Psyllid ID: psy4150

---

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-----
Protein Sequence
MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSGEPVSAMDDEVVIVQNKIKPMQRKRKNNP
Secondary Structure (PSIPRED)
ccccHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccccccccHHHHHHHHHHcHHHHHHHccccccccccHHHHHHHHHHHHHHHHHcccccccEEEEEcccccHHHHHHHHcccccccccEEEEEccccccHHHHHHHHHHHHcccccEEEEccccccccccccccEEEEccccccHHHHHHHHcccccccccEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccHHHHHHccccccHHHHHcccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHccccccccEEEEEEccHHHHHHHHHHHHHccccEEEEEEEcccccccHHHHHHHHHHHHccccEEEEEEEccccccccccEEEEEEEcccccHHHHHHHccccccccccEEEEEEEcccHHHHHHHHHHHHHHHHHHHHccccHHHHHcccccccccccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccEEEEEccccEcccccHHHHcccEHccccccccccHHHHHHHHHHHHHccccccEEccccc
Coil and Loop (DISEMBL)
mlakdkyvkskaqfphinrdlDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVskedgscpilgkdnDLQNLLQQlkpkldinimSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDvlkplepmvkasmfvgqssgvtQQEQKEIMKKFRAGEFNTLIATsvgeegldigeiDLVIcfdaqkspIKMVQRLGrtgrkrngRCVILLTQgreahnfqtsMQTCKSYVEKIINNKSIYANLakngprmipahvtprikCLHIVvkdrvtpakpskkkpkenekaNKKSKKkletdgnsepagkqnktnakktkkqpmmtqsndIRTCFENITKKKKTFIDFLtqssgepvsamdDEVVIVQNKikpmqrkrknnp
Flexible Loop (DISEMBL)
mlakdkyvkskaqfphinrdLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLhaekgettkvIIFANYRVVVAEIFDVLKPLEPMVKASMFvgqssgvtqQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVqrlgrtgrkrngRCVILLtqgreahnfqtsMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLhivvkdrvtpakpskkkpkenekankkskkkletdgnsepagkqnktnakktkkqpmmtqsndirTCFENITKKKKTFIDFLTqssgepvsamddEVVIVqnkikpmqrkrknnp
Low Complexity Region (SEG)
MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPIlgkdndlqnllqqlkpkldINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPakpskkkpkenekankkskkkLETDGNSEPagkqnktnakktkkqPMMTQSNDIRTCFENITKKKKTFIDFLTQSSGEPVSAMDDEVVIVQNKIKPMQRKRKNNP
Disordered region (IsUnstruct)
**************PHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVG************IMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDR********************************************************IRTCFENITKKKKTFIDFLT**************VI****************
Disordered Region (DISOPRED)
**********************RMIQRDFHVTHSLASALENLVTYGLRSFYNNLVE***************DLQNLLQQLKPK***********WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMF*****************KFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTC*******************************************************************************************************************************************************
Disordered Region (DISEMBL)
MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQ*********KEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDR***************************************************TQSNDIRTCFENITKKKKTFIDFLTQSSGEPVSAMDDEVVIVQNKIK**********
Disordered Region (DISPRO)
MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCP*LGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKD*******************************SEPAGKQNKTNAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSGEPVSAMDDEVVIVQNKIK**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSGEPVSAMDDEVVIVQNKIKPMQRKRKNNP
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	395	2.2.26 [Sep-21-2011]
Q8IYD8	2048	Fanconi anemia group M pr	yes	N/A	0.731	0.141	0.355	6e-47
Q8BGE5	2021	Fanconi anemia group M pr	yes	N/A	0.703	0.137	0.344	1e-44
A4RN08	1102	ATP-dependent DNA helicas	N/A	N/A	0.807	0.289	0.347	2e-43
Q2URJ5	1129	ATP-dependent DNA helicas	yes	N/A	0.711	0.248	0.346	4e-41
Q7SDF3	1168	ATP-dependent DNA helicas	N/A	N/A	0.762	0.257	0.321	2e-40
A1CS00	1119	ATP-dependent DNA helicas	N/A	N/A	0.602	0.212	0.356	8e-40
Q2HG76	1134	ATP-dependent DNA helicas	N/A	N/A	0.655	0.228	0.338	1e-39
Q9HE09	783	Putative ATP-dependent RN	yes	N/A	0.622	0.314	0.371	7e-39
Q1DY43	1110	ATP-dependent DNA helicas	N/A	N/A	0.693	0.246	0.326	8e-39
A1D4V5	1111	ATP-dependent DNA helicas	N/A	N/A	0.746	0.265	0.322	2e-38

>sp|Q8IYD8|FANCM_HUMAN Fanconi anemia group M protein OS=Homo sapiens GN=FANCM PE=1 SV=2

 Score =  188 bits (477), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 116/326 (35%), Positives = 188/326 (57%), Gaps = 37/326 (11%)

Query: 1   MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKE 60
           +LA+D++ K+ +  P+I      +I+ +F +  SL    E L   G+RS Y  L  +   
Sbjct: 335 ILARDQFRKNPS--PNIVGIQQGIIEGEFAICISLYHGYELLQQMGMRSLYFFLCGIM-- 390

Query: 61  DGSCPI------LGKDNDLQNLLQQLKPKL------DINIMSS--------EYAWSHLKF 100
           DG+  +      LG++ D   L   L+           N +S+        ++ +SH K 
Sbjct: 391 DGTKGMTRSKNELGRNEDFMKLYNHLECMFARTRSTSANGISAIQQGDKNKKFVYSHPKL 450

Query: 101 IRLREILESHFR-LHAE-----KGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVG 154
            +L E++  HF+  +AE     K + T+V+IF+++R  V EI ++L   +P+++   FVG
Sbjct: 451 KKLEEVVIEHFKSWNAENTTEKKRDETRVMIFSSFRDSVQEIAEMLSQHQPIIRVMTFVG 510

Query: 155 QSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKM 209
            +SG      TQ+EQ E++K+FR G +NTL++T VGEEGLDIGE+DL+ICFD+QKSPI++
Sbjct: 511 HASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDSQKSPIRL 570

Query: 210 VQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMI 269
           VQR+GRTGRKR GR VI+L++GRE   +  S    +S  + I +N+ +  +  +  PRM+
Sbjct: 571 VQRMGRTGRKRQGRIVIILSEGREERIYNQSQSNKRSIYKAISSNRQVL-HFYQRSPRMV 629

Query: 270 PAHVTPRIKCLHIVVKDRVTPAKPSK 295
           P  + P++  +  +      P KPS+
Sbjct: 630 PDGINPKLHKM-FITHGVYEPEKPSR 654

ATPase required for FANCD2 ubiquitination, a key reaction in DNA repair. Binds to ssDNA but not to dsDNA. Recruited to forks stalled by DNA interstrand cross-links, and required for cellular resistance to such lesions.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q8BGE5|FANCM_MOUSE Fanconi anemia group M protein homolog OS=Mus musculus GN=Fancm PE=1 SV=3

 Score =  181 bits (458), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 107/311 (34%), Positives = 173/311 (55%), Gaps = 33/311 (10%)

Query: 1   MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKE 60
           +LA+D++ K+ +  P+I      +I+ +F +  SL    E L   G+RS Y  L  +   
Sbjct: 323 ILARDQFRKNPS--PNIVGIQQGIIEGEFALCISLYHGYELLQQMGMRSLYFFLSGIM-- 378

Query: 61  DGSCPI------LGKDNDLQNLLQQLKPKLDINIMSS-----------EYAWSHLKFIRL 103
           DG+  +      L ++ D   L   L+        S            ++ +SH K  +L
Sbjct: 379 DGTKGMTRARNELSRNEDFMKLYTHLQSAFAPASTSDASAFQRGNKEKKFVYSHPKLKKL 438

Query: 104 REILESHFRLHAEKGET------TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSS 157
            E++  HF+    K  T      ++V+IF+++R  V EI ++L    P+++   FVG +S
Sbjct: 439 EEVILEHFKSWNAKATTEKKCHESRVMIFSSFRDSVEEIAEMLLQHRPVIRVMTFVGHAS 498

Query: 158 G-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQR 212
           G      TQ+EQ +++++FR G +NTL++T VGEEGLDIGE+DL+ICFDAQKSPI+++QR
Sbjct: 499 GKNTKGFTQKEQLQVVRQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDAQKSPIRLIQR 558

Query: 213 LGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAH 272
           +GRTGRKR GR V++L +GRE   +  S    K+  + I  N+ +   L +  PRM+P  
Sbjct: 559 MGRTGRKRQGRIVVILAEGREERTYNQSQSNKKNIYKAISGNRQVL-RLYQGSPRMVPDK 617

Query: 273 VTPRIKCLHIV 283
           + P +  ++I 
Sbjct: 618 INPELHKMYIT 628

ATPase required for FANCD2 ubiquitination, a key reaction in DNA repair. Binds to ssDNA but not to dsDNA. Recruited to forks stalled by DNA interstrand cross-links, and required for cellular resistance to such lesions.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A4RN08|MPH1_MAGO7 ATP-dependent DNA helicase MPH1 OS=Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) GN=MPH1 PE=3 SV=1

 Score =  177 bits (448), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 124/357 (34%), Positives = 193/357 (54%), Gaps = 38/357 (10%)

Query: 3   AKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKED- 61
           A+  ++K   +F   N+ L  M+   F +  SLA A++ L  +G+R FY+NLV    E  
Sbjct: 386 ARQDWMKGPGRF--ANQGLKMMLMAIFTILQSLAHAIKLLNYHGIRPFYDNLVAFRSETE 443

Query: 62  -----GS---CPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRL 113
                GS     ++G+ +  Q ++      L I+  +      H K   L + L ++F +
Sbjct: 444 DKGQKGSKYKRQLIGEQS-FQEMMDLASKWLKIDGFAG-----HPKLTHLCDNLLNYF-M 496

Query: 114 HAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQ-----SSGVTQQEQKEIM 168
            A +G +T+VI+F+ YR    EI  VL   +PM+ AS+FVGQ     S G+ Q++Q E +
Sbjct: 497 DAGEGSSTRVIVFSEYRDSAEEITRVLNVHKPMISASLFVGQADSKKSEGMKQKQQIETI 556

Query: 169 KKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILL 228
            KFR G FN L+ATS+GEEGLDIG++DL+IC+DA  SPI+M+QR+GRTGRKR G+  +LL
Sbjct: 557 AKFRDGIFNVLVATSIGEEGLDIGQVDLIICYDASSSPIRMLQRMGRTGRKRAGKITLLL 616

Query: 229 TQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRI--KCLHIVVKD 286
            +G+E  N+  + Q     ++K+I   S +        R++P  V P +  + + I +++
Sbjct: 617 MKGKEEDNYAKA-QDNYEKMQKLICEGSRFNFRHDLSSRIVPRDVKPEVDKRMVEIPIEN 675

Query: 287 RVTPAKPSKKKPKENEKANKKSKKK-------LETDGNSEPAGKQNKTNAKKTKKQP 336
               + P   +PK      KK+ KK       +ET  NS         +A KTK +P
Sbjct: 676 TQDTSLP---EPKARSTRGKKASKKKFNMPDGVETGFNS--VASMLGISASKTKAKP 727

ATP-dependent DNA helicase involved in error-free DNA damage bypass through homologous recombination.

Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (taxid: 242507)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q2URJ5|MPH1_ASPOR ATP-dependent DNA helicase mph1 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=mph1 PE=3 SV=2

 Score =  169 bits (428), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 108/312 (34%), Positives = 175/312 (56%), Gaps = 31/312 (9%)

Query: 29  FHVTHSLASALENLVTYGLRSFYNNLV------EVSKEDGSCPILGKDNDLQNLLQQLKP 82
           F V  SLA A++ L  +G+  FY +L+      E  K       + +D   + L+  L+P
Sbjct: 595 FTVLASLAHAIDLLKYHGITPFYRHLLHFQSNTEGQKGGKYQRQVVQDESFKKLINHLQP 654

Query: 83  KLDINIMSSEYAWSHLKFIRLREILESHFRLHAE--KGE------TTKVIIFANYRVVVA 134
                  + E+   H K   L+ ++ +HF    E   GE      +T+++IF ++R    
Sbjct: 655 W----TKNPEFI-GHPKLEYLKSVVLNHFMDAGEGSNGEASDSQSSTRIMIFVHFRDSAE 709

Query: 135 EIFDVLKPLEPMVKASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGL 189
           E+  VLK  EPM++  +FVGQSS     G+ Q+ Q +I++KF+ G +NT++ATS+GEEGL
Sbjct: 710 EVTRVLKRYEPMIRPHVFVGQSSAKGSEGMGQKTQLDIVQKFKKGTYNTIVATSIGEEGL 769

Query: 190 DIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSY-- 247
           DIGE+DL++C+D+  SPI+M+QR+GRTGRKR G  V+LL +G+E  ++   ++   +Y  
Sbjct: 770 DIGEVDLIVCYDSSASPIRMLQRMGRTGRKRAGNIVLLLMEGKEEESY---IKAKDNYEK 826

Query: 248 VEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKK 307
           ++++I + S +       PR++PA + P     HI + D    A+ S  +PK   +A K+
Sbjct: 827 MQQMIASGSRFTFHDDISPRILPAGIRPVADKRHIDIPDEN--AEQSLPEPKRRGRAPKR 884

Query: 308 SKKKLETDGNSE 319
             KK     N E
Sbjct: 885 PPKKFHMPDNVE 896

ATP-dependent DNA helicase involved in error-free DNA damage bypass through homologous recombination.

Aspergillus oryzae (strain ATCC 42149 / RIB 40) (taxid: 510516)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q7SDF3|MPH1_NEUCR ATP-dependent DNA helicase mph-1 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=mph-1 PE=3 SV=1

 Score =  166 bits (421), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 105/327 (32%), Positives = 179/327 (54%), Gaps = 26/327 (7%)

Query: 1   MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEV--- 57
           M A++ ++    +  H+N+     +   F +  SLA +++ L  +G++ FYNNL E    
Sbjct: 399 MKARNDWMAGPGR--HVNQGTKFSVIATFAILQSLAHSIKLLNFHGIKPFYNNLAEFRTT 456

Query: 58  -SKEDGSCPILGK----DNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFR 112
             ++ G    L +    D + Q ++  ++  + I+         H K   L E L +HF 
Sbjct: 457 EEEKGGKGSKLKRQVLEDENFQKMMDMIEGWMKIDGF-----LGHPKLEYLCETLVNHF- 510

Query: 113 LHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQ-----SSGVTQQEQKEI 167
           + A +G  T+ I+F+ YR    EI  +L   +P++KA++FVGQ     S G+ Q++Q E 
Sbjct: 511 MDAGEGSNTRAIVFSEYRDSAEEIVRILNK-QPLIKATVFVGQADSKRSEGMKQKQQIET 569

Query: 168 MKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVIL 227
           ++KF+ G  N L+ATS+GEEGLDIG++DL++C+DA  SPI+M+QR+GRTGRKR G  V+L
Sbjct: 570 IEKFKNGAHNVLVATSIGEEGLDIGQVDLIVCYDASASPIRMLQRMGRTGRKRAGNIVLL 629

Query: 228 LTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRI--KCLHIVVK 285
           L +G+E   F  +     + ++++I   S +        R++P  + P +  K + I ++
Sbjct: 630 LMKGKEEDKFNEAKDNYAT-MQRMICEGSRFTFRHDLSSRIVPRDIRPEVEKKVVEIPLE 688

Query: 286 DRVTPAKPSKKKPKENEKANKKSKKKL 312
           +   P  P  K+     +  K +KKK 
Sbjct: 689 NSQNPELPEPKRSAARMR-TKPAKKKF 714

ATP-dependent DNA helicase involved in error-free DNA damage bypass through homologous recombination.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|A1CS00|MPH1_ASPCL ATP-dependent DNA helicase mph1 OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=mph1 PE=3 SV=1

 Score =  164 bits (416), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 96/269 (35%), Positives = 160/269 (59%), Gaps = 31/269 (11%)

Query: 29  FHVTHSLASALENLVTYGLRSFYNNLVEV-SKEDGSCP-----ILGKDNDLQNLLQQLKP 82
           F V  SLA A++ L  +G+  FY +LV   S  DG         + +D   + L+  L+P
Sbjct: 577 FTVLASLAHAIDLLKYHGITPFYRHLVHFRSNTDGQKGGKYQRQIVQDESFKKLMNHLQP 636

Query: 83  KLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGE---------TTKVIIFANYRVVV 133
                  + E+   H K   L++++ +HF + A +G           T++++FA++R   
Sbjct: 637 W----TKNPEFI-GHPKLEYLKQVVLNHF-MDAGEGSGADGNHTRSATRIMVFAHFRDSA 690

Query: 134 AEIFDVLKPLEPMVKASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNTLIATSVGEEG 188
            EI  VLK  EP+++  +FVGQSS     G+ Q+ Q  I++KF+ G++NT++ATS+GEEG
Sbjct: 691 EEIVRVLKRYEPLIRPHVFVGQSSAKGSEGMDQKTQLSIVQKFKKGDYNTIVATSIGEEG 750

Query: 189 LDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSY- 247
           LDIGE+DL++C+D+  SPI+M+QR+GRTGRKR G  V+LL QG+E  ++   ++   +Y 
Sbjct: 751 LDIGEVDLIVCYDSSASPIRMLQRMGRTGRKRAGNIVLLLMQGKEEESY---IRAKDNYE 807

Query: 248 -VEKIINNKSIYANLAKNGPRMIPAHVTP 275
            ++++I + + +A      PR++P  + P
Sbjct: 808 KMQEMIASGTRFAFHDDTSPRILPPGIRP 836

ATP-dependent DNA helicase involved in error-free DNA damage bypass through homologous recombination.

Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) (taxid: 344612)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q2HG76|MPH1_CHAGB ATP-dependent DNA helicase MPH1 OS=Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) GN=MPH1 PE=3 SV=1

 Score =  164 bits (415), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 96/284 (33%), Positives = 156/284 (54%), Gaps = 25/284 (8%)

Query: 16  HINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGK------ 69
           H N+ +  M+   F +  SLA  ++ L  +G++ FYN L E    +   P  G       
Sbjct: 444 HANQGVKFMMMAVFSILQSLAHLIKLLNFHGIKPFYNGLAEFRSSEEGKPGQGSKLKRQL 503

Query: 70  --DNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFA 127
             D   Q ++  ++       M  E    H K   L E L +HF + A +   T+ I+F+
Sbjct: 504 LADESFQRMMALIE-----RWMRMEEFNGHPKLTYLCETLVNHF-IDAGENSNTRAIVFS 557

Query: 128 NYRVVVAEIFDVLKPLEPMVKASMFVGQ-----SSGVTQQEQKEIMKKFRAGEFNTLIAT 182
            YR    EI  +L   +P+++A++FVGQ     S G+ Q++Q E ++KF+ G FN L+AT
Sbjct: 558 EYRDSAEEIVRLLN-NQPLIRATVFVGQADSKRSEGMKQKQQIETIEKFKNGGFNVLVAT 616

Query: 183 SVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQ 242
           S+GEEGLDIG++DL++C+DA  SPI+M+QR+GRTGRKR G  V+LL +G+E   F   ++
Sbjct: 617 SIGEEGLDIGQVDLIVCYDASASPIRMLQRMGRTGRKRAGNIVLLLMKGKEEEKF---LE 673

Query: 243 TCKSY--VEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVV 284
              +Y  ++++I N   +        R++P  + P +   H+ +
Sbjct: 674 AKDNYQKMQQLICNGDGFTFRHDLSTRIVPRDIRPEVDKRHVDI 717

ATP-dependent DNA helicase involved in error-free DNA damage bypass through homologous recombination.

Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) (taxid: 306901)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9HE09|MFH2_SCHPO Putative ATP-dependent RNA helicase mfh2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mfh2 PE=3 SV=1

 Score =  161 bits (408), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 98/264 (37%), Positives = 146/264 (55%), Gaps = 18/264 (6%)

Query: 25  IQRDFHVTHSLASALENLVTYGLRSFYNNLVEV-----SKEDGSCPILGKDNDLQNLLQQ 79
           I   F +  S A     L  +G+  FY  LVE       K  G    L         L+ 
Sbjct: 377 IMSCFTLLISCAHITYLLDCHGIIQFYQKLVETKNKAEGKGSGQSFWLFTSKPFAFYLEH 436

Query: 80  LKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDV 139
           L  K+         + +H K   L E+L+ HF+  +E  +  +V+IF  +R     I   
Sbjct: 437 LHNKIQ------GLSLNHPKMNHLLELLKEHFKDTSEGYQNQRVMIFTEFRNTAEYITTT 490

Query: 140 LKPLEPMVKASMFVGQ-----SSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEI 194
           L  + PMV+AS+F+GQ     S+G+ Q +QKE + +FRAG  NTL+ATS+GEEGLDIG+ 
Sbjct: 491 LLAIRPMVRASLFIGQANSAYSTGMNQMQQKETIDQFRAGVINTLVATSIGEEGLDIGDT 550

Query: 195 DLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINN 254
           D++IC+DA  SPI+ +QR+GRTGRK++G+  +LLT+  E   ++ S Q     V+K+I +
Sbjct: 551 DMIICYDASSSPIRTIQRMGRTGRKKSGKVFVLLTEDCEDSKWERS-QVSYRRVQKVIES 609

Query: 255 KSIYANLAKNGPRMIPAHVTPRIK 278
               A L K+ PR+IP+++ P  K
Sbjct: 610 GKKIA-LKKDVPRLIPSNIQPIFK 632

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q1DY43|MPH1_COCIM ATP-dependent DNA helicase MPH1 OS=Coccidioides immitis (strain RS) GN=MPH1 PE=3 SV=1

 Score =  161 bits (407), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 100/306 (32%), Positives = 171/306 (55%), Gaps = 32/306 (10%)

Query: 29  FHVTHSLASALENLVTYGLRSFYNNLVEVS------KEDGSCPI-LGKDNDLQNLLQQLK 81
           F V  SLA A++ L  +G+  FY NLV         K+ G C   +  D + + L+ +L+
Sbjct: 595 FTVLASLAHAIDLLKYHGIGPFYRNLVSFEDSVLKEKKGGKCASQIVADGNFKVLMSKLR 654

Query: 82  PKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEK--GET------TKVIIFANYRVVV 133
                +  ++E    H K   LR  + +HF     K  G++      T+V+IF+++R   
Sbjct: 655 -----SWTNTEEFIGHPKLEYLRRAILNHFLDAGGKNGGDSEGSDSNTRVMIFSHFRDSA 709

Query: 134 AEIFDVLKPLEPMVKASMFVGQ-----SSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEG 188
            EI  VL+  +P V+  +FVGQ     S G+ Q+ Q E++ KF+ G +NT++ATS+GEEG
Sbjct: 710 EEIVRVLRKHQPFVRPHVFVGQANAKGSEGMDQKTQLEVVGKFKTGTYNTIVATSIGEEG 769

Query: 189 LDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYV 248
           LDIGE+DL+IC+D   SPI+M+QR+GRTGRKR G  ++LL++G+E  ++  +  + +  +
Sbjct: 770 LDIGEVDLIICYDGHSSPIRMLQRMGRTGRKRAGNIILLLSKGKEEESYSKAKDSYEK-M 828

Query: 249 EKIINNKSIYANLAKNGPRMIPAHVTPRI--KCLHIVVKDRVTPAKPSKKKPKENEKANK 306
           +++I + S +        R++P  + P    K + I +++    ++    +P +  +A K
Sbjct: 829 QQLIASGSRFTFHTDKSSRIVPQDIQPEAEEKMIEIPIEN----SQLGLPEPAKRSRAPK 884

Query: 307 KSKKKL 312
           +  KK 
Sbjct: 885 RPPKKF 890

ATP-dependent DNA helicase involved in error-free DNA damage bypass through homologous recombination.

Coccidioides immitis (strain RS) (taxid: 246410)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|A1D4V5|MPH1_NEOFI ATP-dependent DNA helicase MPH1 OS=Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) GN=mph1 PE=3 SV=1

 Score =  160 bits (405), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 106/329 (32%), Positives = 177/329 (53%), Gaps = 34/329 (10%)

Query: 29  FHVTHSLASALENLVTYGLRSFYNNLVEV-SKEDGSCP-----ILGKDNDLQNLLQQLKP 82
           F V  SLA A++ L  +G+  FY +L+   S  DG         + +D   + L+  L+P
Sbjct: 570 FTVLASLAHAIDLLKYHGITPFYRHLLHFQSNTDGQKGGKYQRQIVQDESFKKLMNHLQP 629

Query: 83  KLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGE-----------TTKVIIFANYRV 131
                  + E+   H K   L++++ +HF    ++GE            T+++IF ++R 
Sbjct: 630 W----TKNPEFI-GHPKLEYLKQVVLNHF---MDRGEGTAANGDQSQSATRIMIFVHFRD 681

Query: 132 VVAEIFDVLKPLEPMVKASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNTLIATSVGE 186
              E+  VLK  EP+++  +FVGQSS     G+ Q+ Q  I++KF+ G +NT++ATS+GE
Sbjct: 682 SAEEVVRVLKRYEPLIRPHVFVGQSSAKGSEGMDQKTQLSIVQKFKKGTYNTIVATSIGE 741

Query: 187 EGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKS 246
           EGLDIGE+DL++C+D+  SPI+M+QR+GRTGRKR G  V+LL QG+E  ++  +    + 
Sbjct: 742 EGLDIGEVDLIVCYDSSASPIRMLQRMGRTGRKRAGNIVLLLMQGKEEESYIKAKDNYEK 801

Query: 247 YVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANK 306
            ++++I + + +       PR++P  V P  +   I +    T A     +P++  +  K
Sbjct: 802 -MQQMIASGTRFTFHDDTSPRILPPGVRPVAEKRQIDIPVENTQA--DLPEPRKRARPPK 858

Query: 307 KSKKKLETDGNSEPA-GKQNKTNAKKTKK 334
           +  KK     + E    K +    K TKK
Sbjct: 859 RPPKKFHMPDDVETGFAKASSLTGKVTKK 887

ATP-dependent DNA helicase involved in error-free DNA damage bypass through homologous recombination.

Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) (taxid: 331117)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	395
328698487	2033	PREDICTED: hypothetical protein LOC10016	0.630	0.122	0.471	5e-61
405953921	2327	Fanconi anemia group M protein [Crassost	0.670	0.113	0.413	3e-50
321472411	657	hypothetical protein DAPPUDRAFT_48010 [D	0.675	0.406	0.395	1e-49
432938949	1928	PREDICTED: Fanconi anemia group M protei	0.703	0.144	0.372	6e-49
410898563	1899	PREDICTED: Fanconi anemia group M protei	0.703	0.146	0.372	8e-48
307207083	1344	Fanconi anemia group M protein [Harpegna	0.843	0.247	0.332	1e-47
345306292	2081	PREDICTED: LOW QUALITY PROTEIN: Fanconi	0.772	0.146	0.351	1e-47
395504025	1871	PREDICTED: Fanconi anemia group M protei	0.701	0.148	0.375	3e-47
307176233	1323	Fanconi anemia group M protein [Camponot	0.643	0.191	0.361	4e-47
47230040	1724	unnamed protein product [Tetraodon nigro	0.708	0.162	0.370	6e-47

>gi|328698487|ref|XP_001948012.2| PREDICTED: hypothetical protein LOC100166297 [Acyrthosiphon pisum]

 Score =  241 bits (615), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 124/263 (47%), Positives = 177/263 (67%), Gaps = 14/263 (5%)

Query: 28  DFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDIN 87
           DF +  SLA ALE L  YG++ FY   +E+ KE   C  L  D D QNLL  +  +L+  
Sbjct: 444 DFTICMSLAYALELLTIYGVKVFYLQSLEM-KETHKC--LSNDADFQNLLHGINKELN-- 498

Query: 88  IMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMV 147
             S +  WSH K   L++I++++F     +  ++K+IIF  YR+VV E+F++LK     V
Sbjct: 499 --SQDLTWSHPKLFELKKIVQNYFGFKNVEA-SSKIIIFCQYRLVVVEVFELLKTFGSSV 555

Query: 148 KASMFVGQS----SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQ 203
           K  MFVGQS     G+ Q+EQ E+M +F++G+FN LIATSV EEGLDIG++DL+IC +A 
Sbjct: 556 KPVMFVGQSLKEKGGLRQKEQLEVMSRFKSGDFNVLIATSVAEEGLDIGDVDLIICLEAN 615

Query: 204 KSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAK 263
           KSPIK VQRLGRTGRKR+G+C+ LLT+G+E   + +S+ + K+ V K++ NK+I + LA 
Sbjct: 616 KSPIKFVQRLGRTGRKRSGKCITLLTEGKEQIKYNSSVSSSKTLVIKMLKNKAILSKLAP 675

Query: 264 NGPRMIPAHVTPRIKCLHIVVKD 286
            GPR++P H+ P  +CL I VK+
Sbjct: 676 EGPRLVPKHIHP--QCLMIHVKE 696

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405953921|gb|EKC21486.1| Fanconi anemia group M protein [Crassostrea gigas]

 Score =  205 bits (522), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 120/290 (41%), Positives = 166/290 (57%), Gaps = 25/290 (8%)

Query: 24  MIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGS----------CPILGKDNDL 73
           M++ DF +  SL    E +  +GLRS YN L    K D             P  G   DL
Sbjct: 382 MVEGDFALAISLYHGYELVQLHGLRSLYNFLDGAMKGDKGHGRTKTELMKIPDFG---DL 438

Query: 74  QNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKG-----ETTKVIIFAN 128
            N+L +   K++    +      H K  +L E++  HF+     G     +TT+++IF+ 
Sbjct: 439 MNMLHEKFGKMNGQENAQAINLGHPKLAKLEEVVLDHFKSVEGSGTEQNEQTTRIMIFSQ 498

Query: 129 YRVVVAEIFDVLKPLEPMVKASMFVGQSS------GVTQQEQKEIMKKFRAGEFNTLIAT 182
           YR  V EI ++L+  EP VKA  F+GQSS      G TQ+EQ ++MKKFR G +NTL+AT
Sbjct: 499 YRDSVEEITNMLRRHEPKVKAMSFIGQSSAGKATKGFTQKEQLKVMKKFREGRYNTLVAT 558

Query: 183 SVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQ 242
            VGEEGLDIGE+DL+IC+DA KSPI++VQR+GRTGRKR GR V+L+TQG+E   +   + 
Sbjct: 559 CVGEEGLDIGEVDLIICYDASKSPIRLVQRMGRTGRKRQGRIVMLVTQGKEEQIYNQGIY 618

Query: 243 TCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAK 292
           + KS + K I N +      ++ PRMIP  V P+   + I VK    P K
Sbjct: 619 SKKS-IHKAILNSAKTLQFYQSNPRMIPEGVEPKSHKMFITVKQAYKPNK 667

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|321472411|gb|EFX83381.1| hypothetical protein DAPPUDRAFT_48010 [Daphnia pulex]

 Score =  203 bits (517), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 115/291 (39%), Positives = 172/291 (59%), Gaps = 24/291 (8%)

Query: 4   KDKYVKSKAQ-FPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLV-EVSKED 61
           +DK+ ++    FP   R    +++ DF +  +L  ALE L+ +G+R FYN L  +    D
Sbjct: 356 RDKFRQNPPDNFP---RSRSGIMEGDFALCITLTHALELLLQHGIRGFYNFLAGKTDAAD 412

Query: 62  GSC------PILGKDNDLQNLLQQLKPKL--DINIMSSEYAWSHLKFIRLREILESHFRL 113
           G          LGK      ++  LK K   D  I S   A SH K  RL+EI+  HF+ 
Sbjct: 413 GETGHNRTRTELGKVTGFIEMMSDLKSKFGNDCQIGS---AVSHPKLTRLKEIVLEHFQK 469

Query: 114 HAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSS--------GVTQQEQK 165
             ++G  T+V+IF+ YR  V EI  +L+   P++KA  FVG  +        G TQ +Q 
Sbjct: 470 AEKEGRPTRVMIFSQYRDSVNEIVALLEEYAPLIKAMSFVGHGNSSGGVKTKGFTQADQI 529

Query: 166 EIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCV 225
            I+K+F  G++NTL+AT VGEEGLDIG++D++IC+D  KSP+++VQR GRTGR+R+GR V
Sbjct: 530 RIIKQFSEGDYNTLVATCVGEEGLDIGDVDMIICYDVHKSPVRLVQRCGRTGRQRDGRIV 589

Query: 226 ILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPR 276
           +L+T+G+E H +   M   K+ ++ I+ N  +   L K  PR+IP H++PR
Sbjct: 590 MLMTEGKEEHTYNQCMSQKKNLLKNIVGNPKLKEFLLKQEPRLIPRHLSPR 640

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|432938949|ref|XP_004082559.1| PREDICTED: Fanconi anemia group M protein homolog [Oryzias latipes]

 Score =  201 bits (510), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 112/301 (37%), Positives = 177/301 (58%), Gaps = 23/301 (7%)

Query: 1   MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKE 60
           +LA+D++ K+    PHI      M++ DF +  SL    E L+  GLRS +  +  +   
Sbjct: 345 ILARDQFRKNPP--PHIKSPQQGMLEGDFALCISLYHGYELLMQMGLRSLFFYVQGIM-- 400

Query: 61  DGSCPILGKDNDLQNLLQQLKPKLDINIM--------SSEYAWSHLKFIRLREILESHFR 112
           DGS  +    N+LQ     +    ++  M         + + +SH K  +L E++  HFR
Sbjct: 401 DGSREMSRTKNELQRTPTFMDLYHEMEAMFVKPSAGPDAPFVYSHPKLKKLEEVVLQHFR 460

