE-EEe--------CCCCHHHHHHHHcccccCCe
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASE-ALH--------GDISQHQRERTLNGFRQGKF  115 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~-~lh--------g~~~~~~R~~~~~~f~~g~~  115 (470)
                      ..|++.+..+++.+   ..+.++|||++.+++++.|...|.+ +..+. .+-        .+|+|++|.+++++|+.|.+
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            46778788887644   2457999999999999999999986 33332 332        36999999999999999999


Q ss_pred             eEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChh
Q 012133          116 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS  171 (470)
Q Consensus       116 ~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~  171 (470)
                      +|||||+++++|||||++++||.|++-.|+..++||.|||||. +.|.+++|++..
T Consensus       427 nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~g  481 (542)
T COG1111         427 NVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEG  481 (542)
T ss_pred             eEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecC
Confidence            9999999999999999999999999999999999999999998 899999999876

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.78  E-value=5.5e-18  Score=180.78  Aligned_cols=164  Identities=19%  Similarity=0.207  Sum_probs=126.9

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHH-HHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~-~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|.-.+..++.+-|--+.  +.+... .+....... -.+.+....|..++...+. .+....++||||+|++.++.+
T Consensus       365 mTGTa~~~~~Ef~~iY~l~v--~~IPt~-kp~~r~d~~-d~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~l  440 (762)
T TIGR03714       365 MTGTGKVAEKEFIETYSLSV--VKIPTN-KPIIRIDYP-DKIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIY  440 (762)
T ss_pred             cCCCChhHHHHHHHHhCCCE--EEcCCC-CCeeeeeCC-CeEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHH
Confidence            67887666666666554332  333211 111111111 1233455678877777664 445678999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC---------CccEEEEecCCCChhHHHHH
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP---------NVDLIIHYELPNDPETFVHR  151 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip---------~v~~VI~~~~p~~~~~y~qr  151 (470)
                      +..|.+ ++++..||+++.+.++..+.++++.+  .|+||||+++||+||+         .+.+|++|++|..... +||
T Consensus       441 s~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr  517 (762)
T TIGR03714       441 SELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQL  517 (762)
T ss_pred             HHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHh
Confidence            999985 89999999999999999888888876  7999999999999999         9999999999988776 999


Q ss_pred             hcccCCCCCCCeEEEeeChhhH
Q 012133          152 SGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       152 ~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                      +|||||.|.+|.+++|++..+.
T Consensus       518 ~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       518 RGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             hhcccCCCCceeEEEEEccchh
Confidence            9999999999999999998663

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.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.78  E-value=1.9e-17  Score=178.43  Aligned_cols=138  Identities=28%  Similarity=0.422  Sum_probs=119.7

Q ss_pred             HHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC
Q 012133           53 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP  131 (470)
Q Consensus        53 ~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip  131 (470)
                      .++..+......+.++||||+|++.++.|++.|.. ++.+..+|+++++.+|..+++.|+.|++.|||||+++++|+|+|
T Consensus       434 ~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp  513 (652)
T PRK05298        434 DLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIP  513 (652)
T ss_pred             HHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCcccc
Confidence            34444444455678999999999999999999985 78999999999999999999999999999999999999999999


Q ss_pred             CccEEEEecC-----CCChhHHHHHhcccCCCCCCCeEEEeeCh---------hhHHHHHHHHHHhCCCccccC
Q 012133          132 NVDLIIHYEL-----PNDPETFVHRSGRTGRAGKEGTAILMFTS---------SQRRTVRSLERDVGCKFEFVS  191 (470)
Q Consensus       132 ~v~~VI~~~~-----p~~~~~y~qr~GR~gR~g~~g~~i~l~~~---------~~~~~~~~i~~~~~~~~~~~~  191 (470)
                      ++++||++|.     |.+..+|+||+|||||. ..|.+++|++.         .+...++.++..++.+...++
T Consensus       514 ~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  586 (652)
T PRK05298        514 EVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITP  586 (652)
T ss_pred             CCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCC
Confidence            9999999885     78999999999999997 78999999984         466777778877777666543

>PRK00254 ski2-like helicase; Provisional

Probab=99.77  E-value=8.6e-18  Score=184.29  Aligned_cols=111  Identities=26%  Similarity=0.442  Sum_probs=94.7

Q ss_pred             HcCCCeEEEEeCchHHHHHHHHHHhc----------------------------------CCcEEEEeCCCCHHHHHHHH
Q 012133           62 YAKGGKTIVFTQTKRDADEVSLALTS----------------------------------IIASEALHGDISQHQRERTL  107 (470)
Q Consensus        62 ~~~~~~~lVF~~t~~~~~~l~~~l~~----------------------------------~~~~~~lhg~~~~~~R~~~~  107 (470)
                      ...+.++||||+|++.|+.++..|..                                  ...+.++|++|++++|..++
T Consensus       235 i~~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve  314 (720)
T PRK00254        235 VKKGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIE  314 (720)
T ss_pred             HHhCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHH
Confidence            34568999999999999887766531                                  12488999999999999999


Q ss_pred             cccccCCeeEEEecccccccCCCCCccEEEE-------ecCCC-ChhHHHHHhcccCCCC--CCCeEEEeeChhh
Q 012133          108 NGFRQGKFTVLVATDVAARGLDIPNVDLIIH-------YELPN-DPETFVHRSGRTGRAG--KEGTAILMFTSSQ  172 (470)
Q Consensus       108 ~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~-------~~~p~-~~~~y~qr~GR~gR~g--~~g~~i~l~~~~~  172 (470)
                      +.|++|.++|||||+++++|||+|.+++||.       ++.|. +..+|+||+||+||.+  ..|.+++++...+
T Consensus       315 ~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        315 DAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             HHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcc
Confidence            9999999999999999999999999999994       45544 5679999999999975  6799999987654

>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=99.77  E-value=4.7e-18  Score=145.82  Aligned_cols=128  Identities=47%  Similarity=0.776  Sum_probs=113.2

Q ss_pred             eEEEEEEcCcccHHHHHHHHHHHHc-CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCee
Q 012133           39 IKLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        39 i~~~~~~~~~~~k~~~l~~ll~~~~-~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                      +.+++...+ +.|...+..++.... ...++||||+++..++.+++.|.+ ...+..+|+.++..+|..+++.|+++..+
T Consensus         2 i~~~~~~~~-~~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~   80 (131)
T cd00079           2 IKQYVLPVE-DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIV   80 (131)
T ss_pred             cEEEEEECC-HHHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCc
Confidence            344555543 367777888876553 567999999999999999999985 68899999999999999999999999999


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEe
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  167 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l  167 (470)
                      |||+|+++++|+|+|.+++||.+++|++...|+|++||++|.|+.+.++++
T Consensus        81 ili~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          81 VLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             EEEEcChhhcCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            999999999999999999999999999999999999999999988887764

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.77  E-value=4.2e-18  Score=180.64  Aligned_cols=165  Identities=21%  Similarity=0.240  Sum_probs=129.3

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHH-HHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~-ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|...+...+.+-|--+.+.|..  . .+....... -.+.....+|..++.. +...+..+.++||||+|++.++.|
T Consensus       346 mTGTa~te~~E~~~iY~l~vv~IPt--n-kp~~R~d~~-d~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~l  421 (745)
T TIGR00963       346 MTGTAKTEEEEFEKIYNLEVVVVPT--N-RPVIRKDLS-DLVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELL  421 (745)
T ss_pred             cCCCcHHHHHHHHHHhCCCEEEeCC--C-CCeeeeeCC-CeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHH
Confidence            6888877777777766544333321  1 111111111 1122333456655544 445566788999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCC-------ccEEEEecCCCChhHHHHHhc
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN-------VDLIIHYELPNDPETFVHRSG  153 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~-------v~~VI~~~~p~~~~~y~qr~G  153 (470)
                      +..|.+ ++++..||+.  +.+|+..+..|+.+...|+||||+|+||+||+.       .-+||+++.|.+...|.|+.|
T Consensus       422 s~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~G  499 (745)
T TIGR00963       422 SNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRG  499 (745)
T ss_pred             HHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhc
Confidence            999985 8999999999  889999999999999999999999999999998       459999999999999999999


Q ss_pred             ccCCCCCCCeEEEeeChhhH
Q 012133          154 RTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       154 R~gR~g~~g~~i~l~~~~~~  173 (470)
                      ||||.|.+|.+.+|++..+.
T Consensus       500 RtGRqG~~G~s~~~ls~eD~  519 (745)
T TIGR00963       500 RSGRQGDPGSSRFFLSLEDN  519 (745)
T ss_pred             cccCCCCCcceEEEEeccHH
Confidence            99999999999999998764

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.77  E-value=6.1e-18  Score=170.42  Aligned_cols=145  Identities=20%  Similarity=0.284  Sum_probs=104.8

Q ss_pred             CEEeecCCHHHHHHHHHH--cCCCcEEEeecccc-----------------cccccceEEEEEEcCcccHHHHHHHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKY--LDNPLNIDLVGNQD-----------------EKLAEGIKLYAISTTATSKRTILSDLITV   61 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~--l~~p~~i~~~~~~~-----------------~~~~~~i~~~~~~~~~~~k~~~l~~ll~~   61 (470)
                      |++|||+|+++.+..+..  +..|..+ +.+...                 ..+.+.+.+.+.. ....+.+.+..+++.
T Consensus       185 i~lSAT~~~~~~~~l~~~~~~~~~~~~-v~g~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~l~~l~~~  262 (357)
T TIGR03158       185 VFLSATPDPALILRLQNAKQAGVKIAP-IDGEKYQFPDNPELEADNKTQSFRPVLPPVELELIP-APDFKEEELSELAEE  262 (357)
T ss_pred             EEEecCCCHHHHHHHHhccccCceeee-ecCcccccCCChhhhccccccccceeccceEEEEEe-CCchhHHHHHHHHHH
Confidence            579999999988877654  4444322 222200                 0112356665555 334455544444332


Q ss_pred             ----H--cCCCeEEEEeCchHHHHHHHHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCC
Q 012133           62 ----Y--AKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN  132 (470)
Q Consensus        62 ----~--~~~~~~lVF~~t~~~~~~l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~  132 (470)
                          +  ....++||||+|++.++.+++.|.+   .+.+..+||.+++.+|+++.      +..||||||++++|||+|.
T Consensus       263 i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~~------~~~iLVaTdv~~rGiDi~~  336 (357)
T TIGR03158       263 VIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERAM------QFDILLGTSTVDVGVDFKR  336 (357)
T ss_pred             HHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHhc------cCCEEEEecHHhcccCCCC
Confidence                2  2457999999999999999999985   35788999999999998664      6789999999999999998


Q ss_pred             ccEEEEecCCCChhHHHHHhcccC
Q 012133          133 VDLIIHYELPNDPETFVHRSGRTG  156 (470)
Q Consensus       133 v~~VI~~~~p~~~~~y~qr~GR~g  156 (470)
                      + +|| ++ |.+.++|+||+||+|
T Consensus       337 ~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       337 D-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             c-eEE-EC-CCCHHHHhhhcccCC
Confidence            7 566 45 889999999999986

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

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.76  E-value=1.6e-17  Score=177.96  Aligned_cols=129  Identities=25%  Similarity=0.429  Sum_probs=114.0

Q ss_pred             HHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC
Q 012133           53 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP  131 (470)
Q Consensus        53 ~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip  131 (470)
                      .++..+......+.++||||+|++.++.|++.|.+ ++.+..+|+++++.+|.++++.|+.|++.|||||+++++|+|+|
T Consensus       430 ~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP  509 (655)
T TIGR00631       430 DLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLP  509 (655)
T ss_pred             HHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeC
Confidence            34444444556678999999999999999999985 78999999999999999999999999999999999999999999


Q ss_pred             CccEEEEec-----CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHH
Q 012133          132 NVDLIIHYE-----LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  182 (470)
Q Consensus       132 ~v~~VI~~~-----~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~  182 (470)
                      ++++||++|     .|.+..+|+||+|||||. ..|.++++++..+..+.+.|++.
T Consensus       510 ~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~ai~~~  564 (655)
T TIGR00631       510 EVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSMQKAIEET  564 (655)
T ss_pred             CCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHHHHHHH
Confidence            999999998     799999999999999998 78999999998766666555443

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

>PRK01172 ski2-like helicase; Provisional

Probab=99.75  E-value=2.3e-17  Score=180.05  Aligned_cols=109  Identities=25%  Similarity=0.369  Sum_probs=92.1

Q ss_pred             HcCCCeEEEEeCchHHHHHHHHHHhcC--------------------------CcEEEEeCCCCHHHHHHHHcccccCCe
Q 012133           62 YAKGGKTIVFTQTKRDADEVSLALTSI--------------------------IASEALHGDISQHQRERTLNGFRQGKF  115 (470)
Q Consensus        62 ~~~~~~~lVF~~t~~~~~~l~~~l~~~--------------------------~~~~~lhg~~~~~~R~~~~~~f~~g~~  115 (470)
                      ....+++||||+|++.++.++..|...                          ..+..+|++|++++|..+++.|++|.+
T Consensus       233 ~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i  312 (674)
T PRK01172        233 VNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYI  312 (674)
T ss_pred             HhCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCC
Confidence            446789999999999999999888532                          147789999999999999999999999


Q ss_pred             eEEEecccccccCCCCCccEEEEec---------CCCChhHHHHHhcccCCCC--CCCeEEEeeChh
Q 012133          116 TVLVATDVAARGLDIPNVDLIIHYE---------LPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  171 (470)
Q Consensus       116 ~iLVaTdv~~~Gidip~v~~VI~~~---------~p~~~~~y~qr~GR~gR~g--~~g~~i~l~~~~  171 (470)
                      +|||||+++++|||+|...+|| ++         .|.++.+|.||+||+||.|  ..|.+++++...
T Consensus       313 ~VLvaT~~la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~  378 (674)
T PRK01172        313 KVIVATPTLAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASP  378 (674)
T ss_pred             eEEEecchhhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCc
Confidence            9999999999999999875555 33         3568889999999999998  467788876543

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

Probab=99.74  E-value=2.3e-17  Score=180.22  Aligned_cols=178  Identities=22%  Similarity=0.331  Sum_probs=143.7

Q ss_pred             CEEeecCCHHHHHHHHHHc--CCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYL--DNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l--~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |.+|||....|++-+-..|  .+|..+.-.     ...+++.+........+....+...+..+.+...+||||.++.+|
T Consensus       424 iALTATAT~~v~~DIi~~L~l~~~~~~~~s-----fnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~c  498 (941)
T KOG0351|consen  424 IALTATATERVREDVIRSLGLRNPELFKSS-----FNRPNLKYEVSPKTDKDALLDILEESKLRHPDQSGIIYCLSRKEC  498 (941)
T ss_pred             EEeehhccHHHHHHHHHHhCCCCcceeccc-----CCCCCceEEEEeccCccchHHHHHHhhhcCCCCCeEEEeCCcchH
Confidence            4579999888777444444  466644321     223445433333322344444445555666788999999999999


Q ss_pred             HHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           79 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +.++..|.+ ++.+..+|++|+..+|+.+.+.|..++++|+|||=+...|||-|||..||||.+|++.+.|.|-+||+||
T Consensus       499 e~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGR  578 (941)
T KOG0351|consen  499 EQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGR  578 (941)
T ss_pred             HHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCc
Confidence            999999996 6799999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHHHHh
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLERDV  183 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~~~~  183 (470)
                      .|....|++||...+...++.+...-
T Consensus       579 DG~~s~C~l~y~~~D~~~l~~ll~s~  604 (941)
T KOG0351|consen  579 DGLPSSCVLLYGYADISELRRLLTSG  604 (941)
T ss_pred             CCCcceeEEecchhHHHHHHHHHHcc
Confidence            99999999999999887777665443

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.74  E-value=5.2e-17  Score=173.76  Aligned_cols=164  Identities=23%  Similarity=0.266  Sum_probs=127.5

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHH-HHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~-~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|...+...+.+-|--+.  |.+... .+....... -.+......|..+|...+. .+....++||||+|++.++.|
T Consensus       381 mTGTa~~e~~Ef~~iY~l~v--v~IPtn-kp~~r~d~~-d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~l  456 (796)
T PRK12906        381 MTGTAKTEEEEFREIYNMEV--ITIPTN-RPVIRKDSP-DLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERL  456 (796)
T ss_pred             cCCCCHHHHHHHHHHhCCCE--EEcCCC-CCeeeeeCC-CeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHH
Confidence            68888776666666564442  323211 111111111 1223344567777776664 456778999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCC---CCcc-----EEEEecCCCChhHHHHHh
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI---PNVD-----LIIHYELPNDPETFVHRS  152 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidi---p~v~-----~VI~~~~p~~~~~y~qr~  152 (470)
                      +..|.+ ++++..||+++.+.++..+.+.++.|.  |+|||++|+||+||   ++|.     |||+++.|.+...|.|+.
T Consensus       457 s~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~  534 (796)
T PRK12906        457 SHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLR  534 (796)
T ss_pred             HHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHh
Confidence            999985 799999999999888888888888765  99999999999999   4899     999999999999999999


Q ss_pred             cccCCCCCCCeEEEeeChhh
Q 012133          153 GRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~~  172 (470)
                      |||||.|.+|.+.+|++.++
T Consensus       535 GRtGRqG~~G~s~~~~sleD  554 (796)
T PRK12906        535 GRSGRQGDPGSSRFYLSLED  554 (796)
T ss_pred             hhhccCCCCcceEEEEeccc
Confidence            99999999999999998765

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=99.73  E-value=2.1e-16  Score=165.08  Aligned_cols=106  Identities=17%  Similarity=0.315  Sum_probs=90.9

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc--------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccE
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS--------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL  135 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~--------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~  135 (470)
                      -.+.++||.+-+..+..|...|..        .+.+.++|+.++..++.++.+....+..++|++|++++..|.|.++.+
T Consensus       642 i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~  721 (1282)
T KOG0921|consen  642 IDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVY  721 (1282)
T ss_pred             CccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeE
Confidence            357899999999999999887753        267999999999999999999999999999999999999999999988


Q ss_pred             EEEecCC------------------CChhHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          136 IIHYELP------------------NDPETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       136 VI~~~~p------------------~~~~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                      ||+.+.-                  .+..+.+||.||++|. ++|.|+.++..
T Consensus       722 vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~lcs~  773 (1282)
T KOG0921|consen  722 VIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFHLCSR  773 (1282)
T ss_pred             EEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccccccHH
Confidence            8844321                  2566779999999998 79999988765

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.72  E-value=2e-17  Score=168.45  Aligned_cols=241  Identities=19%  Similarity=0.298  Sum_probs=181.3

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHH-HHHHHHHH--cCCCeEEEEeCchHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTI-LSDLITVY--AKGGKTIVFTQTKRD   77 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~-l~~ll~~~--~~~~~~lVF~~t~~~   77 (470)
                      |++||||..  +++.. |+.+...+.+.+..     -.++..|...+.++..++ +.+.+..+  ...+.+|||.+..++
T Consensus       504 iVtSATm~a--~kf~n-fFgn~p~f~IpGRT-----yPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqed  575 (1042)
T KOG0924|consen  504 IVTSATMDA--QKFSN-FFGNCPQFTIPGRT-----YPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQED  575 (1042)
T ss_pred             EEeeccccH--HHHHH-HhCCCceeeecCCc-----cceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcc
Confidence            578999974  45555 45555556664432     345667777776666544 44444433  345899999998887


Q ss_pred             HHHHHHHHhc-----------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEec------
Q 012133           78 ADEVSLALTS-----------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE------  140 (470)
Q Consensus        78 ~~~l~~~l~~-----------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~------  140 (470)
                      ++-.+..+..           .+.+.+|++.||+..+.++++.-..+..+++|||++|+..|.||.+.+||+.+      
T Consensus       576 iE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kv  655 (1042)
T KOG0924|consen  576 IECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKV  655 (1042)
T ss_pred             hhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeee
Confidence            6665554431           26799999999999999999999999999999999999999999999999644      


Q ss_pred             ------------CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHH
Q 012133          141 ------------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVA  208 (470)
Q Consensus       141 ------------~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~  208 (470)
                                  .|.+..+-.||+||+||.+ +|.||.+|+...+             ...+.+.+.+||....+..++.
T Consensus       656 yn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe~ay-------------~~eml~stvPEIqRTNl~nvVL  721 (1042)
T KOG0924|consen  656 YNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTEDAY-------------KNEMLPSTVPEIQRTNLSNVVL  721 (1042)
T ss_pred             cccccccceeEEEechhccchhhccccCCCC-CcceeeehhhhHH-------------HhhcccCCCchhhhcchhhHHH
Confidence                        4667788899999999994 9999999988542             1223345567888888889999


Q ss_pred             HHcccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCcccccCCCCeEEEEE
Q 012133          209 TLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL  268 (470)
Q Consensus       209 ~l~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r~l~~~~~~~~~~~~  268 (470)
                      .|+++..+++..|     ++++.++.+.+..++-.|.-+.+.....-|+.....|+.+++
T Consensus       722 lLkslgV~dll~F-----dFmD~Pped~~~~sly~Lw~LGAl~~~g~LT~lG~~MvefpL  776 (1042)
T KOG0924|consen  722 LLKSLGVDDLLKF-----DFMDPPPEDNLLNSLYQLWTLGALDNTGQLTPLGRKMVEFPL  776 (1042)
T ss_pred             HHHhcChhhhhCC-----CcCCCCHHHHHHHHHHHHHHhhccccCCccchhhHHhhhCCC
Confidence            9999887777777     778888888899999988877766555556666666766655

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.72  E-value=1.5e-16  Score=167.42  Aligned_cols=112  Identities=18%  Similarity=0.213  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEec-cccccc
Q 012133           51 KRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT-DVAARG  127 (470)
Q Consensus        51 k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaT-dv~~~G  127 (470)
                      +..+|..++..+ ..+.++||||+++++++.|++.|.+ ++.+..+||+|++++|.++++.|++++..||||| +++++|
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            444555554433 3457899999999999999999985 7899999999999999999999999999999998 999999


Q ss_pred             CCCCCccEEEEecCCCChhHHHHHhcccCCCCCCC
Q 012133          128 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG  162 (470)
Q Consensus       128 idip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g  162 (470)
                      +|+|++++||++.++.+...|+||+||++|.+...
T Consensus       409 ~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K  443 (501)
T PHA02558        409 ISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSK  443 (501)
T ss_pred             cccccccEEEEecCCcchhhhhhhhhccccCCCCC
Confidence            99999999999999999999999999999986544

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

Probab=99.71  E-value=5e-16  Score=166.66  Aligned_cols=140  Identities=24%  Similarity=0.427  Sum_probs=112.5

Q ss_pred             HHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhcC--CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC
Q 012133           54 ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI--IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP  131 (470)
Q Consensus        54 ~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~~--~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip  131 (470)
                      ++..+.+...+...+|||+||+..++.++..|.+.  ..+..+||.++.++|..+.++|++|+.+++|||..++-|||+-
T Consensus       242 ~~~~i~~~v~~~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG  321 (814)
T COG1201         242 LYERIAELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIG  321 (814)
T ss_pred             HHHHHHHHHhhcCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccC
Confidence            33444444445579999999999999999999863  6899999999999999999999999999999999999999999


Q ss_pred             CccEEEEecCCCChhHHHHHhcccCC-CCCCCeEEEeeChhh--HHHHHHHHHHhCCCccccCCC
Q 012133          132 NVDLIIHYELPNDPETFVHRSGRTGR-AGKEGTAILMFTSSQ--RRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       132 ~v~~VI~~~~p~~~~~y~qr~GR~gR-~g~~g~~i~l~~~~~--~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      +|++||||..|.++..++||+||+|+ .+.....+++....+  ..........+.-+++.+.+|
T Consensus       322 ~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~r~dllE~~vi~~~a~~g~le~~~i~  386 (814)
T COG1201         322 DIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAEDRDDLLECLVLADLALEGKLERIKIP  386 (814)
T ss_pred             CceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecCHHHHHHHHHHHHHHHhCCcccCCCC
Confidence            99999999999999999999999986 456677777766632  122233344445555555444

>PRK09401 reverse gyrase; Reviewed

Probab=99.71  E-value=6.5e-17  Score=182.69  Aligned_cols=143  Identities=22%  Similarity=0.267  Sum_probs=116.1

Q ss_pred             CEEeecCCHH-HHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHH--
Q 012133            1 MLFSATMPSW-VKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD--   77 (470)
Q Consensus         1 llfSATlp~~-i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~--   77 (470)
                      |+||||+++. +..   .++.++..+.+..  ......+|.+.|+.++  ++.+.|..+++.+.  ..+||||+|++.  
T Consensus       272 ilfSAT~~~~~~~~---~l~~~ll~~~v~~--~~~~~rnI~~~yi~~~--~k~~~L~~ll~~l~--~~~LIFv~t~~~~~  342 (1176)
T PRK09401        272 VVSSATGRPRGNRV---KLFRELLGFEVGS--PVFYLRNIVDSYIVDE--DSVEKLVELVKRLG--DGGLIFVPSDKGKE  342 (1176)
T ss_pred             EEEeCCCCccchHH---HHhhccceEEecC--cccccCCceEEEEEcc--cHHHHHHHHHHhcC--CCEEEEEecccChH
Confidence            5899999875 332   2345565566532  2335677888888765  67777888887653  589999999777  


Q ss_pred             -HHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEe----cccccccCCCCC-ccEEEEecCCC------C
Q 012133           78 -ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELPN------D  144 (470)
Q Consensus        78 -~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVa----Tdv~~~Gidip~-v~~VI~~~~p~------~  144 (470)
                       +++|++.|.. ++.+..+||+|     ++.+++|++|+++||||    ||+++||||+|+ |.+||||++|.      .
T Consensus       343 ~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~  417 (1176)
T PRK09401        343 YAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEE  417 (1176)
T ss_pred             HHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccc
Confidence             9999999985 79999999999     23469999999999999    699999999999 89999999998      7


Q ss_pred             hhHHHHHhcccCC
Q 012133          145 PETFVHRSGRTGR  157 (470)
Q Consensus       145 ~~~y~qr~GR~gR  157 (470)
                      .+.|.||++|+-.
T Consensus       418 ~~~~~~~~~r~~~  430 (1176)
T PRK09401        418 ELAPPFLLLRLLS  430 (1176)
T ss_pred             cccCHHHHHHHHh
Confidence            7899999999864

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.70  E-value=1.9e-16  Score=170.54  Aligned_cols=165  Identities=22%  Similarity=0.257  Sum_probs=128.0

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHH-HcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~-~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|...+..++.+-|--+.+.|..  . .+....+.. -.+......|..+|...+.. +....++||||+|++.++.|
T Consensus       539 MTGTA~te~~Ef~~iY~L~Vv~IPT--n-rP~~R~D~~-d~vy~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~L  614 (1025)
T PRK12900        539 MTGTAETEASEFFEIYKLDVVVIPT--N-KPIVRKDMD-DLVYKTRREKYNAIVLKVEELQKKGQPVLVGTASVEVSETL  614 (1025)
T ss_pred             cCCCChhHHHHHHHHhCCcEEECCC--C-CCcceecCC-CeEecCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHH
Confidence            6778776666666666444333321  1 111111111 12234455788777777753 45678999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC---Ccc-----EEEEecCCCChhHHHHHh
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP---NVD-----LIIHYELPNDPETFVHRS  152 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip---~v~-----~VI~~~~p~~~~~y~qr~  152 (470)
                      +..|.. ++++..||+  .+.+|+..+..|+.+...|+||||+|+||+||+   .|.     +||+++.|.+...|.||.
T Consensus       615 s~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~  692 (1025)
T PRK12900        615 SRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLR  692 (1025)
T ss_pred             HHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHh
Confidence            999984 899999997  589999999999999999999999999999999   554     458999999999999999


Q ss_pred             cccCCCCCCCeEEEeeChhhH
Q 012133          153 GRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~~~  173 (470)
                      |||||.|.+|.+++|++..+.
T Consensus       693 GRtGRqGdpGsS~ffvSleD~  713 (1025)
T PRK12900        693 GRAGRQGDPGESVFYVSLEDE  713 (1025)
T ss_pred             hhhhcCCCCcceEEEechhHH
Confidence            999999999999999998764

>TIGR01054 rgy reverse gyrase

Probab=99.69  E-value=3.2e-16  Score=177.28  Aligned_cols=129  Identities=21%  Similarity=0.355  Sum_probs=102.5

Q ss_pred             EEeec-CCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCch---HH
Q 012133            2 LFSAT-MPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK---RD   77 (470)
Q Consensus         2 lfSAT-lp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~---~~   77 (470)
                      +|||| +|..++.   .+++++..+++..  ......++.+.|+.+..  +...|..+++.+  ...+||||+|+   +.
T Consensus       271 ~~SAT~~p~~~~~---~l~r~ll~~~v~~--~~~~~r~I~~~~~~~~~--~~~~L~~ll~~l--~~~~IVFv~t~~~~~~  341 (1171)
T TIGR01054       271 VSSATGRPRGKRA---KLFRELLGFEVGG--GSDTLRNVVDVYVEDED--LKETLLEIVKKL--GTGGIVYVSIDYGKEK  341 (1171)
T ss_pred             EEeCCCCccccHH---HHcccccceEecC--ccccccceEEEEEeccc--HHHHHHHHHHHc--CCCEEEEEeccccHHH
Confidence            58999 6766542   3556666676632  23456778888876543  345566777665  36899999999   99


Q ss_pred             HHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEe----cccccccCCCCC-ccEEEEecCCC
Q 012133           78 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELPN  143 (470)
Q Consensus        78 ~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVa----Tdv~~~Gidip~-v~~VI~~~~p~  143 (470)
                      |++|++.|.+ ++.+..+||+|++    .++++|++|+++||||    ||+++||||+|+ |++||||++|.
T Consensus       342 a~~l~~~L~~~g~~a~~lhg~~~~----~~l~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       342 AEEIAEFLENHGVKAVAYHATKPK----EDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             HHHHHHHHHhCCceEEEEeCCCCH----HHHHHHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCCC
Confidence            9999999985 7999999999973    6899999999999999    599999999999 89999998773

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.

>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=99.69  E-value=4.7e-17  Score=127.09  Aligned_cols=76  Identities=39%  Similarity=0.768  Sum_probs=72.3

Q ss_pred             HHh-cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           84 ALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        84 ~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      .|+ .++.+..+|+++++.+|+.+++.|+++...|||||+++++|||+|++++||++++|+++..|+|++||++|.|
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            344 3789999999999999999999999999999999999999999999999999999999999999999999975

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 ....

>PRK09694 helicase Cas3; Provisional

Probab=99.69  E-value=6.5e-15  Score=161.39  Aligned_cols=107  Identities=25%  Similarity=0.449  Sum_probs=90.7

Q ss_pred             HHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhcC----CcEEEEeCCCCHHHH----HHHHccc-ccCC---eeEE
Q 012133           51 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI----IASEALHGDISQHQR----ERTLNGF-RQGK---FTVL  118 (470)
Q Consensus        51 k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~~----~~~~~lhg~~~~~~R----~~~~~~f-~~g~---~~iL  118 (470)
                      ...++..+++.....+++||||||++.|+++++.|++.    ..+..+|+.+++.+|    +++++.| ++++   .+||
T Consensus       546 ~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~IL  625 (878)
T PRK09694        546 DLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRIL  625 (878)
T ss_pred             HHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEE
Confidence            34566667766667789999999999999999999853    479999999999999    4577788 6665   4799


Q ss_pred             EecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCC
Q 012133          119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  160 (470)
Q Consensus       119 VaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~  160 (470)
                      |||+++++|||| +++++|....|  .+.|+||+||++|.++
T Consensus       626 VaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        626 VATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             EECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            999999999999 58999998777  6799999999999874

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.68  E-value=6.2e-16  Score=165.11  Aligned_cols=119  Identities=24%  Similarity=0.334  Sum_probs=102.0

Q ss_pred             cHHHHHHHHHHHHc-CCCeEEEEeCchHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHcccccC-CeeEEEeccccccc
Q 012133           50 SKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQG-KFTVLVATDVAARG  127 (470)
Q Consensus        50 ~k~~~l~~ll~~~~-~~~~~lVF~~t~~~~~~l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g-~~~iLVaTdv~~~G  127 (470)
                      .|+.++..+++.+. .+.++||||.+...++.+++.|.    +..|||.+++.+|+++++.|+++ .+++||+|+++.+|
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 NKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG----KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTS  555 (732)
T ss_pred             HHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC----CceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccc
Confidence            45666677776653 56799999999999999988873    56799999999999999999975 78999999999999


Q ss_pred             CCCCCccEEEEecCCC-ChhHHHHHhcccCCCCCCCeE-------EEeeChhh
Q 012133          128 LDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTA-------ILMFTSSQ  172 (470)
Q Consensus       128 idip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~-------i~l~~~~~  172 (470)
                      ||+|++++||+++.|. +...|+||+||++|.+..+.+       |.|++..+
T Consensus       556 IDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT  608 (732)
T TIGR00603       556 IDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDT  608 (732)
T ss_pred             cCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCc
Confidence            9999999999999985 999999999999998766554       67777643

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).

>PRK14701 reverse gyrase; Provisional

Probab=99.68  E-value=1.5e-16  Score=183.42  Aligned_cols=167  Identities=17%  Similarity=0.233  Sum_probs=130.2

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHH---
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD---   77 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~---   77 (470)
                      |+||||+++.- ++ .++++++..+.+.  .......++.+.|+.+....+ ..|..+++..  ...+||||+|++.   
T Consensus       273 l~~SAT~~~r~-~~-~~l~~~~l~f~v~--~~~~~lr~i~~~yi~~~~~~k-~~L~~ll~~~--g~~gIVF~~t~~~~e~  345 (1638)
T PRK14701        273 IVASATGKAKG-DR-VKLYRELLGFEVG--SGRSALRNIVDVYLNPEKIIK-EHVRELLKKL--GKGGLIFVPIDEGAEK  345 (1638)
T ss_pred             EEEecCCCchh-HH-HHHhhcCeEEEec--CCCCCCCCcEEEEEECCHHHH-HHHHHHHHhC--CCCeEEEEeccccchH
Confidence            46899999641 12 2345677777663  233456778888887655545 4566777665  3689999999875   


Q ss_pred             HHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEec----ccccccCCCCC-ccEEEEecCCC---ChhHH
Q 012133           78 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT----DVAARGLDIPN-VDLIIHYELPN---DPETF  148 (470)
Q Consensus        78 ~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaT----dv~~~Gidip~-v~~VI~~~~p~---~~~~y  148 (470)
                      |++|++.|.. ++.+..+|++     |..++++|++|+++|||||    ++++||||+|+ |.+||||++|.   +.+.|
T Consensus       346 ae~la~~L~~~Gi~a~~~h~~-----R~~~l~~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~  420 (1638)
T PRK14701        346 AEEIEKYLLEDGFKIELVSAK-----NKKGFDLFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLE  420 (1638)
T ss_pred             HHHHHHHHHHCCCeEEEecch-----HHHHHHHHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhc
Confidence            5899999985 8999999995     8899999999999999999    59999999999 99999999999   88877


Q ss_pred             HHHh-------------cccCCCCCCCeEEEeeChhhHHHHHHH
Q 012133          149 VHRS-------------GRTGRAGKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       149 ~qr~-------------GR~gR~g~~g~~i~l~~~~~~~~~~~i  179 (470)
                      .|..             +|++|.|.+..++..+...+...++.+
T Consensus       421 ~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~~~~~~~~~~~  464 (1638)
T PRK14701        421 DPTIYRILGLLSEILKIEEELKEGIPIEGVLDVFPEDVEFLRSI  464 (1638)
T ss_pred             ccchhhhhcchHHHHHhhhhcccCCcchhHHHhHHHHHHHHHHH
Confidence            6655             999999988888766666665555544

>PRK13766 Hef nuclease; Provisional

Probab=99.68  E-value=9e-16  Score=170.34  Aligned_cols=122  Identities=35%  Similarity=0.558  Sum_probs=109.4

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCC--------CCHHHHHHHHcccccCCee
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGD--------ISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~--------~~~~~R~~~~~~f~~g~~~  116 (470)
                      ..|.+.|.++|+..   ..+.++||||+++..++.|++.|.. ++.+..+||.        |++.+|.+++++|++++++
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 7888899986        9999999999999999999


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChh
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS  171 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~  171 (470)
                      |||||+++++|+|+|++++||+||+|++...|+||+||+||.+ ++.+++|+...
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            9999999999999999999999999999999999999999985 58888887753

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=99.67  E-value=3.7e-16  Score=168.27  Aligned_cols=238  Identities=19%  Similarity=0.266  Sum_probs=170.8

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccc--------------cceEEEEEE------------cCcccHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLA--------------EGIKLYAIS------------TTATSKRTI   54 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~--------------~~i~~~~~~------------~~~~~k~~~   54 (470)
                      ||||||+..+   +.+.|+.....|.+.+...+...              ....++...            ...+-..++
T Consensus       323 ILMSAT~dae---~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~L  399 (924)
T KOG0920|consen  323 ILMSATLDAE---LFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDL  399 (924)
T ss_pred             EEeeeecchH---HHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHH
Confidence            6999999843   56777777766766443211100              000111000            011123455


Q ss_pred             HHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc--------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc
Q 012133           55 LSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS--------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  123 (470)
Q Consensus        55 l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~--------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv  123 (470)
                      +.+++..+   ...+.+|||.+...++..+++.|..        .+.+.++|+.|+..+++.+++....|..+||+||++
T Consensus       400 i~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNI  479 (924)
T KOG0920|consen  400 IEDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNI  479 (924)
T ss_pred             HHHHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhhh
Confidence            66666544   3467999999999999999999963        156889999999999999999999999999999999


Q ss_pred             ccccCCCCCccEEEE--------ecCCC----------ChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCC
Q 012133          124 AARGLDIPNVDLIIH--------YELPN----------DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGC  185 (470)
Q Consensus       124 ~~~Gidip~v~~VI~--------~~~p~----------~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~  185 (470)
                      |+.+|.|+||.+||+        ||+-.          +...-.||.||+||. ++|.||.+|+...+..+         
T Consensus       480 AETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~~~~---------  549 (924)
T KOG0920|consen  480 AETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRYEKL---------  549 (924)
T ss_pred             HhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhhhhc---------
Confidence            999999999999994        45433          445558999999999 89999999998553211         


Q ss_pred             CccccCCCCHHHHHHHHHHHHHHHHcccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCccccc
Q 012133          186 KFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLIN  258 (470)
Q Consensus       186 ~~~~~~~p~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r~l~~  258 (470)
                          ...-+.+|++...+++++..++-+....+.   +...++++.++++++..|+..|..+.+....-.|+.
T Consensus       550 ----~~~~q~PEilR~pL~~l~L~iK~l~~~~~~---~fLskaldpP~~~~v~~a~~~L~~igaL~~~e~LT~  615 (924)
T KOG0920|consen  550 ----MLAYQLPEILRTPLEELCLHIKVLEQGSIK---AFLSKALDPPPADAVDLAIERLKQIGALDESEELTP  615 (924)
T ss_pred             ----ccccCChHHHhChHHHhhheeeeccCCCHH---HHHHHhcCCCChHHHHHHHHHHHHhccccCcccchH
Confidence                111345688888888888888866666665   445688899999999999988876655544445543

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=99.67  E-value=1.7e-15  Score=159.05  Aligned_cols=123  Identities=33%  Similarity=0.555  Sum_probs=106.0

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc----CCcEEEEeC--------CCCHHHHHHHHcccccC
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS----IIASEALHG--------DISQHQRERTLNGFRQG  113 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~----~~~~~~lhg--------~~~~~~R~~~~~~f~~g  113 (470)
                      ..|++.|.++|..+   .+..++||||.+++.|..|...|..    .+....+-|        +|+|.++++++++|++|
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            56788888777543   3457999999999999999999873    234444433        69999999999999999


Q ss_pred             CeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhH
Q 012133          114 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       114 ~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                      +++|||||.|+++||||+.|++||-||.-.++...+||.|| ||+ +.|.|+++++..+.
T Consensus       474 ~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa-~ns~~vll~t~~~~  531 (746)
T KOG0354|consen  474 EINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRA-RNSKCVLLTTGSEV  531 (746)
T ss_pred             CccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-ccc-cCCeEEEEEcchhH
Confidence            99999999999999999999999999999999999999999 998 78999999885443

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

Probab=99.65  E-value=1.1e-15  Score=153.46  Aligned_cols=163  Identities=23%  Similarity=0.358  Sum_probs=129.1

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEc-CcccHHHHHHHHHHHH-------cCCCeEEEEe
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAIST-TATSKRTILSDLITVY-------AKGGKTIVFT   72 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~-~~~~k~~~l~~ll~~~-------~~~~~~lVF~   72 (470)
                      |-+|||+-+. +.+++++-.+.+..+      .. +..++.+.+.+ ...+|.+++..|.+..       .-.+++|||+
T Consensus       376 i~LSATVgNp-~elA~~l~a~lV~y~------~R-PVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT  447 (830)
T COG1202         376 IYLSATVGNP-EELAKKLGAKLVLYD------ER-PVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFT  447 (830)
T ss_pred             EEEEeecCCh-HHHHHHhCCeeEeec------CC-CCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEe
Confidence            4589998654 457776644433322      11 23344444444 4678999999988642       1247999999


Q ss_pred             CchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEE---EecCCC-ChhH
Q 012133           73 QTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII---HYELPN-DPET  147 (470)
Q Consensus        73 ~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI---~~~~p~-~~~~  147 (470)
                      +++..|.+|+..|. +++.+.++|++|+..+|+.+...|.++.+.++|+|-+++.|+|+|.-.+|+   -++.-| ++..
T Consensus       448 ~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaMG~~WLs~~E  527 (830)
T COG1202         448 YSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVRE  527 (830)
T ss_pred             cchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHHHHHcccccCCHHH
Confidence            99999999999998 589999999999999999999999999999999999999999999866655   245555 8999


Q ss_pred             HHHHhcccCCCC--CCCeEEEeeChh
Q 012133          148 FVHRSGRTGRAG--KEGTAILMFTSS  171 (470)
Q Consensus       148 y~qr~GR~gR~g--~~g~~i~l~~~~  171 (470)
                      |.||+||+||.+  ..|++|+++.+.
T Consensus       528 F~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         528 FQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             HHHHhcccCCCCcccCceEEEEecCC
Confidence            999999999987  669999998764

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=99.64  E-value=3.3e-16  Score=152.25  Aligned_cols=175  Identities=22%  Similarity=0.362  Sum_probs=135.4

Q ss_pred             CEEeecCCHHHHHHHH--HHcCCCcEEEeecccccccccceEEEEEEc---CcccHHHHHHHHHH-HHc-----------
Q 012133            1 MLFSATMPSWVKKLSR--KYLDNPLNIDLVGNQDEKLAEGIKLYAIST---TATSKRTILSDLIT-VYA-----------   63 (470)
Q Consensus         1 llfSATlp~~i~~l~~--~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~---~~~~k~~~l~~ll~-~~~-----------   63 (470)
                      |.++||....|++-+-  .-|++|+.|--.    +....++  +|-..   .-++-...|.++.. .+.           
T Consensus       180 vALTATA~~~VqEDi~~qL~L~~PVAiFkT----P~FR~NL--FYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~  253 (641)
T KOG0352|consen  180 VALTATANAKVQEDIAFQLKLRNPVAIFKT----PTFRDNL--FYDNHMKSFITDCLTVLADFSSSNLGKHEKASQNKKT  253 (641)
T ss_pred             EEeecccChhHHHHHHHHHhhcCcHHhccC----cchhhhh--hHHHHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCC
Confidence            3579999888877333  346688766321    1111221  11100   01233344444332 221           


Q ss_pred             CCCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP  142 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p  142 (470)
                      ..+--||||.|++.|++++-.|. .++.+..+|.+|...+|.++.++|.++++.||+||.....|+|-|+|.+|||+++|
T Consensus       254 ~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~  333 (641)
T KOG0352|consen  254 FTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPS  333 (641)
T ss_pred             cCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCch
Confidence            12457999999999999999998 48999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHH
Q 012133          143 NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  181 (470)
Q Consensus       143 ~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~  181 (470)
                      .++..|.|.+||+||.|+...|-++|..++...+..|.+
T Consensus       334 qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FLi~  372 (641)
T KOG0352|consen  334 QNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFLVS  372 (641)
T ss_pred             hhhHHHHHhccccccCCCccceeeeecccchHHHHHHHh
Confidence            999999999999999999999999999998877776643

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.64  E-value=3.6e-15  Score=147.24  Aligned_cols=235  Identities=16%  Similarity=0.274  Sum_probs=177.6

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHH-HHHHH--cCCCeEEEEeCchHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD-LITVY--AKGGKTIVFTQTKRD   77 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~-ll~~~--~~~~~~lVF~~t~~~   77 (470)
                      |+||||+...   -.+.|+.++..+.+.+      ...++.+|...+..+.+++..+ +++.+  ...+.+|||.+..++
T Consensus       195 vvmSatl~a~---Kfq~yf~n~Pll~vpg------~~PvEi~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeee  265 (699)
T KOG0925|consen  195 VVMSATLDAE---KFQRYFGNAPLLAVPG------THPVEIFYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEE  265 (699)
T ss_pred             EEeecccchH---HHHHHhCCCCeeecCC------CCceEEEecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHH
Confidence            5799998754   3567888888887743      2346668877777777655444 44443  456899999999999


Q ss_pred             HHHHHHHHhcC----------CcEEEEeCCCCHHHHHHHHcccccC-----CeeEEEecccccccCCCCCccEEEEec--
Q 012133           78 ADEVSLALTSI----------IASEALHGDISQHQRERTLNGFRQG-----KFTVLVATDVAARGLDIPNVDLIIHYE--  140 (470)
Q Consensus        78 ~~~l~~~l~~~----------~~~~~lhg~~~~~~R~~~~~~f~~g-----~~~iLVaTdv~~~Gidip~v~~VI~~~--  140 (470)
                      ++..++.+...          +.|.+||    ++++..+++.....     ..+|+|+|++++..+.|+.|.+||+-+  
T Consensus       266 Ie~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~  341 (699)
T KOG0925|consen  266 IEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFS  341 (699)
T ss_pred             HHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchh
Confidence            99988888631          5789999    55566666665431     368999999999999999999999533  


Q ss_pred             ----------------CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHH
Q 012133          141 ----------------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAE  204 (470)
Q Consensus       141 ----------------~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~  204 (470)
                                      -|.|..+-.||.||+||. ++|+|+.||+++..          +   ..+.+.+.++++++.+.
T Consensus       342 kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~~~----------~---~em~~~typeilrsNL~  407 (699)
T KOG0925|consen  342 KQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF----------E---KEMQPQTYPEILRSNLS  407 (699)
T ss_pred             hhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHHhh----------h---hcCCCCCcHHHHHHhhH
Confidence                            366888889999999998 79999999987432          1   12344567899999999


Q ss_pred             HHHHHHcccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCcccccCCCCeEEEE
Q 012133          205 QVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ  267 (470)
Q Consensus       205 ~~~~~l~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r~l~~~~~~~~~~~  267 (470)
                      .++..|+++..+++-.|     ++++.+.+|.++.||..|.-+.+......|+....-|..++
T Consensus       408 s~VL~LKklgI~dlvhf-----dfmDpPAPEtLMrALE~LnYLaaLdDdGnLT~lG~imSEFP  465 (699)
T KOG0925|consen  408 STVLQLKKLGIDDLVHF-----DFMDPPAPETLMRALEVLNYLAALDDDGNLTSLGEIMSEFP  465 (699)
T ss_pred             HHHHHHHhcCcccccCC-----cCCCCCChHHHHHHHHHhhhhhhhCCCcccchhhhhhhcCC
Confidence            99999999988887777     78888999999999999886666666666665444444333

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

Probab=99.62  E-value=1.8e-14  Score=149.41  Aligned_cols=166  Identities=20%  Similarity=0.278  Sum_probs=127.9

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchH----
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKR----   76 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~----   76 (470)
                      |+||||.-+....+...---|-..|+-    -+.-...|+.+.+  +.+.+.+++..+.+...++.++.|.||-.+    
T Consensus       415 LvMTATPIPRTLAlt~fgDldvS~IdE----lP~GRkpI~T~~i--~~~~~~~v~e~i~~ei~~GrQaY~VcPLIeESE~  488 (677)
T COG1200         415 LVMTATPIPRTLALTAFGDLDVSIIDE----LPPGRKPITTVVI--PHERRPEVYERIREEIAKGRQAYVVCPLIEESEK  488 (677)
T ss_pred             EEEeCCCchHHHHHHHhccccchhhcc----CCCCCCceEEEEe--ccccHHHHHHHHHHHHHcCCEEEEEecccccccc
Confidence            589999766554444322223333321    1222244555544  346777778888777778889999998765    


Q ss_pred             ----HHHHHHHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC-ChhHH
Q 012133           77 ----DADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-DPETF  148 (470)
Q Consensus        77 ----~~~~l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~y  148 (470)
                          .|+++++.|..   .+.+..+||.|+.+++++++++|++++++|||||.|.+.|||+|+.+++|.++.-. -..++
T Consensus       489 l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFGLaQL  568 (677)
T COG1200         489 LELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQL  568 (677)
T ss_pred             chhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEechhhhhHHHH
Confidence                45566677764   35699999999999999999999999999999999999999999999988887654 78899


Q ss_pred             HHHhcccCCCCCCCeEEEeeChhh
Q 012133          149 VHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       149 ~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      .|-.||+||...+..|++++.+..
T Consensus       569 HQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         569 HQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             HHhccccCCCCcceEEEEEeCCCC
Confidence            999999999999999999999866

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

Probab=99.59  E-value=2.2e-14  Score=136.54  Aligned_cols=175  Identities=19%  Similarity=0.290  Sum_probs=124.6

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHH------HHHHHHHH-HcCCCeEEEEeC
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT------ILSDLITV-YAKGGKTIVFTQ   73 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~------~l~~ll~~-~~~~~~~lVF~~   73 (470)
                      |.+|||.|+++++-+..-  +-..+.+.. +-+..+..+..+...-++..++.      .|..+|+. ...+.++|||++
T Consensus       237 IylTATp~k~l~r~~~~g--~~~~~klp~-RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p  313 (441)
T COG4098         237 IYLTATPTKKLERKILKG--NLRILKLPA-RFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFP  313 (441)
T ss_pred             EEEecCChHHHHHHhhhC--CeeEeecch-hhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEec
Confidence            578999998866544322  222344332 22333334444555555544431      34455543 345679999999


Q ss_pred             chHHHHHHHHHHhcC---CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEE-ecC-CCChhHH
Q 012133           74 TKRDADEVSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-YEL-PNDPETF  148 (470)
Q Consensus        74 t~~~~~~l~~~l~~~---~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~-~~~-p~~~~~y  148 (470)
                      +.+..++++..|++.   ..+..+|+.  ...|.+.+++||+|+++|||+|.+++||+.+|+|+++|. ..- -.+.+.+
T Consensus       314 ~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~vfTesaL  391 (441)
T COG4098         314 EIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESAL  391 (441)
T ss_pred             chHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEecCCcccccHHHH
Confidence            999999999999754   346788987  667899999999999999999999999999999998664 332 2488999


Q ss_pred             HHHhcccCCCC--CCCeEEEeeChhhHHHHHHHH
Q 012133          149 VHRSGRTGRAG--KEGTAILMFTSSQRRTVRSLE  180 (470)
Q Consensus       149 ~qr~GR~gR~g--~~g~~i~l~~~~~~~~~~~i~  180 (470)
                      +|.+||+||.-  ..|.++.|-......+.+...
T Consensus       392 VQIaGRvGRs~~~PtGdv~FFH~G~skaM~~A~k  425 (441)
T COG4098         392 VQIAGRVGRSLERPTGDVLFFHYGKSKAMKQARK  425 (441)
T ss_pred             HHHhhhccCCCcCCCCcEEEEeccchHHHHHHHH
Confidence            99999999954  468888887776655555443

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.58  E-value=9.2e-15  Score=151.53  Aligned_cols=159  Identities=21%  Similarity=0.323  Sum_probs=115.7

Q ss_pred             EEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecC--------CC----------ChhHHHHHh
Q 012133           91 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL--------PN----------DPETFVHRS  152 (470)
Q Consensus        91 ~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~--------p~----------~~~~y~qr~  152 (470)
                      |.+|++-|+.+.+.++++....|..-++|||+||+..|.||.|.+||+++.        -.          |..+--||+
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            677889999999999999999999999999999999999999999995442        22          344457999


Q ss_pred             cccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHHHHHHHHHHHHHHcccCccchhhhHHHHHHHHHhh
Q 012133          153 GRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEK  232 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~l~~~~  232 (470)
                      ||+||.| +|+||.||+..-.          ...|+..   +.++|+..-++.++..++.++...+..|     .+-..+
T Consensus       687 GRAGRtg-pGHcYRLYSSAVf----------~~~Fe~f---S~PEIlk~Pve~lvLqMKsMnI~kVvnF-----PFPtpP  747 (1172)
T KOG0926|consen  687 GRAGRTG-PGHCYRLYSSAVF----------SNDFEEF---SLPEILKKPVESLVLQMKSMNIDKVVNF-----PFPTPP  747 (1172)
T ss_pred             cccCCCC-CCceeehhhhHHh----------hcchhhh---ccHHHhhCcHHHHHHHHHhcCccceecC-----CCCCCc
Confidence            9999995 9999999987322          1123322   3568889999999999999887776665     222334


Q ss_pred             CHHHHHHHHHHHcCCCCCCCCcccccCCCCeEEEEE
Q 012133          233 GTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQL  268 (470)
Q Consensus       233 ~~~~l~~al~~l~~~~~~~~~r~l~~~~~~~~~~~~  268 (470)
                      +..+|.+|.-.|.-+.+......++..+..|..+++
T Consensus       748 d~~~L~~Aer~L~~LgALd~~g~lT~lGk~mS~FPl  783 (1172)
T KOG0926|consen  748 DRSALEKAERRLKALGALDSNGGLTKLGKAMSLFPL  783 (1172)
T ss_pred             cHHHHHHHHHHHHHhccccccCCcccccchhccccc
Confidence            456676666666555554444445544444444444

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.54  E-value=1.9e-14  Score=112.71  Aligned_cols=80  Identities=53%  Similarity=0.867  Sum_probs=74.3

Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .+++.|.. .+.+..+|+++++++|..+++.|+++...|||+|+++++|+|+|++++||.+++|++...|+|++||++|.
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            45566654 68899999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 012133          159 G  159 (470)
Q Consensus       159 g  159 (470)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            4

>TIGR00595 priA primosomal protein N'

Probab=99.53  E-value=1.3e-13  Score=144.61  Aligned_cols=94  Identities=27%  Similarity=0.432  Sum_probs=78.1

Q ss_pred             HHHHHHHHhc---CCcEEEEeCCCCHHHH--HHHHcccccCCeeEEEecccccccCCCCCccEEE--EecC----CC---
Q 012133           78 ADEVSLALTS---IIASEALHGDISQHQR--ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII--HYEL----PN---  143 (470)
Q Consensus        78 ~~~l~~~l~~---~~~~~~lhg~~~~~~R--~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI--~~~~----p~---  143 (470)
                      ++++++.|.+   ..++..+|+++++.++  ++++++|++++.+|||+|+++++|+|+|+|++|+  ++|.    |.   
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            5777788775   3578999999987766  8999999999999999999999999999999885  5664    32   


Q ss_pred             ---ChhHHHHHhcccCCCCCCCeEEEeeChh
Q 012133          144 ---DPETFVHRSGRTGRAGKEGTAILMFTSS  171 (470)
Q Consensus       144 ---~~~~y~qr~GR~gR~g~~g~~i~l~~~~  171 (470)
                         ....|+|++||+||.++.|.+++.....
T Consensus       351 ~E~~~~ll~q~~GRagR~~~~g~viiqt~~p  381 (505)
T TIGR00595       351 AERGFQLLTQVAGRAGRAEDPGQVIIQTYNP  381 (505)
T ss_pred             HHHHHHHHHHHHhccCCCCCCCEEEEEeCCC
Confidence               2467899999999999999998765433

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).

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

Probab=99.51  E-value=1.5e-12  Score=130.64  Aligned_cols=133  Identities=26%  Similarity=0.417  Sum_probs=115.5

Q ss_pred             cCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccc
Q 012133           46 TTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  124 (470)
Q Consensus        46 ~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~  124 (470)
                      ....+..+++..+.+....+.++||-+-|++.|+.|.++|.. ++++..+|+++..-+|.+++..+|.|.+.|||.-+++
T Consensus       427 p~~~QvdDL~~EI~~r~~~~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLL  506 (663)
T COG0556         427 PTKGQVDDLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLL  506 (663)
T ss_pred             cCCCcHHHHHHHHHHHHhcCCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhh
Confidence            334466677777777677789999999999999999999985 8999999999999999999999999999999999999


Q ss_pred             cccCCCCCccEEEEec-----CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHH
Q 012133          125 ARGLDIPNVDLIIHYE-----LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       125 ~~Gidip~v~~VI~~~-----~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i  179 (470)
                      -+|||+|.|.+|...|     +..|..++||-+||++|. -.|.+|++.+.-...+.+.|
T Consensus       507 REGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN-~~GkvIlYAD~iT~sM~~Ai  565 (663)
T COG0556         507 REGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAI  565 (663)
T ss_pred             hccCCCcceeEEEEeecCccccccccchHHHHHHHHhhc-cCCeEEEEchhhhHHHHHHH
Confidence            9999999999998776     456899999999999996 68999999876555544444

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.51  E-value=1.6e-13  Score=149.00  Aligned_cols=119  Identities=29%  Similarity=0.511  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc---C-----------------------------------CcEEE
Q 012133           52 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---I-----------------------------------IASEA   93 (470)
Q Consensus        52 ~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~---~-----------------------------------~~~~~   93 (470)
                      ..++..++..+..++++||||+++..+...++.|.+   .                                   ..+..
T Consensus       240 ~~~~~~v~~~~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~Gvaf  319 (766)
T COG1204         240 NLALELVLESLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAF  319 (766)
T ss_pred             HHHHHHHHHHHhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccc
Confidence            455566667777889999999999999999888872   0                                   13567


Q ss_pred             EeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEE----Eec-----CCCChhHHHHHhcccCCCC--CCC
Q 012133           94 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII----HYE-----LPNDPETFVHRSGRTGRAG--KEG  162 (470)
Q Consensus        94 lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI----~~~-----~p~~~~~y~qr~GR~gR~g--~~g  162 (470)
                      +|++|+.++|..+.+.|+.|.++|||||+.++.|+|+|.-.+||    -|+     .+.++-+|+|++||+||.|  ..|
T Consensus       320 HhAGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G  399 (766)
T COG1204         320 HHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYG  399 (766)
T ss_pred             cccCCCHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCC
Confidence            89999999999999999999999999999999999999877777    466     5668899999999999987  557


Q ss_pred             eEEEeeCh
Q 012133          163 TAILMFTS  170 (470)
Q Consensus       163 ~~i~l~~~  170 (470)
                      ..+++.+.
T Consensus       400 ~~~i~~~~  407 (766)
T COG1204         400 EAIILATS  407 (766)
T ss_pred             cEEEEecC
Confidence            77777733

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

Probab=99.50  E-value=1.4e-12  Score=142.62  Aligned_cols=175  Identities=18%  Similarity=0.293  Sum_probs=135.6

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |-+|||.-+....++-.-++|-..|...+..    ...|+.|...-   +..-+=..+++.+..++++-...|..+++++
T Consensus       746 LTLSATPIPRTL~Msm~GiRdlSvI~TPP~~----R~pV~T~V~~~---d~~~ireAI~REl~RgGQvfYv~NrV~~Ie~  818 (1139)
T COG1197         746 LTLSATPIPRTLNMSLSGIRDLSVIATPPED----RLPVKTFVSEY---DDLLIREAILRELLRGGQVFYVHNRVESIEK  818 (1139)
T ss_pred             EEeeCCCCcchHHHHHhcchhhhhccCCCCC----CcceEEEEecC---ChHHHHHHHHHHHhcCCEEEEEecchhhHHH
Confidence            4589997777777777777787777653221    12333333222   2222223355666788999999999999999


Q ss_pred             HHHHHhcC---CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC-ChhHHHHHhcccC
Q 012133           81 VSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTG  156 (470)
Q Consensus        81 l~~~l~~~---~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~g  156 (470)
                      +++.|+.-   ..+.+.||.|+..+-+.++..|-+++++|||||.+.+.|||||+++.+|..+.-. -..++.|..||+|
T Consensus       819 ~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGLsQLyQLRGRVG  898 (1139)
T COG1197         819 KAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVG  898 (1139)
T ss_pred             HHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEeccccccHHHHHHhccccC
Confidence            99999863   5699999999999999999999999999999999999999999999988655443 6889999999999


Q ss_pred             CCCCCCeEEEeeChh------hHHHHHHHHHH
Q 012133          157 RAGKEGTAILMFTSS------QRRTVRSLERD  182 (470)
Q Consensus       157 R~g~~g~~i~l~~~~------~~~~~~~i~~~  182 (470)
                      |..+.+.||++|.+.      ..++++.|++.
T Consensus       899 RS~~~AYAYfl~p~~k~lT~~A~kRL~aI~~~  930 (1139)
T COG1197         899 RSNKQAYAYFLYPPQKALTEDAEKRLEAIASF  930 (1139)
T ss_pred             CccceEEEEEeecCccccCHHHHHHHHHHHhh
Confidence            999999999999853      34566666553

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=99.49  E-value=1.9e-13  Score=131.28  Aligned_cols=167  Identities=23%  Similarity=0.359  Sum_probs=129.7

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHH---HHHHHcCCCeEEEEeCchHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD---LITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~---ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      ++||....|.+-++..+.-...++....   -..+++.+.... .+.+..+.+.+   +|+-.......||||-++++++
T Consensus       256 ltatatn~vl~d~k~il~ie~~~tf~a~---fnr~nl~yev~q-kp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~e  331 (695)
T KOG0353|consen  256 LTATATNHVLDDAKDILCIEAAFTFRAG---FNRPNLKYEVRQ-KPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCE  331 (695)
T ss_pred             eehhhhcchhhHHHHHHhHHhhheeecc---cCCCCceeEeee-CCCChHHHHHHHHHHhccccCCCcceEEEeccccHH
Confidence            6788777777777766542222222111   112344433333 33344444444   4433335568899999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHH--------
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH--------  150 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~q--------  150 (470)
                      +++..|+. ++.+..+|..|.+.++.-+-+.+-.++++|+|||-....|||-|+|.+||+..+|.+++.|.|        
T Consensus       332 kva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyqasarillr  411 (695)
T KOG0353|consen  332 KVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQASARILLR  411 (695)
T ss_pred             HHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHHHHHHHHHH
Confidence            99999985 799999999999999999999999999999999999999999999999999999999999999        


Q ss_pred             -----------------------------------HhcccCCCCCCCeEEEeeChhhH
Q 012133          151 -----------------------------------RSGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       151 -----------------------------------r~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                                                         ..||+||.+.+..||++|.-.+.
T Consensus       412 mtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~di  469 (695)
T KOG0353|consen  412 MTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFADI  469 (695)
T ss_pred             HhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEechHHH
Confidence                                               78999999999999999876554

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.48  E-value=5.8e-13  Score=144.53  Aligned_cols=100  Identities=23%  Similarity=0.366  Sum_probs=81.4

Q ss_pred             HHHHHHHHHhc---CCcEEEEeCCCCH--HHHHHHHcccccCCeeEEEecccccccCCCCCccEEE--EecCCCCh----
Q 012133           77 DADEVSLALTS---IIASEALHGDISQ--HQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII--HYELPNDP----  145 (470)
Q Consensus        77 ~~~~l~~~l~~---~~~~~~lhg~~~~--~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI--~~~~p~~~----  145 (470)
                      -++.+++.|.+   ...+..+|+++.+  .++++++++|++++++|||+|+++++|+|+|+|++|+  ++|.+.+.    
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            45677777775   4679999999974  5789999999999999999999999999999999985  44544332    


Q ss_pred             ------hHHHHHhcccCCCCCCCeEEEeeChhhHHHH
Q 012133          146 ------ETFVHRSGRTGRAGKEGTAILMFTSSQRRTV  176 (470)
Q Consensus       146 ------~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~  176 (470)
                            ..|+|++||+||.++.|.+++.....+...+
T Consensus       518 a~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~~~~~  554 (679)
T PRK05580        518 ASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVI  554 (679)
T ss_pred             hHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCCCHHH
Confidence                  5789999999999999999987665443333

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.47  E-value=2.4e-13  Score=148.81  Aligned_cols=169  Identities=22%  Similarity=0.252  Sum_probs=118.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccH--HHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSK--RTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k--~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      ||||||+|+..++..+.++.+...+..........................  ...+..+.....+..+++|.|||+..|
T Consensus       374 ll~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kvlvI~NTV~~A  453 (733)
T COG1203         374 LLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELISEEVKEGKKVLVIVNTVDRA  453 (733)
T ss_pred             EEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhhhhhHhhhhcchhhhccCCcEEEEEecHHHH
Confidence            689999999999988887765554433211000000000001101111111  123344445556778999999999999


Q ss_pred             HHHHHHHhcCC-cEEEEeCCCCHHHHHHHHcccc----cCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhc
Q 012133           79 DEVSLALTSII-ASEALHGDISQHQRERTLNGFR----QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG  153 (470)
Q Consensus        79 ~~l~~~l~~~~-~~~~lhg~~~~~~R~~~~~~f~----~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~G  153 (470)
                      .++++.|+... .+..||+.+...+|.+.++.++    .....|+|||+|++.|+|+. .+++|--  +..+++++||+|
T Consensus       454 ie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-fd~mITe--~aPidSLIQR~G  530 (733)
T COG1203         454 IELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-FDVLITE--LAPIDSLIQRAG  530 (733)
T ss_pred             HHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-cCeeeec--CCCHHHHHHHHH
Confidence            99999999644 5999999999999998888554    45789999999999999995 6776642  456789999999


Q ss_pred             ccCCCC--CCCeEEEeeChhh
Q 012133          154 RTGRAG--KEGTAILMFTSSQ  172 (470)
Q Consensus       154 R~gR~g--~~g~~i~l~~~~~  172 (470)
                      |++|.|  ..+..+++.....
T Consensus       531 Rv~R~g~~~~~~~~v~~~~~~  551 (733)
T COG1203         531 RVNRHGKKENGKIYVYNDEER  551 (733)
T ss_pred             HHhhcccccCCceeEeecccC
Confidence            999999  5677777765443

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.47  E-value=1.2e-12  Score=141.27  Aligned_cols=165  Identities=19%  Similarity=0.182  Sum_probs=124.1

