Citrus Sinensis ID: 012794

---

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------
Protein Sequence
MLNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN
Secondary Structure (PSIPRED)
cHHHHcccccEEEEEcccccccccEEEEEEEEccccHHHHHHHHHHHccccccEEEEccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHcccccEEEEEcccccccccccccEEEEcccccccccccccccccccccccccEEEEEcccHHHHHHHHHHHHccccEEcccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccccccccccccccccEEEccccccccccccccHHHHHHHHHccccccccccEEEEEcccccEEEEEccHHHHHHHHHHccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHccccEEEEEEcccEEEcccEEEEEEEEccHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHccccHHHHcccccHHHHHHHHHHHHccccEEEEEEcHHHccccccccEEEEEccccccccHEEEEccccccccccEEEEEEEcHHHHHHHHHHHHHHcccEEEcccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHccccccccccccccccccccEEEEEEcccccccccHHHHHHHHHHHcccccHHccEEEEEccccEEEEEEEccHHHHHHHHHHHccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccc
Coil and Loop (DISEMBL)
MLNYFVMFshstqvgnqdEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEAlhgdisqhqrertlngfrqgkFTVLVATDVaargldipnvdliihyelpndpetfvhrsgrtgragkegTAILMFTSSQRRTVRslerdvgckfefvsppvveDVLESSAEQVVATLngvhpesvefftPTAQRLIEEKGTDALAAALAQLsgfsrppssrslinheqgWVTLQLTRDSAFSRGFMSARSVMGflsdvyptaadeigKIHIiaddrvqgavfDLPEEIAKELLnkqippgntiskitklpalqddgpssdnygrfssrdrfsrgggsrfsrggarggargggsmdrrgfrssrswgsddedgfsssrggrsfrsgnnrgsrfstssdddwliggsrssrsssrdsrsfggacfncgksghrasecpn
Flexible Loop (DISEMBL)
MLNYFVMFSHSTQVGNQDEKLAEGIKLYAisttatskrtiLSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRsgrtgragkegtailmftssqrrtvrslerdvgckfefvSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKEllnkqippgntISKItklpalqddgpssdnygrfssrdrfsrgggsrfsrggarggargggsmdrrgfrssrswgsddedgfsssrggrsfrsgnnrgsrfstssdddwliggsrssrsssrdsrsfggacfncgksghrasecpn
Low Complexity Region (SEG)
MLNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYgrfssrdrfsrgggsrfsrggarggargggsmdrrgfrssrswgsddEDgfsssrggrsfrsgnnrgsrfstssDDDWLIggsrssrsssrdsrsfggACFNCGKSGHRASECPN
Disordered region (IsUnstruct)
***YFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVH************TAILMFTS**RRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALA*************LINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNK**********************************************************************************************************************************************
Disordered Region (DISOPRED)
MLNYF**FSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALA****************************DSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISK*********************************************************************************************************************FNCGKSGH*******
Disordered Region (DISEMBL)
MLNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRD******************************************************SGNNRGSRFSTSSDDDWLI***************FGGACFNCGK**********
Disordered Region (DISPRO)
MLNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFS*************GWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPAL*****************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	456	2.2.26 [Sep-21-2011]
Q8L7S8	748	DEAD-box ATP-dependent RN	no	no	0.739	0.450	0.842	1e-163
Q0DM51	758	DEAD-box ATP-dependent RN	yes	no	0.734	0.441	0.814	1e-161
Q0D8N0	602	DEAD-box ATP-dependent RN	no	no	0.379	0.287	0.617	5e-57
Q9LUW5	616	DEAD-box ATP-dependent RN	no	no	0.370	0.274	0.621	2e-55
Q0ILZ4	628	DEAD-box ATP-dependent RN	no	no	0.350	0.254	0.637	2e-55
Q9LUW6	610	DEAD-box ATP-dependent RN	no	no	0.370	0.277	0.585	3e-53
Q650T9	696	DEAD-box ATP-dependent RN	no	no	0.673	0.441	0.387	8e-48
Q9JIK5	851	Nucleolar RNA helicase 2	yes	no	0.774	0.414	0.349	8e-48
Q9NR30	783	Nucleolar RNA helicase 2	yes	no	0.791	0.461	0.354	9e-47
Q3B8Q1	782	Nucleolar RNA helicase 2	yes	no	0.804	0.469	0.347	2e-46

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

 Score =  575 bits (1483), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 284/337 (84%), Positives = 315/337 (93%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+QDEKLAEGIKLYAI+TT+TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLAL++
Sbjct: 314 VGDQDEKLAEGIKLYAIATTSTSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALSN 373

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            IA+EALHGDISQHQRERTLN FRQGKFTVLVATDVA+RGLDIPNVDL+IHYELPNDPET
Sbjct: 374 SIATEALHGDISQHQRERTLNAFRQGKFTVLVATDVASRGLDIPNVDLVIHYELPNDPET 433

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGKEG+AILM TSSQ+RTVRSLERDVGC FEF+SPP V D+LESSA+QVV
Sbjct: 434 FVHRSGRTGRAGKEGSAILMHTSSQKRTVRSLERDVGCHFEFISPPTVGDLLESSADQVV 493

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATLNGVHP+S++FF+ TAQ+L EEKGTDALAAALA LSGFS+PPSSRSL++HE+GWVTLQ
Sbjct: 494 ATLNGVHPDSIKFFSATAQKLYEEKGTDALAAALAHLSGFSQPPSSRSLLSHEKGWVTLQ 553

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           L RD   +RGF+SARSV GFLSD+Y TAADE+GKI +IADDR+QGAVFDLPEEIAKELL 
Sbjct: 554 LIRDPTNARGFLSARSVTGFLSDLYRTAADEVGKIFLIADDRIQGAVFDLPEEIAKELLE 613

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRF 350
           K +P GN++S ITKLP LQDDGPSSDNYGRFSSRDR 
Sbjct: 614 KDVPEGNSLSMITKLPPLQDDGPSSDNYGRFSSRDRM 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 =  569 bits (1467), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 273/335 (81%), Positives = 308/335 (91%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+QDEKLAEGIKLYAI  T+TSKRT+LSDLITVYAKGGKTIVFT+TKRDADEVSLALT+
Sbjct: 314 VGDQDEKLAEGIKLYAIPLTSTSKRTVLSDLITVYAKGGKTIVFTKTKRDADEVSLALTN 373

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET
Sbjct: 374 SIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 433

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGK GTAILMFT+SQRRTVRSLERDVGC+F+F+SPP +EDVLESSAE V+
Sbjct: 434 FVHRSGRTGRAGKAGTAILMFTNSQRRTVRSLERDVGCRFDFISPPAIEDVLESSAEHVI 493

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATL GVH ES+++F P A+RL EE G +ALA+ALA LSGFS+PPSSRSLI+HEQGWVTLQ
Sbjct: 494 ATLRGVHTESIQYFIPAAERLQEELGPNALASALAHLSGFSQPPSSRSLISHEQGWVTLQ 553

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRD  + RGF S RSV GFLSDV   AADE+GKI + AD++VQGAVFDLPEEIA++LL+
Sbjct: 554 LTRDPGYGRGFFSPRSVTGFLSDVSSAAADEVGKIFLTADEKVQGAVFDLPEEIARDLLS 613

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRD 348
            ++PPGNTI+K+TKLPALQDDGP++D+YGRFS+ D
Sbjct: 614 MELPPGNTITKVTKLPALQDDGPATDSYGRFSNSD 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 =  222 bits (565), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 108/175 (61%), Positives = 137/175 (78%), Gaps = 2/175 (1%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG++D+KL EGI LY+I++    K +IL  LI  +A GGK IVFTQTKR+AD ++ A+  
Sbjct: 291 VGDEDQKLPEGISLYSIASEHYGKPSILGPLIKEHANGGKCIVFTQTKREADRLAYAMGR 350

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
             A +ALHGDISQ+QRERTL+GFR G+F +LVATDVAARGLDIPNVDL+IHYELPN  E 
Sbjct: 351 SYACQALHGDISQNQRERTLSGFRDGRFNILVATDVAARGLDIPNVDLVIHYELPNTSEL 410

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESS 188
           FVHRSGRT RAGK+G+AIL++T+ Q R VR +E+D+GCKF  +  P +E   E+S
Sbjct: 411 FVHRSGRTARAGKKGSAILIYTNDQARAVRIIEQDIGCKFTEL--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 =  216 bits (551), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 105/169 (62%), Positives = 130/169 (76%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+ D+KLA+GI  Y+I   +  + +I+  L+T +AKGGK IVFTQTKRDAD +S AL  
Sbjct: 312 VGDSDQKLADGITTYSIIADSYGRASIIGPLVTEHAKGGKCIVFTQTKRDADRLSYALAR 371

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
               EALHGDISQ QRERTL GFR G F +LVATDVAARGLD+PNVDLIIHYELPN+ ET
Sbjct: 372 SFKCEALHGDISQSQRERTLAGFRDGHFNILVATDVAARGLDVPNVDLIIHYELPNNTET 431

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE 182
           FVHR+GRTGRAGK+G+AIL+++  Q R V+ +ER+VG +F  +    VE
Sbjct: 432 FVHRTGRTGRAGKKGSAILIYSQDQSRAVKIIEREVGSRFTELPSIAVE 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 =  216 bits (551), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 102/160 (63%), Positives = 124/160 (77%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG  D+KLAEGI LY+I++   +K  +L +LI  +AKGGK IVFTQTKRDAD +S  +  
Sbjct: 305 VGEDDQKLAEGISLYSIASEGHAKPAVLGELIKEHAKGGKCIVFTQTKRDADRLSYTMGR 364

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
               +ALHGDI+Q QRERTL GFR+G F +L+ATDVAARGLDIPNVDL+IH+ELPN  E 
Sbjct: 365 SFQCQALHGDITQAQRERTLKGFREGHFNILIATDVAARGLDIPNVDLVIHFELPNSSEL 424

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKF 173
           FVHRSGRTGRAGK+G AI+M +  Q R +R +E DVGCKF
Sbjct: 425 FVHRSGRTGRAGKKGKAIVMHSYQQSRAIRMVENDVGCKF 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 =  209 bits (532), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 99/169 (58%), Positives = 128/169 (75%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+ D+KLA+GI +Y+I+  +  + +I+  L+  + KGGK IVFTQTKRDAD ++  L  
Sbjct: 324 VGDSDQKLADGITMYSIAADSYGRASIIGPLVKEHGKGGKCIVFTQTKRDADRLAFGLAK 383

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
               EALHGDISQ QRERTL GFR G F++LVATDVAARGLD+PNVDL+IHYELPN+ ET
Sbjct: 384 SYKCEALHGDISQAQRERTLAGFRDGNFSILVATDVAARGLDVPNVDLVIHYELPNNTET 443

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE 182
           FVHR+GRTGRAGK+G+AIL+    Q R V+ +E++VG +F  +    VE
Sbjct: 444 FVHRTGRTGRAGKKGSAILIHGQDQTRAVKMIEKEVGSRFNELPSIAVE 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 =  191 bits (486), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 127/328 (38%), Positives = 184/328 (56%), Gaps = 21/328 (6%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG++  K +  ++  A+     ++  ++ D+I  Y++GG+TI+FT+TK  A +    L+ 
Sbjct: 332 VGDEKLKASASVRHLALPCNRAARAQVIPDIIRCYSRGGRTIIFTETKESASD----LSG 387

Query: 74  IIA-SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
           +IA S ALHGD++Q QRE  L GFR GKF VLVAT+VAARGLDI +V LII  E P D E
Sbjct: 388 LIAGSRALHGDVAQAQREVILAGFRSGKFLVLVATNVAARGLDINDVQLIIQCEPPRDVE 447

Query: 133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
            ++HRSGRTGRAG  G A+++F    +  V  +ER+ G KFE +S P   DV +S+  + 
Sbjct: 448 AYIHRSGRTGRAGNTGVAVMLFEPRYKFNVNRIERESGVKFEHISAPQPTDVAQSAGTEA 507

Query: 193 VATLNGVHPESVEFFTPTAQRLIEEKG---TDALAAALAQLSGFSRPPSSRSLINHEQGW 249
              ++ V    +  F   A++L+   G    D LA ALA+  G++     RSL++     
Sbjct: 508 AEAISSVSDSVIPVFREQAEQLLNSSGMSAVDLLAKALAKAVGYTD-IKKRSLLSSMDNH 566

Query: 250 VTLQL-TRDSAFSRGFMSARSVMGFLSDVYPT--AADEIGKIHIIADDRVQGAVFDLPE- 305
            TL L T  S ++ GF     V+  L    P    AD  G I I AD    GAVFD+P  
Sbjct: 567 TTLLLQTGRSVYAAGF-----VLSTLKRFMPEERLADVKG-ITITADG--TGAVFDVPSA 618

Query: 306 EIAKELLNKQIPPGNTISKITKLPALQD 333
           E+   +   Q     T+ ++ +LP LQ+
Sbjct: 619 EVEDYIQGAQNAAMVTVEEVKQLPPLQE 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 =  191 bits (486), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 139/398 (34%), Positives = 212/398 (53%), Gaps = 45/398 (11%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALT 72
           +G + +K A  ++  AI    T +  ++ D+I VY+   G+TI+F +TK+DA E+S    
Sbjct: 472 IGKKTQKAAITVEHLAIKCHWTERAAVIGDVIRVYSGHQGRTIIFCETKKDAQELSQNTC 531

Query: 73  SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
               +++LHGDI Q QRE TL GFR G F VLVAT+VAARGLDIP VDL++    P D E
Sbjct: 532 IKQDAQSLHGDIPQKQREITLKGFRNGNFGVLVATNVAARGLDIPEVDLVVQSCPPKDVE 591

Query: 133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
           +++HRSGRTGRAG+ G  I  + + +   +  +E+  G KF+ +  P   +++++S++  
Sbjct: 592 SYIHRSGRTGRAGRTGVCICFYQNKEEYQLAQVEQKAGIKFKRIGVPSATEIIKASSKDA 651

Query: 193 VATLNGVHPESVEFFTPTAQRLIEEKG-TDALAAALAQLSGFSRPPSSRSLINHEQGWVT 251
           +  L+ V P ++  F  +A++LIEEKG  +ALAAALA +SG +     RSLIN + G+VT
Sbjct: 652 IRLLDSVPPTAISHFKQSAEKLIEEKGAVEALAAALAHISGATS-VDQRSLINSQAGFVT 710

Query: 252 LQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAV---------FD 302
           +            +     M  +S  +    +++G+     D +V+G V         FD
Sbjct: 711 M-----------ILRCSIEMPNISYAWKELKEQLGE---SIDAKVKGMVFLKGKLGVCFD 756

Query: 303 LPEEIAKELLNKQIPPGN-TISKITKLPALQDDGPSSDNYGRFSSRD------RFSRGGG 355
           +  E   E+  K        ++  T+ P L  +GP     GR   RD      R  RGG 
Sbjct: 757 VRTEAVTEIQEKWHDSRRWQLTVATEQPEL--EGPPDGYRGRMGQRDGSRGAFRGQRGGS 814

Query: 356 SRFSRGGARGGAR--------GGGSMDRRGFRSSRSWG 385
             F   G RGG+R        GG    +R F  S+++G
Sbjct: 815 RNFRGQGQRGGSRNFRGQRPGGGNRGQKRSF--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 =  188 bits (477), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 144/406 (35%), Positives = 216/406 (53%), Gaps = 45/406 (11%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALT 72
           +G + +K A  ++  AI    T +  ++ D+I VY+   G+TI+F +TK++A E+S    
Sbjct: 400 IGKKTQKTAITVEHLAIKCHWTQRAAVIGDVIRVYSGHQGRTIIFCETKKEAQELSQNSA 459

Query: 73  SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
               +++LHGDI Q QRE TL GFR G F VLVAT+VAARGLDIP VDL+I    P D E
Sbjct: 460 IKQDAQSLHGDIPQKQREITLKGFRNGSFGVLVATNVAARGLDIPEVDLVIQSSPPKDVE 519

Query: 133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
           +++HRSGRTGRAG+ G  I  +   +   +  +E+  G KF+ +  P   +++++S++  
Sbjct: 520 SYIHRSGRTGRAGRTGVCICFYQHKEEYQLVQVEQKAGIKFKRIGVPSATEIIKASSKDA 579

Query: 193 VATLNGVHPESVEFFTPTAQRLIEEKG-TDALAAALAQLSGFSRPPSSRSLINHEQGWVT 251
           +  L+ V P ++  F  +A++LIEEKG  +ALAAALA +SG +     RSLIN   G+VT
Sbjct: 580 IRLLDSVPPTAISHFKQSAEKLIEEKGAVEALAAALAHISGATS-VDQRSLINSNVGFVT 638

Query: 252 LQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAV---------FD 302
           +            +     M  +S  +    +++G+     D +V+G V         FD
Sbjct: 639 M-----------ILQCSIEMPNISYAWKELKEQLGE---EIDSKVKGMVFLKGKLGVCFD 684

Query: 303 LPEEIAKELLNKQIPPGN-TISKITKLPALQDDGPSSDNYGRFSSRDRFSRG------GG 355
           +P     E+  K        +S  T+ P L  +GP  + YG F  +   SRG      G 
Sbjct: 685 VPTASVTEIQEKWHDSRRWQLSVATEQPEL--EGP-REGYGGFRGQREGSRGFRGQRDGN 741

Query: 356 SRF--SRGGARG--GARGGGSMDRRGFRSSRSWGSDDEDGFSSSRG 397
            RF   R G+RG  G R GG     G +S+RS     +  FS + G
Sbjct: 742 RRFRGQREGSRGPRGQRSGG-----GNKSNRSQNKGQKRSFSKAFG 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|Q3B8Q1|DDX21_RAT Nucleolar RNA helicase 2 OS=Rattus norvegicus GN=Ddx21 PE=2 SV=1

 Score =  187 bits (474), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 140/403 (34%), Positives = 212/403 (52%), Gaps = 36/403 (8%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALT 72
           +G + +K A  ++  AI    T +  ++ D+I VY+   G+TI+F +TK+DA E+S    
Sbjct: 396 IGKKTQKAAITVEHLAIKCHWTERAAVIGDVIRVYSGHQGRTIIFCETKKDAQELSQNTC 455

Query: 73  SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
               +++LHGDI Q QRE TL GFR G F VLVAT+VAARGLDIP VDL++    P D E
Sbjct: 456 IKQDAQSLHGDIPQKQREITLKGFRNGNFGVLVATNVAARGLDIPEVDLVVQSCPPKDVE 515

Query: 133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
           +++HRSGRTGRAG+ G  I  +   +   +  +E+  G KF+ +  P   +++++S++  
Sbjct: 516 SYIHRSGRTGRAGRTGVCICFYQHKEEYQLAQVEQKAGIKFKRIGVPSATEIIKASSKDA 575

Query: 193 VATLNGVHPESVEFFTPTAQRLIEEKG-TDALAAALAQLSGFSRPPSSRSLINHEQGWVT 251
           +  L+ V P ++  F  +A++LIEEKG  +ALAAALA +SG +     RSLIN + G+VT
Sbjct: 576 IRLLDSVPPTAIGHFKQSAEKLIEEKGAVEALAAALAHISGATS-VDQRSLINSQAGFVT 634

Query: 252 LQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAV---------FD 302
           +            +     M  +S  +    +++G+     D +V+G V         FD
Sbjct: 635 M-----------ILRCSVEMPNISYAWKELKEQLGE---SIDAKVKGMVFLKGKLGVCFD 680

Query: 303 LPEEIAKELLNKQIPPGN-TISKITKLPALQDDGPSSDNYGRFSSRD------RFSRGGG 355
           +  E   E+  K        ++  T+ P L  +GP     G    RD      R  RGG 
Sbjct: 681 VRTEAVTEIKEKWHDSRRWQLTVATEQPEL--EGPPEGYRGGRGQRDGSRGSFRGQRGGS 738

Query: 356 SRFSRGGARGGARG-GGSMDRRGFRSSRSWGSDDEDGFSSSRG 397
             F   G RGG+R   G     G +S+RS     +  FS + G
Sbjct: 739 RNFRGQGQRGGSRNFRGQRPGGGNKSNRSPNKGQKRSFSKAFG 781

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.

Rattus norvegicus (taxid: 10116)

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	456
225450401	764	PREDICTED: DEAD-box ATP-dependent RNA he	0.942	0.562	0.795	0.0
224124522	775	predicted protein [Populus trichocarpa]	0.936	0.550	0.787	0.0
118489724	481	unknown [Populus trichocarpa x Populus d	0.936	0.887	0.790	0.0
224124506	735	predicted protein [Populus trichocarpa]	0.938	0.582	0.803	0.0
356505715	771	PREDICTED: DEAD-box ATP-dependent RNA he	0.960	0.568	0.785	0.0
356534927	736	PREDICTED: DEAD-box ATP-dependent RNA he	0.925	0.573	0.764	0.0
357511641	753	DEAD-box ATP-dependent RNA helicase [Med	0.934	0.565	0.780	0.0
255543078	772	dead box ATP-dependent RNA helicase, put	0.925	0.546	0.747	1e-180
356574052	736	PREDICTED: DEAD-box ATP-dependent RNA he	0.921	0.570	0.761	1e-180
343172316	782	DEAD-box ATP-dependent RNA helicase, par	0.932	0.543	0.726	1e-178

>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 =  672 bits (1735), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/446 (79%), Positives = 382/446 (85%), Gaps = 16/446 (3%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+ DEKLAEGIKLYAI TTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS+ALT+
Sbjct: 328 VGDHDEKLAEGIKLYAIPTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSMALTN 387

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET
Sbjct: 388 SIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 447

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGKEGTAILMFTSSQRRTV+SLERDVGCKFEF+SPP +E+VLESSAEQVV
Sbjct: 448 FVHRSGRTGRAGKEGTAILMFTSSQRRTVKSLERDVGCKFEFISPPAIEEVLESSAEQVV 507

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATLNGVHPESVEFFTPTAQ+LIEEKGT ALAAALA LSGFS+PPS RSLI+HEQGWVTLQ
Sbjct: 508 ATLNGVHPESVEFFTPTAQKLIEEKGTGALAAALAHLSGFSQPPSFRSLISHEQGWVTLQ 567

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRDS +SRGF+SARSV GFLSDVYPTAADE+GKI+++AD+RVQGAVFDLPEEIAKELLN
Sbjct: 568 LTRDSGYSRGFLSARSVTGFLSDVYPTAADELGKIYLVADERVQGAVFDLPEEIAKELLN 627

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSM 373
           KQ+PPGNTISKITKLPALQDDGP+ D YGRFS+RDR S            RGG+R     
Sbjct: 628 KQMPPGNTISKITKLPALQDDGPAGDYYGRFSNRDRSS------------RGGSRERRGS 675

Query: 374 DRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLI---GGSRSSRSS 430
                R S     DD     + RGGRSFRS NN  SR   +S+DDWLI     +RSS S 
Sbjct: 676 RISRGRGSSWGSDDDGGDDLNRRGGRSFRSNNN-WSRNLRTSEDDWLIGGRRSNRSSSSF 734

Query: 431 SRDSRSFGGACFNCGKSGHRASECPN 456
               RSFGG+CF CG+SGHRASECPN
Sbjct: 735 GSRERSFGGSCFTCGRSGHRASECPN 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 =  670 bits (1729), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 349/443 (78%), Positives = 376/443 (84%), Gaps = 16/443 (3%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+Q+EKLAEGIKLYA+S TA SKRTILSDL+TVYAKGGKTI+FTQTKRDADEVS+ALT+
Sbjct: 345 VGDQEEKLAEGIKLYALSATAASKRTILSDLVTVYAKGGKTIIFTQTKRDADEVSMALTN 404

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDLIIHYELPND ET
Sbjct: 405 TIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLIIHYELPNDAET 464

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD GCKFEFVSPP +E+VLESSAEQVV
Sbjct: 465 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDAGCKFEFVSPPAIEEVLESSAEQVV 524

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATL+GVHPESVEFFTPTAQ+LIEE+GT+ALAAALA LSGFS+PPSSRSLI+H QGW TLQ
Sbjct: 525 ATLSGVHPESVEFFTPTAQKLIEEQGTNALAAALAHLSGFSQPPSSRSLISHAQGWATLQ 584

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRD  +SRGF+SARSV GFLSDVYP AADE+GKIH+IAD+RVQGAVFDLPEEIAKELLN
Sbjct: 585 LTRDPTYSRGFLSARSVTGFLSDVYPAAADEVGKIHVIADERVQGAVFDLPEEIAKELLN 644

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSM 373
           KQIPPGNTI+KITKLPALQDDGP  D YGRFSSRDR                     G  
Sbjct: 645 KQIPPGNTIAKITKLPALQDDGPPGDFYGRFSSRDR--------------PARGGPRGQR 690

Query: 374 DRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRD 433
                   R  G D +DG +  RGGRS  S  N  S+ S SS DDWLIGG RSSR  SRD
Sbjct: 691 GGFRSSRGRGSGRDSDDGGTYRRGGRS-NSNENSWSQMSRSSGDDWLIGGRRSSRPPSRD 749

Query: 434 SRSFGGACFNCGKSGHRASECPN 456
            RSFGG+CFNCG+SGHRASECPN
Sbjct: 750 -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 =  670 bits (1729), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/443 (79%), Positives = 377/443 (85%), Gaps = 16/443 (3%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+Q+EKLAEGIKLYA+S TA SKRTILSDL+TVYAKGGKTI+FTQTKRDADEVS+ALT+
Sbjct: 51  VGDQEEKLAEGIKLYALSATAASKRTILSDLVTVYAKGGKTIIFTQTKRDADEVSMALTN 110

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDLIIHYELPND ET
Sbjct: 111 TIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLIIHYELPNDAET 170

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD GCKFEFVSPP +E+VLESSAEQVV
Sbjct: 171 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDAGCKFEFVSPPAIEEVLESSAEQVV 230

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATL+GVHPESVEFFTPTAQ+LIEE+GT+ALAAALA LSGFS+PPSSRSLI+HEQGW TLQ
Sbjct: 231 ATLSGVHPESVEFFTPTAQKLIEEQGTNALAAALAHLSGFSQPPSSRSLISHEQGWATLQ 290

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRD  +SRGF+SARSV GFLSDVYP AADE+GKIH+IAD+RVQGAVFDLPEEIAKELLN
Sbjct: 291 LTRDPTYSRGFLSARSVTGFLSDVYPAAADEVGKIHVIADERVQGAVFDLPEEIAKELLN 350

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSM 373
           KQIPPGNTI+KITKLPALQDDGP  D YGRFSSRDR                     G  
Sbjct: 351 KQIPPGNTIAKITKLPALQDDGPPGDFYGRFSSRDR--------------PARGGPRGQR 396

Query: 374 DRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRD 433
                   R  G D +DG +  RGGRS  S  N  S+ S SS DDWLIGG RSSR  SRD
Sbjct: 397 GGFRSSRGRGSGRDSDDGGTYRRGGRS-NSNENSWSQMSRSSGDDWLIGGRRSSRPPSRD 455

Query: 434 SRSFGGACFNCGKSGHRASECPN 456
            RSFGG+CFNCG+SGHRASECPN
Sbjct: 456 -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 =  667 bits (1720), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/443 (80%), Positives = 384/443 (86%), Gaps = 15/443 (3%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+++EKLAEGIKLYAISTTATSKRTILSDL+TVYAKG KTI+FT+TKRDADEVS+ALT 
Sbjct: 308 VGDREEKLAEGIKLYAISTTATSKRTILSDLVTVYAKGEKTIIFTRTKRDADEVSMALTQ 367

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDLIIHYELPNDPET
Sbjct: 368 SIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLIIHYELPNDPET 427

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGKEGTAILMFT+SQRRTVRSLERD GCKFEFVSPP +E++LESS EQVV
Sbjct: 428 FVHRSGRTGRAGKEGTAILMFTNSQRRTVRSLERDAGCKFEFVSPPAIEELLESSTEQVV 487

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATLNGVHPESVEFFTPTAQ+LIEE+GT ALAAALA LSGFSRPPSSRSLI+HEQGW TLQ
Sbjct: 488 ATLNGVHPESVEFFTPTAQKLIEEQGTSALAAALAHLSGFSRPPSSRSLISHEQGWTTLQ 547

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRD  +SRGF+SARSV GFLSDVYP AADEIGKIH+IAD+RVQGAVFDLPEEIAKELLN
Sbjct: 548 LTRDPTYSRGFLSARSVTGFLSDVYPAAADEIGKIHLIADERVQGAVFDLPEEIAKELLN 607

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSM 373
           KQ+PPGNTI KITKLPALQDDGP SD YGRFSSRDR +RGG      G      +G G  
Sbjct: 608 KQLPPGNTIEKITKLPALQDDGPPSDFYGRFSSRDRPARGGPRGQRGGFRSSRGQGSGRY 667

Query: 374 DRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRD 433
                       SDDE   ++ RGGRS  + N R S  S SS DDWL+GG RSSR SSRD
Sbjct: 668 ------------SDDEG--TNRRGGRSNSNENTR-SWMSRSSGDDWLVGGRRSSRPSSRD 712

Query: 434 SRSFGGACFNCGKSGHRASECPN 456
           SRSFGG+CFNCG+SGHRASECPN
Sbjct: 713 SRSFGGSCFNCGRSGHRASECPN 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 =  659 bits (1699), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 351/447 (78%), Positives = 386/447 (86%), Gaps = 9/447 (2%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+++EKLAEGIKLYAI+ TATSKRTILSDL+TVYAKGGKTIVFTQTKRDADEVSL+LT+
Sbjct: 322 VGDEEEKLAEGIKLYAIAATATSKRTILSDLVTVYAKGGKTIVFTQTKRDADEVSLSLTN 381

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            I SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET
Sbjct: 382 SIMSEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 441

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGK+G AIL++TSSQRRTVRSLERDVGCKFEFVS P +E+VLESSAEQVV
Sbjct: 442 FVHRSGRTGRAGKQGNAILLYTSSQRRTVRSLERDVGCKFEFVSAPAMEEVLESSAEQVV 501

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATL GVHPESV+FFTPTAQRLIEE+GT ALAAALAQLSGFSRPPSSRSLI HEQGW+TLQ
Sbjct: 502 ATLGGVHPESVQFFTPTAQRLIEEQGTSALAAALAQLSGFSRPPSSRSLITHEQGWITLQ 561

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRDS  SR + SARS+ GFLSDVYP AADE+GKIH+IAD++VQGAVFDLPEEIAKELLN
Sbjct: 562 LTRDSD-SRRYFSARSITGFLSDVYPAAADEVGKIHLIADEKVQGAVFDLPEEIAKELLN 620

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSM 373
           + IPPGNT+SKITKLP+LQDDGP SD YGRFS RDR SR G +      +RGG+    S 
Sbjct: 621 RDIPPGNTVSKITKLPSLQDDGPPSDFYGRFSDRDRSSRRGSTSRGGFSSRGGS---ASR 677

Query: 374 DRRGFRSSRSWGSDDE-DGF---SSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRS 429
           DRRGF+SSR W  +D  D F   SS RGGR+F++GN+       SS DDWLIGG R S  
Sbjct: 678 DRRGFKSSRGWDVEDSGDDFGDQSSRRGGRNFKTGNSWSRAAGKSSGDDWLIGGGRRSSR 737

Query: 430 SSRDSRSFGGACFNCGKSGHRASECPN 456
            S   R FGG CFNCG+SGHRAS+CPN
Sbjct: 738 PSSSDR-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 =  641 bits (1654), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/445 (76%), Positives = 367/445 (82%), Gaps = 23/445 (5%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG Q+EKLAEGIKLYA+  TATSKRT+LSDLITVYAKGGKTIVFTQTK+DADEVS+ALTS
Sbjct: 303 VGEQEEKLAEGIKLYALLATATSKRTVLSDLITVYAKGGKTIVFTQTKKDADEVSMALTS 362

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL+IHYELPND ET
Sbjct: 363 SIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLVIHYELPNDAET 422

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGKEGTAILM+TSSQRRTVRSLERDVG KFEFVSPP VE++LESSAEQVV
Sbjct: 423 FVHRSGRTGRAGKEGTAILMYTSSQRRTVRSLERDVGSKFEFVSPPAVEEILESSAEQVV 482

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATLN VHPESVEFFT TAQ+L+EE+G  ALAAALAQ+SGFS+PPS RSLINHEQGW TLQ
Sbjct: 483 ATLNRVHPESVEFFTATAQKLVEEQGARALAAALAQMSGFSQPPSCRSLINHEQGWTTLQ 542

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRDS  S  + SARSV GFLSDVY  AADE+GKIH+IAD+RVQGAVFDLPEEIAKELLN
Sbjct: 543 LTRDSDTSGRYFSARSVTGFLSDVYSQAADEVGKIHLIADERVQGAVFDLPEEIAKELLN 602

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSM 373
           K +P GNTISKITKLP LQD+ P+SD YG+FS RDR                 +   GS 
Sbjct: 603 KDMPSGNTISKITKLPPLQDNEPASDFYGKFSDRDR-----------------SNPRGSR 645

Query: 374 DRRGFRSS--RSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSS 431
           D+RGFRSS  R  G D  D F   RGGRSFRSGNNR      SS +DWLIGGS  S   S
Sbjct: 646 DQRGFRSSRGREGGQDSNDEF--GRGGRSFRSGNNRSRTTGKSSGNDWLIGGSSRSSRFS 703

Query: 432 RDSRS--FGGACFNCGKSGHRASEC 454
             +R    GGACFNCGK GHRAS+C
Sbjct: 704 SSNRDGGHGGACFNCGKPGHRASDC 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 =  641 bits (1653), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 349/447 (78%), Positives = 381/447 (85%), Gaps = 21/447 (4%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+++EKLAEGIKLYAIS T+TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT+
Sbjct: 318 VGDEEEKLAEGIKLYAISATSTSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTN 377

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            I SEALHGDISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDLIIHYELPNDPET
Sbjct: 378 SITSEALHGDISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLIIHYELPNDPET 437

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGK GTAILMFT SQRRTVRSLERDVGCKFEFV+ P VEDVLESSAEQVV
Sbjct: 438 FVHRSGRTGRAGKLGTAILMFTGSQRRTVRSLERDVGCKFEFVNAPSVEDVLESSAEQVV 497

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
            TLNGVHPES+ FFTPTAQ+LIEEKGT ALAAALAQ+SGFS+PPSSRSLI HEQGWVTLQ
Sbjct: 498 VTLNGVHPESIAFFTPTAQKLIEEKGTTALAAALAQMSGFSQPPSSRSLITHEQGWVTLQ 557

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRDS  S+ + SARSV GFLSDVY  AADE+GK+H+IAD+RVQGAVFDLPE+IAKELL+
Sbjct: 558 LTRDSENSQRYFSARSVTGFLSDVYSKAADEVGKVHLIADERVQGAVFDLPEDIAKELLD 617

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSM 373
           K IP GNTISK+TKLP LQDDGP SD YG+FS R+R +R GGSR  RG            
Sbjct: 618 KDIPAGNTISKVTKLPPLQDDGPPSDFYGKFSDRERNNRRGGSRDGRGFR---------- 667

Query: 374 DRRGFRSSRSW----GSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRS 429
                 SSR W    GSDD+ G SS RGGRS++SGN+  S+   SS DDWLIGG +SSRS
Sbjct: 668 ------SSRGWDGGRGSDDDFGDSSRRGGRSYKSGNS-WSKPERSSRDDWLIGGRQSSRS 720

Query: 430 SSRDSRSFGGACFNCGKSGHRASECPN 456
           SS  +RSF G CF CG+SGHRAS+CPN
Sbjct: 721 SSSPNRSFAGTCFTCGESGHRASDCPN 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 =  638 bits (1646), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 344/460 (74%), Positives = 376/460 (81%), Gaps = 38/460 (8%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+Q+EKLAEGIKLYAIST ATSKR+ILSDL+TVYAKGGKTI+FTQTKRDADEVS+ LT+
Sbjct: 330 VGDQEEKLAEGIKLYAISTNATSKRSILSDLVTVYAKGGKTIIFTQTKRDADEVSMVLTN 389

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA+RGLDIPNVDL+IHYELPNDPET
Sbjct: 390 SIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVASRGLDIPNVDLVIHYELPNDPET 449

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGKEGTA+LMFTSSQRRTV+SLERDVGC+FEFVSPP  E+VLESSAEQV+
Sbjct: 450 FVHRSGRTGRAGKEGTAVLMFTSSQRRTVKSLERDVGCRFEFVSPPGTEEVLESSAEQVI 509

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATL+GVHPESV FFTPTAQRLIEE+GT ALAAALAQLSGFS+PPSSRSLI+HEQGW TLQ
Sbjct: 510 ATLSGVHPESVGFFTPTAQRLIEEQGTSALAAALAQLSGFSQPPSSRSLISHEQGWTTLQ 569

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRD ++SRGF+SARSV GFLSDVY  AADE+GKIHIIAD++VQGAVFDLPEEIAKELLN
Sbjct: 570 LTRDPSYSRGFLSARSVTGFLSDVYTAAADEVGKIHIIADEKVQGAVFDLPEEIAKELLN 629

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSM 373
           KQ+PPGNTISKITKLP+LQDDGP SD YGRFSSRDR  RGGG       +  G       
Sbjct: 630 KQLPPGNTISKITKLPSLQDDGPPSDFYGRFSSRDRPPRGGGRGQRGSRSSQGWG----- 684

Query: 374 DRRGFRSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSS------ 427
                       SDD+D            +    G  FS SS DDWLIGG RSS      
Sbjct: 685 -----GGRGGRNSDDDDD-----------TFRRGGRSFSRSSSDDWLIGGGRSSRPSPRG 728

Query: 428 RSSSRD-----------SRSFGGACFNCGKSGHRASECPN 456
           RSS RD            RSFGG+CFNCG+SGHRAS+CPN
Sbjct: 729 RSSPRDWSSPRDRSSPRDRSFGGSCFNCGRSGHRASDCPN 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 =  637 bits (1642), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 339/445 (76%), Positives = 369/445 (82%), Gaps = 25/445 (5%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG Q+EKLAEGIKLYA+S TA+SKRT+LSDLITVYAKGGKTIVFTQTK+DADEVS+ALTS
Sbjct: 305 VGEQEEKLAEGIKLYALSATASSKRTVLSDLITVYAKGGKTIVFTQTKKDADEVSMALTS 364

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL+IHYELPND ET
Sbjct: 365 SIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLVIHYELPNDAET 424

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGKEGTAILM+TSSQRRTVRSLERDVGCKFEFVSPP +E++LESSAEQVV
Sbjct: 425 FVHRSGRTGRAGKEGTAILMYTSSQRRTVRSLERDVGCKFEFVSPPAMEEILESSAEQVV 484

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATLN VHPESV+FF  TAQ+L+EE+G  ALAAALAQ+SGFS+PPS RSLINHEQGW TLQ
Sbjct: 485 ATLNRVHPESVDFFIATAQKLVEEQGARALAAALAQMSGFSQPPSCRSLINHEQGWTTLQ 544

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           LTRD   S  + SARSV GFLSDVY  AADE+GKIH+IAD+RVQGAVFDLPEEIAKELL 
Sbjct: 545 LTRDPDTSARYFSARSVTGFLSDVYSPAADEVGKIHLIADERVQGAVFDLPEEIAKELLT 604

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSRDRFSRGGGSRFSRGGARGGARGGGSM 373
           K +P GNTISKITKLP LQDD P+SD YG+FS RDR +R                  GS 
Sbjct: 605 KDLPSGNTISKITKLPPLQDDEPASDFYGKFSDRDRSNR-----------------RGSR 647

Query: 374 DRRGFRSSRSW--GSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSS 431
           D+RGFRSSR W  G D +D F   +GGRSFRSGN    R   SS DDWLIGGS  S   S
Sbjct: 648 DQRGFRSSRGWEGGQDSDDEF--GQGGRSFRSGNK--FRMGKSSGDDWLIGGSSRSSRFS 703

Query: 432 RDSRS--FGGACFNCGKSGHRASEC 454
             +RS   GGACFNCGK GHRAS+C
Sbjct: 704 SSNRSGGHGGACFNCGKPGHRASDC 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 =  630 bits (1626), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 334/460 (72%), Positives = 375/460 (81%), Gaps = 35/460 (7%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
           VG+++EKLAEGIKLYAIS+TA SKRT+LSD+ITVYAKGGKTIVFTQTKRDADEVSLAL++
Sbjct: 337 VGDREEKLAEGIKLYAISSTAASKRTMLSDVITVYAKGGKTIVFTQTKRDADEVSLALSN 396

Query: 74  IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
            I SEALHGDISQHQRERTLNGFRQGKF+VLVATDVA+RGLDIPNVDL++HYE+PNDPET
Sbjct: 397 SIPSEALHGDISQHQRERTLNGFRQGKFSVLVATDVASRGLDIPNVDLVVHYEMPNDPET 456

Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
           FVHRSGRTGRAGKEGTA+LM+TS+QRRTVRSLERDVGC F +V  P VE+VL SSA+QVV
Sbjct: 457 FVHRSGRTGRAGKEGTALLMYTSNQRRTVRSLERDVGCHFGYVGAPSVEEVLVSSADQVV 516

Query: 194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
           ATL GVHPES++FFTPTAQ+L+EE+GT ALAAA+A LSGFS+PPS++SL++HEQGWVTLQ
Sbjct: 517 ATLRGVHPESIKFFTPTAQKLLEEQGTGALAAAIAHLSGFSQPPSAKSLLSHEQGWVTLQ 576

Query: 254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
           L+RDS FSRG+MSARSVMGFLSDVYPTAADE+GKI +IAD+RVQGAVFDLPEEIAKELL 
Sbjct: 577 LSRDSVFSRGYMSARSVMGFLSDVYPTAADEVGKIQLIADERVQGAVFDLPEEIAKELLK 636

Query: 314 KQIPPGNTISKITKLPALQDDGPSSDNYGRFSSR---------DRFSRGGGSRFSRGGAR 364
           K++PPGNT+SKI+KLPALQDD P SDNYGRFS R         DR   GGGSR SRG   
Sbjct: 637 KELPPGNTLSKISKLPALQDDAPPSDNYGRFSGRGRGSRGGMSDRRGSGGGSRTSRGWG- 695

Query: 365 GGARGGGSMDRRGFRSSRSWGSDDEDGFSSS--RGGRSFRSGNNR--GSRFSTSSDDDWL 420
                            RS  SD EDG S S  RGGRS R   NR      S+SS DDWL
Sbjct: 696 -----------------RSQDSDFEDGGSDSFRRGGRSPRPSTNRWSSGSSSSSSGDDWL 738

Query: 421 I----GGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN 456
           I      SRSS    R    F GACFNCGKSGHRA+ECP 
Sbjct: 739 IGGGRSSSRSSPMGGRRDGQFSGACFNCGKSGHRATECPT 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	456
TAIR|locus:504955106	748	emb1138 "embryo defective 1138	0.719	0.438	0.841	2.4e-153
TAIR|locus:2087852	616	PMH2 "putative mitochondrial R	0.370	0.274	0.621	1.2e-51
TAIR|locus:2087832	610	PMH1 "putative mitochondrial R	0.405	0.303	0.562	3.6e-50
ZFIN|ZDB-GENE-031113-10	759	ddx21 "DEAD (Asp-Glu-Ala-Asp)	0.710	0.426	0.389	9.4e-50
UNIPROTKB|E2RPT4	687	DDX50 "Uncharacterized protein	0.703	0.467	0.374	8.5e-49
UNIPROTKB|F1MMK3	737	DDX50 "Uncharacterized protein	0.703	0.435	0.374	1.2e-48
UNIPROTKB|E2QTT0	738	DDX50 "Uncharacterized protein	0.703	0.434	0.374	1.2e-48
MGI|MGI:2182303	734	Ddx50 "DEAD (Asp-Glu-Ala-Asp)	0.703	0.437	0.368	2.5e-48
UNIPROTKB|Q9BQ39	737	DDX50 "ATP-dependent RNA helic	0.703	0.435	0.374	2.7e-48
UNIPROTKB|E1BW15	693	DDX50 "Uncharacterized protein	0.526	0.346	0.432	2.6e-47

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

 Score = 1425 (506.7 bits), Expect = 2.4e-153, Sum P(2) = 2.4e-153
 Identities = 276/328 (84%), Positives = 307/328 (93%)

Query:    14 VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
             VG+QDEKLAEGIKLYAI+TT+TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLAL++
Sbjct:   314 VGDQDEKLAEGIKLYAIATTSTSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALSN 373

Query:    74 IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
              IA+EALHGDISQHQRERTLN FRQGKFTVLVATDVA+RGLDIPNVDL+IHYELPNDPET
Sbjct:   374 SIATEALHGDISQHQRERTLNAFRQGKFTVLVATDVASRGLDIPNVDLVIHYELPNDPET 433

Query:   134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
             FVHRSGRTGRAGKEG+AILM TSSQ+RTVRSLERDVGC FEF+SPP V D+LESSA+QVV
Sbjct:   434 FVHRSGRTGRAGKEGSAILMHTSSQKRTVRSLERDVGCHFEFISPPTVGDLLESSADQVV 493

Query:   194 ATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQ 253
             ATLNGVHP+S++FF+ TAQ+L EEKGTDALAAALA LSGFS+PPSSRSL++HE+GWVTLQ
Sbjct:   494 ATLNGVHPDSIKFFSATAQKLYEEKGTDALAAALAHLSGFSQPPSSRSLLSHEKGWVTLQ 553

Query:   254 LTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLN 313
             L RD   +RGF+SARSV GFLSD+Y TAADE+GKI +IADDR+QGAVFDLPEEIAKELL 
Sbjct:   554 LIRDPTNARGFLSARSVTGFLSDLYRTAADEVGKIFLIADDRIQGAVFDLPEEIAKELLE 613

Query:   314 KQIPPGNTISKITKLPALQDDGPSSDNY 341
             K +P GN++S ITKLP LQDDGPSSDNY
Sbjct:   614 KDVPEGNSLSMITKLPPLQDDGPSSDNY 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 = 536 (193.7 bits), Expect = 1.2e-51, P = 1.2e-51
 Identities = 105/169 (62%), Positives = 130/169 (76%)

Query:    14 VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
             VG+ D+KLA+GI  Y+I   +  + +I+  L+T +AKGGK IVFTQTKRDAD +S AL  
Sbjct:   312 VGDSDQKLADGITTYSIIADSYGRASIIGPLVTEHAKGGKCIVFTQTKRDADRLSYALAR 371

Query:    74 IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
                 EALHGDISQ QRERTL GFR G F +LVATDVAARGLD+PNVDLIIHYELPN+ ET
Sbjct:   372 SFKCEALHGDISQSQRERTLAGFRDGHFNILVATDVAARGLDVPNVDLIIHYELPNNTET 431

Query:   134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE 182
             FVHR+GRTGRAGK+G+AIL+++  Q R V+ +ER+VG +F  +    VE
Sbjct:   432 FVHRTGRTGRAGKKGSAILIYSQDQSRAVKIIEREVGSRFTELPSIAVE 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 = 522 (188.8 bits), Expect = 3.6e-50, P = 3.6e-50
 Identities = 104/185 (56%), Positives = 133/185 (71%)

Query:    14 VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS 73
             VG+ D+KLA+GI +Y+I+  +  + +I+  L+  + KGGK IVFTQTKRDAD ++  L  
Sbjct:   324 VGDSDQKLADGITMYSIAADSYGRASIIGPLVKEHGKGGKCIVFTQTKRDADRLAFGLAK 383

Query:    74 IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
                 EALHGDISQ QRERTL GFR G F++LVATDVAARGLD+PNVDL+IHYELPN+ ET
Sbjct:   384 SYKCEALHGDISQAQRERTLAGFRDGNFSILVATDVAARGLDVPNVDLVIHYELPNNTET 443

Query:   134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVV 193
             FVHR+GRTGRAGK+G+AIL+    Q R V+ +E++VG +F  +    VE    S  E V 
Sbjct:   444 FVHRTGRTGRAGKKGSAILIHGQDQTRAVKMIEKEVGSRFNELPSIAVERGSASMFEGVG 503

Query:   194 ATLNG 198
             A   G
Sbjct:   504 ARSGG 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 = 520 (188.1 bits), Expect = 9.4e-50, P = 9.4e-50
 Identities = 131/336 (38%), Positives = 194/336 (57%)

Query:     8 FSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADE 66
             F H   +G + +K A  ++  AI+   + + +++ D+I VY+   G+TIVF +TK++A E
Sbjct:   374 FIHVDLIGKKTQKAATTVEHLAIACHWSQRASVIGDVIQVYSGSHGRTIVFCETKKEATE 433

Query:    67 VSLALTSIIAS-EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY 125
             +SL  TSI  S ++LHGDI Q QRE TL GFR G F VLVAT+VAARGLDIP VDL+I  
Sbjct:   434 LSLN-TSIKQSAQSLHGDIPQKQREVTLKGFRNGSFEVLVATNVAARGLDIPEVDLVIQS 492

Query:   126 ELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVL 185
               PND E+++HRSGRTGRAG+ G  I  +   +   ++ +E+  G  F+ V  P   D++
Sbjct:   493 SPPNDVESYIHRSGRTGRAGRTGICICFYQRKEESQLKFVEQKAGITFKRVGVPTAYDII 552

Query:   186 ESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLIN 244
             +SS++  V  L+ V   +V +F   AQ LI+++G  +ALAAALA +SG +     RSLIN
Sbjct:   553 QSSSKDAVRFLDSVPAVAVGYFREAAQELIQQRGAVEALAAALAHISG-ATSLEQRSLIN 611

Query:   245 HEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLP 304
              E G+ ++ L+          + R +   L +        I   H++     +G  FD+P
Sbjct:   612 SEPGFSSMILSCSQEMHSISFAWRGLKEQLGEEID---QHIS--HMVFIKGKKGVCFDVP 666

Query:   305 EEIAKELLNK-QIPPGNTISKITKLPALQDD-GPSS 338
                 KE+  K Q     T+S  T+LP L+    P+S
Sbjct:   667 VSKLKEVQEKWQDSRRWTLSTATQLPELEQSLRPNS 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|E2RPT4 DDX50 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 509 (184.2 bits), Expect = 8.5e-49, P = 8.5e-49
 Identities = 124/331 (37%), Positives = 190/331 (57%)

Query:    14 VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALT 72
             VG   +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++   
Sbjct:   353 VGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPH 412

Query:    73 SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
                 ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E
Sbjct:   413 IKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVE 472

Query:   133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
             +++HRSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   
Sbjct:   473 SYIHRSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDA 532

Query:   193 VATLNGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVT 251
             + +L  V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT
Sbjct:   533 IRSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVT 591

Query:   252 LQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKEL 311
             + L           + + +   LS     A  +I ++ ++  +   G  FD+P   ++ L
Sbjct:   592 MTLESPEEIQDVSCAWKELNRKLSS---NAVSQITRMCLLKGN--MGVCFDVPTTESERL 646

Query:   312 LNKQIPPGNTISKITKLPALQD--DGPSSDN 340
               +       +S   KLP +++  DG +S N
Sbjct:   647 QAEWHDSDWILSLPAKLPEIEEYYDGNTSSN 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|F1MMK3 DDX50 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 509 (184.2 bits), Expect = 1.2e-48, P = 1.2e-48
 Identities = 124/331 (37%), Positives = 190/331 (57%)

Query:    14 VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALT 72
             VG   +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++   
Sbjct:   351 VGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPH 410

Query:    73 SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
                 ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E
Sbjct:   411 IKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVE 470

Query:   133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
             +++HRSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   
Sbjct:   471 SYIHRSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDA 530

Query:   193 VATLNGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVT 251
             + +L  V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT
Sbjct:   531 IRSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVT 589

Query:   252 LQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKEL 311
             + L           + + +   LS     A  +I ++ ++  +   G  FD+P   ++ L
Sbjct:   590 MTLESPEEIQDVSCAWKELNRKLSS---NAVSQITRMCLLKGN--MGVCFDVPTTESERL 644

Query:   312 LNKQIPPGNTISKITKLPALQD--DGPSSDN 340
               +       +S   KLP +++  DG +S N
Sbjct:   645 QAEWHDSDWILSVPAKLPEIEEYYDGNTSSN 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 = 509 (184.2 bits), Expect = 1.2e-48, P = 1.2e-48
 Identities = 124/331 (37%), Positives = 190/331 (57%)

Query:    14 VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALT 72
             VG   +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++   
Sbjct:   352 VGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPH 411

Query:    73 SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
                 ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E
Sbjct:   412 IKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVE 471

Query:   133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
             +++HRSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   
Sbjct:   472 SYIHRSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDA 531

Query:   193 VATLNGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVT 251
             + +L  V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT
Sbjct:   532 IRSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVT 590

Query:   252 LQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKEL 311
             + L           + + +   LS     A  +I ++ ++  +   G  FD+P   ++ L
Sbjct:   591 MTLESPEEIQDVSCAWKELNRKLSS---NAVSQITRMCLLKGN--MGVCFDVPTTESERL 645

Query:   312 LNKQIPPGNTISKITKLPALQD--DGPSSDN 340
               +       +S   KLP +++  DG +S N
Sbjct:   646 QAEWHDSDWILSLPAKLPEIEEYYDGNTSSN 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

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

 Score = 506 (183.2 bits), Expect = 2.5e-48, P = 2.5e-48
 Identities = 122/331 (36%), Positives = 189/331 (57%)

Query:    14 VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALT 72
             VG   +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++   
Sbjct:   348 VGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPH 407

Query:    73 SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
                 ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E
Sbjct:   408 IKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVE 467

Query:   133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
             +++HRSGRTGRAG+ G  +  +   +R  +R +E+  G  F+ V  P   D+++S +   
Sbjct:   468 SYIHRSGRTGRAGRTGICVCFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDA 527

Query:   193 VATLNGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVT 251
             + +L  V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT
Sbjct:   528 IRSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVT 586

Query:   252 LQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKEL 311
             + L           + + +   LS     A   + ++ ++  +   G  FD+P   ++ L
Sbjct:   587 MTLESPEEIQDVSCAWKELNRKLSS---NAVSHVTRMCLLKGN--MGVCFDVPTSESERL 641

Query:   312 LNKQIPPGNTISKITKLPALQD--DGPSSDN 340
               +       +S   KLP +++  DG +S N
Sbjct:   642 QAEWHDSDWILSVPAKLPEIEEYYDGNTSSN 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|Q9BQ39 DDX50 "ATP-dependent RNA helicase DDX50" [Homo sapiens (taxid:9606)]

 Score = 506 (183.2 bits), Expect = 2.7e-48, P = 2.7e-48
 Identities = 124/331 (37%), Positives = 190/331 (57%)

Query:    14 VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALT 72
             VG   +K A  ++  AI    + +  ++ D++ VY+   G+ I+F +TK++  E+++   
Sbjct:   351 VGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPH 410

Query:    73 SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
                 ++ LHGDI+Q QRE TL GFR+G F VLVAT+VAARGLDIP VDL+I    P D E
Sbjct:   411 IKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVE 470

Query:   133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
             +++HRSGRTGRAG+ G  I  +   +R  +R +E+  G  F+ V  P   D+++S +   
Sbjct:   471 SYIHRSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDA 530

Query:   193 VATLNGVHPESVEFFTPTAQRLIEEKGT-DALAAALAQLSGFSRPPSSRSLINHEQGWVT 251
             + +L  V   +V+FF P+AQRLIEEKG  DALAAALA +SG S     RSLI  ++G+VT
Sbjct:   531 IRSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSF-EPRSLITSDKGFVT 589

Query:   252 LQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKEL 311
             + L           + + +   LS     A  +I ++ ++  +   G  FD+P   ++ L
Sbjct:   590 MTLESLEEIQDVSCAWKELNRKLSS---NAVSQITRMCLLKGN--MGVCFDVPTTESERL 644

Query:   312 LNKQIPPGNTISKITKLPALQD--DGPSSDN 340
               +       +S   KLP +++  DG +S N
Sbjct:   645 QAEWHDSDWILSVPAKLPEIEEYYDGNTSSN 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

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

 Score = 495 (179.3 bits), Expect = 2.6e-47, P = 2.6e-47
 Identities = 105/243 (43%), Positives = 156/243 (64%)

Query:    14 VGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKG-GKTIVFTQTKRDADEVSLALT 72
             +G + +K A  ++  AI    + +  ++ D+I VY+   G+TIVF +TK+DA+E++L  +
Sbjct:   327 IGRKTQKAATTVEHLAIECHWSQRAAVIGDVIQVYSGSYGRTIVFCETKKDANELALNAS 386

Query:    73 SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPE 132
                  ++LHGDI Q QRE TL GFR G F VLVAT+VAARGLDIP VDL++    P D E
Sbjct:   387 IKQDCQSLHGDIPQKQREITLKGFRNGAFKVLVATNVAARGLDIPEVDLVVQSSPPKDVE 446

Query:   133 TFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQV 192
             +++HRSGRTGRAG+ G  I  +   +   +R +E   G  F+ V  P   D++++S++  
Sbjct:   447 SYIHRSGRTGRAGRTGICICFYQRKEENQLRYVEVKAGITFKRVGVPTATDIIKASSKDA 506

Query:   193 VATLNGVHPESVEFFTPTAQRLIEEKG-TDALAAALAQLSGFSRPPSSRSLINHEQGWVT 251
             +  L+ V   ++E+F  +AQ LIEEKG  +ALAAALA +SG +     RSL+N + G+VT
Sbjct:   507 IRCLDSVPQTAIEYFKESAQLLIEEKGPVNALAAALAHISG-ATSIEQRSLLNSDVGFVT 565

Query:   252 LQL 254
             + L
Sbjct:   566 MVL 568

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

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

---

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	0.8149	0.7346	0.4419	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

Fail to connect to STRING server

---

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	456
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	4e-42
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	4e-39
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	2e-34
pfam08152	97	pfam08152, GUCT, GUCT (NUC152) domain	7e-29
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-27
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-27
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	2e-27
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-26
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	5e-26
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	2e-25
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	4e-24
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	9e-24
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	9e-24
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	2e-19
cd12938	74	cd12938, GUCT_Hera, RNA-binding GUCT-like domain f	3e-19
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	6e-16
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	3e-15
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	1e-13
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	3e-13
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	9e-13
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	6e-09
TIGR00631	655	TIGR00631, uvrb, excinuclease ABC, B subunit	4e-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	5e-07
COG1197	1139	COG1197, Mfd, Transcription-repair coupling factor	5e-07
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	1e-06
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	2e-06
TIGR01587	358	TIGR01587, cas3_core, CRISPR-associated helicase C	3e-06
smart00343	17	smart00343, ZnF_C2HC, zinc finger	5e-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	1e-04
cd09639	353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	2e-04
PRK05580	679	PRK05580, PRK05580, primosome assembly protein Pri	5e-04
COG4098	441	COG4098, comFA, Superfamily II DNA/RNA helicase re	5e-04
PRK05298	652	PRK05298, PRK05298, excinuclease ABC subunit B; Pr	7e-04
PRK10917	681	PRK10917, PRK10917, ATP-dependent DNA helicase Rec	8e-04
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	0.001
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	0.002
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	0.002
PRK00254	720	PRK00254, PRK00254, ski2-like helicase; Provisiona	0.002
pfam06682	317	pfam06682, DUF1183, Protein of unknown function (D	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 =  156 bits (395), Expect = 4e-42
 Identities = 74/237 (31%), Positives = 115/237 (48%), Gaps = 12/237 (5%)

Query: 16  NQDEKLAEGIKLYAIST-TATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
            + E+  + IK + +   +   K  +L  L+    +G + IVF +TKR  +E++ +L   
Sbjct: 238 EKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDEG-RVIVFVRTKRLVEELAESLRKR 296

Query: 75  -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
                ALHGD+ Q +R+R L  F+ G+  VLVATDVAARGLDIP+V  +I+Y+LP DPE 
Sbjct: 297 GFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPED 356

Query: 134 FVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFE-FVSPPVVEDVLESSAEQ 191
           +VHR GRTGRAG++G AI   T   + + ++ +E+ +  K    V  P+ E       + 
Sbjct: 357 YVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLLKT 416

Query: 192 VVATLNGVHPESVE-------FFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRS 241
               L      S E                +    +  LA    ++ G     +   
Sbjct: 417 TRPGLEEESDISDEIKKLKSSKKALLRGLGVRFTLSKLLANLGKEIPGAGDAVTIDP 473

Length = 513

>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

 Score =  137 bits (347), Expect = 4e-39
 Identities = 57/119 (47%), Positives = 81/119 (68%), Gaps = 2/119 (1%)

Query: 37  KRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLN 94
           K   L +L+  +  KGGK ++F  +K+  DE++  L    I   ALHGD SQ +RE  L 
Sbjct: 13  KLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLK 72

Query: 95  GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM 153
            FR+G+  VLVATDV ARG+D+PNV ++I+Y+LP  P +++ R GR GRAG++GTAIL+
Sbjct: 73  DFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131

Length = 131

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

 Score =  133 bits (338), Expect = 2e-34
 Identities = 54/127 (42%), Positives = 78/127 (61%), Gaps = 1/127 (0%)

Query: 54  TIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR 112
            +VF  TK++  EV+ AL +   ++ ALHGD+ Q  R++ L  F     +VLVATDVAAR
Sbjct: 245 CVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAAR 304

Query: 113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCK 172
           GLDI  ++ +I+YEL  DPE  VHR GRTGRAG +G A+ +    + +   ++E  +G K
Sbjct: 305 GLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRK 364

Query: 173 FEFVSPP 179
             +   P
Sbjct: 365 LNWEPLP 371

Length = 460

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

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

Query: 232 GFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHII 291
           G++     RSL+  E+G+VTLQLT          + +S+  FL D      D I  + ++
Sbjct: 1   GYTSI-KQRSLLTSEEGYVTLQLTSGRPIPTPSFAWKSLRRFLPD---EKVDSIKGMTLL 56

Query: 292 ADDRVQGAVFDLPEEIAKELLNKQIPP-GNTISKITKLPALQD 333
           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|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score =  114 bits (288), Expect = 2e-27
 Identities = 56/156 (35%), Positives = 84/156 (53%), Gaps = 2/156 (1%)

Query: 14  VGNQDEKLAEGIKLYAISTTATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLAL- 71
           VG+ D      IK          KR  L  L+  +   G K ++F +TK+ AD ++  L 
Sbjct: 339 VGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELR 398

Query: 72  TSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP 131
                +  +HGD  Q +R   LN F+ GK  +++ATDVA+RGLD+ +V  +I+++ PN  
Sbjct: 399 LDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQI 458

Query: 132 ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
           E +VHR GRTGRAG +G +    T  + R  R L +
Sbjct: 459 EDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVK 494

Length = 545

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

 Score =  114 bits (288), Expect = 2e-27
 Identities = 73/200 (36%), Positives = 110/200 (55%), Gaps = 27/200 (13%)

Query: 54  TIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR 112
            I+F +TK    EV+ AL  +   S AL+GD++Q  RE+TL   + G+  +L+ATDVAAR
Sbjct: 248 AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAAR 307

Query: 113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCK 172
           GLD+  + L+++Y++P D E++VHR GRTGRAG+ G A+L   + +RR +R++ER +   
Sbjct: 308 GLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLT 367

Query: 173 FEFVSPP---------------VVEDVLESS-AEQVVATLNGVHPESVEFFTPTAQRLIE 216
              V  P                V+  LESS  +Q  A L  + P +            E
Sbjct: 368 IPEVELPNAELLGKRRLEKFAAKVQQQLESSDLDQYRALLAKIQPTAEG----------E 417

Query: 217 EKGTDALAAALAQLSGFSRP 236
           E   + LAAAL +++   RP
Sbjct: 418 ELDLETLAAALLKMAQGERP 437

Length = 629

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

 Score =  103 bits (260), Expect = 2e-27
 Identities = 39/71 (54%), Positives = 52/71 (73%)

Query: 75  IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF 134
           I    LHG +SQ +RE  L  FR GK  VLVATDVA RG+D+P+V+L+I+Y+LP +P ++
Sbjct: 8   IKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASY 67

Query: 135 VHRSGRTGRAG 145
           + 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|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score =  110 bits (277), Expect = 2e-26
 Identities = 59/134 (44%), Positives = 83/134 (61%), Gaps = 6/134 (4%)

Query: 37  KRTILSDLITVYAKGG--KTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTL 93
           KR +LS +I    KG   + +VFT+TK  A+ ++  L    I S A+HG+ SQ  R R L
Sbjct: 232 KRELLSQMI---GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRAL 288

Query: 94  NGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM 153
             F+ G   VLVATD+AARGLDI  +  +++YELPN PE +VHR GRTGRA   G A+ +
Sbjct: 289 ADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSL 348

Query: 154 FTSSQRRTVRSLER 167
               + + +R +E+
Sbjct: 349 VCVDEHKLLRDIEK 362

Length = 456

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

 Score =  109 bits (274), Expect = 5e-26
 Identities = 42/100 (42%), Positives = 65/100 (65%), Gaps = 1/100 (1%)

Query: 53  KTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA 111
           ++IVF +T+    E++  L    I    L G++ Q +R   +     G+  VLVATDVAA
Sbjct: 247 RSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAA 306

Query: 112 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
           RG+DI +V  +I++++P   +T++HR GRTGRAG++GTAI
Sbjct: 307 RGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAI 346

Length = 434

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

 Score = 98.8 bits (247), Expect = 2e-25
 Identities = 42/82 (51%), Positives = 55/82 (67%), Gaps = 1/82 (1%)

Query: 65  DEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 123
           +E++  L  + I    LHG +SQ +RE  L+ F  GK  VLVATDVA RGLD+P VDL+I
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 124 HYELPNDPETFVHRSGRTGRAG 145
            Y+LP  P +++ R GR GRAG
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score =  104 bits (260), Expect = 4e-24
 Identities = 57/154 (37%), Positives = 84/154 (54%), Gaps = 4/154 (2%)

Query: 27  LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDIS 85
           +YA++   + K  +L +L+T      + +VF   K +   +   L    I +  L GD+ 
Sbjct: 314 VYAVA--GSDKYKLLYNLVT-QNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVP 370

Query: 86  QHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG 145
           QH+R +TL GFR+GK  VLVATDVA RG+ I  +  +I++ LP DP+ +VHR GRTGRAG
Sbjct: 371 QHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAG 430

Query: 146 KEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP 179
             G +I          +  +E  +G K     PP
Sbjct: 431 ASGVSISFAGEDDAFQLPEIEELLGRKISCEMPP 464

Length = 475

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

 Score =  102 bits (257), Expect = 9e-24
 Identities = 46/104 (44%), Positives = 64/104 (61%), Gaps = 9/104 (8%)

Query: 53  KTIVFTQTKRDADEVSLALTSIIASEA-----LHGDISQHQRERTLNGFRQGKFTVLVAT 107
           + I+F  TK   +E+       +A++      L GD++Q +R R L  F +G   +LVAT
Sbjct: 257 RAIIFANTKHRCEEI----WGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVAT 312

Query: 108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
           DVAARGL IP V  + +Y+LP+D E +VHR GRTGRAG  G +I
Sbjct: 313 DVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSI 356

Length = 423

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

 Score =  102 bits (255), Expect = 9e-24
 Identities = 51/156 (32%), Positives = 84/156 (53%), Gaps = 9/156 (5%)

Query: 17  QDEKLAEGIKLYAISTTATS-KRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSLALT 72
           +DE   EGI+ + ++      K   L DL   +T+     + I++  T+R  D ++  + 
Sbjct: 233 KDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTIT----QAIIYCNTRRKVDYLTKKMH 288

Query: 73  S-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP 131
                   +HGD+ Q  R+  +  FR G   VL+ TD+ ARG+D+  V L+I+Y+LP  P
Sbjct: 289 ERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASP 348

Query: 132 ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
           E ++HR GR+GR G++G AI   T      ++ +ER
Sbjct: 349 ENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIER 384

Length = 401

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

 Score = 90.8 bits (225), Expect = 2e-19
 Identities = 52/116 (44%), Positives = 73/116 (62%), Gaps = 2/116 (1%)

Query: 37  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNG 95
           K+T+L  L++  ++G +T+VF  TK   + V+  L         L GD+ Q +RE  LN 
Sbjct: 244 KQTLLLGLLS-RSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNR 302

Query: 96  FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
           F++G+  +LVATDVAARGL I  V  + +Y+LP D E +VHR GRT R G+EG AI
Sbjct: 303 FQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAI 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 = 81.6 bits (202), Expect = 3e-19
 Identities = 42/81 (51%), Positives = 47/81 (58%), Gaps = 7/81 (8%)

Query: 239 SRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQG 298
            RSL+  E+GW TLQLT          S R  +G LS     AAD +GKI I+AD    G
Sbjct: 1   PRSLLTGEEGWTTLQLTGSR--LLPPGSVRRAVGLLSRA---AADGVGKIRILAD--AGG 53

Query: 299 AVFDLPEEIAKELLNKQIPPG 319
           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|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]

 Score = 79.7 bits (197), Expect = 6e-16
 Identities = 42/120 (35%), Positives = 64/120 (53%), Gaps = 11/120 (9%)

Query: 50  KGGKTIVFTQTKRDADEVSLALTSI--------IASEALHGD--ISQHQRERTLNGFRQG 99
              + IVFT+ +  A+E+   L  I        I   +  GD  +SQ +++  ++ FR+G
Sbjct: 365 GDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKG 424

Query: 100 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR 159
           ++ 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 = 78.0 bits (193), Expect = 3e-15
 Identities = 49/132 (37%), Positives = 69/132 (52%), Gaps = 24/132 (18%)

Query: 50  KGGKTIVFTQTKRD-ADEVSLALTSI-IASEALHGD--------ISQHQRERTLNGFRQG 99
              + IVFTQ  RD A+++   L    I +    G         +SQ ++   L+ FR G
Sbjct: 364 PDSRIIVFTQY-RDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAG 422

Query: 100 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPET-FVHRSGRTGRAGKEGTA-ILM---- 153
           +F VLV+T VA  GLDIP+VDL+I YE P   E   + R GRTGR  +EG   +L+    
Sbjct: 423 EFNVLVSTSVAEEGLDIPSVDLVIFYE-PVPSEIRSIQRKGRTGR-QEEGRVVVLIAKGT 480

Query: 154 -----FTSSQRR 160
                + 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 = 72.1 bits (177), Expect = 1e-13
 Identities = 40/146 (27%), Positives = 63/146 (43%), Gaps = 2/146 (1%)

Query: 20  KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA 79
            L    +   I+  +  K   +  L+  +A+G KT++F      A E++    +    EA
Sbjct: 252 TLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGIVEA 311

Query: 80  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
           + G+  + +RE  L  FR G   VLV   V   G+DIP+ D++I          F+ R G
Sbjct: 312 ITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLG 371

Query: 140 RTGRA--GKEGTAILMFTSSQRRTVR 163
           R  R   GKE T  L ++        
Sbjct: 372 RGLRPAEGKEDTLALDYSLVPDDLGE 397

Length = 442

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

 Score = 71.0 bits (174), Expect = 3e-13
 Identities = 36/108 (33%), Positives = 62/108 (57%), Gaps = 2/108 (1%)

Query: 55  IVFTQTKRDADEVSLALTSIIASEAL--HGDISQHQRERTLNGFRQGKFTVLVATDVAAR 112
           +VF  ++  AD ++ A+T +   +AL  HG+ S  +R   +  F  G+  V+VAT V  R
Sbjct: 371 VVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGR 430

Query: 113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRR 160
           G+D+  V  +I +++PN  + ++H+ GR  R G++GTAI+      R 
Sbjct: 431 GVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRN 478

Length = 518

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

 Score = 70.0 bits (172), Expect = 9e-13
 Identities = 37/118 (31%), Positives = 62/118 (52%), Gaps = 1/118 (0%)

Query: 49  AKGGKTIVFTQTKRDADEVSLAL-TSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 107
                 I++  T++  +E++  L  + I++ A H  +S  +RER    F   +  V+VAT
Sbjct: 228 QLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVAT 287

Query: 108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 165
           +    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: 55  IVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG 113
           I++  +++  +E++  L S  I++ A H  +S   R      F      V+VAT+    G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287

Query: 114 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS 156
           +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: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           KG   I++  +++ +++V+ +L ++ IA+ A H  +    R+   + F++ +  V+VAT 
Sbjct: 225 KGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATV 284

Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL 165
               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: 240 RSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYP-TAADEIGKIHIIADDRVQG 298
           RSL+   +G+ TL L      +    S   V   L    P    + I  + + AD +  G
Sbjct: 1   RSLLTSHEGYTTLLLK----SNTPIRSPGYVWNALRRYLPEDIVESIKGMTLTADGK--G 54

Query: 299 AVFDLPEEIAKELLNKQIP-PGNTISKITKLP 329
           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 = 6e-09
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 2/93 (2%)

Query: 53  KTIVFTQTKRDADEVSLALTSI--IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA 110
            T++FT T+  A+ ++  L  +     E  HG +S+  R       ++G+   +VAT   
Sbjct: 255 TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSL 314

Query: 111 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
             G+DI ++DL+I    P     F+ R GR G 
Sbjct: 315 ELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347

Length = 814

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

 Score = 55.0 bits (133), Expect = 4e-08
 Identities = 43/140 (30%), Positives = 70/140 (50%), Gaps = 16/140 (11%)

Query: 40  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 98
           +LS++    A+  + +V T TK+ A++++  L  + I    LH +I   +R   +   R 
Sbjct: 431 LLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRL 490

Query: 99  GKFTVLVATDVAARGLDIPNVDLI-IHYELPNDPETFVHRSGRT-----GRAGK--EGTA 150
           G+F VLV  ++   GLD+P V L+ I   L  D E F+ RS R+     GRA +   G  
Sbjct: 491 GEFDVLVGINLLREGLDLPEVSLVAI---LDADKEGFL-RSERSLIQTIGRAARNVNGKV 546

Query: 151 ILM---FTSSQRRTVRSLER 167
           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: 40  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 98
           +LS++    AK  + +V T TK+ A++++  L  + I    LH DI   +R   +   R 
Sbjct: 435 LLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRL 494

Query: 99  GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAI 151
           G+F VLV  ++   GLD+P V L+    L  D E F+ RS R+     GRA +   G  I
Sbjct: 495 GEFDVLVGINLLREGLDLPEVSLVA--ILDADKEGFL-RSERSLIQTIGRAARNVNGKVI 551

Query: 152 L---MFTSSQRRTVRSLER 167
           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: 80  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 135
            HG +++++ E  +  F +G+F VLV T +   G+DIPN + II        + F    +
Sbjct: 692 AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTII----IERADKFGLAQL 747

Query: 136 HR-SGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
           ++  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 = 52.1 bits (125), Expect = 5e-07
 Identities = 49/203 (24%), Positives = 78/203 (38%), Gaps = 34/203 (16%)

Query: 46  TVYAKG--GKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFT 102
           T  +KG  G+TIVFT ++R   E++ ALT   + +   H  +   +R+     F   +  
Sbjct: 433 TESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELA 492

Query: 103 VLVATDVAARGLDIPNVDLIIH-YELPND---PETFVHRSGRTGRAG--KEGTAILM--- 153
            +V T   A G+D P   +I     +  +      F    GR GR      G   L+   
Sbjct: 493 AVVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEP 552

Query: 154 ---FTSSQRRTVRSLERDVGCKFEFVSPP---VVEDVLESSAEQVVAT---------LNG 198
              + +S   T    E +V  K    S P   +VE   E   E V+A+         +  
Sbjct: 553 GKKYHASMEET----EDEVAFKL-LESEPEPVIVEYDEEDEEENVLASAGVTNSLSVIER 607

Query: 199 VHPESVEFFTPTAQRL--IEEKG 219
           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 = 5e-07
 Identities = 25/99 (25%), Positives = 43/99 (43%), Gaps = 23/99 (23%)

Query: 81  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS-- 138
           HG + + + E  +  F  G++ VLV T +   G+DIPN + II           + R+  
Sbjct: 836 HGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTII-----------IERADK 884

Query: 139 ----------GRTGRAGKEGTAILMFTSSQRRTVRSLER 167
                     GR GR+ K+  A  ++   +  T  + +R
Sbjct: 885 FGLAQLYQLRGRVGRSNKQAYAYFLYPPQKALTEDAEKR 923

Length = 1139

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

 Score = 50.8 bits (122), Expect = 1e-06
 Identities = 29/112 (25%), Positives = 53/112 (47%), Gaps = 17/112 (15%)

Query: 62  RDADEVSLALTSIIASEA---LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN 118
           + A+ +   L           LHG +   ++E  +  FR+G+  +LVAT V   G+D+PN
Sbjct: 467 KAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN 526

Query: 119 VDLIIHYELPNDPETF----VHR-SGRTGRAGKEGTAILMF-----TSSQRR 160
             +++      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|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 43.6 bits (104), Expect = 2e-06
 Identities = 10/18 (55%), Positives = 12/18 (66%)

Query: 439 GACFNCGKSGHRASECPN 456
             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|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3

 Score = 48.6 bits (116), Expect = 3e-06
 Identities = 32/118 (27%), Positives = 49/118 (41%), Gaps = 10/118 (8%)

Query: 36  SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA---LHGDISQHQRER- 91
            + + L  L+    KGGK  +   T   A E    L      E    LH   ++  R + 
Sbjct: 207 GEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKK 266

Query: 92  ---TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK 146
               L   ++ +  V+VAT V    LDI + D++I    P D  + + R GR  R G+
Sbjct: 267 EAELLEEMKKNEKFVIVATQVIEASLDI-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|197667 smart00343, ZnF_C2HC, zinc finger

 Score = 42.4 bits (101), Expect = 5e-06
 Identities = 10/16 (62%), Positives = 13/16 (81%)

Query: 441 CFNCGKSGHRASECPN 456
           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: 31  STTATSKRTILSDLITVYAKGG-KTIVFTQTKRDADEVSLALTSIIASEALHGDISQH-- 87
            +   S    L+ L  +  + G +T+VF ++++   +V L   S        G       
Sbjct: 285 ESIRRSALAELATLAALLVRNGIQTLVFFRSRK---QVELLYLSPRRRLVREGGKLLDAV 341

Query: 88  ----------QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET-FVH 136
                     +R R    F++G+   ++AT+    G+DI ++D +I Y  P      F  
Sbjct: 342 STYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQ 401

Query: 137 RSGRTGRAGKEGTAILMFTSS--QRRTVRSLERDVGCKFEFVSPPVVEDV 184
           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: 62  RDADEVSLALTSIIASEA---LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN 118
           + A+E+   L S +       +HG +   +++  +  F++G+  +LVAT V   G+D+PN
Sbjct: 492 QAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPN 551

Query: 119 VDLIIHYELPNDPETF----VH--RSGRTGRAGKEGTAILMFTS 156
             +++      + 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: 81  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----HYELPNDPETFV 135
           HG + + + ER +N F   +F VLV T +   G+DIP  + II     H+ L       +
Sbjct: 842 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ-----L 896

Query: 136 HR-SGRTGRAGKEGTAIL-------MFTSSQRR--TVRSLERDVGCKF 173
           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 = 47.0 bits (112), Expect = 1e-05
 Identities = 26/106 (24%), Positives = 54/106 (50%), Gaps = 1/106 (0%)

Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +G   I++  ++   ++ +  L S  I++ A H  +    R      F++    ++VAT 
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATV 294

Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 154
               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 = 1e-04
 Identities = 37/136 (27%), Positives = 61/136 (44%), Gaps = 6/136 (4%)

Query: 81  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 140
           HG +S+ QR  T    + G+   +VAT     G+D+  VDL+I    P    + + R GR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367

Query: 141 TGRAGKEGTAILMFTSSQRRTVRS---LERDVGCKFEFVSPPVVEDVLESSAEQVVATLN 197
            G      +  L F  ++R  V S   +E     + E ++PP   + L+  A+Q VA   
Sbjct: 368 AGHQVGGVSKGLFFPRTRRDLVDSAVIVECMFAGRLENLTPP--HNPLDVLAQQTVAAA- 424

Query: 198 GVHPESVEFFTPTAQR 213
            +    V+ +    +R
Sbjct: 425 AMDALQVDEWYSRVRR 440

Length = 1490

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

 Score = 43.2 bits (102), Expect = 2e-04
 Identities = 33/119 (27%), Positives = 49/119 (41%), Gaps = 12/119 (10%)

Query: 36  SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA---LHGDISQHQRER- 91
            + + L  L+    KGG   +   T   A E    L      E    +H   ++  R + 
Sbjct: 203 GEISSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKK 262

Query: 92  ----TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK 146
                L   +  KF V+VAT V    LDI +VD++I    P D  + + R GR  R G+
Sbjct: 263 EAELLLEFKKSEKF-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|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: 90  ERTLNGFRQGKFTVLVATDVAARGLDIPNV--------DLIIHYELPNDP----ETF--- 134
           E+ L  F +G+  +L+ T + A+G D PNV        DL +      D      TF   
Sbjct: 470 EQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFS---PDFRASERTFQLL 526

Query: 135 --VHRSGRTGRAGKEGTAIL 152
             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 = 5e-04
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 85  SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL-IIHYELPN-DPETFVHRSGRTG 142
            QH++E+ +  FR GK T+L+ T +  RG+  PNVD+ ++  E         V  +GR G
Sbjct: 341 DQHRKEK-VEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVG 399

Query: 143 RAGKEGTAILMF 154
           R+ +  T  ++F
Sbjct: 400 RSLERPTGDVLF 411

Length = 441

>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: 49  AKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVAT 107
           AKG + +V T TKR A++++  L  + I    LH DI   +R   +   R G+F VLV  
Sbjct: 444 AKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGI 503

Query: 108 DVAARGLDIPNVDLI-IHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 152
           ++   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 = 8e-04
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 11/80 (13%)

Query: 80  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 135
           LHG +   +++  +  F+ G+  +LVAT V   G+D+PN  +++      + E F    +
Sbjct: 511 LHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIE----NAERFGLAQL 566

Query: 136 H--RSGRTGRAGKEGTAILM 153
           H  R GR GR   +   +L+
Sbjct: 567 HQLR-GRVGRGAAQSYCVLL 585

Length = 681

>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: 22  AEGIKLYAISTTATSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEVSLA----LTSIIA 76
             G     +  +A+++   +L+DL+   A+G +T+ F +++R A+ V+      L  +  
Sbjct: 244 LTGENGAPVRRSASAEAADLLADLV---AEGARTLTFVRSRRGAELVAAIARRLLGEVDP 300

Query: 77  SEALH------GDISQHQR--ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 128
             A        G + + +R  ER L   R G+   +  T+    G+DI  +D ++    P
Sbjct: 301 DLAERVAAYRAGYLPEDRRELERAL---RDGELLGVATTNALELGVDISGLDAVVIAGFP 357

Query: 129 NDPETFVHRSGRTGRAGKEGTAILM 153
               +   ++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: 55  IVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVAARG 113
           I++  ++ D ++V+  L       A  HG +   QR      + + +  ++ AT     G
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG 743

Query: 114 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS 157
           ++ P+V  +IH+ LP   E +    GR GR G+  + +L ++ S
Sbjct: 744 INKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYS 787

Length = 1195

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

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 5/31 (16%)

Query: 431 SRD---SRSFGG--ACFNCGKSGHRASECPN 456
           SR+   +    G  +C+NCGK+GH + ECP 
Sbjct: 40  SRECPSAPGGRGERSCYNCGKTGHLSRECPE 70

Length = 148

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

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 47/207 (22%), Positives = 79/207 (38%), Gaps = 48/207 (23%)

Query: 50  KGGKTIVFTQTKRDADEVSLALTSIIAS---------------------------EALHG 82
           KG   +VF  T+R A++ +L L   I                             +AL G
Sbjct: 237 KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRG 296

Query: 83  DISQH-----QRERTL--NGFRQGKFTVLVATDVAARGLDIPNVDLII-------HYELP 128
            ++ H     + ER L  + FR+G   V+ AT   + G+++P   +II       ++   
Sbjct: 297 GVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWE 356

Query: 129 NDPETFVHRS-GRTGRA--GKEGTAILMFTSSQRRTVRSLERDVGCKFE-FVSPPVVEDV 184
           + P   + +  GR GR    + G AI++ T+ +   +  +ER +  K E   S    E  
Sbjct: 357 DIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKL--MERYIFGKPEKLFSMLSNESA 414

Query: 185 LESSAEQVVATLN-GVHPESVEFFTPT 210
             S    ++         E V F   T
Sbjct: 415 FRSQVLALITNFGVSNFKELVNFLERT 441

Length = 720

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

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 29/113 (25%), Positives = 36/113 (31%), Gaps = 10/113 (8%)

Query: 332 QDDGPSSDNY-GRFSSRDRFSRGGGSRFSRGGARGGARGGGSMDRRGFRSSRSWGSDDED 390
              G         F S      G G+  S G   GG R G      GF +    G     
Sbjct: 206 GGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYGSGGTRSGQGGWGPGFWTGLGAG----- 260

Query: 391 GFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSS----RDSRSFGG 439
           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|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA ligase-associated

 Score = 39.8 bits (94), Expect = 0.003
 Identities = 32/110 (29%), Positives = 48/110 (43%), Gaps = 6/110 (5%)

Query: 54  TIVFTQTKRDADEVSLALTSIIASEAL-----HGDISQHQRERTLNGFRQGKFTVLVATD 108
           T+VFT T+  A+    AL       AL     HG + + QR         G+   +V T 
Sbjct: 250 TLVFTNTRSQAELWFQALWEANPEFALPIALHHGSLDREQRRWVEAAMAAGRLRAVVCTS 309

Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG-RAGKEGTAILMFTSS 157
               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	456
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	99.97
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.97
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.97
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.97
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.96
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.96
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.95
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.95
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.95
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	99.95
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.95
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.94
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.94
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.94
PTZ00110	545	helicase; Provisional	99.93
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.93
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.92
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.92
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.92
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.92
KOG0327	397	consensus Translation initiation factor 4F, helica	99.91
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	99.91
PTZ00424	401	helicase 45; Provisional	99.91
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.91
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.9
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.89
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.89
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.89
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.88
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.88
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.87
PRK04914	956	ATP-dependent helicase HepA; Validated	99.87
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.86
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.86
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.86
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.86
KOG4284	980	consensus DEAD box protein [Transcription]	99.85
PHA02653	675	RNA helicase NPH-II; Provisional	99.85
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.85
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.85
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.81
PRK13767	876	ATP-dependent helicase; Provisional	99.8
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.8
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.8
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.79
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.79
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.79
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.78
PRK05298	652	excinuclease ABC subunit B; Provisional	99.77
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.77
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.76
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.75
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.75
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.74
PRK02362	737	ski2-like helicase; Provisional	99.74
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.73
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.73
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.73
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.73
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.73
PRK10689	1147	transcription-repair coupling factor; Provisional	99.72
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.7
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.69
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.68
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.67
PRK00254	720	ski2-like helicase; Provisional	99.67
PRK13766	773	Hef nuclease; Provisional	99.67
KOG0354	746	consensus DEAD-box like helicase [General function	99.66
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.64
PHA02558	501	uvsW UvsW helicase; Provisional	99.64
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.63
PRK09401	1176	reverse gyrase; Reviewed	99.62
PRK01172	674	ski2-like helicase; Provisional	99.61
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.6
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.59
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.58
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.54
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.53
COG1202	830	Superfamily II helicase, archaea-specific [General	99.53
PRK14701	1638	reverse gyrase; Provisional	99.48
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.48
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.47
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.46
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.39
PF08152	97	GUCT: GUCT (NUC152) domain; InterPro: IPR012562 Th	99.38
PRK09694	878	helicase Cas3; Provisional	99.38
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.38
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.36
COG1204	766	Superfamily II helicase [General function predicti	99.36
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.36
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.35
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.35
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.3
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.3
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.28
PRK05580	679	primosome assembly protein PriA; Validated	99.27
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.25
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	99.25
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.24
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.21
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.2
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.16
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.12
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.1
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.03
COG1205	851	Distinct helicase family with a unique C-terminal	99.03
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.99
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	98.98
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	98.89
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	98.89
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.89
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.87
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.79
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	98.78
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	98.77
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	98.74
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.73
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.71
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.67
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.63
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.61
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	98.6
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.56
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.53
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.48
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.47
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.43
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	98.43
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.4
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	98.36
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	98.25
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.24
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	98.16
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	98.16
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	98.15
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.15
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.09
KOG1002	791	consensus Nucleotide excision repair protein RAD16	98.09
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	98.07
KOG1123	776	consensus RNA polymerase II transcription initiati	98.06
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.03
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	98.03
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	98.01
COG4096	875	HsdR Type I site-specific restriction-modification	97.98
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.93
COG1198	730	PriA Primosomal protein N' (replication factor Y)	97.89
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.88
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	97.83
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	97.78
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.78
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	97.49
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	97.38
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	97.31
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.29
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	97.26
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	97.25
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.19
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	97.18
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.17
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.12
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.06
COG4889	1518	Predicted helicase [General function prediction on	97.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	96.97
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	96.96
PF13871	278	Helicase_C_4: Helicase_C-like	96.84
TIGR00595	505	priA primosomal protein N'. All proteins in this f	96.84
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	96.76
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	96.71
PTZ00110	545	helicase; Provisional	96.66
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	96.65
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	96.64
PRK05580	679	primosome assembly protein PriA; Validated	96.61
KOG4439	901	consensus RNA polymerase II transcription terminat	96.6
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.55
KOG0334	997	consensus RNA helicase [RNA processing and modific	96.5
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	96.29
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	96.26
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.05
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	96.01
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	96.0
PRK14873	665	primosome assembly protein PriA; Provisional	96.0
PF13696	32	zf-CCHC_2: Zinc knuckle	95.93
smart00343	26	ZnF_C2HC zinc finger.	95.72
PTZ00368	148	universal minicircle sequence binding protein (UMS	95.63
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	95.45
PF13917	42	zf-CCHC_3: Zinc knuckle	95.29
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	95.28
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	95.25
PRK10689	1147	transcription-repair coupling factor; Provisional	95.16
COG1198	730	PriA Primosomal protein N' (replication factor Y)	95.13
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	94.99
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	94.98
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	94.97
PTZ00368	148	universal minicircle sequence binding protein (UMS	94.8
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	94.78
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	94.77
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	94.58
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	94.55
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	94.47
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	94.31
KOG0347	731	consensus RNA helicase [RNA processing and modific	94.28
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	94.16
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	93.6
PRK14701	1638	reverse gyrase; Provisional	93.57
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	93.49
KOG1001	674	consensus Helicase-like transcription factor HLTF/	93.37
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	93.26
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	93.17
PRK14873	665	primosome assembly protein PriA; Provisional	92.93
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	92.03
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	91.73
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	91.61
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	91.58
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	91.41
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	91.27
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	91.24
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	91.16
PRK13766	773	Hef nuclease; Provisional	91.04
KOG0343	758	consensus RNA Helicase [RNA processing and modific	90.78
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	90.77
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	90.73
PF15288	40	zf-CCHC_6: Zinc knuckle	90.46
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	90.37
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	89.92
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	89.27
PRK09401	1176	reverse gyrase; Reviewed	89.08
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	88.34
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	87.21
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	87.03
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	87.02
PF14392	49	zf-CCHC_4: Zinc knuckle	86.42
KOG2340	698	consensus Uncharacterized conserved protein [Funct	85.74
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	85.7
KOG0346	569	consensus RNA helicase [RNA processing and modific	85.08
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	84.61
KOG0298	1394	consensus DEAD box-containing helicase-like transc	84.35
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	83.29
PF12683	275	DUF3798: Protein of unknown function (DUF3798); In	82.41
PRK13767	876	ATP-dependent helicase; Provisional	82.3

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=4e-44  Score=384.56  Aligned_cols=304  Identities=26%  Similarity=0.395  Sum_probs=257.6

Q ss_pred             ccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeC
Q 012794            4 YFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHG   82 (456)
Q Consensus         4 ~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg   82 (456)
                      |++++..|.+.  ........+.+.|+.+....|.+.|..+|... ...++||||+|+..+++|++.|.. ++.+..+||
T Consensus       201 ~l~~~~~i~i~--~~~~~~~~i~q~~~~v~~~~k~~~L~~~L~~~-~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhg  277 (629)
T PRK11634        201 FMKEPQEVRIQ--SSVTTRPDISQSYWTVWGMRKNEALVRFLEAE-DFDAAIIFVRTKNATLEVAEALERNGYNSAALNG  277 (629)
T ss_pred             HcCCCeEEEcc--CccccCCceEEEEEEechhhHHHHHHHHHHhc-CCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeC
Confidence            44445444433  22344567888888888888999999988765 347899999999999999999985 789999999


Q ss_pred             CCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHH
Q 012794           83 DISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTV  162 (456)
Q Consensus        83 ~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~  162 (456)
                      +|++.+|++++++|++++++||||||++++|||+|+|++|||||+|.++++|+||+|||||+|+.|.+++|+.+.+...+
T Consensus       278 d~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l  357 (629)
T PRK11634        278 DMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLL  357 (629)
T ss_pred             CCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcC-CcchhhhhHHHHHHHHhh-----cCHHHHHHHHHHHhCCCCC
Q 012794          163 RSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGV-HPESVEFFTPTAQRLIEE-----KGTDALAAALAQLSGFSRP  236 (456)
Q Consensus       163 ~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~-~~~~~~~~~~~~~~ll~~-----~~~~~~a~ala~~~~~~~~  236 (456)
                      +.|++.++..++.+.+|..+++.+.....+...+... ..+.++.|.+++++|++.     .+++.+|++|+.+..-..+
T Consensus       358 ~~ie~~~~~~i~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~a~~~~~~~~~~  437 (629)
T PRK11634        358 RNIERTMKLTIPEVELPNAELLGKRRLEKFAAKVQQQLESSDLDQYRALLAKIQPTAEGEELDLETLAAALLKMAQGERP  437 (629)
T ss_pred             HHHHHHhCCCcceecCCcHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhhccccCCHHHHHHHHHHHHcCCCc
Confidence            9999999999999999999999888888887776543 335577888888888864     6789999999988642211


Q ss_pred             ------C-----C---Ccc-----------------cc--C---CCCceEEEEEeecCccccCCCChhHHHHHHHhhCCC
Q 012794          237 ------P-----S---SRS-----------------LI--N---HEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPT  280 (456)
Q Consensus       237 ------~-----~---~r~-----------------l~--~---~~~g~~t~~~~~~~~~~~~~~~~~~i~~~l~~~~~~  280 (456)
                            +     .   .+.                 ..  .   ...+|++++|+.|+   ++++.|++|+++|++..++
T Consensus       438 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~---~~~~~~~~~~~~i~~~~~~  514 (629)
T PRK11634        438 LILPPDAPMRPKREFRDRDDRGPRDRNDRGPRGDREDRPRRERRDVGDMQLYRIEVGR---DDGVEVRHIVGAIANEGDI  514 (629)
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccCCCCEEEEEeccc---ccCCCHHHHHHHHHhhcCC
Confidence                  0     0   000                 00  0   12269999999999   8999999999999999999


Q ss_pred             CCCccccEEEeecCccceeeeecCHHHHHHHHhhcCC
Q 012794          281 AADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIP  317 (456)
Q Consensus       281 ~~~~ig~i~~~~~~~~~~~~~dv~~~~a~~~~~~~~~  317 (456)
                      ...+||+|+|+++|    |+||||+++++++++....
T Consensus       515 ~~~~ig~i~i~~~~----s~v~~~~~~~~~~~~~~~~  547 (629)
T PRK11634        515 SSRYIGNIKLFASH----STIELPKGMPGEVLQHFTR  547 (629)
T ss_pred             ChhhCCcEEEeCCc----eEEEcChhhHHHHHHHhcc
Confidence            99999999999999    7999999999999987543

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

Probab=100.00  E-value=4.4e-33  Score=284.92  Aligned_cols=167  Identities=43%  Similarity=0.638  Sum_probs=155.0

Q ss_pred             cccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHC--CCCcEEEEcCChHHHHHHHHHHHh-cCCEEE
Q 012794            3 NYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYA--KGGKTIVFTQTKRDADEVSLALTS-IIASEA   79 (456)
Q Consensus         3 ~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~--~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~   79 (456)
                      +||+++..|++......++..+|.|+...+++..|...|..+|..+.  +..|+||||+|++.|++|+..|.. .+.+.+
T Consensus       291 ~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~  370 (519)
T KOG0331|consen  291 DFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVA  370 (519)
T ss_pred             HHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceee
Confidence            57788888888877788899999999999999999999999999884  567999999999999999999996 699999


Q ss_pred             EeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhH
Q 012794           80 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  159 (456)
Q Consensus        80 lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~  159 (456)
                      |||+++|.+|+.+|+.|++|+..||||||||+||||||+|++|||||+|.++++|+||+|||||+|++|++++|++..+.
T Consensus       371 iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~  450 (519)
T KOG0331|consen  371 IHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNA  450 (519)
T ss_pred             ecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             HHHHHHHHHh
Q 012794          160 RTVRSLERDV  169 (456)
Q Consensus       160 ~~~~~ie~~~  169 (456)
                      .....+.+.+
T Consensus       451 ~~a~~l~~~l  460 (519)
T KOG0331|consen  451 KLARELIKVL  460 (519)
T ss_pred             HHHHHHHHHH
Confidence            7666665443

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

Probab=99.97  E-value=1.1e-31  Score=250.20  Aligned_cols=163  Identities=34%  Similarity=0.599  Sum_probs=152.1

Q ss_pred             CcccccccCeeEEEEEcCccc-HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHH
Q 012794           16 NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTL   93 (456)
Q Consensus        16 ~~~~~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l   93 (456)
                      +..+++.+.|++||+.+..++ |.+.|.+|...+. -.++||||||+..++.|.+.+.. .+.+..+||+|+|++|++++
T Consensus       231 krdeltlEgIKqf~v~ve~EewKfdtLcdLYd~Lt-ItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im  309 (400)
T KOG0328|consen  231 KRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLT-ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIM  309 (400)
T ss_pred             ecCCCchhhhhhheeeechhhhhHhHHHHHhhhhe-hheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHH
Confidence            355678889999999888765 9999999988764 47999999999999999999995 78999999999999999999


Q ss_pred             hcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCc
Q 012794           94 NGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKF  173 (456)
Q Consensus        94 ~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~  173 (456)
                      +.||.++.+|||+|||.+||||+|.|++|||||+|.+.+.|+||+||.||.|++|++|-|+...+...++.||+++...+
T Consensus       310 ~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~lrdieq~yst~i  389 (400)
T KOG0328|consen  310 NDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILRDIEQYYSTQI  389 (400)
T ss_pred             HHhhcCCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHHHHHHHHHHHhhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             eecCCC
Q 012794          174 EFVSPP  179 (456)
Q Consensus       174 ~~~~~p  179 (456)
                      +.++..
T Consensus       390 ~emp~n  395 (400)
T KOG0328|consen  390 DEMPMN  395 (400)
T ss_pred             ccccch
Confidence            877654

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

Probab=99.97  E-value=2.5e-30  Score=272.89  Aligned_cols=181  Identities=38%  Similarity=0.594  Sum_probs=159.6

Q ss_pred             cccccCCCccccCCcccccccCeeEEEEEcCccc-HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEE
Q 012794            3 NYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEAL   80 (456)
Q Consensus         3 ~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~l   80 (456)
                      +|++++..|.+.......+...|+|+++.+...+ |+.+|..++.... ..++||||+|+..|+.|+..|.. ++.+..|
T Consensus       225 ~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~~-~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~l  303 (513)
T COG0513         225 RYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDED-EGRVIVFVRTKRLVEELAESLRKRGFKVAAL  303 (513)
T ss_pred             HHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHHhcCC-CCeEEEEeCcHHHHHHHHHHHHHCCCeEEEe
Confidence            4566666555554455558899999999999876 9999999998764 35899999999999999999995 7999999


Q ss_pred             eCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh-hH
Q 012794           81 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QR  159 (456)
Q Consensus        81 hg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-e~  159 (456)
                      ||+|+|++|.++++.|++++++|||||||++||||||+|++|||||+|.++++|+||+|||||+|++|.+++|+.+. |.
T Consensus       304 hG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~  383 (513)
T COG0513         304 HGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEV  383 (513)
T ss_pred             cCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999986 89


Q ss_pred             HHHHHHHHHhCCCce-ecCCCCHHHH
Q 012794          160 RTVRSLERDVGCKFE-FVSPPVVEDV  184 (456)
Q Consensus       160 ~~~~~ie~~~~~~~~-~~~~p~~~~i  184 (456)
                      ..+..+++.+...++ ...+|..+..
T Consensus       384 ~~l~~ie~~~~~~~~~~~~~~~~~~~  409 (513)
T COG0513         384 KKLKRIEKRLERKLPSAVLLPLDEPE  409 (513)
T ss_pred             HHHHHHHHHHhccccccccCCcchhh
Confidence            999999999877755 4555554433

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.97  E-value=1.9e-29  Score=264.26  Aligned_cols=229  Identities=31%  Similarity=0.456  Sum_probs=198.7

Q ss_pred             ccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCC
Q 012794           22 AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK  100 (456)
Q Consensus        22 ~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~  100 (456)
                      ...++++++.++...|.+.|..++.... ..++||||+|++.|+.|++.|.. ++.+..+||+|++.+|+.+++.|++|.
T Consensus       214 ~~~i~~~~~~~~~~~k~~~l~~ll~~~~-~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~  292 (460)
T PRK11776        214 LPAIEQRFYEVSPDERLPALQRLLLHHQ-PESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRS  292 (460)
T ss_pred             CCCeeEEEEEeCcHHHHHHHHHHHHhcC-CCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCC
Confidence            4558888888888889999999997653 57899999999999999999985 789999999999999999999999999


Q ss_pred             eEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCCC
Q 012794          101 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPV  180 (456)
Q Consensus       101 ~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p~  180 (456)
                      ++|||||+++++|||+|++++|||||+|.+.++|+||+|||||+|+.|.+++|+.+.+...++.+++.++..+++..+|.
T Consensus       293 ~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i~~~~~~~~~~~~l~~  372 (460)
T PRK11776        293 CSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLPS  372 (460)
T ss_pred             CcEEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHHHHHHHHHHHhCCCCceecCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999988888776664


Q ss_pred             HHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHHHHHHHHHhCCCCCCCCccccCCCCceEEEEEeecCcc
Q 012794          181 VEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAF  260 (456)
Q Consensus       181 ~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~a~ala~~~~~~~~~~~r~l~~~~~g~~t~~~~~~~~~  260 (456)
                      .....                                                ..        .....+.++.+..++  
T Consensus       373 ~~~~~------------------------------------------------~~--------~~~~~~~~l~i~~~~--  394 (460)
T PRK11776        373 LSPLS------------------------------------------------GV--------PLLPEMVTLCIDGGK--  394 (460)
T ss_pred             hhhcc------------------------------------------------cc--------cCCCCeEEEEEeccc--
Confidence            22100                                                00        012347788888776  


Q ss_pred             ccCCCChhHHHHHHHhhCCCCCCccccEEEeecCccceeeeecCHHHHHHHHhh
Q 012794          261 SRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNK  314 (456)
Q Consensus       261 ~~~~~~~~~i~~~l~~~~~~~~~~ig~i~~~~~~~~~~~~~dv~~~~a~~~~~~  314 (456)
                       ...+.+.++++.+.........++|.|.+.+.+    ++++++...++.++..
T Consensus       395 -~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~----~~~~~~~~~~~~~~~~  443 (460)
T PRK11776        395 -KDKLRPGDILGALTGDAGLDGAQIGKINVTDFH----AYVAVERAVAKKALKK  443 (460)
T ss_pred             -ccCCCccchHHHhhcccCCChhhcCCccccccc----ceeecchhhHHHHHHH
Confidence             567788889999988887888889999998887    6999999988888855

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

Probab=99.97  E-value=1.9e-30  Score=251.27  Aligned_cols=163  Identities=34%  Similarity=0.536  Sum_probs=152.5

Q ss_pred             CcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHh
Q 012794           16 NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLN   94 (456)
Q Consensus        16 ~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~   94 (456)
                      .+...+.++++|+|+.++..+|...|..||+... +..+||||+|..+++.++-.|.. ++.+..|||+|+|..|.-.++
T Consensus       266 s~ky~tv~~lkQ~ylfv~~k~K~~yLV~ll~e~~-g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~  344 (476)
T KOG0330|consen  266 SSKYQTVDHLKQTYLFVPGKDKDTYLVYLLNELA-GNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALN  344 (476)
T ss_pred             cchhcchHHhhhheEeccccccchhHHHHHHhhc-CCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHH
Confidence            4566777889999999999999999999998774 58999999999999999999996 899999999999999999999


Q ss_pred             cccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCce
Q 012794           95 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE  174 (456)
Q Consensus        95 ~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~  174 (456)
                      +|+++..+|||||||++||+|+|.|++|||||+|.+..+||||+|||+|+|++|++|.+++..|.+.+.+||..++.+..
T Consensus       345 ~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE~~~gkkl~  424 (476)
T KOG0330|consen  345 KFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIEHALGKKLP  424 (476)
T ss_pred             HHhccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHHHHHHHhcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             ecCCC
Q 012794          175 FVSPP  179 (456)
Q Consensus       175 ~~~~p  179 (456)
                      ...++
T Consensus       425 ~~~~~  429 (476)
T KOG0330|consen  425 EYKVD  429 (476)
T ss_pred             ccCcc
Confidence            54443

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

Probab=99.97  E-value=8e-30  Score=253.58  Aligned_cols=228  Identities=28%  Similarity=0.389  Sum_probs=183.8

Q ss_pred             cCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCC
Q 012794            7 MFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDIS   85 (456)
Q Consensus         7 ~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~   85 (456)
                      .+..|+.+......+.+.++|-|+.++...++-+|..+|+.+....++||||+|...+..+++.|.. .+.|..+||.++
T Consensus       286 d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~  365 (543)
T KOG0342|consen  286 DPVFVNVDDGGERETHERLEQGYVVAPSDSRFSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQK  365 (543)
T ss_pred             CceEeecCCCCCcchhhcccceEEeccccchHHHHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCc
Confidence            5788999999999999999999999999888999999998886668999999999999999999985 688999999999


Q ss_pred             HHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794           86 QHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus        86 ~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      |..|..+...|++.+.-|||||||+|||+|+|+|++||+||+|.++++||||+|||||.|++|.+++++.++|..+++.|
T Consensus       366 Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~L  445 (543)
T KOG0342|consen  366 QNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYL  445 (543)
T ss_pred             ccccchHHHHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCCCceecCCCCH-HHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHH-----Hh--hcCHHHHHHHHHHHhCCCCCC
Q 012794          166 ERDVGCKFEFVSPPVV-EDVLESSAEQVVATLNGVHPESVEFFTPTAQRL-----IE--EKGTDALAAALAQLSGFSRPP  237 (456)
Q Consensus       166 e~~~~~~~~~~~~p~~-~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l-----l~--~~~~~~~a~ala~~~~~~~~~  237 (456)
                      +   ..+++..+.|.. .+.++...+.++..-........+.|..++.-+     ..  ..+.-.++ +++..+|++.+|
T Consensus       446 K---~lpl~~~e~~~~~~~~v~~~~~~li~~~y~~~~aak~ay~syl~~y~s~slk~~~~~~~l~La-~~~~s~gf~~pp  521 (543)
T KOG0342|consen  446 K---KLPLEEFEFPPLKPEDVQSQLEKLISKNYSLKEAAKEAYKSYLGAYNSHSLKDIFNVNLLELA-AVAKSFGFSVPP  521 (543)
T ss_pred             h---hCCCcccCCCCCCHHHHHHHHHHHHHHHhhHHHHHHHHHHhhhhhccchhhhcccccchhhHH-HHHHHcCCCCCc
Confidence            8   445555554443 333344455555433223222333333332211     11  11223455 888999988765


Q ss_pred             C
Q 012794          238 S  238 (456)
Q Consensus       238 ~  238 (456)
                      .
T Consensus       522 ~  522 (543)
T KOG0342|consen  522 A  522 (543)
T ss_pred             c
Confidence            3

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

Probab=99.96  E-value=1.1e-29  Score=253.58  Aligned_cols=164  Identities=36%  Similarity=0.542  Sum_probs=143.6

Q ss_pred             cccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEe
Q 012794            3 NYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALH   81 (456)
Q Consensus         3 ~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lh   81 (456)
                      .||..+.. .+++ ...+....|+|..+.+..+.|...|..+|..+ ...++|||+||++.|+.||+.|.+ ++.+..||
T Consensus       472 ~ylr~pv~-vtig-~~gk~~~rveQ~v~m~~ed~k~kkL~eil~~~-~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlH  548 (673)
T KOG0333|consen  472 SYLRRPVV-VTIG-SAGKPTPRVEQKVEMVSEDEKRKKLIEILESN-FDPPIIIFVNTKKGADALAKILEKAGYKVTTLH  548 (673)
T ss_pred             HHhhCCeE-EEec-cCCCCccchheEEEEecchHHHHHHHHHHHhC-CCCCEEEEEechhhHHHHHHHHhhccceEEEee
Confidence            35554433 2333 44456677899999999999999999999876 457999999999999999999996 89999999


Q ss_pred             CCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHH
Q 012794           82 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT  161 (456)
Q Consensus        82 g~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~  161 (456)
                      |+-+|+||+.+|+.|+.+..+||||||||+||||||+|.+|||||++.++++|+||||||||||+.|++++|+++.+...
T Consensus       549 g~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~v  628 (673)
T KOG0333|consen  549 GGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTAV  628 (673)
T ss_pred             CCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988665


Q ss_pred             HHHHHHHh
Q 012794          162 VRSLERDV  169 (456)
Q Consensus       162 ~~~ie~~~  169 (456)
                      +..|.+.+
T Consensus       629 ~ydLkq~l  636 (673)
T KOG0333|consen  629 FYDLKQAL  636 (673)
T ss_pred             HHHHHHHH
Confidence            55554443

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

Probab=99.96  E-value=3e-28  Score=233.64  Aligned_cols=164  Identities=30%  Similarity=0.542  Sum_probs=152.8

Q ss_pred             cccccccCeeEEEEEcCcccHHHHHHHHHHHHCC--CCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHH
Q 012794           17 QDEKLAEGIKLYAISTTATSKRTILSDLITVYAK--GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTL   93 (456)
Q Consensus        17 ~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~--~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l   93 (456)
                      ....+.+++.+-|+.++...|-..|..+|..+..  .+.++||++|..+|+.|+..|.. .+.+..||+.|+|.+|...+
T Consensus       218 ~~vstvetL~q~yI~~~~~vkdaYLv~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aL  297 (442)
T KOG0340|consen  218 DGVSTVETLYQGYILVSIDVKDAYLVHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAAL  297 (442)
T ss_pred             CCCCchhhhhhheeecchhhhHHHHHHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHH
Confidence            4456778899999999999999999999988754  67899999999999999999986 68999999999999999999


Q ss_pred             hcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCc
Q 012794           94 NGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKF  173 (456)
Q Consensus        94 ~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~  173 (456)
                      .+|+.+.++||||||||+||+|||.|++|||||+|.++.+|+||+|||+|||+.|.++.++++.+...+..||+.++.++
T Consensus       298 srFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~~igkKl  377 (442)
T KOG0340|consen  298 SRFRSNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEEEIGKKL  377 (442)
T ss_pred             HHHhhcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHHHHhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             eecCCCC
Q 012794          174 EFVSPPV  180 (456)
Q Consensus       174 ~~~~~p~  180 (456)
                      .....-+
T Consensus       378 ~e~~~~~  384 (442)
T KOG0340|consen  378 TEYNKVQ  384 (442)
T ss_pred             ccccccc
Confidence            7755443

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

Probab=99.95  E-value=6.8e-28  Score=232.45  Aligned_cols=166  Identities=31%  Similarity=0.522  Sum_probs=149.1

Q ss_pred             cccccccCeeEEEEEcCc-ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHh
Q 012794           17 QDEKLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLN   94 (456)
Q Consensus        17 ~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~   94 (456)
                      .++.+.++|+++|+.|+. .+|.++|.+|..... -+++||||.|++.|..|+..|.. ++.+..|||+|.-.+|..+++
T Consensus       296 ~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~t-igqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~  374 (477)
T KOG0332|consen  296 REELALDNIKQLYVLCACRDDKYQALVNLYGLLT-IGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIID  374 (477)
T ss_pred             hhhccccchhhheeeccchhhHHHHHHHHHhhhh-hhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHH
Confidence            556788999999999886 579999999776553 47999999999999999999985 899999999999999999999


Q ss_pred             cccCCCeEEEEeccccccccCcCccceEEecCCCC------ChhHHHHHhcccccCCCCceEEEeeCh-hhHHHHHHHHH
Q 012794           95 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAILMFTS-SQRRTVRSLER  167 (456)
Q Consensus        95 ~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~------~~~~y~qr~GR~gR~g~~g~~i~~~~~-~e~~~~~~ie~  167 (456)
                      .||.|+.+|||+|+|+|||||++.|++|||||+|.      |.++|+||+|||||.|++|.+|.|+.. .....+..|++
T Consensus       375 ~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~  454 (477)
T KOG0332|consen  375 RFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQK  454 (477)
T ss_pred             HHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHH
Confidence            99999999999999999999999999999999995      799999999999999999999999875 46788889999


Q ss_pred             HhCCCceecCCCCHHH
Q 012794          168 DVGCKFEFVSPPVVED  183 (456)
Q Consensus       168 ~~~~~~~~~~~p~~~~  183 (456)
                      +++.++..+.+...+|
T Consensus       455 ~F~~~i~~~~~~d~~E  470 (477)
T KOG0332|consen  455 HFNMKIKRLDPDDLDE  470 (477)
T ss_pred             HHhhcceecCCccHHH
Confidence            9988888777644443

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.95  E-value=3.2e-27  Score=237.22  Aligned_cols=231  Identities=24%  Similarity=0.309  Sum_probs=178.6

Q ss_pred             ccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh---cCCEEEEeC
Q 012794            6 VMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHG   82 (456)
Q Consensus         6 ~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~---~~~~~~lhg   82 (456)
                      ++|..|.+-......++.+++|+|+.++..+|+++|--+|..+. ..+.|||+.|++++..+++.+.+   ++.+..|||
T Consensus       269 ~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~shl-k~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G  347 (758)
T KOG0343|consen  269 KDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIKSHL-KKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHG  347 (758)
T ss_pred             CCCcEEEEeccccccChhhhhheEEEEehhhHHHHHHHHHHhcc-ccceEEEEehhhHHHHHHHHHHhcCCCCceeeecc
Confidence            45666655555667889999999999999999999999999885 48999999999999999999874   688999999


Q ss_pred             CCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh-HHH
Q 012794           83 DISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ-RRT  161 (456)
Q Consensus        83 ~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e-~~~  161 (456)
                      .|+|..|..++.+|-....-||+|||+++||||+|.|+|||++|.|.++++||||+|||+|....|.+++++++.| ..+
T Consensus       348 ~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~  427 (758)
T KOG0343|consen  348 TMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAM  427 (758)
T ss_pred             chhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999998 566


Q ss_pred             HHHHHHHhCCCceecCCC-CHHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHH------HHHHHHHhCCC
Q 012794          162 VRSLERDVGCKFEFVSPP-VVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDAL------AAALAQLSGFS  234 (456)
Q Consensus       162 ~~~ie~~~~~~~~~~~~p-~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~------a~ala~~~~~~  234 (456)
                      +..|++.. ++++.+.+. ....-+...++.++..-..+..-.-..|..++..+....++..+      +.|++..+|++
T Consensus       428 l~~Lq~k~-I~i~~i~i~~~k~~~i~~~l~~ll~~~~eLk~~aqka~isY~rsi~~~rdK~~f~~~~l~~~afa~s~Gl~  506 (758)
T KOG0343|consen  428 LKKLQKKK-IPIKEIKIDPEKLTSIRNKLEALLAKDPELKEYAQKAFISYLRSIYLMRDKRVFDVEKLDIEAFADSLGLP  506 (758)
T ss_pred             HHHHHHcC-CCHHhhccCHHHhhhHHHHHHHHHhhCHHHHHHHHHHHHHHHHHHHhhccchhhcchhccHHHHHHhcCCC
Confidence            66676654 555554333 11111222333333222222222234555666665554443322      66788888877


Q ss_pred             CCCC
Q 012794          235 RPPS  238 (456)
Q Consensus       235 ~~~~  238 (456)
                      ..|+
T Consensus       507 ~~p~  510 (758)
T KOG0343|consen  507 GTPR  510 (758)
T ss_pred             CCch
Confidence            6665

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

Probab=99.95  E-value=1.4e-27  Score=232.33  Aligned_cols=163  Identities=35%  Similarity=0.562  Sum_probs=149.5

Q ss_pred             cccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEe
Q 012794            3 NYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-SIIASEALH   81 (456)
Q Consensus         3 ~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lh   81 (456)
                      +|++. +.+.+|+.-.-.....|+|..+....++|++++..++..+....++||||..+..|+.|...|. +++.+..||
T Consensus       418 sY~Ke-p~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lH  496 (629)
T KOG0336|consen  418 SYLKE-PMIVYVGSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLH  496 (629)
T ss_pred             HhhhC-ceEEEecccceeeeeeeeeeEEecccHHHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcccchhhcc
Confidence            35544 4777888877777788999998888999999999999999888999999999999999999888 689999999


Q ss_pred             CCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHH
Q 012794           82 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT  161 (456)
Q Consensus        82 g~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~  161 (456)
                      |+-.|.+|+.+++.|+.|.++||||||+++||||+|+|+||+|||+|.+++.|+||+|||||+|++|++++|++-.+...
T Consensus       497 G~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~  576 (629)
T KOG0336|consen  497 GNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSM  576 (629)
T ss_pred             CChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999888776


Q ss_pred             HHHHH
Q 012794          162 VRSLE  166 (456)
Q Consensus       162 ~~~ie  166 (456)
                      ...|-
T Consensus       577 a~eLI  581 (629)
T KOG0336|consen  577 AEELI  581 (629)
T ss_pred             HHHHH
Confidence            66553

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

Probab=99.95  E-value=7.9e-28  Score=227.73  Aligned_cols=173  Identities=25%  Similarity=0.446  Sum_probs=159.7

Q ss_pred             ccccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEE
Q 012794            2 LNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEAL   80 (456)
Q Consensus         2 ~~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~l   80 (456)
                      .+||++|-.|.+.   ++.++..|.|||..+.+.+|+.-|..|+..+. -.++|||||+...++.||+.+.+ ++.|..+
T Consensus       277 ~~~l~kPy~INLM---~eLtl~GvtQyYafV~e~qKvhCLntLfskLq-INQsIIFCNS~~rVELLAkKITelGyscyyi  352 (459)
T KOG0326|consen  277 DRHLKKPYEINLM---EELTLKGVTQYYAFVEERQKVHCLNTLFSKLQ-INQSIIFCNSTNRVELLAKKITELGYSCYYI  352 (459)
T ss_pred             HHhccCcceeehh---hhhhhcchhhheeeechhhhhhhHHHHHHHhc-ccceEEEeccchHhHHHHHHHHhccchhhHH
Confidence            4566666666654   56778899999999999999999999998774 47899999999999999999986 8999999


Q ss_pred             eCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHH
Q 012794           81 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRR  160 (456)
Q Consensus        81 hg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~  160 (456)
                      |+.|.|+.|.+++..|++|..+.|||||.+.||||+++|++|||||+|.+.++|+||+||.||.|..|.+|.+++-.++.
T Consensus       353 HakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf  432 (459)
T KOG0326|consen  353 HAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRF  432 (459)
T ss_pred             HHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCCceecCC
Q 012794          161 TVRSLERDVGCKFEFVSP  178 (456)
Q Consensus       161 ~~~~ie~~~~~~~~~~~~  178 (456)
                      .+..||+.++..+++++.
T Consensus       433 ~L~~IE~eLGtEI~pip~  450 (459)
T KOG0326|consen  433 NLYRIEQELGTEIKPIPS  450 (459)
T ss_pred             hHHHHHHHhccccccCCC
Confidence            999999999998887654

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

Probab=99.95  E-value=1.9e-27  Score=235.34  Aligned_cols=178  Identities=30%  Similarity=0.433  Sum_probs=154.4

Q ss_pred             cccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh---cCCEEEEe
Q 012794            5 FVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALH   81 (456)
Q Consensus         5 l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~---~~~~~~lh   81 (456)
                      |.++..|.+-..+...++..+..+|+.|.+..|+..|.++|..+ ..+++|||.+|+..++..+..|..   ...+..+|
T Consensus       210 LRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~~L~~~-~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iH  288 (567)
T KOG0345|consen  210 LRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNNN-KDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIH  288 (567)
T ss_pred             ccCceeeeecccccccCchhhcceeeEecHHHHHHHHHHHHhcc-ccccEEEEecCcchHHHHHHHHHHHhCCCcEEEec
Confidence            34555555555555558889999999999999999999999875 468999999999999999988874   46789999


Q ss_pred             CCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHH
Q 012794           82 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT  161 (456)
Q Consensus        82 g~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~  161 (456)
                      |.|.+.+|.++++.|++..-.+|+||||+|||||||+|++||+||+|.++..|+||+|||+|+|+.|.+|+|+.+.|..+
T Consensus       289 GK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~aY  368 (567)
T KOG0345|consen  289 GKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEAY  368 (567)
T ss_pred             chhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHHH
Confidence            99999999999999999888899999999999999999999999999999999999999999999999999999998888


Q ss_pred             HHHHHHHhCCCceecCCCCHHH
Q 012794          162 VRSLERDVGCKFEFVSPPVVED  183 (456)
Q Consensus       162 ~~~ie~~~~~~~~~~~~p~~~~  183 (456)
                      +..+.-.-....+.+..|....
T Consensus       369 veFl~i~~~v~le~~~~e~~~~  390 (567)
T KOG0345|consen  369 VEFLRIKGKVELERIDTEKASL  390 (567)
T ss_pred             HHHHHhcCccchhhhcccccch
Confidence            8877544445566666665544

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=1e-26  Score=241.20  Aligned_cols=157  Identities=35%  Similarity=0.520  Sum_probs=142.9

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      .....+++.++......|..+|..++... ...++||||+|+..|+.|+..|.. ++.+..+||+|++++|..+++.|++
T Consensus       225 ~~~~~i~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~  303 (423)
T PRK04837        225 KTGHRIKEELFYPSNEEKMRLLQTLIEEE-WPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTR  303 (423)
T ss_pred             cCCCceeEEEEeCCHHHHHHHHHHHHHhc-CCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHc
Confidence            34566777777777778999999888765 357999999999999999999985 7899999999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecC
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  177 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~  177 (456)
                      |+++||||||++++|||+|+|++|||||+|.++++|+||+|||||+|+.|.+++|+.+.+...+..|++++...++...
T Consensus       304 g~~~vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i~~~~~~~~~~~~  382 (423)
T PRK04837        304 GDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAIETYIGHSIPVSK  382 (423)
T ss_pred             CCCcEEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHHHHHhCCCCCCcc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999998887765433

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.94  E-value=3.9e-26  Score=238.81  Aligned_cols=155  Identities=37%  Similarity=0.563  Sum_probs=141.3

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      .....+.+++..+....|.++|..++... ...++||||+|+..|+.|++.|.. ++.+..+||+|++.+|.+++++|++
T Consensus       215 ~~~~~i~~~~~~~~~~~k~~~l~~l~~~~-~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~  293 (456)
T PRK10590        215 TASEQVTQHVHFVDKKRKRELLSQMIGKG-NWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKS  293 (456)
T ss_pred             ccccceeEEEEEcCHHHHHHHHHHHHHcC-CCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHc
Confidence            34566788888888888888888887654 457999999999999999999985 7899999999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCcee
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF  175 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~  175 (456)
                      |+++|||||+++++|||+|+|++||||++|.++++|+||+|||||+|..|.+++|+...+...++.+++.+...++.
T Consensus       294 g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie~~l~~~~~~  370 (456)
T PRK10590        294 GDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEIPR  370 (456)
T ss_pred             CCCcEEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHHHHhcCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999888766543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=7.7e-26  Score=241.77  Aligned_cols=154  Identities=36%  Similarity=0.530  Sum_probs=140.2

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      .....+.++++.+...+|+.+|..++... ...++||||+|+..|+.|++.|.+ ++.+..|||+|++.+|+++++.|++
T Consensus       227 ~~~~~i~q~~~~~~~~~k~~~L~~ll~~~-~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~  305 (572)
T PRK04537        227 ITAARVRQRIYFPADEEKQTLLLGLLSRS-EGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQK  305 (572)
T ss_pred             ccccceeEEEEecCHHHHHHHHHHHHhcc-cCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHc
Confidence            44566788888777788888888888654 467999999999999999999985 7899999999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCce
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE  174 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~  174 (456)
                      ++++||||||++++|||+|+|++|||||+|.++++|+||+|||||.|+.|.+++|+.+.+...+..|++++..+++
T Consensus       306 G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i~~~~~~~~~  381 (572)
T PRK04537        306 GQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQKIP  381 (572)
T ss_pred             CCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHHHHHHcCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999998889999888776554

>PTZ00110 helicase; Provisional

Probab=99.93  E-value=8.3e-26  Score=240.55  Aligned_cols=151  Identities=35%  Similarity=0.566  Sum_probs=136.6

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHC-CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhccc
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR   97 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~-~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr   97 (456)
                      ....++++.+..+....|...|..++.... ...++||||+|++.|+.|+..|.. ++.+..+||+|++.+|+.+++.|+
T Consensus       345 ~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~  424 (545)
T PTZ00110        345 TACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFK  424 (545)
T ss_pred             ccCCCeeEEEEEEechhHHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHh
Confidence            345678888877777889888988887764 567999999999999999999984 789999999999999999999999


Q ss_pred             CCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhC
Q 012794           98 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  170 (456)
Q Consensus        98 ~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~  170 (456)
                      +++++||||||++++|||+|+|++|||||+|.++++|+||+|||||+|+.|.+++|+++.+...+..|.+.+.
T Consensus       425 ~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~~~~~l~~~l~  497 (545)
T PTZ00110        425 TGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLR  497 (545)
T ss_pred             cCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999988777777665544

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.93  E-value=5.9e-25  Score=228.74  Aligned_cols=154  Identities=31%  Similarity=0.529  Sum_probs=138.8

Q ss_pred             ccccCeeEEEEEcCc-ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhccc
Q 012794           20 KLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR   97 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr   97 (456)
                      .....+.++++.+.. .+|.++|..++... ...++||||+|++.|+.|+..|.. ++.+..+||+|++.+|..+++.|+
T Consensus       214 ~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~-~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~  292 (434)
T PRK11192        214 RERKKIHQWYYRADDLEHKTALLCHLLKQP-EVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLT  292 (434)
T ss_pred             ccccCceEEEEEeCCHHHHHHHHHHHHhcC-CCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHh
Confidence            344567787776654 67899998888643 357999999999999999999985 789999999999999999999999


Q ss_pred             CCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCce
Q 012794           98 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE  174 (456)
Q Consensus        98 ~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~  174 (456)
                      +|+++||||||++++|||+|+|++|||||+|.+.+.|+||+|||||+|..|.+++++...+...+..+++++...+.
T Consensus       293 ~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i~~~~~~~~~  369 (434)
T PRK11192        293 DGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIEEPLK  369 (434)
T ss_pred             CCCCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecHHHHHHHHHHHHHHhcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999988765543

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

Probab=99.92  E-value=2.2e-25  Score=224.97  Aligned_cols=147  Identities=44%  Similarity=0.691  Sum_probs=131.7

Q ss_pred             cccccCeeEEEEEcCcccHHHHHHHHHHHHC---CCC-----cEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHH
Q 012794           19 EKLAEGIKLYAISTTATSKRTILSDLITVYA---KGG-----KTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQR   89 (456)
Q Consensus        19 ~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~---~~~-----~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R   89 (456)
                      -.++.+|.|..+.+...+|...|.++|....   ...     +++|||+|++.|++|+..|.. .+.+..+||+.+|.+|
T Consensus       297 g~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er  376 (482)
T KOG0335|consen  297 GSTSENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIER  376 (482)
T ss_pred             ccccccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHH
Confidence            3456788898888999899888888887543   233     899999999999999999985 8999999999999999


Q ss_pred             HHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794           90 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus        90 ~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      +++++.|+++++.|||||+|++||||+|+|+||||||+|.+..+|+||||||||+|+.|.++.|+........+.|
T Consensus       377 ~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L  452 (482)
T KOG0335|consen  377 EQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIAKAL  452 (482)
T ss_pred             HHHHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999986555444444

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.92  E-value=1.5e-24  Score=228.14  Aligned_cols=154  Identities=34%  Similarity=0.586  Sum_probs=140.6

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      ....+++++.+.+...+|..+|..++... ...++||||+++++|+.+++.|.+ ++.+..+||+|++.+|.++++.|++
T Consensus       305 ~~~~~~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~  383 (475)
T PRK01297        305 VASDTVEQHVYAVAGSDKYKLLYNLVTQN-PWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFRE  383 (475)
T ss_pred             CCCCcccEEEEEecchhHHHHHHHHHHhc-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhC
Confidence            34456777777777778988888888654 357999999999999999999985 7889999999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCce
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE  174 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~  174 (456)
                      |+++|||||+++++|||+|++++||+|++|.++.+|+||+||+||.|+.|.+++|+...+...+..+++.++.+++
T Consensus       384 G~~~vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~~~~~~~~~~~  459 (475)
T PRK01297        384 GKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKIS  459 (475)
T ss_pred             CCCcEEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHHHHHHhCCCCc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999987764

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.92  E-value=6.3e-26  Score=227.90  Aligned_cols=184  Identities=32%  Similarity=0.456  Sum_probs=159.0

Q ss_pred             ccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCC
Q 012794            6 VMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDI   84 (456)
Q Consensus         6 ~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~   84 (456)
                      .++..||+...  ..++.++..-.+.|+..+|--.|..+|..|  ++++|||||+.+.+..|+-.|.. .+....||+.|
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 GKPKIIDLTPQ--SATASTLTESLIECPPLEKDLYLYYFLTRY--PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASM  497 (731)
T ss_pred             CCCeeEecCcc--hhHHHHHHHHhhcCCccccceeEEEEEeec--CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHH
Confidence            35667777643  345666777777787777777777777666  48999999999999999999986 68889999999


Q ss_pred             CHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHH
Q 012794           85 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS  164 (456)
Q Consensus        85 ~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~  164 (456)
                      .|.+|.+.|++|++..--|||||||||||||||.|+|||||.+|.+.+.|+||+|||+||+..|+.++|+.|.+...+.+
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             HHHHhCCCceecCCCCHHHHHHHHHHHHH
Q 012794          165 LERDVGCKFEFVSPPVVEDVLESSAEQVV  193 (456)
Q Consensus       165 ie~~~~~~~~~~~~p~~~~i~~~~~~~~~  193 (456)
                      |.+-+....+.-..|..+.++....+++.
T Consensus       578 L~ktL~k~~dlpifPv~~~~m~~lkeRvr  606 (731)
T KOG0347|consen  578 LCKTLKKKEDLPIFPVETDIMDALKERVR  606 (731)
T ss_pred             HHHHHhhccCCCceeccHHHHHHHHHHHH
Confidence            98888877766557777777766665553

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

Probab=99.92  E-value=3.4e-24  Score=227.31  Aligned_cols=151  Identities=27%  Similarity=0.453  Sum_probs=134.0

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHC-CCCcEEEEcCChHHHHHHHHHHHh--cCCEEEEeCCCCHHHHHHHHhcc
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGF   96 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~-~~~~~IIF~~t~~~a~~l~~~L~~--~~~~~~lhg~~~~~~R~~~l~~F   96 (456)
                      .....++++.+.+....|...|.+++.... ...++||||+|+..|+.|+..|..  ++.+..+||+|++.+|..+++.|
T Consensus       335 ~~~~~v~q~~~~~~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~F  414 (518)
T PLN00206        335 RPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSF  414 (518)
T ss_pred             CCCcceeEEEEeccchhHHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHH
Confidence            344567888888888788888888876543 235899999999999999999973  68899999999999999999999


Q ss_pred             cCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhC
Q 012794           97 RQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  170 (456)
Q Consensus        97 r~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~  170 (456)
                      ++|+++|||||+++++|||+|+|++|||||+|.++++|+||+|||||+|..|.+++|+++.+...+..+.+.+.
T Consensus       415 r~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~~~l~  488 (518)
T PLN00206        415 LVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLK  488 (518)
T ss_pred             HCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999988777777766554

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

Probab=99.91  E-value=1.6e-24  Score=210.73  Aligned_cols=170  Identities=31%  Similarity=0.556  Sum_probs=154.1

Q ss_pred             cccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCC
Q 012794            5 FVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGD   83 (456)
Q Consensus         5 l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~   83 (456)
                      |+..+...++..+. ++.+.|+|+|+.+...+|++.|.++.+   .-.+++|||||++.++.|...|.. .+.+.++|++
T Consensus       221 f~~~pv~i~vkk~~-ltl~gikq~~i~v~k~~k~~~l~dl~~---~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d  296 (397)
T KOG0327|consen  221 FMREPVRILVKKDE-LTLEGIKQFYINVEKEEKLDTLCDLYR---RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGD  296 (397)
T ss_pred             hccCceEEEecchh-hhhhheeeeeeeccccccccHHHHHHH---hhhcceEEecchhhHHHHHHHHhhCCceEEEeecc
Confidence            34334444444333 778999999999999999999999988   347899999999999999999975 7899999999


Q ss_pred             CCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHH
Q 012794           84 ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVR  163 (456)
Q Consensus        84 ~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~  163 (456)
                      |.|.+|..++..|+.|..+|||+|+.++||||+..+.+||||++|...+.|+||+||+||.|++|.++.+++..+...++
T Consensus       297 ~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk  376 (397)
T KOG0327|consen  297 MEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLK  376 (397)
T ss_pred             cchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCceecCC
Q 012794          164 SLERDVGCKFEFVSP  178 (456)
Q Consensus       164 ~ie~~~~~~~~~~~~  178 (456)
                      .+|+++...++.++.
T Consensus       377 ~ie~~y~~~i~e~p~  391 (397)
T KOG0327|consen  377 DIEKFYNTPIEELPS  391 (397)
T ss_pred             hHHHhcCCcceeccc
Confidence            999999998887654

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

Probab=99.91  E-value=2.7e-24  Score=214.57  Aligned_cols=151  Identities=33%  Similarity=0.571  Sum_probs=134.6

Q ss_pred             cccccccCeeEEEEEcCc---ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHH
Q 012794           17 QDEKLAEGIKLYAISTTA---TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERT   92 (456)
Q Consensus        17 ~~~~~~~~i~~~~~~~~~---~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~   92 (456)
                      +...++..+.|.|+.+.+   ..+..+|..|+.... ..++|||+.|++.|..+.-.|- -++.+..|||.|+|.||...
T Consensus       390 ~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf-~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRles  468 (691)
T KOG0338|consen  390 PNKDTAPKLTQEFIRIRPKREGDREAMLASLITRTF-QDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLES  468 (691)
T ss_pred             CccccchhhhHHHheeccccccccHHHHHHHHHHhc-ccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHH
Confidence            445566667777776543   357788888887653 6899999999999999988776 37899999999999999999


Q ss_pred             HhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHH
Q 012794           93 LNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  168 (456)
Q Consensus        93 l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~  168 (456)
                      +++|++.+++||||||+|+|||||+.|..||||..|.+++.|+||+|||+|+|+.|.+++|+...++..++.|-+.
T Consensus       469 L~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~  544 (691)
T KOG0338|consen  469 LEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKS  544 (691)
T ss_pred             HHHHHhccCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999988666

>PTZ00424 helicase 45; Provisional

Probab=99.91  E-value=1.3e-23  Score=216.39  Aligned_cols=159  Identities=31%  Similarity=0.570  Sum_probs=141.2

Q ss_pred             ccccCeeEEEEEcCc-ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhccc
Q 012794           20 KLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR   97 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr   97 (456)
                      .....++++++.+.. ..+...+..++... ...++||||+|++.++.+++.|.. .+.+..+||+|++.+|..+++.|+
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~  314 (401)
T PTZ00424        236 LTLEGIRQFYVAVEKEEWKFDTLCDLYETL-TITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFR  314 (401)
T ss_pred             cccCCceEEEEecChHHHHHHHHHHHHHhc-CCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHH
Confidence            345667788777664 45677777776654 357899999999999999999985 689999999999999999999999


Q ss_pred             CCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecC
Q 012794           98 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  177 (456)
Q Consensus        98 ~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~  177 (456)
                      +|+++|||||+++++|||+|++++||+|++|.+..+|+||+||+||.|+.|.|++|+++.+...+..+++.+...++..+
T Consensus       315 ~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~  394 (401)
T PTZ00424        315 SGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMP  394 (401)
T ss_pred             cCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHHHHHHHHHHHHHHCCcccccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999988777654


Q ss_pred             CC
Q 012794          178 PP  179 (456)
Q Consensus       178 ~p  179 (456)
                      +.
T Consensus       395 ~~  396 (401)
T PTZ00424        395 ME  396 (401)
T ss_pred             cc
Confidence            43

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

Probab=99.91  E-value=2.8e-23  Score=227.72  Aligned_cols=168  Identities=21%  Similarity=0.314  Sum_probs=139.2

Q ss_pred             cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh---------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEe
Q 012794           36 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---------IIASEALHGDISQHQRERTLNGFRQGKFTVLVA  106 (456)
Q Consensus        36 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~---------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVa  106 (456)
                      .+..+|..++.   .+.++||||+|++.|+.|+..|..         ...+..+||+|++++|.+++++|++|++++|||
T Consensus       259 ~~~~~l~~l~~---~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVa  335 (742)
T TIGR03817       259 EAADLLADLVA---EGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVAT  335 (742)
T ss_pred             HHHHHHHHHHH---CCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEE
Confidence            35555666554   357999999999999999998764         246789999999999999999999999999999


Q ss_pred             ccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeC--hhhHHHHHHHHHHhCCCceec-CCCCHHH
Q 012794          107 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT--SSQRRTVRSLERDVGCKFEFV-SPPVVED  183 (456)
Q Consensus       107 Tdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~--~~e~~~~~~ie~~~~~~~~~~-~~p~~~~  183 (456)
                      ||++++|||||++++||||++|.++++|+||+|||||+|+.|.+++++.  +.+...+..+++.+..+++.. ..|....
T Consensus       336 Td~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~~~e~~~~~~~n~~  415 (742)
T TIGR03817       336 TNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDRPVEATVFDPDNPY  415 (742)
T ss_pred             CchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcCCCccceeCCCcHH
Confidence            9999999999999999999999999999999999999999999999986  567778888888888887664 4577777


Q ss_pred             HHHHHHHHHHHHHhcCCcchhhhh
Q 012794          184 VLESSAEQVVATLNGVHPESVEFF  207 (456)
Q Consensus       184 i~~~~~~~~~~~l~~~~~~~~~~~  207 (456)
                      ++..++..+..++ .+..+..+.|
T Consensus       416 il~~hl~~aa~e~-~l~~~~~~~~  438 (742)
T TIGR03817       416 VLGPHLCCAAAEL-PLTEADLELF  438 (742)
T ss_pred             HHHHHHHHHHhcC-CCChHHHHhh
Confidence            7777666665444 3333334444

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.

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

Probab=99.90  E-value=2.2e-23  Score=209.10  Aligned_cols=152  Identities=28%  Similarity=0.437  Sum_probs=135.2

Q ss_pred             cccccCeeEEEEEcCcccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHhc---------------------
Q 012794           19 EKLAEGIKLYAISTTATSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI---------------------   74 (456)
Q Consensus        19 ~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~~---------------------   74 (456)
                      -.+++++.+.|..+|+.-++..|..+|...   .+..++|||..|.+.++.-+..|...                     
T Consensus       390 ~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~  469 (708)
T KOG0348|consen  390 FAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLF  469 (708)
T ss_pred             ccCcHHhhhceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhh
Confidence            346778889999999998888888877643   33568999999999999988877531                     


Q ss_pred             --CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEE
Q 012794           75 --IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL  152 (456)
Q Consensus        75 --~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~  152 (456)
                        .++.-|||.|+|++|..+++.|+...-.||+||||++||||+|+|.+||+||+|.++++|+||+|||+|+|.+|.+++
T Consensus       470 ~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alL  549 (708)
T KOG0348|consen  470 MDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALL  549 (708)
T ss_pred             hcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEE
Confidence              247789999999999999999999988899999999999999999999999999999999999999999999999999


Q ss_pred             eeChhhHHHHHHHHHHhC
Q 012794          153 MFTSSQRRTVRSLERDVG  170 (456)
Q Consensus       153 ~~~~~e~~~~~~ie~~~~  170 (456)
                      |+.|.|.+++..++....
T Consensus       550 fL~P~Eaey~~~l~~~~~  567 (708)
T KOG0348|consen  550 FLLPSEAEYVNYLKKHHI  567 (708)
T ss_pred             EecccHHHHHHHHHhhcc
Confidence            999999999988877643

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.89  E-value=3e-22  Score=210.28  Aligned_cols=132  Identities=27%  Similarity=0.462  Sum_probs=118.4

Q ss_pred             cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccccccc
Q 012794           36 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  114 (456)
Q Consensus        36 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gi  114 (456)
                      ..++.|..++....++..+||||+|+++|+.++..|.. ++.+..+|++|++++|+.+++.|++++++|||||+++++||
T Consensus       211 ~~~~~l~~~l~~~~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GI  290 (470)
T TIGR00614       211 KILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGI  290 (470)
T ss_pred             cHHHHHHHHHHHhcCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccC
Confidence            34444555555344556779999999999999999985 78999999999999999999999999999999999999999


Q ss_pred             CcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHH
Q 012794          115 DIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  167 (456)
Q Consensus       115 dip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~  167 (456)
                      |+|+|++||||++|.+++.|+||+|||||.|..+.|++|+.+.+...++.+..
T Consensus       291 D~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~~  343 (470)
T TIGR00614       291 NKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLM  343 (470)
T ss_pred             CcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechhHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999998887777643

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

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.89  E-value=1e-22  Score=200.30  Aligned_cols=169  Identities=22%  Similarity=0.400  Sum_probs=148.2

Q ss_pred             ccccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEE
Q 012794            2 LNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEAL   80 (456)
Q Consensus         2 ~~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~l   80 (456)
                      .+++...+.|-.+.+.+-..++++.||++.|...+|+.+|..|++...-.+++|||+||.+.+..|.-.|.. +++..+|
T Consensus       219 KkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~DKflllyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciL  298 (569)
T KOG0346|consen  219 KKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEEDKFLLLYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCIL  298 (569)
T ss_pred             HHHhccCCeEEEeccccCCCcccceEEEEEeccchhHHHHHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhh
Confidence            345554555555555555678999999999999999999999998765679999999999999999998886 7999999


Q ss_pred             eCCCCHHHHHHHHhcccCCCeEEEEeccc-----------------------------------cccccCcCccceEEec
Q 012794           81 HGDISQHQRERTLNGFRQGKFTVLVATDV-----------------------------------AARGLDIPNVDLIIHY  125 (456)
Q Consensus        81 hg~~~~~~R~~~l~~Fr~g~~~vLVaTdv-----------------------------------~~~Gidip~v~~VI~~  125 (456)
                      .|.||..-|..++++|..|.++||||||.                                   ++||||+.+|..||||
T Consensus       299 NseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNF  378 (569)
T KOG0346|consen  299 NSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNF  378 (569)
T ss_pred             cccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCccccccccCchhchhccccchheeeeeec
Confidence            99999999999999999999999999981                                   3499999999999999


Q ss_pred             CCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhC
Q 012794          126 ELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  170 (456)
Q Consensus       126 ~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~  170 (456)
                      |+|.++.+||||+|||+|++++|+++.|+.+.+..-...||..+.
T Consensus       379 D~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~~~~  423 (569)
T KOG0346|consen  379 DFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLESILK  423 (569)
T ss_pred             CCCCchHHHHHhccccccCCCCCceEEEecchHHhhhhHHHHHHh
Confidence            999999999999999999999999999999998876666665554

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

Probab=99.89  E-value=4e-22  Score=219.29  Aligned_cols=130  Identities=21%  Similarity=0.368  Sum_probs=117.2

Q ss_pred             HHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCc
Q 012794           38 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI  116 (456)
Q Consensus        38 ~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidi  116 (456)
                      +..|..++.......++||||+|+..|+.|+..|.. ++.+.++||+|++++|+.++++|++++++|||||+++++|||+
T Consensus       667 le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDk  746 (1195)
T PLN03137        667 LEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINK  746 (1195)
T ss_pred             HHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCc
Confidence            345555555443456899999999999999999985 8999999999999999999999999999999999999999999


Q ss_pred             CccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHH
Q 012794          117 PNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  167 (456)
Q Consensus       117 p~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~  167 (456)
                      |+|++||||++|.+++.|+||+|||||.|..+.|++||...+...++.+..
T Consensus       747 PDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI~  797 (1195)
T PLN03137        747 PDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMIS  797 (1195)
T ss_pred             cCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999888776666643

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

Probab=99.88  E-value=3.3e-23  Score=200.74  Aligned_cols=124  Identities=35%  Similarity=0.627  Sum_probs=112.8

Q ss_pred             cCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccc
Q 012794           32 TTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  110 (456)
Q Consensus        32 ~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~  110 (456)
                      +..+.|+..|.+.|...  ..++||||..+..++.+.++|- ++..++++||+-.|++|...++.|+.|+-+|||||||+
T Consensus       404 VkqEaKiVylLeCLQKT--~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVA  481 (610)
T KOG0341|consen  404 VKQEAKIVYLLECLQKT--SPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVA  481 (610)
T ss_pred             HHhhhhhhhHHHHhccC--CCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecch
Confidence            45556666666655543  4689999999999999999987 78999999999999999999999999999999999999


Q ss_pred             ccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh
Q 012794          111 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS  157 (456)
Q Consensus       111 ~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  157 (456)
                      +.|+|+|++.||||||+|.+++.|+||+|||||.|++|.+.+|+...
T Consensus       482 SKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~  528 (610)
T KOG0341|consen  482 SKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKN  528 (610)
T ss_pred             hccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeeccc
Confidence            99999999999999999999999999999999999999999998765

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

Probab=99.88  E-value=2.4e-22  Score=204.56  Aligned_cols=152  Identities=32%  Similarity=0.534  Sum_probs=135.3

Q ss_pred             cccccccCeeEEEEEcC-cccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHH--hcCCEEEEeCCCCHHHHHHHH
Q 012794           17 QDEKLAEGIKLYAISTT-ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT--SIIASEALHGDISQHQRERTL   93 (456)
Q Consensus        17 ~~~~~~~~i~~~~~~~~-~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~--~~~~~~~lhg~~~~~~R~~~l   93 (456)
                      ..+.+..+|+|..+.+- ...|+.++..++..- -..++|||+.+.+.|.+|...|.  ..+.+.++||+.++.+|+.++
T Consensus       353 ~~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~  431 (593)
T KOG0344|consen  353 LRNSANETVDQELVFCGSEKGKLLALRQLVASG-FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETM  431 (593)
T ss_pred             cchhHhhhhhhhheeeecchhHHHHHHHHHhcc-CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHH
Confidence            33445667777766654 457888888888765 35799999999999999999994  578999999999999999999


Q ss_pred             hcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHh
Q 012794           94 NGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  169 (456)
Q Consensus        94 ~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~  169 (456)
                      ++||.|++.|||||++++||||+.+|++|||||+|.+.-+|+||+||+||+|+.|.+|+||+..+...++.++...
T Consensus       432 ~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae~~  507 (593)
T KOG0344|consen  432 ERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAEVM  507 (593)
T ss_pred             HHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999988888876654

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.87  E-value=1.8e-21  Score=210.02  Aligned_cols=130  Identities=22%  Similarity=0.460  Sum_probs=117.3

Q ss_pred             cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccccccc
Q 012794           36 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  114 (456)
Q Consensus        36 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gi  114 (456)
                      .++..|..++... .+.++||||+|+++|+.++..|.. ++.+..+|++|++++|.++++.|++++++|||||+++++||
T Consensus       222 ~~~~~l~~~l~~~-~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GI  300 (607)
T PRK11057        222 KPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGI  300 (607)
T ss_pred             chHHHHHHHHHhc-CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccC
Confidence            3445555555443 467999999999999999999985 78999999999999999999999999999999999999999


Q ss_pred             CcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHH
Q 012794          115 DIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  166 (456)
Q Consensus       115 dip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie  166 (456)
                      |+|+|++||||++|.++++|+||+|||||.|..+.|++|+.+.+...++.+.
T Consensus       301 Dip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~~~~  352 (607)
T PRK11057        301 NKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  352 (607)
T ss_pred             CCCCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999998877776654

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.87  E-value=5.2e-21  Score=211.75  Aligned_cols=164  Identities=17%  Similarity=0.234  Sum_probs=144.1

Q ss_pred             ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHH-h-cCCEEEEeCCCCHHHHHHHHhcccCC--CeEEEEecccc
Q 012794           35 TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-S-IIASEALHGDISQHQRERTLNGFRQG--KFTVLVATDVA  110 (456)
Q Consensus        35 ~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~-~-~~~~~~lhg~~~~~~R~~~l~~Fr~g--~~~vLVaTdv~  110 (456)
                      ..|++.|.++++... ..|+||||+++.+++.|++.|. . ++.+..+||+|++.+|+++++.|+++  ..+|||||+++
T Consensus       478 d~Ki~~L~~~L~~~~-~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvg  556 (956)
T PRK04914        478 DPRVEWLIDFLKSHR-SEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIG  556 (956)
T ss_pred             CHHHHHHHHHHHhcC-CCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhh
Confidence            458888888887663 6899999999999999999995 3 78999999999999999999999984  69999999999


Q ss_pred             ccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCC--CceecCCCCHHHHHHHH
Q 012794          111 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGC--KFEFVSPPVVEDVLESS  188 (456)
Q Consensus       111 ~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~--~~~~~~~p~~~~i~~~~  188 (456)
                      ++|+|++.+++|||||+|++++.|+||+||++|.|+++.+.+++...+......|.+.+..  .+-...+|+..++.+..
T Consensus       557 seGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i~~~~~~~l~ife~~~~~~~~v~~~~  636 (956)
T PRK04914        557 SEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHEGLNAFEHTCPTGRALYDEF  636 (956)
T ss_pred             ccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccCCCCHHHHHHHHHhhhcCceeccCCCHHHHHHHH
Confidence            9999999999999999999999999999999999999988888776666667777776654  66778999999999988


Q ss_pred             HHHHHHHHhcC
Q 012794          189 AEQVVATLNGV  199 (456)
Q Consensus       189 ~~~~~~~l~~~  199 (456)
                      ...+...+..-
T Consensus       637 ~~~l~~~l~~~  647 (956)
T PRK04914        637 GDELIPYLASP  647 (956)
T ss_pred             HHHHHHHHhCC
Confidence            88888777544

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

Probab=99.86  E-value=1.8e-21  Score=194.17  Aligned_cols=151  Identities=28%  Similarity=0.500  Sum_probs=136.1

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHH-h----cCCEEEEeCCCCHHHHHHHHh
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-S----IIASEALHGDISQHQRERTLN   94 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~-~----~~~~~~lhg~~~~~~R~~~l~   94 (456)
                      .++..+.|+++.+....|.-.+..+|... +..++|+|+++.+.+..++..|. .    .+.+..+.|.+++..|.+.++
T Consensus       399 slp~~l~~~~vv~~~~~kpl~~~~lI~~~-k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~  477 (620)
T KOG0350|consen  399 SLPSSLSHRLVVTEPKFKPLAVYALITSN-KLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLE  477 (620)
T ss_pred             ecChhhhhceeecccccchHhHHHHHHHh-hcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHH
Confidence            45667889999888888988899999876 45899999999999999999987 2    356777899999999999999


Q ss_pred             cccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCC
Q 012794           95 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGC  171 (456)
Q Consensus        95 ~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~  171 (456)
                      +|..|.++||||||+++||||+-+|+.|||||+|.+..+|+||+|||+|||+.|.|+++....+...+.++-+..+.
T Consensus       478 ~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~~~~  554 (620)
T KOG0350|consen  478 KFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKKTNL  554 (620)
T ss_pred             HHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHHHHHHHHhcc
Confidence            99999999999999999999999999999999999999999999999999999999999999988877777666654

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

Probab=99.86  E-value=9.7e-22  Score=196.15  Aligned_cols=149  Identities=34%  Similarity=0.535  Sum_probs=132.4

Q ss_pred             cccccccCeeEEEEEcCcc-cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHh
Q 012794           17 QDEKLAEGIKLYAISTTAT-SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLN   94 (456)
Q Consensus        17 ~~~~~~~~i~~~~~~~~~~-~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~   94 (456)
                      +.....+.|.|....++.. .|+..|..-|......+++|||+.-+..+++|+..|. +.+.+..|||+|.|++|.++|.
T Consensus       433 ~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls  512 (731)
T KOG0339|consen  433 EVGEANEDITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLS  512 (731)
T ss_pred             ehhccccchhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHH
Confidence            4555667788887777664 6788777766666667899999999999999999998 6899999999999999999999


Q ss_pred             cccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794           95 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus        95 ~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      +|+++...||||||+++||+|||++..|||||+-.|++.|+||+|||||+|.+|++++|+++.+..+.-.|
T Consensus       513 ~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~fAG~L  583 (731)
T KOG0339|consen  513 KFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHL  583 (731)
T ss_pred             HHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechhhHHHhhHH
Confidence            99999999999999999999999999999999999999999999999999999999999999886544433

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.86  E-value=3.9e-21  Score=206.83  Aligned_cols=153  Identities=33%  Similarity=0.548  Sum_probs=141.8

Q ss_pred             cccccccCeeEEEEEcC-cccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHh
Q 012794           17 QDEKLAEGIKLYAISTT-ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLN   94 (456)
Q Consensus        17 ~~~~~~~~i~~~~~~~~-~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~   94 (456)
                      ........|++....++ ...|+.-|..||..+....++||||...+.|+.+.+.|.+ ++.|..|||+.+|.+|..+++
T Consensus       578 ~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~  657 (997)
T KOG0334|consen  578 GRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIE  657 (997)
T ss_pred             cceeEeccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHH
Confidence            44456677888888888 7789999999998887789999999999999999999986 788889999999999999999


Q ss_pred             cccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHh
Q 012794           95 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  169 (456)
Q Consensus        95 ~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~  169 (456)
                      .|+++.+++||||+++++|||+.++.+|||||+|...+.|+||+|||||+|++|.|++|+.+.+..+.-.|.+.+
T Consensus       658 dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~al  732 (997)
T KOG0334|consen  658 DFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKAL  732 (997)
T ss_pred             HHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999998888888888877

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.86  E-value=5.6e-21  Score=209.98  Aligned_cols=191  Identities=19%  Similarity=0.293  Sum_probs=141.2

Q ss_pred             CeeEEEEEcCcccHH-----HHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeCCCCHHHHHHHHh
Q 012794           24 GIKLYAISTTATSKR-----TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLN   94 (456)
Q Consensus        24 ~i~~~~~~~~~~~k~-----~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg~~~~~~R~~~l~   94 (456)
                      .|+++|+.+...+++     .+|..++..  ..+++||||+++.+++.+++.|.+    .+.+..|||+|++++|.++++
T Consensus       179 pVe~~y~~~~~~~~~~~~v~~~l~~~l~~--~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~  256 (819)
T TIGR01970       179 PVEIRYLPLRGDQRLEDAVSRAVEHALAS--ETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIK  256 (819)
T ss_pred             eeeeEEeecchhhhHHHHHHHHHHHHHHh--cCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHh
Confidence            578888876655443     223333322  357899999999999999999985    477899999999999999999


Q ss_pred             cccCCCeEEEEeccccccccCcCccceEEecCCCC------------------ChhHHHHHhcccccCCCCceEEEeeCh
Q 012794           95 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------------------DPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus        95 ~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~------------------~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      .|++|+.+||||||++++|||||+|++|||+++|.                  +..+|+||+|||||. ++|.||.+++.
T Consensus       257 ~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~  335 (819)
T TIGR01970       257 PDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSE  335 (819)
T ss_pred             hcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCH
Confidence            99999999999999999999999999999999885                  234699999999999 79999999998


Q ss_pred             hhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHHHHHHHHHhCCCCC
Q 012794          157 SQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRP  236 (456)
Q Consensus       157 ~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~a~ala~~~~~~~~  236 (456)
                      .+...   +..+.           ..||+...+..++..+..........|     .+++.+..+++.+|+..|..+...
T Consensus       336 ~~~~~---l~~~~-----------~PEI~r~~L~~~~L~l~~~g~~~~~~~-----~~l~~P~~~~i~~a~~~L~~lgal  396 (819)
T TIGR01970       336 EQHQR---LPAQD-----------EPEILQADLSGLALELAQWGAKDPSDL-----RWLDAPPSVALAAARQLLQRLGAL  396 (819)
T ss_pred             HHHHh---hhcCC-----------CcceeccCcHHHHHHHHHcCCCChhhC-----CCCCCcCHHHHHHHHHHHHHCCCC
Confidence            76433   22221           223333444445544544332222222     356677778888888877655444

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.

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.85  E-value=2.1e-21  Score=198.39  Aligned_cols=155  Identities=26%  Similarity=0.420  Sum_probs=137.0

Q ss_pred             CccccccCCCccccCCcccccccCeeEEEEEcCcc--------cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHH
Q 012794            1 MLNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTAT--------SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT   72 (456)
Q Consensus         1 i~~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~--------~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~   72 (456)
                      |.+|+-++..|.+..+.  .....|+||++.++..        .|++.|..+++.+ +..++||||+....|+-++..|.
T Consensus       217 Lsk~mrdp~lVr~n~~d--~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~i-py~QAlVF~~~~sra~~~a~~L~  293 (980)
T KOG4284|consen  217 LSKFMRDPALVRFNADD--VQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSI-PYVQALVFCDQISRAEPIATHLK  293 (980)
T ss_pred             HHHHhcccceeecccCC--ceeechhheeeeccCCcchHHHHHHHHHHHHHHHhhC-chHHHHhhhhhhhhhhHHHHHhh
Confidence            35677788888777443  4566889998876553        3788888888766 46899999999999999999999


Q ss_pred             -hcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEE
Q 012794           73 -SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI  151 (456)
Q Consensus        73 -~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i  151 (456)
                       .++.|.++.|.|+|.+|..+++.+|+-..+|||+||+.+||||-++|++|||.|.|.|.++|.|||||+||.|..|.++
T Consensus       294 ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aV  373 (980)
T KOG4284|consen  294 SSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAV  373 (980)
T ss_pred             ccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeE
Confidence             5899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeChhh
Q 012794          152 LMFTSSQ  158 (456)
Q Consensus       152 ~~~~~~e  158 (456)
                      +|+...+
T Consensus       374 T~~~~~~  380 (980)
T KOG4284|consen  374 TLLEDER  380 (980)
T ss_pred             EEeccch
Confidence            9987554

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.85  E-value=1.9e-20  Score=201.41  Aligned_cols=200  Identities=16%  Similarity=0.205  Sum_probs=139.1

Q ss_pred             cccccCCCccccCCcccccccCeeEEEEEcCc----------ccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHH
Q 012794            3 NYFVMFSHSTQVGNQDEKLAEGIKLYAISTTA----------TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLAL   71 (456)
Q Consensus         3 ~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~----------~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L   71 (456)
                      +||.++..|...    ..+...|+++|+....          ..+..++..+.... ...+++||||+++.+++.+++.|
T Consensus       340 ~~~~~p~~I~I~----grt~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~~~~g~iLVFlpg~~ei~~l~~~L  415 (675)
T PHA02653        340 EFFPNPAFVHIP----GGTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTPPKGSSGIVFVASVSQCEEYKKYL  415 (675)
T ss_pred             HHhcCCcEEEeC----CCcCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhcccCCcEEEEECcHHHHHHHHHHH
Confidence            455555444432    2344678888875431          22333333333222 23468999999999999999999


Q ss_pred             Hh---cCCEEEEeCCCCHHHHHHHHhcc-cCCCeEEEEeccccccccCcCccceEEecC---CCC---------ChhHHH
Q 012794           72 TS---IIASEALHGDISQHQRERTLNGF-RQGKFTVLVATDVAARGLDIPNVDLIIHYE---LPN---------DPETFV  135 (456)
Q Consensus        72 ~~---~~~~~~lhg~~~~~~R~~~l~~F-r~g~~~vLVaTdv~~~Gidip~v~~VI~~~---~p~---------~~~~y~  135 (456)
                      .+   .+.+.+|||+|++.  ++++++| ++++.+||||||+|++|||||+|++||+++   .|.         +.++|+
T Consensus       416 ~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~  493 (675)
T PHA02653        416 EKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRT  493 (675)
T ss_pred             HhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEECCCccCCCcccCcccccCHHHHH
Confidence            85   47899999999985  5677777 789999999999999999999999999999   665         888999


Q ss_pred             HHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHH
Q 012794          136 HRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLI  215 (456)
Q Consensus       136 qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll  215 (456)
                      ||+|||||. ++|.|+.|+++.+...+.+                   +..+.+..++..++.......+.      .++
T Consensus       494 QRaGRAGR~-~~G~c~rLyt~~~~~pI~r-------------------i~~~~L~~~vL~lk~~g~~~~~~------~~l  547 (675)
T PHA02653        494 QRKGRVGRV-SPGTYVYFYDLDLLKPIKR-------------------IDSEFLHNYILYAKYFNLTLPED------LFV  547 (675)
T ss_pred             HhccCcCCC-CCCeEEEEECHHHhHHHHH-------------------HhHHHHHHHHHHHHHcCCCCccc------ccC
Confidence            999999999 7999999999876422211                   11122344444444333222221      156


Q ss_pred             hhcCHHHHHHHHHHHhCCC
Q 012794          216 EEKGTDALAAALAQLSGFS  234 (456)
Q Consensus       216 ~~~~~~~~a~ala~~~~~~  234 (456)
                      +.++++++.+|+..|..+.
T Consensus       548 dpP~~~~l~~A~~~L~~lg  566 (675)
T PHA02653        548 IPSNLDRLRKTEEYIDSFN  566 (675)
T ss_pred             CCCCHHHHHHHHHHHHHcC
Confidence            7777788877777775443

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.85  E-value=1.4e-20  Score=202.96  Aligned_cols=133  Identities=27%  Similarity=0.510  Sum_probs=120.7

Q ss_pred             CcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccc
Q 012794           33 TATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  111 (456)
Q Consensus        33 ~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~  111 (456)
                      ....+...|.+++.... +.++||||+|++.|+.+++.|.. ++.+..+|++|++++|+.+++.|+++.++|||||++++
T Consensus       207 ~~~~~~~~l~~~l~~~~-~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~  285 (591)
T TIGR01389       207 KKNNKQKFLLDYLKKHR-GQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFG  285 (591)
T ss_pred             eCCCHHHHHHHHHHhcC-CCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhh
Confidence            34456777777776543 57899999999999999999985 78999999999999999999999999999999999999


Q ss_pred             cccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHH
Q 012794          112 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  166 (456)
Q Consensus       112 ~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie  166 (456)
                      +|||+|+|++||+|++|.+++.|+|++||+||.|..+.|++++.+.+...++.+.
T Consensus       286 ~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~~~i  340 (591)
T TIGR01389       286 MGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRI  340 (591)
T ss_pred             ccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999998887776654

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.85  E-value=1.1e-20  Score=207.98  Aligned_cols=192  Identities=18%  Similarity=0.264  Sum_probs=146.6

Q ss_pred             CeeEEEEEcCcccHHH-----HHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeCCCCHHHHHHHHh
Q 012794           24 GIKLYAISTTATSKRT-----ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLN   94 (456)
Q Consensus        24 ~i~~~~~~~~~~~k~~-----~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg~~~~~~R~~~l~   94 (456)
                      .|+++|+.++...++.     +|..++..  ..+.+||||+++.+++.+++.|.+    .+.+..|||+|++++|.++++
T Consensus       182 pV~~~y~~~~~~~~~~~~v~~~l~~~l~~--~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~  259 (812)
T PRK11664        182 PVERRYQPLPAHQRFDEAVARATAELLRQ--ESGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAIL  259 (812)
T ss_pred             cceEEeccCchhhhHHHHHHHHHHHHHHh--CCCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhc
Confidence            5788888776655543     23333322  358999999999999999999985    467889999999999999999


Q ss_pred             cccCCCeEEEEeccccccccCcCccceEEecCCCC------------------ChhHHHHHhcccccCCCCceEEEeeCh
Q 012794           95 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------------------DPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus        95 ~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~------------------~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      .|++|+.+||||||++++|||||+|++|||++++.                  +.++|+||+|||||. .+|.||.++++
T Consensus       260 ~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~  338 (812)
T PRK11664        260 PAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSK  338 (812)
T ss_pred             cccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCH
Confidence            99999999999999999999999999999988774                  346899999999999 69999999998


Q ss_pred             hhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHHHHHHHHHhCCCCC
Q 012794          157 SQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRP  236 (456)
Q Consensus       157 ~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~a~ala~~~~~~~~  236 (456)
                      .+...   +           ..-+..||+...+..++..+..........|     .+++.+.+.++.+|+..|..+...
T Consensus       339 ~~~~~---l-----------~~~~~PEI~r~dL~~~~L~l~~~g~~~~~~~-----~~ld~P~~~~~~~A~~~L~~lgal  399 (812)
T PRK11664        339 EQAER---A-----------AAQSEPEILHSDLSGLLLELLQWGCHDPAQL-----SWLDQPPAAALAAAKRLLQQLGAL  399 (812)
T ss_pred             HHHhh---C-----------ccCCCCceeccchHHHHHHHHHcCCCCHHhC-----CCCCCCCHHHHHHHHHHHHHCCCC
Confidence            76432   1           1122335666666666666655433222222     467778888888888888655444


Q ss_pred             C
Q 012794          237 P  237 (456)
Q Consensus       237 ~  237 (456)
                      .
T Consensus       400 d  400 (812)
T PRK11664        400 D  400 (812)
T ss_pred             C
Confidence            3

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.81  E-value=3.6e-19  Score=189.24  Aligned_cols=133  Identities=21%  Similarity=0.239  Sum_probs=112.9

Q ss_pred             eeEEEEEcCcccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeE
Q 012794           25 IKLYAISTTATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        25 i~~~~~~~~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  102 (456)
                      ..+.++.++..+|...|.+++... ..+.++||||+|++.++.|+..|.+ ++.+.+|||++.  +|+..+..|+.+...
T Consensus       446 ~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~--~rE~~ii~~ag~~g~  523 (656)
T PRK12898        446 HLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGTRSVAASERLSALLREAGLPHQVLNAKQD--AEEAAIVARAGQRGR  523 (656)
T ss_pred             ecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcH--HHHHHHHHHcCCCCc
Confidence            445566677778999999988764 3457899999999999999999985 899999999865  455555555555567


Q ss_pred             EEEeccccccccCcC---ccc-----eEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhH
Q 012794          103 VLVATDVAARGLDIP---NVD-----LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  159 (456)
Q Consensus       103 vLVaTdv~~~Gidip---~v~-----~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~  159 (456)
                      |+||||+++||+||+   +|.     +||+|++|.+...|+||+|||||+|.+|.+++|++..|.
T Consensus       524 VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        524 ITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             EEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhHH
Confidence            999999999999999   676     999999999999999999999999999999999997653

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.80  E-value=1.3e-18  Score=194.47  Aligned_cols=142  Identities=23%  Similarity=0.340  Sum_probs=111.5

Q ss_pred             HCCCCcEEEEcCChHHHHHHHHHHHhc-------CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccc
Q 012794           48 YAKGGKTIVFTQTKRDADEVSLALTSI-------IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  120 (456)
Q Consensus        48 ~~~~~~~IIF~~t~~~a~~l~~~L~~~-------~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~  120 (456)
                      ...+.++||||||+..|+.++..|.+.       ..+.++||+|++++|..++++|++|.++|||||+++++|||+|+++
T Consensus       281 i~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~Vd  360 (876)
T PRK13767        281 IKEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYID  360 (876)
T ss_pred             HhcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCCCc
Confidence            345689999999999999999999752       4689999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCCChhHHHHHhcccccC-CCCceEEEeeChh-h-HHHHHHHHHHhCCCceecCCCC-HHHHHHHHH
Q 012794          121 LIIHYELPNDPETFVHRSGRTGRA-GKEGTAILMFTSS-Q-RRTVRSLERDVGCKFEFVSPPV-VEDVLESSA  189 (456)
Q Consensus       121 ~VI~~~~p~~~~~y~qr~GR~gR~-g~~g~~i~~~~~~-e-~~~~~~ie~~~~~~~~~~~~p~-~~~i~~~~~  189 (456)
                      +||+++.|.++.+|+||+||+||. +.....+++.... + ......++......++.+.+|. ..+++..++
T Consensus       361 ~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~~~~l~e~~~~~~~~~~~~ie~~~~~~~~~dvl~q~i  433 (876)
T PRK13767        361 LVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVDRDDLVECAVLLKKAREGKIDRVHIPKNPLDVLAQHI  433 (876)
T ss_pred             EEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcCchhHHHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHH
Confidence            999999999999999999999986 4434444444322 2 2233344455555666665554 345544333

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.80  E-value=9.4e-19  Score=199.86  Aligned_cols=150  Identities=25%  Similarity=0.408  Sum_probs=116.6

Q ss_pred             HHHHHHCCCCcEEEEcCChHHHHHHHHHHHhcC----------------------------------CEEEEeCCCCHHH
Q 012794           43 DLITVYAKGGKTIVFTQTKRDADEVSLALTSII----------------------------------ASEALHGDISQHQ   88 (456)
Q Consensus        43 ~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~~----------------------------------~~~~lhg~~~~~~   88 (456)
                      .++..+..+.++||||||+..|+.++..|.+.+                                  .+.++||+|++++
T Consensus       236 ~il~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkee  315 (1490)
T PRK09751        236 GILDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQ  315 (1490)
T ss_pred             HHHHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHH
Confidence            445444456899999999999999999887421                                  1568999999999


Q ss_pred             HHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccC-CCCceEEEeeChhhHHHHH---H
Q 012794           89 RERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA-GKEGTAILMFTSSQRRTVR---S  164 (456)
Q Consensus        89 R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~-g~~g~~i~~~~~~e~~~~~---~  164 (456)
                      |..+++.|++|++++||||+.+++||||++|++|||++.|.++.+|+||+||+||. +....++++... ....++   .
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 333445543332 222222   4


Q ss_pred             HHHHhCCCceecCCCCHH-HHHHHHHHHHH
Q 012794          165 LERDVGCKFEFVSPPVVE-DVLESSAEQVV  193 (456)
Q Consensus       165 ie~~~~~~~~~~~~p~~~-~i~~~~~~~~~  193 (456)
                      ++.++...++.+.+|... +++..++-.++
T Consensus       395 ve~~l~g~iE~~~~p~nplDVLaqqiva~a  424 (1490)
T PRK09751        395 VECMFAGRLENLTPPHNPLDVLAQQTVAAA  424 (1490)
T ss_pred             HHHHhcCCCCccCCCCChHHHHHHHHHHHH
Confidence            677788888887666544 56554444333

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.80  E-value=2.2e-18  Score=186.92  Aligned_cols=126  Identities=21%  Similarity=0.282  Sum_probs=113.3

Q ss_pred             cCcccHHHHHHHHHHH-HCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           32 TTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        32 ~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      +...+|..+|..++.. +....++||||+|++.++.|+..|.+ ++.+.+||+++.+.++..+..+++.+  +|+||||+
T Consensus       408 ~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdm  485 (790)
T PRK09200        408 VTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNM  485 (790)
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccc
Confidence            4556788888887754 35678999999999999999999995 89999999999999998888888866  79999999


Q ss_pred             cccccCc---Cccc-----eEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhH
Q 012794          110 AARGLDI---PNVD-----LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  159 (456)
Q Consensus       110 ~~~Gidi---p~v~-----~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~  159 (456)
                      |+||+||   |.|.     +||++++|.+...|+||+|||||+|.+|.+++|++..+.
T Consensus       486 AgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD~  543 (790)
T PRK09200        486 AGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLEDD  543 (790)
T ss_pred             hhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchHH
Confidence            9999999   7998     999999999999999999999999999999999987553

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

Probab=99.79  E-value=1.2e-19  Score=178.11  Aligned_cols=163  Identities=32%  Similarity=0.439  Sum_probs=151.2