Query: 113 LHAEKGE----TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSS------GVTQQ 162
           + AE       +T+V+IF+++R  V EI  +L    P+++   F+GQ+S      G TQ+
Sbjct: 461 VWAESNSDNHVSTRVMIFSSFRESVQEIAAMLNRHSPLIRVMTFMGQASAGKGVKGFTQK 520

Query: 163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNG 222
           EQ E++++FR G FNTL++T VGEEGLDIGE+DL++CFDAQK+PI++VQR+GRTGRKR G
Sbjct: 521 EQLEVVQRFRQGGFNTLVSTCVGEEGLDIGEVDLIVCFDAQKNPIRLVQRMGRTGRKRQG 580

Query: 223 RCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHI 282
           R V++L +GRE   +  S    +S  + I  NK+ + ++  N PRM+P  + P +  ++I
Sbjct: 581 RIVVVLAEGREERTYNQSQSNKRSVYKSITGNKNGF-HMYHNSPRMLPEGLNPSLHKMYI 639

Query: 283 V 283
            
Sbjct: 640 T 640

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|410898563|ref|XP_003962767.1| PREDICTED: Fanconi anemia group M protein homolog [Takifugu rubripes]

 Score =  197 bits (501), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 111/298 (37%), Positives = 177/298 (59%), Gaps = 20/298 (6%)

Query: 1   MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKE 60
           +LA+D++ K+    PHI      +++ DF +  SL    E L+  GLRS +     +   
Sbjct: 354 ILARDQFRKNP--LPHIKGPQQGVLEGDFALCISLYHGYELLMQMGLRSLFLYFQGIM-- 409

Query: 61  DGSCPILGKDNDLQ------NLLQQLKPKLDINIMSSE--YAWSHLKFIRLREILESHFR 112
           DGS  +    N+LQ      +L Q+++         S+  + +SH K  +L +++  HFR
Sbjct: 410 DGSREMSRARNELQRTPVFMDLYQEMEAMFVKQSAESDEPFIYSHPKLQKLEDVVLQHFR 469

Query: 113 LHAEKGE-TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSS------GVTQQEQK 165
           L A   E +T+V+IF+++R  V EI  +L    P+++   F+GQ+S      G TQ+EQ 
Sbjct: 470 LRAGSSEVSTRVMIFSSFRESVQEIAAMLNRHAPLIRVMTFMGQASAGKGVKGFTQKEQL 529

Query: 166 EIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCV 225
           E++ +FR G FNTL++T VGEEGLDIGE+DL++CFDAQK+P ++VQR+GRTGRKR GR V
Sbjct: 530 EVVHRFRQGGFNTLVSTCVGEEGLDIGEVDLIVCFDAQKNPTRLVQRMGRTGRKRQGRIV 589

Query: 226 ILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIV 283
           ++L++GRE   +  S    ++  + I  NK  + ++  + PRM+P  + P +  +HI 
Sbjct: 590 VILSEGREERTYNQSQSNKRNVYKSITGNKCRF-HMYPSSPRMLPQGLIPTLHKMHIT 646

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|307207083|gb|EFN84892.1| Fanconi anemia group M protein [Harpegnathos saltator]

 Score =  197 bits (500), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 121/364 (33%), Positives = 200/364 (54%), Gaps = 31/364 (8%)

Query: 25  IQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLK--- 81
           I +  ++  ++  A + ++ +GLR+F     +  +       +  +N L+ LL  ++   
Sbjct: 297 IMKTLNILLTMYHAYDLMIRHGLRAF----CKFYQNHSDKFWMNNENQLRQLLYDIETYL 352

Query: 82  -------PKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVA 134
                  P   ++ M +   + H KF +L+E+LE HFR +  +   T+ I+F  YR +V 
Sbjct: 353 GPFPDILPNGHVSEMPTNIMFGHNKFYKLKELLERHFRKNNGENADTRAIVFVEYRDIVN 412

Query: 135 EIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEI 194
           E++ +L   +P+++  MFVGQ+S   Q++Q + ++ FR    N LI+TS+GEEGLD+GE+
Sbjct: 413 EVYILLLQSKPLIRPQMFVGQASQ-KQKQQIKALEDFRNNHVNVLISTSIGEEGLDVGEV 471

Query: 195 DLVICFD-AQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIIN 253
           DL+ICFD +Q SP ++VQR+GRTGRKR+G  +IL+T G+E  N ++++    S   KI+N
Sbjct: 472 DLIICFDVSQHSPTRLVQRMGRTGRKRDGHIIILVTDGKEYENLKSTLSKRNSINNKILN 531

Query: 254 NKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKKSK-KKL 312
             +I+++L ++ PRMIP   TP    +HI    + TP   SK+K K   K N+ S  K+ 
Sbjct: 532 TSNIFSSLYQSNPRMIPNQFTPECHMMHITPVQK-TPNVSSKRKKKRVNKENEASSIKQK 590

Query: 313 ETDGNSEPAGKQNK--TNAKKTKKQ-------PMMTQSNDIRTCFE----NITKKKKTFI 359
           ET  N+       K  TN K  +KQ        + TQS ++    +     +       I
Sbjct: 591 ETTSNNAGESLMMKFLTNNKYEQKQNGACNIYTLTTQSGNVHNTIDPNHVKLLSDDNAGI 650

Query: 360 DFLT 363
           DF+T
Sbjct: 651 DFMT 654

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345306292|ref|XP_003428451.1| PREDICTED: LOW QUALITY PROTEIN: Fanconi anemia group M protein-like, partial [Ornithorhynchus anatinus]

 Score =  196 bits (499), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 121/344 (35%), Positives = 199/344 (57%), Gaps = 39/344 (11%)

Query: 1   MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKE 60
           +LA+D++ K+ +  P++      +++    +  SL    E L   GLRSFY  L  +   
Sbjct: 270 VLARDQFRKNPS--PNVVGIQQGVVEGQLALCISLYHGFELLQQMGLRSFYMFLRGIM-- 325

Query: 61  DGSCPI------LGKDND---LQNLLQQLKPKL------DINIMSSEYA-------WSHL 98
           DG+  +      LG++ D   L  LL+ + P        ++ I ++          +SH 
Sbjct: 326 DGTKGLARSRNELGRNGDFMKLYKLLEGMFPDSRTPTGSNVGIGATRIGHEDQKIFYSHP 385

Query: 99  KFIRLREILESHFRLH-----AEKG-ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMF 152
           K  +L E++  HFR       +E G ++T+V+IF+++R  V EI D+L    P+++A  F
Sbjct: 386 KLKKLEEVVVEHFRTWKDHRVSENGCDSTRVMIFSSFRDSVQEIADMLHQHHPVIRAMSF 445

Query: 153 VGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPI 207
           VG +SG      TQ+EQ E++++FR G +NTL++T VGEEGLDIGE+DL++CFDAQKSPI
Sbjct: 446 VGHASGKNVKGFTQKEQLEVVRQFRDGGYNTLVSTCVGEEGLDIGEVDLIVCFDAQKSPI 505

Query: 208 KMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPR 267
           ++VQR+GRTGRKR GR V++L++GRE   +  S    KS  + I  N   + +  ++ PR
Sbjct: 506 RLVQRMGRTGRKRQGRIVVILSEGREERMYNQSQSNRKSIYKAIAGNSKAF-HFYQDSPR 564

Query: 268 MIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKKSKKK 311
           M+P  + P++  +  +  +   PAKPSK  P+++  ++   K++
Sbjct: 565 MVPEGINPKLHKM-FITPETPEPAKPSKTLPRKSSLSSSGGKQR 607

Source: Ornithorhynchus anatinus

Species: Ornithorhynchus anatinus

Genus: Ornithorhynchus

Family: Ornithorhynchidae

Order: Monotremata

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395504025|ref|XP_003756361.1| PREDICTED: Fanconi anemia group M protein, partial [Sarcophilus harrisii]

 Score =  195 bits (496), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 118/314 (37%), Positives = 177/314 (56%), Gaps = 37/314 (11%)

Query: 1   MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKE 60
           +LA+D + K+ +  PH       +I+ DF +  SL    E L   G+RS Y  L  +   
Sbjct: 349 ILARDLFRKNSS--PHTLGGQQGIIEGDFAICISLYHGYELLQQMGMRSLYIFLCGIM-- 404

Query: 61  DGSCPI------LGKDNDLQNLLQQLKPKLDINIMSSE---------------YAWSHLK 99
           DG+  +      L ++     L +QL         +SE               + +SH K
Sbjct: 405 DGTKGMTRTKNELSRNEQFMELFEQLGNMFSDRNTTSEIVDGNPIQRGHNDKKFIYSHPK 464

Query: 100 FIRLREILESHFRLHAEKGET-----TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVG 154
             +L E++  HFR   ++  T     T+V+IF+++R  V EI ++L   +P V+   FVG
Sbjct: 465 LKKLEEVVVEHFRTWKDQNSTEKKCDTRVMIFSSFRDSVQEIAEMLHH-QPTVRVMTFVG 523

Query: 155 QSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKM 209
            +SG     +TQ+EQ E++K+FR G +NTL++T VGEEGLDIGE+DL+ICFDAQKSP+++
Sbjct: 524 HASGKSTKGLTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDAQKSPVRL 583

Query: 210 VQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMI 269
           VQR+GRTGRKR GR V++LT+GRE   +  S Q+CK  + K I+  S   N  +  PRMI
Sbjct: 584 VQRMGRTGRKRQGRIVVILTEGREECAYNRS-QSCKRSIYKAISGNSRAFNFYQGSPRMI 642

Query: 270 PAHVTPRIKCLHIV 283
           P  + P++  + I 
Sbjct: 643 PDGIYPKLHKMFIA 656

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|307176233|gb|EFN65868.1| Fanconi anemia group M protein [Camponotus floridanus]

 Score =  195 bits (495), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 98/271 (36%), Positives = 169/271 (62%), Gaps = 17/271 (6%)

Query: 25  IQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLK--- 81
           I +  ++  ++  A E +V +GLR+F     +  +       +  +N LQ+LL  ++   
Sbjct: 297 IMKTLNILLTMYHAYELMVRHGLRAF----CKFYQNHSDKFWMNNENQLQSLLNDIEVYL 352

Query: 82  -------PKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVA 134
                  P  D+  + ++  + H KF +L+E+LE HF+ + ++ + T+ I+F  YR +V 
Sbjct: 353 GPFPDILPNGDVPEIPADLVFGHNKFHKLKELLEHHFKYNNDR-QDTRAIVFIEYRDIVN 411

Query: 135 EIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEI 194
           E++ +L   +P+++  MFVGQ+S   Q++Q + ++ FR+   N LI+TS+GEEGLD+GE+
Sbjct: 412 EVYILLLKSKPLIRPQMFVGQASQ-KQKQQIKALEDFRSNHVNVLISTSIGEEGLDVGEV 470

Query: 195 DLVICFD-AQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIIN 253
           DL+ICFD +Q SPI++VQR+GRTGRKR+G  ++L+T G+E  N ++++    S   KI+N
Sbjct: 471 DLIICFDVSQHSPIRLVQRMGRTGRKRDGHIIVLVTDGKEHENLKSTLSKRDSLNNKILN 530

Query: 254 NKSIYANLAKNGPRMIPAHVTPRIKCLHIVV 284
             +I+++L +N PRMIP   TP    +HI+ 
Sbjct: 531 TSNIFSSLYENNPRMIPNQFTPECYKMHIIA 561

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|47230040|emb|CAG10454.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  194 bits (493), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 121/327 (37%), Positives = 182/327 (55%), Gaps = 47/327 (14%)

Query: 1   MLAKDKYVKS-----KAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLV 55
           +LA+D++ K+     KAQ  + +     +++ DF +  SL    E L+  GLRS +    
Sbjct: 394 ILARDQFRKNPPQHIKAQH-YTSGPQQGVLEGDFALCISLYHGYELLMQMGLRSLFLYFQ 452

Query: 56  EVSKEDGSCPILGKDNDLQ------NLLQQL-----KP----KLDINIMS-------SEY 93
            +   DGS  +    N+LQ      +L Q++     KP    K D N +S         +
Sbjct: 453 GIM--DGSREMSRAKNELQRTPTFMDLYQEMEAMFVKPSAENKFDSNCVSLLREGSDEPF 510

Query: 94  AWSHLKFIRLREILESHFRLHAEKGE----------TTKVIIFANYRVVVAEIFDVLKPL 143
            +SH K  +L E++  HFRL AE             +T+V+IF+++R  V EI  +L   
Sbjct: 511 VYSHPKLQKLEEVVLQHFRLWAESSADKNGCGAQEVSTRVMIFSSFRESVQEIAAMLNRH 570

Query: 144 EPMVKASMFVGQSS------GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLV 197
            P+++   F+GQ+S      G TQ+EQ E++ +FR G FNTL++T VGEEGLDIGE+DL+
Sbjct: 571 APLIRVMTFMGQASAGKGVKGFTQKEQLEVVHRFRQGGFNTLVSTCVGEEGLDIGEVDLI 630

Query: 198 ICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSI 257
           +CFDAQK+P ++VQR+GRTGRKR GR V++L+ GRE   +  S    +S  + I  NKS 
Sbjct: 631 VCFDAQKNPTRLVQRMGRTGRKRQGRIVVILSAGREERTYNQSQSNKRSVYKAITGNKSG 690

Query: 258 YANLAKNGPRMIPAHVTPRIKCLHIVV 284
           +  L  N PRM+P  + P +  +HI  
Sbjct: 691 F-RLYPNSPRMLPQGLNPTLHKMHITC 716

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

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	395
UNIPROTKB|B2RTQ9	2022	FANCM "FANCM protein" [Homo sa	0.486	0.094	0.426	1.4e-44
UNIPROTKB|Q8IYD8	2048	FANCM "Fanconi anemia group M	0.486	0.093	0.426	1.5e-44
ZFIN|ZDB-GENE-090929-1	1761	fancm "Fanconi anemia, complem	0.488	0.109	0.446	1.6e-43
UNIPROTKB|J9NY43	2022	FANCM "Uncharacterized protein	0.481	0.093	0.420	3.6e-42
UNIPROTKB|E2RNF7	2047	FANCM "Uncharacterized protein	0.481	0.092	0.420	3.8e-42
UNIPROTKB|J9P777	2048	FANCM "Uncharacterized protein	0.481	0.092	0.420	3.8e-42
UNIPROTKB|F1NE03	1836	Gga.50035 "Uncharacterized pro	0.486	0.104	0.436	1e-41
UNIPROTKB|I3LAY7	2028	FANCM "Uncharacterized protein	0.481	0.093	0.430	2.4e-41
UNIPROTKB|F1SI11	2054	FANCM "Uncharacterized protein	0.481	0.092	0.430	2.5e-41
UNIPROTKB|A4RN08	1102	MPH1 "ATP-dependent DNA helica	0.453	0.162	0.430	6e-39

UNIPROTKB|B2RTQ9 FANCM "FANCM protein" [Homo sapiens (taxid:9606)]

 Score = 430 (156.4 bits), Expect = 1.4e-44, Sum P(3) = 1.4e-44
 Identities = 87/204 (42%), Positives = 138/204 (67%)

Query:    90 SSEYAWSHLKFIRLREILESHFRL-HAE-----KGETTKVIIFANYRVVVAEIFDVLKPL 143
             + ++ +SH K  +L E++  HF+  +AE     K + T+V+IF+++R  V EI ++L   
Sbjct:   414 NKKFVYSHPKLKKLEEVVIEHFKSWNAENTTEKKRDETRVMIFSSFRDSVQEIAEMLSQH 473

Query:   144 EPMVKASMFVGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI 198
             +P+++   FVG +SG      TQ+EQ E++K+FR G +NTL++T VGEEGLDIGE+DL+I
Sbjct:   474 QPIIRVMTFVGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLII 533

Query:   199 CFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIY 258
             CFD+QKSPI++VQR+GRTGRKR GR VI+L++GRE   +  S    +S  + I +N+ + 
Sbjct:   534 CFDSQKSPIRLVQRMGRTGRKRQGRIVIILSEGREERIYNQSQSNKRSIYKAISSNRQVL 593

Query:   259 ANLAKNGPRMIPAHVTPRIKCLHI 282
              +  +  PRM+P  + P++  + I
Sbjct:   594 -HFYQRSPRMVPDGINPKLHKMFI 616

GO:0003677 "DNA binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q8IYD8 FANCM "Fanconi anemia group M protein" [Homo sapiens (taxid:9606)]

 Score = 430 (156.4 bits), Expect = 1.5e-44, Sum P(3) = 1.5e-44
 Identities = 87/204 (42%), Positives = 138/204 (67%)

Query:    90 SSEYAWSHLKFIRLREILESHFRL-HAE-----KGETTKVIIFANYRVVVAEIFDVLKPL 143
             + ++ +SH K  +L E++  HF+  +AE     K + T+V+IF+++R  V EI ++L   
Sbjct:   440 NKKFVYSHPKLKKLEEVVIEHFKSWNAENTTEKKRDETRVMIFSSFRDSVQEIAEMLSQH 499

Query:   144 EPMVKASMFVGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI 198
             +P+++   FVG +SG      TQ+EQ E++K+FR G +NTL++T VGEEGLDIGE+DL+I
Sbjct:   500 QPIIRVMTFVGHASGKSTKGFTQKEQLEVVKQFRDGGYNTLVSTCVGEEGLDIGEVDLII 559

Query:   199 CFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIY 258
             CFD+QKSPI++VQR+GRTGRKR GR VI+L++GRE   +  S    +S  + I +N+ + 
Sbjct:   560 CFDSQKSPIRLVQRMGRTGRKRQGRIVIILSEGREERIYNQSQSNKRSIYKAISSNRQVL 619

Query:   259 ANLAKNGPRMIPAHVTPRIKCLHI 282
              +  +  PRM+P  + P++  + I
Sbjct:   620 -HFYQRSPRMVPDGINPKLHKMFI 642

GO:0004518 "nuclease activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0043240 "Fanconi anaemia nuclear complex" evidence=IDA

GO:0003682 "chromatin binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0071821 "FANCM-MHF complex" evidence=IDA

GO:0000712 "resolution of meiotic recombination intermediates" evidence=IMP

GO:0031297 "replication fork processing" evidence=IMP

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

ZFIN|ZDB-GENE-090929-1 fancm "Fanconi anemia, complementation group M" [Danio rerio (taxid:7955)]

 Score = 455 (165.2 bits), Expect = 1.6e-43, Sum P(2) = 1.6e-43
 Identities = 91/204 (44%), Positives = 136/204 (66%)

Query:    89 MSSEYAWSHLKFIRLREILESHFRLHAEKGET----TKVIIFANYRVVVAEIFDVLKPLE 144
             +   Y ++H K  +L E++  HF+  AE  +     T+V+IF++YR  V EI ++L   +
Sbjct:   399 LEEPYVYTHPKLQKLDEVVLRHFQTCAESSDVSAVDTRVMIFSSYRESVQEIAEMLNRHQ 458

Query:   145 PMVKASMFVGQSS------GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI 198
             P+V+   F+GQ+S      G TQ+EQ E++ +FR G FNTL++T VGEEGLDIGE+DL++
Sbjct:   459 PLVRVMTFMGQASAGRGVRGFTQKEQLEVVWRFREGGFNTLVSTCVGEEGLDIGEVDLIV 518

Query:   199 CFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIY 258
             CFDAQKSPI++VQR+GRTGR+R GR V++L +GRE   +  S    +S  + I+ NK  +
Sbjct:   519 CFDAQKSPIRLVQRMGRTGRQRQGRIVVILAEGREERTYNQSQSNRRSINKSIMGNKHSF 578

Query:   259 ANLAKNGPRMIPAHVTPRIKCLHI 282
               +  + PRM+PA VTP +  +HI
Sbjct:   579 -QMFSDSPRMLPADVTPALHKMHI 601

GO:0003677 "DNA binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|J9NY43 FANCM "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 425 (154.7 bits), Expect = 3.6e-42, Sum P(3) = 3.6e-42
 Identities = 85/202 (42%), Positives = 133/202 (65%)

Query:    92 EYAWSHLKFIRLREILESHFR------LHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP 145
             ++ +SH K  +L E++  HF+         +K + T+V+IF+++R  V EI ++L   +P
Sbjct:   416 KFFYSHPKLKKLEEVVLEHFKSWNIQNTSEKKCDETRVMIFSSFRDSVQEIAEMLLQHQP 475

Query:   146 MVKASMFVGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICF 200
             +++   FVG +SG      TQ+EQ E++K+FR+G +NTL++T VGEEGLDIGE+DL+ICF
Sbjct:   476 VIRVMTFVGHASGKSMKGFTQKEQLEVVKQFRSGGYNTLVSTCVGEEGLDIGEVDLIICF 535

Query:   201 DAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYAN 260
             DAQKSPI++VQR+GRTGRKR GR V++L +GRE   +  S    +S  + I  N+ +  +
Sbjct:   536 DAQKSPIRLVQRMGRTGRKRKGRIVVILAEGREERTYNQSQSNKRSIYKAISGNRQVL-H 594

Query:   261 LAKNGPRMIPAHVTPRIKCLHI 282
               +  PRM+P  + P +  + I
Sbjct:   595 FYQGSPRMVPDGINPELHKMFI 616

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RNF7 FANCM "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 425 (154.7 bits), Expect = 3.8e-42, Sum P(3) = 3.8e-42
 Identities = 85/202 (42%), Positives = 133/202 (65%)

Query:    92 EYAWSHLKFIRLREILESHFR------LHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP 145
             ++ +SH K  +L E++  HF+         +K + T+V+IF+++R  V EI ++L   +P
Sbjct:   442 KFFYSHPKLKKLEEVVLEHFKSWNIQNTSEKKCDETRVMIFSSFRDSVQEIAEMLLQHQP 501

Query:   146 MVKASMFVGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICF 200
             +++   FVG +SG      TQ+EQ E++K+FR+G +NTL++T VGEEGLDIGE+DL+ICF
Sbjct:   502 VIRVMTFVGHASGKSMKGFTQKEQLEVVKQFRSGGYNTLVSTCVGEEGLDIGEVDLIICF 561

Query:   201 DAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYAN 260
             DAQKSPI++VQR+GRTGRKR GR V++L +GRE   +  S    +S  + I  N+ +  +
Sbjct:   562 DAQKSPIRLVQRMGRTGRKRKGRIVVILAEGREERTYNQSQSNKRSIYKAISGNRQVL-H 620

Query:   261 LAKNGPRMIPAHVTPRIKCLHI 282
               +  PRM+P  + P +  + I
Sbjct:   621 FYQGSPRMVPDGINPELHKMFI 642

GO:0071821 "FANCM-MHF complex" evidence=IEA

GO:0043240 "Fanconi anaemia nuclear complex" evidence=IEA

GO:0031297 "replication fork processing" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000712 "resolution of meiotic recombination intermediates" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004518 "nuclease activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|J9P777 FANCM "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 425 (154.7 bits), Expect = 3.8e-42, Sum P(3) = 3.8e-42
 Identities = 85/202 (42%), Positives = 133/202 (65%)

Query:    92 EYAWSHLKFIRLREILESHFR------LHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP 145
             ++ +SH K  +L E++  HF+         +K + T+V+IF+++R  V EI ++L   +P
Sbjct:   442 KFFYSHPKLKKLEEVVLEHFKSWNIQNTSEKKCDETRVMIFSSFRDSVQEIAEMLLQHQP 501

Query:   146 MVKASMFVGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICF 200
             +++   FVG +SG      TQ+EQ E++K+FR+G +NTL++T VGEEGLDIGE+DL+ICF
Sbjct:   502 VIRVMTFVGHASGKSMKGFTQKEQLEVVKQFRSGGYNTLVSTCVGEEGLDIGEVDLIICF 561

Query:   201 DAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYAN 260
             DAQKSPI++VQR+GRTGRKR GR V++L +GRE   +  S    +S  + I  N+ +  +
Sbjct:   562 DAQKSPIRLVQRMGRTGRKRKGRIVVILAEGREERTYNQSQSNKRSIYKAISGNRQVL-H 620

Query:   261 LAKNGPRMIPAHVTPRIKCLHI 282
               +  PRM+P  + P +  + I
Sbjct:   621 FYQGSPRMVPDGINPELHKMFI 642

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1NE03 Gga.50035 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 429 (156.1 bits), Expect = 1.0e-41, Sum P(3) = 1.0e-41
 Identities = 90/206 (43%), Positives = 132/206 (64%)

Query:    92 EYAWSHLKFIRLREILESHFRLH----AEKGET---TKVIIFANYRVVVAEIFDVLKPLE 144
             E+ +SH K  +L EI+  HF+         G T   T+V+IF+++R  V EI ++L    
Sbjct:   275 EFIYSHPKLKKLEEIVIEHFKSRKTDQTTSGGTCVDTRVMIFSSFRDSVQEIAEMLSRFS 334

Query:   145 PMVKASMFVGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC 199
             P+V+   FVG S+G      TQ+EQ E++K+FR G +NTL++T VGEEGLDIGE+DL+IC
Sbjct:   335 PVVRVMTFVGHSTGKSTKGFTQKEQLEVVKRFREGGYNTLVSTCVGEEGLDIGEVDLIIC 394

Query:   200 FDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYA 259
             FDAQKSPI++VQR+GRTGR+R GR V++L +GRE   +  S    +S  + I  NK ++ 
Sbjct:   395 FDAQKSPIRLVQRMGRTGRQRQGRVVVILAEGREERTYNQSQSNRRSIQKAISGNKMLH- 453

Query:   260 NLAKNGPRMIPAHVTPRIKCLHIVVK 285
                ++ PRMIP  + P +  + I  +
Sbjct:   454 -FYQHSPRMIPEGINPELHRMFITAE 478

GO:0003677 "DNA binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0000712 "resolution of meiotic recombination intermediates" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0031297 "replication fork processing" evidence=IEA

GO:0043240 "Fanconi anaemia nuclear complex" evidence=IEA

GO:0071821 "FANCM-MHF complex" evidence=IEA

UNIPROTKB|I3LAY7 FANCM "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 433 (157.5 bits), Expect = 2.4e-41, Sum P(2) = 2.4e-41
 Identities = 87/202 (43%), Positives = 137/202 (67%)

Query:    92 EYAWSHLKFIRLREILESHFRL-HAE-----KGETTKVIIFANYRVVVAEIFDVLKPLEP 145
             ++ +SH K  +L E++  HF+  +A+     K + T+V+IF+++R  V EI ++L   +P
Sbjct:   425 KFCYSHPKLKKLEEVVVEHFKSWNAQNTSDKKCDKTRVMIFSSFRDSVQEIAEMLLRHQP 484

Query:   146 MVKASMFVGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICF 200
             +++   FVG +SG      TQ+EQ E++K+FR+G +NTL++T VGEEGLDIGE+DL+ICF
Sbjct:   485 IIRVMTFVGHASGKSMKGFTQKEQLEVVKQFRSGGYNTLVSTCVGEEGLDIGEVDLIICF 544

Query:   201 DAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYAN 260
             DAQKSPI++VQR+GRTGRKR GR V++L +GRE   +  S    +S  + I  NK +  +
Sbjct:   545 DAQKSPIRLVQRMGRTGRKRQGRIVVILAEGREERTYNQSQSNKRSIYKAISGNKQVL-H 603

Query:   261 LAKNGPRMIPAHVTPRIKCLHI 282
               +  PRM+P  ++P++  + I
Sbjct:   604 FYQGSPRMVPEGISPQLHKMFI 625

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1SI11 FANCM "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 433 (157.5 bits), Expect = 2.5e-41, Sum P(2) = 2.5e-41
 Identities = 87/202 (43%), Positives = 137/202 (67%)

Query:    92 EYAWSHLKFIRLREILESHFRL-HAE-----KGETTKVIIFANYRVVVAEIFDVLKPLEP 145
             ++ +SH K  +L E++  HF+  +A+     K + T+V+IF+++R  V EI ++L   +P
Sbjct:   451 KFCYSHPKLKKLEEVVVEHFKSWNAQNTSDKKCDKTRVMIFSSFRDSVQEIAEMLLRHQP 510

Query:   146 MVKASMFVGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICF 200
             +++   FVG +SG      TQ+EQ E++K+FR+G +NTL++T VGEEGLDIGE+DL+ICF
Sbjct:   511 IIRVMTFVGHASGKSMKGFTQKEQLEVVKQFRSGGYNTLVSTCVGEEGLDIGEVDLIICF 570

Query:   201 DAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYAN 260
             DAQKSPI++VQR+GRTGRKR GR V++L +GRE   +  S    +S  + I  NK +  +
Sbjct:   571 DAQKSPIRLVQRMGRTGRKRQGRIVVILAEGREERTYNQSQSNKRSIYKAISGNKQVL-H 629

Query:   261 LAKNGPRMIPAHVTPRIKCLHI 282
               +  PRM+P  ++P++  + I
Sbjct:   630 FYQGSPRMVPEGISPQLHKMFI 651

GO:0071821 "FANCM-MHF complex" evidence=IEA

GO:0043240 "Fanconi anaemia nuclear complex" evidence=IEA

GO:0031297 "replication fork processing" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000712 "resolution of meiotic recombination intermediates" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004518 "nuclease activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|A4RN08 MPH1 "ATP-dependent DNA helicase MPH1" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 374 (136.7 bits), Expect = 6.0e-39, Sum P(2) = 6.0e-39
 Identities = 80/186 (43%), Positives = 119/186 (63%)

Query:    97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQ- 155
             H K   L + L ++F + A +G +T+VI+F+ YR    EI  VL   +PM+ AS+FVGQ 
Sbjct:   481 HPKLTHLCDNLLNYF-MDAGEGSSTRVIVFSEYRDSAEEITRVLNVHKPMISASLFVGQA 539

Query:   156 ----SSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQ 211
                 S G+ Q++Q E + KFR G FN L+ATS+GEEGLDIG++DL+IC+DA  SPI+M+Q
Sbjct:   540 DSKKSEGMKQKQQIETIAKFRDGIFNVLVATSIGEEGLDIGQVDLIICYDASSSPIRMLQ 599

Query:   212 RLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPA 271
             R+GRTGRKR G+  +LL +G+E  N+  +    +  ++K+I   S +        R++P 
Sbjct:   600 RMGRTGRKRAGKITLLLMKGKEEDNYAKAQDNYEK-MQKLICEGSRFNFRHDLSSRIVPR 658

Query:   272 HVTPRI 277
              V P +
Sbjct:   659 DVKPEV 664

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	0.691

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	395
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	5e-53
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	9e-40
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	1e-23
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	3e-21
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	1e-19
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	9e-19
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-14
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	7e-11
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	2e-09
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-09
cd12091	122	cd12091, FANCM_ID, insert domain of FANCM helicase	3e-08
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	6e-08
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	5e-07
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-06
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-06
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	3e-06
cd09639	353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	6e-06
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	6e-06
TIGR00631	655	TIGR00631, uvrb, excinuclease ABC, B subunit	6e-06
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-05
TIGR00580	926	TIGR00580, mfd, transcription-repair coupling fact	1e-05
COG1205	851	COG1205, COG1205, Distinct helicase family with a	1e-05
TIGR01587	358	TIGR01587, cas3_core, CRISPR-associated helicase C	3e-05
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	2e-04
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	3e-04
PRK05298	652	PRK05298, PRK05298, excinuclease ABC subunit B; Pr	5e-04
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	5e-04
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	0.001
COG1200	677	COG1200, RecG, RecG-like helicase [DNA replication	0.003
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	0.003
COG1197	1139	COG1197, Mfd, Transcription-repair coupling factor	0.003
COG4098	441	COG4098, comFA, Superfamily II DNA/RNA helicase re	0.004
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	0.004

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

 Score =  184 bits (469), Expect = 5e-53
 Identities = 91/229 (39%), Positives = 129/229 (56%), Gaps = 23/229 (10%)

Query: 34  SLASALENLVTYGLRSFYNNLVEVSKE-----DGSCPILGKDNDLQNLLQQLKPKLDINI 88
            LA ALE L T G+R FY  L ++ +E       +   L  D          K  L + I
Sbjct: 286 KLAHALELLETQGIRPFYQYLEKLEEEATKGGSKAAKSLLADPYF-------KRALRLLI 338

Query: 89  MSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVK 148
            + E    H K  +LREIL+       EK   ++VI+F  YR    EI + LK +    +
Sbjct: 339 RADESGVEHPKLEKLREILKEQL----EKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKAR 394

Query: 149 ASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQ 203
              F+GQ+S     G++Q+EQKEI+ +FR GE+N L+ATSVGEEGLDI E+DLVI ++  
Sbjct: 395 -VRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPV 453

Query: 204 KSPIKMVQRLGRTGRKRNGRCVILLTQG-REAHNFQTSMQTCKSYVEKI 251
            S I+ +QR GRTGRKR GR V+L+T+G R+   + +S +  +  +E I
Sbjct: 454 PSEIRSIQRKGRTGRKRKGRVVVLVTEGTRDEAYYYSSRRKEQKMIESI 502

Length = 542

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

 Score =  150 bits (381), Expect = 9e-40
 Identities = 63/140 (45%), Positives = 91/140 (65%), Gaps = 11/140 (7%)

Query: 97  HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQS 156
           H K  +LREI++   +L        ++I+F  YR    +I D+L+  +  +KA  FVGQ+
Sbjct: 346 HPKLEKLREIVKE--QLGKNPDS--RIIVFTQYRDTAEKIVDLLE--KEGIKAVRFVGQA 399

Query: 157 S-----GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQ 211
           S     G++Q+EQ EI+ KFRAGEFN L++TSV EEGLDI  +DLVI ++   S I+ +Q
Sbjct: 400 SKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQ 459