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHH-HHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~-ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|...+..++.+-|-.+.+.|..  . .+....... -.+......|..++.. +...+..+.++||||+|++.++.|
T Consensus       385 MTGTa~te~~Ef~~iY~l~Vv~IPt--n-kp~~R~d~~-d~v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~l  460 (896)
T PRK13104        385 MTGTADTEAYEFQQIYNLEVVVIPT--N-RSMIRKDEA-DLVYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFL  460 (896)
T ss_pred             CCCCChhHHHHHHHHhCCCEEECCC--C-CCcceecCC-CeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHH
Confidence            6788877766676666444333321  1 111111111 1222334556655544 445667788999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCc---------------------------
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV---------------------------  133 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v---------------------------  133 (470)
                      +..|.+ ++++..||+.+.+.+++.+.+.|+.|  .|+||||+|+||+||.-=                           
T Consensus       461 s~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G--~VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~  538 (896)
T PRK13104        461 SQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPG--AVTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQ  538 (896)
T ss_pred             HHHHHHcCCCeEeecCCCChHHHHHHHhCCCCC--cEEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhh
Confidence            999985 89999999999999999999999998  499999999999999521                           


Q ss_pred             -----------cEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhH
Q 012133          134 -----------DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       134 -----------~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                                 =+||-...+.|..-=-|-.||+||.|.+|.+.+|++-+|.
T Consensus       539 ~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~  589 (896)
T PRK13104        539 KRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDN  589 (896)
T ss_pred             hhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence                       1688888888888889999999999999999999887653

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.44  E-value=1.3e-12  Score=140.97  Aligned_cols=164  Identities=21%  Similarity=0.195  Sum_probs=127.0

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHH-HcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~-~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|...+...+.+-|--+.+.|..  . .+....... -.+.....+|..+|...+.. +....++||||+|++.++.|
T Consensus       371 mTGTa~te~~E~~~iY~l~vv~IPt--n-kp~~r~d~~-d~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~L  446 (830)
T PRK12904        371 MTGTADTEAEEFREIYNLDVVVIPT--N-RPMIRIDHP-DLIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELL  446 (830)
T ss_pred             cCCCcHHHHHHHHHHhCCCEEEcCC--C-CCeeeeeCC-CeEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHH
Confidence            6888877777777766444333321  1 111111111 12233445777777777744 45678999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCc---------------------------
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV---------------------------  133 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v---------------------------  133 (470)
                      ++.|.+ ++++..||+.  +.+|+..+.+|+.+...|+||||+|+||+||+-=                           
T Consensus       447 s~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~  524 (830)
T PRK12904        447 SKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQ  524 (830)
T ss_pred             HHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHh
Confidence            999985 7999999996  8899999999999999999999999999999742                           


Q ss_pred             -----------cEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhh
Q 012133          134 -----------DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       134 -----------~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                                 =|||-...|.|..---|-.||+||.|.+|.+-+|++-+|
T Consensus       525 ~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~lSleD  574 (830)
T PRK12904        525 EEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLED  574 (830)
T ss_pred             hhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEEEEcCc
Confidence                       168888899999999999999999999999999988765

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.41  E-value=5.5e-12  Score=135.96  Aligned_cols=165  Identities=20%  Similarity=0.245  Sum_probs=123.9

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHH-HHHHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~-l~~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|.-.+..++.+-|--+.+.|..  . .+.......-. +......|..+ +..+...+..+.++||||+|++.++.|
T Consensus       390 MTGTa~te~~Ef~~iY~l~Vv~IPT--n-kp~~R~d~~d~-iy~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~l  465 (908)
T PRK13107        390 MTGTADTEAFEFQHIYGLDTVVVPT--N-RPMVRKDMADL-VYLTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELL  465 (908)
T ss_pred             ccCCChHHHHHHHHHhCCCEEECCC--C-CCccceeCCCc-EEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHH
Confidence            6778777766666666444333321  1 11111111111 12233455444 445555667788999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCC----------------------------
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN----------------------------  132 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~----------------------------  132 (470)
                      +..|.+ ++++..||+.+++.+++.+.+.|+.|.  |+||||+|+||+||.-                            
T Consensus       466 s~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~  543 (908)
T PRK13107        466 ARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQI  543 (908)
T ss_pred             HHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHh
Confidence            999985 899999999999999999999999987  9999999999999962                            


Q ss_pred             ----c-----cEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhH
Q 012133          133 ----V-----DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       133 ----v-----~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                          |     =+||-...+.|..-=-|-.||+||.|.+|.+.+|++-+|.
T Consensus       544 ~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        544 RHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             hHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCcH
Confidence                1     1688888888988889999999999999999999887664

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=99.35  E-value=1.6e-11  Score=133.17  Aligned_cols=174  Identities=21%  Similarity=0.315  Sum_probs=123.9

Q ss_pred             EEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCccc---HHHH-----HHHHHHHHcCCCeEEEEeC
Q 012133            2 LFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS---KRTI-----LSDLITVYAKGGKTIVFTQ   73 (470)
Q Consensus         2 lfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~---k~~~-----l~~ll~~~~~~~~~lVF~~   73 (470)
                      =+|||||+ -.+.+.....++.-+-.....-.  +..+.+.++-+....   +.++     ..++++...+ .++|||+-
T Consensus       479 GLSATLPN-y~DV~~Fl~v~~~glf~fd~syR--pvPL~qq~Igi~ek~~~~~~qamNe~~yeKVm~~agk-~qVLVFVH  554 (1674)
T KOG0951|consen  479 GLSATLPN-YEDVASFLRVDPEGLFYFDSSYR--PVPLKQQYIGITEKKPLKRFQAMNEACYEKVLEHAGK-NQVLVFVH  554 (1674)
T ss_pred             eecccCCc-hhhhHHHhccCcccccccCcccC--cCCccceEeccccCCchHHHHHHHHHHHHHHHHhCCC-CcEEEEEE
Confidence            37999996 34455433345544433222222  345666777655432   2222     2334444333 89999999


Q ss_pred             chHHHHHHHHHHhcC--------------------------------------CcEEEEeCCCCHHHHHHHHcccccCCe
Q 012133           74 TKRDADEVSLALTSI--------------------------------------IASEALHGDISQHQRERTLNGFRQGKF  115 (470)
Q Consensus        74 t~~~~~~l~~~l~~~--------------------------------------~~~~~lhg~~~~~~R~~~~~~f~~g~~  115 (470)
                      +++++.+.|..++..                                      +.+.++|++|+..+|..+.+.|++|.+
T Consensus       555 sRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R~dR~~~EdLf~~g~i  634 (1674)
T KOG0951|consen  555 SRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNRKDRELVEDLFADGHI  634 (1674)
T ss_pred             echHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCcchHHHHHHHHhcCce
Confidence            999888888777511                                      357889999999999999999999999


Q ss_pred             eEEEecccccccCCCCCccEEE----EecCC------CChhHHHHHhcccCCCC--CCCeEEEeeChhhHHHHHHH
Q 012133          116 TVLVATDVAARGLDIPNVDLII----HYELP------NDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       116 ~iLVaTdv~~~Gidip~v~~VI----~~~~p------~~~~~y~qr~GR~gR~g--~~g~~i~l~~~~~~~~~~~i  179 (470)
                      +|||+|-.+++|+++|.-+++|    .|++-      .++.+.+||.||+||..  ..|..+++....+..++..+
T Consensus       635 qvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~~se~qyyls~  710 (1674)
T KOG0951|consen  635 QVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSELQYYLSL  710 (1674)
T ss_pred             eEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeeccCchHhhhhHHh
Confidence            9999999999999999988888    46643      47889999999999976  55777777766665555443

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.34  E-value=6.4e-12  Score=139.47  Aligned_cols=136  Identities=18%  Similarity=0.355  Sum_probs=112.3

Q ss_pred             cccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccC---CeeEEEecc
Q 012133           48 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQG---KFTVLVATD  122 (470)
Q Consensus        48 ~~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g---~~~iLVaTd  122 (470)
                      ...|+.+|..+|..+ ..+.++|||+......+.|.+.|. .++....|||.++..+|..+++.|...   ...+|++|.
T Consensus       469 ~SgKl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTr  548 (1033)
T PLN03142        469 NSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTR  548 (1033)
T ss_pred             hhhHHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEecc
Confidence            357888888888655 356799999999999999999987 478999999999999999999999753   356789999


Q ss_pred             cccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEE--EeeChh--hHHHHHHHHHHh
Q 012133          123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI--LMFTSS--QRRTVRSLERDV  183 (470)
Q Consensus       123 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i--~l~~~~--~~~~~~~i~~~~  183 (470)
                      ++..|||+..+++||+||+||++..+.|+++|+.|.|+...|.  .|++..  |...++...+.+
T Consensus       549 AGGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIEEkIlera~~Kl  613 (1033)
T PLN03142        549 AGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKL  613 (1033)
T ss_pred             ccccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999775544  444442  344555444443

>PF08152 GUCT: GUCT (NUC152) domain; InterPro: IPR012562 This is the C-terminal domain found in the RNA helicase II / Gu protein family []

Probab=99.30  E-value=3.8e-12  Score=102.65  Aligned_cols=95  Identities=38%  Similarity=0.563  Sum_probs=53.4

Q ss_pred             CCCCCCCCcccccCCCCeEEEEEeeCCccccCCcchhhHHhHhhhhcCc-CcCccccEEEeecCccceeEeecCHHHHHH
Q 012133          246 GFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPT-AADEIGKIHIIADDRVQGAVFDLPEEIAKE  324 (470)
Q Consensus       246 ~~~~~~~~r~l~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~-~~~~Ig~I~i~~~~~~~ga~fdv~~~~a~~  324 (470)
                      |+++ ++.|||+++.++++|+.+.+..+    .-++..++..|.+..+. ..++|++|++++|.  +|++||||++.+++
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-IKQRSLLTSEEGFVTLQLTCSRE----IRSPGYAWRILRRQLSEEIADKVKGMTLLKDK--MGAVFDVPSEIAEE   73 (97)
T ss_dssp             S-S--------------EEEEEEE-SS------SSTHHHHHHHHHHS-HHHHTT-EEEEE-TTS--SEEEEEEEHHHHHH
T ss_pred             CCCC-CCccccccCCCCCEEEEEEcCCc----CCCchhHHHHHHHhcCHHHHHhhCcEEEecCC--CEEEEEChHHHHHH
Confidence            4566 78899999999999999988863    45678888888877654 56789999999986  69999999999999


Q ss_pred             HHhhcCCC-CCeEEEeccCCCccC
Q 012133          325 LLNKQIPP-GNTISKITKLPALQD  347 (470)
Q Consensus       325 i~~~~~~~-g~~i~~~~~lP~~~~  347 (470)
                      +++.+... ++.++++++||++++
T Consensus        74 ~~~~~~~~~~~~l~v~~~LPeL~e   97 (97)
T PF08152_consen   74 FLAKWEDSRGWQLSVATELPELQE   97 (97)
T ss_dssp             HHHH--SS-S-EEE----------
T ss_pred             HHHhCcccCCcEEEEcccCcCccC
Confidence            99998875 899999999999974

; GO: 0003723 RNA binding, 0004386 helicase activity, 0005524 ATP binding, 0005634 nucleus; PDB: 2E29_A.

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=99.30  E-value=1.4e-11  Score=131.28  Aligned_cols=116  Identities=29%  Similarity=0.488  Sum_probs=98.3

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcC---------------------------------------CcEEEEeCCCCHHHHH
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSI---------------------------------------IASEALHGDISQHQRE  104 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~---------------------------------------~~~~~lhg~~~~~~R~  104 (470)
                      ++.++||||++++.|+.++..+.+.                                       +.+.++|.+++.++|+
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            4457999999999999988666421                                       2578899999999999


Q ss_pred             HHHcccccCCeeEEEecccccccCCCCCccEEEEe---cC-CCChhHHHHHhcccCCCC--CCCeEEEeeChhhHHHHHH
Q 012133          105 RTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY---EL-PNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRS  178 (470)
Q Consensus       105 ~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~---~~-p~~~~~y~qr~GR~gR~g--~~g~~i~l~~~~~~~~~~~  178 (470)
                      .+...|++|.+.|++||+.++.|+++|...++|-.   .. +.+.-+|.||+|||||+|  ..|.+|+++...+......
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   22 347889999999999997  6699999999988766654


Q ss_pred             H
Q 012133          179 L  179 (470)
Q Consensus       179 i  179 (470)
                      +
T Consensus       619 l  619 (1008)
T KOG0950|consen  619 L  619 (1008)
T ss_pred             H
Confidence            4

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=99.29  E-value=8.3e-11  Score=126.07  Aligned_cols=176  Identities=19%  Similarity=0.302  Sum_probs=121.4

Q ss_pred             EEeecCCHHHHHHHHHHcCCCc-EEEeecccccccccceEEEEEEcCcc---cHHHH-----HHHHHHHHcCCCeEEEEe
Q 012133            2 LFSATMPSWVKKLSRKYLDNPL-NIDLVGNQDEKLAEGIKLYAISTTAT---SKRTI-----LSDLITVYAKGGKTIVFT   72 (470)
Q Consensus         2 lfSATlp~~i~~l~~~~l~~p~-~i~~~~~~~~~~~~~i~~~~~~~~~~---~k~~~-----l~~ll~~~~~~~~~lVF~   72 (470)
                      -+|||+|+ +++++...--+|. -+..-...-.  +..+.+..+-.+..   ...+.     ...+++.+..+.+++|||
T Consensus       280 gLSATlPN-~eDvA~fL~vn~~~glfsFd~~yR--PvpL~~~~iG~k~~~~~~~~~~~d~~~~~kv~e~~~~g~qVlvFv  356 (1230)
T KOG0952|consen  280 GLSATLPN-YEDVARFLRVNPYAGLFSFDQRYR--PVPLTQGFIGIKGKKNRQQKKNIDEVCYDKVVEFLQEGHQVLVFV  356 (1230)
T ss_pred             EeeccCCC-HHHHHHHhcCCCccceeeeccccc--ccceeeeEEeeecccchhhhhhHHHHHHHHHHHHHHcCCeEEEEE
Confidence            48999995 6777764333432 2222111111  22344444433332   22222     233455666788999999


Q ss_pred             CchHHHHHHHHHHhcC------------------------CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccC
Q 012133           73 QTKRDADEVSLALTSI------------------------IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  128 (470)
Q Consensus        73 ~t~~~~~~l~~~l~~~------------------------~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gi  128 (470)
                      .++..+...|+.|.+.                        .....+|++|..++|..+.+.|..|.++||+||..++.|+
T Consensus       357 hsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~cTaTLAwGV  436 (1230)
T KOG0952|consen  357 HSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIKVLCCTATLAWGV  436 (1230)
T ss_pred             ecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCceEEEecceeeecc
Confidence            9999999998888531                        1356789999999999999999999999999999999999


Q ss_pred             CCCCccEEE----EecCCC------ChhHHHHHhcccCCCC--CCCeEEEeeChhhHHHHHHHH
Q 012133          129 DIPNVDLII----HYELPN------DPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRSLE  180 (470)
Q Consensus       129 dip~v~~VI----~~~~p~------~~~~y~qr~GR~gR~g--~~g~~i~l~~~~~~~~~~~i~  180 (470)
                      ++|+-.++|    .||.-.      ..-+.+|..||+||..  ..|.++++.+.+....+..|.
T Consensus       437 NLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~Y~sLl  500 (1230)
T KOG0952|consen  437 NLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDHYESLL  500 (1230)
T ss_pred             CCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHHHHHHH
Confidence            999765555    244322      4556799999999965  779999998876655555543

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

Probab=99.29  E-value=3.9e-11  Score=132.28  Aligned_cols=165  Identities=21%  Similarity=0.392  Sum_probs=126.8

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcC---------cccHHHHHHHHHHH-HcCCCeEEE
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTT---------ATSKRTILSDLITV-YAKGGKTIV   70 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~---------~~~k~~~l~~ll~~-~~~~~~~lV   70 (470)
                      |+.|||+-..- .+++.+...+..+.+.   +...+....++.+..+         ..++...+..++.. +..+-++||
T Consensus       236 i~~SAT~~np~-e~~~~l~~~~f~~~v~---~~g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~~~~~~~~~~~tL~  311 (851)
T COG1205         236 ICTSATLANPG-EFAEELFGRDFEVPVD---EDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTLV  311 (851)
T ss_pred             EEEeccccChH-HHHHHhcCCcceeecc---CCCCCCCceEEEEeCCcchhhhhhcccchHHHHHHHHHHHHHcCceEEE
Confidence            56899997654 4566666655554432   2233444555555555         23555555555543 345679999


Q ss_pred             EeCchHHHHHHHHHHh-----cC----CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecC
Q 012133           71 FTQTKRDADEVSLALT-----SI----IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL  141 (470)
Q Consensus        71 F~~t~~~~~~l~~~l~-----~~----~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~  141 (470)
                      |+.+++.++.++....     ..    ..+..++++|...+|.+++..|++|+..++++|+.++-||||-+++.||.+..
T Consensus       312 F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ldavi~~g~  391 (851)
T COG1205         312 FFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGY  391 (851)
T ss_pred             EEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehhhhhHhhcCC
Confidence            9999999999963322     23    35888999999999999999999999999999999999999999999999999


Q ss_pred             CC-ChhHHHHHhcccCCCCCCCeEEEeeC
Q 012133          142 PN-DPETFVHRSGRTGRAGKEGTAILMFT  169 (470)
Q Consensus       142 p~-~~~~y~qr~GR~gR~g~~g~~i~l~~  169 (470)
                      |. +..+++||+||+||.++....++++.
T Consensus       392 P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~  420 (851)
T COG1205         392 PGVSVLSFRQRAGRAGRRGQESLVLVVLR  420 (851)
T ss_pred             CCchHHHHHHhhhhccCCCCCceEEEEeC
Confidence            99 89999999999999987777777665

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

Probab=99.25  E-value=4.5e-11  Score=123.80  Aligned_cols=104  Identities=32%  Similarity=0.521  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC
Q 012133           53 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP  131 (470)
Q Consensus        53 ~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip  131 (470)
                      ..+..++..+....++|||+.++.+++.++..+.. .+ +..+.+..++.+|.++++.|+.+.+++||++.++.+|+|+|
T Consensus       271 ~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP  349 (442)
T COG1061         271 AAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIP  349 (442)
T ss_pred             HHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCC
Confidence            33344444333457999999999999999999985 45 88999999999999999999999999999999999999999


Q ss_pred             CccEEEEecCCCChhHHHHHhcccCC
Q 012133          132 NVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus       132 ~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +++++|...+..++..|+||+||.-|
T Consensus       350 ~~~~~i~~~~t~S~~~~~Q~lGR~LR  375 (442)
T COG1061         350 DADVLIILRPTGSRRLFIQRLGRGLR  375 (442)
T ss_pred             CCcEEEEeCCCCcHHHHHHHhhhhcc
Confidence            99999999999999999999999999

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=99.24  E-value=4.5e-10  Score=119.31  Aligned_cols=106  Identities=28%  Similarity=0.400  Sum_probs=90.4

Q ss_pred             CeEEEEeCchHHHHHHHHHHhcC----------------------------------------CcEEEEeCCCCHHHHHH
Q 012133           66 GKTIVFTQTKRDADEVSLALTSI----------------------------------------IASEALHGDISQHQRER  105 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~~----------------------------------------~~~~~lhg~~~~~~R~~  105 (470)
                      -++||||-+++.|++.++.|...                                        -.+.++||++-+--++-
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            48999999999999999998631                                        13678999999999999


Q ss_pred             HHcccccCCeeEEEecccccccCCCCCccEEEEec--------CCCChhHHHHHhcccCCCC--CCCeEEEeeChh
Q 012133          106 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE--------LPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  171 (470)
Q Consensus       106 ~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~--------~p~~~~~y~qr~GR~gR~g--~~g~~i~l~~~~  171 (470)
                      +...|..|-++||+||..++.|||+|.-.+|+..=        .--.+-.|.||+||+||.|  .+|++|++....
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            99999999999999999999999999888777311        1126789999999999988  779999987654

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

Probab=99.23  E-value=3.9e-10  Score=127.53  Aligned_cols=93  Identities=23%  Similarity=0.404  Sum_probs=81.9

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhcC----------CcEEEEeCCCCHHHHHHHHcccccCCe-eEEEecccccccCCCCCc
Q 012133           65 GGKTIVFTQTKRDADEVSLALTSI----------IASEALHGDISQHQRERTLNGFRQGKF-TVLVATDVAARGLDIPNV  133 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~~----------~~~~~lhg~~~~~~R~~~~~~f~~g~~-~iLVaTdv~~~Gidip~v  133 (470)
                      .+++||||.++++|+.+++.|.+.          ..+..+|++++  ++.+++++|+++.. +|||+++++.+|+|+|.|
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            479999999999999998887632          14667999986  46789999999876 699999999999999999


Q ss_pred             cEEEEecCCCChhHHHHHhcccCCCC
Q 012133          134 DLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus       134 ~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      ++||.+.++.|...|+||+||+.|.-
T Consensus       776 ~~vVf~rpvkS~~lf~QmIGRgtR~~  801 (1123)
T PRK11448        776 CNLVFLRRVRSRILYEQMLGRATRLC  801 (1123)
T ss_pred             cEEEEecCCCCHHHHHHHHhhhccCC
Confidence            99999999999999999999999963

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.22  E-value=2.5e-10  Score=115.08  Aligned_cols=200  Identities=19%  Similarity=0.247  Sum_probs=132.8

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCc---------ccHHHHHHHHH-HHHcCCCeEEEEe
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA---------TSKRTILSDLI-TVYAKGGKTIVFT   72 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~---------~~k~~~l~~ll-~~~~~~~~~lVF~   72 (470)
                      .|||+-..++-....+  +-..++++.....  +..-+++.+..++         +.+.....+++ +....+-++|-||
T Consensus       457 ~~~~~K~~~~~~~~~~--~~~E~~Li~~DGS--Ps~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~~~R~IAFC  532 (1034)
T KOG4150|consen  457 GDTPYKDRTRLRSELA--NLSELELVTIDGS--PSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEMVQHGLRCIAFC  532 (1034)
T ss_pred             CCCCcCCHHHHHHHhc--CCcceEEEEecCC--CCccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHHHHcCCcEEEec
Confidence            3677776665444433  2223333322211  3334555554432         12222223333 3334567999999


Q ss_pred             CchHHHHHHHHHHhcC---------CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC
Q 012133           73 QTKRDADEVSLALTSI---------IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN  143 (470)
Q Consensus        73 ~t~~~~~~l~~~l~~~---------~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~  143 (470)
                      ++++.|+.+....++-         -.+..+.|+.+.++|.++...+-.|+..-+|||++++-||||-.++.|++.++|.
T Consensus       533 ~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LDAVl~~GFP~  612 (1034)
T KOG4150|consen  533 PSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLDAVLHLGFPG  612 (1034)
T ss_pred             cHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccceeEEEccCch
Confidence            9999999876655431         1255678999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHHHhcccCCCCCCCeEEEee--ChhhHHHHHHHHHHhCCCccccCCCCH-HHHHHHHHHHH
Q 012133          144 DPETFVHRSGRTGRAGKEGTAILMF--TSSQRRTVRSLERDVGCKFEFVSPPVV-EDVLESSAEQV  206 (470)
Q Consensus       144 ~~~~y~qr~GR~gR~g~~g~~i~l~--~~~~~~~~~~i~~~~~~~~~~~~~p~~-~~~~~~~~~~~  206 (470)
                      +...+.|..||+||.+++..+++++  .|-+..++..-+......-..+.+... .-+++..++-+
T Consensus       613 S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y~~HP~~l~~~pN~EL~LD~~N~~iL~~HlQCA  678 (1034)
T KOG4150|consen  613 SIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYYMSHPDKLFGSPNEELHLDSQNKHVLMQHLQCA  678 (1034)
T ss_pred             hHHHHHHHhccccccCCCceEEEEEeccchhhHhhcCcHHHhCCCcceeEEecccHHHHHHHHhHH
Confidence            9999999999999998887665544  456666666555555443333333333 33444444333

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=99.16  E-value=1.1e-10  Score=120.96  Aligned_cols=107  Identities=24%  Similarity=0.425  Sum_probs=90.2

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhcC----------------------------------------CcEEEEeCCCCHHHHH
Q 012133           65 GGKTIVFTQTKRDADEVSLALTSI----------------------------------------IASEALHGDISQHQRE  104 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~~----------------------------------------~~~~~lhg~~~~~~R~  104 (470)
                      ..++|||+-++++|+.+|..+.+.                                        -.+.++|++|-+--++
T Consensus       383 ~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE  462 (1041)
T KOG0948|consen  383 YLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKE  462 (1041)
T ss_pred             CCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHhccccccccchHHHHH
Confidence            358999999999999999888641                                        0367789999999999


Q ss_pred             HHHcccccCCeeEEEecccccccCCCCCccEEEE----ec---CCC-ChhHHHHHhcccCCCC--CCCeEEEeeChh
Q 012133          105 RTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE---LPN-DPETFVHRSGRTGRAG--KEGTAILMFTSS  171 (470)
Q Consensus       105 ~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~----~~---~p~-~~~~y~qr~GR~gR~g--~~g~~i~l~~~~  171 (470)
                      .+.-.|.+|-+++|.||...+.|+|+|.-++|+-    +|   +.| +.-.|+|++||+||.|  ..|.||++++..
T Consensus       463 ~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDek  539 (1041)
T KOG0948|consen  463 VIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEK  539 (1041)
T ss_pred             HHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccCCcceeeecccceEEecccccccCCCCCceEEEEecCc
Confidence            9999999999999999999999999998877762    22   122 6778999999999988  569999998753

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.97  E-value=8.2e-09  Score=110.88  Aligned_cols=163  Identities=19%  Similarity=0.229  Sum_probs=112.8

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHH-HHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILS-DLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~-~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|.-.+-.++.+-|-.+.+.|..  . .+.......- .+......|..++. .+...+..+.++||.|.|.+..+.|
T Consensus       367 MTGTA~te~~Ef~~iY~l~Vv~IPT--n-kP~~R~D~~d-~iy~t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~l  442 (925)
T PRK12903        367 MTGTAKTEEQEFIDIYNMRVNVVPT--N-KPVIRKDEPD-SIFGTKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETL  442 (925)
T ss_pred             cCCCCHHHHHHHHHHhCCCEEECCC--C-CCeeeeeCCC-cEEEcHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHH
Confidence            6788766666666666443333321  1 1111111110 12233345554444 4555667788999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccC-CeeEEEecccccccCCCCCcc--------EEEEecCCCChhHHHHH
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFTVLVATDVAARGLDIPNVD--------LIIHYELPNDPETFVHR  151 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g-~~~iLVaTdv~~~Gidip~v~--------~VI~~~~p~~~~~y~qr  151 (470)
                      +..|.+ +++..+|++.-  .+++..+-. +.| .-.|.|||++|.||.||.--.        |||....|.+..---|-
T Consensus       443 s~~L~~~gi~h~vLNAk~--~e~EA~IIa-~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQL  519 (925)
T PRK12903        443 HELLLEANIPHTVLNAKQ--NAREAEIIA-KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQL  519 (925)
T ss_pred             HHHHHHCCCCceeecccc--hhhHHHHHH-hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHH
Confidence            999985 78888998873  334433332 223 467999999999999996332        89999999999888999


Q ss_pred             hcccCCCCCCCeEEEeeChhh
Q 012133          152 SGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       152 ~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      .||+||.|.+|.+-+|++-.+
T Consensus       520 rGRaGRQGDpGss~f~lSLeD  540 (925)
T PRK12903        520 RGRSGRQGDVGESRFFISLDD  540 (925)
T ss_pred             hcccccCCCCCcceEEEecch
Confidence            999999999999998888665

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=98.89  E-value=8.7e-09  Score=104.26  Aligned_cols=105  Identities=26%  Similarity=0.377  Sum_probs=85.3

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc--CCcEEEEeCCCCHHHHHHHHccccc--CCeeEEEecccccccCCCCCccEEEEe
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQ--GKFTVLVATDVAARGLDIPNVDLIIHY  139 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~--~~~~~~lhg~~~~~~R~~~~~~f~~--g~~~iLVaTdv~~~Gidip~v~~VI~~  139 (470)
                      +.+.|||-. +++++..+...+.+  ...+.+|+|.||++.|.+.-..|.+  ++++||||||++.+|+|+ +|+-||.|
T Consensus       356 k~GDCvV~F-Skk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~  433 (700)
T KOG0953|consen  356 KPGDCVVAF-SKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFY  433 (700)
T ss_pred             CCCCeEEEe-ehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEe
Confidence            345665543 67788899998885  3559999999999999999999987  889999999999999999 68888877


Q ss_pred             cCC---------CChhHHHHHhcccCCCC---CCCeEEEeeCh
Q 012133          140 ELP---------NDPETFVHRSGRTGRAG---KEGTAILMFTS  170 (470)
Q Consensus       140 ~~p---------~~~~~y~qr~GR~gR~g---~~g~~i~l~~~  170 (470)
                      ++-         .+..+..|-+||+||.+   ..|.+.+|..+
T Consensus       434 sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~e  476 (700)
T KOG0953|consen  434 SLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHSE  476 (700)
T ss_pred             ecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeHh
Confidence            653         46778899999999976   45777776544

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.88  E-value=5.4e-08  Score=103.27  Aligned_cols=164  Identities=18%  Similarity=0.192  Sum_probs=114.3

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHH-HHHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l-~~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|...+..++.+-|--+.  +.+.. ..+........ .+......|..++ ..+.+.+..+.++||.|.+.+..+.|
T Consensus       368 MTGTa~t~~~Ef~~iY~l~V--v~IPt-nkp~~R~d~~d-~iy~t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~l  443 (764)
T PRK12326        368 MTGTAVAAGEQLRQFYDLGV--SVIPP-NKPNIREDEAD-RVYATAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEEL  443 (764)
T ss_pred             ecCCChhHHHHHHHHhCCcE--EECCC-CCCceeecCCC-ceEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHH
Confidence            78888777777777665442  22221 11111111111 1222334555444 44556667888999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCC----------cc-----EEEEecCCCCh
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN----------VD-----LIIHYELPNDP  145 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~----------v~-----~VI~~~~p~~~  145 (470)
                      +..|.+ +++..+|++.-...+-+.+-+.=+  .-.|.|||++|.||.||.-          |.     |||-...|.|.
T Consensus       444 s~~L~~~gI~h~vLNAk~~~~EA~IIa~AG~--~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSr  521 (764)
T PRK12326        444 AERLRAAGVPAVVLNAKNDAEEARIIAEAGK--YGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSE  521 (764)
T ss_pred             HHHHHhCCCcceeeccCchHhHHHHHHhcCC--CCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchH
Confidence            999985 789999988744333222222212  3579999999999999962          22     79999999999


Q ss_pred             hHHHHHhcccCCCCCCCeEEEeeChhh
Q 012133          146 ETFVHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       146 ~~y~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      ..-.|-.||+||.|.+|.+.+|++-++
T Consensus       522 RID~QLrGRaGRQGDpGss~f~lSleD  548 (764)
T PRK12326        522 RLDNQLRGRAGRQGDPGSSVFFVSLED  548 (764)
T ss_pred             HHHHHHhcccccCCCCCceeEEEEcch
Confidence            999999999999999999999988766

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=98.78  E-value=5.7e-08  Score=101.69  Aligned_cols=168  Identities=20%  Similarity=0.282  Sum_probs=128.0

Q ss_pred             HHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHh-cCC
Q 012133           12 KKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SII   89 (470)
Q Consensus        12 ~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~-~~~   89 (470)
                      .-..++....|..++-.   ++-.+.....+  .+....|+.+|.+||..+ ..+.+||||..-....+-|..+.. ++|
T Consensus       438 ~mQLRKccnHPYLF~g~---ePg~pyttdeh--Lv~nSGKm~vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y  512 (971)
T KOG0385|consen  438 MMQLRKCCNHPYLFDGA---EPGPPYTTDEH--LVTNSGKMLVLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGY  512 (971)
T ss_pred             HHHHHHhcCCccccCCC---CCCCCCCcchH--HHhcCcceehHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCc
Confidence            33556677788877643   22112222112  234567899999998654 567799999999999998888877 588


Q ss_pred             cEEEEeCCCCHHHHHHHHcccccC---CeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCC--eE
Q 012133           90 ASEALHGDISQHQRERTLNGFRQG---KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG--TA  164 (470)
Q Consensus        90 ~~~~lhg~~~~~~R~~~~~~f~~g---~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g--~~  164 (470)
                      ...-|.|.++.++|...++.|...   ..-.|++|.+...|||+...+.||.||-.|+|..-+|..-|++|.|+.-  .+
T Consensus       513 ~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V  592 (971)
T KOG0385|consen  513 EYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVV  592 (971)
T ss_pred             eeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEE
Confidence            999999999999999999999864   3557899999999999999999999999999999999999999999654  45


Q ss_pred             EEeeChh--hHHHHHHHHHHhC
Q 012133          165 ILMFTSS--QRRTVRSLERDVG  184 (470)
Q Consensus       165 i~l~~~~--~~~~~~~i~~~~~  184 (470)
                      |.|++..  |...+++-+..+.
T Consensus       593 ~RLitentVEe~IveRA~~KL~  614 (971)
T KOG0385|consen  593 YRLITENTVEEKIVERAAAKLR  614 (971)
T ss_pred             EEEeccchHHHHHHHHHHHHhc
Confidence            5566654  3444555444443

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.77  E-value=1.5e-07  Score=102.42  Aligned_cols=165  Identities=19%  Similarity=0.176  Sum_probs=112.1

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHH-HHHHHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-~l~~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|.-.+..++.+-|--+.  |.+... .+.......-. +......|.. ++..++..+..+.++||-|.+.+..+.|
T Consensus       509 mTGTa~~e~~Ef~~iY~l~v--~~iPt~-kp~~r~d~~d~-iy~t~~~k~~ai~~ei~~~~~~grPvLigt~si~~se~l  584 (970)
T PRK12899        509 MTGTAITESREFKEIYNLYV--LQVPTF-KPCLRIDHNDE-FYMTEREKYHAIVAEIASIHRKGNPILIGTESVEVSEKL  584 (970)
T ss_pred             cCCCCHHHHHHHHHHhCCCE--EECCCC-CCceeeeCCCc-EecCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHH
Confidence            67787666566655554332  322211 11111111111 2233345554 4455666777788999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCC---cc-----EEEEecCCCChhHHHHHh
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN---VD-----LIIHYELPNDPETFVHRS  152 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~---v~-----~VI~~~~p~~~~~y~qr~  152 (470)
                      +..|.+ +++..+|+..-...+-+.+-+.=+  .-.|.|||++|.||.||.-   |.     +||....|.+...-.|-.
T Consensus       585 s~~L~~~gi~h~vLNak~~~~Ea~iia~AG~--~g~VTIATNmAGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~  662 (970)
T PRK12899        585 SRILRQNRIEHTVLNAKNHAQEAEIIAGAGK--LGAVTVATNMAGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLR  662 (970)
T ss_pred             HHHHHHcCCcceecccchhhhHHHHHHhcCC--CCcEEEeeccccCCcccccCchHHhcCCcEEEeeccCchHHHHHHHh
Confidence            999984 788888888733333333322222  3579999999999999942   22     789999999999999999


Q ss_pred             cccCCCCCCCeEEEeeChhhH
Q 012133          153 GRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~~~  173 (470)
                      ||+||.|.+|.+.+|++-.+.
T Consensus       663 GRagRQGdpGss~f~lSlEDd  683 (970)
T PRK12899        663 GRCARLGDPGAAKFFLSFEDR  683 (970)
T ss_pred             cccccCCCCCceeEEEEcchH
Confidence            999999999999999887663

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

Probab=98.76  E-value=1.2e-07  Score=101.95  Aligned_cols=177  Identities=19%  Similarity=0.296  Sum_probs=114.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccH-----HHHHHHHHHHHcCCCeEEEEeCch
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSK-----RTILSDLITVYAKGGKTIVFTQTK   75 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k-----~~~l~~ll~~~~~~~~~lVF~~t~   75 (470)
                      ||-|||..-+-...+  -......+.+.........+.+....+.......     ..+|..+-+.+..+.++|||+|.+
T Consensus       353 vLgSATPSLES~~~~--~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~geQ~llflnRR  430 (730)
T COG1198         353 VLGSATPSLESYANA--ESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGEQVLLFLNRR  430 (730)
T ss_pred             EEecCCCCHHHHHhh--hcCceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHHHHHHhcCCeEEEEEccC
Confidence            467999765543333  2222344555433332223333333222222122     344555555667788999999965


Q ss_pred             H------------------------------------------------------------HHHHHHHHHhc---CCcEE
Q 012133           76 R------------------------------------------------------------DADEVSLALTS---IIASE   92 (470)
Q Consensus        76 ~------------------------------------------------------------~~~~l~~~l~~---~~~~~   92 (470)
                      -                                                            -++++.+.|.+   ..++.
T Consensus       431 Gys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~GterieeeL~~~FP~~rv~  510 (730)
T COG1198         431 GYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGTERIEEELKRLFPGARII  510 (730)
T ss_pred             CccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCeeEEecccHHHHHHHHHHHCCCCcEE
Confidence            5                                                            34555555554   34677


Q ss_pred             EEeCCCCHH--HHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecC------C---C---ChhHHHHHhcccCCC
Q 012133           93 ALHGDISQH--QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL------P---N---DPETFVHRSGRTGRA  158 (470)
Q Consensus        93 ~lhg~~~~~--~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~------p---~---~~~~y~qr~GR~gR~  158 (470)
                      .+.++....  .-+..++.|.+|+.+|||.|++++.|.|+|+|++|...|.      |   .   ....+.|-+||+||.
T Consensus       511 r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll~QvaGRAgR~  590 (730)
T COG1198         511 RIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAGRAGRA  590 (730)
T ss_pred             EEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchHHHHHHHHHHHHhhhccC
Confidence            788876543  3567899999999999999999999999999999764332      2   1   234558999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHH
Q 012133          159 GKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i  179 (470)
                      +++|.+++-....+...++.+
T Consensus       591 ~~~G~VvIQT~~P~hp~i~~~  611 (730)
T COG1198         591 GKPGEVVIQTYNPDHPAIQAL  611 (730)
T ss_pred             CCCCeEEEEeCCCCcHHHHHH
Confidence            999999887766554444444

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=98.75  E-value=5.3e-08  Score=106.44  Aligned_cols=131  Identities=18%  Similarity=0.367  Sum_probs=110.6

Q ss_pred             ccHHHHHHHHHHHHcC-CCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHccccc---CCeeEEEeccc
Q 012133           49 TSKRTILSDLITVYAK-GGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQ---GKFTVLVATDV  123 (470)
Q Consensus        49 ~~k~~~l~~ll~~~~~-~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~---g~~~iLVaTdv  123 (470)
                      .-|+-+|..||..+.. +.+||||..-....+-|+++|. ++|+..-|.|.+.-+.|+.+|+.|..   ..+..|+||.+
T Consensus       682 SGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRA  761 (1373)
T KOG0384|consen  682 SGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRA  761 (1373)
T ss_pred             cCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEeccc
Confidence            3455566677755543 4799999999999999999998 58999999999999999999999985   46889999999


Q ss_pred             ccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCC--eEEEeeChh--hHHHHHHH
Q 012133          124 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG--TAILMFTSS--QRRTVRSL  179 (470)
Q Consensus       124 ~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g--~~i~l~~~~--~~~~~~~i  179 (470)
                      ..-|||+...+.||.||--|+|..=+|...|++|.|++-  .+|.|++..  |..++++-
T Consensus       762 GGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEilERA  821 (1373)
T KOG0384|consen  762 GGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEILERA  821 (1373)
T ss_pred             CcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHHHHHHHH
Confidence            999999999999999999999999999999999999664  466677764  34444443

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.74  E-value=9e-08  Score=103.30  Aligned_cols=126  Identities=25%  Similarity=0.407  Sum_probs=88.3

Q ss_pred             CEEeecCCHH--HHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCc---h
Q 012133            1 MLFSATMPSW--VKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQT---K   75 (470)
Q Consensus         1 llfSATlp~~--i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t---~   75 (470)
                      |+.|||..+.  -..+.+..|.    +++-  .......+|...|+..   .-.+.+..+++.+.  .-.|||++.   +
T Consensus       280 vvsSATg~~rg~R~~LfReLlg----FevG--~~~~~LRNIvD~y~~~---~~~e~~~elvk~lG--~GgLIfV~~d~G~  348 (1187)
T COG1110         280 VVSSATGKPRGSRLKLFRELLG----FEVG--SGGEGLRNIVDIYVES---ESLEKVVELVKKLG--DGGLIFVPIDYGR  348 (1187)
T ss_pred             EEeeccCCCCCchHHHHHHHhC----CccC--ccchhhhheeeeeccC---ccHHHHHHHHHHhC--CCeEEEEEcHHhH
Confidence            4579997543  1234444443    1111  1223345676677665   33444556666664  367999999   9


Q ss_pred             HHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEec----ccccccCCCCC-ccEEEEecCC
Q 012133           76 RDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT----DVAARGLDIPN-VDLIIHYELP  142 (470)
Q Consensus        76 ~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaT----dv~~~Gidip~-v~~VI~~~~p  142 (470)
                      +.+++|++.|.. ++.+..+|+.     .++.++.|..|++++||..    .++.||||+|. +.++|.|+.|
T Consensus       349 e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvP  416 (1187)
T COG1110         349 EKAEELAEYLRSHGINAELIHAE-----KEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVP  416 (1187)
T ss_pred             HHHHHHHHHHHhcCceEEEeecc-----chhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCC
Confidence            999999999995 7999999984     3788999999999999876    48999999995 5678866644

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.69  E-value=2.3e-07  Score=100.79  Aligned_cols=164  Identities=21%  Similarity=0.210  Sum_probs=112.5

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHH-HHHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l-~~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|...+...+.+-|--+.+.|..   ..+.......-. +......|..++ ..+...+..+.+|||-|.|.+..+.|
T Consensus       390 MTGTa~te~~Ef~~iY~l~Vv~IPT---nkP~~R~D~~d~-vy~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~l  465 (913)
T PRK13103        390 MTGTADTEAFEFRQIYGLDVVVIPP---NKPLARKDFNDL-VYLTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHM  465 (913)
T ss_pred             CCCCCHHHHHHHHHHhCCCEEECCC---CCCcccccCCCe-EEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHH
Confidence            6788877766676666444333321   111111111111 223334555444 44556667788999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC-----------------------------
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP-----------------------------  131 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip-----------------------------  131 (470)
                      +..|.+ +++..+|+......+-+.+-+.=+  .-.|.|||++|.||.||.                             
T Consensus       466 s~~L~~~gi~h~VLNAk~~~~EA~IIa~AG~--~GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~  543 (913)
T PRK13103        466 SNLLKKEGIEHKVLNAKYHEKEAEIIAQAGR--PGALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQK  543 (913)
T ss_pred             HHHHHHcCCcHHHhccccchhHHHHHHcCCC--CCcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHh
Confidence            999985 777777777644333333332222  457999999999999994                             


Q ss_pred             ---Ccc-----EEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhh
Q 012133          132 ---NVD-----LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       132 ---~v~-----~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                         .|.     +||-...|.|..-=.|-.||+||.|.+|.+-+|++-.+
T Consensus       544 ~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlED  592 (913)
T PRK13103        544 RHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  592 (913)
T ss_pred             HHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCc
Confidence               122     68888899999999999999999999999999988755

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.67  E-value=4.6e-07  Score=99.07  Aligned_cols=164  Identities=21%  Similarity=0.216  Sum_probs=113.9

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHH-HHHHHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-~l~~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|...+-.++.+-|--+.+.|..  . .+....... -.+......|.. ++..+...+..+.++||-|.|.+..+.|
T Consensus       569 MTGTA~tea~Ef~~IY~L~Vv~IPT--n-rP~~R~D~~-D~vy~t~~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~l  644 (1112)
T PRK12901        569 MTGTAETEAGEFWDIYKLDVVVIPT--N-RPIARKDKE-DLVYKTKREKYNAVIEEITELSEAGRPVLVGTTSVEISELL  644 (1112)
T ss_pred             cCCCCHHHHHHHHHHhCCCEEECCC--C-CCcceecCC-CeEecCHHHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHH
Confidence            6778877766676666444333321  1 111111111 122223345544 4555666777888999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC---Cc-----cEEEEecCCCChhHHHHHh
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP---NV-----DLIIHYELPNDPETFVHRS  152 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip---~v-----~~VI~~~~p~~~~~y~qr~  152 (470)
                      +..|.. +++..+|++.....+-+.+-+.=+  .-.|-|||++|.||.||.   .|     =+||-...+.|...--|-.
T Consensus       645 S~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~--~GaVTIATNMAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLr  722 (1112)
T PRK12901        645 SRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQ--PGTVTIATNMAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLR  722 (1112)
T ss_pred             HHHHHHcCCcHHHhhccchhhHHHHHHhcCC--CCcEEEeccCcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHh
Confidence            999984 788777877754444433333322  357899999999999995   22     2788899999999999999


Q ss_pred             cccCCCCCCCeEEEeeChhh
Q 012133          153 GRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~~  172 (470)
                      ||+||.|.+|.+.+|++-.+
T Consensus       723 GRaGRQGDPGsS~f~lSLED  742 (1112)
T PRK12901        723 GRAGRQGDPGSSQFYVSLED  742 (1112)
T ss_pred             cccccCCCCCcceEEEEccc
Confidence            99999999999999888665

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.66  E-value=1e-08  Score=55.60  Aligned_cols=17  Identities=59%  Similarity=1.499  Sum_probs=15.9

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+|++.||+++|||+
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            39999999999999996

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

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

Probab=98.64  E-value=4e-07  Score=102.09  Aligned_cols=106  Identities=21%  Similarity=0.261  Sum_probs=76.4

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcC---CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccE--EEE
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL--IIH  138 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~---~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~--VI~  138 (470)
                      ..+++|||+++.+..+.++..|...   .....+..+.. ..|.+++++|++++..||++|+.+.+|||+|+..+  ||.
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            4579999999999999999998741   12223333333 57899999999999999999999999999998774  555


Q ss_pred             ecCCCC------------------------------hhHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          139 YELPND------------------------------PETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       139 ~~~p~~------------------------------~~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                      ..+|..                              ...+.|.+||.=|....--++++++.
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                              12236888999887543334444444

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.

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

Probab=98.61  E-value=3.5e-07  Score=100.85  Aligned_cols=104  Identities=25%  Similarity=0.439  Sum_probs=86.0

Q ss_pred             CeEEEEeCchHHHHHHHHHHhcC-----------------------------C-------------cEEEEeCCCCHHHH
Q 012133           66 GKTIVFTQTKRDADEVSLALTSI-----------------------------I-------------ASEALHGDISQHQR  103 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~~-----------------------------~-------------~~~~lhg~~~~~~R  103 (470)
                      -++|+|+-++..|+.++..+...                             +             .+.++|++|-+..+
T Consensus       380 lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K  459 (1041)
T COG4581         380 LPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIK  459 (1041)
T ss_pred             CceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHH
Confidence            48999999999999988776410                             1             13468999999999


Q ss_pred             HHHHcccccCCeeEEEecccccccCCCCCccEEE----Eec----CCCChhHHHHHhcccCCCC--CCCeEEEeeC
Q 012133          104 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII----HYE----LPNDPETFVHRSGRTGRAG--KEGTAILMFT  169 (470)
Q Consensus       104 ~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI----~~~----~p~~~~~y~qr~GR~gR~g--~~g~~i~l~~  169 (470)
                      ..+.+.|..|.++||+||.+.+.|||+|.-++|+    .+|    -+-++..|+|+.||+||.|  ..|.+|++-.
T Consensus       460 ~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~  535 (1041)
T COG4581         460 ELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEP  535 (1041)
T ss_pred             HHHHHHHhccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecC
Confidence            9999999999999999999999999999877766    122    2347899999999999988  5688888743

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=98.54  E-value=9.2e-07  Score=93.26  Aligned_cols=124  Identities=19%  Similarity=0.324  Sum_probs=107.5

Q ss_pred             CcccHHHHHHHHHH-HHcCCCeEEEEeCchHHHHHHHHHHh--cCCcEEEEeCCCCHHHHHHHHcccccCC-ee-EEEec
Q 012133           47 TATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALT--SIIASEALHGDISQHQRERTLNGFRQGK-FT-VLVAT  121 (470)
Q Consensus        47 ~~~~k~~~l~~ll~-~~~~~~~~lVF~~t~~~~~~l~~~l~--~~~~~~~lhg~~~~~~R~~~~~~f~~g~-~~-iLVaT  121 (470)
                      ...-|+.+|..+|+ ++..+.++|+|..++...+-|...|.  ++|...-+.|..+...|..++++|.++. +. .|++|
T Consensus       527 k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTT  606 (923)
T KOG0387|consen  527 KRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTT  606 (923)
T ss_pred             hhcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEe
Confidence            34578999999885 55667799999999999999999998  4899999999999999999999999764 33 57899


Q ss_pred             ccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeE--EEeeCh
Q 012133          122 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA--ILMFTS  170 (470)
Q Consensus       122 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~--i~l~~~  170 (470)
                      .|..-|+|+...+-||.|||-|+|.+-.|..-|+-|.|++-.+  |.|++.
T Consensus       607 rvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~  657 (923)
T KOG0387|consen  607 RVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTA  657 (923)
T ss_pred             cccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecC
Confidence            9999999999999999999999999999999999999966544  445554

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=98.52  E-value=8.3e-07  Score=95.30  Aligned_cols=119  Identities=18%  Similarity=0.261  Sum_probs=93.1

Q ss_pred             ccHHHHHHHHHHHHcC--CCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCC---eeEEEecc
Q 012133           49 TSKRTILSDLITVYAK--GGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK---FTVLVATD  122 (470)
Q Consensus        49 ~~k~~~l~~ll~~~~~--~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~---~~iLVaTd  122 (470)
                      ..|+..|..++....+  ..++.+..|.+...+.+..... +++.+..|||.|+..+|+.+++.|.+..   .-.|.+|-
T Consensus       577 s~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsK  656 (776)
T KOG0390|consen  577 SGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSK  656 (776)
T ss_pred             hhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecc
Confidence            4567777777643321  2344444555555555555444 4899999999999999999999998743   33567889


Q ss_pred             cccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEe
Q 012133          123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  167 (470)
Q Consensus       123 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l  167 (470)
                      +.+.||++-..+.||.+|++|+|..-.|.+.|+-|.|++-.|+++
T Consensus       657 Agg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iY  701 (776)
T KOG0390|consen  657 AGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIY  701 (776)
T ss_pred             cccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEE
Confidence            999999999999999999999999999999999999988777765

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=98.51  E-value=1.1e-06  Score=95.48  Aligned_cols=123  Identities=20%  Similarity=0.335  Sum_probs=100.8

Q ss_pred             cccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCC--eeEEEeccc
Q 012133           48 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK--FTVLVATDV  123 (470)
Q Consensus        48 ~~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~--~~iLVaTdv  123 (470)
                      +..|++.|.-||..+ ..+.++|||+.-.+..+-|...|. .++.-.-|.|...-++|+..+++|....  +..|++|..
T Consensus      1258 DcGKLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrS 1337 (1958)
T KOG0391|consen 1258 DCGKLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRS 1337 (1958)
T ss_pred             ccchHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccC
Confidence            347888888888655 456799999999999999999998 4677888999999999999999998754  567899999


Q ss_pred             ccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCC--CCeEEEeeCh
Q 012133          124 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK--EGTAILMFTS  170 (470)
Q Consensus       124 ~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~--~g~~i~l~~~  170 (470)
                      ...|||+-..+.||.||-.|++..-.|.--|+.|.|+  .-..|.|++.
T Consensus      1338 ggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIYRLISe 1386 (1958)
T KOG0391|consen 1338 GGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIYRLISE 1386 (1958)
T ss_pred             CccccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEEEeecc
Confidence            9999999999999999999988776665555555553  3455566655

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.48  E-value=4.4e-06  Score=90.67  Aligned_cols=123  Identities=20%  Similarity=0.211  Sum_probs=76.6

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHH-HHHHHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-~l~~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|.-.+-..+.+-|--+.+.|  ... .+....... -.+......|.. ++..++..+..+.++||-|.|.+..+.|
T Consensus       365 MTGTa~te~~Ef~~iY~l~vv~I--Ptn-kp~~R~d~~-d~v~~t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~l  440 (870)
T CHL00122        365 MTGTAKTEELEFEKIYNLEVVCI--PTH-RPMLRKDLP-DLIYKDELSKWRAIADECLQMHQTGRPILIGTTTIEKSELL  440 (870)
T ss_pred             cCCCCHHHHHHHHHHhCCCEEEC--CCC-CCccceeCC-CeEEeCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHH
Confidence            67888766666666564433322  211 111111111 122233334544 4555666777888999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHH-HHHcccccCCeeEEEecccccccCCC
Q 012133           82 SLALTS-IIASEALHGDISQHQRE-RTLNGFRQGKFTVLVATDVAARGLDI  130 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~-~~~~~f~~g~~~iLVaTdv~~~Gidi  130 (470)
                      +..|.+ +++..+|++.-.+.+++ +++.. .-..-.|.|||++|.||.||
T Consensus       441 s~~L~~~gi~h~vLNAk~~~~~~EA~IIA~-AG~~G~VTIATNMAGRGTDI  490 (870)
T CHL00122        441 SQLLKEYRLPHQLLNAKPENVRRESEIVAQ-AGRKGSITIATNMAGRGTDI  490 (870)
T ss_pred             HHHHHHcCCccceeeCCCccchhHHHHHHh-cCCCCcEEEeccccCCCcCe
Confidence            999985 88899999873222222 23322 22245799999999999998

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.39  E-value=2.1e-06  Score=94.08  Aligned_cols=122  Identities=21%  Similarity=0.344  Sum_probs=101.2

Q ss_pred             ccHHHHHHHHHHHHc---------------CCCeEEEEeCchHHHHHHHHHHhc-CC---cEEEEeCCCCHHHHHHHHcc
Q 012133           49 TSKRTILSDLITVYA---------------KGGKTIVFTQTKRDADEVSLALTS-II---ASEALHGDISQHQRERTLNG  109 (470)
Q Consensus        49 ~~k~~~l~~ll~~~~---------------~~~~~lVF~~t~~~~~~l~~~l~~-~~---~~~~lhg~~~~~~R~~~~~~  109 (470)
                      ..|+.+|.+||..-.               .+.++||||.-+..++-+.+.|.+ .+   .-..|.|.+++.+|.++.++
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            467888998885431               235899999999999999888764 32   23478999999999999999


Q ss_pred             cccC-CeeEE-EecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeE--EEeeCh
Q 012133          110 FRQG-KFTVL-VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA--ILMFTS  170 (470)
Q Consensus       110 f~~g-~~~iL-VaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~--i~l~~~  170 (470)
                      |.++ .++|| ++|.|..-|+|+...+.||.++-.|++..-+|.+-|++|.|++-++  |.|++.
T Consensus      1389 FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlItr 1453 (1549)
T KOG0392|consen 1389 FNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLITR 1453 (1549)
T ss_pred             hcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCceeeeeeeehhc
Confidence            9998 68876 6778999999999999999999999999999999999999977554  444443

>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=98.36  E-value=4.8e-07  Score=69.52  Aligned_cols=61  Identities=21%  Similarity=0.401  Sum_probs=48.3

Q ss_pred             EEEEEeeCCccccCCcchhhHHhHhhhhcCcCcCccccEEEeecCccceeEeecCHHHHHHHHhhcCC
Q 012133          264 VTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIP  331 (470)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~Ig~I~i~~~~~~~ga~fdv~~~~a~~i~~~~~~  331 (470)
                      |+++++.++   +++++|++|+++|++..++...+||+|++.+++    +||+||++.++++++....
T Consensus         1 vrl~in~Gr---~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~~----S~vev~~~~a~~v~~~l~~   61 (74)
T PF03880_consen    1 VRLFINVGR---KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDNF----SFVEVPEEVAEKVLEALNG   61 (74)
T ss_dssp             -EEEES-SG---GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-----EEEEE-TT-HHHHHHHHTT
T ss_pred             CEEEEEccc---ccCCCHHHHHHHHHhccCCCHHhEEEEEEeeeE----EEEEECHHHHHHHHHHhcC
Confidence            578999998   899999999999999999999999999999997    7999999999999987653

; PDB: 2G0C_A 3MOJ_B.

>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=98.36  E-value=2.9e-05  Score=79.20  Aligned_cols=178  Identities=16%  Similarity=0.206  Sum_probs=131.9

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCc-EEEeecccc-----cccccceEEEEEEcCccc-------HHH-----HHHHHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPL-NIDLVGNQD-----EKLAEGIKLYAISTTATS-------KRT-----ILSDLITVY   62 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~-~i~~~~~~~-----~~~~~~i~~~~~~~~~~~-------k~~-----~l~~ll~~~   62 (470)
                      |+||+.+.+++..+.+.++.|.. .|.+.....     ..+...++|.+...+..+       +.+     +|..+.+ -
T Consensus       219 ii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~~~iLP~l~~-~  297 (442)
T PF06862_consen  219 IIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSSPADDPDARFKYFTKKILPQLKR-D  297 (442)
T ss_pred             EEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCCcchhhhHHHHHHHHHHHHHhhh-c
Confidence            68999999999999999877653 344433222     234556777777644332       222     2222322 2


Q ss_pred             cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc--cccccCCCCCccEEEEe
Q 012133           63 AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD--VAARGLDIPNVDLIIHY  139 (470)
Q Consensus        63 ~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd--v~~~Gidip~v~~VI~~  139 (470)
                      .....+|||+++--+-..|..+|.+ .+....+|--.++.+-.++-..|.+|+.+||+.|.  ..=+=..|..|.+||.|
T Consensus       298 ~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~irGi~~viFY  377 (442)
T PF06862_consen  298 SKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIRGIRHVIFY  377 (442)
T ss_pred             cCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceecCCcEEEEE
Confidence            2457999999999998999999985 78889999999999999999999999999999997  33455667889999999


Q ss_pred             cCCCChhHHHHHhcccCCCC------CCCeEEEeeChhhHHHHHHH
Q 012133          140 ELPNDPETFVHRSGRTGRAG------KEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       140 ~~p~~~~~y~qr~GR~gR~g------~~g~~i~l~~~~~~~~~~~i  179 (470)
                      .+|..+.-|...+.-.....      ....|.++|+.-+.-.+++|
T Consensus       378 ~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErI  423 (442)
T PF06862_consen  378 GPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERI  423 (442)
T ss_pred             CCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHH
Confidence            99999999977775544432      25789999999776665554

; GO: 0005634 nucleus

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.32  E-value=1.7e-05  Score=86.18  Aligned_cols=124  Identities=19%  Similarity=0.184  Sum_probs=76.7

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHH-HHHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTIL-SDLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l-~~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      ||.|.-.+..++.+-|-.+.+.|..  . .+.......- .+......|..++ ..+...+..+.++||-|.|.+..+.|
T Consensus       380 MTGTa~te~~Ef~~iY~l~Vv~IPT--n-kP~~R~d~~d-~vy~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~l  455 (939)
T PRK12902        380 MTGTAKTEEVEFEKTYKLEVTVIPT--N-RPRRRQDWPD-QVYKTEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELL  455 (939)
T ss_pred             cCCCCHHHHHHHHHHhCCcEEEcCC--C-CCeeeecCCC-eEEcCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHH
Confidence            6778766666666666444333321  1 1111111111 1222334555444 45556677888999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHH-HHHcccccCCeeEEEecccccccCCCC
Q 012133           82 SLALTS-IIASEALHGDISQHQRE-RTLNGFRQGKFTVLVATDVAARGLDIP  131 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~-~~~~~f~~g~~~iLVaTdv~~~Gidip  131 (470)
                      +..|.+ +++..+|+..--+.+++ +++.. .-..-.|-|||++|.||.||.
T Consensus       456 s~~L~~~gi~h~vLNAk~~~~~~EA~IIa~-AG~~GaVTIATNMAGRGTDIk  506 (939)
T PRK12902        456 SALLQEQGIPHNLLNAKPENVEREAEIVAQ-AGRKGAVTIATNMAGRGTDII  506 (939)
T ss_pred             HHHHHHcCCchheeeCCCcchHhHHHHHHh-cCCCCcEEEeccCCCCCcCEe
Confidence            999985 78888899863222233 23322 222357899999999999983

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=98.19  E-value=1.8e-05  Score=83.66  Aligned_cols=124  Identities=21%  Similarity=0.333  Sum_probs=104.9

Q ss_pred             ccHHHHHHHHHHHHc-CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCC--eeEEEecccc
Q 012133           49 TSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK--FTVLVATDVA  124 (470)
Q Consensus        49 ~~k~~~l~~ll~~~~-~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~--~~iLVaTdv~  124 (470)
                      +.|...|..||..+. ++.+||||..-....+-|...|.. .+...-|.|...-.+|+.+++.|...+  .-.|++|.+.
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            467888888886654 457999999999999988888874 788899999999999999999998654  4568999999


Q ss_pred             cccCCCCCccEEEEecCCCChhHHHHHhcccCCCCC--CCeEEEeeChhh
Q 012133          125 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK--EGTAILMFTSSQ  172 (470)
Q Consensus       125 ~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~--~g~~i~l~~~~~  172 (470)
                      .-|||+...++||.+|+-.+|-.-.|.--|++|.|+  +-+++.|++...
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            999999999999999999988888888888888884  456677777643

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=98.19  E-value=1.6e-05  Score=80.10  Aligned_cols=107  Identities=24%  Similarity=0.349  Sum_probs=88.8

Q ss_pred             ccHHHHHHHHHHHHc-CCCeEEEEeCchHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHccccc-CCeeEEEecccccc
Q 012133           49 TSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQ-GKFTVLVATDVAAR  126 (470)
Q Consensus        49 ~~k~~~l~~ll~~~~-~~~~~lVF~~t~~~~~~l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~-g~~~iLVaTdv~~~  126 (470)
                      ..|..+..-||+.++ .+.++|||..+.-...+.+-.|.+    -.|+|..+|.+|.++++.|+. ..++.+.-+.|...
T Consensus       526 P~KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~K----pfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVgDt  601 (776)
T KOG1123|consen  526 PNKFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLGK----PFIYGPTSQNERMKILQNFQTNPKVNTIFLSKVGDT  601 (776)
T ss_pred             cchhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHcCC----ceEECCCchhHHHHHHHhcccCCccceEEEeeccCc
Confidence            467777777887664 467999999998877777766654    458999999999999999995 46888899999999


Q ss_pred             cCCCCCccEEEEecCCC-ChhHHHHHhcccCCCC
Q 012133          127 GLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAG  159 (470)
Q Consensus       127 Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g  159 (470)
                      .||+|..+++|+...-. +...-.||.||.-|+.
T Consensus       602 SiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAK  635 (776)
T KOG1123|consen  602 SIDLPEANVLIQISSHGGSRRQEAQRLGRILRAK  635 (776)
T ss_pred             cccCCcccEEEEEcccccchHHHHHHHHHHHHHh
Confidence            99999999999876554 6777889999999975

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=98.10  E-value=1.7e-05  Score=82.87  Aligned_cols=122  Identities=20%  Similarity=0.335  Sum_probs=105.0

Q ss_pred             ccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCC-eeEEEeccccc
Q 012133           49 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK-FTVLVATDVAA  125 (470)
Q Consensus        49 ~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~-~~iLVaTdv~~  125 (470)
                      +.|+..|..||..+ ..+.++|+|..-.+..+.+.++|. +.+...-|.|.....+|..++.+|+... +-.|++|.+..
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            46777888888655 456799999999999999999998 5899999999999999999999999755 45679999999


Q ss_pred             ccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCC--eEEEeeCh
Q 012133          126 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG--TAILMFTS  170 (470)
Q Consensus       126 ~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g--~~i~l~~~  170 (470)
                      -||++...+.||.||..|++..-.|..-|+.|-|++-  ++|.|++.
T Consensus      1107 LGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~r 1153 (1185)
T KOG0388|consen 1107 LGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITR 1153 (1185)
T ss_pred             ccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeeccc
Confidence            9999999999999999999999999999999998654  45555543

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

Probab=98.09  E-value=4.3e-05  Score=79.01  Aligned_cols=219  Identities=16%  Similarity=0.236  Sum_probs=129.8

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----ccccc-CCCCCc
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNV  133 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~~G-idip~v  133 (470)
                      ...+||.+||++.|.++++.+..     .+.+.+++|+.+...+..-+++    .+.|+|||+     .++.| +|+..|
T Consensus       165 ~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~----gvdiviaTPGRl~d~le~g~~~l~~v  240 (519)
T KOG0331|consen  165 GPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLER----GVDVVIATPGRLIDLLEEGSLNLSRV  240 (519)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhc----CCcEEEeCChHHHHHHHcCCccccce
Confidence            45799999999999999888763     2559999999999988877776    689999997     45555 888999


Q ss_pred             cEEEE--------ecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHHH-HHHHHH
Q 012133          134 DLIIH--------YELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDV-LESSAE  204 (470)
Q Consensus       134 ~~VI~--------~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~~-~~~~~~  204 (470)
                      .++|.        .++-.++..+++.+.+.-|      -.++++..-...++.|...+-.....+.+-...+. ....+.
T Consensus       241 ~ylVLDEADrMldmGFe~qI~~Il~~i~~~~r------Qtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~  314 (519)
T KOG0331|consen  241 TYLVLDEADRMLDMGFEPQIRKILSQIPRPDR------QTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIR  314 (519)
T ss_pred             eEEEeccHHhhhccccHHHHHHHHHhcCCCcc------cEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchh
Confidence            99883        4455678888888888766      34455544445555555544333333322222111 111112


Q ss_pred             HHHHHHcccCccchhhhHHHHHHHHHh------------hCHHHHHHHHHHHcCCCC---------CCCCcccccCCCCe
Q 012133          205 QVVATLNGVHPESVEFFTPTAQRLIEE------------KGTDALAAALAQLSGFSR---------PPSSRSLINHEQGW  263 (470)
Q Consensus       205 ~~~~~l~~~~~~~~~~~~~~a~~l~~~------------~~~~~l~~al~~l~~~~~---------~~~~r~l~~~~~~~  263 (470)
                      ++++.+...  +......+.+++....            ...+.|+..+... ++..         ..+...|...+++-
T Consensus       315 qive~~~~~--~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~-~~~a~~iHGd~sQ~eR~~~L~~FreG~  391 (519)
T KOG0331|consen  315 QIVEVCDET--AKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRK-GWPAVAIHGDKSQSERDWVLKGFREGK  391 (519)
T ss_pred             hhhhhcCHH--HHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhc-CcceeeecccccHHHHHHHHHhcccCC
Confidence            222211100  0011111111111100            0122333333331 1111         11222344567788


Q ss_pred             EEEEEeeCCccccCCcchhhHHhHhhhhcCcCcCc
Q 012133          264 VTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADE  298 (470)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~  298 (470)
                      ..+.|.++.  +.++++..+|-..|+...|...++
T Consensus       392 ~~vLVATdV--AaRGLDi~dV~lVInydfP~~vEd  424 (519)
T KOG0331|consen  392 SPVLVATDV--AARGLDVPDVDLVINYDFPNNVED  424 (519)
T ss_pred             cceEEEccc--ccccCCCccccEEEeCCCCCCHHH
Confidence            889999987  678899999988888888866654

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

Probab=98.06  E-value=6.7e-05  Score=84.92  Aligned_cols=80  Identities=21%  Similarity=0.252  Sum_probs=61.5