Q ss_pred             cccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhc
Q 012794           17 QDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNG   95 (456)
Q Consensus        17 ~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~   95 (456)
                      -+.++.+.+++.++.+...+|..+|..++.....+.++||||.|+.+|+.+...|.. ++.+..+++.|.+..|..-+.+
T Consensus       227 vetkise~lk~~f~~~~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~  306 (529)
T KOG0337|consen  227 VETKISELLKVRFFRVRKAEKEAALLSILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRD  306 (529)
T ss_pred             hhhhcchhhhhheeeeccHHHHHHHHHHHhccccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhcccc
Confidence            345778888999999999999999999998776678999999999999999999985 8899999999999999999999


Q ss_pred             ccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCcee
Q 012794           96 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF  175 (456)
Q Consensus        96 Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~  175 (456)
                      |+.++..+||.||+++||+|||-.+.|||||+|.+...|+||+||+.|+|++|.+|.++.+.+..++-.|...++.++..
T Consensus       307 F~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~yl~DL~lflgr~~~~  386 (529)
T KOG0337|consen  307 FRGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPYLLDLQLFLGRPLIF  386 (529)
T ss_pred             ccCCccceEEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecccchhhhhhhhhcCCceee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999887765


Q ss_pred             cCCC
Q 012794          176 VSPP  179 (456)
Q Consensus       176 ~~~p  179 (456)
                      ...+
T Consensus       387 ~~~~  390 (529)
T KOG0337|consen  387 AISH  390 (529)
T ss_pred             ccch
Confidence            5444

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

Probab=99.79  E-value=2.1e-18  Score=180.41  Aligned_cols=119  Identities=31%  Similarity=0.552  Sum_probs=112.9

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCC
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP  128 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p  128 (456)
                      ..+..||||.|++.|+.+|+.|.. ++.+..+|++|+.++|+.+.++|..++++|+|||.+..+|||-|+|.+||||++|
T Consensus       229 ~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP  308 (590)
T COG0514         229 LSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLP  308 (590)
T ss_pred             cCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCC
Confidence            456789999999999999999995 7999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHH
Q 012794          129 NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  168 (456)
Q Consensus       129 ~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~  168 (456)
                      .++++|+|-+||+||.|....|++|+.+.+..+.+.+.+.
T Consensus       309 ~s~EsYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i~~  348 (590)
T COG0514         309 GSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQ  348 (590)
T ss_pred             CCHHHHHHHHhhccCCCCcceEEEeeccccHHHHHHHHHh
Confidence            9999999999999999999999999999998887777554

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.79  E-value=1.2e-18  Score=195.94  Aligned_cols=190  Identities=17%  Similarity=0.312  Sum_probs=141.0

Q ss_pred             CeeEEEEEcCccc---HHHHHHHHH---HHH--CCCCcEEEEcCChHHHHHHHHHHHh-cC---CEEEEeCCCCHHHHHH
Q 012794           24 GIKLYAISTTATS---KRTILSDLI---TVY--AKGGKTIVFTQTKRDADEVSLALTS-II---ASEALHGDISQHQRER   91 (456)
Q Consensus        24 ~i~~~~~~~~~~~---k~~~L~~ll---~~~--~~~~~~IIF~~t~~~a~~l~~~L~~-~~---~~~~lhg~~~~~~R~~   91 (456)
                      .|+++|..+....   +.+.+..++   ..+  ...+++||||+++.+++.+++.|.+ .+   .+.+|||+|++++|.+
T Consensus       251 pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~  330 (1294)
T PRK11131        251 PVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNR  330 (1294)
T ss_pred             cceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHH
Confidence            4677777654321   233333333   222  3457899999999999999999985 33   3778999999999999


Q ss_pred             HHhcccCCCeEEEEeccccccccCcCccceEEecC---------------CC---CChhHHHHHhcccccCCCCceEEEe
Q 012794           92 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE---------------LP---NDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus        92 ~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~---------------~p---~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      +++.  .+..+||||||++++|||||+|++|||++               +|   .+.++|+||+|||||. .+|.||.+
T Consensus       331 Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rL  407 (1294)
T PRK11131        331 VFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRL  407 (1294)
T ss_pred             Hhcc--cCCeeEEEeccHHhhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEe
Confidence            9987  46789999999999999999999999986               33   4568999999999999 69999999


Q ss_pred             eChhhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHHHHHHHHHhCC
Q 012794          154 FTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGF  233 (456)
Q Consensus       154 ~~~~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~a~ala~~~~~  233 (456)
                      |++.+...   +..           -+..||+...+..++..++.+....+..|     .+++.++++++..++..|..+
T Consensus       408 yte~d~~~---~~~-----------~~~PEIlR~~L~~viL~lk~lgl~di~~F-----~fldpP~~~~i~~al~~L~~L  468 (1294)
T PRK11131        408 YSEDDFLS---RPE-----------FTDPEILRTNLASVILQMTALGLGDIAAF-----PFVEAPDKRNIQDGVRLLEEL  468 (1294)
T ss_pred             CCHHHHHh---hhc-----------ccCCccccCCHHHHHHHHHHcCCCCccee-----eCCCCCCHHHHHHHHHHHHHC
Confidence            99866432   211           13345666667777777766554444444     367778888898888887654


Q ss_pred             CC
Q 012794          234 SR  235 (456)
Q Consensus       234 ~~  235 (456)
                      ..
T Consensus       469 gA  470 (1294)
T PRK11131        469 GA  470 (1294)
T ss_pred             CC
Confidence            43

>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=99.78  E-value=3.8e-18  Score=146.83  Aligned_cols=128  Identities=47%  Similarity=0.776  Sum_probs=114.3

Q ss_pred             eeEEEEEcCcccHHHHHHHHHHHHC-CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeE
Q 012794           25 IKLYAISTTATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        25 i~~~~~~~~~~~k~~~L~~ll~~~~-~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  102 (456)
                      |++++...+. .|...+..++.... ...++||||+++..++.+++.|.+ ...+..+|++++..+|..+++.|+++...
T Consensus         2 i~~~~~~~~~-~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~   80 (131)
T cd00079           2 IKQYVLPVED-EKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIV   80 (131)
T ss_pred             cEEEEEECCH-HHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCc
Confidence            4566665543 78888888887653 467999999999999999999985 67899999999999999999999999999


Q ss_pred             EEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      |||+|.++++|+|+|.+++||.+++|++...|+|++||++|.|+.+.++++
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

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.77  E-value=1.7e-17  Score=179.99  Aligned_cols=141  Identities=27%  Similarity=0.381  Sum_probs=120.4

Q ss_pred             HHHHHHHHHH-HHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccccccc
Q 012794           37 KRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  114 (456)
Q Consensus        37 k~~~L~~ll~-~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gi  114 (456)
                      +++.|...|. ....+.++||||+|+..++.|++.|.. ++.+..+|+++++.+|..+++.|+.|++.|||||+++++|+
T Consensus       431 q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGf  510 (652)
T PRK05298        431 QVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGL  510 (652)
T ss_pred             cHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCc
Confidence            4444444443 345567999999999999999999985 78999999999999999999999999999999999999999


Q ss_pred             CcCccceEEecCC-----CCChhHHHHHhcccccCCCCceEEEeeCh---------hhHHHHHHHHHHhCCCceecCC
Q 012794          115 DIPNVDLIIHYEL-----PNDPETFVHRSGRTGRAGKEGTAILMFTS---------SQRRTVRSLERDVGCKFEFVSP  178 (456)
Q Consensus       115 dip~v~~VI~~~~-----p~~~~~y~qr~GR~gR~g~~g~~i~~~~~---------~e~~~~~~ie~~~~~~~~~~~~  178 (456)
                      |+|++++||++|.     |.+.++|+||+|||||. ..|.+++|+..         .+...++.++..++.+...++.
T Consensus       511 dlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  587 (652)
T PRK05298        511 DIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITPK  587 (652)
T ss_pred             cccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCCh
Confidence            9999999998874     78999999999999996 78999999983         5667777888777766655443

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

Probab=99.77  E-value=3.7e-18  Score=171.84  Aligned_cols=122  Identities=33%  Similarity=0.553  Sum_probs=107.7

Q ss_pred             ccHHHHHHHHHHHHC---CCCcEEEEcCChHHHHHHHHHHHh-cCCEE-EEe--------CCCCHHHHHHHHhcccCCCe
Q 012794           35 TSKRTILSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS-IIASE-ALH--------GDISQHQRERTLNGFRQGKF  101 (456)
Q Consensus        35 ~~k~~~L~~ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~-~lh--------g~~~~~~R~~~l~~Fr~g~~  101 (456)
                      ..|++.|.++++...   .+.++|||++.+++|+.|+..|.+ +..+. .+-        .+|+|.++.+++++|++|.+
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            368888888887652   357999999999999999999986 44442 222        36999999999999999999


Q ss_pred             EEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh
Q 012794          102 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS  157 (456)
Q Consensus       102 ~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  157 (456)
                      +|||||+|+++|||||++++||.|++-.|.-.++||.|||||. +.|.++++++..
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 789999998866

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.76  E-value=7.3e-18  Score=187.44  Aligned_cols=113  Identities=24%  Similarity=0.426  Sum_probs=103.4

Q ss_pred             HHHHHCCCCcEEEEcCChHHHHHHHHHHHh---cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccc
Q 012794           44 LITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD  120 (456)
Q Consensus        44 ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~  120 (456)
                      ++.....+++++|||++++.++.+++.|.+   .+.+..+||+|++.+|++++++|++|+++|||||+++++|||+|+++
T Consensus       653 i~~el~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~  732 (926)
T TIGR00580       653 IRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNAN  732 (926)
T ss_pred             HHHHHHcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCC
Confidence            344445678999999999999999999986   46799999999999999999999999999999999999999999999


Q ss_pred             eEEecCCCC-ChhHHHHHhcccccCCCCceEEEeeCh
Q 012794          121 LIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       121 ~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      +||+++.|. +..+|+||+||+||.++.|.|++++.+
T Consensus       733 ~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~  769 (926)
T TIGR00580       733 TIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPH  769 (926)
T ss_pred             EEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECC
Confidence            999999875 688999999999999999999999864

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.75  E-value=3.9e-17  Score=175.82  Aligned_cols=127  Identities=21%  Similarity=0.259  Sum_probs=111.9

Q ss_pred             EEcCcccHHHHHHHHHHH-HCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec
Q 012794           30 ISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT  107 (456)
Q Consensus        30 ~~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT  107 (456)
                      +.+...+|..++...+.. +....++||||+|++.++.|+..|.+ ++.+.+||+++.+.++..+.++++.+  .|+|||
T Consensus       402 i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIAT  479 (762)
T TIGR03714       402 IYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVAT  479 (762)
T ss_pred             EEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEc
Confidence            344556788877776654 45678999999999999999999985 89999999999999998888888877  699999


Q ss_pred             cccccccCcC---------ccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhH
Q 012794          108 DVAARGLDIP---------NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  159 (456)
Q Consensus       108 dv~~~Gidip---------~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~  159 (456)
                      |+|+||+||+         .+.+|+++++|..... +||+|||||+|.+|.+++|++..+.
T Consensus       480 dmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       480 SMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             cccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchh
Confidence            9999999999         9999999999998777 9999999999999999999987653

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.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.75  E-value=1.2e-17  Score=188.51  Aligned_cols=191  Identities=15%  Similarity=0.256  Sum_probs=139.7

Q ss_pred             CeeEEEEEcCc------ccHHHHHHHHHHHH--CCCCcEEEEcCChHHHHHHHHHHHh-c---CCEEEEeCCCCHHHHHH
Q 012794           24 GIKLYAISTTA------TSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-I---IASEALHGDISQHQRER   91 (456)
Q Consensus        24 ~i~~~~~~~~~------~~k~~~L~~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~-~---~~~~~lhg~~~~~~R~~   91 (456)
                      .|+.+|.....      .++.+.+..++..+  ...+.+|||++++.+++.+++.|.+ .   +.+..|||+|++++|.+
T Consensus       244 PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~  323 (1283)
T TIGR01967       244 PVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQR  323 (1283)
T ss_pred             cceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHH
Confidence            45566654432      12444444444332  2357999999999999999999984 2   45889999999999999


Q ss_pred             HHhcccCCCeEEEEeccccccccCcCccceEEecCCC------------------CChhHHHHHhcccccCCCCceEEEe
Q 012794           92 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP------------------NDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus        92 ~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p------------------~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      +++.+.  ..+||||||++++|||||+|.+||+++++                  .+.++|+||+|||||.+ +|.||.+
T Consensus       324 vf~~~~--~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRL  400 (1283)
T TIGR01967       324 VFQPHS--GRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVA-PGICIRL  400 (1283)
T ss_pred             HhCCCC--CceEEEeccHHHhccccCCeeEEEeCCCccccccccccCccccCCccCCHHHHHHHhhhhCCCC-CceEEEe
Confidence            987653  46899999999999999999999999853                  36689999999999997 9999999


Q ss_pred             eChhhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHHHHHHHHHhCC
Q 012794          154 FTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGF  233 (456)
Q Consensus       154 ~~~~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~a~ala~~~~~  233 (456)
                      |+..+...+   ..           -+..||+...+..++..+.......+..|     .+++.+..+++..++..|..+
T Consensus       401 yte~~~~~~---~~-----------~~~PEIlR~~L~~viL~l~~lg~~di~~f-----~fldpP~~~~i~~A~~~L~~L  461 (1283)
T TIGR01967       401 YSEEDFNSR---PE-----------FTDPEILRTNLASVILQMLALRLGDIAAF-----PFIEAPDPRAIRDGFRLLEEL  461 (1283)
T ss_pred             cCHHHHHhh---hh-----------ccCcccccccHHHHHHHHHhcCCCCcccc-----cCCCCCCHHHHHHHHHHHHHC
Confidence            998764322   11           12335666667777777665443333333     467778888888888888655


Q ss_pred             CCC
Q 012794          234 SRP  236 (456)
Q Consensus       234 ~~~  236 (456)
                      ...
T Consensus       462 GAl  464 (1283)
T TIGR01967       462 GAL  464 (1283)
T ss_pred             CCC
Confidence            443

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.74  E-value=1.5e-17  Score=179.52  Aligned_cols=132  Identities=24%  Similarity=0.387  Sum_probs=114.3

Q ss_pred             cHHHHHHHHHH-HHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccc
Q 012794           36 SKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG  113 (456)
Q Consensus        36 ~k~~~L~~ll~-~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~G  113 (456)
                      .+++.|..-|. ....+.++||||+|++.++.|++.|.+ ++.+..+|++|++.+|.++++.|++|++.|||||+++++|
T Consensus       426 ~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rG  505 (655)
T TIGR00631       426 GQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREG  505 (655)
T ss_pred             chHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCC
Confidence            34444444443 445678999999999999999999985 7899999999999999999999999999999999999999


Q ss_pred             cCcCccceEEecC-----CCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHH
Q 012794          114 LDIPNVDLIIHYE-----LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  168 (456)
Q Consensus       114 idip~v~~VI~~~-----~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~  168 (456)
                      +|+|++++||++|     .|.+..+|+||+|||||. ..|.+++|+...+..+.+.|++.
T Consensus       506 fDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~ai~~~  564 (655)
T TIGR00631       506 LDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSMQKAIEET  564 (655)
T ss_pred             eeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHHHHHHH
Confidence            9999999999988     899999999999999998 68999999987665555555443

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

>PRK02362 ski2-like helicase; Provisional

Probab=99.74  E-value=2.2e-17  Score=182.46  Aligned_cols=130  Identities=27%  Similarity=0.453  Sum_probs=106.3

Q ss_pred             HHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc-------------------------------------CCEEEEeC
Q 012794           40 ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------------IASEALHG   82 (456)
Q Consensus        40 ~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~-------------------------------------~~~~~lhg   82 (456)
                      .+..++..+..++++||||+|+..|+.+|..|...                                     ..+.++|+
T Consensus       232 ~~~~~~~~~~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHa  311 (737)
T PRK02362        232 TLNLVLDTLEEGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHA  311 (737)
T ss_pred             HHHHHHHHHHcCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecC
Confidence            33444444446789999999999999998877531                                     25789999


Q ss_pred             CCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEe----cC-----CCCChhHHHHHhcccccCCCC--ceEE
Q 012794           83 DISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE-----LPNDPETFVHRSGRTGRAGKE--GTAI  151 (456)
Q Consensus        83 ~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~----~~-----~p~~~~~y~qr~GR~gR~g~~--g~~i  151 (456)
                      +|++.+|+.+++.|++|.++|||||+++++|+|+|.+.+||+    ||     .|.++.+|+||+|||||.|..  |.++
T Consensus       312 gl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~i  391 (737)
T PRK02362        312 GLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAV  391 (737)
T ss_pred             CCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEE
Confidence            999999999999999999999999999999999999999997    66     689999999999999999854  8999


Q ss_pred             EeeChhhHHHHHHHHHHhC
Q 012794          152 LMFTSSQRRTVRSLERDVG  170 (456)
Q Consensus       152 ~~~~~~e~~~~~~ie~~~~  170 (456)
                      +++...+. ..+.+++++.
T Consensus       392 i~~~~~~~-~~~~~~~~l~  409 (737)
T PRK02362        392 LLAKSYDE-LDELFERYIW  409 (737)
T ss_pred             EEecCchh-HHHHHHHHHh
Confidence            99876431 2233444553

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.73  E-value=6.2e-17  Score=173.35  Aligned_cols=125  Identities=26%  Similarity=0.286  Sum_probs=112.0

Q ss_pred             CcccHHHHHHH-HHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccc
Q 012794           33 TATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  110 (456)
Q Consensus        33 ~~~~k~~~L~~-ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~  110 (456)
                      ...+|..++.+ +...+..+.++||||+|++.++.|+..|.+ ++.+.+||++  +.+|+..+.+|+.+...|+||||+|
T Consensus       386 t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmA  463 (745)
T TIGR00963       386 TEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMA  463 (745)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccc
Confidence            34467666654 555567788999999999999999999995 8999999999  8999999999999999999999999


Q ss_pred             ccccCcCc-------cceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhH
Q 012794          111 ARGLDIPN-------VDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  159 (456)
Q Consensus       111 ~~Gidip~-------v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~  159 (456)
                      +||+||+.       ..|||+++.|.+...|.|++|||||+|.+|.+..|++..+.
T Consensus       464 gRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD~  519 (745)
T TIGR00963       464 GRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLEDN  519 (745)
T ss_pred             cCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccHH
Confidence            99999998       55999999999999999999999999999999999987653

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.73  E-value=2.5e-17  Score=167.10  Aligned_cols=119  Identities=25%  Similarity=0.374  Sum_probs=101.2

Q ss_pred             ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cC--CEEEEeCCCCHHHHHH----HHhcccCCCeEEEEec
Q 012794           35 TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-II--ASEALHGDISQHQRER----TLNGFRQGKFTVLVAT  107 (456)
Q Consensus        35 ~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~--~~~~lhg~~~~~~R~~----~l~~Fr~g~~~vLVaT  107 (456)
                      ..+...+..++.....+.++||||+|++.|+.+++.|.+ ..  .+..+||+|++.+|.+    +++.|++++..|||||
T Consensus       206 ~~~~~~l~~l~~~~~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT  285 (358)
T TIGR01587       206 VGEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVAT  285 (358)
T ss_pred             ccCHHHHHHHHHHhhCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEEC
Confidence            356777788887666678999999999999999999985 33  4899999999999976    4899999999999999


Q ss_pred             cccccccCcCccceEEecCCCCChhHHHHHhcccccCCCC----ceEEEeeCh
Q 012794          108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE----GTAILMFTS  156 (456)
Q Consensus       108 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~----g~~i~~~~~  156 (456)
                      +++++|||++ +++||++..|  +++|+||+||+||.|+.    +.++++...
T Consensus       286 ~~~~~GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~  335 (358)
T TIGR01587       286 QVIEASLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIA  335 (358)
T ss_pred             cchhceeccC-CCEEEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeec
Confidence            9999999996 8899998776  78999999999998854    356666554

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.73  E-value=4.7e-17  Score=177.73  Aligned_cols=129  Identities=22%  Similarity=0.410  Sum_probs=105.8

Q ss_pred             eeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCCh--------HHHHHHHHHHHhc---CCEEEEeCCCCHHHHHHHH
Q 012794           25 IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK--------RDADEVSLALTSI---IASEALHGDISQHQRERTL   93 (456)
Q Consensus        25 i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~--------~~a~~l~~~L~~~---~~~~~lhg~~~~~~R~~~l   93 (456)
                      ++.+++..  ..+..++..+......+.+++|||++.        ..++.+++.|.+.   +.+..+||+|++.+|++++
T Consensus       447 i~~~~~~~--~~~~~~~~~i~~~~~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~  524 (681)
T PRK10917        447 ITTVVIPD--SRRDEVYERIREEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVM  524 (681)
T ss_pred             cEEEEeCc--ccHHHHHHHHHHHHHcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHH
Confidence            44444332  233334444444455678999999964        4566777777753   5799999999999999999


Q ss_pred             hcccCCCeEEEEeccccccccCcCccceEEecCCCC-ChhHHHHHhcccccCCCCceEEEeeC
Q 012794           94 NGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFT  155 (456)
Q Consensus        94 ~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~~~~  155 (456)
                      ++|++|+++|||||+++++|||+|++++||+++.|. ....|+||+||+||.|..|.|++++.
T Consensus       525 ~~F~~g~~~ILVaT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~  587 (681)
T PRK10917        525 AAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYK  587 (681)
T ss_pred             HHHHcCCCCEEEECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEEC
Confidence            999999999999999999999999999999999997 57889999999999999999999995

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

Probab=99.73  E-value=1.1e-17  Score=164.53  Aligned_cols=106  Identities=38%  Similarity=0.642  Sum_probs=100.2

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecC
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE  126 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~  126 (456)
                      -.++||||.|+..|+.|.+.+.+    .+.|++|||+..+.+|.+.++.|++..++.||||||++|||||..+.++||.-
T Consensus       505 mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invt  584 (725)
T KOG0349|consen  505 MDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVT  584 (725)
T ss_pred             cCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEe
Confidence            46899999999999999999873    38999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhHHHHHhcccccCCCCceEEEeeCh
Q 012794          127 LPNDPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       127 ~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      +|.+...|+||+||+||+-+-|.+|.++..
T Consensus       585 lpd~k~nyvhrigrvgraermglaislvat  614 (725)
T KOG0349|consen  585 LPDDKTNYVHRIGRVGRAERMGLAISLVAT  614 (725)
T ss_pred             cCcccchhhhhhhccchhhhcceeEEEeec
Confidence            999999999999999999999999988753

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.73  E-value=5.8e-17  Score=175.80  Aligned_cols=120  Identities=23%  Similarity=0.404  Sum_probs=103.0

Q ss_pred             cHHHHHHHHHHHHCCCCcEEEEcCCh--------HHHHHHHHHHHh---cCCEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           36 SKRTILSDLITVYAKGGKTIVFTQTK--------RDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        36 ~k~~~L~~ll~~~~~~~~~IIF~~t~--------~~a~~l~~~L~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      .+..++..+.+....+.+++|||++.        ..++.+++.|.+   .+.+..+||+|++++|++++++|++|+++||
T Consensus       433 ~~~~~~~~i~~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~IL  512 (630)
T TIGR00643       433 EKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDIL  512 (630)
T ss_pred             hHHHHHHHHHHHHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEE
Confidence            34444555555555678999999976        456677777764   4679999999999999999999999999999


Q ss_pred             EeccccccccCcCccceEEecCCCC-ChhHHHHHhcccccCCCCceEEEeeC
Q 012794          105 VATDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFT  155 (456)
Q Consensus       105 VaTdv~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~~~~  155 (456)
                      |||+++++|||+|++++||+++.|. ....|+||+||+||.|++|.|++++.
T Consensus       513 VaT~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       513 VATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             EECceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            9999999999999999999999986 68889999999999999999999983

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.72  E-value=5.8e-17  Score=183.89  Aligned_cols=127  Identities=20%  Similarity=0.355  Sum_probs=106.1

Q ss_pred             HHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh---cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCc
Q 012794           42 SDLITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN  118 (456)
Q Consensus        42 ~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~  118 (456)
                      ..++..+..+++++||||+++.++.+++.|.+   .+.+.++||+|++.+|++++.+|++|+++|||||+++++|||+|+
T Consensus       800 ~~il~el~r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~  879 (1147)
T PRK10689        800 EAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPT  879 (1147)
T ss_pred             HHHHHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhccccccc
Confidence            33444444568999999999999999999985   367999999999999999999999999999999999999999999


Q ss_pred             cceEEecCCC-CChhHHHHHhcccccCCCCceEEEeeChh------hHHHHHHHHHH
Q 012794          119 VDLIIHYELP-NDPETFVHRSGRTGRAGKEGTAILMFTSS------QRRTVRSLERD  168 (456)
Q Consensus       119 v~~VI~~~~p-~~~~~y~qr~GR~gR~g~~g~~i~~~~~~------e~~~~~~ie~~  168 (456)
                      +++||..+.. .+...|+||+|||||.++.|.|++++...      ....++.|++.
T Consensus       880 v~~VIi~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~~~~~~~~~~rl~~~~~~  936 (1147)
T PRK10689        880 ANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASL  936 (1147)
T ss_pred             CCEEEEecCCCCCHHHHHHHhhccCCCCCceEEEEEeCCCcccCHHHHHHHHHHHHh
Confidence            9999954432 35668999999999999999999998542      34455555554

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

Probab=99.70  E-value=1.1e-16  Score=174.02  Aligned_cols=129  Identities=23%  Similarity=0.336  Sum_probs=99.1

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHH-HHH-CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHH-----H
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLI-TVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRE-----R   91 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll-~~~-~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~-----~   91 (456)
                      ....++.++ +.++...|+..+...+ ..+ ...+++||||||++.|+.|++.|.+ .+  ..|||+|+|.+|+     +
T Consensus       240 l~a~ki~q~-v~v~~e~Kl~~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~  316 (844)
T TIGR02621       240 LAAKKIVKL-VPPSDEKFLSTMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKE  316 (844)
T ss_pred             ccccceEEE-EecChHHHHHHHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHH
Confidence            444566665 3444444554333322 212 2357899999999999999999985 33  8999999999999     8


Q ss_pred             HHhcccC----CC-------eEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCc-eEEEee
Q 012794           92 TLNGFRQ----GK-------FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG-TAILMF  154 (456)
Q Consensus        92 ~l~~Fr~----g~-------~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g-~~i~~~  154 (456)
                      ++++|++    +.       ..|||||+++++||||+. ++||++..|  .++|+||+||++|+|+.+ ..++++
T Consensus       317 il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv  388 (844)
T TIGR02621       317 IFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVV  388 (844)
T ss_pred             HHHHHhccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEE
Confidence            8999987    43       689999999999999987 888987766  699999999999999754 435555

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.

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.69  E-value=3.4e-16  Score=169.06  Aligned_cols=125  Identities=27%  Similarity=0.330  Sum_probs=111.0

Q ss_pred             cCcccHHHHHHHHHH-HHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           32 TTATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        32 ~~~~~k~~~L~~ll~-~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      .....|..+|.+.+. .+..+.++||||+|++.++.|+..|.+ ++.+.+||+++.+.+++.+.++++.|.  |+|||++
T Consensus       420 ~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnm  497 (796)
T PRK12906        420 PTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNM  497 (796)
T ss_pred             cCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEecc
Confidence            344568777777664 446678999999999999999999985 899999999999888888888888777  9999999


Q ss_pred             cccccCc---Cccc-----eEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          110 AARGLDI---PNVD-----LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       110 ~~~Gidi---p~v~-----~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      |+||+||   ++|.     |||+++.|.+...|.|+.|||||.|.+|.+..|++..+
T Consensus       498 AGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD  554 (796)
T PRK12906        498 AGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLED  554 (796)
T ss_pred             ccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccc
Confidence            9999999   4899     99999999999999999999999999999999988664

>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=99.68  E-value=7.6e-17  Score=126.91  Aligned_cols=76  Identities=39%  Similarity=0.768  Sum_probs=72.3

Q ss_pred             HHH-hcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCC
Q 012794           70 ALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG  145 (456)
Q Consensus        70 ~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g  145 (456)
                      .|. .++.+..+||+|++.+|+.+++.|+++...|||||+++++|||+|.+++||++++|+++..|+|++||++|.|
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            355 3789999999999999999999999999999999999999999999999999999999999999999999976

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 ....

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.67  E-value=9.6e-16  Score=166.71  Aligned_cols=126  Identities=26%  Similarity=0.312  Sum_probs=112.0

Q ss_pred             cCcccHHHHHHHHHHH-HCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           32 TTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        32 ~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      ....+|..+|...+.. +..+.++||||+|++.++.|+..|.. ++.+.+||+  .|.+|+..+.+|+.+...|+||||+
T Consensus       578 ~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNM  655 (1025)
T PRK12900        578 KTRREKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNM  655 (1025)
T ss_pred             cCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccC
Confidence            4555788888887754 45678999999999999999999985 899999997  5999999999999999999999999


Q ss_pred             cccccCcC---ccc-----eEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhH
Q 012794          110 AARGLDIP---NVD-----LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  159 (456)
Q Consensus       110 ~~~Gidip---~v~-----~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~  159 (456)
                      |+||+||+   .|.     +||+++.|.+...|.|++|||||+|.+|.+++|++..+.
T Consensus       656 AGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~  713 (1025)
T PRK12900        656 AGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDE  713 (1025)
T ss_pred             cCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHH
Confidence            99999999   554     459999999999999999999999999999999987653

>PRK00254 ski2-like helicase; Provisional

Probab=99.67  E-value=4.8e-16  Score=171.34  Aligned_cols=125  Identities=26%  Similarity=0.405  Sum_probs=100.2

Q ss_pred             CCCCcEEEEcCChHHHHHHHHHHHh----------------------------------cCCEEEEeCCCCHHHHHHHHh
Q 012794           49 AKGGKTIVFTQTKRDADEVSLALTS----------------------------------IIASEALHGDISQHQRERTLN   94 (456)
Q Consensus        49 ~~~~~~IIF~~t~~~a~~l~~~L~~----------------------------------~~~~~~lhg~~~~~~R~~~l~   94 (456)
                      ..+.++||||+|+..|+.++..|..                                  ...+.++|++|++++|..+++
T Consensus       236 ~~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~  315 (720)
T PRK00254        236 KKGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIED  315 (720)
T ss_pred             HhCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHH
Confidence            3468999999999999888766632                                  124889999999999999999


Q ss_pred             cccCCCeEEEEeccccccccCcCccceEEe-------cCCCC-ChhHHHHHhcccccCC--CCceEEEeeChhhHHHHHH
Q 012794           95 GFRQGKFTVLVATDVAARGLDIPNVDLIIH-------YELPN-DPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRS  164 (456)
Q Consensus        95 ~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~-------~~~p~-~~~~y~qr~GR~gR~g--~~g~~i~~~~~~e~~~~~~  164 (456)
                      .|++|.++|||||+++++|+|+|.+++||.       ++.|. ++.+|+||+|||||.|  ..|.+++++...+..  +.
T Consensus       316 ~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~~~--~~  393 (720)
T PRK00254        316 AFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPS--KL  393 (720)
T ss_pred             HHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcchH--HH
Confidence            999999999999999999999999999994       55544 5779999999999975  679999998765422  12


Q ss_pred             HHHHhCCCcee
Q 012794          165 LERDVGCKFEF  175 (456)
Q Consensus       165 ie~~~~~~~~~  175 (456)
                      +++++...++.
T Consensus       394 ~~~~~~~~pe~  404 (720)
T PRK00254        394 MERYIFGKPEK  404 (720)
T ss_pred             HHHHHhCCchh
Confidence            44454444433

>PRK13766 Hef nuclease; Provisional

Probab=99.67  E-value=5.9e-16  Score=172.34  Aligned_cols=121  Identities=35%  Similarity=0.555  Sum_probs=109.4

Q ss_pred             ccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCC--------CCHHHHHHHHhcccCCCeE
Q 012794           35 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGD--------ISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        35 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~--------~~~~~R~~~l~~Fr~g~~~  102 (456)
                      ..|++.|.++|...   ..+.++||||+++.+|+.|++.|.. ++.+..+||.        |++.+|..++++|+++.++
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            46888899988764   3568999999999999999999974 7888899886        9999999999999999999


Q ss_pred             EEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeCh
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      |||||+++++|+|+|++++||+||+|++...|+||+||+||.+. +.+++++..
T Consensus       426 vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~  478 (773)
T PRK13766        426 VLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAK  478 (773)
T ss_pred             EEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeC
Confidence            99999999999999999999999999999999999999999864 777777754

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=99.66  E-value=2.6e-15  Score=159.25  Aligned_cols=123  Identities=33%  Similarity=0.555  Sum_probs=106.1

Q ss_pred             ccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeC--------CCCHHHHHHHHhcccCC
Q 012794           35 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS----IIASEALHG--------DISQHQRERTLNGFRQG   99 (456)
Q Consensus        35 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg--------~~~~~~R~~~l~~Fr~g   99 (456)
                      ..|++.|..+|..+   .+..++||||.|++.|+.|...|..    ++++..+-|        +|+|.++.+++++|++|
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            57888888877654   4567999999999999999999873    234444433        79999999999999999


Q ss_pred             CeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhH
Q 012794          100 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  159 (456)
Q Consensus       100 ~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~  159 (456)
                      +++|||||+|+++||||+.|++||-||.-.++-..+||.|| ||+ +.|.++++++..+.
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 57888888875443

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.64  E-value=1.8e-15  Score=162.96  Aligned_cols=120  Identities=23%  Similarity=0.331  Sum_probs=103.7

Q ss_pred             ccHHHHHHHHHHHHC-CCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccCC-CeEEEEecccccc
Q 012794           35 TSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQG-KFTVLVATDVAAR  112 (456)
Q Consensus        35 ~~k~~~L~~ll~~~~-~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~g-~~~vLVaTdv~~~  112 (456)
                      ..|+.++..|+..+. .+.++||||.+...++.++..|.    +..|||++++.+|++++++|+++ .+++||+|+++.+
T Consensus       479 p~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~----~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgde  554 (732)
T TIGR00603       479 PNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG----KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDT  554 (732)
T ss_pred             hHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC----CceEECCCCHHHHHHHHHHHHhCCCccEEEEeccccc
Confidence            467777778887663 56799999999999999988773    56799999999999999999975 8899999999999


Q ss_pred             ccCcCccceEEecCCCC-ChhHHHHHhcccccCCCCceE-------EEeeChhh
Q 012794          113 GLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTA-------ILMFTSSQ  158 (456)
Q Consensus       113 Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~-------i~~~~~~e  158 (456)
                      |||+|++++||+++.|. +...|+||+||++|.++.+.+       |.|++..+
T Consensus       555 GIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT  608 (732)
T TIGR00603       555 SIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDT  608 (732)
T ss_pred             ccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCc
Confidence            99999999999999985 999999999999999866654       66776543

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).

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.64  E-value=2.6e-15  Score=158.90  Aligned_cols=113  Identities=18%  Similarity=0.212  Sum_probs=99.1

Q ss_pred             cHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec-ccccc
Q 012794           36 SKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT-DVAAR  112 (456)
Q Consensus        36 ~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT-dv~~~  112 (456)
                      .+..+|..++..+ ..+.++||||++.++++.|++.|.+ +..+..+||+|++++|..+++.|++++..||||| +++++
T Consensus       328 ~Rn~~I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~e  407 (501)
T PHA02558        328 KRNKWIANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFST  407 (501)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceecc
Confidence            3445555555433 3457899999999999999999985 7899999999999999999999999999999998 99999


Q ss_pred             ccCcCccceEEecCCCCChhHHHHHhcccccCCCCc
Q 012794          113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG  148 (456)
Q Consensus       113 Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g  148 (456)
                      |+|+|++++||++.++.+...|+||+||++|.+...
T Consensus       408 G~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K  443 (501)
T PHA02558        408 GISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSK  443 (501)
T ss_pred             ccccccccEEEEecCCcchhhhhhhhhccccCCCCC
Confidence            999999999999999999999999999999987544

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

Probab=99.63  E-value=2.1e-15  Score=166.20  Aligned_cols=133  Identities=23%  Similarity=0.407  Sum_probs=119.8

Q ss_pred             HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccC
Q 012794           37 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  115 (456)
Q Consensus        37 k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gid  115 (456)
                      .+..+...+..+.+...+||||.++.+|++++..|.+ ++.+..+|++|+..+|+.+..+|-.++++|+|||=+..+|||
T Consensus       471 ~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGId  550 (941)
T KOG0351|consen  471 ALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGID  550 (941)
T ss_pred             chHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCC
Confidence            3444444555566788999999999999999999996 789999999999999999999999999999999999999999


Q ss_pred             cCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHh
Q 012794          116 IPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  169 (456)
Q Consensus       116 ip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~  169 (456)
                      .|+|..||||.+|.+.+.|.|-+||+||.|....|++|+...+...++.+-..-
T Consensus       551 K~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~s~  604 (941)
T KOG0351|consen  551 KPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADISELRRLLTSG  604 (941)
T ss_pred             CCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEecchhHHHHHHHHHHcc
Confidence            999999999999999999999999999999999999999998877777664443

>PRK09401 reverse gyrase; Reviewed

Probab=99.62  E-value=1.4e-15  Score=173.09  Aligned_cols=101  Identities=25%  Similarity=0.399  Sum_probs=87.6

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHH---HHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhc
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD---ADEVSLALTS-IIASEALHGDISQHQRERTLNG   95 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~---a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~   95 (456)
                      ....+|.|.|+.+.  +|...|..++....  .++||||+|+..   |+.|++.|.. ++.+..+||+|     ++.+++
T Consensus       301 ~~~rnI~~~yi~~~--~k~~~L~~ll~~l~--~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~  371 (1176)
T PRK09401        301 FYLRNIVDSYIVDE--DSVEKLVELVKRLG--DGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEK  371 (1176)
T ss_pred             cccCCceEEEEEcc--cHHHHHHHHHHhcC--CCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHH
Confidence            45678899988766  67778888887653  589999999777   9999999995 89999999999     334699


Q ss_pred             ccCCCeEEEEe----ccccccccCcCc-cceEEecCCCC
Q 012794           96 FRQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELPN  129 (456)
Q Consensus        96 Fr~g~~~vLVa----Tdv~~~Gidip~-v~~VI~~~~p~  129 (456)
                      |++|+++||||    ||+++||||+|+ |.+||||++|.
T Consensus       372 F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~  410 (1176)
T PRK09401        372 FEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPK  410 (1176)
T ss_pred             HHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCC
Confidence            99999999999    699999999999 89999999996

>PRK01172 ski2-like helicase; Provisional

Probab=99.61  E-value=5.9e-15  Score=161.80  Aligned_cols=109  Identities=25%  Similarity=0.369  Sum_probs=92.3

Q ss_pred             HCCCCcEEEEcCChHHHHHHHHHHHhc--------------------------CCEEEEeCCCCHHHHHHHHhcccCCCe
Q 012794           48 YAKGGKTIVFTQTKRDADEVSLALTSI--------------------------IASEALHGDISQHQRERTLNGFRQGKF  101 (456)
Q Consensus        48 ~~~~~~~IIF~~t~~~a~~l~~~L~~~--------------------------~~~~~lhg~~~~~~R~~~l~~Fr~g~~  101 (456)
                      ...++++||||+|++.|+.++..|...                          ..+.++|++|++++|..+++.|++|.+
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            345689999999999999999888632                          147789999999999999999999999


Q ss_pred             EEEEeccccccccCcCccceEEecC---------CCCChhHHHHHhcccccCC--CCceEEEeeChh
Q 012794          102 TVLVATDVAARGLDIPNVDLIIHYE---------LPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  157 (456)
Q Consensus       102 ~vLVaTdv~~~Gidip~v~~VI~~~---------~p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~  157 (456)
                      +|||||+++++|+|+|...+|| ++         .|.++.+|.||+|||||.|  ..|.+++++...
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         3568899999999999998  457788876543

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

Probab=99.60  E-value=2.3e-14  Score=155.26  Aligned_cols=151  Identities=25%  Similarity=0.399  Sum_probs=117.3

Q ss_pred             HHHCCCCcEEEEcCChHHHHHHHHHHHhc--CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEE
Q 012794           46 TVYAKGGKTIVFTQTKRDADEVSLALTSI--IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII  123 (456)
Q Consensus        46 ~~~~~~~~~IIF~~t~~~a~~l~~~L~~~--~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI  123 (456)
                      .....+..+|||+||+..|+.|+..|.+.  ..+.++||.++.++|..+.++|++|+++++|||..++-|||+-+|++||
T Consensus       248 ~~v~~~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdlVI  327 (814)
T COG1201         248 ELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVI  327 (814)
T ss_pred             HHHhhcCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCceEEE
Confidence            33344568999999999999999999963  6899999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCChhHHHHHhccccc-CCCCceEEEeeChhh--HHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhc
Q 012794          124 HYELPNDPETFVHRSGRTGR-AGKEGTAILMFTSSQ--RRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNG  198 (456)
Q Consensus       124 ~~~~p~~~~~y~qr~GR~gR-~g~~g~~i~~~~~~e--~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~  198 (456)
                      |+..|.++..++||+||+|+ .+.....+++....+  ....-.........++.+.+|..  -+...+.+++..+..
T Consensus       328 q~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~r~dllE~~vi~~~a~~g~le~~~i~~~--~LDVLaq~ivg~~~~  403 (814)
T COG1201         328 QLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAEDRDDLLECLVLADLALEGKLERIKIPKN--PLDVLAQQIVGMALE  403 (814)
T ss_pred             EeCCcHHHHHHhHhccccccccCCcccEEEEecCHHHHHHHHHHHHHHHhCCcccCCCCCc--chhHHHHHHHHHHhh
Confidence            99999999999999999987 455566676666532  22333344455556665555533  233344455444433

>TIGR01054 rgy reverse gyrase

Probab=99.59  E-value=5.1e-15  Score=168.71  Aligned_cols=101  Identities=20%  Similarity=0.366  Sum_probs=85.9

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCCh---HHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhc
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTK---RDADEVSLALTS-IIASEALHGDISQHQRERTLNG   95 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~---~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~   95 (456)
                      ....+|.|.|+.+..  +...|.+++..+  +.++||||+|+   +.|++|+..|.+ ++.+..+||+|++    .++++
T Consensus       299 ~~~r~I~~~~~~~~~--~~~~L~~ll~~l--~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l~~  370 (1171)
T TIGR01054       299 DTLRNVVDVYVEDED--LKETLLEIVKKL--GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDYEK  370 (1171)
T ss_pred             ccccceEEEEEeccc--HHHHHHHHHHHc--CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHHHH
Confidence            455678888876544  345567777665  36899999999   999999999985 7999999999973    68999


Q ss_pred             ccCCCeEEEEe----ccccccccCcCc-cceEEecCCC
Q 012794           96 FRQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELP  128 (456)
Q Consensus        96 Fr~g~~~vLVa----Tdv~~~Gidip~-v~~VI~~~~p  128 (456)
                      |++|+++||||    ||+++||||+|+ |++|||||+|
T Consensus       371 Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P  408 (1171)
T TIGR01054       371 FAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVP  408 (1171)
T ss_pred             HHcCCCCEEEEeccccCcccccCCCCccccEEEEECCC
Confidence            99999999999    599999999999 8999998877

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.58  E-value=1e-14  Score=148.00  Aligned_cols=109  Identities=23%  Similarity=0.353  Sum_probs=86.6

Q ss_pred             CeeEEEEEcCcccHHHHHHHHHHHH------CCCCcEEEEcCChHHHHHHHHHHHh-c--CCEEEEeCCCCHHHHHHHHh
Q 012794           24 GIKLYAISTTATSKRTILSDLITVY------AKGGKTIVFTQTKRDADEVSLALTS-I--IASEALHGDISQHQRERTLN   94 (456)
Q Consensus        24 ~i~~~~~~~~~~~k~~~L~~ll~~~------~~~~~~IIF~~t~~~a~~l~~~L~~-~--~~~~~lhg~~~~~~R~~~l~   94 (456)
                      .+++.++. ....|...+..+++..      ..+.++||||+|+..|+.++..|.+ +  +.+..+||.+++.+|++++ 
T Consensus       240 ~i~~~~~~-~~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~~-  317 (357)
T TIGR03158       240 PVELELIP-APDFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERAM-  317 (357)
T ss_pred             ceEEEEEe-CCchhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHhc-
Confidence            56666655 4445555554444422      2457999999999999999999985 2  5688899999999998664 


Q ss_pred             cccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccc
Q 012794           95 GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG  142 (456)
Q Consensus        95 ~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~g  142 (456)
                           +..||||||++++|||+|.+ +|| ++ |.+.++|+||+||||
T Consensus       318 -----~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       318 -----QFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             -----cCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence                 67899999999999999987 566 45 899999999999986

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.

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=99.54  E-value=1.4e-14  Score=142.82  Aligned_cols=114  Identities=25%  Similarity=0.482  Sum_probs=109.1

Q ss_pred             CcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCC
Q 012794           52 GKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPND  130 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~  130 (456)
                      +-.||||.|+++|+++|-.|. .++.+.++|.+|...+|.++.+++-++++.||+||....+|+|-|+|.+|||+++|.+
T Consensus       256 GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn  335 (641)
T KOG0352|consen  256 GCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQN  335 (641)
T ss_pred             cceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchhh
Confidence            457999999999999999998 5899999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794          131 PETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus       131 ~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      +..|.|-+||+||.|+...|-++|...+...+..|
T Consensus       336 ~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FL  370 (641)
T KOG0352|consen  336 LAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFL  370 (641)
T ss_pred             hHHHHHhccccccCCCccceeeeecccchHHHHHH
Confidence            99999999999999999999999999988877766

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.53  E-value=2.6e-14  Score=112.41  Aligned_cols=80  Identities=53%  Similarity=0.867  Sum_probs=74.3

Q ss_pred             HHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccC
Q 012794           66 EVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  144 (456)
Q Consensus        66 ~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  144 (456)
                      .+++.|.. .+.+..+||+|++++|..+++.|+++...|||+|+++++|+|+|.+++||.+++|++...|+|++||++|.
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            45566664 68899999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 012794          145 G  145 (456)
Q Consensus       145 g  145 (456)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            5

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

Probab=99.53  E-value=2.6e-14  Score=145.53  Aligned_cols=133  Identities=23%  Similarity=0.386  Sum_probs=113.0

Q ss_pred             eeEEEEEc-CcccHHHHHHHHHHHH-------CCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhc
Q 012794           25 IKLYAIST-TATSKRTILSDLITVY-------AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNG   95 (456)
Q Consensus        25 i~~~~~~~-~~~~k~~~L~~ll~~~-------~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~   95 (456)
                      ++.+.+.+ ...+|.+++..|.+..       .-.+++|||++++..|.+||..|. +++++.++|++|++.+|..+...
T Consensus       406 lErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~  485 (830)
T COG1202         406 LERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERA  485 (830)
T ss_pred             hhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHH
Confidence            44444444 4678999999988743       124799999999999999999999 58999999999999999999999


Q ss_pred             ccCCCeEEEEeccccccccCcCccceEE---ecCCCC-ChhHHHHHhcccccCC--CCceEEEeeChh
Q 012794           96 FRQGKFTVLVATDVAARGLDIPNVDLII---HYELPN-DPETFVHRSGRTGRAG--KEGTAILMFTSS  157 (456)
Q Consensus        96 Fr~g~~~vLVaTdv~~~Gidip~v~~VI---~~~~p~-~~~~y~qr~GR~gR~g--~~g~~i~~~~~~  157 (456)
                      |.++.+.++|+|-+++-|+|+|.-.+|+   -++.-| ++..|.|++||+||.+  ..|++++++.+.
T Consensus       486 F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         486 FAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             HhcCCcceEeehhhhhcCCCCchHHHHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCC
Confidence            9999999999999999999999877665   355555 8999999999999977  568999988654

>PRK14701 reverse gyrase; Provisional

Probab=99.48  E-value=5.8e-14  Score=163.41  Aligned_cols=138  Identities=17%  Similarity=0.264  Sum_probs=112.7

Q ss_pred             cccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHH---HHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHh
Q 012794           19 EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD---ADEVSLALTS-IIASEALHGDISQHQRERTLN   94 (456)
Q Consensus        19 ~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~---a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~   94 (456)
                      .....+|.|.|+.+....| ..|.++++..  +..+||||+|++.   |++|++.|.. ++.+..+|++     |..+++
T Consensus       301 ~~~lr~i~~~yi~~~~~~k-~~L~~ll~~~--g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~  372 (1638)
T PRK14701        301 RSALRNIVDVYLNPEKIIK-EHVRELLKKL--GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFD  372 (1638)
T ss_pred             CCCCCCcEEEEEECCHHHH-HHHHHHHHhC--CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHH
Confidence            3456788999987765555 4677777655  4689999999875   5899999985 8999999996     899999


Q ss_pred             cccCCCeEEEEec----cccccccCcCc-cceEEecCCCC---ChhHHHHHh-------------cccccCCCCceEEEe
Q 012794           95 GFRQGKFTVLVAT----DVAARGLDIPN-VDLIIHYELPN---DPETFVHRS-------------GRTGRAGKEGTAILM  153 (456)
Q Consensus        95 ~Fr~g~~~vLVaT----dv~~~Gidip~-v~~VI~~~~p~---~~~~y~qr~-------------GR~gR~g~~g~~i~~  153 (456)
                      +|++|+++|||||    ++++||||+|+ |.+|||||+|.   +++.|.|-.             ||++|.|....+++.
T Consensus       373 ~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~  452 (1638)
T PRK14701        373 LFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLD  452 (1638)
T ss_pred             HHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhHHH
Confidence            9999999999999    59999999998 99999999999   888777765             999998877777655


Q ss_pred             eChhhHHHHHH
Q 012794          154 FTSSQRRTVRS  164 (456)
Q Consensus       154 ~~~~e~~~~~~  164 (456)
                      +.......++.
T Consensus       453 ~~~~~~~~~~~  463 (1638)
T PRK14701        453 VFPEDVEFLRS  463 (1638)
T ss_pred             hHHHHHHHHHH
Confidence            55555444443

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

Probab=99.48  E-value=1.6e-13  Score=142.60  Aligned_cols=210  Identities=19%  Similarity=0.294  Sum_probs=159.5

Q ss_pred             ccccccCCCccccCCcccccccCeeEEEEEcCcccHHHH-HHHHHHHH--CCCCcEEEEcCChHHHHHHHHHHHhc---C
Q 012794            2 LNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTI-LSDLITVY--AKGGKTIVFTQTKRDADEVSLALTSI---I   75 (456)
Q Consensus         2 ~~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~-L~~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~~---~   75 (456)
                      ..||+..+.+...+..-     .|+.+|...+..+.++. +..+++.+  .+.+.+|||....++++.+++.|.+.   .
T Consensus       211 S~yF~~a~i~~i~GR~f-----PVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~  285 (674)
T KOG0922|consen  211 SEYFNNAPILTIPGRTF-----PVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACELLRERAKSL  285 (674)
T ss_pred             HHHhcCCceEeecCCCC-----ceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhc
Confidence            35677666666555443     67888887776665444 34444444  45678999999999999999999753   1


Q ss_pred             ------CEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecC------------------CCCCh
Q 012794           76 ------ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE------------------LPNDP  131 (456)
Q Consensus        76 ------~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~------------------~p~~~  131 (456)
                            .+.++||.|+.+++.++++.-..|..+|+++|++|+..|.||.+.+||+.+                  .|.|.
T Consensus       286 ~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISk  365 (674)
T KOG0922|consen  286 PEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISK  365 (674)
T ss_pred             cccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechH
Confidence                  246799999999999999999999999999999999999999999999655                  36688


Q ss_pred             hHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhhhhHHHH
Q 012794          132 ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTA  211 (456)
Q Consensus       132 ~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~  211 (456)
                      .+-.||+||+||.+ +|+|+-+|+..+.              +.++..+..|+....+..++..++.+...++-.|    
T Consensus       366 asA~QRaGRAGRt~-pGkcyRLYte~~~--------------~~~~~~~~PEI~R~~Ls~~vL~Lkalgi~d~l~F----  426 (674)
T KOG0922|consen  366 ASANQRAGRAGRTG-PGKCYRLYTESAY--------------DKMPLQTVPEIQRVNLSSAVLQLKALGINDPLRF----  426 (674)
T ss_pred             HHHhhhcccCCCCC-CceEEEeeeHHHH--------------hhcccCCCCceeeechHHHHHHHHhcCCCCcccC----
Confidence            89999999999986 8999999998663              2233444556666777777777777655444333    


Q ss_pred             HHHHhhcCHHHHHHHHHHHhCCCCC
Q 012794          212 QRLIEEKGTDALAAALAQLSGFSRP  236 (456)
Q Consensus       212 ~~ll~~~~~~~~a~ala~~~~~~~~  236 (456)
                       ++++.+.++.+..||..|..+...
T Consensus       427 -~f~d~P~~~~l~~AL~~L~~lgal  450 (674)
T KOG0922|consen  427 -PFIDPPPPEALEEALEELYSLGAL  450 (674)
T ss_pred             -CCCCCCChHHHHHHHHHHHhcCcc
Confidence             567778888899999888654433

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

Probab=99.47  E-value=1.3e-14  Score=134.57  Aligned_cols=131  Identities=27%  Similarity=0.544  Sum_probs=107.2

Q ss_pred             cccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCC
Q 012794            5 FVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDI   84 (456)
Q Consensus         5 l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~   84 (456)
                      |+..+.-.+|.++...+...++|+|+.....+|...|.+||..+.- .+++||+.+...       |             
T Consensus       238 FmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~LeF-NQVvIFvKsv~R-------l-------------  296 (387)
T KOG0329|consen  238 FMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLEF-NQVVIFVKSVQR-------L-------------  296 (387)
T ss_pred             hhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhhh-cceeEeeehhhh-------h-------------
Confidence            4445566678888899999999999999999999999999988754 789999987654       1             


Q ss_pred             CHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh-hHHHHH
Q 012794           85 SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVR  163 (456)
Q Consensus        85 ~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-e~~~~~  163 (456)
                      +          |   ..+ ||||++..||+||..+++|+|||+|.+.++|+||++||||.|.+|.+|+|++.. +...+.
T Consensus       297 ~----------f---~kr-~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn  362 (387)
T KOG0329|consen  297 S----------F---QKR-LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILN  362 (387)
T ss_pred             h----------h---hhh-hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhc
Confidence            0          2   112 899999999999999999999999999999999999999999999999998754 444444


Q ss_pred             HHHHHhC
Q 012794          164 SLERDVG  170 (456)
Q Consensus       164 ~ie~~~~  170 (456)
                      .+.....
T Consensus       363 ~vqdRf~  369 (387)
T KOG0329|consen  363 PVQDRFE  369 (387)
T ss_pred             hhhHhhh
Confidence            4444433

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

Probab=99.46  E-value=3.7e-13  Score=147.01  Aligned_cols=210  Identities=19%  Similarity=0.288  Sum_probs=157.1

Q ss_pred             ccccccCCCccccCCcccccccCeeEEEEEcCc-cc-HHHHHHHHHHHH--CCCCcEEEEcCChHHHHHHHHHHHh-c--
Q 012794            2 LNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTA-TS-KRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-I--   74 (456)
Q Consensus         2 ~~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~-~~-k~~~L~~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~-~--   74 (456)
                      .+||++.+.+...+...     .|+.+|..... .. -.+.+...+..+  ...+.+|||.+-.++.+.+++.|.+ .  
T Consensus       211 s~~f~~apvi~i~GR~f-----PVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~~~~L~~~~l~  285 (845)
T COG1643         211 SAYFGNAPVIEIEGRTY-----PVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERTAEWLEKAELG  285 (845)
T ss_pred             HHHcCCCCEEEecCCcc-----ceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHHHHHHHhcccc
Confidence            35666665565554443     56777755443 33 344555555544  3367999999999999999999985 2  


Q ss_pred             --CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCC------------------CCChhHH
Q 012794           75 --IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL------------------PNDPETF  134 (456)
Q Consensus        75 --~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~------------------p~~~~~y  134 (456)
                        +.+.+|||.|+.+++.++++.-..++-+|++||+||+.+|.||+|.+||+.++                  |.+-.+.
T Consensus       286 ~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA  365 (845)
T COG1643         286 DDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASA  365 (845)
T ss_pred             CCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCcccccccccccCceeeeEEEechhhh
Confidence              56889999999999999999988888889999999999999999999996553                  4578889


Q ss_pred             HHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcc-hhhhhHHHHHH
Q 012794          135 VHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPE-SVEFFTPTAQR  213 (456)
Q Consensus       135 ~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~  213 (456)
                      .||.||+||.+ +|+||-+|+..+..              ..+.-+..||+...+..++..++..-.. ++..|     .
T Consensus       366 ~QRaGRAGR~~-pGicyRLyse~~~~--------------~~~~~t~PEIlrtdLs~~vL~l~~~G~~~d~~~f-----~  425 (845)
T COG1643         366 DQRAGRAGRTG-PGICYRLYSEEDFL--------------AFPEFTLPEILRTDLSGLVLQLKSLGIGQDIAPF-----P  425 (845)
T ss_pred             hhhccccccCC-CceEEEecCHHHHH--------------hcccCCChhhhhcchHHHHHHHHhcCCCCCcccC-----c
Confidence            99999999985 89999999985532              1233456688888888888888776542 33333     4


Q ss_pred             HHhhcCHHHHHHHHHHHhCCCCC
Q 012794          214 LIEEKGTDALAAALAQLSGFSRP  236 (456)
Q Consensus       214 ll~~~~~~~~a~ala~~~~~~~~  236 (456)
                      +++.++...+.+|+..|..+...
T Consensus       426 fld~P~~~~i~~A~~~L~~LGAl  448 (845)
T COG1643         426 FLDPPPEAAIQAALTLLQELGAL  448 (845)
T ss_pred             cCCCCChHHHHHHHHHHHHcCCc
Confidence            66777778888877777654433

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

Probab=99.39  E-value=8.7e-12  Score=131.00  Aligned_cols=134  Identities=21%  Similarity=0.389  Sum_probs=111.9

Q ss_pred             cCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHH--------HHHHHHHHHh---cCCEEEEeCCCCHHHHHH
Q 012794           23 EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD--------ADEVSLALTS---IIASEALHGDISQHQRER   91 (456)
Q Consensus        23 ~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~--------a~~l~~~L~~---~~~~~~lhg~~~~~~R~~   91 (456)
                      ..|.-+++.  .+.+.+++..+.....++.++.|.|+-.++        |.++++.|..   .+.+..+||.|+.+++++
T Consensus       447 kpI~T~~i~--~~~~~~v~e~i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~  524 (677)
T COG1200         447 KPITTVVIP--HERRPEVYERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDA  524 (677)
T ss_pred             CceEEEEec--cccHHHHHHHHHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHH
Confidence            445565554  345666777777777788999999987554        4566667764   256899999999999999


Q ss_pred             HHhcccCCCeEEEEeccccccccCcCccceEEecCCCC-ChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794           92 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus        92 ~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      +|++|++++++|||||.|.+.|||+|+.+++|.++.-. -..+..|-.||+||...+..|++++.+..
T Consensus       525 vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         525 VMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             HHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            99999999999999999999999999999988877643 78899999999999999999999998765

>PF08152 GUCT: GUCT (NUC152) domain; InterPro: IPR012562 This is the C-terminal domain found in the RNA helicase II / Gu protein family []

Probab=99.38  E-value=5.8e-13  Score=108.78  Aligned_cols=95  Identities=38%  Similarity=0.563  Sum_probs=53.3

Q ss_pred             CCCCCCCCccccCCCCceEEEEEeecCccccCCCChhHHHHHHHhhCCC-CCCccccEEEeecCccceeeeecCHHHHHH
Q 012794          232 GFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPT-AADEIGKIHIIADDRVQGAVFDLPEEIAKE  310 (456)
Q Consensus       232 ~~~~~~~~r~l~~~~~g~~t~~~~~~~~~~~~~~~~~~i~~~l~~~~~~-~~~~ig~i~~~~~~~~~~~~~dv~~~~a~~  310 (456)
                      |+.+ ++.|||+++.+|++|+.+..+.+    .-.+..++..|.+..+. ..+.|++|+++++.  +|+|||||++.+++
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            3556 78899999999999999988753    45677888888877664 56789999999986  69999999999999


Q ss_pred             HHhhcCCC-CCceeecccCCCccC
Q 012794          311 LLNKQIPP-GNTISKITKLPALQD  333 (456)
Q Consensus       311 ~~~~~~~~-g~~l~~~t~LP~l~~  333 (456)
                      +++.|.+. ++.++++++||+|++
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            99999985 999999999999974

; GO: 0003723 RNA binding, 0004386 helicase activity, 0005524 ATP binding, 0005634 nucleus; PDB: 2E29_A.

>PRK09694 helicase Cas3; Provisional

Probab=99.38  E-value=2.7e-12  Score=142.03  Aligned_cols=107  Identities=25%  Similarity=0.449  Sum_probs=90.6

Q ss_pred             HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc----CCEEEEeCCCCHHHH----HHHHhcc-cCCC---eEEE
Q 012794           37 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI----IASEALHGDISQHQR----ERTLNGF-RQGK---FTVL  104 (456)
Q Consensus        37 k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~----~~~~~lhg~~~~~~R----~~~l~~F-r~g~---~~vL  104 (456)
                      ...++..+++....++++||||||++.|+++++.|.+.    ..+..+|+.+++.+|    +++++.| ++++   ..||
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            34556666666666789999999999999999999853    469999999999999    4677888 6665   4799


Q ss_pred             EeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCC
Q 012794          105 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  146 (456)
Q Consensus       105 VaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~  146 (456)
                      |||+|+++|||| ++++||....|  ++.|+||+||++|.+.
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 58999998887  6899999999999874

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.38  E-value=1.1e-11  Score=135.18  Aligned_cols=125  Identities=22%  Similarity=0.243  Sum_probs=107.4

Q ss_pred             cCcccHHHHHHH-HHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           32 TTATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        32 ~~~~~k~~~L~~-ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      .....|..++.+ +...+..+.++||||+|++.++.|+..|.+ ++.+.+||+.+.+.+++.+.++|+.|.  |+||||+
T Consensus       424 ~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNm  501 (896)
T PRK13104        424 LTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNM  501 (896)
T ss_pred             cCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCCc--EEEeccC
Confidence            344567665554 555667789999999999999999999995 899999999999999999999999995  9999999


Q ss_pred             cccccCcCc---------------------------------c-----ceEEecCCCCChhHHHHHhcccccCCCCceEE
Q 012794          110 AARGLDIPN---------------------------------V-----DLIIHYELPNDPETFVHRSGRTGRAGKEGTAI  151 (456)
Q Consensus       110 ~~~Gidip~---------------------------------v-----~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i  151 (456)
                      |+||+||.=                                 |     -|||-...+.+...--|-.||+||.|.+|.+-
T Consensus       502 AGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~  581 (896)
T PRK13104        502 AGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSR  581 (896)
T ss_pred             ccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceE
Confidence            999999851                                 1     26888889999999999999999999999998


Q ss_pred             EeeChhh
Q 012794          152 LMFTSSQ  158 (456)
Q Consensus       152 ~~~~~~e  158 (456)
                      .|++-.+
T Consensus       582 f~lSleD  588 (896)
T PRK13104        582 FYLSLED  588 (896)
T ss_pred             EEEEcCc
Confidence            8877544

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

Probab=99.36  E-value=2.1e-12  Score=133.42  Aligned_cols=207  Identities=17%  Similarity=0.274  Sum_probs=154.0

Q ss_pred             CeeEEEEEcCcccHHHHHHH-HHHHH--CCCCcEEEEcCChHHHHHHHHHHHhc----------CCEEEEeCCCCHHHHH
Q 012794           24 GIKLYAISTTATSKRTILSD-LITVY--AKGGKTIVFTQTKRDADEVSLALTSI----------IASEALHGDISQHQRE   90 (456)
Q Consensus        24 ~i~~~~~~~~~~~k~~~L~~-ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~~----------~~~~~lhg~~~~~~R~   90 (456)
                      .|+.+|-..+..+.+++... +++.+  .+.+.+|||..-.++.+.+.+.|...          +.+.+||+.||...+.
T Consensus       443 PVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQa  522 (902)
T KOG0923|consen  443 PVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQA  522 (902)
T ss_pred             ceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHH
Confidence            46777877787777665444 44443  34578999999998888877777531          4578999999999999


Q ss_pred             HHHhcccCCCeEEEEeccccccccCcCccceEEecC------------------CCCChhHHHHHhcccccCCCCceEEE
Q 012794           91 RTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE------------------LPNDPETFVHRSGRTGRAGKEGTAIL  152 (456)
Q Consensus        91 ~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~------------------~p~~~~~y~qr~GR~gR~g~~g~~i~  152 (456)
                      ++++.--.|..+|++||++|+..|.|++|.+||+-+                  .|.+..+-.||+||+||.| +|+|+-
T Consensus       523 kIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfR  601 (902)
T KOG0923|consen  523 KIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFR  601 (902)
T ss_pred             hhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEE
Confidence            999999999999999999999999999999999644                  3567888899999999997 899999


Q ss_pred             eeChhhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHHHHHHHHHhC
Q 012794          153 MFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSG  232 (456)
Q Consensus       153 ~~~~~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~a~ala~~~~  232 (456)
                      +|+...  +...+|.        .   +..+|....+..++..|+++--.++-+|     ++++.+..+.|..+|..|..
T Consensus       602 LYt~~a--Y~~eLE~--------~---t~PEIqRtnL~nvVL~LkSLGI~Dl~~F-----dFmDpPp~etL~~aLE~Lya  663 (902)
T KOG0923|consen  602 LYTAWA--YEHELEE--------M---TVPEIQRTNLGNVVLLLKSLGIHDLIHF-----DFLDPPPTETLLKALEQLYA  663 (902)
T ss_pred             eechhh--hhhhhcc--------C---CCcceeeccchhHHHHHHhcCcchhccc-----ccCCCCChHHHHHHHHHHHH
Confidence            998743  3333332        2   2235556677777777777654444444     56777888999999999877


Q ss_pred             CCCCCCCccccCCCCce
Q 012794          233 FSRPPSSRSLINHEQGW  249 (456)
Q Consensus       233 ~~~~~~~r~l~~~~~g~  249 (456)
                      +......-.|+.....|
T Consensus       664 LGALn~~GeLTk~GrrM  680 (902)
T KOG0923|consen  664 LGALNHLGELTKLGRRM  680 (902)
T ss_pred             hhccccccchhhhhhhh
Confidence            66554444444333333

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.36  E-value=4.5e-12  Score=138.81  Aligned_cols=118  Identities=28%  Similarity=0.506  Sum_probs=100.4

Q ss_pred             HHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc--------------------------------------CCEEE
Q 012794           38 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI--------------------------------------IASEA   79 (456)
Q Consensus        38 ~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~--------------------------------------~~~~~   79 (456)
                      ..++..++..+..++++||||+++..+...|..|.+.                                      ..+..
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            5555666666777899999999999999999888731                                      03677


Q ss_pred             EeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEE----ecC-----CCCChhHHHHHhcccccCC--CCc
Q 012794           80 LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII----HYE-----LPNDPETFVHRSGRTGRAG--KEG  148 (456)
Q Consensus        80 lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI----~~~-----~p~~~~~y~qr~GR~gR~g--~~g  148 (456)
                      +|++|+.++|..+.+.|++|+++|||||+.+|+|+|+|.-.+||    -|+     .+.++-+|+|+.|||||.|  ..|
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            89999999999999999999999999999999999999888888    466     5678999999999999988  557


Q ss_pred             eEEEeeC
Q 012794          149 TAILMFT  155 (456)
Q Consensus       149 ~~i~~~~  155 (456)
                      .++++..
T Consensus       400 ~~~i~~~  406 (766)
T COG1204         400 EAIILAT  406 (766)
T ss_pred             cEEEEec
Confidence            7777763

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.36  E-value=7.6e-12  Score=136.15  Aligned_cols=125  Identities=24%  Similarity=0.245  Sum_probs=109.7

Q ss_pred             cCcccHHHHHHHHHHH-HCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           32 TTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        32 ~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      ....+|..+|...+.. +..+.++||||+|++.++.|+..|.+ ++.+..||+.  +.+|+..+.+|+.+...|+||||+
T Consensus       410 ~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNm  487 (830)
T PRK12904        410 KTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNM  487 (830)
T ss_pred             ECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEeccc
Confidence            3555788888877754 45678999999999999999999985 7999999996  899999999999999999999999


Q ss_pred             cccccCcCcc--------------------------------------ceEEecCCCCChhHHHHHhcccccCCCCceEE
Q 012794          110 AARGLDIPNV--------------------------------------DLIIHYELPNDPETFVHRSGRTGRAGKEGTAI  151 (456)
Q Consensus       110 ~~~Gidip~v--------------------------------------~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i  151 (456)
                      |+||+||+-=                                      -|||-...|.+...--|-.||+||.|.+|.+-
T Consensus       488 AGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~  567 (830)
T PRK12904        488 AGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSR  567 (830)
T ss_pred             ccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCcee
Confidence            9999999742                                      27888999999999999999999999999998


Q ss_pred             EeeChhh
Q 012794          152 LMFTSSQ  158 (456)
Q Consensus       152 ~~~~~~e  158 (456)
                      .|++-.+
T Consensus       568 f~lSleD  574 (830)
T PRK12904        568 FYLSLED  574 (830)
T ss_pred             EEEEcCc
Confidence            8887544

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.35  E-value=5.9e-12  Score=140.82  Aligned_cols=137  Identities=18%  Similarity=0.362  Sum_probs=113.7

Q ss_pred             CcccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCC---CeEEEEec
Q 012794           33 TATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQG---KFTVLVAT  107 (456)
Q Consensus        33 ~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g---~~~vLVaT  107 (456)
                      ....|+.+|..||..+ ..+.++|||+......+.|...|. .++....|||.++..+|..+++.|.+.   .+-+|++|
T Consensus       468 e~SgKl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLST  547 (1033)
T PLN03142        468 ENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLST  547 (1033)
T ss_pred             hhhhHHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEec
Confidence            3457899999988765 346799999999999999999998 478999999999999999999999753   35678999


Q ss_pred             cccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe--eCh--hhHHHHHHHHHHh
Q 012794          108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM--FTS--SQRRTVRSLERDV  169 (456)
Q Consensus       108 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~--~~~--~e~~~~~~ie~~~  169 (456)
                      .+++.|||+..+++||+||+||++..+.|+++|+.|.|++..+.++  ++.  -|...+....+++
T Consensus       548 rAGGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIEEkIlera~~Kl  613 (1033)
T PLN03142        548 RAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKL  613 (1033)
T ss_pred             cccccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999987655544  332  2445555444443

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.35  E-value=1.9e-11  Score=133.03  Aligned_cols=123  Identities=24%  Similarity=0.307  Sum_probs=106.5

Q ss_pred             cccHHHHH-HHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccc
Q 012794           34 ATSKRTIL-SDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  111 (456)
Q Consensus        34 ~~~k~~~L-~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~  111 (456)
                      ...|..++ .++...+..+.++||||+|++.++.|+..|.. ++.+.+||+.+++.+++.+.++|+.|.  |+||||+|+
T Consensus       431 ~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAG  508 (908)
T PRK13107        431 ADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAG  508 (908)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcC
Confidence            34555444 44555667788999999999999999999985 899999999999999999999999998  999999999


Q ss_pred             cccCcCc--------------------------------c-----ceEEecCCCCChhHHHHHhcccccCCCCceEEEee
Q 012794          112 RGLDIPN--------------------------------V-----DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF  154 (456)
Q Consensus       112 ~Gidip~--------------------------------v-----~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~  154 (456)
                      ||+||.=                                |     -|||-...+.+...--|-.||+||.|.+|.+..|+
T Consensus       509 RGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~l  588 (908)
T PRK13107        509 RGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYL  588 (908)
T ss_pred             CCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEE
Confidence            9999861                                1     27888899999999999999999999999998888


Q ss_pred             Chhh
Q 012794          155 TSSQ  158 (456)
Q Consensus       155 ~~~e  158 (456)
                      +-.+
T Consensus       589 SlED  592 (908)
T PRK13107        589 SMED  592 (908)
T ss_pred             EeCc
Confidence            7554

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=99.30  E-value=1.5e-11  Score=119.87  Aligned_cols=127  Identities=25%  Similarity=0.473  Sum_probs=111.0

Q ss_pred             cHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccc
Q 012794           36 SKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  111 (456)
Q Consensus        36 ~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~  111 (456)
                      +.-+.+.++.+.+   -.+...||||-++..+++++..|++ ++.+..+|..|.+.++.-+-+.+..++++|+|||-+..
T Consensus       299 n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafg  378 (695)
T KOG0353|consen  299 NEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFG  378 (695)
T ss_pred             ChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeec
Confidence            3444455555443   3456789999999999999999996 79999999999999999999999999999999999999


Q ss_pred             cccCcCccceEEecCCCCChhHHHH-------------------------------------------HhcccccCCCCc
Q 012794          112 RGLDIPNVDLIIHYELPNDPETFVH-------------------------------------------RSGRTGRAGKEG  148 (456)
Q Consensus       112 ~Gidip~v~~VI~~~~p~~~~~y~q-------------------------------------------r~GR~gR~g~~g  148 (456)
                      +|||-|+|.+||+..+|.+++.|.|                                           -.||+||.+.+.
T Consensus       379 mgidkpdvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a  458 (695)
T KOG0353|consen  379 MGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKA  458 (695)
T ss_pred             ccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcc
Confidence            9999999999999999999999999                                           789999999999


Q ss_pred             eEEEeeChhhHHHH
Q 012794          149 TAILMFTSSQRRTV  162 (456)
Q Consensus       149 ~~i~~~~~~e~~~~  162 (456)
                      .||++|.-.+...+
T Consensus       459 ~cilyy~~~difk~  472 (695)
T KOG0353|consen  459 DCILYYGFADIFKI  472 (695)
T ss_pred             cEEEEechHHHHhH
Confidence            99999976554333

>TIGR00595 priA primosomal protein N'

Probab=99.30  E-value=1e-11  Score=131.11  Aligned_cols=99  Identities=25%  Similarity=0.448  Sum_probs=80.6

Q ss_pred             HHHHHHHHHhc---CCEEEEeCCCCHHHH--HHHHhcccCCCeEEEEeccccccccCcCccceEE--ecCC----CC---
Q 012794           64 ADEVSLALTSI---IASEALHGDISQHQR--ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII--HYEL----PN---  129 (456)
Q Consensus        64 a~~l~~~L~~~---~~~~~lhg~~~~~~R--~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI--~~~~----p~---  129 (456)
                      ++.+++.|.+.   ..+..+|+++++.++  +++++.|++++++|||+|+++++|+|+|+|++|+  ++|.    |.   
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            57777878753   578899999988766  8999999999999999999999999999999875  6664    32   


Q ss_pred             ---ChhHHHHHhcccccCCCCceEEEeeChhhHHHH
Q 012794          130 ---DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTV  162 (456)
Q Consensus       130 ---~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~  162 (456)
                         ....|+|++||+||.++.|.+++.....+...+
T Consensus       351 ~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~~~~~  386 (505)
T TIGR00595       351 AERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAI  386 (505)
T ss_pred             HHHHHHHHHHHHhccCCCCCCCEEEEEeCCCCCHHH
Confidence               256789999999999999999876544443333

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=99.28  E-value=4.7e-11  Score=121.37  Aligned_cols=128  Identities=27%  Similarity=0.423  Sum_probs=110.0

Q ss_pred             cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccccccc
Q 012794           36 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  114 (456)
Q Consensus        36 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gi  114 (456)
                      +--+++.++-.....+.++||-+-|+++|+.|+++|.. ++++..+|+++..-+|.+++..+|.|.++|||.-+++-+||
T Consensus       431 QvdDL~~EI~~r~~~~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGL  510 (663)
T COG0556         431 QVDDLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGL  510 (663)
T ss_pred             cHHHHHHHHHHHHhcCCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccC
Confidence            34455556555566789999999999999999999995 89999999999999999999999999999999999999999


Q ss_pred             CcCccceEEecC-----CCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHH
Q 012794          115 DIPNVDLIIHYE-----LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS  164 (456)
Q Consensus       115 dip~v~~VI~~~-----~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~  164 (456)
                      |+|.|.+|..+|     +..+..+.+|-+|||+|- -.|.+|++...-...+-+.
T Consensus       511 DiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN-~~GkvIlYAD~iT~sM~~A  564 (663)
T COG0556         511 DLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKA  564 (663)
T ss_pred             CCcceeEEEEeecCccccccccchHHHHHHHHhhc-cCCeEEEEchhhhHHHHHH
Confidence            999999988766     567999999999999995 4789999876544443333

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.27  E-value=3.1e-11  Score=131.96  Aligned_cols=103  Identities=23%  Similarity=0.363  Sum_probs=83.7

Q ss_pred             HHHHHHHHHHh---cCCEEEEeCCCCH--HHHHHHHhcccCCCeEEEEeccccccccCcCccceEE--ecCCCCC-----
Q 012794           63 DADEVSLALTS---IIASEALHGDISQ--HQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII--HYELPND-----  130 (456)
Q Consensus        63 ~a~~l~~~L~~---~~~~~~lhg~~~~--~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI--~~~~p~~-----  130 (456)
                      .++.+++.|.+   ...+..+|+++.+  .+++++++.|++++++|||+|+++++|+|+|+|++|+  ++|.+.+     
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   3578999999975  5789999999999999999999999999999999985  5565543     


Q ss_pred             -----hhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794          131 -----PETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus       131 -----~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                           ...|+|++||+||.++.|.+++.....+...++.+
T Consensus       518 a~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~~~~~~~~  557 (679)
T PRK05580        518 ASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQAL  557 (679)
T ss_pred             hHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCCCHHHHHH
Confidence                 36799999999999999999987665554444433

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

Probab=99.25  E-value=6e-11  Score=123.63  Aligned_cols=107  Identities=32%  Similarity=0.508  Sum_probs=96.3

Q ss_pred             cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccccccc
Q 012794           36 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  114 (456)
Q Consensus        36 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gi  114 (456)
                      .|...+..++..+....++||||.++.+++.++..+.. .+ +..+.++.++.+|+.+++.|+.+.+++||++.++..|+
T Consensus       268 ~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGv  346 (442)
T COG1061         268 RKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGV  346 (442)
T ss_pred             HHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeecccee
Confidence            45555555555544467999999999999999999985 45 88999999999999999999999999999999999999


Q ss_pred             CcCccceEEecCCCCChhHHHHHhccccc
Q 012794          115 DIPNVDLIIHYELPNDPETFVHRSGRTGR  143 (456)
Q Consensus       115 dip~v~~VI~~~~p~~~~~y~qr~GR~gR  143 (456)
                      |+|+++++|...+..+...|+||+||.-|
T Consensus       347 DiP~~~~~i~~~~t~S~~~~~Q~lGR~LR  375 (442)
T COG1061         347 DIPDADVLIILRPTGSRRLFIQRLGRGLR  375 (442)
T ss_pred             cCCCCcEEEEeCCCCcHHHHHHHhhhhcc
Confidence            99999999999999999999999999999

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

Probab=99.25  E-value=1.8e-11  Score=126.97  Aligned_cols=205  Identities=19%  Similarity=0.300  Sum_probs=143.0

Q ss_pred             cccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHH-HHHHHH--CCCCcEEEEcCChHHHHHHHHHHHh------
Q 012794            3 NYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILS-DLITVY--AKGGKTIVFTQTKRDADEVSLALTS------   73 (456)
Q Consensus         3 ~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~-~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~------   73 (456)
                      +||.+-+...+-+...     .|+.+|...+-++..++.. ..+..+  ...+.+|||..-.+.++..+..+..      
T Consensus       517 nfFgn~p~f~IpGRTy-----PV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~~~i~~~l~ql~  591 (1042)
T KOG0924|consen  517 NFFGNCPQFTIPGRTY-----PVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLEQLD  591 (1042)
T ss_pred             HHhCCCceeeecCCcc-----ceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHHHHHHHHHHhhh
Confidence            4455444444443332     5677777777766655433 344433  3357899999887776665555542      


Q ss_pred             -----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecC------------------CCCC
Q 012794           74 -----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE------------------LPND  130 (456)
Q Consensus        74 -----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~------------------~p~~  130 (456)
                           .+.+.++++.||+..+.++++.-..+..+++|||++|+..|.||.+.+||+.+                  .|.+
T Consensus       592 ~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS  671 (1042)
T KOG0924|consen  592 SAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPIS  671 (1042)
T ss_pred             cCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeeecccccccceeEEEech
Confidence                 15688999999999999999999999999999999999999999999999765                  4667


Q ss_pred             hhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhhhhHHH
Q 012794          131 PETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPT  210 (456)
Q Consensus       131 ~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~  210 (456)
                      ...-.||+||+||.+ +|+||-+|+....  ...           +-+.+..||....+..++..|+.+..+++..|   
T Consensus       672 ~AnA~QRaGRAGRt~-pG~cYRlYTe~ay--~~e-----------ml~stvPEIqRTNl~nvVLlLkslgV~dll~F---  734 (1042)
T KOG0924|consen  672 QANADQRAGRAGRTG-PGTCYRLYTEDAY--KNE-----------MLPSTVPEIQRTNLSNVVLLLKSLGVDDLLKF---  734 (1042)
T ss_pred             hccchhhccccCCCC-CcceeeehhhhHH--Hhh-----------cccCCCchhhhcchhhHHHHHHhcChhhhhCC---
Confidence            788899999999986 8999999987431  111           12233456777777777777776655444443   


Q ss_pred             HHHHHhhcCHHHHHHHHHHHh
Q 012794          211 AQRLIEEKGTDALAAALAQLS  231 (456)
Q Consensus       211 ~~~ll~~~~~~~~a~ala~~~  231 (456)
                        ++++.+..+.+..+|-.|.
T Consensus       735 --dFmD~Pped~~~~sly~Lw  753 (1042)
T KOG0924|consen  735 --DFMDPPPEDNLLNSLYQLW  753 (1042)
T ss_pred             --CcCCCCHHHHHHHHHHHHH
Confidence              3444444566666666654

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

Probab=99.24  E-value=4.8e-10  Score=124.17  Aligned_cols=116  Identities=22%  Similarity=0.406  Sum_probs=103.1

Q ss_pred             HHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc---CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcC
Q 012794           41 LSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP  117 (456)
Q Consensus        41 L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~---~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip  117 (456)
                      =..|++++..++++-..+|..+..+++++.|...   ..+.+.||.|+..+-+.+|..|-+++++|||||.+.+.|||||
T Consensus       793 reAI~REl~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIP  872 (1139)
T COG1197         793 REAILRELLRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIP  872 (1139)
T ss_pred             HHHHHHHHhcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCC
Confidence            3456677778999999999999999999999864   4689999999999999999999999999999999999999999


Q ss_pred             ccceEEecCCC-CChhHHHHHhcccccCCCCceEEEeeCh
Q 012794          118 NVDLIIHYELP-NDPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       118 ~v~~VI~~~~p-~~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      +++.+|..+.. .-..+..|..||+||..+.+.||+++.+
T Consensus       873 nANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~  912 (1139)
T COG1197         873 NANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPP  912 (1139)
T ss_pred             CCceEEEeccccccHHHHHHhccccCCccceEEEEEeecC
Confidence            99988754433 3678899999999999999999999975

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

Probab=99.21  E-value=2.7e-10  Score=110.28  Aligned_cols=121  Identities=23%  Similarity=0.427  Sum_probs=95.4

Q ss_pred             HHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHhc---CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccC
Q 012794           40 ILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  115 (456)
Q Consensus        40 ~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~~---~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gid  115 (456)
                      .|..+|+.. ..+.+++||+++.+..+++++.|+..   ..++.+|+.  ...|.+..++||+|++.+||+|.+++||+.
T Consensus       293 kl~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVT  370 (441)
T COG4098         293 KLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVT  370 (441)
T ss_pred             HHHHHHHHHHhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccc
Confidence            455555544 45679999999999999999999753   356788987  456888999999999999999999999999


Q ss_pred             cCccceEE-ecCC-CCChhHHHHHhcccccCC--CCceEEEeeChhhHHHH
Q 012794          116 IPNVDLII-HYEL-PNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTV  162 (456)
Q Consensus       116 ip~v~~VI-~~~~-p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~e~~~~  162 (456)
                      +|+|+++| ...- -.+.+..+|.+||+||.-  ..|.++.|-......+.
T Consensus       371 fp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~G~skaM~  421 (441)
T COG4098         371 FPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYGKSKAMK  421 (441)
T ss_pred             cccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEeccchHHHH
Confidence            99999865 4433 358899999999999954  45777766554444433

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

Probab=99.20  E-value=3.6e-10  Score=128.61  Aligned_cols=93  Identities=23%  Similarity=0.429  Sum_probs=82.1

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhc-------C---CEEEEeCCCCHHHHHHHHhcccCCCe-EEEEeccccccccCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSI-------I---ASEALHGDISQHQRERTLNGFRQGKF-TVLVATDVAARGLDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~-------~---~~~~lhg~~~~~~R~~~l~~Fr~g~~-~vLVaTdv~~~Gidip~v  119 (456)
                      .+++||||.++++|+.+++.|.+.       +   .+..+||+++  ++..++++|+++.. +|||+++++..|+|+|.|
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            479999999999999998887642       1   3567899986  46789999999876 799999999999999999


Q ss_pred             ceEEecCCCCChhHHHHHhcccccCC
Q 012794          120 DLIIHYELPNDPETFVHRSGRTGRAG  145 (456)
Q Consensus       120 ~~VI~~~~p~~~~~y~qr~GR~gR~g  145 (456)
                      .+||.+.++.|...|+||+||+.|.-
T Consensus       776 ~~vVf~rpvkS~~lf~QmIGRgtR~~  801 (1123)
T PRK11448        776 CNLVFLRRVRSRILYEQMLGRATRLC  801 (1123)
T ss_pred             cEEEEecCCCCHHHHHHHHhhhccCC
Confidence            99999999999999999999999953

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=99.16  E-value=2.5e-10  Score=124.85  Aligned_cols=181  Identities=18%  Similarity=0.292  Sum_probs=141.5