Query: 212 RLGRTGRKRNGRCVILLTQG 231
           R GRTGR+  GR V+L+ +G
Sbjct: 460 RKGRTGRQEEGRVVVLIAKG 479

Length = 773

>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 = 95.0 bits (237), Expect = 1e-23
 Identities = 43/130 (33%), Positives = 74/130 (56%), Gaps = 12/130 (9%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K   L E+L    + H +KG   KV+IF   + ++ E+ ++L+  +P +K +   G    
Sbjct: 13  KLEALLELL----KEHLKKGG--KVLIFCPSKKMLDELAELLR--KPGIKVAALHGD--- 61

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
            +Q+E++E++K FR GE   L+AT V   G+D+  + +VI +D   SP   +QR+GR GR
Sbjct: 62  GSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGR 121

Query: 219 -KRNGRCVIL 227
             + G  ++L
Sbjct: 122 AGQKGTAILL 131

Length = 131

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

 Score = 86.4 bits (215), Expect = 3e-21
 Identities = 25/62 (40%), Positives = 43/62 (69%)

Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
            G++Q+E++EI++ FR G+   L+AT V   G+D+ +++LVI +D   +P   +QR+GR 
Sbjct: 15  GGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASYIQRIGRA 74

Query: 217 GR 218
           GR
Sbjct: 75  GR 76

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

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

 Score = 82.3 bits (204), Expect = 1e-19
 Identities = 29/63 (46%), Positives = 42/63 (66%)

Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
            G++Q+E++EI+ KF  G+   L+AT V E GLD+  +DLVI +D   SP   +QR+GR 
Sbjct: 19  GGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78

Query: 217 GRK 219
           GR 
Sbjct: 79  GRA 81

Length = 82

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

 Score = 87.5 bits (217), Expect = 9e-19
 Identities = 47/241 (19%), Positives = 87/241 (36%), Gaps = 15/241 (6%)

Query: 97  HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQS 156
             K   L ++L+          +  +VI+F   + +V E+ + L+      K +      
Sbjct: 258 EEKLELLLKLLKDE--------DEGRVIVFVRTKRLVEELAESLRKRG--FKVAAL---H 304

Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
             + Q+E+   ++KF+ GE   L+AT V   GLDI ++  VI +D    P   V R+GRT
Sbjct: 305 GDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRT 364

Query: 217 GR-KRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTP 275
           GR  R G  +  +T+  E    +   +  +  +   +         AK      P     
Sbjct: 365 GRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLLKTTRPGLEEE 424

Query: 276 RIKCLHI-VVKDRVTPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKTKK 334
                 I  +K                 K      K++   G++     + +  +  +  
Sbjct: 425 SDISDEIKKLKSSKKALLRGLGVRFTLSKLLANLGKEIPGAGDAVTIDPELERRSPNSAD 484

Query: 335 Q 335
            
Sbjct: 485 D 485

Length = 513

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

 Score = 73.4 bits (181), Expect = 3e-14
 Identities = 58/217 (26%), Positives = 94/217 (43%), Gaps = 34/217 (15%)

Query: 119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT 178
           E T+ I+F   R  V E+   L   +  +      G+   + Q ++ E +K+   G  N 
Sbjct: 244 EVTRSIVFVRTRERVHELAGWL--RKAGINCCYLEGE---MVQAKRNEAIKRLTDGRVNV 298

Query: 179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQGREAHNF 237
           L+AT V   G+DI ++  VI FD  +S    + R+GRTGR  R G  + L+    EAH+ 
Sbjct: 299 LVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLV----EAHD- 353

Query: 238 QTSMQTCKSYVEKIINNKSIYANLAKNGPRMI----PAHVTPRIKCLHIVVKDRVTPAKP 293
              +   + Y+E+ +              R+I    P    P  K      K     AK 
Sbjct: 354 HLLLGKIERYIEEPLK------------ARVIDELRPKTKAPSEKKTGKPSKK--VLAKR 399

Query: 294 SKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAK 330
           ++KK KE EK   K + +     +++  GK+ K +  
Sbjct: 400 AEKKEKEKEKPKVKKRHR-----DTKNIGKRRKPSGT 431

Length = 434

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

 Score = 63.2 bits (154), Expect = 7e-11
 Identities = 32/123 (26%), Positives = 54/123 (43%), Gaps = 11/123 (8%)

Query: 102 RLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVT- 160
           R    +      HA      K +IFA+         +    +  +  A   V   +G T 
Sbjct: 268 RKIAAVRGLLLKHAR---GDKTLIFASDV-------EHAYEIAKLFLAPGIVEAITGETP 317

Query: 161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR 220
           ++E++ I+++FR G    L+   V +EG+DI + D++I      S    +QRLGR  R  
Sbjct: 318 KEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRPA 377

Query: 221 NGR 223
            G+
Sbjct: 378 EGK 380

Length = 442

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

 Score = 59.2 bits (144), Expect = 2e-09
 Identities = 38/147 (25%), Positives = 69/147 (46%), Gaps = 20/147 (13%)

Query: 83  KLDINIMSSEYAWSHLKFI------RLREILESHFRLHAEKGETTKVIIFANYRVVVAEI 136
           KL+I ++S      + + +      R+ E+++ H             +IF N R     +
Sbjct: 220 KLEIKVISPVEDLIYDEELWAALYERIAELVKKH----------RTTLIFTNTRSGAERL 269

Query: 137 FDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDL 196
              LK L P +           ++++ + E+ ++ + GE   ++ATS  E G+DIG+IDL
Sbjct: 270 AFRLKKLGPDIIEV----HHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDL 325

Query: 197 VICFDAQKSPIKMVQRLGRTGRKRNGR 223
           VI   + KS  + +QR+GR G +    
Sbjct: 326 VIQLGSPKSVNRFLQRIGRAGHRLGEV 352

Length = 814

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

 Score = 56.8 bits (137), Expect = 9e-09
 Identities = 35/98 (35%), Positives = 51/98 (52%), Gaps = 7/98 (7%)

Query: 122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTLI 180
           +V++FAN +  V  I + L      VK  +   Q SG V Q ++ + ++ FR G+   L+
Sbjct: 337 RVMVFANRKDEVRRIEERL------VKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLV 390

Query: 181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           AT V   G+ I  I  VI F   + P   V R+GRTGR
Sbjct: 391 ATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGR 428

Length = 475

>gnl|CDD|213060 cd12091, FANCM_ID, insert domain of FANCM helicase and similar proteins

 Score = 51.5 bits (124), Expect = 3e-08
 Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 8/86 (9%)

Query: 1   MLAKDKYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKE 60
           + A+DK+  +        +     I+ DF +  SLA A+E L+ +G+R FY+ L E++ E
Sbjct: 38  LQARDKFRANPPGNNEGQK---GSIEGDFALLISLAHAMELLLEHGIRPFYDYLKEIATE 94

Query: 61  DGSCPI-----LGKDNDLQNLLQQLK 81
             S        L  + + + L+ +L+
Sbjct: 95  TKSKKSKSKKELANNPNFKELMDELE 120

FANCM and related proteins, like Mph1 and Fml1, are DNA junction-specific helicases/translocases that bind to and process perturbed replication forks and intermediates of homologous recombination. FANCM contains an N-terminal superfamily 2 helicase (SF2) domain, although FANCM, in contrast to other members of this family, does not exhibit DNA helicase activity. The SF2 helicase domain is comprised of 3 structural domains, the 2 generally conserved helicase domains and a helical domain inserted between the two domains. FANCM is a component of the Fanconi anaemia (FA) core complex. FA is a rare genetic disease in humans that is associated with progressive bone marrow failure, a variety of developmental abnormalities, and a high incidence of cancer. A key role of this complex is to monoubiquitination of FANCD2 and FANCI during S-phase and in response to DNA damage. The role of FANCM during this process seems to be the recruitment of the complex to chromatin. Length = 122

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

 Score = 54.1 bits (130), Expect = 6e-08
 Identities = 33/99 (33%), Positives = 53/99 (53%), Gaps = 7/99 (7%)

Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
           T+ II+ N R  V    D L   + M +    V    G + Q+++  IM++FR+G    L
Sbjct: 268 TQAIIYCNTRRKV----DYLT--KKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVL 321

Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           I T +   G+D+ ++ LVI +D   SP   + R+GR+GR
Sbjct: 322 ITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGR 360

Length = 401

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

 Score = 51.4 bits (124), Expect = 5e-07
 Identities = 48/157 (30%), Positives = 74/157 (47%), Gaps = 16/157 (10%)

Query: 163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTG 217
           E+ EI++  R GEF+ L+  ++  EGLD+ E+ LV   DA K     S   ++Q +GR  
Sbjct: 484 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAA 543

Query: 218 RKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRI 277
           R  NG+ VIL      A     SMQ      E+      +  N  ++G  + P  +  +I
Sbjct: 544 RNVNGK-VILY-----ADKITDSMQKAIDETER-RREIQMAYN-EEHG--ITPQTIKKKI 593

Query: 278 KCLHIVVKDRV-TPAKPSKKKPKENEKANKKSKKKLE 313
           + +     +     AK  KK  K ++K  +K  KKLE
Sbjct: 594 RDILDGEYEEDEYKAKIEKKASKMSKKELEKLIKKLE 630

Length = 663

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

 Score = 50.2 bits (121), Expect = 1e-06
 Identities = 27/100 (27%), Positives = 47/100 (47%), Gaps = 15/100 (15%)

Query: 124 IIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGV-----TQQEQKEIMKKFRAGEFNT 178
           ++F N +    E+ D L             G S+        Q+++ +++ +F     + 
Sbjct: 246 VVFCNTKKECQEVADALN----------AQGFSALALHGDLEQRDRDQVLVRFANRSCSV 295

Query: 179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           L+AT V   GLDI  ++ VI ++  + P   V R+GRTGR
Sbjct: 296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGR 335

Length = 460

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

 Score = 49.1 bits (117), Expect = 3e-06
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK- 219
           Q  +++ +++ + G  + LIAT V   GLD+  I LV+ +D        V R+GRTGR  
Sbjct: 281 QALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340

Query: 220 RNGRCVILLTQGRE 233
           R GR  +L  + RE
Sbjct: 341 RAGR-ALLFVENRE 353

Length = 629

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

 Score = 49.2 bits (117), Expect = 3e-06
 Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 149 ASMFVGQS--SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSP 206
           + +F+ +S    V+++++    +  ++GE   ++ATS  E G+D+G +DLVI      S 
Sbjct: 299 SDVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSV 358

Query: 207 IKMVQRLGRTGRKRNG 222
              +QR+GR G +  G
Sbjct: 359 ASGLQRIGRAGHQVGG 374

Length = 1490

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

 Score = 47.4 bits (113), Expect = 6e-06
 Identities = 32/117 (27%), Positives = 53/117 (45%), Gaps = 10/117 (8%)

Query: 122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK--FRAGEFNTL 179
            V I  N      E +  LK   P  +  +   + +    + +KE      F+  E   +
Sbjct: 220 SVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFT-EKDRAKKEAELLLEFKKSEKFVI 278

Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPI-KMVQRLGRTGRK--RNGRCVILLTQGRE 233
           +AT V E  LDI  +D++I    + +PI  ++QRLGR  R   +NG  V ++T   +
Sbjct: 279 VATQVIEASLDI-SVDVMI---TELAPIDSLIQRLGRLHRYGEKNGEEVYIITDAPD 331

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|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score = 47.8 bits (114), Expect = 6e-06
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           Q+E+  ++ +F+ G+   +IAT V   GLD+ ++  VI FD        V R+GRTGR
Sbjct: 413 QEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGR 470

Length = 545

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

 Score = 48.1 bits (115), Expect = 6e-06
 Identities = 31/85 (36%), Positives = 45/85 (52%), Gaps = 11/85 (12%)

Query: 163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTG 217
           E+ EI++  R GEF+ L+  ++  EGLD+ E+ LV   DA K     S   ++Q +GR  
Sbjct: 480 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAA 539

Query: 218 RKRNGRCVILLTQGREAHNFQTSMQ 242
           R  NG+ VI+      A     SMQ
Sbjct: 540 RNVNGK-VIMY-----ADKITDSMQ 558

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

 Score = 47.3 bits (112), Expect = 1e-05
 Identities = 41/152 (26%), Positives = 68/152 (44%), Gaps = 11/152 (7%)

Query: 117 KGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGE 175
           + E  + ++F N +  V     V + LE   +    VG  SG V Q++++ ++ +F+ G+
Sbjct: 254 RSEGARTMVFVNTKAFVER---VARTLE---RHGYRVGVLSGDVPQKKRESLLNRFQKGQ 307

Query: 176 FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAH 235
              L+AT V   GL I  +  V  +D        V R+GRT R       I     R A 
Sbjct: 308 LEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYA- 366

Query: 236 NFQTSMQTCKSYVEKIINNKSIYANLAKNGPR 267
               S+   ++Y+E+ I  + + A L    PR
Sbjct: 367 ---MSLPDIEAYIEQKIPVEPVTAELLTPLPR 395

Length = 572

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

 Score = 47.4 bits (113), Expect = 1e-05
 Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 3/88 (3%)

Query: 133 VAEIFDVLKPLEPMV-KASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDI 191
           +  I  +   L  +V +A + +     +T+ E +E+M +F  GEF  L+ T++ E G+DI
Sbjct: 670 IESIEKLATQLRELVPEARIAIAHGQ-MTENELEEVMLEFYKGEFQVLVCTTIIETGIDI 728

Query: 192 GEIDLVICFDAQKSPIKMVQRL-GRTGR 218
              + +I   A K  +  + +L GR GR
Sbjct: 729 PNANTIIIERADKFGLAQLYQLRGRVGR 756

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

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 8/82 (9%)

Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPI----KMVQR 212
           +G+ ++E++ I  +F+ GE   +IAT+  E G+DIG +D VI   A   P        QR
Sbjct: 346 AGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVI---AYGYPGVSVLSFRQR 402

Query: 213 LGRTGRKRNGRCVILLTQGREA 234
            GR GR R    ++L+    + 
Sbjct: 403 AGRAGR-RGQESLVLVVLRSDP 423

Length = 851

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

 Score = 45.1 bits (107), Expect = 3e-05
 Identities = 31/123 (25%), Positives = 50/123 (40%), Gaps = 12/123 (9%)

Query: 122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK--FRAGEFNTL 179
           K+ I  N      E +  LK   P  +  +   + +    + +KE       +  E   +
Sbjct: 224 KIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFT-EKDRAKKEAELLEEMKKNEKFVI 282

Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPI-KMVQRLGRTGRK----RNGRCVILLTQGREA 234
           +AT V E  LDI   D++I    + +PI  ++QRLGR  R          V ++T   E 
Sbjct: 283 VATQVIEASLDI-SADVMI---TELAPIDSLIQRLGRLHRYGRKNGENFEVYIITIAPEG 338

Query: 235 HNF 237
             F
Sbjct: 339 KLF 341

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

 Score = 43.0 bits (102), Expect = 2e-04
 Identities = 32/98 (32%), Positives = 48/98 (48%), Gaps = 7/98 (7%)

Query: 122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTLI 180
           + IIFAN +    EI+  L            VG  +G V Q+++  I+++F  G+ + L+
Sbjct: 257 RAIIFANTKHRCEEIWGHLA------ADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILV 310

Query: 181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           AT V   GL I  +  V  +D        V R+GRTGR
Sbjct: 311 ATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGR 348

Length = 423

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

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 23/87 (26%), Positives = 42/87 (48%)

Query: 160 TQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK 219
           + +E++E+MK F  GE   ++AT V   G+D+  +  VI FD   +  + + ++GR  R 
Sbjct: 403 SMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRM 462

Query: 220 RNGRCVILLTQGREAHNFQTSMQTCKS 246
                 I+     + + F   +   KS
Sbjct: 463 GEKGTAIVFVNEEDRNLFPELVALLKS 489

Length = 518

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

 Score = 42.0 bits (100), Expect = 5e-04
 Identities = 30/71 (42%), Positives = 38/71 (53%), Gaps = 14/71 (19%)

Query: 166 EIMKKFRAGEFNTLIATSVG----EEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRT 216
           EI++  R GEF+ L    VG     EGLDI E+ LV   DA K     S   ++Q +GR 
Sbjct: 487 EIIRDLRLGEFDVL----VGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRA 542

Query: 217 GRKRNGRCVIL 227
            R  NG+ VIL
Sbjct: 543 ARNVNGK-VIL 552

Length = 652

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

 Score = 41.7 bits (98), Expect = 5e-04
 Identities = 19/48 (39%), Positives = 29/48 (60%)

Query: 171 FRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           F++G+   L+AT +   GLDI E+  V+ ++    P   V R+GRTGR
Sbjct: 291 FKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGR 338

Length = 456

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

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 24/87 (27%), Positives = 48/87 (55%), Gaps = 4/87 (4%)

Query: 133 VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIG 192
              +++ LK   P     +  G+   +   E++ +M++FR GE + L+AT+V E G+D+ 
Sbjct: 469 AEALYERLKKAFPKYNVGLLHGR---MKSDEKEAVMEEFREGEVDILVATTVIEVGVDVP 525

Query: 193 EIDLVICFDAQKSPIKMVQRL-GRTGR 218
              +++  DA++  +  + +L GR GR
Sbjct: 526 NATVMVIEDAERFGLSQLHQLRGRVGR 552

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

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

 Score = 39.5 bits (93), Expect = 0.003
 Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 133 VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDI 191
             E+++ LK   P +K  +  G+       E+  +M+ F+ GE + L+AT+V E G+D+
Sbjct: 494 AEELYEELKSFLPELKVGLVHGRMKP---AEKDAVMEAFKEGEIDILVATTVIEVGVDV 549

Length = 677

>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional

 Score = 39.5 bits (93), Expect = 0.003
 Identities = 20/52 (38%), Positives = 35/52 (67%)

Query: 166 EIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTG 217
           E+ +K + GE   +++++  E G+DIG IDLV+   + KS  +++QR+GR G
Sbjct: 331 EVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAG 382

Length = 876

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

 Score = 39.6 bits (93), Expect = 0.003
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 133 VAEIFDVLKPLEPMV-KASMFV--GQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGL 189
           V  I    + L  +V +A + V  GQ   + ++E +E+M  F  GE++ L+ T++ E G+
Sbjct: 813 VESIEKKAERLRELVPEARIAVAHGQ---MRERELEEVMLDFYNGEYDVLVCTTIIETGI 869

Query: 190 DIGEIDLVICFDAQK 204
           DI   + +I   A K
Sbjct: 870 DIPNANTIIIERADK 884

Length = 1139

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

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 9/100 (9%)

Query: 123 VIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIAT 182
           V+IF      + ++   LK   P    +    +      Q +KE ++ FR G+   LI T
Sbjct: 308 VLIFFPEIETMEQVAAALKKKLPKETIASVHSED-----QHRKEKVEAFRDGKITLLITT 362

Query: 183 SVGEEGLDIGEIDLVICFDAQKSPIK---MVQRLGRTGRK 219
           ++ E G+    +D+ +   A+        +VQ  GR GR 
Sbjct: 363 TILERGVTFPNVDVFV-LGAEHRVFTESALVQIAGRVGRS 401

Length = 441

>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 43/200 (21%), Positives = 79/200 (39%), Gaps = 30/200 (15%)

Query: 24  MIQRDFHVTHSLASA-LENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKP 82
               +  V   L SA L   +   L+       EV +    CP   +          LK 
Sbjct: 364 EALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDE--------PGLKR 415

Query: 83  KLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKP 142
           K  +++              + E ++        K    KV++  N      E+++ LK 
Sbjct: 416 KERVDVEDGPQEE---LIELISEEVKE------GK----KVLVIVNTVDRAIELYEKLKE 462

Query: 143 LEPMVKASMFVGQ-SSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFD 201
             P  K  +   + +    +++++E+ K F+  E   ++AT V E G+DI + D++I   
Sbjct: 463 KGP--KVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-DFDVLI--- 516

Query: 202 AQKSPIK-MVQRLGRTGRKR 220
            + +PI  ++QR GR  R  
Sbjct: 517 TELAPIDSLIQRAGRVNRHG 536

Length = 733

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	395
KOG0331|consensus	519		100.0
KOG0330|consensus	476		100.0
KOG0333|consensus	673		100.0
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	100.0
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.98
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.98
KOG0338|consensus	691		99.97
KOG0342|consensus	543		99.96
KOG0326|consensus	459		99.96
KOG0343|consensus	758		99.96
KOG0328|consensus	400		99.96
KOG0340|consensus	442		99.96
KOG0335|consensus	482		99.96
KOG0341|consensus	610		99.96
KOG0345|consensus	567		99.95
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.95
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.95
KOG0336|consensus	629		99.95
PTZ00110	545	helicase; Provisional	99.94
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.94
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.94
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.94
KOG0332|consensus	477		99.94
KOG0354|consensus	746		99.94
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.94
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.94
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.94
PRK05298	652	excinuclease ABC subunit B; Provisional	99.93
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.93
KOG0348|consensus	708		99.92
KOG0339|consensus	731		99.92
KOG0327|consensus	397		99.91
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.91
KOG4284|consensus	980		99.9
KOG0346|consensus	569		99.9
PTZ00424	401	helicase 45; Provisional	99.9
KOG0334|consensus	997		99.9
KOG0344|consensus	593		99.9
KOG0347|consensus	731		99.89
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.89
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.88
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.88
PRK13766	773	Hef nuclease; Provisional	99.88
KOG0350|consensus	620		99.87
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.85
KOG0337|consensus	529		99.84
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.83
PRK04914	956	ATP-dependent helicase HepA; Validated	99.82
PHA02653	675	RNA helicase NPH-II; Provisional	99.82
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.81
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.79
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.79
PRK13767	876	ATP-dependent helicase; Provisional	99.79
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.78
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.78
PRK10689	1147	transcription-repair coupling factor; Provisional	99.78
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.78
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.78
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.76
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.74
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.74
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.73
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.72
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.71
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.71
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.7
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.7
PRK00254	720	ski2-like helicase; Provisional	99.69
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.68
PRK02362	737	ski2-like helicase; Provisional	99.68
KOG0349|consensus	725		99.68
PHA02558	501	uvsW UvsW helicase; Provisional	99.67
PRK01172	674	ski2-like helicase; Provisional	99.66
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.65
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.65
KOG0329|consensus	387		99.64
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.63
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.63
PRK09401	1176	reverse gyrase; Reviewed	99.62
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.59
COG1202	830	Superfamily II helicase, archaea-specific [General	99.58
KOG0351|consensus	941		99.57
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.56
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.5
PRK14701	1638	reverse gyrase; Provisional	99.49
KOG0352|consensus	641		99.47
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.45
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.43
PRK09694	878	helicase Cas3; Provisional	99.41
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.4
PRK05580	679	primosome assembly protein PriA; Validated	99.36
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.35
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.34
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.31
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.27
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.27
COG1204	766	Superfamily II helicase [General function predicti	99.26
COG1205	851	Distinct helicase family with a unique C-terminal	99.26
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.25
KOG4150|consensus	1034		99.22
KOG0353|consensus	695		99.15
KOG0387|consensus	923		99.09
KOG0392|consensus	1549		99.08
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.05
KOG0385|consensus	971		99.03
KOG0384|consensus	1373		99.0
KOG0951|consensus	1674		98.99
KOG0952|consensus	1230		98.91
KOG0950|consensus	1008		98.9
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.89
KOG0391|consensus	1958		98.87
KOG0388|consensus	1185		98.86
KOG0922|consensus	674		98.83
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	98.82
KOG0389|consensus	941		98.81
KOG1002|consensus	791		98.71
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.69
KOG0923|consensus	902		98.68
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.68
KOG0390|consensus	776		98.65
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.63
KOG0953|consensus	700		98.57
KOG0920|consensus	924		98.55
KOG0924|consensus	1042		98.52
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.52
KOG0947|consensus	1248		98.51
KOG1123|consensus	776		98.48
KOG0948|consensus	1041		98.39
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.37
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.34
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.33
KOG1000|consensus	689		98.29
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.27
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.25
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.22
KOG1015|consensus	1567		98.19
COG4096	875	HsdR Type I site-specific restriction-modification	98.08
KOG0949|consensus	1330		98.07
KOG0386|consensus	1157		98.04
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.03
KOG0926|consensus	1172		98.03
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.02
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.86
KOG4439|consensus	901		97.83
KOG0925|consensus	699		97.81
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.78
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.71
PF02151	36	UVR: UvrB/uvrC motif; InterPro: IPR001943 During t	97.68
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	97.68
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.65
COG4889	1518	Predicted helicase [General function prediction on	97.54
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.47
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.22
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.14
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	97.07
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	96.91
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	96.9
PF13871	278	Helicase_C_4: Helicase_C-like	96.74
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	96.6
PRK14873	665	primosome assembly protein PriA; Provisional	96.38
KOG1001|consensus	674		96.36
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.35
KOG0701|consensus	1606		96.35
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	96.28
PRK05580	679	primosome assembly protein PriA; Validated	96.05
TIGR00595	505	priA primosomal protein N'. All proteins in this f	96.05
KOG1016|consensus	1387		96.04
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	95.85
PRK14873	665	primosome assembly protein PriA; Provisional	95.4
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	95.27
PRK10689	1147	transcription-repair coupling factor; Provisional	94.47
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	94.28
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.27
KOG0921|consensus	1282		94.13
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	93.47
PRK07883	557	hypothetical protein; Validated	93.32
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	92.97
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	92.95
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	92.9
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	92.09
PRK12306	519	uvrC excinuclease ABC subunit C; Reviewed	91.53
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	91.43
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	91.34
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	91.19
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	91.16
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	91.15
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	91.1
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	91.06
COG3880	176	Modulator of heat shock repressor CtsR, McsA [Sign	90.89
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	90.79
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	90.57
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	90.16
PRK14701	1638	reverse gyrase; Provisional	90.07
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	89.96
KOG0331|consensus	519		89.94
KOG1513|consensus	1300		89.6
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	89.47
KOG0298|consensus	1394		89.4
KOG0347|consensus	731		89.07
KOG0951|consensus	1674		88.66
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	88.5
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	88.21
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	87.41
KOG2340|consensus	698		87.27
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	87.17
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	86.58
PF04364	137	DNA_pol3_chi: DNA polymerase III chi subunit, HolC	85.91
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	85.88
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	85.61
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	84.08
PRK09401	1176	reverse gyrase; Reviewed	83.55
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	83.35
PTZ00110	545	helicase; Provisional	82.2
KOG0343|consensus	758		81.66
KOG1133|consensus	821		81.33
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	80.74

>KOG0331|consensus

Probab=100.00  E-value=5.7e-35  Score=295.66  Aligned_cols=197  Identities=25%  Similarity=0.292  Sum_probs=162.4

Q ss_pred             HHHHHHHhcchHHHHHHHHhC---CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccc-cceeeeccccH
Q psy4150          25 IQRDFHVTHSLASALENLVTY---GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINI-MSSEYAWSHLK   99 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~---g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~-~~~~~~~~~~K   99 (395)
                      -|||.|++|||.++++.|..+   ..+|+++||||.|.++. ....++.++.-+.+..........+. .....+....|
T Consensus       246 DEADrMldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K  325 (519)
T KOG0331|consen  246 DEADRMLDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAK  325 (519)
T ss_pred             ccHHhhhccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHH
Confidence            399999999999999999886   45789999999999985 33455555544433322211111111 11112335668


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ...|..+|..+..     ..++|+||||+|++.|+.|+..|+..+  +.+..|||   +.+|.+|..+|+.|++|++.||
T Consensus       326 ~~~l~~lL~~~~~-----~~~~KvIIFc~tkr~~~~l~~~l~~~~--~~a~~iHG---d~sQ~eR~~~L~~FreG~~~vL  395 (519)
T KOG0331|consen  326 LRKLGKLLEDISS-----DSEGKVIIFCETKRTCDELARNLRRKG--WPAVAIHG---DKSQSERDWVLKGFREGKSPVL  395 (519)
T ss_pred             HHHHHHHHHHHhc-----cCCCcEEEEecchhhHHHHHHHHHhcC--cceeeecc---cccHHHHHHHHHhcccCCcceE
Confidence            8999999988752     467899999999999999999999998  99999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      |||||++||||||+|++|||||+|.++++|+||+|||||+| .|.++.|++..
T Consensus       396 VATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~  448 (519)
T KOG0331|consen  396 VATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSD  448 (519)
T ss_pred             EEcccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHH
Confidence            99999999999999999999999999999999999999985 78889888764

>KOG0330|consensus

Probab=100.00  E-value=2.3e-33  Score=269.76  Aligned_cols=208  Identities=20%  Similarity=0.265  Sum_probs=166.9

Q ss_pred             hHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccccc-ccccCChhHHHHHHhhcccccccccceeee--cccc
Q psy4150          24 MIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDGSC-PILGKDNDLQNLLQQLKPKLDINIMSSEYA--WSHL   98 (395)
Q Consensus        24 ~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~~~-~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~--~~~~   98 (395)
                      |-|||..++|.|.+.++.+...  .-|++++|||||+..++.. +..+.+|.-+..-....   ....+.|.|.  ....
T Consensus       210 lDEADrlLd~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~---tv~~lkQ~ylfv~~k~  286 (476)
T KOG0330|consen  210 LDEADRLLDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQ---TVDHLKQTYLFVPGKD  286 (476)
T ss_pred             hchHHhhhhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhc---chHHhhhheEeccccc
Confidence            4499999999999998887774  5689999999999988432 22223332111111100   0111333444  4556


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      |-..|..||.+.        .+..+||||+|+.+++.++-.|+..|  +.+..+||   .|++..|...++.|++|.++|
T Consensus       287 K~~yLV~ll~e~--------~g~s~iVF~~t~~tt~~la~~L~~lg--~~a~~LhG---qmsq~~Rlg~l~~Fk~~~r~i  353 (476)
T KOG0330|consen  287 KDTYLVYLLNEL--------AGNSVIVFCNTCNTTRFLALLLRNLG--FQAIPLHG---QMSQSKRLGALNKFKAGARSI  353 (476)
T ss_pred             cchhHHHHHHhh--------cCCcEEEEEeccchHHHHHHHHHhcC--cceecccc---hhhHHHHHHHHHHHhccCCcE
Confidence            888899998874        35889999999999999999999999  99999999   999999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhHHHHHHHHcccc
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKS  256 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~~~~  256 (395)
                      ||||||++||+|+|.|++|||||.|.+..+||||+||+||+| +|.++.+++..+-         +.+..|+..++.+.
T Consensus       354 Lv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDv---------e~~qrIE~~~gkkl  423 (476)
T KOG0330|consen  354 LVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDV---------ELVQRIEHALGKKL  423 (476)
T ss_pred             EEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhh---------HHHHHHHHHHhcCC
Confidence            999999999999999999999999999999999999999996 8999999987332         33577888887754

>KOG0333|consensus

Probab=100.00  E-value=4e-33  Score=276.21  Aligned_cols=197  Identities=24%  Similarity=0.338  Sum_probs=165.6

Q ss_pred             hHHHHHHHhcchHHHHHHHHhC---------------------------CCcchhhhccccCcccc-ccccccCChhHHH
Q psy4150          24 MIQRDFHVTHSLASALENLVTY---------------------------GLRSFYNNLVEVSKEDG-SCPILGKDNDLQN   75 (395)
Q Consensus        24 ~lead~~~~~~l~~~~~~L~~~---------------------------g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~   75 (395)
                      +.|+|.|++|||.+++..++++                           .+||+++|+||+|+.+. .++.++.+|-++.
T Consensus       402 ldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vt  481 (673)
T KOG0333|consen  402 LDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVT  481 (673)
T ss_pred             ccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEE
Confidence            4489999999999987776652                           13889999999998774 5667777775554


Q ss_pred             HHHhhcccccccccceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEecc
Q psy4150          76 LLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQ  155 (395)
Q Consensus        76 ~v~~~~~~~~~~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~  155 (395)
                      +-....+..... ..-.+...+.|+.+|.++|...+        ..++|||+|+++.|+.|++.|.+.|  +++..||| 
T Consensus       482 ig~~gk~~~rve-Q~v~m~~ed~k~kkL~eil~~~~--------~ppiIIFvN~kk~~d~lAk~LeK~g--~~~~tlHg-  549 (673)
T KOG0333|consen  482 IGSAGKPTPRVE-QKVEMVSEDEKRKKLIEILESNF--------DPPIIIFVNTKKGADALAKILEKAG--YKVTTLHG-  549 (673)
T ss_pred             eccCCCCccchh-eEEEEecchHHHHHHHHHHHhCC--------CCCEEEEEechhhHHHHHHHHhhcc--ceEEEeeC-
Confidence            333333222222 22345567889999999998853        4799999999999999999999999  99999999 


Q ss_pred             CCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         156 SSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       156 ~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                        +-+|++|..+|.+|+.|..+||||||+++||||||+|++|||||++++...|+||||||||+| .|.++.|++..+.+
T Consensus       550 --~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~  627 (673)
T KOG0333|consen  550 --GKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTA  627 (673)
T ss_pred             --CccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhH
Confidence              999999999999999999999999999999999999999999999999999999999999998 78889998887654

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

Probab=100.00  E-value=1.5e-32  Score=273.28  Aligned_cols=239  Identities=22%  Similarity=0.317  Sum_probs=199.2

Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      ....+...|....+.+++.+.....   ..+.|+||.+-|+++|++|+++|.+.|  +++.++|+   ++..-+|.++++
T Consensus       419 lDP~ievRp~~~QvdDL~~EI~~r~---~~~eRvLVTtLTKkmAEdLT~Yl~e~g--ikv~YlHS---didTlER~eIir  490 (663)
T COG0556         419 LDPEIEVRPTKGQVDDLLSEIRKRV---AKNERVLVTTLTKKMAEDLTEYLKELG--IKVRYLHS---DIDTLERVEIIR  490 (663)
T ss_pred             CCCceeeecCCCcHHHHHHHHHHHH---hcCCeEEEEeehHHHHHHHHHHHHhcC--ceEEeeec---cchHHHHHHHHH
Confidence            3333445566666666666654431   346999999999999999999999999  99999999   999999999999


Q ss_pred             HHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC-----ChhhHhhhccccccccCceEEEEEeCCchhhHHHHHHHHh
Q psy4150         170 KFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTC  244 (395)
Q Consensus       170 ~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~-----s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~~~~  244 (395)
                      ++|.|.++|||+.|++.+|||+|+|++|.++|+.+     |..++||.+|||+|+-.|.++++      .+.++.+|+.+
T Consensus       491 dLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN~~GkvIlY------AD~iT~sM~~A  564 (663)
T COG0556         491 DLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILY------ADKITDSMQKA  564 (663)
T ss_pred             HHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHHHHHHHhhccCCeEEEE------chhhhHHHHHH
Confidence            99999999999999999999999999999999876     89999999999999999999999      67788899999


Q ss_pred             HHHHHHHHcccchhhhhcccCCCCCCCCcchhhhhhcccccccCCCCCCCCCCchhhHHhhhcchhhhccCCCCCccccc
Q psy4150         245 KSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQ  324 (395)
Q Consensus       245 ~~~i~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  324 (395)
                      ..+.++....+.+||..|+..|..+.+.+...+........ ..         ........++++++.+           
T Consensus       565 i~ET~RRR~iQ~~yN~~hgItP~ti~K~i~d~l~~~~~~~~-~~---------~~~~~~~~~~~~~e~~-----------  623 (663)
T COG0556         565 IDETERRREIQMAYNEEHGITPQTIKKKIRDILDGEYEEDE-YK---------AKIEKKASKMSKKELE-----------  623 (663)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCchhhhhhhhHhhhhhhhhhh-hh---------hhcccccccCCHHHHH-----------
Confidence            99999999999999999999999988887766554322100 00         0000113345666666           


Q ss_pred             ccchhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhcCC
Q psy4150         325 NKTNAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSGE  368 (395)
Q Consensus       325 ~k~~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~~~  368 (395)
                         ..|++|+++|.+||++|+  ||.||++||+|.+|++++.+.
T Consensus       624 ---~~I~~Le~~M~~aA~~l~--FE~Aa~lRD~i~~L~~~~~~~  662 (663)
T COG0556         624 ---KLIKKLEKEMKEAAKNLE--FEEAARLRDEIKELKEELLGK  662 (663)
T ss_pred             ---HHHHHHHHHHHHHHHhCC--HHHHHHHHHHHHHHHHHhccc
Confidence               899999999999999999  999999999999999988653

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

Probab=99.98  E-value=1e-31  Score=266.66  Aligned_cols=221  Identities=39%  Similarity=0.572  Sum_probs=181.0

Q ss_pred             cchhHHHHHHHhcchHHHHHHHHhCCCcchhhhccccCcccc-----ccccccCChhHHHHHHhhcccccccccceeeec
Q psy4150          21 LDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDG-----SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAW   95 (395)
Q Consensus        21 ~~~~lead~~~~~~l~~~~~~L~~~g~r~~~~fsatl~~~~~-----~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~   95 (395)
                      ...-+..-+...+.+.+++++|.+||+++++.|+..+.....     ..+.++.++.+...+..+...       .....
T Consensus       273 ~~~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~~l~e~~~~~~sk~a~~l~~d~~~~~al~~~~~~-------~~~~v  345 (542)
T COG1111         273 DKFRLLSVLAEAIKLAHALELLETQGIRPFYQYLEKLEEEATKGGSKAAKSLLADPYFKRALRLLIRA-------DESGV  345 (542)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHhcccchHHHHHHhcChhhHHHHHHHHHh-------ccccC
Confidence            334456678888999999999999999999999986654331     246778888777665443211       22356


Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCC-----CCCHHHHHHHHHH
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSS-----GVTQQEQKEIMKK  170 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~-----~~~~~~R~~~l~~  170 (395)
                      .|||++.+.+++.+++..    +++.|+|||++.|++|+.+.++|.+.++..+ ..|.|+++     ||+|.++.+++++
T Consensus       346 ~HPKl~~l~eilke~~~k----~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~-~rFiGQa~r~~~~GMsQkeQ~eiI~~  420 (542)
T COG1111         346 EHPKLEKLREILKEQLEK----NGDSRVIVFTEYRDTAEEIVNFLKKIGIKAR-VRFIGQASREGDKGMSQKEQKEIIDQ  420 (542)
T ss_pred             CCccHHHHHHHHHHHHhc----CCCceEEEEehhHhHHHHHHHHHHhcCCcce-eEEeeccccccccccCHHHHHHHHHH
Confidence            899999999999999876    6679999999999999999999999996555 57888543     8999999999999


Q ss_pred             HhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchhhHHHHHHHHhHHHHHH
Q psy4150         171 FRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEK  250 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~  250 (395)
                      |+.|+++|||||+++++|||||+|++||+|++-+|+..+|||.|||||.+.|.+++|++.++-+..|...-.+..+.+.+
T Consensus       421 Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~r~Grv~vLvt~gtrdeayy~~s~rke~~m~e  500 (542)
T COG1111         421 FRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKRKGRVVVLVTEGTRDEAYYYSSRRKEQKMIE  500 (542)
T ss_pred             HhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccCCCCeEEEEEecCchHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999986554444333244555555


Q ss_pred             HHc
Q psy4150         251 IIN  253 (395)
Q Consensus       251 ~i~  253 (395)
                      .+.
T Consensus       501 ~i~  503 (542)
T COG1111         501 SIR  503 (542)
T ss_pred             HHH
Confidence            443

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

Probab=99.98  E-value=2.8e-32  Score=283.16  Aligned_cols=199  Identities=22%  Similarity=0.328  Sum_probs=162.7

Q ss_pred             hHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeecccc--
Q psy4150          24 MIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHL--   98 (395)
Q Consensus        24 ~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~--   98 (395)
                      +-|||.|++|||.+.++.+...  ..+|+++||||++..+. ....++.+|..+.+-... .......+.|.|.....  
T Consensus       180 lDEADrmLd~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~-~~~~~~~i~q~~~~v~~~~  258 (513)
T COG0513         180 LDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEK-LERTLKKIKQFYLEVESEE  258 (513)
T ss_pred             eccHhhhhcCCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEcccc-ccccccCceEEEEEeCCHH
Confidence            3499999999999999998886  45999999999998663 445566666533322111 10122335566665442  


Q ss_pred             -HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          99 -KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        99 -K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                       |+..|..++...        ...++||||+|+..|+.|+..|...|  +++..|||   +|+|.+|.++++.|++|+++
T Consensus       259 ~k~~~L~~ll~~~--------~~~~~IVF~~tk~~~~~l~~~l~~~g--~~~~~lhG---~l~q~~R~~~l~~F~~g~~~  325 (513)
T COG0513         259 EKLELLLKLLKDE--------DEGRVIVFVRTKRLVEELAESLRKRG--FKVAALHG---DLPQEERDRALEKFKDGELR  325 (513)
T ss_pred             HHHHHHHHHHhcC--------CCCeEEEEeCcHHHHHHHHHHHHHCC--CeEEEecC---CCCHHHHHHHHHHHHcCCCC
Confidence             888887777653        34579999999999999999999999  99999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhH
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHN  236 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~  236 (395)
                      ||||||+++||||||+|++|||||+|.+++.|+||+|||||+| .|.++.|+++..+...
T Consensus       326 vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~  385 (513)
T COG0513         326 VLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKK  385 (513)
T ss_pred             EEEEechhhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHH
Confidence            9999999999999999999999999999999999999999997 7888999887434433

>KOG0338|consensus

Probab=99.97  E-value=4.2e-32  Score=268.13  Aligned_cols=210  Identities=21%  Similarity=0.277  Sum_probs=160.7

Q ss_pred             hhHHhhcCCCCCCcccccch-hHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHh
Q psy4150           4 KDKYVKSKAQFPHINRDLDR-MIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQ   79 (395)
Q Consensus         4 ~~~~~~~~~~~~~i~~~~~~-~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~   79 (395)
                      -|+-+++  |+-++-...-- +-|||.|++-||.+.++.|...  .-||+++|||||+..+. .....+..|- .-.+..
T Consensus       314 IDHlrNs--~sf~ldsiEVLvlDEADRMLeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPv-rifvd~  390 (691)
T KOG0338|consen  314 IDHLRNS--PSFNLDSIEVLVLDEADRMLEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPV-RIFVDP  390 (691)
T ss_pred             HHHhccC--CCccccceeEEEechHHHHHHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCe-EEEeCC
Confidence            3666666  44444444322 4599999999999998887764  67999999999998773 1111122221 000000


Q ss_pred             hcccccccccceeeec-----cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEec
Q psy4150          80 LKPKLDINIMSSEYAW-----SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVG  154 (395)
Q Consensus        80 ~~~~~~~~~~~~~~~~-----~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg  154 (395)
                      .. . .-..+.|.|.-     .+.+-..|..++...|.        .++||||.|+..|..|.-+|.-.|  +++.-+||
T Consensus       391 ~~-~-~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf~--------~~~ivFv~tKk~AHRl~IllGLlg--l~agElHG  458 (691)
T KOG0338|consen  391 NK-D-TAPKLTQEFIRIRPKREGDREAMLASLITRTFQ--------DRTIVFVRTKKQAHRLRILLGLLG--LKAGELHG  458 (691)
T ss_pred             cc-c-cchhhhHHHheeccccccccHHHHHHHHHHhcc--------cceEEEEehHHHHHHHHHHHHHhh--chhhhhcc
Confidence            00 0 00002333332     33455566667776664        699999999999999999999999  99999999


Q ss_pred             cCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         155 QSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       155 ~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                         .++|.+|.+.++.|+.++++|||||||++|||||++|.+||||++|.+...|+||+|||+|+| .|.++.|+.+.
T Consensus       459 ---sLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~  533 (691)
T KOG0338|consen  459 ---SLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGES  533 (691)
T ss_pred             ---cccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccc
Confidence               999999999999999999999999999999999999999999999999999999999999996 89999998876

>KOG0342|consensus

Probab=99.96  E-value=2.7e-30  Score=254.95  Aligned_cols=207  Identities=19%  Similarity=0.291  Sum_probs=167.9

Q ss_pred             CCCCcccccchhH--HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccc-cccCChhHHHHHHhhcccccc
Q psy4150          13 QFPHINRDLDRMI--QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCP-ILGKDNDLQNLLQQLKPKLDI   86 (395)
Q Consensus        13 ~~~~i~~~~~~~l--ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~-~l~~~~~~~~~v~~~~~~~~~   86 (395)
                      ++..+-..++..+  |||..++|||.+.++.+...  ..||+++||||.+..+. .++ .+..++.|+.++....... +
T Consensus       223 t~~f~~r~~k~lvlDEADrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~T-h  301 (543)
T KOG0342|consen  223 TSGFLFRNLKCLVLDEADRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERET-H  301 (543)
T ss_pred             CCcchhhccceeEeecchhhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcch-h
Confidence            3445555555533  99999999999998888775  57899999999998885 233 2334577777665444322 2


Q ss_pred             cccceeeecc--ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHH
Q psy4150          87 NIMSSEYAWS--HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQ  164 (395)
Q Consensus        87 ~~~~~~~~~~--~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R  164 (395)
                      ..+.|.|+.+  ..++-.|..+|.++..       ..++||||.|+..+..+++.|....  +.|..|||   +++|..|
T Consensus       302 e~l~Qgyvv~~~~~~f~ll~~~LKk~~~-------~~KiiVF~sT~~~vk~~~~lL~~~d--lpv~eiHg---k~~Q~kR  369 (543)
T KOG0342|consen  302 ERLEQGYVVAPSDSRFSLLYTFLKKNIK-------RYKIIVFFSTCMSVKFHAELLNYID--LPVLEIHG---KQKQNKR  369 (543)
T ss_pred             hcccceEEeccccchHHHHHHHHHHhcC-------CceEEEEechhhHHHHHHHHHhhcC--Cchhhhhc---CCccccc
Confidence            3355555543  3356677777777643       3899999999999999999999888  99999999   9999999


Q ss_pred             HHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         165 KEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       165 ~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      ..+..+|+..+.-|||||||++||+|+|+|++||+||+|.++.+||||+|||||.| .|.+++++.+++
T Consensus       370 T~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~E  438 (543)
T KOG0342|consen  370 TSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWE  438 (543)
T ss_pred             chHHHHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhH
Confidence            99999999999999999999999999999999999999999999999999999996 788888877644

>KOG0326|consensus

Probab=99.96  E-value=5.8e-30  Score=240.93  Aligned_cols=207  Identities=20%  Similarity=0.250  Sum_probs=174.7

Q ss_pred             hhHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceee--eccc
Q psy4150          23 RMIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEY--AWSH   97 (395)
Q Consensus        23 ~~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~--~~~~   97 (395)
                      -+-|||.+++..|...++.|.+.  .-+|.++||||+|-.+. .....+..|..+.+...+...-    +.|.|  +.++
T Consensus       232 V~DEADKlLs~~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~eLtl~G----vtQyYafV~e~  307 (459)
T KOG0326|consen  232 VMDEADKLLSVDFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEELTLKG----VTQYYAFVEER  307 (459)
T ss_pred             EechhhhhhchhhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhhhhhhcc----hhhheeeechh
Confidence            35599999999999999998886  57899999999998773 3345666777777777665433    33444  4556


Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .|+..|..++..+.-        .+.|||||+...+|.|+..+.+.|  +.|.++|+   .|.|+.|..++.+|++|.++
T Consensus       308 qKvhCLntLfskLqI--------NQsIIFCNS~~rVELLAkKITelG--yscyyiHa---kM~Q~hRNrVFHdFr~G~cr  374 (459)
T KOG0326|consen  308 QKVHCLNTLFSKLQI--------NQSIIFCNSTNRVELLAKKITELG--YSCYYIHA---KMAQEHRNRVFHDFRNGKCR  374 (459)
T ss_pred             hhhhhHHHHHHHhcc--------cceEEEeccchHhHHHHHHHHhcc--chhhHHHH---HHHHhhhhhhhhhhhccccc
Confidence            688888887776533        689999999999999999999999  99999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhHHHHHHHHccc
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNK  255 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~~~  255 (395)
                      .|||||++.||||++.|++|||||+|++.++|+||+||.||.| -|-++.+++.++...         ...|++.++..
T Consensus       375 nLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~---------L~~IE~eLGtE  444 (459)
T KOG0326|consen  375 NLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFN---------LYRIEQELGTE  444 (459)
T ss_pred             eeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhh---------HHHHHHHhccc
Confidence            9999999999999999999999999999999999999999998 688999988755433         34577777653

>KOG0343|consensus

Probab=99.96  E-value=7.3e-30  Score=254.26  Aligned_cols=206  Identities=20%  Similarity=0.256  Sum_probs=175.4

Q ss_pred             hHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeee--cccc
Q psy4150          24 MIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYA--WSHL   98 (395)
Q Consensus        24 ~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~--~~~~   98 (395)
                      +-|||.+++|||...++-|.++  ..||+++||||-++.+. .++.-+.+|.|+.+..+..... ...+.|.|+  ....
T Consensus       221 LDEADR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~at-P~~L~Q~y~~v~l~~  299 (758)
T KOG0343|consen  221 LDEADRMLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAAT-PSNLQQSYVIVPLED  299 (758)
T ss_pred             eccHHHHHHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccC-hhhhhheEEEEehhh
Confidence            3399999999999999998886  67999999999988774 5666678888887653321111 112334443  4567


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      |+..|...|..|..        .++|||+.|++.+..+++.+.+..|+++...|||   .|+|..|.++..+|-....-|
T Consensus       300 Ki~~L~sFI~shlk--------~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G---~~~Q~~R~ev~~~F~~~~~~v  368 (758)
T KOG0343|consen  300 KIDMLWSFIKSHLK--------KKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHG---TMSQKKRIEVYKKFVRKRAVV  368 (758)
T ss_pred             HHHHHHHHHHhccc--------cceEEEEehhhHHHHHHHHHHhcCCCCceeeecc---chhHHHHHHHHHHHHHhcceE
Confidence            99999999988764        7999999999999999999999999999999999   999999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHH
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~  241 (395)
                      |+|||+++||||+|.|++||+||+|-++.+||||+||++|.. .|.+++++++.+++..+..+.
T Consensus       369 LF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq  432 (758)
T KOG0343|consen  369 LFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQ  432 (758)
T ss_pred             EEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHH
Confidence            999999999999999999999999999999999999999995 899999999888666555444

>KOG0328|consensus

Probab=99.96  E-value=8.8e-30  Score=236.31  Aligned_cols=206  Identities=19%  Similarity=0.282  Sum_probs=160.6

Q ss_pred             hHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeec---cc
Q psy4150          24 MIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAW---SH   97 (395)
Q Consensus        24 ~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~---~~   97 (395)
                      +-|+|.|+.-||.+..--+-.+  +-.|..++|||+|+++. ....++.+|  +.++...... ....+.+.|..   +.
T Consensus       175 LDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdp--vrilvkrdel-tlEgIKqf~v~ve~Ee  251 (400)
T KOG0328|consen  175 LDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDP--VRILVKRDEL-TLEGIKQFFVAVEKEE  251 (400)
T ss_pred             eccHHHHHHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCc--eeEEEecCCC-chhhhhhheeeechhh
Confidence            3499999999999775444443  34788999999998873 445666666  2222221111 11123344442   34


Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .|++.|+++...+        .-.+++|||||+..+++|.+.|++..  +.+..+||   +|.+++|.+++.+|++|..+
T Consensus       252 wKfdtLcdLYd~L--------tItQavIFcnTk~kVdwLtekm~~~n--ftVssmHG---Dm~qkERd~im~dFRsg~Sr  318 (400)
T KOG0328|consen  252 WKFDTLCDLYDTL--------TITQAVIFCNTKRKVDWLTEKMREAN--FTVSSMHG---DMEQKERDKIMNDFRSGKSR  318 (400)
T ss_pred             hhHhHHHHHhhhh--------ehheEEEEecccchhhHHHHHHHhhC--ceeeeccC---CcchhHHHHHHHHhhcCCce
Confidence            4888888877654        24799999999999999999999998  99999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhHHHHHHHHcc
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCKSYVEKIINN  254 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~~  254 (395)
                      ||+|||+.+||+|+|.|++|||||+|.+...||||+||.||.| .|.++.|+...+-         +....|++.++.
T Consensus       319 vLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~---------~~lrdieq~yst  387 (400)
T KOG0328|consen  319 VLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDL---------RILRDIEQYYST  387 (400)
T ss_pred             EEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHH---------HHHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999996 7888888765332         334566666654

>KOG0340|consensus

Probab=99.96  E-value=2.9e-29  Score=239.14  Aligned_cols=218  Identities=22%  Similarity=0.268  Sum_probs=165.5

Q ss_pred             cccchhH--HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCccccccccccCChhHHHHHHhhcccccccccceeee
Q psy4150          19 RDLDRMI--QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYA   94 (395)
Q Consensus        19 ~~~~~~l--ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~   94 (395)
                      ..++.++  |||.++.-.|.+.++-+.+.  .-||+++|+||++.........-....+-..+...........+.+.|.
T Consensus       152 ~rlkflVlDEADrvL~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI  231 (442)
T KOG0340|consen  152 QRLKFLVLDEADRVLAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYI  231 (442)
T ss_pred             hceeeEEecchhhhhccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhhee
Confidence            3344443  99999999999998888775  4479999999998766321111111001111111111111222344444


Q ss_pred             --ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 --WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 --~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                        ..+.|-..|..+|...-.     ...+.++|||||...|+.|+..|+..+  +++..+||   .|+|.+|...+..|+
T Consensus       232 ~~~~~vkdaYLv~~Lr~~~~-----~~~~simIFvnttr~cQ~l~~~l~~le--~r~~~lHs---~m~Q~eR~~aLsrFr  301 (442)
T KOG0340|consen  232 LVSIDVKDAYLVHLLRDFEN-----KENGSIMIFVNTTRECQLLSMTLKNLE--VRVVSLHS---QMPQKERLAALSRFR  301 (442)
T ss_pred             ecchhhhHHHHHHHHhhhhh-----ccCceEEEEeehhHHHHHHHHHHhhhc--eeeeehhh---cchHHHHHHHHHHHh
Confidence              445577788888877533     256889999999999999999999999  99999999   999999999999999


Q ss_pred             cCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhHHHHHHH
Q psy4150         173 AGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCKSYVEKI  251 (395)
Q Consensus       173 ~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~  251 (395)
                      ++..+|||||||++||+|||.|++|||||.|.+|..||||+||++|+| .|.++.++++.+ .        +....|++.
T Consensus       302 s~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rD-v--------~l~~aiE~~  372 (442)
T KOG0340|consen  302 SNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRD-V--------ELLQAIEEE  372 (442)
T ss_pred             hcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhh-H--------HHHHHHHHH
Confidence            999999999999999999999999999999999999999999999996 788888888433 3        234667777


Q ss_pred             Hccc
Q psy4150         252 INNK  255 (395)
Q Consensus       252 i~~~  255 (395)
                      ++..
T Consensus       373 igkK  376 (442)
T KOG0340|consen  373 IGKK  376 (442)
T ss_pred             Hhcc
Confidence            7764

>KOG0335|consensus

Probab=99.96  E-value=1.8e-29  Score=252.02  Aligned_cols=200  Identities=21%  Similarity=0.228  Sum_probs=156.3

Q ss_pred             hHHHHHHHh-cchHHHHHHHHhC------CCcchhhhccccCcccc-ccccccCC-hhHHHHHHhhcccccccccceeee
Q psy4150          24 MIQRDFHVT-HSLASALENLVTY------GLRSFYNNLVEVSKEDG-SCPILGKD-NDLQNLLQQLKPKLDINIMSSEYA   94 (395)
Q Consensus        24 ~lead~~~~-~~l~~~~~~L~~~------g~r~~~~fsatl~~~~~-~~~~l~~~-~~~~~~v~~~~~~~~~~~~~~~~~   94 (395)
                      +-|||+|++ |||.+.++.|..+      +.+|+++||||+|.... ....++.+ ..++.+. .+............++
T Consensus       232 LDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~-rvg~~~~ni~q~i~~V  310 (482)
T KOG0335|consen  232 LDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVG-RVGSTSENITQKILFV  310 (482)
T ss_pred             ecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEe-eeccccccceeEeeee
Confidence            349999999 9999999999886      47899999999998873 22222222 1111111 1111111111223345


Q ss_pred             ccccHHHHHHHHHHHHHHh-hhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          95 WSHLKFIRLREILESHFRL-HAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~-~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      ....|...|+++|...... +.......+++|||.|++.|..|+.+|...+  +++..+||   +.++.+|.+.++.|++
T Consensus       311 ~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~--~~~~sIhg---~~tq~er~~al~~Fr~  385 (482)
T KOG0335|consen  311 NEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNG--YPAKSIHG---DRTQIEREQALNDFRN  385 (482)
T ss_pred             cchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCC--CCceeecc---hhhhhHHHHHHHHhhc
Confidence            5567999999998875432 2222335589999999999999999999999  99999999   9999999999999999


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEe
Q psy4150         174 GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLT  229 (395)
Q Consensus       174 g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~  229 (395)
                      |.+.|||||+|++||||||+|.+|||||+|.+..+|+||||||||.| .|.++.|+.
T Consensus       386 g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n  442 (482)
T KOG0335|consen  386 GKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFN  442 (482)
T ss_pred             CCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEec
Confidence            99999999999999999999999999999999999999999999998 566666665

>KOG0341|consensus

Probab=99.96  E-value=2.7e-29  Score=241.37  Aligned_cols=198  Identities=25%  Similarity=0.372  Sum_probs=158.7

Q ss_pred             hHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCccccccccccCChhHHHHHHh----hcccccccccceeeeccc
Q psy4150          24 MIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQ----LKPKLDINIMSSEYAWSH   97 (395)
Q Consensus        24 ~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~~~~~l~~~~~~~~~v~~----~~~~~~~~~~~~~~~~~~   97 (395)
                      +-|||.|++|||.+++..+.++  +.||+++||||||+.+   +.+..++-...+..+    ....+... ....|+...
T Consensus       332 lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KI---Q~FAkSALVKPvtvNVGRAGAAsldVi-QevEyVkqE  407 (610)
T KOG0341|consen  332 LDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKI---QNFAKSALVKPVTVNVGRAGAASLDVI-QEVEYVKQE  407 (610)
T ss_pred             hhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHH---HHHHHhhcccceEEecccccccchhHH-HHHHHHHhh
Confidence            4599999999999999999887  8899999999999877   333333322222111    11111111 122344555


Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .|+-.|++-|..         ...++||||..+..++.+.+||--.|  +.+..+||   +.+|++|...++.|+.|+-+
T Consensus       408 aKiVylLeCLQK---------T~PpVLIFaEkK~DVD~IhEYLLlKG--VEavaIHG---GKDQedR~~ai~afr~gkKD  473 (610)
T KOG0341|consen  408 AKIVYLLECLQK---------TSPPVLIFAEKKADVDDIHEYLLLKG--VEAVAIHG---GKDQEDRHYAIEAFRAGKKD  473 (610)
T ss_pred             hhhhhHHHHhcc---------CCCceEEEeccccChHHHHHHHHHcc--ceeEEeec---CcchhHHHHHHHHHhcCCCc
Confidence            566655554422         35789999999999999999999999  99999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHH
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQT  239 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~  239 (395)
                      |||||||++.|+|+|++.+|||||+|...+.|+||+|||||.| .|.+..|+....++..+..
T Consensus       474 VLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~~esvLlD  536 (610)
T KOG0341|consen  474 VLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQEESVLLD  536 (610)
T ss_pred             eEEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccchHHHHHH
Confidence            9999999999999999999999999999999999999999997 7888889988877765543

>KOG0345|consensus

Probab=99.95  E-value=3.4e-28  Score=238.85  Aligned_cols=196  Identities=20%  Similarity=0.249  Sum_probs=159.8

Q ss_pred             hHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcc-cccccccceeeeccccH
Q psy4150          24 MIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKP-KLDINIMSSEYAWSHLK   99 (395)
Q Consensus        24 ~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~-~~~~~~~~~~~~~~~~K   99 (395)
                      +-|||..++|||...++.|.++  ..|.+-+||||.+.++. ..+.-+.+|--+.+-..... .+..-.+.+..+....|
T Consensus       163 LDEADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK  242 (567)
T KOG0345|consen  163 LDEADRLLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEK  242 (567)
T ss_pred             ecchHhHhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHH
Confidence            4499999999999999998886  57899999999988774 33455556533332222110 01101122333445569


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      +..|.++|..+        ...++|||+.|+.++++.+..|...........+||   .|++..|..+++.|+...-.||
T Consensus       243 ~~~lv~~L~~~--------~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHG---K~~q~~R~k~~~~F~~~~~~vl  311 (567)
T KOG0345|consen  243 LSQLVHLLNNN--------KDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHG---KMSQKARAKVLEAFRKLSNGVL  311 (567)
T ss_pred             HHHHHHHHhcc--------ccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecc---hhcchhHHHHHHHHHhccCceE
Confidence            99999988773        458999999999999999999988755688999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      +||||++||||||+|++||+||+|.++.+|+||+|||||+| .|.+++|+.+
T Consensus       312 ~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p  363 (567)
T KOG0345|consen  312 FCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNP  363 (567)
T ss_pred             EeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecc
Confidence            99999999999999999999999999999999999999996 8999999887

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.95  E-value=4.3e-27  Score=249.43  Aligned_cols=225  Identities=20%  Similarity=0.311  Sum_probs=170.1

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .+++.|.+.|.....      .+.++||||+|+..++.|+++|.+.|  +.+.++||   ++++.+|.++++.|+.|++.
T Consensus       426 ~qi~~Ll~eI~~~~~------~g~~vLIf~~tk~~ae~L~~~L~~~g--i~~~~lh~---~~~~~eR~~~l~~fr~G~i~  494 (655)
T TIGR00631       426 GQVDDLLSEIRQRVA------RNERVLVTTLTKKMAEDLTDYLKELG--IKVRYLHS---EIDTLERVEIIRDLRLGEFD  494 (655)
T ss_pred             chHHHHHHHHHHHHc------CCCEEEEEECCHHHHHHHHHHHhhhc--cceeeeeC---CCCHHHHHHHHHHHhcCCce
Confidence            356666666655433      36899999999999999999999998  99999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcC-----CCCChhhHhhhccccccccCceEEEEEeCCchhhHHHHHHHHhHHHHHHHH
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFD-----AQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKII  252 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d-----~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i  252 (395)
                      |||||+++++|+|+|++++||++|     .|.+..+|+||+|||||...|.+++|+...+....      .+........
T Consensus       495 VLV~t~~L~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~~~G~vi~~~~~~~~~~~------~ai~~~~~~~  568 (655)
T TIGR00631       495 VLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQ------KAIEETERRR  568 (655)
T ss_pred             EEEEcChhcCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCCCCCEEEEEEcCCCHHHH------HHHHHHHhHH
Confidence            999999999999999999999999     79999999999999999999999888776554322      3334443444


Q ss_pred             cccchhhhhcccCCCCCCCCcchhhhhhcccccccCCCCCCCCCCchhhHHhhhcchhhhccCCCCCcccccccchhhhh
Q psy4150         253 NNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKT  332 (395)
Q Consensus       253 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~  332 (395)
                      ..+..++..+...|..+.+.+...+........  . .....   ... ....+++++++.              +.+++
T Consensus       569 ~iq~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~--~-~~~~~---~~~-~~~~~~~~~~~~--------------~~i~~  627 (655)
T TIGR00631       569 KIQMAYNEEHGITPQTIRKPIRDILDIELKEKE--D-AAKKK---KKG-EDLSDLSKKELK--------------KLIKQ  627 (655)
T ss_pred             HHHhhhhhhcCCCCcccCcchHHHhhhhhhccc--c-hhhcc---ccc-cccccCCHHHHH--------------HHHHH
Confidence            444566677777888877766654432111100  0 00000   000 000112334444              79999


Q ss_pred             hccchhhhhHHHHHHHHhhhhchhhHHHHH
Q psy4150         333 KKQPMMTQSNDIRTCFENITKKKKTFIDFL  362 (395)
Q Consensus       333 ~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~  362 (395)
                      |+++|.+||++|+  ||.||.+||+|..|+
T Consensus       628 l~~~M~~aa~~l~--FE~Aa~~RD~i~~L~  655 (655)
T TIGR00631       628 LEKEMKQAARNLE--FEEAARLRDEILELK  655 (655)
T ss_pred             HHHHHHHHHHccC--HHHHHHHHHHHHhcC
Confidence            9999999999999  999999999999875

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

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=1e-27  Score=243.98  Aligned_cols=191  Identities=21%  Similarity=0.267  Sum_probs=147.5

Q ss_pred             HHHHHHHhcchHHHHHHHHhC----CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccce--eeeccc
Q psy4150          25 IQRDFHVTHSLASALENLVTY----GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSS--EYAWSH   97 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~----g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~--~~~~~~   97 (395)
                      .|+|.+++++|...+..+...    ..++.+.||||++.... .+...+.++.++.+.....   ....+.+  .+....
T Consensus       164 DEad~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~---~~~~i~~~~~~~~~~  240 (423)
T PRK04837        164 DEADRMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQK---TGHRIKEELFYPSNE  240 (423)
T ss_pred             ecHHHHhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCc---CCCceeEEEEeCCHH
Confidence            399999999998887776653    23567899999987552 2223334443322111100   0011122  223345


Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .|...|..++..        ....++||||+++..|+.+++.|...|  +.+.++||   +|++.+|..++++|+.|+++
T Consensus       241 ~k~~~l~~ll~~--------~~~~~~lVF~~t~~~~~~l~~~L~~~g--~~v~~lhg---~~~~~~R~~~l~~F~~g~~~  307 (423)
T PRK04837        241 EKMRLLQTLIEE--------EWPDRAIIFANTKHRCEEIWGHLAADG--HRVGLLTG---DVAQKKRLRILEEFTRGDLD  307 (423)
T ss_pred             HHHHHHHHHHHh--------cCCCeEEEEECCHHHHHHHHHHHHhCC--CcEEEecC---CCChhHHHHHHHHHHcCCCc
Confidence            577777666654        235799999999999999999999988  99999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      ||||||+++||||+|+|++||+||+|.+..+|+||+|||||.| .|.+++|+++.
T Consensus       308 vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~  362 (423)
T PRK04837        308 ILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEE  362 (423)
T ss_pred             EEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHH
Confidence            9999999999999999999999999999999999999999997 78888887653

>KOG0336|consensus

Probab=99.95  E-value=4e-28  Score=234.71  Aligned_cols=195  Identities=18%  Similarity=0.252  Sum_probs=154.4

Q ss_pred             HHHHHHHhcchHHHHHHHHh--CCCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeec--cccH
Q psy4150          25 IQRDFHVTHSLASALENLVT--YGLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAW--SHLK   99 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~--~g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~--~~~K   99 (395)
                      -|||.|++|||..++..++-  .+.||+.+-|||.|..++ ....++.+|-.+ .+..+. ....+.+.|.+..  ...|
T Consensus       374 DEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v-~vGsLd-L~a~~sVkQ~i~v~~d~~k  451 (629)
T KOG0336|consen  374 DEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIV-YVGSLD-LVAVKSVKQNIIVTTDSEK  451 (629)
T ss_pred             cchhhhhcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEE-Eecccc-eeeeeeeeeeEEecccHHH
Confidence            49999999999998776433  488999999999999885 334455555221 122221 1122223344433  3446