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcCCc---EEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCc--cEEEE
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSIIA---SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV--DLIIH  138 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~~~---~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v--~~VI~  138 (470)
                      .++++|||+++.+..+.+++.|.....   ...+.=+++...|.+++++|+.++-.||++|....+|||+|+-  .+||.
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            467999999999999999999974321   2222223444567889999998888899999999999999964  67877


Q ss_pred             ecCCC
Q 012133          139 YELPN  143 (470)
Q Consensus       139 ~~~p~  143 (470)
                      ..+|.
T Consensus       831 ~kLPF  835 (928)
T PRK08074        831 VRLPF  835 (928)
T ss_pred             ecCCC
Confidence            66553

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=98.06  E-value=3.6e-05  Score=83.15  Aligned_cols=82  Identities=28%  Similarity=0.459  Sum_probs=71.6

Q ss_pred             EEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEec-CCCChhHHHHHhcccCCCC--CCCeEEEe
Q 012133           91 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE-LPNDPETFVHRSGRTGRAG--KEGTAILM  167 (470)
Q Consensus        91 ~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~-~p~~~~~y~qr~GR~gR~g--~~g~~i~l  167 (470)
                      +.++|++|....|..+.-.||.|...||+||..++-|||+|.-++|+--| +--++-.|.|++||+||.|  ..|.++++
T Consensus       965 iG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~Fm 1044 (1330)
T KOG0949|consen  965 IGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVFM 1044 (1330)
T ss_pred             ccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEEE
Confidence            56689999999999999999999999999999999999999887777655 3448899999999999988  56888888


Q ss_pred             eChhh
Q 012133          168 FTSSQ  172 (470)
Q Consensus       168 ~~~~~  172 (470)
                      --|..
T Consensus      1045 giP~~ 1049 (1330)
T KOG0949|consen 1045 GIPRQ 1049 (1330)
T ss_pred             eCcHH
Confidence            76644

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

Probab=98.06  E-value=3e-05  Score=87.57  Aligned_cols=119  Identities=19%  Similarity=0.302  Sum_probs=102.6

Q ss_pred             cHHHHHHHHH-H-HHcCCC--eEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccC--CeeEEEecc
Q 012133           50 SKRTILSDLI-T-VYAKGG--KTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG--KFTVLVATD  122 (470)
Q Consensus        50 ~k~~~l~~ll-~-~~~~~~--~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g--~~~iLVaTd  122 (470)
                      .|...+.+++ . ......  ++|||++.....+-+...+.. .+....++|.++.++|..+++.|.++  ..-+|++|.
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 3 334445  899999999999999999986 46899999999999999999999985  456678889


Q ss_pred             cccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEee
Q 012133          123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF  168 (470)
Q Consensus       123 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~  168 (470)
                      +...|+++...++||++|+.|++....|...|+.|.|++..+.++-
T Consensus       772 agg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r  817 (866)
T COG0553         772 AGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYR  817 (866)
T ss_pred             ccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEE
Confidence            9999999999999999999999999999999999998776655543

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=98.03  E-value=2.2e-05  Score=83.92  Aligned_cols=60  Identities=12%  Similarity=0.080  Sum_probs=41.8

Q ss_pred             CCeEEEEEeeCCccccCCcchhhHHhHhhhhcCcCcCccccEEEeecCccceeEeecCHHHHHHHHhhcC
Q 012133          261 QGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQI  330 (470)
Q Consensus       261 ~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~Ig~I~i~~~~~~~ga~fdv~~~~a~~i~~~~~  330 (470)
                      ++..|-.++++.   +..++|-.|+-|-+++.......|.+++-|.+       ++|..+.|..|..+..
T Consensus      1044 EKIRTRAIS~K~---MslVsPLQLLLF~SrKVqsdgq~IV~VDdWIk-------lqIshEaAAcItgLr~ 1103 (1282)
T KOG0921|consen 1044 EKIRTRAISCKQ---MSLVSPLQLLLFGSRKVQSDGQGIVRVDDWIK-------LQISHEAAACITGLRP 1103 (1282)
T ss_pred             hhhhhheecccC---ccccChHHHhhhhhhhccccCcceEEeeceee-------EeccHHHHHHHhhhHH
Confidence            334455566655   55678888888888777666656777776654       8999999988765543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=98.01  E-value=0.00012  Score=76.67  Aligned_cols=68  Identities=22%  Similarity=0.359  Sum_probs=52.4

Q ss_pred             eEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCCccE
Q 012133           67 KTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVDL  135 (470)
Q Consensus        67 ~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~v~~  135 (470)
                      ++||.+||++.|.++++.+..     .+.+..++|+++...+...+.    +..+|||+|+      .....+++..+.+
T Consensus        77 ~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~----~~~~IiV~TP~rL~~~~~~~~~~l~~v~~  152 (456)
T PRK10590         77 RALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLR----GGVDVLVATPGRLLDLEHQNAVKLDQVEI  152 (456)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHc----CCCcEEEEChHHHHHHHHcCCcccccceE
Confidence            799999999999999888763     356788999998776554432    3679999996      2345568888998


Q ss_pred             EEE
Q 012133          136 IIH  138 (470)
Q Consensus       136 VI~  138 (470)
                      ||.
T Consensus       153 lVi  155 (456)
T PRK10590        153 LVL  155 (456)
T ss_pred             EEe
Confidence            874

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

Probab=97.99  E-value=3e-05  Score=82.89  Aligned_cols=92  Identities=25%  Similarity=0.366  Sum_probs=76.7

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhcCC------cEEEEeCCCCHHHHHHHHccccc--CCeeEEEecccccccCCCCCccEE
Q 012133           65 GGKTIVFTQTKRDADEVSLALTSII------ASEALHGDISQHQRERTLNGFRQ--GKFTVLVATDVAARGLDIPNVDLI  136 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~~~------~~~~lhg~~~~~~R~~~~~~f~~--g~~~iLVaTdv~~~Gidip~v~~V  136 (470)
                      -+|+||||.+..+|+.+...|.+.+      -+..|.++-.+.++  .++.|..  .-.+|.|+.|++..|||+|.|..+
T Consensus       426 ~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~~~~q~--~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nl  503 (875)
T COG4096         426 IGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAEQAQA--LIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNL  503 (875)
T ss_pred             cCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccchhhHH--HHHHHHhcCCCCceEEehhhhhcCCCchheeee
Confidence            3699999999999999999997532      37788888655543  3555543  346789999999999999999999


Q ss_pred             EEecCCCChhHHHHHhcccCCC
Q 012133          137 IHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus       137 I~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      |.+..-.|...|.||+||.-|.
T Consensus       504 VF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         504 VFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             eehhhhhhHHHHHHHhcCcccc
Confidence            9999999999999999999884

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

Probab=97.97  E-value=9.1e-05  Score=80.90  Aligned_cols=93  Identities=18%  Similarity=0.212  Sum_probs=73.9

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhcC------CcEEEEeCCCCHH---------------------HHHHHHccccc-CCee
Q 012133           65 GGKTIVFTQTKRDADEVSLALTSI------IASEALHGDISQH---------------------QRERTLNGFRQ-GKFT  116 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~~------~~~~~lhg~~~~~---------------------~R~~~~~~f~~-g~~~  116 (470)
                      ..+++|||.++..|..+++.|.+.      ..+.++++..+..                     ....++++|++ +.++
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            479999999999999999888642      3455666553322                     22468889976 5789


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      |||++|++..|+|.|.++.++...+-.+. .++|.+||+.|.
T Consensus       594 ilIVvdmllTGFDaP~l~tLyldKplk~h-~LlQai~R~nR~  634 (667)
T TIGR00348       594 LLIVVDMLLTGFDAPILNTLYLDKPLKYH-GLLQAIARTNRI  634 (667)
T ss_pred             EEEEEcccccccCCCccceEEEecccccc-HHHHHHHHhccc
Confidence            99999999999999999999987766654 589999999994

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

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=97.94  E-value=0.00013  Score=79.13  Aligned_cols=123  Identities=20%  Similarity=0.306  Sum_probs=106.2

Q ss_pred             cccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCC---eeEEEecc
Q 012133           48 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK---FTVLVATD  122 (470)
Q Consensus        48 ~~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~---~~iLVaTd  122 (470)
                      ..-|+++|.++|-.+ ..+.++|.||.-....+-+..+|. +.+.-.-+.|.....+|-..++.|..-.   +..|++|.
T Consensus       708 ~sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~Fllstr  787 (1157)
T KOG0386|consen  708 VSGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTR  787 (1157)
T ss_pred             hccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeec
Confidence            357899999998655 457899999999998888888888 5788889999999999999999998643   56789999


Q ss_pred             cccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       123 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                      ....|+|+...+.||.||.-|++....|+--|+.|.|+.-.+-++...
T Consensus       788 agglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~  835 (1157)
T KOG0386|consen  788 AGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLI  835 (1157)
T ss_pred             ccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeee
Confidence            999999999999999999999999999999999999976665555443

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

Probab=97.92  E-value=0.0002  Score=78.54  Aligned_cols=94  Identities=20%  Similarity=0.234  Sum_probs=70.2

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcCCc--EEEEeCCCCHHHHHHHHcccccCCe-eEEEecccccccCCCCCc--cEEEE
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSIIA--SEALHGDISQHQRERTLNGFRQGKF-TVLVATDVAARGLDIPNV--DLIIH  138 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~~~--~~~lhg~~~~~~R~~~~~~f~~g~~-~iLVaTdv~~~Gidip~v--~~VI~  138 (470)
                      .++++|||+++.+..+.+++.+.....  ....++..+.   .+.+++|+...- -++|+|..+.+|||+|+-  ..||.
T Consensus       478 ~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~~---~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI  554 (654)
T COG1199         478 SPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDER---EELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVI  554 (654)
T ss_pred             cCCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCcH---HHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEE
Confidence            356999999999999999999985332  4455555444   477888876544 899999999999999865  56776


Q ss_pred             ecCCC------------------------------ChhHHHHHhcccCCCCC
Q 012133          139 YELPN------------------------------DPETFVHRSGRTGRAGK  160 (470)
Q Consensus       139 ~~~p~------------------------------~~~~y~qr~GR~gR~g~  160 (470)
                      ..+|.                              -...+.|-+||.=|.-.
T Consensus       555 ~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~  606 (654)
T COG1199         555 VGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSED  606 (654)
T ss_pred             EecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCC
Confidence            66553                              23344899999999643

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=97.91  E-value=4.3e-05  Score=76.92  Aligned_cols=122  Identities=19%  Similarity=0.251  Sum_probs=98.9

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccC-CeeE-EEecc
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFTV-LVATD  122 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g-~~~i-LVaTd  122 (470)
                      +.|+++|..-|..+   ...-+.|||..-....+.+.-.|.+ ++.|+-|-|.|++++|..+++.|++. .++| ||+-.
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            35677766544333   2234889999999999999888886 89999999999999999999999975 4555 46667


Q ss_pred             cccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC--CCCeEEEeeCh
Q 012133          123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG--KEGTAILMFTS  170 (470)
Q Consensus       123 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g--~~g~~i~l~~~  170 (470)
                      +...-+++....+|+..|+-|++..-.|.--|..|.|  ++-.++.|+-.
T Consensus       699 AGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iE  748 (791)
T KOG1002|consen  699 AGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIE  748 (791)
T ss_pred             cCceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehh
Confidence            7888899999999999999999999888888888887  56667777655

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

Probab=97.88  E-value=6.3e-05  Score=83.79  Aligned_cols=77  Identities=16%  Similarity=0.160  Sum_probs=58.0

Q ss_pred             cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC--CccEEEEe
Q 012133           63 AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP--NVDLIIHY  139 (470)
Q Consensus        63 ~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip--~v~~VI~~  139 (470)
                      ..++++||++++.+..+.+++.|.. .+.+ ...+.-.  .+.+++++|+++...||++|...-+|||+|  +...||..
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            4568999999999999999999874 2333 4444321  245689999988889999999999999997  34555655


Q ss_pred             cCC
Q 012133          140 ELP  142 (470)
Q Consensus       140 ~~p  142 (470)
                      .+|
T Consensus       722 kLP  724 (820)
T PRK07246        722 RLP  724 (820)
T ss_pred             cCC
Confidence            555

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.79  E-value=0.00015  Score=79.55  Aligned_cols=78  Identities=26%  Similarity=0.398  Sum_probs=58.3

Q ss_pred             cCCCeEEEEeCchHHHHHHHHHHhcCC-cEEEEeCCCCHHHHHHHHcccc----cCCeeEEEecccccccCCCCC--ccE
Q 012133           63 AKGGKTIVFTQTKRDADEVSLALTSII-ASEALHGDISQHQRERTLNGFR----QGKFTVLVATDVAARGLDIPN--VDL  135 (470)
Q Consensus        63 ~~~~~~lVF~~t~~~~~~l~~~l~~~~-~~~~lhg~~~~~~R~~~~~~f~----~g~~~iLVaTdv~~~Gidip~--v~~  135 (470)
                      ...+.+|||+++.+..++++..|.... .-...++..   .+.++++.|+    .++-.||++|....+|||+|+  +.+
T Consensus       532 ~~~gg~LVlFtSy~~l~~v~~~l~~~~~~~ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~  608 (697)
T PRK11747        532 EKHKGSLVLFASRRQMQKVADLLPRDLRLMLLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQ  608 (697)
T ss_pred             hcCCCEEEEeCcHHHHHHHHHHHHHhcCCcEEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEE
Confidence            345679999999999999999987422 233446643   4667776666    356789999999999999986  677


Q ss_pred             EEEecCCC
Q 012133          136 IIHYELPN  143 (470)
Q Consensus       136 VI~~~~p~  143 (470)
                      ||...+|.
T Consensus       609 vII~kLPF  616 (697)
T PRK11747        609 VIITKIPF  616 (697)
T ss_pred             EEEEcCCC
Confidence            88777663

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.76  E-value=0.0002  Score=77.70  Aligned_cols=164  Identities=20%  Similarity=0.169  Sum_probs=103.7

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHH-HHHHHHHHHHcCCCeEEEEeCchHHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKR-TILSDLITVYAKGGKTIVFTQTKRDADEV   81 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~-~~l~~ll~~~~~~~~~lVF~~t~~~~~~l   81 (470)
                      |+.|.-.+..++..-|..+.+.|...   .+....+.... +......|. .++.++...+..+.++||-+.+.+..+.+
T Consensus       370 mTGTa~te~~EF~~iY~l~vv~iPTn---rp~~R~D~~D~-vy~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~l  445 (822)
T COG0653         370 MTGTADTEEEEFDVIYGLDVVVIPTN---RPIIRLDEPDL-VYKTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELL  445 (822)
T ss_pred             CCCcchhhhhhhhhccCCceeeccCC---CcccCCCCccc-cccchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchhH
Confidence            45666666666666665554444321   11111111111 112223444 45556667778889999999999999999


Q ss_pred             HHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCcc-----------EEEEecCCCChhHHH
Q 012133           82 SLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD-----------LIIHYELPNDPETFV  149 (470)
Q Consensus        82 ~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~-----------~VI~~~~p~~~~~y~  149 (470)
                      .+.|.+ +++..+|...-..  |+.-+-...-..-.|-|||++|.||.||.--.           +||-..--.|..---
T Consensus       446 s~~L~~~~i~h~VLNAk~h~--~EA~Iia~AG~~gaVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDn  523 (822)
T COG0653         446 SKLLRKAGIPHNVLNAKNHA--REAEIIAQAGQPGAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDN  523 (822)
T ss_pred             HHHHHhcCCCceeeccccHH--HHHHHHhhcCCCCccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHHH
Confidence            999985 7887788777543  33333333322346889999999999994222           344443333444445


Q ss_pred             HHhcccCCCCCCCeEEEeeChhh
Q 012133          150 HRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       150 qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      |--||+||.|.+|.+-.+++-.+
T Consensus       524 QLRGRsGRQGDpG~S~F~lSleD  546 (822)
T COG0653         524 QLRGRAGRQGDPGSSRFYLSLED  546 (822)
T ss_pred             HhhcccccCCCcchhhhhhhhHH
Confidence            89999999999999888877655

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

Probab=97.75  E-value=8.4e-05  Score=66.70  Aligned_cols=105  Identities=24%  Similarity=0.396  Sum_probs=70.4

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcCC---cEEEEeCCCCHHHHHHHHcccccCCeeEEEecc--cccccCCCCC--ccEE
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSII---ASEALHGDISQHQRERTLNGFRQGKFTVLVATD--VAARGLDIPN--VDLI  136 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~~---~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd--v~~~Gidip~--v~~V  136 (470)
                      .++.+|||+++.+..+.+.+.+....   ....+.-  ...++.++++.|+.+.-.||+++.  .+.+|||+|+  +..|
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            45899999999999999999987532   1222332  356788999999999999999998  9999999996  6678


Q ss_pred             EEecCCC----Ch--------------------------hHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          137 IHYELPN----DP--------------------------ETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       137 I~~~~p~----~~--------------------------~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                      |...+|.    ++                          ....|-+||.-|....--++++++.
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            8888774    11                          1116889999998554444444444

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=97.72  E-value=0.0007  Score=73.21  Aligned_cols=120  Identities=18%  Similarity=0.232  Sum_probs=100.4

Q ss_pred             ccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHhc----C-------------------CcEEEEeCCCCHHHHH
Q 012133           49 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS----I-------------------IASEALHGDISQHQRE  104 (470)
Q Consensus        49 ~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~~----~-------------------~~~~~lhg~~~~~~R~  104 (470)
                      +.|+-+|.+||... ..+.++|||..+....+.|..+|..    +                   ..-..|.|..+..+|+
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            56777888888654 4567999999999998888888752    1                   1346688999999999


Q ss_pred             HHHcccccCC----eeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEee
Q 012133          105 RTLNGFRQGK----FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF  168 (470)
Q Consensus       105 ~~~~~f~~g~----~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~  168 (470)
                      ++.+.|.+-.    .-.||+|.+..-|||+-..+-||.+|..|++.--+|-+=|+-|.|+.-.||++-
T Consensus      1205 k~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYR 1272 (1567)
T KOG1015|consen 1205 KWAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYR 1272 (1567)
T ss_pred             HHHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehh
Confidence            9999998632    347899999999999999999999999999999999999999999887777763

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=97.69  E-value=0.00054  Score=65.85  Aligned_cols=12  Identities=25%  Similarity=0.313  Sum_probs=5.6

Q ss_pred             eecCHHHHHHHH
Q 012133          315 FDLPEEIAKELL  326 (470)
Q Consensus       315 fdv~~~~a~~i~  326 (470)
                      .|+.+..|.++-
T Consensus       284 ~~~Re~Taski~  295 (465)
T KOG3973|consen  284 MDRRERTASKIH  295 (465)
T ss_pred             cchhhhhhhhhc
Confidence            455545444443

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=97.64  E-value=0.0003  Score=71.15  Aligned_cols=105  Identities=18%  Similarity=0.379  Sum_probs=91.2

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccC-CeeE-EEecccccccCCCCCccEEEEec
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFTV-LVATDVAARGLDIPNVDLIIHYE  140 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g-~~~i-LVaTdv~~~Gidip~v~~VI~~~  140 (470)
                      ...|.|||+--....+.|...+.+ ++...-|.|..+...|....+.|+.. +++| +++-.++..|+++...+.||...
T Consensus       491 ~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaE  570 (689)
T KOG1000|consen  491 PPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAE  570 (689)
T ss_pred             CCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEE
Confidence            456999999999999999999984 89999999999999999999999964 3454 34557889999999999999999


Q ss_pred             CCCChhHHHHHhcccCCCCCCCeEEEee
Q 012133          141 LPNDPETFVHRSGRTGRAGKEGTAILMF  168 (470)
Q Consensus       141 ~p~~~~~y~qr~GR~gR~g~~g~~i~l~  168 (470)
                      ++|++..++|.=-|+.|.|++..+.+.|
T Consensus       571 L~wnPgvLlQAEDRaHRiGQkssV~v~y  598 (689)
T KOG1000|consen  571 LHWNPGVLLQAEDRAHRIGQKSSVFVQY  598 (689)
T ss_pred             ecCCCceEEechhhhhhccccceeeEEE
Confidence            9999999999999999999776655544

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

Probab=97.59  E-value=0.001  Score=67.61  Aligned_cols=107  Identities=15%  Similarity=0.257  Sum_probs=75.5

Q ss_pred             eEEEEeCchHHHHHHHHHHh---c--CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCCccE
Q 012133           67 KTIVFTQTKRDADEVSLALT---S--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVDL  135 (470)
Q Consensus        67 ~~lVF~~t~~~~~~l~~~l~---~--~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~v~~  135 (470)
                      -.||.|+|++.|.++...-+   +  ++.+.++||++|..++...|+.    ...|+|||+      |--.++|+..|++
T Consensus       298 i~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~----g~EivVaTPgRlid~VkmKatn~~rvS~  373 (731)
T KOG0339|consen  298 IGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKE----GAEIVVATPGRLIDMVKMKATNLSRVSY  373 (731)
T ss_pred             eEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhc----CCeEEEechHHHHHHHHhhcccceeeeE
Confidence            35778899999988866554   3  4779999999999999888873    679999998      5567899999998


Q ss_pred             EEEe--------cCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhC
Q 012133          136 IIHY--------ELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  184 (470)
Q Consensus       136 VI~~--------~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~  184 (470)
                      +|.-        ++-..+.+..|-+       ++-...++++..-...++.+.+.+-
T Consensus       374 LV~DEadrmfdmGfe~qVrSI~~hi-------rpdrQtllFsaTf~~kIe~lard~L  423 (731)
T KOG0339|consen  374 LVLDEADRMFDMGFEPQVRSIKQHI-------RPDRQTLLFSATFKKKIEKLARDIL  423 (731)
T ss_pred             EEEechhhhhccccHHHHHHHHhhc-------CCcceEEEeeccchHHHHHHHHHHh
Confidence            7732        2223455555555       3445556666655566666655543

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.40  E-value=0.0032  Score=69.57  Aligned_cols=79  Identities=15%  Similarity=0.257  Sum_probs=57.6

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcC-C-------cEEEEeCCCCHHHHHHHHccccc----CCeeEEEec--ccccccCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSI-I-------ASEALHGDISQHQRERTLNGFRQ----GKFTVLVAT--DVAARGLD  129 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~-~-------~~~~lhg~~~~~~R~~~~~~f~~----g~~~iLVaT--dv~~~Gid  129 (470)
                      .++.+|||+++-...+.+++.+.+. +       ....+-+. ...++..+++.|+.    +.-.||+|+  ..+.+|||
T Consensus       521 ~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~-~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGID  599 (705)
T TIGR00604       521 IPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETK-DAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGID  599 (705)
T ss_pred             CCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCC-CcchHHHHHHHHHHHHhcCCceEEEEecCCcccCccc
Confidence            3588999999999999988877631 1       11222221 12577889999964    355699998  88999999


Q ss_pred             CCC--ccEEEEecCCC
Q 012133          130 IPN--VDLIIHYELPN  143 (470)
Q Consensus       130 ip~--v~~VI~~~~p~  143 (470)
                      +++  ...||...+|.
T Consensus       600 f~~~~~r~ViivGlPf  615 (705)
T TIGR00604       600 FCDDLGRAVIMVGIPY  615 (705)
T ss_pred             cCCCCCcEEEEEccCC
Confidence            986  56788888775

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).

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

Probab=97.34  E-value=0.00026  Score=75.02  Aligned_cols=210  Identities=20%  Similarity=0.278  Sum_probs=114.9

Q ss_pred             EEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----ccccc-CCCCCccE
Q 012133           68 TIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNVDL  135 (470)
Q Consensus        68 ~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~~G-idip~v~~  135 (470)
                      +||++||++.|.++++.+..      .+.+..++|+++...+...++.   + .+|||+|+     .+.++ +++..+.+
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            99999999999999988863      3568999999998888766666   4 89999997     55665 99999999


Q ss_pred             EEE------ec--CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHHH--HH------
Q 012133          136 IIH------YE--LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVED--VL------  199 (470)
Q Consensus       136 VI~------~~--~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~~--~~------  199 (470)
                      +|.      .|  +..+++..+-.+-       .-..+++++..-...+..+.+.+-.++..+.+.....  ..      
T Consensus       178 lVlDEADrmLd~Gf~~~i~~I~~~~p-------~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~  250 (513)
T COG0513         178 LVLDEADRMLDMGFIDDIEKILKALP-------PDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQF  250 (513)
T ss_pred             EEeccHhhhhcCCCHHHHHHHHHhCC-------cccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEE
Confidence            884      22  2223332222221       1355555554433346666555544443322220000  00      


Q ss_pred             -------HHHHHHHHHHHcccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCC---------CCCCcccccCCCCe
Q 012133          200 -------ESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSR---------PPSSRSLINHEQGW  263 (470)
Q Consensus       200 -------~~~~~~~~~~l~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~---------~~~~r~l~~~~~~~  263 (470)
                             +.....+...+........-.|...-.      ..+.|+..|.. .|+..         ..+.+.+.....+-
T Consensus       251 ~~~v~~~~~k~~~L~~ll~~~~~~~~IVF~~tk~------~~~~l~~~l~~-~g~~~~~lhG~l~q~~R~~~l~~F~~g~  323 (513)
T COG0513         251 YLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKR------LVEELAESLRK-RGFKVAALHGDLPQEERDRALEKFKDGE  323 (513)
T ss_pred             EEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCcHH------HHHHHHHHHHH-CCCeEEEecCCCCHHHHHHHHHHHHcCC
Confidence                   012222222233222221111111000      01111211211 12211         11122233345677


Q ss_pred             EEEEEeeCCccccCCcchhhHHhHhhhhcCcCcC
Q 012133          264 VTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAAD  297 (470)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~  297 (470)
                      ..+.|.++.  +.++++..+|...++...+...+
T Consensus       324 ~~vLVaTDv--aaRGiDi~~v~~VinyD~p~~~e  355 (513)
T COG0513         324 LRVLVATDV--AARGLDIPDVSHVINYDLPLDPE  355 (513)
T ss_pred             CCEEEEech--hhccCCccccceeEEccCCCCHH
Confidence            788888887  56788999888888888775444

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.31  E-value=7.6e-05  Score=46.32  Aligned_cols=16  Identities=44%  Similarity=1.333  Sum_probs=15.5

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      |+.|++.|||.+|||+
T Consensus        11 C~~C~~~GH~i~dCP~   26 (32)
T PF13696_consen   11 CHRCGQKGHWIQDCPT   26 (32)
T ss_pred             eecCCCCCccHhHCCC
Confidence            9999999999999995

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=97.29  E-value=0.0033  Score=67.65  Aligned_cols=78  Identities=18%  Similarity=0.143  Sum_probs=61.3

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcCCc-EEEEeCCCCHHHHHHHHcccccC----CeeEEEecccccccCCC--------
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSIIA-SEALHGDISQHQRERTLNGFRQG----KFTVLVATDVAARGLDI--------  130 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~~~-~~~lhg~~~~~~R~~~~~~f~~g----~~~iLVaTdv~~~Gidi--------  130 (470)
                      ..+.+||.+.+....+.+++.|...+. ...+.|+.+  .+..++++|+..    .-.||++|+.+-+|||+        
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            467999999999999999999986542 455666543  345677888863    68999999999999999        


Q ss_pred             --CCccEEEEecCCC
Q 012133          131 --PNVDLIIHYELPN  143 (470)
Q Consensus       131 --p~v~~VI~~~~p~  143 (470)
                        ..+++||...+|.
T Consensus       547 ~G~~Ls~ViI~kLPF  561 (636)
T TIGR03117       547 KDNLLTDLIITCAPF  561 (636)
T ss_pred             CCCcccEEEEEeCCC
Confidence              3578898877773

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.26  E-value=0.00076  Score=74.46  Aligned_cols=49  Identities=16%  Similarity=0.160  Sum_probs=37.6

Q ss_pred             EecccccccCCCCC----------------------c----------cEEEEecCCCChhHHHH--HhcccCCCCCCCeE
Q 012133          119 VATDVAARGLDIPN----------------------V----------DLIIHYELPNDPETFVH--RSGRTGRAGKEGTA  164 (470)
Q Consensus       119 VaTdv~~~Gidip~----------------------v----------~~VI~~~~p~~~~~y~q--r~GR~gR~g~~g~~  164 (470)
                      |+|.+.+.|+|+|.                      +          ++||.|++-.+..--+|  |++|++|.   +.+
T Consensus       431 ~~~~~~~e~~d~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~L~e~~P~~VImYEP~~sfIR~IEvyra~r~~r~---~rV  507 (814)
T TIGR00596       431 FEIIDEENDIDIYSGAEFDNLPQHITHFLWGERDEYVLRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLRP---LRV  507 (814)
T ss_pred             ccccccccccccchhhccccccceeeeecccccchhhHHHHHhhhCCCEEEEECCChHHHHHHHHHHccCCCCC---cEE
Confidence            77888999999997                      5          89999997766555566  67766664   678


Q ss_pred             EEeeCh
Q 012133          165 ILMFTS  170 (470)
Q Consensus       165 i~l~~~  170 (470)
                      |+|+..
T Consensus       508 yfL~y~  513 (814)
T TIGR00596       508 YFLYYG  513 (814)
T ss_pred             EEEEEC
Confidence            877764

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

>COG4889 Predicted helicase [General function prediction only]

Probab=97.17  E-value=0.00024  Score=76.14  Aligned_cols=101  Identities=21%  Similarity=0.409  Sum_probs=79.4

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc--------------C--CcEEEEeCCCCHHHHHHHHc---ccccCCeeEEEecccccc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS--------------I--IASEALHGDISQHQRERTLN---GFRQGKFTVLVATDVAAR  126 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~--------------~--~~~~~lhg~~~~~~R~~~~~---~f~~g~~~iLVaTdv~~~  126 (470)
                      .++|-||.+.++..++++.+..              .  +.+..+.|.|...+|...+.   .|...+++||---..+.+
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            3689999998888888766532              1  34556678899888855443   456678999988899999


Q ss_pred             cCCCCCccEEEEecCCCChhHHHHHhcccCCCC---CCCeEEE
Q 012133          127 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG---KEGTAIL  166 (470)
Q Consensus       127 Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g---~~g~~i~  166 (470)
                      |||+|.++-||.+++..+..+.+|.+||+.|--   +-|..|+
T Consensus       541 GVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIIL  583 (1518)
T COG4889         541 GVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIIL  583 (1518)
T ss_pred             CCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEE
Confidence            999999999999999999999999999999932   2355544

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.14  E-value=0.0075  Score=64.91  Aligned_cols=69  Identities=10%  Similarity=0.187  Sum_probs=53.1

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----cccc--cCCCCCc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR--GLDIPNV  133 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~~--Gidip~v  133 (470)
                      .++||.++|++.+.++++.+.+     .+.+..+||+.+...+...++.    ..+|||+|+     .+..  .+++..+
T Consensus        85 ~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~----~~dIiV~TP~rL~~~l~~~~~~~l~~v  160 (572)
T PRK04537         85 PRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQ----GVDVIIATPGRLIDYVKQHKVVSLHAC  160 (572)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhC----CCCEEEECHHHHHHHHHhccccchhhe
Confidence            5899999999999999887763     3678899999988877666643    578999996     3322  3667778


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      .+||.
T Consensus       161 ~~lVi  165 (572)
T PRK04537        161 EICVL  165 (572)
T ss_pred             eeeEe
Confidence            87764

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

Probab=97.02  E-value=0.0067  Score=62.15  Aligned_cols=69  Identities=17%  Similarity=0.298  Sum_probs=50.9

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----ccccc-CCCCCcc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNVD  134 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~~G-idip~v~  134 (470)
                      ..+||..||++.+++++..-++     .+.+...+++.+-.++..-+    ...+.|||||+     +.++| |.++++.
T Consensus       153 P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~----~~gcdIlvaTpGrL~d~~e~g~i~l~~~k  228 (482)
T KOG0335|consen  153 PRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFI----KRGCDILVATPGRLKDLIERGKISLDNCK  228 (482)
T ss_pred             CceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhh----ccCccEEEecCchhhhhhhcceeehhhCc
Confidence            5799999999999999988775     35678888885544443333    33799999996     55655 7777777


Q ss_pred             EEEE
Q 012133          135 LIIH  138 (470)
Q Consensus       135 ~VI~  138 (470)
                      ++|.
T Consensus       229 ~~vL  232 (482)
T KOG0335|consen  229 FLVL  232 (482)
T ss_pred             EEEe
Confidence            7663

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

Probab=96.99  E-value=0.0016  Score=64.22  Aligned_cols=132  Identities=17%  Similarity=0.247  Sum_probs=86.1

Q ss_pred             HHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc----
Q 012133           52 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD----  122 (470)
Q Consensus        52 ~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd----  122 (470)
                      +.+|..|+.. .+...+||.+||++.|.++++.++.     ++.+..|-|+|....+...+.+    +..|||||+    
T Consensus       117 LPIl~~LL~~-p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~k----kPhilVaTPGrL~  191 (476)
T KOG0330|consen  117 LPILQRLLQE-PKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSK----KPHILVATPGRLW  191 (476)
T ss_pred             HHHHHHHHcC-CCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhc----CCCEEEeCcHHHH
Confidence            3455555542 2346899999999999999988873     4789999999987765544433    678899998    


Q ss_pred             --cc-cccCCCCCccEEE--------EecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccC
Q 012133          123 --VA-ARGLDIPNVDLII--------HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  191 (470)
Q Consensus       123 --v~-~~Gidip~v~~VI--------~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~  191 (470)
                        +. ..|+.+..+.+.|        +.|+-...+.++-++-       ...-.+|++..-...+++|+...-..+..+.
T Consensus       192 dhl~~Tkgf~le~lk~LVlDEADrlLd~dF~~~ld~ILk~ip-------~erqt~LfsATMt~kv~kL~rasl~~p~~v~  264 (476)
T KOG0330|consen  192 DHLENTKGFSLEQLKFLVLDEADRLLDMDFEEELDYILKVIP-------RERQTFLFSATMTKKVRKLQRASLDNPVKVA  264 (476)
T ss_pred             HHHHhccCccHHHhHHHhhchHHhhhhhhhHHHHHHHHHhcC-------ccceEEEEEeecchhhHHHHhhccCCCeEEe
Confidence              22 5777777777665        4455445555555553       2344566666555666677655544444444


Q ss_pred             CCCH
Q 012133          192 PPVV  195 (470)
Q Consensus       192 ~p~~  195 (470)
                      .+..
T Consensus       265 ~s~k  268 (476)
T KOG0330|consen  265 VSSK  268 (476)
T ss_pred             ccch
Confidence            4443

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=96.84  E-value=0.0042  Score=69.19  Aligned_cols=89  Identities=17%  Similarity=0.159  Sum_probs=67.4

Q ss_pred             EEEeCchHHHHHHHHHHhc-----C--CcEEEEeCCCCHHHHHHHHccc----------------------cc----CCe
Q 012133           69 IVFTQTKRDADEVSLALTS-----I--IASEALHGDISQHQRERTLNGF----------------------RQ----GKF  115 (470)
Q Consensus        69 lVF~~t~~~~~~l~~~l~~-----~--~~~~~lhg~~~~~~R~~~~~~f----------------------~~----g~~  115 (470)
                      ||-+++++.+..+++.|..     .  +.+.++|+..+...|..+++..                      ++    +..
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            7778888888888887753     1  3477899999877776655442                      11    356


Q ss_pred             eEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCC
Q 012133          116 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  160 (470)
Q Consensus       116 ~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~  160 (470)
                      .|+|+|+|++.|+|+. .+++|-  -|.+..+++||+||+.|.+.
T Consensus       840 ~i~v~Tqv~E~g~D~d-fd~~~~--~~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       840 FIVLATPVEEVGRDHD-YDWAIA--DPSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             eEEEEeeeEEEEeccc-CCeeee--ccCcHHHHHHHhhccccccc
Confidence            8999999999999994 455553  36788999999999999763

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.

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

Probab=96.75  E-value=0.015  Score=59.49  Aligned_cols=112  Identities=14%  Similarity=0.192  Sum_probs=74.2

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-------cccccCCCCCc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-------VAARGLDIPNV  133 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-------v~~~Gidip~v  133 (470)
                      -++||.|||++.+.+++...++     .+.+...-|+|+-+.++.+++.    ...|+|||+       --..++|+.++
T Consensus       253 TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs----~PDIVIATPGRlIDHlrNs~sf~ldsi  328 (691)
T KOG0338|consen  253 TRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRS----RPDIVIATPGRLIDHLRNSPSFNLDSI  328 (691)
T ss_pred             eeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhh----CCCEEEecchhHHHHhccCCCccccce
Confidence            4899999999998888776553     3667777899999999999987    678999998       23456777777


Q ss_pred             cEEEEecCCCChh--------HHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCcc
Q 012133          134 DLIIHYELPNDPE--------TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE  188 (470)
Q Consensus       134 ~~VI~~~~p~~~~--------~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~  188 (470)
                      .++|.-....-.+        .+++.+-       ......|++..--..++.|.+..-.++.
T Consensus       329 EVLvlDEADRMLeegFademnEii~lcp-------k~RQTmLFSATMteeVkdL~slSL~kPv  384 (691)
T KOG0338|consen  329 EVLVLDEADRMLEEGFADEMNEIIRLCP-------KNRQTMLFSATMTEEVKDLASLSLNKPV  384 (691)
T ss_pred             eEEEechHHHHHHHHHHHHHHHHHHhcc-------ccccceeehhhhHHHHHHHHHhhcCCCe
Confidence            7777543332222        2333332       2234556666555556666555444443

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.64  E-value=0.028  Score=61.17  Aligned_cols=63  Identities=10%  Similarity=0.131  Sum_probs=44.6

Q ss_pred             HHHHcccccCCeeEEEecc----cccccCCCCCccEEEEecC------CC------ChhHHHHHhcccCCCCCCCeEEEe
Q 012133          104 ERTLNGFRQGKFTVLVATD----VAARGLDIPNVDLIIHYEL------PN------DPETFVHRSGRTGRAGKEGTAILM  167 (470)
Q Consensus       104 ~~~~~~f~~g~~~iLVaTd----v~~~Gidip~v~~VI~~~~------p~------~~~~y~qr~GR~gR~g~~g~~i~l  167 (470)
                      +.+++.|.. +..|||+|+    +++     +++++|+..|.      |.      ....+.|-+||+||..+.|.+++.
T Consensus       462 d~~l~~~~~-~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfRA~Er~~qll~qvagragr~~~~G~V~iq  535 (665)
T PRK14873        462 DQVVDTVDA-GPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVV  535 (665)
T ss_pred             HHHHHhhcc-CCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcChHHHHHHHHHHHHHhhcCCCCCCEEEEE
Confidence            357788864 899999999    555     35677664442      22      233447899999999899999998


Q ss_pred             eChhh
Q 012133          168 FTSSQ  172 (470)
Q Consensus       168 ~~~~~  172 (470)
                      ..++.
T Consensus       536 ~~p~~  540 (665)
T PRK14873        536 AESSL  540 (665)
T ss_pred             eCCCC
Confidence            65443

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=96.59  E-value=0.012  Score=62.32  Aligned_cols=119  Identities=15%  Similarity=0.257  Sum_probs=92.2

Q ss_pred             ccHHHHHHHHHHHH--cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHccccc--CCeeEE-Eecc
Q 012133           49 TSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ--GKFTVL-VATD  122 (470)
Q Consensus        49 ~~k~~~l~~ll~~~--~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~--g~~~iL-VaTd  122 (470)
                      +.|+..+..++..+  ....+++|...-.....-+...|.+ ++....+||.+..++|+.+++.|..  +..+|+ ++=.
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            45555555555433  3446777666665656666777875 6778899999999999999999964  445554 5557


Q ss_pred             cccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEe
Q 012133          123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  167 (470)
Q Consensus       123 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l  167 (470)
                      ..+.|||+-..+|+|..|+-|++.-=.|.+-|.-|.|++-.+++.
T Consensus       808 AGGVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V~Ih  852 (901)
T KOG4439|consen  808 AGGVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDVFIH  852 (901)
T ss_pred             cCcceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCceEEE
Confidence            788999999999999999999999999999999999988777664

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

Probab=96.56  E-value=0.016  Score=57.65  Aligned_cols=273  Identities=15%  Similarity=0.214  Sum_probs=137.8

Q ss_pred             CHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHH--HHHHHHHHHH--------cCCCeEEEEeCchHH
Q 012133            8 PSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKR--TILSDLITVY--------AKGGKTIVFTQTKRD   77 (470)
Q Consensus         8 p~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~--~~l~~ll~~~--------~~~~~~lVF~~t~~~   77 (470)
                      |+-++++.+.-+..|..|.-  ..++.+.+.+...-+......|.  .++.-++...        .....+||+++|++.
T Consensus       229 pevmenIkK~GFqKPtPIqS--QaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreL  306 (629)
T KOG0336|consen  229 PEVMENIKKTGFQKPTPIQS--QAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTREL  306 (629)
T ss_pred             HHHHHHHHhccCCCCCcchh--cccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHH
Confidence            44455566666777777743  34555556666555555544442  1122122111        123479999999999


Q ss_pred             HHHHHHHHh----cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCCccEEEEec------C
Q 012133           78 ADEVSLALT----SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVDLIIHYE------L  141 (470)
Q Consensus        78 ~~~l~~~l~----~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~v~~VI~~~------~  141 (470)
                      +.++.....    +++...+++|+-...++.+.+++    ...|+|||+      ...--||+..|+++|.-.      +
T Consensus       307 alqie~e~~kysyng~ksvc~ygggnR~eqie~lkr----gveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDM  382 (629)
T KOG0336|consen  307 ALQIEGEVKKYSYNGLKSVCVYGGGNRNEQIEDLKR----GVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDM  382 (629)
T ss_pred             HHHHHhHHhHhhhcCcceEEEecCCCchhHHHHHhc----CceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhcc
Confidence            888765554    35778888888766666555554    689999997      234446777777776422      1


Q ss_pred             CCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCcccc-----------------CCCCHHHHHHHHHH
Q 012133          142 PNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV-----------------SPPVVEDVLESSAE  204 (470)
Q Consensus       142 p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~-----------------~~p~~~~~~~~~~~  204 (470)
                      -..+  -+.++=   -.=++-...++.+..-..-+++|...+-...-.+                 -+++..+.+ +..+
T Consensus       383 gFEp--qIrkil---ldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~-~~~~  456 (629)
T KOG0336|consen  383 GFEP--QIRKIL---LDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKL-EIVQ  456 (629)
T ss_pred             cccH--HHHHHh---hhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEecccHHHH-HHHH
Confidence            1111  111110   0013334455555555556666655543332211                 112222211 1111


Q ss_pred             HHHHHHcccCccchhhhH--HHHHHHHHhhCHHHHHHHHHHHcC-CCCCCCCcccccCCCCeEEEEEeeCCccccCCcch
Q 012133          205 QVVATLNGVHPESVEFFT--PTAQRLIEEKGTDALAAALAQLSG-FSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSA  281 (470)
Q Consensus       205 ~~~~~l~~~~~~~~~~~~--~~a~~l~~~~~~~~l~~al~~l~~-~~~~~~~r~l~~~~~~~~~~~~~~~~~~~~~~~~~  281 (470)
                      .++..+.+ +...+-+..  ..|..|-.++....+.+.  .|.| -++....+++...+.+.+++++.++.  +.++++.
T Consensus       457 ~f~~~ms~-ndKvIiFv~~K~~AD~LSSd~~l~gi~~q--~lHG~r~Q~DrE~al~~~ksG~vrILvaTDl--aSRGlDv  531 (629)
T KOG0336|consen  457 FFVANMSS-NDKVIIFVSRKVMADHLSSDFCLKGISSQ--SLHGNREQSDREMALEDFKSGEVRILVATDL--ASRGLDV  531 (629)
T ss_pred             HHHHhcCC-CceEEEEEechhhhhhccchhhhcccchh--hccCChhhhhHHHHHHhhhcCceEEEEEech--hhcCCCc
Confidence            11111111 111111110  011111111111111110  0111 11222334455667889999999987  6788999


Q ss_pred             hhHHhHhhhhcCcCcC
Q 012133          282 RSVMGFLSDVYPTAAD  297 (470)
Q Consensus       282 ~~v~~~l~~~~~~~~~  297 (470)
                      .||.+.++..++..-+
T Consensus       532 ~DiTHV~NyDFP~nIe  547 (629)
T KOG0336|consen  532 PDITHVYNYDFPRNIE  547 (629)
T ss_pred             hhcceeeccCCCccHH
Confidence            9999998888775443

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.55  E-value=0.019  Score=63.07  Aligned_cols=92  Identities=21%  Similarity=0.265  Sum_probs=72.6

Q ss_pred             cccHHHHHHHHH-HHHcCCCeEEEEeCchHHHHHHHHHHhc--CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccc
Q 012133           48 ATSKRTILSDLI-TVYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  124 (470)
Q Consensus        48 ~~~k~~~l~~ll-~~~~~~~~~lVF~~t~~~~~~l~~~l~~--~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~  124 (470)
                      ...|..+...++ ..+..+.++||.+||++.+.++++.|++  +..+..+|++++..+|.+.+.++.++..+|+|+|..+
T Consensus       172 GSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsa  251 (679)
T PRK05580        172 GSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSA  251 (679)
T ss_pred             CChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHH
Confidence            345666554444 3344567999999999999999999986  4578999999999999999999999999999999754


Q ss_pred             cccCCCCCccEEEEec
Q 012133          125 ARGLDIPNVDLIIHYE  140 (470)
Q Consensus       125 ~~Gidip~v~~VI~~~  140 (470)
                      .. +.+.++.+||.-+
T Consensus       252 l~-~p~~~l~liVvDE  266 (679)
T PRK05580        252 LF-LPFKNLGLIIVDE  266 (679)
T ss_pred             hc-ccccCCCEEEEEC
Confidence            32 5677888888544

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=96.53  E-value=0.001  Score=44.46  Aligned_cols=16  Identities=50%  Similarity=1.273  Sum_probs=15.3

Q ss_pred             ccccCCCCCccCCCCC
Q 012133          454 ACFNCGKSGHRASECP  469 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~  469 (470)
                      .|.+|++.|||+.|||
T Consensus         6 ~CqkC~~~GH~tyeC~   21 (42)
T PF13917_consen    6 RCQKCGQKGHWTYECP   21 (42)
T ss_pred             cCcccCCCCcchhhCC
Confidence            4999999999999999

>PF13871 Helicase_C_4: Helicase_C-like

Probab=96.53  E-value=0.011  Score=57.05  Aligned_cols=79  Identities=20%  Similarity=0.369  Sum_probs=59.3

Q ss_pred             HHHcccccCCeeEEEecccccccCCCCCc--------cEEEEecCCCChhHHHHHhcccCCCCCC-CeEEEeeC---hhh
Q 012133          105 RTLNGFRQGKFTVLVATDVAARGLDIPNV--------DLIIHYELPNDPETFVHRSGRTGRAGKE-GTAILMFT---SSQ  172 (470)
Q Consensus       105 ~~~~~f~~g~~~iLVaTdv~~~Gidip~v--------~~VI~~~~p~~~~~y~qr~GR~gR~g~~-g~~i~l~~---~~~  172 (470)
                      ...+.|.+|+..|+|.|+.++.||.+..-        .+-|...+||+.+..+|..||+.|.++. ...|.++.   +-|
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            45678999999999999999999988532        3566789999999999999999999854 33344333   235


Q ss_pred             HHHHHHHHHHh
Q 012133          173 RRTVRSLERDV  183 (470)
Q Consensus       173 ~~~~~~i~~~~  183 (470)
                      +.....+.+.+
T Consensus       132 ~Rfas~va~rL  142 (278)
T PF13871_consen  132 RRFASTVARRL  142 (278)
T ss_pred             HHHHHHHHHHH
Confidence            55555555544

>smart00343 ZnF_C2HC zinc finger

Probab=96.53  E-value=0.001  Score=39.79  Aligned_cols=15  Identities=67%  Similarity=1.688  Sum_probs=14.7

Q ss_pred             cccCCCCCccCCCCC
Q 012133          455 CFNCGKSGHRASECP  469 (470)
Q Consensus       455 c~~c~~~gh~~~~c~  469 (470)
                      |++|++.||++++||
T Consensus         2 C~~CG~~GH~~~~C~   16 (26)
T smart00343        2 CYNCGKEGHIARDCP   16 (26)
T ss_pred             CccCCCCCcchhhCC
Confidence            999999999999998

>TIGR00595 priA primosomal protein N'

Probab=96.53  E-value=0.016  Score=61.36  Aligned_cols=90  Identities=20%  Similarity=0.246  Sum_probs=71.7

Q ss_pred             ccHHHHHHHHHH-HHcCCCeEEEEeCchHHHHHHHHHHhc--CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccccc
Q 012133           49 TSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  125 (470)
Q Consensus        49 ~~k~~~l~~ll~-~~~~~~~~lVF~~t~~~~~~l~~~l~~--~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~  125 (470)
                      .-|.++...++. .+..+.++||.+|++..+.++++.|++  ...+..+|+.++..+|.++..+..+++.+|+|+|..+.
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            456665555443 344567999999999999999999986  35688999999999999999999999999999997544


Q ss_pred             ccCCCCCccEEEEe
Q 012133          126 RGLDIPNVDLIIHY  139 (470)
Q Consensus       126 ~Gidip~v~~VI~~  139 (470)
                      . +.++++.+||.-
T Consensus        88 f-~p~~~l~lIIVD  100 (505)
T TIGR00595        88 F-LPFKNLGLIIVD  100 (505)
T ss_pred             c-CcccCCCEEEEE
Confidence            3 567788888843

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).

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=96.43  E-value=0.0072  Score=53.02  Aligned_cols=67  Identities=21%  Similarity=0.269  Sum_probs=37.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 012133          393 RSSRSWGSDDEDGFSSSRGGRS-FRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN  470 (470)
Q Consensus       393 ~~~~~~g~~g~~~~~~~~g~~~-~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~g~~c~~c~~~gh~~~~c~~  470 (470)
                      ..|+.|+..||.++.+...... ....+..++..|+....-.....           .+....||+|++.||+++|||+
T Consensus        28 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~-----------~~~~~~C~~Cg~~GH~~~~C~~   95 (148)
T PTZ00368         28 RPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPP-----------GSGPRSCYNCGQTGHISRECPN   95 (148)
T ss_pred             ccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCccc-----------CCCCcccCcCCCCCcccccCCC
Confidence            5688899999988877543211 11234444433322111100000           0112359999999999999985

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=96.41  E-value=0.012  Score=51.57  Aligned_cols=68  Identities=22%  Similarity=0.282  Sum_probs=38.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 012133          393 RSSRSWGSDDEDGFSSSRGGR-SFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN  470 (470)
Q Consensus       393 ~~~~~~g~~g~~~~~~~~g~~-~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~g~~c~~c~~~gh~~~~c~~  470 (470)
                      ..|+.|+..||.+..++.... +....+..++..++....-....-   +       ++....||+|++.||+++|||+
T Consensus        53 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~---~-------~~~~~~C~~Cg~~gH~~~~C~~  121 (148)
T PTZ00368         53 RSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAK---G-------GAARRACYNCGGEGHISRDCPN  121 (148)
T ss_pred             cccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCccc---c-------cccchhhcccCcCCcchhcCCC
Confidence            468889999998887754321 112234444433332111100000   0       1122359999999999999995

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.38  E-value=0.014  Score=64.28  Aligned_cols=91  Identities=16%  Similarity=0.255  Sum_probs=72.3

Q ss_pred             ccHHHH-HHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           49 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        49 ~~k~~~-l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      .-|..+ +..++.....+.++||.+||+..|.+.++.+.+     ++.+..+||+++.++|.++++.+.+|...|+|+|.
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            455433 333444455667999999999999999888764     37799999999999999999999999999999997


Q ss_pred             c-ccccCCCCCccEEEEe
Q 012133          123 V-AARGLDIPNVDLIIHY  139 (470)
Q Consensus       123 v-~~~Gidip~v~~VI~~  139 (470)
                      . +...+.+.++.+||.-
T Consensus       373 ~ll~~~v~~~~l~lvVID  390 (681)
T PRK10917        373 ALIQDDVEFHNLGLVIID  390 (681)
T ss_pred             HHhcccchhcccceEEEe
Confidence            4 4445778899988853

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=96.31  E-value=0.0014  Score=61.74  Aligned_cols=16  Identities=56%  Similarity=1.479  Sum_probs=15.4

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||.||++|||+.|||.
T Consensus       163 cyrcGkeghwskEcP~  178 (346)
T KOG0109|consen  163 CYRCGKEGHWSKECPV  178 (346)
T ss_pred             heeccccccccccCCc
Confidence            9999999999999995

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.28  E-value=0.022  Score=61.97  Aligned_cols=92  Identities=18%  Similarity=0.275  Sum_probs=74.8

Q ss_pred             cccHHHHHHHHHH-HHcCCCeEEEEeCchHHHHHHHHHHhcCC---cEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc
Q 012133           48 ATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSII---ASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  123 (470)
Q Consensus        48 ~~~k~~~l~~ll~-~~~~~~~~lVF~~t~~~~~~l~~~l~~~~---~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv  123 (470)
                      .+.|.+++.+++. .+..++++||.++....+.++.+.|+..+   .+..+|+++++.+|.+...+.++|+.+|+|.|-.
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            3467777777764 34567799999999999999999998644   5899999999999999999999999999999975


Q ss_pred             ccccCCCCCccEEEEec
Q 012133          124 AARGLDIPNVDLIIHYE  140 (470)
Q Consensus       124 ~~~Gidip~v~~VI~~~  140 (470)
                      +. =.-++++.+||..+
T Consensus       250 Av-FaP~~~LgLIIvdE  265 (665)
T PRK14873        250 AV-FAPVEDLGLVAIWD  265 (665)
T ss_pred             eE-EeccCCCCEEEEEc
Confidence            43 34567778888544

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=96.18  E-value=0.0023  Score=40.54  Aligned_cols=15  Identities=60%  Similarity=1.052  Sum_probs=11.3

Q ss_pred             ccccCCCCCccCCCC
Q 012133          454 ACFNCGKSGHRASEC  468 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c  468 (470)
                      -|++|++..|||+||
T Consensus         4 ~CprC~kg~Hwa~~C   18 (36)
T PF14787_consen    4 LCPRCGKGFHWASEC   18 (36)
T ss_dssp             C-TTTSSSCS-TTT-
T ss_pred             cCcccCCCcchhhhh
Confidence            399999999999999

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=96.05  E-value=0.023  Score=62.01  Aligned_cols=90  Identities=17%  Similarity=0.271  Sum_probs=71.6

Q ss_pred             ccHHHH-HHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           49 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        49 ~~k~~~-l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      .-|..+ +..++.......+++|.+||+..|.++++.+.+     ++.+..+||+++.++|..+++.+.+++..|+|+|.
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            455433 333445555667999999999999999887764     47899999999999999999999999999999997


Q ss_pred             cc-cccCCCCCccEEEE
Q 012133          123 VA-ARGLDIPNVDLIIH  138 (470)
Q Consensus       123 v~-~~Gidip~v~~VI~  138 (470)
                      .. ...+.+.++.+||.
T Consensus       347 ~ll~~~~~~~~l~lvVI  363 (630)
T TIGR00643       347 ALIQEKVEFKRLALVII  363 (630)
T ss_pred             HHHhccccccccceEEE
Confidence            43 44577888888884

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=95.87  E-value=0.045  Score=61.61  Aligned_cols=117  Identities=18%  Similarity=0.303  Sum_probs=87.0

Q ss_pred             HHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----------------------CCcEEEEeCCCCHHHHHHHHcccccCC
Q 012133           58 LITVYAKGGKTIVFTQTKRDADEVSLALTS-----------------------IIASEALHGDISQHQRERTLNGFRQGK  114 (470)
Q Consensus        58 ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----------------------~~~~~~lhg~~~~~~R~~~~~~f~~g~  114 (470)
                      +.+.....+++|||+++++.|..++..|-.                       .++..+=|-+|+..++..+-..|..|.
T Consensus      1352 i~~~a~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~ 1431 (1674)
T KOG0951|consen 1352 IVRHAGNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGA 1431 (1674)
T ss_pred             HHHHhcCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCc
Confidence            333335668999999999999888765421                       023333388999999999999999999


Q ss_pred             eeEEEecccccccCCCCCccEEE-----Eec------CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHH
Q 012133          115 FTVLVATDVAARGLDIPNVDLII-----HYE------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       115 ~~iLVaTdv~~~Gidip~v~~VI-----~~~------~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i  179 (470)
                      ++|+|...- -.|+-... ++||     .||      .+.+.....|++|++.|+   +.|+++.....+.+++++
T Consensus      1432 i~v~v~s~~-~~~~~~~~-~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~~---~k~vi~~~~~~k~yykkf 1502 (1674)
T KOG0951|consen 1432 IQVCVMSRD-CYGTKLKA-HLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASGA---GKCVIMCHTPKKEYYKKF 1502 (1674)
T ss_pred             EEEEEEEcc-cccccccc-eEEEEecceeecccccccccCchhHHHHHhhhhcCC---ccEEEEecCchHHHHHHh
Confidence            999988755 66766643 3344     233      355788899999999984   699999998888887765

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=95.86  E-value=0.033  Score=62.96  Aligned_cols=90  Identities=17%  Similarity=0.225  Sum_probs=71.0

Q ss_pred             ccHHHHHH-HHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           49 TSKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        49 ~~k~~~l~-~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      .-|..+.. .++.......+++|.+||+..|.+.++.+.+     .+.+..+++.++..++.++++.+++|+++|||+|.
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            45554332 3344444568999999999999999988874     24678899999999999999999999999999996


Q ss_pred             -cccccCCCCCccEEEE
Q 012133          123 -VAARGLDIPNVDLIIH  138 (470)
Q Consensus       123 -v~~~Gidip~v~~VI~  138 (470)
                       ++...+.+.++.+||.
T Consensus       563 ~ll~~~v~f~~L~llVI  579 (926)
T TIGR00580       563 KLLQKDVKFKDLGLLII  579 (926)
T ss_pred             HHhhCCCCcccCCEEEe
Confidence             4555678889998885

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.