Q ss_pred             cHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh--------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           36 SKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS--------IIASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        36 ~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~--------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      -..+++..++..+   ...+.+|||.+...++..+.+.|..        .+.+.++|+.|+..+++.++..--.|..+||
T Consensus       395 id~~Li~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKII  474 (924)
T KOG0920|consen  395 IDYDLIEDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKII  474 (924)
T ss_pred             ccHHHHHHHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhh
Confidence            4567777777655   3357899999999999999999963        1457889999999999999999999999999


Q ss_pred             EeccccccccCcCccceEEecC--------CCC----------ChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHH
Q 012794          105 VATDVAARGLDIPNVDLIIHYE--------LPN----------DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  166 (456)
Q Consensus       105 VaTdv~~~Gidip~v~~VI~~~--------~p~----------~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie  166 (456)
                      +||++|+..|.|++|-+||+.+        +-.          +...-.||.||+||. ++|.||-+|+......+.   
T Consensus       475 laTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~~~~~---  550 (924)
T KOG0920|consen  475 LATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRYEKLM---  550 (924)
T ss_pred             hhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhhhhcc---
Confidence            9999999999999999999644        322          455569999999998 699999999875432211   


Q ss_pred             HHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHHHHHHHHHhCC
Q 012794          167 RDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGF  233 (456)
Q Consensus       167 ~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~a~ala~~~~~  233 (456)
                                ..-+..|++...++++...++-+....+.   +.+..+++.+.++++..|+..|..+
T Consensus       551 ----------~~~q~PEilR~pL~~l~L~iK~l~~~~~~---~fLskaldpP~~~~v~~a~~~L~~i  604 (924)
T KOG0920|consen  551 ----------LAYQLPEILRTPLEELCLHIKVLEQGSIK---AFLSKALDPPPADAVDLAIERLKQI  604 (924)
T ss_pred             ----------cccCChHHHhChHHHhhheeeeccCCCHH---HHHHHhcCCCChHHHHHHHHHHHHh
Confidence                      11235577777888888777755555444   5677889999999888888777643

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.12  E-value=1.2e-09  Score=109.84  Aligned_cols=204  Identities=17%  Similarity=0.307  Sum_probs=150.5

Q ss_pred             ccccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHH-HHHHH--CCCCcEEEEcCChHHHHHHHHHHHh-c---
Q 012794            2 LNYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSD-LITVY--AKGGKTIVFTQTKRDADEVSLALTS-I---   74 (456)
Q Consensus         2 ~~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~-ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~-~---   74 (456)
                      +.||.+.+.+.+-+      ...++.+|...+..+.++...+ +++.+  ...+.+|||....++++..++.+.. .   
T Consensus       207 q~yf~n~Pll~vpg------~~PvEi~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L  280 (699)
T KOG0925|consen  207 QRYFGNAPLLAVPG------THPVEIFYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKISREVDNL  280 (699)
T ss_pred             HHHhCCCCeeecCC------CCceEEEecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhh
Confidence            34565555444332      3456778888788777776555 44444  3468999999999999999988873 1   


Q ss_pred             ------CCEEEEeCCCCHHHHHHHHhcccC---C--CeEEEEeccccccccCcCccceEEecC-----------------
Q 012794           75 ------IASEALHGDISQHQRERTLNGFRQ---G--KFTVLVATDVAARGLDIPNVDLIIHYE-----------------  126 (456)
Q Consensus        75 ------~~~~~lhg~~~~~~R~~~l~~Fr~---g--~~~vLVaTdv~~~Gidip~v~~VI~~~-----------------  126 (456)
                            +.+.+||    ++++..+++....   +  ..+|+|+|++++..+.++.|.+||+-+                 
T Consensus       281 ~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesll  356 (699)
T KOG0925|consen  281 GPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLL  356 (699)
T ss_pred             ccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeee
Confidence                  4688898    4455555544432   2  358999999999999999999999755                 


Q ss_pred             -CCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhh
Q 012794          127 -LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVE  205 (456)
Q Consensus       127 -~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~  205 (456)
                       .|.+..+-.||.||+||. ++|+|+.+|++.-          +..   .+.+.+..+++++.+..++..++...-+++-
T Consensus       357 v~PISkasA~qR~gragrt-~pGkcfrLYte~~----------~~~---em~~~typeilrsNL~s~VL~LKklgI~dlv  422 (699)
T KOG0925|consen  357 VSPISKASAQQRAGRAGRT-RPGKCFRLYTEEA----------FEK---EMQPQTYPEILRSNLSSTVLQLKKLGIDDLV  422 (699)
T ss_pred             eccchHhHHHHHhhhccCC-CCCceEEeecHHh----------hhh---cCCCCCcHHHHHHhhHHHHHHHHhcCccccc
Confidence             367888889999999997 6899999998632          111   2344456789999999999999988777766


Q ss_pred             hhHHHHHHHHhhcCHHHHHHHHHHHhCCC
Q 012794          206 FFTPTAQRLIEEKGTDALAAALAQLSGFS  234 (456)
Q Consensus       206 ~~~~~~~~ll~~~~~~~~a~ala~~~~~~  234 (456)
                      +|     ++++.+.|+.++.||-.|-.+.
T Consensus       423 hf-----dfmDpPAPEtLMrALE~LnYLa  446 (699)
T KOG0925|consen  423 HF-----DFMDPPAPETLMRALEVLNYLA  446 (699)
T ss_pred             CC-----cCCCCCChHHHHHHHHHhhhhh
Confidence            66     6778888999998887775433

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=99.10  E-value=2.3e-10  Score=123.21  Aligned_cols=116  Identities=29%  Similarity=0.487  Sum_probs=98.3

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhc---------------------------------------CCEEEEeCCCCHHHHH
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSI---------------------------------------IASEALHGDISQHQRE   90 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~---------------------------------------~~~~~lhg~~~~~~R~   90 (456)
                      .+.++||||++|..|+.+|..+...                                       +.++++|.+++.++|+
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            4557999999999999988666421                                       1478899999999999


Q ss_pred             HHHhcccCCCeEEEEeccccccccCcCccceEEec---C-CCCChhHHHHHhcccccCC--CCceEEEeeChhhHHHHHH
Q 012794           91 RTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY---E-LPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRS  164 (456)
Q Consensus        91 ~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~---~-~p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~e~~~~~~  164 (456)
                      .+...|++|.+.|++||+.++.|+++|...++|-+   + .+.+.-.|.||+|||||+|  ..|.+|+++.+.+......
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            99999999999999999999999999999998853   3 2347889999999999998  5589999999888765554


Q ss_pred             H
Q 012794          165 L  165 (456)
Q Consensus       165 i  165 (456)
                      +
T Consensus       619 l  619 (1008)
T KOG0950|consen  619 L  619 (1008)
T ss_pred             H
Confidence            3

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=99.03  E-value=1.8e-09  Score=116.01  Aligned_cols=106  Identities=28%  Similarity=0.416  Sum_probs=91.0

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-cC---------------------------------------CEEEEeCCCCHHHHHH
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-II---------------------------------------ASEALHGDISQHQRER   91 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-~~---------------------------------------~~~~lhg~~~~~~R~~   91 (456)
                      -++||||-+++.|++.|+.|.. .+                                       .++++||++-+-.++-
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            4899999999999999999864 11                                       4788999999999999


Q ss_pred             HHhcccCCCeEEEEeccccccccCcCccceEEec----C----CCCChhHHHHHhcccccCC--CCceEEEeeChh
Q 012794           92 TLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY----E----LPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  157 (456)
Q Consensus        92 ~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~----~----~p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~  157 (456)
                      +.--|..|-++||+||...|+|+|+|.-.+|+..    |    .-..+-.|.|++|||||-|  .+|++|++....
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            9999999999999999999999999998888832    1    1236789999999999987  778888887643

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

Probab=99.03  E-value=1.8e-09  Score=120.16  Aligned_cols=151  Identities=23%  Similarity=0.400  Sum_probs=117.8

Q ss_pred             ccccCeeEEEEEcC---------cccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHH----HHH-hc----CCEEEE
Q 012794           20 KLAEGIKLYAISTT---------ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSL----ALT-SI----IASEAL   80 (456)
Q Consensus        20 ~~~~~i~~~~~~~~---------~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~----~L~-~~----~~~~~l   80 (456)
                      ..+...+++.+..+         ..++...+..++... ..+-++|+|+.++..|+.++.    .+. ..    ..+..+
T Consensus       265 g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~  344 (851)
T COG1205         265 GSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTY  344 (851)
T ss_pred             CCCCCceEEEEeCCcchhhhhhcccchHHHHHHHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeec
Confidence            33445556666555         235555556555543 456799999999999999973    332 22    357888


Q ss_pred             eCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCC-ChhHHHHHhcccccCCCCceEEEeeC--hh
Q 012794           81 HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFT--SS  157 (456)
Q Consensus        81 hg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~~~~--~~  157 (456)
                      +++|...+|.+++..|++|++.++++|++++-||||-+++.||.++.|. +..+++||.||+||.++....++++.  +.
T Consensus       345 ~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~  424 (851)
T COG1205         345 RAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPL  424 (851)
T ss_pred             cccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCcc
Confidence            9999999999999999999999999999999999999999999999999 89999999999999987776666654  33


Q ss_pred             hHHHHHHHHHHhC
Q 012794          158 QRRTVRSLERDVG  170 (456)
Q Consensus       158 e~~~~~~ie~~~~  170 (456)
                      +..++..-+....
T Consensus       425 d~yy~~~p~~~~~  437 (851)
T COG1205         425 DSYYLRHPEELLE  437 (851)
T ss_pred             chhhhhCcHhhhh
Confidence            5566666666655

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=98.99  E-value=7.1e-09  Score=114.07  Aligned_cols=140  Identities=21%  Similarity=0.352  Sum_probs=106.0

Q ss_pred             CeeEEEEEcCcc---cHHHHHHH-----HHHHHCCCCcEEEEcCChHHHHHHHHHHHhc---------------------
Q 012794           24 GIKLYAISTTAT---SKRTILSD-----LITVYAKGGKTIVFTQTKRDADEVSLALTSI---------------------   74 (456)
Q Consensus        24 ~i~~~~~~~~~~---~k~~~L~~-----ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~---------------------   74 (456)
                      .++|.++-+..+   .+.++.++     +++... ..++|||+.+++++.+.|..++..                     
T Consensus       512 PL~qq~Igi~ek~~~~~~qamNe~~yeKVm~~ag-k~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eil  590 (1674)
T KOG0951|consen  512 PLKQQYIGITEKKPLKRFQAMNEACYEKVLEHAG-KNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREIL  590 (1674)
T ss_pred             CccceEeccccCCchHHHHHHHHHHHHHHHHhCC-CCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhh
Confidence            456666655443   23333333     333333 489999999999999888877621                     


Q ss_pred             -----------------CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEE----ecCC------
Q 012794           75 -----------------IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII----HYEL------  127 (456)
Q Consensus        75 -----------------~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI----~~~~------  127 (456)
                                       +..+.+|++|+..+|..+.+.|++|.++|||+|-.+|+|+|+|.-+++|    -|++      
T Consensus       591 rtea~~~kn~dLkdLLpygfaIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~  670 (1674)
T KOG0951|consen  591 RTEAGQAKNPDLKDLLPYGFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWT  670 (1674)
T ss_pred             hhhhhcccChhHHHHhhccceeeccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccc
Confidence                             2478899999999999999999999999999999999999999988888    3543      


Q ss_pred             CCChhHHHHHhcccccCC--CCceEEEeeChhhHHHHHH
Q 012794          128 PNDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRS  164 (456)
Q Consensus       128 p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~e~~~~~~  164 (456)
                      +.++.+.+||.||+||.+  ..|..+++....+..+...
T Consensus       671 elsp~dv~qmlgragrp~~D~~gegiiit~~se~qyyls  709 (1674)
T KOG0951|consen  671 ELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSELQYYLS  709 (1674)
T ss_pred             cCCHHHHHHHHhhcCCCccCcCCceeeccCchHhhhhHH
Confidence            347899999999999976  4567777766666554444

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.98  E-value=7.2e-09  Score=105.99  Aligned_cols=143  Identities=20%  Similarity=0.298  Sum_probs=113.7

Q ss_pred             CCCCcEEEEcCChHHHHHHHHHHHhcC---------CEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCcc
Q 012794           49 AKGGKTIVFTQTKRDADEVSLALTSII---------ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNV  119 (456)
Q Consensus        49 ~~~~~~IIF~~t~~~a~~l~~~L~~~~---------~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v  119 (456)
                      ..+-++|-||+.++.|+.|....++.+         .+..+.|+.+.++|.++...+-.|+..-+|||++++-||||..+
T Consensus       523 ~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~L  602 (1034)
T KOG4150|consen  523 QHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHL  602 (1034)
T ss_pred             HcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccc
Confidence            456799999999999998866554321         24556799999999999999999999999999999999999999


Q ss_pred             ceEEecCCCCChhHHHHHhcccccCCCCceEEEee--ChhhHHHHHHHHHHhCCCceecCCCCHH-HHHHHHHHH
Q 012794          120 DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF--TSSQRRTVRSLERDVGCKFEFVSPPVVE-DVLESSAEQ  191 (456)
Q Consensus       120 ~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~--~~~e~~~~~~ie~~~~~~~~~~~~p~~~-~i~~~~~~~  191 (456)
                      +.|++.++|.+...+.|..||+||.++...++.++  .|-+..++..-+..+..+-..+.+.... -++..+++-
T Consensus       603 DAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y~~HP~~l~~~pN~EL~LD~~N~~iL~~HlQC  677 (1034)
T KOG4150|consen  603 DAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYYMSHPDKLFGSPNEELHLDSQNKHVLMQHLQC  677 (1034)
T ss_pred             eeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHhhcCcHHHhCCCcceeEEecccHHHHHHHHhH
Confidence            99999999999999999999999998887665554  4667888887777777655555444443 333444433

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=98.89  E-value=9.4e-09  Score=105.20  Aligned_cols=163  Identities=19%  Similarity=0.224  Sum_probs=112.5

Q ss_pred             ccCCCccccCCcccccccCeeEEEE-EcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh--cCCEEEEeC
Q 012794            6 VMFSHSTQVGNQDEKLAEGIKLYAI-STTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHG   82 (456)
Q Consensus         6 ~~~~~i~~v~~~~~~~~~~i~~~~~-~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~--~~~~~~lhg   82 (456)
                      ..+..+++|.+--..+.++++...+ ...+-.-.+.+..-++.+. .+.||| |-+++.+-.+...+.+  ...+++++|
T Consensus       312 GepsvldlV~~i~k~TGd~vev~~YeRl~pL~v~~~~~~sl~nlk-~GDCvV-~FSkk~I~~~k~kIE~~g~~k~aVIYG  389 (700)
T KOG0953|consen  312 GEPSVLDLVRKILKMTGDDVEVREYERLSPLVVEETALGSLSNLK-PGDCVV-AFSKKDIFTVKKKIEKAGNHKCAVIYG  389 (700)
T ss_pred             CCchHHHHHHHHHhhcCCeeEEEeecccCcceehhhhhhhhccCC-CCCeEE-EeehhhHHHHHHHHHHhcCcceEEEec
Confidence            3566777777666677777665544 2322222222233333333 455655 3366778888888874  356999999


Q ss_pred             CCCHHHHHHHHhcccC--CCeEEEEeccccccccCcCccceEEecCC---------CCChhHHHHHhcccccCC---CCc
Q 012794           83 DISQHQRERTLNGFRQ--GKFTVLVATDVAARGLDIPNVDLIIHYEL---------PNDPETFVHRSGRTGRAG---KEG  148 (456)
Q Consensus        83 ~~~~~~R~~~l~~Fr~--g~~~vLVaTdv~~~Gidip~v~~VI~~~~---------p~~~~~y~qr~GR~gR~g---~~g  148 (456)
                      +||++.|.+.-..|.+  +..+||||||+..+|+|+ ++..||.|++         |.++.+..|-+|||||.|   ..|
T Consensus       390 sLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G  468 (700)
T KOG0953|consen  390 SLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQG  468 (700)
T ss_pred             CCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCc
Confidence            9999999999999987  789999999999999998 5777777664         346888999999999986   346


Q ss_pred             eEEEeeChhhHHHHHHHHHHhCCCcee
Q 012794          149 TAILMFTSSQRRTVRSLERDVGCKFEF  175 (456)
Q Consensus       149 ~~i~~~~~~e~~~~~~ie~~~~~~~~~  175 (456)
                      .+.++..    +.+..+.+.+..++++
T Consensus       469 ~vTtl~~----eDL~~L~~~l~~p~ep  491 (700)
T KOG0953|consen  469 EVTTLHS----EDLKLLKRILKRPVEP  491 (700)
T ss_pred             eEEEeeH----hhHHHHHHHHhCCchH
Confidence            6666644    3455555555544443

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.89  E-value=1.4e-08  Score=107.48  Aligned_cols=115  Identities=23%  Similarity=0.384  Sum_probs=86.1

Q ss_pred             EEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCC--------C----------ChhHHHHHh
Q 012794           77 SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP--------N----------DPETFVHRS  138 (456)
Q Consensus        77 ~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p--------~----------~~~~y~qr~  138 (456)
                      |.+|++=|+.+.+.++++.--.|..-++|||+||+..|.||.|.+||+.+.-        .          +..+--||+
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            4556777889999999999999998999999999999999999999975532        2          344558999


Q ss_pred             cccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCCCHHHHHHHHHHHHHHHHhcCCcchhh
Q 012794          139 GRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVE  205 (456)
Q Consensus       139 GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p~~~~i~~~~~~~~~~~l~~~~~~~~~  205 (456)
                      ||+||.| .|.||-+|+..=.          ...|+..   +..+|++...+.++..++.+.-..+.
T Consensus       687 GRAGRtg-pGHcYRLYSSAVf----------~~~Fe~f---S~PEIlk~Pve~lvLqMKsMnI~kVv  739 (1172)
T KOG0926|consen  687 GRAGRTG-PGHCYRLYSSAVF----------SNDFEEF---SLPEILKKPVESLVLQMKSMNIDKVV  739 (1172)
T ss_pred             cccCCCC-CCceeehhhhHHh----------hcchhhh---ccHHHhhCcHHHHHHHHHhcCcccee
Confidence            9999997 8999999976321          1122222   23467777777888777776554433

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.89  E-value=2.2e-08  Score=108.90  Aligned_cols=99  Identities=25%  Similarity=0.467  Sum_probs=79.5

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCC---hHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhc
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQT---KRDADEVSLALTS-IIASEALHGDISQHQRERTLNG   95 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t---~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~   95 (456)
                      ....+|.+.|+..   .-...+..+++.+..  -.|||+++   ++.|++|++.|.. ++.+..+|+.     .++.++.
T Consensus       309 ~~LRNIvD~y~~~---~~~e~~~elvk~lG~--GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~  378 (1187)
T COG1110         309 EGLRNIVDIYVES---ESLEKVVELVKKLGD--GGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KEEALED  378 (1187)
T ss_pred             hhhhheeeeeccC---ccHHHHHHHHHHhCC--CeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----chhhhhh
Confidence            4456777777766   334445566766643  57999999   9999999999995 7999999985     3788999


Q ss_pred             ccCCCeEEEEec----cccccccCcC-ccceEEecCCC
Q 012794           96 FRQGKFTVLVAT----DVAARGLDIP-NVDLIIHYELP  128 (456)
Q Consensus        96 Fr~g~~~vLVaT----dv~~~Gidip-~v~~VI~~~~p  128 (456)
                      |..|++++||.+    .++-||||+| .+.++|.|+.|
T Consensus       379 F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvP  416 (1187)
T COG1110         379 FEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVP  416 (1187)
T ss_pred             hccCceeEEEEecccccceeecCCchhheeEEEEecCC
Confidence            999999999876    5899999999 56788888866

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=98.87  E-value=2.4e-08  Score=108.60  Aligned_cols=122  Identities=20%  Similarity=0.364  Sum_probs=96.0

Q ss_pred             HHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-c-----------------------CCEEEEeCCCCHHHHHHHHhcccC
Q 012794           43 DLITVYAKGGKTIVFTQTKRDADEVSLALTS-I-----------------------IASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        43 ~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~-----------------------~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      ++++.+..+.+++|||.++..+...|+.|.+ .                       .....+|++|....|..+.+.|+.
T Consensus       341 kv~e~~~~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~  420 (1230)
T KOG0952|consen  341 KVVEFLQEGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKE  420 (1230)
T ss_pred             HHHHHHHcCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhc
Confidence            3444556678999999999999999988863 1                       135678999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEE----ecCCC------CChhHHHHHhcccccCC--CCceEEEeeChhhHHHHHH
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLII----HYELP------NDPETFVHRSGRTGRAG--KEGTAILMFTSSQRRTVRS  164 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI----~~~~p------~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~e~~~~~~  164 (456)
                      |.++||+||..+|+|+|+|+-.+||    .||.-      ..+-+.+|..|||||..  ..|.++++.+......+..
T Consensus       421 G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~Y~s  498 (1230)
T KOG0952|consen  421 GHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDHYES  498 (1230)
T ss_pred             CCceEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHHHHH
Confidence            9999999999999999999765555    23322      24667899999999965  7799998877654444433

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.79  E-value=6.6e-08  Score=105.02  Aligned_cols=123  Identities=23%  Similarity=0.319  Sum_probs=97.2

Q ss_pred             CcccHHHHHHH-HHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCC-CeEEEEeccc
Q 012794           33 TATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFTVLVATDV  109 (456)
Q Consensus        33 ~~~~k~~~L~~-ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g-~~~vLVaTdv  109 (456)
                      ....|..++.. +...+.++.++||.|.|.+..+.|+..|.+ ++...+|+..  +.+++..+-+ +.| .-.|.|||++
T Consensus       407 t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk--~~e~EA~IIa-~AG~~GaVTIATNM  483 (925)
T PRK12903        407 TKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAK--QNAREAEIIA-KAGQKGAITIATNM  483 (925)
T ss_pred             cHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeeccc--chhhHHHHHH-hCCCCCeEEEeccc
Confidence            44456555544 555667788999999999999999999995 7888888886  4455544433 334 3578999999


Q ss_pred             cccccCcCccc--------eEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          110 AARGLDIPNVD--------LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       110 ~~~Gidip~v~--------~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      |.||.||.--.        |||....|.+...--|..||+||.|.+|.+-.|++-.+
T Consensus       484 AGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD  540 (925)
T PRK12903        484 AGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDD  540 (925)
T ss_pred             ccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecch
Confidence            99999986322        89999999999999999999999999999888876544

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

Probab=98.78  E-value=5.2e-08  Score=101.12  Aligned_cols=119  Identities=21%  Similarity=0.297  Sum_probs=89.4

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh---c--CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec-----cccccc-cCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS---I--IASEALHGDISQHQRERTLNGFRQGKFTVLVAT-----DVAARG-LDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~---~--~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT-----dv~~~G-idip~v  119 (456)
                      ...+||.++|++.|.++.+.+..   .  +.+.+++|+.+...+..-+++    .++|+|||     |.+..| +|+..|
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            34699999999999999888764   2  559999999999999888887    78999999     578888 999999


Q ss_pred             ceEE--------ecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCC
Q 012794          120 DLII--------HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  179 (456)
Q Consensus       120 ~~VI--------~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p  179 (456)
                      .++|        ++++-.+++.+++.+.++-|      ..++++.+-...++.|...+-.....+.+-
T Consensus       241 ~ylVLDEADrMldmGFe~qI~~Il~~i~~~~r------Qtlm~saTwp~~v~~lA~~fl~~~~~i~ig  302 (519)
T KOG0331|consen  241 TYLVLDEADRMLDMGFEPQIRKILSQIPRPDR------QTLMFSATWPKEVRQLAEDFLNNPIQINVG  302 (519)
T ss_pred             eEEEeccHHhhhccccHHHHHHHHHhcCCCcc------cEEEEeeeccHHHHHHHHHHhcCceEEEec
Confidence            9988        56677789999999988766      344444444444555544433244444433

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=98.77  E-value=6.4e-09  Score=109.38  Aligned_cols=106  Identities=25%  Similarity=0.423  Sum_probs=90.3

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhc-C---------------------------------------CEEEEeCCCCHHHHH
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSI-I---------------------------------------ASEALHGDISQHQRE   90 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~-~---------------------------------------~~~~lhg~~~~~~R~   90 (456)
                      ..++|||+-++++|+.+|..+.+. +                                       .+.++|++|-+--++
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            468999999999999999888642 1                                       477889999999999


Q ss_pred             HHHhcccCCCeEEEEeccccccccCcCccceEEe----cCCC----CChhHHHHHhcccccCC--CCceEEEeeCh
Q 012794           91 RTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YELP----NDPETFVHRSGRTGRAG--KEGTAILMFTS  156 (456)
Q Consensus        91 ~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~----~~~p----~~~~~y~qr~GR~gR~g--~~g~~i~~~~~  156 (456)
                      .+.--|.+|-+++|+||...+.|||+|.-++|+-    ||--    .+.-.|+|++|||||-|  ..|.||+++..
T Consensus       463 ~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDe  538 (1041)
T KOG0948|consen  463 VIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDE  538 (1041)
T ss_pred             HHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccCCcceeeecccceEEecccccccCCCCCceEEEEecC
Confidence            9999999999999999999999999999888873    3321    26678999999999988  45888888864

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

Probab=98.74  E-value=1.2e-06  Score=94.15  Aligned_cols=118  Identities=16%  Similarity=0.281  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHhc--------CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEe
Q 012794           38 RTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI--------IASEALHGDISQHQRERTLNGFRQGKFTVLVA  106 (456)
Q Consensus        38 ~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~~--------~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVa  106 (456)
                      ..++..++..+   .-.+-++||.+-....-.|...|..+        +.+..+|+.++..++.++.+....+..++++.
T Consensus       627 f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~s  706 (1282)
T KOG0921|consen  627 FGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILS  706 (1282)
T ss_pred             hHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccc
Confidence            34444444433   22568999999999998888877532        56888999999999999999999999999999


Q ss_pred             ccccccccCcCccceEEecCC------------------CCChhHHHHHhcccccCCCCceEEEeeCh
Q 012794          107 TDVAARGLDIPNVDLIIHYEL------------------PNDPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       107 Tdv~~~Gidip~v~~VI~~~~------------------p~~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      |.++..-|.+.++..||+.+.                  -.+....+||.||++|. ++|.|..+++.
T Consensus       707 tniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~lcs~  773 (1282)
T KOG0921|consen  707 TNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFHLCSR  773 (1282)
T ss_pred             cceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccccccHH
Confidence            999999999999888775442                  12556679999999997 57888877654

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.73  E-value=3.6e-08  Score=109.02  Aligned_cols=116  Identities=23%  Similarity=0.321  Sum_probs=93.1

Q ss_pred             HHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhcC-CEEEEeCCCCHHHHHHHHhccc----CCCeEEEEecccccccc
Q 012794           40 ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSII-ASEALHGDISQHQRERTLNGFR----QGKFTVLVATDVAARGL  114 (456)
Q Consensus        40 ~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~~-~~~~lhg~~~~~~R~~~l~~Fr----~g~~~vLVaTdv~~~Gi  114 (456)
                      .+..+......+.+++|-|||+..|.+++..|+... .+..+|+.+....|.+.++.++    .....|+|||.|++.|+
T Consensus       429 ~~~~~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagv  508 (733)
T COG1203         429 LIELISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGV  508 (733)
T ss_pred             hhhcchhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEe
Confidence            344444555677899999999999999999999644 5999999999999998887544    45778999999999999


Q ss_pred             CcCccceEEecCCCCChhHHHHHhcccccCC--CCceEEEeeChhh
Q 012794          115 DIPNVDLIIHYELPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQ  158 (456)
Q Consensus       115 dip~v~~VI~~~~p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~e  158 (456)
                      |++ .+++|-=  +..+++++||+||++|-|  ..+..+++.....
T Consensus       509 Did-fd~mITe--~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~~~  551 (733)
T COG1203         509 DID-FDVLITE--LAPIDSLIQRAGRVNRHGKKENGKIYVYNDEER  551 (733)
T ss_pred             ccc-cCeeeec--CCCHHHHHHHHHHHhhcccccCCceeEeecccC
Confidence            996 6665532  345889999999999999  5677777765443

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=98.71  E-value=8.4e-08  Score=105.89  Aligned_cols=136  Identities=18%  Similarity=0.351  Sum_probs=113.4

Q ss_pred             cccHHHHHHHHHHHHC-CCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccC---CCeEEEEecc
Q 012794           34 ATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQ---GKFTVLVATD  108 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~~-~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~---g~~~vLVaTd  108 (456)
                      ..-|+.+|..||..+. .+.++|||.......+-|+++|. ++|...-|-|.+.-+.|+.+++.|..   ..+-.|+||-
T Consensus       681 sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTR  760 (1373)
T KOG0384|consen  681 SSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTR  760 (1373)
T ss_pred             hcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecc
Confidence            3456677777776663 35799999999999999999999 58999999999999999999999986   3578999999


Q ss_pred             ccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCce--EEEeeChh--hHHHHHHHHHHh
Q 012794          109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGT--AILMFTSS--QRRTVRSLERDV  169 (456)
Q Consensus       109 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~--~i~~~~~~--e~~~~~~ie~~~  169 (456)
                      +..-|||+-..+.||.||-.|++..-+|...||+|.|++-.  +|-|++..  |..++++..+.+
T Consensus       761 AGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEilERAk~Km  825 (1373)
T KOG0384|consen  761 AGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEILERAKLKM  825 (1373)
T ss_pred             cCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999997754  45556543  455555443333

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.67  E-value=4e-07  Score=97.70  Aligned_cols=124  Identities=21%  Similarity=0.257  Sum_probs=95.1

Q ss_pred             CcccHHHHHH-HHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccc
Q 012794           33 TATSKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  110 (456)
Q Consensus        33 ~~~~k~~~L~-~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~  110 (456)
                      ....|..++. ++...+..+.++||.|.+.+..+.|+..|.+ +++..+|+..-...+-+.+-++=+  .-.|.|||++|
T Consensus       408 t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa~AG~--~gaVTIATNMA  485 (764)
T PRK12326        408 TAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEEARIIAEAGK--YGAVTVSTQMA  485 (764)
T ss_pred             CHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhHHHHHHhcCC--CCcEEEEecCC
Confidence            3445655444 4556677889999999999999999999995 788888988633222222223222  34689999999


Q ss_pred             ccccCcC----------cc-----ceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          111 ARGLDIP----------NV-----DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       111 ~~Gidip----------~v-----~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      .||.||.          .|     -|||-...|.+...-.|-.||+||.|.+|.+..|++-.+
T Consensus       486 GRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleD  548 (764)
T PRK12326        486 GRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLED  548 (764)
T ss_pred             CCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            9999986          22     279999999999999999999999999999988887544

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=98.63  E-value=1.7e-07  Score=101.39  Aligned_cols=128  Identities=19%  Similarity=0.250  Sum_probs=96.6

Q ss_pred             eEEEEEcCcccHHHHHHHHHHHHCC--CCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCC--
Q 012794           26 KLYAISTTATSKRTILSDLITVYAK--GGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK--  100 (456)
Q Consensus        26 ~~~~~~~~~~~k~~~L~~ll~~~~~--~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~--  100 (456)
                      ++.........|+..|..++.....  ..++++..|.+...+.+..... .++.+..|||.|+..+|+.+++.|.+..  
T Consensus       568 ~~~~~~~~ks~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~  647 (776)
T KOG0390|consen  568 KLDAGDGSKSGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESP  647 (776)
T ss_pred             ccccccchhhhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCC
Confidence            3333334445678888888754421  1233333444544444444443 4789999999999999999999998743  


Q ss_pred             -eEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794          101 -FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus       101 -~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                       .-.|.+|.+.+.||++-..+.||.||++|++..-.|++.|+.|.|++-.|+++
T Consensus       648 ~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iY  701 (776)
T KOG0390|consen  648 SFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIY  701 (776)
T ss_pred             ceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEE
Confidence             23556788999999999999999999999999999999999999999888876

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=98.61  E-value=2.6e-07  Score=97.86  Aligned_cols=139  Identities=20%  Similarity=0.350  Sum_probs=115.4

Q ss_pred             cCcccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCC---eEEEEe
Q 012794           32 TTATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK---FTVLVA  106 (456)
Q Consensus        32 ~~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~---~~vLVa  106 (456)
                      +...-|+.+|..||..+ ..+.++|||.......+-|..++. ++|...-|-|.++.++|...++.|....   +-.|++
T Consensus       467 v~nSGKm~vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLS  546 (971)
T KOG0385|consen  467 VTNSGKMLVLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLS  546 (971)
T ss_pred             HhcCcceehHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEe
Confidence            45567999999988765 567899999999999998888887 6788999999999999999999998643   557899


Q ss_pred             ccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe--eChh--hHHHHHHHHHHhC
Q 012794          107 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM--FTSS--QRRTVRSLERDVG  170 (456)
Q Consensus       107 Tdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~--~~~~--e~~~~~~ie~~~~  170 (456)
                      |-+..-|||+...+.||.||..|++..-+|..-||+|.|++..+.+|  ++..  |...+++.+.++.
T Consensus       547 TRAGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentVEe~IveRA~~KL~  614 (971)
T KOG0385|consen  547 TRAGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTVEEKIVERAAAKLR  614 (971)
T ss_pred             ccccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccchHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999977655544  5543  4455555555443

>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=98.60  E-value=4.4e-08  Score=76.22  Aligned_cols=61  Identities=21%  Similarity=0.401  Sum_probs=48.7

Q ss_pred             EEEEEeecCccccCCCChhHHHHHHHhhCCCCCCccccEEEeecCccceeeeecCHHHHHHHHhhcCC
Q 012794          250 VTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIP  317 (456)
Q Consensus       250 ~t~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~ig~i~~~~~~~~~~~~~dv~~~~a~~~~~~~~~  317 (456)
                      ++++++.|+   +++++|++|+++|++..++..++||+|+|.++|    |+|+||+++++++++....
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            589999998   899999999999999999999999999999999    7999999999999987553

; PDB: 2G0C_A 3MOJ_B.

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.56  E-value=1.4e-06  Score=95.97  Aligned_cols=124  Identities=23%  Similarity=0.300  Sum_probs=96.0

Q ss_pred             cCcccHHHH-HHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCC-CeEEEEecc
Q 012794           32 TTATSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFTVLVATD  108 (456)
Q Consensus        32 ~~~~~k~~~-L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g-~~~vLVaTd  108 (456)
                      .....|..+ +.+++..+..+.++||-|.+.+..+.|+..|.+ ++...+|+..  +.+++..+-+ ..| .-.|.|||+
T Consensus       548 ~t~~~k~~ai~~ei~~~~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak--~~~~Ea~iia-~AG~~g~VTIATN  624 (970)
T PRK12899        548 MTEREKYHAIVAEIASIHRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAK--NHAQEAEIIA-GAGKLGAVTVATN  624 (970)
T ss_pred             cCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccc--hhhhHHHHHH-hcCCCCcEEEeec
Confidence            333456544 455667777788999999999999999999985 7888888886  3344433322 123 346899999


Q ss_pred             ccccccCcC---ccc-----eEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          109 VAARGLDIP---NVD-----LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       109 v~~~Gidip---~v~-----~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      +|.||.||.   .|.     |||....|.+...--|-.||+||.|.+|.+..|++-.+
T Consensus       625 mAGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlED  682 (970)
T PRK12899        625 MAGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFED  682 (970)
T ss_pred             cccCCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            999999984   222     79999999999999999999999999999988887554

>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=98.53  E-value=4.7e-08  Score=54.14  Aligned_cols=17  Identities=59%  Similarity=1.499  Sum_probs=16.1

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
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            49999999999999996

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 ....

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.48  E-value=9e-07  Score=97.81  Aligned_cols=119  Identities=21%  Similarity=0.345  Sum_probs=102.2

Q ss_pred             ccHHHHHHHHHHHHC---------------CCCcEEEEcCChHHHHHHHHHHHh-cC-CE--EEEeCCCCHHHHHHHHhc
Q 012794           35 TSKRTILSDLITVYA---------------KGGKTIVFTQTKRDADEVSLALTS-II-AS--EALHGDISQHQRERTLNG   95 (456)
Q Consensus        35 ~~k~~~L~~ll~~~~---------------~~~~~IIF~~t~~~a~~l~~~L~~-~~-~~--~~lhg~~~~~~R~~~l~~   95 (456)
                      ..|+.+|..||....               .+.++||||.-|..++.+.+.|.+ ++ .+  ..|-|.+++.+|.++.++
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            468999999987541               246899999999999999988875 33 23  367899999999999999


Q ss_pred             ccCC-CeEEE-EeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794           96 FRQG-KFTVL-VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus        96 Fr~g-~~~vL-VaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      |.++ .++|| ++|.|..-|+|+...+.||.++-.|++-.-+|.+-||+|.|++.++-++
T Consensus      1389 FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVNVy 1448 (1549)
T KOG0392|consen 1389 FNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVNVY 1448 (1549)
T ss_pred             hcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCceeeeee
Confidence            9998 78877 5778999999999999999999999999999999999999988766554

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.47  E-value=2.6e-06  Score=94.21  Aligned_cols=124  Identities=24%  Similarity=0.287  Sum_probs=95.4

Q ss_pred             CcccHHH-HHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccc
Q 012794           33 TATSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  110 (456)
Q Consensus        33 ~~~~k~~-~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~  110 (456)
                      ....|.. ++.++...+..+.++||-|.+.+..+.|+..|.. ++...+|+......+-+.+-++=+  .-.|-|||++|
T Consensus       609 t~~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~--~GaVTIATNMA  686 (1112)
T PRK12901        609 TKREKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQ--PGTVTIATNMA  686 (1112)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCC--CCcEEEeccCc
Confidence            3345654 4455666777889999999999999999999984 787777777643333333334323  33588999999


Q ss_pred             ccccCcC---cc-----ceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          111 ARGLDIP---NV-----DLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       111 ~~Gidip---~v-----~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      .||.||.   .|     -+||-...+.|...--|-.||+||.|.+|.+..|++-.+
T Consensus       687 GRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLED  742 (1112)
T PRK12901        687 GRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLED  742 (1112)
T ss_pred             CCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEccc
Confidence            9999985   22     379999999999999999999999999999888876544

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=98.43  E-value=1e-06  Score=93.77  Aligned_cols=121  Identities=18%  Similarity=0.347  Sum_probs=106.4

Q ss_pred             CcccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHH--hcCCEEEEeCCCCHHHHHHHHhcccCCC-eE-EEEec
Q 012794           33 TATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT--SIIASEALHGDISQHQRERTLNGFRQGK-FT-VLVAT  107 (456)
Q Consensus        33 ~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~--~~~~~~~lhg~~~~~~R~~~l~~Fr~g~-~~-vLVaT  107 (456)
                      ...-|+.+|..|+... ..+.++|+|..|+.+.+-|...|.  ++|...-+.|..+.+.|..+++.|.++. +. .|++|
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            3456899999998765 456799999999999999999998  4899999999999999999999999764 33 57889


Q ss_pred             cccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794          108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus       108 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      .|..-|+|+...+-||.||+.|++.+-.|..-|+.|.|++-.+++|
T Consensus       607 rvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VY  652 (923)
T KOG0387|consen  607 RVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVY  652 (923)
T ss_pred             cccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEE
Confidence            9999999999999999999999999999999999999977655554

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=98.43  E-value=1.9e-06  Score=94.71  Aligned_cols=120  Identities=20%  Similarity=0.339  Sum_probs=100.5

Q ss_pred             cccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCC--eEEEEeccc
Q 012794           34 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK--FTVLVATDV  109 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~--~~vLVaTdv  109 (456)
                      ..-|++.|.-||..+ ..+.++|||+...++.+-|...|. .++...-|.|...-++|+..+++|....  +..|++|-.
T Consensus      1258 DcGKLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrS 1337 (1958)
T KOG0391|consen 1258 DCGKLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRS 1337 (1958)
T ss_pred             ccchHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccC
Confidence            346788887777655 446799999999999999999998 4777888999999999999999998653  467788999


Q ss_pred             cccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794          110 AARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus       110 ~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      -..|||+-..+.||.||-.|++..-.|.--|+.|.|+...+.++
T Consensus      1338 ggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIY 1381 (1958)
T KOG0391|consen 1338 GGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIY 1381 (1958)
T ss_pred             CccccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEE
Confidence            99999999999999999999998888888888888866544444

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.40  E-value=4.5e-06  Score=91.78  Aligned_cols=124  Identities=25%  Similarity=0.304  Sum_probs=94.4

Q ss_pred             cCcccHHHHHH-HHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCC-CeEEEEecc
Q 012794           32 TTATSKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFTVLVATD  108 (456)
Q Consensus        32 ~~~~~k~~~L~-~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g-~~~vLVaTd  108 (456)
                      .....|..++. ++...+..+.++||-|.|.+..+.|+..|.+ ++...+|+..-.  +++..+-+ +.| .-.|.|||+
T Consensus       429 ~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk~~--~~EA~IIa-~AG~~GaVTIATN  505 (913)
T PRK13103        429 LTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAKYH--EKEAEIIA-QAGRPGALTIATN  505 (913)
T ss_pred             cCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccccc--hhHHHHHH-cCCCCCcEEEecc
Confidence            34445655544 4556667789999999999999999999985 777777777633  34433322 223 346899999


Q ss_pred             ccccccCcC--------------------------------cc-----ceEEecCCCCChhHHHHHhcccccCCCCceEE
Q 012794          109 VAARGLDIP--------------------------------NV-----DLIIHYELPNDPETFVHRSGRTGRAGKEGTAI  151 (456)
Q Consensus       109 v~~~Gidip--------------------------------~v-----~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i  151 (456)
                      +|.||.||.                                .|     -|||-...|.+...--|-.||+||.|.+|.+-
T Consensus       506 MAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~  585 (913)
T PRK13103        506 MAGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSR  585 (913)
T ss_pred             CCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceE
Confidence            999999984                                12     27888999999999999999999999999998


Q ss_pred             EeeChhh
Q 012794          152 LMFTSSQ  158 (456)
Q Consensus       152 ~~~~~~e  158 (456)
                      .|++-.+
T Consensus       586 f~lSlED  592 (913)
T PRK13103        586 FYLSLED  592 (913)
T ss_pred             EEEEcCc
Confidence            8887543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=98.36  E-value=1.4e-05  Score=84.03  Aligned_cols=67  Identities=22%  Similarity=0.392  Sum_probs=51.4

Q ss_pred             cEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----c-cccccCcCccce
Q 012794           53 KTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----V-AARGLDIPNVDL  121 (456)
Q Consensus        53 ~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v-~~~Gidip~v~~  121 (456)
                      ++||.|+|++.|.++.+.+..     .+.+..++|+++...+...+.    +..+|||||+     . ....+++..+.+
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            699999999999999988764     256778899998776554443    3679999995     2 234578888888


Q ss_pred             EE
Q 012794          122 II  123 (456)
Q Consensus       122 VI  123 (456)
                      ||
T Consensus       153 lV  154 (456)
T PRK10590        153 LV  154 (456)
T ss_pred             EE
Confidence            77

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

Probab=98.25  E-value=3.8e-06  Score=89.41  Aligned_cols=108  Identities=20%  Similarity=0.349  Sum_probs=75.4

Q ss_pred             EEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-cCcCccce
Q 012794           54 TIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNVDL  121 (456)
Q Consensus        54 ~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-idip~v~~  121 (456)
                      +||+++|++.|.++++.+..      .+.+..++|+++...+...++.   + .+|||||+     .+.++ +++..+.+
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            99999999999999998863      2568899999999888766666   4 99999995     67777 99999998


Q ss_pred             EE--------ecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCC
Q 012794          122 II--------HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCK  172 (456)
Q Consensus       122 VI--------~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~  172 (456)
                      +|        ++++..+++..+..+-.       -..+++++.+-...+..+.+.+-.+
T Consensus       178 lVlDEADrmLd~Gf~~~i~~I~~~~p~-------~~qtllfSAT~~~~i~~l~~~~l~~  229 (513)
T COG0513         178 LVLDEADRMLDMGFIDDIEKILKALPP-------DRQTLLFSATMPDDIRELARRYLND  229 (513)
T ss_pred             EEeccHhhhhcCCCHHHHHHHHHhCCc-------ccEEEEEecCCCHHHHHHHHHHccC
Confidence            88        45555566655555532       3344444433222455554444333

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

Probab=98.24  E-value=1.7e-06  Score=96.31  Aligned_cols=105  Identities=25%  Similarity=0.421  Sum_probs=87.6

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhc-----------------------------C-------------CEEEEeCCCCHHH
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSI-----------------------------I-------------ASEALHGDISQHQ   88 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~-----------------------------~-------------~~~~lhg~~~~~~   88 (456)
                      .-++|+|+-++..|+..+..+...                             +             .+.++|++|-+..
T Consensus       379 ~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~  458 (1041)
T COG4581         379 LLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAI  458 (1041)
T ss_pred             CCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHH
Confidence            468999999999999988776410                             0             2457899999999


Q ss_pred             HHHHHhcccCCCeEEEEeccccccccCcCccceEE----ecC----CCCChhHHHHHhcccccCC--CCceEEEeeC
Q 012794           89 RERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII----HYE----LPNDPETFVHRSGRTGRAG--KEGTAILMFT  155 (456)
Q Consensus        89 R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI----~~~----~p~~~~~y~qr~GR~gR~g--~~g~~i~~~~  155 (456)
                      ++.+...|..|.++||+||.+.+.|||+|.-++|+    .+|    -+.++..|+|+.||+||.|  ..|.+|++-.
T Consensus       459 K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~  535 (1041)
T COG4581         459 KELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEP  535 (1041)
T ss_pred             HHHHHHHHhccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecC
Confidence            99999999999999999999999999999988877    222    3457899999999999988  4577777743

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

Probab=98.16  E-value=1.8e-05  Score=78.39  Aligned_cols=249  Identities=16%  Similarity=0.193  Sum_probs=141.6

Q ss_pred             HHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc----
Q 012794           38 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD----  108 (456)
Q Consensus        38 ~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd----  108 (456)
                      +++|..|+... +.-.++|.++|++.|.++++.+..     ++.+.+|-|+|....+...+.+    +..|||||+    
T Consensus       117 LPIl~~LL~~p-~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~k----kPhilVaTPGrL~  191 (476)
T KOG0330|consen  117 LPILQRLLQEP-KLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSK----KPHILVATPGRLW  191 (476)
T ss_pred             HHHHHHHHcCC-CCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhc----CCCEEEeCcHHHH
Confidence            56666666532 336799999999999999988863     3679999999988766655544    678899996    


Q ss_pred             -cc--ccccCcCccceEE--------ecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecC
Q 012794          109 -VA--ARGLDIPNVDLII--------HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  177 (456)
Q Consensus       109 -v~--~~Gidip~v~~VI--------~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~  177 (456)
                       .+  ..|+.+..+.++|        +.|+-..++.++-.+-       ...-.++++.+-...+.+|.+..-..+..+.
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  3667776666544        6777777777777774       3344555555555666777665555555554


Q ss_pred             CCCHHHHHHHHHHHHHHHHhcCCcchhhhhH-HHHHHHHh--------hcCHHHHHHHHHHHhCCCCCCC---------C
Q 012794          178 PPVVEDVLESSAEQVVATLNGVHPESVEFFT-PTAQRLIE--------EKGTDALAAALAQLSGFSRPPS---------S  239 (456)
Q Consensus       178 ~p~~~~i~~~~~~~~~~~l~~~~~~~~~~~~-~~~~~ll~--------~~~~~~~a~ala~~~~~~~~~~---------~  239 (456)
                      .++.-..+    ..+.+....+.....+.|. .++.++..        ........+.+...+|+...+-         .
T Consensus       265 ~s~ky~tv----~~lkQ~ylfv~~k~K~~yLV~ll~e~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rl  340 (476)
T KOG0330|consen  265 VSSKYQTV----DHLKQTYLFVPGKDKDTYLVYLLNELAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRL  340 (476)
T ss_pred             ccchhcch----HHhhhheEeccccccchhHHHHHHhhcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHH
Confidence            44433322    2222222222222222221 12222211        1223445555555556543221         1


Q ss_pred             ccccCCCCceEEEEEeecCccccCCCChhHHHHHHHhhCCCCCCccccEEEeecCccceeeeecCHHHHHHHHhhcC--C
Q 012794          240 RSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQI--P  317 (456)
Q Consensus       240 r~l~~~~~g~~t~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~ig~i~~~~~~~~~~~~~dv~~~~a~~~~~~~~--~  317 (456)
                      -++...+.+...+++.+|.+                    ...-||..++++.||+    +.--..+|.+++.+...  .
T Consensus       341 g~l~~Fk~~~r~iLv~TDVa--------------------SRGLDip~Vd~VVNyD----iP~~skDYIHRvGRtaRaGr  396 (476)
T KOG0330|consen  341 GALNKFKAGARSILVCTDVA--------------------SRGLDIPHVDVVVNYD----IPTHSKDYIHRVGRTARAGR  396 (476)
T ss_pred             HHHHHHhccCCcEEEecchh--------------------cccCCCCCceEEEecC----CCCcHHHHHHHcccccccCC
Confidence            12223455555666666542                    2345788888888764    44444666677665433  2


Q ss_pred             CCCceeecc
Q 012794          318 PGNTISKIT  326 (456)
Q Consensus       318 ~g~~l~~~t  326 (456)
                      +|..++.+|
T Consensus       397 sG~~ItlVt  405 (476)
T KOG0330|consen  397 SGKAITLVT  405 (476)
T ss_pred             CcceEEEEe
Confidence            455555543

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

Probab=98.16  E-value=2.1e-05  Score=80.23  Aligned_cols=113  Identities=12%  Similarity=0.177  Sum_probs=78.6

Q ss_pred             cEEEEcCChHHHHHHHHHHH---h--cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc------ccccccCcCccce
Q 012794           53 KTIVFTQTKRDADEVSLALT---S--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVDL  121 (456)
Q Consensus        53 ~~IIF~~t~~~a~~l~~~L~---~--~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd------v~~~Gidip~v~~  121 (456)
                      -.||.|+|++.|.+|....+   +  ++.++++||+++.-++.+.|+.    ...|+|||+      |--.++|+..|.+
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            35788999999998865544   3  3779999999999999988884    778999996      3445699999998


Q ss_pred             EE--------ecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCcee
Q 012794          122 II--------HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF  175 (456)
Q Consensus       122 VI--------~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~  175 (456)
                      +|        ++++-..+.++.|.+    |  ....|++|.........+.....+.-++..
T Consensus       374 LV~DEadrmfdmGfe~qVrSI~~hi----r--pdrQtllFsaTf~~kIe~lard~L~dpVrv  429 (731)
T KOG0339|consen  374 LVLDEADRMFDMGFEPQVRSIKQHI----R--PDRQTLLFSATFKKKIEKLARDILSDPVRV  429 (731)
T ss_pred             EEEechhhhhccccHHHHHHHHhhc----C--CcceEEEeeccchHHHHHHHHHHhcCCeeE
Confidence            77        344455677777777    1  234555555554544444444555544443

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

Probab=98.15  E-value=2.1e-05  Score=80.34  Aligned_cols=125  Identities=14%  Similarity=0.209  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHH--CCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc--
Q 012794           38 RTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD--  108 (456)
Q Consensus        38 ~~~L~~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd--  108 (456)
                      +++|.+||-.-  ..-.++||.|+|++.+.+++....+     .+.+...-|+|+-.+++.+|..    ..+|+|||+  
T Consensus       237 lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs----~PDIVIATPGR  312 (691)
T KOG0338|consen  237 LPILERLLYRPKKVAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRS----RPDIVIATPGR  312 (691)
T ss_pred             HHHHHHHhcCcccCcceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhh----CCCEEEecchh
Confidence            45556655221  1235899999999999988776653     2556667799999999999988    788999996  


Q ss_pred             -----ccccccCcCccceEEecCCC--------CChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCc
Q 012794          109 -----VAARGLDIPNVDLIIHYELP--------NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKF  173 (456)
Q Consensus       109 -----v~~~Gidip~v~~VI~~~~p--------~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~  173 (456)
                           --..+.|+.++.++|.-...        .....+++.+       .+....++++.+-...++.|....-.+.
T Consensus       313 lIDHlrNs~sf~ldsiEVLvlDEADRMLeegFademnEii~lc-------pk~RQTmLFSATMteeVkdL~slSL~kP  383 (691)
T KOG0338|consen  313 LIDHLRNSPSFNLDSIEVLVLDEADRMLEEGFADEMNEIIRLC-------PKNRQTMLFSATMTEEVKDLASLSLNKP  383 (691)
T ss_pred             HHHHhccCCCccccceeEEEechHHHHHHHHHHHHHHHHHHhc-------cccccceeehhhhHHHHHHHHHhhcCCC
Confidence                 23456888888887753332        3344456655       3455667777766677777766643333

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.15  E-value=4.4e-05  Score=83.83  Aligned_cols=85  Identities=22%  Similarity=0.258  Sum_probs=60.7

Q ss_pred             CcccHHH-HHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccc
Q 012794           33 TATSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  110 (456)
Q Consensus        33 ~~~~k~~-~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~  110 (456)
                      ....|.. ++.++...+..+.++||-|.|.+..+.|+..|.. +++..+|++.-.+.+++..+-+=.-..-.|.|||++|
T Consensus       405 t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIA~AG~~G~VTIATNMA  484 (870)
T CHL00122        405 DELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPENVRRESEIVAQAGRKGSITIATNMA  484 (870)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCccchhHHHHHHhcCCCCcEEEecccc
Confidence            3334544 5556677778889999999999999999999985 7888899986323233332222122234689999999


Q ss_pred             ccccCcC
Q 012794          111 ARGLDIP  117 (456)
Q Consensus       111 ~~Gidip  117 (456)
                      .||.||-
T Consensus       485 GRGTDI~  491 (870)
T CHL00122        485 GRGTDII  491 (870)
T ss_pred             CCCcCee
Confidence            9998873

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

Probab=98.09  E-value=2.6e-05  Score=88.15  Aligned_cols=120  Identities=19%  Similarity=0.287  Sum_probs=103.6

Q ss_pred             cHHHHHHHHH-HH-HCCCC--cEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCC--CeEEEEecc
Q 012794           36 SKRTILSDLI-TV-YAKGG--KTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG--KFTVLVATD  108 (456)
Q Consensus        36 ~k~~~L~~ll-~~-~~~~~--~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g--~~~vLVaTd  108 (456)
                      .|...+.+++ .. .....  ++|||+......+.+...|.. .+....++|.++.+.|..+++.|.++  ..-+|++|.
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            6888888888 33 33445  899999999999999999986 46899999999999999999999985  445667788


Q ss_pred             ccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeC
Q 012794          109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT  155 (456)
Q Consensus       109 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~  155 (456)
                      +...|+|+...++||+||+.|++....|...|+.|.|++..+.++-.
T Consensus       772 agg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~  818 (866)
T COG0553         772 AGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRL  818 (866)
T ss_pred             ccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEEe
Confidence            99999999999999999999999999999999999998776665543

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=98.09  E-value=2e-05  Score=80.18  Aligned_cols=122  Identities=18%  Similarity=0.242  Sum_probs=99.2

Q ss_pred             ccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCC-CeEEE-Eecc
Q 012794           35 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFTVL-VATD  108 (456)
Q Consensus        35 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g-~~~vL-VaTd  108 (456)
                      +.|+++|.+-|...   ...-+.|||.......+.+.-.|.+ ++.|+-|.|.|++++|..+++.|++. .+.|+ |+-.
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            45777777655433   2335899999999999999999985 89999999999999999999999986 45554 5556


Q ss_pred             ccccccCcCccceEEecCCCCChhHHHHHhcccccCCC--CceEEEeeCh
Q 012794          109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK--EGTAILMFTS  156 (456)
Q Consensus       109 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~--~g~~i~~~~~  156 (456)
                      +....+|+....+|+.+|+-|++..-.|.--|..|.|+  +-.++.|+.+
T Consensus       699 AGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iE  748 (791)
T KOG1002|consen  699 AGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIE  748 (791)
T ss_pred             cCceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehh
Confidence            77777999999999999999999999999999999884  4456666554

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=98.07  E-value=1.8e-05  Score=83.50  Aligned_cols=119  Identities=18%  Similarity=0.313  Sum_probs=104.9

Q ss_pred             ccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCCe-EEEEeccccc
Q 012794           35 TSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKF-TVLVATDVAA  111 (456)
Q Consensus        35 ~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~-~vLVaTdv~~  111 (456)
                      +.|+..|..||..+ ..+.++|+|....++.+.+.++|. +++...-|.|...-..|..++..|+...+ -.|++|-+..
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            46888888888766 446799999999999999999998 57888999999999999999999998654 5678999999


Q ss_pred             cccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794          112 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus       112 ~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      -|||+...+.||.||..|++..-.|..-|+.|.|++..+.++
T Consensus      1107 LGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvy 1148 (1185)
T KOG0388|consen 1107 LGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVY 1148 (1185)
T ss_pred             ccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeee
Confidence            999999999999999999999999999999999977655444

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=98.06  E-value=3.8e-05  Score=78.38  Aligned_cols=110  Identities=24%  Similarity=0.337  Sum_probs=90.2

Q ss_pred             cCcccHHHHHHHHHHHHC-CCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccC-CCeEEEEeccc
Q 012794           32 TTATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQ-GKFTVLVATDV  109 (456)
Q Consensus        32 ~~~~~k~~~L~~ll~~~~-~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~-g~~~vLVaTdv  109 (456)
                      +-...|..+..-||+.+. .+.++|||....-...+.|-.|.+    ..|+|..+|.+|.++|+.|+- ..++-++-+.|
T Consensus       523 vMNP~KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~K----pfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKV  598 (776)
T KOG1123|consen  523 VMNPNKFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLGK----PFIYGPTSQNERMKILQNFQTNPKVNTIFLSKV  598 (776)
T ss_pred             ecCcchhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHcCC----ceEECCCchhHHHHHHHhcccCCccceEEEeec
Confidence            334457777777887664 467999999988777777666643    468999999999999999985 47888999999


Q ss_pred             cccccCcCccceEEecCCCC-ChhHHHHHhcccccCC
Q 012794          110 AARGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAG  145 (456)
Q Consensus       110 ~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g  145 (456)
                      ....||+|..+++|+..... +..+-.||.||.-|+.
T Consensus       599 gDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAK  635 (776)
T KOG1123|consen  599 GDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAK  635 (776)
T ss_pred             cCccccCCcccEEEEEcccccchHHHHHHHHHHHHHh
Confidence            99999999999999876554 6788899999999975

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

Probab=98.03  E-value=4.3e-05  Score=86.32  Aligned_cols=106  Identities=20%  Similarity=0.244  Sum_probs=77.2

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhc---CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccc--eEEe
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVD--LIIH  124 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~---~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~--~VI~  124 (456)
                      ..+++|||+++.+..+.++..|...   .....+..+.. ..|.++++.|++++..||++|+.+.+|||+|...  +||.
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            3578999999999999999998741   12233433333 5789999999999999999999999999999776  4666


Q ss_pred             cCCCCC------------------------------hhHHHHHhcccccCCCCceEEEeeCh
Q 012794          125 YELPND------------------------------PETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       125 ~~~p~~------------------------------~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      ..+|..                              ...+.|.+||.=|.....-+++++..
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            666532                              12247889999887644334444443

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.

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=98.03  E-value=1.6e-05  Score=86.56  Aligned_cols=83  Identities=28%  Similarity=0.456  Sum_probs=71.5

Q ss_pred             CEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecC-CCCChhHHHHHhcccccCC--CCceEEE
Q 012794           76 ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE-LPNDPETFVHRSGRTGRAG--KEGTAIL  152 (456)
Q Consensus        76 ~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~-~p~~~~~y~qr~GR~gR~g--~~g~~i~  152 (456)
                      .+.++|++|....|..+.--||.|...||+||..++-|||+|.-++|+--| +--++-.|.|++|||||-|  -.|.++.
T Consensus       964 GiG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~F 1043 (1330)
T KOG0949|consen  964 GIGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVF 1043 (1330)
T ss_pred             cccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEE
Confidence            366789999999999999999999999999999999999999888887666 4568999999999999988  4577666


Q ss_pred             eeChhh
Q 012794          153 MFTSSQ  158 (456)
Q Consensus       153 ~~~~~e  158 (456)
                      +--|..
T Consensus      1044 mgiP~~ 1049 (1330)
T KOG0949|consen 1044 MGIPRQ 1049 (1330)
T ss_pred             EeCcHH
Confidence            655543

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=98.01  E-value=4.4e-05  Score=81.69  Aligned_cols=123  Identities=20%  Similarity=0.326  Sum_probs=104.0

Q ss_pred             ccHHHHHHHHHHHHC-CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCC-e-EEEEecccc
Q 012794           35 TSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK-F-TVLVATDVA  110 (456)
Q Consensus        35 ~~k~~~L~~ll~~~~-~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~-~-~vLVaTdv~  110 (456)
                      +.|...|..||.... ++.++|||.......+-|...|.. .+...-|-|...-..|+.+++.|-..+ + -+|++|.+.
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            468888999887763 457999999999999888888874 678888999999999999999998653 4 467899999


Q ss_pred             ccccCcCccceEEecCCCCChhHHHHHhcccccCCCCc--eEEEeeChh
Q 012794          111 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEG--TAILMFTSS  157 (456)
Q Consensus       111 ~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g--~~i~~~~~~  157 (456)
                      ..|||+...++||.+|+..++-.-.|.--|++|.|++-  +++-|++..
T Consensus       840 G~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~  888 (941)
T KOG0389|consen  840 GFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKS  888 (941)
T ss_pred             cceecccccceEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEEecC
Confidence            99999999999999999999999999999999999664  444455543

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

Probab=97.98  E-value=3.7e-05  Score=83.06  Aligned_cols=92  Identities=25%  Similarity=0.366  Sum_probs=76.6

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhcC------CEEEEeCCCCHHHHHHHHhcccC--CCeEEEEeccccccccCcCccceE
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSII------ASEALHGDISQHQRERTLNGFRQ--GKFTVLVATDVAARGLDIPNVDLI  122 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~~------~~~~lhg~~~~~~R~~~l~~Fr~--g~~~vLVaTdv~~~Gidip~v~~V  122 (456)
                      -.|+||||.+..+|+.+...|.+.+      -+..+.++-.+.++  .++.|..  .-.+|.|+.|++..|||+|.|..+
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            3699999999999999999998532      37778888665543  3555544  345788999999999999999999


Q ss_pred             EecCCCCChhHHHHHhcccccC
Q 012794          123 IHYELPNDPETFVHRSGRTGRA  144 (456)
Q Consensus       123 I~~~~p~~~~~y~qr~GR~gR~  144 (456)
                      |.+-.-.|...|.|++||.-|.
T Consensus       504 VF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         504 VFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             eehhhhhhHHHHHHHhcCcccc
Confidence            9999999999999999999994

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

Probab=97.93  E-value=0.00013  Score=80.28  Aligned_cols=93  Identities=18%  Similarity=0.212  Sum_probs=73.8

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhc------CCEEEEeCCCCHH---------------------HHHHHHhcccC-CCeE
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSI------IASEALHGDISQH---------------------QRERTLNGFRQ-GKFT  102 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~------~~~~~lhg~~~~~---------------------~R~~~l~~Fr~-g~~~  102 (456)
                      ..+++|||.++..|..+++.|.+.      ..++++++.....                     ..+.++++|++ +.++
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            479999999999999999888643      2345566543322                     22478889986 5789


Q ss_pred             EEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccC
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRA  144 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~  144 (456)
                      |||++|++-.|+|.|.+++++..-+-.+. .++|.+||+-|.
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            99999999999999999998877766655 589999999993

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

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

Probab=97.89  E-value=3.5e-05  Score=83.97  Aligned_cols=102  Identities=25%  Similarity=0.458  Sum_probs=78.2

Q ss_pred             HHHHHHHHHh---cCCEEEEeCCCCHHH--HHHHHhcccCCCeEEEEeccccccccCcCccceEE--ecCC----CC---
Q 012794           64 ADEVSLALTS---IIASEALHGDISQHQ--RERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII--HYEL----PN---  129 (456)
Q Consensus        64 a~~l~~~L~~---~~~~~~lhg~~~~~~--R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI--~~~~----p~---  129 (456)
                      ++.+++.|.+   ...++.+-+|.+...  -+..+..|.+|+++|||.|.+++.|.|+|++++|.  +.|.    |+   
T Consensus       493 terieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA  572 (730)
T COG1198         493 TERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRA  572 (730)
T ss_pred             HHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcch
Confidence            4555555554   346777888766543  56789999999999999999999999999999866  4332    21   


Q ss_pred             ---ChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794          130 ---DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus       130 ---~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                         ....+.|-+||+||.+++|.+++-....+...++.+
T Consensus       573 ~Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~  611 (730)
T COG1198         573 SERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAIQAL  611 (730)
T ss_pred             HHHHHHHHHHHHhhhccCCCCCeEEEEeCCCCcHHHHHH
Confidence               356679999999999999999888776666666555

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.88  E-value=0.00029  Score=77.55  Aligned_cols=85  Identities=24%  Similarity=0.245  Sum_probs=60.4

Q ss_pred             CcccHHHHHH-HHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccc
Q 012794           33 TATSKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  110 (456)
Q Consensus        33 ~~~~k~~~L~-~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~  110 (456)
                      ....|..++. ++...+..+.++||-|.|.+..+.|+..|.+ ++...+|+..-.+.+++..+-+=.-..-.|-|||++|
T Consensus       420 t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIa~AG~~GaVTIATNMA  499 (939)
T PRK12902        420 TEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAKPENVEREAEIVAQAGRKGAVTIATNMA  499 (939)
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCCCcchHhHHHHHHhcCCCCcEEEeccCC
Confidence            3345655544 5666677889999999999999999999995 7888889886333333333222111133589999999


Q ss_pred             ccccCcC
Q 012794          111 ARGLDIP  117 (456)
Q Consensus       111 ~~Gidip  117 (456)
                      .||.||.
T Consensus       500 GRGTDIk  506 (939)
T PRK12902        500 GRGTDII  506 (939)
T ss_pred             CCCcCEe
Confidence            9998874

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=97.83  E-value=8.9e-05  Score=81.20  Aligned_cols=161  Identities=17%  Similarity=0.237  Sum_probs=120.7

Q ss_pred             cccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCC---eEEEEecc
Q 012794           34 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK---FTVLVATD  108 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~---~~vLVaTd  108 (456)
                      ..-|+++|.++|-.+ ..+.++|.||......+-+..+|. +.+...-|-|.....+|-..++.|..-.   +.+|..|-
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            357899999988766 447899999999988888888887 5677788899999999999999998754   45788999


Q ss_pred             ccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh----hHHHHHHHHHHhCCC-----ceecCCC
Q 012794          109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS----QRRTVRSLERDVGCK-----FEFVSPP  179 (456)
Q Consensus       109 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~----e~~~~~~ie~~~~~~-----~~~~~~p  179 (456)
                      ....|+|+.-++.||.||..|++....|+--|+.|.|+.-.+-++....    +..++.....+++..     ......-
T Consensus       788 agglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~tv~sveE~il~~a~~Kl~~d~kviqag~fdn~  867 (1157)
T KOG0386|consen  788 AGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLITVNSVEEKILAEAFYKLDVDGKVIQAGKFDNK  867 (1157)
T ss_pred             ccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeeehhhHHHHHHHHHHHHhcCchHhhhhcccccCC
Confidence            9999999999999999999999999999999999999776655554433    223333322223222     2223334


Q ss_pred             CHHHHHHHHHHHHHH
Q 012794          180 VVEDVLESSAEQVVA  194 (456)
Q Consensus       180 ~~~~i~~~~~~~~~~  194 (456)
                      +..+-.+..++.++.
T Consensus       868 st~~eR~~~Le~~l~  882 (1157)
T KOG0386|consen  868 STAEEREMFLEQLLE  882 (1157)
T ss_pred             CcHHHHHHHHHHHHh
Confidence            445555555555554

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=97.78  E-value=0.00012  Score=74.78  Aligned_cols=119  Identities=18%  Similarity=0.359  Sum_probs=98.1

Q ss_pred             cHHHHHHHHHHH-----HCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCC-CeEE-EEec
Q 012794           36 SKRTILSDLITV-----YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG-KFTV-LVAT  107 (456)
Q Consensus        36 ~k~~~L~~ll~~-----~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g-~~~v-LVaT  107 (456)
                      .|+..+.+.|..     ..+..|.+|||.-....+.+...+.+ ++..+-+-|..+...|....+.|+.. ++.| +++-
T Consensus       472 aK~~av~eyi~~~~~l~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsI  551 (689)
T KOG1000|consen  472 AKAAAVCEYILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSI  551 (689)
T ss_pred             cccHHHHHHHHhCcccccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEE
Confidence            455555555544     13467999999999999999999984 78889999999999999999999864 4554 3455


Q ss_pred             cccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEee
Q 012794          108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF  154 (456)
Q Consensus       108 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~  154 (456)
                      .++..||++...+.||...+++++-.++|.--|++|.|++..+.++|
T Consensus       552 tA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQkssV~v~y  598 (689)
T KOG1000|consen  552 TAAGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSSVFVQY  598 (689)
T ss_pred             eecccceeeeccceEEEEEecCCCceEEechhhhhhccccceeeEEE
Confidence            78899999999999999999999999999999999999876554443

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

Probab=97.78  E-value=9.3e-05  Score=66.95  Aligned_cols=104  Identities=24%  Similarity=0.406  Sum_probs=70.5

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhcC---CEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc--ccccccCcCc--cceEE
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSII---ASEALHGDISQHQRERTLNGFRQGKFTVLVATD--VAARGLDIPN--VDLII  123 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~~---~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd--v~~~Gidip~--v~~VI  123 (456)
                      ++.+|||+++.+..+.+...+....   ...++.-  .......+++.|+++.-.||+++.  .+.+|||+|+  +..||
T Consensus         9 ~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~vi   86 (167)
T PF13307_consen    9 PGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAVI   86 (167)
T ss_dssp             SSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhheee
Confidence            5899999999999999999887532   1222332  355788999999999999999998  9999999995  66799


Q ss_pred             ecCCCC----Ch--------------------------hHHHHHhcccccCCCCceEEEeeCh
Q 012794          124 HYELPN----DP--------------------------ETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       124 ~~~~p~----~~--------------------------~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      ...+|.    |+                          ....|.+||+=|....--+++++..
T Consensus        87 i~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~  149 (167)
T PF13307_consen   87 IVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDS  149 (167)
T ss_dssp             EES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESG
T ss_pred             ecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcC
Confidence            888774    11                          1237889999997655444444443

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.49  E-value=0.014  Score=63.17  Aligned_cols=68  Identities=10%  Similarity=0.199  Sum_probs=52.7

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc--ccCcCcc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR--GLDIPNV  119 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~--Gidip~v  119 (456)
                      .++||.++|++.|.++++.+..     .+.+..+||+.+...+...++.    ..+|||+|+     .+..  .+++..+
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            5799999999999999887764     2568899999998877766653    678999995     3332  3667777


Q ss_pred             ceEE
Q 012794          120 DLII  123 (456)
Q Consensus       120 ~~VI  123 (456)
                      .+||
T Consensus       161 ~~lV  164 (572)
T PRK04537        161 EICV  164 (572)
T ss_pred             eeeE
Confidence            7766

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=97.38  E-value=0.0033  Score=65.04  Aligned_cols=146  Identities=13%  Similarity=0.200  Sum_probs=108.4

Q ss_pred             ccccCeeEEEEEcCcc-------cHHHHHHH-HHHHHC---CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHH
Q 012794           20 KLAEGIKLYAISTTAT-------SKRTILSD-LITVYA---KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQH   87 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~-------~k~~~L~~-ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~   87 (456)
                      .....|.|.+...+..       .+.+.... ++..+.   ....+|||+++--+=-.|-..|++ .+....+|--.++.
T Consensus       258 ~v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~  337 (442)
T PF06862_consen  258 QVVVQVRQVFQRFDCSSPADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNS  337 (442)
T ss_pred             ccccCCceEEEEecCCCcchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHH
Confidence            3445667776654332       23333332 332222   357899999999888889899985 68888999999999


Q ss_pred             HHHHHHhcccCCCeEEEEecc--ccccccCcCccceEEecCCCCChhHHHHHhcccccCCC------CceEEEeeChhhH
Q 012794           88 QRERTLNGFRQGKFTVLVATD--VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK------EGTAILMFTSSQR  159 (456)
Q Consensus        88 ~R~~~l~~Fr~g~~~vLVaTd--v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~------~g~~i~~~~~~e~  159 (456)
                      +-.++-..|.+|+.+||+.|.  ..-+=..|..+.+||.|.+|..+.-|...+.-......      ...|.++++..+.
T Consensus       338 ~isRAR~~F~~G~~~iLL~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~  417 (442)
T PF06862_consen  338 DISRARSQFFHGRKPILLYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDA  417 (442)
T ss_pred             HHHHHHHHHHcCCceEEEEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHH
Confidence            999999999999999999996  33344667789999999999999999887765554332      5789999998876


Q ss_pred             HHHHHH
Q 012794          160 RTVRSL  165 (456)
Q Consensus       160 ~~~~~i  165 (456)
                      -.++.|
T Consensus       418 ~~LErI  423 (442)
T PF06862_consen  418 LRLERI  423 (442)
T ss_pred             HHHHHH
Confidence            655544

; GO: 0005634 nucleus

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=97.31  E-value=0.0019  Score=70.64  Aligned_cols=122  Identities=17%  Similarity=0.226  Sum_probs=101.4

Q ss_pred             CcccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHh----c-------------------CCEEEEeCCCCHHH
Q 012794           33 TATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS----I-------------------IASEALHGDISQHQ   88 (456)
Q Consensus        33 ~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~----~-------------------~~~~~lhg~~~~~~   88 (456)
                      ..+.|+-+|.+||... .-+.++|||..+....+.|...|.-    +                   .....|-|..+..+
T Consensus      1123 ~~SgKmiLLleIL~mceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~ 1202 (1567)
T KOG1015|consen 1123 EHSGKMILLLEILRMCEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQS 1202 (1567)
T ss_pred             hcCcceehHHHHHHHHHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHH
Confidence            3457888899988755 3467999999999988888777751    1                   12456778899999


Q ss_pred             HHHHHhcccCCC----eEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEee
Q 012794           89 RERTLNGFRQGK----FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF  154 (456)
Q Consensus        89 R~~~l~~Fr~g~----~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~  154 (456)
                      |+++.+.|.+-.    .-.||+|-+..-|||+-..+.||.||..|++..-+|.+=|+.|.|+.--||++-
T Consensus      1203 R~k~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYR 1272 (1567)
T KOG1015|consen 1203 RKKWAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYR 1272 (1567)
T ss_pred             HHHHHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehh
Confidence            999999998642    247899999999999999999999999999999999999999999888877763

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.29  E-value=0.0019  Score=70.90  Aligned_cols=122  Identities=24%  Similarity=0.262  Sum_probs=87.8

Q ss_pred             ccH-HHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccccc
Q 012794           35 TSK-RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR  112 (456)
Q Consensus        35 ~~k-~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~  112 (456)
                      ..| .+++.++...+.++.++||-+.+.+..+.+.+.|.+ +++..+|...-.  .|+..+-++.-..-.|-|||++|.|
T Consensus       412 ~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h--~~EA~Iia~AG~~gaVTiATNMAGR  489 (822)
T COG0653         412 EEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNH--AREAEIIAQAGQPGAVTIATNMAGR  489 (822)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccH--HHHHHHHhhcCCCCccccccccccC
Confidence            345 445556666778899999999999999999999985 777777777644  4444444433223357899999999


Q ss_pred             ccCcCccc-----------eEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          113 GLDIPNVD-----------LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       113 Gidip~v~-----------~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      |.||.--.           +||-..--.+..---|--||+||.|-+|.+..|++-.+
T Consensus       490 GTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSleD  546 (822)
T COG0653         490 GTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  546 (822)
T ss_pred             CcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhhHH
Confidence            99984221           45655555666666799999999998888777665433

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=97.26  E-value=0.002  Score=72.47  Aligned_cols=157  Identities=15%  Similarity=0.219  Sum_probs=105.4

Q ss_pred             ccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc---------
Q 012794            4 YFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI---------   74 (456)
Q Consensus         4 ~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~---------   74 (456)
                      .||+.+.+..++...+...-++.|+........| ..+..+.......+++|||+++++.|..+|..|...         
T Consensus      1313 v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~-~~~~ai~~~a~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l 1391 (1674)
T KOG0951|consen 1313 VFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTK-PTYTAIVRHAGNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYL 1391 (1674)
T ss_pred             eeecCcccCCCceeEEEEEeccchhHHHHHHhhh-hHHHHHHHHhcCCCCeEEEeccchhhhhhhhccchhhccCcHHHH
Confidence            4556666666655554444444443322222222 123344444456789999999999999988665321         


Q ss_pred             --------------CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEE----ecC------CCCC
Q 012794           75 --------------IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII----HYE------LPND  130 (456)
Q Consensus        75 --------------~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI----~~~------~p~~  130 (456)
                                    +...+=|-+|+...++.+-+-|..|.++|+|...- -.|+-...--+||    .||      .+.+
T Consensus      1392 ~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~s~~-~~~~~~~~~lVvvmgt~~ydg~e~~~~~y~ 1470 (1674)
T KOG0951|consen 1392 LSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CYGTKLKAHLVVVMGTQYYDGKEHSYEDYP 1470 (1674)
T ss_pred             HHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEEEcc-cccccccceEEEEecceeecccccccccCc
Confidence                          12222278899999999999999999999998755 6676654333333    233      5667


Q ss_pred             hhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794          131 PETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus       131 ~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      +....|+.|+|.|   .+.|++++....+.+++++
T Consensus      1471 i~~ll~m~G~a~~---~~k~vi~~~~~~k~yykkf 1502 (1674)
T KOG0951|consen 1471 IAELLQMVGLASG---AGKCVIMCHTPKKEYYKKF 1502 (1674)
T ss_pred             hhHHHHHhhhhcC---CccEEEEecCchHHHHHHh
Confidence            8999999999988   6789999998888887765

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

Probab=97.25  E-value=0.0026  Score=62.83  Aligned_cols=54  Identities=20%  Similarity=0.212  Sum_probs=45.2

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      +.-++||++|++.|-++++.|..     .+++.++.|+|+.-.+...|.+    .-.|+|||+
T Consensus        75 giFalvlTPTrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~----rPHvVvatP  133 (442)
T KOG0340|consen   75 GIFALVLTPTRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSD----RPHVVVATP  133 (442)
T ss_pred             cceEEEecchHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhccc----CCCeEecCc
Confidence            34689999999999999999872     3689999999988777777666    778999995

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

Probab=97.19  E-value=0.0036  Score=71.44  Aligned_cols=119  Identities=18%  Similarity=0.221  Sum_probs=81.0

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhcCC---EEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCc--cceEEe
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSIIA---SEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN--VDLIIH  124 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~~~---~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~--v~~VI~  124 (456)
                      ..+++|||+++.+..++++..|.....   ...+.=+++...|.++++.|+++.-.||++|....+|||+|.  +.+||.
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            457999999999999999999974321   222222344456789999999888889999999999999995  467887


Q ss_pred             cCCCC----C--------------------------hhHHHHHhcccccCCCCceEEEeeChh--hHHHHHHHHHH
Q 012794          125 YELPN----D--------------------------PETFVHRSGRTGRAGKEGTAILMFTSS--QRRTVRSLERD  168 (456)
Q Consensus       125 ~~~p~----~--------------------------~~~y~qr~GR~gR~g~~g~~i~~~~~~--e~~~~~~ie~~  168 (456)
                      ..+|.    +                          +-.+.|.+||.=|....--+++++...  ...+-+.+.+.
T Consensus       831 ~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~R~~~k~Yg~~~l~s  906 (928)
T PRK08074        831 VRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLDRRLTTTSYGKYFLES  906 (928)
T ss_pred             ecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEecCccccchHHHHHHHh
Confidence            66663    1                          122378889988875442234444432  33344444333

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=97.18  E-value=0.0053  Score=67.09  Aligned_cols=69  Identities=25%  Similarity=0.290  Sum_probs=53.6

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-cCcCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPN  118 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-idip~  118 (456)
                      ..++||.|+|++.|.++++.+..      .+.+..+||+.+...+...+..    ..+|||+|+     .+.++ +++.+
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            35799999999999999887753      3568889999888776665543    578999994     44444 78888


Q ss_pred             cceEE
Q 012794          119 VDLII  123 (456)
Q Consensus       119 v~~VI  123 (456)
                      +.+||
T Consensus       150 l~~lV  154 (629)
T PRK11634        150 LSGLV  154 (629)
T ss_pred             ceEEE
Confidence            88877

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

Probab=97.17  E-value=0.0065  Score=66.91  Aligned_cols=94  Identities=21%  Similarity=0.253  Sum_probs=71.1

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhcCC--EEEEeCCCCHHHHHHHHhcccCCCe-EEEEeccccccccCcCcc--ceEEec
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSIIA--SEALHGDISQHQRERTLNGFRQGKF-TVLVATDVAARGLDIPNV--DLIIHY  125 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~~~--~~~lhg~~~~~~R~~~l~~Fr~g~~-~vLVaTdv~~~Gidip~v--~~VI~~  125 (456)
                      ++++|||+++.+..+.+++.+.....  ....++..+   +..++++|+...- -++|+|..+.+|||+|.-  ..||..
T Consensus       479 ~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~---~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI~  555 (654)
T COG1199         479 PGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDE---REELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIV  555 (654)
T ss_pred             CCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCc---HHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEEE
Confidence            46899999999999999999985332  344555543   4478888887654 899999999999999854  668877


Q ss_pred             CCCCC------------------------------hhHHHHHhcccccCCCC
Q 012794          126 ELPND------------------------------PETFVHRSGRTGRAGKE  147 (456)
Q Consensus       126 ~~p~~------------------------------~~~y~qr~GR~gR~g~~  147 (456)
                      .+|..                              .....|.+||.=|.-..
T Consensus       556 ~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D  607 (654)
T COG1199         556 GLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDD  607 (654)
T ss_pred             ecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCC
Confidence            76642                              33458999999995433

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.12  E-value=0.0016  Score=72.53  Aligned_cols=40  Identities=20%  Similarity=0.337  Sum_probs=31.3

Q ss_pred             cccHHHHHHHHHHHHC----------CCCcEEEEcCChHHHHHHHHHHHh
Q 012794           34 ATSKRTILSDLITVYA----------KGGKTIVFTQTKRDADEVSLALTS   73 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~~----------~~~~~IIF~~t~~~a~~l~~~L~~   73 (456)
                      ...|...|.++|+.+.          .+.++||||+...+|.+|.+.|..
T Consensus       268 e~PKw~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       268 ENPKWEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             cCCCHHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHh
Confidence            4568888888776532          246799999999999999998865

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

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

Probab=97.06  E-value=0.002  Score=64.69  Aligned_cols=69  Identities=14%  Similarity=0.265  Sum_probs=51.8

Q ss_pred             CCcEEEEcCChHHHHHHHHHHH----hcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----c-cccccCcCccc
Q 012794           51 GGKTIVFTQTKRDADEVSLALT----SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----V-AARGLDIPNVD  120 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~----~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v-~~~Gidip~v~  120 (456)
                      ...+||+++|++.+.++.....    +++...+++|+-...++.+.+++    .+.|+|||+     + ..--||+..++
T Consensus       294 ~p~~lvl~ptreLalqie~e~~kysyng~ksvc~ygggnR~eqie~lkr----gveiiiatPgrlndL~~~n~i~l~siT  369 (629)
T KOG0336|consen  294 GPGVLVLTPTRELALQIEGEVKKYSYNGLKSVCVYGGGNRNEQIEDLKR----GVEIIIATPGRLNDLQMDNVINLASIT  369 (629)
T ss_pred             CCceEEEeccHHHHHHHHhHHhHhhhcCcceEEEecCCCchhHHHHHhc----CceEEeeCCchHhhhhhcCeeeeeeeE
Confidence            3468999999999988765554    34778899988777776666665    789999995     3 23338888888


Q ss_pred             eEE
Q 012794          121 LII  123 (456)
Q Consensus       121 ~VI  123 (456)
                      ++|
T Consensus       370 YlV  372 (629)
T KOG0336|consen  370 YLV  372 (629)
T ss_pred             EEE
Confidence            877

>COG4889 Predicted helicase [General function prediction only]

Probab=97.00  E-value=0.00059  Score=74.02  Aligned_cols=102  Identities=22%  Similarity=0.400  Sum_probs=79.3

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh--------------cCCEEEEe--CCCCHHHHHHHHh---cccCCCeEEEEecccccc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS--------------IIASEALH--GDISQHQRERTLN---GFRQGKFTVLVATDVAAR  112 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~--------------~~~~~~lh--g~~~~~~R~~~l~---~Fr~g~~~vLVaTdv~~~  112 (456)
                      .++|-||.+.++..++++.+..              .+.+.+=|  |.|.-.+|...+.   .|.....+||--.-.+.+
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            4689999999998888876642              13344444  7898888866554   456667888888889999


Q ss_pred             ccCcCccceEEecCCCCChhHHHHHhcccccC--CC-CceEEEe
Q 012794          113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRA--GK-EGTAILM  153 (456)
Q Consensus       113 Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~--g~-~g~~i~~  153 (456)
                      |+|+|.++.||.+++-.+..+.+|.+||+-|-  |+ -|..|+-
T Consensus       541 GVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILP  584 (1518)
T COG4889         541 GVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILP  584 (1518)
T ss_pred             CCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEE
Confidence            99999999999999999999999999999993  22 2555543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=96.97  E-value=0.0017  Score=68.32  Aligned_cols=87  Identities=17%  Similarity=0.219  Sum_probs=61.4

Q ss_pred             cccHHHH-HHHHHHHHCC---CCcEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEE
Q 012794           34 ATSKRTI-LSDLITVYAK---GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTV  103 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~~~---~~~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v  103 (456)
                      -.-|..+ +..++..+..   ..++||.|+|++.|.++++.+..      .+.+..++|+.+...+...++    ...+|
T Consensus        51 GsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~----~~~~I  126 (460)
T PRK11776         51 GSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE----HGAHI  126 (460)
T ss_pred             CCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc----CCCCE
Confidence            3456533 3334443322   23799999999999999987763      356888999999887766665    36789