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      +.....++..+       ....++||||..+..|+.|..-|.-.|  +.+..|||   +-.|.+|+..+++|++|+++||
T Consensus       452 ~~~~~~f~~~m-------s~ndKvIiFv~~K~~AD~LSSd~~l~g--i~~q~lHG---~r~Q~DrE~al~~~ksG~vrIL  519 (629)
T KOG0336|consen  452 LEIVQFFVANM-------SSNDKVIIFVSRKVMADHLSSDFCLKG--ISSQSLHG---NREQSDREMALEDFKSGEVRIL  519 (629)
T ss_pred             HHHHHHHHHhc-------CCCceEEEEEechhhhhhccchhhhcc--cchhhccC---ChhhhhHHHHHHhhhcCceEEE
Confidence            65555555443       446899999999999999999988888  99999999   8999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      ||||+++||||++++.+|+|||+|.+.+.|+||+||+||+| .|..+.|++..+-
T Consensus       520 vaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~  574 (629)
T KOG0336|consen  520 VATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDW  574 (629)
T ss_pred             EEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhH
Confidence            99999999999999999999999999999999999999996 8889988887543

>PTZ00110 helicase; Provisional

Probab=99.94  E-value=3.9e-27  Score=246.61  Aligned_cols=194  Identities=24%  Similarity=0.287  Sum_probs=151.1

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCC-hhHHHHHHhhccccccccccee--eeccccH
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKD-NDLQNLLQQLKPKLDINIMSSE--YAWSHLK   99 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~-~~~~~~v~~~~~~~~~~~~~~~--~~~~~~K   99 (395)
                      |+|.+++++|...+..|...  ..+|++.||||++..+. ....++.. +..+.+ ...... ....+.+.  +.....|
T Consensus       285 EAd~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~v-g~~~l~-~~~~i~q~~~~~~~~~k  362 (545)
T PTZ00110        285 EADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNV-GSLDLT-ACHNIKQEVFVVEEHEK  362 (545)
T ss_pred             hHHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEE-CCCccc-cCCCeeEEEEEEechhH
Confidence            99999999999888877764  56789999999987652 11222211 111000 000000 00111222  2334568


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ...|..+|.....      .+.++||||+|+..|+.|+..|...+  +.+..+||   ++++.+|..++++|++|+++||
T Consensus       363 ~~~L~~ll~~~~~------~~~k~LIF~~t~~~a~~l~~~L~~~g--~~~~~ihg---~~~~~eR~~il~~F~~G~~~IL  431 (545)
T PTZ00110        363 RGKLKMLLQRIMR------DGDKILIFVETKKGADFLTKELRLDG--WPALCIHG---DKKQEERTWVLNEFKTGKSPIM  431 (545)
T ss_pred             HHHHHHHHHHhcc------cCCeEEEEecChHHHHHHHHHHHHcC--CcEEEEEC---CCcHHHHHHHHHHHhcCCCcEE
Confidence            8888888876542      35899999999999999999999888  89999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      |||++++||||||+|++||+||+|.+..+|+||+|||||.| .|.+++|+++.+
T Consensus       432 VaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~  485 (545)
T PTZ00110        432 IATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDK  485 (545)
T ss_pred             EEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcch
Confidence            99999999999999999999999999999999999999996 788888887643

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.94  E-value=3.3e-27  Score=242.80  Aligned_cols=189  Identities=20%  Similarity=0.328  Sum_probs=149.6

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeec--cccHH
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAW--SHLKF  100 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~--~~~K~  100 (395)
                      |+|.+++++|...+..+...  ..++++.||||++.... ....++.++..+.+....    ....+.+.|..  ...|+
T Consensus       155 Ead~~l~~g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~----~~~~i~~~~~~~~~~~k~  230 (460)
T PRK11776        155 EADRMLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH----DLPAIEQRFYEVSPDERL  230 (460)
T ss_pred             CHHHHhCcCcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC----CCCCeeEEEEEeCcHHHH
Confidence            99999999999888777665  45789999999987653 223334444322211110    11112333332  33477


Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEE
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI  180 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLV  180 (395)
                      ..|..+|..+        ...++||||+|+..++.+++.|...+  +.+..+||   +|++.+|..+++.|++|+++|||
T Consensus       231 ~~l~~ll~~~--------~~~~~lVF~~t~~~~~~l~~~L~~~~--~~v~~~hg---~~~~~eR~~~l~~F~~g~~~vLV  297 (460)
T PRK11776        231 PALQRLLLHH--------QPESCVVFCNTKKECQEVADALNAQG--FSALALHG---DLEQRDRDQVLVRFANRSCSVLV  297 (460)
T ss_pred             HHHHHHHHhc--------CCCceEEEECCHHHHHHHHHHHHhCC--CcEEEEeC---CCCHHHHHHHHHHHHcCCCcEEE
Confidence            7777776542        35789999999999999999999998  99999999   99999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       181 aT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      ||+++++|||+|+|++||+||+|.++.+|+||+|||||.| .|.+++++.+.
T Consensus       298 aTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~  349 (460)
T PRK11776        298 ATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPE  349 (460)
T ss_pred             EecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchh
Confidence            9999999999999999999999999999999999999997 67788777654

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.94  E-value=1.1e-26  Score=237.01  Aligned_cols=189  Identities=23%  Similarity=0.310  Sum_probs=143.1

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcc-c-cccccccCChhHHHHHHhhcccccccccceeeecc---cc
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKE-D-GSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWS---HL   98 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~-~-~~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~---~~   98 (395)
                      |+|.+++++|...+..+...  ..++.+.||||++.. . ..+..++.++..+.....   ......+.+.+...   ..
T Consensus       155 Eah~~l~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~---~~~~~~i~~~~~~~~~~~~  231 (434)
T PRK11192        155 EADRMLDMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPS---RRERKKIHQWYYRADDLEH  231 (434)
T ss_pred             CHHHHhCCCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCC---cccccCceEEEEEeCCHHH
Confidence            89999999999988887653  446889999999743 2 122233333321111100   00011122222222   23


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      |...|..++..        ....++||||+++..++.|+..|...+  +.+..+||   +|++.+|..+++.|++|+++|
T Consensus       232 k~~~l~~l~~~--------~~~~~~lVF~~s~~~~~~l~~~L~~~~--~~~~~l~g---~~~~~~R~~~l~~f~~G~~~v  298 (434)
T PRK11192        232 KTALLCHLLKQ--------PEVTRSIVFVRTRERVHELAGWLRKAG--INCCYLEG---EMVQAKRNEAIKRLTDGRVNV  298 (434)
T ss_pred             HHHHHHHHHhc--------CCCCeEEEEeCChHHHHHHHHHHHhCC--CCEEEecC---CCCHHHHHHHHHHHhCCCCcE
Confidence            55555554432        346899999999999999999999988  99999999   999999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      ||||+++++|||+|+|++||+||+|.+...|+||+|||||.| .|.+++++..
T Consensus       299 LVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~  351 (434)
T PRK11192        299 LVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEA  351 (434)
T ss_pred             EEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecH
Confidence            999999999999999999999999999999999999999996 6777777754

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.94  E-value=9.7e-27  Score=239.09  Aligned_cols=205  Identities=17%  Similarity=0.273  Sum_probs=151.1

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeecc--ccHH
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWS--HLKF  100 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~--~~K~  100 (395)
                      |+|.+++++|.+.+..+...  ..+|.+.||||++.... .+..++.++..+.+....   .....+.+.+...  ..|.
T Consensus       157 Eah~ll~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~---~~~~~i~~~~~~~~~~~k~  233 (456)
T PRK10590        157 EADRMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRN---TASEQVTQHVHFVDKKRKR  233 (456)
T ss_pred             cHHHHhccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEeccc---ccccceeEEEEEcCHHHHH
Confidence            99999999998887776654  45688999999987652 223334333222111100   0011122232222  2333


Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEE
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI  180 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLV  180 (395)
                      ..|..++    ..    ....++||||+++..++.|++.|...+  +.+..+||   +|++.+|..++++|++|+++|||
T Consensus       234 ~~l~~l~----~~----~~~~~~lVF~~t~~~~~~l~~~L~~~g--~~~~~lhg---~~~~~~R~~~l~~F~~g~~~iLV  300 (456)
T PRK10590        234 ELLSQMI----GK----GNWQQVLVFTRTKHGANHLAEQLNKDG--IRSAAIHG---NKSQGARTRALADFKSGDIRVLV  300 (456)
T ss_pred             HHHHHHH----Hc----CCCCcEEEEcCcHHHHHHHHHHHHHCC--CCEEEEEC---CCCHHHHHHHHHHHHcCCCcEEE
Confidence            3333333    22    345799999999999999999999988  99999999   99999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhHHHHHHHHccc
Q psy4150         181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNK  255 (395)
Q Consensus       181 aT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~~~  255 (395)
                      ||+++++|||+|+|++||+||+|.++.+|+||+|||||.| .|.++++++..+ .        .....+++.++..
T Consensus       301 aTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d-~--------~~~~~ie~~l~~~  367 (456)
T PRK10590        301 ATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDE-H--------KLLRDIEKLLKKE  367 (456)
T ss_pred             EccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHH-H--------HHHHHHHHHhcCC
Confidence            9999999999999999999999999999999999999996 688887776532 2        2235566666543

>KOG0332|consensus

Probab=99.94  E-value=9e-27  Score=223.32  Aligned_cols=188  Identities=19%  Similarity=0.311  Sum_probs=145.9

Q ss_pred             hcchHHHHHHHHhCCCcchhhhcc-ccCccccccccccCChhHHHHHHhhcccccccc--------------cceeeec-
Q psy4150          32 THSLASALENLVTYGLRSFYNNLV-EVSKEDGSCPILGKDNDLQNLLQQLKPKLDINI--------------MSSEYAW-   95 (395)
Q Consensus        32 ~~~l~~~~~~L~~~g~r~~~~fsa-tl~~~~~~~~~l~~~~~~~~~v~~~~~~~~~~~--------------~~~~~~~-   95 (395)
                      .+.|+++..+|-.+|++....-+. .+|+   .++.++++++|.+-+..+...+..+.              +.+.|.. 
T Consensus       235 vfVlDEAD~Mi~tqG~~D~S~rI~~~lP~---~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C  311 (477)
T KOG0332|consen  235 VFVLDEADVMIDTQGFQDQSIRIMRSLPR---NQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLC  311 (477)
T ss_pred             EEEecchhhhhhcccccccchhhhhhcCC---cceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeec
Confidence            356677777777776654432222 2232   33666677777766665554443332              4444443 


Q ss_pred             --cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          96 --SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        96 --~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                        ...|++.|.+|...        ..-++.||||.|+.+|.+|+..|...|  ..+..+||   +|+..+|..++..||.
T Consensus       312 ~~~~~K~~~l~~lyg~--------~tigqsiIFc~tk~ta~~l~~~m~~~G--h~V~~l~G---~l~~~~R~~ii~~Fr~  378 (477)
T KOG0332|consen  312 ACRDDKYQALVNLYGL--------LTIGQSIIFCHTKATAMWLYEEMRAEG--HQVSLLHG---DLTVEQRAAIIDRFRE  378 (477)
T ss_pred             cchhhHHHHHHHHHhh--------hhhhheEEEEeehhhHHHHHHHHHhcC--ceeEEeec---cchhHHHHHHHHHHhc
Confidence              35688888885433        234899999999999999999999999  99999999   9999999999999999


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEcCCCC------ChhhHhhhcccccccc-CceEEEEEeCCchhh
Q psy4150         174 GEFNTLIATSVGEEGLDIGEIDLVICFDAQK------SPIKMVQRLGRTGRKR-NGRCVILLTQGREAH  235 (395)
Q Consensus       174 g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~------s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~  235 (395)
                      |..+|||+|+|++||||++.|++|||||+|.      ++..|+||+|||||.| .|.++.++.......
T Consensus       379 g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~  447 (477)
T KOG0332|consen  379 GKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMN  447 (477)
T ss_pred             CcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHH
Confidence            9999999999999999999999999999996      7899999999999997 788888777655543

>KOG0354|consensus

Probab=99.94  E-value=4.5e-26  Score=237.70  Aligned_cols=205  Identities=39%  Similarity=0.560  Sum_probs=159.6

Q ss_pred             HHHhcchHHHHHHHHhCCCc--chhhhccccCccccccc--cccCChhHHHHHHhhcccccccccceeeeccccHHHHHH
Q psy4150          29 FHVTHSLASALENLVTYGLR--SFYNNLVEVSKEDGSCP--ILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLR  104 (395)
Q Consensus        29 ~~~~~~l~~~~~~L~~~g~r--~~~~fsatl~~~~~~~~--~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~K~~~L~  104 (395)
                      |..+..+.+.+.+|..+|+|  ..+.+..++..+....+  .+..+..+.......-..+..  +...-...+||++.|.
T Consensus       324 f~~~~~~~~~~~ll~~~gir~~~~l~~~~~f~~e~~~~k~~~~~~e~~~~~~~~~~m~~~~~--l~~~~~~~npkle~l~  401 (746)
T KOG0354|consen  324 FYALHLRKYNLALLISDGIRFVDALDYLEDFYEEVALKKYLKLELEARLIRNFTENMNELEH--LSLDPPKENPKLEKLV  401 (746)
T ss_pred             HHHHHHHHHHHHHHhhcchhhHHHHhhhhhhccccchhHHHHHHhcchhhHHHHHHHHhhhh--hhcCCCccChhHHHHH
Confidence            77777778889999999999  55555556655443222  222222222222211111111  1111136799999999


Q ss_pred             HHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHc-ccCCCCceeEEeccCC-----CCCHHHHHHHHHHHhcCCccE
Q psy4150         105 EILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK-PLEPMVKASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus       105 ~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~-~~~~~~~~~~lhg~~~-----~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      ++|.+++..    .+..|+||||.||.+|+.|..+|. -+.+.+++..+.|++.     +|+|.++.+++++|++|+++|
T Consensus       402 ~~l~e~f~~----~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~Nv  477 (746)
T KOG0354|consen  402 EILVEQFEQ----NPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINV  477 (746)
T ss_pred             HHHHHHhhc----CCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccE
Confidence            999999885    778999999999999999999998 4455589999999664     899999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchhhHHHHHH
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~  241 (395)
                      ||||+|+++||||++|++||+||+..|+..+|||+|| ||+.+|.++++++ +.+...+....
T Consensus       478 LVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa~ns~~vll~t-~~~~~~~E~~~  538 (746)
T KOG0354|consen  478 LVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRARNSKCVLLTT-GSEVIEFERNN  538 (746)
T ss_pred             EEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-ccccCCeEEEEEc-chhHHHHHHHH
Confidence            9999999999999999999999999999999999999 9999999999988 66665555544

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.94  E-value=1.5e-26  Score=245.18  Aligned_cols=190  Identities=21%  Similarity=0.309  Sum_probs=151.7

Q ss_pred             HHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeee--ccccH
Q psy4150          25 IQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYA--WSHLK   99 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~--~~~~K   99 (395)
                      -|+|.++.++|.+.++.+...  ..+++++||||+|..+. ....++.++..+.+.....   ....+.+.|.  ....|
T Consensus       156 DEAd~ml~~gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~---~~~~i~q~~~~v~~~~k  232 (629)
T PRK11634        156 DEADEMLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVT---TRPDISQSYWTVWGMRK  232 (629)
T ss_pred             ccHHHHhhcccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccc---cCCceEEEEEEechhhH
Confidence            399999999999888877664  45789999999998763 2334444543332221111   1111233333  33457


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ...|..+|..        ....++||||+|+..++.|++.|...+  +.+..+||   +|++.+|..+++.|++|+++||
T Consensus       233 ~~~L~~~L~~--------~~~~~~IVF~~tk~~a~~l~~~L~~~g--~~~~~lhg---d~~q~~R~~il~~Fr~G~~~IL  299 (629)
T PRK11634        233 NEALVRFLEA--------EDFDAAIIFVRTKNATLEVAEALERNG--YNSAALNG---DMNQALREQTLERLKDGRLDIL  299 (629)
T ss_pred             HHHHHHHHHh--------cCCCCEEEEeccHHHHHHHHHHHHhCC--CCEEEeeC---CCCHHHHHHHHHHHhCCCCCEE
Confidence            7877777754        234789999999999999999999998  99999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      |||+++++|||+|+|++||+||+|.++.+|+||+|||||+| .|.+++|+.+
T Consensus       300 VATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~  351 (629)
T PRK11634        300 IATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVEN  351 (629)
T ss_pred             EEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEech
Confidence            99999999999999999999999999999999999999997 5888877764

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=2e-26  Score=242.24  Aligned_cols=190  Identities=18%  Similarity=0.250  Sum_probs=145.6

Q ss_pred             HHHHHHHhcchHHHHHHHHhC----CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeee--ccc
Q psy4150          25 IQRDFHVTHSLASALENLVTY----GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYA--WSH   97 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~----g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~--~~~   97 (395)
                      .|+|.+++++|...+..|...    ..+++++||||++..+. .....+.++....+.  .. ......+.+.+.  ...
T Consensus       166 DEAh~lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~--~~-~~~~~~i~q~~~~~~~~  242 (572)
T PRK04537        166 DEADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVE--TE-TITAARVRQRIYFPADE  242 (572)
T ss_pred             cCHHHHhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEec--cc-cccccceeEEEEecCHH
Confidence            499999999999888777664    25789999999987652 222222222111000  00 001111222222  234


Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .|+..|..++..        ..+.++||||+|+..|+.|++.|...+  +.+..+||   +|++.+|..+++.|++|+++
T Consensus       243 ~k~~~L~~ll~~--------~~~~k~LVF~nt~~~ae~l~~~L~~~g--~~v~~lhg---~l~~~eR~~il~~Fr~G~~~  309 (572)
T PRK04537        243 EKQTLLLGLLSR--------SEGARTMVFVNTKAFVERVARTLERHG--YRVGVLSG---DVPQKKRESLLNRFQKGQLE  309 (572)
T ss_pred             HHHHHHHHHHhc--------ccCCcEEEEeCCHHHHHHHHHHHHHcC--CCEEEEeC---CCCHHHHHHHHHHHHcCCCe
Confidence            466666555543        346799999999999999999999998  99999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      ||||||++++|||+|+|++|||||+|.+..+|+||+|||||.| .|.+++|+++
T Consensus       310 VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~  363 (572)
T PRK04537        310 ILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACE  363 (572)
T ss_pred             EEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecH
Confidence            9999999999999999999999999999999999999999997 7888888765

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

Probab=99.94  E-value=2.8e-26  Score=239.03  Aligned_cols=193  Identities=20%  Similarity=0.263  Sum_probs=146.9

Q ss_pred             HHHHHHHhcchHHHHHHHHh-CCCcchhhhccccCcccc-ccccccCChhHHHHHHhhccccccccccee--eeccccHH
Q psy4150          25 IQRDFHVTHSLASALENLVT-YGLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSE--YAWSHLKF  100 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~-~g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~--~~~~~~K~  100 (395)
                      -|+|.++++||...+..+.. .+..|++.||||++..+. ....++.++.++.+-....   ....+.+.  ++....|.
T Consensus       277 DEad~ml~~gf~~~i~~i~~~l~~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~---~~~~v~q~~~~~~~~~k~  353 (518)
T PLN00206        277 DEVDCMLERGFRDQVMQIFQALSQPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNR---PNKAVKQLAIWVETKQKK  353 (518)
T ss_pred             ecHHHHhhcchHHHHHHHHHhCCCCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCC---CCcceeEEEEeccchhHH
Confidence            39999999999887665544 366799999999987653 2222333322111111000   00111122  33345577


Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcc-cCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKP-LEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~-~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ..|.++|.....      ...++||||+++..++.|++.|.. .+  +.+..+||   ++++.+|..+++.|++|+++||
T Consensus       354 ~~l~~~l~~~~~------~~~~~iVFv~s~~~a~~l~~~L~~~~g--~~~~~~Hg---~~~~~eR~~il~~Fr~G~~~IL  422 (518)
T PLN00206        354 QKLFDILKSKQH------FKPPAVVFVSSRLGADLLANAITVVTG--LKALSIHG---EKSMKERREVMKSFLVGEVPVI  422 (518)
T ss_pred             HHHHHHHHhhcc------cCCCEEEEcCCchhHHHHHHHHhhccC--cceEEeeC---CCCHHHHHHHHHHHHCCCCCEE
Confidence            778777765321      246899999999999999999975 46  89999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      |||++++||||+|+|++||+||+|.+..+|+||+|||||.| .|.+++|++..
T Consensus       423 VaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~  475 (518)
T PLN00206        423 VATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEE  475 (518)
T ss_pred             EEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchh
Confidence            99999999999999999999999999999999999999997 67888877653

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.93  E-value=1.7e-25  Score=238.18  Aligned_cols=215  Identities=21%  Similarity=0.341  Sum_probs=160.3

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .++..|.+.|.....      .+.++||||+|+..++.|++.|.+.|  +++.++||   ++++.+|..++..|+.|.+.
T Consensus       430 ~q~~~L~~~L~~~~~------~g~~viIf~~t~~~ae~L~~~L~~~g--i~~~~~h~---~~~~~~R~~~l~~f~~g~i~  498 (652)
T PRK05298        430 GQVDDLLSEIRKRVA------KGERVLVTTLTKRMAEDLTDYLKELG--IKVRYLHS---DIDTLERVEIIRDLRLGEFD  498 (652)
T ss_pred             ccHHHHHHHHHHHHh------CCCEEEEEeCCHHHHHHHHHHHhhcc--eeEEEEEC---CCCHHHHHHHHHHHHcCCce
Confidence            356666666655443      36899999999999999999999999  99999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCC-----CCChhhHhhhccccccccCceEEEEEeCCchhhHHHHHHHHhHHHHHHHH
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDA-----QKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKII  252 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~-----p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i  252 (395)
                      |||||+++++|+|+|++++||++|.     |.+..+|+||+|||||...|.+++|++..+....-........+.++..+
T Consensus       499 vlV~t~~L~rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~  578 (652)
T PRK05298        499 VLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQKAIDETERRREIQIAY  578 (652)
T ss_pred             EEEEeCHHhCCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCCCCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999986     78999999999999999889999888754432221111112233343333


Q ss_pred             cccchhhhhcccCCCCCCCCcchhhhhhcccccccCCCCCCCCCCchhhHHhhhcchhhhccCCCCCcccccccchhhhh
Q psy4150         253 NNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKKT  332 (395)
Q Consensus       253 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~  332 (395)
                      +      ..+...|..+.+.+...+...       .   .           ...+..+..+              +.++.
T Consensus       579 ~------~~~~~~~~~~~~~~~~~~~~~-------~---~-----------~~~~~~~~~~--------------~~~~~  617 (652)
T PRK05298        579 N------EEHGITPKTIKKKIRDILDSV-------Y---K-----------KDKLSKKELE--------------KLIKE  617 (652)
T ss_pred             h------hccCCCChhHHHHHHHHHHhh-------h---h-----------hccCCHHHHH--------------HHHHH
Confidence            2      333333433333333322100       0   0           0012222333              68899


Q ss_pred             hccchhhhhHHHHHHHHhhhhchhhHHHHHhhhc
Q psy4150         333 KKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSS  366 (395)
Q Consensus       333 ~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~  366 (395)
                      ++++|..||++|+  ||.||.+||+|..|+..+.
T Consensus       618 l~~~M~~aa~~l~--fE~Aa~~Rd~i~~l~~~~~  649 (652)
T PRK05298        618 LEKQMKEAAKNLE--FEEAARLRDEIKELKEELL  649 (652)
T ss_pred             HHHHHHHHHHhHH--HHHHHHHHHHHHHHHHHhc
Confidence            9999999999999  9999999999999998654

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.93  E-value=1.5e-25  Score=231.43  Aligned_cols=205  Identities=20%  Similarity=0.292  Sum_probs=151.7

Q ss_pred             HHHHHHhcchHHHHHHHHhC----CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceee--ecccc
Q psy4150          26 QRDFHVTHSLASALENLVTY----GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEY--AWSHL   98 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~----g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~--~~~~~   98 (395)
                      |+|.++.++|...+..|..+    +.++++.+|||++.... ....++.++....+...  . .....+.+.+  .....
T Consensus       245 Eah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~--~-~~~~~~~~~~~~~~~~~  321 (475)
T PRK01297        245 EADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPE--N-VASDTVEQHVYAVAGSD  321 (475)
T ss_pred             hHHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccC--c-CCCCcccEEEEEecchh
Confidence            89999999988777666553    34689999999876542 22222233322111100  0 0000111121  23445


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      |...|..++..        ....++||||+++..++.+++.|...+  +.+..+||   ++++.+|.++++.|++|+++|
T Consensus       322 k~~~l~~ll~~--------~~~~~~IVF~~s~~~~~~l~~~L~~~~--~~~~~~~g---~~~~~~R~~~~~~Fr~G~~~v  388 (475)
T PRK01297        322 KYKLLYNLVTQ--------NPWERVMVFANRKDEVRRIEERLVKDG--INAAQLSG---DVPQHKRIKTLEGFREGKIRV  388 (475)
T ss_pred             HHHHHHHHHHh--------cCCCeEEEEeCCHHHHHHHHHHHHHcC--CCEEEEEC---CCCHHHHHHHHHHHhCCCCcE
Confidence            66666666543        345799999999999999999999888  89999999   999999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhHHHHHHHHccc
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNK  255 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~~~  255 (395)
                      ||||+++++|||||+|++||+||+|.+..+|+||+||+||.| .|.+++|+.+. +.        .....+++.++..
T Consensus       389 LvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~-d~--------~~~~~~~~~~~~~  457 (475)
T PRK01297        389 LVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGED-DA--------FQLPEIEELLGRK  457 (475)
T ss_pred             EEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHH-HH--------HHHHHHHHHhCCC
Confidence            999999999999999999999999999999999999999997 67777777643 21        2245677777654

>KOG0348|consensus

Probab=99.92  E-value=3.8e-25  Score=220.10  Aligned_cols=203  Identities=18%  Similarity=0.247  Sum_probs=155.7

Q ss_pred             HHHHHHHhcchHHHHHHHHhC---------C------CcchhhhccccCcccc-ccccccCChhHHHH------------
Q psy4150          25 IQRDFHVTHSLASALENLVTY---------G------LRSFYNNLVEVSKEDG-SCPILGKDNDLQNL------------   76 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~---------g------~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~------------   76 (395)
                      .|+|..++|||...+..|...         .      .+|.++.|||++..+. ....-+.||.++.+            
T Consensus       294 DEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~  373 (708)
T KOG0348|consen  294 DEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDK  373 (708)
T ss_pred             cchhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchh
Confidence            399999999999887776652         1      3788999999987763 22223334433330            


Q ss_pred             -HHhh-cc--------cccccccceeeeccccHHHH--HHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC
Q psy4150          77 -LQQL-KP--------KLDINIMSSEYAWSHLKFIR--LREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE  144 (395)
Q Consensus        77 -v~~~-~~--------~~~~~~~~~~~~~~~~K~~~--L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~  144 (395)
                       +... ..        ......+.+.|...+||+..  |..+|.+++..    ....++|||+.|++.++.-++.|....
T Consensus       374 a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~----~~~qk~iVF~S~~d~VeFHy~lf~~~l  449 (708)
T KOG0348|consen  374 AVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKF----EEKQKMIVFFSCSDSVEFHYSLFSEAL  449 (708)
T ss_pred             hhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhh----hhhceeEEEEechhHHHHHHHHHHhhh
Confidence             0000 00        11112266778888887765  56777777665    445699999999999999888875421


Q ss_pred             ----------C----------CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC
Q psy4150         145 ----------P----------MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK  204 (395)
Q Consensus       145 ----------~----------~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~  204 (395)
                                |          ..+...|||   +|+|++|..+++.|+...-.||+||||++||||+|+|.+||.||+|.
T Consensus       450 ~~~~e~~s~~~~s~g~~~l~~~~k~~rLHG---sm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~  526 (708)
T KOG0348|consen  450 LSHLEGSSGAPDSEGLPPLFMDLKFYRLHG---SMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPF  526 (708)
T ss_pred             hcccccccCCcccCCChhhhhcceEEEecC---chhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCC
Confidence                      0          357788999   99999999999999999888999999999999999999999999999


Q ss_pred             ChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         205 SPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       205 s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      ++.+|+||+|||+|+| .|.+++|+.+.+.+
T Consensus       527 s~adylHRvGRTARaG~kG~alLfL~P~Eae  557 (708)
T KOG0348|consen  527 STADYLHRVGRTARAGEKGEALLFLLPSEAE  557 (708)
T ss_pred             CHHHHHHHhhhhhhccCCCceEEEecccHHH
Confidence            9999999999999998 78888888776654

>KOG0339|consensus

Probab=99.92  E-value=1.1e-25  Score=222.62  Aligned_cols=196  Identities=23%  Similarity=0.244  Sum_probs=160.8

Q ss_pred             hHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHh-hc-ccccccccceeeecccc
Q psy4150          24 MIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQ-LK-PKLDINIMSSEYAWSHL   98 (395)
Q Consensus        24 ~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~-~~-~~~~~~~~~~~~~~~~~   98 (395)
                      +-|+|.|.+|||..++.-|..|  +.||+++|++|++..+. ..+.++.+|  +.+++. +. .--.+.+.+..+.....
T Consensus       376 ~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dp--VrvVqg~vgean~dITQ~V~V~~s~~~  453 (731)
T KOG0339|consen  376 LDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDP--VRVVQGEVGEANEDITQTVSVCPSEEK  453 (731)
T ss_pred             EechhhhhccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCC--eeEEEeehhccccchhheeeeccCcHH
Confidence            3499999999999999999998  78999999999987663 455666666  222211 11 10111112233334556


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      |+.+|..-|.....       .+++||||..+..++.+...|.-.+  +.+..+||   +|+|.+|.++|.+|+.+...|
T Consensus       454 Kl~wl~~~L~~f~S-------~gkvlifVTKk~~~e~i~a~Lklk~--~~v~llhg---dkdqa~rn~~ls~fKkk~~~V  521 (731)
T KOG0339|consen  454 KLNWLLRHLVEFSS-------EGKVLIFVTKKADAEEIAANLKLKG--FNVSLLHG---DKDQAERNEVLSKFKKKRKPV  521 (731)
T ss_pred             HHHHHHHHhhhhcc-------CCcEEEEEeccCCHHHHHHHhcccc--ceeeeecC---chhhHHHHHHHHHHhhcCCce
Confidence            88888776666533       4899999999999999999999999  99999999   999999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      ||+||+++||+||+++..|||||+-.+...|.||+||+||+| .|.++.|+++-+.
T Consensus       522 lvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa  577 (731)
T KOG0339|consen  522 LVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDA  577 (731)
T ss_pred             EEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechhhH
Confidence            999999999999999999999999999999999999999997 7889999987443

>KOG0327|consensus

Probab=99.91  E-value=2.2e-24  Score=208.15  Aligned_cols=202  Identities=19%  Similarity=0.272  Sum_probs=162.1

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeee--ccccHH
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYA--WSHLKF  100 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~--~~~~K~  100 (395)
                      |+|.|++.||.+.+..|..+  ...|..+||||+|.++. ..+.++.+|-.+.+-.+.   +....+.+.|.  ...+|+
T Consensus       177 EaDEmLs~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~---ltl~gikq~~i~v~k~~k~  253 (397)
T KOG0327|consen  177 EADEMLSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDE---LTLEGIKQFYINVEKEEKL  253 (397)
T ss_pred             chHhhhccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchh---hhhhheeeeeeeccccccc
Confidence            89999999999998888886  45699999999998873 345556555322111110   11222334443  345588


Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEE
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI  180 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLV  180 (395)
                      ..|+.+..+          -.+.+|||||++.+..|...|..++  +.+.++||   +|.+.+|..+++.|+.|+.+|||
T Consensus       254 ~~l~dl~~~----------~~q~~if~nt~r~v~~l~~~L~~~~--~~~s~~~~---d~~q~~R~~~~~ef~~gssrvlI  318 (397)
T KOG0327|consen  254 DTLCDLYRR----------VTQAVIFCNTRRKVDNLTDKLRAHG--FTVSAIHG---DMEQNERDTLMREFRSGSSRVLI  318 (397)
T ss_pred             cHHHHHHHh----------hhcceEEecchhhHHHHHHHHhhCC--ceEEEeec---ccchhhhhHHHHHhhcCCceEEe
Confidence            888888773          2678999999999999999998888  99999999   99999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhHHHHHHHHcc
Q psy4150         181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCKSYVEKIINN  254 (395)
Q Consensus       181 aT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~~  254 (395)
                      +|++++||+|+..+++|||||+|....+|+||+||+||.| .|.++.++++.+..         ....+++..+.
T Consensus       319 ttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~---------~lk~ie~~y~~  384 (397)
T KOG0327|consen  319 TTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVR---------DLKDIEKFYNT  384 (397)
T ss_pred             eccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHH---------HHHhHHHhcCC
Confidence            9999999999999999999999999999999999999996 78888888765542         23556665544

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

Probab=99.91  E-value=2.3e-24  Score=232.42  Aligned_cols=151  Identities=17%  Similarity=0.276  Sum_probs=115.4

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccC----C--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLE----P--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGE  193 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~----~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~  193 (395)
                      +.++||||+|+..|+.++..|.+..    +  ..++..+||   ++++.+|.+++++|++|++++|||||++++|||||+
T Consensus       271 ~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hg---g~~~~eR~~ie~~f~~G~i~vLVaTd~lerGIDI~~  347 (742)
T TIGR03817       271 GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRA---GYLPEDRRELERALRDGELLGVATTNALELGVDISG  347 (742)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheec---CCCHHHHHHHHHHHHcCCceEEEECchHhccCCccc
Confidence            4799999999999999999887631    1  257788899   999999999999999999999999999999999999


Q ss_pred             CCEEEEcCCCCChhhHhhhccccccccC-ceEEEEEeCCchhhHHHHHHHHhHHHHHHHHcccchhhhhcccCCCCCCCC
Q psy4150         194 IDLVICFDAQKSPIKMVQRLGRTGRKRN-GRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAH  272 (395)
Q Consensus       194 v~~VI~~d~p~s~~~yiQr~GRagR~~~-g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~i~~~  272 (395)
                      +++||+||+|.+..+|+||+|||||.|. |.+++++.+...+..+       ...+++.++.......+...++..+..|
T Consensus       348 vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~-------~~~~~~~~~~~~e~~~~~~~n~~il~~h  420 (742)
T TIGR03817       348 LDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYL-------VHHPEALFDRPVEATVFDPDNPYVLGPH  420 (742)
T ss_pred             ccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHH-------HhCHHHHhcCCCccceeCCCcHHHHHHH
Confidence            9999999999999999999999999974 5555554433322222       2344556655433323344555555556


Q ss_pred             cchhhhhh
Q psy4150         273 VTPRIKCL  280 (395)
Q Consensus       273 ~~~~~~~~  280 (395)
                      +.+.+.+.
T Consensus       421 l~~aa~e~  428 (742)
T TIGR03817       421 LCCAAAEL  428 (742)
T ss_pred             HHHHHhcC
Confidence            65555444

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.