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=95.82  E-value=0.22  Score=54.49  Aligned_cols=111  Identities=19%  Similarity=0.259  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC
Q 012133           53 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP  131 (470)
Q Consensus        53 ~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip  131 (470)
                      .....|+..+..++++-||+.|...++.+++.... ...+..+++.-+..+   + +.+.  +.+|+|-|+++..|+++.
T Consensus       270 tF~~~L~~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~d---v-~~W~--~~~VviYT~~itvG~Sf~  343 (824)
T PF02399_consen  270 TFFSELLARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLED---V-ESWK--KYDVVIYTPVITVGLSFE  343 (824)
T ss_pred             hHHHHHHHHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccc---c-cccc--ceeEEEEeceEEEEeccc
Confidence            44455566666778889999999998888888775 456777777655442   1 2333  689999999999999997


Q ss_pred             CccE--EEEecCC----CChhHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          132 NVDL--IIHYELP----NDPETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       132 ~v~~--VI~~~~p----~~~~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                      +..+  |.-|=-|    .+..+..|++||+-.. .....+++++.
T Consensus       344 ~~HF~~~f~yvk~~~~gpd~~s~~Q~lgRvR~l-~~~ei~v~~d~  387 (824)
T PF02399_consen  344 EKHFDSMFAYVKPMSYGPDMVSVYQMLGRVRSL-LDNEIYVYIDA  387 (824)
T ss_pred             hhhceEEEEEecCCCCCCcHHHHHHHHHHHHhh-ccCeEEEEEec
Confidence            5542  4433223    3566789999997544 33445554443

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

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=95.34  E-value=0.059  Score=52.24  Aligned_cols=10  Identities=0%  Similarity=0.348  Sum_probs=4.3

Q ss_pred             HHHHHHHHHh
Q 012133          174 RTVRSLERDV  183 (470)
Q Consensus       174 ~~~~~i~~~~  183 (470)
                      ..++.|+..+
T Consensus       165 ~lfe~i~~kl  174 (465)
T KOG3973|consen  165 KLFETIRQKL  174 (465)
T ss_pred             HHHHHHHHHH
Confidence            4444444443

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=95.25  E-value=0.13  Score=55.91  Aligned_cols=70  Identities=23%  Similarity=0.240  Sum_probs=53.8

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----cccc-cCCCCC
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPN  132 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~~-Gidip~  132 (470)
                      ..++||.|||++.|.++++.+..      .+.+..+|++.+...+...++.    ...|||+|+     .+.+ .+++.+
T Consensus        74 ~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~----~~~IVVgTPgrl~d~l~r~~l~l~~  149 (629)
T PRK11634         74 APQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQ----GPQIVVGTPGRLLDHLKRGTLDLSK  149 (629)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcC----CCCEEEECHHHHHHHHHcCCcchhh
Confidence            45899999999999999887653      4678899999887776665543    578999995     3333 478888


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +.+||.
T Consensus       150 l~~lVl  155 (629)
T PRK11634        150 LSGLVL  155 (629)
T ss_pred             ceEEEe
Confidence            888874

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

Probab=95.00  E-value=0.056  Score=59.04  Aligned_cols=92  Identities=24%  Similarity=0.299  Sum_probs=75.7

Q ss_pred             cCcccHHHHHHHHHH-HHcCCCeEEEEeCchHHHHHHHHHHhc--CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           46 TTATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        46 ~~~~~k~~~l~~ll~-~~~~~~~~lVF~~t~~~~~~l~~~l~~--~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      ++-+.|.+++..++. .+..++++||.+|-+....++...+..  +..+.++|++|++.+|.....+.++|+.+|+|.|-
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            455678888888775 446678999999999999999998885  46799999999999999999999999999999996


Q ss_pred             cccccCCCCCccEEEE
Q 012133          123 VAARGLDIPNVDLIIH  138 (470)
Q Consensus       123 v~~~Gidip~v~~VI~  138 (470)
                      .+- =.-++++-+||.
T Consensus       305 SAl-F~Pf~~LGLIIv  319 (730)
T COG1198         305 SAL-FLPFKNLGLIIV  319 (730)
T ss_pred             hhh-cCchhhccEEEE
Confidence            432 344567777773

>PRK10689 transcription-repair coupling factor; Provisional

Probab=94.92  E-value=0.088  Score=60.94  Aligned_cols=92  Identities=15%  Similarity=0.153  Sum_probs=70.0

Q ss_pred             CcccHHHHHHH-HHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEe
Q 012133           47 TATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVA  120 (470)
Q Consensus        47 ~~~~k~~~l~~-ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVa  120 (470)
                      ...-|..+... +........++||.+||+..|.++++.+.+     .+.+..+++..+.+++.++++.++++..+|||+
T Consensus       630 TGsGKT~val~aa~~~~~~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVg  709 (1147)
T PRK10689        630 VGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIG  709 (1147)
T ss_pred             CCcCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEE
Confidence            33456543222 222334568999999999999999988874     246778999999999999999999999999999


Q ss_pred             cc-cccccCCCCCccEEEE
Q 012133          121 TD-VAARGLDIPNVDLIIH  138 (470)
Q Consensus       121 Td-v~~~Gidip~v~~VI~  138 (470)
                      |. .+...+.+.++.+||.
T Consensus       710 Tp~lL~~~v~~~~L~lLVI  728 (1147)
T PRK10689        710 THKLLQSDVKWKDLGLLIV  728 (1147)
T ss_pred             CHHHHhCCCCHhhCCEEEE
Confidence            96 4445567788888774

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=94.86  E-value=0.011  Score=53.04  Aligned_cols=15  Identities=60%  Similarity=1.646  Sum_probs=14.8

Q ss_pred             cccCCCCCccCCCCC
Q 012133          455 CFNCGKSGHRASECP  469 (470)
Q Consensus       455 c~~c~~~gh~~~~c~  469 (470)
                      ||+|||.||.++|||
T Consensus        63 C~nCg~~GH~~~DCP   77 (190)
T COG5082          63 CFNCGQNGHLRRDCP   77 (190)
T ss_pred             cchhcccCcccccCC
Confidence            999999999999999

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=94.61  E-value=0.13  Score=53.32  Aligned_cols=70  Identities=16%  Similarity=0.246  Sum_probs=54.2

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCCcc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVD  134 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~v~  134 (470)
                      .++||.+||++.+.++++.+..     .+.+..++|+.+...+..++..    ..+|||+|+      +....+++.++.
T Consensus        74 ~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~----~~~IlV~Tp~rl~~~~~~~~~~~~~v~  149 (434)
T PRK11192         74 PRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSE----NQDIVVATPGRLLQYIKEENFDCRAVE  149 (434)
T ss_pred             ceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcC----CCCEEEEChHHHHHHHHcCCcCcccCC
Confidence            5899999999999998876652     4678999999988877766643    578999997      223456788888


Q ss_pred             EEEEe
Q 012133          135 LIIHY  139 (470)
Q Consensus       135 ~VI~~  139 (470)
                      +||.-
T Consensus       150 ~lViD  154 (434)
T PRK11192        150 TLILD  154 (434)
T ss_pred             EEEEE
Confidence            88743

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=94.60  E-value=0.19  Score=43.59  Aligned_cols=46  Identities=22%  Similarity=0.302  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHcccccCC-eeEEEecccccccCCCCCc--cEEEEecCCC
Q 012133           98 ISQHQRERTLNGFRQGK-FTVLVATDVAARGLDIPNV--DLIIHYELPN  143 (470)
Q Consensus        98 ~~~~~R~~~~~~f~~g~-~~iLVaTdv~~~Gidip~v--~~VI~~~~p~  143 (470)
                      ....+..++++.|++.. ..||++|.-..+|||+|+-  ..||...+|.
T Consensus        31 ~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492       31 EDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             CChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCC
Confidence            44445678888888654 3799999889999999974  5688777664

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=94.56  E-value=0.13  Score=55.32  Aligned_cols=110  Identities=19%  Similarity=0.262  Sum_probs=89.0

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcC-------------------CcEEEEeCCCCHHHHHHHHcccccC---CeeEEEec
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSI-------------------IASEALHGDISQHQRERTLNGFRQG---KFTVLVAT  121 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~-------------------~~~~~lhg~~~~~~R~~~~~~f~~g---~~~iLVaT  121 (470)
                      .+.++|||.......+.|.+.|.+.                   ..-.-+.|..+..+|++.+++|.+.   ..-+|++|
T Consensus       718 ~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllst  797 (1387)
T KOG1016|consen  718 IGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLST  797 (1387)
T ss_pred             cCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehh
Confidence            3568999999988888887777642                   1234577888999999999999863   24678999


Q ss_pred             ccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhH
Q 012133          122 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       122 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                      .....||++-..+-+|.+|.-|++.--.|.+-|+-|.|+.-.|+++-.--+.
T Consensus       798 rag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlVmD~  849 (1387)
T KOG1016|consen  798 RAGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLVMDN  849 (1387)
T ss_pred             ccccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeehhhh
Confidence            9999999998888999999999999889999999999988888776544433

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=94.51  E-value=0.12  Score=57.27  Aligned_cols=60  Identities=20%  Similarity=0.345  Sum_probs=51.5

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-----C-CcEEE-EeCCCCHHHHHHHHcccccCCeeEEEeccc
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-----I-IASEA-LHGDISQHQRERTLNGFRQGKFTVLVATDV  123 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-----~-~~~~~-lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv  123 (470)
                      +++++++.+||...+.+.++.|.+     . +.+.. +|+.|+.+++++++++|.+|..+|||+|..
T Consensus       124 kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         124 KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             cCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            458999999999999999988874     1 33333 999999999999999999999999999973

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=94.51  E-value=0.015  Score=52.08  Aligned_cols=54  Identities=22%  Similarity=0.327  Sum_probs=32.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccCCCCCccCCCC-C
Q 012133          393 RSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASEC-P  469 (470)
Q Consensus       393 ~~~~~~g~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~g~~c~~c~~~gh~~~~c-~  469 (470)
                      -.|+.||+.||..++|+ .     .-+..|.-     .++.+.--            ....-||+||+.||+++|| |
T Consensus        61 ~~C~nCg~~GH~~~DCP-~-----~iC~~C~~-----~~H~s~~C------------~~~~~C~~Cg~~GH~~~dC~P  115 (190)
T COG5082          61 PVCFNCGQNGHLRRDCP-H-----SICYNCSW-----DGHRSNHC------------PKPKKCYNCGETGHLSRDCNP  115 (190)
T ss_pred             cccchhcccCcccccCC-h-----hHhhhcCC-----CCcccccC------------CcccccccccccCccccccCc
Confidence            46999999999998887 1     11222210     00110000            0112399999999999999 5

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

Probab=94.28  E-value=0.1  Score=53.75  Aligned_cols=55  Identities=18%  Similarity=0.245  Sum_probs=42.8

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      .+...||..+|++.++++.+.-.+     ++.+..+-|+++.+++---+..    -+.|+|||+
T Consensus       321 ~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~----gceiviatP  380 (673)
T KOG0333|consen  321 EGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSM----GCEIVIATP  380 (673)
T ss_pred             cCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhc----cceeeecCc
Confidence            356899999999999999876543     4678889999998876433333    579999997

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=94.15  E-value=0.2  Score=43.58  Aligned_cols=42  Identities=21%  Similarity=0.376  Sum_probs=30.9

Q ss_pred             HHHHHHcccccCCe---eEEEeccc--ccccCCCCCc--cEEEEecCCC
Q 012133          102 QRERTLNGFRQGKF---TVLVATDV--AARGLDIPNV--DLIIHYELPN  143 (470)
Q Consensus       102 ~R~~~~~~f~~g~~---~iLVaTdv--~~~Gidip~v--~~VI~~~~p~  143 (470)
                      +..++++.|++..-   .||+++.-  ..+|||+|+-  ..||...+|.
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            44677778876433   68888876  8999999974  5788777763

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=93.89  E-value=0.044  Score=63.98  Aligned_cols=92  Identities=22%  Similarity=0.403  Sum_probs=75.9

Q ss_pred             eEEEEeCchHHHHHHHHHHhc--CCcEEEEeCCCC-----------HHHHHHHHcccccCCeeEEEecccccccCCCCCc
Q 012133           67 KTIVFTQTKRDADEVSLALTS--IIASEALHGDIS-----------QHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV  133 (470)
Q Consensus        67 ~~lVF~~t~~~~~~l~~~l~~--~~~~~~lhg~~~-----------~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v  133 (470)
                      ..|+|++....+..+.+.+.+  .+.+..+.|.+.           +..+.+++..|....+++|++|.++..|+|++.+
T Consensus       294 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~  373 (1606)
T KOG0701|consen  294 SGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKC  373 (1606)
T ss_pred             hheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhh
Confidence            568999999999998888874  233333444322           2246789999999999999999999999999999


Q ss_pred             cEEEEecCCCChhHHHHHhcccCCC
Q 012133          134 DLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus       134 ~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      +.|+.++.|.....|+|..||+-++
T Consensus       374 ~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  374 NLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhheeccCcchHHHHHHhhcccccc
Confidence            9999999999999999999998554

>PRK14701 reverse gyrase; Provisional

Probab=93.83  E-value=0.19  Score=60.07  Aligned_cols=60  Identities=22%  Similarity=0.316  Sum_probs=52.6

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  123 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv  123 (470)
                      +..++||.+||++.+.++++.|..       .+.+..+||+++..++.++++.++++..+|||+|+-
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            456899999999999999988874       245788999999999999999999999999999974

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=93.82  E-value=0.32  Score=54.15  Aligned_cols=107  Identities=17%  Similarity=0.281  Sum_probs=69.1

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-------cccc--cCCCC
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-------VAAR--GLDIP  131 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-------v~~~--Gidip  131 (470)
                      .-+||.++|++.+.+|.+.+.+     .+.+++.+|+..++++...+++   | ..|+|||.       ++..  =.+|-
T Consensus       439 Pi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkR---g-~eIvV~tpGRmiD~l~~n~grvtnlr  514 (997)
T KOG0334|consen  439 PIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKR---G-AEIVVCTPGRMIDILCANSGRVTNLR  514 (997)
T ss_pred             ceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhc---C-CceEEeccchhhhhHhhcCCcccccc
Confidence            4579999999999999988874     4778999999888877666554   5 78999996       1222  23445


Q ss_pred             CccEEEE------ec--CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHh
Q 012133          132 NVDLIIH------YE--LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  183 (470)
Q Consensus       132 ~v~~VI~------~~--~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~  183 (470)
                      .|++|+.      +|  +-.....++|.+ |.-|      -.++++.+....+..+.+..
T Consensus       515 R~t~lv~deaDrmfdmgfePq~~~Ii~nl-rpdr------QtvlfSatfpr~m~~la~~v  567 (997)
T KOG0334|consen  515 RVTYLVLDEADRMFDMGFEPQITRILQNL-RPDR------QTVLFSATFPRSMEALARKV  567 (997)
T ss_pred             ccceeeechhhhhheeccCcccchHHhhc-chhh------hhhhhhhhhhHHHHHHHHHh
Confidence            5556662      22  222333377888 4444      34555555555566665554

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=93.77  E-value=0.41  Score=50.17  Aligned_cols=70  Identities=19%  Similarity=0.237  Sum_probs=54.8

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----ccc-ccCCCCCc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAA-RGLDIPNV  133 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~-~Gidip~v  133 (470)
                      .++||.+||++.+.++++.+..      .+.+..++|+.+...+...++    ....|+|+|+     .+. ..+++.++
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            4799999999999999887763      367888999999887766665    3678999995     333 45788899


Q ss_pred             cEEEEe
Q 012133          134 DLIIHY  139 (470)
Q Consensus       134 ~~VI~~  139 (470)
                      .+||.-
T Consensus       149 ~~lViD  154 (460)
T PRK11776        149 NTLVLD  154 (460)
T ss_pred             CEEEEE
Confidence            988853

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.72  E-value=0.35  Score=50.08  Aligned_cols=114  Identities=21%  Similarity=0.291  Sum_probs=86.0

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc--ccccCCCCCccEEEEecCC
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV--AARGLDIPNVDLIIHYELP  142 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv--~~~Gidip~v~~VI~~~~p  142 (470)
                      .-+|||.|+--+-..+..++.+ .+....+|--.++..-.++-+.|-.|...||+-|.-  .-+-.+|..|..||.|.+|
T Consensus       553 s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfYqpP  632 (698)
T KOG2340|consen  553 SGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFYQPP  632 (698)
T ss_pred             CceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEecCC
Confidence            4679999999998888888875 455555665555666566677888999999999973  4567889999999999999


Q ss_pred             CChhHH---HHHhcccCCCC----CCCeEEEeeChhhHHHHHHH
Q 012133          143 NDPETF---VHRSGRTGRAG----KEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       143 ~~~~~y---~qr~GR~gR~g----~~g~~i~l~~~~~~~~~~~i  179 (470)
                      ..+.=|   +.+++|+.-.|    ..-.|.++|+.-+.-.++.|
T Consensus       633 ~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~i  676 (698)
T KOG2340|consen  633 NNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLENI  676 (698)
T ss_pred             CCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHHh
Confidence            998766   66777765433    34578889988776554443

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=93.37  E-value=0.14  Score=53.06  Aligned_cols=52  Identities=27%  Similarity=0.387  Sum_probs=47.0

Q ss_pred             eEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           67 KTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        67 ~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      -.|||+||++.|.++.++|..     .+.+..|.|+|+...+++++.+    ...|+|||+
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            389999999999999999863     5889999999999999999988    678999998

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=92.57  E-value=0.059  Score=35.40  Aligned_cols=15  Identities=53%  Similarity=1.260  Sum_probs=13.9

Q ss_pred             cccCCCCCccC--CCCC
Q 012133          455 CFNCGKSGHRA--SECP  469 (470)
Q Consensus       455 c~~c~~~gh~~--~~c~  469 (470)
                      |-+||+.||++  +.||
T Consensus         4 C~~CG~~GH~~t~k~CP   20 (40)
T PF15288_consen    4 CKNCGAFGHMRTNKRCP   20 (40)
T ss_pred             ccccccccccccCccCC
Confidence            99999999998  7788

>PTZ00110 helicase; Provisional

Probab=92.40  E-value=0.65  Score=49.80  Aligned_cols=69  Identities=13%  Similarity=0.193  Sum_probs=52.3

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----cccc-cCCCCCcc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPNVD  134 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~~-Gidip~v~  134 (470)
                      ..+||.+||++.|.++.+.+.+     .+.+..++++.+...+...+..    ...|||+|+     .+.. -+++..+.
T Consensus       204 p~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~----~~~IlVaTPgrL~d~l~~~~~~l~~v~  279 (545)
T PTZ00110        204 PIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRR----GVEILIACPGRLIDFLESNVTNLRRVT  279 (545)
T ss_pred             cEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHc----CCCEEEECHHHHHHHHHcCCCChhhCc
Confidence            4689999999999999888764     3668889999887766555543    478999996     3333 36778888


Q ss_pred             EEEE
Q 012133          135 LIIH  138 (470)
Q Consensus       135 ~VI~  138 (470)
                      +||.
T Consensus       280 ~lVi  283 (545)
T PTZ00110        280 YLVL  283 (545)
T ss_pred             EEEe
Confidence            8774

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

Probab=92.37  E-value=0.53  Score=50.44  Aligned_cols=84  Identities=19%  Similarity=0.300  Sum_probs=70.5

Q ss_pred             HHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc-ccccC
Q 012133           55 LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-AARGL  128 (470)
Q Consensus        55 l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv-~~~Gi  128 (470)
                      +..++..+..+.++.+-+||--.|++-+..+.+     ++.+..+.|.+..++|+++++...+|.++|+|.|-+ +...+
T Consensus       301 ~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V  380 (677)
T COG1200         301 LLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKV  380 (677)
T ss_pred             HHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcce
Confidence            344455666778999999998888887777664     467999999999999999999999999999999964 56679


Q ss_pred             CCCCccEEEE
Q 012133          129 DIPNVDLIIH  138 (470)
Q Consensus       129 dip~v~~VI~  138 (470)
                      ++.++-+||.
T Consensus       381 ~F~~LgLVIi  390 (677)
T COG1200         381 EFHNLGLVII  390 (677)
T ss_pred             eecceeEEEE
Confidence            9999999885

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

Probab=92.31  E-value=2.1  Score=42.75  Aligned_cols=111  Identities=16%  Similarity=0.255  Sum_probs=69.4

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhcC-----------CcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----c-----
Q 012133           65 GGKTIVFTQTKRDADEVSLALTSI-----------IASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----V-----  123 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~~-----------~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v-----  123 (470)
                      ..-.||.|++++.|.+.++.+...           +.+..--|+++-.++..++++    .+.|+|||+     +     
T Consensus       246 GP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~----GvHivVATPGRL~DmL~KK~  321 (610)
T KOG0341|consen  246 GPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRR----GVHIVVATPGRLMDMLAKKI  321 (610)
T ss_pred             CCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhc----CeeEEEcCcchHHHHHHHhh
Confidence            456799999999998887776532           234455689999998888876    689999997     1     


Q ss_pred             ----ccccCCCCCccEEEEecCCCChhHHH-HHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCc
Q 012133          124 ----AARGLDIPNVDLIIHYELPNDPETFV-HRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKF  187 (470)
Q Consensus       124 ----~~~Gidip~v~~VI~~~~p~~~~~y~-qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~  187 (470)
                          +-|-+.+...+-.|+.++-.++.+.. +-.|        -...+|++..-...++.+.+..-.+.
T Consensus       322 ~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~--------QRQTLLFSATMP~KIQ~FAkSALVKP  382 (610)
T KOG0341|consen  322 MSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKG--------QRQTLLFSATMPKKIQNFAKSALVKP  382 (610)
T ss_pred             ccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhh--------hhheeeeeccccHHHHHHHHhhcccc
Confidence                22334445555566666666654432 2221        13345566555555555555444333

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

Probab=92.30  E-value=0.5  Score=53.65  Aligned_cols=89  Identities=17%  Similarity=0.259  Sum_probs=72.4

Q ss_pred             cHHHHHH-HHHHHHcCCCeEEEEeCchHHHHHHHHHHhc---C--CcEEEEeCCCCHHHHHHHHcccccCCeeEEEec-c
Q 012133           50 SKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTS---I--IASEALHGDISQHQRERTLNGFRQGKFTVLVAT-D  122 (470)
Q Consensus        50 ~k~~~l~-~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~---~--~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaT-d  122 (470)
                      -|.++.. ...+....++++.|.+||.-.|++=++.+.+   +  +.+..|.-=.+.+++.++++..++|+++|||.| .
T Consensus       627 GKTEVAmRAAFkAV~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHr  706 (1139)
T COG1197         627 GKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHR  706 (1139)
T ss_pred             cHHHHHHHHHHHHhcCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechH
Confidence            3444333 3334445678999999999999999988875   2  457778888899999999999999999999999 6


Q ss_pred             cccccCCCCCccEEEE
Q 012133          123 VAARGLDIPNVDLIIH  138 (470)
Q Consensus       123 v~~~Gidip~v~~VI~  138 (470)
                      ++...|-+.|+-+||.
T Consensus       707 LL~kdv~FkdLGLlII  722 (1139)
T COG1197         707 LLSKDVKFKDLGLLII  722 (1139)
T ss_pred             hhCCCcEEecCCeEEE
Confidence            8888999999999885

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

Probab=92.26  E-value=1.9  Score=44.72  Aligned_cols=71  Identities=30%  Similarity=0.352  Sum_probs=57.9

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc--CC---cEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCCc
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS--II---ASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNV  133 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~--~~---~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~v  133 (470)
                      ++++|+..||+-.+.+-+..+.+  ++   .+..|.|..++++|.+....     .+|+|||+      +.+-=||+.++
T Consensus        58 ~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~~w~~-----~kVfvaTPQvveNDl~~Grid~~dv  132 (542)
T COG1111          58 GGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELWAK-----KKVFVATPQVVENDLKAGRIDLDDV  132 (542)
T ss_pred             CCeEEEecCCchHHHHHHHHHHHHhCCChhheeeecCCCChHHHHHHHhh-----CCEEEeccHHHHhHHhcCccChHHc
Confidence            34899999999999988888875  33   47899999999999988764     78999996      45556999999


Q ss_pred             cEEEEec
Q 012133          134 DLIIHYE  140 (470)
Q Consensus       134 ~~VI~~~  140 (470)
                      .++|.-.
T Consensus       133 ~~lifDE  139 (542)
T COG1111         133 SLLIFDE  139 (542)
T ss_pred             eEEEech
Confidence            9988433

>TIGR01054 rgy reverse gyrase

Probab=92.13  E-value=0.3  Score=56.79  Aligned_cols=59  Identities=19%  Similarity=0.339  Sum_probs=50.1

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-----CCc---EEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-----IIA---SEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-----~~~---~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      ...++||.+||++.+.++++.+.+     ++.   +..+||+++..+|...++.++++..+|||+|+
T Consensus       120 ~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp  186 (1171)
T TIGR01054       120 KGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTT  186 (1171)
T ss_pred             cCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            457899999999999999888864     223   23589999999999999999988899999997

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.

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=91.67  E-value=0.074  Score=51.33  Aligned_cols=18  Identities=39%  Similarity=1.324  Sum_probs=16.1

Q ss_pred             CccccCCCCCccCCCCCC
Q 012133          453 GACFNCGKSGHRASECPN  470 (470)
Q Consensus       453 ~~c~~c~~~gh~~~~c~~  470 (470)
                      .-||+||+.|||++|||+
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~  161 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPE  161 (261)
T ss_pred             CccCCCCcCCcchhhCCC
Confidence            349999999999999993

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=91.38  E-value=0.071  Score=37.17  Aligned_cols=17  Identities=53%  Similarity=1.411  Sum_probs=15.7

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+||.-||..++||.
T Consensus        33 ~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   33 FCFHCGRIGHSDKECPK   49 (49)
T ss_pred             hhcCCCCcCcCHhHcCC
Confidence            49999999999999984

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

Probab=91.00  E-value=1.7  Score=41.10  Aligned_cols=110  Identities=19%  Similarity=0.257  Sum_probs=72.4

Q ss_pred             eEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCCcc
Q 012133           67 KTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVD  134 (470)
Q Consensus        67 ~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~v~  134 (470)
                      .+||.|.|++.|.++.+...+      ..++.+++|+|+.+.-+++++.    -..|+|+|+      +-.+.+++.+|.
T Consensus       112 svlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~----~PhivVgTPGrilALvr~k~l~lk~vk  187 (387)
T KOG0329|consen  112 SVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN----CPHIVVGTPGRILALVRNRSLNLKNVK  187 (387)
T ss_pred             EEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhC----CCeEEEcCcHHHHHHHHhccCchhhcc
Confidence            689999999999999876653      3578999999999888888776    568999998      456778888888


Q ss_pred             EEEEecCCC-----ChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHh
Q 012133          135 LIIHYELPN-----DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  183 (470)
Q Consensus       135 ~VI~~~~p~-----~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~  183 (470)
                      +.|.-...+     +...-+|.+=|.--   ..+.+.+++..-...++-+.+..
T Consensus       188 hFvlDEcdkmle~lDMrRDvQEifr~tp---~~KQvmmfsatlskeiRpvC~kF  238 (387)
T KOG0329|consen  188 HFVLDECDKMLEQLDMRRDVQEIFRMTP---HEKQVMMFSATLSKEIRPVCHKF  238 (387)
T ss_pred             eeehhhHHHHHHHHHHHHHHHHHhhcCc---ccceeeeeeeecchhhHHHHHhh
Confidence            876433222     22223555555422   23344444443333444444443

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=90.99  E-value=1.2  Score=46.20  Aligned_cols=69  Identities=9%  Similarity=0.196  Sum_probs=52.1

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCCcc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVD  134 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~v~  134 (470)
                      .++||.+||++.|.++++.+..     .+.+..++|+.+...+...++.    ..+|||+|+      +-..-+++.++.
T Consensus        84 ~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~----~~~IlV~TP~~l~~~l~~~~~~l~~v~  159 (423)
T PRK04837         84 PRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLES----GVDILIGTTGRLIDYAKQNHINLGAIQ  159 (423)
T ss_pred             ceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcC----CCCEEEECHHHHHHHHHcCCccccccc
Confidence            5799999999999998776542     4678889999877666555542    578999997      123457888899


Q ss_pred             EEEE
Q 012133          135 LIIH  138 (470)
Q Consensus       135 ~VI~  138 (470)
                      +||.
T Consensus       160 ~lVi  163 (423)
T PRK04837        160 VVVL  163 (423)
T ss_pred             EEEE
Confidence            8884

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=90.67  E-value=0.054  Score=58.83  Aligned_cols=119  Identities=16%  Similarity=0.202  Sum_probs=93.5

Q ss_pred             cccHHHHHHHHHHHHc-CC-CeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCC-ee-EEEecc
Q 012133           48 ATSKRTILSDLITVYA-KG-GKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK-FT-VLVATD  122 (470)
Q Consensus        48 ~~~k~~~l~~ll~~~~-~~-~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~-~~-iLVaTd  122 (470)
                      ...|+..+..+|.... .. .++|||+.-..-+..+...|. ..+....+-|.|+..+|.+++..|..+. .+ .|++..
T Consensus       520 ~s~ki~~~~~~l~~~~~s~~~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slk  599 (674)
T KOG1001|consen  520 ESSKIYAFLKILQAKEMSEQPKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLK  599 (674)
T ss_pred             hhhhhHHHHHHHhhccCCCCCceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHH
Confidence            3455555555554321 11 499999999888888777776 3667778889999999999999999643 33 457788


Q ss_pred             cccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEE
Q 012133          123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL  166 (470)
Q Consensus       123 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~  166 (470)
                      +...|+++-...+|+..|+-|++..-.|.+-|+.|.|+.-.+.+
T Consensus       600 ag~~glnlt~a~~v~~~d~~wnp~~eeQaidR~hrigq~k~v~v  643 (674)
T KOG1001|consen  600 AGKVGLNLTAASHVLLMDPWWNPAVEEQAIDRAHRIGQTKPVKV  643 (674)
T ss_pred             HhhhhhchhhhhHHHhhchhcChHHHHHHHHHHHHhcccceeee
Confidence            99999999999999999999999999999999999986655544

>cd00268 DEADc DEAD-box helicases

Probab=90.21  E-value=2.3  Score=38.75  Aligned_cols=70  Identities=19%  Similarity=0.245  Sum_probs=50.6

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc-----c-cccCCCCCc
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----A-ARGLDIPNV  133 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv-----~-~~Gidip~v  133 (470)
                      ..++||.+++++.+.+.+..+..     .+.+..+|++.+..+....++    ....|+|+|..     + ..-.+++++
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            45899999999999988877653     356788999988876655554    45789999952     2 222566777


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      +++|.
T Consensus       145 ~~lIv  149 (203)
T cd00268         145 KYLVL  149 (203)
T ss_pred             CEEEE
Confidence            77764

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=90.08  E-value=1.1  Score=47.17  Aligned_cols=75  Identities=23%  Similarity=0.315  Sum_probs=59.9

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccc-ccc------C-CCCCcc
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA-ARG------L-DIPNVD  134 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~-~~G------i-dip~v~  134 (470)
                      ..+.+||.+|+++.+.+....|.. ++.+..+++..+..++..++..+..+..+||++|+-. ...      + ....+.
T Consensus        50 ~~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~  129 (470)
T TIGR00614        50 SDGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGIT  129 (470)
T ss_pred             cCCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcC
Confidence            457899999999999888887774 7889999999999999999999999999999999732 111      2 445677


Q ss_pred             EEEE
Q 012133          135 LIIH  138 (470)
Q Consensus       135 ~VI~  138 (470)
                      +||.
T Consensus       130 ~iVi  133 (470)
T TIGR00614       130 LIAV  133 (470)
T ss_pred             EEEE
Confidence            7663

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

>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=88.83  E-value=4.3  Score=38.53  Aligned_cols=88  Identities=15%  Similarity=0.212  Sum_probs=66.4

Q ss_pred             CCcEEEEeCCCCHHHHHHHHcccccCC----eeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccC-CCCCCC
Q 012133           88 IIASEALHGDISQHQRERTLNGFRQGK----FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG-RAGKEG  162 (470)
Q Consensus        88 ~~~~~~lhg~~~~~~R~~~~~~f~~g~----~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~g-R~g~~g  162 (470)
                      .+.+..++++-+...     -.+.++.    ..|+|.=+.++||+.++.+.......-+...+++.||.=--| |.|-..
T Consensus       110 ~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgRwFGYR~gY~d  184 (239)
T PF10593_consen  110 GIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGRWFGYRPGYED  184 (239)
T ss_pred             CceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhhcccCCccccc
Confidence            488999998765543     3444443    889999999999999999998888888888999999864444 555567


Q ss_pred             eEEEeeChhhHHHHHHHH
Q 012133          163 TAILMFTSSQRRTVRSLE  180 (470)
Q Consensus       163 ~~i~l~~~~~~~~~~~i~  180 (470)
                      .|-++.++.-...+..|.
T Consensus       185 l~Ri~~~~~l~~~f~~i~  202 (239)
T PF10593_consen  185 LCRIYMPEELYDWFRHIA  202 (239)
T ss_pred             ceEEecCHHHHHHHHHHH
Confidence            888888776666665554

This domain is found associated with a helicase domain of superfamily type II [].

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=88.62  E-value=0.18  Score=47.89  Aligned_cols=17  Identities=41%  Similarity=1.324  Sum_probs=15.6

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      -||+||+.|||-..||.
T Consensus       178 ~CyRCGqkgHwIqnCpT  194 (427)
T COG5222         178 VCYRCGQKGHWIQNCPT  194 (427)
T ss_pred             eEEecCCCCchhhcCCC
Confidence            39999999999999983

>PRK13766 Hef nuclease; Provisional

Probab=88.18  E-value=5.4  Score=44.79  Aligned_cols=73  Identities=25%  Similarity=0.352  Sum_probs=55.1

Q ss_pred             cCCCeEEEEeCchHHHHHHHHHHhcC-----CcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc------ccccCCCC
Q 012133           63 AKGGKTIVFTQTKRDADEVSLALTSI-----IASEALHGDISQHQRERTLNGFRQGKFTVLVATDV------AARGLDIP  131 (470)
Q Consensus        63 ~~~~~~lVF~~t~~~~~~l~~~l~~~-----~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv------~~~Gidip  131 (470)
                      ...+++||.+||+..+++.++.+.+.     ..+..++|+.+..+|.+....     ..|+|+|+-      ...-+++.
T Consensus        56 ~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~r~~~~~~-----~~iiv~T~~~l~~~l~~~~~~~~  130 (773)
T PRK13766         56 KKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWEK-----AKVIVATPQVIENDLIAGRISLE  130 (773)
T ss_pred             hCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEEeCCCCHHHHHHHHhC-----CCEEEECHHHHHHHHHcCCCChh
Confidence            35689999999999998888877642     267889999999988776653     579999962      23446777


Q ss_pred             CccEEEEec
Q 012133          132 NVDLIIHYE  140 (470)
Q Consensus       132 ~v~~VI~~~  140 (470)
                      ++++||.-+
T Consensus       131 ~~~liVvDE  139 (773)
T PRK13766        131 DVSLLIFDE  139 (773)
T ss_pred             hCcEEEEEC
Confidence            888888543

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=88.13  E-value=0.38  Score=46.37  Aligned_cols=16  Identities=56%  Similarity=1.545  Sum_probs=14.3

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||.|++.+|.++|||+
T Consensus       167 c~~c~~~~h~~~~C~~  182 (261)
T KOG4400|consen  167 CFRCGKVGHGSRDCPS  182 (261)
T ss_pred             cccCCCcceecccCCc
Confidence            9999999999999984

>PRK09401 reverse gyrase; Reviewed

Probab=87.88  E-value=1.4  Score=51.36  Aligned_cols=92  Identities=21%  Similarity=0.284  Sum_probs=61.2

Q ss_pred             EcCcccHHHHHHHHHH-HHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEE--EEeCCCCHHHHHHHHcccccCCee
Q 012133           45 STTATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS-----IIASE--ALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        45 ~~~~~~k~~~l~~ll~-~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~--~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                      .....-|...+.-++. ...+..++||.+||++.+.++++.+..     .+.+.  ..|+.++.+++.+.++.++.+..+
T Consensus       102 ApTGsGKT~f~l~~~~~l~~~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~  181 (1176)
T PRK09401        102 APTGVGKTTFGLVMSLYLAKKGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFD  181 (1176)
T ss_pred             cCCCCCHHHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCC
Confidence            3344456543222222 223467999999999999999998874     23333  345667788888888888888899


Q ss_pred             EEEecc-----cccccCCCCCccEEE
Q 012133          117 VLVATD-----VAARGLDIPNVDLII  137 (470)
Q Consensus       117 iLVaTd-----v~~~Gidip~v~~VI  137 (470)
                      |+|+|+     .+. .+....+++||
T Consensus       182 IlV~Tp~rL~~~~~-~l~~~~~~~lV  206 (1176)
T PRK09401        182 ILVTTSQFLSKNFD-ELPKKKFDFVF  206 (1176)
T ss_pred             EEEECHHHHHHHHH-hccccccCEEE
Confidence            999995     222 34444577766

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=87.88  E-value=2.6  Score=44.31  Aligned_cols=70  Identities=11%  Similarity=0.190  Sum_probs=51.2

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc------ccccCCCCCcc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV------AARGLDIPNVD  134 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv------~~~Gidip~v~  134 (470)
                      .++||.++|++.+.++++.+..     .+.+..++|+.+...+.+.+   .....+|||+|+-      ....+.+.++.
T Consensus       163 ~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~---~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~  239 (475)
T PRK01297        163 PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQL---EARFCDILVATPGRLLDFNQRGEVHLDMVE  239 (475)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHH---hCCCCCEEEECHHHHHHHHHcCCcccccCc
Confidence            5899999999999998887763     36788899988766544333   3456789999972      23356677788


Q ss_pred             EEEE
Q 012133          135 LIIH  138 (470)
Q Consensus       135 ~VI~  138 (470)
                      +||.
T Consensus       240 ~lVi  243 (475)
T PRK01297        240 VMVL  243 (475)
T ss_pred             eEEe
Confidence            8774

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=87.56  E-value=4.5  Score=35.35  Aligned_cols=86  Identities=17%  Similarity=0.246  Sum_probs=56.2

Q ss_pred             ccHHHHHH-HHHHHHcC--CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHH-HHHHHHcccccCCeeEEE
Q 012133           49 TSKRTILS-DLITVYAK--GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQH-QRERTLNGFRQGKFTVLV  119 (470)
Q Consensus        49 ~~k~~~l~-~ll~~~~~--~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~-~R~~~~~~f~~g~~~iLV  119 (470)
                      .-|..... .++..+.+  ..++||.+|+++.++++.+.+.+     .+.+..+|++.+.. +....+    .+...|||
T Consensus        25 sGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilv  100 (169)
T PF00270_consen   25 SGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVL----SNQADILV  100 (169)
T ss_dssp             SSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHH----HTTSSEEE
T ss_pred             CccHHHHHHHHHhhhccCCCceEEEEeecccccccccccccccccccccccccccccccccccccccc----cccccccc
Confidence            45654433 33333322  35999999999999999988874     25788999998855 444444    44689999


Q ss_pred             eccc------ccccCCCCCccEEEE
Q 012133          120 ATDV------AARGLDIPNVDLIIH  138 (470)
Q Consensus       120 aTdv------~~~Gidip~v~~VI~  138 (470)
                      +|..      ....+++..+++||.
T Consensus       101 ~T~~~l~~~~~~~~~~~~~~~~iVi  125 (169)
T PF00270_consen  101 TTPEQLLDLISNGKINISRLSLIVI  125 (169)
T ss_dssp             EEHHHHHHHHHTTSSTGTTESEEEE
T ss_pred             cCcchhhccccccccccccceeecc
Confidence            9962      222345566666663

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=87.18  E-value=2.3  Score=46.08  Aligned_cols=74  Identities=15%  Similarity=0.162  Sum_probs=58.9

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccccc------ccCCCCCccEE
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA------RGLDIPNVDLI  136 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~------~Gidip~v~~V  136 (470)
                      ..+.+||.+|++..+.+....|.. ++.+..+|+.++..++..+++....+..+||+.|+-.-      .-+...++.+|
T Consensus        52 ~~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~i  131 (591)
T TIGR01389        52 LKGLTVVISPLISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALV  131 (591)
T ss_pred             cCCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEE
Confidence            457899999999998887777764 78899999999999999999999999999999886321      12334456666


Q ss_pred             E
Q 012133          137 I  137 (470)
Q Consensus       137 I  137 (470)
                      |
T Consensus       132 V  132 (591)
T TIGR01389       132 A  132 (591)
T ss_pred             E
Confidence            6

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.

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

Probab=86.85  E-value=4.6  Score=45.04  Aligned_cols=70  Identities=13%  Similarity=0.199  Sum_probs=51.6

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-cccccC---------C
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-VAARGL---------D  129 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-v~~~Gi---------d  129 (470)
                      +..++||.+||++.+.++...|..    .+.+..++|+.+..+|..+.+     ..+|||+|+ .+..++         .
T Consensus        80 ~~~~aL~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~~i~~-----~~~IivtTPd~L~~~~L~~~~~~~~~  154 (742)
T TIGR03817        80 PRATALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERRWARE-----HARYVLTNPDMLHRGILPSHARWARF  154 (742)
T ss_pred             CCcEEEEEcChHHHHHHHHHHHHHhccCCeEEEEEeCCCCHHHHHHHhc-----CCCEEEEChHHHHHhhccchhHHHHH
Confidence            346899999999999999988874    367888999999888754433     368999995 332221         2


Q ss_pred             CCCccEEEE
Q 012133          130 IPNVDLIIH  138 (470)
Q Consensus       130 ip~v~~VI~  138 (470)
                      +.++.+||.
T Consensus       155 l~~l~~vVi  163 (742)
T TIGR03817       155 LRRLRYVVI  163 (742)
T ss_pred             HhcCCEEEE
Confidence            567888874

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.

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

Probab=86.22  E-value=2.7  Score=48.29  Aligned_cols=59  Identities=17%  Similarity=0.211  Sum_probs=50.5

Q ss_pred             CCCeEEEEeCchHHHH-HHHHHHhcCCcEEEEeCCCCHHHHHHHHccccc--CCeeEEEecc
Q 012133           64 KGGKTIVFTQTKRDAD-EVSLALTSIIASEALHGDISQHQRERTLNGFRQ--GKFTVLVATD  122 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~-~l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~--g~~~iLVaTd  122 (470)
                      ..+.+||.+|+++.+. ++..++..++.+..+.+.++..++..+++.+..  +.++||++|+
T Consensus       499 ~~GiTLVISPLiSLmqDQV~~L~~~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTP  560 (1195)
T PLN03137        499 CPGITLVISPLVSLIQDQIMNLLQANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTP  560 (1195)
T ss_pred             cCCcEEEEeCHHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEECh
Confidence            3578999999999986 555555568999999999999999999998876  8899999997

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=85.97  E-value=0.95  Score=49.16  Aligned_cols=53  Identities=23%  Similarity=0.415  Sum_probs=45.7

Q ss_pred             cccccCCeeEEEecccccccCCCCCccEEE--------EecCCCChhHHHHHhcccCCCCC
Q 012133          108 NGFRQGKFTVLVATDVAARGLDIPNVDLII--------HYELPNDPETFVHRSGRTGRAGK  160 (470)
Q Consensus       108 ~~f~~g~~~iLVaTdv~~~Gidip~v~~VI--------~~~~p~~~~~y~qr~GR~gR~g~  160 (470)
                      ++|.+|+-.|-|-+.++..||.++.-.-|+        -..+||+.+.-||..|||.|.++
T Consensus       851 qrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQ  911 (1300)
T KOG1513|consen  851 QRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQ  911 (1300)
T ss_pred             hhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccc
Confidence            578889988999999999999997665554        47899999999999999999873

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=85.77  E-value=2.5  Score=50.30  Aligned_cols=70  Identities=16%  Similarity=0.210  Sum_probs=54.0

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----------------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc----
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----------------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV----  123 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----------------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv----  123 (470)
                      ..++|+.+|+++.+.++.+.|+.                 .+.+..+||+.++.+|.+.++.    ...|||+|+-    
T Consensus        37 ~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V~vrtGDt~~~eR~rll~~----ppdILVTTPEsL~~  112 (1490)
T PRK09751         37 TSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRVGIRTGDTPAQERSKLTRN----PPDILITTPESLYL  112 (1490)
T ss_pred             CCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEEEEEECCCCHHHHHHHhcC----CCCEEEecHHHHHH
Confidence            35899999999999988877641                 3568899999999999877654    5789999972    


Q ss_pred             -cc-cc-CCCCCccEEEE
Q 012133          124 -AA-RG-LDIPNVDLIIH  138 (470)
Q Consensus       124 -~~-~G-idip~v~~VI~  138 (470)
                       +. +. ..+.+|++||.
T Consensus       113 LLtsk~r~~L~~Vr~VIV  130 (1490)
T PRK09751        113 MLTSRARETLRGVETVII  130 (1490)
T ss_pred             HHhhhhhhhhccCCEEEE
Confidence             22 22 35788999885

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=84.77  E-value=3.6  Score=43.16  Aligned_cols=109  Identities=14%  Similarity=0.183  Sum_probs=67.7

Q ss_pred             eEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----c--ccccCCCCCcc
Q 012133           67 KTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----V--AARGLDIPNVD  134 (470)
Q Consensus        67 ~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v--~~~Gidip~v~  134 (470)
                      -+||..||++.|.++.+.|.+     .+.+-.+-|+..-+.     +.-|-..++|||||+     -  -.-.++-+++.
T Consensus       143 GalIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~-----E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~lQ  217 (758)
T KOG0343|consen  143 GALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKF-----ELERISQMNILVCTPGRLLQHMDENPNFSTSNLQ  217 (758)
T ss_pred             eeEEecchHHHHHHHHHHHHHHhhccccccceeecCchhHH-----HHHhhhcCCeEEechHHHHHHhhhcCCCCCCcce
Confidence            689999999999999999974     377878888865432     222224689999998     1  23345556666


Q ss_pred             EEEE--------ecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCc
Q 012133          135 LIIH--------YELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKF  187 (470)
Q Consensus       135 ~VI~--------~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~  187 (470)
                      ++|.        +++-...+..+--+       .+-...+|++......++.|.+..-.++
T Consensus       218 mLvLDEADR~LDMGFk~tL~~Ii~~l-------P~~RQTLLFSATqt~svkdLaRLsL~dP  271 (758)
T KOG0343|consen  218 MLVLDEADRMLDMGFKKTLNAIIENL-------PKKRQTLLFSATQTKSVKDLARLSLKDP  271 (758)
T ss_pred             EEEeccHHHHHHHhHHHHHHHHHHhC-------ChhheeeeeecccchhHHHHHHhhcCCC
Confidence            6663        22222333333222       1234466677666677777776644443

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=84.42  E-value=4.4  Score=44.11  Aligned_cols=59  Identities=19%  Similarity=0.240  Sum_probs=52.0

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      ..+.+||.+|+++.+.+....|.. ++.+..+++.++..++..+++..+.+.+++|++|+
T Consensus        64 ~~g~tlVisPl~sL~~dqv~~l~~~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tP  123 (607)
T PRK11057         64 LDGLTLVVSPLISLMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAP  123 (607)
T ss_pred             cCCCEEEEecHHHHHHHHHHHHHHcCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEECh
Confidence            457899999999999988888774 68899999999999999999999999999999985

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=84.11  E-value=27  Score=30.24  Aligned_cols=70  Identities=11%  Similarity=-0.016  Sum_probs=39.6

Q ss_pred             CCeEEEEEeeCCccccCCcchhhHHhHhhhhcCcCcCccccEEEeecC----ccceeEeec-CHHHHHHHHhhcCC---C
Q 012133          261 QGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADD----RVQGAVFDL-PEEIAKELLNKQIP---P  332 (470)
Q Consensus       261 ~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~Ig~I~i~~~~----~~~ga~fdv-~~~~a~~i~~~~~~---~  332 (470)
                      ....+|+|..-    ...++..+|..++....     .|..+.+..+.    ....+|++. ..+.|+.+++....   .
T Consensus        32 ~~~~~lfVgnL----~~~~te~~L~~~F~~~G-----~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~  102 (144)
T PLN03134         32 LMSTKLFIGGL----SWGTDDASLRDAFAHFG-----DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELN  102 (144)
T ss_pred             CCCCEEEEeCC----CCCCCHHHHHHHHhcCC-----CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            33456777533    23578888888876543     36666666442    134577777 45666666654322   3


Q ss_pred             CCeEEEe
Q 012133          333 GNTISKI  339 (470)
Q Consensus       333 g~~i~~~  339 (470)
                      +..+.+-
T Consensus       103 Gr~l~V~  109 (144)
T PLN03134        103 GRHIRVN  109 (144)
T ss_pred             CEEEEEE
Confidence            4444443

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

Probab=83.78  E-value=6  Score=40.73  Aligned_cols=106  Identities=19%  Similarity=0.346  Sum_probs=68.1

Q ss_pred             eEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----cccc---cCCCCC
Q 012133           67 KTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR---GLDIPN  132 (470)
Q Consensus        67 ~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~~---Gidip~  132 (470)
                      -+||..||++.+.+|.+.+..      .+.+..+-|+.+.++   -++.|++...+|||+|+     ++.+   .+|+..
T Consensus        81 galIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~---Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rs  157 (567)
T KOG0345|consen   81 GALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEE---DIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRS  157 (567)
T ss_pred             eEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHH---HHHHHHHhCCcEEEeCchhHHHHHhchhhhccccc
Confidence            579999999999988776652      367888889966654   45667777889999997     3333   566667


Q ss_pred             ccEEEE--------ecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHH
Q 012133          133 VDLIIH--------YELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  182 (470)
Q Consensus       133 v~~VI~--------~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~  182 (470)
                      +.++|.        +++-.+..+.+-+.-+--|.|       |++.........|.+.
T Consensus       158 Le~LVLDEADrLldmgFe~~~n~ILs~LPKQRRTG-------LFSATq~~~v~dL~ra  208 (567)
T KOG0345|consen  158 LEILVLDEADRLLDMGFEASVNTILSFLPKQRRTG-------LFSATQTQEVEDLARA  208 (567)
T ss_pred             cceEEecchHhHhcccHHHHHHHHHHhcccccccc-------cccchhhHHHHHHHHh
Confidence            777773        334445555555555444433       3444444444444443

>PRK13767 ATP-dependent helicase; Provisional

Probab=83.68  E-value=3.5  Score=46.89  Aligned_cols=69  Identities=16%  Similarity=0.186  Sum_probs=49.9

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----------------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccc-c--
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----------------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA-A--  125 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----------------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~-~--  125 (470)
                      .++|+.+|+++.+.++++.|..                 .+.+...||+.++.++.+.++.    ...|||+|+-. .  
T Consensus        85 ~~~LyIsPtraLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~----~p~IlVtTPE~L~~l  160 (876)
T PRK13767         85 VYCLYVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKK----PPHILITTPESLAIL  160 (876)
T ss_pred             eEEEEEcCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhC----CCCEEEecHHHHHHH
Confidence            4699999999999887664321                 3467889999999998877764    56899999721 1  


Q ss_pred             ---cc--CCCCCccEEEE
Q 012133          126 ---RG--LDIPNVDLIIH  138 (470)
Q Consensus       126 ---~G--idip~v~~VI~  138 (470)
                         ..  -.+.++.+||.
T Consensus       161 l~~~~~~~~l~~l~~VVI  178 (876)
T PRK13767        161 LNSPKFREKLRTVKWVIV  178 (876)
T ss_pred             hcChhHHHHHhcCCEEEE
Confidence               11  13567888874

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

Probab=83.43  E-value=5.6  Score=42.39  Aligned_cols=70  Identities=16%  Similarity=0.204  Sum_probs=48.2

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----cc-cccCCCCCc
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VA-ARGLDIPNV  133 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~-~~Gidip~v  133 (470)
                      ..++||.+||++.|.++.+.+..     .+.+..+.++.+..++...+.   . ...|||+|+     .+ ...+++.++
T Consensus       196 ~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~---~-~~~IiV~TPgrL~~~l~~~~~~l~~v  271 (518)
T PLN00206        196 NPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQ---Q-GVELIVGTPGRLIDLLSKHDIELDNV  271 (518)
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhc---C-CCCEEEECHHHHHHHHHcCCccchhe
Confidence            45899999999999888776652     245666777665554433332   2 468999995     33 346778888


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      .+||.
T Consensus       272 ~~lVi  276 (518)
T PLN00206        272 SVLVL  276 (518)
T ss_pred             eEEEe
Confidence            88774

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=83.16  E-value=1.2  Score=39.48  Aligned_cols=16  Identities=38%  Similarity=1.259  Sum_probs=14.5

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      |++||+.||+.+.|-+
T Consensus       103 ~~r~G~rg~~~r~~~~  118 (195)
T KOG0107|consen  103 CYRCGERGHIGRNCKD  118 (195)
T ss_pred             cccCCCcccccccccc
Confidence            9999999999999953

>KOG4284 consensus DEAD box protein [Transcription]

Probab=81.35  E-value=13  Score=39.98  Aligned_cols=69  Identities=13%  Similarity=0.187  Sum_probs=51.1

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCC
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPN  132 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~  132 (470)
                      ..+.+|.++|++-+.++.+.+.+      ++.|.++-|+.+-+.-..-+     .+.+|+|.|+      +--+-+|+..
T Consensus        93 ~~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rl-----k~~rIvIGtPGRi~qL~el~~~n~s~  167 (980)
T KOG4284|consen   93 HIQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRL-----KQTRIVIGTPGRIAQLVELGAMNMSH  167 (980)
T ss_pred             cceeEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhh-----hhceEEecCchHHHHHHHhcCCCccc
Confidence            45789999999999999887763      46788888987665433333     3577999998      3344578888


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      |++.|.
T Consensus       168 vrlfVL  173 (980)
T KOG4284|consen  168 VRLFVL  173 (980)
T ss_pred             eeEEEe
Confidence            888774

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=80.81  E-value=2.4  Score=48.50  Aligned_cols=100  Identities=19%  Similarity=0.254  Sum_probs=71.3

Q ss_pred             cCCCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecC
Q 012133           63 AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL  141 (470)
Q Consensus        63 ~~~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~  141 (470)
                      ....++|||+.-....+.+...+. +.+..... +.  -++-...+..|++ --..|+-+...+.|+++-+..||++.++
T Consensus      1219 ~~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~-~~--t~d~~dc~~~fk~-I~clll~~~~~~~GLNL~eA~Hvfl~eP 1294 (1394)
T KOG0298|consen 1219 NEQEKVIVFSQWSVVLDVKELRYLMNLIKKQLD-GE--TEDFDDCIICFKS-IDCLLLFVSKGSKGLNLIEATHVFLVEP 1294 (1394)
T ss_pred             CcCceEEEEEehHHHHHHHHHHHHhhhhHhhhc-cC--Ccchhhhhhhccc-ceEEEEEeccCcccccHHhhhhhheecc
Confidence            445799999987766666655554 23322211 11  2344556677776 3345677888999999999999999999


Q ss_pred             CCChhHHHHHhcccCCCCCCCeEEE
Q 012133          142 PNDPETFVHRSGRTGRAGKEGTAIL  166 (470)
Q Consensus       142 p~~~~~y~qr~GR~gR~g~~g~~i~  166 (470)
                      -.++..-.|.+||..|.|++-..++
T Consensus      1295 iLN~~~E~QAigRvhRiGQ~~pT~V 1319 (1394)
T KOG0298|consen 1295 ILNPGDEAQAIGRVHRIGQKRPTFV 1319 (1394)
T ss_pred             ccCchHHHhhhhhhhhcccccchhh
Confidence            9999999999999999996654433

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

Probab=80.37  E-value=4.7  Score=41.81  Aligned_cols=73  Identities=18%  Similarity=0.224  Sum_probs=52.7

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHH-HHHHHHcccccCCeeEEEecc-------cccccCCCCC
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQH-QRERTLNGFRQGKFTVLVATD-------VAARGLDIPN  132 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~-~R~~~~~~f~~g~~~iLVaTd-------v~~~Gidip~  132 (470)
                      =++||.++|+..+.+++..+..     ++.|..+.|.-+-+ +..+....-....++|||+|+       -...++|+..
T Consensus       216 LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~  295 (620)
T KOG0350|consen  216 LRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKH  295 (620)
T ss_pred             eEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhh
Confidence            4899999999999999998874     35566666654433 334444555556789999998       2367888888


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +.++|.
T Consensus       296 LrfLVI  301 (620)
T KOG0350|consen  296 LRFLVI  301 (620)
T ss_pred             ceEEEe
Confidence            887663

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=80.30  E-value=5.9  Score=30.92  Aligned_cols=43  Identities=19%  Similarity=0.169  Sum_probs=32.2

Q ss_pred             HHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCC
Q 012133           57 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDIS   99 (470)
Q Consensus        57 ~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~   99 (470)
                      ..+..+....++++||.+-..+...+..|+. ++.+..|.|+++
T Consensus        43 ~~~~~~~~~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~   86 (90)
T cd01524          43 DRLNELPKDKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYK   86 (90)
T ss_pred             HHHHhcCCCCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHH
Confidence            3334445667999999987778888888874 568888999874

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	470
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		6e-38
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		1e-28
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		1e-27
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		5e-27
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		5e-27
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-26
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-26
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-26
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-26
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-25
2jgn_A	185	Ddx3 Helicase Domain Length = 185		1e-23
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-23
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		4e-23
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		2e-22
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		1e-20
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		2e-20
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		2e-20
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		5e-20
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		8e-20
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		1e-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
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		9e-19
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-18
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-18
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-18
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		3e-18
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		7e-18
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		7e-18
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		8e-18
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		2e-17
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		6e-17
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		4e-16
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		4e-16
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		5e-16
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		5e-16
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		1e-15
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		3e-15
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		4e-15
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		4e-15
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		4e-15
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		6e-13
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		8e-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		7e-08
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		9e-07
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		4e-06
2eyq_A	1151	Crystal Structure Of Escherichia Coli Transcription		5e-06
2fwr_A	472	Structure Of Archaeoglobus Fulgidis Xpb Length = 47		1e-05
2fzl_A	219	Structure Of C-Terminal Domain Of Archaeoglobus Ful		2e-05
3v4r_A	667	Crystal Structure Of A Uvrb Dimer-Dna Complex Lengt		8e-05
2d7d_A	661	Structural Insights Into The Cryptic Dna Dependent		8e-05
2fdc_A	658	Structural Basis Of Dna Damage Recognition And Proc		1e-04
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
1t5l_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Po		1e-04
3uwx_B	683	Crystal Structure Of Uvra-Uvrb Complex Length = 683		1e-04
4i1s_A	243	Melanoma Differentiation Associated Protein-5 Helic		2e-04
1c4o_A	664	Crystal Structure Of The Dna Nucleotide Excision Re		3e-04
1d2m_A	665	Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleot		3e-04
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		5e-04
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		5e-04
2p6r_A	702	Crystal Structure Of Superfamily 2 Helicase Hel308		6e-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 =  155 bits (391), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 114/289 (39%), Positives = 168/289 (58%), Gaps = 17/289 (5%)
Query: 43  AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 101
           A+      +  +LSDL+ V A   + +VFT+TK + +E++  L  +   ++ALHGD+SQ 
Sbjct: 7   AVPAPVRGRLEVLSDLLYV-ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQG 65
Query: 102 QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 161
           +RER +  FRQG+  VLVATDVAARGLDIP VDL++HY +P+  E + HRSGRTGRAG+ 
Sbjct: 66  ERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRG 125
Query: 162 GTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFF 221
           G  +L++   +RR V +LER VG +F+ V+PP  E+VLE+    ++A L  V  +    +
Sbjct: 126 GRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLY 185
Query: 222 TPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVT-------LQLTRDSAF 274
              A RL  E   + +AA LA L G +   + RSL+  E+GW T       L L R  A 
Sbjct: 186 QDFAGRLFAEGRVEVVAALLALLLGGAP--AERSLLTGEEGWRTYKATGPRLSLPRLVAL 243
Query: 275 SRG-----FMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLP 318
            +G        A +  GF  D+ P A  E+  + +    RV+G + ++P
Sbjct: 244 LKGQGLEVGKVAEAEGGFYVDLRPEARPEVAGLRLEPARRVEG-LLEIP 291

>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 (358), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 87/190 (45%), Positives = 123/190 (64%), Gaps = 2/190 (1%)
Query: 43  AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 101
           A+      +  +LSDL+ V A   + +VFT+TK + +E++  L  +   ++ALHGD+SQ 
Sbjct: 10  AVPAPVRGRLEVLSDLLYV-ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQG 68
Query: 102 QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 161
           +RER L  FRQG+  VLVATDVAARGLDIP VDL++HY LP+  E + HRSGRTGRAG+ 
Sbjct: 69  ERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRG 128
Query: 162 GTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFF 221
           G  +L++   +RR V +LER VG +F+ V+PP  E+VLE+    ++A L  V  +    +
Sbjct: 129 GRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLY 188
Query: 222 TPTAQRLIEE 231
              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 =  124 bits (311), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 71/172 (41%), Positives = 99/172 (57%), Gaps = 7/172 (4%)
Query: 1   MLFSATMPSWVKKLSRKYLDNP--LNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL 58
           M+FSAT P  ++ L+R +LD    L +  VG+  E + + +    +    + KR+ L DL
Sbjct: 214 MMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKV----VWVEESDKRSFLLDL 269
Query: 59  ITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEALHGDISQHQRERTLNGFRQGKFTV 117
           +    K   T+VF +TK+ AD +         A  ++HGD SQ  RE  L+ FR GK  +
Sbjct: 270 LNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPI 329
Query: 118 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT 169
           LVAT VAARGLDI NV  +I+++LP+D E +VHR GRTGR G  G A   F 
Sbjct: 330 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFN 381

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

Iteration: 1
 Score =  120 bits (302), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 66/182 (36%), Positives = 105/182 (57%), Gaps = 9/182 (4%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +LFSAT P  +  L++KY  +   I        K+   I+   +      +   L  L+ 
Sbjct: 182 LLFSATXPREILNLAKKYXGDYSFIK------AKINANIEQSYVEVNENERFEALCRLLK 235
Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLV 119
              K    +VF +TKRD  E++  L  I   + A+HGD+SQ QRE+ +  F+Q K  +L+
Sbjct: 236 --NKEFYGLVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILI 293
Query: 120 ATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 179
           ATDV +RG+D+ +++ +I+Y LP +PE++ HR GRTGRAGK+G AI +    + + +R +
Sbjct: 294 ATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLRYI 353
Query: 180 ER 181
           ER
Sbjct: 354 ER 355

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

Iteration: 1
 Score =  119 bits (297), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 68/202 (33%), Positives = 114/202 (56%), Gaps = 5/202 (2%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLI 59
           +L SAT+P  + +++ K++ +P+ I  +  +DE   EGIK + ++      K   L DL 
Sbjct: 193 VLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY 250
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
                  + ++F  TKR  D ++  +        ++HGD+ Q +RE  +  FR G   VL
Sbjct: 251 DTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 309
Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           ++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+GR G++G AI    +   R +R 
Sbjct: 310 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRD 369
Query: 179 LERDVGCKFEFVSPPVVEDVLE 200
           +E+    + + +   V + +LE
Sbjct: 370 IEQYYSTQIDEMPMNVADLILE 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 =  119 bits (297), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 68/202 (33%), Positives = 114/202 (56%), Gaps = 5/202 (2%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLI 59
           +L SAT+P  + +++ K++ +P+ I  +  +DE   EGIK + ++      K   L DL 
Sbjct: 215 VLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY 272
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
                  + ++F  TKR  D ++  +        ++HGD+ Q +RE  +  FR G   VL
Sbjct: 273 DTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 331
Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           ++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+GR G++G AI    +   R +R 
Sbjct: 332 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRD 391
Query: 179 LERDVGCKFEFVSPPVVEDVLE 200
           +E+    + + +   V + +LE
Sbjct: 392 IEQYYSTQIDEMPMNVADLILE 413

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

Iteration: 1
 Score =  117 bits (294), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 65/183 (35%), Positives = 106/183 (57%), Gaps = 5/183 (2%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLI 59
           +L SAT+P  V +++ K++ +P+ I  +  +DE   EGIK + ++      K   L DL 
Sbjct: 178 VLISATLPHEVLEMTNKFMTDPIRI--LVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY 235
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
                  + ++F  TKR  D ++  +        ++HGD+ Q +RE  +  FR G   VL
Sbjct: 236 DTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 294
Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           ++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+GR G++G A+    +   R +R 
Sbjct: 295 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRD 354
Query: 179 LER 181
           +E+
Sbjct: 355 IEQ 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 =  117 bits (294), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 65/183 (35%), Positives = 106/183 (57%), Gaps = 5/183 (2%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLI 59
           +L SAT+P  + +++ K++ +P+ I  +  +DE   EGIK + ++      K   L DL 
Sbjct: 215 VLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY 272
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
                  + ++F  TKR  D ++  +        ++HGD+ Q +RE  +  FR G   VL
Sbjct: 273 DTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 331
Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           ++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+GR G++G AI    +   R +R 
Sbjct: 332 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRD 391
Query: 179 LER 181
           +E+
Sbjct: 392 IEQ 394

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

Iteration: 1
 Score =  117 bits (294), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 65/183 (35%), Positives = 106/183 (57%), Gaps = 5/183 (2%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLI 59
           +L SAT+P  + +++ K++ +P+ I  +  +DE   EGIK + ++      K   L DL 
Sbjct: 214 VLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY 271
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
                  + ++F  TKR  D ++  +        ++HGD+ Q +RE  +  FR G   VL
Sbjct: 272 DTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 330
Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           ++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+GR G++G AI    +   R +R 
Sbjct: 331 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRD 390
Query: 179 LER 181
           +E+
Sbjct: 391 IEQ 393

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

Iteration: 1
 Score =  117 bits (293), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 64/183 (34%), Positives = 106/183 (57%), Gaps = 5/183 (2%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLI 59
           +L SAT+P  + +++ K++ +P+ I  +  +DE   EGIK + ++      K   L DL 
Sbjct: 178 VLISATLPHEILEMTNKFMTDPIRI--LVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY 235
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
                  + ++F  TKR  D ++  +        ++HGD+ Q +RE  +  FR G   VL
Sbjct: 236 DTLTIT-QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 294
Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           ++TDV ARGLD+P V LII+Y+LPN+ E ++HR GR+GR G++G A+    +   R +R 
Sbjct: 295 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRD 354
Query: 179 LER 181
           +E+
Sbjct: 355 IEQ 357

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

Iteration: 1
 Score =  112 bits (280), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 66/179 (36%), Positives = 107/179 (59%), Gaps = 9/179 (5%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPL--NIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL 58
           ++FSAT P  +++++ ++L N +   I +VG     + + I  Y ++  A  KR+ L ++
Sbjct: 240 LMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTI--YEVNKYA--KRSKLIEI 295
Query: 59  ITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTV 117
           ++  A G  TIVF +TKR AD ++  L+     + ++HGD  Q QRE+ L  F+ G   V
Sbjct: 296 LSEQADG--TIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKV 353
Query: 118 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTV 176
           L+AT VA+RGLDI N+  +I+Y++P+  + +VHR GRTGR G  G A   F   + R +
Sbjct: 354 LIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAI 412

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

Iteration: 1
 Score =  107 bits (268), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 59/135 (43%), Positives = 78/135 (57%), Gaps = 1/135 (0%)
Query: 36  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEAL 94
           +E I    +    + KR+ L DL+    K   T+VF +TK+ AD +         A  ++
Sbjct: 17  SENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSI 76
Query: 95  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 154
           HGD SQ  RE  L+ FR GK  +LVAT VAARGLDI NV  +I+++LP+D E +VHR GR
Sbjct: 77  HGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGR 136
Query: 155 TGRAGKEGTAILMFT 169
           TGR G  G A   F 
Sbjct: 137 TGRVGNLGLATSFFN 151

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

Iteration: 1
 Score =  107 bits (266), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 65/177 (36%), Positives = 101/177 (57%), Gaps = 19/177 (10%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIK-LYAISTTATSKRTILSDLI 59
           +LFSAT    V++ ++K + N   ++L  N  E   + IK LY        K  +L++L 
Sbjct: 181 VLFSATFADAVRQYAKKIVPNANTLELQTN--EVNVDAIKQLYMDCKNEADKFDVLTELY 238
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-----LHGDISQHQRERTLNGFRQGK 114
            V   G  +I+F  TK+ A+     L   + SE      LHGD+   +R+R ++ FR+G+
Sbjct: 239 GVMTIGS-SIIFVATKKTAN----VLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGR 293
Query: 115 FTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 165
             VL+ T+V ARG+DIP V ++++Y+LP       DP T++HR GRTGR G++G AI
Sbjct: 294 SKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 350

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

Iteration: 1
 Score =  105 bits (263), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 64/177 (36%), Positives = 101/177 (57%), Gaps = 19/177 (10%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIK-LYAISTTATSKRTILSDLI 59
           +LFSAT    V++ ++K + N   ++L  N  E   + IK LY        K  +L++L 
Sbjct: 181 VLFSATFADAVRQYAKKIVPNANTLELQTN--EVNVDAIKQLYMDCKNEADKFDVLTELY 238
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-----LHGDISQHQRERTLNGFRQGK 114
            +   G  +I+F  TK+ A+     L   + SE      LHGD+   +R+R ++ FR+G+
Sbjct: 239 GLMTIGS-SIIFVATKKTAN----VLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGR 293
Query: 115 FTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 165
             VL+ T+V ARG+DIP V ++++Y+LP       DP T++HR GRTGR G++G AI
Sbjct: 294 SKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 350

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

Iteration: 1
 Score =  103 bits (257), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 52/143 (36%), Positives = 88/143 (61%), Gaps = 2/143 (1%)
Query: 43  AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 101
            I     +K ++L D++         I+F +TK   ++++  L  +    + +HG + Q 
Sbjct: 14  VIQVREENKFSLLKDVLMT-ENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQE 72
Query: 102 QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 161
            R   +N F++G++  LVATDVAARG+DI N+ L+I+Y+LP + E++VHR+GRTGRAG +
Sbjct: 73  DRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNK 132
Query: 162 GTAILMFTSSQRRTVRSLERDVG 184
           G AI   T+ ++R +  +E  +G
Sbjct: 133 GKAISFVTAFEKRFLADIEEYIG 155

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

Iteration: 1
 Score = 97.4 bits (241), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 58/187 (31%), Positives = 101/187 (54%), Gaps = 9/187 (4%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +LFSAT P  VK+   K+L  P  I+L+   +E   +GI  Y        +R  L  L T
Sbjct: 198 LLFSATFPLTVKEFMVKHLHKPYEINLM---EELTLKGITQYY---AFVEERQKLHCLNT 251
Query: 61  VYAKG--GKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTV 117
           +++K    + I+F  +    + ++  +T +  +    H  + Q +R +  + FRQGK   
Sbjct: 252 LFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRT 311
Query: 118 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVR 177
           LV +D+  RG+DI  V+++I+++ P   ET++HR GR+GR G  G AI +   + R  + 
Sbjct: 312 LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLY 371
Query: 178 SLERDVG 184
            +E+++G
Sbjct: 372 KIEQELG 378

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

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 64/182 (35%), Positives = 107/182 (58%), Gaps = 5/182 (2%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLI 59
           +L SATMPS V ++++K++ +P+ I  +  ++E   EGI+ + I+      K   L DL 
Sbjct: 218 VLLSATMPSDVLEVTKKFMRDPIRI--LVKKEELTLEGIRQFYINVEREEWKLDTLCDLY 275
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
                  + ++F  T+R  D ++  + +      A+HGD+ Q +R+  +  FR G   VL
Sbjct: 276 ETLTIT-QAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVL 334
Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           + TD+ ARG+D+  V L+I+Y+LP + E ++HR GR GR G++G AI M T   +RT+R 
Sbjct: 335 ITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRD 394
Query: 179 LE 180
           +E
Sbjct: 395 IE 396

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

Iteration: 1
 Score = 96.7 bits (239), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 64/182 (35%), Positives = 107/182 (58%), Gaps = 5/182 (2%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLI 59
           +L SATMPS V ++++K++ +P+ I  +  ++E   EGI+ + I+      K   L DL 
Sbjct: 192 VLLSATMPSDVLEVTKKFMRDPIRI--LVKKEELTLEGIRQFYINVEREEWKLDTLCDLY 249
Query: 60  TVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVL 118
                  + ++F  T+R  D ++  + +      A+HGD+ Q +R+  +  FR G   VL
Sbjct: 250 ETLTIT-QAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVL 308
Query: 119 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 178
           + TD+ ARG+D+  V L+I+Y+LP + E ++HR GR GR G++G AI M T   +RT+R 
Sbjct: 309 ITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRD 368
Query: 179 LE 180
           +E
Sbjct: 369 IE 370

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

Iteration: 1
 Score = 95.1 bits (235), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 53/158 (33%), Positives = 87/158 (55%), Gaps = 30/158 (18%)
Query: 21  NPLNIDLVG-------NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQ 73
           N +N+D +        N+ +K     +LY + T  +S       +I V  K    +++ +
Sbjct: 2   NEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSS-------IIFVATKKTANVLYGK 54
Query: 74  TKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV 133
            K +  EVS+          LHGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V
Sbjct: 55  LKSEGHEVSI----------LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTV 104
Query: 134 DLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 165
            ++++Y+LP       DP T++HR GRTGR G++G AI
Sbjct: 105 SMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 142

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

Iteration: 1
 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 60/168 (35%), Positives = 93/168 (55%), Gaps = 19/168 (11%)
Query: 2   LFSATMPSWVKKLSRKYLDNPLNIDL---VGNQDEKLAEGIKLYAISTTATSKRTILSDL 58
           LFSAT+P  ++K+ + ++ N   I+    + N + K         +     SK   L + 
Sbjct: 165 LFSATIPEEIRKVVKDFITNYEEIEACIGLANVEHKFVH------VKDDWRSKVQALRE- 217
Query: 59  ITVYAKGGKTIVFTQTK-RDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTV 117
                K    IVF +T+ R A  V L   +I     L GD+ Q  R R ++ FR+G++ +
Sbjct: 218 ----NKDKGVIVFVRTRNRVAKLVRLFDNAI----ELRGDLPQSVRNRNIDAFREGEYDM 269
Query: 118 LVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
           L+ TDVA+RGLDIP V+ +I+++ P D  T++HR GRTGR G++G AI
Sbjct: 270 LITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAI 317

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

Iteration: 1
 Score = 94.0 bits (232), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/158 (33%), Positives = 86/158 (54%), Gaps = 30/158 (18%)
Query: 21  NPLNIDLVG-------NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQ 73
           N +N+D +        N+ +K     +LY + T  +S       +I V  K    +++ +
Sbjct: 3   NEVNVDAIKQLYXDCKNEADKFDVLTELYGVXTIGSS-------IIFVATKKTANVLYGK 55
Query: 74  TKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV 133
            K +  EVS+          LHGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V
Sbjct: 56  LKSEGHEVSI----------LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTV 105
Query: 134 DLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 165
             +++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 = 93.2 bits (230), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 53/158 (33%), Positives = 86/158 (54%), Gaps = 30/158 (18%)
Query: 21  NPLNIDLVG-------NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQ 73
           N +N+D +        N+ +K     +LY + T  +S       +I V  K    +++ +
Sbjct: 4   NEVNVDAIKQLYXDCKNEADKFDVLTELYGLXTIGSS-------IIFVATKKTANVLYGK 56
Query: 74  TKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV 133
            K +  EVS+          LHGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V
Sbjct: 57  LKSEGHEVSI----------LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTV 106
Query: 134 DLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 165
             +++Y+LP       DP T++HR GRTGR G++G AI
Sbjct: 107 SXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 144

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

Iteration: 1
 Score = 91.3 bits (225), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 63/193 (32%), Positives = 109/193 (56%), Gaps = 11/193 (5%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKR----TILS 56
           +L SATMP+ V +++ K++ NP+ I  +  +DE   EGIK + ++      +    T L 
Sbjct: 198 VLLSATMPNDVLEVTTKFMRNPVRI--LVKKDELTLEGIKQFYVNVEEEEYKYECLTDLY 255
Query: 57  DLITVYAKGGKTIVFTQTKRDADEVSLAL-TSIIASEALHGDISQHQRERTLNGFRQGKF 115
           D I+V     + ++F  T+R  +E++  L        A++ D+ Q +R+  +  FR G  
Sbjct: 256 DSISV----TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSS 311
Query: 116 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT 175
            +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR GR GR G++G AI   T+     
Sbjct: 312 RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGA 371
Query: 176 VRSLERDVGCKFE 188
           +R LE+    + E
Sbjct: 372 MRELEKFYSTQIE 384