Q ss_pred             EEecc-----cccc-ccCcCccceEEe
Q 012794          104 LVATD-----VAAR-GLDIPNVDLIIH  124 (456)
Q Consensus       104 LVaTd-----v~~~-Gidip~v~~VI~  124 (456)
                      +|+|+     .+.+ .+++.++.+||.
T Consensus       127 vV~Tp~rl~~~l~~~~~~l~~l~~lVi  153 (460)
T PRK11776        127 IVGTPGRILDHLRKGTLDLDALNTLVL  153 (460)
T ss_pred             EEEChHHHHHHHHcCCccHHHCCEEEE
Confidence            99994     4444 478889998873

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

Probab=96.96  E-value=0.0026  Score=65.77  Aligned_cols=68  Identities=21%  Similarity=0.357  Sum_probs=52.7

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec-----cccccc-cCcCccc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT-----DVAARG-LDIPNVD  120 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT-----dv~~~G-idip~v~  120 (456)
                      ..+||++||++.|++++..-.+     .+.+...+|+.+...+..    +-...++|||||     |++++| |.++++.
T Consensus       153 P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~----~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k  228 (482)
T KOG0335|consen  153 PRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLR----FIKRGCDILVATPGRLKDLIERGKISLDNCK  228 (482)
T ss_pred             CceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhh----hhccCccEEEecCchhhhhhhcceeehhhCc
Confidence            5799999999999999887764     256788888854444333    333489999999     588888 8999998


Q ss_pred             eEE
Q 012794          121 LII  123 (456)
Q Consensus       121 ~VI  123 (456)
                      ++|
T Consensus       229 ~~v  231 (482)
T KOG0335|consen  229 FLV  231 (482)
T ss_pred             EEE
Confidence            777

>PF13871 Helicase_C_4: Helicase_C-like

Probab=96.84  E-value=0.029  Score=54.61  Aligned_cols=79  Identities=20%  Similarity=0.369  Sum_probs=61.3

Q ss_pred             HHHhcccCCCeEEEEeccccccccCcCcc--------ceEEecCCCCChhHHHHHhcccccCCCC-ceEEEeeC---hhh
Q 012794           91 RTLNGFRQGKFTVLVATDVAARGLDIPNV--------DLIIHYELPNDPETFVHRSGRTGRAGKE-GTAILMFT---SSQ  158 (456)
Q Consensus        91 ~~l~~Fr~g~~~vLVaTdv~~~Gidip~v--------~~VI~~~~p~~~~~y~qr~GR~gR~g~~-g~~i~~~~---~~e  158 (456)
                      ...+.|.+|+..|+|.|+.++.||.+..-        .+-|...+||+.+..+|..||+.|.++. ...|.++.   +-|
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            56679999999999999999999988632        2566789999999999999999999864 33344432   346


Q ss_pred             HHHHHHHHHHh
Q 012794          159 RRTVRSLERDV  169 (456)
Q Consensus       159 ~~~~~~ie~~~  169 (456)
                      +.+...+.+.+
T Consensus       132 ~Rfas~va~rL  142 (278)
T PF13871_consen  132 RRFASTVARRL  142 (278)
T ss_pred             HHHHHHHHHHH
Confidence            66666666655

>TIGR00595 priA primosomal protein N'

Probab=96.84  E-value=0.014  Score=62.07  Aligned_cols=89  Identities=20%  Similarity=0.267  Sum_probs=71.1

Q ss_pred             ccHHHHHHHHHH-HHCCCCcEEEEcCChHHHHHHHHHHHhc--CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccc
Q 012794           35 TSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSI--IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  111 (456)
Q Consensus        35 ~~k~~~L~~ll~-~~~~~~~~IIF~~t~~~a~~l~~~L~~~--~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~  111 (456)
                      .-|..+...++. .+..+.++||.+|+...+.++++.|.+.  ..+..+|++++..+|.+++.+.+++..+|+|+|..+.
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            457666555443 3345678999999999999999999863  5688999999999999999999999999999997544


Q ss_pred             cccCcCccceEEe
Q 012794          112 RGLDIPNVDLIIH  124 (456)
Q Consensus       112 ~Gidip~v~~VI~  124 (456)
                      . +.++++.+||.
T Consensus        88 f-~p~~~l~lIIV   99 (505)
T TIGR00595        88 F-LPFKNLGLIIV   99 (505)
T ss_pred             c-CcccCCCEEEE
Confidence            3 45778888773

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=96.76  E-value=0.0072  Score=66.04  Aligned_cols=23  Identities=22%  Similarity=0.179  Sum_probs=12.2

Q ss_pred             cccc-EEEeecCccceeeeecCHHHHHH
Q 012794          284 EIGK-IHIIADDRVQGAVFDLPEEIAKE  310 (456)
Q Consensus       284 ~ig~-i~~~~~~~~~~~~~dv~~~~a~~  310 (456)
                      ..|. |-.++|-    .-+++.-+.|..
T Consensus      1074 sdgq~IV~VDdW----IklqIshEaAAc 1097 (1282)
T KOG0921|consen 1074 SDGQGIVRVDDW----IKLQISHEAAAC 1097 (1282)
T ss_pred             ccCcceEEeece----eeEeccHHHHHH
Confidence            3444 5555554    456666555543

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=96.71  E-value=0.016  Score=65.28  Aligned_cols=77  Identities=16%  Similarity=0.160  Sum_probs=58.2

Q ss_pred             CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcC--ccceEEec
Q 012794           49 AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIP--NVDLIIHY  125 (456)
Q Consensus        49 ~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip--~v~~VI~~  125 (456)
                      ..++++||++++.+..+.++..|.. .+.+ ...|.-.  .+.+++++|+++.-.||++|....+|||+|  ....||..
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            3468999999999999999999874 2333 3444221  246689999998888999999999999997  35556655


Q ss_pred             CCC
Q 012794          126 ELP  128 (456)
Q Consensus       126 ~~p  128 (456)
                      .+|
T Consensus       722 kLP  724 (820)
T PRK07246        722 RLP  724 (820)
T ss_pred             cCC
Confidence            555

>PTZ00110 helicase; Provisional

Probab=96.66  E-value=0.03  Score=60.32  Aligned_cols=68  Identities=13%  Similarity=0.223  Sum_probs=52.3

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-cCcCccc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNVD  120 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-idip~v~  120 (456)
                      ..+||.++|++.|.++.+.+..     .+.+.+++|+.+...+...+..    ..+|||+|+     .+..+ +++..+.
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     2567889999887766655543    578999995     44444 6788888


Q ss_pred             eEE
Q 012794          121 LII  123 (456)
Q Consensus       121 ~VI  123 (456)
                      +||
T Consensus       280 ~lV  282 (545)
T PTZ00110        280 YLV  282 (545)
T ss_pred             EEE
Confidence            877

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=96.65  E-value=0.015  Score=64.38  Aligned_cols=77  Identities=26%  Similarity=0.402  Sum_probs=58.4

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhcC-CEEEEeCCCCHHHHHHHHhcccC----CCeEEEEeccccccccCcCc--cceE
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSII-ASEALHGDISQHQRERTLNGFRQ----GKFTVLVATDVAARGLDIPN--VDLI  122 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~~-~~~~lhg~~~~~~R~~~l~~Fr~----g~~~vLVaTdv~~~Gidip~--v~~V  122 (456)
                      ..+.+|||+++.+..++++..|.... .-...++..   .+.++++.|++    +.-.||++|....+|||+|.  +.+|
T Consensus       533 ~~gg~LVlFtSy~~l~~v~~~l~~~~~~~ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~v  609 (697)
T PRK11747        533 KHKGSLVLFASRRQMQKVADLLPRDLRLMLLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQV  609 (697)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHhcCCcEEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEE
Confidence            45679999999999999999987422 223446643   46778877764    56779999999999999985  6788


Q ss_pred             EecCCCC
Q 012794          123 IHYELPN  129 (456)
Q Consensus       123 I~~~~p~  129 (456)
                      |...+|.
T Consensus       610 II~kLPF  616 (697)
T PRK11747        610 IITKIPF  616 (697)
T ss_pred             EEEcCCC
Confidence            8777663

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=96.64  E-value=0.0085  Score=62.54  Aligned_cols=68  Identities=16%  Similarity=0.276  Sum_probs=53.0

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc------ccccccCcCccc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVD  120 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd------v~~~Gidip~v~  120 (456)
                      .++||.++|++.|.++++.+..     .+.+..++|+.+...+..++..    ..+|||+|+      +....+++.++.
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            5799999999999998876653     3678899999998887766653    678999996      222446788888


Q ss_pred             eEE
Q 012794          121 LII  123 (456)
Q Consensus       121 ~VI  123 (456)
                      +||
T Consensus       150 ~lV  152 (434)
T PRK11192        150 TLI  152 (434)
T ss_pred             EEE
Confidence            877

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.61  E-value=0.014  Score=64.42  Aligned_cols=91  Identities=21%  Similarity=0.277  Sum_probs=72.4

Q ss_pred             CcccHHHHHHHHHH-HHCCCCcEEEEcCChHHHHHHHHHHHh--cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           33 TATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        33 ~~~~k~~~L~~ll~-~~~~~~~~IIF~~t~~~a~~l~~~L~~--~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      .-.-|..+...++. .+..+.++||.++|++.+.++++.|.+  +..+..+||+++..+|.+.+.+..++..+|+|+|..
T Consensus       171 TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrs  250 (679)
T PRK05580        171 TGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARS  250 (679)
T ss_pred             CCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccH
Confidence            34567766655443 334567899999999999999999986  357899999999999999999999999999999975


Q ss_pred             cccccCcCccceEEe
Q 012794          110 AARGLDIPNVDLIIH  124 (456)
Q Consensus       110 ~~~Gidip~v~~VI~  124 (456)
                      +.. +.+.++.+||.
T Consensus       251 al~-~p~~~l~liVv  264 (679)
T PRK05580        251 ALF-LPFKNLGLIIV  264 (679)
T ss_pred             Hhc-ccccCCCEEEE
Confidence            433 56778888774

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=96.60  E-value=0.013  Score=62.57  Aligned_cols=120  Identities=15%  Similarity=0.255  Sum_probs=93.5

Q ss_pred             cccHHHHHHHHHHHH--CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC--CCeEEE-Eec
Q 012794           34 ATSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ--GKFTVL-VAT  107 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~--g~~~vL-VaT  107 (456)
                      .+-|+..+..+++.+  ....++||...-.....-+...|.+ ++....+||.+..++|+.+++.|..  +..+|+ +.=
T Consensus       727 ~S~Ki~~~l~~le~i~~~skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSL  806 (901)
T KOG4439|consen  727 PSCKIAMVLEILETILTSSKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSL  806 (901)
T ss_pred             chhHHHHHHHHHHHHhhcccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEE
Confidence            345666666655544  3446777766666666667777775 6778889999999999999999964  445655 455


Q ss_pred             cccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794          108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus       108 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      .+-+.|||+-..+|+|..|+.|++.--.|.+-|.-|.|++-.+++.
T Consensus       807 tAGGVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V~Ih  852 (901)
T KOG4439|consen  807 TAGGVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDVFIH  852 (901)
T ss_pred             ccCcceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCceEEE
Confidence            6778899999999999999999999999999999999987766654

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.55  E-value=0.0085  Score=66.22  Aligned_cols=91  Identities=16%  Similarity=0.253  Sum_probs=72.3

Q ss_pred             cccHHH-HHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec
Q 012794           34 ATSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT  107 (456)
Q Consensus        34 ~~~k~~-~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT  107 (456)
                      -+-|.. .+..++.....+.+++|.+||+..|.++++.+.+     ++.+..+||+++..+|..+++.+.+|.++|+|+|
T Consensus       292 GSGKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT  371 (681)
T PRK10917        292 GSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGT  371 (681)
T ss_pred             CCcHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEch
Confidence            345643 3334444455667999999999999999988874     2678999999999999999999999999999999


Q ss_pred             cc-cccccCcCccceEEe
Q 012794          108 DV-AARGLDIPNVDLIIH  124 (456)
Q Consensus       108 dv-~~~Gidip~v~~VI~  124 (456)
                      .. +...+.+.++.+||.
T Consensus       372 ~~ll~~~v~~~~l~lvVI  389 (681)
T PRK10917        372 HALIQDDVEFHNLGLVII  389 (681)
T ss_pred             HHHhcccchhcccceEEE
Confidence            74 344577889998883

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=96.50  E-value=0.033  Score=62.08  Aligned_cols=106  Identities=18%  Similarity=0.292  Sum_probs=70.6

Q ss_pred             cEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-------ccccc--cCcCc
Q 012794           53 KTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-------VAARG--LDIPN  118 (456)
Q Consensus        53 ~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-------v~~~G--idip~  118 (456)
                      =+||.|+|++.+.+|.+.+..     .+.+++++|+..++++...+++   | ..|+|||.       ++..|  .+|-.
T Consensus       440 i~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkR---g-~eIvV~tpGRmiD~l~~n~grvtnlrR  515 (997)
T KOG0334|consen  440 IALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKR---G-AEIVVCTPGRMIDILCANSGRVTNLRR  515 (997)
T ss_pred             eEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhc---C-CceEEeccchhhhhHhhcCCccccccc
Confidence            479999999999999988764     3678999999888877666655   5 78999994       33334  56666


Q ss_pred             cceEEe--------cCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHh
Q 012794          119 VDLIIH--------YELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  169 (456)
Q Consensus       119 v~~VI~--------~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~  169 (456)
                      +++||.        +.+-.....++|.+ |+.|      ..++++.+....+..+.+.+
T Consensus       516 ~t~lv~deaDrmfdmgfePq~~~Ii~nl-rpdr------QtvlfSatfpr~m~~la~~v  567 (997)
T KOG0334|consen  516 VTYLVLDEADRMFDMGFEPQITRILQNL-RPDR------QTVLFSATFPRSMEALARKV  567 (997)
T ss_pred             cceeeechhhhhheeccCcccchHHhhc-chhh------hhhhhhhhhhHHHHHHHHHh
Confidence            777662        22323333488888 4333      34555555545566655543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=96.29  E-value=0.015  Score=63.79  Aligned_cols=89  Identities=17%  Similarity=0.280  Sum_probs=71.7

Q ss_pred             ccHHHH-HHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           35 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        35 ~~k~~~-L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      .-|..+ +..++.....+.+++|.+||+..|.++++.+.+     ++.+..+||+++..+|..+++...+++++|+|+|.
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            456443 334555555677999999999999999988864     36789999999999999999999999999999997


Q ss_pred             ccc-cccCcCccceEE
Q 012794          109 VAA-RGLDIPNVDLII  123 (456)
Q Consensus       109 v~~-~Gidip~v~~VI  123 (456)
                      .+- ..+.+.++.+||
T Consensus       347 ~ll~~~~~~~~l~lvV  362 (630)
T TIGR00643       347 ALIQEKVEFKRLALVI  362 (630)
T ss_pred             HHHhccccccccceEE
Confidence            544 347788888877

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=96.26  E-value=0.043  Score=59.63  Aligned_cols=78  Identities=18%  Similarity=0.143  Sum_probs=61.4

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhcCC-EEEEeCCCCHHHHHHHHhcccCC----CeEEEEeccccccccCc--------
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSIIA-SEALHGDISQHQRERTLNGFRQG----KFTVLVATDVAARGLDI--------  116 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~~~-~~~lhg~~~~~~R~~~l~~Fr~g----~~~vLVaTdv~~~Gidi--------  116 (456)
                      ..+.++|.+.+....+.+++.|...+. ...+.|+.+  .+..++++|+..    .-.||++|+.+-.|||+        
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            467999999999999999999986543 345567643  345678888874    67899999999999999        


Q ss_pred             --CccceEEecCCCC
Q 012794          117 --PNVDLIIHYELPN  129 (456)
Q Consensus       117 --p~v~~VI~~~~p~  129 (456)
                        ..+++||..-+|.
T Consensus       547 ~G~~Ls~ViI~kLPF  561 (636)
T TIGR03117       547 KDNLLTDLIITCAPF  561 (636)
T ss_pred             CCCcccEEEEEeCCC
Confidence              3578898777763

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.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.05  E-value=0.024  Score=64.45  Aligned_cols=90  Identities=17%  Similarity=0.226  Sum_probs=70.8

Q ss_pred             ccHHHHHH-HHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc-----CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           35 TSKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTSI-----IASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        35 ~~k~~~L~-~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      .-|..+.. .++.....+.+++|.+||+..|.+.++.+.+.     +.+..+++.++..++.++++.+++|+++|||+|.
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            45654332 33444445689999999999999999988742     4678899999999999999999999999999997


Q ss_pred             -ccccccCcCccceEEe
Q 012794          109 -VAARGLDIPNVDLIIH  124 (456)
Q Consensus       109 -v~~~Gidip~v~~VI~  124 (456)
                       ++...+.+.++.+||.
T Consensus       563 ~ll~~~v~f~~L~llVI  579 (926)
T TIGR00580       563 KLLQKDVKFKDLGLLII  579 (926)
T ss_pred             HHhhCCCCcccCCEEEe
Confidence             4445578888888773

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.

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

Probab=96.01  E-value=0.052  Score=56.43  Aligned_cols=69  Identities=16%  Similarity=0.209  Sum_probs=48.8

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc-ccCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~-Gidip~v  119 (456)
                      +..+||..+|++.+.++.+.-.+     ++.++.+-|+++.+++---+..    ...|+|||+     +++. -+=+..|
T Consensus       322 gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~----gceiviatPgrLid~Lenr~lvl~qc  397 (673)
T KOG0333|consen  322 GPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSM----GCEIVIATPGRLIDSLENRYLVLNQC  397 (673)
T ss_pred             CceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhc----cceeeecCchHHHHHHHHHHHHhccC
Confidence            56899999999999998765542     3678889999998877444444    578999995     3332 2334555


Q ss_pred             ceEE
Q 012794          120 DLII  123 (456)
Q Consensus       120 ~~VI  123 (456)
                      ++||
T Consensus       398 tyvv  401 (673)
T KOG0333|consen  398 TYVV  401 (673)
T ss_pred             ceEe
Confidence            5555

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

Probab=96.00  E-value=0.07  Score=59.59  Aligned_cols=87  Identities=14%  Similarity=0.168  Sum_probs=58.3

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-ccccc---------cC
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-VAARG---------LD  115 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-v~~~G---------id  115 (456)
                      +..++||.+||++.|.++...|..    .+.+..++|+.+..+|..+.+     ..+|||+|+ .+..+         ..
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    356788999999887754432     368999995 33222         12


Q ss_pred             cCccceEEecC-------CCCChhHHHHHhccc
Q 012794          116 IPNVDLIIHYE-------LPNDPETFVHRSGRT  141 (456)
Q Consensus       116 ip~v~~VI~~~-------~p~~~~~y~qr~GR~  141 (456)
                      +.++.+||.=.       +-.....++.|+-|.
T Consensus       155 l~~l~~vViDEah~~~g~fg~~~~~il~rL~ri  187 (742)
T TIGR03817       155 LRRLRYVVIDECHSYRGVFGSHVALVLRRLRRL  187 (742)
T ss_pred             HhcCCEEEEeChhhccCccHHHHHHHHHHHHHH
Confidence            56788877311       112345556665544

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.

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.00  E-value=0.035  Score=60.87  Aligned_cols=91  Identities=19%  Similarity=0.269  Sum_probs=74.3

Q ss_pred             cccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHhcC---CEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           34 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTSII---ASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~~~---~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      -+.|.++...++... ..++++||.++....+.++.+.|...+   .++.+|++++..+|.+.+.+.++|+.+|+|.|-.
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            456878777777654 457799999999999999999999644   4889999999999999999999999999999965


Q ss_pred             cccccCcCccceEEec
Q 012794          110 AARGLDIPNVDLIIHY  125 (456)
Q Consensus       110 ~~~Gidip~v~~VI~~  125 (456)
                      +.. +-++++.+||..
T Consensus       250 AvF-aP~~~LgLIIvd  264 (665)
T PRK14873        250 AVF-APVEDLGLVAIW  264 (665)
T ss_pred             eEE-eccCCCCEEEEE
Confidence            433 455677777743

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=95.93  E-value=0.0029  Score=40.23  Aligned_cols=17  Identities=41%  Similarity=1.257  Sum_probs=15.8

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      -|+.|++.||.-+|||+
T Consensus        10 ~C~~C~~~GH~i~dCP~   26 (32)
T PF13696_consen   10 VCHRCGQKGHWIQDCPT   26 (32)
T ss_pred             EeecCCCCCccHhHCCC
Confidence            49999999999999995

>smart00343 ZnF_C2HC zinc finger

Probab=95.72  E-value=0.0045  Score=37.60  Aligned_cols=15  Identities=67%  Similarity=1.688  Sum_probs=14.7

Q ss_pred             cccCCCCCcCcCCCC
Q 012794          441 CFNCGKSGHRASECP  455 (456)
Q Consensus       441 ~~~c~~~gh~~~~~p  455 (456)
                      |++|++.||++++||
T Consensus         2 C~~CG~~GH~~~~C~   16 (26)
T smart00343        2 CYNCGKEGHIARDCP   16 (26)
T ss_pred             CccCCCCCcchhhCC
Confidence            999999999999998

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=95.63  E-value=0.029  Score=49.60  Aligned_cols=67  Identities=19%  Similarity=0.293  Sum_probs=36.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCcccCCCCCcCcCCCCC
Q 012794          379 RSSRSWGSDDEDGFSSSRGG-RSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN  456 (456)
Q Consensus       379 ~~~~~~g~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~~~~~~~c~~~gh~~~~~p~  456 (456)
                      ..++.|+..+|....++... ......+..++     ..+|+...     ..... ..+....||+|++.||+++|||+
T Consensus        28 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg-----~~GH~~~~-----Cp~~~-~~~~~~~C~~Cg~~GH~~~~C~~   95 (148)
T PTZ00368         28 RPCYKCGEPGHLSRECPSAPGGRGERSCYNCG-----KTGHLSRE-----CPEAP-PGSGPRSCYNCGQTGHISRECPN   95 (148)
T ss_pred             ccCccCCCCCcCcccCcCCCCCCCCcccCCCC-----CcCcCccc-----CCCcc-cCCCCcccCcCCCCCcccccCCC
Confidence            35677899998877775432 11122344333     22222100     00000 00123469999999999999985

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=95.45  E-value=0.054  Score=61.20  Aligned_cols=90  Identities=17%  Similarity=0.171  Sum_probs=65.6

Q ss_pred             EEEEcCChHHHHHHHHHHHhc-------CCEEEEeCCCCHHHHHHHHhcc----------------------cC----CC
Q 012794           54 TIVFTQTKRDADEVSLALTSI-------IASEALHGDISQHQRERTLNGF----------------------RQ----GK  100 (456)
Q Consensus        54 ~IIF~~t~~~a~~l~~~L~~~-------~~~~~lhg~~~~~~R~~~l~~F----------------------r~----g~  100 (456)
                      .||=.++...+-.+|..|...       +.+.++|+..+...|..+++..                      ++    +.
T Consensus       759 GliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~  838 (1110)
T TIGR02562       759 GLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNH  838 (1110)
T ss_pred             EEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCC
Confidence            367777777788888877632       3477889998777776655442                      11    35


Q ss_pred             eEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCC
Q 012794          101 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  146 (456)
Q Consensus       101 ~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~  146 (456)
                      ..|+|+|.|++.|+|+. .+++|-  -|.++.+++|++||+-|.+.
T Consensus       839 ~~i~v~Tqv~E~g~D~d-fd~~~~--~~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       839 LFIVLATPVEEVGRDHD-YDWAIA--DPSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             CeEEEEeeeEEEEeccc-CCeeee--ccCcHHHHHHHhhccccccc
Confidence            67999999999999984 444432  35678999999999999763

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.

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=95.29  E-value=0.0098  Score=40.50  Aligned_cols=18  Identities=50%  Similarity=1.141  Sum_probs=16.2

Q ss_pred             CCcccCCCCCcCcCCCCC
Q 012794          439 GACFNCGKSGHRASECPN  456 (456)
Q Consensus       439 ~~~~~c~~~gh~~~~~p~  456 (456)
                      ..|.+|++.||+..+||+
T Consensus         5 ~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    5 VRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CcCcccCCCCcchhhCCC
Confidence            459999999999999993

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

Probab=95.28  E-value=0.15  Score=52.78  Aligned_cols=109  Identities=17%  Similarity=0.234  Sum_probs=69.4

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cc-------cc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VA-------AR  112 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~-------~~  112 (456)
                      .-.+||.|+|++.|.+++..++.      .+.+..+-|+-....   ..++..+ .++|||||+     .+       .+
T Consensus       154 ~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~---e~~kl~k-~~niliATPGRLlDHlqNt~~f~~r  229 (543)
T KOG0342|consen  154 GTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSV---EADKLVK-GCNILIATPGRLLDHLQNTSGFLFR  229 (543)
T ss_pred             CeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchH---HHHHhhc-cccEEEeCCchHHhHhhcCCcchhh
Confidence            34789999999999988776653      245666667643332   2333333 789999995     11       12


Q ss_pred             c---cCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhC
Q 012794          113 G---LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  170 (456)
Q Consensus       113 G---idip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~  170 (456)
                      -   +=+...+++...+++.+++.++-...+       -...++++......++.+.+..-
T Consensus       230 ~~k~lvlDEADrlLd~GF~~di~~Ii~~lpk-------~rqt~LFSAT~~~kV~~l~~~~L  283 (543)
T KOG0342|consen  230 NLKCLVLDEADRLLDIGFEEDVEQIIKILPK-------QRQTLLFSATQPSKVKDLARGAL  283 (543)
T ss_pred             ccceeEeecchhhhhcccHHHHHHHHHhccc-------cceeeEeeCCCcHHHHHHHHHhh
Confidence            1   223455666678888888888888763       23445556556666676666543

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

Probab=95.25  E-value=0.12  Score=51.91  Aligned_cols=108  Identities=16%  Similarity=0.250  Sum_probs=71.0

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhc-----------CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccc---
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSI-----------IASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAA---  111 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~-----------~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~---  111 (456)
                      +.-.||.|++++.|.+....+...           +.+..--|+++-.++..++.+    .+.|+|||+     +++   
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            345799999999999887766532           234444589999999888877    789999995     332   


Q ss_pred             ------cccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHh
Q 012794          112 ------RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  169 (456)
Q Consensus       112 ------~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~  169 (456)
                            |=+-+...+..|++++-.++.++.--.       +.-...++++.+-...++.+.+..
T Consensus       322 ~sLd~CRyL~lDEADRmiDmGFEddir~iF~~F-------K~QRQTLLFSATMP~KIQ~FAkSA  378 (610)
T KOG0341|consen  322 MSLDACRYLTLDEADRMIDMGFEDDIRTIFSFF-------KGQRQTLLFSATMPKKIQNFAKSA  378 (610)
T ss_pred             ccHHHHHHhhhhhHHHHhhccchhhHHHHHHHH-------hhhhheeeeeccccHHHHHHHHhh
Confidence                  334445566677888888776543322       122345556655555555555443

>PRK10689 transcription-repair coupling factor; Provisional

Probab=95.16  E-value=0.075  Score=61.87  Aligned_cols=91  Identities=15%  Similarity=0.163  Sum_probs=69.5

Q ss_pred             CcccHHHHHHH-HHHHHCCCCcEEEEcCChHHHHHHHHHHHhc-----CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEe
Q 012794           33 TATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTSI-----IASEALHGDISQHQRERTLNGFRQGKFTVLVA  106 (456)
Q Consensus        33 ~~~~k~~~L~~-ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVa  106 (456)
                      .-.-|..+... +......+.+++|.|||+..|.+++..+.+.     +.+..+++..+..++.++++.++++.++|||+
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            34567653322 2222345689999999999999999988742     46778999999999999999999999999999


Q ss_pred             cc-ccccccCcCccceEE
Q 012794          107 TD-VAARGLDIPNVDLII  123 (456)
Q Consensus       107 Td-v~~~Gidip~v~~VI  123 (456)
                      |. .+...+.+.++.+||
T Consensus       710 Tp~lL~~~v~~~~L~lLV  727 (1147)
T PRK10689        710 THKLLQSDVKWKDLGLLI  727 (1147)
T ss_pred             CHHHHhCCCCHhhCCEEE
Confidence            96 444456777888877

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

Probab=95.13  E-value=0.048  Score=59.97  Aligned_cols=92  Identities=23%  Similarity=0.285  Sum_probs=76.2

Q ss_pred             EcCcccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHh--cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec
Q 012794           31 STTATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT  107 (456)
Q Consensus        31 ~~~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~--~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT  107 (456)
                      -++-+-|.++...++... ..++++||.++-.....++...|..  +..+.++|++|++.+|..+..+.++|+.+|+|.|
T Consensus       224 GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGt  303 (730)
T COG1198         224 GVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGT  303 (730)
T ss_pred             CCCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEe
Confidence            356678999888888655 5567999999999999999999985  4678999999999999999999999999999998


Q ss_pred             cccccccCcCccceEE
Q 012794          108 DVAARGLDIPNVDLII  123 (456)
Q Consensus       108 dv~~~Gidip~v~~VI  123 (456)
                      -.|- -.-++++-+||
T Consensus       304 RSAl-F~Pf~~LGLII  318 (730)
T COG1198         304 RSAL-FLPFKNLGLII  318 (730)
T ss_pred             chhh-cCchhhccEEE
Confidence            6432 23456777766

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

Probab=94.99  E-value=0.2  Score=53.66  Aligned_cols=69  Identities=16%  Similarity=0.225  Sum_probs=48.0

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh---c--CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc-ccCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS---I--IASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~---~--~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~-Gidip~v  119 (456)
                      ...+||.++|++.|.++.+.+..   .  +.+..+.|+.+..++...+.   . ..+|||+|+     .+.+ .+++..+
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            35799999999999988776653   2  45667777766554433332   2 478999994     4433 5788888


Q ss_pred             ceEE
Q 012794          120 DLII  123 (456)
Q Consensus       120 ~~VI  123 (456)
                      .+||
T Consensus       272 ~~lV  275 (518)
T PLN00206        272 SVLV  275 (518)
T ss_pred             eEEE
Confidence            8877

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

Probab=94.98  E-value=0.56  Score=44.73  Aligned_cols=68  Identities=21%  Similarity=0.288  Sum_probs=54.3

Q ss_pred             cEEEEcCChHHHHHHHHHHH---hc---CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc------ccccccCcCccc
Q 012794           53 KTIVFTQTKRDADEVSLALT---SI---IASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVD  120 (456)
Q Consensus        53 ~~IIF~~t~~~a~~l~~~L~---~~---~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd------v~~~Gidip~v~  120 (456)
                      .+||.|.|++.|-++.....   ++   .++.+++|+|+-+.-+++++.    -..|+|+|+      +-.+-+++.++.
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            57999999999999977654   33   468999999999888888876    668999997      334558888888


Q ss_pred             eEEe
Q 012794          121 LIIH  124 (456)
Q Consensus       121 ~VI~  124 (456)
                      +.|.
T Consensus       188 hFvl  191 (387)
T KOG0329|consen  188 HFVL  191 (387)
T ss_pred             eeeh
Confidence            8663

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=94.97  E-value=0.29  Score=48.21  Aligned_cols=9  Identities=0%  Similarity=0.287  Sum_probs=3.4

Q ss_pred             HHHHHHHHh
Q 012794          161 TVRSLERDV  169 (456)
Q Consensus       161 ~~~~ie~~~  169 (456)
                      .+..|+..+
T Consensus       166 lfe~i~~kl  174 (465)
T KOG3973|consen  166 LFETIRQKL  174 (465)
T ss_pred             HHHHHHHHH
Confidence            333333333

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=94.80  E-value=0.12  Score=45.72  Aligned_cols=68  Identities=21%  Similarity=0.310  Sum_probs=37.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCcccCCCCCcCcCCCCC
Q 012794          379 RSSRSWGSDDEDGFSSSRGGR-SFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASECPN  456 (456)
Q Consensus       379 ~~~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~~~~~~~c~~~gh~~~~~p~  456 (456)
                      ..++.++..+|....++.... .....+..++.     .+|+...     ......++.....||+|++.||+++|||+
T Consensus        53 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~-----~GH~~~~-----C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~  121 (148)
T PTZ00368         53 RSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQ-----TGHISRE-----CPNRAKGGAARRACYNCGGEGHISRDCPN  121 (148)
T ss_pred             cccCCCCCcCcCcccCCCcccCCCCcccCcCCC-----CCccccc-----CCCcccccccchhhcccCcCCcchhcCCC
Confidence            356778889998877754321 12223444442     2222100     00000001223469999999999999995

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=94.78  E-value=0.25  Score=43.27  Aligned_cols=47  Identities=21%  Similarity=0.330  Sum_probs=35.3

Q ss_pred             CCCHHHHHHHHhcccCCC-eEEEEeccccccccCcCc--cceEEecCCCC
Q 012794           83 DISQHQRERTLNGFRQGK-FTVLVATDVAARGLDIPN--VDLIIHYELPN  129 (456)
Q Consensus        83 ~~~~~~R~~~l~~Fr~g~-~~vLVaTdv~~~Gidip~--v~~VI~~~~p~  129 (456)
                      +....+...+++.|++.. ..||++|.-..+|||+|+  +..||...+|.
T Consensus        30 ~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492       30 GEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             CCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCC
Confidence            344445678888888654 379999988999999996  45788777764

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=94.77  E-value=0.36  Score=53.70  Aligned_cols=78  Identities=15%  Similarity=0.240  Sum_probs=57.2

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-cC-------CEEEEeCCCCHHHHHHHHhcccC----CCeEEEEec--cccccccCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-II-------ASEALHGDISQHQRERTLNGFRQ----GKFTVLVAT--DVAARGLDI  116 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~~-------~~~~lhg~~~~~~R~~~l~~Fr~----g~~~vLVaT--dv~~~Gidi  116 (456)
                      ++.+|||.++....+.+++.+.. ++       ..+.+-+. ...+++.+++.|+.    +.-.||+|+  ..+++|||+
T Consensus       522 pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~-~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGIDf  600 (705)
T TIGR00604       522 PDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETK-DAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGIDF  600 (705)
T ss_pred             CCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCC-CcchHHHHHHHHHHHHhcCCceEEEEecCCcccCcccc
Confidence            57899999999999998887763 11       11222121 12577889999964    345699998  899999999


Q ss_pred             Cc--cceEEecCCCC
Q 012794          117 PN--VDLIIHYELPN  129 (456)
Q Consensus       117 p~--v~~VI~~~~p~  129 (456)
                      ++  +..||..++|.
T Consensus       601 ~~~~~r~ViivGlPf  615 (705)
T TIGR00604       601 CDDLGRAVIMVGIPY  615 (705)
T ss_pred             CCCCCcEEEEEccCC
Confidence            85  57798888886

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).

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=94.58  E-value=0.21  Score=43.85  Aligned_cols=42  Identities=21%  Similarity=0.373  Sum_probs=31.2

Q ss_pred             HHHHHHhcccCCCe---EEEEeccc--cccccCcCc--cceEEecCCCC
Q 012794           88 QRERTLNGFRQGKF---TVLVATDV--AARGLDIPN--VDLIIHYELPN  129 (456)
Q Consensus        88 ~R~~~l~~Fr~g~~---~vLVaTdv--~~~Gidip~--v~~VI~~~~p~  129 (456)
                      +..++++.|++..-   .||+++.-  ..+|||+|+  +..||...+|.
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            34677788876433   58888876  999999996  56788877774

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

Probab=94.55  E-value=0.36  Score=50.32  Aligned_cols=70  Identities=29%  Similarity=0.340  Sum_probs=57.6

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh--cC---CEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc------ccccccCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS--II---ASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~--~~---~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd------v~~~Gidip~v  119 (456)
                      .+++|+.+||+-.+.+-+..+.+  ++   .+++|.|..++++|+.....     .+|+|||+      +.+-=||+.++
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            34899999999999999998875  33   47899999999999988765     57999994      44444999999


Q ss_pred             ceEEec
Q 012794          120 DLIIHY  125 (456)
Q Consensus       120 ~~VI~~  125 (456)
                      .+||.=
T Consensus       133 ~~lifD  138 (542)
T COG1111         133 SLLIFD  138 (542)
T ss_pred             eEEEec
Confidence            998843

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

Probab=94.47  E-value=0.5  Score=48.79  Aligned_cols=106  Identities=19%  Similarity=0.349  Sum_probs=71.4

Q ss_pred             cEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc---ccCcCc
Q 012794           53 KTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR---GLDIPN  118 (456)
Q Consensus        53 ~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~---Gidip~  118 (456)
                      -+||.++|++.|.++.+.+..      .+.+..+-|+.+..   +-++.|++...+|||+|+     ++.+   .+|+-.
T Consensus        81 galIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~---~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rs  157 (567)
T KOG0345|consen   81 GALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVE---EDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRS  157 (567)
T ss_pred             eEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHH---HHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccc
Confidence            479999999999988776642      25688899996654   446678888899999995     4444   466657


Q ss_pred             cceEE--------ecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHH
Q 012794          119 VDLII--------HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  168 (456)
Q Consensus       119 v~~VI--------~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~  168 (456)
                      ++++|        .+++-.++..++-+.-+--|.|       +++.++...+..|.+.
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            77766        4666667777776665543433       3444444445555443

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=94.31  E-value=0.023  Score=66.64  Aligned_cols=93  Identities=22%  Similarity=0.383  Sum_probs=77.4

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh--cCCEEEEeCCCC-----------HHHHHHHHhcccCCCeEEEEeccccccccCcCc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS--IIASEALHGDIS-----------QHQRERTLNGFRQGKFTVLVATDVAARGLDIPN  118 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~--~~~~~~lhg~~~-----------~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~  118 (456)
                      -..||||+.+..+..+.+.+.+  ...+..+.|.+.           +..+++++..|....+++|++|.++..|+|++.
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~  372 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPK  372 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhh
Confidence            3569999999999999988874  233444444432           224678999999999999999999999999999


Q ss_pred             cceEEecCCCCChhHHHHHhcccccC
Q 012794          119 VDLIIHYELPNDPETFVHRSGRTGRA  144 (456)
Q Consensus       119 v~~VI~~~~p~~~~~y~qr~GR~gR~  144 (456)
                      ++.|+.++.|.....|+|..||+-.+
T Consensus       373 ~~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  373 CNLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhhheeccCcchHHHHHHhhcccccc
Confidence            99999999999999999999997654

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=94.28  E-value=0.077  Score=55.55  Aligned_cols=66  Identities=23%  Similarity=0.376  Sum_probs=53.8

Q ss_pred             EEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-c---CcCcc
Q 012794           54 TIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-L---DIPNV  119 (456)
Q Consensus        54 ~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-i---dip~v  119 (456)
                      +|||++|++.|.++.+.|..     .+.+..|.|+|+...+++++++    .-+|+|||+     ++..+ .   ++.+|
T Consensus       266 ~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATPGRlweli~e~n~~l~~~k~v  341 (731)
T KOG0347|consen  266 ALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATPGRLWELIEEDNTHLGNFKKV  341 (731)
T ss_pred             eEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc----CCCEEEecchHHHHHHHhhhhhhhhhhhc
Confidence            89999999999999998863     4789999999999999999998    678999997     33332 2   45666


Q ss_pred             ceEE
Q 012794          120 DLII  123 (456)
Q Consensus       120 ~~VI  123 (456)
                      .++|
T Consensus       342 kcLV  345 (731)
T KOG0347|consen  342 KCLV  345 (731)
T ss_pred             eEEE
Confidence            6655

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=94.16  E-value=0.087  Score=58.92  Aligned_cols=60  Identities=20%  Similarity=0.376  Sum_probs=51.5

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhc------CCEE-EEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSI------IASE-ALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~------~~~~-~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      ++++++|.+||...+.++++.|.+.      +.+. .+|+.|+.++++.++++|.+|.++|||+|..
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            4689999999999999999998742      2222 2899999999999999999999999999963

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=93.60  E-value=0.23  Score=54.05  Aligned_cols=109  Identities=20%  Similarity=0.290  Sum_probs=88.8

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhc-C------------------CEEEEeCCCCHHHHHHHHhcccCC---CeEEEEecc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSI-I------------------ASEALHGDISQHQRERTLNGFRQG---KFTVLVATD  108 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~-~------------------~~~~lhg~~~~~~R~~~l~~Fr~g---~~~vLVaTd  108 (456)
                      +.++|||.......+.|.+.|.+. +                  .-.-+.|-.+...|++.+++|.+.   .+-+|++|-
T Consensus       719 g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllstr  798 (1387)
T KOG1016|consen  719 GEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLSTR  798 (1387)
T ss_pred             CceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehhc
Confidence            568999999888888887777642 1                  123456778889999999999863   346888999


Q ss_pred             ccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhH
Q 012794          109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR  159 (456)
Q Consensus       109 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~  159 (456)
                      ...-|||+-..+-+|.+|.-|++.--.|.+-|+-|.|++..|+++-.-.+.
T Consensus       799 ag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlVmD~  849 (1387)
T KOG1016|consen  799 AGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLVMDN  849 (1387)
T ss_pred             cccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeehhhh
Confidence            999999998888999999999999999999999999999888887554443

>PRK14701 reverse gyrase; Provisional

Probab=93.57  E-value=0.2  Score=60.23  Aligned_cols=60  Identities=22%  Similarity=0.316  Sum_probs=52.7

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      ++.++||.+||++.+.+++..|..       .+.+.++||+++..++.++++.++++..+|||+|+-
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            456899999999999999998875       245788999999999999999999999999999973

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

Probab=93.49  E-value=0.095  Score=51.39  Aligned_cols=111  Identities=18%  Similarity=0.273  Sum_probs=68.7

Q ss_pred             CcEEEEcCChHHHHHHHHHH---Hhc--CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec-----cccccc-cCcCccc
Q 012794           52 GKTIVFTQTKRDADEVSLAL---TSI--IASEALHGDISQHQRERTLNGFRQGKFTVLVAT-----DVAARG-LDIPNVD  120 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L---~~~--~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT-----dv~~~G-idip~v~  120 (456)
                      -++||.++|++.|.+..+..   .++  +.+.+..|+.+-  |..++.-  +..+.++|+|     |.+..| -|+.++.
T Consensus       154 IQ~~ilVPtrelALQtSqvc~~lskh~~i~vmvttGGT~l--rDDI~Rl--~~~VH~~vgTPGRIlDL~~KgVa~ls~c~  229 (459)
T KOG0326|consen  154 IQAIILVPTRELALQTSQVCKELSKHLGIKVMVTTGGTSL--RDDIMRL--NQTVHLVVGTPGRILDLAKKGVADLSDCV  229 (459)
T ss_pred             eeEEEEeecchhhHHHHHHHHHHhcccCeEEEEecCCccc--ccceeee--cCceEEEEcCChhHHHHHhcccccchhce
Confidence            47899999999888766544   443  567777888543  3333332  3478999999     577888 4677777


Q ss_pred             eEEe--------cCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHH-HHHHHhCCCc
Q 012794          121 LIIH--------YELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVR-SLERDVGCKF  173 (456)
Q Consensus       121 ~VI~--------~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~-~ie~~~~~~~  173 (456)
                      ++|.        .++-..++..+.-.-       +...+++|+..-...++ .+.+++..+.
T Consensus       230 ~lV~DEADKlLs~~F~~~~e~li~~lP-------~~rQillySATFP~tVk~Fm~~~l~kPy  284 (459)
T KOG0326|consen  230 ILVMDEADKLLSVDFQPIVEKLISFLP-------KERQILLYSATFPLTVKGFMDRHLKKPY  284 (459)
T ss_pred             EEEechhhhhhchhhhhHHHHHHHhCC-------ccceeeEEecccchhHHHHHHHhccCcc
Confidence            6663        334445666666663       34556666654433333 3444444443

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=93.37  E-value=0.049  Score=59.59  Aligned_cols=119  Identities=16%  Similarity=0.202  Sum_probs=95.5

Q ss_pred             cccHHHHHHHHHHHHC-CC-CcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCC-eE-EEEecc
Q 012794           34 ATSKRTILSDLITVYA-KG-GKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGK-FT-VLVATD  108 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~~-~~-~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~-~~-vLVaTd  108 (456)
                      .+.|+..+..+|.... .. .++|||+.-...++.+...|. ..+....+-|.|+..+|.+++..|..+. .+ .|++..
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            4566666666665331 12 389999999998888888776 3566667779999999999999999653 33 346778


Q ss_pred             ccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEE
Q 012794          109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL  152 (456)
Q Consensus       109 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~  152 (456)
                      +...|+++-...+|+..|+-|++..-.|.+-|+.|.|+.-.+.+
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            99999999999999999999999999999999999997765555

>TIGR01054 rgy reverse gyrase

Probab=93.26  E-value=0.19  Score=58.81  Aligned_cols=75  Identities=17%  Similarity=0.314  Sum_probs=56.6

Q ss_pred             cccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHhc-----CCE---EEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           34 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTSI-----IAS---EALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~---~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      ..-|...+.-++..+ ..+.++||.+||++.|.++++.+...     +.+   ..+||+++..+++..++.++++..+||
T Consensus       103 GsGKT~f~l~~~~~l~~~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIl  182 (1171)
T TIGR01054       103 GVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDIL  182 (1171)
T ss_pred             CCCHHHHHHHHHHHHHhcCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEE
Confidence            356765333222222 34578999999999999999888742     222   358999999999999999999989999


Q ss_pred             Eecc
Q 012794          105 VATD  108 (456)
Q Consensus       105 VaTd  108 (456)
                      |+|+
T Consensus       183 V~Tp  186 (1171)
T TIGR01054       183 ITTT  186 (1171)
T ss_pred             EECH
Confidence            9996

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

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

Probab=93.17  E-value=0.36  Score=52.18  Aligned_cols=86  Identities=19%  Similarity=0.286  Sum_probs=71.4

Q ss_pred             HHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccc-c
Q 012794           39 TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA-R  112 (456)
Q Consensus        39 ~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~-~  112 (456)
                      -++..++..+..+.++...+||--.|++.+..+.+     ++.+..|.|.+..++|+++++...+|.++|+|.|-++- .
T Consensus       299 VA~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd  378 (677)
T COG1200         299 VALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQD  378 (677)
T ss_pred             HHHHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhc
Confidence            33444555666788999999998888888877764     46789999999999999999999999999999997654 5


Q ss_pred             ccCcCccceEEe
Q 012794          113 GLDIPNVDLIIH  124 (456)
Q Consensus       113 Gidip~v~~VI~  124 (456)
                      .+++.++-+||.
T Consensus       379 ~V~F~~LgLVIi  390 (677)
T COG1200         379 KVEFHNLGLVII  390 (677)
T ss_pred             ceeecceeEEEE
Confidence            688988888874

>PRK14873 primosome assembly protein PriA; Provisional

Probab=92.93  E-value=0.33  Score=53.38  Aligned_cols=69  Identities=12%  Similarity=0.158  Sum_probs=47.5

Q ss_pred             HHHHhcccCCCeEEEEecc----ccccccCcCccceEEecC------CCC------ChhHHHHHhcccccCCCCceEEEe
Q 012794           90 ERTLNGFRQGKFTVLVATD----VAARGLDIPNVDLIIHYE------LPN------DPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus        90 ~~~l~~Fr~g~~~vLVaTd----v~~~Gidip~v~~VI~~~------~p~------~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      +.+++.|.. +.+|||+|.    +++     +++++|+..|      .|.      ....+.|-+||+||..+.|.+++.
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            357888874 899999998    555     3566665433      222      245568999999999999999988


Q ss_pred             eChhhHHHHHHH
Q 012794          154 FTSSQRRTVRSL  165 (456)
Q Consensus       154 ~~~~e~~~~~~i  165 (456)
                      ..+ +...++.+
T Consensus       536 ~~p-~~~~~~~l  546 (665)
T PRK14873        536 AES-SLPTVQAL  546 (665)
T ss_pred             eCC-CCHHHHHH
Confidence            643 33444433

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=92.03  E-value=0.69  Score=48.08  Aligned_cols=69  Identities=10%  Similarity=0.202  Sum_probs=51.5

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccc-cccCcCccc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAA-RGLDIPNVD  120 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~-~Gidip~v~  120 (456)
                      .++||.++|++.|.++++.+..     .+.+..++|+.+...+...++.    ..+|||+|+     .+. .-+++..+.
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            4799999999999998776642     3678889999887666555532    578999996     222 347888888


Q ss_pred             eEEe
Q 012794          121 LIIH  124 (456)
Q Consensus       121 ~VI~  124 (456)
                      +||.
T Consensus       160 ~lVi  163 (423)
T PRK04837        160 VVVL  163 (423)
T ss_pred             EEEE
Confidence            8773

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

Probab=91.73  E-value=1.3  Score=45.17  Aligned_cols=70  Identities=17%  Similarity=0.224  Sum_probs=51.7

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc------ccccccCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd------v~~~Gidip~v  119 (456)
                      +-+++|..+|++.+.+.-+.++.     .+.+.++.|+-+.+++-..+..    .-+|++||+      .++.-+++..|
T Consensus        90 g~RalilsptreLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~----npDii~ATpgr~~h~~vem~l~l~sv  165 (529)
T KOG0337|consen   90 GLRALILSPTRELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNE----NPDIIIATPGRLLHLGVEMTLTLSSV  165 (529)
T ss_pred             ccceeeccCcHHHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhcc----CCCEEEecCceeeeeehheeccccce
Confidence            35899999999999888777763     2566767777666665555543    678999996      45556888899


Q ss_pred             ceEEe
Q 012794          120 DLIIH  124 (456)
Q Consensus       120 ~~VI~  124 (456)
                      .+||.
T Consensus       166 eyVVf  170 (529)
T KOG0337|consen  166 EYVVF  170 (529)
T ss_pred             eeeee
Confidence            99994

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=91.61  E-value=0.075  Score=48.30  Aligned_cols=16  Identities=56%  Similarity=1.545  Sum_probs=15.1

Q ss_pred             CcccCCCCCcCcCCCC
Q 012794          440 ACFNCGKSGHRASECP  455 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p  455 (456)
                      .||+||+-||..+|||
T Consensus        62 ~C~nCg~~GH~~~DCP   77 (190)
T COG5082          62 VCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccchhcccCcccccCC
Confidence            3999999999999999

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

Probab=91.58  E-value=0.73  Score=52.77  Aligned_cols=88  Identities=17%  Similarity=0.279  Sum_probs=70.9

Q ss_pred             cHHHHHHH-HHHHHCCCCcEEEEcCChHHHHHHHHHHHhc-----CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec-c
Q 012794           36 SKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTSI-----IASEALHGDISQHQRERTLNGFRQGKFTVLVAT-D  108 (456)
Q Consensus        36 ~k~~~L~~-ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT-d  108 (456)
                      -|.++..+ .......++++.|.|||.-.|++-++.+++.     +.+..|.-=.+.+++..+++..++|+++|||.| .
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            45544333 3344455789999999999999999999853     356777777889999999999999999999999 4


Q ss_pred             ccccccCcCccceEE
Q 012794          109 VAARGLDIPNVDLII  123 (456)
Q Consensus       109 v~~~Gidip~v~~VI  123 (456)
                      ++...|-+.++-+||
T Consensus       707 LL~kdv~FkdLGLlI  721 (1139)
T COG1197         707 LLSKDVKFKDLGLLI  721 (1139)
T ss_pred             hhCCCcEEecCCeEE
Confidence            777788888888877

>cd00268 DEADc DEAD-box helicases

Probab=91.41  E-value=3  Score=38.17  Aligned_cols=69  Identities=22%  Similarity=0.350  Sum_probs=50.9

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-cCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-idip~v  119 (456)
                      ..++||.|+|+..+.+.+..+..     .+.+..++|+.+..+....++    ....|+|+|.     .+..+ .+++++
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            45899999999999998877653     356788899988876655544    4678999995     23233 677788


Q ss_pred             ceEE
Q 012794          120 DLII  123 (456)
Q Consensus       120 ~~VI  123 (456)
                      ++||
T Consensus       145 ~~lI  148 (203)
T cd00268         145 KYLV  148 (203)
T ss_pred             CEEE
Confidence            8877

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.

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=91.27  E-value=0.088  Score=47.86  Aligned_cols=54  Identities=19%  Similarity=0.364  Sum_probs=32.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCcccCCCCCcCcCCC-C
Q 012794          379 RSSRSWGSDDEDGFSSSRGGRSFRSGNNRGSRFSTSSDDDWLIGGSRSSRSSSRDSRSFGGACFNCGKSGHRASEC-P  455 (456)
Q Consensus       379 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~~~~~~~~~c~~~gh~~~~~-p  455 (456)
                      .-|..||..||..++|+ .  .=...|.+.+        |.     +...       .-.--|++||+-||.++|| |
T Consensus        61 ~~C~nCg~~GH~~~DCP-~--~iC~~C~~~~--------H~-----s~~C-------~~~~~C~~Cg~~GH~~~dC~P  115 (190)
T COG5082          61 PVCFNCGQNGHLRRDCP-H--SICYNCSWDG--------HR-----SNHC-------PKPKKCYNCGETGHLSRDCNP  115 (190)
T ss_pred             cccchhcccCcccccCC-h--hHhhhcCCCC--------cc-----cccC-------CcccccccccccCccccccCc
Confidence            35778999999888888 2  1122222111        11     0000       0013499999999999999 5

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=91.24  E-value=0.11  Score=33.84  Aligned_cols=15  Identities=60%  Similarity=1.052  Sum_probs=11.4

Q ss_pred             CcccCCCCCcCcCCC
Q 012794          440 ACFNCGKSGHRASEC  454 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~  454 (456)
                      -|++|++..|.|+||
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            499999999999999

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=91.16  E-value=0.81  Score=48.36  Aligned_cols=59  Identities=24%  Similarity=0.338  Sum_probs=52.9

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      ..+.+||.+||++.+.+....|.. ++.+..++++.+..++..++..++.+.++||++|+
T Consensus        50 ~~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TP  109 (470)
T TIGR00614        50 SDGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTP  109 (470)
T ss_pred             cCCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            357899999999999988888875 78899999999999999999999999999999996

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

>PRK13766 Hef nuclease; Provisional

Probab=91.04  E-value=3  Score=46.93  Aligned_cols=70  Identities=26%  Similarity=0.413  Sum_probs=53.7

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhc--C---CEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc------ccccccCcCc
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSI--I---ASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPN  118 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~--~---~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd------v~~~Gidip~  118 (456)
                      ..+++||.|+|+..+++.++.+...  +   .+..++|+.+..+|.+.+..     ..|+|+|+      .+..-+++.+
T Consensus        57 ~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~r~~~~~~-----~~iiv~T~~~l~~~l~~~~~~~~~  131 (773)
T PRK13766         57 KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWEK-----AKVIVATPQVIENDLIAGRISLED  131 (773)
T ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEEeCCCCHHHHHHHHhC-----CCEEEECHHHHHHHHHcCCCChhh
Confidence            4689999999999999988888752  2   67889999999988776643     47999995      2334467778


Q ss_pred             cceEEe
Q 012794          119 VDLIIH  124 (456)
Q Consensus       119 v~~VI~  124 (456)
                      +++||.
T Consensus       132 ~~liVv  137 (773)
T PRK13766        132 VSLLIF  137 (773)
T ss_pred             CcEEEE
Confidence            888774

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=90.78  E-value=1.2  Score=47.06  Aligned_cols=110  Identities=14%  Similarity=0.190  Sum_probs=74.2

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc--ccCcCcc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR--GLDIPNV  119 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~--Gidip~v  119 (456)
                      --+||..+|++.|.++.+.|.+     .+.+..+-|+..-+     .+.-|-..++|||||+     .+-.  .++-+++
T Consensus       142 lGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k-----~E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~l  216 (758)
T KOG0343|consen  142 LGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVK-----FELERISQMNILVCTPGRLLQHMDENPNFSTSNL  216 (758)
T ss_pred             ceeEEecchHHHHHHHHHHHHHHhhccccccceeecCchhH-----HHHHhhhcCCeEEechHHHHHHhhhcCCCCCCcc
Confidence            3689999999999999999974     26777777875432     2233334689999996     2222  3445566


Q ss_pred             ceEE--------ecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCc
Q 012794          120 DLII--------HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKF  173 (456)
Q Consensus       120 ~~VI--------~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~  173 (456)
                      .++|        .+++-...+.++--+       ......++++.++...++.|.+..-.+.
T Consensus       217 QmLvLDEADR~LDMGFk~tL~~Ii~~l-------P~~RQTLLFSATqt~svkdLaRLsL~dP  271 (758)
T KOG0343|consen  217 QMLVLDEADRMLDMGFKKTLNAIIENL-------PKKRQTLLFSATQTKSVKDLARLSLKDP  271 (758)
T ss_pred             eEEEeccHHHHHHHhHHHHHHHHHHhC-------ChhheeeeeecccchhHHHHHHhhcCCC
Confidence            6555        456666667766655       3455677777777777888877744433

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

Probab=90.77  E-value=1.4  Score=42.79  Aligned_cols=119  Identities=13%  Similarity=0.143  Sum_probs=68.2

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh---c--CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-cCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS---I--IASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~---~--~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-idip~v  119 (456)
                      ..++||..||++.|.++.+.+..   .  +.|.+.-|+.+-.+-.+.++.    ...|+..|+     +..++ +.--+|
T Consensus        95 ~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~----G~hvVsGtPGrv~dmikr~~L~tr~v  170 (400)
T KOG0328|consen   95 ETQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDY----GQHVVSGTPGRVLDMIKRRSLRTRAV  170 (400)
T ss_pred             eeeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcc----cceEeeCCCchHHHHHHhccccccce
Confidence            46799999999999999887763   2  445555566655544444442    446777774     55555 777777


Q ss_pred             ceEEecCCC--CChhHHHHHhcccccCCCCceEEEeeChh-hHHHHHHHHHHhCCCce
Q 012794          120 DLIIHYELP--NDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFE  174 (456)
Q Consensus       120 ~~VI~~~~p--~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-e~~~~~~ie~~~~~~~~  174 (456)
                      .++|.-...  .+. -+-+.+=+.-|.=.++..+++++.. ....++..+++..-++.
T Consensus       171 kmlVLDEaDemL~k-gfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvr  227 (400)
T KOG0328|consen  171 KMLVLDEADEMLNK-GFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVR  227 (400)
T ss_pred             eEEEeccHHHHHHh-hHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCcee
Confidence            776642211  111 2223333344444556666665543 44555555555544443

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

Probab=90.73  E-value=2.7  Score=44.30  Aligned_cols=114  Identities=11%  Similarity=0.209  Sum_probs=66.9

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhcC-------CEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-------ccccccCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSII-------ASEALHGDISQHQRERTLNGFRQGKFTVLVATD-------VAARGLDI  116 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~~-------~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-------v~~~Gidi  116 (456)
                      +--+||.++|++.|.++++.+.+.+       .+..+-|+-...++.    ++| ..++|||+|+       .--..|++
T Consensus       211 G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKA----RLR-KGiNILIgTPGRLvDHLknT~~i~~  285 (708)
T KOG0348|consen  211 GPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKA----RLR-KGINILIGTPGRLVDHLKNTKSIKF  285 (708)
T ss_pred             CceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHH----HHh-cCceEEEcCchHHHHHHhccchhee
Confidence            3468999999999999998887532       233333433222222    222 2689999996       12345788


Q ss_pred             CccceEE--------ecCCCCChhHHHHHhcccccCCCCc------eEEEeeChhhHHHHHHHHHHh
Q 012794          117 PNVDLII--------HYELPNDPETFVHRSGRTGRAGKEG------TAILMFTSSQRRTVRSLERDV  169 (456)
Q Consensus       117 p~v~~VI--------~~~~p~~~~~y~qr~GR~gR~g~~g------~~i~~~~~~e~~~~~~ie~~~  169 (456)
                      ..+.|||        ..++-.++..++..++-.-++-.+-      ..-++++.+-...+.+|....
T Consensus       286 s~LRwlVlDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~s  352 (708)
T KOG0348|consen  286 SRLRWLVLDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLS  352 (708)
T ss_pred             eeeeEEEecchhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhcc
Confidence            8888888        3556677777777775433332121      233444444444455554443

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=90.46  E-value=0.13  Score=34.43  Aligned_cols=16  Identities=50%  Similarity=1.213  Sum_probs=13.9

Q ss_pred             CcccCCCCCcCcCC--CC
Q 012794          440 ACFNCGKSGHRASE--CP  455 (456)
Q Consensus       440 ~~~~c~~~gh~~~~--~p  455 (456)
                      .|-+||.-||++++  ||
T Consensus         3 kC~~CG~~GH~~t~k~CP   20 (40)
T PF15288_consen    3 KCKNCGAFGHMRTNKRCP   20 (40)
T ss_pred             cccccccccccccCccCC
Confidence            49999999999854  98

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=90.37  E-value=1.5  Score=48.57  Aligned_cols=113  Identities=18%  Similarity=0.235  Sum_probs=76.4

Q ss_pred             cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccccccc
Q 012794           36 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGL  114 (456)
Q Consensus        36 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gi  114 (456)
                      +.......|+..+..++++-||++|...++.+++.... ...+..+++.-+..+   + +.+  ++.+|+|=|+++..|+
T Consensus       267 ~~~tF~~~L~~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~d---v-~~W--~~~~VviYT~~itvG~  340 (824)
T PF02399_consen  267 DETTFFSELLARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLED---V-ESW--KKYDVVIYTPVITVGL  340 (824)
T ss_pred             chhhHHHHHHHHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccc---c-ccc--cceeEEEEeceEEEEe
Confidence            44555666676776778888999999999998888775 455667777654442   2 222  3689999999999999


Q ss_pred             CcCccce--EEec--CCC--CChhHHHHHhcccccCCCCceEEEeeC
Q 012794          115 DIPNVDL--IIHY--ELP--NDPETFVHRSGRTGRAGKEGTAILMFT  155 (456)
Q Consensus       115 dip~v~~--VI~~--~~p--~~~~~y~qr~GR~gR~g~~g~~i~~~~  155 (456)
                      ++.....  |+-|  ...  .+..+..|++||+-... ....++++.
T Consensus       341 Sf~~~HF~~~f~yvk~~~~gpd~~s~~Q~lgRvR~l~-~~ei~v~~d  386 (824)
T PF02399_consen  341 SFEEKHFDSMFAYVKPMSYGPDMVSVYQMLGRVRSLL-DNEIYVYID  386 (824)
T ss_pred             ccchhhceEEEEEecCCCCCCcHHHHHHHHHHHHhhc-cCeEEEEEe
Confidence            9975532  3323  111  35667899999985543 334444443

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

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=89.92  E-value=3.7  Score=36.05  Aligned_cols=86  Identities=19%  Similarity=0.276  Sum_probs=57.9

Q ss_pred             ccHHHHHH-HHHHHHC--CCCcEEEEcCChHHHHHHHHHHHhc-----CCEEEEeCCCCHH-HHHHHHhcccCCCeEEEE
Q 012794           35 TSKRTILS-DLITVYA--KGGKTIVFTQTKRDADEVSLALTSI-----IASEALHGDISQH-QRERTLNGFRQGKFTVLV  105 (456)
Q Consensus        35 ~~k~~~L~-~ll~~~~--~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~~~lhg~~~~~-~R~~~l~~Fr~g~~~vLV  105 (456)
                      .-|..... .++....  +..++||.+++++.++++...+.+.     +.+..+|++.+.. +....+    ....+|||
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            45754444 3333332  2349999999999999999888742     4688899998855 344444    44688999


Q ss_pred             ecc-----cc-ccccCcCccceEEe
Q 012794          106 ATD-----VA-ARGLDIPNVDLIIH  124 (456)
Q Consensus       106 aTd-----v~-~~Gidip~v~~VI~  124 (456)
                      +|.     .. ...+++..+++||.
T Consensus       101 ~T~~~l~~~~~~~~~~~~~~~~iVi  125 (169)
T PF00270_consen  101 TTPEQLLDLISNGKINISRLSLIVI  125 (169)
T ss_dssp             EEHHHHHHHHHTTSSTGTTESEEEE
T ss_pred             cCcchhhccccccccccccceeecc
Confidence            994     22 22357777887773

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 ....

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=89.27  E-value=1.7  Score=45.91  Aligned_cols=69  Identities=10%  Similarity=0.208  Sum_probs=50.4

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cc-ccccCcCccc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VA-ARGLDIPNVD  120 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~-~~Gidip~v~  120 (456)
                      .++||.++|++.|.++++.+..     .+.+..++|+.+...+.+.   +.....+|||+|+     .. ...+.+..+.
T Consensus       163 ~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~---~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~  239 (475)
T PRK01297        163 PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQ---LEARFCDILVATPGRLLDFNQRGEVHLDMVE  239 (475)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHH---HhCCCCCEEEECHHHHHHHHHcCCcccccCc
Confidence            5799999999999999887763     2568889998876554433   3345678999996     22 2346677888


Q ss_pred             eEE
Q 012794          121 LII  123 (456)
Q Consensus       121 ~VI  123 (456)
                      +||
T Consensus       240 ~lV  242 (475)
T PRK01297        240 VMV  242 (475)
T ss_pred             eEE
Confidence            777

>PRK09401 reverse gyrase; Reviewed

Probab=89.08  E-value=1.1  Score=52.61  Aligned_cols=90  Identities=22%  Similarity=0.315  Sum_probs=60.2

Q ss_pred             CcccHHHHHHHHHHH-HCCCCcEEEEcCChHHHHHHHHHHHhc-----CCEEEE--eCCCCHHHHHHHHhcccCCCeEEE
Q 012794           33 TATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTSI-----IASEAL--HGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        33 ~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~~~l--hg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      ...-|...+.-++.. ..++.++||.+||++.|.++++.+...     +.+..+  |+.++..++...++.++++..+||
T Consensus       104 TGsGKT~f~l~~~~~l~~~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~Il  183 (1176)
T PRK09401        104 TGVGKTTFGLVMSLYLAKKGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDIL  183 (1176)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEE
Confidence            345676443322222 234678999999999999999998742     233333  566778888888889998889999


Q ss_pred             Eecc-----ccccccCcCccceEE
Q 012794          105 VATD-----VAARGLDIPNVDLII  123 (456)
Q Consensus       105 VaTd-----v~~~Gidip~v~~VI  123 (456)
                      |+|+     .+. .+....+++||
T Consensus       184 V~Tp~rL~~~~~-~l~~~~~~~lV  206 (1176)
T PRK09401        184 VTTSQFLSKNFD-ELPKKKFDFVF  206 (1176)
T ss_pred             EECHHHHHHHHH-hccccccCEEE
Confidence            9995     222 33434466655

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=88.34  E-value=2  Score=46.76  Aligned_cols=59  Identities=15%  Similarity=0.196  Sum_probs=52.6

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      ..+.+||.+|++..+.+....|.. ++.+..+|++++..++..++..+..+.++||++|+
T Consensus        52 ~~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tp  111 (591)
T TIGR01389        52 LKGLTVVISPLISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAP  111 (591)
T ss_pred             cCCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECh
Confidence            357899999999998888888875 78899999999999999999999999999999985

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=87.21  E-value=1.7  Score=51.88  Aligned_cols=70  Identities=16%  Similarity=0.227  Sum_probs=53.8

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----------------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----------------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----  108 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----------------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----  108 (456)
                      ..++|+.+++++.+.++.+.|..                 .+.+..+||+.++.+|.+.++.    ..+|||+|+     
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            35799999999999999887742                 3567889999999999877654    678999995     


Q ss_pred             ccc-cc-cCcCccceEEe
Q 012794          109 VAA-RG-LDIPNVDLIIH  124 (456)
Q Consensus       109 v~~-~G-idip~v~~VI~  124 (456)
                      ++. +. ..+.+|.+||.
T Consensus       113 LLtsk~r~~L~~Vr~VIV  130 (1490)
T PRK09751        113 MLTSRARETLRGVETVII  130 (1490)
T ss_pred             HHhhhhhhhhccCCEEEE
Confidence            222 22 35788998883

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

Probab=87.03  E-value=2.3  Score=49.21  Aligned_cols=58  Identities=17%  Similarity=0.231  Sum_probs=49.8

Q ss_pred             CCcEEEEcCChHHHH-HHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccC--CCeEEEEecc
Q 012794           51 GGKTIVFTQTKRDAD-EVSLALTSIIASEALHGDISQHQRERTLNGFRQ--GKFTVLVATD  108 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~-~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~--g~~~vLVaTd  108 (456)
                      .+.+||.+|+++.+. ++...+..++.+..+.++++..++..+++.+..  +.++||++|+
T Consensus       500 ~GiTLVISPLiSLmqDQV~~L~~~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTP  560 (1195)
T PLN03137        500 PGITLVISPLVSLIQDQIMNLLQANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTP  560 (1195)
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEECh
Confidence            568999999999987 555555568899999999999999999998876  8899999997

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=87.02  E-value=0.28  Score=47.68  Aligned_cols=18  Identities=39%  Similarity=1.324  Sum_probs=16.2

Q ss_pred             CCcccCCCCCcCcCCCCC
Q 012794          439 GACFNCGKSGHRASECPN  456 (456)
Q Consensus       439 ~~~~~c~~~gh~~~~~p~  456 (456)
                      .-||+|++.||++.|||+
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~  161 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPE  161 (261)
T ss_pred             CccCCCCcCCcchhhCCC
Confidence            459999999999999993

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=86.42  E-value=0.26  Score=34.78  Aligned_cols=17  Identities=53%  Similarity=1.411  Sum_probs=15.5

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      -|++||.-||-.++||-
T Consensus        33 ~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   33 FCFHCGRIGHSDKECPK   49 (49)
T ss_pred             hhcCCCCcCcCHhHcCC
Confidence            39999999999999983

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=85.74  E-value=2.5  Score=44.55  Aligned_cols=113  Identities=21%  Similarity=0.285  Sum_probs=82.2

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc--cccccCcCccceEEecCCC
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV--AARGLDIPNVDLIIHYELP  128 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv--~~~Gidip~v~~VI~~~~p  128 (456)
                      .-+|||.++--.--.|-.++++ .+....+|---++.+-.++-+-|-.|..+||+-|.=  .-+-.+|..|.-||.|.+|
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            4579999998888888888874 455455555455555566677888999999999964  3456888999999999999


Q ss_pred             CChhHH---HHHhcccccCC----CCceEEEeeChhhHHHHHH
Q 012794          129 NDPETF---VHRSGRTGRAG----KEGTAILMFTSSQRRTVRS  164 (456)
Q Consensus       129 ~~~~~y---~qr~GR~gR~g----~~g~~i~~~~~~e~~~~~~  164 (456)
                      ..+.=|   +.+++|+.-.|    ..-+|.++|+..+.-.+..
T Consensus       633 ~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~  675 (698)
T KOG2340|consen  633 NNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLEN  675 (698)
T ss_pred             CCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHH
Confidence            998766   56676664433    2357888888766544433

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases

Probab=85.70  E-value=7.2  Score=37.35  Aligned_cols=87  Identities=15%  Similarity=0.219  Sum_probs=66.1

Q ss_pred             CCEEEEeCCCCHHHHHHHHhcccCC----CeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccc-cCCCCce
Q 012794           75 IASEALHGDISQHQRERTLNGFRQG----KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG-RAGKEGT  149 (456)
Q Consensus        75 ~~~~~lhg~~~~~~R~~~l~~Fr~g----~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~g-R~g~~g~  149 (456)
                      +.+..++++.+...     -.|.++    ...|+|.=+.++||+.++.+.+....--+...+++.||.=-.| |.|-...
T Consensus       111 ~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgRwFGYR~gY~dl  185 (239)
T PF10593_consen  111 IEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGRWFGYRPGYEDL  185 (239)
T ss_pred             ceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhhcccCCcccccc
Confidence            77888887755433     234433    3789999999999999999999999988999999999975555 5555678


Q ss_pred             EEEeeChhhHHHHHHHH
Q 012794          150 AILMFTSSQRRTVRSLE  166 (456)
Q Consensus       150 ~i~~~~~~e~~~~~~ie  166 (456)
                      |-++.++.-...+..|.
T Consensus       186 ~Ri~~~~~l~~~f~~i~  202 (239)
T PF10593_consen  186 CRIYMPEELYDWFRHIA  202 (239)
T ss_pred             eEEecCHHHHHHHHHHH
Confidence            88888776666665553

This domain is found associated with a helicase domain of superfamily type II [].

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=85.08  E-value=2.5  Score=43.48  Aligned_cols=66  Identities=18%  Similarity=0.204  Sum_probs=47.9

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccccc--CcC
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARGL--DIP  117 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~Gi--dip  117 (456)
                      ..++|.++|++.|.+++..+.+       .+.++-+..+|+......++..    ...|+|+|+     .++.|+  ...
T Consensus        94 ~sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d----~pdIvV~TP~~ll~~~~~~~~~~~~  169 (569)
T KOG0346|consen   94 PSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMD----LPDIVVATPAKLLRHLAAGVLEYLD  169 (569)
T ss_pred             ceeEEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHcc----CCCeEEeChHHHHHHHhhccchhhh
Confidence            4689999999999999887764       2566777788888776666655    778999996     455554  333


Q ss_pred             ccce
Q 012794          118 NVDL  121 (456)
Q Consensus       118 ~v~~  121 (456)
                      .+.+
T Consensus       170 ~l~~  173 (569)
T KOG0346|consen  170 SLSF  173 (569)
T ss_pred             heee
Confidence            4443

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=84.61  E-value=0.4  Score=46.29  Aligned_cols=16  Identities=56%  Similarity=1.479  Sum_probs=15.3

Q ss_pred             cccCCCCCcCcCCCCC
Q 012794          441 CFNCGKSGHRASECPN  456 (456)
Q Consensus       441 ~~~c~~~gh~~~~~p~  456 (456)
                      |+.||++||.+.|||.
T Consensus       163 cyrcGkeghwskEcP~  178 (346)
T KOG0109|consen  163 CYRCGKEGHWSKECPV  178 (346)
T ss_pred             heeccccccccccCCc
Confidence            9999999999999994

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=84.35  E-value=1.6  Score=50.28  Aligned_cols=112  Identities=19%  Similarity=0.251  Sum_probs=77.4

Q ss_pred             cHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCCeEE-EEecccc
Q 012794           36 SKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTV-LVATDVA  110 (456)
Q Consensus        36 ~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v-LVaTdv~  110 (456)
                      .|++.+...+..+   ....++|||+.-....+.+...+. +++.... -++  -+.-...+..|++  +++ |+-+...
T Consensus      1203 ~kI~~v~~~il~iK~k~~qekvIvfsqws~~ldV~e~~~~~N~I~~~~-~~~--t~d~~dc~~~fk~--I~clll~~~~~ 1277 (1394)
T KOG0298|consen 1203 TKIDSVVIAILYIKFKNEQEKVIVFSQWSVVLDVKELRYLMNLIKKQL-DGE--TEDFDDCIICFKS--IDCLLLFVSKG 1277 (1394)
T ss_pred             cCchhHHHHHHHHhccCcCceEEEEEehHHHHHHHHHHHHhhhhHhhh-ccC--Ccchhhhhhhccc--ceEEEEEeccC
Confidence            4544443333222   335689999988777776666665 3332221 121  2334566777876  554 4678889


Q ss_pred             ccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEE
Q 012794          111 ARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL  152 (456)
Q Consensus       111 ~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~  152 (456)
                      +-|+|+-+..||+..++-.++..-.|.+||..|.|++-...+
T Consensus      1278 ~~GLNL~eA~Hvfl~ePiLN~~~E~QAigRvhRiGQ~~pT~V 1319 (1394)
T KOG0298|consen 1278 SKGLNLIEATHVFLVEPILNPGDEAQAIGRVHRIGQKRPTFV 1319 (1394)
T ss_pred             cccccHHhhhhhheeccccCchHHHhhhhhhhhcccccchhh
Confidence            999999999999999999999999999999999997754443

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=83.29  E-value=4.7  Score=44.09  Aligned_cols=59  Identities=19%  Similarity=0.240  Sum_probs=52.2

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      ..+.+||.+|+++.+.+....|.. ++.+..+++.++..++..++...+.+.+++|++|+
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            357899999999999988888875 68889999999999999999999999999999985

>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria

Probab=82.41  E-value=5.6  Score=38.43  Aligned_cols=133  Identities=19%  Similarity=0.259  Sum_probs=74.1

Q ss_pred             CeeEEEEEcCcc-cHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCC
Q 012794           24 GIKLYAISTTAT-SKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK  100 (456)
Q Consensus        24 ~i~~~~~~~~~~-~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~  100 (456)
                      .|+|..+..... +--..+..++... .+.-++|||++...-+...-+.+++ .-.+..+-+.+..  --.+++.    .
T Consensus        33 ~I~h~tyPdnf~~e~EttIskI~~lAdDp~mKaIVv~q~vpGt~~af~kIkekRpDIl~ia~~~~E--Dp~~i~~----~  106 (275)
T PF12683_consen   33 MIKHVTYPDNFMSEQETTISKIVSLADDPDMKAIVVSQAVPGTAEAFRKIKEKRPDILLIAGEPHE--DPEVISS----A  106 (275)
T ss_dssp             EEEEEE--TTGGGCHHHHHHHHHGGGG-TTEEEEEEE-SS---HHHHHHHHHH-TTSEEEESS--S---HHHHHH----H
T ss_pred             eEEEEeCCCcccchHHHHHHHHHHhccCCCccEEEEeCCCcchHHHHHHHHhcCCCeEEEcCCCcC--CHHHHhh----c
Confidence            577877766543 3333444555422 4567999999998887777777774 3445555555322  2233444    4


Q ss_pred             eEEEEeccccccccCcCc------cceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCce
Q 012794          101 FTVLVATDVAARGLDIPN------VDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE  174 (456)
Q Consensus       101 ~~vLVaTdv~~~Gidip~------v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~  174 (456)
                      ++|.|.+|...+|..++.      +...|||.+|.+.. |....-                  ....++.-.+.++++|.
T Consensus       107 aDi~~~~D~~~~G~~i~~~Ak~mGAktFVh~sfprhms-~~~l~~------------------Rr~~M~~~C~~lGi~fv  167 (275)
T PF12683_consen  107 ADIVVNPDEISRGYTIVWAAKKMGAKTFVHYSFPRHMS-YELLAR------------------RRDIMEEACKDLGIKFV  167 (275)
T ss_dssp             SSEEEE--HHHHHHHHHHHHHHTT-S-EEEEEETTGGG-SHHHHH------------------HHHHHHHHHHHCT--EE
T ss_pred             cCeEeccchhhccHHHHHHHHHcCCceEEEEechhhcc-hHHHHH------------------HHHHHHHHHHHcCCeEE
Confidence            678999999999988764      35688998888765 333221                  23667777888899998


Q ss_pred             ecCCCCH
Q 012794          175 FVSPPVV  181 (456)
Q Consensus       175 ~~~~p~~  181 (456)
                      ....|.+
T Consensus       168 ~~taPDP  174 (275)
T PF12683_consen  168 EVTAPDP  174 (275)
T ss_dssp             EEEE---
T ss_pred             EEeCCCC
Confidence            8766653

They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.