>KOG4284|consensus

Probab=99.90  E-value=2e-24  Score=218.52  Aligned_cols=202  Identities=19%  Similarity=0.262  Sum_probs=169.3

Q ss_pred             hHHHHHHHh-cchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeecccc-
Q psy4150          24 MIQRDFHVT-HSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHL-   98 (395)
Q Consensus        24 ~lead~~~~-~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~-   98 (395)
                      +-|||..++ -+|.+.+++|...  ..||.+.||||.|.... ....+|.+|.++..-......+...+  ..+..+.+ 
T Consensus       173 LDEADkL~~t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQ--yv~~~~s~n  250 (980)
T KOG4284|consen  173 LDEADKLMDTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQ--YVVAKCSPN  250 (980)
T ss_pred             eccHHhhhchhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhh--eeeeccCCc
Confidence            348998888 7888889988774  67999999999998763 56788999998877666555554443  11222223 


Q ss_pred             --------HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          99 --------KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        99 --------K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                              |+..|.+++..        -+..++||||+....|+-++.+|...|  +.|.++.|   .|+|.+|..++..
T Consensus       251 nsveemrlklq~L~~vf~~--------ipy~QAlVF~~~~sra~~~a~~L~ssG--~d~~~ISg---aM~Q~~Rl~a~~~  317 (980)
T KOG4284|consen  251 NSVEEMRLKLQKLTHVFKS--------IPYVQALVFCDQISRAEPIATHLKSSG--LDVTFISG---AMSQKDRLLAVDQ  317 (980)
T ss_pred             chHHHHHHHHHHHHHHHhh--------CchHHHHhhhhhhhhhhHHHHHhhccC--CCeEEecc---ccchhHHHHHHHH
Confidence                    55555555544        456789999999999999999999999  99999999   9999999999999


Q ss_pred             HhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHH
Q psy4150         171 FRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTS  240 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~  240 (395)
                      ++.-.++|||+||+.+||||-+.|++|||.|+|.+..+|.||||||||.| .|.++.|++.+.+...|..+
T Consensus       318 lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e~~~f~~m  388 (980)
T KOG4284|consen  318 LRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERELKGFTAM  388 (980)
T ss_pred             hhhceEEEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchhhhhhHHH
Confidence            99999999999999999999999999999999999999999999999998 79999999998887666443

>KOG0346|consensus

Probab=99.90  E-value=3.4e-24  Score=209.23  Aligned_cols=196  Identities=17%  Similarity=0.247  Sum_probs=160.0

Q ss_pred             HHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCccccccc-cccCChhHHHHHHhhcccccccccceee--eccccH
Q psy4150          25 IQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDGSCP-ILGKDNDLQNLLQQLKPKLDINIMSSEY--AWSHLK   99 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~~~~-~l~~~~~~~~~v~~~~~~~~~~~~~~~~--~~~~~K   99 (395)
                      -|||.++..|+.+.+..|.++  ..-|.++.|||++..+...+ .++.+|-...+-...  ....+.+.|.+  +...+|
T Consensus       177 DEADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~e--l~~~dqL~Qy~v~cse~DK  254 (569)
T KOG0346|consen  177 DEADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGE--LPNPDQLTQYQVKCSEEDK  254 (569)
T ss_pred             chhhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEecccc--CCCcccceEEEEEeccchh
Confidence            499999999999999999887  45688999999998875433 344555433222111  11122233333  356679


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      +-.++.+|.-.+-.       +++||||||.+.|..|--+|...|  ++.+++.|   .|+...|..++++|..|-++++
T Consensus       255 flllyallKL~LI~-------gKsliFVNtIdr~YrLkLfLeqFG--iksciLNs---eLP~NSR~Hii~QFNkG~Ydiv  322 (569)
T KOG0346|consen  255 FLLLYALLKLRLIR-------GKSLIFVNTIDRCYRLKLFLEQFG--IKSCILNS---ELPANSRCHIIEQFNKGLYDIV  322 (569)
T ss_pred             HHHHHHHHHHHHhc-------CceEEEEechhhhHHHHHHHHHhC--cHhhhhcc---cccccchhhHHHHhhCcceeEE
Confidence            99888888776554       899999999999999999999999  99999999   9999999999999999999999


Q ss_pred             EEcCc-----------------------------------cccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-Cce
Q psy4150         180 IATSV-----------------------------------GEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGR  223 (395)
Q Consensus       180 VaT~v-----------------------------------~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~  223 (395)
                      ||||.                                   ++||||+.+|..|||||+|.++.+||||+|||||++ .|.
T Consensus       323 IAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~Gt  402 (569)
T KOG0346|consen  323 IATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGT  402 (569)
T ss_pred             EEccCccchhhhhccccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCCCc
Confidence            99991                                   359999999999999999999999999999999996 788


Q ss_pred             EEEEEeCCchh
Q psy4150         224 CVILLTQGREA  234 (395)
Q Consensus       224 ~i~l~~~~~e~  234 (395)
                      ++.|+.+.++.
T Consensus       403 alSfv~P~e~~  413 (569)
T KOG0346|consen  403 ALSFVSPKEEF  413 (569)
T ss_pred             eEEEecchHHh
Confidence            88888876554

>PTZ00424 helicase 45; Provisional

Probab=99.90  E-value=7.1e-24  Score=213.83  Aligned_cols=189  Identities=22%  Similarity=0.312  Sum_probs=137.5

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeeccc---cH
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSH---LK   99 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~---~K   99 (395)
                      |+|.+...++...+..+...  ...+.+.+|||++.... ....++.++....+ ..  .......+.+.+....   .+
T Consensus       178 Eah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~-~~--~~~~~~~~~~~~~~~~~~~~~  254 (401)
T PTZ00424        178 EADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILV-KK--DELTLEGIRQFYVAVEKEEWK  254 (401)
T ss_pred             cHHHHHhcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEe-CC--CCcccCCceEEEEecChHHHH
Confidence            88888888877554444333  34678899999986541 11122222211100 00  0011111222232222   24


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ...+..++..        ....++||||+|+..++.+++.|...+  +.+..+||   ++++.+|..+++.|++|+++||
T Consensus       255 ~~~l~~~~~~--------~~~~~~ivF~~t~~~~~~l~~~l~~~~--~~~~~~h~---~~~~~~R~~i~~~f~~g~~~vL  321 (401)
T PTZ00424        255 FDTLCDLYET--------LTITQAIIYCNTRRKVDYLTKKMHERD--FTVSCMHG---DMDQKDRDLIMREFRSGSTRVL  321 (401)
T ss_pred             HHHHHHHHHh--------cCCCeEEEEecCcHHHHHHHHHHHHCC--CcEEEEeC---CCCHHHHHHHHHHHHcCCCCEE
Confidence            4444444332        235789999999999999999999888  89999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      |||+++++|||+|+|++||+||+|.+..+|+||+||+||.| .|.+++++++
T Consensus       322 vaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~  373 (401)
T PTZ00424        322 ITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTP  373 (401)
T ss_pred             EEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcH
Confidence            99999999999999999999999999999999999999996 7778877754

>KOG0334|consensus

Probab=99.90  E-value=3.5e-24  Score=227.68  Aligned_cols=192  Identities=22%  Similarity=0.323  Sum_probs=157.8

Q ss_pred             hHHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeee---ccc
Q psy4150          24 MIQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYA---WSH   97 (395)
Q Consensus        24 ~lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~---~~~   97 (395)
                      +.|||.|++|||.+.+-.|+.+  ..||+.+||||++..+. ....++..| +. ++......+ ...+.+.+.   ..+
T Consensus       521 ~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~P-ve-iiv~~~svV-~k~V~q~v~V~~~e~  597 (997)
T KOG0334|consen  521 LDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKP-VE-IIVGGRSVV-CKEVTQVVRVCAIEN  597 (997)
T ss_pred             echhhhhheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCC-ee-EEEccceeE-eccceEEEEEecCch
Confidence            4599999999999887777775  67999999999998763 223344433 22 111121111 111233322   367


Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .|+.+|.+||.+...       ..++||||.....|+.|.+-|.+.|  +.+..+||   +.++.+|..++++|++|.++
T Consensus       598 eKf~kL~eLl~e~~e-------~~~tiiFv~~qe~~d~l~~~L~~ag--~~~~slHG---gv~q~dR~sti~dfK~~~~~  665 (997)
T KOG0334|consen  598 EKFLKLLELLGERYE-------DGKTIIFVDKQEKADALLRDLQKAG--YNCDSLHG---GVDQHDRSSTIEDFKNGVVN  665 (997)
T ss_pred             HHHHHHHHHHHHHhh-------cCCEEEEEcCchHHHHHHHHHHhcC--cchhhhcC---CCchHHHHhHHHHHhccCce
Confidence            899999999988765       4899999999999999999999888  89999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      +||||+++++|||+.++.+|||||+|.....|+||+|||||.| .|.+++|+.+
T Consensus       666 LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p  719 (997)
T KOG0334|consen  666 LLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITP  719 (997)
T ss_pred             EEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeCh
Confidence            9999999999999999999999999999999999999999996 7888888887

>KOG0344|consensus

Probab=99.90  E-value=1e-23  Score=212.58  Aligned_cols=190  Identities=21%  Similarity=0.351  Sum_probs=140.8

Q ss_pred             HHHHHHhc-chHHHHHHHHhC---CCcchhhhccccCccccc-cccccCChhHHHHHHhhcccccccccceeeec---cc
Q psy4150          26 QRDFHVTH-SLASALENLVTY---GLRSFYNNLVEVSKEDGS-CPILGKDNDLQNLLQQLKPKLDINIMSSEYAW---SH   97 (395)
Q Consensus        26 ead~~~~~-~l~~~~~~L~~~---g~r~~~~fsatl~~~~~~-~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~---~~   97 (395)
                      |+|..+.- +|..++.-|...   ..-..-+||||++..+.- +...+.+. ..-++. ..+.. ...+.|...+   ..
T Consensus       296 EaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~-~~vivg-~~~sa-~~~V~QelvF~gse~  372 (593)
T KOG0344|consen  296 EADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDL-KRVIVG-LRNSA-NETVDQELVFCGSEK  372 (593)
T ss_pred             hHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccc-eeEEEe-cchhH-hhhhhhhheeeecch
Confidence            88988888 777665555442   333455788988876621 11111111 000110 11100 1112233332   34


Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHc-ccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK-PLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~-~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      .|+-.+.+++..-        -..++|||+.+.+.|..|...|. -.+  +.+.++||   +.++.+|.++++.|+.|++
T Consensus       373 ~K~lA~rq~v~~g--------~~PP~lIfVQs~eRak~L~~~L~~~~~--i~v~vIh~---e~~~~qrde~~~~FR~g~I  439 (593)
T KOG0344|consen  373 GKLLALRQLVASG--------FKPPVLIFVQSKERAKQLFEELEIYDN--INVDVIHG---ERSQKQRDETMERFRIGKI  439 (593)
T ss_pred             hHHHHHHHHHhcc--------CCCCeEEEEecHHHHHHHHHHhhhccC--cceeeEec---ccchhHHHHHHHHHhccCe
Confidence            4777777777663        35799999999999999999994 444  99999999   9999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         177 NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       177 ~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      +|||||++++||||+.+|++|||||+|.+..+|+||+||+||+| .|.++.|+++.
T Consensus       440 wvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~  495 (593)
T KOG0344|consen  440 WVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQ  495 (593)
T ss_pred             eEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccc
Confidence            99999999999999999999999999999999999999999997 78999998873

>KOG0347|consensus

Probab=99.89  E-value=3.1e-23  Score=207.07  Aligned_cols=212  Identities=19%  Similarity=0.200  Sum_probs=145.0

Q ss_pred             HHHHHHhcchHHHHHHHHhC-------CCcchhhhccccCcccc---------ccccccCChhHHHHHHhhccccccccc
Q psy4150          26 QRDFHVTHSLASALENLVTY-------GLRSFYNNLVEVSKEDG---------SCPILGKDNDLQNLLQQLKPKLDINIM   89 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~-------g~r~~~~fsatl~~~~~---------~~~~l~~~~~~~~~v~~~~~~~~~~~~   89 (395)
                      |+|+|+.-|..+.+..|..+       ..+|++.||||++-...         ..+..-.+..+..++..+.-.-  +. 
T Consensus       348 EaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~--kp-  424 (731)
T KOG0347|consen  348 EADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRG--KP-  424 (731)
T ss_pred             cHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccC--CC-
Confidence            88999888877665555442       46899999999875331         1122222333333333322110  00 


Q ss_pred             ceeeeccccHHHHHHHHHHHHHHh---hhc-------cCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCC
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRL---HAE-------KGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGV  159 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~---~~~-------~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~  159 (395)
                        .+....+-...-..+.+..+.-   ..+       ....+++|||||+.+.+..|+-+|...+  +.+..||.   .|
T Consensus       425 --kiiD~t~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~ryPGrTlVF~NsId~vKRLt~~L~~L~--i~p~~LHA---~M  497 (731)
T KOG0347|consen  425 --KIIDLTPQSATASTLTESLIECPPLEKDLYLYYFLTRYPGRTLVFCNSIDCVKRLTVLLNNLD--IPPLPLHA---SM  497 (731)
T ss_pred             --eeEecCcchhHHHHHHHHhhcCCccccceeEEEEEeecCCceEEEechHHHHHHHHHHHhhcC--CCCchhhH---HH
Confidence              1111111111111111111110   000       1237899999999999999999999999  99999999   99


Q ss_pred             CHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHH
Q psy4150         160 TQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQ  238 (395)
Q Consensus       160 ~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~  238 (395)
                      .|.+|...+++|+.....|||||||++||||||.|.+||+|-+|.+..-|+||.|||+|++ .|..++++.+ .+...  
T Consensus       498 ~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P-~e~~~--  574 (731)
T KOG0347|consen  498 IQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGP-QEVGP--  574 (731)
T ss_pred             HHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeCh-HHhHH--
Confidence            9999999999999999999999999999999999999999999999999999999999997 5555555554 44433  


Q ss_pred             HHHHHhHHHHHHHHcccc
Q psy4150         239 TSMQTCKSYVEKIINNKS  256 (395)
Q Consensus       239 ~~~~~~~~~i~~~i~~~~  256 (395)
                            +..+.+.+....
T Consensus       575 ------~~KL~ktL~k~~  586 (731)
T KOG0347|consen  575 ------LKKLCKTLKKKE  586 (731)
T ss_pred             ------HHHHHHHHhhcc
Confidence                  344555555443

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

Probab=99.89  E-value=1.9e-22  Score=219.14  Aligned_cols=106  Identities=23%  Similarity=0.336  Sum_probs=100.6

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      +..+||||+|+..|+.++..|...|  +.+..+||   +|++.+|..+++.|+.|+++|||||+++++|||+|+|++||+
T Consensus       680 ~esgIIYC~SRke~E~LAe~L~~~G--ika~~YHA---GLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIH  754 (1195)
T PLN03137        680 DECGIIYCLSRMDCEKVAERLQEFG--HKAAFYHG---SMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIH  754 (1195)
T ss_pred             CCCceeEeCchhHHHHHHHHHHHCC--CCeeeeeC---CCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEE
Confidence            4679999999999999999999999  99999999   999999999999999999999999999999999999999999


Q ss_pred             cCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         200 FDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       200 ~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      ||+|.+++.|+||+|||||.| .|.+++|+..
T Consensus       755 ydlPkSiEsYyQriGRAGRDG~~g~cILlys~  786 (1195)
T PLN03137        755 HSLPKSIEGYHQECGRAGRDGQRSSCVLYYSY  786 (1195)
T ss_pred             cCCCCCHHHHHhhhcccCCCCCCceEEEEecH
Confidence            999999999999999999997 6777777654

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.88  E-value=2e-22  Score=207.90  Aligned_cols=108  Identities=21%  Similarity=0.373  Sum_probs=101.1

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      .+.++||||+|++.++.++..|...|  +.+..+||   +|++.+|..+++.|+.|+++|||||+++++|||+|+|++||
T Consensus       225 ~~~~~IIF~~s~~~~e~la~~L~~~g--~~~~~~H~---~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI  299 (470)
T TIGR00614       225 KGKSGIIYCPSRKKSEQVTASLQNLG--IAAGAYHA---GLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVI  299 (470)
T ss_pred             CCCceEEEECcHHHHHHHHHHHHhcC--CCeeEeeC---CCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEE
Confidence            35677999999999999999999998  99999999   99999999999999999999999999999999999999999


Q ss_pred             EcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         199 CFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       199 ~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      +||+|.+...|+||+|||||.| .|.+++++...
T Consensus       300 ~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~  333 (470)
T TIGR00614       300 HYSLPKSMESYYQESGRAGRDGLPSECHLFYAPA  333 (470)
T ss_pred             EeCCCCCHHHHHhhhcCcCCCCCCceEEEEechh
Confidence            9999999999999999999997 66777776654

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

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.88  E-value=8.3e-22  Score=209.05  Aligned_cols=110  Identities=18%  Similarity=0.346  Sum_probs=102.5

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEE
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLV  197 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~V  197 (395)
                      ..+.++||||+|++.|+.++..|...|  +.+..+||   +|++.+|..++++|+.|+++|||||+++++|||+|+|++|
T Consensus       234 ~~~~~~IIFc~tr~~~e~la~~L~~~g--~~v~~~Ha---~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~V  308 (607)
T PRK11057        234 QRGKSGIIYCNSRAKVEDTAARLQSRG--ISAAAYHA---GLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFV  308 (607)
T ss_pred             cCCCCEEEEECcHHHHHHHHHHHHhCC--CCEEEecC---CCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEE
Confidence            346799999999999999999999998  99999999   9999999999999999999999999999999999999999


Q ss_pred             EEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         198 ICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       198 I~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      |+||+|.|..+|+||+|||||.| .|.+++|+...+
T Consensus       309 I~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d  344 (607)
T PRK11057        309 VHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD  344 (607)
T ss_pred             EEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHH
Confidence            99999999999999999999997 677777766543

>PRK13766 Hef nuclease; Provisional

Probab=99.88  E-value=1.7e-21  Score=212.48  Aligned_cols=190  Identities=38%  Similarity=0.627  Sum_probs=151.2

Q ss_pred             hcchHHHHHHHHhCCCcchhhhccccCccc------cccccccCChhHHHHHHhhcccccccccceeeeccccHHHHHHH
Q psy4150          32 THSLASALENLVTYGLRSFYNNLVEVSKED------GSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLRE  105 (395)
Q Consensus        32 ~~~l~~~~~~L~~~g~r~~~~fsatl~~~~------~~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~K~~~L~~  105 (395)
                      .+.+.++..++..++...++.|+.++....      .....+..++.+...+....          .....+||+..|.+
T Consensus       285 ~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~----------~~~~~~pK~~~L~~  354 (773)
T PRK13766        285 AMKLRHAVELLETQGVEALRRYLERLREEARSSGGSKASKRLVEDPRFRKAVRKAK----------ELDIEHPKLEKLRE  354 (773)
T ss_pred             HHHHHHHHHHHHHhCHHHHHHHHHHHHhhccccCCcHHHHHHHhCHHHHHHHHHHH----------hcccCChHHHHHHH
Confidence            344566777777777777777766543222      01223444444444443221          11345799999999


Q ss_pred             HHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEecc-----CCCCCHHHHHHHHHHHhcCCccEEE
Q psy4150         106 ILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQ-----SSGVTQQEQKEIMKKFRAGEFNTLI  180 (395)
Q Consensus       106 lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~-----~~~~~~~~R~~~l~~Fk~g~~~vLV  180 (395)
                      +|.+.+..    ..+.++||||+++++|+.|+++|...+  +.+..+||.     +++|++.+|..++.+|+.|+++|||
T Consensus       355 il~~~~~~----~~~~kvlIF~~~~~t~~~L~~~L~~~~--~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLv  428 (773)
T PRK13766        355 IVKEQLGK----NPDSRIIVFTQYRDTAEKIVDLLEKEG--IKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLV  428 (773)
T ss_pred             HHHHHHhc----CCCCeEEEEeCcHHHHHHHHHHHHhCC--CceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEE
Confidence            99988754    467899999999999999999998888  889999995     3359999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchhhHH
Q psy4150         181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNF  237 (395)
Q Consensus       181 aT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~  237 (395)
                      ||+++++|+|+|.|++||+||+|+++..|+||+||+||.|.|.++++++.++.++.+
T Consensus       429 aT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~~~v~~l~~~~t~ee~~  485 (773)
T PRK13766        429 STSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEEGRVVVLIAKGTRDEAY  485 (773)
T ss_pred             ECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCCCEEEEEEeCCChHHHH
Confidence            999999999999999999999999999999999999999999999999988765543

>KOG0350|consensus

Probab=99.87  E-value=5.4e-22  Score=196.49  Aligned_cols=113  Identities=27%  Similarity=0.469  Sum_probs=102.2

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHc-ccC-CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCC
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLK-PLE-PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEID  195 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~-~~~-~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~  195 (395)
                      ....++|+|+++..++..|+..|. ..+ +.+++..+.|   +++...|.+.++.|..|+++||||||+++||||+.+|+
T Consensus       427 ~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~---~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~  503 (620)
T KOG0350|consen  427 NKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTG---QLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVD  503 (620)
T ss_pred             hhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhh---hhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccc
Confidence            346899999999999999999998 332 3478888999   99999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         196 LVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       196 ~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      .|||||+|.+..+|+||+|||||+| .|.++.++...+.
T Consensus       504 ~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~  542 (620)
T KOG0350|consen  504 NVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEK  542 (620)
T ss_pred             eEeecCCCchhhHHHHhhcccccccCCceEEEeeccccc
Confidence            9999999999999999999999997 7888888776544

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.85  E-value=7.9e-21  Score=201.28  Aligned_cols=122  Identities=23%  Similarity=0.336  Sum_probs=108.3

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      ...+...+.++|..+        .+.++||||+|+..|+.+++.|...|  +.+..+||   +|++.+|..+++.|..|+
T Consensus       208 ~~~~~~~l~~~l~~~--------~~~~~IIf~~sr~~~e~la~~L~~~g--~~~~~~H~---~l~~~~R~~i~~~F~~g~  274 (591)
T TIGR01389       208 KNNKQKFLLDYLKKH--------RGQSGIIYASSRKKVEELAERLESQG--ISALAYHA---GLSNKVRAENQEDFLYDD  274 (591)
T ss_pred             CCCHHHHHHHHHHhc--------CCCCEEEEECcHHHHHHHHHHHHhCC--CCEEEEEC---CCCHHHHHHHHHHHHcCC
Confidence            345666666666542        35789999999999999999999988  99999999   999999999999999999


Q ss_pred             ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         176 FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       176 ~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      ++|||||+++++|||+|+|++||+||+|.|..+|+|++|||||.| .|.+++++..
T Consensus       275 ~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~  330 (591)
T TIGR01389       275 VKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSP  330 (591)
T ss_pred             CcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCH
Confidence            999999999999999999999999999999999999999999998 5666655544

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.

>KOG0337|consensus

Probab=99.84  E-value=1.2e-21  Score=190.68  Aligned_cols=196  Identities=19%  Similarity=0.200  Sum_probs=157.3

Q ss_pred             HHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCccc-cccccccCChhHHHHHHhhcccccccc-cceeeeccccHH
Q psy4150          25 IQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKED-GSCPILGKDNDLQNLLQQLKPKLDINI-MSSEYAWSHLKF  100 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~-~~~~~l~~~~~~~~~v~~~~~~~~~~~-~~~~~~~~~~K~  100 (395)
                      -|+|..+.|||.+.+..+...  +-+|+++||||+|+.. ...+.-+.+|-++.+-  ....+.... ..-.++....|.
T Consensus       171 dEadrlfemgfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRld--vetkise~lk~~f~~~~~a~K~  248 (529)
T KOG0337|consen  171 DEADRLFEMGFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLD--VETKISELLKVRFFRVRKAEKE  248 (529)
T ss_pred             hhhhHHHhhhhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEee--hhhhcchhhhhheeeeccHHHH
Confidence            489999999999987777664  6789999999999763 2223333344333211  111111111 222334566788


Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEE
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI  180 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLV  180 (395)
                      ..|+.++..+..       ..+++|||.|+..++.+...|+..|  +.+..+.|   .|++..|..-+.+|+.+...+||
T Consensus       249 aaLl~il~~~~~-------~~~t~vf~~tk~hve~~~~ll~~~g--~~~s~iys---slD~~aRk~~~~~F~~~k~~~lv  316 (529)
T KOG0337|consen  249 AALLSILGGRIK-------DKQTIVFVATKHHVEYVRGLLRDFG--GEGSDIYS---SLDQEARKINGRDFRGRKTSILV  316 (529)
T ss_pred             HHHHHHHhcccc-------ccceeEEecccchHHHHHHHHHhcC--CCcccccc---ccChHhhhhccccccCCccceEE
Confidence            888888877644       4789999999999999999999999  88999999   99999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       181 aT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      .||+++||+|||-.+.|||||+|.+..-|+||+||++|+| .|.+|.++.+.+..
T Consensus       317 vTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~  371 (529)
T KOG0337|consen  317 VTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDP  371 (529)
T ss_pred             EehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecccch
Confidence            9999999999999999999999999999999999999997 89999998876654

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

Probab=99.83  E-value=3.6e-20  Score=198.49  Aligned_cols=183  Identities=17%  Similarity=0.258  Sum_probs=130.0

Q ss_pred             HHHHHHhcchHHHHHHHHhC----C-C--cchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeec-c
Q psy4150          26 QRDFHVTHSLASALENLVTY----G-L--RSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAW-S   96 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~----g-~--r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~-~   96 (395)
                      |+|  ++++|.+.+..|...    + .  +|+++||||++.... ....++.++....+..   .......+.+.+.. .
T Consensus       179 EAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~---~~l~a~ki~q~v~v~~  253 (844)
T TIGR02621       179 EAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLK---KRLAAKKIVKLVPPSD  253 (844)
T ss_pred             hhh--hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeeccc---ccccccceEEEEecCh
Confidence            899  889999998888773    1 1  589999999987652 1122333332222211   11111112232222 2


Q ss_pred             ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHH-----HHHHHH
Q psy4150          97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQK-----EIMKKF  171 (395)
Q Consensus        97 ~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~-----~~l~~F  171 (395)
                      ..|+..+...+...+.     ..++++||||||+..|+.+++.|.+.+  +  ..+||   +|++.+|.     .++++|
T Consensus       254 e~Kl~~lv~~L~~ll~-----e~g~~vLVF~NTv~~Aq~L~~~L~~~g--~--~lLHG---~m~q~dR~~~~~~~il~~F  321 (844)
T TIGR02621       254 EKFLSTMVKELNLLMK-----DSGGAILVFCRTVKHVRKVFAKLPKEK--F--ELLTG---TLRGAERDDLVKKEIFNRF  321 (844)
T ss_pred             HHHHHHHHHHHHHHHh-----hCCCcEEEEECCHHHHHHHHHHHHhcC--C--eEeeC---CCCHHHHhhHHHHHHHHHH
Confidence            3355555554444332     235789999999999999999999877  5  89999   99999999     889999


Q ss_pred             hc----CC-------ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC--ceEEEEE
Q psy4150         172 RA----GE-------FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN--GRCVILL  228 (395)
Q Consensus       172 k~----g~-------~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~--g~~i~l~  228 (395)
                      +.    |.       ..|||||+++++||||+. ++||++..|  ..+|+||+||+||.|.  +..+.++
T Consensus       322 k~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv  388 (844)
T TIGR02621       322 LPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVV  388 (844)
T ss_pred             hccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEE
Confidence            87    54       789999999999999986 899998877  6899999999999963  3334444

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.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.82  E-value=1.1e-19  Score=198.58  Aligned_cols=113  Identities=21%  Similarity=0.336  Sum_probs=103.9

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHc-ccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK-PLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~-~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ..+|++.|.++|..+        .+.++||||+++.++..|.+.|. ..|  +++..+||   +|++.+|.++++.|+++
T Consensus       477 ~d~Ki~~L~~~L~~~--------~~~KvLVF~~~~~t~~~L~~~L~~~~G--i~~~~ihG---~~s~~eR~~~~~~F~~~  543 (956)
T PRK04914        477 FDPRVEWLIDFLKSH--------RSEKVLVICAKAATALQLEQALREREG--IRAAVFHE---GMSIIERDRAAAYFADE  543 (956)
T ss_pred             cCHHHHHHHHHHHhc--------CCCeEEEEeCcHHHHHHHHHHHhhccC--eeEEEEEC---CCCHHHHHHHHHHHhcC
Confidence            457888888888663        35799999999999999999995 567  99999999   99999999999999985


Q ss_pred             --CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC
Q psy4150         175 --EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN  221 (395)
Q Consensus       175 --~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~  221 (395)
                        .++|||||+++++|+|++.+++|||||+|||+..|+||+||+||.|+
T Consensus       544 ~~~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ  592 (956)
T PRK04914        544 EDGAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQ  592 (956)
T ss_pred             CCCccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCC
Confidence              69999999999999999999999999999999999999999999984

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.82  E-value=2.1e-20  Score=198.36  Aligned_cols=191  Identities=16%  Similarity=0.114  Sum_probs=131.0

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCccccccccccCChhHHHHHHhhcccccccccceeeeccc------
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSH------   97 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~------   97 (395)
                      |+|.+..++ +-.+.++...  ..++.++||||++........++.++.++.+.    ... ...+.+.|....      
T Consensus       299 EaHEr~~~~-DllL~llk~~~~~~rq~ILmSATl~~dv~~l~~~~~~p~~I~I~----grt-~~pV~~~yi~~~~~~~~~  372 (675)
T PHA02653        299 EVHEHDQIG-DIIIAVARKHIDKIRSLFLMTATLEDDRDRIKEFFPNPAFVHIP----GGT-LFPISEVYVKNKYNPKNK  372 (675)
T ss_pred             ccccCccch-hHHHHHHHHhhhhcCEEEEEccCCcHhHHHHHHHhcCCcEEEeC----CCc-CCCeEEEEeecCcccccc
Confidence            676666655 2223333322  34689999999986653333444444333221    110 011223332111      


Q ss_pred             -----cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHH-
Q psy4150          98 -----LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKF-  171 (395)
Q Consensus        98 -----~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~F-  171 (395)
                           .....+..++....     ...++++||||+++..++.+++.|.+..+.+.+..+||   +|++.  .+++++| 
T Consensus       373 ~~y~~~~k~~~l~~L~~~~-----~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG---~Lsq~--eq~l~~ff  442 (675)
T PHA02653        373 RAYIEEEKKNIVTALKKYT-----PPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHG---KVPNI--DEILEKVY  442 (675)
T ss_pred             hhhhHHHHHHHHHHHHHhh-----cccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccC---CcCHH--HHHHHHHh
Confidence                 11111222222211     12346899999999999999999998744489999999   99975  5677887 


Q ss_pred             hcCCccEEEEcCccccCCCCCCCCEEEEcC---CCC---------ChhhHhhhccccccccCceEEEEEeCCc
Q psy4150         172 RAGEFNTLIATSVGEEGLDIGEIDLVICFD---AQK---------SPIKMVQRLGRTGRKRNGRCVILLTQGR  232 (395)
Q Consensus       172 k~g~~~vLVaT~v~~~GlDip~v~~VI~~d---~p~---------s~~~yiQr~GRagR~~~g~~i~l~~~~~  232 (395)
                      +.|+.+||||||++++|||||+|++||++|   .|.         |..+|+||+|||||.+.|.++.++++.+
T Consensus       443 ~~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~~~G~c~rLyt~~~  515 (675)
T PHA02653        443 SSKNPSIIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRVSPGTYVYFYDLDL  515 (675)
T ss_pred             ccCceeEEeccChhhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCCCCCeEEEEECHHH
Confidence            789999999999999999999999999999   564         7889999999999999999999987654

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.81  E-value=6.2e-20  Score=182.62  Aligned_cols=121  Identities=24%  Similarity=0.272  Sum_probs=100.4

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHH----HHHHHhc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKE----IMKKFRA  173 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~----~l~~Fk~  173 (395)
                      .+...+..++...       ..+.++||||+|++.|+.+++.|.+.++...+..+||   ++++.+|..    +++.|++
T Consensus       207 ~~~~~l~~l~~~~-------~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~---~~~~~~r~~~~~~~~~~f~~  276 (358)
T TIGR01587       207 GEISSLERLLEFI-------KKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHS---RFTEKDRAKKEAELLEEMKK  276 (358)
T ss_pred             cCHHHHHHHHHHh-------hCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEEC---CCCHHHHHHHHHHHHHHhcC
Confidence            4666666666443       2358999999999999999999998885567999999   999999976    4899999


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC-----ceEEEEEeCC
Q psy4150         174 GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN-----GRCVILLTQG  231 (395)
Q Consensus       174 g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~-----g~~i~l~~~~  231 (395)
                      |...|||||+++++|+|++ +++||+++.|  +.+|+||+||+||.|.     |.++++...+
T Consensus       277 ~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~  336 (358)
T TIGR01587       277 NEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAP  336 (358)
T ss_pred             CCCeEEEECcchhceeccC-CCEEEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecC
Confidence            9999999999999999996 8999999877  7899999999999852     2555554433

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.