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 60/186 (32%), Positives = 99/186 (53%), Gaps = 15/186 (8%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL-- 58
           +LFSAT    V K ++K + +P N+  +  ++E L    + Y + ++   K   L +L  
Sbjct: 204 LLFSATFEDSVWKFAQKVVPDP-NVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYG 262
Query: 59  -ITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFT 116
            IT+     + ++F  T++ A  ++  L+      AL  G++   QR   +  FR+GK  
Sbjct: 263 AITI----AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK 318
Query: 117 VLVATDVAARGLDIPNVDLIIHYELPNDP------ETFVHRSGRTGRAGKEGTAILMFTS 170
           VLV T+V ARG+D+  V ++I+++LP D       ET++HR GRTGR GK G A+ M  S
Sbjct: 319 VLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 378
Query: 171 SQRRTV 176
                +
Sbjct: 379 KHSMNI 384

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 60/186 (32%), Positives = 99/186 (53%), Gaps = 15/186 (8%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL-- 58
           +LFSAT    V K ++K + +P N+  +  ++E L    + Y + ++   K   L +L  
Sbjct: 220 LLFSATFEDSVWKFAQKVVPDP-NVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYG 278
Query: 59  -ITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFT 116
            IT+     + ++F  T++ A  ++  L+      AL  G++   QR   +  FR+GK  
Sbjct: 279 AITI----AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK 334
Query: 117 VLVATDVAARGLDIPNVDLIIHYELPNDP------ETFVHRSGRTGRAGKEGTAILMFTS 170
           VLV T+V ARG+D+  V ++I+++LP D       ET++HR GRTGR GK G A+ M  S
Sbjct: 335 VLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 394
Query: 171 SQRRTV 176
                +
Sbjct: 395 KHSMNI 400

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 60/186 (32%), Positives = 99/186 (53%), Gaps = 15/186 (8%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL-- 58
           +LFSAT    V K ++K + +P N+  +  ++E L    + Y + ++   K   L +L  
Sbjct: 271 LLFSATFEDSVWKFAQKVVPDP-NVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYG 329
Query: 59  -ITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFT 116
            IT+     + ++F  T++ A  ++  L+      AL  G++   QR   +  FR+GK  
Sbjct: 330 AITI----AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK 385
Query: 117 VLVATDVAARGLDIPNVDLIIHYELPNDP------ETFVHRSGRTGRAGKEGTAILMFTS 170
           VLV T+V ARG+D+  V ++I+++LP D       ET++HR GRTGR GK G A+ M  S
Sbjct: 386 VLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 445
Query: 171 SQRRTV 176
                +
Sbjct: 446 KHSMNI 451

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 60/186 (32%), Positives = 99/186 (53%), Gaps = 15/186 (8%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDL-- 58
           +LFSAT    V K ++K + +P N+  +  ++E L    + Y + ++   K   L +L  
Sbjct: 241 LLFSATFEDSVWKFAQKVVPDP-NVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYG 299
Query: 59  -ITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFT 116
            IT+     + ++F  T++ A  ++  L+      AL  G++   QR   +  FR+GK  
Sbjct: 300 AITI----AQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEK 355
Query: 117 VLVATDVAARGLDIPNVDLIIHYELPNDP------ETFVHRSGRTGRAGKEGTAILMFTS 170
           VLV T+V ARG+D+  V ++I+++LP D       ET++HR GRTGR GK G A+ M  S
Sbjct: 356 VLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 415
Query: 171 SQRRTV 176
                +
Sbjct: 416 KHSMNI 421

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

Iteration: 1
 Score = 88.6 bits (218), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 84/165 (50%), Gaps = 1/165 (0%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           M+FSAT+   ++ + RK++ +P+ I  V ++ +    G++ Y +      K   L DL+ 
Sbjct: 188 MMFSATLSKEIRPVCRKFMQDPMEI-FVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLD 246
Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           V       I     +R      L +     + A+H  + Q +R      F+  +  +LVA
Sbjct: 247 VLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVA 306
Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
           T++  RG+DI  V++  +Y++P D +T++HR  R GR G +G AI
Sbjct: 307 TNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAI 351

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

Iteration: 1
 Score = 88.6 bits (218), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 84/165 (50%), Gaps = 1/165 (0%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           M+FSAT+   ++ + RK++ +P+ I  V ++ +    G++ Y +      K   L DL+ 
Sbjct: 188 MMFSATLSKEIRPVCRKFMQDPMEI-FVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLD 246
Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           V       I     +R      L +     + A+H  + Q +R      F+  +  +LVA
Sbjct: 247 VLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVA 306
Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
           T++  RG+DI  V++  +Y++P D +T++HR  R GR G +G AI
Sbjct: 307 TNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAI 351

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

Iteration: 1
 Score = 88.2 bits (217), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 84/165 (50%), Gaps = 1/165 (0%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           M+FSAT+   ++ + RK++ +P+ I  V ++ +    G++ Y +      K   L DL+ 
Sbjct: 187 MMFSATLSKEIRPVCRKFMQDPMEI-FVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLD 245
Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA 120
           V       I     +R      L +     + A+H  + Q +R      F+  +  +LVA
Sbjct: 246 VLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVA 305
Query: 121 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
           T++  RG+DI  V++  +Y++P D +T++HR  R GR G +G AI
Sbjct: 306 TNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAI 350

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

Iteration: 1
 Score = 86.7 bits (213), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 40/98 (40%), Positives = 61/98 (62%), Gaps = 1/98 (1%)
Query: 68  TIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR 126
            ++F + K D D +    L   + + A+HG   Q +R + +  FR+GK  VLVATDVA++
Sbjct: 57  VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 127 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA 164
           GLD P +  +I+Y++P + E +VHR GRTG +G  G A
Sbjct: 117 GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIA 154

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

Iteration: 1
 Score = 85.5 bits (210), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 62/193 (32%), Positives = 105/193 (54%), Gaps = 11/193 (5%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKR----TILS 56
           +L SAT P+ V +++ K+  NP+ I  +  +DE   EGIK + ++      +    T L 
Sbjct: 197 VLLSATXPNDVLEVTTKFXRNPVRI--LVKKDELTLEGIKQFYVNVEEEEYKYECLTDLY 254
Query: 57  DLITVYAKGGKTIVFTQTKRDADEVSLAL-TSIIASEALHGDISQHQRERTLNGFRQGKF 115
           D I+V     + ++F  T+R  +E++  L        A++ D+ Q +R+     FR G  
Sbjct: 255 DSISV----TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSS 310
Query: 116 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT 175
            +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR GR GR G++G AI   T+     
Sbjct: 311 RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGA 370
Query: 176 VRSLERDVGCKFE 188
            R LE+    + E
Sbjct: 371 XRELEKFYSTQIE 383

>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 = 82.8 bits (203), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 87/165 (52%), Gaps = 5/165 (3%)
Query: 21  NPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE 80
           +P  I+L+   +E   +G+  Y    T   K   L+ L +   +  ++I+F  + +  + 
Sbjct: 4   DPYEINLM---EELTLKGVTQYYAYVTERQKVHCLNTLFSR-LQINQSIIFCNSSQRVEL 59
Query: 81  VSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY 139
           ++  ++ +  +   +H  + Q  R R  + FR G    LV TD+  RG+DI  V+++I++
Sbjct: 60  LAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINF 119
Query: 140 ELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG 184
           + P   ET++HR GR+GR G  G AI + T   R  ++S+E  +G
Sbjct: 120 DFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLG 164

>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 = 82.4 bits (202), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 59/197 (29%), Positives = 98/197 (49%), Gaps = 23/197 (11%)
Query: 1   MLFSATMPSWVKKLSRKYLDNP--LNIDLVGNQDEKLAEGI-------KLYAISTTATSK 51
           +LFSAT+   V+KL+   ++    L +D V   + +  E I       + +A S  A  +
Sbjct: 217 LLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVE 276
Query: 52  RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASE--------ALHGDISQHQR 103
              +   I       K I+F  T +     +  L SI+ +E          HG I+Q++R
Sbjct: 277 H--IKKQIKERDSNYKAIIFAPTVK----FTSFLCSILKNEFKKDLPILEFHGKITQNKR 330
Query: 104 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGT 163
              +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR GRT R+GKEG+
Sbjct: 331 TSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGS 390
Query: 164 AILMFTSSQRRTVRSLE 180
           ++L     +   VR LE
Sbjct: 391 SVLFICKDELPFVRELE 407

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

Iteration: 1
 Score = 82.4 bits (202), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 56/195 (28%), Positives = 95/195 (48%), Gaps = 19/195 (9%)
Query: 1   MLFSATMPSWVKKLSRKYLDNP--LNIDLVGNQDEKLAEGIKLYAISTTATSKRTI---- 54
           +LFSAT+   V+KL+   ++    L +D V   + +  E I    + +   +        
Sbjct: 217 LLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVE 276
Query: 55  -LSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASE--------ALHGDISQHQRER 105
            +   I       K I+F  T +     +  L SI+ +E          HG I+Q++R  
Sbjct: 277 HIKKQIKERDSNYKAIIFAPTVK----FTSFLCSILKNEFKKDLPILEFHGKITQNKRTS 332
Query: 106 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
            +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR GRT R+GKEG+++
Sbjct: 333 LVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSV 392
Query: 166 LMFTSSQRRTVRSLE 180
           L     +   VR LE
Sbjct: 393 LFICKDELPFVRELE 407

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

Iteration: 1
 Score = 82.4 bits (202), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 59/197 (29%), Positives = 98/197 (49%), Gaps = 23/197 (11%)
Query: 1   MLFSATMPSWVKKLSRKYLDNP--LNIDLVGNQDEKLAEGI-------KLYAISTTATSK 51
           +LFSAT+   V+KL+   ++    L +D V   + +  E I       + +A S  A  +
Sbjct: 268 LLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVE 327
Query: 52  RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASE--------ALHGDISQHQR 103
              +   I       K I+F  T +     +  L SI+ +E          HG I+Q++R
Sbjct: 328 H--IKKQIKERDSNYKAIIFAPTVK----FTSFLCSILKNEFKKDLPILEFHGKITQNKR 381
Query: 104 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGT 163
              +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR GRT R+GKEG+
Sbjct: 382 TSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGS 441
Query: 164 AILMFTSSQRRTVRSLE 180
           ++L     +   VR LE
Sbjct: 442 SVLFICKDELPFVRELE 458

>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 = 1e-15,   Method: Compositional matrix adjust.
 Identities = 40/100 (40%), Positives = 65/100 (65%), Gaps = 1/100 (1%)
Query: 67  KTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA 125
           ++IVF + +    E++  L    I +  L G++ Q +R   +    +G+  VLVATDVAA
Sbjct: 32  RSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAA 91
Query: 126 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
           RG+DIP+V  + ++++P   +T++HR GRT RAG++GTAI
Sbjct: 92  RGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAI 131

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 67/110 (60%), Gaps = 7/110 (6%)
Query: 66  GKTIVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVA 124
           G+ I+F QT+R+A  +++ +       +L  G+++  QR   +  FR GK  VL+ T+V 
Sbjct: 35  GQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVC 94
Query: 125 ARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAILMF 168
           ARG+D+  V ++++++LP       D ET++HR GRTGR GK+G A  M 
Sbjct: 95  ARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMI 144

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 94  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 153
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 154 RTGRAGKEGTAILMFTSSQRRTVRSLE 180
           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 = 79.3 bits (194), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 94  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 153
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 154 RTGRAGKEGTAILMFTSSQRRTVRSLE 180
           RT R+GKEG+++L     +   VR LE
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE 152

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 94  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 153
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 154 RTGRAGKEGTAILMFTSSQRRTVRSLE 180
           RT R+GKEG+++L     +   VR LE
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE 152

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 86/157 (54%), Gaps = 9/157 (5%)
Query: 37  EGIKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL-TSIIAS 91
           EGIK + ++      +    T L D I+V     + ++F  T+R  +E++  L       
Sbjct: 2   EGIKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLRNDKFTV 57
Query: 92  EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHR 151
            A++ D+ Q +R+  +  FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR
Sbjct: 58  SAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 117
Query: 152 SGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 188
            GR GR G++G AI   T+     +R LE+    + E
Sbjct: 118 IGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIE 154

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 62/128 (48%)
Query: 38  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 97
           G++ Y +      K   L DL+ V       I     +R      L +     + A+H  
Sbjct: 5   GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 64
Query: 98  ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 157
           + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R GR
Sbjct: 65  MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 124
Query: 158 AGKEGTAI 165
            G +G AI
Sbjct: 125 FGTKGLAI 132

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 38/113 (33%), Positives = 55/113 (48%), Gaps = 9/113 (7%)
Query: 64  KGGKTIVFTQTKRDADEVSLALTS-------IIASEALHGD--ISQHQRERTLNGFRQGK 114
           +  K IVFT  +  A ++   L          +   +   D  +SQ +++  L+ F +G+
Sbjct: 360 QNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE 419
Query: 115 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM 167
           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: 58  LITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFT 116
           LI    KG   I++  +++D+++V+++L ++ I + A H ++    +      +   +  
Sbjct: 260 LINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQ 319
Query: 117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 168
           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: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +G   I++  ++   ++ +  L S  I++ A H  +  + R      F++    ++VAT 
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV 294
Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 168
               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 = 7e-08,   Method: Compositional matrix adjust.
 Identities = 26/106 (24%), Positives = 54/106 (50%), Gaps = 1/106 (0%)
Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +G   I++  ++   ++ +  L S  I++ A H  +  + R      F++    ++VAT 
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV 294
Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 168
               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 = 51.6 bits (122), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 47/79 (59%), Gaps = 9/79 (11%)
Query: 94  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 149
           +HG +SQ +++R +  F +G++ +LV+T V   G+D+P  ++++      +PE F    +
Sbjct: 619 MHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMV----IENPERFGLAQL 674
Query: 150 HR-SGRTGRAGKEGTAILM 167
           H+  GR GR G+E    L+
Sbjct: 675 HQLRGRVGRGGQEAYCFLV 693

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 41/147 (27%), Positives = 71/147 (48%), Gaps = 21/147 (14%)
Query: 49  TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-----SIIASEALH-------- 95
           T  R  + +  T   +  + I+FT+T++ A  +S  +T     + +  +A H        
Sbjct: 384 TKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSS 443
Query: 96  --GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 153
               ++Q++++  ++ FR GK  +L+AT VA  GLDI   +++I Y L  +    V   G
Sbjct: 444 EFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARG 503
Query: 154 RTGRAGKEGTAILMFTSS----QRRTV 176
           R  RA  E T +L+  S     +R TV
Sbjct: 504 R-ARAD-ESTYVLVAHSGSGVIERETV 528

>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair Coupling Factor Length = 1151

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 21/112 (18%)
Query: 95  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----HYELPNDPETFV 149
           HG + + + ER +N F   +F VLV T +   G+DIP  + II     H+ L       +
Sbjct: 845 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ-----L 899
Query: 150 HR-SGRTGRAGKEGTAIL-------MFTSSQRR--TVRSLERDVGCKFEFVS 191
           H+  GR GR+  +  A L       M T +Q+R   + SLE D+G  F   +
Sbjct: 900 HQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLE-DLGAGFALAT 950

>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb Length = 472

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 35/156 (22%), Positives = 72/156 (46%), Gaps = 9/156 (5%)
Query: 24  NIDLVGNQDEKLAEGIKLYA----ISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDAD 79
            I +    DE+  E ++ +     I+  + +K   L +++  + K  K I+FT+     +
Sbjct: 305 KIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKD-KIIIFTRH----N 359
Query: 80  EVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY 139
           E+   ++ +    A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +  
Sbjct: 360 ELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIM 419
Query: 140 ELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT 175
                   ++ 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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/141 (23%), Positives = 67/141 (47%), Gaps = 9/141 (6%)
Query: 24  NIDLVGNQDEKLAEGIKLYA----ISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDAD 79
            I +    DE+  E ++ +     I+  + +K   L +++  + K  K I+FT+     +
Sbjct: 70  KIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKD-KIIIFTRH----N 124
Query: 80  EVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY 139
           E+   ++ +    A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +  
Sbjct: 125 ELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIM 184
Query: 140 ELPNDPETFVHRSGRTGRAGK 160
                   ++ R GR  R  K
Sbjct: 185 SGSGSAREYIQRLGRILRPSK 205

>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex Length = 667

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 11/111 (9%)
Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +  + +V T TK+ +++++  L  I I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 450 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 509
Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 166
           +   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 = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 11/111 (9%)
Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +  + +V T TK+ +++++  L  I I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 166
           +   GLDIP V L+    L  D E F+ RS R+     GRA +  EG  I+
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNAEGRVIM 551

>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 = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 171
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555

>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In Complex With Atp Length = 657

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 443 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 502
Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 171
           +   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 = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 171
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555

>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 = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 171
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555

>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex Length = 683

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 64  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 122
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 469 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 528
Query: 123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 171
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 529 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 580

>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 = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/155 (25%), Positives = 70/155 (45%), Gaps = 34/155 (21%)
Query: 2   LFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITV 61
           +F  T+    KK+ +K  +NP        ++EKL             T  R  + +  T 
Sbjct: 106 IFLXTLFLRNKKILKKLAENP------EYENEKL-------------TKLRNTIXEHFTR 146
Query: 62  YAKGGKTIVFTQTKRDADEVSLALT-----SIIASEALH----------GDISQHQRERT 106
             +  + I+FT+T++ A  +S  +T     + +  +A H             +Q+++   
Sbjct: 147 TEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSSEFKPXTQNEQREV 206
Query: 107 LNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL 141
           ++ FR GK  +L+AT VA  GLDI   +++I Y L
Sbjct: 207 ISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL 241

>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair Enzyme Uvrb From Thermus Thermophilus Length = 664

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 63  AKGGKTIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 121
           A+G +T+V   T R A+E+ S  +   I +  LH ++   +R+  +   R G +  LV  
Sbjct: 437 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI 496
Query: 122 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK 160
           ++   GLDIP V L+    L  D E F+ RS R+     GRA +
Sbjct: 497 NLLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAAR 537

>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide Excision Repair Enzyme Length = 665

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 63  AKGGKTIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 121
           A+G +T+V   T R A+E+ S  +   I +  LH ++   +R+  +   R G +  LV  
Sbjct: 438 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI 497
Query: 122 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK 160
           ++   GLDIP V L+    L  D E F+ RS R+     GRA +
Sbjct: 498 NLLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAAR 538

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 14/28 (50%), Positives = 24/28 (85%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLV 28
           +LFSAT+PSW K+L+ +Y+ NP+ I+++
Sbjct: 179 LLFSATLPSWAKRLAERYMKNPVLINVI 206

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 14/28 (50%), Positives = 24/28 (85%)
Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLV 28
           +LFSAT+PSW K+L+ +Y+ NP+ I+++
Sbjct: 179 LLFSATLPSWAKRLAERYMKNPVLINVI 206

>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 = 6e-04,   Method: Compositional matrix adjust.
 Identities = 40/167 (23%), Positives = 68/167 (40%), Gaps = 41/167 (24%)
Query: 48  ATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSIIA----SEAL-------- 94
           +TS+R    +L+    A+ G  +VF  T+R A++ ++ L++I A    +E L        
Sbjct: 224 STSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEEN 283
Query: 95  -------------------HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL 135
                              H  +   QR    + FR+G   V+VAT   A G+++P   +
Sbjct: 284 EGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRV 343
Query: 136 IIH-------YELPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQR 173
           I+        Y        +   +GR GR G  + G AI++     R
Sbjct: 344 IVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR 390

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	470
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
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.97
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.97
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.96
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.96
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.96
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.96
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.96
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.96
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.96
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.96
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.96
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.96
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.95
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.95
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.95
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.95
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.95
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.94
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.89
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.93
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.93
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.92
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.92
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.92
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.91
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.88
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.87
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.86
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.86
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.86
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.85
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.85
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.85
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.84
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.84
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.84
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.84
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.83
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.83
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.83
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.83
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.83
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.83
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.83
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.83
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.82
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.82
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.82
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.82
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.81
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.81
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.81
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.81
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.79
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.78
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.77
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.76
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.75
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.75
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.74
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.71
3h1t_A	590	Type I site-specific restriction-modification syst	99.71
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.7
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.7
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.65
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.6
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.56
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.39
2e29_A	92	ATP-dependent RNA helicase DDX50; ATP binding, hyd	99.06
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.57
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.56
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.38
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	98.25
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	98.21
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.17
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.13
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	98.12
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	98.08
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	98.06
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	98.01
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	98.01
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	97.99
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.92
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.92
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.89
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	97.88
3i31_A	88	Heat resistant RNA dependent ATPase; RNA helicase,	97.77
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	97.74
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	97.63
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.61
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	97.56
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.56
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.43
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	97.43
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.32
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.22
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.17
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.13
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	96.63
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.53
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	96.42
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	95.84
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	95.7
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	94.45
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	94.06
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	93.69
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	93.05
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	92.34
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	91.46
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	91.39
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	90.64
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	90.51
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	90.43
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	90.41
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	90.27
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	89.92
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	89.58
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	89.58
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	89.28
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	87.94
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	87.87
3bor_A	237	Human initiation factor 4A-II; translation initiat	87.61
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	86.92
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	86.75
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	85.46
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	85.14
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	84.76
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	84.3
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	84.02
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	83.84
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	83.15
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	82.89
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	82.63
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	82.17
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	81.44
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	81.07

>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=1.1e-44  Score=354.29  Aligned_cols=289  Identities=38%  Similarity=0.595  Sum_probs=252.4

Q ss_pred             ceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCee
Q 012133           38 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        38 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                      +++|+++.++..+|.++|.++++.+. .+++||||+|++.++.+++.|.. ++.+..+||+|++.+|+.+++.|++++++
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            46789999999999999999998874 78999999999999999999975 78999999999999999999999999999


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHH
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE  196 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~  196 (470)
                      |||||+++++|||+|+|++||+|++|++.++|+||+||+||.|++|.|++|+++.+...++.+++.++.+++.+.+|+.+
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             HHHHHHHHHHHHHHcccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHcCCCCCCCCcccccCCCCeEEEEEeeCCcccc
Q 012133          197 DVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSR  276 (470)
Q Consensus       197 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~~~~~~~~~r~l~~~~~~~~~~~~~~~~~~~~  276 (470)
                      ++.+..+..++..+..+....++.|.+.++++++++.++.++++|+.+++...  .++++++...+|++++++.++   .
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            99999999999999988888899999999999999999999999999998776  678898889999999999987   3


Q ss_pred             CCcchhhHHhHhhhhcCcCcCccccEEEeecCccceeEeecCHHHHHHHHhhcCCCCCeEEEeccCCCccCCC
Q 012133          277 GFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDG  349 (470)
Q Consensus       277 ~~~~~~~v~~~l~~~~~~~~~~Ig~I~i~~~~~~~ga~fdv~~~~a~~i~~~~~~~g~~i~~~~~lP~~~~~~  349 (470)
                      ..  |++++ .|++. +.   +||+|++.++    ++|||||++.++      ...++.++++++||+++++.
T Consensus       236 ~~--~~~~~-~i~~~-~~---~ig~i~~~~~----~~~~dvp~~~~~------~~~~~~~~~~~~~p~~~~~~  291 (300)
T 3i32_A          236 SL--PRLVA-LLKGQ-GL---EVGKVAEAEG----GFYVDLRPEARP------EVAGLRLEPARRVEGLLEIP  291 (300)
T ss_dssp             CH--HHHHH-HHHHT-TC---CCCCEEEETT----EEEECBCSSCCC------CCTTCEEEEC----------
T ss_pred             CC--cHHHH-HHHhc-CC---eECcEEEeCC----EEEEEeCHHHcC------cCCCcEEEecccCCCCccCC
Confidence            33  99997 66654 33   8999999766    489999999888      34689999999999998764

>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=1.1e-34  Score=270.38  Aligned_cols=207  Identities=44%  Similarity=0.699  Sum_probs=193.5

Q ss_pred             ceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCee
Q 012133           38 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        38 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                      .+.+.++.++...|.++|.++++.. ..+++||||++++.++.+++.|.. ++.+..+||+|++.+|.++++.|+++.++
T Consensus         5 ~~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~   83 (212)
T 3eaq_A            5 TYEEEAVPAPVRGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVR   83 (212)
T ss_dssp             CBCCEEEECCTTSHHHHHHHHHHHH-CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCC
T ss_pred             ceeeeEEeCCHHHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCe
Confidence            3456788888899999999999876 568999999999999999999985 89999999999999999999999999999


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCCCHH
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE  196 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p~~~  196 (470)
                      |||||+++++|||+|++++||+|++|+++.+|+||+||+||.|++|.|++|+++.+...++.+++.++.+++.+.+|..+
T Consensus        84 vlvaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~  163 (212)
T 3eaq_A           84 VLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPE  163 (212)
T ss_dssp             EEEECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHHHHSSCCEECCCCCHH
T ss_pred             EEEecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHHHhcCcCeecCCCCHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcccCccchhhhHHHHHHHHHhhCHHHHHHHHHHHc
Q 012133          197 DVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLS  245 (470)
Q Consensus       197 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~l~~~~~~~~l~~al~~l~  245 (470)
                      ++.+..++.++..+..........|.+.++++++++++++++++|++|+
T Consensus       164 ei~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~l~~al~~ll  212 (212)
T 3eaq_A          164 EVLEAKWRHLLARLARVPEKDYRLYQDFAGRLFAEGRVEVVAALLALLL  212 (212)
T ss_dssp             HHHHHHHHHHHHHHTTSCHHHHTTTHHHHHHHHHHTCHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCHHHHHHHHHhhC
Confidence            9999999999999999887777899999999999999999999999874

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

Probab=99.97  E-value=2.7e-29  Score=224.09  Aligned_cols=155  Identities=34%  Similarity=0.613  Sum_probs=146.3

Q ss_pred             cccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccC
Q 012133           35 LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG  113 (470)
Q Consensus        35 ~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g  113 (470)
                      .+.+|+|+++.++.+.|.+.|.++++.. ...++||||++++.++.+++.|.. ++.+..+||+|++.+|..+++.|+++
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            4567999999999999999999999876 557999999999999999999985 78999999999999999999999999


Q ss_pred             CeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCcccc
Q 012133          114 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV  190 (470)
Q Consensus       114 ~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~  190 (470)
                      +++|||||+++++|+|+|++++||+|++|+++.+|+||+||++|.|++|.+++|+++.+...++.|++.++.+++++
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            99999999999999999999999999999999999999999999999999999999999999999999998887654

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

Probab=99.97  E-value=1e-29  Score=262.06  Aligned_cols=180  Identities=34%  Similarity=0.561  Sum_probs=159.2

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+|+++.++++.++.++..+.+..  .......+.+.++.+....|...|.+++....  .++||||+|++.++.
T Consensus       240 l~~SAT~~~~~~~~~~~~l~~~~~i~~~~--~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~--~~~lVF~~t~~~a~~  315 (434)
T 2db3_A          240 LMFSATFPEEIQRMAGEFLKNYVFVAIGI--VGGACSDVKQTIYEVNKYAKRSKLIEILSEQA--DGTIVFVETKRGADF  315 (434)
T ss_dssp             EEEESCCCHHHHHHHHTTCSSCEEEEESS--TTCCCTTEEEEEEECCGGGHHHHHHHHHHHCC--TTEEEECSSHHHHHH
T ss_pred             EEEeccCCHHHHHHHHHhccCCEEEEecc--ccccccccceEEEEeCcHHHHHHHHHHHHhCC--CCEEEEEeCcHHHHH
Confidence            58999999999999999999998887642  23445678888888888899988888887653  359999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +++.|.+ ++.+..+||++++.+|+++++.|++++.+|||||+++++|||+|+|++||+||+|.+.++|+||+|||||.|
T Consensus       316 l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g  395 (434)
T 2db3_A          316 LASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG  395 (434)
T ss_dssp             HHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTT
T ss_pred             HHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCC
Confidence            9999985 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChh-hHHHHHHHHHHhC
Q 012133          160 KEGTAILMFTSS-QRRTVRSLERDVG  184 (470)
Q Consensus       160 ~~g~~i~l~~~~-~~~~~~~i~~~~~  184 (470)
                      +.|.+++|+++. +...++.|.+.+.
T Consensus       396 ~~G~a~~~~~~~~~~~~~~~l~~~l~  421 (434)
T 2db3_A          396 NNGRATSFFDPEKDRAIAADLVKILE  421 (434)
T ss_dssp             CCEEEEEEECTTTCGGGHHHHHHHHH
T ss_pred             CCCEEEEEEeccccHHHHHHHHHHHH
Confidence            999999999954 4555555655543

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

Probab=99.96  E-value=2.2e-29  Score=227.36  Aligned_cols=161  Identities=28%  Similarity=0.502  Sum_probs=145.3

Q ss_pred             cccceEEEEEEcCccc-HHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHccccc
Q 012133           35 LAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ  112 (470)
Q Consensus        35 ~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~  112 (470)
                      ++.+|+|+++.++... |.+.|..+++.. ..+++||||++++.++.++..|.. ++.+..+||+|++.+|.++++.|++
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            4578999999998765 999998888765 567999999999999999999985 7899999999999999999999999


Q ss_pred             CCeeEEEecccccccCCCCCccEEEEecCC------CChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCC
Q 012133          113 GKFTVLVATDVAARGLDIPNVDLIIHYELP------NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCK  186 (470)
Q Consensus       113 g~~~iLVaTdv~~~Gidip~v~~VI~~~~p------~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~  186 (470)
                      ++++|||||+++++|+|+|++++||+||+|      .+..+|+||+||+||.|+.|.+++|+++.+...++.+++.++.+
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      89999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCHH
Q 012133          187 FEFVSPPVVE  196 (470)
Q Consensus       187 ~~~~~~p~~~  196 (470)
                      ++.++++..+
T Consensus       163 ~~~~~~~~~~  172 (175)
T 2rb4_A          163 IKQLNAEDMD  172 (175)
T ss_dssp             CEEECSSCCC
T ss_pred             ccccCCchhc
Confidence            9888776544

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

Probab=99.96  E-value=2.4e-29  Score=230.26  Aligned_cols=168  Identities=27%  Similarity=0.393  Sum_probs=132.8

Q ss_pred             HHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEE
Q 012133           15 SRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEA   93 (470)
Q Consensus        15 ~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~   93 (470)
                      ..+||++|..|.+..  ......+|.++++.++.+.|...|.+++...  ..++||||++++.++.+++.|.. ++.+..
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            457999999998743  3355678999999999999999988888653  46899999999999999999984 899999


Q ss_pred             EeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChh-h
Q 012133           94 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-Q  172 (470)
Q Consensus        94 lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~-~  172 (470)
                      +||+|++.+|.++++.|++++.+|||||+++++|+|+|++++||+||+|+++++|+||+||++|.|++|.+++|+++. +
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             HHHHHHHHHHhCCC
Q 012133          173 RRTVRSLERDVGCK  186 (470)
Q Consensus       173 ~~~~~~i~~~~~~~  186 (470)
                      ...++.|++.+...
T Consensus       164 ~~~~~~l~~~l~~~  177 (191)
T 2p6n_A          164 ESVLMDLKALLLEA  177 (191)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHc
Confidence            67777777766433

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

Probab=99.96  E-value=8.6e-29  Score=264.37  Aligned_cols=192  Identities=27%  Similarity=0.402  Sum_probs=161.4

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeec--ccccccccceEEEEEEcCcc--cHHHHHHHHHH---HHcCCCeEEEEeC
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVG--NQDEKLAEGIKLYAISTTAT--SKRTILSDLIT---VYAKGGKTIVFTQ   73 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~--~~~~~~~~~i~~~~~~~~~~--~k~~~l~~ll~---~~~~~~~~lVF~~   73 (470)
                      |+||||+|+.+.++++.++.+|..+.+..  .........+.+.++.....  .+..++..++.   ......++||||+
T Consensus       217 l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~  296 (579)
T 3sqw_A          217 LLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAP  296 (579)
T ss_dssp             EEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECS
T ss_pred             EEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecchhhhHHHHHHHHHHHHhhcCCCCcEEEECC
Confidence            58999999999999999999887765532  22333445666666655442  23333433333   3245679999999


Q ss_pred             chHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHH
Q 012133           74 TKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFV  149 (470)
Q Consensus        74 t~~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~  149 (470)
                      |++.++.+++.|.+    .+.+..+||+|++.+|.++++.|++++.+|||||+++++|||+|+|++||+|++|.+++.|+
T Consensus       297 t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~  376 (579)
T 3sqw_A          297 TVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYI  376 (579)
T ss_dssp             SHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHH
T ss_pred             cHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCCcccCCEEEEcCCCCCHHHhh
Confidence            99999999999974    68899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCC
Q 012133          150 HRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  192 (470)
Q Consensus       150 qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~  192 (470)
                      ||+|||||.|+.|.|++|+++.+...++.|++.....+.....
T Consensus       377 Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~~~~  419 (579)
T 3sqw_A          377 HRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEK  419 (579)
T ss_dssp             HHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCEEEE
T ss_pred             hhccccccCCCCceEEEEEcccHHHHHHHHHHHhCCCcccccC
Confidence            9999999999999999999999999999999998887766543

>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=99.96  E-value=6.8e-29  Score=223.51  Aligned_cols=156  Identities=23%  Similarity=0.451  Sum_probs=143.6

Q ss_pred             ccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCC
Q 012133           36 AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK  114 (470)
Q Consensus        36 ~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~  114 (470)
                      +.+|+|+++.++.++|...|.++++.. ...++||||++++.++.+++.|.. ++.+..+||+|++.+|..+++.|++++
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            467899999999999999999999876 567999999999999999999985 789999999999999999999999999


Q ss_pred             eeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChh-hHHHHHHHHHHhCCCccccCC
Q 012133          115 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFVSP  192 (470)
Q Consensus       115 ~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~-~~~~~~~i~~~~~~~~~~~~~  192 (470)
                      .+|||||+++++|+|+|++++||+||+|+++..|+||+||++|.|+.|.+++|+++. +...++.|++.+..+++.++.
T Consensus        82 ~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  160 (172)
T 1t5i_A           82 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPD  160 (172)
T ss_dssp             CSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC-
T ss_pred             CcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCCh
Confidence            999999999999999999999999999999999999999999999999999999875 568889999999988877643

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

Probab=99.96  E-value=1.1e-28  Score=220.54  Aligned_cols=156  Identities=31%  Similarity=0.584  Sum_probs=139.7

Q ss_pred             cceEEEEEEcCccc-HHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCC
Q 012133           37 EGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK  114 (470)
Q Consensus        37 ~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~  114 (470)
                      .+|+|+|+.++.++ |.+.|.++++.. ...++||||++++.++.++..|.. ++.+..+||+|++.+|.++++.|++++
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            35788888888777 999999999876 568999999999999999999985 789999999999999999999999999


Q ss_pred             eeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCC
Q 012133          115 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       115 ~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      .+|||||+++++|+|+|++++||+|++|+++.+|+||+||+||.|++|.+++|+++.+...++.+++.++..++.++.+
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            9999999999999999999999999999999999999999999999999999999999999999999999888877654

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

Probab=99.96  E-value=1.3e-28  Score=251.67  Aligned_cols=183  Identities=39%  Similarity=0.563  Sum_probs=162.8

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+|+++..+++.++.++..+.+.  ........+.+.++.+....|...|.++++......++||||++++.++.
T Consensus       214 i~~SAT~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~  291 (417)
T 2i4i_A          214 MMFSATFPKEIQMLARDFLDEYIFLAVG--RVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADS  291 (417)
T ss_dssp             EEEESCCCHHHHHHHHHHCSSCEEEEEC------CCSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHH
T ss_pred             EEEEEeCCHHHHHHHHHHcCCCEEEEeC--CCCCCccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHH
Confidence            5799999999999999999999877653  23345677888888888889999999998877667899999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +++.|.+ ++.+..+||+|++++|.++++.|++++.+|||||+++++|||+|++++||+|++|++..+|+||+||+||.|
T Consensus       292 l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g  371 (417)
T 2i4i_A          292 LEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG  371 (417)
T ss_dssp             HHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--
T ss_pred             HHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCC
Confidence            9999985 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCC
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGC  185 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~  185 (470)
                      +.|.+++|+++.+...++.|.+.+..
T Consensus       372 ~~g~~~~~~~~~~~~~~~~l~~~~~~  397 (417)
T 2i4i_A          372 NLGLATSFFNERNINITKDLLDLLVE  397 (417)
T ss_dssp             CCEEEEEEECGGGGGGHHHHHHHHHH
T ss_pred             CCceEEEEEccccHHHHHHHHHHHHH
Confidence            99999999999998888888776643

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.96  E-value=1.3e-28  Score=251.40  Aligned_cols=190  Identities=34%  Similarity=0.599  Sum_probs=170.3

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCccc-HHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      |+||||+|+.+.++++.++.+|..+.+.  ........+.++++.+.... |...|..++... ...++||||++++.++
T Consensus       214 i~~SAT~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~-~~~~~lVf~~~~~~~~  290 (410)
T 2j0s_A          214 VLISATLPHEILEMTNKFMTDPIRILVK--RDELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVD  290 (410)
T ss_dssp             EEEESCCCHHHHTTGGGTCSSCEEECCC--GGGCSCTTEEEEEEEESSTTHHHHHHHHHHHHH-TSSEEEEECSSHHHHH
T ss_pred             EEEEcCCCHHHHHHHHHHcCCCEEEEec--CccccCCCceEEEEEeCcHHhHHHHHHHHHHhc-CCCcEEEEEcCHHHHH
Confidence            5899999999999999999999877553  23344567777777766554 888888888776 4579999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .+++.|.. ++.+..+||+|++.+|.++++.|++++.+|||||+++++|||+|++++||+|++|++...|+||+||+||.
T Consensus       291 ~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~  370 (410)
T 2j0s_A          291 WLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRY  370 (410)
T ss_dssp             HHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGG
T ss_pred             HHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCC
Confidence            99999985 78999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCC
Q 012133          159 GKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      |++|.+++|+++.+...++.|++.++..++.++..
T Consensus       371 g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~  405 (410)
T 2j0s_A          371 GRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN  405 (410)
T ss_dssp             GCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSC
T ss_pred             CCceEEEEEecHHHHHHHHHHHHHhCCCceecccc
Confidence            99999999999999999999999999998887654

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.96  E-value=3e-28  Score=259.22  Aligned_cols=191  Identities=26%  Similarity=0.406  Sum_probs=160.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeec--ccccccccceEEEEEEcCcc-cH-HHHHHHHHH---HHcCCCeEEEEeC
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVG--NQDEKLAEGIKLYAISTTAT-SK-RTILSDLIT---VYAKGGKTIVFTQ   73 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~--~~~~~~~~~i~~~~~~~~~~-~k-~~~l~~ll~---~~~~~~~~lVF~~   73 (470)
                      |+||||+|+.+.++++.++.++..+.+..  .........+.+.++..... .+ ...+..++.   ......++||||+
T Consensus       268 l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~  347 (563)
T 3i5x_A          268 LLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAP  347 (563)
T ss_dssp             EEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECS
T ss_pred             EEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECchhHhhHHHHHHHHHHHHhhcCCCCcEEEEcC
Confidence            58999999999999999999887665432  22233445666666655432 22 233333333   3345679999999


Q ss_pred             chHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHH
Q 012133           74 TKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFV  149 (470)
Q Consensus        74 t~~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~  149 (470)
                      |++.++.+++.|..    .+.+..+|++|++.+|.++++.|++++.+|||||+++++|||+|+|++||+|++|.++++|+
T Consensus       348 s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~  427 (563)
T 3i5x_A          348 TVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYI  427 (563)
T ss_dssp             CHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHH
T ss_pred             cHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCCcccCCEEEEECCCCchhhhh
Confidence            99999999999974    68899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccC
Q 012133          150 HRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  191 (470)
Q Consensus       150 qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~  191 (470)
                      ||+|||||.|+.|.+++|+.+.+...++.|++.....++...
T Consensus       428 Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~~~~~~  469 (563)
T 3i5x_A          428 HRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQE  469 (563)
T ss_dssp             HHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCCCCEEE
T ss_pred             hhcCccccCCCCceEEEEEchhHHHHHHHHHHHhCCCccccc
Confidence            999999999999999999999999999999999888776544

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.96  E-value=9.7e-28  Score=243.95  Aligned_cols=189  Identities=30%  Similarity=0.517  Sum_probs=171.8

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+|..+.+++..++.+|..+.+..   ......+.+++..+....|...+..++... ...++||||++++.++.
T Consensus       198 i~lSAT~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~-~~~~~lVf~~~~~~~~~  273 (400)
T 1s2m_A          198 LLFSATFPLTVKEFMVKHLHKPYEINLME---ELTLKGITQYYAFVEERQKLHCLNTLFSKL-QINQAIIFCNSTNRVEL  273 (400)
T ss_dssp             EEEESCCCHHHHHHHHHHCSSCEEESCCS---SCBCTTEEEEEEECCGGGHHHHHHHHHHHS-CCSEEEEECSSHHHHHH
T ss_pred             EEEEecCCHHHHHHHHHHcCCCeEEEecc---ccccCCceeEEEEechhhHHHHHHHHHhhc-CCCcEEEEEecHHHHHH
Confidence            57999999999999999999988776532   234567888888888888999888888765 56799999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +++.|.. ++.+..+|++|++.+|.++++.|++++.+|||||+++++|+|+|++++||+|++|++..+|+||+||+||.|
T Consensus       274 l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g  353 (400)
T 1s2m_A          274 LAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFG  353 (400)
T ss_dssp             HHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTT
T ss_pred             HHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCC
Confidence            9999985 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCccccCCC
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      ++|.|++|+++.+...++.|++.++.+++.++..
T Consensus       354 ~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~  387 (400)
T 1s2m_A          354 HLGLAINLINWNDRFNLYKIEQELGTEIAAIPAT  387 (400)
T ss_dssp             CCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSS
T ss_pred             CCceEEEEeccchHHHHHHHHHHhCCCccccccc
Confidence            9999999999999999999999999988876543

>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=1.6e-28  Score=223.63  Aligned_cols=155  Identities=39%  Similarity=0.548  Sum_probs=128.4

Q ss_pred             cccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccc
Q 012133           33 EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR  111 (470)
Q Consensus        33 ~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~  111 (470)
                      ..++.+|+++++.++...|...|.++|+...+..++||||++++.++.+++.|.. ++.+..+||+|++.+|.++++.|+
T Consensus        14 ~~~~~~i~q~~~~v~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~   93 (185)
T 2jgn_A           14 GSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFR   93 (185)
T ss_dssp             --CCTTEEEEEEECCGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHH
T ss_pred             CCCCCCceEEEEEeCcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHH
Confidence            3456789999999999999999999998875678999999999999999999985 789999999999999999999999


Q ss_pred             cCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCc
Q 012133          112 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKF  187 (470)
Q Consensus       112 ~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~  187 (470)
                      +++++|||||+++++|+|+|++++||+||+|+++.+|+||+||++|.|++|.+++|+++.+...++.+++.+....
T Consensus        94 ~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~l~~~~  169 (185)
T 2jgn_A           94 SGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAK  169 (185)
T ss_dssp             HTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHHHHHHTT
T ss_pred             cCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHHHHHhcc
Confidence            9999999999999999999999999999999999999999999999999999999999999888888888775443

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.95  E-value=1.2e-27  Score=243.90  Aligned_cols=195  Identities=31%  Similarity=0.503  Sum_probs=165.9

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCc-ccHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      |+||||+|+++..+++.++.++..+.+..  .......+.++++.+.. ..+...|..++... ...++||||++++.++
T Consensus       204 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lvf~~~~~~~~  280 (412)
T 3fht_A          204 LLFSATFEDSVWKFAQKVVPDPNVIKLKR--EEETLDTIKQYYVLCSSRDEKFQALCNLYGAI-TIAQAMIFCHTRKTAS  280 (412)
T ss_dssp             EEEESCCCHHHHHHHHHHSSSCEEECCCG--GGSSCTTEEEEEEECSSHHHHHHHHHHHHHHH-SSSEEEEECSSHHHHH
T ss_pred             EEEEeecCHHHHHHHHHhcCCCeEEeecc--ccccccCceEEEEEcCChHHHHHHHHHHHhhc-CCCCEEEEeCCHHHHH
Confidence            57999999999999999999998887643  33445677777776654 46777787877765 5589999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC------ChhHHHHHh
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRS  152 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~------~~~~y~qr~  152 (470)
                      .+++.|.+ .+.+..+||+|++.+|.++++.|++++.+|||||+++++|||+|++++||+|++|+      +..+|+||+
T Consensus       281 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~  360 (412)
T 3fht_A          281 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRI  360 (412)
T ss_dssp             HHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHH
T ss_pred             HHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeeccc
Confidence            99999985 78999999999999999999999999999999999999999999999999999994      678999999


Q ss_pred             cccCCCCCCCeEEEeeChhh-HHHHHHHHHHhCCCccccCCCCHHHH
Q 012133          153 GRTGRAGKEGTAILMFTSSQ-RRTVRSLERDVGCKFEFVSPPVVEDV  198 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~~-~~~~~~i~~~~~~~~~~~~~p~~~~~  198 (470)
                      ||+||.|+.|.+++++++.+ ...++.+++.+...++.++.+..+++
T Consensus       361 GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  407 (412)
T 3fht_A          361 GRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLDEI  407 (412)
T ss_dssp             TTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC--------
T ss_pred             CcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccCCCccHHHH
Confidence            99999999999999998764 88999999999999988876654443

>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=99.95  E-value=3.5e-27  Score=238.86  Aligned_cols=191  Identities=24%  Similarity=0.463  Sum_probs=170.4

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+|+.+..+++.++.+|..+.+... .......+.++++.+....|...|..+++.. ...++||||++++.++.
T Consensus       188 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~-~~~~~lvf~~~~~~~~~  265 (391)
T 1xti_A          188 MMFSATLSKEIRPVCRKFMQDPMEIFVDDE-TKLTLHGLQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIA  265 (391)
T ss_dssp             EEEESSCCSTHHHHHHHHCSSCEEEECCCC-CCCCCTTCEEEEEECCGGGHHHHHHHHHHHS-CCSEEEEECSCHHHHHH
T ss_pred             EEEEeeCCHHHHHHHHHHcCCCeEEEecCc-cccCcccceEEEEEcCchhHHHHHHHHHHhc-CCCcEEEEeCcHHHHHH
Confidence            579999999999999999999988865432 2334567788888888889999998888776 66899999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +++.|.. ++.+..+|++|++++|.++++.|++++.+|||||+++++|+|+|++++||+|++|++...|+||+||++|.|
T Consensus       266 l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g  345 (391)
T 1xti_A          266 LAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG  345 (391)
T ss_dssp             HHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSC
T ss_pred             HHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCC
Confidence            9999985 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChh-hHHHHHHHHHHhCCCccccCCC
Q 012133          160 KEGTAILMFTSS-QRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       160 ~~g~~i~l~~~~-~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      ++|.+++++++. +...++.+++.+..+++.++..
T Consensus       346 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  380 (391)
T 1xti_A          346 TKGLAITFVSDENDAKILNDVQDRFEVNISELPDE  380 (391)
T ss_dssp             CCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCSC
T ss_pred             CceEEEEEEcccchHHHHHHHHHHhcCChhhCCcc
Confidence            999999999876 5677899999988888776543

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.95  E-value=4.7e-28  Score=247.12  Aligned_cols=190  Identities=34%  Similarity=0.588  Sum_probs=153.7

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcc-cHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTAT-SKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      |+||||+|..+..+++.++.+|..+.+.  ........+.++++.+... .+...|..++... ...++||||++++.++
T Consensus       218 i~~SAT~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lvf~~~~~~~~  294 (414)
T 3eiq_A          218 VLLSATMPSDVLEVTKKFMRDPIRILVK--KEELTLEGIRQFYINVEREEWKLDTLCDLYETL-TITQAVIFINTRRKVD  294 (414)
T ss_dssp             EEECSCCCHHHHHHHTTTCSSCEEECCC--CCCCCTTSCCEEEEECSSSTTHHHHHHHHHHSS-CCSSCEEECSCHHHHH
T ss_pred             EEEEEecCHHHHHHHHHHcCCCEEEEec--CCccCCCCceEEEEEeChHHhHHHHHHHHHHhC-CCCcEEEEeCCHHHHH
Confidence            5899999999999999999998877653  2334456677777766554 4888888887665 5579999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .+++.|.. .+.+..+|++|++++|.++++.|++++.+|||||+++++|||+|++++||+|++|++..+|+||+||+||.
T Consensus       295 ~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~  374 (414)
T 3eiq_A          295 WLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRF  374 (414)
T ss_dssp             HHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC---
T ss_pred             HHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCC
Confidence            99999985 78999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCC
Q 012133          159 GKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      |++|.|++|+++.+...++.+++.++..++.++..
T Consensus       375 g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (414)
T 3eiq_A          375 GRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLN  409 (414)
T ss_dssp             ----CEEEEECSTHHHHHHHHHHHTTCCCEECCC-
T ss_pred             CCCceEEEEEcHHHHHHHHHHHHHHcCCccccChh
Confidence            99999999999999999999999999988877543

>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=99.95  E-value=6.1e-27  Score=236.88  Aligned_cols=196  Identities=32%  Similarity=0.567  Sum_probs=167.3

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCc-ccHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      |+||||+|+.+..+++.++.++..+.+..  .......+.+.+..+.. ..+...+..++... ...++||||++++.++
T Consensus       181 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lvf~~~~~~~~  257 (395)
T 3pey_A          181 VLFSATFADAVRQYAKKIVPNANTLELQT--NEVNVDAIKQLYMDCKNEADKFDVLTELYGLM-TIGSSIIFVATKKTAN  257 (395)
T ss_dssp             EEEESCCCHHHHHHHHHHSCSCEEECCCG--GGCSCTTEEEEEEECSSHHHHHHHHHHHHTTT-TSSEEEEECSCHHHHH
T ss_pred             EEEEecCCHHHHHHHHHhCCCCeEEEccc--cccccccccEEEEEcCchHHHHHHHHHHHHhc-cCCCEEEEeCCHHHHH
Confidence            57999999999999999999988876543  23345567777766644 46667777666554 5589999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC------ChhHHHHHh
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRS  152 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~------~~~~y~qr~  152 (470)
                      .+++.|.. ++.+..+|++|++.+|.++++.|++++.+|||||+++++|||+|++++||+|++|+      ++.+|+||+
T Consensus       258 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~  337 (395)
T 3pey_A          258 VLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRI  337 (395)
T ss_dssp             HHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHH
T ss_pred             HHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhc
Confidence            99999985 78999999999999999999999999999999999999999999999999999999      999999999


Q ss_pred             cccCCCCCCCeEEEeeCh-hhHHHHHHHHHHhC-CCccccCCCCHHHHH
Q 012133          153 GRTGRAGKEGTAILMFTS-SQRRTVRSLERDVG-CKFEFVSPPVVEDVL  199 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~-~~~~~~~~i~~~~~-~~~~~~~~p~~~~~~  199 (470)
                      ||+||.|+.|.+++++.+ .+...++.+++.+. ..+..++.+..+++.
T Consensus       338 GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~  386 (395)
T 3pey_A          338 GRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVE  386 (395)
T ss_dssp             TTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTTSCCCEECCSSCHHHHH
T ss_pred             cccccCCCCceEEEEEechHHHHHHHHHHHHhCCceeecCChHHHHHHH
Confidence            999999999999999986 55678888888887 777777766655443

>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=99.95  E-value=8.3e-27  Score=233.55  Aligned_cols=183  Identities=36%  Similarity=0.606  Sum_probs=165.5

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+|.++.++++.++.++..+...      ....+.+.++.+....+.+.|..+++  ....++||||++++.++.
T Consensus       182 i~~SAT~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~l~~~l~--~~~~~~lvf~~~~~~~~~  253 (367)
T 1hv8_A          182 LLFSATMPREILNLAKKYMGDYSFIKAK------INANIEQSYVEVNENERFEALCRLLK--NKEFYGLVFCKTKRDTKE  253 (367)
T ss_dssp             EEECSSCCHHHHHHHHHHCCSEEEEECC------SSSSSEEEEEECCGGGHHHHHHHHHC--STTCCEEEECSSHHHHHH
T ss_pred             EEEeeccCHHHHHHHHHHcCCCeEEEec------CCCCceEEEEEeChHHHHHHHHHHHh--cCCCcEEEEECCHHHHHH
Confidence            5799999999999999999887776542      12466778888888888888877775  356799999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCC
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  159 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  159 (470)
                      +++.|.+ ++.+..+|+++++.+|.++++.|++++.+|||||+++++|+|+|++++||++++|+++.+|+||+||++|.|
T Consensus       254 l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g  333 (367)
T 1hv8_A          254 LASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAG  333 (367)
T ss_dssp             HHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSS
T ss_pred             HHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCC
Confidence            9999985 789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEeeChhhHHHHHHHHHHhCCCccccC
Q 012133          160 KEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  191 (470)
Q Consensus       160 ~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~  191 (470)
                      ++|.+++++++.+...++.|++.++.+++.++
T Consensus       334 ~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  365 (367)
T 1hv8_A          334 KKGKAISIINRREYKKLRYIERAMKLKIKKLK  365 (367)
T ss_dssp             SCCEEEEEECTTSHHHHHHHHHHHTCCCCCBC
T ss_pred             CccEEEEEEcHHHHHHHHHHHHHhCCCCceec
Confidence            99999999999999999999999998887654

>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=99.94  E-value=2.5e-28  Score=254.81  Aligned_cols=193  Identities=32%  Similarity=0.498  Sum_probs=25.5

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCc-ccHHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      |+||||+|.++..+++.++.+|..|.+..  .......+.++++.+.. ..+...|..++... ...++||||++++.++
T Consensus       271 i~~SAT~~~~~~~~~~~~~~~~~~i~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lvF~~s~~~~~  347 (479)
T 3fmp_B          271 LLFSATFEDSVWKFAQKVVPDPNVIKLKR--EEETLDTIKQYYVLCSSRDEKFQALCNLYGAI-TIAQAMIFCHTRKTAS  347 (479)
T ss_dssp             EEEESCCCHHHHHHHHHHSSSEEEEEEC----------------------------------------------------
T ss_pred             EEEeCCCCHHHHHHHHHHcCCCeEEeccc--cccCcCCceEEEEEeCCHHHHHHHHHHHHhhc-cCCceEEEeCcHHHHH
Confidence            58999999999999999999998887743  23345566666666554 46667777766554 4579999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC------ChhHHHHHh
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRS  152 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~------~~~~y~qr~  152 (470)
                      .+++.|.. .+.+..+||+|++.+|..+++.|++++.+|||||+++++|||+|++++||+||+|.      +...|+||+
T Consensus       348 ~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~  427 (479)
T 3fmp_B          348 WLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRI  427 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHh
Confidence            99999985 78899999999999999999999999999999999999999999999999999995      568999999


Q ss_pred             cccCCCCCCCeEEEeeChhh-HHHHHHHHHHhCCCccccCCCCHH
Q 012133          153 GRTGRAGKEGTAILMFTSSQ-RRTVRSLERDVGCKFEFVSPPVVE  196 (470)
Q Consensus       153 GR~gR~g~~g~~i~l~~~~~-~~~~~~i~~~~~~~~~~~~~p~~~  196 (470)
                      ||+||.|+.|.+++|+++.+ ...++.|++.+..+++.+.....+
T Consensus       428 GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~  472 (479)
T 3fmp_B          428 GRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLD  472 (479)
T ss_dssp             ---------------------------------------------
T ss_pred             cccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceECCCccHH
Confidence            99999999999999998765 778888888888777766554433

>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=99.89  E-value=1.3e-28  Score=221.17  Aligned_cols=153  Identities=29%  Similarity=0.506  Sum_probs=139.9

Q ss_pred             ceEEEEEEcCc-ccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCe
Q 012133           38 GIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF  115 (470)
Q Consensus        38 ~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~  115 (470)
                      +|.|+++.++. +.|..+|..+++.. ...++||||++++.++.+++.|.. ++.+..+||+|++.+|.++++.|++++.
T Consensus         3 ~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~   81 (170)
T 2yjt_D            3 KIHQWYYRADDLEHKTALLVHLLKQP-EATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRV   81 (170)
Confidence            56778888877 88999999888764 457999999999999999999985 7889999999999999999999999999


Q ss_pred             eEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccC
Q 012133          116 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  191 (470)
Q Consensus       116 ~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~  191 (470)
                      +|||||+++++|+|+|++++||+|++|+++..|+||+||++|.|+.|.+++++++.+...++.+++.++..++...
T Consensus        82 ~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (170)
T 2yjt_D           82 NVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARV  157 (170)
Confidence            9999999999999999999999999999999999999999999999999999999999999999888777765543

>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=99.93  E-value=1.5e-27  Score=241.61  Aligned_cols=189  Identities=33%  Similarity=0.580  Sum_probs=25.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCccc-HHHHHHHHHHHHcCCCeEEEEeCchHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~~lVF~~t~~~~~   79 (470)
                      |+||||+|+.+.++...++.+|..+.+..  .......+.++++.+.... +...+..+++.. ...++||||++++.++
T Consensus       197 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lVf~~~~~~~~  273 (394)
T 1fuu_A          197 VLLSATMPNDVLEVTTKFMRNPVRILVKK--DELTLEGIKQFYVNVEEEEYKYECLTDLYDSI-SVTQAVIFCNTRRKVE  273 (394)
T ss_dssp             EEECSSCCHHHHHHHHHHCCSCEEEEECC---------------------------------------------------
T ss_pred             EEEEEecCHHHHHHHHHhcCCCeEEEecC--ccccCCCceEEEEEcCchhhHHHHHHHHHhcC-CCCcEEEEECCHHHHH
Confidence            57999999999999999999998886642  2333455666666555443 677777777654 4579999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCC
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  158 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  158 (470)
                      .+++.|.+ ++.+..+||+|++++|.++++.|++++.+|||||+++++|+|+|++++||++++|+++.+|+||+||+||.
T Consensus       274 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~  353 (394)
T 1fuu_A          274 ELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRF  353 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCC
Confidence            99999985 68899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCeEEEeeChhhHHHHHHHHHHhCCCccccCC
Q 012133          159 GKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  192 (470)
Q Consensus       159 g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~  192 (470)
                      |++|.|++++++.+...++.+++.++..++.++.
T Consensus       354 g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  387 (394)
T 1fuu_A          354 GRKGVAINFVTNEDVGAMRELEKFYSTQIEELPS  387 (394)
T ss_dssp             ----------------------------------
T ss_pred             CCCceEEEEEchhHHHHHHHHHHHhCCcccccCc
Confidence            9999999999999999999999988887776544

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.93  E-value=2.6e-25  Score=236.89  Aligned_cols=175  Identities=19%  Similarity=0.331  Sum_probs=142.5

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHH---cCCCeEEEEeCchHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVY---AKGGKTIVFTQTKRD   77 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~   77 (470)
                      |+||||+++.+.+.+..++..+..+.+...   ....++.+.... ....+...+..+++.+   ....++||||+|++.
T Consensus       204 i~lSAT~~~~v~~~i~~~l~~~~~~~~~~~---~~r~nl~~~v~~-~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~  279 (591)
T 2v1x_A          204 IGLTATATNHVLTDAQKILCIEKCFTFTAS---FNRPNLYYEVRQ-KPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKD  279 (591)
T ss_dssp             EEEESSCCHHHHHHHHHHTTCCSCEEEECC---CCCTTEEEEEEE-CCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHH
T ss_pred             EEEecCCCHHHHHHHHHHhCCCCcEEEecC---CCCcccEEEEEe-CCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHH
Confidence            579999999998888888875544433321   122344433333 2233334444444433   256899999999999


Q ss_pred             HHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccC
Q 012133           78 ADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG  156 (470)
Q Consensus        78 ~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~g  156 (470)
                      ++++++.|.. ++.+..+|++|++++|.++++.|++++++|||||+++++|||+|+|++||+|++|.+++.|+||+||+|
T Consensus       280 ~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaG  359 (591)
T 2v1x_A          280 SEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG  359 (591)
T ss_dssp             HHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSC
T ss_pred             HHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCC
Confidence            9999999985 789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCeEEEeeChhhHHHHHHH
Q 012133          157 RAGKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       157 R~g~~g~~i~l~~~~~~~~~~~i  179 (470)
                      |.|+++.|++||.+.+...++.+
T Consensus       360 R~G~~g~~i~l~~~~D~~~~~~~  382 (591)
T 2v1x_A          360 RDDMKADCILYYGFGDIFRISSM  382 (591)
T ss_dssp             TTSSCEEEEEEECHHHHHHHHHH
T ss_pred             cCCCCceEEEEEChHHHHHHHHH
Confidence            99999999999999887666655

>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=99.92  E-value=4.7e-24  Score=224.58  Aligned_cols=174  Identities=20%  Similarity=0.383  Sum_probs=142.4

Q ss_pred             CEEeecCCHHHHHHHHHHc--CCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSATMPSWVKKLSRKYL--DNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l--~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |+||||+++.+.+.+...+  .+|..+ +...    ...++.+..  .....+...|.+++... ...++||||+|++.+
T Consensus       178 i~lSAT~~~~~~~~i~~~l~~~~~~~~-~~~~----~r~~l~~~v--~~~~~~~~~l~~~l~~~-~~~~~IVf~~sr~~~  249 (523)
T 1oyw_A          178 MALTATADDTTRQDIVRLLGLNDPLIQ-ISSF----DRPNIRYML--MEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKV  249 (523)
T ss_dssp             EEEESCCCHHHHHHHHHHHTCCSCEEE-ECCC----CCTTEEEEE--EECSSHHHHHHHHHHHT-TTCCEEEECSSHHHH
T ss_pred             EEEeCCCCHHHHHHHHHHhCCCCCeEE-eCCC----CCCceEEEE--EeCCCHHHHHHHHHHhc-CCCcEEEEeCCHHHH
Confidence            5799999998765444333  345433 2211    123443333  23356677777777654 567999999999999


Q ss_pred             HHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCC
Q 012133           79 DEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR  157 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR  157 (470)
                      +.+++.|.. ++.+..+|++|++++|.++++.|++++.+|||||+++++|||+|+|++||+|++|+++++|+||+||+||
T Consensus       250 e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR  329 (523)
T 1oyw_A          250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGR  329 (523)
T ss_dssp             HHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCT
T ss_pred             HHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccC
Confidence            999999985 7899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCeEEEeeChhhHHHHHHHHHH
Q 012133          158 AGKEGTAILMFTSSQRRTVRSLERD  182 (470)
Q Consensus       158 ~g~~g~~i~l~~~~~~~~~~~i~~~  182 (470)
                      .|+++.|++|+++.+...++.+...
T Consensus       330 ~g~~~~~~l~~~~~d~~~~~~~~~~  354 (523)
T 1oyw_A          330 DGLPAEAMLFYDPADMAWLRRCLEE  354 (523)
T ss_dssp             TSSCEEEEEEECHHHHHHHHHHHHT
T ss_pred             CCCCceEEEEeCHHHHHHHHHHHhc
Confidence            9999999999999888777766543

>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=99.92  E-value=7.5e-25  Score=216.85  Aligned_cols=172  Identities=29%  Similarity=0.532  Sum_probs=144.4

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ++||||+|+.+.++...++.++..+...     .....+.+.++.+....+..+  ..+.. ....++||||++++.++.
T Consensus       164 ~~~SAT~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~lvf~~~~~~~~~  235 (337)
T 2z0m_A          164 GLFSATIPEEIRKVVKDFITNYEEIEAC-----IGLANVEHKFVHVKDDWRSKV--QALRE-NKDKGVIVFVRTRNRVAK  235 (337)
T ss_dssp             EEEESCCCHHHHHHHHHHSCSCEEEECS-----GGGGGEEEEEEECSSSSHHHH--HHHHT-CCCSSEEEECSCHHHHHH
T ss_pred             EEEeCcCCHHHHHHHHHhcCCceeeecc-----cccCCceEEEEEeChHHHHHH--HHHHh-CCCCcEEEEEcCHHHHHH
Confidence            3689999999999999999988777532     234556777777665544322  33332 356899999999999999


Q ss_pred             HHHHHhcCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCC
Q 012133           81 VSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  160 (470)
Q Consensus        81 l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~  160 (470)
                      +++.|.   .+..+|++|++.+|.++++.|++++.+|||||+++++|+|+|++++||+|++|+++.+|+||+||+||.|+
T Consensus       236 l~~~l~---~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~  312 (337)
T 2z0m_A          236 LVRLFD---NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGR  312 (337)
T ss_dssp             HHTTCT---TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGC
T ss_pred             HHHHhh---hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCC
Confidence            998886   58899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeEEEeeChhhHHHHHHHHHHhC
Q 012133          161 EGTAILMFTSSQRRTVRSLERDVG  184 (470)
Q Consensus       161 ~g~~i~l~~~~~~~~~~~i~~~~~  184 (470)
                      +|.+++++. .+...++.|++.++
T Consensus       313 ~g~~~~~~~-~~~~~~~~i~~~~~  335 (337)
T 2z0m_A          313 KGEAITFIL-NEYWLEKEVKKVSQ  335 (337)
T ss_dssp             CEEEEEEES-SCHHHHHHHC----
T ss_pred             CceEEEEEe-CcHHHHHHHHHHhc
Confidence            999999999 78888888876654

>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=99.91  E-value=2.3e-24  Score=235.93  Aligned_cols=164  Identities=17%  Similarity=0.361  Sum_probs=133.4

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHH-HHHHHHHHH--cCCCeEEEEeCchHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRT-ILSDLITVY--AKGGKTIVFTQTKRD   77 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~-~l~~ll~~~--~~~~~~lVF~~t~~~   77 (470)
                      |+||||++.+  .+ ..|+.++..+.+...     ...++++|+..+..++.. ++..++..+  ...+++||||+++++
T Consensus       244 Il~SAT~~~~--~l-~~~~~~~~vi~v~gr-----~~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~  315 (773)
T 2xau_A          244 IIMSATLDAE--KF-QRYFNDAPLLAVPGR-----TYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDE  315 (773)
T ss_dssp             EEEESCSCCH--HH-HHHTTSCCEEECCCC-----CCCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHH
T ss_pred             EEEeccccHH--HH-HHHhcCCCcccccCc-----ccceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHH
Confidence            5899999753  34 456666666665332     234777777766666543 333343332  356899999999999


Q ss_pred             HHHHHHHHhc------------CCcEEEEeCCCCHHHHHHHHcccc-----cCCeeEEEecccccccCCCCCccEEEEec
Q 012133           78 ADEVSLALTS------------IIASEALHGDISQHQRERTLNGFR-----QGKFTVLVATDVAARGLDIPNVDLIIHYE  140 (470)
Q Consensus        78 ~~~l~~~l~~------------~~~~~~lhg~~~~~~R~~~~~~f~-----~g~~~iLVaTdv~~~Gidip~v~~VI~~~  140 (470)
                      ++.+++.|.+            .+.+.++||+|++++|.++++.|+     +|..+|||||+++++|||||+|++||+++
T Consensus       316 i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g  395 (773)
T 2xau_A          316 IEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPG  395 (773)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECS
T ss_pred             HHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCC
Confidence            9999999873            467999999999999999999999     99999999999999999999999999988