>PRK13767 ATP-dependent helicase; Provisional

Probab=82.30  E-value=4  Score=46.65  Aligned_cols=69  Identities=14%  Similarity=0.163  Sum_probs=49.8

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----------------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc-----
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----------------IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----  109 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----------------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv-----  109 (456)
                      .++|+.+||++.+.++...|..                 .+.+...||+.++.++.+.+..    ..+|||+|+-     
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            3699999999999988765431                 2457889999999998877765    5689999962     


Q ss_pred             cccc---cCcCccceEEe
Q 012794          110 AARG---LDIPNVDLIIH  124 (456)
Q Consensus       110 ~~~G---idip~v~~VI~  124 (456)
                      +...   -.+.++.+||.
T Consensus       161 l~~~~~~~~l~~l~~VVI  178 (876)
T PRK13767        161 LNSPKFREKLRTVKWVIV  178 (876)
T ss_pred             hcChhHHHHHhcCCEEEE
Confidence            1111   13567888773

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	456
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		4e-38
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		4e-34
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		4e-26
2jgn_A	185	Ddx3 Helicase Domain Length = 185		8e-24
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-23
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		8e-23
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		8e-23
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-22
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-22
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		2e-22
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-22
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-22
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		4e-21
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		3e-20
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		5e-20
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		1e-19
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		3e-19
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		5e-19
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		5e-18
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		3e-17
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		6e-17
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		1e-15
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		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
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		5e-15
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		5e-15
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		5e-15
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		6e-15
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		6e-15
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		7e-15
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-14
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-14
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-14
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-14
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-13
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		7e-13
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		9e-13
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		5e-12
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		5e-12
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		5e-12
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		7e-12
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		5e-09
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		3e-08
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		4e-08
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		8e-08
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		1e-06
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		5e-06
2eyq_A	1151	Crystal Structure Of Escherichia Coli Transcription		6e-06
2fwr_A	472	Structure Of Archaeoglobus Fulgidis Xpb Length = 47		8e-06
2fzl_A	219	Structure Of C-Terminal Domain Of Archaeoglobus Ful		1e-05
3v4r_A	667	Crystal Structure Of A Uvrb Dimer-Dna Complex Lengt		5e-05
2d7d_A	661	Structural Insights Into The Cryptic Dna Dependent		5e-05
1d9z_A	657	Crystal Structure Of The Dna Repair Protein Uvrb In		8e-05
1d9x_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Le		8e-05
2fdc_A	658	Structural Basis Of Dna Damage Recognition And Proc		8e-05
1t5l_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Po		8e-05
3uwx_B	683	Crystal Structure Of Uvra-Uvrb Complex Length = 683		9e-05
1d2m_A	665	Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleot		3e-04
1c4o_A	664	Crystal Structure Of The Dna Nucleotide Excision Re		3e-04
4i1s_A	243	Melanoma Differentiation Associated Protein-5 Helic		3e-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 (393), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 114/289 (39%), Positives = 168/289 (58%), Gaps = 17/289 (5%)
Query: 29  AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 87
           A+      +  +LSDL+ V A   + +VFT+TK + +E++  L  +   ++ALHGD+SQ 
Sbjct: 7   AVPAPVRGRLEVLSDLLYV-ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQG 65
Query: 88  QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 147
           +RER +  FRQG+  VLVATDVAARGLDIP VDL++HY +P+  E + HRSGRTGRAG+ 
Sbjct: 66  ERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRG 125
Query: 148 GTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFF 207
           G  +L++   +RR V +LER VG +F+ V+PP  E+VLE+    ++A L  V  +    +
Sbjct: 126 GRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLY 185
Query: 208 TPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVT-------LQLTRDSAF 260
              A RL  E   + +AA LA L G +   + RSL+  E+GW T       L L R  A 
Sbjct: 186 QDFAGRLFAEGRVEVVAALLALLLGGAP--AERSLLTGEEGWRTYKATGPRLSLPRLVAL 243
Query: 261 SRG-----FMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLP 304
            +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: 29  AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 87
           A+      +  +LSDL+ V A   + +VFT+TK + +E++  L  +   ++ALHGD+SQ 
Sbjct: 10  AVPAPVRGRLEVLSDLLYV-ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQG 68
Query: 88  QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 147
           +RER L  FRQG+  VLVATDVAARGLDIP VDL++HY LP+  E + HRSGRTGRAG+ 
Sbjct: 69  ERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRG 128
Query: 148 GTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFF 207
           G  +L++   +RR V +LER VG +F+ V+PP  E+VLE+    ++A L  V  +    +
Sbjct: 129 GRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLY 188
Query: 208 TPTAQRLIEE 217
              A RL  E
Sbjct: 189 QDFAGRLFAE 198

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

Iteration: 1
 Score =  115 bits (289), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 51/114 (44%), Positives = 80/114 (70%), Gaps = 1/114 (0%)
Query: 55  IVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG 113
           +VF +TKRD  E++  L  I   + A+HGD+SQ QRE+ +  F+Q K  +L+ATDV +RG
Sbjct: 242 LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRG 301
Query: 114 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
           +D+ +++ +I+Y LP +PE++ HR GRTGRAGK+G AI +    + + +R +ER
Sbjct: 302 IDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISIINRREYKKLRYIER 355

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

Iteration: 1
 Score =  108 bits (269), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 60/145 (41%), Positives = 80/145 (55%), Gaps = 1/145 (0%)
Query: 22  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEAL 80
           +E I    +    + KR+ L DL+    K   T+VF +TK+ AD +         A  ++
Sbjct: 17  SENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSI 76
Query: 81  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 140
           HGD SQ  RE  L+ FR GK  +LVAT VAARGLDI NV  +I+++LP+D E +VHR GR
Sbjct: 77  HGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGR 136
Query: 141 TGRAGKEGTAILMFTSSQRRTVRSL 165
           TGR G  G A   F        + L
Sbjct: 137 TGRVGNLGLATSFFNERNINITKDL 161

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

Iteration: 1
 Score =  107 bits (267), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/150 (40%), Positives = 85/150 (56%), Gaps = 5/150 (3%)
Query: 7   MFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADE 66
           +F    +VG+  E + + +    +    + KR+ L DL+    K   T+VF +TK+ AD 
Sbjct: 236 IFLAVGRVGSTSENITQKV----VWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADS 291
Query: 67  VS-LALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHY 125
           +         A  ++HGD SQ  RE  L+ FR GK  +LVAT VAARGLDI NV  +I++
Sbjct: 292 LEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINF 351
Query: 126 ELPNDPETFVHRSGRTGRAGKEGTAILMFT 155
           +LP+D E +VHR GRTGR G  G A   F 
Sbjct: 352 DLPSDIEEYVHRIGRTGRVGNLGLATSFFN 381

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

Iteration: 1
 Score =  105 bits (261), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 60/173 (34%), Positives = 95/173 (54%), Gaps = 3/173 (1%)
Query: 16  NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
            +DE   EGIK + ++      K   L DL        + ++F  TKR  D ++  +   
Sbjct: 220 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 278
Query: 75  -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
                ++HGD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E 
Sbjct: 279 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 338
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLE 186
           ++HR GR+GR G++G AI    +   R +R +E+    + + +   V + +LE
Sbjct: 339 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE 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 =  104 bits (260), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 60/173 (34%), Positives = 95/173 (54%), Gaps = 3/173 (1%)
Query: 16  NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
            +DE   EGIK + ++      K   L DL        + ++F  TKR  D ++  +   
Sbjct: 242 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 300
Query: 75  -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
                ++HGD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E 
Sbjct: 301 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 360
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLE 186
           ++HR GR+GR G++G AI    +   R +R +E+    + + +   V + +LE
Sbjct: 361 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE 413

>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 =  103 bits (257), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 57/154 (37%), Positives = 87/154 (56%), Gaps = 3/154 (1%)
Query: 16  NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
            +DE   EGIK + ++      K   L DL        + ++F  TKR  D ++  +   
Sbjct: 242 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 300
Query: 75  -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
                ++HGD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E 
Sbjct: 301 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 360
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
           ++HR GR+GR G++G AI    +   R +R +E+
Sbjct: 361 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQ 394

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

Iteration: 1
 Score =  103 bits (257), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 57/154 (37%), Positives = 87/154 (56%), Gaps = 3/154 (1%)
Query: 16  NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
            +DE   EGIK + ++      K   L DL        + ++F  TKR  D ++  +   
Sbjct: 241 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 299
Query: 75  -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
                ++HGD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E 
Sbjct: 300 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 359
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
           ++HR GR+GR G++G AI    +   R +R +E+
Sbjct: 360 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQ 393

>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: 29  AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQH 87
            I     +K ++L D++         I+F +TK   ++++  L  +    + +HG + Q 
Sbjct: 14  VIQVREENKFSLLKDVLMT-ENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQE 72
Query: 88  QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE 147
            R   +N F++G++  LVATDVAARG+DI N+ L+I+Y+LP + E++VHR+GRTGRAG +
Sbjct: 73  DRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNK 132
Query: 148 GTAILMFTSSQRRTVRSLERDVG 170
           G AI   T+ ++R +  +E  +G
Sbjct: 133 GKAISFVTAFEKRFLADIEEYIG 155

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

Iteration: 1
 Score =  103 bits (257), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 56/154 (36%), Positives = 87/154 (56%), Gaps = 3/154 (1%)
Query: 16  NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
            +DE   EGIK + ++      K   L DL        + ++F  TKR  D ++  +   
Sbjct: 205 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 263
Query: 75  -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
                ++HGD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E 
Sbjct: 264 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 323
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
           ++HR GR+GR G++G A+    +   R +R +E+
Sbjct: 324 YIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQ 357

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

Iteration: 1
 Score =  103 bits (256), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 56/154 (36%), Positives = 87/154 (56%), Gaps = 3/154 (1%)
Query: 16  NQDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI 74
            +DE   EGIK + ++      K   L DL        + ++F  TKR  D ++  +   
Sbjct: 205 KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT-QAVIFCNTKRKVDWLTEKMREA 263
Query: 75  -IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET 133
                ++HGD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E 
Sbjct: 264 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 323
Query: 134 FVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER 167
           ++HR GR+GR G++G A+    +   R +R +E+
Sbjct: 324 YIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQ 357

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

Iteration: 1
 Score = 99.0 bits (245), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 55/137 (40%), Positives = 84/137 (61%), Gaps = 5/137 (3%)
Query: 27  LYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDIS 85
           +Y ++  A  KR+ L ++++  A G  TIVF +TKR AD ++  L+     + ++HGD  
Sbjct: 280 IYEVNKYA--KRSKLIEILSEQADG--TIVFVETKRGADFLASFLSEKEFPTTSIHGDRL 335
Query: 86  QHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAG 145
           Q QRE+ L  F+ G   VL+AT VA+RGLDI N+  +I+Y++P+  + +VHR GRTGR G
Sbjct: 336 QSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395
Query: 146 KEGTAILMFTSSQRRTV 162
             G A   F   + R +
Sbjct: 396 NNGRATSFFDPEKDRAI 412

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

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 80/137 (58%), Gaps = 16/137 (11%)
Query: 26  KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-----L 80
           +LY        K  +L++L  V   G  +I+F  TK+ A+     L   + SE      L
Sbjct: 219 QLYMDCKNEADKFDVLTELYGVMTIGS-SIIFVATKKTAN----VLYGKLKSEGHEVSIL 273
Query: 81  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETF 134
           HGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V ++++Y+LP       DP T+
Sbjct: 274 HGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATY 333
Query: 135 VHRSGRTGRAGKEGTAI 151
           +HR GRTGR G++G AI
Sbjct: 334 IHRIGRTGRFGRKGVAI 350

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

Iteration: 1
 Score = 95.5 bits (236), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 47/119 (39%), Positives = 73/119 (61%), Gaps = 16/119 (13%)
Query: 39  TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQ 98
           TI S +I V  K    +++ + K +  EVS+          LHGD+   +R+R ++ FR+
Sbjct: 242 TIGSSIIFVATKKTANVLYGKLKSEGHEVSI----------LHGDLQTQERDRLIDDFRE 291
Query: 99  GKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 151
           G+  VL+ T+V ARG+DIP V ++++Y+LP       DP T++HR GRTGR G++G AI
Sbjct: 292 GRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 350

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 47/119 (39%), Positives = 73/119 (61%), Gaps = 16/119 (13%)
Query: 39  TILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQ 98
           TI S +I V  K    +++ + K +  EVS+          LHGD+   +R+R ++ FR+
Sbjct: 34  TIGSSIIFVATKKTANVLYGKLKSEGHEVSI----------LHGDLQTQERDRLIDDFRE 83
Query: 99  GKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAI 151
           G+  VL+ T+V ARG+DIP V ++++Y+LP       DP T++HR GRTGR G++G AI
Sbjct: 84  GRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAI 142

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

Iteration: 1
 Score = 93.2 bits (230), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 79/137 (57%), Gaps = 16/137 (11%)
Query: 26  KLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEA-----L 80
           +LY        K  +L++L  V   G  +I+F  TK+ A+     L   + SE      L
Sbjct: 12  QLYXDCKNEADKFDVLTELYGVXTIGS-SIIFVATKKTAN----VLYGKLKSEGHEVSIL 66
Query: 81  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETF 134
           HGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V  +++Y+LP       DP T+
Sbjct: 67  HGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATY 126
Query: 135 VHRSGRTGRAGKEGTAI 151
           +HR GRTGR G++G AI
Sbjct: 127 IHRIGRTGRFGRKGVAI 143

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

Iteration: 1
 Score = 92.4 bits (228), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 50/142 (35%), Positives = 80/142 (56%), Gaps = 23/142 (16%)
Query: 16  NQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSII 75
           N+ +K     +LY + T  +S       +I V  K    +++ + K +  EVS+      
Sbjct: 20  NEADKFDVLTELYGLXTIGSS-------IIFVATKKTANVLYGKLKSEGHEVSI------ 66
Query: 76  ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN------ 129
               LHGD+   +R+R ++ FR+G+  VL+ T+V ARG+DIP V  +++Y+LP       
Sbjct: 67  ----LHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQA 122
Query: 130 DPETFVHRSGRTGRAGKEGTAI 151
           DP T++HR GRTGR G++G AI
Sbjct: 123 DPATYIHRIGRTGRFGRKGVAI 144

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

Iteration: 1
 Score = 89.0 bits (219), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/99 (45%), Positives = 66/99 (66%), Gaps = 5/99 (5%)
Query: 54  TIVFTQTK-RDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR 112
            IVF +T+ R A  V L   +I     L GD+ Q  R R ++ FR+G++ +L+ TDVA+R
Sbjct: 223 VIVFVRTRNRVAKLVRLFDNAI----ELRGDLPQSVRNRNIDAFREGEYDMLITTDVASR 278
Query: 113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
           GLDIP V+ +I+++ P D  T++HR GRTGR G++G AI
Sbjct: 279 GLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAI 317

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

Iteration: 1
 Score = 86.7 bits (213), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 40/98 (40%), Positives = 61/98 (62%), Gaps = 1/98 (1%)
Query: 54  TIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR 112
            ++F + K D D +    L   + + A+HG   Q +R + +  FR+GK  VLVATDVA++
Sbjct: 57  VLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK 116
Query: 113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTA 150
           GLD P +  +I+Y++P + E +VHR GRTG +G  G A
Sbjct: 117 GLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIA 154

>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: 53  KTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA 111
           ++IVF + +    E++  L    I +  L G++ Q +R   +    +G+  VLVATDVAA
Sbjct: 32  RSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAA 91
Query: 112 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
           RG+DIP+V  + ++++P   +T++HR GRT RAG++GTAI
Sbjct: 92  RGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAI 131

>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 = 80.9 bits (198), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 83/159 (52%), Gaps = 2/159 (1%)
Query: 13  QVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT 72
           ++   +E   +G+  Y    T   K   L+ L +   +  ++I+F  + +  + ++  ++
Sbjct: 7   EINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSR-LQINQSIIFCNSSQRVELLAKKIS 65
Query: 73  SI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP 131
            +  +   +H  + Q  R R  + FR G    LV TD+  RG+DI  V+++I+++ P   
Sbjct: 66  QLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLA 125
Query: 132 ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG 170
           ET++HR GR+GR G  G AI + T   R  ++S+E  +G
Sbjct: 126 ETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLG 164

>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: 52  GKTIVFTQTKRDADEVSLALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVA 110
           G+ I+F QT+R+A  +++ +       +L  G+++  QR   +  FR GK  VL+ T+V 
Sbjct: 35  GQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVC 94
Query: 111 ARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAILMF 154
           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: 80  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 140 RTGRAGKEGTAILMFTSSQRRTVRSLE 166
           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: 80  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 140 RTGRAGKEGTAILMFTSSQRRTVRSLE 166
           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: 80  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 66  FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 125
Query: 140 RTGRAGKEGTAILMFTSSQRRTVRSLE 166
           RT R+GKEG+++L     +   VR LE
Sbjct: 126 RTARSGKEGSSVLFICKDELPFVRELE 152

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

Iteration: 1
 Score = 79.0 bits (193), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 86/152 (56%), Gaps = 3/152 (1%)
Query: 17  QDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI- 74
           ++E   EGI+ + I+      K   L DL        + ++F  T+R  D ++  + +  
Sbjct: 246 KEELTLEGIRQFYINVEREEWKLDTLCDLYETLTIT-QAVIFINTRRKVDWLTEKMHARD 304
Query: 75  IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF 134
               A+HGD+ Q +R+  +  FR G   VL+ TD+ ARG+D+  V L+I+Y+LP + E +
Sbjct: 305 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 364
Query: 135 VHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 166
           +HR GR GR G++G AI M T   +RT+R +E
Sbjct: 365 IHRIGRGGRFGRKGVAINMVTEEDKRTLRDIE 396

>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 = 79.0 bits (193), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 34/87 (39%), Positives = 55/87 (63%)
Query: 80  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
            HG I+Q++R   +  F++ +  +LV TDV ARG+D PNV  ++   +P++   ++HR G
Sbjct: 321 FHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIG 380
Query: 140 RTGRAGKEGTAILMFTSSQRRTVRSLE 166
           RT R+GKEG+++L     +   VR LE
Sbjct: 381 RTARSGKEGSSVLFICKDELPFVRELE 407

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

Iteration: 1
 Score = 79.0 bits (193), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 42/122 (34%), Positives = 68/122 (55%), Gaps = 12/122 (9%)
Query: 53  KTIVFTQTKRDADEVSLALTSIIASE--------ALHGDISQHQRERTLNGFRQGKFTVL 104
           K I+F  T +     +  L SI+ +E          HG I+Q++R   +  F++ +  +L
Sbjct: 290 KAIIFAPTVK----FTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGIL 345
Query: 105 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 164
           V TDV ARG+D PNV  ++   +P++   ++HR GRT R+GKEG+++L     +   VR 
Sbjct: 346 VCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRE 405
Query: 165 LE 166
           LE
Sbjct: 406 LE 407

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

Iteration: 1
 Score = 78.6 bits (192), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 42/122 (34%), Positives = 68/122 (55%), Gaps = 12/122 (9%)
Query: 53  KTIVFTQTKRDADEVSLALTSIIASE--------ALHGDISQHQRERTLNGFRQGKFTVL 104
           K I+F  T +     +  L SI+ +E          HG I+Q++R   +  F++ +  +L
Sbjct: 341 KAIIFAPTVK----FTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGIL 396
Query: 105 VATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRS 164
           V TDV ARG+D PNV  ++   +P++   ++HR GRT R+GKEG+++L     +   VR 
Sbjct: 397 VCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRE 456
Query: 165 LE 166
           LE
Sbjct: 457 LE 458

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

Iteration: 1
 Score = 78.6 bits (192), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 86/152 (56%), Gaps = 3/152 (1%)
Query: 17  QDEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI- 74
           ++E   EGI+ + I+      K   L DL        + ++F  T+R  D ++  + +  
Sbjct: 220 KEELTLEGIRQFYINVEREEWKLDTLCDLYETLTIT-QAVIFINTRRKVDWLTEKMHARD 278
Query: 75  IASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF 134
               A+HGD+ Q +R+  +  FR G   VL+ TD+ ARG+D+  V L+I+Y+LP + E +
Sbjct: 279 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 338
Query: 135 VHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE 166
           +HR GR GR G++G AI M T   +RT+R +E
Sbjct: 339 IHRIGRGGRFGRKGVAINMVTEEDKRTLRDIE 370

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

Iteration: 1
 Score = 78.6 bits (192), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 41/137 (29%), Positives = 77/137 (56%), Gaps = 3/137 (2%)
Query: 37  KRTILSDLITVYAKG--GKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTL 93
           +R  L  L T+++K    + I+F  +    + ++  +T +  +    H  + Q +R +  
Sbjct: 242 ERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVF 301
Query: 94  NGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM 153
           + FRQGK   LV +D+  RG+DI  V+++I+++ P   ET++HR GR+GR G  G AI +
Sbjct: 302 HEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINL 361
Query: 154 FTSSQRRTVRSLERDVG 170
              + R  +  +E+++G
Sbjct: 362 INWNDRFNLYKIEQELG 378

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

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 81/165 (49%), Gaps = 29/165 (17%)
Query: 4   YFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD 63
           Y+V+ S      ++DEK      LY   T A +       +I  + +   + +  +  ++
Sbjct: 310 YYVLCS------SRDEKFQALCNLYGAITIAQA-------MIFCHTRKTASWLAAELSKE 356
Query: 64  ADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 123
             +V+L          L G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I
Sbjct: 357 GHQVAL----------LSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI 406
Query: 124 HYELPNDP------ETFVHRSGRTGRAGKEGTAILMFTSSQRRTV 162
           +++LP D       ET++HR GRTGR GK G A+ M  S     +
Sbjct: 407 NFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 451

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

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 50/160 (31%), Positives = 84/160 (52%), Gaps = 14/160 (8%)
Query: 13  QVGNQDEKLAEGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSL 69
           ++  ++E L    + Y + ++   K   L +L   IT+     + ++F  T++ A  ++ 
Sbjct: 266 KLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAA 321
Query: 70  ALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 128
            L+      AL  G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I+++LP
Sbjct: 322 ELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 381
Query: 129 NDP------ETFVHRSGRTGRAGKEGTAILMFTSSQRRTV 162
            D       ET++HR GRTGR GK G A+ M  S     +
Sbjct: 382 VDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 421

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

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 50/160 (31%), Positives = 84/160 (52%), Gaps = 14/160 (8%)
Query: 13  QVGNQDEKLAEGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSL 69
           ++  ++E L    + Y + ++   K   L +L   IT+     + ++F  T++ A  ++ 
Sbjct: 229 KLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAA 284
Query: 70  ALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 128
            L+      AL  G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I+++LP
Sbjct: 285 ELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 344
Query: 129 NDP------ETFVHRSGRTGRAGKEGTAILMFTSSQRRTV 162
            D       ET++HR GRTGR GK G A+ M  S     +
Sbjct: 345 VDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNI 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 = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 50/154 (32%), Positives = 83/154 (53%), Gaps = 14/154 (9%)
Query: 13  QVGNQDEKLAEGIKLYAISTTATSKRTILSDL---ITVYAKGGKTIVFTQTKRDADEVSL 69
           ++  ++E L    + Y + ++   K   L +L   IT+     + ++F  T++ A  ++ 
Sbjct: 245 KLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI----AQAMIFCHTRKTASWLAA 300
Query: 70  ALTSIIASEAL-HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELP 128
            L+      AL  G++   QR   +  FR+GK  VLV T+V ARG+D+  V ++I+++LP
Sbjct: 301 ELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 360
Query: 129 NDP------ETFVHRSGRTGRAGKEGTAILMFTS 156
            D       ET++HR GRTGR GK G A+ M  S
Sbjct: 361 VDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDS 394

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

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 52/163 (31%), Positives = 89/163 (54%), Gaps = 9/163 (5%)
Query: 17  QDEKLAEGIKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL- 71
           +DE   EGIK + ++      +    T L D I+V     + ++F  T+R  +E++  L 
Sbjct: 226 KDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLR 281
Query: 72  TSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP 131
                  A++ D+ Q +R+  +  FR G   +L++TD+ ARG+D+  V L+I+Y+LP + 
Sbjct: 282 NDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANK 341
Query: 132 ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 174
           E ++HR GR GR G++G AI   T+     +R LE+    + E
Sbjct: 342 ENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIE 384

>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 = 7e-13,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 86/157 (54%), Gaps = 9/157 (5%)
Query: 23  EGIKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL-TSIIAS 77
           EGIK + ++      +    T L D I+V     + ++F  T+R  +E++  L       
Sbjct: 2   EGIKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLRNDKFTV 57
Query: 78  EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHR 137
            A++ D+ Q +R+  +  FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR
Sbjct: 58  SAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHR 117
Query: 138 SGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 174
            GR GR G++G AI   T+     +R LE+    + E
Sbjct: 118 IGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIE 154

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 52/163 (31%), Positives = 87/163 (53%), Gaps = 9/163 (5%)
Query: 17  QDEKLAEGIKLYAISTTATSKR----TILSDLITVYAKGGKTIVFTQTKRDADEVSLAL- 71
           +DE   EGIK + ++      +    T L D I+V     + ++F  T+R  +E++  L 
Sbjct: 225 KDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISV----TQAVIFCNTRRKVEELTTKLR 280
Query: 72  TSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDP 131
                  A++ D+ Q +R+     FR G   +L++TD+ ARG+D+  V L+I+Y+LP + 
Sbjct: 281 NDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANK 340
Query: 132 ETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFE 174
           E ++HR GR GR G++G AI   T+      R LE+    + E
Sbjct: 341 ENYIHRIGRGGRFGRKGVAINFVTNEDVGAXRELEKFYSTQIE 383

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 62/128 (48%)
Query: 24  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 83
           G++ Y +      K   L DL+ V       I     +R      L +     + A+H  
Sbjct: 224 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 283
Query: 84  ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
           + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R GR
Sbjct: 284 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 343
Query: 144 AGKEGTAI 151
            G +G AI
Sbjct: 344 FGTKGLAI 351

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 62/128 (48%)
Query: 24  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 83
           G++ Y +      K   L DL+ V       I     +R      L +     + A+H  
Sbjct: 224 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 283
Query: 84  ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
           + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R GR
Sbjct: 284 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 343
Query: 144 AGKEGTAI 151
            G +G AI
Sbjct: 344 FGTKGLAI 351

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 62/128 (48%)
Query: 24  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 83
           G++ Y +      K   L DL+ V       I     +R      L +     + A+H  
Sbjct: 223 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 282
Query: 84  ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
           + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R GR
Sbjct: 283 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 342
Query: 144 AGKEGTAI 151
            G +G AI
Sbjct: 343 FGTKGLAI 350

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 62/128 (48%)
Query: 24  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGD 83
           G++ Y +      K   L DL+ V       I     +R      L +     + A+H  
Sbjct: 5   GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 64
Query: 84  ISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
           + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R GR
Sbjct: 65  MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 124
Query: 144 AGKEGTAI 151
            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 = 59.3 bits (142), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 38/113 (33%), Positives = 55/113 (48%), Gaps = 9/113 (7%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTS-------IIASEALHGD--ISQHQRERTLNGFRQGK 100
           +  K IVFT  +  A ++   L          +   +   D  +SQ +++  L+ F +G+
Sbjct: 360 QNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE 419
Query: 101 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM 153
           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 = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/112 (25%), Positives = 57/112 (50%), Gaps = 1/112 (0%)
Query: 44  LITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFT 102
           LI    KG   I++  +++D+++V+++L ++ I + A H ++    +      +   +  
Sbjct: 260 LINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQ 319
Query: 103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 154
           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 = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/106 (24%), Positives = 55/106 (51%), Gaps = 1/106 (0%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +G   I++  ++   ++ +  L S  I++ A H  +  + R      F++    ++VAT 
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV 294
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 154
               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 = 55.1 bits (131), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 26/106 (24%), Positives = 54/106 (50%), Gaps = 1/106 (0%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +G   I++  ++   ++ +  L S  I++ A H  +  + R      F++    ++VAT 
Sbjct: 235 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV 294
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 154
               G++ PNV  ++H+++P + E++   +GR GR G    A L +
Sbjct: 295 AFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFY 340

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 47/79 (59%), Gaps = 9/79 (11%)
Query: 80  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETF----V 135
           +HG +SQ +++R +  F +G++ +LV+T V   G+D+P  ++++      +PE F    +
Sbjct: 619 MHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMV----IENPERFGLAQL 674
Query: 136 HR-SGRTGRAGKEGTAILM 153
           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 = 5e-06,   Method: Compositional matrix adjust.
 Identities = 41/147 (27%), Positives = 71/147 (48%), Gaps = 21/147 (14%)
Query: 35  TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-----SIIASEALH-------- 81
           T  R  + +  T   +  + I+FT+T++ A  +S  +T     + +  +A H        
Sbjct: 384 TKLRNTIMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSS 443
Query: 82  --GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSG 139
               ++Q++++  ++ FR GK  +L+AT VA  GLDI   +++I Y L  +    V   G
Sbjct: 444 EFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARG 503
Query: 140 RTGRAGKEGTAILMFTSS----QRRTV 162
           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 = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 21/112 (18%)
Query: 81  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----HYELPNDPETFV 135
           HG + + + ER +N F   +F VLV T +   G+DIP  + II     H+ L       +
Sbjct: 845 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ-----L 899
Query: 136 HR-SGRTGRAGKEGTAIL-------MFTSSQRR--TVRSLERDVGCKFEFVS 177
           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 = 48.5 bits (114), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 35/158 (22%), Positives = 72/158 (45%), Gaps = 9/158 (5%)
Query: 8   FSHSTQVGNQDEKLAEGIKLYA----ISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD 63
           F+        DE+  E ++ +     I+  + +K   L +++  + K  K I+FT+    
Sbjct: 303 FNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKD-KIIIFTRH--- 358
Query: 64  ADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 123
            +E+   ++ +    A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +
Sbjct: 359 -NELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGV 417
Query: 124 HYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT 161
                     ++ R GR  R  K     +++    R T
Sbjct: 418 IMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGT 455

>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus Xpb Length = 219

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 33/143 (23%), Positives = 67/143 (46%), Gaps = 9/143 (6%)
Query: 8   FSHSTQVGNQDEKLAEGIKLYA----ISTTATSKRTILSDLITVYAKGGKTIVFTQTKRD 63
           F+        DE+  E ++ +     I+  + +K   L +++  + K  K I+FT+    
Sbjct: 68  FNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKD-KIIIFTRH--- 123
Query: 64  ADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII 123
            +E+   ++ +    A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +
Sbjct: 124 -NELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGV 182
Query: 124 HYELPNDPETFVHRSGRTGRAGK 146
                     ++ R GR  R  K
Sbjct: 183 IMSGSGSAREYIQRLGRILRPSK 205

>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex Length = 667

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 11/111 (9%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +  + +V T TK+ +++++  L  I I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 450 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 509
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 152
           +   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 = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 11/111 (9%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +  + +V T TK+ +++++  L  I I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK--EGTAIL 152
           +   GLDIP V L+    L  D E F+ RS R+     GRA +  EG  I+
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNAEGRVIM 551

>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In Complex With Atp Length = 657

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 443 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 502
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
           +   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 = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 504 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 555

>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX Length = 658

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
           +   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 = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 444 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
           +   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 = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 50  KGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFTVLVATD 108
           +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R GK+ VLV  +
Sbjct: 469 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 528
Query: 109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGKEGTA-ILMFTSS 157
           +   GLDIP V L+    L  D E F+ RS R+     GRA +     ++M+  +
Sbjct: 529 LLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAARNANGHVIMYADT 580

>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: 49  AKGGKTIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 107
           A+G +T+V   T R A+E+ S  +   I +  LH ++   +R+  +   R G +  LV  
Sbjct: 438 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI 497
Query: 108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK 146
           ++   GLDIP V L+    L  D E F+ RS R+     GRA +
Sbjct: 498 NLLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAAR 538

>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair Enzyme Uvrb From Thermus Thermophilus Length = 664

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 9/104 (8%)
Query: 49  AKGGKTIVFTQTKRDADEV-SLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT 107
           A+G +T+V   T R A+E+ S  +   I +  LH ++   +R+  +   R G +  LV  
Sbjct: 437 ARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI 496
Query: 108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRT-----GRAGK 146
           ++   GLDIP V L+    L  D E F+ RS R+     GRA +
Sbjct: 497 NLLREGLDIPEVSLVAI--LDADKEGFL-RSERSLIQTIGRAAR 537

>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase Domain Complex With Inhibitor Non-structural Protein V Length = 243

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 53/108 (49%), Gaps = 15/108 (13%)
Query: 35  TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALT-----SIIASEALH-------- 81
           T  R  + +  T   +  + I+FT+T++ A  +S  +T     + +  +A H        
Sbjct: 134 TKLRNTIXEHFTRTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIGAGHSS 193
Query: 82  --GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL 127
                +Q+++   ++ FR GK  +L+AT VA  GLDI   +++I Y L
Sbjct: 194 EFKPXTQNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL 241

>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In Complex With Unwound Dna Length = 702

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 40/167 (23%), Positives = 68/167 (40%), Gaps = 41/167 (24%)
Query: 34  ATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSIIA----SEAL-------- 80
           +TS+R    +L+    A+ G  +VF  T+R A++ ++ L++I A    +E L        
Sbjct: 224 STSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEEN 283
Query: 81  -------------------HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL 121
                              H  +   QR    + FR+G   V+VAT   A G+++P   +
Sbjct: 284 EGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRV 343
Query: 122 IIH-------YELPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQR 159
           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	456
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
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.97
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
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.96
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.96
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.9
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.92
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.92
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.92
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.92
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.91
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.91
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.91
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.91
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.9
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.9
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.9
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.87
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.87
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.86
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.86
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.85
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.84
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.84
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.84
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.83
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.83
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.82
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.82
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.81
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.81
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.8
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.8
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.79
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.79
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.79
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.78
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.77
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.77
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.77
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.77
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.77
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.76
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.76
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.74
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.74
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.74
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.74
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.74
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.72
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.72
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.71
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.7
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.69
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.68
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.68
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.68
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.66
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.66
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.65
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.63
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.62
3h1t_A	590	Type I site-specific restriction-modification syst	99.6
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.59
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.57
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.54
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.27
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	98.34
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	98.27
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.25
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.05
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.98
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.92
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.8
3i31_A	88	Heat resistant RNA dependent ATPase; RNA helicase,	97.79
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.61
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.53
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.45
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.44
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	97.42
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.41
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.41
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	97.38
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.38
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.34
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.27
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.19
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.17
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.1
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.05
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	97.01
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	96.99
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	96.97
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	96.91
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	96.75
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	96.69
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	96.06
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	96.05
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.03
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	95.63
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	95.44
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	95.08
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	94.5
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	94.27
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	94.19
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	94.1
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	94.03
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	93.33
3bor_A	237	Human initiation factor 4A-II; translation initiat	92.86
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	92.86
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	92.66
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	92.61
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	92.55
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	92.36
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	92.28
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	92.03
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	91.37
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	91.35
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	91.14
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	89.49
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	89.04
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	88.82
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	88.11
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	87.87
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	87.62
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	87.36
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	86.44
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	86.28
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	85.17
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	84.84
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	84.81
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	84.59
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	84.39
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	81.15
3b6e_A	216	Interferon-induced helicase C domain-containing P;	80.75

>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=5.4e-46  Score=365.92  Aligned_cols=289  Identities=38%  Similarity=0.587  Sum_probs=253.6

Q ss_pred             CeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeE
Q 012794           24 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        24 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  102 (456)
                      +++|+++.++..+|+++|.+++..+. ..++||||+|+++++.|+..|.. ++.+.+|||+|++.+|+.+++.|++|+++
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            57899999999999999999998875 68999999999999999999985 78999999999999999999999999999


Q ss_pred             EEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCCCHH
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE  182 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p~~~  182 (456)
                      |||||+++++|||+|++++||+|++|++.++|+||+|||||+|+.|.|++|+++.+...++.+++.++..++.+.+|+.+
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             HHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHHHHHHHHHhCCCCCCCCccccCCCCceEEEEEeecCcccc
Q 012794          183 DVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSR  262 (456)
Q Consensus       183 ~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~a~ala~~~~~~~~~~~r~l~~~~~g~~t~~~~~~~~~~~  262 (456)
                      ++.+..+..++..+..+.....+.|.+++++++++..++.+++||+.+++...  ..+++++..++|+|++++.++   .
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            99999999999999888888899999999999999999999999999998776  678898889999999999987   3


Q ss_pred             CCCChhHHHHHHHhhCCCCCCccccEEEeecCccceeeeecCHHHHHHHHhhcCCCCCceeecccCCCccCCC
Q 012794          263 GFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIPPGNTISKITKLPALQDDG  335 (456)
Q Consensus       263 ~~~~~~~i~~~l~~~~~~~~~~ig~i~~~~~~~~~~~~~dv~~~~a~~~~~~~~~~g~~l~~~t~LP~l~~~~  335 (456)
                      ..  |++|+ .|... +.   +||.|+|.+++    +|||||++.++      ..++++++++++||+|+..+
T Consensus       236 ~~--~~~~~-~i~~~-~~---~ig~i~~~~~~----~~~dvp~~~~~------~~~~~~~~~~~~~p~~~~~~  291 (300)
T 3i32_A          236 SL--PRLVA-LLKGQ-GL---EVGKVAEAEGG----FYVDLRPEARP------EVAGLRLEPARRVEGLLEIP  291 (300)
T ss_dssp             CH--HHHHH-HHHHT-TC---CCCCEEEETTE----EEECBCSSCCC------CCTTCEEEEC----------
T ss_pred             CC--cHHHH-HHHhc-CC---eECcEEEeCCE----EEEEeCHHHcC------cCCCcEEEecccCCCCccCC
Confidence            33  99997 55553 33   99999997775    89999999987      34689999999999999875

>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=8.3e-35  Score=272.65  Aligned_cols=207  Identities=44%  Similarity=0.700  Sum_probs=194.4

Q ss_pred             CeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeE
Q 012794           24 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        24 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  102 (456)
                      .+.+.++.++...|+++|.+++.... .+++||||+|+.+++.++..|.. ++.+..+||+|++.+|+++++.|+++.++
T Consensus         5 ~~~~~~~~~~~~~k~~~l~~ll~~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~   83 (212)
T 3eaq_A            5 TYEEEAVPAPVRGRLEVLSDLLYVAS-PDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVR   83 (212)
T ss_dssp             CBCCEEEECCTTSHHHHHHHHHHHHC-CSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCC
T ss_pred             ceeeeEEeCCHHHHHHHHHHHHHhCC-CCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCe
Confidence            46788888999999999999998764 68999999999999999999985 78999999999999999999999999999


Q ss_pred             EEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCCCHH
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVE  182 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p~~~  182 (456)
                      |||||+++++|||+|++++||+|++|++++.|+||+|||||.|+.|.|++|+++.+...++.+++.++..++.+.+|+.+
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             HHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHhhcCHHHHHHHHHHHh
Q 012794          183 DVLESSAEQVVATLNGVHPESVEFFTPTAQRLIEEKGTDALAAALAQLS  231 (456)
Q Consensus       183 ~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ll~~~~~~~~a~ala~~~  231 (456)
                      ++.+.....++..+..........|.+.+++++++++++++++||++++
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            9999999999999998877777899999999999999999999999873

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

Probab=99.97  E-value=1.2e-29  Score=227.45  Aligned_cols=157  Identities=34%  Similarity=0.601  Sum_probs=147.5

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      ....+|+|+++.++..+|+.+|.+++... ...++||||+|+..++.+++.|.. ++.+..+||+|++.+|..+++.|++
T Consensus         5 ~~~~~i~~~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~   83 (163)
T 2hjv_A            5 LTTRNIEHAVIQVREENKFSLLKDVLMTE-NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKR   83 (163)
T ss_dssp             -CCCCEEEEEEECCGGGHHHHHHHHHHHH-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             cCcccceEEEEECChHHHHHHHHHHHHhc-CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHc
Confidence            45667999999999999999999999876 457999999999999999999985 7899999999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecC
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  177 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~  177 (456)
                      ++++|||||+++++|+|+|++++||+|++|+++..|+||+||+||.|++|.+++|+.+.+...++.+++.++.++++++
T Consensus        84 g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  162 (163)
T 2hjv_A           84 GEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQKIE  162 (163)
T ss_dssp             TSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHHHHHTSCCEECC
T ss_pred             CCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHHHHHHHHHCCCcCccC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999998887653

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

Probab=99.97  E-value=8.3e-30  Score=231.22  Aligned_cols=162  Identities=28%  Similarity=0.495  Sum_probs=147.0

Q ss_pred             ccccCeeEEEEEcCccc-HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhccc
Q 012794           20 KLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR   97 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr   97 (456)
                      .++.+|+|+|+.++..+ |+.+|.+++... ...++||||+|+..++.++..|.. ++.+..+||+|++.+|..+++.|+
T Consensus         3 ~~~~~i~q~~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~   81 (175)
T 2rb4_A            3 LTLNNIRQYYVLCEHRKDKYQALCNIYGSI-TIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFR   81 (175)
T ss_dssp             CCBCCEEEEEEECSSHHHHHHHHHHHHTTS-CCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHH
T ss_pred             CccCCceEEEEEcCChHhHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHH
Confidence            45678999999998765 999999988765 457999999999999999999985 789999999999999999999999


Q ss_pred             CCCeEEEEeccccccccCcCccceEEecCCC------CChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCC
Q 012794           98 QGKFTVLVATDVAARGLDIPNVDLIIHYELP------NDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGC  171 (456)
Q Consensus        98 ~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p------~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~  171 (456)
                      ++.++|||||+++++|+|+|++++||+||+|      .+..+|+||+||+||.|+.|.+++|+.+.+...+..+++.++.
T Consensus        82 ~g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~  161 (175)
T 2rb4_A           82 DGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNS  161 (175)
T ss_dssp             TTSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHHHHHHTC
T ss_pred             cCCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHHHHHhcC
Confidence            9999999999999999999999999999999      8999999999999999999999999999999999999999999


Q ss_pred             CceecCCCCHH
Q 012794          172 KFEFVSPPVVE  182 (456)
Q Consensus       172 ~~~~~~~p~~~  182 (456)
                      .++.++++..+
T Consensus       162 ~~~~~~~~~~~  172 (175)
T 2rb4_A          162 SIKQLNAEDMD  172 (175)
T ss_dssp             CCEEECSSCCC
T ss_pred             cccccCCchhc
Confidence            99988877554

>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=2.9e-29  Score=227.19  Aligned_cols=157  Identities=23%  Similarity=0.443  Sum_probs=144.3

Q ss_pred             cccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCC
Q 012794           21 LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQG   99 (456)
Q Consensus        21 ~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g   99 (456)
                      ++.+|+|+++.++..+|+.+|.+++... +..++||||+|+..++.++..|.. ++.+..+||+|++.+|+.+++.|+++
T Consensus         2 ~~~~i~q~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g   80 (172)
T 1t5i_A            2 SLHGLQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF   80 (172)
T ss_dssp             ---CCEEEEEECCGGGHHHHHHHHHHHS-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             ccCCeEEEEEECChHHHHHHHHHHHHhC-CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCC
Confidence            3568999999999999999999999876 467999999999999999999985 78999999999999999999999999


Q ss_pred             CeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh-hHHHHHHHHHHhCCCceecCC
Q 012794          100 KFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFVSP  178 (456)
Q Consensus       100 ~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-e~~~~~~ie~~~~~~~~~~~~  178 (456)
                      .++|||||+++++|+|+|++++||+||+|++++.|+||+||+||.|+.|.+++|+.+. +...++.+++.+...++.++.
T Consensus        81 ~~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  160 (172)
T 1t5i_A           81 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPD  160 (172)
T ss_dssp             SCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC-
T ss_pred             CCcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCCh
Confidence            9999999999999999999999999999999999999999999999999999999875 578899999999988887654

>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=5.5e-29  Score=223.60  Aligned_cols=156  Identities=31%  Similarity=0.584  Sum_probs=140.8

Q ss_pred             cCeeEEEEEcCccc-HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCC
Q 012794           23 EGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK  100 (456)
Q Consensus        23 ~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~  100 (456)
                      .+|+|+|+.++..+ |+++|.+++... ...++||||+|++.++.++..|.. ++.+..+||+|++.+|..+++.|++++
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            46899999988877 999999999876 468999999999999999999985 789999999999999999999999999


Q ss_pred             eEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCCC
Q 012794          101 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPP  179 (456)
Q Consensus       101 ~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~p  179 (456)
                      ++|||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++++.+.+...+..+++.++..++.++.+
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            9999999999999999999999999999999999999999999999999999999999999999999999988877655

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

Probab=99.96  E-value=3.5e-29  Score=230.60  Aligned_cols=165  Identities=26%  Similarity=0.382  Sum_probs=133.1

Q ss_pred             cccccCCCccccCCcccccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEe
Q 012794            3 NYFVMFSHSTQVGNQDEKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALH   81 (456)
Q Consensus         3 ~~l~~~~~i~~v~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lh   81 (456)
                      +|++++..|.+-  ....+..+|+|+++.++...|+..|.+++...  ..++||||+|+..++.+++.|.. ++.+..+|
T Consensus        10 ~~~~~p~~i~v~--~~~~~~~~i~q~~~~~~~~~K~~~L~~~l~~~--~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lh   85 (191)
T 2p6n_A           10 GVDLGTENLYFQ--SMGAASLDVIQEVEYVKEEAKMVYLLECLQKT--PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIH   85 (191)
T ss_dssp             --------------------CCSEEEEEECCGGGHHHHHHHHHTTS--CSCEEEECSCHHHHHHHHHHHHHHTCCEEEEC
T ss_pred             cccCCCEEEEEC--CCCCCCcCceEEEEEcChHHHHHHHHHHHHhC--CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEe
Confidence            678888777653  33456789999999999999999999988653  46899999999999999999985 78999999


Q ss_pred             CCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh-hHH
Q 012794           82 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRR  160 (456)
Q Consensus        82 g~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-e~~  160 (456)
                      |+|++.+|+++++.|++++++|||||+++++|||+|++++||+||+|++++.|+||+|||||.|++|.+++|+++. +..
T Consensus        86 g~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~  165 (191)
T 2p6n_A           86 GGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDES  165 (191)
T ss_dssp             TTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHH
T ss_pred             CCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999876 677


Q ss_pred             HHHHHHHHhCC
Q 012794          161 TVRSLERDVGC  171 (456)
Q Consensus       161 ~~~~ie~~~~~  171 (456)
                      .++.|++.+..
T Consensus       166 ~~~~l~~~l~~  176 (191)
T 2p6n_A          166 VLMDLKALLLE  176 (191)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            77777776543

>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=7.1e-29  Score=227.39  Aligned_cols=154  Identities=40%  Similarity=0.559  Sum_probs=128.6

Q ss_pred             cccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhccc
Q 012794           19 EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR   97 (456)
Q Consensus        19 ~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr   97 (456)
                      ..+..+|+|+++.++...|+..|.+++....+..++||||+|+..++.|+..|.. ++.+..+||+|++.+|+.+++.|+
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            4567789999999999999999999998876678999999999999999999985 789999999999999999999999


Q ss_pred             CCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCC
Q 012794           98 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCK  172 (456)
Q Consensus        98 ~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~  172 (456)
                      +++++|||||+++++|+|+|++++||+||+|+++.+|+||+||+||.|+.|.+++|+++.+...++.+++.+...
T Consensus        94 ~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~l~~~  168 (185)
T 2jgn_A           94 SGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEA  168 (185)
T ss_dssp             HTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHHHHHHT
T ss_pred             cCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999999999999999999999999988888888776543

>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=99.90  E-value=7.5e-29  Score=223.92  Aligned_cols=154  Identities=29%  Similarity=0.505  Sum_probs=141.8

Q ss_pred             cCeeEEEEEcCc-ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCC
Q 012794           23 EGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGK  100 (456)
Q Consensus        23 ~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~  100 (456)
                      .+|+|+++.++. ..|+.+|.+++... ...++||||+|+..++.+++.|.. ++.+..+||+|++.+|..+++.|++++
T Consensus         2 ~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~   80 (170)
T 2yjt_D            2 KKIHQWYYRADDLEHKTALLVHLLKQP-EATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGR   80 (170)
Confidence            367888888888 88999999998764 457999999999999999999985 788999999999999999999999999


Q ss_pred             eEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecC
Q 012794          101 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  177 (456)
Q Consensus       101 ~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~  177 (456)
                      ++|||||+++++|+|+|++++||+|++|+++..|+||+||+||.|+.|.+++++.+.+...++.+++.++..++...
T Consensus        81 ~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (170)
T 2yjt_D           81 VNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARV  157 (170)
Confidence            99999999999999999999999999999999999999999999999999999999999999999888877665543

>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=99.92  E-value=4.8e-25  Score=227.86  Aligned_cols=149  Identities=36%  Similarity=0.590  Sum_probs=133.4

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      .....+.+.++.+....|...|.+++....  .++||||+|++.|+.+++.|.+ ++.+..+||+|++.+|+++++.|++
T Consensus       271 ~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~--~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~  348 (434)
T 2db3_A          271 GACSDVKQTIYEVNKYAKRSKLIEILSEQA--DGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKN  348 (434)
T ss_dssp             CCCTTEEEEEEECCGGGHHHHHHHHHHHCC--TTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHT
T ss_pred             ccccccceEEEEeCcHHHHHHHHHHHHhCC--CCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHc
Confidence            345678899888999899999999887653  4599999999999999999985 7899999999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh-hHHHHHHHHHHhC
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVG  170 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-e~~~~~~ie~~~~  170 (456)
                      ++.+|||||+++++|||+|+|++|||||+|.++++|+||+|||||+|+.|.+++|+.+. +...+..|.+.+.
T Consensus       349 g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~  421 (434)
T 2db3_A          349 GSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILE  421 (434)
T ss_dssp             SSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHH
T ss_pred             CCCcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999854 4555555555543

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

Probab=99.92  E-value=1.2e-24  Score=232.89  Aligned_cols=161  Identities=26%  Similarity=0.408  Sum_probs=137.4

Q ss_pred             ccccccCeeEEEEEcCcc--cHHHHHHHHHH---HHCCCCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeCCCCHHH
Q 012794           18 DEKLAEGIKLYAISTTAT--SKRTILSDLIT---VYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQ   88 (456)
Q Consensus        18 ~~~~~~~i~~~~~~~~~~--~k~~~L~~ll~---~~~~~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg~~~~~~   88 (456)
                      .......+.+.++.+...  .+..++..++.   ......++||||+|+..|+.+++.|.+    .+.+..+||+|++.+
T Consensus       250 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~  329 (579)
T 3sqw_A          250 EPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNK  329 (579)
T ss_dssp             SCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHH
T ss_pred             ccccccccceEEEEecchhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHH
Confidence            344455677776665542  23344443333   324567999999999999999999984    678999999999999


Q ss_pred             HHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHH
Q 012794           89 RERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  168 (456)
Q Consensus        89 R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~  168 (456)
                      |.++++.|++++++|||||+++++|||+|+|++||+|++|.+++.|+||+|||||+|+.|.|++|+.+.+..+++.|++.
T Consensus       330 R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~  409 (579)
T 3sqw_A          330 RTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDA  409 (579)
T ss_dssp             HHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHH
T ss_pred             HHHHHHHhhcCCCeEEEEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCCceecCC
Q 012794          169 VGCKFEFVSP  178 (456)
Q Consensus       169 ~~~~~~~~~~  178 (456)
                      ....++....
T Consensus       410 ~~~~~~~~~~  419 (579)
T 3sqw_A          410 KNIVIAKQEK  419 (579)
T ss_dssp             HCCCCCEEEE
T ss_pred             hCCCcccccC
Confidence            9887766543

>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=99.92  E-value=1.7e-24  Score=220.88  Aligned_cols=161  Identities=35%  Similarity=0.601  Sum_probs=147.4

Q ss_pred             ccccccCeeEEEEEcCccc-HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhc
Q 012794           18 DEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNG   95 (456)
Q Consensus        18 ~~~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~   95 (456)
                      .......+.+++..+.... |...|.+++.... ..++||||+|++.++.+++.|.. ++.+..+||+|++.+|+++++.
T Consensus       243 ~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~-~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~  321 (410)
T 2j0s_A          243 DELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT-ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKE  321 (410)
T ss_dssp             GGCSCTTEEEEEEEESSTTHHHHHHHHHHHHHT-SSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHH
T ss_pred             ccccCCCceEEEEEeCcHHhHHHHHHHHHHhcC-CCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHH
Confidence            3445667888888776654 8999999888764 57999999999999999999985 7899999999999999999999


Q ss_pred             ccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCcee
Q 012794           96 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF  175 (456)
Q Consensus        96 Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~  175 (456)
                      |++++++|||||+++++|||+|++++||+|++|++...|+||+||+||.|++|.+++|+.+.+...++.++++++..++.
T Consensus       322 f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~  401 (410)
T 2j0s_A          322 FRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDE  401 (410)
T ss_dssp             HHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEE
T ss_pred             HHCCCCCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHHHHHHHHHHHhCCCcee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             cCCC
Q 012794          176 VSPP  179 (456)
Q Consensus       176 ~~~p  179 (456)
                      ++.+
T Consensus       402 ~~~~  405 (410)
T 2j0s_A          402 MPMN  405 (410)
T ss_dssp             CCSC
T ss_pred             cccc
Confidence            7654

>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=99.92  E-value=3.3e-24  Score=228.33  Aligned_cols=159  Identities=26%  Similarity=0.411  Sum_probs=135.8

Q ss_pred             cccccCeeEEEEEcCcc-cH-HHHHHHHHH---HHCCCCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeCCCCHHHH
Q 012794           19 EKLAEGIKLYAISTTAT-SK-RTILSDLIT---VYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQR   89 (456)
Q Consensus        19 ~~~~~~i~~~~~~~~~~-~k-~~~L~~ll~---~~~~~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg~~~~~~R   89 (456)
                      ......+.+.++..... .+ ..++..++.   ......++||||+|+..|+.++..|.+    .+.+..+||+|++.+|
T Consensus       302 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R  381 (563)
T 3i5x_A          302 PEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKR  381 (563)
T ss_dssp             CSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHH
T ss_pred             ccccccCceEEEECchhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHH
Confidence            34455666666655442 22 333333333   334567999999999999999999984    6789999999999999


Q ss_pred             HHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHh
Q 012794           90 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV  169 (456)
Q Consensus        90 ~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~  169 (456)
                      +.+++.|++++++|||||+++++|||+|+|++||+|++|.+++.|+||+|||||+|+.|.+++|+.+.+...++.|++..
T Consensus       382 ~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~  461 (563)
T 3i5x_A          382 TSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAK  461 (563)
T ss_dssp             HHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCEEEEcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCceecC
Q 012794          170 GCKFEFVS  177 (456)
Q Consensus       170 ~~~~~~~~  177 (456)
                      ...++...
T Consensus       462 ~~~~~~~~  469 (563)
T 3i5x_A          462 NIVIAKQE  469 (563)
T ss_dssp             CCCCCEEE
T ss_pred             CCCccccc
Confidence            88776544

>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=99.91  E-value=7e-24  Score=215.48  Aligned_cols=159  Identities=26%  Similarity=0.488  Sum_probs=147.7

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      .....+.+++..+....|...|..++... ...++||||+++++++.+++.|.. ++.+..+||+|++.+|..+++.|++
T Consensus       228 ~~~~~~~~~~~~~~~~~k~~~l~~~~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~  306 (400)
T 1s2m_A          228 LTLKGITQYYAFVEERQKLHCLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQ  306 (400)
T ss_dssp             CBCTTEEEEEEECCGGGHHHHHHHHHHHS-CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             cccCCceeEEEEechhhHHHHHHHHHhhc-CCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhc
Confidence            34567888888888889999999988765 457999999999999999999985 7899999999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCC
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  178 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~  178 (456)
                      ++++|||||+++++|+|+|++++||++++|.+...|+||+||+||.|+.|.|++++.+.+...++.|++.++..++.++.
T Consensus       307 g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~  386 (400)
T 1s2m_A          307 GKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPA  386 (400)
T ss_dssp             TSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCS
T ss_pred             CCCcEEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHHHHHHHHHHhCCCcccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999887664


Q ss_pred             C
Q 012794          179 P  179 (456)
Q Consensus       179 p  179 (456)
                      .
T Consensus       387 ~  387 (400)
T 1s2m_A          387 T  387 (400)
T ss_dssp             S
T ss_pred             c
Confidence            4

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

Probab=99.91  E-value=2.1e-24  Score=220.36  Aligned_cols=151  Identities=40%  Similarity=0.579  Sum_probs=137.8

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      .....+.+.++.+....|...|.+++.......++||||+|+++++.+++.|.+ ++.+..+||+|++++|.++++.|++
T Consensus       245 ~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~  324 (417)
T 2i4i_A          245 STSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRS  324 (417)
T ss_dssp             -CCSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHc
Confidence            455678888888898999999999998776678999999999999999999985 7899999999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhC
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  170 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~  170 (456)
                      ++.+|||||+++++|||+|++++||+|++|.+...|+||+||+||.|+.|.+++|+.+.+...+..+.+.+.
T Consensus       325 g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~~~~  396 (417)
T 2i4i_A          325 GKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLV  396 (417)
T ss_dssp             TSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHHHHH
T ss_pred             CCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999888888877664

>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=99.91  E-value=9.2e-24  Score=214.92  Aligned_cols=166  Identities=30%  Similarity=0.511  Sum_probs=142.2

Q ss_pred             ccccccCeeEEEEEcCc-ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhc
Q 012794           18 DEKLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNG   95 (456)
Q Consensus        18 ~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~   95 (456)
                      .......+.++++.+.. ..|...|..++.... ..++||||+|+++|+.++..|.+ ++.+..+||+|++.+|.++++.
T Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~  311 (412)
T 3fht_A          233 EEETLDTIKQYYVLCSSRDEKFQALCNLYGAIT-IAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIER  311 (412)
T ss_dssp             GGSSCTTEEEEEEECSSHHHHHHHHHHHHHHHS-SSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHH
T ss_pred             ccccccCceEEEEEcCChHHHHHHHHHHHhhcC-CCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHH
Confidence            34456677888777665 568888888887764 57999999999999999999985 7899999999999999999999


Q ss_pred             ccCCCeEEEEeccccccccCcCccceEEecCCC------CChhHHHHHhcccccCCCCceEEEeeChh-hHHHHHHHHHH
Q 012794           96 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELP------NDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERD  168 (456)
Q Consensus        96 Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p------~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-e~~~~~~ie~~  168 (456)
                      |++++++|||||+++++|||+|++++||+|++|      .+..+|+||+||+||.|+.|.+++++.+. +...++.+++.
T Consensus       312 f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~  391 (412)
T 3fht_A          312 FREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEH  391 (412)
T ss_dssp             HHTTSCSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHH
T ss_pred             HHCCCCcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHHHHH
Confidence            999999999999999999999999999999999      46789999999999999999999999866 48899999999


Q ss_pred             hCCCceecCCCCHHHH
Q 012794          169 VGCKFEFVSPPVVEDV  184 (456)
Q Consensus       169 ~~~~~~~~~~p~~~~i  184 (456)
                      ++..++.+..+..+++
T Consensus       392 ~~~~~~~~~~~~~~~~  407 (412)
T 3fht_A          392 FNKKIERLDTDDLDEI  407 (412)
T ss_dssp             HTCCCEEC--------
T ss_pred             HCCccccCCCccHHHH
Confidence            9999998877665544

>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=99.91  E-value=5.6e-24  Score=216.85  Aligned_cols=161  Identities=34%  Similarity=0.576  Sum_probs=130.7

Q ss_pred             ccccccCeeEEEEEcCcc-cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhc
Q 012794           18 DEKLAEGIKLYAISTTAT-SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNG   95 (456)
Q Consensus        18 ~~~~~~~i~~~~~~~~~~-~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~   95 (456)
                      .......+.++++.+... .|...|..++... ...++||||+++++++.+++.|.. .+.+..+||+|++.+|.++++.
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~  325 (414)
T 3eiq_A          247 EELTLEGIRQFYINVEREEWKLDTLCDLYETL-TITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMRE  325 (414)
T ss_dssp             CCCCTTSCCEEEEECSSSTTHHHHHHHHHHSS-CCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHH
T ss_pred             CccCCCCceEEEEEeChHHhHHHHHHHHHHhC-CCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHH
Confidence            344556777888776654 4888888888765 457999999999999999999985 7899999999999999999999


Q ss_pred             ccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCcee
Q 012794           96 FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF  175 (456)
Q Consensus        96 Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~  175 (456)
                      |++++.+|||||+++++|||+|++++||+|++|.+...|+||+||+||.|++|.|++++++.+...++.+++.++..++.
T Consensus       326 f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (414)
T 3eiq_A          326 FRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEE  405 (414)
T ss_dssp             HSCC---CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHHHHHHHHHHHTTCCCEE
T ss_pred             HHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHHHHHHHHcCCccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998888


Q ss_pred             cCCC
Q 012794          176 VSPP  179 (456)
Q Consensus       176 ~~~p  179 (456)
                      ++..
T Consensus       406 ~~~~  409 (414)
T 3eiq_A          406 MPLN  409 (414)
T ss_dssp             CCC-
T ss_pred             cChh
Confidence            7543

>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=99.90  E-value=3.3e-23  Score=209.52  Aligned_cols=160  Identities=23%  Similarity=0.434  Sum_probs=145.6

Q ss_pred             cccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhccc
Q 012794           19 EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR   97 (456)
Q Consensus        19 ~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr   97 (456)
                      ......+.++++.+....|...|.+++... ...++||||+++++++.+++.|.. ++.+..+||+|++.+|.++++.|+
T Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~  297 (391)
T 1xti_A          219 KLTLHGLQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFK  297 (391)
T ss_dssp             CCCCTTCEEEEEECCGGGHHHHHHHHHHHS-CCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             ccCcccceEEEEEcCchhHHHHHHHHHHhc-CCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHh
Confidence            344567888888888899999999998876 568999999999999999999985 789999999999999999999999


Q ss_pred             CCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh-hHHHHHHHHHHhCCCceec
Q 012794           98 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFV  176 (456)
Q Consensus        98 ~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-e~~~~~~ie~~~~~~~~~~  176 (456)
                      +++.+|||||+++++|+|+|++++||++++|+++..|+||+||+||.|+.|.+++++.+. +...++.+++.+..+++.+
T Consensus       298 ~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  377 (391)
T 1xti_A          298 DFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISEL  377 (391)
T ss_dssp             TTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCCEEC
T ss_pred             cCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCChhhC
Confidence            999999999999999999999999999999999999999999999999999999999866 5677899999998888776


Q ss_pred             CCC
Q 012794          177 SPP  179 (456)
Q Consensus       177 ~~p  179 (456)
                      +..
T Consensus       378 ~~~  380 (391)
T 1xti_A          378 PDE  380 (391)
T ss_dssp             CSC
T ss_pred             Ccc
Confidence            543

>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=99.90  E-value=6.2e-23  Score=207.20  Aligned_cols=165  Identities=32%  Similarity=0.576  Sum_probs=143.7

Q ss_pred             ccccCeeEEEEEcCc-ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhccc
Q 012794           20 KLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR   97 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr   97 (456)
                      .....+.+.+..+.. ..|...|..++... ...++||||+++++++.+++.|.. ++.+..+||+|++.+|.++++.|+
T Consensus       212 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~  290 (395)
T 3pey_A          212 VNVDAIKQLYMDCKNEADKFDVLTELYGLM-TIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFR  290 (395)
T ss_dssp             CSCTTEEEEEEECSSHHHHHHHHHHHHTTT-TSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             cccccccEEEEEcCchHHHHHHHHHHHHhc-cCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHH
Confidence            445567777776644 56788887777654 458999999999999999999985 789999999999999999999999


Q ss_pred             CCCeEEEEeccccccccCcCccceEEecCCCC------ChhHHHHHhcccccCCCCceEEEeeCh-hhHHHHHHHHHHhC
Q 012794           98 QGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAILMFTS-SQRRTVRSLERDVG  170 (456)
Q Consensus        98 ~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~------~~~~y~qr~GR~gR~g~~g~~i~~~~~-~e~~~~~~ie~~~~  170 (456)
                      +++++|||||+++++|||+|++++||+|++|.      ++.+|+||+||+||.|+.|.+++++.+ .+...++.+++.++
T Consensus       291 ~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~  370 (395)
T 3pey_A          291 EGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFG  370 (395)
T ss_dssp             TTSCCEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTT
T ss_pred             CCCCCEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999      999999999999999999999999985 56778889999988


Q ss_pred             -CCceecCCCCHHHHH
Q 012794          171 -CKFEFVSPPVVEDVL  185 (456)
Q Consensus       171 -~~~~~~~~p~~~~i~  185 (456)
                       ..+..++.+..+++.
T Consensus       371 ~~~~~~~~~~~~~~~~  386 (395)
T 3pey_A          371 DIEMTRVPTDDWDEVE  386 (395)
T ss_dssp             SCCCEECCSSCHHHHH
T ss_pred             CceeecCChHHHHHHH
Confidence             777777776665443

>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=99.90  E-value=6.5e-23  Score=204.98  Aligned_cols=153  Identities=36%  Similarity=0.616  Sum_probs=142.4

Q ss_pred             cCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCe
Q 012794           23 EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF  101 (456)
Q Consensus        23 ~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~  101 (456)
                      ..+.+.++.+....|...|..++.  ....++||||+|+++++.+++.|.. ++.+..+||+|++.+|.++++.|++++.
T Consensus       212 ~~~~~~~~~~~~~~~~~~l~~~l~--~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~  289 (367)
T 1hv8_A          212 ANIEQSYVEVNENERFEALCRLLK--NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI  289 (367)
T ss_dssp             SSSEEEEEECCGGGHHHHHHHHHC--STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSS
T ss_pred             CCceEEEEEeChHHHHHHHHHHHh--cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCC
Confidence            467788888888899988888776  3567999999999999999999985 7899999999999999999999999999


Q ss_pred             EEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecC
Q 012794          102 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  177 (456)
Q Consensus       102 ~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~  177 (456)
                      +|||||+++++|+|+|++++||++++|.++.+|+||+||+||.|+.|.+++++.+.+...++.|++.++.+++.+.
T Consensus       290 ~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  365 (367)
T 1hv8_A          290 RILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKLK  365 (367)
T ss_dssp             SEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCCCBC
T ss_pred             eEEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHHHHHHHHHHHhCCCCceec
Confidence            9999999999999999999999999999999999999999999999999999999999999999999998887654

>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=99.87  E-value=2e-21  Score=205.33  Aligned_cols=134  Identities=21%  Similarity=0.438  Sum_probs=122.6

Q ss_pred             CcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccc
Q 012794           33 TATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA  111 (456)
Q Consensus        33 ~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~  111 (456)
                      ....+...|.+++... ++.++||||+|++.++.+++.|.. ++.+..+||+|++++|+++++.|++++++|||||++++
T Consensus       219 ~~~~~~~~l~~~l~~~-~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~  297 (523)
T 1oyw_A          219 EKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFG  297 (523)
T ss_dssp             ECSSHHHHHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSC
T ss_pred             eCCCHHHHHHHHHHhc-CCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhh
Confidence            3456777777777665 567999999999999999999985 78999999999999999999999999999999999999


Q ss_pred             cccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHH
Q 012794          112 RGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLER  167 (456)
Q Consensus       112 ~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~  167 (456)
                      +|||+|+|++||+|++|.+++.|+||+||+||.|+.+.+++++.+.+...++.+..
T Consensus       298 ~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~~~~~  353 (523)
T 1oyw_A          298 MGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLE  353 (523)
T ss_dssp             TTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHH
T ss_pred             CCCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999988877776644

>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=99.87  E-value=3.5e-24  Score=223.78  Aligned_cols=162  Identities=30%  Similarity=0.497  Sum_probs=0.0

Q ss_pred             ccccCeeEEEEEcCc-ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhccc
Q 012794           20 KLAEGIKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR   97 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr   97 (456)
                      .....+.++++.+.. ..|...|..++... ...++||||+|+..|+.++..|.. .+.+..+||+|++.+|..+++.|+
T Consensus       302 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~  380 (479)
T 3fmp_B          302 ETLDTIKQYYVLCSSRDEKFQALCNLYGAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFR  380 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCcCCceEEEEEeCCHHHHHHHHHHHHhhc-cCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHH
Confidence            445667777776654 46777777777655 357999999999999999999985 788999999999999999999999


Q ss_pred             CCCeEEEEeccccccccCcCccceEEecCCCC------ChhHHHHHhcccccCCCCceEEEeeChhh-HHHHHHHHHHhC
Q 012794           98 QGKFTVLVATDVAARGLDIPNVDLIIHYELPN------DPETFVHRSGRTGRAGKEGTAILMFTSSQ-RRTVRSLERDVG  170 (456)
Q Consensus        98 ~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~------~~~~y~qr~GR~gR~g~~g~~i~~~~~~e-~~~~~~ie~~~~  170 (456)
                      +|+++|||||+++++|||+|++++||+||+|.      +...|+||+|||||.|+.|.+++|+.+.+ ...++.|++.++
T Consensus       381 ~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~  460 (479)
T 3fmp_B          381 EGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFN  460 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCCCcEEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhC
Confidence            99999999999999999999999999999995      67899999999999999999999998665 788888888888


Q ss_pred             CCceecCCCCHH
Q 012794          171 CKFEFVSPPVVE  182 (456)
Q Consensus       171 ~~~~~~~~p~~~  182 (456)
                      ..++.+..+..+
T Consensus       461 ~~~~~l~~~~~~  472 (479)
T 3fmp_B          461 KKIERLDTDDLD  472 (479)
T ss_dssp             ------------
T ss_pred             CCceECCCccHH
Confidence            777766554433

>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=99.86  E-value=2.4e-21  Score=207.37  Aligned_cols=129  Identities=23%  Similarity=0.400  Sum_probs=115.6

Q ss_pred             HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccC
Q 012794           37 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  115 (456)
Q Consensus        37 k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gid  115 (456)
                      ++..|.+++.......++||||+|++.|++|++.|.. ++.+..+|++|++.+|.++++.|++++++|||||+++++|||
T Consensus       253 ~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID  332 (591)
T 2v1x_A          253 FIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGID  332 (591)
T ss_dssp             HHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCC
T ss_pred             HHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCC
Confidence            3444444443333567999999999999999999985 789999999999999999999999999999999999999999


Q ss_pred             cCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794          116 IPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus       116 ip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      +|+|++||+|++|.+++.|+||+||+||.|+++.|++|+.+.+...+..+
T Consensus       333 ~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~~  382 (591)
T 2v1x_A          333 KPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSM  382 (591)
T ss_dssp             CSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHH
T ss_pred             cccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHHHHHHHH
Confidence            99999999999999999999999999999999999999999887766655

>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=99.86  E-value=1.4e-23  Score=212.35  Aligned_cols=158  Identities=31%  Similarity=0.568  Sum_probs=0.0

Q ss_pred             ccccCeeEEEEEcCccc-HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhccc
Q 012794           20 KLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFR   97 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr   97 (456)
                      .....+.++++.+.... |...|..++... ...++||||+|+++++.+++.|.. ++.+..+||+|++.+|.++++.|+
T Consensus       228 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~  306 (394)
T 1fuu_A          228 LTLEGIKQFYVNVEEEEYKYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFR  306 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCCCceEEEEEcCchhhHHHHHHHHHhcC-CCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHH
Confidence            33455666666655543 777788877655 357999999999999999999985 788999999999999999999999


Q ss_pred             CCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecC
Q 012794           98 QGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVS  177 (456)
Q Consensus        98 ~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~  177 (456)
                      +++.+|||||+++++|+|+|++++||++++|.++..|+||+||+||.|++|.+++++.+.+...++.+++.++..++.++
T Consensus       307 ~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  386 (394)
T 1fuu_A          307 SGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELP  386 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHHHhCCcccccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998888777654


Q ss_pred             C
Q 012794          178 P  178 (456)
Q Consensus       178 ~  178 (456)
                      .
T Consensus       387 ~  387 (394)
T 1fuu_A          387 S  387 (394)
T ss_dssp             -
T ss_pred             c
Confidence            4

>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=99.85  E-value=1.3e-20  Score=212.19  Aligned_cols=167  Identities=17%  Similarity=0.243  Sum_probs=146.5

Q ss_pred             cCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh--cCCEEEEeCCCCHHHHHHHHhcccCCC--eEEEEec
Q 012794           32 TTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQGK--FTVLVAT  107 (456)
Q Consensus        32 ~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~--~~~~~~lhg~~~~~~R~~~l~~Fr~g~--~~vLVaT  107 (456)
                      +....|...|.+++... +..++||||+++..++.|+..|..  ++.+..+||+|++.+|++++++|++++  ++|||||
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            34567999999999874 578999999999999999999983  789999999999999999999999998  9999999


Q ss_pred             cccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHh--CCCceecCCCCHHHHH
Q 012794          108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDV--GCKFEFVSPPVVEDVL  185 (456)
Q Consensus       108 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~--~~~~~~~~~p~~~~i~  185 (456)
                      +++++|||+|++++||+||+|+++..|+||+||++|.|+.+.+++++...+....+.|.+.+  +.++....+|...++.
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            99999999999999999999999999999999999999999877776655555556666666  6667778889999999


Q ss_pred             HHHHHHHHHHHhcC
Q 012794          186 ESSAEQVVATLNGV  199 (456)
Q Consensus       186 ~~~~~~~~~~l~~~  199 (456)
                      +...+.+...+...
T Consensus       644 ~~~~~~l~~~l~~~  657 (968)
T 3dmq_A          644 DSVYNDLINYLASP  657 (968)
T ss_dssp             HHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHhcc
Confidence            98888888877654

>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=99.84  E-value=7.7e-21  Score=187.84  Aligned_cols=143  Identities=29%  Similarity=0.538  Sum_probs=120.9

Q ss_pred             cccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccCCC
Q 012794           21 LAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGK  100 (456)
Q Consensus        21 ~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~  100 (456)
                      ....+.+.++.+....+..+  ..+.. ....++||||+|+++++.+++.|.   .+..+||+|++.+|.++++.|++++
T Consensus       193 ~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~lvf~~~~~~~~~l~~~l~---~~~~~~~~~~~~~r~~~~~~f~~~~  266 (337)
T 2z0m_A          193 GLANVEHKFVHVKDDWRSKV--QALRE-NKDKGVIVFVRTRNRVAKLVRLFD---NAIELRGDLPQSVRNRNIDAFREGE  266 (337)
T ss_dssp             GGGGEEEEEEECSSSSHHHH--HHHHT-CCCSSEEEECSCHHHHHHHHTTCT---TEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             ccCCceEEEEEeChHHHHHH--HHHHh-CCCCcEEEEEcCHHHHHHHHHHhh---hhhhhcCCCCHHHHHHHHHHHHcCC
Confidence            34556777777666544322  33332 356899999999999999988876   5889999999999999999999999


Q ss_pred             eEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhC
Q 012794          101 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVG  170 (456)
Q Consensus       101 ~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~  170 (456)
                      ++|||||+++++|+|+|++++||++++|.++..|+||+||+||.|+.|.+++++. .+...++.|++.++
T Consensus       267 ~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~~~~~~~i~~~~~  335 (337)
T 2z0m_A          267 YDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL-NEYWLEKEVKKVSQ  335 (337)
T ss_dssp             CSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES-SCHHHHHHHC----
T ss_pred             CcEEEEcCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe-CcHHHHHHHHHHhc
Confidence            9999999999999999999999999999999999999999999999999999999 88888888877654

>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=99.84  E-value=1.6e-21  Score=211.34  Aligned_cols=128  Identities=21%  Similarity=0.263  Sum_probs=114.1

Q ss_pred             EEEcCcccHHHHHHHHHHH-HCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEe
Q 012794           29 AISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVA  106 (456)
Q Consensus        29 ~~~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVa  106 (456)
                      ++.+...+|..+|.+++.. +..+.++||||+|++.++.|+..|.. ++.+.+|||++.+.+|..+.++|+.+  .||||
T Consensus       409 ~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIA  486 (844)
T 1tf5_A          409 LIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIA  486 (844)
T ss_dssp             EEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEE
T ss_pred             EEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEe
Confidence            4456777899888887764 34567899999999999999999995 89999999999988888888888876  58999


Q ss_pred             ccccccccCcC--------ccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          107 TDVAARGLDIP--------NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       107 Tdv~~~Gidip--------~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      ||+|+||+||+        ++.+||||++|.+.+.|+||+|||||+|.+|.+++|++..+
T Consensus       487 TdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD  546 (844)
T 1tf5_A          487 TNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  546 (844)
T ss_dssp             ETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             CCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHH
Confidence            99999999999        78899999999999999999999999999999999998665

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

Probab=99.84  E-value=1.5e-20  Score=198.79  Aligned_cols=125  Identities=20%  Similarity=0.334  Sum_probs=70.5

Q ss_pred             ccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHhc-------------CCEEEEeCCCCHHHHHHHHhcccC
Q 012794           35 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI-------------IASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        35 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~~-------------~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      ..|+..|.++|...   ....++||||+++.+++.|+..|...             .....+||+|++.+|.+++++|++
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            56888888888654   56789999999999999999999742             234556788999999999999999


Q ss_pred             -CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHH
Q 012794           99 -GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT  161 (456)
Q Consensus        99 -g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~  161 (456)
                       +.++|||||+++++|||+|+|++||+||+|+++..|+||+|| ||. +.|.+++|++..+...
T Consensus       451 ~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~  512 (556)
T 4a2p_A          451 SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVE  512 (556)
T ss_dssp             ---CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHHHHH
T ss_pred             cCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcchHH
Confidence             999999999999999999999999999999999999999999 999 7899999998776543

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

Probab=99.83  E-value=2.6e-20  Score=190.61  Aligned_cols=139  Identities=22%  Similarity=0.417  Sum_probs=119.4

Q ss_pred             cccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEE-EEeCCCCHHHHHHHHhcc
Q 012794           19 EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASE-ALHGDISQHQRERTLNGF   96 (456)
Q Consensus        19 ~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~-~lhg~~~~~~R~~~l~~F   96 (456)
                      .....++.+.++.+   +|.+.|.+++...  +.++||||+|+..|+.++..|.. ++.+. .+||+    +|+  ++.|
T Consensus       225 ~~~~~~i~~~~~~~---~~~~~l~~~l~~~--~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f  293 (414)
T 3oiy_A          225 VSVARNITHVRISS---RSKEKLVELLEIF--RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDF  293 (414)
T ss_dssp             CCCCCSEEEEEESS---CCHHHHHHHHHHH--CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHH
T ss_pred             ccccccchheeecc---CHHHHHHHHHHHc--CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHH
Confidence            34456778887766   4566677777764  48999999999999999999985 78887 89995    444  9999


Q ss_pred             cCCCeEEEEe----ccccccccCcCc-cceEEecCCC--CChhHHHHHhcccccCC----CCceEEEeeChhhHHHHHHH
Q 012794           97 RQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELP--NDPETFVHRSGRTGRAG----KEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus        97 r~g~~~vLVa----Tdv~~~Gidip~-v~~VI~~~~p--~~~~~y~qr~GR~gR~g----~~g~~i~~~~~~e~~~~~~i  165 (456)
                      ++|+++||||    |+++++|||+|+ |++||+|++|  .++.+|+||+|||||.|    ++|.+++++  .+...++.+
T Consensus       294 ~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l  371 (414)
T 3oiy_A          294 KVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESL  371 (414)
T ss_dssp             HTTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC--CCHHHHHHH
T ss_pred             hCCCCeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE--ccHHHHHHH
Confidence            9999999999    999999999999 9999999999  99999999999999987    589999999  566777888


Q ss_pred             HHHhC
Q 012794          166 ERDVG  170 (456)
Q Consensus       166 e~~~~  170 (456)
                      ++.++
T Consensus       372 ~~~~~  376 (414)
T 3oiy_A          372 KTRLL  376 (414)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            88777

>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=99.82  E-value=9.8e-21  Score=208.23  Aligned_cols=136  Identities=16%  Similarity=0.331  Sum_probs=116.0

Q ss_pred             cCeeEEEEEcCcccHHHH-HHHHHHHH--CCCCcEEEEcCChHHHHHHHHHHHh------------cCCEEEEeCCCCHH
Q 012794           23 EGIKLYAISTTATSKRTI-LSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS------------IIASEALHGDISQH   87 (456)
Q Consensus        23 ~~i~~~~~~~~~~~k~~~-L~~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~------------~~~~~~lhg~~~~~   87 (456)
                      ..++++|+..+..++... +..++..+  ...+++||||+++++++.+++.|..            .+.+.+|||+|+++
T Consensus       272 ~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~  351 (773)
T 2xau_A          272 YPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPH  351 (773)
T ss_dssp             CCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHH
T ss_pred             cceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHH
Confidence            357777777666655433 33343332  3468999999999999999999873            45689999999999


Q ss_pred             HHHHHHhccc-----CCCeEEEEeccccccccCcCccceEEecCC------------------CCChhHHHHHhcccccC
Q 012794           88 QRERTLNGFR-----QGKFTVLVATDVAARGLDIPNVDLIIHYEL------------------PNDPETFVHRSGRTGRA  144 (456)
Q Consensus        88 ~R~~~l~~Fr-----~g~~~vLVaTdv~~~Gidip~v~~VI~~~~------------------p~~~~~y~qr~GR~gR~  144 (456)
                      +|.++++.|+     +|..+|||||+++++|||||+|++||++++                  |.+.++|+||+|||||.
T Consensus       352 eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~  431 (773)
T 2xau_A          352 QQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT  431 (773)
T ss_dssp             HHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS
T ss_pred             HHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC
Confidence            9999999999     999999999999999999999999999888                  89999999999999999


Q ss_pred             CCCceEEEeeChhhH
Q 012794          145 GKEGTAILMFTSSQR  159 (456)
Q Consensus       145 g~~g~~i~~~~~~e~  159 (456)
                       ..|.|++|+++.+.
T Consensus       432 -~~G~~~~l~~~~~~  445 (773)
T 2xau_A          432 -RPGKCFRLYTEEAF  445 (773)
T ss_dssp             -SSEEEEESSCHHHH
T ss_pred             -CCCEEEEEecHHHh
Confidence             79999999987654

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

Probab=99.82  E-value=5.6e-20  Score=193.97  Aligned_cols=129  Identities=24%  Similarity=0.357  Sum_probs=93.4

Q ss_pred             ccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHhc-----CCE--------EEEeCCCCHHHHHHHHhcccC
Q 012794           35 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI-----IAS--------EALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        35 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~--------~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      ..|+..|.++|...   .+..++||||+++.+++.|+..|...     +.+        ..+||+|++.+|.+++++|++
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            46888888888654   45689999999999999999999842     333        445669999999999999999


Q ss_pred             -CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794           99 -GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus        99 -g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                       +.++|||||+++++|||+|+|++||+||+|+++..|+||+|| ||. +.|.+++|+++.+......+
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 89999999998776555444

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

Probab=99.81  E-value=1.8e-20  Score=204.21  Aligned_cols=130  Identities=22%  Similarity=0.361  Sum_probs=83.5

Q ss_pred             cccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-c----CCEEEE--------eCCCCHHHHHHHHhccc
Q 012794           34 ATSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-I----IASEAL--------HGDISQHQRERTLNGFR   97 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-~----~~~~~l--------hg~~~~~~R~~~l~~Fr   97 (456)
                      ...|+..|.+++...   .+..++||||+++.+|+.|++.|.. .    +.+..+        |++|++.+|.+++++|+
T Consensus       378 ~~~k~~~L~~ll~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~  457 (696)
T 2ykg_A          378 ENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFK  457 (696)
T ss_dssp             CCHHHHHHHHHHHHHHTTCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC--------------------------
T ss_pred             CCHHHHHHHHHHHHHhccCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHH
Confidence            456888899988765   3467999999999999999999985 3    788888        55999999999999999


Q ss_pred             C-CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794           98 Q-GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus        98 ~-g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      + |+++|||||+++++|||+|+|++||+||+|+++++|+||+|| ||. +.|.++++++..+......+
T Consensus       458 ~~g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~~~~~  524 (696)
T 2ykg_A          458 ASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIEKEQI  524 (696)
T ss_dssp             ---CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC-----------CCCEEEEEESCHHHHHHHHH
T ss_pred             hcCCccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHHHHHHH
Confidence            8 999999999999999999999999999999999999999999 998 78999999998776555444

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.81  E-value=1.3e-19  Score=192.49  Aligned_cols=141  Identities=22%  Similarity=0.251  Sum_probs=115.4

Q ss_pred             EEEcCcccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEe
Q 012794           29 AISTTATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVA  106 (456)
Q Consensus        29 ~~~~~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVa  106 (456)
                      .+.....+|..+|..++... ..+.++||||+|++.++.|+..|.+ ++.+.+|||++.+.++..+.++|+.+  .|+||
T Consensus       451 ~vy~t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVA  528 (822)
T 3jux_A          451 LVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIA  528 (822)
T ss_dssp             EEESSHHHHHHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEE
T ss_pred             EEEecHHHHHHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEE
Confidence            34566778888888877643 4568999999999999999999995 89999999995555555556667666  59999


Q ss_pred             ccccccccCcC--------ccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhH-------HHHHHHHHHhCC
Q 012794          107 TDVAARGLDIP--------NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQR-------RTVRSLERDVGC  171 (456)
Q Consensus       107 Tdv~~~Gidip--------~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~-------~~~~~ie~~~~~  171 (456)
                      ||+|+||+||+        ...+||++++|.+.+.|+||+|||||+|.+|.+++|++..+.       ..+..+.+.++.
T Consensus       529 TdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~l~r~fg~~~~~~~m~~~~~  608 (822)
T 3jux_A          529 TNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDLLRIFGSEQIGKVMNILKI  608 (822)
T ss_dssp             ETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSHHHHHTTHHHHHHHHHHSSC
T ss_pred             cchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHHHHHhhhHHHHHHHHHHcCC
Confidence            99999999998        566999999999999999999999999999999999987662       344445555543

>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=99.80  E-value=3.1e-19  Score=193.28  Aligned_cols=128  Identities=23%  Similarity=0.398  Sum_probs=112.7

Q ss_pred             HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccC
Q 012794           37 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  115 (456)
Q Consensus        37 k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gid  115 (456)
                      +..++..|......+.++||||+|+..|+.|++.|.. ++.+..+|++|++.+|.++++.|++|+++|||||+++++|+|
T Consensus       431 ~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlD  510 (661)
T 2d7d_A          431 IDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLD  510 (661)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCC
T ss_pred             HHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcc
Confidence            3444455555445668999999999999999999985 789999999999999999999999999999999999999999


Q ss_pred             cCccceEEecCC-----CCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794          116 IPNVDLIIHYEL-----PNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus       116 ip~v~~VI~~~~-----p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      +|+|++||+++.     |.+.++|+||+|||||. ..|.+++|+.+.+....+.|
T Consensus       511 ip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~~~~~~i  564 (661)
T 2d7d_A          511 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-AEGRVIMYADKITKSMEIAI  564 (661)
T ss_dssp             CTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCCHHHHHHH
T ss_pred             cCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCCHHHHHHH
Confidence            999999999997     99999999999999998 78999999988665544444

>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=99.80  E-value=7.9e-20  Score=197.63  Aligned_cols=128  Identities=25%  Similarity=0.247  Sum_probs=115.4

Q ss_pred             EEEcCcccHHHHHHHHHHH-HCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEe
Q 012794           29 AISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVA  106 (456)
Q Consensus        29 ~~~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVa  106 (456)
                      ++.+...+|..+|.+++.. +..+.++||||+|++.++.|+..|.+ ++.+.+||+++.+.++..+.++|+.|  .|+||
T Consensus       418 ~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIA  495 (853)
T 2fsf_A          418 LVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIA  495 (853)
T ss_dssp             EEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEE
T ss_pred             EEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEe
Confidence            4556778899999888754 45668999999999999999999985 89999999999988898899999988  59999


Q ss_pred             ccccccccCcCc--------------------------------c-----ceEEecCCCCChhHHHHHhcccccCCCCce
Q 012794          107 TDVAARGLDIPN--------------------------------V-----DLIIHYELPNDPETFVHRSGRTGRAGKEGT  149 (456)
Q Consensus       107 Tdv~~~Gidip~--------------------------------v-----~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~  149 (456)
                      ||+|+||+||+.                                |     .+||++++|.+.+.|+||+|||||+|.+|.
T Consensus       496 TnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~  575 (853)
T 2fsf_A          496 TNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGS  575 (853)
T ss_dssp             ESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEE
T ss_pred             cccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCee
Confidence            999999999987                                3     699999999999999999999999999999


Q ss_pred             EEEeeChhh
Q 012794          150 AILMFTSSQ  158 (456)
Q Consensus       150 ~i~~~~~~e  158 (456)
                      +++|++..+
T Consensus       576 s~~fls~eD  584 (853)
T 2fsf_A          576 SRFYLSMED  584 (853)
T ss_dssp             EEEEEETTS
T ss_pred             EEEEecccH
Confidence            999998765

>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=99.79  E-value=3.8e-19  Score=197.02  Aligned_cols=124  Identities=20%  Similarity=0.337  Sum_probs=75.7

Q ss_pred             ccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHhc-------------CCEEEEeCCCCHHHHHHHHhcccC
Q 012794           35 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI-------------IASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        35 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~~-------------~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      ..|+..|..+|...   ....++||||+++.+++.|+..|...             ..+..+||+|++.+|..++++|++
T Consensus       612 ~~K~~~L~~lL~~~~~~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~  691 (797)
T 4a2q_A          612 NPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKT  691 (797)
T ss_dssp             CHHHHHHHHHHHHHHHHCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC--------------------------
T ss_pred             ChHHHHHHHHHHHHhccCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhc
Confidence            56888888888753   45689999999999999999999742             345667899999999999999999


Q ss_pred             -CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHH
Q 012794           99 -GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRR  160 (456)
Q Consensus        99 -g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~  160 (456)
                       +.++|||||+++++|||+|+|++||+||+|+++..|+||+|| ||. +.|.+++|++..+..
T Consensus       692 ~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~e  752 (797)
T 4a2q_A          692 SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (797)
T ss_dssp             --CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHHHH
T ss_pred             cCCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcHH
Confidence             999999999999999999999999999999999999999999 999 899999999876643

>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=99.79  E-value=6.9e-19  Score=190.68  Aligned_cols=130  Identities=24%  Similarity=0.402  Sum_probs=114.4

Q ss_pred             HHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCc
Q 012794           38 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDI  116 (456)
Q Consensus        38 ~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidi  116 (456)
                      ..++..|......+.++||||+|+..++.|++.|.. ++.+..+|++|++.+|.++++.|++|+++|||||+++++|+|+
T Consensus       426 ~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDi  505 (664)
T 1c4o_A          426 LDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDI  505 (664)
T ss_dssp             HHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCC
T ss_pred             HHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccC
Confidence            333444444444578999999999999999999985 7899999999999999999999999999999999999999999


Q ss_pred             CccceEEecCC-----CCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHH
Q 012794          117 PNVDLIIHYEL-----PNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERD  168 (456)
Q Consensus       117 p~v~~VI~~~~-----p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~  168 (456)
                      |+|++||+++.     |.+..+|+||+|||||.+ .|.+++++.+.+....+.|++.
T Consensus       506 p~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~~~~~~~i~~~  561 (664)
T 1c4o_A          506 PEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSEAMQRAIEET  561 (664)
T ss_dssp             TTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCHHHHHHHHHH
T ss_pred             CCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCCHHHHHHHHHH
Confidence            99999999997     999999999999999995 8999999988777666666543

>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=99.79  E-value=3e-19  Score=184.06  Aligned_cols=125  Identities=33%  Similarity=0.532  Sum_probs=112.9

Q ss_pred             CcccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeC--------CCCHHHHHHHHhcccCCC
Q 012794           33 TATSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHG--------DISQHQRERTLNGFRQGK  100 (456)
Q Consensus        33 ~~~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg--------~~~~~~R~~~l~~Fr~g~  100 (456)
                      ....|+..|.++|..+   ....++||||+++..++.+++.|.. ++.+..+||        +|++.+|+++++.|+++.
T Consensus       340 ~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~  419 (494)
T 1wp9_A          340 LDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE  419 (494)
T ss_dssp             CSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTS
T ss_pred             CCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCC
Confidence            4557888899988775   4678999999999999999999985 789999999        999999999999999999


Q ss_pred             eEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          101 FTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       101 ~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      ++|||||+++++|||+|++++||+|++|+++..|+||+||+||.|+ |.+++|+.+.+
T Consensus       420 ~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t  476 (494)
T 1wp9_A          420 FNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGT  476 (494)
T ss_dssp             CSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTS
T ss_pred             ceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCC
Confidence            9999999999999999999999999999999999999999999998 99999988653

>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=3e-19  Score=172.98  Aligned_cols=122  Identities=16%  Similarity=0.289  Sum_probs=96.5

Q ss_pred             cCcccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHh--cCCEEEEeCCCCHHHHHHHHhcccCC-CeE-EEEe
Q 012794           32 TTATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQG-KFT-VLVA  106 (456)
Q Consensus        32 ~~~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~--~~~~~~lhg~~~~~~R~~~l~~Fr~g-~~~-vLVa  106 (456)
                      .....|+..|.++|... ..+.++||||+++..++.|+..|..  ++.+..+||++++.+|+++++.|+++ .++ +||+
T Consensus        92 ~~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~s  171 (271)
T 1z5z_A           92 VRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLS  171 (271)
T ss_dssp             STTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEE
T ss_pred             cccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEe
Confidence            34568999999998765 3568999999999999999999984  78899999999999999999999998 677 7899