>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=99.79  E-value=1e-18  Score=147.50  Aligned_cols=118  Identities=33%  Similarity=0.599  Sum_probs=107.2

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .|...+.+++..+..      .+.++||||++...++.+.+.|.+.+  ..+.++||   +++..+|..++..|+.|...
T Consensus        12 ~k~~~i~~~i~~~~~------~~~~~lvf~~~~~~~~~~~~~l~~~~--~~~~~~~~---~~~~~~~~~~~~~f~~~~~~   80 (131)
T cd00079          12 EKLEALLELLKEHLK------KGGKVLIFCPSKKMLDELAELLRKPG--IKVAALHG---DGSQEEREEVLKDFREGEIV   80 (131)
T ss_pred             HHHHHHHHHHHhccc------CCCcEEEEeCcHHHHHHHHHHHHhcC--CcEEEEEC---CCCHHHHHHHHHHHHcCCCc
Confidence            588888888877532      36899999999999999999998866  88999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEE
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVI  226 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~  226 (395)
                      +|+||+++++|+|+|.+++||.++.|++...|+|++||++|.| .|.+++
T Consensus        81 ili~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~  130 (131)
T cd00079          81 VLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAIL  130 (131)
T ss_pred             EEEEcChhhcCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEe
Confidence            9999999999999999999999999999999999999999998 555543

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.79  E-value=1.8e-19  Score=202.77  Aligned_cols=98  Identities=29%  Similarity=0.433  Sum_probs=88.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC-------------------------------CCceeEEeccCCCCCHHHHHHHH
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP-------------------------------MVKASMFVGQSSGVTQQEQKEIM  168 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~-------------------------------~~~~~~lhg~~~~~~~~~R~~~l  168 (395)
                      ..++||||||+..|+.++..|.+...                               .+.+.++||   +|++.+|..++
T Consensus       244 ~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHG---sLSkeeR~~IE  320 (1490)
T PRK09751        244 HRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHG---SVSKEQRAITE  320 (1490)
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccc---cCCHHHHHHHH
Confidence            47899999999999999999976421                               012445667   99999999999


Q ss_pred             HHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc
Q psy4150         169 KKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR  220 (395)
Q Consensus       169 ~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~  220 (395)
                      +.|++|++++||||+++++||||++|++||+|+.|.+..+|+||+||+||..
T Consensus       321 ~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~  372 (1490)
T PRK09751        321 QALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQV  372 (1490)
T ss_pred             HHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCC
Confidence            9999999999999999999999999999999999999999999999999984

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.79  E-value=1.1e-18  Score=191.82  Aligned_cols=110  Identities=26%  Similarity=0.431  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC----CCceeEEeccCCCCCHHHHHHHHHHHhcCCc
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP----MVKASMFVGQSSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~----~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      ..+...|......      +.++||||+|+..|+.++..|.+..+    ...+.++||   +|++.+|..+++.|++|++
T Consensus       271 ~~l~~~L~~~i~~------~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg---~ls~~~R~~ve~~fk~G~i  341 (876)
T PRK13767        271 EALYETLHELIKE------HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHS---SLSREVRLEVEEKLKRGEL  341 (876)
T ss_pred             HHHHHHHHHHHhc------CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeC---CCCHHHHHHHHHHHHcCCC
Confidence            3444555554432      47899999999999999999987432    256888888   9999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccc
Q psy4150         177 NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK  219 (395)
Q Consensus       177 ~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~  219 (395)
                      +|||||+++++|||+|+|++||+||.|.+..+|+||+||+||.
T Consensus       342 ~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~  384 (876)
T PRK13767        342 KVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHR  384 (876)
T ss_pred             eEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCC
Confidence            9999999999999999999999999999999999999999997

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.78  E-value=9.6e-19  Score=183.72  Aligned_cols=127  Identities=14%  Similarity=0.143  Sum_probs=106.7

Q ss_pred             eeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          92 EYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        92 ~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .|.....|...|.+++.....      .+.++||||+|+..++.|+..|.+.|  +++..|||   +++  +|...+..|
T Consensus       451 v~~t~~~K~~aL~~~i~~~~~------~~~pvLIft~t~~~se~L~~~L~~~g--i~~~~Lhg---~~~--~rE~~ii~~  517 (656)
T PRK12898        451 VFLTAAAKWAAVAARVRELHA------QGRPVLVGTRSVAASERLSALLREAG--LPHQVLNA---KQD--AEEAAIVAR  517 (656)
T ss_pred             EEeCHHHHHHHHHHHHHHHHh------cCCCEEEEeCcHHHHHHHHHHHHHCC--CCEEEeeC---CcH--HHHHHHHHH
Confidence            344556688888888876432      24679999999999999999999999  99999999   755  555566667


Q ss_pred             hcCCccEEEEcCccccCCCCC---CCC-----EEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         172 RAGEFNTLIATSVGEEGLDIG---EID-----LVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       172 k~g~~~vLVaT~v~~~GlDip---~v~-----~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      +.+...|+||||+++||+||+   +|.     +||+||.|.|...|+||+|||||.| .|.++++++..
T Consensus       518 ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~e  586 (656)
T PRK12898        518 AGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLE  586 (656)
T ss_pred             cCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechh
Confidence            767778999999999999999   676     9999999999999999999999998 67777777653

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

Probab=99.78  E-value=1.3e-18  Score=179.71  Aligned_cols=110  Identities=23%  Similarity=0.369  Sum_probs=103.0

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEE
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLV  197 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~V  197 (395)
                      ......||||.|++.++.+++.|...|  +.+..+||   +|+..+|..+.+.|..+++.|+|||.+++.|||-|+|.+|
T Consensus       228 ~~~~~GIIYc~sRk~~E~ia~~L~~~g--~~a~~YHa---Gl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfV  302 (590)
T COG0514         228 QLSKSGIIYCLTRKKVEELAEWLRKNG--ISAGAYHA---GLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFV  302 (590)
T ss_pred             ccCCCeEEEEeeHHhHHHHHHHHHHCC--CceEEecC---CCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEE
Confidence            345779999999999999999999998  99999999   9999999999999999999999999999999999999999


Q ss_pred             EEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         198 ICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       198 I~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      |+||+|.|.++|+|-+|||||.| ...+++++.+.+
T Consensus       303 iH~~lP~s~EsYyQE~GRAGRDG~~a~aill~~~~D  338 (590)
T COG0514         303 IHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPED  338 (590)
T ss_pred             EEecCCCCHHHHHHHHhhccCCCCcceEEEeecccc
Confidence            99999999999999999999998 566777776655

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.78  E-value=7.9e-19  Score=195.95  Aligned_cols=108  Identities=23%  Similarity=0.321  Sum_probs=96.2

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      +++++|||+++..++.+++.|.+..|.+++..+||   +|++.+|.+++.+|++|+++|||||+++++|||+|+|++||+
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG---~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi  885 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHG---QMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIII  885 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeC---CCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEE
Confidence            47999999999999999999999877789999999   999999999999999999999999999999999999999996


Q ss_pred             cCCC-CChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         200 FDAQ-KSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       200 ~d~p-~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      .+++ .+...|+||+||+||.| .|.+++++..
T Consensus       886 ~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~  918 (1147)
T PRK10689        886 ERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPH  918 (1147)
T ss_pred             ecCCCCCHHHHHHHhhccCCCCCceEEEEEeCC
Confidence            6554 35668999999999997 5666655543

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.78  E-value=1.2e-18  Score=186.60  Aligned_cols=130  Identities=17%  Similarity=0.196  Sum_probs=112.9

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..|.....|...|.+.+.....      .+.++||||+|+..++.|+..|.+.|  +++..+||   ++.+.++..+...
T Consensus       405 ~i~~~~~~K~~al~~~i~~~~~------~~~pvLIf~~t~~~se~l~~~L~~~g--i~~~~L~~---~~~~~e~~~i~~a  473 (790)
T PRK09200        405 KVFVTLDEKYKAVIEEVKERHE------TGRPVLIGTGSIEQSETFSKLLDEAG--IPHNLLNA---KNAAKEAQIIAEA  473 (790)
T ss_pred             eEEcCHHHHHHHHHHHHHHHHh------cCCCEEEEeCcHHHHHHHHHHHHHCC--CCEEEecC---CccHHHHHHHHHc
Confidence            4455667788888888866422      36899999999999999999999999  99999999   8889888888888


Q ss_pred             HhcCCccEEEEcCccccCCCC---CCCC-----EEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         171 FRAGEFNTLIATSVGEEGLDI---GEID-----LVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDi---p~v~-----~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      ++.|  .|+||||+++||+||   |+|.     +||+||+|.+...|+||+|||||.| .|.++++++..++
T Consensus       474 g~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD~  543 (790)
T PRK09200        474 GQKG--AVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLEDD  543 (790)
T ss_pred             CCCC--eEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchHH
Confidence            7766  799999999999999   7998     9999999999999999999999998 6777777766443

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.78  E-value=6.4e-19  Score=192.94  Aligned_cols=109  Identities=27%  Similarity=0.415  Sum_probs=100.3

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      +++++|||+++..++.+++.|.+..|.+++..+||   +|++.+|..++++|++|+++|||||+++++|||+|+|++||+
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG---~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi  736 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELVPEARIAIAHG---QMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIII  736 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecC---CCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEE
Confidence            58999999999999999999998766689999999   999999999999999999999999999999999999999999


Q ss_pred             cCCCC-ChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         200 FDAQK-SPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       200 ~d~p~-s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      +++|. +..+|+||+||+||.| .|.|++++...
T Consensus       737 ~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       737 ERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             ecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            99976 6779999999999996 67777776543

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.

>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=99.76  E-value=1.5e-18  Score=134.82  Aligned_cols=77  Identities=39%  Similarity=0.664  Sum_probs=73.9

Q ss_pred             HHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccc
Q psy4150         139 VLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR  218 (395)
Q Consensus       139 ~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR  218 (395)
                      +|...+  +.+..+||   ++++.+|..+++.|++|...|||||+++++|+|+|.+++||+|++|+|+..|+|++||+||
T Consensus         2 ~L~~~~--~~~~~i~~---~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R   76 (78)
T PF00271_consen    2 FLEKKG--IKVAIIHG---DMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGR   76 (78)
T ss_dssp             HHHHTT--SSEEEEST---TSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSST
T ss_pred             ChHHCC--CcEEEEEC---CCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCC
Confidence            566777  99999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q psy4150         219 KR  220 (395)
Q Consensus       219 ~~  220 (395)
                      .|
T Consensus        77 ~g   78 (78)
T PF00271_consen   77 IG   78 (78)
T ss_dssp             TT
T ss_pred             CC
Confidence            75

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 ....

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.74  E-value=2.2e-17  Score=177.39  Aligned_cols=127  Identities=21%  Similarity=0.379  Sum_probs=105.7

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCc--------HHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHH
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANY--------RVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEI  167 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t--------~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~  167 (395)
                      ...+...+.+.+.....      .+.+++|||++        ...++.+++.|.+..+.+++..+||   +|++.+|..+
T Consensus       453 ~~~~~~~~~~~i~~~~~------~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG---~m~~~eR~~i  523 (681)
T PRK10917        453 PDSRRDEVYERIREEIA------KGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHG---RMKPAEKDAV  523 (681)
T ss_pred             CcccHHHHHHHHHHHHH------cCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeC---CCCHHHHHHH
Confidence            34455566666665543      36899999995        4567788888888765589999999   9999999999


Q ss_pred             HHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC-ChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         168 MKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-SPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       168 l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~-s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      +++|++|+++|||||+++++|+|+|++++||+||+|. ....|.||+||+||.| .|.|++++..+
T Consensus       524 ~~~F~~g~~~ILVaT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~  589 (681)
T PRK10917        524 MAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDP  589 (681)
T ss_pred             HHHHHcCCCCEEEECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCC
Confidence            9999999999999999999999999999999999997 5778888999999997 67777666433

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.74  E-value=1.2e-17  Score=177.51  Aligned_cols=130  Identities=17%  Similarity=0.203  Sum_probs=112.3

Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      ...|.....|...+.+.+.+...      .+.++||||+|+..++.|+..|.+.|  +++..+||   .+++.++..+..
T Consensus       400 d~i~~~~~~K~~ai~~~i~~~~~------~~~pvLIft~s~~~se~ls~~L~~~g--i~~~~L~a---~~~~~E~~ii~~  468 (762)
T TIGR03714       400 DKIYATLPEKLMATLEDVKEYHE------TGQPVLLITGSVEMSEIYSELLLREG--IPHNLLNA---QNAAKEAQIIAE  468 (762)
T ss_pred             CeEEECHHHHHHHHHHHHHHHhh------CCCCEEEEECcHHHHHHHHHHHHHCC--CCEEEecC---CChHHHHHHHHH
Confidence            34566777899999888876533      36899999999999999999999999  99999999   999999888877


Q ss_pred             HHhcCCccEEEEcCccccCCCCC---------CCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         170 KFRAGEFNTLIATSVGEEGLDIG---------EIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       170 ~Fk~g~~~vLVaT~v~~~GlDip---------~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      .|+.|  .|+||||+++||+||+         ++.+|++|++|..... +||+|||||.| .|.+++|++..+.
T Consensus       469 ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       469 AGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             cCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchh
Confidence            77776  7999999999999999         9999999999988766 99999999998 6777777766443

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.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.73  E-value=5.1e-17  Score=173.25  Aligned_cols=123  Identities=22%  Similarity=0.388  Sum_probs=103.6

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcH--------HHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYR--------VVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~--------~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ....+...+...+..      +.+++|||++.        ..++.+++.|.+..+.+.+..+||   +|++.+|..++++
T Consensus       433 ~~~~~~~~i~~~l~~------g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG---~m~~~eR~~i~~~  503 (630)
T TIGR00643       433 EKDIVYEFIEEEIAK------GRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHG---RMKSDEKEAVMEE  503 (630)
T ss_pred             hHHHHHHHHHHHHHh------CCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeC---CCCHHHHHHHHHH
Confidence            345566666555433      58999999875        567788888887655689999999   9999999999999


Q ss_pred             HhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC-ChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         171 FRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-SPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~-s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      |++|+++|||||+++++|||+|++++||+||+|. +...|.||+||+||.| .|.|++++..
T Consensus       504 F~~g~~~ILVaT~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~~  565 (630)
T TIGR00643       504 FREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKN  565 (630)
T ss_pred             HHcCCCCEEEECceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEECC
Confidence            9999999999999999999999999999999997 6778889999999997 6777766633

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.72  E-value=4.7e-17  Score=172.17  Aligned_cols=131  Identities=17%  Similarity=0.131  Sum_probs=114.2

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..|.....|+.++.+.+.+...      .+.++||||+|+..++.|++.|.+.|  +++..+||   .  +.+|...+..
T Consensus       382 ~i~~t~~~k~~ai~~~i~~~~~------~grpvLV~t~si~~se~ls~~L~~~g--i~~~~Lna---~--q~~rEa~ii~  448 (745)
T TIGR00963       382 LVYKTEEEKWKAVVDEIKERHA------KGQPVLVGTTSVEKSELLSNLLKERG--IPHNVLNA---K--NHEREAEIIA  448 (745)
T ss_pred             eEEcCHHHHHHHHHHHHHHHHh------cCCCEEEEeCcHHHHHHHHHHHHHcC--CCeEEeeC---C--hHHHHHHHHH
Confidence            3445566788887776655433      37899999999999999999999999  99999999   5  8899999999


Q ss_pred             HhcCCccEEEEcCccccCCCCCC-------CCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         171 FRAGEFNTLIATSVGEEGLDIGE-------IDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDip~-------v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      |+.+...|+||||+++||+||+.       ..+||+++.|.|...|.||+|||||.| .|.+.++++..++.
T Consensus       449 ~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD~l  520 (745)
T TIGR00963       449 QAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLEDNL  520 (745)
T ss_pred             hcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccHHH
Confidence            99999999999999999999998       559999999999999999999999998 68888888776543

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.

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.71  E-value=3.4e-17  Score=177.61  Aligned_cols=109  Identities=24%  Similarity=0.333  Sum_probs=99.2

Q ss_pred             CccEEEEcCcHHHHHHHHHHHccc-CCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPL-EPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~-~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      .+.+|||++++..++.+++.|.+. ++.+.+..+||   +|++.+|..+++.|++|..+||||||++++|||||+|++||
T Consensus       209 ~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg---~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VI  285 (819)
T TIGR01970       209 TGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYG---ELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVI  285 (819)
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecC---CCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEE
Confidence            478999999999999999999873 23488999999   99999999999999999999999999999999999999999


Q ss_pred             EcCCCC------------------ChhhHhhhccccccccCceEEEEEeCC
Q psy4150         199 CFDAQK------------------SPIKMVQRLGRTGRKRNGRCVILLTQG  231 (395)
Q Consensus       199 ~~d~p~------------------s~~~yiQr~GRagR~~~g~~i~l~~~~  231 (395)
                      +++.|.                  |..+|+||.|||||.+.|.||.++++.
T Consensus       286 D~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~~~G~cyrL~t~~  336 (819)
T TIGR01970       286 DSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCYRLWSEE  336 (819)
T ss_pred             EcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCCCCCEEEEeCCHH
Confidence            999986                  234699999999999999999998753

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.71  E-value=1.6e-17  Score=184.48  Aligned_cols=188  Identities=17%  Similarity=0.175  Sum_probs=127.2

Q ss_pred             HHH-HHHhcchHHH--HHHHHhCCCcchhhhccccCccccccccccCChhHHHHHHhhcccccccccceeeeccc-----
Q psy4150          26 QRD-FHVTHSLASA--LENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSH-----   97 (395)
Q Consensus        26 ead-~~~~~~l~~~--~~~L~~~g~r~~~~fsatl~~~~~~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-----   97 (395)
                      |+| +++.++|.-.  ...+...+..+.+.+|||++... ....+. +...+.+    ....  ..+...|....     
T Consensus       194 EAHERsLn~DfLLg~Lk~lL~~rpdlKvILmSATid~e~-fs~~F~-~apvI~V----~Gr~--~pVei~y~p~~~~~~~  265 (1294)
T PRK11131        194 EAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPER-FSRHFN-NAPIIEV----SGRT--YPVEVRYRPIVEEADD  265 (1294)
T ss_pred             CccccccccchHHHHHHHhhhcCCCceEEEeeCCCCHHH-HHHHcC-CCCEEEE----cCcc--ccceEEEeecccccch
Confidence            777 5666666532  22333334568899999997432 222222 2211111    1110  11222332211     


Q ss_pred             cHHHHHHHH---HHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC-CCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          98 LKFIRLREI---LESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE-PMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        98 ~K~~~L~~l---L~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~-~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      .+.+.+..+   +..+..     ...+.+|||+++...++.+++.|.+.+ +.+.+..+||   ++++.+|..+++.  .
T Consensus       266 ~~~d~l~~ll~~V~~l~~-----~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg---~Ls~~eQ~~Vf~~--~  335 (1294)
T PRK11131        266 TERDQLQAIFDAVDELGR-----EGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYA---RLSNSEQNRVFQS--H  335 (1294)
T ss_pred             hhHHHHHHHHHHHHHHhc-----CCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeeccc---CCCHHHHHHHhcc--c
Confidence            123333333   333221     346789999999999999999999876 2234677888   9999999999986  5


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEcC---------------CC---CChhhHhhhccccccccCceEEEEEeCC
Q psy4150         174 GEFNTLIATSVGEEGLDIGEIDLVICFD---------------AQ---KSPIKMVQRLGRTGRKRNGRCVILLTQG  231 (395)
Q Consensus       174 g~~~vLVaT~v~~~GlDip~v~~VI~~d---------------~p---~s~~~yiQr~GRagR~~~g~~i~l~~~~  231 (395)
                      |..+||||||++++|||||+|++||+++               +|   .|..+|+||+|||||.+.|.|+.++++.
T Consensus       336 g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~~~G~c~rLyte~  411 (1294)
T PRK11131        336 SGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLYSED  411 (1294)
T ss_pred             CCeeEEEeccHHhhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCCCCcEEEEeCCHH
Confidence            8899999999999999999999999986               33   3557899999999999999999998754

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.70  E-value=1.5e-16  Score=169.04  Aligned_cols=128  Identities=24%  Similarity=0.384  Sum_probs=107.1

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC-
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG-  174 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g-  174 (395)
                      .+.|+..+..++..|-      ..+.++||||.+...++.++..|.       +.++||   ++++.+|..++++|+.| 
T Consensus       478 np~K~~~~~~Li~~he------~~g~kiLVF~~~~~~l~~~a~~L~-------~~~I~G---~ts~~ER~~il~~Fr~~~  541 (732)
T TIGR00603       478 NPNKFRACQFLIRFHE------QRGDKIIVFSDNVFALKEYAIKLG-------KPFIYG---PTSQQERMQILQNFQHNP  541 (732)
T ss_pred             ChHHHHHHHHHHHHHh------hcCCeEEEEeCCHHHHHHHHHHcC-------CceEEC---CCCHHHHHHHHHHHHhCC
Confidence            3456666666665542      246899999999999999998873       346899   99999999999999975 


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCC-ChhhHhhhccccccccCc-e-------EEEEEeCCchhhHHHH
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQK-SPIKMVQRLGRTGRKRNG-R-------CVILLTQGREAHNFQT  239 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~-s~~~yiQr~GRagR~~~g-~-------~i~l~~~~~e~~~~~~  239 (395)
                      .+++||+|+++.+|||+|++++||+++.|. |...|+||+||++|.+.+ .       +|.+++.++.+..+..
T Consensus       542 ~i~vLv~SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E~~~s~  615 (732)
T TIGR00603       542 KVNTIFLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYST  615 (732)
T ss_pred             CccEEEEecccccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchHHHHHH
Confidence            889999999999999999999999999984 999999999999999633 2       2778888888877653

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).

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.70  E-value=4.3e-17  Score=177.06  Aligned_cols=110  Identities=24%  Similarity=0.343  Sum_probs=99.4

Q ss_pred             CccEEEEcCcHHHHHHHHHHHccc-CCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPL-EPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~-~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      .+.+|||++++..++.+++.|... +..+.+..+||   +|++.+|..++..|+.|..+||||||++++|||||+|++||
T Consensus       212 ~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg---~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VI  288 (812)
T PRK11664        212 SGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYG---ALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVV  288 (812)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeC---CCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEE
Confidence            578999999999999999999862 23488999999   99999999999999999999999999999999999999999


Q ss_pred             EcCCCCC------------------hhhHhhhccccccccCceEEEEEeCCc
Q psy4150         199 CFDAQKS------------------PIKMVQRLGRTGRKRNGRCVILLTQGR  232 (395)
Q Consensus       199 ~~d~p~s------------------~~~yiQr~GRagR~~~g~~i~l~~~~~  232 (395)
                      +++.++.                  ..+|+||.|||||.+.|.||.++++..
T Consensus       289 D~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~~~G~cyrL~t~~~  340 (812)
T PRK11664        289 DSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICLHLYSKEQ  340 (812)
T ss_pred             ECCCcccccccccCCcceeEEEeechhhhhhhccccCCCCCcEEEEecCHHH
Confidence            9887753                  358999999999999999999987643

>PRK00254 ski2-like helicase; Provisional

Probab=99.69  E-value=7.6e-17  Score=174.54  Aligned_cols=193  Identities=17%  Similarity=0.235  Sum_probs=123.3

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCccccccccccCChhHHHHHHhhcccccccc-cceeee-ccccHH-
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINI-MSSEYA-WSHLKF-  100 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~~~~~l~~~~~~~~~v~~~~~~~~~~~-~~~~~~-~~~~K~-  100 (395)
                      |++.+.+.+....++.+...  +..+.+.+|||++.....+.++.. ..+.   ....+...... ..+.+. ....+. 
T Consensus       146 E~H~l~~~~rg~~le~il~~l~~~~qiI~lSATl~n~~~la~wl~~-~~~~---~~~rpv~l~~~~~~~~~~~~~~~~~~  221 (720)
T PRK00254        146 EIHLIGSYDRGATLEMILTHMLGRAQILGLSATVGNAEELAEWLNA-ELVV---SDWRPVKLRKGVFYQGFLFWEDGKIE  221 (720)
T ss_pred             CcCccCCccchHHHHHHHHhcCcCCcEEEEEccCCCHHHHHHHhCC-cccc---CCCCCCcceeeEecCCeeeccCcchh
Confidence            55666555666666666654  346788899998754322222211 1100   01111000000 001111 111111 


Q ss_pred             ---HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC----------------------C---------C
Q psy4150         101 ---IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE----------------------P---------M  146 (395)
Q Consensus       101 ---~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~----------------------~---------~  146 (395)
                         .....++.+....      +.++||||+|+..|+.++..|....                      +         .
T Consensus       222 ~~~~~~~~~~~~~i~~------~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~  295 (720)
T PRK00254        222 RFPNSWESLVYDAVKK------GKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALR  295 (720)
T ss_pred             cchHHHHHHHHHHHHh------CCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHh
Confidence               2223334343332      5799999999999998887664210                      0         0


Q ss_pred             CceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE-------cCCCC-ChhhHhhhcccccc
Q psy4150         147 VKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC-------FDAQK-SPIKMVQRLGRTGR  218 (395)
Q Consensus       147 ~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~-------~d~p~-s~~~yiQr~GRagR  218 (395)
                      ..+.++||   +|++.+|..+++.|++|.++|||||+++++|+|+|.+++||.       ++.|. +..+|+||+|||||
T Consensus       296 ~gv~~hHa---gl~~~eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR  372 (720)
T PRK00254        296 GGVAFHHA---GLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGR  372 (720)
T ss_pred             hCEEEeCC---CCCHHHHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCC
Confidence            24677788   999999999999999999999999999999999999999994       56555 56799999999999


Q ss_pred             cc---CceEEEEEeCC
Q psy4150         219 KR---NGRCVILLTQG  231 (395)
Q Consensus       219 ~~---~g~~i~l~~~~  231 (395)
                      .|   .|.+++++...
T Consensus       373 ~~~d~~G~~ii~~~~~  388 (720)
T PRK00254        373 PKYDEVGEAIIVATTE  388 (720)
T ss_pred             CCcCCCceEEEEecCc
Confidence            85   57788777653

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.68  E-value=1.6e-16  Score=169.40  Aligned_cols=131  Identities=19%  Similarity=0.190  Sum_probs=113.3

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..|.....|...+.+.+.....      .+.++||||+|+..++.|+..|.+.|  +++..+|+   ++.+.++..+.+.
T Consensus       417 ~i~~t~~~K~~al~~~i~~~~~------~g~pvLI~t~si~~se~ls~~L~~~g--i~~~~Lna---~~~~~Ea~ii~~a  485 (796)
T PRK12906        417 LLYPTLDSKFNAVVKEIKERHA------KGQPVLVGTVAIESSERLSHLLDEAG--IPHAVLNA---KNHAKEAEIIMNA  485 (796)
T ss_pred             eEEcCHHHHHHHHHHHHHHHHh------CCCCEEEEeCcHHHHHHHHHHHHHCC--CCeeEecC---CcHHHHHHHHHhc
Confidence            3455667788888888866432      47899999999999999999999999  99999999   8888888888887


Q ss_pred             HhcCCccEEEEcCccccCCCC---CCCC-----EEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         171 FRAGEFNTLIATSVGEEGLDI---GEID-----LVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDi---p~v~-----~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      ++.|.  |+||||+++||+||   ++|.     +||+++.|.|...|.|+.|||||.| +|.+.++++..++.
T Consensus       486 g~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD~l  556 (796)
T PRK12906        486 GQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDDL  556 (796)
T ss_pred             CCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccchH
Confidence            77777  99999999999999   4899     9999999999999999999999998 68888777766443

>PRK02362 ski2-like helicase; Provisional

Probab=99.68  E-value=2e-16  Score=171.66  Aligned_cols=109  Identities=17%  Similarity=0.263  Sum_probs=94.3

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC----------------------------------CCceeEEeccCCCCCHHHHH
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP----------------------------------MVKASMFVGQSSGVTQQEQK  165 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~----------------------------------~~~~~~lhg~~~~~~~~~R~  165 (395)
                      ++++||||+|+..|+.++..|.....                                  ...+.++||   +|++.+|.
T Consensus       243 ~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHa---gl~~~eR~  319 (737)
T PRK02362        243 GGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHA---GLSREHRE  319 (737)
T ss_pred             CCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecC---CCCHHHHH
Confidence            58999999999999999988865321                                  024667788   99999999


Q ss_pred             HHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE----cC-----CCCChhhHhhhcccccccc---CceEEEEEeCC
Q psy4150         166 EIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC----FD-----AQKSPIKMVQRLGRTGRKR---NGRCVILLTQG  231 (395)
Q Consensus       166 ~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~----~d-----~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~  231 (395)
                      .+++.|++|.++|||||+++++|+|+|.+.+||+    ||     .|.+..+|+||+|||||.|   .|.+++++...
T Consensus       320 ~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~  397 (737)
T PRK02362        320 LVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSY  397 (737)
T ss_pred             HHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCc
Confidence            9999999999999999999999999999999997    77     5889999999999999997   37777776554

>KOG0349|consensus

Probab=99.68  E-value=7.9e-17  Score=157.60  Aligned_cols=114  Identities=24%  Similarity=0.347  Sum_probs=105.8

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCC-CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEE
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEP-MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLV  197 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~-~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~V  197 (395)
                      .-.++||||.|+..|+.|..++.+.|. .+.+.++||   +..+.+|.+.++.|+.+..+.|||||+++|||||..+.++
T Consensus       504 ~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhg---DrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~  580 (725)
T KOG0349|consen  504 AMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHG---DRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFM  580 (725)
T ss_pred             ccCceEEEEeccccchHHHHHHHHcCCccceeEEEec---CCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceE
Confidence            457999999999999999999998764 689999999   9999999999999999999999999999999999999999


Q ss_pred             EEcCCCCChhhHhhhccccccc-cCceEEEEEeCCchhh
Q psy4150         198 ICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQGREAH  235 (395)
Q Consensus       198 I~~d~p~s~~~yiQr~GRagR~-~~g~~i~l~~~~~e~~  235 (395)
                      ||..+|.....|+||+||+||+ +-|-++.++....+.-
T Consensus       581 invtlpd~k~nyvhrigrvgraermglaislvat~~ekv  619 (725)
T KOG0349|consen  581 INVTLPDDKTNYVHRIGRVGRAERMGLAISLVATVPEKV  619 (725)
T ss_pred             EEEecCcccchhhhhhhccchhhhcceeEEEeeccchhe
Confidence            9999999999999999999999 6899998887766543

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.67  E-value=2.9e-16  Score=163.28  Aligned_cols=99  Identities=23%  Similarity=0.336  Sum_probs=93.4

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEc-CccccCCCCCCCCEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIAT-SVGEEGLDIGEIDLVI  198 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT-~v~~~GlDip~v~~VI  198 (395)
                      +.++||||++.++++.|++.|.+.+  +++.++||   ++++.+|..+++.|+.|...||||| ++++||+|+|++++||
T Consensus       344 ~~~~lV~~~~~~h~~~L~~~L~~~g--~~v~~i~G---~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vI  418 (501)
T PHA02558        344 GENTFVMFKYVEHGKPLYEMLKKVY--DKVYYVSG---EVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVI  418 (501)
T ss_pred             CCCEEEEEEEHHHHHHHHHHHHHcC--CCEEEEeC---CCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEE
Confidence            5789999999999999999999988  89999999   9999999999999999999999998 8999999999999999


Q ss_pred             EcCCCCChhhHhhhccccccccCce
Q psy4150         199 CFDAQKSPIKMVQRLGRTGRKRNGR  223 (395)
Q Consensus       199 ~~d~p~s~~~yiQr~GRagR~~~g~  223 (395)
                      +++++.+...|+||+||++|.+.|+
T Consensus       419 l~~p~~s~~~~~QriGR~~R~~~~K  443 (501)
T PHA02558        419 FAHPSKSKIIVLQSIGRVLRKHGSK  443 (501)
T ss_pred             EecCCcchhhhhhhhhccccCCCCC
Confidence            9999999999999999999996544