Q ss_pred             C------------------CCChhHHHHHhcccCCCCCCCeEEEeeChhhH
Q 012133          141 L------------------PNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       141 ~------------------p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                      +                  |.+..+|+||+|||||. ++|.||+|+++.+.
T Consensus       396 ~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          396 FSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             EEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             CccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHHh
Confidence            7                  89999999999999999 89999999987654

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

Probab=99.88  E-value=7.8e-23  Score=209.09  Aligned_cols=165  Identities=22%  Similarity=0.398  Sum_probs=131.6

Q ss_pred             CEEeec-CCHHHH-HHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSAT-MPSWVK-KLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSAT-lp~~i~-~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |+|||| +|..+. .+.+.++.    +.+.  ........+.+.++.+   ++.+.|..+++..  +.++||||++++.+
T Consensus       197 i~~SAT~~~~~~~~~~~~~~~~----~~~~--~~~~~~~~i~~~~~~~---~~~~~l~~~l~~~--~~~~lVF~~~~~~~  265 (414)
T 3oiy_A          197 VVSSATAKPRGIRPLLFRDLLN----FTVG--RLVSVARNITHVRISS---RSKEKLVELLEIF--RDGILIFAQTEEEG  265 (414)
T ss_dssp             EESSCCSSCCSSTTHHHHHHHS----CCSS--CCCCCCCSEEEEEESS---CCHHHHHHHHHHH--CSSEEEEESSHHHH
T ss_pred             EEEecCCCcchhHHHHHHHhhc----cCcC--ccccccccchheeecc---CHHHHHHHHHHHc--CCCEEEEECCHHHH
Confidence            578999 676655 34444433    2221  2233456777777665   4556667777664  48999999999999


Q ss_pred             HHHHHHHhc-CCcEE-EEeCCCCHHHHHHHHcccccCCeeEEEe----cccccccCCCCC-ccEEEEecCC--CChhHHH
Q 012133           79 DEVSLALTS-IIASE-ALHGDISQHQRERTLNGFRQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELP--NDPETFV  149 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~-~lhg~~~~~~R~~~~~~f~~g~~~iLVa----Tdv~~~Gidip~-v~~VI~~~~p--~~~~~y~  149 (470)
                      +.+++.|.. ++.+. .+||+    +|+  ++.|++++++||||    |+++++|||+|+ |++||+|++|  .+..+|+
T Consensus       266 ~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~  339 (414)
T 3oiy_A          266 KELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYI  339 (414)
T ss_dssp             HHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHH
T ss_pred             HHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHH
Confidence            999999985 78888 89995    444  99999999999999    999999999999 9999999999  9999999


Q ss_pred             HHhcccCCCC----CCCeEEEeeChhhHHHHHHHHHHhC
Q 012133          150 HRSGRTGRAG----KEGTAILMFTSSQRRTVRSLERDVG  184 (470)
Q Consensus       150 qr~GR~gR~g----~~g~~i~l~~~~~~~~~~~i~~~~~  184 (470)
                      ||+||+||.|    ++|.+++|+  .+...++.|++.++
T Consensus       340 qr~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l~~~~~  376 (414)
T 3oiy_A          340 QASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLL  376 (414)
T ss_dssp             HHHGGGCCEETTEECCEEEEEEC--CCHHHHHHHHHHHH
T ss_pred             HHhCccccCCCCCCcceEEEEEE--ccHHHHHHHHHHhc
Confidence            9999999987    589999999  56677777777776

>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=99.87  E-value=8.3e-23  Score=219.49  Aligned_cols=163  Identities=18%  Similarity=0.201  Sum_probs=132.8

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceE-EEEEEcCcccHHHHHHHHHHH-HcCCCeEEEEeCchHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIK-LYAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~-~~~~~~~~~~k~~~l~~ll~~-~~~~~~~lVF~~t~~~~~~   80 (470)
                      ||+|...+...+.+.|..+  ++.+.  . ......+. ..++.+...+|..+|..++.. +....++||||+|++.++.
T Consensus       373 mTGTa~te~~e~~~iY~l~--vv~IP--t-n~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~  447 (844)
T 1tf5_A          373 MTGTAKTEEEEFRNIYNMQ--VVTIP--T-NRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSEL  447 (844)
T ss_dssp             EESCCGGGHHHHHHHHCCC--EEECC--C-SSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHH
T ss_pred             CCcccchhHHHHHHHhCCc--eEEec--C-CCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHH
Confidence            7899988888888887544  23332  1 11112222 124456667888888887754 4456789999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC--------CccEEEEecCCCChhHHHHH
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP--------NVDLIIHYELPNDPETFVHR  151 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip--------~v~~VI~~~~p~~~~~y~qr  151 (470)
                      |+..|.+ ++++.+||+++.+.+|..+.+.|+.+  .||||||+|+||+||+        ++.+||||++|.+.+.|+||
T Consensus       448 Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr  525 (844)
T 1tf5_A          448 ISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQL  525 (844)
T ss_dssp             HHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHH
T ss_pred             HHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhh
Confidence            9999985 89999999999999998888888766  6999999999999999        78899999999999999999


Q ss_pred             hcccCCCCCCCeEEEeeChhh
Q 012133          152 SGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       152 ~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      +|||||+|++|.+++|++..+
T Consensus       526 ~GRTGRqG~~G~s~~~vs~eD  546 (844)
T 1tf5_A          526 RGRSGRQGDPGITQFYLSMED  546 (844)
T ss_dssp             HTTSSGGGCCEEEEEEEETTS
T ss_pred             cCccccCCCCCeEEEEecHHH
Confidence            999999999999999998765

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

Probab=99.86  E-value=7.9e-23  Score=222.77  Aligned_cols=129  Identities=22%  Similarity=0.364  Sum_probs=81.6

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc-C----CcEEEE--------eCCCCHHHHHHHHccccc
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-I----IASEAL--------HGDISQHQRERTLNGFRQ  112 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~-~----~~~~~l--------hg~~~~~~R~~~~~~f~~  112 (470)
                      ..|...|.+++...   ....++||||++++.++.|++.|.. .    +.+..+        |++|++++|.+++++|++
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            45777777887654   3557999999999999999999985 3    788888        569999999999999998


Q ss_pred             -CCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHH
Q 012133          113 -GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       113 -g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i  179 (470)
                       |+++|||||+++++|||+|+|++||+||+|+++++|+||+|| ||. +.|.+++|++..+....+.+
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 88999999998776554444

>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=99.86  E-value=5.8e-21  Score=205.94  Aligned_cols=130  Identities=22%  Similarity=0.395  Sum_probs=114.1

Q ss_pred             cHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccC
Q 012133           50 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  128 (470)
Q Consensus        50 ~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gi  128 (470)
                      .+..++..+......+.++||||+|+..++.|++.|.. ++.+..+|+++++.+|.++++.|++|+++|||||+++++|+
T Consensus       430 ~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~Gl  509 (661)
T 2d7d_A          430 QIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGL  509 (661)
T ss_dssp             HHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTC
T ss_pred             hHHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCc
Confidence            33444455555555678999999999999999999985 78999999999999999999999999999999999999999


Q ss_pred             CCCCccEEEEecC-----CCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHH
Q 012133          129 DIPNVDLIIHYEL-----PNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  180 (470)
Q Consensus       129 dip~v~~VI~~~~-----p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~  180 (470)
                      |+|+|++||+++.     |.+.++|+||+||+||. .+|.+++|+++.+..+.+.|+
T Consensus       510 Dip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~~~~~~i~  565 (661)
T 2d7d_A          510 DIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-AEGRVIMYADKITKSMEIAIN  565 (661)
T ss_dssp             CCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCCHHHHHHHH
T ss_pred             ccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCCHHHHHHHH
Confidence            9999999999997     99999999999999998 799999999987655544443

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.86  E-value=5.2e-21  Score=201.34  Aligned_cols=164  Identities=21%  Similarity=0.214  Sum_probs=130.2

Q ss_pred             EEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEE-EEEEcCcccHHHHHHHHHHH-HcCCCeEEEEeCchHHHH
Q 012133            2 LFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKL-YAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDAD   79 (470)
Q Consensus         2 lfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~-~~~~~~~~~k~~~l~~ll~~-~~~~~~~lVF~~t~~~~~   79 (470)
                      -||+|+..+...+.+.|-.+  +|.+..   ..+...+.+ ..+......|..+|...+.. +....++||||+|++.++
T Consensus       414 GMTGTa~te~~Ef~~iY~l~--vv~IPt---nkp~~R~d~~d~vy~t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE  488 (822)
T 3jux_A          414 GMTGTAKTEESEFVQVYGME--VVVIPT---HKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSE  488 (822)
T ss_dssp             EEESSCGGGHHHHHHHSCCC--EEECCC---SSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESSHHHHH
T ss_pred             EECCCCchHHHHHHHHhCCe--EEEECC---CCCcceeecCcEEEecHHHHHHHHHHHHHHHhhCCCCEEEEECCHHHHH
Confidence            38999999888888777433  443321   122222322 23445667788887777754 345689999999999999


Q ss_pred             HHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCC--------CccEEEEecCCCChhHHHH
Q 012133           80 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP--------NVDLIIHYELPNDPETFVH  150 (470)
Q Consensus        80 ~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip--------~v~~VI~~~~p~~~~~y~q  150 (470)
                      .|+..|.+ ++++.+||+++.+.++..+.+.++.+  .|+||||+|+||+||+        ++.+||++++|.+.+.|+|
T Consensus       489 ~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~q  566 (822)
T 3jux_A          489 LLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQ  566 (822)
T ss_dssp             HHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHH
T ss_pred             HHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHH
Confidence            99999985 89999999996666666666667655  6999999999999998        5569999999999999999


Q ss_pred             HhcccCCCCCCCeEEEeeChhh
Q 012133          151 RSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       151 r~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      |+|||||+|.+|.+++|++..+
T Consensus       567 riGRTGRqG~~G~a~~fvsleD  588 (822)
T 3jux_A          567 LRGRAGRQGDPGESIFFLSLED  588 (822)
T ss_dssp             HHTTSSCSSCCCEEEEEEETTS
T ss_pred             hhCccccCCCCeeEEEEechhH
Confidence            9999999999999999998876

>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=99.85  E-value=1.6e-20  Score=202.61  Aligned_cols=131  Identities=24%  Similarity=0.392  Sum_probs=115.2

Q ss_pred             HHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCC
Q 012133           51 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  129 (470)
Q Consensus        51 k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gid  129 (470)
                      +..++..+......+.++||||+|+..++.|++.|.+ ++.+..+|++|++.+|.++++.|+.|+++|||||+++++|+|
T Consensus       425 ~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlD  504 (664)
T 1c4o_A          425 ILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLD  504 (664)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCC
T ss_pred             HHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCcc
Confidence            3344444444455678999999999999999999985 789999999999999999999999999999999999999999


Q ss_pred             CCCccEEEEecC-----CCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHH
Q 012133          130 IPNVDLIIHYEL-----PNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  182 (470)
Q Consensus       130 ip~v~~VI~~~~-----p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~  182 (470)
                      +|+|++||+++.     |.+..+|+||+||+||. .+|.+++|+++.+..+.+.|++.
T Consensus       505 ip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~~~~~~i~~~  561 (664)
T 1c4o_A          505 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-ARGEVWLYADRVSEAMQRAIEET  561 (664)
T ss_dssp             CTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTS-TTCEEEEECSSCCHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcC-CCCEEEEEEcCCCHHHHHHHHHH
Confidence            999999999997     89999999999999999 58999999998777666666543

>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=99.85  E-value=8.4e-23  Score=210.58  Aligned_cols=115  Identities=23%  Similarity=0.287  Sum_probs=96.1

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEE----
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----  138 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~----  138 (470)
                      ..+++||||++++.++.+++.|.. ++.+..+||    ++|+++++.|++++++|||||+++++|||+| +++||+    
T Consensus       176 ~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~  250 (440)
T 1yks_A          176 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTA  250 (440)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCcc
Confidence            357999999999999999999985 789999999    4688999999999999999999999999999 999986    


Q ss_pred             ---------------ecCCCChhHHHHHhcccCCC-CCCCeEEEee---ChhhHHHHHHHHHHh
Q 012133          139 ---------------YELPNDPETFVHRSGRTGRA-GKEGTAILMF---TSSQRRTVRSLERDV  183 (470)
Q Consensus       139 ---------------~~~p~~~~~y~qr~GR~gR~-g~~g~~i~l~---~~~~~~~~~~i~~~~  183 (470)
                                     |+.|.+.++|+||+||+||. +++|.|++|+   ++.+...++.++..+
T Consensus       251 ~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~  314 (440)
T 1yks_A          251 FKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASM  314 (440)
T ss_dssp             EEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHH
T ss_pred             ceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhhhhhhhhHHh
Confidence                           89999999999999999998 6899999997   566767777777665

>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=99.85  E-value=4.7e-22  Score=212.53  Aligned_cols=157  Identities=17%  Similarity=0.220  Sum_probs=122.6

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+|..+..+++   .++..+.+....               +......++..+. .  ..+++||||+|++.++.
T Consensus       312 il~SAT~~~~~~~~~~---~~~~~~~v~~~~---------------~~~~~~~ll~~l~-~--~~~~~LVF~~s~~~a~~  370 (618)
T 2whx_A          312 IFMTATPPGSTDPFPQ---SNSPIEDIEREI---------------PERSWNTGFDWIT-D--YQGKTVWFVPSIKAGND  370 (618)
T ss_dssp             EEECSSCTTCCCSSCC---CSSCEEEEECCC---------------CSSCCSSSCHHHH-H--CCSCEEEECSSHHHHHH
T ss_pred             EEEECCCchhhhhhhc---cCCceeeecccC---------------CHHHHHHHHHHHH-h--CCCCEEEEECChhHHHH
Confidence            5899999987554332   245555443210               1111111222222 2  35799999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEE--------------------EEe
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI--------------------IHY  139 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~V--------------------I~~  139 (470)
                      +++.|.+ ++.+..+|++    +|+++++.|++++.+||||||++++|||+| |++|                    |+|
T Consensus       371 l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~  445 (618)
T 2whx_A          371 IANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAG  445 (618)
T ss_dssp             HHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEE
T ss_pred             HHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCceEEcc
Confidence            9999985 7899999985    788899999999999999999999999997 9888                    788


Q ss_pred             cCCCChhHHHHHhcccCCCC-CCCeEEEeeC---hhhHHHHHHHHHHh
Q 012133          140 ELPNDPETFVHRSGRTGRAG-KEGTAILMFT---SSQRRTVRSLERDV  183 (470)
Q Consensus       140 ~~p~~~~~y~qr~GR~gR~g-~~g~~i~l~~---~~~~~~~~~i~~~~  183 (470)
                      ++|.+.++|+||+|||||.+ ++|.+++|++   +.+...++.+++.+
T Consensus       446 d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i  493 (618)
T 2whx_A          446 PIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKM  493 (618)
T ss_dssp             EEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHH
T ss_pred             cccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHh
Confidence            88999999999999999996 5999999998   77777777777765

>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=99.84  E-value=5.2e-22  Score=224.31  Aligned_cols=188  Identities=18%  Similarity=0.284  Sum_probs=142.4

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ++||||++.. ..+++.++.++..+.+.  .......++.++++   ..++...|..+++..  +.++||||+|++.|+.
T Consensus       219 ~l~SAT~t~~-~~~~~~~~~~~~~i~v~--~~~~~~~~i~~~~~---~~~k~~~L~~ll~~~--~~~~LVF~~t~~~a~~  290 (1054)
T 1gku_B          219 CLMVSTATAK-KGKKAELFRQLLNFDIG--SSRITVRNVEDVAV---NDESISTLSSILEKL--GTGGIIYARTGEEAEE  290 (1054)
T ss_dssp             EEEECCCCSC-CCTTHHHHHHHHCCCCS--CCEECCCCEEEEEE---SCCCTTTTHHHHTTS--CSCEEEEESSHHHHHH
T ss_pred             EEEEecCCCc-hhHHHHHhhcceEEEcc--CcccCcCCceEEEe---chhHHHHHHHHHhhc--CCCEEEEEcCHHHHHH
Confidence            4899999987 65666666555555442  22334456777776   245666667777543  5789999999999999


Q ss_pred             HHHHHhcCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEe----cccccccCCCCCc-cEEEEecCC-------------
Q 012133           81 VSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVA----TDVAARGLDIPNV-DLIIHYELP-------------  142 (470)
Q Consensus        81 l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVa----Tdv~~~Gidip~v-~~VI~~~~p-------------  142 (470)
                      +++.|...+.+..+||+|     .+++++|++|+++||||    |+++++|||+|+| ++||+|++|             
T Consensus       291 l~~~L~~~~~v~~lhg~~-----~~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~~  365 (1054)
T 1gku_B          291 IYESLKNKFRIGIVTATK-----KGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPSFRVTIEDIDSLS  365 (1054)
T ss_dssp             HHHTTTTSSCEEECTTSS-----SHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCCEEEEECSCGGGSC
T ss_pred             HHHHHhhccCeeEEeccH-----HHHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEEEeCCCcccccccccccCh
Confidence            999998668999999998     37788999999999999    9999999999995 999999999             


Q ss_pred             ----------------------------------------------------------CChhHHHHHhcccCCCCCCC--
Q 012133          143 ----------------------------------------------------------NDPETFVHRSGRTGRAGKEG--  162 (470)
Q Consensus       143 ----------------------------------------------------------~~~~~y~qr~GR~gR~g~~g--  162 (470)
                                                                                .+..+|+||+|||||.+..|  
T Consensus       366 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~~  445 (1054)
T 1gku_B          366 PQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLT  445 (1054)
T ss_dssp             HHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTEEEEECHHHHHHHHHTTCCEETTEEC
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecceecCcHHHHhhhhchhhhccCCCCc
Confidence                                                                      78999999999999987665  


Q ss_pred             eEEEeeChhhHHHHHHHHHHhC---CCccccCCCCHHHHHHH
Q 012133          163 TAILMFTSSQRRTVRSLERDVG---CKFEFVSPPVVEDVLES  201 (470)
Q Consensus       163 ~~i~l~~~~~~~~~~~i~~~~~---~~~~~~~~p~~~~~~~~  201 (470)
                      .++.++...+...++.|++.++   ..+..+..+..+++++.
T Consensus       446 ~g~~~~~~~d~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~  487 (1054)
T 1gku_B          446 KGASFLLEDDSELLSAFIERAKLYDIEFKSIDEVDFEKLSRE  487 (1054)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTTSSCCCBCSCCCHHHHHHH
T ss_pred             eEEEEEEecCHHHHHHHHHHHhhccCccccCCcCCHHHHHHh
Confidence            4666666667778888888776   45555666666666554

>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=99.84  E-value=2.2e-20  Score=209.47  Aligned_cols=167  Identities=17%  Similarity=0.243  Sum_probs=145.4

Q ss_pred             cCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc--CCcEEEEeCCCCHHHHHHHHcccccCC--eeEEEec
Q 012133           46 TTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGK--FTVLVAT  121 (470)
Q Consensus        46 ~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~--~~~~~~lhg~~~~~~R~~~~~~f~~g~--~~iLVaT  121 (470)
                      +....|...|..+++.. ...++||||+++..++.+++.|..  ++.+..+||+|++.+|++++++|++++  ++|||||
T Consensus       485 ~~~~~K~~~L~~ll~~~-~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT  563 (968)
T 3dmq_A          485 WNFDPRVEWLMGYLTSH-RSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCS  563 (968)
T ss_dssp             TTTSHHHHHHHHHHHHT-SSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECS
T ss_pred             cCccHHHHHHHHHHHhC-CCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEec
Confidence            34457888898888773 678999999999999999999983  789999999999999999999999998  9999999


Q ss_pred             ccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHh--CCCccccCCCCHHHHH
Q 012133          122 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV--GCKFEFVSPPVVEDVL  199 (470)
Q Consensus       122 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~--~~~~~~~~~p~~~~~~  199 (470)
                      +++++|||+|++++||+||+|+++..|+||+||++|.|+.+.+++++...+....+.|.+.+  +.++....+|...++.
T Consensus       564 ~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~ee~i~~~~~~k~~~~~~~~~~~~~i~  643 (968)
T 3dmq_A          564 EIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRTIY  643 (968)
T ss_dssp             CCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSHHHHHHHHHHHTTCCSSSCCSSHHHHH
T ss_pred             chhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEecCCChHHHHHHHHHHhCCCceecCCCCHHHHH
Confidence            99999999999999999999999999999999999999999877776655545555566666  5666677889999999


Q ss_pred             HHHHHHHHHHHccc
Q 012133          200 ESSAEQVVATLNGV  213 (470)
Q Consensus       200 ~~~~~~~~~~l~~~  213 (470)
                      +...+++...+...
T Consensus       644 ~~~~~~l~~~l~~~  657 (968)
T 3dmq_A          644 DSVYNDLINYLASP  657 (968)
T ss_dssp             HHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHhcc
Confidence            98888888887754

>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=99.84  E-value=1e-20  Score=206.36  Aligned_cols=111  Identities=28%  Similarity=0.530  Sum_probs=101.5

Q ss_pred             HcCCCeEEEEeCchHHHHHHHHHHhcC-------------------------------CcEEEEeCCCCHHHHHHHHccc
Q 012133           62 YAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------IASEALHGDISQHQRERTLNGF  110 (470)
Q Consensus        62 ~~~~~~~lVF~~t~~~~~~l~~~l~~~-------------------------------~~~~~lhg~~~~~~R~~~~~~f  110 (470)
                      +.+.+++||||+++++++.++..|...                               ..+.++|++|++++|..+++.|
T Consensus       239 ~~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f  318 (702)
T 2p6r_A          239 VAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAF  318 (702)
T ss_dssp             HHTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHH
T ss_pred             HhcCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHH
Confidence            346789999999999999999888631                               3588899999999999999999


Q ss_pred             ccCCeeEEEecccccccCCCCCccEEEE----ec---CCCChhHHHHHhcccCCCC--CCCeEEEeeChhh
Q 012133          111 RQGKFTVLVATDVAARGLDIPNVDLIIH----YE---LPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQ  172 (470)
Q Consensus       111 ~~g~~~iLVaTdv~~~Gidip~v~~VI~----~~---~p~~~~~y~qr~GR~gR~g--~~g~~i~l~~~~~  172 (470)
                      ++|.++|||||+++++|||+|++++||+    ||   .|.+..+|+||+||+||.|  ..|.|+++++..+
T Consensus       319 ~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  389 (702)
T 2p6r_A          319 RRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  389 (702)
T ss_dssp             HTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             HCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCcc
Confidence            9999999999999999999999999998    66   7899999999999999988  5899999999877

>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=99.84  E-value=3.7e-21  Score=206.29  Aligned_cols=163  Identities=21%  Similarity=0.187  Sum_probs=134.1

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEE-EEEEcCcccHHHHHHHHHHH-HcCCCeEEEEeCchHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKL-YAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~-~~~~~~~~~k~~~l~~ll~~-~~~~~~~lVF~~t~~~~~~   80 (470)
                      ||+|...+...+.+.|-.+  +|.+.   .......+.+ .++.+....|..+|.+++.. +....++||||+|++.++.
T Consensus       382 mTGTa~te~~ef~~iY~l~--vv~IP---tn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~  456 (853)
T 2fsf_A          382 MTGTADTEAFEFSSIYKLD--TVVVP---TNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSEL  456 (853)
T ss_dssp             EECTTCCCHHHHHHHHCCE--EEECC---CSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHH
T ss_pred             CCCCchhHHHHHHHHhCCc--EEEcC---CCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHH
Confidence            7899988888888777433  33332   1222222222 24556677899888887754 4566799999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCc--------------------------
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV--------------------------  133 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v--------------------------  133 (470)
                      |+..|.+ ++++.+||+++.+.++..+.++|+.|  .|+||||+|+||+||+..                          
T Consensus       457 Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~  534 (853)
T 2fsf_A          457 VSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQ  534 (853)
T ss_dssp             HHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHH
T ss_pred             HHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhh
Confidence            9999985 89999999999999999999999988  699999999999999973                          


Q ss_pred             -----------cEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhh
Q 012133          134 -----------DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       134 -----------~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                                 .+||+|+.|.+...|+||+|||||+|.+|.+++|++..+
T Consensus       535 ~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD  584 (853)
T 2fsf_A          535 VRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMED  584 (853)
T ss_dssp             HHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             hhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccH
Confidence                       599999999999999999999999999999999998776

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

Probab=99.83  E-value=1.2e-21  Score=210.77  Aligned_cols=115  Identities=17%  Similarity=0.254  Sum_probs=103.2

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEE----
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----  138 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~----  138 (470)
                      ..+++||||++++.++.+++.|.. .+.+..|||.    +|+++++.|++++++|||||+++++|||+| +++|||    
T Consensus       409 ~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~  483 (673)
T 2wv9_A          409 YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRKS  483 (673)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCEE
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCCc
Confidence            568999999999999999999985 7899999994    799999999999999999999999999999 999998    


Q ss_pred             ----------------ecCCCChhHHHHHhcccCCC-CCCCeEEEee---ChhhHHHHHHHHHHh
Q 012133          139 ----------------YELPNDPETFVHRSGRTGRA-GKEGTAILMF---TSSQRRTVRSLERDV  183 (470)
Q Consensus       139 ----------------~~~p~~~~~y~qr~GR~gR~-g~~g~~i~l~---~~~~~~~~~~i~~~~  183 (470)
                                      |++|.+.++|+||+||+||. +++|.|++|+   ++.+...++.++..+
T Consensus       484 ~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~  548 (673)
T 2wv9_A          484 VKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKI  548 (673)
T ss_dssp             CCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHH
T ss_pred             ccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHH
Confidence                            67899999999999999999 7999999996   466666666666554

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.83  E-value=3.8e-20  Score=209.29  Aligned_cols=116  Identities=25%  Similarity=0.408  Sum_probs=97.8

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CC---------------------------------------cEEEEeCCCCHHHH
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-II---------------------------------------ASEALHGDISQHQR  103 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~---------------------------------------~~~~lhg~~~~~~R  103 (470)
                      ...++||||++++.|+.++..|.. .+                                       .+.++||+|++.+|
T Consensus       440 ~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R  519 (1108)
T 3l9o_A          440 KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILK  519 (1108)
T ss_dssp             TCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHH
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHH
Confidence            346999999999999999998853 11                                       17999999999999


Q ss_pred             HHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC--------ChhHHHHHhcccCCCC--CCCeEEEeeChh-h
Q 012133          104 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN--------DPETFVHRSGRTGRAG--KEGTAILMFTSS-Q  172 (470)
Q Consensus       104 ~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~--------~~~~y~qr~GR~gR~g--~~g~~i~l~~~~-~  172 (470)
                      +.+++.|++|.++|||||+++++|||+|++++||+++.|+        ++.+|+||+|||||.|  ..|.||+++.+. +
T Consensus       520 ~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~~~  599 (1108)
T 3l9o_A          520 EVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKME  599 (1108)
T ss_dssp             HHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCCCC
T ss_pred             HHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCCcC
Confidence            9999999999999999999999999999999999877644        6667999999999999  689999998875 3


Q ss_pred             HHHHHHH
Q 012133          173 RRTVRSL  179 (470)
Q Consensus       173 ~~~~~~i  179 (470)
                      ...++.+
T Consensus       600 ~~~~~~l  606 (1108)
T 3l9o_A          600 PQVAKGM  606 (1108)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4444444

>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=99.83  E-value=2.2e-20  Score=197.50  Aligned_cols=124  Identities=20%  Similarity=0.337  Sum_probs=69.5

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhcC-------------CcEEEEeCCCCHHHHHHHHccccc
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI-------------IASEALHGDISQHQRERTLNGFRQ  112 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~~-------------~~~~~lhg~~~~~~R~~~~~~f~~  112 (470)
                      ..|...|.++|...   ....++||||+++..++.|++.|...             .....+|++|++++|.+++++|++
T Consensus       371 ~~K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~  450 (556)
T 4a2p_A          371 NPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKT  450 (556)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC---------------------------
T ss_pred             ChHHHHHHHHHHHHhcCCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcc
Confidence            56788888887543   56789999999999999999999742             234566788999999999999999


Q ss_pred             -CCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHH
Q 012133          113 -GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRR  174 (470)
Q Consensus       113 -g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~  174 (470)
                       ++++|||||+++++|||+|+|++||+||+|+++..|+||+|| ||. ++|.+++|+++.+..
T Consensus       451 ~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~  511 (556)
T 4a2p_A          451 SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  511 (556)
T ss_dssp             ---CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHHHH
T ss_pred             cCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcchH
Confidence             999999999999999999999999999999999999999999 999 899999999986643

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

Probab=99.83  E-value=5.7e-20  Score=200.89  Aligned_cols=115  Identities=27%  Similarity=0.469  Sum_probs=99.5

Q ss_pred             HHHHHcCCCeEEEEeCchHHHHHHHHHHhcC-------------------------------------CcEEEEeCCCCH
Q 012133           58 LITVYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------------IASEALHGDISQ  100 (470)
Q Consensus        58 ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~~-------------------------------------~~~~~lhg~~~~  100 (470)
                      +.+.+...+++||||+++++++.+++.|.+.                                     ..+.++|++|++
T Consensus       245 ~~~~~~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~  324 (715)
T 2va8_A          245 TLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSK  324 (715)
T ss_dssp             HHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCH
T ss_pred             HHHHHhcCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCH
Confidence            3344456789999999999999999998742                                     248999999999


Q ss_pred             HHHHHHHcccccCCeeEEEecccccccCCCCCccEEEE----ec-------CCCChhHHHHHhcccCCCC--CCCeEEEe
Q 012133          101 HQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE-------LPNDPETFVHRSGRTGRAG--KEGTAILM  167 (470)
Q Consensus       101 ~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~----~~-------~p~~~~~y~qr~GR~gR~g--~~g~~i~l  167 (470)
                      ++|..+++.|++|.++|||||+++++|||+|++++||+    ||       .|.+..+|+||+||+||.+  .+|.|+++
T Consensus       325 ~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l  404 (715)
T 2va8_A          325 ALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVV  404 (715)
T ss_dssp             HHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEE
T ss_pred             HHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEE
Confidence            99999999999999999999999999999999999999    99       8999999999999999987  58999999


Q ss_pred             eChhh
Q 012133          168 FTSSQ  172 (470)
Q Consensus       168 ~~~~~  172 (470)
                      ++..+
T Consensus       405 ~~~~~  409 (715)
T 2va8_A          405 VRDKE  409 (715)
T ss_dssp             CSCGG
T ss_pred             eCCch
Confidence            98765

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.83  E-value=3.4e-20  Score=202.77  Aligned_cols=127  Identities=24%  Similarity=0.344  Sum_probs=107.8

Q ss_pred             HcCCCeEEEEeCchHHHHHHHHHHhcC----------------------------------CcEEEEeCCCCHHHHHHHH
Q 012133           62 YAKGGKTIVFTQTKRDADEVSLALTSI----------------------------------IASEALHGDISQHQRERTL  107 (470)
Q Consensus        62 ~~~~~~~lVF~~t~~~~~~l~~~l~~~----------------------------------~~~~~lhg~~~~~~R~~~~  107 (470)
                      +.+.+++||||++++.++.++..|.+.                                  ..+.++|++|++++|..++
T Consensus       234 ~~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~  313 (720)
T 2zj8_A          234 IRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVE  313 (720)
T ss_dssp             HHTTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHH
T ss_pred             HhCCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHH
Confidence            346689999999999999999988631                                  2489999999999999999


Q ss_pred             cccccCCeeEEEecccccccCCCCCccEEEE----ec----CCCChhHHHHHhcccCCCC--CCCeEEEeeChhhHHHHH
Q 012133          108 NGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE----LPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVR  177 (470)
Q Consensus       108 ~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~----~~----~p~~~~~y~qr~GR~gR~g--~~g~~i~l~~~~~~~~~~  177 (470)
                      +.|++|.++|||||+++++|||+|++++||+    ||    .|.+..+|+||+||+||.+  ..|.|+++++..+..  .
T Consensus       314 ~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~--~  391 (720)
T 2zj8_A          314 ENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPR--E  391 (720)
T ss_dssp             HHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSCHH--H
T ss_pred             HHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCccHH--H
Confidence            9999999999999999999999999999998    77    6899999999999999987  579999999987622  2


Q ss_pred             HHHHHhCCCcccc
Q 012133          178 SLERDVGCKFEFV  190 (470)
Q Consensus       178 ~i~~~~~~~~~~~  190 (470)
                      .+++.+...++.+
T Consensus       392 ~~~~~~~~~~~~i  404 (720)
T 2zj8_A          392 VMNHYIFGKPEKL  404 (720)
T ss_dssp             HHHHHTTSCCCCC
T ss_pred             HHHHHhcCCCCCc
Confidence            3344554444444

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

Probab=99.83  E-value=2.4e-20  Score=210.90  Aligned_cols=182  Identities=20%  Similarity=0.352  Sum_probs=136.4

Q ss_pred             CEEeec-CCHHHHH-HHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHH
Q 012133            1 MLFSAT-MPSWVKK-LSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDA   78 (470)
Q Consensus         1 llfSAT-lp~~i~~-l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~   78 (470)
                      |+|||| .|..+.. +.+.++.    +.+.  .......++.+.++.+   ++...|..+++..  +.++||||++++.+
T Consensus       254 ll~SAT~~p~~~~~~~~~~~l~----i~v~--~~~~~~~~i~~~~~~~---~k~~~L~~ll~~~--~~~~LVF~~s~~~a  322 (1104)
T 4ddu_A          254 VVSSATAKPRGIRPLLFRDLLN----FTVG--RLVSVARNITHVRISS---RSKEKLVELLEIF--RDGILIFAQTEEEG  322 (1104)
T ss_dssp             EEECBSSCCCSSTTHHHHHHTC----CCCC--BCCCCCCCEEEEEESC---CCHHHHHHHHHHH--CSSEEEEESSSHHH
T ss_pred             EEEcCCCCcHHHHHHHhhccee----EEec--cCCCCcCCceeEEEec---CHHHHHHHHHHhc--CCCEEEEECcHHHH
Confidence            589999 6766553 3333333    3322  2334466788888766   4566667777664  38999999999999


Q ss_pred             HHHHHHHhc-CCcEE-EEeCCCCHHHHHHHHcccccCCeeEEEe----cccccccCCCCC-ccEEEEecCCC--------
Q 012133           79 DEVSLALTS-IIASE-ALHGDISQHQRERTLNGFRQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELPN--------  143 (470)
Q Consensus        79 ~~l~~~l~~-~~~~~-~lhg~~~~~~R~~~~~~f~~g~~~iLVa----Tdv~~~Gidip~-v~~VI~~~~p~--------  143 (470)
                      +.++..|.. ++.+. .+||+     |++ +++|++|+++||||    |+++++|||+|+ |++|||||+|.        
T Consensus       323 ~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~~~~Sle~~  396 (1104)
T 4ddu_A          323 KELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSMRFSLELD  396 (1104)
T ss_dssp             HHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSCSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCEEEEECSSS
T ss_pred             HHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCCCEEEEecCCCCeeEecCcCCCCCCEEEEECCCCCCCCcccc
Confidence            999999985 78898 99993     555 99999999999999    999999999999 99999999998        


Q ss_pred             ----------------------------------------------------------------ChhHHHHHhcccCCCC
Q 012133          144 ----------------------------------------------------------------DPETFVHRSGRTGRAG  159 (470)
Q Consensus       144 ----------------------------------------------------------------~~~~y~qr~GR~gR~g  159 (470)
                                                                                      |..+|+||+|||||.+
T Consensus       397 ~~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~i~~~~~~l~~~~~~~~~~~pd~~tYihr~GRtgR~~  476 (1104)
T 4ddu_A          397 KAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVVKDEDLELIIPDVYTYIQASGRSSRIL  476 (1104)
T ss_dssp             SCCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCSSEEETTTTEEEEECHHHHHHHHHTTCCEE
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHhhccceEEecCCeeEEEecChhhhhcccCchhccc
Confidence                                                                            8889999999999954


Q ss_pred             ----CCCeEEEeeChhhHHHHHHHHHHhC----CCccccCCCCHHHHHHH
Q 012133          160 ----KEGTAILMFTSSQRRTVRSLERDVG----CKFEFVSPPVVEDVLES  201 (470)
Q Consensus       160 ----~~g~~i~l~~~~~~~~~~~i~~~~~----~~~~~~~~p~~~~~~~~  201 (470)
                          ..|.+++++  ++...++.|++.+.    ..+..+.....+++++.
T Consensus       477 ~gg~~~Glsi~~~--~d~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  524 (1104)
T 4ddu_A          477 NGVLVKGVSVIFE--EDEEIFESLKTRLLLIAEEEIIEEAEANWKELVHE  524 (1104)
T ss_dssp             TTEECCEEEEEEC--CCHHHHHHHHHHHHHHTCCCEEEGGGCCHHHHHHH
T ss_pred             CCCcccceEEEEE--ecHHHHHHHHHHHhhhcccccccccccCHHHHHHH
Confidence                356777777  55566777766664    34444443444554443

>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=99.83  E-value=6.5e-20  Score=202.62  Aligned_cols=123  Identities=20%  Similarity=0.338  Sum_probs=72.2

Q ss_pred             cHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhcC-------------CcEEEEeCCCCHHHHHHHHccccc-
Q 012133           50 SKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI-------------IASEALHGDISQHQRERTLNGFRQ-  112 (470)
Q Consensus        50 ~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~~-------------~~~~~lhg~~~~~~R~~~~~~f~~-  112 (470)
                      .|...|..+|...   ....++||||+++..++.|++.|...             ..+..+|++|++.+|.+++++|++ 
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            3555566666532   45689999999999999999999742             345667899999999999999999 


Q ss_pred             CCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHH
Q 012133          113 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRR  174 (470)
Q Consensus       113 g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~  174 (470)
                      +.++|||||+++++|||+|+|++||+||+|+++..|+||+|| ||. ++|.+++|+++.+..
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 899999999886643

>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=99.83  E-value=2.2e-20  Score=193.07  Aligned_cols=123  Identities=33%  Similarity=0.545  Sum_probs=109.3

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeC--------CCCHHHHHHHHcccccCCee
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHG--------DISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg--------~~~~~~R~~~~~~f~~g~~~  116 (470)
                      ..|...|.++|..+   ....++||||++++.++.+++.|.. ++.+..+||        +|++++|++++++|++++.+
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            34666667777654   4678999999999999999999985 789999999        99999999999999999999


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhh
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      |||||+++++|||+|++++||+|++|+++..|+||+||++|.|+ |.+++|+++.+
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            99999999999999999999999999999999999999999987 99999998754

>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=99.82  E-value=8.9e-20  Score=195.91  Aligned_cols=164  Identities=21%  Similarity=0.212  Sum_probs=133.1

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceE-EEEEEcCcccHHHHHHHHHHH-HcCCCeEEEEeCchHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIK-LYAISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~-~~~~~~~~~~k~~~l~~ll~~-~~~~~~~lVF~~t~~~~~~   80 (470)
                      ||.|+..+...+.+.|-.+  ++.+..   ......+. ..++.+....|..+|...+.. +....++||||+|++.++.
T Consensus       401 MTGTa~te~~Ef~~iY~l~--vv~IPt---n~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~  475 (922)
T 1nkt_A          401 MTGTAQTEAAELHEIYKLG--VVSIPT---NMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEY  475 (922)
T ss_dssp             EESCCGGGHHHHHHHHCCE--EEECCC---SSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHH
T ss_pred             cccCchhHHHHHHHHhCCC--eEEeCC---CCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHH
Confidence            7899988888888877433  343321   11122222 124456667888888777754 4456789999999999999


Q ss_pred             HHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCc--------------------------
Q 012133           81 VSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV--------------------------  133 (470)
Q Consensus        81 l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v--------------------------  133 (470)
                      |+..|.+ ++++.+||+++.+.++..+.+.|+.|  .|+||||+|+||+||+.+                          
T Consensus       476 Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  553 (922)
T 1nkt_A          476 LSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYE  553 (922)
T ss_dssp             HHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHH
T ss_pred             HHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhH
Confidence            9999985 89999999999888888888999987  699999999999999975                          


Q ss_pred             --------------------------cEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhH
Q 012133          134 --------------------------DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       134 --------------------------~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                                                .+||+|+.|.+...|+||+|||||+|.+|.+++|++..+.
T Consensus       554 ~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          554 AAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHH
Confidence                                      4999999999999999999999999999999999987664

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

Probab=99.82  E-value=3e-19  Score=200.30  Aligned_cols=116  Identities=25%  Similarity=0.416  Sum_probs=103.1

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CC---------------------------------------cEEEEeCCCCHHHH
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-II---------------------------------------ASEALHGDISQHQR  103 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~---------------------------------------~~~~lhg~~~~~~R  103 (470)
                      ...++||||+++..|+.+++.|.. .+                                       .+.++||+|++.+|
T Consensus       342 ~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR  421 (1010)
T 2xgj_A          342 KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILK  421 (1010)
T ss_dssp             TCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHH
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHH
Confidence            345899999999999999988864 22                                       27899999999999


Q ss_pred             HHHHcccccCCeeEEEecccccccCCCCCccEEEE----ecC----CCChhHHHHHhcccCCCCC--CCeEEEeeChh-h
Q 012133          104 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YEL----PNDPETFVHRSGRTGRAGK--EGTAILMFTSS-Q  172 (470)
Q Consensus       104 ~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~----~~~----p~~~~~y~qr~GR~gR~g~--~g~~i~l~~~~-~  172 (470)
                      +.+++.|++|.++|||||+++++|||+|++++||+    ||.    |.++.+|+||+||+||.|.  .|.|++++++. +
T Consensus       422 ~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e  501 (1010)
T 2xgj_A          422 EVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKME  501 (1010)
T ss_dssp             HHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCC
T ss_pred             HHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCC
Confidence            99999999999999999999999999999999999    999    8999999999999999985  59999999865 5


Q ss_pred             HHHHHHH
Q 012133          173 RRTVRSL  179 (470)
Q Consensus       173 ~~~~~~i  179 (470)
                      ...++.+
T Consensus       502 ~~~~~~l  508 (1010)
T 2xgj_A          502 PQVAKGM  508 (1010)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4555554

>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=99.82  E-value=1.8e-20  Score=199.42  Aligned_cols=123  Identities=25%  Similarity=0.380  Sum_probs=106.0

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEE-----
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----  137 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI-----  137 (470)
                      ..+++||||+|++.++++++.|.+ ++.+..+||+|++++       |+++..+||||||++++|||+| |++||     
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~  466 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTC  466 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEE
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCcc
Confidence            568999999999999999999985 789999999999875       4455669999999999999997 99988     


Q ss_pred             -----Eec-----------CCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHH--H--HHHHHHhCCCccccCCCCHH
Q 012133          138 -----HYE-----------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT--V--RSLERDVGCKFEFVSPPVVE  196 (470)
Q Consensus       138 -----~~~-----------~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~--~--~~i~~~~~~~~~~~~~p~~~  196 (470)
                           |||           +|.+.++|+||+||+|| +++|. ++|+++.+...  +  +.|++..+..+.+..+|..+
T Consensus       467 ~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~~~l~~~~i~~~~~~~~~~~~l~~~~  543 (666)
T 3o8b_A          467 VTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGERPSGMFDSSVLCECYDAGCAWYELTPAE  543 (666)
T ss_dssp             EEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCCBCSSBCCHHHHHHHHHHHHHTSCCCHHH
T ss_pred             cccccccccccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecchhhcccccHHHHHHHhcCCcccccCCchH
Confidence                 677           89999999999999999 89999 99998877554  4  77777777777777666543

>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=99.82  E-value=1.9e-21  Score=201.51  Aligned_cols=102  Identities=19%  Similarity=0.318  Sum_probs=92.9

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEE-----
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-----  138 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~-----  138 (470)
                      .+++||||++++.++.+++.|.. ++.+..+|++    +|+++++.|++++.+|||||+++++|||+|+ ++||+     
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~  264 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSV  264 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEEC
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCccc
Confidence            57999999999999999999985 7899999995    7889999999999999999999999999999 99999     


Q ss_pred             ---------------ecCCCChhHHHHHhcccCCCCC-CCeEEEeeChh
Q 012133          139 ---------------YELPNDPETFVHRSGRTGRAGK-EGTAILMFTSS  171 (470)
Q Consensus       139 ---------------~~~p~~~~~y~qr~GR~gR~g~-~g~~i~l~~~~  171 (470)
                                     |++|.+..+|+||+||+||.|+ +|.+++|+++.
T Consensus       265 ~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          265 KPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             CEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             ccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence                           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=99.81  E-value=9.8e-20  Score=207.04  Aligned_cols=164  Identities=18%  Similarity=0.261  Sum_probs=134.1

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      |+||||+++....++...+.++..|...    ......+..+....   .+..++..++..+..++++||||++++.++.
T Consensus       755 l~lSATp~p~~l~~~~~~~~~~~~i~~~----~~~r~~i~~~~~~~---~~~~i~~~il~~l~~g~qvlvf~~~v~~~~~  827 (1151)
T 2eyq_A          755 LTLTATPIPRTLNMAMSGMRDLSIIATP----PARRLAVKTFVREY---DSMVVREAILREILRGGQVYYLYNDVENIQK  827 (1151)
T ss_dssp             EEEESSCCCHHHHHHHTTTSEEEECCCC----CCBCBCEEEEEEEC---CHHHHHHHHHHHHTTTCEEEEECCCSSCHHH
T ss_pred             EEEcCCCChhhHHHHHhcCCCceEEecC----CCCccccEEEEecC---CHHHHHHHHHHHHhcCCeEEEEECCHHHHHH
Confidence            5799999887777776666655444321    11123444444432   3445556666666678999999999999999


Q ss_pred             HHHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecC-CCChhHHHHHhcccC
Q 012133           81 VSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL-PNDPETFVHRSGRTG  156 (470)
Q Consensus        81 l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~-p~~~~~y~qr~GR~g  156 (470)
                      +++.|.+   .+.+..+||+|++.+|++++++|++++++|||||+++++|||+|++++||+++. ++++..|+||+||+|
T Consensus       828 l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~~~~~~~l~~l~Qr~GRvg  907 (1151)
T 2eyq_A          828 AAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVG  907 (1151)
T ss_dssp             HHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCC
T ss_pred             HHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEeCCCCCCHHHHHHHHhccC
Confidence            9999985   468999999999999999999999999999999999999999999999999988 579999999999999


Q ss_pred             CCCCCCeEEEeeChh
Q 012133          157 RAGKEGTAILMFTSS  171 (470)
Q Consensus       157 R~g~~g~~i~l~~~~  171 (470)
                      |.++.|.|++++.+.
T Consensus       908 R~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          908 RSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             BTTBCEEEEEEECCG
T ss_pred             cCCCceEEEEEECCc
Confidence            999999999998764

>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=99.81  E-value=3.8e-20  Score=191.40  Aligned_cols=101  Identities=19%  Similarity=0.304  Sum_probs=93.5

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEec---
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE---  140 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~---  140 (470)
                      .+++||||+|++.++.+++.|.+ ++.+..+|+++.    +++++.|++++.+|||||+++++|||+|+ ++||||+   
T Consensus       188 ~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~  262 (451)
T 2jlq_A          188 QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCL  262 (451)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEE
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcc
Confidence            57999999999999999999985 788999999853    57999999999999999999999999999 9999998   


Q ss_pred             -----------------CCCChhHHHHHhcccCCCCC-CCeEEEeeCh
Q 012133          141 -----------------LPNDPETFVHRSGRTGRAGK-EGTAILMFTS  170 (470)
Q Consensus       141 -----------------~p~~~~~y~qr~GR~gR~g~-~g~~i~l~~~  170 (470)
                                       .|.+.++|+||+||+||.|+ +|.+++|+..
T Consensus       263 ~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          263 KPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             EEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             cccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence                             99999999999999999997 8899888754

>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=99.81  E-value=2.8e-20  Score=202.70  Aligned_cols=103  Identities=28%  Similarity=0.518  Sum_probs=89.0

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-------CCcEEEEeCC--------CCHHHHHHHHcccccCCeeEEEecccccccCC
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-------IIASEALHGD--------ISQHQRERTLNGFRQGKFTVLVATDVAARGLD  129 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-------~~~~~~lhg~--------~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gid  129 (470)
                      ..++||||++++.++.|++.|..       ++.+..+||+        |++.+|.+++++|++++++|||||+++++|||
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       4889999999        99999999999999999999999999999999


Q ss_pred             CCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          130 IPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       130 ip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                      +|+|++||+||+|+++..|+||+||++|.|   .+++++..
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            999999999999999999999999975543   55555443

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

Probab=99.81  E-value=4.2e-20  Score=195.17  Aligned_cols=129  Identities=24%  Similarity=0.355  Sum_probs=92.1

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhcC-----Cc--------EEEEeCCCCHHHHHHHHccccc
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI-----IA--------SEALHGDISQHQRERTLNGFRQ  112 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~~-----~~--------~~~lhg~~~~~~R~~~~~~f~~  112 (470)
                      ..|...|..+|...   ....++||||++++.++.|++.|...     +.        ...+||+|++++|.+++++|++
T Consensus       370 ~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~  449 (555)
T 3tbk_A          370 NPKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRA  449 (555)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC------------------------
T ss_pred             CHHHHHHHHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhc
Confidence            46777888877643   35689999999999999999999742     33        3445669999999999999999


Q ss_pred             -CCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHH
Q 012133          113 -GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       113 -g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i  179 (470)
                       ++++|||||+++++|||+|+|++||+||+|+++..|+||+|| ||. +.|.+++|+++.+......+
T Consensus       450 ~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~~~~  515 (555)
T 3tbk_A          450 SGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIEKEKA  515 (555)
T ss_dssp             --CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHHHHHHHH
T ss_pred             CCCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCHHHHHHH
Confidence             999999999999999999999999999999999999999999 999 89999999998776544443

>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=99.79  E-value=5e-20  Score=200.78  Aligned_cols=172  Identities=17%  Similarity=0.279  Sum_probs=124.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchH----
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKR----   76 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~----   76 (470)
                      |+||||+++....+.  +..+.....+. . .......+..++  .+......++..+.+......+++|||++.+    
T Consensus       520 L~mSATp~p~tl~~~--~~g~~~~s~i~-~-~p~~r~~i~~~~--~~~~~~~~l~~~i~~~l~~g~qvlVf~~~ie~se~  593 (780)
T 1gm5_A          520 LVMSATPIPRSMALA--FYGDLDVTVID-E-MPPGRKEVQTML--VPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDK  593 (780)
T ss_dssp             EEEESSCCCHHHHHH--HTCCSSCEEEC-C-CCSSCCCCEECC--CCSSTHHHHHHHHHHHTTTSCCBCCBCCCC-----
T ss_pred             EEEeCCCCHHHHHHH--HhCCcceeeee-c-cCCCCcceEEEE--eccchHHHHHHHHHHHHhcCCcEEEEecchhhhhh
Confidence            589999877654433  33332211111 1 111112333322  2333444444445455566789999999764    


Q ss_pred             ----HHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCC-ChhH
Q 012133           77 ----DADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-DPET  147 (470)
Q Consensus        77 ----~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~  147 (470)
                          .++.+++.|..    .+.+..+||+|++++|++++++|++|+++|||||+++++|||+|++++||++++|. +...
T Consensus       594 l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDiP~v~~VIi~d~~r~~l~~  673 (780)
T 1gm5_A          594 LNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQ  673 (780)
T ss_dssp             ---CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTH
T ss_pred             hhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccccCCCCCEEEEeCCCCCCHHH
Confidence                46778888876    35789999999999999999999999999999999999999999999999999996 7889


Q ss_pred             HHHHhcccCCCCCCCeEEEeeChhhHHHHHH
Q 012133          148 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRS  178 (470)
Q Consensus       148 y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~  178 (470)
                      |+||+||+||.+++|.|++++++.+....+.
T Consensus       674 l~Qr~GRaGR~g~~g~~ill~~~~~~~~~~r  704 (780)
T 1gm5_A          674 LHQLRGRVGRGGQEAYCFLVVGDVGEEAMER  704 (780)
T ss_dssp             HHHHHHTSCCSSTTCEEECCCCSCCHHHHHH
T ss_pred             HHHHhcccCcCCCCCEEEEEECCCChHHHHH
Confidence            9999999999999999999998533333333

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

Probab=99.78  E-value=4.1e-19  Score=170.98  Aligned_cols=124  Identities=15%  Similarity=0.273  Sum_probs=97.1

Q ss_pred             CcccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHhc--CCcEEEEeCCCCHHHHHHHHcccccC-Cee-EEEec
Q 012133           47 TATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQG-KFT-VLVAT  121 (470)
Q Consensus        47 ~~~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~~--~~~~~~lhg~~~~~~R~~~~~~f~~g-~~~-iLVaT  121 (470)
                      ....|+..|.++|... ..+.++||||+++..++.|+..|..  ++.+..+||++++++|.++++.|+++ .++ +||+|
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            4568999999988654 4568999999999999999999974  78899999999999999999999998 676 78999


Q ss_pred             ccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeE--EEeeCh
Q 012133          122 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA--ILMFTS  170 (470)
Q Consensus       122 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~--i~l~~~  170 (470)
                      +++++|||++.+++||+||+||++..|+||+||++|.|+...+  +.|++.
T Consensus       173 ~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~  223 (271)
T 1z5z_A          173 KAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISV  223 (271)
T ss_dssp             CTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEET
T ss_pred             hhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeC
Confidence            9999999999999999999999999999999999999977665  444444

>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=99.77  E-value=1.5e-18  Score=194.40  Aligned_cols=123  Identities=20%  Similarity=0.345  Sum_probs=75.5

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhcC-------------CcEEEEeCCCCHHHHHHHHccccc
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI-------------IASEALHGDISQHQRERTLNGFRQ  112 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~~-------------~~~~~lhg~~~~~~R~~~~~~f~~  112 (470)
                      ..|...|.++|...   ....++||||++++.++.|++.|...             ..+..+||+|++.+|.+++++|++
T Consensus       612 ~~K~~~L~~lL~~~~~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~  691 (936)
T 4a2w_A          612 NPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKT  691 (936)
T ss_dssp             CHHHHHHHHHHHHTTTSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC--------------------------
T ss_pred             CHHHHHHHHHHHHHhccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhc
Confidence            46778888888664   35689999999999999999999842             235567899999999999999999


Q ss_pred             -CCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhH
Q 012133          113 -GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  173 (470)
Q Consensus       113 -g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~  173 (470)
                       +.++|||||+++++|||+|+|++||+||+|+++..|+||+|| ||. +.|.+++|++..+.
T Consensus       692 ~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~  751 (936)
T 4a2w_A          692 SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  751 (936)
T ss_dssp             --CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHHH
T ss_pred             cCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCH
Confidence             999999999999999999999999999999999999999999 999 88999999987654

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

Probab=99.76  E-value=4.7e-19  Score=182.11  Aligned_cols=100  Identities=19%  Similarity=0.283  Sum_probs=88.7

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccE-------
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL-------  135 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~-------  135 (470)
                      ..+++||||++++.++.+++.|.+ .+.+..+||+    +|++++++|++++++|||||+++++|||+| +.+       
T Consensus       170 ~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~  244 (431)
T 2v6i_A          170 FDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKT  244 (431)
T ss_dssp             CSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCcc
Confidence            357999999999999999999985 7899999997    578899999999999999999999999999 554       


Q ss_pred             ----------EEEecCCCChhHHHHHhcccCCCCC-CCeEEEee
Q 012133          136 ----------IIHYELPNDPETFVHRSGRTGRAGK-EGTAILMF  168 (470)
Q Consensus       136 ----------VI~~~~p~~~~~y~qr~GR~gR~g~-~g~~i~l~  168 (470)
                                ||+++.|.+.++|+||+||+||.+. .+.++++.
T Consensus       245 ~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          245 IKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             EEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             ccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence                      6788999999999999999999985 45555554

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

Probab=99.75  E-value=1.1e-17  Score=187.50  Aligned_cols=126  Identities=25%  Similarity=0.327  Sum_probs=101.1

Q ss_pred             HHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CC---------------------------------------cE
Q 012133           52 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-II---------------------------------------AS   91 (470)
Q Consensus        52 ~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~---------------------------------------~~   91 (470)
                      ...|..++... ...++||||++++.|+.++..|.. ++                                       .+
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            33444444443 457999999999999999998864 22                                       47


Q ss_pred             EEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCC---------CChhHHHHHhcccCCCC--C
Q 012133           92 EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP---------NDPETFVHRSGRTGRAG--K  160 (470)
Q Consensus        92 ~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p---------~~~~~y~qr~GR~gR~g--~  160 (470)
                      .++|++|++.+|+.+++.|++|.++|||||+++++|||+|++.+|| +++|         .++.+|+||+|||||.|  .
T Consensus       403 ~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~~~VVi-~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~  481 (997)
T 4a4z_A          403 AVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTVIF-SSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDS  481 (997)
T ss_dssp             EEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCCSEEEE-SCSEEEETTEEEECCHHHHHHHHGGGCCTTTCS
T ss_pred             eeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCCceEEE-eccccccCccCCCCCHHHHhHHhcccccCCCCc
Confidence            9999999999999999999999999999999999999999955544 4444         49999999999999988  6


Q ss_pred             CCeEEEeeC--hhhHHHHHHH
Q 012133          161 EGTAILMFT--SSQRRTVRSL  179 (470)
Q Consensus       161 ~g~~i~l~~--~~~~~~~~~i  179 (470)
                      .|.||+++.  ..+...++.+
T Consensus       482 ~G~vi~l~~~~~~~~~~~~~~  502 (997)
T 4a4z_A          482 TGTVIVMAYNSPLSIATFKEV  502 (997)
T ss_dssp             SEEEEEECCSSCCCHHHHHHH
T ss_pred             ceEEEEecCCCcchHHHHHHH
Confidence            788888883  3344555544

>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=99.75  E-value=5.8e-20  Score=191.03  Aligned_cols=114  Identities=25%  Similarity=0.452  Sum_probs=101.7

Q ss_pred             cccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccccccc
Q 012133           48 ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG  127 (470)
Q Consensus        48 ~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~G  127 (470)
                      ...|...|.+++... ...++||||++++.++.+++.|.    +..+|+++++.+|++++++|++++++|||||+++++|
T Consensus       333 ~~~k~~~l~~~l~~~-~~~k~lvF~~~~~~~~~l~~~l~----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~G  407 (472)
T 2fwr_A          333 SKNKIRKLREILERH-RKDKIIIFTRHNELVYRISKVFL----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEG  407 (472)
T ss_dssp             CSHHHHHHHHHHHHT-SSSCBCCBCSCHHHHHHHHHHTT----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSS
T ss_pred             ChHHHHHHHHHHHhC-CCCcEEEEECCHHHHHHHHHHhC----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcC
Confidence            345677888888774 57899999999999999999874    6679999999999999999999999999999999999


Q ss_pred             CCCCCccEEEEecCCCChhHHHHHhcccCCCCCC-CeEEE
Q 012133          128 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE-GTAIL  166 (470)
Q Consensus       128 idip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~-g~~i~  166 (470)
                      +|+|++++||++++|+++..|+||+||++|.++. ..+++
T Consensus       408 ldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i  447 (472)
T 2fwr_A          408 IDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVL  447 (472)
T ss_dssp             SCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEE
T ss_pred             cccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEE
Confidence            9999999999999999999999999999999844 34443

>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=99.74  E-value=2e-17  Score=193.68  Aligned_cols=176  Identities=15%  Similarity=0.203  Sum_probs=130.0

Q ss_pred             CEEeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEEEEEEcCcccHH-------HHHHHHHHHHcCCCeEEEEeC
Q 012133            1 MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKR-------TILSDLITVYAKGGKTIVFTQ   73 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~~~~~~~~~~k~-------~~l~~ll~~~~~~~~~lVF~~   73 (470)
                      |+||||+|+ .++++++.-.++..+........  +..++++....+.....       ..+...+..+...+++||||+
T Consensus      1087 I~lSATl~N-~~dla~WL~~~~~~~~~~~~~~R--PvpL~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~lVF~~ 1163 (1724)
T 4f92_B         1087 VALSSSLSN-AKDVAHWLGCSATSTFNFHPNVR--PVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVP 1163 (1724)
T ss_dssp             EEEESCBTT-HHHHHHHHTCCSTTEEECCGGGC--SSCEEEEEEEECCCSHHHHHHTTHHHHHHHHHHHCSSSCEEEEES
T ss_pred             EEEeCCCCC-HHHHHHHhCCCCCCeEEeCCCCC--CCCeEEEEEeccCCCchhhhhhhcchHHHHHHHhcCCCCeeeeCC
Confidence            579999985 56777765444433322222222  22344433332222221       223344556667789999999


Q ss_pred             chHHHHHHHHHHhc-----------------------------------CCcEEEEeCCCCHHHHHHHHcccccCCeeEE
Q 012133           74 TKRDADEVSLALTS-----------------------------------IIASEALHGDISQHQRERTLNGFRQGKFTVL  118 (470)
Q Consensus        74 t~~~~~~l~~~l~~-----------------------------------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iL  118 (470)
                      |++.|+.++..|..                                   ...+..+|++|++.+|..+++.|++|.++||
T Consensus      1164 sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE~lF~~G~i~VL 1243 (1724)
T 4f92_B         1164 SRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVV 1243 (1724)
T ss_dssp             SHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHHHHHHHTSBCEE
T ss_pred             CHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHHHHHHCCCCeEE
Confidence            99999988876631                                   0258899999999999999999999999999


Q ss_pred             EecccccccCCCCCccEEEE----e------cCCCChhHHHHHhcccCCCCC--CCeEEEeeChhhHHHHHHH
Q 012133          119 VATDVAARGLDIPNVDLIIH----Y------ELPNDPETFVHRSGRTGRAGK--EGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       119 VaTdv~~~Gidip~v~~VI~----~------~~p~~~~~y~qr~GR~gR~g~--~g~~i~l~~~~~~~~~~~i  179 (470)
                      |||+++++|||+|.+.+||.    |      ..|.++.+|+||+|||||+|.  .|.|++++.+.+...++++
T Consensus      1244 vaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~~~~~~~~l 1316 (1724)
T 4f92_B         1244 VASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKF 1316 (1724)
T ss_dssp             EEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGGGHHHHHHH
T ss_pred             EEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecchHHHHHHHH
Confidence            99999999999999999993    2      346789999999999999985  7999999999887777665

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

Probab=99.71  E-value=3.9e-17  Score=175.39  Aligned_cols=122  Identities=20%  Similarity=0.284  Sum_probs=104.2

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHccccc--CCeeEEEecccccccCCCCCccEEEEecC-
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ--GKFTVLVATDVAARGLDIPNVDLIIHYEL-  141 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~--g~~~iLVaTdv~~~Gidip~v~~VI~~~~-  141 (470)
                      ...||||+|+++++.+++.|.+ .+.+.++||+|++++|.++++.|++  +.++|||||+++++|||+ +|++||++++ 
T Consensus       321 ~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~  399 (677)
T 3rc3_A          321 PGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLI  399 (677)
T ss_dssp             TTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSB
T ss_pred             CCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCcc
Confidence            4558899999999999999985 7899999999999999999999999  889999999999999999 8999999999 


Q ss_pred             -------------CCChhHHHHHhcccCCCCCC---CeEEEeeChhhHHHHHHHHHHhCCCccc
Q 012133          142 -------------PNDPETFVHRSGRTGRAGKE---GTAILMFTSSQRRTVRSLERDVGCKFEF  189 (470)
Q Consensus       142 -------------p~~~~~y~qr~GR~gR~g~~---g~~i~l~~~~~~~~~~~i~~~~~~~~~~  189 (470)
                                   |.+..+|+||+|||||.|+.   |.|++++.. +...++.+.......++.
T Consensus       400 k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~~~-d~~~~~~~~~~~~~~i~~  462 (677)
T 3rc3_A          400 KPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNHE-DLSLLKEILKRPVDPIRA  462 (677)
T ss_dssp             C-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESSTT-HHHHHHHHHHSCCCCCCC
T ss_pred             ccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEecc-hHHHHHHHHhcCcchhhh
Confidence                         78999999999999999854   677776554 444556665554444444

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

Probab=99.71  E-value=3.3e-17  Score=175.12  Aligned_cols=101  Identities=21%  Similarity=0.302  Sum_probs=88.5

Q ss_pred             HHHHcCCCeEEEEeCchHHHHHHHHHHhcCC---------cEEEEeCCCCHHHHHHHHcccccCCee---EEEecccccc
Q 012133           59 ITVYAKGGKTIVFTQTKRDADEVSLALTSII---------ASEALHGDISQHQRERTLNGFRQGKFT---VLVATDVAAR  126 (470)
Q Consensus        59 l~~~~~~~~~lVF~~t~~~~~~l~~~l~~~~---------~~~~lhg~~~~~~R~~~~~~f~~g~~~---iLVaTdv~~~  126 (470)
                      +.......++||||++++.|+.+++.|.+..         .+..+||++++ +|++++++|++++.+   |||||+++++
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            3333456899999999999999999997421         27889999864 799999999998766   8999999999


Q ss_pred             cCCCCCccEEEEecCCCChhHHHHHhcccCCCCC
Q 012133          127 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  160 (470)
Q Consensus       127 Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~  160 (470)
                      |||+|++++||++++|+++..|+||+||++|.+.
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            9999999999999999999999999999999764

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

Probab=99.70  E-value=2e-17  Score=173.54  Aligned_cols=117  Identities=14%  Similarity=0.170  Sum_probs=98.4

Q ss_pred             HHHHHHHHHHH-cCC-CeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEec-cccccc
Q 012133           52 RTILSDLITVY-AKG-GKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT-DVAARG  127 (470)
Q Consensus        52 ~~~l~~ll~~~-~~~-~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaT-dv~~~G  127 (470)
                      ...+.+++... ... .++|||++ .+.++.|++.|.+ ...+..+||+|++.+|+++++.|++++.+||||| +++++|
T Consensus       333 ~~~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~G  411 (510)
T 2oca_A          333 NKWIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTG  411 (510)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHS
T ss_pred             HHHHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcc
Confidence            33444554433 233 45666666 8889999999986 4689999999999999999999999999999999 999999


Q ss_pred             CCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeC
Q 012133          128 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT  169 (470)
Q Consensus       128 idip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~  169 (470)
                      ||+|++++||++++|+++..|+||+||+||.++.+.++++++
T Consensus       412 iDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          412 ISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             CCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             cccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            999999999999999999999999999999998775555544

>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=99.70  E-value=3.1e-17  Score=191.96  Aligned_cols=175  Identities=20%  Similarity=0.344  Sum_probs=126.8