Q ss_pred             ccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794          107 TDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus       107 Tdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      |+++++|||++.+++||+||+||++..|+||+||++|.|+++.++++
T Consensus       172 t~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~  218 (271)
T 1z5z_A          172 VKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVH  218 (271)
T ss_dssp             CCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEE
T ss_pred             hhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEE
Confidence            99999999999999999999999999999999999999987765443

>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=99.77  E-value=1.9e-18  Score=187.32  Aligned_cols=129  Identities=24%  Similarity=0.282  Sum_probs=114.0

Q ss_pred             EEEcCcccHHHHHHHHHHH-HCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEe
Q 012794           29 AISTTATSKRTILSDLITV-YAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVA  106 (456)
Q Consensus        29 ~~~~~~~~k~~~L~~ll~~-~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVa  106 (456)
                      ++.+...+|..+|...+.. +..+.++||||+|++.++.|+..|.+ ++.+.+||+++.+.++..+.++|+.|  .|+||
T Consensus       437 ~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIA  514 (922)
T 1nkt_A          437 LIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVA  514 (922)
T ss_dssp             EEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEE
T ss_pred             EEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEe
Confidence            4456677899888887754 45567999999999999999999985 89999999999888888888999988  58999


Q ss_pred             ccccccccCcCcc----------------------------------------------------ceEEecCCCCChhHH
Q 012794          107 TDVAARGLDIPNV----------------------------------------------------DLIIHYELPNDPETF  134 (456)
Q Consensus       107 Tdv~~~Gidip~v----------------------------------------------------~~VI~~~~p~~~~~y  134 (456)
                      ||+|+||+||+.+                                                    .+||+++.|.+...|
T Consensus       515 TnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy  594 (922)
T 1nkt_A          515 TNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRID  594 (922)
T ss_dssp             ETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHH
T ss_pred             cchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHH
Confidence            9999999999964                                                    599999999999999


Q ss_pred             HHHhcccccCCCCceEEEeeChhhH
Q 012794          135 VHRSGRTGRAGKEGTAILMFTSSQR  159 (456)
Q Consensus       135 ~qr~GR~gR~g~~g~~i~~~~~~e~  159 (456)
                      +||+|||||+|.+|.+++|++..+.
T Consensus       595 ~qr~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          595 NQLRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             HHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             HHHhcccccCCCCeeEEEEechhHH
Confidence            9999999999999999999987654

>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=99.77  E-value=1.7e-19  Score=186.70  Aligned_cols=114  Identities=23%  Similarity=0.288  Sum_probs=96.0

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEe-----
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-----  124 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~-----  124 (456)
                      ..++||||+|++.|+.+++.|.. ++.+..+||    ++|+++++.|++++++|||||+++++|||+| +++||+     
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~  251 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAF  251 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccc
Confidence            57999999999999999999985 789999999    4688999999999999999999999999999 999986     


Q ss_pred             --------------cCCCCChhHHHHHhcccccC-CCCceEEEee---ChhhHHHHHHHHHHh
Q 012794          125 --------------YELPNDPETFVHRSGRTGRA-GKEGTAILMF---TSSQRRTVRSLERDV  169 (456)
Q Consensus       125 --------------~~~p~~~~~y~qr~GR~gR~-g~~g~~i~~~---~~~e~~~~~~ie~~~  169 (456)
                                    ++.|.+.++|+||+|||||. +++|.|++|+   ++.+...++.++..+
T Consensus       252 ~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~  314 (440)
T 1yks_A          252 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASM  314 (440)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHH
T ss_pred             eeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhhhhhhhhHHh
Confidence                          88999999999999999998 6899999996   567777777777765

>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=1.4e-18  Score=195.28  Aligned_cols=124  Identities=20%  Similarity=0.337  Sum_probs=76.5

Q ss_pred             ccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHhc-------------CCEEEEeCCCCHHHHHHHHhcccC
Q 012794           35 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTSI-------------IASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        35 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~~-------------~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      ..|+..|.++|...   ..+.++||||+|+.+++.|+..|...             ..+..+||+|++.+|.+++++|++
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            56888888888764   34689999999999999999999842             235566899999999999999999


Q ss_pred             -CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHH
Q 012794           99 -GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRR  160 (456)
Q Consensus        99 -g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~  160 (456)
                       |.++|||||+++++|||+|+|++||+||+|+++..|+||+|| ||. +.|.+++|++..+..
T Consensus       692 ~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~e  752 (936)
T 4a2w_A          692 SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (936)
T ss_dssp             --CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHHHH
T ss_pred             cCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCHH
Confidence             999999999999999999999999999999999999999999 999 789999998876543

>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=99.77  E-value=3.7e-19  Score=201.87  Aligned_cols=158  Identities=18%  Similarity=0.296  Sum_probs=125.6

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccCC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQG   99 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~g   99 (456)
                      ....++.++++   ..+|...|.+++...  +.++||||+|++.|+.++..|...+.+..+||+|     ..+++.|++|
T Consensus       249 ~~~~~i~~~~~---~~~k~~~L~~ll~~~--~~~~LVF~~t~~~a~~l~~~L~~~~~v~~lhg~~-----~~~l~~F~~G  318 (1054)
T 1gku_B          249 ITVRNVEDVAV---NDESISTLSSILEKL--GTGGIIYARTGEEAEEIYESLKNKFRIGIVTATK-----KGDYEKFVEG  318 (1054)
T ss_dssp             ECCCCEEEEEE---SCCCTTTTHHHHTTS--CSCEEEEESSHHHHHHHHHTTTTSSCEEECTTSS-----SHHHHHHHHT
T ss_pred             cCcCCceEEEe---chhHHHHHHHHHhhc--CCCEEEEEcCHHHHHHHHHHHhhccCeeEEeccH-----HHHHHHHHcC
Confidence            44556777776   345667777777654  5789999999999999999998558999999998     4788999999


Q ss_pred             CeEEEEe----ccccccccCcCcc-ceEEecCCC----------------------------------------------
Q 012794          100 KFTVLVA----TDVAARGLDIPNV-DLIIHYELP----------------------------------------------  128 (456)
Q Consensus       100 ~~~vLVa----Tdv~~~Gidip~v-~~VI~~~~p----------------------------------------------  128 (456)
                      +++||||    |+++++|||+|+| ++||++|+|                                              
T Consensus       319 ~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  398 (1054)
T 1gku_B          319 EIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVRE  398 (1054)
T ss_dssp             SCSEEEEECC------CCSCCTTTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHH
T ss_pred             CCcEEEEecCCCCeeEeccccCCcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence            9999999    9999999999996 999999999                                              


Q ss_pred             -------------------------CChhHHHHHhcccccCCCCc--eEEEeeChhhHHHHHHHHHHhC---CCceecCC
Q 012794          129 -------------------------NDPETFVHRSGRTGRAGKEG--TAILMFTSSQRRTVRSLERDVG---CKFEFVSP  178 (456)
Q Consensus       129 -------------------------~~~~~y~qr~GR~gR~g~~g--~~i~~~~~~e~~~~~~ie~~~~---~~~~~~~~  178 (456)
                                               .|..+|+||+|||||+|+.|  .+++++...+...+..|++.++   ..+..+..
T Consensus       399 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~~~l~~~l~~~~~~~~~~~~  478 (1054)
T 1gku_B          399 ILKKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFIERAKLYDIEFKSIDE  478 (1054)
T ss_dssp             HHHHHHTTSCCSCSSSEEETTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECSCHHHHHHHHHHHHTTSSCCCBCSC
T ss_pred             HHHHHhccccccccceeEeecceecCcHHHHhhhhchhhhccCCCCceEEEEEEecCHHHHHHHHHHHhhccCccccCCc
Confidence                                     78999999999999987665  4777777777888888888877   45566666


Q ss_pred             CCHHHHHHH
Q 012794          179 PVVEDVLES  187 (456)
Q Consensus       179 p~~~~i~~~  187 (456)
                      +..+++++.
T Consensus       479 ~~~~~l~~~  487 (1054)
T 1gku_B          479 VDFEKLSRE  487 (1054)
T ss_dssp             CCHHHHHHH
T ss_pred             CCHHHHHHh
Confidence            666666654

>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=99.77  E-value=1.9e-18  Score=188.34  Aligned_cols=103  Identities=28%  Similarity=0.518  Sum_probs=88.7

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-------cCCEEEEeCC--------CCHHHHHHHHhcccCCCeEEEEeccccccccC
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-------IIASEALHGD--------ISQHQRERTLNGFRQGKFTVLVATDVAARGLD  115 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-------~~~~~~lhg~--------~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gid  115 (456)
                      ..++||||+|+.+++.|++.|..       ++.+..+||+        |++.+|.+++++|++|+++|||||+++++|||
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             cCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeCh
Q 012794          116 IPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       116 ip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      +|+|++||+||+|+++..|+||+||++|.|   .+++++.+
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            999999999999999999999999976543   44555443

>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=99.76  E-value=9.6e-19  Score=187.92  Aligned_cols=114  Identities=17%  Similarity=0.271  Sum_probs=103.9

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceE-------
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLI-------  122 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~V-------  122 (456)
                      .+++||||+|++.|+.+++.|.. ++.+..||++    +|+++++.|++++++||||||++++|||+| +++|       
T Consensus       355 ~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~  429 (618)
T 2whx_A          355 QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCL  429 (618)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEE
T ss_pred             CCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECccee
Confidence            57999999999999999999985 7899999985    688899999999999999999999999998 8888       


Q ss_pred             -------------EecCCCCChhHHHHHhcccccCC-CCceEEEeeC---hhhHHHHHHHHHHh
Q 012794          123 -------------IHYELPNDPETFVHRSGRTGRAG-KEGTAILMFT---SSQRRTVRSLERDV  169 (456)
Q Consensus       123 -------------I~~~~p~~~~~y~qr~GR~gR~g-~~g~~i~~~~---~~e~~~~~~ie~~~  169 (456)
                                   |+|++|.+.++|+||+|||||+| .+|.+++|+.   +.+...++.+++.+
T Consensus       430 ~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i  493 (618)
T 2whx_A          430 KPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKM  493 (618)
T ss_dssp             EEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHH
T ss_pred             cceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHh
Confidence                         77788999999999999999996 4899999997   77777888888765

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

Probab=99.76  E-value=1.2e-18  Score=188.61  Aligned_cols=115  Identities=17%  Similarity=0.254  Sum_probs=103.5

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEe----
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----  124 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~----  124 (456)
                      ..+++||||+|+++++.+++.|.. .+.+..|||+    +|+++++.|++++++|||||+++++|||+| +++|||    
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            468999999999999999999985 7899999994    799999999999999999999999999999 999998    


Q ss_pred             ----------------cCCCCChhHHHHHhcccccC-CCCceEEEee---ChhhHHHHHHHHHHh
Q 012794          125 ----------------YELPNDPETFVHRSGRTGRA-GKEGTAILMF---TSSQRRTVRSLERDV  169 (456)
Q Consensus       125 ----------------~~~p~~~~~y~qr~GR~gR~-g~~g~~i~~~---~~~e~~~~~~ie~~~  169 (456)
                                      |++|.+.++|+||+|||||. +++|.|++|+   .+.+...++.++..+
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                            67899999999999999998 7899999996   566666666666654

>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=99.74  E-value=1.7e-18  Score=185.59  Aligned_cols=123  Identities=25%  Similarity=0.380  Sum_probs=106.3

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEE-----
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----  123 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI-----  123 (456)
                      ..+++||||+|++.++.+++.|.+ ++.+..+||+|++++       |+++..+||||||++++|||+| |++||     
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            468999999999999999999985 789999999999874       5556669999999999999997 99988     


Q ss_pred             -----ecC-----------CCCChhHHHHHhcccccCCCCceEEEeeChhhHHH--H--HHHHHHhCCCceecCCCCHH
Q 012794          124 -----HYE-----------LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRT--V--RSLERDVGCKFEFVSPPVVE  182 (456)
Q Consensus       124 -----~~~-----------~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~--~--~~ie~~~~~~~~~~~~p~~~  182 (456)
                           |||           +|.+.++|+||+||||| +++|. ++|+++.+...  +  ..+++..+..+++..+|..+
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 99999 99998877554  4  77777777777777776544

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

Probab=99.74  E-value=7.3e-18  Score=191.57  Aligned_cols=155  Identities=19%  Similarity=0.365  Sum_probs=123.7

Q ss_pred             cccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEE-EEeCCCCHHHHHHHHhcc
Q 012794           19 EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASE-ALHGDISQHQRERTLNGF   96 (456)
Q Consensus        19 ~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~-~lhg~~~~~~R~~~l~~F   96 (456)
                      .....++.+.++.+   +|...|..++...  +.++||||+|+..|+.|+..|.. ++.+. .+||+     |.+ ++.|
T Consensus       282 ~~~~~~i~~~~~~~---~k~~~L~~ll~~~--~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F  350 (1104)
T 4ddu_A          282 VSVARNITHVRISS---RSKEKLVELLEIF--RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDF  350 (1104)
T ss_dssp             CCCCCCEEEEEESC---CCHHHHHHHHHHH--CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHH
T ss_pred             CCCcCCceeEEEec---CHHHHHHHHHHhc--CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHH
Confidence            34566788888766   4566677777765  48999999999999999999985 78888 99993     555 9999


Q ss_pred             cCCCeEEEEe----ccccccccCcCc-cceEEecCCCC------------------------------------------
Q 012794           97 RQGKFTVLVA----TDVAARGLDIPN-VDLIIHYELPN------------------------------------------  129 (456)
Q Consensus        97 r~g~~~vLVa----Tdv~~~Gidip~-v~~VI~~~~p~------------------------------------------  129 (456)
                      ++|+++||||    |+++++|||+|+ |++|||||+|.                                          
T Consensus       351 ~~G~~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~~~~Sle~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~  430 (1104)
T 4ddu_A          351 KVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKE  430 (1104)
T ss_dssp             HHTSCSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCEEEEECSSSSCCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHH
T ss_pred             HCCCCCEEEEecCCCCeeEecCcCCCCCCEEEEECCCCCCCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999    999999999999 99999999998                                          


Q ss_pred             ------------------------------ChhHHHHHhcccccCCC----CceEEEeeChhhHHHHHHHHHHhC----C
Q 012794          130 ------------------------------DPETFVHRSGRTGRAGK----EGTAILMFTSSQRRTVRSLERDVG----C  171 (456)
Q Consensus       130 ------------------------------~~~~y~qr~GR~gR~g~----~g~~i~~~~~~e~~~~~~ie~~~~----~  171 (456)
                                                    |+.+|+||+|||||.+.    +|.+++++  .+...++.|++.+.    .
T Consensus       431 ~l~~~~~~~~i~~~~~~l~~~~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~--~d~~~~~~l~~~~~~~~~~  508 (1104)
T 4ddu_A          431 HLTQKEFVEKVKEMFRGVVVKDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLLLIAEE  508 (1104)
T ss_dssp             CCCHHHHHHHHHHHCCSSEEETTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEEC--CCHHHHHHHHHHHHHHTCC
T ss_pred             HhccHHHHHHHhhccceEEecCCeeEEEecChhhhhcccCchhcccCCCcccceEEEEE--ecHHHHHHHHHHHhhhccc
Confidence                                          88899999999999653    45666666  56677777777664    4


Q ss_pred             CceecCCCCHHHHHH
Q 012794          172 KFEFVSPPVVEDVLE  186 (456)
Q Consensus       172 ~~~~~~~p~~~~i~~  186 (456)
                      .+.++.....+++++
T Consensus       509 ~~~~~~~~~~~~~~~  523 (1104)
T 4ddu_A          509 EIIEEAEANWKELVH  523 (1104)
T ss_dssp             CEEEGGGCCHHHHHH
T ss_pred             ccccccccCHHHHHH
Confidence            444444444455544

>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=99.74  E-value=1.9e-17  Score=180.85  Aligned_cols=119  Identities=26%  Similarity=0.515  Sum_probs=105.3

Q ss_pred             HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc-------------------------------CCEEEEeCCCC
Q 012794           37 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------IASEALHGDIS   85 (456)
Q Consensus        37 k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~-------------------------------~~~~~lhg~~~   85 (456)
                      +..++.+++   ..++++||||+|+++++.++..|...                               ..+.++||+|+
T Consensus       231 ~~~~~~~~~---~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~  307 (702)
T 2p6r_A          231 FEELVEECV---AENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLL  307 (702)
T ss_dssp             HHHHHHHHH---HTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSC
T ss_pred             HHHHHHHHH---hcCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCC
Confidence            455554444   35789999999999999999988632                               35888999999


Q ss_pred             HHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEe----cC---CCCChhHHHHHhcccccCC--CCceEEEeeCh
Q 012794           86 QHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE---LPNDPETFVHRSGRTGRAG--KEGTAILMFTS  156 (456)
Q Consensus        86 ~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~----~~---~p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~  156 (456)
                      +++|..+++.|++|.++|||||+++++|||+|++++||+    ||   .|.+..+|+||+|||||.|  ..|.|++++..
T Consensus       308 ~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~  387 (702)
T 2p6r_A          308 NGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGK  387 (702)
T ss_dssp             HHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCG
T ss_pred             HHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecC
Confidence            999999999999999999999999999999999999998    66   7899999999999999988  57999999998


Q ss_pred             hh
Q 012794          157 SQ  158 (456)
Q Consensus       157 ~e  158 (456)
                      .+
T Consensus       388 ~~  389 (702)
T 2p6r_A          388 RD  389 (702)
T ss_dssp             GG
T ss_pred             cc
Confidence            77

>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=99.74  E-value=1.8e-17  Score=181.58  Aligned_cols=136  Identities=24%  Similarity=0.329  Sum_probs=112.3

Q ss_pred             cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc----------------------------------CCEEEEe
Q 012794           36 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI----------------------------------IASEALH   81 (456)
Q Consensus        36 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~----------------------------------~~~~~lh   81 (456)
                      .+..++.+++   .+++++||||+|+++|+.++..|.+.                                  ..+.++|
T Consensus       225 ~~~~~~~~~~---~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h  301 (720)
T 2zj8_A          225 SWEELVYDAI---RKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHH  301 (720)
T ss_dssp             STTHHHHHHH---HTTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEEC
T ss_pred             HHHHHHHHHH---hCCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeec
Confidence            3444444444   35689999999999999999988742                                  1489999


Q ss_pred             CCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEe----cC----CCCChhHHHHHhcccccCC--CCceEE
Q 012794           82 GDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE----LPNDPETFVHRSGRTGRAG--KEGTAI  151 (456)
Q Consensus        82 g~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~----~~----~p~~~~~y~qr~GR~gR~g--~~g~~i  151 (456)
                      ++|++.+|..+++.|++|.++|||||+++++|||+|++++||+    ||    .|.+..+|+||+|||||.|  ..|.|+
T Consensus       302 ~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~  381 (720)
T 2zj8_A          302 AGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGI  381 (720)
T ss_dssp             TTSCHHHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEE
T ss_pred             CCCCHHHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEE
Confidence            9999999999999999999999999999999999999999998    77    6899999999999999988  578999


Q ss_pred             EeeChhhHHHHHHHHHHhCCCceec
Q 012794          152 LMFTSSQRRTVRSLERDVGCKFEFV  176 (456)
Q Consensus       152 ~~~~~~e~~~~~~ie~~~~~~~~~~  176 (456)
                      +++++.+.  ...+++++...++.+
T Consensus       382 ~l~~~~~~--~~~~~~~~~~~~~~i  404 (720)
T 2zj8_A          382 IVSTSDDP--REVMNHYIFGKPEKL  404 (720)
T ss_dssp             EECSSSCH--HHHHHHHTTSCCCCC
T ss_pred             EEecCccH--HHHHHHHhcCCCCCc
Confidence            99988762  233445555444444

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

Probab=99.74  E-value=2.2e-17  Score=180.73  Aligned_cols=129  Identities=26%  Similarity=0.431  Sum_probs=104.3

Q ss_pred             HHCCCCcEEEEcCChHHHHHHHHHHHhc-------------------------------------CCEEEEeCCCCHHHH
Q 012794           47 VYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------------IASEALHGDISQHQR   89 (456)
Q Consensus        47 ~~~~~~~~IIF~~t~~~a~~l~~~L~~~-------------------------------------~~~~~lhg~~~~~~R   89 (456)
                      .+..++++||||+|+++++.++..|.+.                                     ..+.++||+|++.+|
T Consensus       248 ~~~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r  327 (715)
T 2va8_A          248 SLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALR  327 (715)
T ss_dssp             HHTTTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHH
T ss_pred             HHhcCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHH
Confidence            3446789999999999999999998742                                     248999999999999


Q ss_pred             HHHHhcccCCCeEEEEeccccccccCcCccceEEe----cC-------CCCChhHHHHHhcccccCC--CCceEEEeeCh
Q 012794           90 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE-------LPNDPETFVHRSGRTGRAG--KEGTAILMFTS  156 (456)
Q Consensus        90 ~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~----~~-------~p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~  156 (456)
                      ..+++.|++|.++|||||+++++|||+|++++||+    ||       .|.+..+|+||+|||||.|  ..|.|+++++.
T Consensus       328 ~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~  407 (715)
T 2va8_A          328 DLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRD  407 (715)
T ss_dssp             HHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEECSC
T ss_pred             HHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCC
Confidence            99999999999999999999999999999999999    99       8999999999999999988  47999999987


Q ss_pred             hhHHHHHHHHHHhCCCceec
Q 012794          157 SQRRTVRSLERDVGCKFEFV  176 (456)
Q Consensus       157 ~e~~~~~~ie~~~~~~~~~~  176 (456)
                      .+. ....+++++....+.+
T Consensus       408 ~~~-~~~~~~~~l~~~~e~~  426 (715)
T 2va8_A          408 KED-VDRVFKKYVLSDVEPI  426 (715)
T ss_dssp             GGG-HHHHHHHTTSSCCCCC
T ss_pred             chH-HHHHHHHHHcCCCCCc
Confidence            653 2223444444444443

>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=99.72  E-value=1.1e-17  Score=173.64  Aligned_cols=101  Identities=19%  Similarity=0.304  Sum_probs=93.6

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecC---
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYE---  126 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~---  126 (456)
                      .+++||||+|+++|+.+++.|.+ ++.+..+|+++.    +++++.|++|+++|||||+++++|||+|+ ++||||+   
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            56999999999999999999985 788999999864    57999999999999999999999999999 9999999   


Q ss_pred             -----------------CCCChhHHHHHhcccccCCC-CceEEEeeCh
Q 012794          127 -----------------LPNDPETFVHRSGRTGRAGK-EGTAILMFTS  156 (456)
Q Consensus       127 -----------------~p~~~~~y~qr~GR~gR~g~-~g~~i~~~~~  156 (456)
                                       .|.+.++|+||+|||||.|+ .|.+++|+..
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 8889888743

>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=99.72  E-value=1.8e-18  Score=179.80  Aligned_cols=102  Identities=19%  Similarity=0.318  Sum_probs=92.8

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEe-----
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-----  124 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~-----  124 (456)
                      .+++||||+|++.|+.+++.|.. ++.+..||++    +|+++++.|++|+++|||||+++++|||+|+ ++||+     
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    6889999999999999999999999999999 99999     


Q ss_pred             ---------------cCCCCChhHHHHHhcccccCCC-CceEEEeeChh
Q 012794          125 ---------------YELPNDPETFVHRSGRTGRAGK-EGTAILMFTSS  157 (456)
Q Consensus       125 ---------------~~~p~~~~~y~qr~GR~gR~g~-~g~~i~~~~~~  157 (456)
                                     |++|.+.++|+||+|||||.|+ +|.+++|+.+.
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 89999999874

>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=4.1e-17  Score=176.31  Aligned_cols=122  Identities=20%  Similarity=0.284  Sum_probs=104.4

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC--CCeEEEEeccccccccCcCccceEEecCC-
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ--GKFTVLVATDVAARGLDIPNVDLIIHYEL-  127 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~--g~~~vLVaTdv~~~Gidip~v~~VI~~~~-  127 (456)
                      ...||||+|+++++.+++.|.+ .+.+.++||+|++++|+++++.|++  +.++|||||+++++|||+ ++++||++++ 
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            4569999999999999999985 7899999999999999999999999  889999999999999999 8999999999 


Q ss_pred             -------------CCChhHHHHHhcccccCCCC---ceEEEeeChhhHHHHHHHHHHhCCCcee
Q 012794          128 -------------PNDPETFVHRSGRTGRAGKE---GTAILMFTSSQRRTVRSLERDVGCKFEF  175 (456)
Q Consensus       128 -------------p~~~~~y~qr~GR~gR~g~~---g~~i~~~~~~e~~~~~~ie~~~~~~~~~  175 (456)
                                   |.+..+|+||+|||||.|..   |.|++++.. +...++.+.......++.
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                         88999999999999999964   666666544 445556665554444444

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

Probab=99.70  E-value=9.5e-17  Score=180.97  Aligned_cols=115  Identities=24%  Similarity=0.410  Sum_probs=102.5

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-cC---------------------------------------CEEEEeCCCCHHHHH
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-II---------------------------------------ASEALHGDISQHQRE   90 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~~---------------------------------------~~~~lhg~~~~~~R~   90 (456)
                      ..++||||+|+..|+.++..|.. .+                                       .+.++||+|++.+|+
T Consensus       343 ~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~  422 (1010)
T 2xgj_A          343 YNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKE  422 (1010)
T ss_dssp             CCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHH
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHH
Confidence            46899999999999999988864 22                                       278899999999999


Q ss_pred             HHHhcccCCCeEEEEeccccccccCcCccceEEe----cCC----CCChhHHHHHhcccccCCC--CceEEEeeChh-hH
Q 012794           91 RTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YEL----PNDPETFVHRSGRTGRAGK--EGTAILMFTSS-QR  159 (456)
Q Consensus        91 ~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~----~~~----p~~~~~y~qr~GR~gR~g~--~g~~i~~~~~~-e~  159 (456)
                      .+++.|++|.++|||||+++++|||+|++++||+    ||.    |.++..|+||+|||||.|.  .|.|++++.+. +.
T Consensus       423 ~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e~  502 (1010)
T 2xgj_A          423 VIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEP  502 (1010)
T ss_dssp             HHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCCH
T ss_pred             HHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCCH
Confidence            9999999999999999999999999999999999    999    8999999999999999996  59999999865 54


Q ss_pred             HHHHHH
Q 012794          160 RTVRSL  165 (456)
Q Consensus       160 ~~~~~i  165 (456)
                      ..+..+
T Consensus       503 ~~~~~l  508 (1010)
T 2xgj_A          503 QVAKGM  508 (1010)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            455544

>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=99.69  E-value=5.7e-17  Score=184.32  Aligned_cols=116  Identities=25%  Similarity=0.408  Sum_probs=97.3

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cC---------------------------------------CEEEEeCCCCHHHH
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-II---------------------------------------ASEALHGDISQHQR   89 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~---------------------------------------~~~~lhg~~~~~~R   89 (456)
                      ...++||||+|+..|+.++..|.. .+                                       .+.++||+|++.+|
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            356999999999999999998753 11                                       17899999999999


Q ss_pred             HHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCC--------ChhHHHHHhcccccCC--CCceEEEeeChh-h
Q 012794           90 ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPN--------DPETFVHRSGRTGRAG--KEGTAILMFTSS-Q  158 (456)
Q Consensus        90 ~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~--------~~~~y~qr~GR~gR~g--~~g~~i~~~~~~-e  158 (456)
                      +.+++.|++|.++|||||+++++|||+|++++||+++.|+        ++..|+||+|||||.|  ..|.|++++.+. +
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            9999999999999999999999999999999999887643        6677999999999999  678999988765 3


Q ss_pred             HHHHHHH
Q 012794          159 RRTVRSL  165 (456)
Q Consensus       159 ~~~~~~i  165 (456)
                      ...+..+
T Consensus       600 ~~~~~~l  606 (1108)
T 3l9o_A          600 PQVAKGM  606 (1108)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            3344444

>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=99.68  E-value=1.5e-17  Score=173.01  Aligned_cols=116  Identities=25%  Similarity=0.446  Sum_probs=104.1

Q ss_pred             CcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccccc
Q 012794           33 TATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR  112 (456)
Q Consensus        33 ~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~  112 (456)
                      ....|...|.+++... .+.++||||++++.++.+++.|.    +..+||++++.+|++++++|++++++|||||+++++
T Consensus       332 ~~~~k~~~l~~~l~~~-~~~k~lvF~~~~~~~~~l~~~l~----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~  406 (472)
T 2fwr_A          332 NSKNKIRKLREILERH-RKDKIIIFTRHNELVYRISKVFL----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDE  406 (472)
T ss_dssp             SCSHHHHHHHHHHHHT-SSSCBCCBCSCHHHHHHHHHHTT----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCS
T ss_pred             cChHHHHHHHHHHHhC-CCCcEEEEECCHHHHHHHHHHhC----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhc
Confidence            4557888899988874 56899999999999999998874    678999999999999999999999999999999999


Q ss_pred             ccCcCccceEEecCCCCChhHHHHHhcccccCCCC-ceEEEe
Q 012794          113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE-GTAILM  153 (456)
Q Consensus       113 Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~-g~~i~~  153 (456)
                      |+|+|++++||++++|+++..|+||+||++|.|+. +.++++
T Consensus       407 Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~  448 (472)
T 2fwr_A          407 GIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLY  448 (472)
T ss_dssp             SSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEE
T ss_pred             CcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEE
Confidence            99999999999999999999999999999999854 454443

>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=99.68  E-value=1.3e-16  Score=182.26  Aligned_cols=121  Identities=21%  Similarity=0.354  Sum_probs=110.0

Q ss_pred             HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh---cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccc
Q 012794           37 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG  113 (456)
Q Consensus        37 k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~G  113 (456)
                      +..++..++..+..++++||||+++++++.+++.|.+   .+.+..+||+|++.+|++++++|++++++|||||+++++|
T Consensus       798 ~~~i~~~il~~l~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~G  877 (1151)
T 2eyq_A          798 SMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETG  877 (1151)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGG
T ss_pred             HHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceee
Confidence            4455566677776788999999999999999999985   4689999999999999999999999999999999999999


Q ss_pred             cCcCccceEEecCC-CCChhHHHHHhcccccCCCCceEEEeeChh
Q 012794          114 LDIPNVDLIIHYEL-PNDPETFVHRSGRTGRAGKEGTAILMFTSS  157 (456)
Q Consensus       114 idip~v~~VI~~~~-p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  157 (456)
                      ||+|++++||+++. +.++.+|+||+||+||.|+.|.|++++.+.
T Consensus       878 iDip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          878 IDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             SCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             ecccCCcEEEEeCCCCCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            99999999999988 579999999999999999999999998764

>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=99.68  E-value=1.4e-17  Score=182.57  Aligned_cols=124  Identities=21%  Similarity=0.385  Sum_probs=104.3

Q ss_pred             HHHHHHHHHHHHCCCCcEEEEcCChH--------HHHHHHHHHHh----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           37 KRTILSDLITVYAKGGKTIVFTQTKR--------DADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        37 k~~~L~~ll~~~~~~~~~IIF~~t~~--------~a~~l~~~L~~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      ...++..+.+....+.+++|||++.+        .++.+++.|.+    .+.+..+||+|++.+|++++++|++|+++||
T Consensus       564 ~~~l~~~i~~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~IL  643 (780)
T 1gm5_A          564 VNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDIL  643 (780)
T ss_dssp             HHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBC
T ss_pred             HHHHHHHHHHHHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEE
Confidence            34444444455566789999999764        47778888876    3578999999999999999999999999999


Q ss_pred             EeccccccccCcCccceEEecCCCC-ChhHHHHHhcccccCCCCceEEEeeChhhHH
Q 012794          105 VATDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTSSQRR  160 (456)
Q Consensus       105 VaTdv~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~  160 (456)
                      |||+++++|||+|++++||+++.|. +...|+||+||+||.|+.|.|++++.+.+..
T Consensus       644 VaT~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~~~~  700 (780)
T 1gm5_A          644 VSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEE  700 (780)
T ss_dssp             CCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHH
T ss_pred             EECCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECCCChH
Confidence            9999999999999999999999996 7899999999999999999999999743333

>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=99.66  E-value=2.3e-16  Score=165.31  Aligned_cols=120  Identities=17%  Similarity=0.295  Sum_probs=103.5

Q ss_pred             cccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHh--cCCEEEEeCCCCHHHHHHHHhcccCC-CeE-EEEecc
Q 012794           34 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQG-KFT-VLVATD  108 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~--~~~~~~lhg~~~~~~R~~~l~~Fr~g-~~~-vLVaTd  108 (456)
                      ...|+..|.+++... ..+.++||||+++..++.++..|..  ++.+..+||++++.+|+++++.|+++ ..+ +||+|+
T Consensus       323 ~s~K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~  402 (500)
T 1z63_A          323 RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK  402 (500)
T ss_dssp             TCHHHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECC
T ss_pred             cchhHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecc
Confidence            457888888888765 4578999999999999999999984  68899999999999999999999998 565 789999


Q ss_pred             ccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794          109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus       109 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      ++++|||+|.+++||+||+|+++..|+||+||++|.|+...++++
T Consensus       403 ~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~  447 (500)
T 1z63_A          403 AGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVH  447 (500)
T ss_dssp             CC-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEE
T ss_pred             cccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEE
Confidence            999999999999999999999999999999999999987766444

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

Probab=99.66  E-value=5.4e-16  Score=174.76  Aligned_cols=136  Identities=23%  Similarity=0.315  Sum_probs=107.5

Q ss_pred             EEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cC-------------------------------
Q 012794           28 YAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-II-------------------------------   75 (456)
Q Consensus        28 ~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~-------------------------------   75 (456)
                      ++...+...+...|..++... ...++||||+|++.|+.++..|.. ++                               
T Consensus       314 ~~~~~~~~~~~~~li~~l~~~-~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~  392 (997)
T 4a4z_A          314 FTQDGPSKKTWPEIVNYLRKR-ELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQIL  392 (997)
T ss_dssp             ---CCCCTTHHHHHHHHHHHT-TCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHH
T ss_pred             ccccccchhHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHH
Confidence            344445566777777777654 457999999999999999998864 22                               


Q ss_pred             --------CEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCC---------CCChhHHHHHh
Q 012794           76 --------ASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL---------PNDPETFVHRS  138 (456)
Q Consensus        76 --------~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~---------p~~~~~y~qr~  138 (456)
                              .+.++|++|++.+|+.+++.|++|.++|||||+++++|||+|++.+|+ +++         |.++.+|+||+
T Consensus       393 ~l~~~l~~gi~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~~~VVi-~~~~k~dg~~~~~~s~~~y~Qr~  471 (997)
T 4a4z_A          393 KTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTVIF-SSIRKHDGNGLRELTPGEFTQMA  471 (997)
T ss_dssp             HHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCCSEEEE-SCSEEEETTEEEECCHHHHHHHH
T ss_pred             HHHHHhhcCeeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCCceEEE-eccccccCccCCCCCHHHHhHHh
Confidence                    478999999999999999999999999999999999999999955555 444         44999999999


Q ss_pred             cccccCC--CCceEEEeeC--hhhHHHHHHH
Q 012794          139 GRTGRAG--KEGTAILMFT--SSQRRTVRSL  165 (456)
Q Consensus       139 GR~gR~g--~~g~~i~~~~--~~e~~~~~~i  165 (456)
                      |||||.|  ..|.+++++.  ..+...++.+
T Consensus       472 GRAGR~G~~~~G~vi~l~~~~~~~~~~~~~~  502 (997)
T 4a4z_A          472 GRAGRRGLDSTGTVIVMAYNSPLSIATFKEV  502 (997)
T ss_dssp             GGGCCTTTCSSEEEEEECCSSCCCHHHHHHH
T ss_pred             cccccCCCCcceEEEEecCCCcchHHHHHHH
Confidence            9999988  5678888873  3344455444

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

Probab=99.65  E-value=1.6e-16  Score=163.90  Aligned_cols=99  Identities=19%  Similarity=0.297  Sum_probs=88.6

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccce--------
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDL--------  121 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~--------  121 (456)
                      .+++||||+|+++++.+++.|.+ .+.+..+||+    +|+++++.|++|+++|||||+++++|||+| +.+        
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~  245 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTI  245 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccc
Confidence            57999999999999999999985 7889999997    578899999999999999999999999999 554        


Q ss_pred             ---------EEecCCCCChhHHHHHhcccccCCC-CceEEEee
Q 012794          122 ---------IIHYELPNDPETFVHRSGRTGRAGK-EGTAILMF  154 (456)
Q Consensus       122 ---------VI~~~~p~~~~~y~qr~GR~gR~g~-~g~~i~~~  154 (456)
                               ||+++.|.+.++|+||+||+||.|. .+.++++.
T Consensus       246 ~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          246 KPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             EEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             cceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence                     6788999999999999999999985 45555555

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

Probab=99.63  E-value=5.1e-16  Score=163.04  Aligned_cols=118  Identities=14%  Similarity=0.173  Sum_probs=99.9

Q ss_pred             HHHHHHHHHHHH-CC-CCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec-ccccc
Q 012794           37 KRTILSDLITVY-AK-GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT-DVAAR  112 (456)
Q Consensus        37 k~~~L~~ll~~~-~~-~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT-dv~~~  112 (456)
                      +...+.+++... .. ..++||||+ .++++.|++.|.+ ...+..+||+|++.+|+++++.|++++++||||| +++++
T Consensus       332 ~~~~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~  410 (510)
T 2oca_A          332 RNKWIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFST  410 (510)
T ss_dssp             HHHHHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhc
Confidence            444555555543 22 345677777 8889999999985 5689999999999999999999999999999999 99999


Q ss_pred             ccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeC
Q 012794          113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT  155 (456)
Q Consensus       113 Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~  155 (456)
                      |+|+|++++||++++|+++..|+|++||+||.|+.+.+++++.
T Consensus       411 GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          411 GISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             SCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             ccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            9999999999999999999999999999999998774444443

>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=99.62  E-value=2.7e-15  Score=162.25  Aligned_cols=120  Identities=13%  Similarity=0.242  Sum_probs=107.6

Q ss_pred             cccHHHHHHHHHHHH--CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCe---EEEEec
Q 012794           34 ATSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF---TVLVAT  107 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~---~vLVaT  107 (456)
                      ...|+.+|..++...  ..+.++||||+++..++.|+..|.. ++.+..+||+|++.+|++++++|+++..   .+||+|
T Consensus       397 ~s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st  476 (644)
T 1z3i_X          397 LSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSS  476 (644)
T ss_dssp             GSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEG
T ss_pred             cChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEec
Confidence            356888888888765  2468999999999999999999984 8999999999999999999999999865   489999


Q ss_pred             cccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEe
Q 012794          108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILM  153 (456)
Q Consensus       108 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~  153 (456)
                      ++++.|||++.+++||+||+|+++..|+|++||++|.|++..++++
T Consensus       477 ~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~  522 (644)
T 1z3i_X          477 KAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIY  522 (644)
T ss_dssp             GGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEE
T ss_pred             ccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEE
Confidence            9999999999999999999999999999999999999977655544

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

Probab=99.60  E-value=1.7e-15  Score=162.04  Aligned_cols=101  Identities=21%  Similarity=0.302  Sum_probs=88.6

Q ss_pred             HHHHCCCCcEEEEcCChHHHHHHHHHHHhcC---------CEEEEeCCCCHHHHHHHHhcccCCCeE---EEEecccccc
Q 012794           45 ITVYAKGGKTIVFTQTKRDADEVSLALTSII---------ASEALHGDISQHQRERTLNGFRQGKFT---VLVATDVAAR  112 (456)
Q Consensus        45 l~~~~~~~~~IIF~~t~~~a~~l~~~L~~~~---------~~~~lhg~~~~~~R~~~l~~Fr~g~~~---vLVaTdv~~~  112 (456)
                      +.......++||||+++.+|+.+++.|.+..         .+..+||++++ +|++++++|++++.+   |||||+++++
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            4444456899999999999999999997421         27789999864 799999999998766   8899999999


Q ss_pred             ccCcCccceEEecCCCCChhHHHHHhcccccCCC
Q 012794          113 GLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGK  146 (456)
Q Consensus       113 Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~  146 (456)
                      |||+|++++||++++|.++..|+||+||++|.+.
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

>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=99.59  E-value=4.8e-15  Score=174.41  Aligned_cols=124  Identities=19%  Similarity=0.261  Sum_probs=106.2

Q ss_pred             HHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc-----------------------------------CCEEEEeCCCCH
Q 012794           42 SDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-----------------------------------IASEALHGDISQ   86 (456)
Q Consensus        42 ~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~-----------------------------------~~~~~lhg~~~~   86 (456)
                      ...+..+...+++||||+|+..|+.+|..|...                                   ..+.++|++|++
T Consensus      1146 ~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~ 1225 (1724)
T 4f92_B         1146 YHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSP 1225 (1724)
T ss_dssp             HHHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCH
T ss_pred             HHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCH
Confidence            344555667789999999999999888766321                                   248899999999


Q ss_pred             HHHHHHHhcccCCCeEEEEeccccccccCcCccceEEe----------cCCCCChhHHHHHhcccccCCC--CceEEEee
Q 012794           87 HQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----------YELPNDPETFVHRSGRTGRAGK--EGTAILMF  154 (456)
Q Consensus        87 ~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~----------~~~p~~~~~y~qr~GR~gR~g~--~g~~i~~~  154 (456)
                      .+|..+++.|++|.++|||||+++++|||+|.+.+||.          ...|.++.+|+||+|||||+|.  .|.|++++
T Consensus      1226 ~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~ 1305 (1724)
T 4f92_B         1226 MERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMC 1305 (1724)
T ss_dssp             HHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEE
T ss_pred             HHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEe
Confidence            99999999999999999999999999999999999993          3357799999999999999985  69999999


Q ss_pred             ChhhHHHHHHH
Q 012794          155 TSSQRRTVRSL  165 (456)
Q Consensus       155 ~~~e~~~~~~i  165 (456)
                      .+.+...++.+
T Consensus      1306 ~~~~~~~~~~l 1316 (1724)
T 4f92_B         1306 QGSKKDFFKKF 1316 (1724)
T ss_dssp             EGGGHHHHHHH
T ss_pred             cchHHHHHHHH
Confidence            98887776655

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

Probab=99.57  E-value=1.7e-14  Score=159.79  Aligned_cols=138  Identities=17%  Similarity=0.336  Sum_probs=118.1

Q ss_pred             cccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCCe---EEEEecc
Q 012794           34 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKF---TVLVATD  108 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~---~vLVaTd  108 (456)
                      ...|+.+|..+|..+ ..+.++||||.....++.|+..|. .++.+..+||.+++.+|.++++.|+++..   .+||+|.
T Consensus       554 ~s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~  633 (800)
T 3mwy_W          554 SSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTR  633 (800)
T ss_dssp             TCHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHH
T ss_pred             cChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecc
Confidence            356899999999876 346799999999999999999998 48999999999999999999999998654   4999999


Q ss_pred             ccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEE--eeCh--hhHHHHHHHHHHhCC
Q 012794          109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL--MFTS--SQRRTVRSLERDVGC  171 (456)
Q Consensus       109 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~--~~~~--~e~~~~~~ie~~~~~  171 (456)
                      +++.|||++.+++||+||+|+++..++||+||++|.|++..+.+  |++.  -|...++.++++...
T Consensus       634 agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe~i~~~~~~K~~l  700 (800)
T 3mwy_W          634 AGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMIL  700 (800)
T ss_dssp             HHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHHHHHHHHHHHTTS
T ss_pred             cccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999997765544  3443  366667766666544

>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=99.54  E-value=6.7e-15  Score=173.22  Aligned_cols=117  Identities=22%  Similarity=0.377  Sum_probs=100.1

Q ss_pred             CCCCcEEEEcCChHHHHHHHHHHHhc--------------------------------------CCEEEEeCCCCHHHHH
Q 012794           49 AKGGKTIVFTQTKRDADEVSLALTSI--------------------------------------IASEALHGDISQHQRE   90 (456)
Q Consensus        49 ~~~~~~IIF~~t~~~a~~l~~~L~~~--------------------------------------~~~~~lhg~~~~~~R~   90 (456)
                      ....++||||+|++.|+.+|..|.+.                                      ..+.++|++|++.+|.
T Consensus       315 ~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~  394 (1724)
T 4f92_B          315 AGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRT  394 (1724)
T ss_dssp             CSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHH
T ss_pred             hcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHH
Confidence            34578999999999999888877421                                      1378999999999999


Q ss_pred             HHHhcccCCCeEEEEeccccccccCcCccceEEe----cC------CCCChhHHHHHhcccccCC--CCceEEEeeChhh
Q 012794           91 RTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH----YE------LPNDPETFVHRSGRTGRAG--KEGTAILMFTSSQ  158 (456)
Q Consensus        91 ~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~----~~------~p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~e  158 (456)
                      .+++.|++|.++|||||+++++|||+|.+++||.    |+      .|.++.+|+||+|||||+|  ..|.+++++...+
T Consensus       395 ~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~  474 (1724)
T 4f92_B          395 LVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGE  474 (1724)
T ss_dssp             HHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTT
T ss_pred             HHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchh
Confidence            9999999999999999999999999999999995    44      3568999999999999987  5699999988877


Q ss_pred             HHHHHHH
Q 012794          159 RRTVRSL  165 (456)
Q Consensus       159 ~~~~~~i  165 (456)
                      ...+..+
T Consensus       475 ~~~~~~l  481 (1724)
T 4f92_B          475 LQYYLSL  481 (1724)
T ss_dssp             CCHHHHH
T ss_pred             HHHHHHH
Confidence            6555544

>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=99.27  E-value=6.7e-11  Score=133.16  Aligned_cols=120  Identities=11%  Similarity=0.111  Sum_probs=94.0

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-c------------CCE-EEEeCC----------C----------CHH---------
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-I------------IAS-EALHGD----------I----------SQH---------   87 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~------------~~~-~~lhg~----------~----------~~~---------   87 (456)
                      ..++||||+++..|..+++.|.+ .            +.+ +++|++          |          ++.         
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            35899999999999999999874 2            345 445542          2          322         


Q ss_pred             --------------------HHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCC
Q 012794           88 --------------------QRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE  147 (456)
Q Consensus        88 --------------------~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~  147 (456)
                                          +|..++++|+++.++|||+||++.+|+|+|.+ .|+++|.|.+...|+|++||++|.+..
T Consensus       617 ~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~  695 (1038)
T 2w00_A          617 REYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDA  695 (1038)
T ss_dssp             HHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCT
T ss_pred             HHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCC
Confidence                                48889999999999999999999999999999 788999999999999999999998753


Q ss_pred             ----ceEEEeeChhhHHHHHHHHHHhCCC
Q 012794          148 ----GTAILMFTSSQRRTVRSLERDVGCK  172 (456)
Q Consensus       148 ----g~~i~~~~~~e~~~~~~ie~~~~~~  172 (456)
                          |.++.|+.. .......|..+....
T Consensus       696 ~K~~G~IVdf~~~-~~~l~~Al~~y~~~~  723 (1038)
T 2w00_A          696 TKTFGNIVTFRDL-ERSTIDAITLFGDKN  723 (1038)
T ss_dssp             TCCSEEEEESSCC-HHHHHHHHHHTSCSS
T ss_pred             CCCcEEEEEcccc-HHHHHHHHHHHhCCC
Confidence                666666653 444455555555443

>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=3e-10  Score=90.45  Aligned_cols=89  Identities=22%  Similarity=0.297  Sum_probs=73.4

Q ss_pred             HhCCCCCCCCccccCCCCceEEEEEeecCccccCCCChhHHHHHHHhhCCC-CCCccccEEEeecCccceeeeecCHHHH
Q 012794          230 LSGFSRPPSSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPT-AADEIGKIHIIADDRVQGAVFDLPEEIA  308 (456)
Q Consensus       230 ~~~~~~~~~~r~l~~~~~g~~t~~~~~~~~~~~~~~~~~~i~~~l~~~~~~-~~~~ig~i~~~~~~~~~~~~~dv~~~~a  308 (456)
                      ++|+++ +++|||+++.+|++|+.+..+.    ..-.+..++.+|.+..+. ..++|++|+++++.  +|++||||++.+
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            467777 5569999999999999998875    345788899999985543 55689999999986  599999999999


Q ss_pred             HHHHhhcCCCCCceeec
Q 012794          309 KELLNKQIPPGNTISKI  325 (456)
Q Consensus       309 ~~~~~~~~~~g~~l~~~  325 (456)
                      ++++..|.+..+.++++
T Consensus        75 ~~~~~~~~~~~~~l~v~   91 (92)
T 2e29_A           75 ERLQAEWHDSDWILSVP   91 (92)
T ss_dssp             HHHHHHCCSSSCEEECC
T ss_pred             HHHHhhCCCCceEEEec
Confidence            99999987644767665

>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=98.34  E-value=1.6e-07  Score=56.51  Aligned_cols=18  Identities=44%  Similarity=1.198  Sum_probs=16.4

Q ss_pred             CCcccCCCCCcCcCCCCC
Q 012794          439 GACFNCGKSGHRASECPN  456 (456)
Q Consensus       439 ~~~~~c~~~gh~~~~~p~  456 (456)
                      ..||+||++||+|+|||+
T Consensus         3 ~~Cf~CG~~GH~ardC~~   20 (26)
T 1dsq_A            3 PVCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTC
T ss_pred             CeeEeCCCCCcccccCCC
Confidence            459999999999999995

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=98.27  E-value=4.9e-07  Score=69.50  Aligned_cols=61  Identities=16%  Similarity=0.275  Sum_probs=52.4

Q ss_pred             EEEEEeecCccccCCCChhHHHHHHHhhCCCCCCccccEEEeecCccceeeeecCHHHHHHHHhhcCC
Q 012794          250 VTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIP  317 (456)
Q Consensus       250 ~t~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~ig~i~~~~~~~~~~~~~dv~~~~a~~~~~~~~~  317 (456)
                      +|++++.++   ++++.|++|+++|++...+...+||+|+|+++|    |+|+||++.++++++....
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            378899998   899999999999999999999999999999998    7999999999999987654

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.25  E-value=1e-05  Score=88.18  Aligned_cols=38  Identities=24%  Similarity=0.310  Sum_probs=33.6

Q ss_pred             eEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          121 LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       121 ~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      |||-...+.|...-.|-.||+||.|.+|.+..|++-.+
T Consensus       662 hVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeD  699 (997)
T 2ipc_A          662 FIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDD  699 (997)
T ss_dssp             CEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSS
T ss_pred             EEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECCh
Confidence            79999999999999999999999999999887766443

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.05  E-value=5.6e-06  Score=87.36  Aligned_cols=101  Identities=16%  Similarity=0.243  Sum_probs=63.8

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEE--eccccccccCcCc----cceEE
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLV--ATDVAARGLDIPN----VDLII  123 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLV--aTdv~~~Gidip~----v~~VI  123 (456)
                      ..+.+|||+++...++++++.|.. + ...+++..  ..|+++++.|+++. .||+  +|+.+.+|||+|+    +.+||
T Consensus       383 ~~g~~lvff~S~~~~~~v~~~l~~-~-~~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~Vi  457 (540)
T 2vl7_A          383 SSKSVLVFFPSYEMLESVRIHLSG-I-PVIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFESLV  457 (540)
T ss_dssp             CSSEEEEEESCHHHHHHHHTTCTT-S-CEEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHhcc-C-ceEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccEEE
Confidence            457899999999999999988764 2 24556654  46889999999864 4665  8999999999997    89999


Q ss_pred             ecCCCCCh------------------------------hHHHHHhcccccCCCCceEEEeeC
Q 012794          124 HYELPNDP------------------------------ETFVHRSGRTGRAGKEGTAILMFT  155 (456)
Q Consensus       124 ~~~~p~~~------------------------------~~y~qr~GR~gR~g~~g~~i~~~~  155 (456)
                      ++++|...                              ..+.|.+||+-|....--+++++.
T Consensus       458 i~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD  519 (540)
T 2vl7_A          458 LAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCD  519 (540)
T ss_dssp             EESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEES
T ss_pred             EECCCCCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEc
Confidence            99998521                              224689999988643322344444

>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=97.98  E-value=1.7e-06  Score=53.42  Aligned_cols=17  Identities=53%  Similarity=1.300  Sum_probs=15.7

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||||+++||+++|||.
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            49999999999999984

>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=97.92  E-value=3.1e-06  Score=56.11  Aligned_cols=17  Identities=41%  Similarity=1.085  Sum_probs=15.9

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|++.||+|+|||+
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            49999999999999995

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=97.80  E-value=2.1e-05  Score=52.09  Aligned_cols=17  Identities=47%  Similarity=1.331  Sum_probs=16.0

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
T Consensus        23 ~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           23 GCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             SCTTTCCSSSCTTTSCC
T ss_pred             ccccCCCCCCccCcCcC
Confidence            49999999999999996

>3i31_A Heat resistant RNA dependent ATPase; RNA helicase, RNA recognition motif, ATP-binding, helicase, nucleotide-binding; 1.80A {Thermus thermophilus}

Probab=97.79  E-value=4.5e-05  Score=57.99  Aligned_cols=78  Identities=24%  Similarity=0.326  Sum_probs=62.0

Q ss_pred             CCccccCCCCceEEEEEeecCccccCCCChhHHHHHHHhhCCCCCCccccEEEeecCccceeeeecCHHHHHHHHhhcCC
Q 012794          238 SSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQIP  317 (456)
Q Consensus       238 ~~r~l~~~~~g~~t~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~ig~i~~~~~~~~~~~~~dv~~~~a~~~~~~~~~  317 (456)
                      .++||+++++||+|+.++..      .++...++.+|.....    +||+|..-..    |+++||+.++..      ..
T Consensus         2 ~~~SLLTGEEGw~Tlkl~G~------rLS~~R~VAlLk~aG~----~iGkI~~~~~----gayaDlr~e~l~------~~   61 (88)
T 3i31_A            2 AERSLLTGEEGWRTYKATGP------RLSLPRLVALLKGQGL----EVGKVAEAEG----GFYVDLRPEARP------EV   61 (88)
T ss_dssp             CCBCTTTCCBSCEEEEEECT------TCCHHHHHHHHHHTTC----CEEEEEEETT----EEEEEECTTCCC------CC
T ss_pred             CcccccccCcceEEEEEecc------cccHHHHHHHHHHccc----ccccEEeccc----eeEEecChHHcc------cc
Confidence            46899999999999999754      3899999999987544    9999997655    689999988766      22


Q ss_pred             CCCceeecccCCCccCCC
Q 012794          318 PGNTISKITKLPALQDDG  335 (456)
Q Consensus       318 ~g~~l~~~t~LP~l~~~~  335 (456)
                      .++.+.+.+.+|.+.+.+
T Consensus        62 ~~~~~e~A~~v~~~~E~p   79 (88)
T 3i31_A           62 AGLRLEPARRVEGLLEIP   79 (88)
T ss_dssp             TTCEEEECCSCCCCC---
T ss_pred             ccceehhhhhccccccCC
Confidence            788899999998887654

>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=97.61  E-value=1.5e-05  Score=56.90  Aligned_cols=17  Identities=41%  Similarity=1.085  Sum_probs=15.9

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+||+.||+++|||+
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            49999999999999995

>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=97.53  E-value=7.2e-05  Score=52.13  Aligned_cols=16  Identities=50%  Similarity=1.475  Sum_probs=15.4

Q ss_pred             cccCCCCCcCcCCCCC
Q 012794          441 CFNCGKSGHRASECPN  456 (456)
Q Consensus       441 ~~~c~~~gh~~~~~p~  456 (456)
                      ||+|+++||+++|||+
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

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=97.45  E-value=4e-05  Score=50.09  Aligned_cols=17  Identities=35%  Similarity=1.087  Sum_probs=16.0

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
T Consensus        21 ~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           21 VCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             TCSSCCCTTGGGGTTCC
T ss_pred             eEccCCCcCCccCcCcC
Confidence            49999999999999997

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.44  E-value=5.1e-05  Score=53.94  Aligned_cols=18  Identities=50%  Similarity=1.252  Sum_probs=16.1

Q ss_pred             CCcccCCCCCcCcCCCCC
Q 012794          439 GACFNCGKSGHRASECPN  456 (456)
Q Consensus       439 ~~~~~c~~~gh~~~~~p~  456 (456)
                      ..||+||++||+++|||+
T Consensus         8 ~~C~kCGk~GH~~k~Cp~   25 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCPT   25 (55)
T ss_dssp             CCCTTTCCTTSCGGGCSG
T ss_pred             CccccCCCcCcccccCCC
Confidence            349999999999999993

>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=97.42  E-value=0.0012  Score=64.52  Aligned_cols=120  Identities=13%  Similarity=0.127  Sum_probs=84.6

Q ss_pred             CcccHHHHHHHHHHHHC-CCCcEEEEcCChHHHHHHHHHHH-hcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccc
Q 012794           33 TATSKRTILSDLITVYA-KGGKTIVFTQTKRDADEVSLALT-SIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVA  110 (456)
Q Consensus        33 ~~~~k~~~L~~ll~~~~-~~~~~IIF~~t~~~a~~l~~~L~-~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~  110 (456)
                      ..+.|+.+|.+||.... .+.++|||++...+.+-|...|. +++...-+-|.....++ +.    .+....|.+.|...
T Consensus       106 ~~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~~-k~----~~~~~~i~Lltsag  180 (328)
T 3hgt_A          106 ENSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAA-AA----NDFSCTVHLFSSEG  180 (328)
T ss_dssp             HTCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSC
T ss_pred             HcCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhhh-hc----ccCCceEEEEECCC
Confidence            35689999999998773 45699999999999999999888 47777888887544322 21    23455665556666


Q ss_pred             ccccC-----cCccceEEecCCCCChhHH-HHHhcccccCC----CCceEEEeeChh
Q 012794          111 ARGLD-----IPNVDLIIHYELPNDPETF-VHRSGRTGRAG----KEGTAILMFTSS  157 (456)
Q Consensus       111 ~~Gid-----ip~v~~VI~~~~p~~~~~y-~qr~GR~gR~g----~~g~~i~~~~~~  157 (456)
                      .-|+|     +...+.||.||.-+++..= +|++-|+.|.+    +.-.+|-+++..
T Consensus       181 ~~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~  237 (328)
T 3hgt_A          181 INFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAIN  237 (328)
T ss_dssp             CCTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETT
T ss_pred             CCCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCC
Confidence            66676     6788999999999999885 89888888863    344566666554

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=97.41  E-value=9.5e-05  Score=54.07  Aligned_cols=17  Identities=35%  Similarity=0.847  Sum_probs=15.9

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
T Consensus        32 ~C~~Cg~~GH~ar~C~~   48 (61)
T 2ihx_A           32 RCQLCNGMGHNAKQCRK   48 (61)
T ss_dssp             BCTTTCCBSSCGGGCCC
T ss_pred             eeCCCCCCCCCcCCCcC
Confidence            49999999999999995

>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=97.41  E-value=0.00022  Score=52.39  Aligned_cols=16  Identities=31%  Similarity=0.818  Sum_probs=15.4

Q ss_pred             cccCCCCCcCcCCCCC
Q 012794          441 CFNCGKSGHRASECPN  456 (456)
Q Consensus       441 ~~~c~~~gh~~~~~p~  456 (456)
                      ||+|+++||+++|||+
T Consensus        32 C~~Cg~~GH~ar~Cp~   47 (63)
T 2cqf_A           32 CHFCQSISHMVASCPL   47 (63)
T ss_dssp             CTTTCCSSSCTTTCTG
T ss_pred             cCCcCCcCCccCcCCC
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=97.38  E-value=0.00015  Score=62.97  Aligned_cols=16  Identities=31%  Similarity=0.818  Sum_probs=15.6

Q ss_pred             cccCCCCCcCcCCCCC
Q 012794          441 CFNCGKSGHRASECPN  456 (456)
Q Consensus       441 ~~~c~~~gh~~~~~p~  456 (456)
                      ||+|+++||+++|||+
T Consensus       122 C~~Cg~~GH~~r~Cp~  137 (148)
T 3ts2_A          122 CHFCQSINHMVASCPL  137 (148)
T ss_dssp             CTTTCCSSCCGGGCTT
T ss_pred             ccccCCcCCEeccCcC
Confidence            9999999999999996

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=97.38  E-value=0.00021  Score=54.26  Aligned_cols=17  Identities=29%  Similarity=0.763  Sum_probs=15.8

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
T Consensus        48 ~C~~Cg~~GH~ar~Cp~   64 (74)
T 2li8_A           48 KCHFCQSISHMVASCPL   64 (74)
T ss_dssp             CCTTTCCTTSCGGGCTT
T ss_pred             ccCCcCCcCCccCcCcC
Confidence            39999999999999995

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=97.34  E-value=6.6e-05  Score=49.64  Aligned_cols=17  Identities=59%  Similarity=1.341  Sum_probs=15.7

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
T Consensus         2 ~C~~Cg~~GH~a~~C~~   18 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQ   18 (39)
T ss_dssp             BCTTTCCBSSCTTTCCS
T ss_pred             eeeccCCCCcccccCCC
Confidence            39999999999999994

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=97.27  E-value=9.6e-05  Score=48.24  Aligned_cols=17  Identities=53%  Similarity=1.339  Sum_probs=15.7

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
T Consensus         2 ~C~~Cg~~GH~~~~C~~   18 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRA   18 (37)
T ss_dssp             CBSSSCCSSCCTTTSSC
T ss_pred             cccccCCCCcchhhCcC
Confidence            39999999999999995

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=97.19  E-value=0.00027  Score=53.65  Aligned_cols=18  Identities=44%  Similarity=1.027  Sum_probs=16.1

Q ss_pred             CCcccCCCCCcCcCCCCC
Q 012794          439 GACFNCGKSGHRASECPN  456 (456)
Q Consensus       439 ~~~~~c~~~gh~~~~~p~  456 (456)
                      ..||+|+++||+++|||+
T Consensus        25 ~~C~~Cg~~GH~a~~C~~   42 (74)
T 2li8_A           25 DRCYNCGGLDHHAKECKL   42 (74)
T ss_dssp             SCCTTTCCSSSCTTTCSS
T ss_pred             CcccccCCcCcCcccCCC
Confidence            349999999999999983

>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=97.17  E-value=0.00016  Score=52.67  Aligned_cols=18  Identities=39%  Similarity=0.905  Sum_probs=16.3

Q ss_pred             CCcccCCCCCcCcCCCCC
Q 012794          439 GACFNCGKSGHRASECPN  456 (456)
Q Consensus       439 ~~~~~c~~~gh~~~~~p~  456 (456)
                      ..||+|+++||+++|||+
T Consensus        31 ~~C~~Cg~~GH~ar~C~~   48 (60)
T 1cl4_A           31 GLCPRCKRGKHWANECKS   48 (60)
T ss_dssp             CSCSSCSSCSSCSTTCCC
T ss_pred             cceeECCCCCCccCcCCC
Confidence            349999999999999995

>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=97.10  E-value=0.00017  Score=50.27  Aligned_cols=17  Identities=53%  Similarity=1.300  Sum_probs=15.8

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
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            49999999999999984

>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=97.05  E-value=0.00033  Score=51.46  Aligned_cols=18  Identities=44%  Similarity=1.027  Sum_probs=16.1

Q ss_pred             CCcccCCCCCcCcCCCCC
Q 012794          439 GACFNCGKSGHRASECPN  456 (456)
Q Consensus       439 ~~~~~c~~~gh~~~~~p~  456 (456)
                      ..||+|+++||+++|||+
T Consensus         8 ~~C~~Cg~~GH~a~~C~~   25 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKL   25 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCS
T ss_pred             CcccccCCCCcChhhCCC
Confidence            349999999999999994

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=97.01  E-value=0.00017  Score=56.02  Aligned_cols=18  Identities=39%  Similarity=1.030  Sum_probs=16.4

Q ss_pred             CCcccCCCCCcCcCCCCC
Q 012794          439 GACFNCGKSGHRASECPN  456 (456)
Q Consensus       439 ~~~~~c~~~gh~~~~~p~  456 (456)
                      ..||+||+.||+++|||+
T Consensus        47 ~~CYnCG~~GH~~rdC~~   64 (83)
T 3nyb_B           47 IYCYNCGGKGHFGDDCKE   64 (83)
T ss_dssp             CBCSSSSCBSSCGGGCSS
T ss_pred             CeecccCCCCcCcccCCc
Confidence            459999999999999995

>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=96.99  E-value=0.00022  Score=50.90  Aligned_cols=17  Identities=41%  Similarity=1.304  Sum_probs=15.8

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
T Consensus        35 ~C~~Cg~~GH~~~~C~~   51 (55)
T 1a1t_A           35 GCWKCGKEGHQMKDCTE   51 (55)
T ss_dssp             BCTTTCCBSSCGGGCSS
T ss_pred             EeCCCCCcCCccCCCcC
Confidence            39999999999999995

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=96.97  E-value=0.0002  Score=52.26  Aligned_cols=17  Identities=41%  Similarity=1.327  Sum_probs=15.9

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
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            49999999999999995

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=96.91  E-value=0.002  Score=54.02  Aligned_cols=19  Identities=37%  Similarity=0.957  Sum_probs=17.2

Q ss_pred             CCCcccCCCCCcCcCCCCC
Q 012794          438 GGACFNCGKSGHRASECPN  456 (456)
Q Consensus       438 ~~~~~~c~~~gh~~~~~p~  456 (456)
                      ...||+|++.||+|+|||+
T Consensus       105 ~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A          105 TIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCCTTTTSSSCTTTTTSCC
T ss_pred             CCCcCCCCCCCcCcccCcC
Confidence            3569999999999999996

>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=96.75  E-value=0.00039  Score=49.58  Aligned_cols=17  Identities=59%  Similarity=1.318  Sum_probs=15.7

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|+++||+++|||+
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            49999999999999984

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=96.69  E-value=0.0063  Score=65.05  Aligned_cols=103  Identities=20%  Similarity=0.268  Sum_probs=68.1

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc--ccccccCcCc--cceEEecC
Q 012794           51 GGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATD--VAARGLDIPN--VDLIIHYE  126 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd--v~~~Gidip~--v~~VI~~~  126 (456)
                      ++.+|||+++....+++++.|. .+... ..-+++...+..+++.|+ +.-.||++|.  ...+|||+|+  +.+||...
T Consensus       448 ~g~~lvlF~Sy~~l~~v~~~l~-~~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~  524 (620)
T 4a15_A          448 KKNTIVYFPSYSLMDRVENRVS-FEHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAG  524 (620)
T ss_dssp             CSCEEEEESCHHHHHHHTSSCC-SCCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHH-hcchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEc
Confidence            5789999999999999988776 22222 444555678999999999 7778999975  9999999984  56799888


Q ss_pred             CCCCh-----------------------------hHHHHHhcccccCCCCceEEEeeCh
Q 012794          127 LPNDP-----------------------------ETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       127 ~p~~~-----------------------------~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      +|...                             ....|.+||+=|.-..--+++++..
T Consensus       525 lPfp~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~  583 (620)
T 4a15_A          525 LPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDK  583 (620)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECG
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEcc
Confidence            77421                             1126899999886544334444443

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

Probab=96.06  E-value=0.016  Score=58.14  Aligned_cols=88  Identities=15%  Similarity=0.210  Sum_probs=68.6

Q ss_pred             ccHHH-HHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           35 TSKRT-ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        35 ~~k~~-~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      .-|.. .+..++.....+.++||.+||++.+.++++.+..    .+.+..+||+++..++...++.+..+..+|+|+|+-
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            45654 3333344445678999999999999999999986    568999999999999888888888888999999962


Q ss_pred             -----cccccCcCccceEE
Q 012794          110 -----AARGLDIPNVDLII  123 (456)
Q Consensus       110 -----~~~Gidip~v~~VI  123 (456)
                           +.. +++..+.+||
T Consensus       127 ~l~~~l~~-~~~~~~~~iV  144 (414)
T 3oiy_A          127 FVSKNREK-LSQKRFDFVF  144 (414)
T ss_dssp             HHHHCHHH-HTTCCCSEEE
T ss_pred             HHHHHHHH-hccccccEEE
Confidence                 222 5666788877

>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=96.05  E-value=0.014  Score=64.04  Aligned_cols=90  Identities=20%  Similarity=0.286  Sum_probs=70.9

Q ss_pred             ccHHHH-HHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           35 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        35 ~~k~~~-L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      .-|..+ +..++.....+.++||.++|+..|.++++.+.+     ++.+..+||+++..++..+++.+.++..+|+|+|.
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            456433 333444444467999999999999999988864     37899999999999999999999999999999997


Q ss_pred             c-cccccCcCccceEEe
Q 012794          109 V-AARGLDIPNVDLIIH  124 (456)
Q Consensus       109 v-~~~Gidip~v~~VI~  124 (456)
                      . +...+++.++.+||.
T Consensus       480 ~ll~~~~~~~~l~lVVI  496 (780)
T 1gm5_A          480 ALIQEDVHFKNLGLVII  496 (780)
T ss_dssp             THHHHCCCCSCCCEEEE
T ss_pred             HHHhhhhhccCCceEEe
Confidence            4 334578888888883

>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=96.03  E-value=0.002  Score=55.74  Aligned_cols=17  Identities=47%  Similarity=1.085  Sum_probs=15.7

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||||++.||+|++||+
T Consensus        99 ~C~~Cg~~GH~a~~C~~  115 (148)
T 3ts2_A           99 RCYNCGGLDHHAKECKL  115 (148)
T ss_dssp             CCTTTCCSSCCGGGCCS
T ss_pred             cccEeCCccchhhhCCC
Confidence            39999999999999984

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=95.63  E-value=0.019  Score=47.94  Aligned_cols=18  Identities=28%  Similarity=0.709  Sum_probs=16.3

Q ss_pred             CCcccCCCCCcCcCCCCC
Q 012794          439 GACFNCGKSGHRASECPN  456 (456)
Q Consensus       439 ~~~~~c~~~gh~~~~~p~  456 (456)
                      ..||+|++.||+++|||+
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            459999999999999995

>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=95.44  E-value=0.094  Score=48.40  Aligned_cols=69  Identities=16%  Similarity=0.236  Sum_probs=54.2

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc-ccCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~-Gidip~v  119 (456)
                      ..++||.|+|++.+.++++.+..     .+.+..++|+.+...+...+..    ..+|+|+|+     .+.. .+++.++
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            46799999999999999887764     4688999999998877766654    578999995     3333 3678888


Q ss_pred             ceEE
Q 012794          120 DLII  123 (456)
Q Consensus       120 ~~VI  123 (456)
                      .+||
T Consensus       178 ~~lV  181 (242)
T 3fe2_A          178 TYLV  181 (242)
T ss_dssp             CEEE
T ss_pred             cEEE
Confidence            8877

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

Probab=95.08  E-value=0.041  Score=62.62  Aligned_cols=90  Identities=14%  Similarity=0.194  Sum_probs=70.0

Q ss_pred             cccHHHHH-HHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           34 ATSKRTIL-SDLITVYAKGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        34 ~~~k~~~L-~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      ..-|..+. ..++.....+.++||.+||++.|.++++.|..    .+.+..+||+++..++...++.+.++..+|||+|+
T Consensus       103 GSGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp  182 (1104)
T 4ddu_A          103 GVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFST  182 (1104)
T ss_dssp             TCCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEH
T ss_pred             CCcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECH
Confidence            34575433 33344445678999999999999999999986    35899999999998888889999999899999995


Q ss_pred             c-----cccccCcCccceEEe
Q 012794          109 V-----AARGLDIPNVDLIIH  124 (456)
Q Consensus       109 v-----~~~Gidip~v~~VI~  124 (456)
                      -     +.. +++.++.+||.
T Consensus       183 ~rL~~~l~~-l~~~~l~~lVi  202 (1104)
T 4ddu_A          183 QFVSKNREK-LSQKRFDFVFV  202 (1104)
T ss_dssp             HHHHHSHHH-HHTSCCSEEEE
T ss_pred             HHHHHHHHh-hcccCcCEEEE
Confidence            2     222 56678888773

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=94.50  E-value=0.27  Score=51.41  Aligned_cols=75  Identities=12%  Similarity=0.139  Sum_probs=52.2

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec--cccccccCcC-----ccceE
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVAT--DVAARGLDIP-----NVDLI  122 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT--dv~~~Gidip-----~v~~V  122 (456)
                      ..+.+|||+++....+++++.+  ...+.+-.-+++.   ..+++.|+...-.||+||  ....+|||+|     .+..|
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--SLPKYVESEDSSV---EDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDV  466 (551)
T ss_dssp             CSSEEEEEESCHHHHHHHHTTC--CSSEEECCSSCCH---HHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEEE
T ss_pred             CCCCEEEEecCHHHHHHHHHhc--CCcEEEcCCCCCH---HHHHHHHHhcCCeEEEEEecceecccccccccCCcceeEE
Confidence            3578999999999999988732  2223222234554   456677753334799998  6999999999     36788


Q ss_pred             EecCCCC
Q 012794          123 IHYELPN  129 (456)
Q Consensus       123 I~~~~p~  129 (456)
                      |...+|.
T Consensus       467 iI~~lPf  473 (551)
T 3crv_A          467 VIVGIPY  473 (551)
T ss_dssp             EEESCCC
T ss_pred             EEEcCCC
Confidence            8777664

>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=94.27  E-value=0.24  Score=45.00  Aligned_cols=70  Identities=14%  Similarity=0.262  Sum_probs=48.0

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cc-ccccCcCcc
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VA-ARGLDIPNV  119 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~-~~Gidip~v  119 (456)
                      ...++||.++|++.+.++++.+.+    .+.+..++|+.+...+...+..    ..+|+|+|+     .+ ...+++..+
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            456899999999999999998875    3678889998876655544433    578999995     22 234677888


Q ss_pred             ceEE
Q 012794          120 DLII  123 (456)
Q Consensus       120 ~~VI  123 (456)
                      .+||
T Consensus       169 ~~lV  172 (228)
T 3iuy_A          169 TYLV  172 (228)
T ss_dssp             CEEE
T ss_pred             eEEE
Confidence            8777

>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=94.19  E-value=0.39  Score=44.52  Aligned_cols=70  Identities=19%  Similarity=0.261  Sum_probs=52.7

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccc--cccCcCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAA--RGLDIPN  118 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~--~Gidip~  118 (456)
                      ..++||.++|++.+.++++.+.+     .+.+..++|+.+...+...+..    ..+|+|+|+     .+.  ..+++..
T Consensus       111 ~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~l~~  186 (249)
T 3ber_A          111 RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAK----KPHIIIATPGRLIDHLENTKGFNLRA  186 (249)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHT----CCSEEEECHHHHHHHHHHSTTCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCcCccc
Confidence            45799999999999999987763     3678899999887766555543    678999995     222  3467788


Q ss_pred             cceEEe
Q 012794          119 VDLIIH  124 (456)
Q Consensus       119 v~~VI~  124 (456)
                      +++||.
T Consensus       187 ~~~lVi  192 (249)
T 3ber_A          187 LKYLVM  192 (249)
T ss_dssp             CCEEEE
T ss_pred             cCEEEE
Confidence            887773

>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=94.10  E-value=0.36  Score=44.60  Aligned_cols=68  Identities=18%  Similarity=0.217  Sum_probs=50.3

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc-ccCcCccc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPNVD  120 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~-Gidip~v~  120 (456)
                      .++||.|+|++.+.++++.+..     .+.+..++|+.+...+...+.    ...+|+|+|+     .+.. .+++..+.
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            4899999999999999888764     256788899887665554443    2578999995     2222 36777888


Q ss_pred             eEE
Q 012794          121 LII  123 (456)
Q Consensus       121 ~VI  123 (456)
                      +||
T Consensus       177 ~lV  179 (253)
T 1wrb_A          177 YIV  179 (253)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            777

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=94.03  E-value=0.14  Score=58.43  Aligned_cols=89  Identities=15%  Similarity=0.178  Sum_probs=70.2

Q ss_pred             ccHHHHHH-HHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc-----CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           35 TSKRTILS-DLITVYAKGGKTIVFTQTKRDADEVSLALTSI-----IASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        35 ~~k~~~L~-~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      .-|..+.. .++.....+.++||.|+|+..|.+.++.+.+.     +.+..+++..+..++..+++.+.++.++|+|+|.
T Consensus       635 sGKT~val~aa~~~~~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~  714 (1151)
T 2eyq_A          635 FGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTH  714 (1151)
T ss_dssp             TTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECT
T ss_pred             CCHHHHHHHHHHHHHHhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            45654332 23333445679999999999999999988742     5688899999999999999999999999999995


Q ss_pred             -ccccccCcCccceEE
Q 012794          109 -VAARGLDIPNVDLII  123 (456)
Q Consensus       109 -v~~~Gidip~v~~VI  123 (456)
                       .+...+.+.++.+||
T Consensus       715 ~ll~~~~~~~~l~lvI  730 (1151)
T 2eyq_A          715 KLLQSDVKFKDLGLLI  730 (1151)
T ss_dssp             HHHHSCCCCSSEEEEE
T ss_pred             HHHhCCccccccceEE
Confidence             445558888888877

>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=93.33  E-value=0.65  Score=41.08  Aligned_cols=86  Identities=22%  Similarity=0.234  Sum_probs=59.7

Q ss_pred             cccHHHH-HHHHHHHHC------CCCcEEEEcCChHHHHHHHHHHHh---cCCEEEEeCCCCHHHHHHHHhcccCCCeEE
Q 012794           34 ATSKRTI-LSDLITVYA------KGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTV  103 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~~------~~~~~IIF~~t~~~a~~l~~~L~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v  103 (456)
                      ..-|..+ +..++....      ...++||.|+|++.+.++++.+.+   .+.+..++|+.+...+...+..    ..+|
T Consensus        48 GsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~i  123 (207)
T 2gxq_A           48 GTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLR----GADA  123 (207)
T ss_dssp             TSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHHH----CCSE
T ss_pred             CChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhhC----CCCE
Confidence            3567654 444444432      346899999999999999999885   3678889998876655544433    5789


Q ss_pred             EEecc-----cccc-ccCcCccceEE
Q 012794          104 LVATD-----VAAR-GLDIPNVDLII  123 (456)
Q Consensus       104 LVaTd-----v~~~-Gidip~v~~VI  123 (456)
                      +|+|+     .+.. .+++..+++||
T Consensus       124 ~v~T~~~l~~~~~~~~~~~~~~~~iV  149 (207)
T 2gxq_A          124 VVATPGRALDYLRQGVLDLSRVEVAV  149 (207)
T ss_dssp             EEECHHHHHHHHHHTSSCCTTCSEEE
T ss_pred             EEECHHHHHHHHHcCCcchhhceEEE
Confidence            99995     2222 36677888777

>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=92.86  E-value=0.66  Score=42.43  Aligned_cols=86  Identities=14%  Similarity=0.214  Sum_probs=51.0

Q ss_pred             ccHHHH-HHHHHHHHC---CCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEE
Q 012794           35 TSKRTI-LSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  105 (456)
Q Consensus        35 ~~k~~~-L~~ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLV  105 (456)
                      .-|..+ +..++....   ...++||.++|++.+.++++.+..     .+.+..++|+......   ++.+..+..+|+|
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            456543 334444332   346899999999999999998874     2567778887654332   3344556688999


Q ss_pred             ecc-----ccccc-cCcCccceEE
Q 012794          106 ATD-----VAARG-LDIPNVDLII  123 (456)
Q Consensus       106 aTd-----v~~~G-idip~v~~VI  123 (456)
                      +|+     .+.++ +++..+.+||
T Consensus       155 ~Tp~~l~~~l~~~~~~~~~~~~lV  178 (237)
T 3bor_A          155 GTPGRVFDMLNRRYLSPKWIKMFV  178 (237)
T ss_dssp             ECHHHHHHHHHTTSSCSTTCCEEE
T ss_pred             ECHHHHHHHHHhCCcCcccCcEEE
Confidence            994     33333 6677788777

>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=92.86  E-value=0.61  Score=41.98  Aligned_cols=85  Identities=18%  Similarity=0.189  Sum_probs=51.8

Q ss_pred             cccHHHH-HHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           34 ATSKRTI-LSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      ..-|..+ +..++...   ....++||.++|++.+.++++.+..     .+.+..++|+.+..++...+   .  ..+|+
T Consensus        61 GsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~--~~~ii  135 (224)
T 1qde_A           61 GTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL---R--DAQIV  135 (224)
T ss_dssp             TSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C---T--TCSEE
T ss_pred             CCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcC---C--CCCEE
Confidence            3567654 44445443   2345899999999999999988764     35788889987665544333   2  27899


Q ss_pred             Eeccc------cccccCcCccceEE
Q 012794          105 VATDV------AARGLDIPNVDLII  123 (456)
Q Consensus       105 VaTdv------~~~Gidip~v~~VI  123 (456)
                      |+|.-      ....+++..+.+||
T Consensus       136 v~Tp~~l~~~~~~~~~~~~~~~~iV  160 (224)
T 1qde_A          136 VGTPGRVFDNIQRRRFRTDKIKMFI  160 (224)
T ss_dssp             EECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             EECHHHHHHHHHhCCcchhhCcEEE
Confidence            99952      12346677788777

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=92.66  E-value=0.68  Score=41.58  Aligned_cols=87  Identities=16%  Similarity=0.228  Sum_probs=57.4

Q ss_pred             cccHHHH-HHHHHHHHCC---CCcEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEE
Q 012794           34 ATSKRTI-LSDLITVYAK---GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTV  103 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~~~---~~~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v  103 (456)
                      ..-|..+ +..++.....   ..++||.|+|++.+.++++.+.+      .+.+..++|+.+...+...+.   ++..+|
T Consensus        61 GsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~---~~~~~i  137 (220)
T 1t6n_A           61 GMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK---KNCPHI  137 (220)
T ss_dssp             TSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHH---HSCCSE
T ss_pred             CCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHh---cCCCCE
Confidence            3457543 3333333322   34899999999999999888764      367889999998776655543   345689


Q ss_pred             EEeccc-----cc-cccCcCccceEE
Q 012794          104 LVATDV-----AA-RGLDIPNVDLII  123 (456)
Q Consensus       104 LVaTdv-----~~-~Gidip~v~~VI  123 (456)
                      +|+|.-     +. ..+++..+++||
T Consensus       138 ~v~T~~~l~~~~~~~~~~~~~~~~lV  163 (220)
T 1t6n_A          138 VVGTPGRILALARNKSLNLKHIKHFI  163 (220)
T ss_dssp             EEECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             EEeCHHHHHHHHHhCCCCcccCCEEE
Confidence            999952     11 235566666666

>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=92.61  E-value=0.7  Score=47.96  Aligned_cols=74  Identities=19%  Similarity=0.188  Sum_probs=60.0

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccc------cccCcCccceE
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAA------RGLDIPNVDLI  122 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~------~Gidip~v~~V  122 (456)
                      ..+.+||.++++..+.+....|.. ++.+..+|+..+..++..++..+..+..+|||+|+-.-      .-++...+.+|
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            357899999999999999999985 78899999999999999999999999999999995211      12334556665


Q ss_pred             E
Q 012794          123 I  123 (456)
Q Consensus       123 I  123 (456)
                      |
T Consensus       144 V  144 (523)
T 1oyw_A          144 A  144 (523)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=92.55  E-value=1.2  Score=41.53  Aligned_cols=69  Identities=16%  Similarity=0.257  Sum_probs=51.7

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc--ccCcCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR--GLDIPN  118 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~--Gidip~  118 (456)
                      ..++||.++|++.|.++++.+.+     .+.+..++|+.........+..    ..+|+|+|+     .+..  .+++..
T Consensus       126 ~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~Iiv~Tp~~l~~~~~~~~~~~~~~  201 (262)
T 3ly5_A          126 GTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGN----GINIIVATPGRLLDHMQNTPGFMYKN  201 (262)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHCTTCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcC----CCCEEEEcHHHHHHHHHccCCccccc
Confidence            56899999999999999998875     2467888999887766555443    478999994     2222  467778


Q ss_pred             cceEE
Q 012794          119 VDLII  123 (456)
Q Consensus       119 v~~VI  123 (456)
                      +.+||
T Consensus       202 l~~lV  206 (262)
T 3ly5_A          202 LQCLV  206 (262)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            88777

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=92.36  E-value=0.73  Score=41.91  Aligned_cols=68  Identities=12%  Similarity=0.220  Sum_probs=48.5

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc-----ccc--ccCcCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV-----AAR--GLDIPN  118 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv-----~~~--Gidip~  118 (456)
                      ..++||.|+|++.+.++++.+..     .+.+..++|+.+.......+     ...+|+|+|.-     +..  .+++..
T Consensus        97 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~~~~  171 (236)
T 2pl3_A           97 GLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFHATD  171 (236)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCccccc
Confidence            56899999999999999988874     26788899987766554444     25789999952     222  356677


Q ss_pred             cceEE
Q 012794          119 VDLII  123 (456)
Q Consensus       119 v~~VI  123 (456)
                      +.+||
T Consensus       172 ~~~lV  176 (236)
T 2pl3_A          172 LQMLV  176 (236)
T ss_dssp             CCEEE
T ss_pred             ccEEE
Confidence            77776

>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=92.28  E-value=0.33  Score=49.03  Aligned_cols=69  Identities=12%  Similarity=0.203  Sum_probs=53.6

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-cCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-LDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-idip~v  119 (456)
                      ..++||.++|++.|.++++.+.+     .+.+..++|+.+...+...+..    ..+|+|+|+     .+.++ +++..+
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            35899999999999999988874     2568889999988776665543    678999995     33444 677888


Q ss_pred             ceEE
Q 012794          120 DLII  123 (456)
Q Consensus       120 ~~VI  123 (456)
                      .+||
T Consensus       205 ~~lV  208 (434)
T 2db3_A          205 RFVV  208 (434)
T ss_dssp             CEEE
T ss_pred             CeEE
Confidence            8877

>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=92.03  E-value=0.71  Score=41.96  Aligned_cols=85  Identities=15%  Similarity=0.190  Sum_probs=58.1