Q ss_pred             CEEeecCCHHHHHHHHHHcC-CCc-EEEeecccccccccceEEEEEEcCcccH---HHHHHHHH----HHHcCCCeEEEE
Q 012133            1 MLFSATMPSWVKKLSRKYLD-NPL-NIDLVGNQDEKLAEGIKLYAISTTATSK---RTILSDLI----TVYAKGGKTIVF   71 (470)
Q Consensus         1 llfSATlp~~i~~l~~~~l~-~p~-~i~~~~~~~~~~~~~i~~~~~~~~~~~k---~~~l~~ll----~~~~~~~~~lVF   71 (470)
                      |.+|||+|+ ++++++ |+. ++. .+.+..... + +..++++++.......   ...+..++    ..+....++|||
T Consensus       248 I~LSATl~N-~~dvA~-wL~~~~~~~~~~~~~~~-R-PvpL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~LVF  323 (1724)
T 4f92_B          248 IGLSATLPN-YEDVAT-FLRVDPAKGLFYFDNSF-R-PVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVF  323 (1724)
T ss_dssp             EEEECSCTT-HHHHHH-HTTCCHHHHEEECCGGG-C-SSCEEEECCEECCCCHHHHHHHHHHHHHHHHTTCCSSCCEEEE
T ss_pred             EEEecccCC-HHHHHH-HhCCCCCCCeEEECCCC-c-cCccEEEEeccCCcchhhhhHHHHHHHHHHHHHHhcCCcEEEE
Confidence            579999985 566766 444 322 222222111 1 2345555554444322   22233222    222345799999


Q ss_pred             eCchHHHHHHHHHHhcC--------------------------------------CcEEEEeCCCCHHHHHHHHcccccC
Q 012133           72 TQTKRDADEVSLALTSI--------------------------------------IASEALHGDISQHQRERTLNGFRQG  113 (470)
Q Consensus        72 ~~t~~~~~~l~~~l~~~--------------------------------------~~~~~lhg~~~~~~R~~~~~~f~~g  113 (470)
                      |+|++.|+.+++.|.+.                                      ..+.++|++|++.+|..+++.|++|
T Consensus       324 ~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~~vE~~F~~G  403 (1724)
T 4f92_B          324 VHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADK  403 (1724)
T ss_dssp             CSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHHHHHHHHHCC
Confidence            99999999888877420                                      2478999999999999999999999


Q ss_pred             CeeEEEecccccccCCCCCccEEEE----ecC------CCChhHHHHHhcccCCCC--CCCeEEEeeChhhHHHHHHH
Q 012133          114 KFTVLVATDVAARGLDIPNVDLIIH----YEL------PNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       114 ~~~iLVaTdv~~~Gidip~v~~VI~----~~~------p~~~~~y~qr~GR~gR~g--~~g~~i~l~~~~~~~~~~~i  179 (470)
                      .++|||||+++++|||+|.+++||.    |++      |.++.+|+||+|||||.|  ..|.+++++.+.+...+..+
T Consensus       404 ~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~~~~~~~l  481 (1724)
T 4f92_B          404 HIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSL  481 (1724)
T ss_dssp             CCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTTCCHHHHH
T ss_pred             CCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchhHHHHHHH
Confidence            9999999999999999999999995    543      568999999999999987  57999999988776555554

>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=99.65  E-value=4.8e-16  Score=162.61  Aligned_cols=118  Identities=17%  Similarity=0.305  Sum_probs=101.2

Q ss_pred             ccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHhc--CCcEEEEeCCCCHHHHHHHHcccccC-Cee-EEEeccc
Q 012133           49 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQG-KFT-VLVATDV  123 (470)
Q Consensus        49 ~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~~--~~~~~~lhg~~~~~~R~~~~~~f~~g-~~~-iLVaTdv  123 (470)
                      ..|...+.+++... ..+.++||||+++..++.+++.|..  ++.+..+||++++++|+++++.|+++ ..+ +||+|++
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            56777777777654 4668999999999999999999984  78899999999999999999999988 455 7999999


Q ss_pred             ccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEE
Q 012133          124 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL  166 (470)
Q Consensus       124 ~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~  166 (470)
                      +++|+|+|.+++||+||+||++..|+||+||++|.|+...+++
T Consensus       404 ~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v  446 (500)
T 1z63_A          404 GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIV  446 (500)
T ss_dssp             C-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEE
T ss_pred             ccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEE
Confidence            9999999999999999999999999999999999997766543

>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=99.60  E-value=4.7e-15  Score=159.77  Aligned_cols=134  Identities=12%  Similarity=0.254  Sum_probs=112.0

Q ss_pred             ccHHHHHHHHHHHHc--CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCe---eEEEecc
Q 012133           49 TSKRTILSDLITVYA--KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF---TVLVATD  122 (470)
Q Consensus        49 ~~k~~~l~~ll~~~~--~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~---~iLVaTd  122 (470)
                      +.|+.+|..++....  ...++||||+++..++.|+..|.. ++.+..+||++++++|++++++|+++..   .+||+|+
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            467788888886652  468999999999999999999984 8999999999999999999999999865   4899999


Q ss_pred             cccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEE--eeChh--hHHHHHHHHHH
Q 012133          123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL--MFTSS--QRRTVRSLERD  182 (470)
Q Consensus       123 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~--l~~~~--~~~~~~~i~~~  182 (470)
                      ++++|||++.+++||+||+||++..|+|++||++|.|+...+++  |++..  |...++.++.+
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            99999999999999999999999999999999999997665444  44432  33344444333

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

Probab=99.56  E-value=1.9e-14  Score=158.72  Aligned_cols=137  Identities=18%  Similarity=0.322  Sum_probs=116.2

Q ss_pred             ccHHHHHHHHHHHH-cCCCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCCe---eEEEeccc
Q 012133           49 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKF---TVLVATDV  123 (470)
Q Consensus        49 ~~k~~~l~~ll~~~-~~~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~---~iLVaTdv  123 (470)
                      ..|+.+|..+|..+ ..+.++||||..+..++.|...|. .++.+..|||.+++.+|+++++.|+++..   .+||+|.+
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            46788888888766 345799999999999999999998 48999999999999999999999998554   59999999


Q ss_pred             ccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeE--EEeeChh--hHHHHHHHHHHhCC
Q 012133          124 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA--ILMFTSS--QRRTVRSLERDVGC  185 (470)
Q Consensus       124 ~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~--i~l~~~~--~~~~~~~i~~~~~~  185 (470)
                      ++.|||++.+++||+||+||++..++||+||+.|.|+...+  +.|++..  |...++.+.++...
T Consensus       635 gg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe~i~~~~~~K~~l  700 (800)
T 3mwy_W          635 GGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMIL  700 (800)
T ss_dssp             HTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHHHHHHHHHHHTTS
T ss_pred             ccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999966544  4455543  55666666666543

>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=99.39  E-value=2.1e-12  Score=144.47  Aligned_cols=119  Identities=11%  Similarity=0.110  Sum_probs=92.3

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-C------------CcE-EEEeCC----------C----------CHH---------
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-I------------IAS-EALHGD----------I----------SQH---------  101 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-~------------~~~-~~lhg~----------~----------~~~---------  101 (470)
                      ..++||||+++..|..+++.|.+ .            +.+ .++|++          |          ++.         
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            35899999999999999999864 1            445 455542          2          322         


Q ss_pred             --------------------HHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCC
Q 012133          102 --------------------QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE  161 (470)
Q Consensus       102 --------------------~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~  161 (470)
                                          +|..++++|++++++|||+|+++.+|+|+|.+ .|+++|.|.+...|+|++||++|....
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                                47889999999999999999999999999999 788999999999999999999998743


Q ss_pred             ----CeEEEeeChhhHHHHHHHHHHhCC
Q 012133          162 ----GTAILMFTSSQRRTVRSLERDVGC  185 (470)
Q Consensus       162 ----g~~i~l~~~~~~~~~~~i~~~~~~  185 (470)
                          |.++.|+.. .....+.|..+...
T Consensus       696 ~K~~G~IVdf~~~-~~~l~~Al~~y~~~  722 (1038)
T 2w00_A          696 TKTFGNIVTFRDL-ERSTIDAITLFGDK  722 (1038)
T ss_dssp             TCCSEEEEESSCC-HHHHHHHHHHTSCS
T ss_pred             CCCcEEEEEcccc-HHHHHHHHHHHhCC
Confidence                666666653 33444455444433

>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=99.06  E-value=3.9e-10  Score=88.50  Aligned_cols=89  Identities=22%  Similarity=0.294  Sum_probs=73.7

Q ss_pred             HcCCCCCCCCcccccCCCCeEEEEEeeCCccccCCcchhhHHhHhhhhcC-cCcCccccEEEeecCccceeEeecCHHHH
Q 012133          244 LSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYP-TAADEIGKIHIIADDRVQGAVFDLPEEIA  322 (470)
Q Consensus       244 l~~~~~~~~~r~l~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~-~~~~~Ig~I~i~~~~~~~ga~fdv~~~~a  322 (470)
                      ++|+++ +++|||+++.++++|+.+....    ..-.|..++.+|++..+ ...++|++|++++|.  +|++||||++.+
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----EIQDVSCAWKELNRKLSSNAVSQITRMCLLKGN--MGVCFDVPTTES   74 (92)
T ss_dssp             CCSCSC-CCCCCCCCCCCCEEEEEEECSS----CCSSTHHHHHHHHHHSCHHHHTTCEEEEECTTS--SEEEEEEEHHHH
T ss_pred             CCCcCC-CCCcccccCCCCCEEEEEecCC----cccchHHHHHHHHHhcCHHHHhhhCeEEEecCC--CEEEEECcHHHH
Confidence            467887 5669999999999999998876    35678999999998554 456789999999986  599999999999


Q ss_pred             HHHHhhcCCCCCeEEEe
Q 012133          323 KELLNKQIPPGNTISKI  339 (470)
Q Consensus       323 ~~i~~~~~~~g~~i~~~  339 (470)
                      +++++.+....+.++++
T Consensus        75 ~~~~~~~~~~~~~l~v~   91 (92)
T 2e29_A           75 ERLQAEWHDSDWILSVP   91 (92)
T ss_dssp             HHHHHHCCSSSCEEECC
T ss_pred             HHHHhhCCCCceEEEec
Confidence            99999977634666664

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=98.57  E-value=1.9e-08  Score=59.51  Aligned_cols=17  Identities=47%  Similarity=1.300  Sum_probs=15.9

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+||++||||||||+
T Consensus         4 ~Cf~CG~~GH~ardC~~   20 (26)
T 1dsq_A            4 VCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             BCTTTCCBSSCTTTTTC
T ss_pred             eeEeCCCCCcccccCCC
Confidence            49999999999999995

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.56  E-value=8.4e-07  Score=95.84  Aligned_cols=163  Identities=20%  Similarity=0.220  Sum_probs=111.8

Q ss_pred             EeecCCHHHHHHHHHHcCCCcEEEeecccccccccceEE-EEEEcCcccHHHHH-HHHHHHHcCCCeEEEEeCchHHHHH
Q 012133            3 FSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKL-YAISTTATSKRTIL-SDLITVYAKGGKTIVFTQTKRDADE   80 (470)
Q Consensus         3 fSATlp~~i~~l~~~~l~~p~~i~~~~~~~~~~~~~i~~-~~~~~~~~~k~~~l-~~ll~~~~~~~~~lVF~~t~~~~~~   80 (470)
                      ||.|...+...+.+.|--+.  |.+..   +.+.....+ -.+......|..++ ..+...+..+.++||+|.|.+..+.
T Consensus       384 MTGTA~tE~~Ef~~iY~l~V--v~IPT---n~p~~R~D~~d~vy~t~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE~  458 (997)
T 2ipc_A          384 MTGTAKTEEKEFQEIYGMDV--VVVPT---NRPVIRKDFPDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSER  458 (997)
T ss_dssp             EESSCGGGHHHHHHHHCCCE--EECCC---SSCCCCEEEEEEEESSHHHHHHHHHHHHHHHHHHTCCEEEECSSHHHHHH
T ss_pred             cCCCchHHHHHHHHHhCCCE--EEcCC---CCCcccccCCCeEEcCHHHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHHH
Confidence            78999888888887775552  33321   111121221 22334445666554 4555566778899999999999999


Q ss_pred             HHHHHh--------------------------------------------------------------------------
Q 012133           81 VSLALT--------------------------------------------------------------------------   86 (470)
Q Consensus        81 l~~~l~--------------------------------------------------------------------------   86 (470)
                      |+..|.                                                                          
T Consensus       459 LS~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~  538 (997)
T 2ipc_A          459 LSQMLKEPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLA  538 (997)
T ss_dssp             HHHHHHCGGGGHHHHHHHHHHHHHHHTTCCSHHHHHHHHHTSSSTTCSHHHHSGGGGGCCSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhccccchhhhhhhhhhhhhhhhccccchhhhhhhhhccccccccccccccccccccccccccccccchhhhhhH
Confidence            999887                                                                          


Q ss_pred             --c-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCc-------------------c----------
Q 012133           87 --S-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV-------------------D----------  134 (470)
Q Consensus        87 --~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v-------------------~----------  134 (470)
                        + +++..+|.+.--..+-+.+-+.=+  .-.|-|||++|.||.||.-=                   .          
T Consensus       539 ~~~~gI~H~VLNAK~he~EAeIIAqAG~--~GaVTIATNMAGRGTDIkLggn~e~~~~~~~~~~~~~~~~~~~~~~~~~~  616 (997)
T 2ipc_A          539 VLRQGIPHQVLNAKHHAREAEIVAQAGR--SKTVTIATNMAGRGTDIKLGGNPEYLAAALLEKEGFDRYEWKVELFIKKM  616 (997)
T ss_dssp             HHHHCCCCCEECSSSHHHHHHHHHTTTS--TTCEEEECSSTTTTSCCCSSCCHHHHHHHTTSSSCSSTTHHHHHHHHHHH
T ss_pred             HHHcCCCeeeccccchHHHHHHHHhcCC--CCeEEEEecccCCCcCeecCCCHHHHHHHHHHhhcccccccccccccccc
Confidence              1 355666666633333222222222  34689999999999999522                   1          


Q ss_pred             ---------------------------------------------EEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeC
Q 012133          135 ---------------------------------------------LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT  169 (470)
Q Consensus       135 ---------------------------------------------~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~  169 (470)
                                                                   +||-...+.|...=.|-.||+||.|.+|.+.+|++
T Consensus       617 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~V~e~GGLhVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LS  696 (997)
T 2ipc_A          617 VAGKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVS  696 (997)
T ss_dssp             HHTCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTCCCCEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEE
T ss_pred             cccchhhccccchhhhhhhhHHHHHHHhhhhhhhhhhHHHhcCCeEEEeccCCchHHHHHHHhcccccCCCCCCeEEEEE
Confidence                                                         78999999999999999999999999999988877


Q ss_pred             hhh
Q 012133          170 SSQ  172 (470)
Q Consensus       170 ~~~  172 (470)
                      -.+
T Consensus       697 LeD  699 (997)
T 2ipc_A          697 FDD  699 (997)
T ss_dssp             SSS
T ss_pred             CCh
Confidence            655

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=98.38  E-value=9.6e-08  Score=62.24  Aligned_cols=17  Identities=41%  Similarity=1.085  Sum_probs=15.9

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+|++.||||+|||+
T Consensus        12 ~C~~Cgk~GH~ardCP~   28 (40)
T 1a6b_B           12 QCAYCKEKGHWAKDCPK   28 (40)
T ss_dssp             SCSSSCCTTCCTTSCSS
T ss_pred             eeeECCCCCcchhhCcC
Confidence            39999999999999995

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=98.25  E-value=9.3e-07  Score=57.82  Aligned_cols=16  Identities=50%  Similarity=1.404  Sum_probs=15.6

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||+|+++||+++|||+
T Consensus        24 C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           24 CWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CTTTCCSSSCTTTSCC
T ss_pred             cccCCCCCCccCcCcC
Confidence            9999999999999996

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=98.21  E-value=4.6e-07  Score=65.49  Aligned_cols=47  Identities=19%  Similarity=0.296  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 012133          393 RSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN  470 (470)
Q Consensus       393 ~~~~~~g~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~g~~c~~c~~~gh~~~~c~~  470 (470)
                      +.|++|++.||.++.+........                   .            ......||+|+++||||+|||+
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~~~~~~-------------------~------------~~~~~~C~~Cg~~GH~ar~C~~   48 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEHAHNNA-------------------E------------PKVPGLCPRCKRGKHWANECKS   48 (60)
T ss_dssp             ----------------------------------------------------------CCCSCSSCSSCSSCSTTCCC
T ss_pred             CccccCCCCCcCHhhCcCCCCCcc-------------------c------------cCCCcceeECCCCCCccCcCCC
Confidence            468899999998887754321100                   0            0012239999999999999995

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=98.17  E-value=4.2e-07  Score=55.21  Aligned_cols=17  Identities=53%  Similarity=1.300  Sum_probs=15.6

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .|||||++||+|+|||.
T Consensus         8 ~C~nCgk~GH~ar~C~~   24 (29)
T 1nc8_A            8 RCWNCGKEGHSARQCRA   24 (29)
T ss_dssp             BCTTTSCBSSCGGGCCS
T ss_pred             EEEECCccccCHhHCcc
Confidence            39999999999999984

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=98.13  E-value=5.3e-07  Score=63.40  Aligned_cols=17  Identities=41%  Similarity=1.085  Sum_probs=15.8

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+|||.||||+|||+
T Consensus        25 ~C~~Cge~GH~ardCp~   41 (56)
T 1u6p_A           25 QCAYCKEKGHWAKDCPK   41 (56)
T ss_dssp             BCSSSCCBSSCGGGCTT
T ss_pred             cceeCCCCCcccccCcC
Confidence            39999999999999995

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=98.12  E-value=1.7e-06  Score=55.82  Aligned_cols=16  Identities=38%  Similarity=1.153  Sum_probs=15.5

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||+|+++||+|+|||+
T Consensus        22 C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           22 CFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             CSSCCCTTGGGGTTCC
T ss_pred             EccCCCcCCccCcCcC
Confidence            9999999999999996

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.08  E-value=5e-06  Score=60.49  Aligned_cols=40  Identities=18%  Similarity=0.302  Sum_probs=30.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 012133          393 RSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN  470 (470)
Q Consensus       393 ~~~~~~g~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~g~~c~~c~~~gh~~~~c~~  470 (470)
                      ..|++|++.||..+.+.....                                      ...||+|+++||+|+|||+
T Consensus         8 ~~C~~Cg~~GH~a~~C~~~~~--------------------------------------~~~C~~Cg~~GH~ar~Cp~   47 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKLPPQ--------------------------------------PKKCHFCQSISHMVASCPL   47 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCSCCC--------------------------------------SSCCTTTCCSSSCTTTCTG
T ss_pred             CcccccCCCCcChhhCCCCCC--------------------------------------CCccCCcCCcCCccCcCCC
Confidence            468999999998877743210                                      0129999999999999994

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=98.06  E-value=3e-06  Score=58.35  Aligned_cols=16  Identities=50%  Similarity=1.475  Sum_probs=15.4

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||+|+++||+++|||+
T Consensus        30 C~~Cg~~GH~~~~C~~   45 (49)
T 2ec7_A           30 CWKCGKTGHVMAKCPE   45 (49)
T ss_dssp             CSSSCCSSCCGGGCCS
T ss_pred             eCcCCCcCCccCCCcC
Confidence            9999999999999995

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=98.01  E-value=4.2e-06  Score=63.57  Aligned_cols=61  Identities=16%  Similarity=0.275  Sum_probs=51.6

Q ss_pred             EEEEEeeCCccccCCcchhhHHhHhhhhcCcCcCccccEEEeecCccceeEeecCHHHHHHHHhhcCC
Q 012133          264 VTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIP  331 (470)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~Ig~I~i~~~~~~~ga~fdv~~~~a~~i~~~~~~  331 (470)
                      +|++++.++   ++++.|.+|+++|++...+...+||+|++.+++    +||++|.+.++++++.+..
T Consensus         1 ~~~~i~~Gr---k~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~~----s~v~v~~~~~~~~~~~l~~   61 (76)
T 2g0c_A            1 MKLYFNGGK---KKKIRAVDFVGTIAKIDGVSADDIGIITIMDNA----SYVEILNGKGPHVLKVMKN   61 (76)
T ss_dssp             CEEEESCCC---C----CHHHHHHHHTSTTCCGGGEEEEEECSSC----EEEEECTTCHHHHHHHHTT
T ss_pred             CEEEEeCCC---ccCCCHHHHHHHHHHccCCChhhccEEEEeCCc----EEEEECHHHHHHHHHHhcc
Confidence            367888888   889999999999999999999999999999987    7999999999999987654

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=98.01  E-value=3e-06  Score=61.28  Aligned_cols=44  Identities=20%  Similarity=0.295  Sum_probs=31.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 012133          393 RSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN  470 (470)
Q Consensus       393 ~~~~~~g~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~g~~c~~c~~~gh~~~~c~~  470 (470)
                      ..|+.|++.||.++.+......+                                  .....||+|+++||+|+|||+
T Consensus         5 ~~C~~Cg~~GH~a~~C~~~~~~~----------------------------------~~~~~C~~Cg~~GH~ar~C~~   48 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQCPKKRKSG----------------------------------NSRERCQLCNGMGHNAKQCRK   48 (61)
T ss_dssp             TBCSSSCCBTCCGGGCTTTTSSS----------------------------------CCCSBCTTTCCBSSCGGGCCC
T ss_pred             CcccccCCCCeehhhCcCCcCCC----------------------------------CCCCeeCCCCCCCCCcCCCcC
Confidence            45889999999888775431100                                  001239999999999999995

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=97.99  E-value=9.8e-06  Score=85.14  Aligned_cols=75  Identities=16%  Similarity=0.287  Sum_probs=49.7

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHcccccCCeeEEE--ecccccccCCCCC----ccEEE
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLV--ATDVAARGLDIPN----VDLII  137 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLV--aTdv~~~Gidip~----v~~VI  137 (470)
                      .++.+|||++|....+++++.|.. +. ..+++..  .+|.++++.|+.+. .||+  +|+.+.+|||+|+    +.+||
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            457999999999999999988864 33 4456654  56888999998864 5666  8999999999997    88999


Q ss_pred             EecCCC
Q 012133          138 HYELPN  143 (470)
Q Consensus       138 ~~~~p~  143 (470)
                      ++++|.
T Consensus       458 i~~lPf  463 (540)
T 2vl7_A          458 LAGLPY  463 (540)
T ss_dssp             EESCCC
T ss_pred             EECCCC
Confidence            999985

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.92  E-value=3.4e-06  Score=59.05  Aligned_cols=16  Identities=56%  Similarity=1.481  Sum_probs=15.4

Q ss_pred             ccccCCCCCccCCCCC
Q 012133          454 ACFNCGKSGHRASECP  469 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~  469 (470)
                      .||+||++|||++|||
T Consensus         9 ~C~kCGk~GH~~k~Cp   24 (55)
T 2ysa_A            9 TCFRCGKPGHYIKNCP   24 (55)
T ss_dssp             CCTTTCCTTSCGGGCS
T ss_pred             ccccCCCcCcccccCC
Confidence            4999999999999999

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=97.92  E-value=1.1e-05  Score=60.60  Aligned_cols=16  Identities=31%  Similarity=0.818  Sum_probs=15.4

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||+|+++||+|+|||+
T Consensus        49 C~~Cg~~GH~ar~Cp~   64 (74)
T 2li8_A           49 CHFCQSISHMVASCPL   64 (74)
T ss_dssp             CTTTCCTTSCGGGCTT
T ss_pred             cCCcCCcCCccCcCcC
Confidence            9999999999999995

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=97.89  E-value=4.7e-06  Score=58.95  Aligned_cols=16  Identities=44%  Similarity=1.375  Sum_probs=15.4

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||+|+++||+|+|||+
T Consensus        36 C~~Cg~~GH~~~~C~~   51 (55)
T 1a1t_A           36 CWKCGKEGHQMKDCTE   51 (55)
T ss_dssp             CTTTCCBSSCGGGCSS
T ss_pred             eCCCCCcCCccCCCcC
Confidence            9999999999999995

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=97.88  E-value=9.5e-06  Score=69.77  Aligned_cols=40  Identities=18%  Similarity=0.302  Sum_probs=31.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccCCCCCccCCCCCC
Q 012133          393 RSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN  470 (470)
Q Consensus       393 ~~~~~~g~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~g~~c~~c~~~gh~~~~c~~  470 (470)
                      ..|++||+.||.++.|.....                                      ...||+|+++||++||||+
T Consensus        98 ~~C~~Cg~~GH~a~~C~~~~~--------------------------------------~~~C~~Cg~~GH~~r~Cp~  137 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECKLPPQ--------------------------------------PKKCHFCQSINHMVASCPL  137 (148)
T ss_dssp             CCCTTTCCSSCCGGGCCSCCC--------------------------------------CCCCTTTCCSSCCGGGCTT
T ss_pred             CcccEeCCccchhhhCCCCCC--------------------------------------CCcccccCCcCCEeccCcC
Confidence            569999999998887754210                                      0129999999999999995

>3i31_A Heat resistant RNA dependent ATPase; RNA helicase, RNA recognition motif, ATP-binding, helicase, nucleotide-binding; 1.80A {Thermus thermophilus}

Probab=97.77  E-value=4.6e-05  Score=56.91  Aligned_cols=77  Identities=25%  Similarity=0.350  Sum_probs=60.9

Q ss_pred             CCcccccCCCCeEEEEEeeCCccccCCcchhhHHhHhhhhcCcCcCccccEEEeecCccceeEeecCHHHHHHHHhhcCC
Q 012133          252 SSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIP  331 (470)
Q Consensus       252 ~~r~l~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~Ig~I~i~~~~~~~ga~fdv~~~~a~~i~~~~~~  331 (470)
                      .++||++++++|+|+.+...+      ++...++.+|.+...    +||+|+.+..    |+|.|++.+..+      ..
T Consensus         2 ~~~SLLTGEEGw~Tlkl~G~r------LS~~R~VAlLk~aG~----~iGkI~~~~~----gayaDlr~e~l~------~~   61 (88)
T 3i31_A            2 AERSLLTGEEGWRTYKATGPR------LSLPRLVALLKGQGL----EVGKVAEAEG----GFYVDLRPEARP------EV   61 (88)
T ss_dssp             CCBCTTTCCBSCEEEEEECTT------CCHHHHHHHHHHTTC----CEEEEEEETT----EEEEEECTTCCC------CC
T ss_pred             CcccccccCcceEEEEEeccc------ccHHHHHHHHHHccc----ccccEEeccc----eeEEecChHHcc------cc
Confidence            468999999999999996544      788888888876543    8999998765    699999888766      34


Q ss_pred             CCCeEEEeccCCCccCC
Q 012133          332 PGNTISKITKLPALQDD  348 (470)
Q Consensus       332 ~g~~i~~~~~lP~~~~~  348 (470)
                      .++.++++..+|.+.+.
T Consensus        62 ~~~~~e~A~~v~~~~E~   78 (88)
T 3i31_A           62 AGLRLEPARRVEGLLEI   78 (88)
T ss_dssp             TTCEEEECCSCCCCC--
T ss_pred             ccceehhhhhccccccC
Confidence            78888888888888664

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=97.74  E-value=0.00019  Score=76.56  Aligned_cols=104  Identities=20%  Similarity=0.260  Sum_probs=68.1

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc--cccccCCCCC--ccEEEEe
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATD--VAARGLDIPN--VDLIIHY  139 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd--v~~~Gidip~--v~~VI~~  139 (470)
                      .++.+|||+++....+++++.|. .+... ..-+++..++.+++++|+ +.-.||++|.  .+.+|||+|+  ...||..
T Consensus       447 ~~g~~lvlF~Sy~~l~~v~~~l~-~~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~  523 (620)
T 4a15_A          447 VKKNTIVYFPSYSLMDRVENRVS-FEHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILA  523 (620)
T ss_dssp             HCSCEEEEESCHHHHHHHTSSCC-SCCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEES
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHH-hcchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEE
Confidence            35789999999999999988876 33322 444455668999999999 7888999975  8999999985  5578888


Q ss_pred             cCCCCh-----------------------------hHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          140 ELPNDP-----------------------------ETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       140 ~~p~~~-----------------------------~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                      .+|...                             ..+.|-+||.=|.-..-=++++++.
T Consensus       524 ~lPfp~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~  583 (620)
T 4a15_A          524 GLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDK  583 (620)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECG
T ss_pred             cCCCCCCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEcc
Confidence            877421                             1126889999997533334444444

>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=97.63  E-value=0.00064  Score=65.74  Aligned_cols=120  Identities=13%  Similarity=0.130  Sum_probs=86.3

Q ss_pred             cccHHHHHHHHHHHHc-CCCeEEEEeCchHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccccc
Q 012133           48 ATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  125 (470)
Q Consensus        48 ~~~k~~~l~~ll~~~~-~~~~~lVF~~t~~~~~~l~~~l~-~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~  125 (470)
                      .+.|+.+|.++|.... .+.++|||++..+..+-|..++. +++....+.|.....+++ .    .+....|.+.|....
T Consensus       107 ~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~~k-~----~~~~~~i~Lltsag~  181 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAAA-A----NDFSCTVHLFSSEGI  181 (328)
T ss_dssp             TCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCC
T ss_pred             cCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhhhh-c----ccCCceEEEEECCCC
Confidence            5689999999997663 45699999999999999999998 578888899885443322 1    234556666566666


Q ss_pred             ccCC-----CCCccEEEEecCCCChhHH-HHHhcccCCCC----CCCeEEEeeChhh
Q 012133          126 RGLD-----IPNVDLIIHYELPNDPETF-VHRSGRTGRAG----KEGTAILMFTSSQ  172 (470)
Q Consensus       126 ~Gid-----ip~v~~VI~~~~p~~~~~y-~qr~GR~gR~g----~~g~~i~l~~~~~  172 (470)
                      -|++     +...+.||.||.-|++..= +|.+-|+.|.+    ++-.+|.|++...
T Consensus       182 ~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~T  238 (328)
T 3hgt_A          182 NFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINS  238 (328)
T ss_dssp             CTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTS
T ss_pred             CCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCC
Confidence            6675     6788999999999999885 89888888862    4567777777644

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=97.61  E-value=1.9e-05  Score=51.53  Aligned_cols=16  Identities=63%  Similarity=1.412  Sum_probs=15.3

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||+|+++||+|+|||+
T Consensus         3 C~~Cg~~GH~a~~C~~   18 (39)
T 2a51_A            3 CFNCGKPGHTARMCRQ   18 (39)
T ss_dssp             CTTTCCBSSCTTTCCS
T ss_pred             eeccCCCCcccccCCC
Confidence            9999999999999984

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=97.56  E-value=0.00028  Score=58.73  Aligned_cols=18  Identities=39%  Similarity=1.030  Sum_probs=16.6

Q ss_pred             CccccCCCCCccCCCCCC
Q 012133          453 GACFNCGKSGHRASECPN  470 (470)
Q Consensus       453 ~~c~~c~~~gh~~~~c~~  470 (470)
                      ..||+|++.||||+|||+
T Consensus       106 ~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A          106 IYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCTTTTSSSCTTTTTSCC
T ss_pred             CCcCCCCCCCcCcccCcC
Confidence            469999999999999996

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=97.56  E-value=2.6e-05  Score=50.18  Aligned_cols=16  Identities=56%  Similarity=1.410  Sum_probs=15.3

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||+|+++||++++||+
T Consensus         3 C~~Cg~~GH~~~~C~~   18 (37)
T 2bl6_A            3 CYNCGKPGHLSSQCRA   18 (37)
T ss_dssp             BSSSCCSSCCTTTSSC
T ss_pred             ccccCCCCcchhhCcC
Confidence            9999999999999985

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=97.43  E-value=4.2e-05  Score=52.53  Aligned_cols=17  Identities=53%  Similarity=1.300  Sum_probs=15.7

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+|+++||+++|||+
T Consensus         8 ~C~~Cg~~GH~a~~C~~   24 (49)
T 2ec7_A            8 RCWNCGKEGHSARQCRA   24 (49)
T ss_dssp             BCTTTCCBTCCTTTCCC
T ss_pred             eeeecCCCCcChhhCcC
Confidence            39999999999999984

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=97.43  E-value=3.2e-05  Score=59.31  Aligned_cols=17  Identities=41%  Similarity=1.179  Sum_probs=15.9

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+||+.||+++|||+
T Consensus        48 ~CYnCG~~GH~~rdC~~   64 (83)
T 3nyb_B           48 YCYNCGGKGHFGDDCKE   64 (83)
T ss_dssp             BCSSSSCBSSCGGGCSS
T ss_pred             eecccCCCCcCcccCCc
Confidence            49999999999999995

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=97.32  E-value=5.4e-05  Score=54.63  Aligned_cols=17  Identities=41%  Similarity=1.327  Sum_probs=15.8

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+|+++||+|+|||+
T Consensus         6 ~C~~Cg~~GH~a~~C~~   22 (61)
T 2ihx_A            6 LCYTCGSPGHYQAQCPK   22 (61)
T ss_dssp             BCSSSCCBTCCGGGCTT
T ss_pred             cccccCCCCeehhhCcC
Confidence            39999999999999995

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.22  E-value=0.00018  Score=52.24  Aligned_cols=17  Identities=47%  Similarity=1.085  Sum_probs=15.6

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+|+++||+++|||+
T Consensus         9 ~C~~Cg~~GH~a~~C~~   25 (63)
T 2cqf_A            9 RCYNCGGLDHHAKECKL   25 (63)
T ss_dssp             CCSSSCCSSSCTTTCCS
T ss_pred             cccccCCCCcChhhCCC
Confidence            39999999999999983

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=97.17  E-value=9.8e-05  Score=52.06  Aligned_cols=17  Identities=59%  Similarity=1.318  Sum_probs=15.7

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+|+++||+|+|||+
T Consensus        14 ~C~~Cg~~GH~a~~C~~   30 (55)
T 1a1t_A           14 KCFNCGKEGHIAKNCRA   30 (55)
T ss_dssp             BCTTTCCBSSCGGGCSS
T ss_pred             ceeeeCCCCcChhhcCC
Confidence            39999999999999984

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=97.13  E-value=0.00033  Score=52.41  Aligned_cols=17  Identities=47%  Similarity=1.085  Sum_probs=15.6

Q ss_pred             ccccCCCCCccCCCCCC
Q 012133          454 ACFNCGKSGHRASECPN  470 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~~  470 (470)
                      .||+|+++||+++|||.
T Consensus        26 ~C~~Cg~~GH~a~~C~~   42 (74)
T 2li8_A           26 RCYNCGGLDHHAKECKL   42 (74)
T ss_dssp             CCTTTCCSSSCTTTCSS
T ss_pred             cccccCCcCcCcccCCC
Confidence            39999999999999983

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=96.63  E-value=0.014  Score=61.13  Aligned_cols=75  Identities=11%  Similarity=0.125  Sum_probs=53.2

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEec--ccccccCCCC-----CccEE
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT--DVAARGLDIP-----NVDLI  136 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaT--dv~~~Gidip-----~v~~V  136 (470)
                      .++.+|||+++....+++++.+  ...+..-.-+++..   ++++.|+...-.||++|  ....+|||+|     .+..|
T Consensus       392 ~~g~~lvlF~Sy~~l~~v~~~~--~~~v~~q~~~~~~~---~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~v  466 (551)
T 3crv_A          392 AKANVLVVFPSYEIMDRVMSRI--SLPKYVESEDSSVE---DLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDV  466 (551)
T ss_dssp             CSSEEEEEESCHHHHHHHHTTC--CSSEEECCSSCCHH---HHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEEE
T ss_pred             CCCCEEEEecCHHHHHHHHHhc--CCcEEEcCCCCCHH---HHHHHHHhcCCeEEEEEecceecccccccccCCcceeEE
Confidence            4679999999999999888732  23333333355544   45666643334799998  6999999999     46788


Q ss_pred             EEecCCC
Q 012133          137 IHYELPN  143 (470)
Q Consensus       137 I~~~~p~  143 (470)
                      |...+|.
T Consensus       467 iI~~lPf  473 (551)
T 3crv_A          467 VIVGIPY  473 (551)
T ss_dssp             EEESCCC
T ss_pred             EEEcCCC
Confidence            8888775

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=96.53  E-value=0.00062  Score=58.37  Aligned_cols=16  Identities=50%  Similarity=1.165  Sum_probs=15.3

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||||++.||+|++||+
T Consensus       100 C~~Cg~~GH~a~~C~~  115 (148)
T 3ts2_A          100 CYNCGGLDHHAKECKL  115 (148)
T ss_dssp             CTTTCCSSCCGGGCCS
T ss_pred             ccEeCCccchhhhCCC
Confidence            9999999999999984

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=96.42  E-value=0.0048  Score=51.16  Aligned_cols=18  Identities=28%  Similarity=0.709  Sum_probs=16.2

Q ss_pred             CccccCCCCCccCCCCCC
Q 012133          453 GACFNCGKSGHRASECPN  470 (470)
Q Consensus       453 ~~c~~c~~~gh~~~~c~~  470 (470)
                      ..||+|++.||+++|||+
T Consensus        65 ~~C~~Cg~~GH~~~~Cp~   82 (124)
T 2lli_A           65 VQCTLCKSKKHSKERCPS   82 (124)
T ss_dssp             CSSSSSCSSCCCTTTCCC
T ss_pred             ccCCCCCcCCcchhhCCC
Confidence            359999999999999995

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=95.84  E-value=0.02  Score=62.43  Aligned_cols=92  Identities=21%  Similarity=0.289  Sum_probs=72.1

Q ss_pred             ccHHHH-HHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           49 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        49 ~~k~~~-l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      .-|..+ +..++.....+.++||.+||+..+.+.++.+.+     ++.+..+||+++..+|..+++.+.++..+|+|+|.
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            455433 333344444567999999999999999888763     47899999999999999999999999999999996


Q ss_pred             -cccccCCCCCccEEEEec
Q 012133          123 -VAARGLDIPNVDLIIHYE  140 (470)
Q Consensus       123 -v~~~Gidip~v~~VI~~~  140 (470)
                       .+...+++.++.+||.-.
T Consensus       480 ~ll~~~~~~~~l~lVVIDE  498 (780)
T 1gm5_A          480 ALIQEDVHFKNLGLVIIDE  498 (780)
T ss_dssp             THHHHCCCCSCCCEEEEES
T ss_pred             HHHhhhhhccCCceEEecc
Confidence             444567888999888543

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

Probab=95.70  E-value=0.023  Score=56.83  Aligned_cols=90  Identities=14%  Similarity=0.200  Sum_probs=69.1

Q ss_pred             ccHHHH-HHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc
Q 012133           49 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  123 (470)
Q Consensus        49 ~~k~~~-l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv  123 (470)
                      .-|..+ +..++.......++||.+||++.+.++++.+.+    .+.+..+||+.+..++...++.+..+..+|+|+|+-
T Consensus        47 sGKT~~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~  126 (414)
T 3oiy_A           47 VGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQ  126 (414)
T ss_dssp             SSHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHH
T ss_pred             CCHHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHH
Confidence            455442 233344445678999999999999999999886    578999999999999888888888888999999973


Q ss_pred             cc----ccCCCCCccEEEE
Q 012133          124 AA----RGLDIPNVDLIIH  138 (470)
Q Consensus       124 ~~----~Gidip~v~~VI~  138 (470)
                      .-    .-+++.++++||.
T Consensus       127 ~l~~~l~~~~~~~~~~iVi  145 (414)
T 3oiy_A          127 FVSKNREKLSQKRFDFVFV  145 (414)
T ss_dssp             HHHHCHHHHTTCCCSEEEE
T ss_pred             HHHHHHHHhccccccEEEE
Confidence            21    1256678888885

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

Probab=94.45  E-value=0.061  Score=60.93  Aligned_cols=92  Identities=15%  Similarity=0.188  Sum_probs=70.8

Q ss_pred             CcccHHHHH-HHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEec
Q 012133           47 TATSKRTIL-SDLITVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT  121 (470)
Q Consensus        47 ~~~~k~~~l-~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaT  121 (470)
                      ...-|..+. .-++.......++||.+||++.+.++++.+..    .+.+..+||+++..+|...++.+.++..+|||+|
T Consensus       102 TGSGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~T  181 (1104)
T 4ddu_A          102 TGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFS  181 (1104)
T ss_dssp             TTCCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEE
T ss_pred             CCCcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEC
Confidence            334565433 22334445678999999999999999999986    3589999999999888888999998889999999


Q ss_pred             cc-----ccccCCCCCccEEEEe
Q 012133          122 DV-----AARGLDIPNVDLIIHY  139 (470)
Q Consensus       122 dv-----~~~Gidip~v~~VI~~  139 (470)
                      +-     +.. +++.++.+||.-
T Consensus       182 p~rL~~~l~~-l~~~~l~~lViD  203 (1104)
T 4ddu_A          182 TQFVSKNREK-LSQKRFDFVFVD  203 (1104)
T ss_dssp             HHHHHHSHHH-HHTSCCSEEEES
T ss_pred             HHHHHHHHHh-hcccCcCEEEEe
Confidence            62     222 566788888853

>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=94.06  E-value=0.95  Score=41.30  Aligned_cols=70  Identities=16%  Similarity=0.229  Sum_probs=54.2

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----ccc-ccCCCCCc
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAA-RGLDIPNV  133 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~-~Gidip~v  133 (470)
                      ..++||.+||++.+.++++.+.+     .+.+..++|+.+...+...+..    ..+|+|+|+     .+. ..+++.++
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            45799999999999999887764     5789999999988877666554    478999996     222 34577888


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      .+||.
T Consensus       178 ~~lVi  182 (242)
T 3fe2_A          178 TYLVL  182 (242)
T ss_dssp             CEEEE
T ss_pred             cEEEE
Confidence            88774

>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=93.69  E-value=0.19  Score=57.26  Aligned_cols=90  Identities=14%  Similarity=0.173  Sum_probs=70.9

Q ss_pred             ccHHHHH-HHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           49 TSKRTIL-SDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        49 ~~k~~~l-~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      .-|..+. ..++.....+.++||.+||+..+.+.++.+.+     .+.+..+++..+..++..+++.+.++..+|+|+|.
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            3454332 23333444667999999999999999988874     35789999999999999999999999999999994


Q ss_pred             -cccccCCCCCccEEEE
Q 012133          123 -VAARGLDIPNVDLIIH  138 (470)
Q Consensus       123 -v~~~Gidip~v~~VI~  138 (470)
                       .+...+.+.++.+||.
T Consensus       715 ~ll~~~~~~~~l~lvIi  731 (1151)
T 2eyq_A          715 KLLQSDVKFKDLGLLIV  731 (1151)
T ss_dssp             HHHHSCCCCSSEEEEEE
T ss_pred             HHHhCCccccccceEEE
Confidence             5556688889988884

>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=93.05  E-value=0.7  Score=42.45  Aligned_cols=69  Identities=17%  Similarity=0.179  Sum_probs=50.9

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc------ccccCCCCCcc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV------AARGLDIPNVD  134 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv------~~~Gidip~v~  134 (470)
                      .++||.++|++.+.++++.+.+     .+.+..++|+.+..++...+.    ...+|+|+|.-      ....+++..+.
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~  176 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQ----MGCHLLVATPGRLVDFIEKNKISLEFCK  176 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHS----SCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhC----CCCCEEEECHHHHHHHHHcCCCChhhCC
Confidence            5899999999999999888763     367888999887665554443    25789999962      12235677888


Q ss_pred             EEEE
Q 012133          135 LIIH  138 (470)
Q Consensus       135 ~VI~  138 (470)
                      +||.
T Consensus       177 ~lVi  180 (253)
T 1wrb_A          177 YIVL  180 (253)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8774

>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=92.34  E-value=0.47  Score=42.85  Aligned_cols=71  Identities=14%  Similarity=0.222  Sum_probs=46.7

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc------ccccCCCCCc
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV------AARGLDIPNV  133 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv------~~~Gidip~v  133 (470)
                      ...++||.++|++.+.++++.+.+    .+.+..++++.+...+...+..    ..+|+|+|+-      ....+++.++
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDISK----GVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHHHS----CCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCcCcccc
Confidence            456899999999999999988874    4678889998776655444432    4789999962      2234556666


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      ++||.
T Consensus       169 ~~lVi  173 (228)
T 3iuy_A          169 TYLVI  173 (228)
T ss_dssp             CEEEE
T ss_pred             eEEEE
Confidence            66663

>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=91.46  E-value=0.91  Score=41.77  Aligned_cols=70  Identities=19%  Similarity=0.255  Sum_probs=51.5

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc-----cc--ccCCCCC
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----AA--RGLDIPN  132 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv-----~~--~Gidip~  132 (470)
                      ..++||.++|++.+.++++.+.+     .+.+..++|+.+...+...+.    ...+|+|+|+-     +.  ..+++..
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            45799999999999999887763     477899999988776655443    25789999962     11  3456677


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       187 ~~~lVi  192 (249)
T 3ber_A          187 LKYLVM  192 (249)
T ss_dssp             CCEEEE
T ss_pred             cCEEEE
Confidence            777664

>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=91.39  E-value=1.9  Score=38.45  Aligned_cols=70  Identities=17%  Similarity=0.238  Sum_probs=50.6

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccc------cccCCCCCc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA------ARGLDIPNV  133 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~------~~Gidip~v  133 (470)
                      .++||.++|++.+.++++.+.+      .+.+..++|+.+..++...+.   .+..+|+|+|.-.      ...+++.++
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            4899999999999999887763      467899999998776655443   3456899999621      223456666


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      ++||.
T Consensus       160 ~~lVi  164 (220)
T 1t6n_A          160 KHFIL  164 (220)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            66663

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=90.64  E-value=2.2  Score=37.97  Aligned_cols=88  Identities=16%  Similarity=0.165  Sum_probs=52.8

Q ss_pred             cCcccHHHH-HHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCee
Q 012133           46 TTATSKRTI-LSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        46 ~~~~~k~~~-l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                      ....-|..+ +..++..+   ....++||.++|++.+.++++.+..     .+.+..++|+.+..++...+.     ..+
T Consensus        59 pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~  133 (224)
T 1qde_A           59 QSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-----DAQ  133 (224)
T ss_dssp             CTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CT-----TCS
T ss_pred             CCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCC-----CCC
Confidence            334566644 33444433   2345899999999999999887763     467888999877665443332     278


Q ss_pred             EEEeccc------ccccCCCCCccEEEE
Q 012133          117 VLVATDV------AARGLDIPNVDLIIH  138 (470)
Q Consensus       117 iLVaTdv------~~~Gidip~v~~VI~  138 (470)
                      |+|+|.-      ....+++..+++||.
T Consensus       134 iiv~Tp~~l~~~~~~~~~~~~~~~~iVi  161 (224)
T 1qde_A          134 IVVGTPGRVFDNIQRRRFRTDKIKMFIL  161 (224)
T ss_dssp             EEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             EEEECHHHHHHHHHhCCcchhhCcEEEE
Confidence            9999962      233466677777774

>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=90.51  E-value=0.59  Score=42.33  Aligned_cols=71  Identities=14%  Similarity=0.205  Sum_probs=50.7

Q ss_pred             CcccHHHH-HHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCee
Q 012133           47 TATSKRTI-LSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        47 ~~~~k~~~-l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                      ...-|..+ +.-++...   ....++||.++|++.+.++++.+.+      .+.+..++|+.+..++...++     ..+
T Consensus        70 TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~  144 (230)
T 2oxc_A           70 SGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-----KCH  144 (230)
T ss_dssp             TTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTT-----SCS
T ss_pred             CCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhcc-----CCC
Confidence            33566544 33344433   2346899999999999999888863      467889999998877665553     478


Q ss_pred             EEEecc
Q 012133          117 VLVATD  122 (470)
Q Consensus       117 iLVaTd  122 (470)
                      |+|+|.
T Consensus       145 Iiv~Tp  150 (230)
T 2oxc_A          145 IAVGSP  150 (230)
T ss_dssp             EEEECH
T ss_pred             EEEECH
Confidence            999996

>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=90.43  E-value=2  Score=37.71  Aligned_cols=88  Identities=23%  Similarity=0.214  Sum_probs=58.5

Q ss_pred             CcccHHHH-HHHHHHHHc------CCCeEEEEeCchHHHHHHHHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCee
Q 012133           47 TATSKRTI-LSDLITVYA------KGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        47 ~~~~k~~~-l~~ll~~~~------~~~~~lVF~~t~~~~~~l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                      ...-|..+ +..++....      ...++||.+||++.+.++++.+.+   .+.+..++++.+...+...+..    ..+
T Consensus        47 TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~  122 (207)
T 2gxq_A           47 TGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLR----GAD  122 (207)
T ss_dssp             TTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHHH----CCS
T ss_pred             CCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhhC----CCC
Confidence            34466544 333444431      346899999999999999998875   3678899998876555444432    478


Q ss_pred             EEEeccc-----c-cccCCCCCccEEEE
Q 012133          117 VLVATDV-----A-ARGLDIPNVDLIIH  138 (470)
Q Consensus       117 iLVaTdv-----~-~~Gidip~v~~VI~  138 (470)
                      |+|+|+-     + ...+++.++++||.
T Consensus       123 i~v~T~~~l~~~~~~~~~~~~~~~~iVi  150 (207)
T 2gxq_A          123 AVVATPGRALDYLRQGVLDLSRVEVAVL  150 (207)
T ss_dssp             EEEECHHHHHHHHHHTSSCCTTCSEEEE
T ss_pred             EEEECHHHHHHHHHcCCcchhhceEEEE
Confidence            9999961     1 22355667777664

>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=90.41  E-value=0.63  Score=48.96  Aligned_cols=75  Identities=12%  Similarity=0.152  Sum_probs=60.4

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHccc--ccCCeeEEEecccc-----------cccCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGF--RQGKFTVLVATDVA-----------ARGLD  129 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f--~~g~~~iLVaTdv~-----------~~Gid  129 (470)
                      ..+.+||.+|+++.+++.++.|.. ++.+..++++++..++..++..+  ..+..+|||+|+-.           ..-++
T Consensus        83 ~~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~  162 (591)
T 2v1x_A           83 SDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYE  162 (591)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHH
T ss_pred             cCCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhh
Confidence            467999999999999999998885 78999999999999998888887  46789999999731           12234


Q ss_pred             CCCccEEEE
Q 012133          130 IPNVDLIIH  138 (470)
Q Consensus       130 ip~v~~VI~  138 (470)
                      +..+.+||.
T Consensus       163 ~~~i~~iVi  171 (591)
T 2v1x_A          163 ARRFTRIAV  171 (591)
T ss_dssp             TTCEEEEEE
T ss_pred             ccCCcEEEE
Confidence            556777663

>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=90.27  E-value=0.6  Score=48.26  Aligned_cols=75  Identities=19%  Similarity=0.177  Sum_probs=60.9

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccccc------ccCCCCCccEE
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA------RGLDIPNVDLI  136 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~------~Gidip~v~~V  136 (470)
                      ..+.+||.+|++..+.+..+.|.. ++.+..+|+..+..++..++..+..+..+|||+|+-.-      .-++..++.+|
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            458999999999999999998885 78899999999999999999999999999999996311      22344566666


Q ss_pred             EE
Q 012133          137 IH  138 (470)
Q Consensus       137 I~  138 (470)
                      |.
T Consensus       144 Vi  145 (523)
T 1oyw_A          144 AV  145 (523)
T ss_dssp             EE
T ss_pred             EE
Confidence            63

>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=89.92  E-value=1.1  Score=39.58  Aligned_cols=70  Identities=19%  Similarity=0.130  Sum_probs=49.4

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc-----cc-ccCCCCC
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----AA-RGLDIPN  132 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv-----~~-~Gidip~  132 (470)
                      ..++||.++|++.+.++++.+.+      .+.+..++|+.+..+....+.    ...+|+|+|+-     +. .-+++..
T Consensus        71 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~  146 (206)
T 1vec_A           71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD----DTVHVVIATPGRILDLIKKGVAKVDH  146 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTT----SCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcC----CCCCEEEeCHHHHHHHHHcCCcCccc
Confidence            35899999999999999888763      467889999988766544432    35789999962     12 2245566


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       147 ~~~lVi  152 (206)
T 1vec_A          147 VQMIVL  152 (206)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            666663

>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=89.58  E-value=0.87  Score=45.70  Aligned_cols=70  Identities=11%  Similarity=0.171  Sum_probs=53.7

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----cccc-cCCCCCc
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPNV  133 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~~-Gidip~v  133 (470)
                      ..++||.+||++.+.++++.+.+     .+.+..+||+.+..++...+..    ..+|+|+|+     .+.+ -+++..+
T Consensus       129 ~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~----~~~Ivv~Tp~~l~~~l~~~~~~l~~~  204 (434)
T 2db3_A          129 RPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITR----GCHVVIATPGRLLDFVDRTFITFEDT  204 (434)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTT----CCSEEEECHHHHHHHHHTTSCCCTTC
T ss_pred             CccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhc----CCCEEEEChHHHHHHHHhCCcccccC
Confidence            35899999999999999988774     3678889999988776655543    579999996     2222 3567888


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      ++||.
T Consensus       205 ~~lVl  209 (434)
T 2db3_A          205 RFVVL  209 (434)
T ss_dssp             CEEEE
T ss_pred             CeEEE
Confidence            88874

>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=89.58  E-value=0.61  Score=52.61  Aligned_cols=76  Identities=17%  Similarity=0.288  Sum_probs=58.6

Q ss_pred             HHcCCCeEEEEeCchHHHHHHHHHHhc-----CC----cEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc-ccccCC-
Q 012133           61 VYAKGGKTIVFTQTKRDADEVSLALTS-----II----ASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-AARGLD-  129 (470)
Q Consensus        61 ~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~----~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv-~~~Gid-  129 (470)
                      ......++||.+||++.+.++++.+..     .+    .+..+||+++..++.+.++.+++  .+|||+|+- +..-+. 
T Consensus        95 ~~~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~  172 (1054)
T 1gku_B           95 LALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRE  172 (1054)
T ss_dssp             HHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTT
T ss_pred             HhhcCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHH
Confidence            334567999999999999999988873     34    78999999999998888888887  899999961 111111 


Q ss_pred             CCCccEEEE
Q 012133          130 IPNVDLIIH  138 (470)
Q Consensus       130 ip~v~~VI~  138 (470)
                      +..+++||.
T Consensus       173 L~~l~~lVi  181 (1054)
T 1gku_B          173 LGHFDFIFV  181 (1054)
T ss_dssp             SCCCSEEEE
T ss_pred             hccCCEEEE
Confidence            557788774

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=89.28  E-value=1.4  Score=40.80  Aligned_cols=71  Identities=15%  Similarity=0.237  Sum_probs=51.6

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----ccc--ccCCCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAA--RGLDIP  131 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~--~Gidip  131 (470)
                      ...++||.+||++.+.++++.+.+     ...+..++|+.....+...+..    ..+|+|+|+     .+.  ..+++.
T Consensus       125 ~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~Iiv~Tp~~l~~~~~~~~~~~~~  200 (262)
T 3ly5_A          125 NGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGN----GINIIVATPGRLLDHMQNTPGFMYK  200 (262)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHCTTCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcC----CCCEEEEcHHHHHHHHHccCCcccc
Confidence            356899999999999999988874     3567888998877665544432    378999995     222  235677


Q ss_pred             CccEEEE
Q 012133          132 NVDLIIH  138 (470)
Q Consensus       132 ~v~~VI~  138 (470)
                      ++.+||.
T Consensus       201 ~l~~lVi  207 (262)
T 3ly5_A          201 NLQCLVI  207 (262)
T ss_dssp             TCCEEEE
T ss_pred             cCCEEEE
Confidence            7777764

>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=87.94  E-value=2.3  Score=41.40  Aligned_cols=71  Identities=17%  Similarity=0.230  Sum_probs=53.7

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccc------cccCCCCC
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA------ARGLDIPN  132 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~------~~Gidip~  132 (470)
                      ..++||.|||+..++++++.+.+      .+.+..++|+.+..++...+.   .+..+|+|+|.-.      ...+++.+
T Consensus        76 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~~~~~iiv~T~~~l~~~~~~~~~~~~~  152 (391)
T 1xti_A           76 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK---KNCPHIVVGTPGRILALARNKSLNLKH  152 (391)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHH---HSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHh---cCCCCEEEECHHHHHHHHHcCCccccc
Confidence            45899999999999998887763      467999999998876665543   3457899999621      23456788


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       153 ~~~vVi  158 (391)
T 1xti_A          153 IKHFIL  158 (391)
T ss_dssp             CSEEEE
T ss_pred             cCEEEE
Confidence            888884

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=87.87  E-value=2.1  Score=38.65  Aligned_cols=54  Identities=15%  Similarity=0.207  Sum_probs=40.7

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      ...++||.+||++.+.++++.+.+     .+.+..+||+.+.......+     ...+|+|+|.
T Consensus        96 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp  154 (236)
T 2pl3_A           96 DGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTP  154 (236)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECH
Confidence            356899999999999999988874     26788999988766554444     2578999996

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=87.61  E-value=1.7  Score=39.46  Aligned_cols=87  Identities=14%  Similarity=0.193  Sum_probs=49.6

Q ss_pred             ccHHHH-HHHHHHHHc---CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEE
Q 012133           49 TSKRTI-LSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  119 (470)
Q Consensus        49 ~~k~~~-l~~ll~~~~---~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLV  119 (470)
                      .-|..+ +..++....   ...++||.++|++.+.++++.+.+     .+.+..++++.+....   ++.+..+..+|+|
T Consensus        78 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~Ilv  154 (237)
T 3bor_A           78 TGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNE---MQKLQAEAPHIVV  154 (237)
T ss_dssp             HHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEE
T ss_pred             CcHHHHHHHHHHHHHHhcCCCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHH---HHHHhcCCCCEEE
Confidence            455533 333344332   346899999999999999988864     3567788887654432   3344455688999


Q ss_pred             ecc-----cccc-cCCCCCccEEEE
Q 012133          120 ATD-----VAAR-GLDIPNVDLIIH  138 (470)
Q Consensus       120 aTd-----v~~~-Gidip~v~~VI~  138 (470)
                      +|+     .+.+ .+++..+++||.
T Consensus       155 ~Tp~~l~~~l~~~~~~~~~~~~lVi  179 (237)
T 3bor_A          155 GTPGRVFDMLNRRYLSPKWIKMFVL  179 (237)
T ss_dssp             ECHHHHHHHHHTTSSCSTTCCEEEE
T ss_pred             ECHHHHHHHHHhCCcCcccCcEEEE
Confidence            994     2222 355666776664

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

Probab=86.92  E-value=1.7  Score=42.79  Aligned_cols=69  Identities=16%  Similarity=0.135  Sum_probs=52.2

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc-----c-cccCCCCCcc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----A-ARGLDIPNVD  134 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv-----~-~~Gidip~v~  134 (470)
                      .++||.+||++.+.++++.+.+     .+.+..+||+.+..++...+..    ..+|+|+|+-     + ...+++..++
T Consensus       102 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~~~~~  177 (417)
T 2i4i_A          102 PISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLER----GCHLLVATPGRLVDMMERGKIGLDFCK  177 (417)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTT----CCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhC----CCCEEEEChHHHHHHHHcCCcChhhCc
Confidence            4799999999999999988763     4678999999888766555432    5789999972     1 2235677888


Q ss_pred             EEEE
Q 012133          135 LIIH  138 (470)
Q Consensus       135 ~VI~  138 (470)
                      +||.
T Consensus       178 ~iVi  181 (417)
T 2i4i_A          178 YLVL  181 (417)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8874

>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=86.75  E-value=1.2  Score=45.87  Aligned_cols=70  Identities=11%  Similarity=0.150  Sum_probs=48.0

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccc-----ccc-C-CCCC
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA-----ARG-L-DIPN  132 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~-----~~G-i-dip~  132 (470)
                      ..++||.+||+..+.+.++.+.+     .+.+..+||+.+...+...+..    ..+|+|+|.-.     ..+ + ++..
T Consensus        55 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~i~v~T~~~l~~~~~~~~~~~~~~  130 (556)
T 4a2p_A           55 KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIE----DSDIIVVTPQILVNSFEDGTLTSLSI  130 (556)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEECCCC-----CHHHHHH----HCSEEEECHHHHHHHHHSSSCCCSTT
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCcchhHHHhhC----CCCEEEECHHHHHHHHHhCccccccc
Confidence            67899999999999998888764     5789999999876654433322    46899999622     222 4 6778


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       131 ~~~vVi  136 (556)
T 4a2p_A          131 FTLMIF  136 (556)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            888874

>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=85.46  E-value=2.1  Score=42.54  Aligned_cols=70  Identities=24%  Similarity=0.344  Sum_probs=54.0

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc--CC---cEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc-cc-----ccCCCCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS--II---ASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-AA-----RGLDIPN  132 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~--~~---~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv-~~-----~Gidip~  132 (470)
                      ...++||.||++..+.+.++.+.+  .+   .+..+||+....++.....     ..+|+|+|.- +.     .-+.+.+
T Consensus        51 ~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~-----~~~ivv~T~~~l~~~~~~~~~~~~~  125 (494)
T 1wp9_A           51 YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA-----RAKVIVATPQTIENDLLAGRISLED  125 (494)
T ss_dssp             SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHH-----HCSEEEECHHHHHHHHHTTSCCTTS
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhcc-----CCCEEEecHHHHHHHHhcCCcchhh
Confidence            568999999999999999998875  33   7999999999887765543     3689999952 21     2456778


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       126 ~~~vIi  131 (494)
T 1wp9_A          126 VSLIVF  131 (494)
T ss_dssp             CSEEEE
T ss_pred             ceEEEE
Confidence            888874

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=85.14  E-value=1.1  Score=40.16  Aligned_cols=71  Identities=14%  Similarity=0.211  Sum_probs=46.0

Q ss_pred             cccHHHH-HHHHHHHHc---CCCeEEEEeCchHHHHHHHHHHhc---------CCcEEEEeCCCCHHHHHHHHcccccCC
Q 012133           48 ATSKRTI-LSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS---------IIASEALHGDISQHQRERTLNGFRQGK  114 (470)
Q Consensus        48 ~~~k~~~-l~~ll~~~~---~~~~~lVF~~t~~~~~~l~~~l~~---------~~~~~~lhg~~~~~~R~~~~~~f~~g~  114 (470)
                      ..-|..+ +.-++..+.   ...++||.++|++.+.++++.+.+         .+.+..++|+.+..++   .+.+. ..
T Consensus        51 GsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~---~~~~~-~~  126 (219)
T 1q0u_A           51 GTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKA---LEKLN-VQ  126 (219)
T ss_dssp             SHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHT---TCCCS-SC
T ss_pred             CChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHH---HHHcC-CC
Confidence            3456543 333344332   246899999999999999887753         3568888988754432   22332 35


Q ss_pred             eeEEEecc
Q 012133          115 FTVLVATD  122 (470)
Q Consensus       115 ~~iLVaTd  122 (470)
                      .+|+|+|.
T Consensus       127 ~~Iiv~Tp  134 (219)
T 1q0u_A          127 PHIVIGTP  134 (219)
T ss_dssp             CSEEEECH
T ss_pred             CCEEEeCH
Confidence            68999995

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

Probab=84.76  E-value=1.2  Score=45.71  Aligned_cols=70  Identities=13%  Similarity=0.219  Sum_probs=50.4

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc-----cccc-C-CCCC
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----AARG-L-DIPN  132 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv-----~~~G-i-dip~  132 (470)
                      ..++||.+||+..+.+.++.+.+     .+.+..+||+.+...+...+..    ..+|+|+|.-     +..+ + ++.+
T Consensus        52 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~i~v~T~~~l~~~~~~~~~~~~~~  127 (555)
T 3tbk_A           52 KGKVVFFANQIPVYEQQATVFSRYFERLGYNIASISGATSDSVSVQHIIE----DNDIIILTPQILVNNLNNGAIPSLSV  127 (555)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECTTTGGGSCHHHHHH----HCSEEEECHHHHHHHHHTSSSCCGGG
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHHhccCCcEEEEEcCCCcchhhHHHHhc----CCCEEEECHHHHHHHHhcCccccccc
Confidence            67899999999999988887764     5789999999876654333322    4789999962     1222 3 5667


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       128 ~~~vVi  133 (555)
T 3tbk_A          128 FTLMIF  133 (555)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            788774

>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}

Probab=84.30  E-value=0.25  Score=28.08  Aligned_cols=16  Identities=38%  Similarity=0.831  Sum_probs=14.9

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      |-+|-.-||+..||+.
T Consensus         6 Ce~CE~FGH~t~~C~d   21 (26)
T 2hqh_E            6 CEICEMFGHWATNCND   21 (26)
T ss_dssp             ETTTTEESSCGGGCCT
T ss_pred             chHHHHhCcccccCCc
Confidence            9999999999999974

>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=84.02  E-value=1.8  Score=47.05  Aligned_cols=70  Identities=10%  Similarity=0.106  Sum_probs=47.5

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc-----ccc-cC-CCCC
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----AAR-GL-DIPN  132 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv-----~~~-Gi-dip~  132 (470)
                      ..++||.|||+..+.+.+..+.+     .+.+..+||+.+...+...+..    ..+|+|+|.-     +.. -+ ++.+
T Consensus       296 ~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~----~~~Ivv~Tp~~l~~~l~~~~~~~~~~  371 (797)
T 4a2q_A          296 KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIE----DSDIIVVTPQILVNSFEDGTLTSLSI  371 (797)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECCC-----CHHHHHH----TCSEEEECHHHHHHHHHSSSCCCGGG
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHhcccCCceEEEEeCCcchhhhHHHhhC----CCCEEEEchHHHHHHHHhcccccccc
Confidence            67999999999999998887763     5889999999876654433322    5789999952     122 23 5667


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       372 ~~~iVi  377 (797)
T 4a2q_A          372 FTLMIF  377 (797)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            788874

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=83.84  E-value=0.25  Score=37.52  Aligned_cols=15  Identities=7%  Similarity=0.000  Sum_probs=4.4

Q ss_pred             cccCCCCCccCCCCC
Q 012133          455 CFNCGKSGHRASECP  469 (470)
Q Consensus       455 c~~c~~~gh~~~~c~  469 (470)
                      ||+|+++||+++||+
T Consensus        27 cY~c~~~gh~~~~c~   41 (83)
T 3nyb_B           27 AYILVDDNEKAKPKV   41 (83)
T ss_dssp             CCCBC----------
T ss_pred             ccccccCCccccccc
Confidence            888888888888885

>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=83.15  E-value=2.5  Score=41.01  Aligned_cols=70  Identities=17%  Similarity=0.202  Sum_probs=52.4

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc------ccccCCCCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV------AARGLDIPN  132 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv------~~~Gidip~  132 (470)
                      ...++||.+|++..+.++++.+.+     .+.+..++|+.+..++...+.     ..+|+|+|.-      ....+++..
T Consensus        88 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~i~v~T~~~l~~~~~~~~~~~~~  162 (394)
T 1fuu_A           88 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-----DAQIVVGTPGRVFDNIQRRRFRTDK  162 (394)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-----HCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-----CCCEEEECHHHHHHHHHhCCcchhh
Confidence            346999999999999999888763     367899999998877665554     3679999952      122455677


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       163 ~~~vIi  168 (394)
T 1fuu_A          163 IKMFIL  168 (394)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            788774

>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=82.89  E-value=3.7  Score=38.79  Aligned_cols=84  Identities=17%  Similarity=0.205  Sum_probs=57.1