Q ss_pred             cccHHHH-HHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEE
Q 012794           34 ATSKRTI-LSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTV  103 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v  103 (456)
                      ..-|..+ +..++...   ....++||.|+|++.+.++++.+..      .+.+..++|+.+..++...++     ..+|
T Consensus        71 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~I  145 (230)
T 2oxc_A           71 GTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-----KCHI  145 (230)
T ss_dssp             TSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTT-----SCSE
T ss_pred             CCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhcc-----CCCE
Confidence            3567544 34444443   2346899999999999999988874      356888999998877665543     4789


Q ss_pred             EEeccc-----cc-cccCcCccceEE
Q 012794          104 LVATDV-----AA-RGLDIPNVDLII  123 (456)
Q Consensus       104 LVaTdv-----~~-~Gidip~v~~VI  123 (456)
                      +|+|.-     +. ..+++..+.+||
T Consensus       146 iv~Tp~~l~~~~~~~~~~~~~~~~lV  171 (230)
T 2oxc_A          146 AVGSPGRIKQLIELDYLNPGSIRLFI  171 (230)
T ss_dssp             EEECHHHHHHHHHTTSSCGGGCCEEE
T ss_pred             EEECHHHHHHHHhcCCcccccCCEEE
Confidence            999962     22 235566666655

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=91.37  E-value=0.46  Score=50.20  Aligned_cols=59  Identities=14%  Similarity=0.186  Sum_probs=52.9

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcc--cCCCeEEEEecc
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGF--RQGKFTVLVATD  108 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~F--r~g~~~vLVaTd  108 (456)
                      ..+.+||.+|+++.+.+.+..|.. ++.+..++++++..++..++..+  ..+..+|||+|+
T Consensus        83 ~~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           83 SDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             cCCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            457999999999999999999986 78999999999999999888888  567899999997

>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=91.35  E-value=0.41  Score=54.17  Aligned_cols=87  Identities=16%  Similarity=0.251  Sum_probs=62.3

Q ss_pred             ccHHHHHHHHH-HHHCCCCcEEEEcCChHHHHHHHHHHHh-----cC----CEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           35 TSKRTILSDLI-TVYAKGGKTIVFTQTKRDADEVSLALTS-----II----ASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        35 ~~k~~~L~~ll-~~~~~~~~~IIF~~t~~~a~~l~~~L~~-----~~----~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      .-|...+..++ .....+.++||.++|++.|.++++.+..     .+    .+..+||+++..++...++.+++  .+|+
T Consensus        82 SGKTl~~lp~l~~~~~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~Il  159 (1054)
T 1gku_B           82 VGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN--FKIV  159 (1054)
T ss_dssp             SCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEE
T ss_pred             CCHHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC--CCEE
Confidence            34543333333 3334567999999999999999998874     24    78899999999998888888887  8999


Q ss_pred             Eeccc-cccccC-cCccceEE
Q 012794          105 VATDV-AARGLD-IPNVDLII  123 (456)
Q Consensus       105 VaTdv-~~~Gid-ip~v~~VI  123 (456)
                      |+|+- +..-+. +..+.+||
T Consensus       160 V~TP~~L~~~l~~L~~l~~lV  180 (1054)
T 1gku_B          160 ITTTQFLSKHYRELGHFDFIF  180 (1054)
T ss_dssp             EEEHHHHHHCSTTSCCCSEEE
T ss_pred             EEcHHHHHHHHHHhccCCEEE
Confidence            99961 111111 55777777

>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=91.14  E-value=1.2  Score=39.41  Aligned_cols=86  Identities=21%  Similarity=0.229  Sum_probs=56.4

Q ss_pred             cccHHH-HHHHHHHHHC---CCCcEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEE
Q 012794           34 ATSKRT-ILSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTV  103 (456)
Q Consensus        34 ~~~k~~-~L~~ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v  103 (456)
                      ..-|.. .+..++....   ...++||.|+|++.+.++++.+..      .+.+..++|+.+..+....+.    ...+|
T Consensus        50 GsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~i  125 (206)
T 1vec_A           50 GTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD----DTVHV  125 (206)
T ss_dssp             SSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTT----SCCSE
T ss_pred             CCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcC----CCCCE
Confidence            345653 3333444332   245799999999999999888863      356888999988766544432    36789


Q ss_pred             EEecc-----ccccc-cCcCccceEE
Q 012794          104 LVATD-----VAARG-LDIPNVDLII  123 (456)
Q Consensus       104 LVaTd-----v~~~G-idip~v~~VI  123 (456)
                      +|+|+     .+..+ +++..+.+||
T Consensus       126 ~v~T~~~l~~~~~~~~~~~~~~~~lV  151 (206)
T 1vec_A          126 VIATPGRILDLIKKGVAKVDHVQMIV  151 (206)
T ss_dssp             EEECHHHHHHHHHTTCSCCTTCCEEE
T ss_pred             EEeCHHHHHHHHHcCCcCcccCCEEE
Confidence            99996     22222 4566677666

>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=89.49  E-value=1.7  Score=42.31  Aligned_cols=87  Identities=16%  Similarity=0.227  Sum_probs=59.8

Q ss_pred             cccHHHH-HHHHHHHHC---CCCcEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEE
Q 012794           34 ATSKRTI-LSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTV  103 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v  103 (456)
                      ..-|..+ +..++....   ...++||.|+|+..++++++.+.+      .+.+..++|+.+.......+.   ++..+|
T Consensus        55 GsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~~~~~i  131 (391)
T 1xti_A           55 GMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLK---KNCPHI  131 (391)
T ss_dssp             CSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHH---HSCCSE
T ss_pred             CCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHh---cCCCCE
Confidence            3467543 333443332   245899999999999999887764      367889999998876665543   355789


Q ss_pred             EEeccc-----c-ccccCcCccceEE
Q 012794          104 LVATDV-----A-ARGLDIPNVDLII  123 (456)
Q Consensus       104 LVaTdv-----~-~~Gidip~v~~VI  123 (456)
                      +|+|.-     + ...+++..+.+||
T Consensus       132 iv~T~~~l~~~~~~~~~~~~~~~~vV  157 (391)
T 1xti_A          132 VVGTPGRILALARNKSLNLKHIKHFI  157 (391)
T ss_dssp             EEECHHHHHHHHHTTSSCCTTCSEEE
T ss_pred             EEECHHHHHHHHHcCCccccccCEEE
Confidence            999952     1 2336677888877

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=89.04  E-value=0.54  Score=42.32  Aligned_cols=86  Identities=14%  Similarity=0.252  Sum_probs=53.6

Q ss_pred             cccHHHH-HHHHHHHHC---CCCcEEEEcCChHHHHHHHHHHHh---------cCCEEEEeCCCCHHHHHHHHhcccCCC
Q 012794           34 ATSKRTI-LSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS---------IIASEALHGDISQHQRERTLNGFRQGK  100 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~---------~~~~~~lhg~~~~~~R~~~l~~Fr~g~  100 (456)
                      ..-|..+ +..++....   ...++||.|+|++.+.++++.+.+         .+.+..++|+.+..+.   .+.+. ..
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            3457544 334444432   245899999999999999887763         3567788888754432   22222 35


Q ss_pred             eEEEEecc-----cccc-ccCcCccceEE
Q 012794          101 FTVLVATD-----VAAR-GLDIPNVDLII  123 (456)
Q Consensus       101 ~~vLVaTd-----v~~~-Gidip~v~~VI  123 (456)
                      .+|+|+|+     .+.. .+++..+.+||
T Consensus       127 ~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lV  155 (219)
T 1q0u_A          127 PHIVIGTPGRINDFIREQALDVHTAHILV  155 (219)
T ss_dssp             CSEEEECHHHHHHHHHTTCCCGGGCCEEE
T ss_pred             CCEEEeCHHHHHHHHHcCCCCcCcceEEE
Confidence            78999995     2222 24556666655

>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=88.82  E-value=0.79  Score=47.15  Aligned_cols=69  Identities=12%  Similarity=0.147  Sum_probs=47.8

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-c-CcCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-L-DIPN  118 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-i-dip~  118 (456)
                      ..++||.|+|+..+.+++..+.+     .+.+..+||+.+...+...+..    ..+|+|+|+     .+..+ + .+..
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            57899999999999999888874     5789999999876655443332    467999995     22333 4 6778


Q ss_pred             cceEE
Q 012794          119 VDLII  123 (456)
Q Consensus       119 v~~VI  123 (456)
                      +++||
T Consensus       131 ~~~vV  135 (556)
T 4a2p_A          131 FTLMI  135 (556)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            88877

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

Probab=88.11  E-value=1.3  Score=43.76  Aligned_cols=68  Identities=18%  Similarity=0.201  Sum_probs=51.6

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc-ccCcCccc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPNVD  120 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~-Gidip~v~  120 (456)
                      .++||.++|++.+.++++.+.+     .+.+..+||+.+..++...+..    ..+|+|+|+     .+.. .+++..+.
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            4699999999999999988864     3678899999888766555432    578999995     2223 35677888


Q ss_pred             eEE
Q 012794          121 LII  123 (456)
Q Consensus       121 ~VI  123 (456)
                      +||
T Consensus       178 ~iV  180 (417)
T 2i4i_A          178 YLV  180 (417)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            877

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

Probab=87.87  E-value=0.77  Score=47.12  Aligned_cols=69  Identities=13%  Similarity=0.220  Sum_probs=50.5

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-c-CcCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-L-DIPN  118 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-i-dip~  118 (456)
                      ..++||.|+|++.+.+++..+.+     .+.+..+||+.+...+...+..    ..+|+|+|.     .+..+ + ++..
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            67899999999999998888864     4789999999876554333322    467999995     22232 3 5677


Q ss_pred             cceEE
Q 012794          119 VDLII  123 (456)
Q Consensus       119 v~~VI  123 (456)
                      +++||
T Consensus       128 ~~~vV  132 (555)
T 3tbk_A          128 FTLMI  132 (555)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            88877

>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=87.62  E-value=1.8  Score=42.96  Aligned_cols=84  Identities=24%  Similarity=0.309  Sum_probs=59.4

Q ss_pred             ccHHHHHHHHHHHH--CCCCcEEEEcCChHHHHHHHHHHHhc--C---CEEEEeCCCCHHHHHHHHhcccCCCeEEEEec
Q 012794           35 TSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTSI--I---ASEALHGDISQHQRERTLNGFRQGKFTVLVAT  107 (456)
Q Consensus        35 ~~k~~~L~~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~~--~---~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT  107 (456)
                      .-|.-....++...  ....++||.|+|+..+.+.++.+.+.  +   .+..+||+....++.....     ..+|+|+|
T Consensus        34 ~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~-----~~~ivv~T  108 (494)
T 1wp9_A           34 LGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA-----RAKVIVAT  108 (494)
T ss_dssp             SCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHH-----HCSEEEEC
T ss_pred             CCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhcc-----CCCEEEec
Confidence            45654444433322  24689999999999999999999853  3   7899999999887766554     35799999


Q ss_pred             cc------cccccCcCccceEE
Q 012794          108 DV------AARGLDIPNVDLII  123 (456)
Q Consensus       108 dv------~~~Gidip~v~~VI  123 (456)
                      .-      ...-+.+..+++||
T Consensus       109 ~~~l~~~~~~~~~~~~~~~~vI  130 (494)
T 1wp9_A          109 PQTIENDLLAGRISLEDVSLIV  130 (494)
T ss_dssp             HHHHHHHHHTTSCCTTSCSEEE
T ss_pred             HHHHHHHHhcCCcchhhceEEE
Confidence            42      11235677788777

>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=87.36  E-value=1.3  Score=48.46  Aligned_cols=69  Identities=12%  Similarity=0.147  Sum_probs=47.9

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-c-CcCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-L-DIPN  118 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-i-dip~  118 (456)
                      ..++||.|+|+..+.+++..+.+     .+.+..+||+.+...+...+..    ..+|+|+|.     .+..+ + .+..
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            67899999999999998887764     5789999999877665444432    578999995     22233 4 5677


Q ss_pred             cceEE
Q 012794          119 VDLII  123 (456)
Q Consensus       119 v~~VI  123 (456)
                      +++||
T Consensus       372 ~~~iV  376 (797)
T 4a2q_A          372 FTLMI  376 (797)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            88877

>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=86.44  E-value=2.4  Score=41.70  Aligned_cols=85  Identities=15%  Similarity=0.233  Sum_probs=59.0

Q ss_pred             ccHHHH-HHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEE
Q 012794           35 TSKRTI-LSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  105 (456)
Q Consensus        35 ~~k~~~-L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLV  105 (456)
                      .-|..+ +..++..+   ....++||.|+|++.+.++++.+..     .+.+..++|+....+....+..    ..+|+|
T Consensus        85 sGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~ivv  160 (410)
T 2j0s_A           85 TGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY----GQHVVA  160 (410)
T ss_dssp             SSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHH----CCSEEE
T ss_pred             CCchHHHHHHHHHHHhhccCCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhc----CCCEEE
Confidence            467533 33344332   2457999999999999999998864     2567888999887776655543    458999


Q ss_pred             ecc-----cccc-ccCcCccceEE
Q 012794          106 ATD-----VAAR-GLDIPNVDLII  123 (456)
Q Consensus       106 aTd-----v~~~-Gidip~v~~VI  123 (456)
                      +|+     .+.. .+++..+++||
T Consensus       161 ~Tp~~l~~~l~~~~~~~~~~~~vV  184 (410)
T 2j0s_A          161 GTPGRVFDMIRRRSLRTRAIKMLV  184 (410)
T ss_dssp             ECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             cCHHHHHHHHHhCCccHhheeEEE
Confidence            994     3333 36677788777

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=86.28  E-value=0.36  Score=44.27  Aligned_cols=87  Identities=17%  Similarity=0.308  Sum_probs=53.2

Q ss_pred             cccHHHH-HHHHHHHHC----CCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEE
Q 012794           34 ATSKRTI-LSDLITVYA----KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTV  103 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~~----~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v  103 (456)
                      ..-|..+ +..++....    ...++||.++|++.+.++++.+.+     .+.+..++++....   ...........+|
T Consensus        76 GsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~I  152 (245)
T 3dkp_A           76 GSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAA---KKFGPKSSKKFDI  152 (245)
T ss_dssp             TSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHH---TTTSTTSCCCCCE
T ss_pred             CCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHH---HHhhhhhcCCCCE
Confidence            3567543 444444442    345799999999999999998875     24566666653221   1122233456789


Q ss_pred             EEecc-----cccc---ccCcCccceEE
Q 012794          104 LVATD-----VAAR---GLDIPNVDLII  123 (456)
Q Consensus       104 LVaTd-----v~~~---Gidip~v~~VI  123 (456)
                      +|+|+     .+..   .+++.++.+||
T Consensus       153 ~v~Tp~~l~~~l~~~~~~~~~~~~~~lV  180 (245)
T 3dkp_A          153 LVTTPNRLIYLLKQDPPGIDLASVEWLV  180 (245)
T ss_dssp             EEECHHHHHHHHHSSSCSCCCTTCCEEE
T ss_pred             EEECHHHHHHHHHhCCCCcccccCcEEE
Confidence            99994     2222   36677777666

>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=85.17  E-value=3.7  Score=39.86  Aligned_cols=84  Identities=17%  Similarity=0.170  Sum_probs=58.0

Q ss_pred             ccHHHH-HHHHHHHHC---CCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEE
Q 012794           35 TSKRTI-LSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  105 (456)
Q Consensus        35 ~~k~~~-L~~ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLV  105 (456)
                      .-|..+ +..++..+.   ...++||.|+|+..+.++++.+.+     .+.+..++|+.+..+....+.     ..+|+|
T Consensus        69 sGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~i~v  143 (394)
T 1fuu_A           69 TGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-----DAQIVV  143 (394)
T ss_dssp             HHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-----HCSEEE
T ss_pred             ChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-----CCCEEE
Confidence            456543 344444332   356999999999999999888764     367888999998877666554     357999


Q ss_pred             eccc-----cc-cccCcCccceEE
Q 012794          106 ATDV-----AA-RGLDIPNVDLII  123 (456)
Q Consensus       106 aTdv-----~~-~Gidip~v~~VI  123 (456)
                      +|.-     +. ..+++..+++||
T Consensus       144 ~T~~~l~~~~~~~~~~~~~~~~vI  167 (394)
T 1fuu_A          144 GTPGRVFDNIQRRRFRTDKIKMFI  167 (394)
T ss_dssp             ECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             ECHHHHHHHHHhCCcchhhCcEEE
Confidence            9942     22 235566777777

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=84.84  E-value=1.7  Score=41.45  Aligned_cols=84  Identities=7%  Similarity=0.044  Sum_probs=54.2

Q ss_pred             cccHHHH-HHHHHHHHCC---CCcEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEE
Q 012794           34 ATSKRTI-LSDLITVYAK---GGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTV  103 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~~~---~~~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v  103 (456)
                      ..-|..+ +..++.....   ..++||.++|++.|.+++..+..      .+.+..++++......       .....+|
T Consensus       141 GsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~-------~~~~~~I  213 (300)
T 3fmo_B          141 GTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-------QKISEQI  213 (300)
T ss_dssp             TSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTT-------CCCCCSE
T ss_pred             CCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhh-------hcCCCCE
Confidence            3457533 4455554422   33799999999999999887763      2456777776543211       1335689


Q ss_pred             EEeccc-----cc--cccCcCccceEEe
Q 012794          104 LVATDV-----AA--RGLDIPNVDLIIH  124 (456)
Q Consensus       104 LVaTdv-----~~--~Gidip~v~~VI~  124 (456)
                      ||+|+-     +.  ..+++..+.+||.
T Consensus       214 lV~TP~~l~~~l~~~~~~~l~~l~~lVl  241 (300)
T 3fmo_B          214 VIGTPGTVLDWCSKLKFIDPKKIKVFVL  241 (300)
T ss_dssp             EEECHHHHHHHHTTTCCCCGGGCSEEEE
T ss_pred             EEECHHHHHHHHHhcCCCChhhceEEEE
Confidence            999962     22  3578889998873

>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=84.81  E-value=3.2  Score=39.28  Aligned_cols=83  Identities=17%  Similarity=0.225  Sum_probs=57.0

Q ss_pred             cccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           34 ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      ..-|..+....+..  ...++||.|+|+..+.++++.+.+     .+.+..+||+.+...+...+.     ..+|+|+|.
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            34675443333322  257999999999999999998874     257888999998876655443     267999995


Q ss_pred             c-----ccc-ccCcCccceEE
Q 012794          109 V-----AAR-GLDIPNVDLII  123 (456)
Q Consensus       109 v-----~~~-Gidip~v~~VI  123 (456)
                      -     +.. -+++..+++||
T Consensus       114 ~~l~~~~~~~~~~~~~~~~iV  134 (337)
T 2z0m_A          114 GRLLDLWSKGVIDLSSFEIVI  134 (337)
T ss_dssp             HHHHHHHHTTSCCGGGCSEEE
T ss_pred             HHHHHHHHcCCcchhhCcEEE
Confidence            2     122 35667777776

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=84.59  E-value=4.8  Score=38.46  Aligned_cols=85  Identities=22%  Similarity=0.294  Sum_probs=57.9

Q ss_pred             cccHHHHHH-HHHHHHC--CCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEE
Q 012794           34 ATSKRTILS-DLITVYA--KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  105 (456)
Q Consensus        34 ~~~k~~~L~-~ll~~~~--~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLV  105 (456)
                      ..-|..+.. .++....  ...++||.|+|+..++++++.+..     .+.+..++|+.........+.     ..+|+|
T Consensus        54 GsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-----~~~iiv  128 (367)
T 1hv8_A           54 GSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVV  128 (367)
T ss_dssp             SSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEE
T ss_pred             CChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-----CCCEEE
Confidence            356755433 3343332  356899999999999999998874     356888899988766555543     467999


Q ss_pred             eccc-----ccc-ccCcCccceEE
Q 012794          106 ATDV-----AAR-GLDIPNVDLII  123 (456)
Q Consensus       106 aTdv-----~~~-Gidip~v~~VI  123 (456)
                      +|.-     +.. .+++..+++||
T Consensus       129 ~T~~~l~~~~~~~~~~~~~~~~iI  152 (367)
T 1hv8_A          129 GTPGRILDHINRGTLNLKNVKYFI  152 (367)
T ss_dssp             ECHHHHHHHHHTTCSCTTSCCEEE
T ss_pred             ecHHHHHHHHHcCCcccccCCEEE
Confidence            9952     222 25677777777

>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=84.39  E-value=4.2  Score=39.64  Aligned_cols=86  Identities=19%  Similarity=0.212  Sum_probs=57.8

Q ss_pred             cccHHHH-HHHHHHHHC---CCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           34 ATSKRTI-LSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        34 ~~~k~~~-L~~ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      ..-|..+ +..++....   ...++||.|+|+..+.++++.+..     .+.+..++|+.........+    ....+|+
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            3467543 333443332   345899999999999999888874     35688889998766544333    2367899


Q ss_pred             Eecc-----cccc-ccCcCccceEE
Q 012794          105 VATD-----VAAR-GLDIPNVDLII  123 (456)
Q Consensus       105 VaTd-----v~~~-Gidip~v~~VI  123 (456)
                      |+|.     .+.+ ..++.++++||
T Consensus       144 v~T~~~l~~~~~~~~~~~~~~~~vI  168 (400)
T 1s2m_A          144 VGTPGRVLDLASRKVADLSDCSLFI  168 (400)
T ss_dssp             EECHHHHHHHHHTTCSCCTTCCEEE
T ss_pred             EEchHHHHHHHHhCCcccccCCEEE
Confidence            9994     2333 36677888877

>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=81.15  E-value=1.8  Score=48.20  Aligned_cols=69  Identities=12%  Similarity=0.147  Sum_probs=46.9

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----ccccc-c-CcCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAARG-L-DIPN  118 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~G-i-dip~  118 (456)
                      ..++||.|+|+..+.+++..+.+     .+.+..+||+.+...+...+..    ..+|+|+|+     .+..+ + .+..
T Consensus       296 ~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~G~~~~~~~~~~~~~----~~~IvI~Tp~~L~~~l~~~~~~~l~~  371 (936)
T 4a2w_A          296 KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIE----DSDIIVVTPQILVNSFEDGTLTSLSI  371 (936)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECCC-----CCHHHHH----HCSEEEECHHHHHHHHHSSSCCCGGG
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEECCcchhhHHHHhcc----CCCEEEecHHHHHHHHHcCccccccC
Confidence            57899999999999998888764     5789999999876654333322    467999995     22222 3 5667


Q ss_pred             cceEE
Q 012794          119 VDLII  123 (456)
Q Consensus       119 v~~VI  123 (456)
                      +++||
T Consensus       372 ~~liV  376 (936)
T 4a2w_A          372 FTLMI  376 (936)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            78777

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=80.75  E-value=1.9  Score=38.01  Aligned_cols=54  Identities=15%  Similarity=0.161  Sum_probs=34.6

Q ss_pred             CCcEEEEcCChHHHHH-HHHHHHh----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           51 GGKTIVFTQTKRDADE-VSLALTS----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~-l~~~L~~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      ..++||+|+|+..+++ +.+.+..    .+.+..++|+.....+...+..    ..+|+|+|.
T Consensus        82 ~~~~lil~p~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~----~~~i~v~T~  140 (216)
T 3b6e_A           82 PGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVK----SCDIIISTA  140 (216)
T ss_dssp             CCCEEEEESSHHHHHHHHHHTHHHHHTTTSCEEECCC---CCCCHHHHHH----HCSEEEEEH
T ss_pred             CCcEEEEECHHHHHHHHHHHHHHHHhccCceEEEEeCCcccchhHHhhcc----CCCEEEECH
Confidence            5789999999999888 5555543    4678888887644322222211    467999995

---

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	456
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	6e-34
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	1e-29
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-26
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	5e-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	2e-18
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	2e-16
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	2e-16
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	5e-16
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	3e-15
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	1e-14
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	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	4e-12
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	1e-07
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	3e-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 = 6e-34
 Identities = 37/180 (20%), Positives = 62/180 (34%), Gaps = 21/180 (11%)

Query: 25  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGD 83
           I+  A+STT          +     KGG+ ++F  +K+  DE++  L ++ I + A +  
Sbjct: 11  IEEVALSTTG-EIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRG 69

Query: 84  ISQHQR----------ERTLNGFRQGKFTVLVATDVAARG---LDIPNVDLIIHYELPND 130
           +                  L     G F  ++  +          +     I    LP D
Sbjct: 70  LDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQD 129

Query: 131 PETFVHRSGRTGRAGKEGTAILMFTSSQRR-TVRSLE----RDVGCKFEFVSPPVVEDVL 185
             +   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 =  114 bits (285), Expect = 1e-29
 Identities = 33/203 (16%), Positives = 64/203 (31%), Gaps = 21/203 (10%)

Query: 37  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGF 96
             + LS ++     G   I++ +T  +A+E+  +L            I    ++     F
Sbjct: 13  SISTLSSILE--KLGTGGIIYARTGEEAEEIYESL-----KNKFRIGIVTATKKGDYEKF 65

Query: 97  RQGKFTVLVAT----DVAARGLDIP-NVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
            +G+   L+ T        RGLD+P  +   +    P+    F            +   +
Sbjct: 66  VEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKL 121

Query: 152 LMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAEQVVATLNGVHPESVEFFTPTA 211
           L +       +  L   V    +      V ++L+    +       V     E   P  
Sbjct: 122 LAYLYRNVDEIERLLPAVERHID-----EVREILKKVMGKERPQAKDVVVREGEVIFPDL 176

Query: 212 QRLIEEKGTDALAAALAQLSGFS 234
           +  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 = 4e-26
 Identities = 47/150 (31%), Positives = 83/150 (55%), Gaps = 3/150 (2%)

Query: 37  KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNG 95
           K   L+DL        + ++F  T+R  +E++  L +      A++ D+ Q +R+  +  
Sbjct: 14  KYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKE 72

Query: 96  FRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFT 155
           FR G   +L++TD+ ARG+D+  V L+I+Y+LP + E ++HR GR GR G++G AI   T
Sbjct: 73  FRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVT 132

Query: 156 SSQRRTVRSLERDVGCKFEFVSPPVVEDVL 185
           +     +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 =  102 bits (254), Expect = 5e-25
 Identities = 41/136 (30%), Positives = 61/136 (44%), Gaps = 13/136 (9%)

Query: 36  SKRTILSDLITVY---AKGGKTIVFTQTKRDADE-VSLALTSIIASEALHGDISQHQR-- 89
            K   L ++I       +  K IVFT  +  A + V+  +   I ++   G  S+     
Sbjct: 143 PKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRG 202

Query: 90  ------ERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
                 +  L+ F +G+F VLVAT V   GLD+P VDL++ YE        + R GRTGR
Sbjct: 203 LSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 262

Query: 144 AGKEGTAILMFTSSQR 159
               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: 18  DEKLAEGIKLYAISTTATS-KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIA 76
           DE   EGIK + ++      K   L DL        + ++F  TKR  D ++  +     
Sbjct: 1   DELTLEGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANF 59

Query: 77  SEA-LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFV 135
           + + +HGD+ Q +RE  +  FR G   VL++TDV ARGLD+P V LII+Y+LPN+ E ++
Sbjct: 60  TVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYI 119

Query: 136 HRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVL 185
           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: 25  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDI 84
           I+   +      +   L  L+    K    +VF +TKRD  E++  L  I          
Sbjct: 4   IEQSYVEVNENERFEALCRLLK--NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGD 61

Query: 85  S-QHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGR 143
             Q QRE+ +  F+Q K  +L+ATDV +RG+D+ +++ +I+Y LP +PE+++HR GRTGR
Sbjct: 62  LSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGR 121

Query: 144 AGKEGTAILMFTSSQRRTVRSLERDVGCKFE 174
           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: 19  EKLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASE 78
           E L    +   I+  + +K   L +++  + +  K I+FT+       +S     +    
Sbjct: 62  EALRAWEEARRIAFNSKNKIRKLREILERH-RKDKIIIFTRHNELVYRIS----KVFLIP 116

Query: 79  ALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS 138
           A+    S+ +RE  L GFR G+F  +V++ V   G+D+P+ ++ +          ++ R 
Sbjct: 117 AITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRL 176

Query: 139 GRTGRAGKEGTAILMFT 155
           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 = 79.4 bits (195), Expect = 2e-18
 Identities = 36/138 (26%), Positives = 55/138 (39%), Gaps = 12/138 (8%)

Query: 25  IKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDI 84
           I+  A+STT        +  + V  KGG+ ++F  +K+  DE++  L       AL  + 
Sbjct: 10  IEEVALSTTGEIPFYGKAIPLEVI-KGGRHLIFCHSKKKCDELAAKL------VALGINA 62

Query: 85  SQHQRERTLNGFRQGKFTVLVATDVAARGLDIPN---VDLIIHYELPNDPETFVHRSGRT 141
             + R   ++        V+VATD    G        +D       P D  +   R GRT
Sbjct: 63  VAYYRGLDVSVIPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRT 122

Query: 142 GRAGKEGTAILMFTSSQR 159
           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 = 75.2 bits (184), Expect = 2e-16
 Identities = 30/118 (25%), Positives = 54/118 (45%), Gaps = 3/118 (2%)

Query: 40  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 98
           ++ ++     +  +T+V T TK+ A++++  L    I    LH +I   +R   +   R 
Sbjct: 20  LIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRL 79

Query: 99  GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS--GRTGRAGKEGTAILMF 154
           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: 22  AEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEAL 80
            +GI  Y        K   L+ L +   +  + I+F  +    + ++        +    
Sbjct: 4   LKGITQYYAFVEERQKLHCLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYS 62

Query: 81  HGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGR 140
           H  + Q +R +  + FRQGK   LV +D+  RG+DI  V+++I+++ P   ET++HR GR
Sbjct: 63  HARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGR 122

Query: 141 TGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSPPVVEDVLESSAE 190
           +GR G  G AI +   + R  +  +E+++G +   + P  ++  L   AE
Sbjct: 123 SGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAI-PATIDKSLY-VAE 170

>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 = 74.2 bits (181), Expect = 5e-16
 Identities = 41/188 (21%), Positives = 68/188 (36%), Gaps = 46/188 (24%)

Query: 21  LAEGIKL-----YAISTTATSKRTILSDLIT-VYAKGGKTIVFTQTKRDADEVSLALTSI 74
           L EG+             +TS+R    +L+    A+ G  +VF  T+R A++ ++ L++I
Sbjct: 4   LVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAI 63

Query: 75  IASEA-------------------------------LHGDISQHQRERTLNGFRQGKFTV 103
            A                                   H  +   QR    + FR+G   V
Sbjct: 64  TAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKV 123

Query: 104 LVATDVAARGLDIPNVDLIIH-------YELPNDPETFVHRSGRTGRAGK--EGTAILMF 154
           +VAT   A G+++P   +I+        Y        +   +GR GR G    G AI++ 
Sbjct: 124 VVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIV 183

Query: 155 TSSQRRTV 162
               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 = 71.7 bits (175), Expect = 3e-15
 Identities = 31/136 (22%), Positives = 58/136 (42%), Gaps = 8/136 (5%)

Query: 40  ILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQ 98
           ++  +    A+G +T+V   T R A+E++  L    I +  LH ++   +R+  +   R 
Sbjct: 20  LMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRL 79

Query: 99  GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRS--GRTGRAGKEGTAILMF-- 154
           G +  LV  ++   GLDIP V L+   +   +      RS     GRA +     +    
Sbjct: 80  GHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYA 139

Query: 155 ---TSSQRRTVRSLER 167
              + + +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: 36  SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLN 94
                L   +    +G   I++  ++   ++ +  L S  I++ A H  +  + R     
Sbjct: 16  KPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQE 74

Query: 95  GFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF 154
            F++    ++VAT     G++ PNV  ++H+++P + E++   +GR GR G    A+L +
Sbjct: 75  KFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 134

Query: 155 TSSQRRTVR 163
             +    +R
Sbjct: 135 DPADMAWLR 143

>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 = 71.9 bits (175), Expect = 1e-14
 Identities = 20/133 (15%), Positives = 40/133 (30%), Gaps = 24/133 (18%)

Query: 44  LITVYAKGGKTIVFTQTKRDADEVSLALTSI-IASEALHGDISQHQRERTLNGFRQGKFT 102
              V    GKT+ F  + +  ++++  L         L       +  +     R   + 
Sbjct: 171 HEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYIK----TRTNDWD 226

Query: 103 VLVATDVAARGLDI-------------------PNVDLIIHYELPNDPETFVHRSGRTGR 143
            +V TD++  G +                        +I+   +P    +   R GR GR
Sbjct: 227 FVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGR 286

Query: 144 AGKEGTAILMFTS 156
             K      ++  
Sbjct: 287 NPKNENDQYIYMG 299

>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: 24  GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVS-LALTSIIASEALHG 82
           G++ Y +      K   L DL+ V  +  + ++F ++ +    ++ L +     + A+H 
Sbjct: 1   GLQQYYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHR 59

Query: 83  DISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTG 142
            + Q +R      F+  +  +LVAT++  RG+DI  V++  +Y++P D +T++HR  R G
Sbjct: 60  GMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAG 119

Query: 143 RAGKEGTAILMFTSSQ-RRTVRSLERDVGCKFEFVSPPV-VEDVLE 186
           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 = 63.1 bits (153), Expect = 4e-12
 Identities = 34/149 (22%), Positives = 59/149 (39%), Gaps = 15/149 (10%)

Query: 78  EALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFV-H 136
              HG + + + ER +N F   +F VLV T +   G+DIP  + II     +     +  
Sbjct: 61  AIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQ 120

Query: 137 RSGRTGRAGKEGTAILMFTSSQRRTVRSLER--------DVGCKFEFVSPPVVEDVLESS 188
             GR GR+  +  A L+    +  T  + +R        D+G  F   +     D+    
Sbjct: 121 LRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALAT----HDLEIRG 176

Query: 189 AEQVVATLNGVHPESVEFFTPTAQRLIEE 217
           A +++        E++ F       L+E 
Sbjct: 177 AGELLGEEQSGSMETIGF--SLYMELLEN 203

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 50.2 bits (119), Expect = 1e-07
 Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 1/97 (1%)

Query: 80  LHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPET-FVHRS 138
           +HG +SQ +++R +  F +G++ +LV+T V   G+D+P  ++++                
Sbjct: 70  MHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLR 129

Query: 139 GRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEF 175
           GR GR G+E    L+        +  L         F
Sbjct: 130 GRVGRGGQEAYCFLVVGDVGEEAMERLRFFTLNTDGF 166

>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 = 3e-06
 Identities = 20/125 (16%), Positives = 39/125 (31%), Gaps = 23/125 (18%)

Query: 51  GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV 109
              T  F  + R A+ ++ +L     +   L+    + +        +Q K   ++ATD+
Sbjct: 36  KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPT----IKQKKPDFILATDI 91

Query: 110 AARGLDIPNV------------------DLIIHYELPNDPETFVHRSGRTGRAGKEGTAI 151
           A  G ++                      + I   L     +   R GR GR        
Sbjct: 92  AEMGANLCVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDS 151

Query: 152 LMFTS 156
             ++ 
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 = 39.8 bits (93), Expect = 1e-05
 Identities = 10/16 (62%), Positives = 10/16 (62%)

Query: 441 CFNCGKSGHRASECPN 456
           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: 438 GGACFNCGKSGHRASECPN 456
              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: 239 SRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTAADE-IGKIHIIADDRVQ 297
            RSLI  ++G+VT+ L                   L+    + A   I ++ ++  +   
Sbjct: 3   PRSLITSDKGFVTMTLE----SLEEIQDVSCAWKELNRKLSSNAVSQITRMCLLKGN--M 56

Query: 298 GAVFDLPEEIAKELLNK 314
           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	456
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.98
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.98
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	99.82
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.81
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.78
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.76
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.76
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.72
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.5
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.46
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.45
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.4
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.22
d2e29a1	85	ATP-dependent RNA helicase DDX50 {Human (Homo sapi	98.73
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.65
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.79
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.58
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.2
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.12
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.97
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	96.44
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	94.99
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	94.41
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	94.32
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	92.51
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	91.41
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	90.7
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	90.03
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	89.6
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	89.4
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	89.19
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	84.54

>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=6.2e-33  Score=248.17  Aligned_cols=159  Identities=35%  Similarity=0.593  Sum_probs=148.9

Q ss_pred             cccccCeeEEEEEcCcc-cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcc
Q 012794           19 EKLAEGIKLYAISTTAT-SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGF   96 (456)
Q Consensus        19 ~~~~~~i~~~~~~~~~~-~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~F   96 (456)
                      +.+.++|+|+|+.++.. .|+++|.++++.+. ..++||||+|+..|+.++..|.. ++.+..+||+|++.+|..+++.|
T Consensus         2 ~~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~-~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   80 (168)
T d2j0sa2           2 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLT-ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEF   80 (168)
T ss_dssp             GCSCTTEEEEEEEESSTTHHHHHHHHHHHHHT-SSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHH
T ss_pred             CCCCCCcEEEEEEecChHHHHHHHHHHHHhCC-CCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHH
Confidence            46778999999998875 59999999998774 57999999999999999999985 78999999999999999999999


Q ss_pred             cCCCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceec
Q 012794           97 RQGKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV  176 (456)
Q Consensus        97 r~g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~  176 (456)
                      ++++++||||||+++||||+|++++|||||+|++++.|+||+|||||.|+.|.+++|+.+.+...++.|++.++..++.+
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            99999999999999999999999999999999999999999999999999999999999999999999999999888776


Q ss_pred             CC
Q 012794          177 SP  178 (456)
Q Consensus       177 ~~  178 (456)
                      +.
T Consensus       161 p~  162 (168)
T d2j0sa2         161 PM  162 (168)
T ss_dssp             CS
T ss_pred             Cc
Confidence            54

>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=1.2e-32  Score=247.22  Aligned_cols=159  Identities=26%  Similarity=0.488  Sum_probs=150.9

Q ss_pred             ccccCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccC
Q 012794           20 KLAEGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQ   98 (456)
Q Consensus        20 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~   98 (456)
                      .+.++|+|+|+.++..+|+.+|.++|+.. +..++||||+|+++|+.|+..|.. ++.+..+||+|++.+|+++++.|++
T Consensus         2 ~tl~~i~q~yi~v~~~~K~~~L~~ll~~~-~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~   80 (171)
T d1s2ma2           2 LTLKGITQYYAFVEERQKLHCLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQ   80 (171)
T ss_dssp             CBCTTEEEEEEECCGGGHHHHHHHHHHHS-CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CCccceEEEEEEcCHHHHHHHHHHHHHhC-CCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhccc
Confidence            56789999999999999999999999876 468999999999999999999995 8999999999999999999999999


Q ss_pred             CCeEEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCC
Q 012794           99 GKFTVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  178 (456)
Q Consensus        99 g~~~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~  178 (456)
                      +.++|||||+++++|||+|++++|||||+|++++.|+||+||+||.|+.|.+++|+.+.+...++.|++.++.+++.++.
T Consensus        81 ~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~~~l~~~~~~~p~  160 (171)
T d1s2ma2          81 GKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPA  160 (171)
T ss_dssp             TSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCS
T ss_pred             CccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHHHHHCCCCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998877665


Q ss_pred             C
Q 012794          179 P  179 (456)
Q Consensus       179 p  179 (456)
                      .
T Consensus       161 ~  161 (171)
T d1s2ma2         161 T  161 (171)
T ss_dssp             S
T ss_pred             c
Confidence            4

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1e-32  Score=245.37  Aligned_cols=153  Identities=31%  Similarity=0.570  Sum_probs=138.8

Q ss_pred             eeEEEEEcCc-ccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeE
Q 012794           25 IKLYAISTTA-TSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        25 i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  102 (456)
                      |+|+|+.+.. +.|+++|.+|++.. +..++||||+|+..+++|+..|.. ++.+..+||+|++.+|..+++.|++++.+
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            6899998865 56999999999876 468999999999999999999985 79999999999999999999999999999


Q ss_pred             EEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceecCC
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFVSP  178 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~~~  178 (456)
                      ||||||+++||||+|+|++|||||+|++++.|+||+|||||.|+.|.+++++++.|...++.|++.++..++.++.
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=99.98  E-value=7.7e-32  Score=238.02  Aligned_cols=152  Identities=36%  Similarity=0.616  Sum_probs=143.7

Q ss_pred             cCeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCe
Q 012794           23 EGIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF  101 (456)
Q Consensus        23 ~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~  101 (456)
                      .+|+|+|+.+...+|+++|.++|+.  .+.++||||+|+++|+.|+..|.. ++.+..+|+++++.+|..++++|++++.
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            5799999999999999999999864  357899999999999999999985 7899999999999999999999999999


Q ss_pred             EEEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHHHHhCCCceec
Q 012794          102 TVLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLERDVGCKFEFV  176 (456)
Q Consensus       102 ~vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie~~~~~~~~~~  176 (456)
                      +|||||+++++|||+|++++||+||+|+++..|+||+||+||.|+.|.+++++.+.|...++.|++.++.+++++
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            999999999999999999999999999999999999999999999999999999999999999999998877654

>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=3e-30  Score=230.69  Aligned_cols=152  Identities=24%  Similarity=0.462  Sum_probs=142.0

Q ss_pred             CeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeE
Q 012794           24 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        24 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  102 (456)
                      .++|+|+.+..++|+++|.++++.+. ..++||||+|++.++.|++.|.+ ++.+..+||+|++.+|..+++.|++++++
T Consensus         1 ~l~q~~v~~~~~~K~~~L~~ll~~~~-~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~   79 (168)
T d1t5ia_           1 GLQQYYVKLKDNEKNRKLFDLLDVLE-FNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR   79 (168)
T ss_dssp             CCEEEEEECCGGGHHHHHHHHHHHSC-CSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             CcEEEEEEeChHHHHHHHHHHHHhCC-CCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccce
Confidence            37899999999999999999998774 57999999999999999999985 79999999999999999999999999999


Q ss_pred             EEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChh-hHHHHHHHHHHhCCCceec
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSS-QRRTVRSLERDVGCKFEFV  176 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-e~~~~~~ie~~~~~~~~~~  176 (456)
                      |||||+++++|+|+|.+++||+|++|.+++.|+||+||+||.|++|.||+|+++. +...+..+++.+...++.+
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            9999999999999999999999999999999999999999999999999999764 6778888999998887764

>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=5.2e-29  Score=228.48  Aligned_cols=137  Identities=20%  Similarity=0.422  Sum_probs=126.3

Q ss_pred             EEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec
Q 012794           29 AISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT  107 (456)
Q Consensus        29 ~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT  107 (456)
                      |..++..+|++.|..+|+.+ +..++||||+|+..|+.|+..|.. ++.+..+||+|++.+|.++++.|++++++|||||
T Consensus         9 y~v~~~~~k~~~L~~~l~~~-~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaT   87 (200)
T d1oywa3           9 YMLMEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVAT   87 (200)
T ss_dssp             EEEEECSSHHHHHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEC
T ss_pred             EEEEcCCcHHHHHHHHHHhc-CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEec
Confidence            33445567999999998876 467999999999999999999985 7999999999999999999999999999999999


Q ss_pred             cccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHH
Q 012794          108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  166 (456)
Q Consensus       108 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie  166 (456)
                      +++++|||+|+|++||||++|.++++|+||+|||||.|++|.+++|+.+.|...++++.
T Consensus        88 d~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~i  146 (200)
T d1oywa3          88 VAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  146 (200)
T ss_dssp             TTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHH
T ss_pred             chhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999888877653

>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=201.88  Aligned_cols=128  Identities=23%  Similarity=0.404  Sum_probs=111.0

Q ss_pred             HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccC
Q 012794           37 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  115 (456)
Q Consensus        37 k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gid  115 (456)
                      ..++|..+.+...++.++||||+|+++|+.|+..|.. ++.+..+||+|++.+|++++++|++|+++|||||+++++|||
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            3456666666666788999999999999999999995 899999999999999999999999999999999999999999


Q ss_pred             cCccceEEecCCCC-----ChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794          116 IPNVDLIIHYELPN-----DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus       116 ip~v~~VI~~~~p~-----~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      +|+|++||+|++|.     +.++|+||+||+||.++ |.+++++........+.+
T Consensus        97 ip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~~~~~~~~i  150 (174)
T d1c4oa2          97 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRVSEAMQRAI  150 (174)
T ss_dssp             CTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSCCHHHHHHH
T ss_pred             CCCCcEEEEeccccccccchhHHHHHHhhhhhhcCC-CeeEEeecCCCHHHHHHH
Confidence            99999999999765     66889999999999874 777777766554444433

>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=7.7e-26  Score=203.60  Aligned_cols=120  Identities=24%  Similarity=0.408  Sum_probs=104.8

Q ss_pred             HHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccC
Q 012794           37 KRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLD  115 (456)
Q Consensus        37 k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gid  115 (456)
                      ..++|..+.+....+.++||||+|+..++.++..|.+ ++.+..+||+|++.+|.+++++|++|+++||||||++++|||
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            3455666665556678999999999999999999985 899999999999999999999999999999999999999999


Q ss_pred             cCccceEEecCCCC-----ChhHHHHHhcccccCCCCceEEEeeChh
Q 012794          116 IPNVDLIIHYELPN-----DPETFVHRSGRTGRAGKEGTAILMFTSS  157 (456)
Q Consensus       116 ip~v~~VI~~~~p~-----~~~~y~qr~GR~gR~g~~g~~i~~~~~~  157 (456)
                      +|+|++|||||+|.     +...|+||+|||||.|.. .+++++...
T Consensus        97 ip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~-~~~~~~~~~  142 (181)
T d1t5la2          97 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANG-HVIMYADTI  142 (181)
T ss_dssp             CTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTC-EEEEECSSC
T ss_pred             CCCCCEEEEecCCcccccccHHHHHHHHHhhccccCc-eeEeecchh
Confidence            99999999999995     689999999999998854 444444433

>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=4.9e-24  Score=183.27  Aligned_cols=124  Identities=28%  Similarity=0.377  Sum_probs=98.6

Q ss_pred             CeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeE
Q 012794           24 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        24 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  102 (456)
                      +|++.++....+.+.......++.+ +.+++||||+|++.|+.|++.|.+ ++.+..+|++|++       +.|++++.+
T Consensus         9 ~I~~~~~~~~~~~~~~~~~i~l~~~-~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~-------~~~~~~~~~   80 (138)
T d1jr6a_           9 NIEEVALSTTGEIPFYGKAIPLEVI-KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDV-------SVIPTNGDV   80 (138)
T ss_dssp             TEEEEECCBCSSEECSSCEECHHHH-TTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCS-------CCCTTSSCE
T ss_pred             CeEEEEeccCChhHHHHhhChHhhc-CCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchh-------hhhhhhhcc
Confidence            4666665544321111101113334 468999999999999999999985 8999999999984       568899999


Q ss_pred             EEEeccccccccCcCccceEEecC----CCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYE----LPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~----~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      ||||||++++||| |++++|||++    +|.++++|+||+||||| |++|. ++|+++.|
T Consensus        81 vlvaTd~~~~GiD-~~v~~Vi~~~~~~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_          81 VVVATDALMTGFT-GDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             EEEESSSSCSSSC-CCBSEEEECSEETTEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             eeehhHHHHhccc-cccceEEEEEecCCCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence            9999999999999 9999999855    69999999999999999 99995 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=6.3e-21  Score=183.85  Aligned_cols=123  Identities=33%  Similarity=0.545  Sum_probs=105.7

Q ss_pred             ccHHHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeC--------CCCHHHHHHHHhcccCCCeE
Q 012794           35 TSKRTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHG--------DISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        35 ~~k~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg--------~~~~~~R~~~l~~Fr~g~~~  102 (456)
                      ..|++.|.++|...   .++.++||||+++..++.+++.|.+ ++.+..+||        +|++.+|..+++.|++|+++
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            35777777777543   4567999999999999999999985 788888866        56777899999999999999


Q ss_pred             EEEeccccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      |||||+++++|||+|++++||+||+|+++..|+||+|||||.+ ++.+++|+++..
T Consensus       222 vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~  276 (286)
T d1wp9a2         222 VLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGT  276 (286)
T ss_dssp             EEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTS
T ss_pred             EEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCC
Confidence            9999999999999999999999999999999999999999975 688888887653

>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=99.82  E-value=1.7e-20  Score=171.46  Aligned_cols=120  Identities=27%  Similarity=0.529  Sum_probs=103.0

Q ss_pred             HHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc-------------------------------CCEEEEeCCCCH
Q 012794           38 RTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI-------------------------------IASEALHGDISQ   86 (456)
Q Consensus        38 ~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~-------------------------------~~~~~lhg~~~~   86 (456)
                      .+++.+++.   .++++||||+|++.|+.+|..|.+.                               ..+.++|++|++
T Consensus        30 ~~l~~~~i~---~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          30 EELVEECVA---ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHHH---TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHH---cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            344444443   5689999999999999998887631                               137889999999


Q ss_pred             HHHHHHHhcccCCCeEEEEeccccccccCcCccceEEe-------cCCCCChhHHHHHhcccccCC--CCceEEEeeChh
Q 012794           87 HQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIH-------YELPNDPETFVHRSGRTGRAG--KEGTAILMFTSS  157 (456)
Q Consensus        87 ~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~-------~~~p~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~  157 (456)
                      .+|..+++.|+++.++|||||+++++|||+|.+++||+       ++.|.++.+|+||+|||||.|  ..|.+++++.+.
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       678899999999999999988  468899988877


Q ss_pred             hHH
Q 012794          158 QRR  160 (456)
Q Consensus       158 e~~  160 (456)
                      +..
T Consensus       187 ~~~  189 (201)
T d2p6ra4         187 DRE  189 (201)
T ss_dssp             GHH
T ss_pred             ChH
Confidence            643

>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=99.81  E-value=8.9e-23  Score=193.08  Aligned_cols=129  Identities=18%  Similarity=0.318  Sum_probs=108.9

Q ss_pred             CeeEEEEEcCcccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccCCCeEE
Q 012794           24 GIKLYAISTTATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTV  103 (456)
Q Consensus        24 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~v  103 (456)
                      +|...++   .++|++.|..+|+.+  +.++||||+|++.|+.|++.|...     +||+|++.+|.+++++|++|+++|
T Consensus         3 ~v~d~~~---~~~~~~~l~~~l~~~--~~~~iif~~~~~~~~~l~~~l~~~-----~hg~~~~~~R~~~~~~f~~g~~~v   72 (248)
T d1gkub2           3 NVEDVAV---NDESISTLSSILEKL--GTGGIIYARTGEEAEEIYESLKNK-----FRIGIVTATKKGDYEKFVEGEIDH   72 (248)
T ss_dssp             CEEEEEE---SCCCTTTTHHHHTTS--CSCEEEEESSHHHHHHHHHTTTTS-----SCEEECTTSSSHHHHHHHHTSCSE
T ss_pred             CEEEEec---CchHHHHHHHHHHHh--CCCEEEEECCHHHHHHHHHHHHHh-----ccCCCCHHHHHHHHHHHHhCCCeE
Confidence            4566664   456888888888754  468999999999999999999753     799999999999999999999999


Q ss_pred             EEec----cccccccCcCc-cceEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHHH
Q 012794          104 LVAT----DVAARGLDIPN-VDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSLE  166 (456)
Q Consensus       104 LVaT----dv~~~Gidip~-v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~ie  166 (456)
                      ||||    +++++|||+|+ |++|||||+|+    |+||+|||||+|+.+.+++++...+...+..+.
T Consensus        73 LVaT~a~~~v~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~  136 (248)
T d1gkub2          73 LIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLL  136 (248)
T ss_dssp             EEEECC------CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTC
T ss_pred             EEEeccccchhhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHHHHHHH
Confidence            9999    89999999996 99999999995    889999999999999999988887766665543

>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=99.78  E-value=1.4e-20  Score=171.73  Aligned_cols=130  Identities=20%  Similarity=0.408  Sum_probs=100.4

Q ss_pred             cHHH-HHHHHHHHHCCCCcEEEEcCChHHHHHH--------HHHHHh----cCCEEEEeCCCCHHHHHHHHhcccCCCeE
Q 012794           36 SKRT-ILSDLITVYAKGGKTIVFTQTKRDADEV--------SLALTS----IIASEALHGDISQHQRERTLNGFRQGKFT  102 (456)
Q Consensus        36 ~k~~-~L~~ll~~~~~~~~~IIF~~t~~~a~~l--------~~~L~~----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~  102 (456)
                      ++.+ ++..+.+.+..+.++.|.||..++.+.+        .+.|.+    .+.+..+||.|++++|++++++|++|+++
T Consensus        13 ~~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~   92 (206)
T d1gm5a4          13 DRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYD   92 (206)
T ss_dssp             STHHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSS
T ss_pred             ccHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEE
Confidence            3444 4444445566778999999876554433        333332    25678899999999999999999999999


Q ss_pred             EEEeccccccccCcCccceEEecCCCC-ChhHHHHHhcccccCCCCceEEEeeChhhHHHHHHH
Q 012794          103 VLVATDVAARGLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTSSQRRTVRSL  165 (456)
Q Consensus       103 vLVaTdv~~~Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~e~~~~~~i  165 (456)
                      |||||+|+++|||+|++++||+++.|. ....|.|..||+||.+.++.|++++.+......+.+
T Consensus        93 iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~rl  156 (206)
T d1gm5a4          93 ILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERL  156 (206)
T ss_dssp             BCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHH
T ss_pred             EEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchhhh
Confidence            999999999999999999999999997 688888889999999999999999986554444444

>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=1.3e-19  Score=165.41  Aligned_cols=109  Identities=25%  Similarity=0.448  Sum_probs=99.8

Q ss_pred             cccHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhcCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccc
Q 012794           34 ATSKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTSIIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARG  113 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~G  113 (456)
                      ...|++.|.+++..+ .+.++||||+++..++.|++.|    .+..+||++++.+|+.+++.|++++++|||||+++++|
T Consensus        77 ~~~K~~~l~~ll~~~-~~~k~lvf~~~~~~~~~l~~~l----~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~G  151 (200)
T d2fwra1          77 SKNKIRKLREILERH-RKDKIIIFTRHNELVYRISKVF----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEG  151 (200)
T ss_dssp             CSHHHHHHHHHHHHT-SSSCBCCBCSCHHHHHHHHHHT----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSS
T ss_pred             cHHHHHHHHHHHHhC-CCCcEEEEeCcHHHHHHHHhhc----CcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcc
Confidence            356899999999876 4689999999999999888766    45678999999999999999999999999999999999


Q ss_pred             cCcCccceEEecCCCCChhHHHHHhcccccCCCC
Q 012794          114 LDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKE  147 (456)
Q Consensus       114 idip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~  147 (456)
                      ||+|.+++||++++|+++..|+||+||++|.++.
T Consensus       152 idl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~  185 (200)
T d2fwra1         152 IDVPDANVGVIMSGSGSAREYIQRLGRILRPSKG  185 (200)
T ss_dssp             SCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTT
T ss_pred             cCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCC
Confidence            9999999999999999999999999999998864

>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=1.5e-19  Score=170.95  Aligned_cols=105  Identities=24%  Similarity=0.363  Sum_probs=92.7

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHH----------HHHHhcccCCCeEEEEecccccc---ccCc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQR----------ERTLNGFRQGKFTVLVATDVAAR---GLDI  116 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R----------~~~l~~Fr~g~~~vLVaTdv~~~---Gidi  116 (456)
                      ++++||||+|++.|++|+..|.+ ++.+..+|++|+++.|          ..+++.|+.+++++||+|+++++   ++|+
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giDi  115 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSL  115 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECCC
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCCC
Confidence            68999999999999999999985 7999999999999887          56788999999999999999999   5777


Q ss_pred             CccceEEecCCCCChhHHHHHhcccccCCCCceEEEeeCh
Q 012794          117 PNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       117 p~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      +.+.+||++++|.++++|+||+||||| |+.|...+++..
T Consensus       116 d~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~  154 (299)
T d1a1va2         116 DPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPG  154 (299)
T ss_dssp             SSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSC
T ss_pred             CcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecC
Confidence            888899999999999999999999999 899987766543

>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=99.72  E-value=3.1e-17  Score=148.42  Aligned_cols=121  Identities=21%  Similarity=0.367  Sum_probs=110.2

Q ss_pred             cHHHHHHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHh---cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecccccc
Q 012794           36 SKRTILSDLITVYAKGGKTIVFTQTKRDADEVSLALTS---IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAAR  112 (456)
Q Consensus        36 ~k~~~L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~---~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~  112 (456)
                      ++..+...+...+..++++.+.||..+.++.+++.|.+   .+.+..+||.|++++++++|.+|++++++|||||.+++.
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            44556667777888899999999999999999998885   468999999999999999999999999999999999999


Q ss_pred             ccCcCccceEEecCCCC-ChhHHHHHhcccccCCCCceEEEeeCh
Q 012794          113 GLDIPNVDLIIHYELPN-DPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       113 Gidip~v~~VI~~~~p~-~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                      |||+|+++++|..+.+. -..++.|..||+||.+..+.|++++..
T Consensus        96 GiDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~  140 (211)
T d2eyqa5          96 GIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPH  140 (211)
T ss_dssp             GSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECC
T ss_pred             ccCCCCCcEEEEecchhccccccccccceeeecCccceEEEEecC
Confidence            99999999999888875 899999999999999999999999864

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.50  E-value=8.5e-14  Score=136.67  Aligned_cols=121  Identities=13%  Similarity=0.231  Sum_probs=106.8

Q ss_pred             cccHHHHHHHHHHHH--CCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCe---EEEEec
Q 012794           34 ATSKRTILSDLITVY--AKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKF---TVLVAT  107 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~--~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~---~vLVaT  107 (456)
                      .+.|+.+|..++...  .++.|+|||++.+...+.|...|.. ++.+..+||.++..+|..+++.|+++..   -+|++|
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            356999999988754  4567999999999999999999984 8899999999999999999999998653   367889


Q ss_pred             cccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEEee
Q 012794          108 DVAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAILMF  154 (456)
Q Consensus       108 dv~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~  154 (456)
                      .+++.|||++.+++||+||++|++..+.|++||+.|.|++..+.++.
T Consensus       179 ~agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~r  225 (346)
T d1z3ix1         179 KAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYR  225 (346)
T ss_dssp             GGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEE
T ss_pred             hhhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEE
Confidence            99999999999999999999999999999999999999876665543

>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=99.46  E-value=8.8e-14  Score=130.06  Aligned_cols=119  Identities=18%  Similarity=0.293  Sum_probs=89.5

Q ss_pred             cccHHHHHHHHHHHH-CCCCcEEEEcCChHHHHHHHHHHHh--cCCEEEEeCCCCHHHHHHHHhcccCC-CeEEEEe-cc
Q 012794           34 ATSKRTILSDLITVY-AKGGKTIVFTQTKRDADEVSLALTS--IIASEALHGDISQHQRERTLNGFRQG-KFTVLVA-TD  108 (456)
Q Consensus        34 ~~~k~~~L~~ll~~~-~~~~~~IIF~~t~~~a~~l~~~L~~--~~~~~~lhg~~~~~~R~~~l~~Fr~g-~~~vLVa-Td  108 (456)
                      .+.|+..|.+++... ..+.++||||+.....+.|...|..  ++.+..+||++++.+|+.+++.|.++ ...|||+ |.
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            456999999988754 4577999999999999999888863  57788899999999999999999876 4666654 57


Q ss_pred             ccccccCcCccceEEecCCCCChhHHHHHhcccccCCCCceEEE
Q 012794          109 VAARGLDIPNVDLIIHYELPNDPETFVHRSGRTGRAGKEGTAIL  152 (456)
Q Consensus       109 v~~~Gidip~v~~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~  152 (456)
                      +++.|+|++.+++||++++||++..+.|++||+.|.|++..+.+
T Consensus       147 ~~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i  190 (244)
T d1z5za1         147 AGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIV  190 (244)
T ss_dssp             TTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEE
T ss_pred             ccccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEE
Confidence            89999999999999999999999999999999999996654443

>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=99.45  E-value=6.4e-14  Score=134.32  Aligned_cols=102  Identities=19%  Similarity=0.293  Sum_probs=85.8

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEE-----
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLII-----  123 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI-----  123 (456)
                      ..+++||||+++++++.+++.|.+ ++.+..+|+++++..    ...|+++..++||||+++++|+|++ +++||     
T Consensus       177 ~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~  251 (305)
T d2bmfa2         177 FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRC  251 (305)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEE
T ss_pred             hCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCc
Confidence            468999999999999999999985 789999999986654    4578899999999999999999995 55554     


Q ss_pred             -----ecCC----------CCChhHHHHHhcccccCCCCceEEEeeCh
Q 012794          124 -----HYEL----------PNDPETFVHRSGRTGRAGKEGTAILMFTS  156 (456)
Q Consensus       124 -----~~~~----------p~~~~~y~qr~GR~gR~g~~g~~i~~~~~  156 (456)
                           +++.          |.+..+|+||+||+||.++.+...++|..
T Consensus       252 ~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~  299 (305)
T d2bmfa2         252 MKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMG  299 (305)
T ss_dssp             EEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECS
T ss_pred             eeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECC
Confidence                 3443          46889999999999999988877777654

>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=99.40  E-value=2.8e-13  Score=129.76  Aligned_cols=100  Identities=19%  Similarity=0.254  Sum_probs=79.4

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccccccccCcCccceEEecCC--
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDVAARGLDIPNVDLIIHYEL--  127 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv~~~Gidip~v~~VI~~~~--  127 (456)
                      .+++||||++..++++++..|.+ ++.+.+|||.++.++++    +|++++.+||||||+++.|||+ +|.+||++++  
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~  110 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTAF  110 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCcee
Confidence            58999999999999999999995 78999999999987765    5678899999999999999999 5999997664  


Q ss_pred             -----------------CCChhHHHHHhcccccCCCCceEEEeeC
Q 012794          128 -----------------PNDPETFVHRSGRTGRAGKEGTAILMFT  155 (456)
Q Consensus       128 -----------------p~~~~~y~qr~GR~gR~g~~g~~i~~~~  155 (456)
                                       |.+..+..||.||+||.+....++.+|.
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         111 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             ceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                             2467888999999999865544555554

>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=99.22  E-value=1.2e-10  Score=101.39  Aligned_cols=125  Identities=22%  Similarity=0.267  Sum_probs=98.5

Q ss_pred             cCcccHHHHHHHHH-HHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc
Q 012794           32 TTATSKRTILSDLI-TVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATDV  109 (456)
Q Consensus        32 ~~~~~k~~~L~~ll-~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv  109 (456)
                      ....+|+.++.+-+ ..+.++.++||+|.|.+.++.|+..|.+ ++...+|+......+-+.+-++-.  .-.|.|||++
T Consensus        14 ~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~Ag~--~g~VtIATNm   91 (175)
T d1tf5a4          14 RTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQ--KGAVTIATNM   91 (175)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTS--TTCEEEEETT
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhccC--CCceeehhhH
Confidence            45557766665544 5566789999999999999999999995 788899998854433333333333  3469999999


Q ss_pred             cccccCcC---ccc-----eEEecCCCCChhHHHHHhcccccCCCCceEEEeeChhh
Q 012794          110 AARGLDIP---NVD-----LIIHYELPNDPETFVHRSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       110 ~~~Gidip---~v~-----~VI~~~~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      |.||.||.   .|.     |||....|.+.....|..||+||.|.+|.+.+|++-.+
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            99999984   232     79999999999999999999999999999988886443

>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=98.73  E-value=1.6e-08  Score=76.48  Aligned_cols=82  Identities=20%  Similarity=0.306  Sum_probs=71.1

Q ss_pred             CCccccCCCCceEEEEEeecCccccCCCChhHHHHHHHhhCCCC-CCccccEEEeecCccceeeeecCHHHHHHHHhhcC
Q 012794          238 SSRSLINHEQGWVTLQLTRDSAFSRGFMSARSVMGFLSDVYPTA-ADEIGKIHIIADDRVQGAVFDLPEEIAKELLNKQI  316 (456)
Q Consensus       238 ~~r~l~~~~~g~~t~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~ig~i~~~~~~~~~~~~~dv~~~~a~~~~~~~~  316 (456)
                      +.|||+++.+|++|+.+..+.    ..-.+..++..|.+..+.. .+.|..|+++++.  +|+|||||++.++++.+.|.
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            469999999999999999875    4568999999999988753 5679999999986  69999999999999999999


Q ss_pred             CCCCceeec
Q 012794          317 PPGNTISKI  325 (456)
Q Consensus       317 ~~g~~l~~~  325 (456)
                      +..+.++++
T Consensus        76 dsr~~ls~~   84 (85)
T d2e29a1          76 DSDWILSVP   84 (85)
T ss_dssp             SSSCEEECC
T ss_pred             ccceEEecC
Confidence            887777765

>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=98.65  E-value=2e-07  Score=82.43  Aligned_cols=126  Identities=25%  Similarity=0.314  Sum_probs=97.4

Q ss_pred             EcCcccHHHHHHH-HHHHHCCCCcEEEEcCChHHHHHHHHHHHh-cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc
Q 012794           31 STTATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTS-IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD  108 (456)
Q Consensus        31 ~~~~~~k~~~L~~-ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd  108 (456)
                      +.....|..++.+ +...+..+.++||.+.+.+..+.|+..|.+ ++...+|+..-  .+|+..+-+=.-..-.|-|||+
T Consensus        13 y~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~--herEAeIIAqAG~~GaVTIATN   90 (219)
T d1nkta4          13 YKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKY--HEQEATIIAVAGRRGGVTVATN   90 (219)
T ss_dssp             ESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSC--HHHHHHHHHTTTSTTCEEEEET
T ss_pred             EcCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhh--HHHHHHHHHhcccCCcEEeecc
Confidence            3455567666555 555667889999999999999999999985 89999999974  4454443332222346899999


Q ss_pred             ccccccCcCc-----------------------------------------------c-----ceEEecCCCCChhHHHH
Q 012794          109 VAARGLDIPN-----------------------------------------------V-----DLIIHYELPNDPETFVH  136 (456)
Q Consensus       109 v~~~Gidip~-----------------------------------------------v-----~~VI~~~~p~~~~~y~q  136 (456)
                      +|.||.||-=                                               |     -|||-.....+...--|
T Consensus        91 MAGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQ  170 (219)
T d1nkta4          91 MAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQ  170 (219)
T ss_dssp             TCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHH
T ss_pred             ccCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEecccccccccccc
Confidence            9999999821                                               1     16888888899999999


Q ss_pred             HhcccccCCCCceEEEeeChhh
Q 012794          137 RSGRTGRAGKEGTAILMFTSSQ  158 (456)
Q Consensus       137 r~GR~gR~g~~g~~i~~~~~~e  158 (456)
                      -.||+||.|.+|.+..|++-.+
T Consensus       171 LRGRsGRQGDPGsSrFflSLeD  192 (219)
T d1nkta4         171 LRGRSGRQGDPGESRFYLSLGD  192 (219)
T ss_dssp             HHHTSSGGGCCEEEEEEEETTS
T ss_pred             ccccccccCCCccceeEEeccH
Confidence            9999999999999988887544

>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=97.79  E-value=2.4e-06  Score=48.97  Aligned_cols=16  Identities=56%  Similarity=1.387  Sum_probs=14.7

Q ss_pred             CcccCCCCCcCcCCCC
Q 012794          440 ACFNCGKSGHRASECP  455 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p  455 (456)
                      -|||||++||.+++|-
T Consensus         8 kCfNCGkeGH~ar~Cr   23 (29)
T d1nc8a_           8 RCWNCGKEGHSARQCR   23 (29)
T ss_dssp             BCTTTSCBSSCGGGCC
T ss_pred             EeecCCccchhhhhcc
Confidence            4999999999999993

>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=97.58  E-value=3.7e-05  Score=50.05  Aligned_cols=16  Identities=44%  Similarity=1.375  Sum_probs=15.5

Q ss_pred             cccCCCCCcCcCCCCC
Q 012794          441 CFNCGKSGHRASECPN  456 (456)
Q Consensus       441 ~~~c~~~gh~~~~~p~  456 (456)
                      ||+|++.||+++|||+
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

>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=97.20  E-value=0.00063  Score=62.46  Aligned_cols=104  Identities=19%  Similarity=0.250  Sum_probs=75.4

Q ss_pred             cccHHHHHHH-HHHHHCCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEec
Q 012794           34 ATSKRTILSD-LITVYAKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVAT  107 (456)
Q Consensus        34 ~~~k~~~L~~-ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaT  107 (456)
                      -+-|..+... ++..+..+.++++.++|.-.|.+.++.+.+     ++.+..+||.++..+|.+++.+.++|+++|+|.|
T Consensus       114 GSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGT  193 (264)
T d1gm5a3         114 GSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGT  193 (264)
T ss_dssp             SSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEEC
T ss_pred             cccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEee
Confidence            3456554443 334445678999999999999999988875     2578999999999999999999999999999999


Q ss_pred             ccccc-ccCcCccceEEecCCCCChhHHHHHhc
Q 012794          108 DVAAR-GLDIPNVDLIIHYELPNDPETFVHRSG  139 (456)
Q Consensus       108 dv~~~-Gidip~v~~VI~~~~p~~~~~y~qr~G  139 (456)
                      -.+-. .+.+.++.+||.=.  ...-.|.||..
T Consensus       194 hsl~~~~~~f~~LglviiDE--qH~fgv~Qr~~  224 (264)
T d1gm5a3         194 HALIQEDVHFKNLGLVIIDE--QHRFGVKQREA  224 (264)
T ss_dssp             TTHHHHCCCCSCCCEEEEES--CCCC-----CC
T ss_pred             hHHhcCCCCccccceeeecc--ccccchhhHHH
Confidence            65544 57778888877332  11224666653

>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=97.12  E-value=7.6e-05  Score=48.50  Aligned_cols=17  Identities=59%  Similarity=1.355  Sum_probs=15.8

Q ss_pred             CcccCCCCCcCcCCCCC
Q 012794          440 ACFNCGKSGHRASECPN  456 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p~  456 (456)
                      .||+|++.||+++|||+
T Consensus         3 ~C~~Cg~~GH~~~~Cp~   19 (42)
T d2exfa1           3 KCFNCGKEGHTARNCRA   19 (42)
T ss_dssp             CCTTTCCSSSCTTTCSS
T ss_pred             ccccCCCcCcCcccCcC
Confidence            49999999999999995

>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=96.97  E-value=0.0013  Score=59.05  Aligned_cols=93  Identities=14%  Similarity=0.149  Sum_probs=76.1

Q ss_pred             cCcccHHHHHHHHH-HHHCCCCcEEEEcCChHHHHHHHHHHHhc-----CCEEEEeCCCCHHHHHHHHhcccCCCeEEEE
Q 012794           32 TTATSKRTILSDLI-TVYAKGGKTIVFTQTKRDADEVSLALTSI-----IASEALHGDISQHQRERTLNGFRQGKFTVLV  105 (456)
Q Consensus        32 ~~~~~k~~~L~~ll-~~~~~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLV  105 (456)
                      +...-|..+....+ ..+..+.++++.+||.-.+.+.++.+.+.     ..+..+|+.++..+|..+++.+.+|+++|||
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            44456766655544 45567889999999999999999999852     4688899999999999999999999999999


Q ss_pred             ecccccc-ccCcCccceEEe
Q 012794          106 ATDVAAR-GLDIPNVDLIIH  124 (456)
Q Consensus       106 aTdv~~~-Gidip~v~~VI~  124 (456)
                      .|-.+-. -+.++++-+||.
T Consensus       164 Gths~l~~~~~f~~LgLiIi  183 (233)
T d2eyqa3         164 GTHKLLQSDVKFKDLGLLIV  183 (233)
T ss_dssp             ECTHHHHSCCCCSSEEEEEE
T ss_pred             eehhhhccCCccccccceee
Confidence            9975544 688888888773

>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=96.44  E-value=0.00061  Score=37.07  Aligned_cols=16  Identities=50%  Similarity=1.362  Sum_probs=15.0

Q ss_pred             CcccCCCCCcCcCCCC
Q 012794          440 ACFNCGKSGHRASECP  455 (456)
Q Consensus       440 ~~~~c~~~gh~~~~~p  455 (456)
                      -||.||+.||+-+||-
T Consensus         4 vcfscgktghikkdck   19 (26)
T d1dsqa_           4 VCFSCGKTGHIKRDCK   19 (26)
T ss_dssp             BCTTTCCBSSCTTTTT
T ss_pred             EEEecCCcccchhhhh
Confidence            4999999999999996

>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=94.99  E-value=0.038  Score=48.71  Aligned_cols=85  Identities=16%  Similarity=0.252  Sum_probs=61.8

Q ss_pred             ccH-HHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEE
Q 012794           35 TSK-RTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  105 (456)
Q Consensus        35 ~~k-~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLV  105 (456)
                      +-| +..+.-++..+   ....++||+|+|++.|.++++.+..     .+.+..++|+.+..+....++.    ..+|||
T Consensus        65 SGKTlayllPil~~l~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~----~~~Ilv  140 (222)
T d2j0sa1          65 TGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY----GQHVVA  140 (222)
T ss_dssp             SSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHH----CCSEEE
T ss_pred             hhhhhhhcccccccccccccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhcc----CCeEEe
Confidence            445 44444455433   2345799999999999999887763     3678889999988877776654    568999


Q ss_pred             ecc------ccccccCcCccceEE
Q 012794          106 ATD------VAARGLDIPNVDLII  123 (456)
Q Consensus       106 aTd------v~~~Gidip~v~~VI  123 (456)
                      +|+      +....+++.++.++|
T Consensus       141 ~TPgrl~~~~~~~~~~~~~l~~lV  164 (222)
T d2j0sa1         141 GTPGRVFDMIRRRSLRTRAIKMLV  164 (222)
T ss_dssp             ECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             CCCCcHHhcccccccccccceeee
Confidence            995      234558888999887

>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=94.41  E-value=0.19  Score=43.22  Aligned_cols=85  Identities=20%  Similarity=0.181  Sum_probs=59.8

Q ss_pred             ccH-HHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh------cCCEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           35 TSK-RTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS------IIASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        35 ~~k-~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~------~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      +-| +..+.-++...   ....++||.|+|++.|.++.+.+..      ...+..++|+.....+...++.    ..+||
T Consensus        51 sGKTlayllP~l~~~~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~----~~~iv  126 (206)
T d1veca_          51 TGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDD----TVHVV  126 (206)
T ss_dssp             STTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTS----CCSEE
T ss_pred             cccccccccchhhcccccccCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHh----ccCeE
Confidence            445 44444455443   2345799999999999999887753      1456777888888877777654    67899


Q ss_pred             Eecc-----c-cccccCcCccceEE
Q 012794          105 VATD-----V-AARGLDIPNVDLII  123 (456)
Q Consensus       105 VaTd-----v-~~~Gidip~v~~VI  123 (456)
                      |+|+     . ....+++.++.++|
T Consensus       127 v~TPgrl~~~~~~~~~~~~~l~~lV  151 (206)
T d1veca_         127 IATPGRILDLIKKGVAKVDHVQMIV  151 (206)
T ss_dssp             EECHHHHHHHHHTTCSCCTTCCEEE
T ss_pred             EeCCccccccccchhccccccceEE
Confidence            9995     2 33347788888877

>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=94.32  E-value=0.2  Score=43.13  Aligned_cols=69  Identities=23%  Similarity=0.283  Sum_probs=53.1

Q ss_pred             CCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc-----cccc-ccCcCcc
Q 012794           51 GGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD-----VAAR-GLDIPNV  119 (456)
Q Consensus        51 ~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd-----v~~~-Gidip~v  119 (456)
                      +.++||.|+|++.|.++.+.+..     ...+..++|+.+..++.+.++     ..+|||+|+     .+.. .+++.++
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     257888999988877666553     367999995     3333 4788999


Q ss_pred             ceEEe
Q 012794          120 DLIIH  124 (456)
Q Consensus       120 ~~VI~  124 (456)
                      .++|.
T Consensus       147 ~~lVi  151 (208)
T d1hv8a1         147 KYFIL  151 (208)
T ss_dssp             CEEEE
T ss_pred             cEEEE
Confidence            88773

>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=92.51  E-value=0.3  Score=42.17  Aligned_cols=85  Identities=19%  Similarity=0.230  Sum_probs=51.3

Q ss_pred             cccH-HHHHHHHHHHHC---CCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           34 ATSK-RTILSDLITVYA---KGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        34 ~~~k-~~~L~~ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      .+-| +..+..++..+.   ....+||+|+|++.+.++...+..     .+.+..++++-+..++...+   +  ..+||
T Consensus        57 GsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~--~~~Iv  131 (212)
T d1qdea_          57 GTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL---R--DAQIV  131 (212)
T ss_dssp             TSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C---T--TCSEE
T ss_pred             ccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHh---c--CCcEE
Confidence            3455 344444554442   345899999999999999888863     24566677765555444332   2  46899


Q ss_pred             Eecc------ccccccCcCccceEE
Q 012794          105 VATD------VAARGLDIPNVDLII  123 (456)
Q Consensus       105 VaTd------v~~~Gidip~v~~VI  123 (456)
                      |+|+      .-...+++.++.++|
T Consensus       132 I~TP~~l~~~~~~~~~~l~~l~~lV  156 (212)
T d1qdea_         132 VGTPGRVFDNIQRRRFRTDKIKMFI  156 (212)
T ss_dssp             EECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             EECCCccccccccCceecCcceEEe
Confidence            9995      234457888999877

>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=91.41  E-value=0.33  Score=42.29  Aligned_cols=72  Identities=18%  Similarity=0.271  Sum_probs=50.3

Q ss_pred             ccHHHH-HHHHHHHHCCCCcEEEEcCChHHHHHHHHHHHhc---------CCEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           35 TSKRTI-LSDLITVYAKGGKTIVFTQTKRDADEVSLALTSI---------IASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        35 ~~k~~~-L~~ll~~~~~~~~~IIF~~t~~~a~~l~~~L~~~---------~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      .-|..+ +..++....++.++||.++|+..++++++.|.+.         ..+..+++..+..++...++...  ..+||
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            346533 2223334456789999999999999999888642         22456678888888888877655  35689


Q ss_pred             Eecc
Q 012794          105 VATD  108 (456)
Q Consensus       105 VaTd  108 (456)
                      |+|+
T Consensus       147 v~Tp  150 (237)
T d1gkub1         147 ITTT  150 (237)
T ss_dssp             EEEH
T ss_pred             ccCh
Confidence            9985

>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=90.70  E-value=0.054  Score=32.99  Aligned_cols=16  Identities=44%  Similarity=1.157  Sum_probs=15.2

Q ss_pred             cccCCCCCcCcCCCCC
Q 012794          441 CFNCGKSGHRASECPN  456 (456)
Q Consensus       441 ~~~c~~~gh~~~~~p~  456 (456)
                      |--|.|.||.++|||.
T Consensus        13 CAyCke~GHW~~dCPk   28 (40)
T d1a6bb_          13 CAYCKEKGHWAKDCPK   28 (40)
T ss_dssp             CSSSCCTTCCTTSCSS
T ss_pred             hHHHhhcCchhhhCcc
Confidence            9999999999999994

>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=90.03  E-value=0.82  Score=39.00  Aligned_cols=86  Identities=16%  Similarity=0.234  Sum_probs=57.0

Q ss_pred             ccH-HHHHHHHHHHHCC---CCcEEEEcCChHHHHHHHHHHHh---c---CCEEEEeCCCCHHHHHHHHhcccCCCeEEE
Q 012794           35 TSK-RTILSDLITVYAK---GGKTIVFTQTKRDADEVSLALTS---I---IASEALHGDISQHQRERTLNGFRQGKFTVL  104 (456)
Q Consensus        35 ~~k-~~~L~~ll~~~~~---~~~~IIF~~t~~~a~~l~~~L~~---~---~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vL  104 (456)
                      +-| +..+.-++.....   ..++||.|+|++.|.++.+.+..   .   +.+..++|+.+.......+..   ...+||
T Consensus        49 sGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~---~~~~il  125 (207)
T d1t6na_          49 MGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK---NCPHIV  125 (207)
T ss_dssp             SCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHH---SCCSEE
T ss_pred             cccccccccceeeeecccCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHh---cCCCEE
Confidence            456 4444455554422   34799999999999999888863   1   357778888887765554432   357899


Q ss_pred             Eecc-----ccc-cccCcCccceEE
Q 012794          105 VATD-----VAA-RGLDIPNVDLII  123 (456)
Q Consensus       105 VaTd-----v~~-~Gidip~v~~VI  123 (456)
                      |+|+     .+. ..+++.++.++|
T Consensus       126 I~TP~rl~~~~~~~~~~l~~l~~lV  150 (207)
T d1t6na_         126 VGTPGRILALARNKSLNLKHIKHFI  150 (207)
T ss_dssp             EECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             EeCcchhhhhccCCceeccccceee
Confidence            9996     222 236667776665

>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=89.60  E-value=0.69  Score=40.49  Aligned_cols=68  Identities=18%  Similarity=0.222  Sum_probs=49.1

Q ss_pred             CcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEEecc------ccccccCcCccc
Q 012794           52 GKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLVATD------VAARGLDIPNVD  120 (456)
Q Consensus        52 ~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTd------v~~~Gidip~v~  120 (456)
                      .++||.|+|++.|.++...+..     .+.+..+.|+.....+.....    ...+|||+|+      +....+++.++.
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            4699999999999999877752     367888888877666554433    2678999996      223346677777


Q ss_pred             eEE
Q 012794          121 LII  123 (456)
Q Consensus       121 ~VI  123 (456)
                      ++|
T Consensus       175 ~lV  177 (238)
T d1wrba1         175 YIV  177 (238)
T ss_dssp             EEE
T ss_pred             eee
Confidence            666

>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=89.40  E-value=0.94  Score=38.44  Aligned_cols=85  Identities=19%  Similarity=0.212  Sum_probs=60.7

Q ss_pred             ccH-HHHHHHHHHHH---CCCCcEEEEcCChHHHHHHHHHHHh-----cCCEEEEeCCCCHHHHHHHHhcccCCCeEEEE
Q 012794           35 TSK-RTILSDLITVY---AKGGKTIVFTQTKRDADEVSLALTS-----IIASEALHGDISQHQRERTLNGFRQGKFTVLV  105 (456)
Q Consensus        35 ~~k-~~~L~~ll~~~---~~~~~~IIF~~t~~~a~~l~~~L~~-----~~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLV  105 (456)
                      .-| +..+..++...   .....+++.+++...+.+....+..     .+.+..++|+.........+..    ...|||
T Consensus        49 sGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~----~~~Ili  124 (206)
T d1s2ma1          49 TGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNE----TVHILV  124 (206)
T ss_dssp             SCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTS----CCSEEE
T ss_pred             chhhhhhccccccccccccccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcc----cceEEE
Confidence            445 33344444433   3346789999999999888776653     3678999999998877766643    688999


Q ss_pred             ecc-----cc-ccccCcCccceEE
Q 012794          106 ATD-----VA-ARGLDIPNVDLII  123 (456)
Q Consensus       106 aTd-----v~-~~Gidip~v~~VI  123 (456)
                      +|+     .+ ...+++.++.++|
T Consensus       125 ~TP~~l~~~l~~~~~~l~~l~~lV  148 (206)
T d1s2ma1         125 GTPGRVLDLASRKVADLSDCSLFI  148 (206)
T ss_dssp             ECHHHHHHHHHTTCSCCTTCCEEE
T ss_pred             ECCcccccccccceeecccceEEE
Confidence            995     23 3347888998877

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {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: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.19  E-value=0.54  Score=40.64  Aligned_cols=86  Identities=15%  Similarity=0.246  Sum_probs=52.7

Q ss_pred             ccH-HHHHHHHHHHHC---CCCcEEEEcCChHHHHHHHHHHHhc-----CCEEEEeCCCCHHHHHHHHhcccCCCeEEEE
Q 012794           35 TSK-RTILSDLITVYA---KGGKTIVFTQTKRDADEVSLALTSI-----IASEALHGDISQHQRERTLNGFRQGKFTVLV  105 (456)
Q Consensus        35 ~~k-~~~L~~ll~~~~---~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLV  105 (456)
                      +-| +..+.-++..+.   ...++||+++|++.|.++++.+...     +.+..++++.....   ..........+|||
T Consensus        60 sGKTlayllp~l~~i~~~~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~IvV  136 (218)
T d2g9na1          60 TGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRA---EVQKLQMEAPHIIV  136 (218)
T ss_dssp             SSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCS---TTTSSSSCCCSEEE
T ss_pred             hhhhhhhhhhhhheecccccCccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhH---HHHHHhcCCCEEEE
Confidence            455 444444554432   2457999999999999999887642     44555555432211   12233344678999


Q ss_pred             ecc-----cccc-ccCcCccceEE
Q 012794          106 ATD-----VAAR-GLDIPNVDLII  123 (456)
Q Consensus       106 aTd-----v~~~-Gidip~v~~VI  123 (456)
                      +|+     .+.+ .+++..+.+||
T Consensus       137 ~TP~rl~~~l~~~~~~~~~l~~lV  160 (218)
T d2g9na1         137 GTPGRVFDMLNRRYLSPKYIKMFV  160 (218)
T ss_dssp             ECHHHHHHHHHTTSSCSTTCCEEE
T ss_pred             eCChhHHHHHhcCCcccccceEEE
Confidence            996     3333 47778888877

>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=84.54  E-value=7.9  Score=31.54  Aligned_cols=69  Identities=26%  Similarity=0.342  Sum_probs=51.9

Q ss_pred             CCCcEEEEcCChHHHHHHHHHHHhc-----CCEEEEeCCCCHHHHHHHHhcccCCCeEEEEeccc------cccccCcCc
Q 012794           50 KGGKTIVFTQTKRDADEVSLALTSI-----IASEALHGDISQHQRERTLNGFRQGKFTVLVATDV------AARGLDIPN  118 (456)
Q Consensus        50 ~~~~~IIF~~t~~~a~~l~~~L~~~-----~~~~~lhg~~~~~~R~~~l~~Fr~g~~~vLVaTdv------~~~Gidip~  118 (456)
                      .+.++||.++++..+++.++.+.+.     ..+..+|++....++...+..     ..++++|..      ...-+.+.+
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            4578999999999999998888752     457888999999988887655     357888842      223355667


Q ss_pred             cceEE
Q 012794          119 VDLII  123 (456)
Q Consensus       119 v~~VI  123 (456)
                      +++||
T Consensus       126 ~~~vI  130 (200)
T d1wp9a1         126 VSLIV  130 (200)
T ss_dssp             CSEEE
T ss_pred             cceEE
Confidence            77777