Q ss_pred             cccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           48 ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        48 ~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      ..-|..+....+..  ...++||.+|++..+.++++.+.+     ...+..+|++.+..++...+.     ..+|+|+|.
T Consensus        41 GsGKT~~~~~~~~~--~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~i~v~T~  113 (337)
T 2z0m_A           41 GSGKTAAYAIPILE--LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-----NADIVVATP  113 (337)
T ss_dssp             TSSHHHHHHHHHHH--HTCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHHHT-----TCSEEEECH
T ss_pred             CCcHHHHHHHHHHh--hcCCEEEEeCCHHHHHHHHHHHHHHhhhcCCcEEEEECCcchHHHHhhcC-----CCCEEEECH
Confidence            34565433332222  357999999999999999988873     367889999998876655443     268999995


Q ss_pred             cc------cccCCCCCccEEEE
Q 012133          123 VA------ARGLDIPNVDLIIH  138 (470)
Q Consensus       123 v~------~~Gidip~v~~VI~  138 (470)
                      -.      ..-+++.++++||.
T Consensus       114 ~~l~~~~~~~~~~~~~~~~iVi  135 (337)
T 2z0m_A          114 GRLLDLWSKGVIDLSSFEIVII  135 (337)
T ss_dssp             HHHHHHHHTTSCCGGGCSEEEE
T ss_pred             HHHHHHHHcCCcchhhCcEEEE
Confidence            21      22345667777774

>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=82.63  E-value=6  Score=37.74  Aligned_cols=87  Identities=22%  Similarity=0.267  Sum_probs=58.9

Q ss_pred             CcccHHHHHH-HHHHHHc--CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEE
Q 012133           47 TATSKRTILS-DLITVYA--KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVL  118 (470)
Q Consensus        47 ~~~~k~~~l~-~ll~~~~--~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iL  118 (470)
                      ...-|..+.. .++....  ...++||.+|++..++++++.+.+     .+.+..++++....++...+.     ..+|+
T Consensus        53 TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-----~~~ii  127 (367)
T 1hv8_A           53 TGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIV  127 (367)
T ss_dssp             SSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEE
T ss_pred             CCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-----CCCEE
Confidence            3346654433 3333332  356899999999999999988874     367888999988766555443     46899


Q ss_pred             Eecccc------cccCCCCCccEEEE
Q 012133          119 VATDVA------ARGLDIPNVDLIIH  138 (470)
Q Consensus       119 VaTdv~------~~Gidip~v~~VI~  138 (470)
                      |+|.-.      ...+++.++++||.
T Consensus       128 v~T~~~l~~~~~~~~~~~~~~~~iIi  153 (367)
T 1hv8_A          128 VGTPGRILDHINRGTLNLKNVKYFIL  153 (367)
T ss_dssp             EECHHHHHHHHHTTCSCTTSCCEEEE
T ss_pred             EecHHHHHHHHHcCCcccccCCEEEE
Confidence            999621      22356777888774

>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=82.17  E-value=4.9  Score=39.36  Aligned_cols=71  Identities=15%  Similarity=0.236  Sum_probs=53.0

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----cccc-cCCCCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPN  132 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~~~-Gidip~  132 (470)
                      ...++||.+||++.+.++++.+.+     .+.+..++++.+..++...+..    ...|+|+|+     .+.+ .+++..
T Consensus       104 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~ivv~Tp~~l~~~l~~~~~~~~~  179 (410)
T 2j0s_A          104 RETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY----GQHVVAGTPGRVFDMIRRRSLRTRA  179 (410)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhc----CCCEEEcCHHHHHHHHHhCCccHhh
Confidence            457999999999999999988764     3678889999887766555542    458999995     2223 466777


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       180 ~~~vVi  185 (410)
T 2j0s_A          180 IKMLVL  185 (410)
T ss_dssp             CCEEEE
T ss_pred             eeEEEE
Confidence            888774

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=81.44  E-value=6.3  Score=38.31  Aligned_cols=87  Identities=17%  Similarity=0.171  Sum_probs=58.2

Q ss_pred             cccHHHH-HHHHHHHHc---CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEE
Q 012133           48 ATSKRTI-LSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVL  118 (470)
Q Consensus        48 ~~~k~~~-l~~ll~~~~---~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iL  118 (470)
                      ..-|..+ +..++....   ...++||.+|++..+.++++.+.+     .+.+..++++.........+    ....+|+
T Consensus        68 GsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~Iv  143 (400)
T 1s2m_A           68 GTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRL----NETVHIL  143 (400)
T ss_dssp             TSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHT----TSCCSEE
T ss_pred             CcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHh----cCCCCEE
Confidence            3456543 333333332   345899999999999999888764     46788899998766544333    2367899


Q ss_pred             Eeccc-----c-cccCCCCCccEEEE
Q 012133          119 VATDV-----A-ARGLDIPNVDLIIH  138 (470)
Q Consensus       119 VaTdv-----~-~~Gidip~v~~VI~  138 (470)
                      |+|.-     + ....++.++++||.
T Consensus       144 v~T~~~l~~~~~~~~~~~~~~~~vIi  169 (400)
T 1s2m_A          144 VGTPGRVLDLASRKVADLSDCSLFIM  169 (400)
T ss_dssp             EECHHHHHHHHHTTCSCCTTCCEEEE
T ss_pred             EEchHHHHHHHHhCCcccccCCEEEE
Confidence            99952     2 23366788888874

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=81.07  E-value=24  Score=35.30  Aligned_cols=58  Identities=16%  Similarity=0.108  Sum_probs=33.0

Q ss_pred             CeEEEEEeeCCccccCCcchhhHHhHhhhhcCcCcCccccEEEeecC----ccceeEeec-CHHHHHHHHhh
Q 012133          262 GWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADD----RVQGAVFDL-PEEIAKELLNK  328 (470)
Q Consensus       262 ~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~Ig~I~i~~~~----~~~ga~fdv-~~~~a~~i~~~  328 (470)
                      ...+|+|..-.    ..++..+|..++..+..     |-.|.|+.+.    ....+||.. ..+.|..+++.
T Consensus       101 ~~~~lfV~nL~----~~~te~~L~~~F~~~G~-----I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~  163 (437)
T 3pgw_S          101 AFKTLFVARVN----YDTTESKLRREFEVYGP-----IKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH  163 (437)
T ss_pred             CCCEEEEeCCC----CCCCHHHHHHHHHHcCC-----eeEEEeeccCCCCCccceEEEeeccHHHHHHHHHH
Confidence            45678885432    35778888888876544     5556665431    123466666 34445555544

---

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	470
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	7e-34
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	2e-29
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	5e-26
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	6e-25
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	1e-24
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	2e-24
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-22
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	1e-19
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	1e-18
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	1e-16
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	2e-16
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-16
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	4e-16
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	2e-15
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	1e-14
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	5e-14
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	3e-12
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	4e-08
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	5e-08
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	6e-08
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	8e-08
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	4e-07
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	5e-07
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	7e-07
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	7e-07
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	1e-06
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	3e-06
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	4e-06
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	1e-05
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.002
d2e29a1	85	d.58.7.5 (A:8-92) ATP-dependent RNA helicase DDX50	2e-04

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score =  126 bits (319), Expect = 7e-34
 Identities = 37/180 (20%), Positives = 62/180 (34%), Gaps = 21/180 (11%)

Query: 39  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGD 97
           I+  A+STT          +     KGG+ ++F  +K+  DE++  L ++ I + A +  
Sbjct: 11  IEEVALSTTG-EIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRG 69

Query: 98  ISQHQR----------ERTLNGFRQGKFTVLVATDVAARG---LDIPNVDLIIHYELPND 144
           +                  L     G F  ++  +          +     I    LP D
Sbjct: 70  LDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQD 129

Query: 145 PETFVHRSGRTGRAGKEGTAILMFTSSQRR-TVRSLE----RDVGCKFEFVSPPVVEDVL 199
             +   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 =  113 bits (283), Expect = 2e-29
 Identities = 33/203 (16%), Positives = 64/203 (31%), Gaps = 21/203 (10%)

Query: 51  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGF 110
             + LS ++     G   I++ +T  +A+E+  +L            I    ++     F
Sbjct: 13  SISTLSSILE--KLGTGGIIYARTGEEAEEIYESL-----KNKFRIGIVTATKKGDYEKF 65

Query: 111 RQGKFTVLVAT----DVAARGLDIP-NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
            +G+   L+ T        RGLD+P  +   +    P+    F            +   +
Sbjct: 66  VEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKL 121

Query: 166 LMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTA 225
           L +       +  L   V    +      V ++L+    +       V     E   P  
Sbjct: 122 LAYLYRNVDEIERLLPAVERHID-----EVREILKKVMGKERPQAKDVVVREGEVIFPDL 176

Query: 226 QRLIEEKGTDALAAALAQLSGFS 248
           +  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 =  101 bits (252), Expect = 5e-26
 Identities = 47/150 (31%), Positives = 83/150 (55%), Gaps = 3/150 (2%)

Query: 51  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNG 109
           K   L+DL        + ++F  T+R  +E++  L +      A++ D+ Q +R+  +  
Sbjct: 14  KYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKE 72

Query: 110 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT 169
           FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR GR GR G++G AI   T
Sbjct: 73  FRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVT 132

Query: 170 SSQRRTVRSLERDVGCKFEFVSPPVVEDVL 199
           +     +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 =  101 bits (253), Expect = 6e-25
 Identities = 41/136 (30%), Positives = 61/136 (44%), Gaps = 13/136 (9%)

Query: 50  SKRTILSDLITVY---AKGGKTIVFTQTKRDADE-VSLALTSIIASEALHGDISQHQR-- 103
            K   L ++I       +  K IVFT  +  A + V+  +   I ++   G  S+     
Sbjct: 143 PKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRG 202

Query: 104 ------ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 157
                 +  L+ F +G+F VLVAT V   GLD+P VDL++ YE        + R GRTGR
Sbjct: 203 LSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 262

Query: 158 AGKEGTAILMFTSSQR 173
               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 = 97.7 bits (242), Expect = 1e-24
 Identities = 60/170 (35%), Positives = 95/170 (55%), Gaps = 4/170 (2%)

Query: 32  DEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIA 90
           DE   EGIK + ++      K   L DL        + ++F  TKR  D ++  +     
Sbjct: 1   DELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANF 59

Query: 91  SEA-LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFV 149
           + + +HGD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++
Sbjct: 60  TVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYI 119

Query: 150 HRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVL 199
           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 = 96.6 bits (239), Expect = 2e-24
 Identities = 51/151 (33%), Positives = 84/151 (55%), Gaps = 3/151 (1%)

Query: 39  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDI 98
           I+   +      +   L  L+    K    +VF +TKRD  E++  L  I          
Sbjct: 4   IEQSYVEVNENERFEALCRLLK--NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGD 61

Query: 99  S-QHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 157
             Q QRE+ +  F+Q K  +L+ATDV +RG+D+ +++ +I+Y LP +PE+++HR GRTGR
Sbjct: 62  LSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGR 121

Query: 158 AGKEGTAILMFTSSQRRTVRSLERDVGCKFE 188
           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 = 93.0 bits (230), Expect = 1e-22
 Identities = 30/137 (21%), Positives = 61/137 (44%), Gaps = 5/137 (3%)

Query: 33  EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASE 92
           E L    +   I+  + +K   L +++  + +  K I+FT+       +S     +    
Sbjct: 62  EALRAWEEARRIAFNSKNKIRKLREILERH-RKDKIIIFTRHNELVYRIS----KVFLIP 116

Query: 93  ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS 152
           A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +          ++ R 
Sbjct: 117 AITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRL 176

Query: 153 GRTGRAGKEGTAILMFT 169
           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 = 80.1 bits (197), Expect = 1e-18
 Identities = 36/138 (26%), Positives = 55/138 (39%), Gaps = 12/138 (8%)

Query: 39  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDI 98
           I+  A+STT        +  + V  KGG+ ++F  +K+  DE++  L       AL  + 
Sbjct: 10  IEEVALSTTGEIPFYGKAIPLEVI-KGGRHLIFCHSKKKCDELAAKL------VALGINA 62

Query: 99  SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN---VDLIIHYELPNDPETFVHRSGRT 155
             + R   ++        V+VATD    G        +D       P D  +   R GRT
Sbjct: 63  VAYYRGLDVSVIPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRT 122

Query: 156 GRAGKEGTAILMFTSSQR 173
           GR GK G         +R
Sbjct: 123 GR-GKPGI-YRFVAPGER 138

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

 Score = 75.6 bits (185), Expect = 1e-16
 Identities = 30/118 (25%), Positives = 54/118 (45%), Gaps = 3/118 (2%)

Query: 54  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 112
           ++ ++     +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R 
Sbjct: 20  LIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRL 79

Query: 113 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS--GRTGRAGKEGTAILMF 168
           GK+ VLV  ++   GLDIP V L+   +   +      RS     GRA +     ++ 
Sbjct: 80  GKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM 137

>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 = 75.1 bits (183), Expect = 2e-16
 Identities = 45/170 (26%), Positives = 83/170 (48%), Gaps = 4/170 (2%)

Query: 36  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEAL 94
            +GI  Y        K   L+ L +   +  + I+F  +    + ++        +    
Sbjct: 4   LKGITQYYAFVEERQKLHCLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYS 62

Query: 95  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 154
           H  + Q +R +  + FRQGK   LV +D+  RG+DI  V+++I+++ P   ET++HR GR
Sbjct: 63  HARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGR 122

Query: 155 TGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAE 204
           +GR G  G AI +   + R  +  +E+++G +   + P  ++  L   AE
Sbjct: 123 SGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAI-PATIDKSLY-VAE 170

>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 = 77.3 bits (189), Expect = 3e-16
 Identities = 23/190 (12%), Positives = 48/190 (25%), Gaps = 45/190 (23%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVGNQDEKLAEGIKLYAISTTATSKRTILSDLIT 60
           +  +AT P       +           +  +                             
Sbjct: 135 IFMTATPPGSRDPFPQSNAPIMDEEREIPERSWNSG---------------------HEW 173

Query: 61  VYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLV 119
           V    GKT+ F  + +  ++++  L         L       +  +     R   +  +V
Sbjct: 174 VTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYIK----TRTNDWDFVV 229

Query: 120 ATDVAARGLDI-------------------PNVDLIIHYELPNDPETFVHRSGRTGRAGK 160
            TD++  G +                        +I+   +P    +   R GR GR  K
Sbjct: 230 TTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPK 289

Query: 161 EGTAILMFTS 170
                 ++  
Sbjct: 290 NENDQYIYMG 299

>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 = 74.6 bits (182), Expect = 4e-16
 Identities = 41/188 (21%), Positives = 68/188 (36%), Gaps = 46/188 (24%)

Query: 35  LAEGIKL-----YAISTTATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSI 88
           L EG+             +TS+R    +L+    A+ G  +VF  T+R A++ ++ L++I
Sbjct: 4   LVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAI 63

Query: 89  IASEA-------------------------------LHGDISQHQRERTLNGFRQGKFTV 117
            A                                   H  +   QR    + FR+G   V
Sbjct: 64  TAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKV 123

Query: 118 LVATDVAARGLDIPNVDLIIH-------YELPNDPETFVHRSGRTGRAGK--EGTAILMF 168
           +VAT   A G+++P   +I+        Y        +   +GR GR G    G AI++ 
Sbjct: 124 VVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIV 183

Query: 169 TSSQRRTV 176
               R   
Sbjct: 184 GKRDREIA 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 = 72.0 bits (176), Expect = 2e-15
 Identities = 31/136 (22%), Positives = 58/136 (42%), Gaps = 8/136 (5%)

Query: 54  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 112
           ++  +    A+G +T+V   T R A+E++  L    I +  LH ++   +R+  +   R 
Sbjct: 20  LMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRL 79

Query: 113 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS--GRTGRAGKEGTAILMF-- 168
           G +  LV  ++   GLDIP V L+   +   +      RS     GRA +     +    
Sbjct: 80  GHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYA 139

Query: 169 ---TSSQRRTVRSLER 181
              + + +R +    R
Sbjct: 140 DRVSEAMQRAIEETNR 155

>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 = 70.5 bits (171), Expect = 1e-14
 Identities = 28/129 (21%), Positives = 60/129 (46%), Gaps = 2/129 (1%)

Query: 50  SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLN 108
                L   +    +G   I++  ++   ++ +  L S  I++ A H  +  + R     
Sbjct: 16  KPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQE 74

Query: 109 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 168
            F++    ++VAT     G++ PNV  ++H+++P + E++   +GR GR G    A+L +
Sbjct: 75  KFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 134

Query: 169 TSSQRRTVR 177
             +    +R
Sbjct: 135 DPADMAWLR 143

>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 = 67.8 bits (164), Expect = 5e-14
 Identities = 37/166 (22%), Positives = 79/166 (47%), Gaps = 4/166 (2%)

Query: 38  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEALHG 96
           G++ Y +      K   L DL+ V  +  + ++F ++ +    ++ L +     + A+H 
Sbjct: 1   GLQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHR 59

Query: 97  DISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG 156
            + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R G
Sbjct: 60  GMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAG 119

Query: 157 RAGKEGTAILMFTSSQ-RRTVRSLERDVGCKFEFVSPPV-VEDVLE 200
           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 = 3e-12
 Identities = 34/149 (22%), Positives = 59/149 (39%), Gaps = 15/149 (10%)

Query: 92  EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFV-H 150
              HG + + + ER +N F   +F VLV T +   G+DIP  + II     +     +  
Sbjct: 61  AIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQ 120

Query: 151 RSGRTGRAGKEGTAILMFTSSQRRTVRSLER--------DVGCKFEFVSPPVVEDVLESS 202
             GR GR+  +  A L+    +  T  + +R        D+G  F   +     D+    
Sbjct: 121 LRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALAT----HDLEIRG 176

Query: 203 AEQVVATLNGVHPESVEFFTPTAQRLIEE 231
           A +++        E++ F       L+E 
Sbjct: 177 AGELLGEEQSGSMETIGF--SLYMELLEN 203

>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 = 51.2 bits (121), Expect = 4e-08
 Identities = 10/28 (35%), Positives = 20/28 (71%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLV 28
           ++FSAT+P  +K   +KY++NP  + ++
Sbjct: 182 LVFSATIPEKLKPFLKKYMENPTFVHVL 209

>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 = 51.1 bits (121), Expect = 5e-08
 Identities = 13/27 (48%), Positives = 17/27 (62%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDL 27
           +LFSAT P  VK+   K+L  P  I+L
Sbjct: 178 LLFSATFPLTVKEFMVKHLHKPYEINL 204

>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 = 50.7 bits (120), Expect = 6e-08
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNID 26
           +L+SAT P  V+K    +L+ P  I+
Sbjct: 181 LLYSATFPLSVQKFMNSHLEKPYEIN 206

>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 = 50.6 bits (120), Expect = 8e-08
 Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 1/97 (1%)

Query: 94  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET-FVHRS 152
           +HG +SQ +++R +  F +G++ +LV+T V   G+D+P  ++++                
Sbjct: 70  MHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLR 129

Query: 153 GRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF 189
           GR GR G+E    L+        +  L         F
Sbjct: 130 GRVGRGGQEAYCFLVVGDVGEEAMERLRFFTLNTDGF 166

>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 = 48.7 bits (115), Expect = 4e-07
 Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 1/29 (3%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDLVG 29
           ++FSAT P  ++KL+  +L N + +  VG
Sbjct: 211 LMFSATFPKEIQKLAADFLYNYIFMT-VG 238

>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 = 47.9 bits (113), Expect = 5e-07
 Identities = 11/25 (44%), Positives = 19/25 (76%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNI 25
           +L SATMP+ V +++ K++ NP+ I
Sbjct: 186 VLLSATMPNDVLEVTTKFMRNPVRI 210

>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 = 47.6 bits (112), Expect = 7e-07
 Identities = 9/25 (36%), Positives = 18/25 (72%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNI 25
           M+FSAT+   ++ + RK++ +P+ I
Sbjct: 181 MMFSATLSKEIRPVCRKFMQDPMEI 205

>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 = 47.5 bits (112), Expect = 7e-07
 Identities = 11/27 (40%), Positives = 21/27 (77%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDL 27
           +L SATMPS V ++++K++ +P+ I +
Sbjct: 190 VLLSATMPSDVLEVTKKFMRDPIRILV 216

>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 = 47.5 bits (112), Expect = 1e-06
 Identities = 8/27 (29%), Positives = 19/27 (70%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDL 27
           +L SAT+P  + +++ K++ +P+ I +
Sbjct: 194 VLISATLPHEILEMTNKFMTDPIRILV 220

>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 = 45.8 bits (108), Expect = 3e-06
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 1   MLFSATMPSWVKKLSRKYLDNPLNIDL 27
           +LFSATMP  +  L++KY+ +   I  
Sbjct: 180 LLFSATMPREILNLAKKYMGDYSFIKA 206

>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 = 46.1 bits (109), Expect = 4e-06
 Identities = 20/125 (16%), Positives = 39/125 (31%), Gaps = 23/125 (18%)

Query: 65  GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV 123
              T  F  + R A+ ++ +L     +   L+    + +        +Q K   ++ATD+
Sbjct: 36  KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPT----IKQKKPDFILATDI 91

Query: 124 AARGLDIPNV------------------DLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 165
           A  G ++                      + I   L     +   R GR GR        
Sbjct: 92  AEMGANLCVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDS 151

Query: 166 LMFTS 170
             ++ 
Sbjct: 152 YYYSE 156

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 10/16 (62%), Positives = 10/16 (62%)

Query: 455 CFNCGKSGHRASECPN 470
           CFNCGK GH A  C  
Sbjct: 4   CFNCGKEGHTARNCRA 19

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 33.7 bits (77), Expect = 0.002
 Identities = 7/19 (36%), Positives = 10/19 (52%)

Query: 452 GGACFNCGKSGHRASECPN 470
              C+ CGK GH+  +C  
Sbjct: 22  KKGCWKCGKEGHQMKDCTE 40

>d2e29a1 d.58.7.5 (A:8-92) ATP-dependent RNA helicase DDX50 {Human (Homo sapiens) [TaxId: 9606]} Length = 85

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]

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 7/77 (9%)

Query: 253 SRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADE-IGKIHIIADDRVQ 311
            RSLI  ++G+VT+ L                   L+    + A   I ++ ++  +   
Sbjct: 3   PRSLITSDKGFVTMTLE----SLEEIQDVSCAWKELNRKLSSNAVSQITRMCLLKGN--M 56

Query: 312 GAVFDLPEEIAKELLNK 328
           G  FD+P   ++ L  +
Sbjct: 57  GVCFDVPTTESERLQAE 73

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	470
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	99.98
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.97
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.97
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.97
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.96
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.93
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.93
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.89
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.84
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.81
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.8
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.79
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.76
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.76
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.74
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.56
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.48
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.43
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.42
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.28
d2e29a1	85	ATP-dependent RNA helicase DDX50 {Human (Homo sapi	98.68
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.66
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	98.16
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.05
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.55
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.35
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.18
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	97.14
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.94
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	93.28
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	93.24
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	93.14
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	92.16
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	91.56
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	89.96
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	88.04
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	87.71
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	86.87
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	83.77
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	81.73

>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=1.7e-32  Score=243.43  Aligned_cols=159  Identities=35%  Similarity=0.592  Sum_probs=147.9

Q ss_pred             cccccceEEEEEEcCcc-cHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHccc
Q 012133           33 EKLAEGIKLYAISTTAT-SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGF  110 (470)
Q Consensus        33 ~~~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f  110 (470)
                      +.+..+|+|+|+.++.+ .|++.|.++++.+ ...++||||++++.++.++..|.. ++.+..+|+++++++|.++++.|
T Consensus         2 ~~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~-~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   80 (168)
T d2j0sa2           2 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEF   80 (168)
T ss_dssp             GCSCTTEEEEEEEESSTTHHHHHHHHHHHHH-TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHH
T ss_pred             CCCCCCcEEEEEEecChHHHHHHHHHHHHhC-CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHH
Confidence            34568999999998775 5999999999876 557999999999999999999985 78999999999999999999999


Q ss_pred             ccCCeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCcccc
Q 012133          111 RQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV  190 (470)
Q Consensus       111 ~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~  190 (470)
                      ++++.+||||||++++|||+|+|++|||||+|++++.|+||+||+||.|+.|.+++|+++.+...++.|++.++.+++.+
T Consensus        81 k~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i~~~~~~~i~e~  160 (168)
T d2j0sa2          81 RSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEM  160 (168)
T ss_dssp             HHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEEC
T ss_pred             hcCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHHHHHHHcCcCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999888777


Q ss_pred             CC
Q 012133          191 SP  192 (470)
Q Consensus       191 ~~  192 (470)
                      +.
T Consensus       161 p~  162 (168)
T d2j0sa2         161 PM  162 (168)
T ss_dssp             CS
T ss_pred             Cc
Confidence            43

>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=3.4e-32  Score=242.60  Aligned_cols=158  Identities=27%  Similarity=0.496  Sum_probs=149.7

Q ss_pred             cccceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccC
Q 012133           35 LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG  113 (470)
Q Consensus        35 ~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g  113 (470)
                      +..+|+|+|+.++..+|...|.++|+.. +..++||||+|++.++.|+..|.. ++.+..+||+|++++|.++++.|+++
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 568999999999999999999985 89999999999999999999999999


Q ss_pred             CeeEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCCC
Q 012133          114 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  193 (470)
Q Consensus       114 ~~~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~p  193 (470)
                      ..+|||||+++++|||+|++++|||||+|+++++|+||+||+||.|+.|.+++|+++.+...++.|++.++.+++.++..
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            99999999999999999999999999999999999999999999999999999999999999999999999888776544

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.98  E-value=2.1e-32  Score=241.48  Aligned_cols=153  Identities=31%  Similarity=0.570  Sum_probs=138.0

Q ss_pred             eEEEEEEcCc-ccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCee
Q 012133           39 IKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        39 i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                      |+|+|+.+.. +.|+++|.++++.. +..++||||+|+..++++++.|.. ++.+..+||+|++++|..+++.|+.++.+
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            5788888754 56999999999876 568999999999999999999985 79999999999999999999999999999


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCccccCC
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  192 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~~~  192 (470)
                      ||||||+++||||+|+|++|||||+|++++.|+||+||+||.|+.|.|++|+++.+...++.|++.++.+++.++.
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            9999999999999999999999999999999999999999999999999999999999999999999998887654

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.97  E-value=1.5e-31  Score=234.51  Aligned_cols=152  Identities=36%  Similarity=0.616  Sum_probs=143.3

Q ss_pred             cceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCe
Q 012133           37 EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF  115 (470)
Q Consensus        37 ~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~  115 (470)
                      .+|+|+|+.++..+|++.|.++|+.  .+.++||||+|+++++.|++.|.. ++.+..+|+++++.+|..++++|++++.
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            5789999999999999999998864  456899999999999999999985 7899999999999999999999999999


Q ss_pred             eEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHHHHhCCCcccc
Q 012133          116 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV  190 (470)
Q Consensus       116 ~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~~~~~~~~~~~  190 (470)
                      +|||||+++++|||+|++++||+||+|+++..|+||+||+||.|++|.+++|+++.|...++.|++.++.+++++
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            999999999999999999999999999999999999999999999999999999999999999999998887654

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=4e-30  Score=228.13  Aligned_cols=152  Identities=24%  Similarity=0.465  Sum_probs=141.7

Q ss_pred             ceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCee
Q 012133           38 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        38 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~  116 (470)
                      .++|+|+.+..++|.++|.++|+.+ ...++||||++++.++.|++.|.+ ++.+..+||+|++++|..+++.|++++++
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            3689999999999999999999887 457999999999999999999985 79999999999999999999999999999


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChh-hHHHHHHHHHHhCCCcccc
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFV  190 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~-~~~~~~~i~~~~~~~~~~~  190 (470)
                      |||||+++++|+|+|.+++||+|++|++++.|+||+||+||.|++|.||+|+++. +...++.+++.+...+..+
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            9999999999999999999999999999999999999999999999999999874 5678888999988887765

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.96  E-value=7.8e-29  Score=225.51  Aligned_cols=141  Identities=21%  Similarity=0.426  Sum_probs=127.3

Q ss_pred             cceEEEEEEcCcccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCe
Q 012133           37 EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF  115 (470)
Q Consensus        37 ~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~  115 (470)
                      ++|.  |..++..+|++.|..+|+.+ ...++||||+|++.++.|+..|.. ++.+..+||+|++++|.++++.|+++++
T Consensus         5 pNi~--y~v~~~~~k~~~L~~~l~~~-~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~   81 (200)
T d1oywa3           5 PNIR--YMLMEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDL   81 (200)
T ss_dssp             TTEE--EEEEECSSHHHHHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCcE--EEEEcCCcHHHHHHHHHHhc-CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccc
Confidence            4453  33344567888888888775 557999999999999999999985 7999999999999999999999999999


Q ss_pred             eEEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHH
Q 012133          116 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  180 (470)
Q Consensus       116 ~iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~  180 (470)
                      +|||||+++++|||+|+|++||||++|+++++|+||+|||||.|++|.+++|+++.|...++++.
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            99999999999999999999999999999999999999999999999999999999888777654

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=99.93  E-value=5.7e-26  Score=199.68  Aligned_cols=128  Identities=23%  Similarity=0.398  Sum_probs=111.4

Q ss_pred             HHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCC
Q 012133           51 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  129 (470)
Q Consensus        51 k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gid  129 (470)
                      ..+++..+.+...++.++||||+|+++++.|+..|.. ++.+..+||+|++.+|++++++|++|+++|||||+++++|||
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            3456666666666788999999999999999999985 899999999999999999999999999999999999999999


Q ss_pred             CCCccEEEEecCCC-----ChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHH
Q 012133          130 IPNVDLIIHYELPN-----DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       130 ip~v~~VI~~~~p~-----~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i  179 (470)
                      +|+|++||+|++|.     +.++|+||+||+||.+ +|.+++++......+.+.+
T Consensus        97 ip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~-~g~~~~~~~~~~~~~~~~i  150 (174)
T d1c4oa2          97 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSEAMQRAI  150 (174)
T ss_dssp             CTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCHHHHHHH
T ss_pred             CCCCcEEEEeccccccccchhHHHHHHhhhhhhcC-CCeeEEeecCCCHHHHHHH
Confidence            99999999999776     5588999999999986 4888888776555444444

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=99.93  E-value=9.2e-26  Score=201.26  Aligned_cols=121  Identities=25%  Similarity=0.425  Sum_probs=105.5

Q ss_pred             HHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCC
Q 012133           51 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  129 (470)
Q Consensus        51 k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gid  129 (470)
                      ..++|..+.+....+.++||||++++.++.++..|.+ ++.+..+||+|++.+|.+++++|++|+++||||||++++|||
T Consensus        17 vd~ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiD   96 (181)
T d1t5la2          17 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLD   96 (181)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCC
T ss_pred             HHHHHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCC
Confidence            3455666666656778999999999999999999985 899999999999999999999999999999999999999999


Q ss_pred             CCCccEEEEecCCC-----ChhHHHHHhcccCCCCCCCeEEEeeChhh
Q 012133          130 IPNVDLIIHYELPN-----DPETFVHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       130 ip~v~~VI~~~~p~-----~~~~y~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      +|+|++|||||+|.     +...|+||+||+||.|. +.+++++....
T Consensus        97 ip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~-~~~~~~~~~~~  143 (181)
T d1t5la2          97 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIMYADTIT  143 (181)
T ss_dssp             CTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSCC
T ss_pred             CCCCCEEEEecCCcccccccHHHHHHHHHhhccccC-ceeEeecchhh
Confidence            99999999999996     68899999999999874 44455544433

>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=99.89  E-value=4.5e-24  Score=181.71  Aligned_cols=99  Identities=29%  Similarity=0.469  Sum_probs=89.6

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEec--
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE--  140 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~--  140 (470)
                      +.+++||||+|++.|++|++.|.+ ++.+..+|++|++       +.|++++.+||||||++++||| |+|++||||+  
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            568999999999999999999985 8999999999985       4688999999999999999999 9999999865  


Q ss_pred             --CCCChhHHHHHhcccCCCCCCCeEEEeeChhh
Q 012133          141 --LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       141 --~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                        +|.++++|+||+||||| |++|. ++|+++.|
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 99996 66777654

>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=99.84  E-value=4.8e-21  Score=183.94  Aligned_cols=123  Identities=33%  Similarity=0.551  Sum_probs=105.6

Q ss_pred             ccHHHHHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeC--------CCCHHHHHHHHcccccCCee
Q 012133           49 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHG--------DISQHQRERTLNGFRQGKFT  116 (470)
Q Consensus        49 ~~k~~~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg--------~~~~~~R~~~~~~f~~g~~~  116 (470)
                      ..|++.|.++|..+   ..+.++||||++++.++.+++.|.+ ++++..+||        .|++.+|..+++.|++++++
T Consensus       142 ~pK~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~  221 (286)
T d1wp9a2         142 HPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFN  221 (286)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCS
T ss_pred             CcHHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCc
Confidence            35777777776432   4567999999999999999999985 688888866        56777899999999999999


Q ss_pred             EEEecccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhh
Q 012133          117 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       117 iLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      |||||+++++|||+|++++||+||+|+++..|+||+||+||. +++.+++|+++..
T Consensus       222 vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~-~~~~~~~l~~~~~  276 (286)
T d1wp9a2         222 VLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH-MPGRVIILMAKGT  276 (286)
T ss_dssp             EEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSC-CCSEEEEEEETTS
T ss_pred             EEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCC-CCCEEEEEEeCCC
Confidence            999999999999999999999999999999999999999997 5788888888753

>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=99.81  E-value=3.2e-20  Score=168.42  Aligned_cols=120  Identities=28%  Similarity=0.534  Sum_probs=102.8

Q ss_pred             HHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhcC-------------------------------CcEEEEeCCCCH
Q 012133           52 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------IASEALHGDISQ  100 (470)
Q Consensus        52 ~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~~-------------------------------~~~~~lhg~~~~  100 (470)
                      .+++.+++   .+++++||||+|++.|+.++..|...                               ..+..+|++|++
T Consensus        30 ~~l~~~~i---~~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          30 EELVEECV---AENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHH---HTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHH---HcCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            34444444   45689999999999999888877531                               137889999999


Q ss_pred             HHHHHHHcccccCCeeEEEecccccccCCCCCccEEEE-------ecCCCChhHHHHHhcccCCCC--CCCeEEEeeChh
Q 012133          101 HQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-------YELPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  171 (470)
Q Consensus       101 ~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~-------~~~p~~~~~y~qr~GR~gR~g--~~g~~i~l~~~~  171 (470)
                      ++|..+++.|+++.++|||||+++++|||+|.+++||+       ++.|.++.+|+||+|||||.|  ..|.+++++.+.
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       677889999999999999988  478999998887


Q ss_pred             hHH
Q 012133          172 QRR  174 (470)
Q Consensus       172 ~~~  174 (470)
                      +..
T Consensus       187 ~~~  189 (201)
T d2p6ra4         187 DRE  189 (201)
T ss_dssp             GHH
T ss_pred             ChH
Confidence            653

>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=99.80  E-value=5.2e-21  Score=173.03  Aligned_cols=128  Identities=20%  Similarity=0.410  Sum_probs=100.8

Q ss_pred             HHHHHHHHHHHcCCCeEEEEeCchHHHHH--------HHHHHhc----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEE
Q 012133           52 RTILSDLITVYAKGGKTIVFTQTKRDADE--------VSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  119 (470)
Q Consensus        52 ~~~l~~ll~~~~~~~~~lVF~~t~~~~~~--------l~~~l~~----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLV  119 (470)
                      ..++..+.+.+..+.++.|.||..+..+.        .++.|.+    .+.+..+||+|++++|++++++|++|+++|||
T Consensus        16 ~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLV   95 (206)
T d1gm5a4          16 NEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILV   95 (206)
T ss_dssp             HHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCC
T ss_pred             HHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEE
Confidence            34444455566777899999987665443        3333332    35688899999999999999999999999999


Q ss_pred             ecccccccCCCCCccEEEEecCCC-ChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHH
Q 012133          120 ATDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  179 (470)
Q Consensus       120 aTdv~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i  179 (470)
                      ||+|+++|||+|++++||+++.|. ..+.|.|..||+||.++++.|++++.+......+++
T Consensus        96 aTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~rl  156 (206)
T d1gm5a4          96 STTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERL  156 (206)
T ss_dssp             CSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHH
T ss_pred             EehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchhhh
Confidence            999999999999999999999997 678888889999999999999999987555444444

>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=99.79  E-value=3.6e-22  Score=187.91  Aligned_cols=122  Identities=18%  Similarity=0.322  Sum_probs=104.5

Q ss_pred             cccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEec----cc
Q 012133           48 ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT----DV  123 (470)
Q Consensus        48 ~~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaT----dv  123 (470)
                      .++|++.|..+|+.+  +.++||||+|++.++.|++.|...     +||+|++.+|.+++++|++|+++|||||    ++
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            356778888888754  468999999999999999999753     7999999999999999999999999999    89


Q ss_pred             ccccCCCCC-ccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhhHHHHHHHH
Q 012133          124 AARGLDIPN-VDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  180 (470)
Q Consensus       124 ~~~Gidip~-v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~i~  180 (470)
                      +++|||+|+ |++|||||+|+    |.||+||+||+|+.+.+++++...+...++.+.
T Consensus        83 ~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~  136 (248)
T d1gkub2          83 LVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLL  136 (248)
T ss_dssp             --CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTC
T ss_pred             hhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHHHHHHH
Confidence            999999996 99999999995    899999999999999999998887766655543

>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=99.76  E-value=1.7e-19  Score=168.70  Aligned_cols=106  Identities=25%  Similarity=0.370  Sum_probs=93.5

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHH----------HHHHcccccCCeeEEEecccccc---cCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQR----------ERTLNGFRQGKFTVLVATDVAAR---GLD  129 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R----------~~~~~~f~~g~~~iLVaTdv~~~---Gid  129 (470)
                      +.+++||||+|++.|++|+..|.+ ++.+..+|++|+++.|          ..+++.|+.++.++||+|+++++   ++|
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            468999999999999999999984 8999999999999887          56788999999999999999999   677


Q ss_pred             CCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          130 IPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       130 ip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                      ++.|.+||+|++|.|+++|+||+||||| |++|...+++..
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~  154 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPG  154 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSC
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecC
Confidence            8888899999999999999999999999 899988776654

>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=99.76  E-value=1.7e-19  Score=163.86  Aligned_cols=108  Identities=25%  Similarity=0.449  Sum_probs=98.7

Q ss_pred             ccHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccC
Q 012133           49 TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  128 (470)
Q Consensus        49 ~~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gi  128 (470)
                      ..|++.|.++++.+ ...++||||+++..++.|++.|    .+..+||++++.+|+.+++.|++++++|||+|+++++||
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            46788888888875 5689999999999999988876    355689999999999999999999999999999999999


Q ss_pred             CCCCccEEEEecCCCChhHHHHHhcccCCCCCC
Q 012133          129 DIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE  161 (470)
Q Consensus       129 dip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~  161 (470)
                      |+|.+++||++++|+++..|+||+||++|.++.
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            999999999999999999999999999998753

>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=99.74  E-value=2.4e-17  Score=147.53  Aligned_cols=122  Identities=21%  Similarity=0.365  Sum_probs=110.4

Q ss_pred             cHHHHHHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc---CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccc
Q 012133           50 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR  126 (470)
Q Consensus        50 ~k~~~l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~---~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~  126 (470)
                      ++..+...+.+.+..++++.+.||..+.++.+++.+.+   .+.+..+||.|+++++++++.+|++++++|||||.+++.
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            44556666667788899999999999999999998885   578999999999999999999999999999999999999


Q ss_pred             cCCCCCccEEEEecCCC-ChhHHHHHhcccCCCCCCCeEEEeeChh
Q 012133          127 GLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTSS  171 (470)
Q Consensus       127 Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~l~~~~  171 (470)
                      |||+|+++++|.++.+. ...++.|..||+||.++.+.||+++.+.
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            99999999999988875 8999999999999999999999998653

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.56  E-value=3.1e-15  Score=143.59  Aligned_cols=103  Identities=18%  Similarity=0.313  Sum_probs=86.7

Q ss_pred             cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEE----
Q 012133           63 AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII----  137 (470)
Q Consensus        63 ~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI----  137 (470)
                      ...+++||||+++++++++++.|.+ ++.+..+|+++++..    ...|+++..++||||+++++|+|++ +++||    
T Consensus       176 ~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~  250 (305)
T d2bmfa2         176 DFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRR  250 (305)
T ss_dssp             SSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCE
T ss_pred             hhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCC
Confidence            3568999999999999999999985 789999999986654    4578889999999999999999994 55554    


Q ss_pred             ------Eec----------CCCChhHHHHHhcccCCCCCCCeEEEeeCh
Q 012133          138 ------HYE----------LPNDPETFVHRSGRTGRAGKEGTAILMFTS  170 (470)
Q Consensus       138 ------~~~----------~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~  170 (470)
                            +++          .|.|..+|+||+||+||.++.+..+++|..
T Consensus       251 ~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~  299 (305)
T d2bmfa2         251 CMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMG  299 (305)
T ss_dssp             EEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECS
T ss_pred             ceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECC
Confidence                  344          356889999999999999988888777764

>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=99.48  E-value=1.7e-13  Score=133.68  Aligned_cols=120  Identities=13%  Similarity=0.242  Sum_probs=105.6

Q ss_pred             cccHHHHHHHHHHHH--cCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCe---eEEEec
Q 012133           48 ATSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF---TVLVAT  121 (470)
Q Consensus        48 ~~~k~~~l~~ll~~~--~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~---~iLVaT  121 (470)
                      .+.|+.+|..+|...  ..+.|+|||++.+...+.|...|.. ++.+..+||.++..+|..+++.|+++..   -+|++|
T Consensus        99 ~S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~  178 (346)
T d1z3ix1          99 LSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSS  178 (346)
T ss_dssp             GSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEG
T ss_pred             cCHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecc
Confidence            356888888888653  3567999999999999999999984 8999999999999999999999987643   367899


Q ss_pred             ccccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeEEEe
Q 012133          122 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  167 (470)
Q Consensus       122 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l  167 (470)
                      .+++.|||++.+++||+||++|++..+.|++||+.|.|+...|.++
T Consensus       179 ~agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~  224 (346)
T d1z3ix1         179 KAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIY  224 (346)
T ss_dssp             GGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEE
T ss_pred             hhhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEE
Confidence            9999999999999999999999999999999999999977655543

>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=99.43  E-value=1.4e-13  Score=128.15  Aligned_cols=123  Identities=15%  Similarity=0.274  Sum_probs=90.5

Q ss_pred             cccHHHHHHHHHHH-HcCCCeEEEEeCchHHHHHHHHHHhc--CCcEEEEeCCCCHHHHHHHHcccccCC-eeEE-Eecc
Q 012133           48 ATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGK-FTVL-VATD  122 (470)
Q Consensus        48 ~~~k~~~l~~ll~~-~~~~~~~lVF~~t~~~~~~l~~~l~~--~~~~~~lhg~~~~~~R~~~~~~f~~g~-~~iL-VaTd  122 (470)
                      .+.|+..|.+++.. ...+.++||||+.....+.+...|.+  .+.+..+||++++.+|+.+++.|+++. ..+| ++|.
T Consensus        67 ~S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~  146 (244)
T d1z5za1          67 RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK  146 (244)
T ss_dssp             TCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECC
T ss_pred             hhhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhcccccc
Confidence            35688888888864 34667999999999999999888863  677888999999999999999998754 5666 5558


Q ss_pred             cccccCCCCCccEEEEecCCCChhHHHHHhcccCCCCCCCeE--EEeeCh
Q 012133          123 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA--ILMFTS  170 (470)
Q Consensus       123 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~--i~l~~~  170 (470)
                      +++.|+|++.+++||++++||++..+.|+.+|+.|.|+...+  +.|+..
T Consensus       147 ~~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~  196 (244)
T d1z5za1         147 AGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISV  196 (244)
T ss_dssp             TTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEET
T ss_pred             ccccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeC
Confidence            999999999999999999999999999999999999965443  434444

>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=99.42  E-value=1.8e-13  Score=130.03  Aligned_cols=101  Identities=19%  Similarity=0.253  Sum_probs=79.9

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecccccccCCCCCccEEEEecC-
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL-  141 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv~~~Gidip~v~~VI~~~~-  141 (470)
                      ..+++||||+++.+++++++.|.+ ++.|.+|||.++.++++    +|++++.+||||||+++.|||+ +|.+||+.++ 
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 78999999999988765    5678899999999999999999 5999996553 


Q ss_pred             ------------------CCChhHHHHHhcccCCCCCCCeEEEeeC
Q 012133          142 ------------------PNDPETFVHRSGRTGRAGKEGTAILMFT  169 (470)
Q Consensus       142 ------------------p~~~~~y~qr~GR~gR~g~~g~~i~l~~  169 (470)
                                        |.+..+..||.||+||.+....++++|.
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         110 FKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             eceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                              2467888999999999865555666654

>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=99.28  E-value=3.1e-11  Score=103.95  Aligned_cols=125  Identities=22%  Similarity=0.271  Sum_probs=99.4

Q ss_pred             cCcccHHHHHHHHH-HHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc
Q 012133           46 TTATSKRTILSDLI-TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  123 (470)
Q Consensus        46 ~~~~~k~~~l~~ll-~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv  123 (470)
                      .....|..++.+-+ ..+..+.++||+|.|.+..+.|+..|.+ +++..+|+.....++-+.+-+.  -..-.|.|||++
T Consensus        14 ~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~A--g~~g~VtIATNm   91 (175)
T d1tf5a4          14 RTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEA--GQKGAVTIATNM   91 (175)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTT--TSTTCEEEEETT
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhc--cCCCceeehhhH
Confidence            34456766655544 5666788999999999999999999986 7889999998654443333333  334579999999


Q ss_pred             ccccCCCC---Ccc-----EEEEecCCCChhHHHHHhcccCCCCCCCeEEEeeChhh
Q 012133          124 AARGLDIP---NVD-----LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       124 ~~~Gidip---~v~-----~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      |.||.||.   .|.     |||....|.+.....|..||+||.|.+|.+.+|++-++
T Consensus        92 AGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          92 AGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             SSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             HHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            99999994   232     79999999999999999999999999999999987654

>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=98.68  E-value=2.7e-08  Score=73.94  Aligned_cols=82  Identities=21%  Similarity=0.317  Sum_probs=70.8

Q ss_pred             CCcccccCCCCeEEEEEeeCCccccCCcchhhHHhHhhhhcCc-CcCccccEEEeecCccceeEeecCHHHHHHHHhhcC
Q 012133          252 SSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPT-AADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQI  330 (470)
Q Consensus       252 ~~r~l~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~-~~~~Ig~I~i~~~~~~~ga~fdv~~~~a~~i~~~~~  330 (470)
                      +.|||+++.++++|+.+.+..    ..-+|..++..|.+..+. ..+.|.+|+++++.  +|++||||++.++++.+.|.
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----EIQDVSCAWKELNRKLSSNAVSQITRMCLLKGN--MGVCFDVPTTESERLQAEWH   75 (85)
T ss_dssp             CCCCCCCCCCCEEEEEEECSS----CCSSTHHHHHHHHHHSCHHHHTTCEEEEECTTS--SEEEEEEEHHHHHHHHHHCC
T ss_pred             ccccccccCCCcEEEEEecCc----cccccHHHHHHHHHHccHHHHHhhheeEEecCC--CEEEEeccHHHHHHHHHHhc
Confidence            469999999999999998876    356899999999998865 35679999999986  69999999999999999998


Q ss_pred             CCCCeEEEe
Q 012133          331 PPGNTISKI  339 (470)
Q Consensus       331 ~~g~~i~~~  339 (470)
                      +..+.++++
T Consensus        76 dsr~~ls~~   84 (85)
T d2e29a1          76 DSDWILSVP   84 (85)
T ss_dssp             SSSCEEECC
T ss_pred             ccceEEecC
Confidence            877777654

>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=98.66  E-value=2e-07  Score=81.36  Aligned_cols=125  Identities=25%  Similarity=0.305  Sum_probs=96.2

Q ss_pred             cCcccHHHHHHH-HHHHHcCCCeEEEEeCchHHHHHHHHHHhc-CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc
Q 012133           46 TTATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  123 (470)
Q Consensus        46 ~~~~~k~~~l~~-ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~-~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv  123 (470)
                      .....|..++.+ +...+....++||.+.|.+..+.|+..|.+ +++..+|++.-.  +|+..+-.=.--.-.|-|||++
T Consensus        14 ~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~h--erEAeIIAqAG~~GaVTIATNM   91 (219)
T d1nkta4          14 KTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYH--EQEATIIAVAGRRGGVTVATNM   91 (219)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCH--HHHHHHHHTTTSTTCEEEEETT
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhH--HHHHHHHHhcccCCcEEeeccc
Confidence            344566655544 446677888999999999999999999985 899999999843  3433332222224578999999


Q ss_pred             ccccCCCCC-----------------------------------------------c-----cEEEEecCCCChhHHHHH
Q 012133          124 AARGLDIPN-----------------------------------------------V-----DLIIHYELPNDPETFVHR  151 (470)
Q Consensus       124 ~~~Gidip~-----------------------------------------------v-----~~VI~~~~p~~~~~y~qr  151 (470)
                      |.||.||.-                                               |     =|||-.....|..-=-|-
T Consensus        92 AGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQL  171 (219)
T d1nkta4          92 AGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQL  171 (219)
T ss_dssp             CSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHH
T ss_pred             cCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccccccc
Confidence            999999932                                               1     167877777888888999


Q ss_pred             hcccCCCCCCCeEEEeeChhh
Q 012133          152 SGRTGRAGKEGTAILMFTSSQ  172 (470)
Q Consensus       152 ~GR~gR~g~~g~~i~l~~~~~  172 (470)
                      .||+||.|.+|.+.+|++-++
T Consensus       172 RGRsGRQGDPGsSrFflSLeD  192 (219)
T d1nkta4         172 RGRSGRQGDPGESRFYLSLGD  192 (219)
T ss_dssp             HHTSSGGGCCEEEEEEEETTS
T ss_pred             cccccccCCCccceeEEeccH
Confidence            999999999999999988765

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=98.16  E-value=1e-06  Score=56.76  Aligned_cols=16  Identities=44%  Similarity=1.375  Sum_probs=15.5

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||+||+.|||++|||+
T Consensus        25 C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1          25 CWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             CSSSCCSSSCTTTCCS
T ss_pred             cccCCCCCeecccCCC
Confidence            9999999999999996

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=98.05  E-value=4.4e-07  Score=50.86  Aligned_cols=14  Identities=64%  Similarity=1.621  Sum_probs=13.9

Q ss_pred             cccCCCCCccCCCC
Q 012133          455 CFNCGKSGHRASEC  468 (470)
Q Consensus       455 c~~c~~~gh~~~~c  468 (470)
                      |||||++||.||+|
T Consensus         9 CfNCGkeGH~ar~C   22 (29)
T d1nc8a_           9 CWNCGKEGHSARQC   22 (29)
T ss_dssp             CTTTSCBSSCGGGC
T ss_pred             eecCCccchhhhhc
Confidence            99999999999999

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=97.55  E-value=1.2e-05  Score=51.53  Aligned_cols=16  Identities=63%  Similarity=1.448  Sum_probs=15.3

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      ||+|++.||+++|||+
T Consensus         4 C~~Cg~~GH~~~~Cp~   19 (42)
T d2exfa1           4 CFNCGKEGHTARNCRA   19 (42)
T ss_dssp             CTTTCCSSSCTTTCSS
T ss_pred             cccCCCcCcCcccCcC
Confidence            9999999999999994

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=97.35  E-value=2.9e-05  Score=41.34  Aligned_cols=16  Identities=50%  Similarity=1.362  Sum_probs=14.9

Q ss_pred             ccccCCCCCccCCCCC
Q 012133          454 ACFNCGKSGHRASECP  469 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~  469 (470)
                      -||.||+.||+-+||-
T Consensus         4 vcfscgktghikkdck   19 (26)
T d1dsqa_           4 VCFSCGKTGHIKRDCK   19 (26)
T ss_dssp             BCTTTCCBSSCTTTTT
T ss_pred             EEEecCCcccchhhhh
Confidence            4999999999999995

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.18  E-value=0.00095  Score=60.69  Aligned_cols=103  Identities=19%  Similarity=0.234  Sum_probs=75.8

Q ss_pred             ccHHHHHHHH-HHHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc
Q 012133           49 TSKRTILSDL-ITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  122 (470)
Q Consensus        49 ~~k~~~l~~l-l~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd  122 (470)
                      +-|..+.... +..+..+.++++.+||...+.+.++.+.+     ++.+..+||.++..+|.+++...++|+++|+|.|-
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            4555444333 34455678999999999999998888774     36799999999999999999999999999999996


Q ss_pred             ccc-ccCCCCCccEEEEecCCCChhHHHHHhc
Q 012133          123 VAA-RGLDIPNVDLIIHYELPNDPETFVHRSG  153 (470)
Q Consensus       123 v~~-~Gidip~v~~VI~~~~p~~~~~y~qr~G  153 (470)
                      .+- ..+.+.++.+||.-.  ...-.|.||-.
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            544 468888898888543  22335666653

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=97.14  E-value=7.6e-05  Score=44.99  Aligned_cols=16  Identities=44%  Similarity=1.157  Sum_probs=15.3

Q ss_pred             cccCCCCCccCCCCCC
Q 012133          455 CFNCGKSGHRASECPN  470 (470)
Q Consensus       455 c~~c~~~gh~~~~c~~  470 (470)
                      |--|.|.|||++|||.
T Consensus        13 CAyCke~GHW~~dCPk   28 (40)
T d1a6bb_          13 CAYCKEKGHWAKDCPK   28 (40)
T ss_dssp             CSSSCCTTCCTTSCSS
T ss_pred             hHHHhhcCchhhhCcc
Confidence            9999999999999994

>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=96.94  E-value=0.0016  Score=58.07  Aligned_cols=94  Identities=14%  Similarity=0.131  Sum_probs=76.6

Q ss_pred             cCcccHHHHHHHHH-HHHcCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEE
Q 012133           46 TTATSKRTILSDLI-TVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  119 (470)
Q Consensus        46 ~~~~~k~~~l~~ll-~~~~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLV  119 (470)
                      +..+-|.++....+ ..+..+.++++.+||...+.+.++.+++     ...+..+|+.++..+|..+++.+.+|+++|||
T Consensus        84 dvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~ivi  163 (233)
T d2eyqa3          84 DVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILI  163 (233)
T ss_dssp             CCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEE
T ss_pred             CCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEE
Confidence            33446665555444 5566788999999999999999999874     25688999999999999999999999999999


Q ss_pred             eccccc-ccCCCCCccEEEEe
Q 012133          120 ATDVAA-RGLDIPNVDLIIHY  139 (470)
Q Consensus       120 aTdv~~-~Gidip~v~~VI~~  139 (470)
                      .|-.+- .-+.++++.+||.-
T Consensus       164 Gths~l~~~~~f~~LgLiIiD  184 (233)
T d2eyqa3         164 GTHKLLQSDVKFKDLGLLIVD  184 (233)
T ss_dssp             ECTHHHHSCCCCSSEEEEEEE
T ss_pred             eehhhhccCCccccccceeee
Confidence            997544 46888899988854

>d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId: 11855]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleocapsid protein from mason-pfizer monkey virus (MPMV)
species: Mason-pfizer monkey virus [TaxId: 11855]

Probab=93.28  E-value=0.016  Score=33.19  Aligned_cols=16  Identities=38%  Similarity=0.862  Sum_probs=14.6

Q ss_pred             ccccCCCCCccCCCCC
Q 012133          454 ACFNCGKSGHRASECP  469 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~  469 (470)
                      -|-+|.+--|||+||-
T Consensus         4 lCPrC~kG~HWa~~Cr   19 (32)
T d1cl4a_           4 LCPRCKRGKHWANECK   19 (32)
T ss_dssp             SCSSCSSCSSCSTTCC
T ss_pred             cCccccCcchHHHHhh
Confidence            3999999999999994

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.24  E-value=0.077  Score=46.29  Aligned_cols=70  Identities=16%  Similarity=0.234  Sum_probs=53.6

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCCc
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNV  133 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~v  133 (470)
                      ..++||+++|++.+.++++.+.+     .+.+..++++.+..+....++.    ...|||+|+      +....+++.++
T Consensus        85 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~----~~~Ilv~TPgrl~~~~~~~~~~~~~l  160 (222)
T d2j0sa1          85 ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY----GQHVVAGTPGRVFDMIRRRSLRTRAI  160 (222)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             CceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhcc----CCeEEeCCCCcHHhcccccccccccc
Confidence            45799999999999999987763     3678899999988777666643    468999996      33455677777


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      .++|.
T Consensus       161 ~~lVl  165 (222)
T d2j0sa1         161 KMLVL  165 (222)
T ss_dssp             CEEEE
T ss_pred             eeeee
Confidence            77763

>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=93.14  E-value=0.017  Score=32.93  Aligned_cols=16  Identities=44%  Similarity=0.781  Sum_probs=14.6

Q ss_pred             ccccCCCCCccCCCCC
Q 012133          454 ACFNCGKSGHRASECP  469 (470)
Q Consensus       454 ~c~~c~~~gh~~~~c~  469 (470)
                      -|-+|.+--|||+||=
T Consensus         4 lCPrC~kG~HWa~~Cr   19 (31)
T d1dsva_           4 LCPRCKKGYHWKSECK   19 (31)
T ss_dssp             BCTTTCSSBSCTTTCC
T ss_pred             cCccccCcchHHHHhh
Confidence            4999999999999994

>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=92.16  E-value=0.22  Score=42.53  Aligned_cols=69  Identities=22%  Similarity=0.254  Sum_probs=52.9

Q ss_pred             CCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc-----cc-cccCCCCCc
Q 012133           65 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VA-ARGLDIPNV  133 (470)
Q Consensus        65 ~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd-----v~-~~Gidip~v  133 (470)
                      ..++||.|+|++.|.++.+.+..     ...+..++|+.+..++.+.++     ..+|||+|+     .+ ...+++.++
T Consensus        72 ~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-----~~~IlV~TP~~l~~~l~~~~~~~~~l  146 (208)
T d1hv8a1          72 GIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLKNV  146 (208)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTTSC
T ss_pred             CcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-----CCCEEEEChHHHHHHHHcCCCCcccC
Confidence            45899999999999999887763     367889999988877666553     368999996     22 445678888


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      .++|.
T Consensus       147 ~~lVi  151 (208)
T d1hv8a1         147 KYFIL  151 (208)
T ss_dssp             CEEEE
T ss_pred             cEEEE
Confidence            87774

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.56  E-value=0.38  Score=40.97  Aligned_cols=71  Identities=18%  Similarity=0.163  Sum_probs=54.3

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIP  131 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip  131 (470)
                      ...++||.++|++.+.++++.+..      ...+..++++.+..++...++.    ...|||+|+      +....+++.
T Consensus        70 ~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~----~~~ivv~TPgrl~~~~~~~~~~~~  145 (206)
T d1veca_          70 DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDD----TVHVVIATPGRILDLIKKGVAKVD  145 (206)
T ss_dssp             CSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTS----CCSEEEECHHHHHHHHHTTCSCCT
T ss_pred             cCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHh----ccCeEEeCCccccccccchhcccc
Confidence            345899999999999999887753      2457788888888877766654    678999996      344457788


Q ss_pred             CccEEEE
Q 012133          132 NVDLIIH  138 (470)
Q Consensus       132 ~v~~VI~  138 (470)
                      ++.++|.
T Consensus       146 ~l~~lVl  152 (206)
T d1veca_         146 HVQMIVL  152 (206)
T ss_dssp             TCCEEEE
T ss_pred             ccceEEE
Confidence            8888774

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.96  E-value=0.44  Score=41.27  Aligned_cols=72  Identities=18%  Similarity=0.265  Sum_probs=50.5

Q ss_pred             ccHHHH-HHHHHHHHcCCCeEEEEeCchHHHHHHHHHHhc---C------CcEEEEeCCCCHHHHHHHHcccccCCeeEE
Q 012133           49 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---I------IASEALHGDISQHQRERTLNGFRQGKFTVL  118 (470)
Q Consensus        49 ~~k~~~-l~~ll~~~~~~~~~lVF~~t~~~~~~l~~~l~~---~------~~~~~lhg~~~~~~R~~~~~~f~~g~~~iL  118 (470)
                      .-|..+ +..++....++.++||.+||+..++++++.+.+   .      ..+..+++..+..++...++...  ...||
T Consensus        69 sGKT~~~~~~~~~~~~~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~Il  146 (237)
T d1gkub1          69 VGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLR--NFKIV  146 (237)
T ss_dssp             SCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGG--GCSEE
T ss_pred             ChHHHHHHHHHHHHHHhcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhcccc--cccee
Confidence            345433 222334445678999999999999999988863   1      23566788888888888777655  35789


Q ss_pred             Eecc
Q 012133          119 VATD  122 (470)
Q Consensus       119 VaTd  122 (470)
                      |+|+
T Consensus       147 v~Tp  150 (237)
T d1gkub1         147 ITTT  150 (237)
T ss_dssp             EEEH
T ss_pred             ccCh
Confidence            9995

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.04  E-value=0.61  Score=39.81  Aligned_cols=89  Identities=16%  Similarity=0.197  Sum_probs=53.2

Q ss_pred             EcCcccHHH-HHHHHHHHH---cCCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCe
Q 012133           45 STTATSKRT-ILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKF  115 (470)
Q Consensus        45 ~~~~~~k~~-~l~~ll~~~---~~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~  115 (470)
                      .....-|.. .+.-++..+   .....+||+++|++.+.++...+..     ...+..+++..+..++...++     ..
T Consensus        54 a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~  128 (212)
T d1qdea_          54 AQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-----DA  128 (212)
T ss_dssp             CCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CT-----TC
T ss_pred             cccccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHhc-----CC
Confidence            334445543 233344433   2345899999999999999888763     245677777665555443332     46


Q ss_pred             eEEEecc------cccccCCCCCccEEEE
Q 012133          116 TVLVATD------VAARGLDIPNVDLIIH  138 (470)
Q Consensus       116 ~iLVaTd------v~~~Gidip~v~~VI~  138 (470)
                      .|||+|+      .-...+++.++.++|.
T Consensus       129 ~IvI~TP~~l~~~~~~~~~~l~~l~~lVl  157 (212)
T d1qdea_         129 QIVVGTPGRVFDNIQRRRFRTDKIKMFIL  157 (212)
T ss_dssp             SEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             cEEEECCCccccccccCceecCcceEEee
Confidence            8999997      3456678889999884

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=87.71  E-value=0.77  Score=39.92  Aligned_cols=69  Identities=17%  Similarity=0.210  Sum_probs=50.1

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCCcc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVD  134 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~v~  134 (470)
                      .++||.++|++.+.++.+.+..     .+.+..++|+....++.+...    ....|||+|+      +-...+++.++.
T Consensus        99 ~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~ivV~TP~~l~~~~~~~~~~l~~v~  174 (238)
T d1wrba1          99 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQ----MGCHLLVATPGRLVDFIEKNKISLEFCK  174 (238)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHS----SCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcc----cCCceeecCHHHHHhHHccCceeccccc
Confidence            4799999999999999877652     467888888877666554433    2578999997      223456667777


Q ss_pred             EEEE
Q 012133          135 LIIH  138 (470)
Q Consensus       135 ~VI~  138 (470)
                      ++|.
T Consensus       175 ~lVi  178 (238)
T d1wrba1         175 YIVL  178 (238)
T ss_dssp             EEEE
T ss_pred             eeee
Confidence            6664

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.87  E-value=0.9  Score=38.49  Aligned_cols=70  Identities=17%  Similarity=0.238  Sum_probs=49.0

Q ss_pred             CeEEEEeCchHHHHHHHHHHhc------CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc------ccccCCCCCc
Q 012133           66 GKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV------AARGLDIPNV  133 (470)
Q Consensus        66 ~~~lVF~~t~~~~~~l~~~l~~------~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv------~~~Gidip~v  133 (470)
                      .++||.++|++.+.++.+.+..      .+.+..++|+.+.......+.   .....|||+|+-      -...+++.++
T Consensus        70 ~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~---~~~~~ilI~TP~rl~~~~~~~~~~l~~l  146 (207)
T d1t6na_          70 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK---KNCPHIVVGTPGRILALARNKSLNLKHI  146 (207)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHH---HSCCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             ceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHH---hcCCCEEEeCcchhhhhccCCceecccc
Confidence            4799999999999999888863      245778888888776554443   235789999972      2234566666


Q ss_pred             cEEEE
Q 012133          134 DLIIH  138 (470)
Q Consensus       134 ~~VI~  138 (470)
                      .++|.
T Consensus       147 ~~lVl  151 (207)
T d1t6na_         147 KHFIL  151 (207)
T ss_dssp             CEEEE
T ss_pred             ceeeh
Confidence            66553

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.77  E-value=2.3  Score=35.61  Aligned_cols=71  Identities=18%  Similarity=0.216  Sum_probs=55.5

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEecc------cccccCCCCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPN  132 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTd------v~~~Gidip~  132 (470)
                      ....+++.+++...+.+....+..     .+.+..++|+.....+...+..    ...|||+|+      +-...+++.+
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~----~~~Ili~TP~~l~~~l~~~~~~l~~  143 (206)
T d1s2ma1          68 NKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNE----TVHILVGTPGRVLDLASRKVADLSD  143 (206)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTS----CCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             ccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcc----cceEEEECCcccccccccceeeccc
Confidence            346789999999999888776652     4789999999998877766643    689999997      3345678889


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +.++|.
T Consensus       144 l~~lV~  149 (206)
T d1s2ma1         144 CSLFIM  149 (206)
T ss_dssp             CCEEEE
T ss_pred             ceEEEe
Confidence            998874

>d1wp9a1 c.37.1.19 (A:1-200) 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=81.73  E-value=3.3  Score=33.95  Aligned_cols=70  Identities=26%  Similarity=0.311  Sum_probs=51.7

Q ss_pred             CCCeEEEEeCchHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHcccccCCeeEEEeccc------ccccCCCCC
Q 012133           64 KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV------AARGLDIPN  132 (470)
Q Consensus        64 ~~~~~lVF~~t~~~~~~l~~~l~~-----~~~~~~lhg~~~~~~R~~~~~~f~~g~~~iLVaTdv------~~~Gidip~  132 (470)
                      ...++|+.+|++..+++.++.+.+     ...+..+|++....+|......     ..|+++|..      ...-+.+.+
T Consensus        51 ~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~-----~~i~i~t~~~~~~~~~~~~~~~~~  125 (200)
T d1wp9a1          51 YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWAR-----AKVIVATPQTIENDLLAGRISLED  125 (200)
T ss_dssp             SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHHH-----CSEEEECHHHHHHHHHTTSCCTTS
T ss_pred             cCCcEEEEcCchHHHHHHHHHHHHhhcccccceeeeecccchhHHHHhhhc-----ccccccccchhHHHHhhhhhhccc
Confidence            567899999999999998888874     2558889999999988877654     468888852      222344556


Q ss_pred             ccEEEE
Q 012133          133 VDLIIH  138 (470)
Q Consensus       133 v~~VI~  138 (470)
                      +++||.
T Consensus       126 ~~~vIi  131 (200)
T d1wp9a1         126 VSLIVF  131 (200)
T ss_dssp             CSEEEE
T ss_pred             cceEEE
Confidence            777664