>PRK01172 ski2-like helicase; Provisional

Probab=99.66  E-value=2.8e-16  Score=169.02  Aligned_cols=109  Identities=22%  Similarity=0.312  Sum_probs=90.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCC-----------------------CceeEEeccCCCCCHHHHHHHHHHHhcCCc
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPM-----------------------VKASMFVGQSSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~-----------------------~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      ++++||||++++.|+.++..|....+.                       ..+.++||   +|++.+|..+++.|++|.+
T Consensus       236 ~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~ha---gl~~~eR~~ve~~f~~g~i  312 (674)
T PRK01172        236 GGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHA---GLSNEQRRFIEEMFRNRYI  312 (674)
T ss_pred             CCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecC---CCCHHHHHHHHHHHHcCCC
Confidence            579999999999999999988654211                       13566777   9999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEcCC---------CCChhhHhhhcccccccc---CceEEEEEeCCc
Q psy4150         177 NTLIATSVGEEGLDIGEIDLVICFDA---------QKSPIKMVQRLGRTGRKR---NGRCVILLTQGR  232 (395)
Q Consensus       177 ~vLVaT~v~~~GlDip~v~~VI~~d~---------p~s~~~yiQr~GRagR~~---~g~~i~l~~~~~  232 (395)
                      +|||||+++++|+|+|.. .||++|.         |.+..+|.||+|||||.|   .|.+++++...+
T Consensus       313 ~VLvaT~~la~Gvnipa~-~VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~  379 (674)
T PRK01172        313 KVIVATPTLAAGVNLPAR-LVIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPA  379 (674)
T ss_pred             eEEEecchhhccCCCcce-EEEEcCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcc
Confidence            999999999999999986 5555554         457889999999999997   577777765543

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.65  E-value=4.2e-16  Score=167.54  Aligned_cols=132  Identities=17%  Similarity=0.184  Sum_probs=114.6

Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      ...|.....|+..|.+.+.....      .+.++||||+|+..++.|+..|...+  +++.+||+     .+.+|...+-
T Consensus       574 d~vy~t~~eK~~Ali~~I~~~~~------~grpVLIft~Sve~sE~Ls~~L~~~g--I~h~vLna-----kq~~REa~Ii  640 (1025)
T PRK12900        574 DLVYKTRREKYNAIVLKVEELQK------KGQPVLVGTASVEVSETLSRMLRAKR--IAHNVLNA-----KQHDREAEIV  640 (1025)
T ss_pred             CeEecCHHHHHHHHHHHHHHHhh------CCCCEEEEeCcHHHHHHHHHHHHHcC--CCceeecC-----CHHHhHHHHH
Confidence            34455667799999998877543      36899999999999999999999999  99999997     4889999999


Q ss_pred             HHhcCCccEEEEcCccccCCCCC---CCC-----EEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         170 KFRAGEFNTLIATSVGEEGLDIG---EID-----LVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       170 ~Fk~g~~~vLVaT~v~~~GlDip---~v~-----~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      .|+.+...|+||||+++||+||+   +|.     +||+++.|.|...|.||+|||||.| +|.+++|++..++.
T Consensus       641 a~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~L  714 (1025)
T PRK12900        641 AEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDEL  714 (1025)
T ss_pred             HhcCCCCeEEEeccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHHH
Confidence            99999999999999999999999   554     4499999999999999999999998 78888887775544

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

Probab=99.65  E-value=5.6e-16  Score=165.64  Aligned_cols=120  Identities=29%  Similarity=0.458  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEE
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI  180 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLV  180 (395)
                      ..+...|.+....      ...+||||||+.++|.++..|.+.++ ..+...||   .++...|..+.++|++|+.+++|
T Consensus       240 ~~~~~~i~~~v~~------~~ttLIF~NTR~~aE~l~~~L~~~~~-~~i~~HHg---SlSre~R~~vE~~lk~G~lravV  309 (814)
T COG1201         240 AALYERIAELVKK------HRTTLIFTNTRSGAERLAFRLKKLGP-DIIEVHHG---SLSRELRLEVEERLKEGELKAVV  309 (814)
T ss_pred             HHHHHHHHHHHhh------cCcEEEEEeChHHHHHHHHHHHHhcC-Cceeeecc---cccHHHHHHHHHHHhcCCceEEE
Confidence            3344444444443      25799999999999999999999874 45555566   99999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccc-c-CceEEEEEeC
Q psy4150         181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-R-NGRCVILLTQ  230 (395)
Q Consensus       181 aT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~-~-~g~~i~l~~~  230 (395)
                      ||+.++-|||+++|++||+|+.|.++..++||+||+|+. + ..+.+++..+
T Consensus       310 ~TSSLELGIDiG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         310 ATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             EccchhhccccCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            999999999999999999999999999999999999998 3 3445555443

>KOG0329|consensus

Probab=99.64  E-value=1.2e-16  Score=147.23  Aligned_cols=162  Identities=19%  Similarity=0.313  Sum_probs=122.7

Q ss_pred             HHHHHHh-cchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeec--cccH
Q psy4150          26 QRDFHVT-HSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAW--SHLK   99 (395)
Q Consensus        26 ead~~~~-~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~--~~~K   99 (395)
                      |.|.|+. +.+..++..+...  .-.|.++||||++++++ .|+.+|.+|  .+++.+....+....+.|.|..  ...|
T Consensus       193 Ecdkmle~lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdP--mEi~vDdE~KLtLHGLqQ~YvkLke~eK  270 (387)
T KOG0329|consen  193 ECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDP--MEIFVDDEAKLTLHGLQQYYVKLKENEK  270 (387)
T ss_pred             hHHHHHHHHHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCc--hhhhccchhhhhhhhHHHHHHhhhhhhh
Confidence            6665544 3334555555443  45788999999999886 899999999  6666666666666667777764  4568


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ..+|.++|..+        ...+++||+.+...                          ++          |   .-+ |
T Consensus       271 Nrkl~dLLd~L--------eFNQVvIFvKsv~R--------------------------l~----------f---~kr-~  302 (387)
T KOG0329|consen  271 NRKLNDLLDVL--------EFNQVVIFVKSVQR--------------------------LS----------F---QKR-L  302 (387)
T ss_pred             hhhhhhhhhhh--------hhcceeEeeehhhh--------------------------hh----------h---hhh-h
Confidence            88888877654        24789999987654                          00          2   122 7


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHH
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNF  237 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~  237 (395)
                      |||++.+||+||..|++|+|||.|.++.+|+||+|||||.| .|-++.++....+...+
T Consensus       303 vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iL  361 (387)
T KOG0329|consen  303 VATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL  361 (387)
T ss_pred             HHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHh
Confidence            99999999999999999999999999999999999999998 67788888776655443

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.63  E-value=8.6e-16  Score=118.85  Aligned_cols=81  Identities=43%  Similarity=0.765  Sum_probs=76.3

Q ss_pred             HHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcc
Q psy4150         135 EIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLG  214 (395)
Q Consensus       135 ~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~G  214 (395)
                      .+++.|...+  +.+..+||   +++..+|..+++.|..|...|||+|+++++|+|+|.++.||.+++|++...|+|++|
T Consensus         2 ~l~~~l~~~~--~~~~~~~~---~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~g   76 (82)
T smart00490        2 ELAELLKELG--IKVARLHG---GLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIG   76 (82)
T ss_pred             HHHHHHHHCC--CeEEEEEC---CCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhc
Confidence            4667777777  89999999   999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q psy4150         215 RTGRKR  220 (395)
Q Consensus       215 RagR~~  220 (395)
                      |++|.|
T Consensus        77 R~~R~g   82 (82)
T smart00490       77 RAGRAG   82 (82)
T ss_pred             ccccCC
Confidence            999975

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.63  E-value=5e-16  Score=173.13  Aligned_cols=124  Identities=19%  Similarity=0.315  Sum_probs=102.6

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC-CCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE-PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~-~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      +...+...+..+..     ...+.+|||+++...++.+++.|.+.+ +.+.+..+||   +|++.+|..+++.+  +..+
T Consensus       263 ~~~~i~~~I~~l~~-----~~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg---~Ls~~eQ~~vf~~~--~~rk  332 (1283)
T TIGR01967       263 QLEAILDAVDELFA-----EGPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYA---RLSNKEQQRVFQPH--SGRR  332 (1283)
T ss_pred             HHHHHHHHHHHHHh-----hCCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccC---CCCHHHHHHHhCCC--CCce
Confidence            45556666655543     235789999999999999999998765 2366788999   99999999987654  3469


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCC------------------ChhhHhhhccccccccCceEEEEEeCCc
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQK------------------SPIKMVQRLGRTGRKRNGRCVILLTQGR  232 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~------------------s~~~yiQr~GRagR~~~g~~i~l~~~~~  232 (395)
                      ||||||++++|||||+|.+||+++++.                  |..+|+||.|||||.+.|.||.++++.+
T Consensus       333 IVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~~G~cyRLyte~~  405 (1283)
T TIGR01967       333 IVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLYSEED  405 (1283)
T ss_pred             EEEeccHHHhccccCCeeEEEeCCCccccccccccCccccCCccCCHHHHHHHhhhhCCCCCceEEEecCHHH
Confidence            999999999999999999999999543                  5679999999999999999999987543

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.62  E-value=7.1e-16  Score=172.79  Aligned_cols=149  Identities=17%  Similarity=0.185  Sum_probs=109.7

Q ss_pred             CcchhhhccccCcc-ccccccccCChhHHHHHHhhcccccccccceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEE
Q psy4150          47 LRSFYNNLVEVSKE-DGSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVII  125 (395)
Q Consensus        47 ~r~~~~fsatl~~~-~~~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iV  125 (395)
                      .++++.||||+++. ...  .++.+..... +..  .......+.+.|.....|...|.+++..+         +.++||
T Consensus       268 ~~q~ilfSAT~~~~~~~~--~l~~~ll~~~-v~~--~~~~~rnI~~~yi~~~~k~~~L~~ll~~l---------~~~~LI  333 (1176)
T PRK09401        268 KGVLVVSSATGRPRGNRV--KLFRELLGFE-VGS--PVFYLRNIVDSYIVDEDSVEKLVELVKRL---------GDGGLI  333 (1176)
T ss_pred             CceEEEEeCCCCccchHH--HHhhccceEE-ecC--cccccCCceEEEEEcccHHHHHHHHHHhc---------CCCEEE
Confidence            46889999999764 311  1111110000 010  01111224455555557888888777542         357999


Q ss_pred             EcCcHHH---HHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEE----cCccccCCCCCC-CCEE
Q psy4150         126 FANYRVV---VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIA----TSVGEEGLDIGE-IDLV  197 (395)
Q Consensus       126 F~~t~~~---ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVa----T~v~~~GlDip~-v~~V  197 (395)
                      ||+|+..   |+.|+++|...|  +++..+||   +|     ...+++|++|+++||||    ||+++||||+|+ |.+|
T Consensus       334 Fv~t~~~~~~ae~l~~~L~~~g--i~v~~~hg---~l-----~~~l~~F~~G~~~VLVatas~tdv~aRGIDiP~~IryV  403 (1176)
T PRK09401        334 FVPSDKGKEYAEELAEYLEDLG--INAELAIS---GF-----ERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYA  403 (1176)
T ss_pred             EEecccChHHHHHHHHHHHHCC--CcEEEEeC---cH-----HHHHHHHHCCCCCEEEEecCCCCceeecCCCCcceeEE
Confidence            9999877   999999999999  99999999   88     23469999999999999    699999999999 8999


Q ss_pred             EEcCCCC------ChhhHhhhccccccc
Q psy4150         198 ICFDAQK------SPIKMVQRLGRTGRK  219 (395)
Q Consensus       198 I~~d~p~------s~~~yiQr~GRagR~  219 (395)
                      ||||+|.      ....|.||+||+...
T Consensus       404 I~y~vP~~~~~~~~~~~~~~~~~r~~~~  431 (1176)
T PRK09401        404 IFYGVPKFKFSLEEELAPPFLLLRLLSL  431 (1176)
T ss_pred             EEeCCCCEEEeccccccCHHHHHHHHhh
Confidence            9999998      678899999999643

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.59  E-value=5.7e-15  Score=147.37  Aligned_cols=87  Identities=22%  Similarity=0.288  Sum_probs=76.1

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      .+.++||||+|+..++.++..|++.+..+.+..+||   .+++.+|.++      ++.+|||||+++++|||++.+ +||
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g---~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi  340 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITG---FAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI  340 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeec---CCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE
Confidence            467999999999999999999998764467888999   8999988654      478999999999999999987 565


Q ss_pred             EcCCCCChhhHhhhccccc
Q psy4150         199 CFDAQKSPIKMVQRLGRTG  217 (395)
Q Consensus       199 ~~d~p~s~~~yiQr~GRag  217 (395)
                       ++ |.+..+|+||+||+|
T Consensus       341 -~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       341 -FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             -EC-CCCHHHHhhhcccCC
Confidence             55 889999999999997

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.

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

Probab=99.58  E-value=7.2e-15  Score=148.38  Aligned_cols=134  Identities=23%  Similarity=0.394  Sum_probs=118.0

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      ...|.+.+..+.+..+..-++....+++|||+++++.|..|+..|...|  +++..+|+   +|+..+|..+...|.+++
T Consensus       416 e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG--~~a~pYHa---GL~y~eRk~vE~~F~~q~  490 (830)
T COG1202         416 ESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKG--LKAAPYHA---GLPYKERKSVERAFAAQE  490 (830)
T ss_pred             chHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCC--cccccccC---CCcHHHHHHHHHHHhcCC
Confidence            5679999999998887775666678899999999999999999999999  99999999   999999999999999999


Q ss_pred             ccEEEEcCccccCCCCCCCCEEE---EcCCCC-ChhhHhhhcccccccc---CceEEEEEeCCchh
Q psy4150         176 FNTLIATSVGEEGLDIGEIDLVI---CFDAQK-SPIKMVQRLGRTGRKR---NGRCVILLTQGREA  234 (395)
Q Consensus       176 ~~vLVaT~v~~~GlDip~v~~VI---~~d~p~-s~~~yiQr~GRagR~~---~g~~i~l~~~~~e~  234 (395)
                      +.++|+|-.++-|+|+|.-.+|+   -.+..| |+..|.|+.|||||.+   .|.+++++.++...
T Consensus       491 l~~VVTTAAL~AGVDFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg~~Y  556 (830)
T COG1202         491 LAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGKKY  556 (830)
T ss_pred             cceEeehhhhhcCCCCchHHHHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCChhh
Confidence            99999999999999999765553   234455 8999999999999995   79999998887544

>KOG0351|consensus

Probab=99.57  E-value=1e-14  Score=158.85  Aligned_cols=109  Identities=24%  Similarity=0.373  Sum_probs=101.4

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEE
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLV  197 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~V  197 (395)
                      .+...+||+|.++.+|+.++..|+..|  +++..+|+   +|+..+|..+.++|-.++++|+|||=+.+.|||.|+|..|
T Consensus       483 ~~~~s~IIYC~sr~~ce~vs~~L~~~~--~~a~~YHA---Gl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~V  557 (941)
T KOG0351|consen  483 HPDQSGIIYCLSRKECEQVSAVLRSLG--KSAAFYHA---GLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFV  557 (941)
T ss_pred             CCCCCeEEEeCCcchHHHHHHHHHHhc--hhhHhhhc---CCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEE
Confidence            567899999999999999999999999  99999999   9999999999999999999999999999999999999999


Q ss_pred             EEcCCCCChhhHhhhccccccccC-ceEEEEEeCC
Q psy4150         198 ICFDAQKSPIKMVQRLGRTGRKRN-GRCVILLTQG  231 (395)
Q Consensus       198 I~~d~p~s~~~yiQr~GRagR~~~-g~~i~l~~~~  231 (395)
                      |+|.+|++.+.|.|-+|||||.|. ..+++|+...
T Consensus       558 iH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~  592 (941)
T KOG0351|consen  558 IHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYA  592 (941)
T ss_pred             EECCCchhHHHHHHhccccCcCCCcceeEEecchh
Confidence            999999999999999999999984 5555555443

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.56  E-value=4.6e-14  Score=155.35  Aligned_cols=136  Identities=18%  Similarity=0.234  Sum_probs=118.8

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ..+.|+..|..+|..+..      .+.+||||++...+.+.|.++|...+  +....++|   +++..+|..+++.|...
T Consensus       468 e~SgKl~lLdkLL~~Lk~------~g~KVLIFSQft~~LdiLed~L~~~g--~~y~rIdG---sts~~eRq~~Id~Fn~~  536 (1033)
T PLN03142        468 ENSGKMVLLDKLLPKLKE------RDSRVLIFSQMTRLLDILEDYLMYRG--YQYCRIDG---NTGGEDRDASIDAFNKP  536 (1033)
T ss_pred             hhhhHHHHHHHHHHHHHh------cCCeEEeehhHHHHHHHHHHHHHHcC--CcEEEECC---CCCHHHHHHHHHHhccc
Confidence            346789888888877643      37899999999999999999999888  89999999   99999999999999763


Q ss_pred             ---CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCc---eEEEEEeCCchhhHHHHHH
Q psy4150         175 ---EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNG---RCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       175 ---~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g---~~i~l~~~~~e~~~~~~~~  241 (395)
                         .+-+|++|.+++.|||+..+++||+||+||||..+.|++||+.|.|+.   .++.|++.++.+..+....
T Consensus       537 ~s~~~VfLLSTrAGGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIEEkIlera  609 (1033)
T PLN03142        537 GSEKFVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERA  609 (1033)
T ss_pred             cCCceEEEEeccccccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHHHHHHHHH
Confidence               345799999999999999999999999999999999999999999843   4567888888777766555

>TIGR01054 rgy reverse gyrase

Probab=99.50  E-value=6.9e-14  Score=157.09  Aligned_cols=98  Identities=24%  Similarity=0.282  Sum_probs=83.1

Q ss_pred             cceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcH---HHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHH
Q psy4150          89 MSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYR---VVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQK  165 (395)
Q Consensus        89 ~~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~---~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~  165 (395)
                      +.+.|.....+...|.++|...         +.++||||+|+   +.|+.|++.|.+.|  +++..+||   ++++    
T Consensus       304 I~~~~~~~~~~~~~L~~ll~~l---------~~~~IVFv~t~~~~~~a~~l~~~L~~~g--~~a~~lhg---~~~~----  365 (1171)
T TIGR01054       304 VVDVYVEDEDLKETLLEIVKKL---------GTGGIVYVSIDYGKEKAEEIAEFLENHG--VKAVAYHA---TKPK----  365 (1171)
T ss_pred             eEEEEEecccHHHHHHHHHHHc---------CCCEEEEEeccccHHHHHHHHHHHHhCC--ceEEEEeC---CCCH----
Confidence            4555555444456666666542         36799999999   99999999999998  99999999   8863    


Q ss_pred             HHHHHHhcCCccEEEE----cCccccCCCCCC-CCEEEEcCCCC
Q psy4150         166 EIMKKFRAGEFNTLIA----TSVGEEGLDIGE-IDLVICFDAQK  204 (395)
Q Consensus       166 ~~l~~Fk~g~~~vLVa----T~v~~~GlDip~-v~~VI~~d~p~  204 (395)
                      .++++|++|+++||||    ||+++||||+|+ |++||+||+|.
T Consensus       366 ~~l~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       366 EDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             HHHHHHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCCC
Confidence            6899999999999999    599999999999 89999999997

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.49  E-value=2e-14  Score=164.69  Aligned_cols=113  Identities=19%  Similarity=0.201  Sum_probs=92.5

Q ss_pred             cceeeecc-ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHH---HHHHHHHHcccCCCCceeEEeccCCCCCHHHH
Q psy4150          89 MSSEYAWS-HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVV---VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQ  164 (395)
Q Consensus        89 ~~~~~~~~-~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~---ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R  164 (395)
                      +.+.|... .+....|.++|..+         +..+||||+|+..   |+.|++.|...|  +++..+||   +     |
T Consensus       307 i~~~yi~~~~~~k~~L~~ll~~~---------g~~gIVF~~t~~~~e~ae~la~~L~~~G--i~a~~~h~---~-----R  367 (1638)
T PRK14701        307 IVDVYLNPEKIIKEHVRELLKKL---------GKGGLIFVPIDEGAEKAEEIEKYLLEDG--FKIELVSA---K-----N  367 (1638)
T ss_pred             cEEEEEECCHHHHHHHHHHHHhC---------CCCeEEEEeccccchHHHHHHHHHHHCC--CeEEEecc---h-----H
Confidence            44555432 22224566655432         3679999999886   589999999999  99999999   4     8


Q ss_pred             HHHHHHHhcCCccEEEEc----CccccCCCCCC-CCEEEEcCCCC---ChhhHhhhc-------------ccccccc
Q psy4150         165 KEIMKKFRAGEFNTLIAT----SVGEEGLDIGE-IDLVICFDAQK---SPIKMVQRL-------------GRTGRKR  220 (395)
Q Consensus       165 ~~~l~~Fk~g~~~vLVaT----~v~~~GlDip~-v~~VI~~d~p~---s~~~yiQr~-------------GRagR~~  220 (395)
                      ..++++|++|+++|||||    ++++||||+|+ |.+||+||+|+   +...|.|..             ||+||.|
T Consensus       368 ~~~l~~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g  444 (1638)
T PRK14701        368 KKGFDLFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEG  444 (1638)
T ss_pred             HHHHHHHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccC
Confidence            899999999999999999    59999999999 99999999999   888777766             9999887

>KOG0352|consensus

Probab=99.47  E-value=2.1e-13  Score=133.77  Aligned_cols=113  Identities=19%  Similarity=0.287  Sum_probs=101.9

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      .+-.||||.|++.||.++-.|...|  +.+..+|.   ++...+|.++.+++-.|++.|++||...+.|+|-|+|.+||+
T Consensus       255 ~GCGIVYCRTR~~cEq~AI~l~~~G--i~A~AYHA---GLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViH  329 (641)
T KOG0352|consen  255 TGCGIVYCRTRNECEQVAIMLEIAG--IPAMAYHA---GLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIH  329 (641)
T ss_pred             CcceEEEeccHHHHHHHHHHhhhcC--cchHHHhc---ccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEe
Confidence            4568999999999999999999999  99999999   999999999999999999999999999999999999999999


Q ss_pred             cCCCCChhhHhhhccccccccCceEEEEEeCCchhhHH
Q psy4150         200 FDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNF  237 (395)
Q Consensus       200 ~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~  237 (395)
                      ||+|.|...|.|-.|||||.|....+-++..-.+.+.+
T Consensus       330 W~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i  367 (641)
T KOG0352|consen  330 WSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNAL  367 (641)
T ss_pred             cCchhhhHHHHHhccccccCCCccceeeeecccchHHH
Confidence            99999999999999999999966665555544444433

>TIGR00595 priA primosomal protein N'

Probab=99.45  E-value=6.1e-13  Score=138.26  Aligned_cols=98  Identities=22%  Similarity=0.334  Sum_probs=79.8

Q ss_pred             HHHHHHHHcccCCCCceeEEeccCCCCCHHHH--HHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC------
Q psy4150         133 VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQ--KEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK------  204 (395)
Q Consensus       133 ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R--~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~------  204 (395)
                      ++.+.+.|.+..|..++..+|+   ++++..+  ..++++|++|+++|||+|+++++|+|+|+|++|+.+|.+.      
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~---d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd  347 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDS---DTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPD  347 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEec---ccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcc
Confidence            6889999999888899999999   8876655  8999999999999999999999999999999996555432      


Q ss_pred             ------ChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         205 ------SPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       205 ------s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                            ....|+|++||+||.+ .|.+++. +...+.
T Consensus       348 ~ra~E~~~~ll~q~~GRagR~~~~g~viiq-t~~p~~  383 (505)
T TIGR00595       348 FRAAERGFQLLTQVAGRAGRAEDPGQVIIQ-TYNPNH  383 (505)
T ss_pred             cchHHHHHHHHHHHHhccCCCCCCCEEEEE-eCCCCC
Confidence                  2467899999999986 4555544 433333

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).

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

Probab=99.43  E-value=1.7e-12  Score=124.53  Aligned_cols=134  Identities=23%  Similarity=0.358  Sum_probs=104.2

Q ss_pred             HHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEE
Q psy4150         102 RLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIA  181 (395)
Q Consensus       102 ~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVa  181 (395)
                      +|..+|+.+...      +.+++||+++....+.++..|++..|.....+.|+     ....|.+.++.||+|++.+||+
T Consensus       293 kl~~~lekq~~~------~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs-----~d~~R~EkV~~fR~G~~~lLiT  361 (441)
T COG4098         293 KLKRWLEKQRKT------GRPVLIFFPEIETMEQVAAALKKKLPKETIASVHS-----EDQHRKEKVEAFRDGKITLLIT  361 (441)
T ss_pred             HHHHHHHHHHhc------CCcEEEEecchHHHHHHHHHHHhhCCccceeeeec-----cCccHHHHHHHHHcCceEEEEE
Confidence            456667666543      78999999999999999999988777677788888     3456899999999999999999


Q ss_pred             cCccccCCCCCCCCEEEEcCCC--CChhhHhhhccccccc--cCceEEEEEeCCchhhHHHHHHHHhHHHHHHH
Q psy4150         182 TSVGEEGLDIGEIDLVICFDAQ--KSPIKMVQRLGRTGRK--RNGRCVILLTQGREAHNFQTSMQTCKSYVEKI  251 (395)
Q Consensus       182 T~v~~~GlDip~v~~VI~~d~p--~s~~~yiQr~GRagR~--~~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~  251 (395)
                      |.+++||+.+|.|++++.-.-.  -+.++++|-.||+||.  ...+-++|+..+....     |..+.++|++.
T Consensus       362 TTILERGVTfp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~G~ska-----M~~A~keIk~M  430 (441)
T COG4098         362 TTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYGKSKA-----MKQARKEIKEM  430 (441)
T ss_pred             eehhhcccccccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEeccchHH-----HHHHHHHHHHH
Confidence            9999999999999987754433  4788999999999998  3444455666554432     22455555554

>PRK09694 helicase Cas3; Provisional

Probab=99.41  E-value=1.2e-12  Score=142.70  Aligned_cols=95  Identities=26%  Similarity=0.413  Sum_probs=83.9

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccC-CCCceeEEeccCCCCCHHHH----HHHHHHH-hcCC---ccEEEEcCccccCCC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLE-PMVKASMFVGQSSGVTQQEQ----KEIMKKF-RAGE---FNTLIATSVGEEGLD  190 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~-~~~~~~~lhg~~~~~~~~~R----~~~l~~F-k~g~---~~vLVaT~v~~~GlD  190 (395)
                      +.++||||||++.|..+++.|++.+ +...+..+||   .++..+|    .++++.| ++|+   ..|||||+++++|||
T Consensus       560 g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHs---rf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLD  636 (878)
T PRK09694        560 GAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHA---RFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLD  636 (878)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeC---CCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheee
Confidence            6789999999999999999999764 3467899999   9999999    4678888 6676   479999999999999


Q ss_pred             CCCCCEEEEcCCCCChhhHhhhcccccccc
Q psy4150         191 IGEIDLVICFDAQKSPIKMVQRLGRTGRKR  220 (395)
Q Consensus       191 ip~v~~VI~~d~p~s~~~yiQr~GRagR~~  220 (395)
                      | +++++|...+|  ..+|+||+||+||.+
T Consensus       637 I-d~DvlItdlaP--idsLiQRaGR~~R~~  663 (878)
T PRK09694        637 L-DFDWLITQLCP--VDLLFQRLGRLHRHH  663 (878)
T ss_pred             c-CCCeEEECCCC--HHHHHHHHhccCCCC
Confidence            9 58999999888  789999999999984

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

Probab=99.40  E-value=2.3e-12  Score=132.15  Aligned_cols=113  Identities=27%  Similarity=0.418  Sum_probs=98.5

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .|...+..++..+.       .+.+++|||.+...+..++..|...+  + +..+.|   ..+..+|..+++.|+.|.++
T Consensus       268 ~~~~~~~~~~~~~~-------~~~~~lif~~~~~~a~~i~~~~~~~~--~-~~~it~---~t~~~eR~~il~~fr~g~~~  334 (442)
T COG1061         268 RKIAAVRGLLLKHA-------RGDKTLIFASDVEHAYEIAKLFLAPG--I-VEAITG---ETPKEEREAILERFRTGGIK  334 (442)
T ss_pred             HHHHHHHHHHHHhc-------CCCcEEEEeccHHHHHHHHHHhcCCC--c-eEEEEC---CCCHHHHHHHHHHHHcCCCC
Confidence            34444444444432       35799999999999999999998877  6 888999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccc--cCce
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK--RNGR  223 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~--~~g~  223 (395)
                      +||++.++.+|+|+|+++++|......|...|+||+||.-|.  |.+.
T Consensus       335 ~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR~~~~k~~  382 (442)
T COG1061         335 VLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRPAEGKED  382 (442)
T ss_pred             EEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhccCCCCCCc
Confidence            999999999999999999999999999999999999999994  4444

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.36  E-value=6.8e-12  Score=134.89  Aligned_cols=104  Identities=24%  Similarity=0.257  Sum_probs=82.9

Q ss_pred             HHHHHHHHHcccCCCCceeEEeccCCCCC--HHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC--C--
Q psy4150         132 VVAEIFDVLKPLEPMVKASMFVGQSSGVT--QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK--S--  205 (395)
Q Consensus       132 ~ae~l~~~L~~~~~~~~~~~lhg~~~~~~--~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~--s--  205 (395)
                      .++.+.+.|.+..|..++..+|+   +++  ..++.+++++|++|+++|||+|+++++|+|+|+|++|+.+|++.  +  
T Consensus       438 G~e~~~e~l~~~fp~~~v~~~~~---d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~p  514 (679)
T PRK05580        438 GTERLEEELAELFPEARILRIDR---DTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSP  514 (679)
T ss_pred             cHHHHHHHHHHhCCCCcEEEEec---cccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCC
Confidence            57788899988877789999999   776  46789999999999999999999999999999999997666542  2  


Q ss_pred             --------hhhHhhhccccccccCceEEEEEeCCchhhHHH
Q psy4150         206 --------PIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQ  238 (395)
Q Consensus       206 --------~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~  238 (395)
                              ...|+|++||+||.+.++.+++.+...+...+.
T Consensus       515 dfra~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~~~~~~  555 (679)
T PRK05580        515 DFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQ  555 (679)
T ss_pred             ccchHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCCCHHHH
Confidence                    357999999999986444444445444443333

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

Probab=99.35  E-value=8.5e-12  Score=129.74  Aligned_cols=134  Identities=21%  Similarity=0.336  Sum_probs=111.6

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHH--------HHHHHHHHHcccCCCCceeEEeccCCCCCHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRV--------VVAEIFDVLKPLEPMVKASMFVGQSSGVTQQ  162 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~--------~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~  162 (395)
                      ..+...+.+...+.+.+.+.+..      +.++.+-|+-.+        .|+.+++.|....|.+++..+||   .|+..
T Consensus       450 ~T~~i~~~~~~~v~e~i~~ei~~------GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HG---rm~~~  520 (677)
T COG1200         450 TTVVIPHERRPEVYERIREEIAK------GRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHG---RMKPA  520 (677)
T ss_pred             EEEEeccccHHHHHHHHHHHHHc------CCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEec---CCChH
Confidence            44556667888888888776654      788999888643        57788899998888899999999   99999


Q ss_pred             HHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC-ChhhHhhhccccccccCceEEEEEeCCch
Q psy4150         163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-SPIKMVQRLGRTGRKRNGRCVILLTQGRE  233 (395)
Q Consensus       163 ~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~-s~~~yiQr~GRagR~~~g~~i~l~~~~~e  233 (395)
                      +..+++++|++|+++|||||.|.+.|||+|+.++.|++|+-. ..+++=|-.||+||.+...+|++++....
T Consensus       521 eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         521 EKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             HHHHHHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            999999999999999999999999999999999999999877 56667777799999975555556555544

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.34  E-value=1e-11  Score=133.52  Aligned_cols=131  Identities=18%  Similarity=0.122  Sum_probs=112.2

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..|.....|+..+.+.+.+...      .+.++||||+|+..++.|+..|.+.|  +++..|||   .  +.+|...+.+
T Consensus       407 ~i~~t~~~K~~aI~~~I~~~~~------~grpVLIft~Si~~se~Ls~~L~~~g--i~~~vLna---k--q~eREa~Iia  473 (830)
T PRK12904        407 LIYKTEKEKFDAVVEDIKERHK------KGQPVLVGTVSIEKSELLSKLLKKAG--IPHNVLNA---K--NHEREAEIIA  473 (830)
T ss_pred             eEEECHHHHHHHHHHHHHHHHh------cCCCEEEEeCcHHHHHHHHHHHHHCC--CceEeccC---c--hHHHHHHHHH
Confidence            4455667799999888876433      36899999999999999999999999  99999999   4  7899999999


Q ss_pred             HhcCCccEEEEcCccccCCCCCCC--------------------------------------CEEEEcCCCCChhhHhhh
Q psy4150         171 FRAGEFNTLIATSVGEEGLDIGEI--------------------------------------DLVICFDAQKSPIKMVQR  212 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDip~v--------------------------------------~~VI~~d~p~s~~~yiQr  212 (395)
                      |+.+...|+||||+++||+||+=-                                      =+||--..|.|..---|-
T Consensus       474 ~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~Ql  553 (830)
T PRK12904        474 QAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQL  553 (830)
T ss_pred             hcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHh
Confidence            999999999999999999999742                                      278888889999999999


Q ss_pred             cccccccc-CceEEEEEeCCchh
Q psy4150         213 LGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       213 ~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      .||+||.| +|.+-+|++-+++.
T Consensus       554 rGRagRQGdpGss~f~lSleD~l  576 (830)
T PRK12904        554 RGRSGRQGDPGSSRFYLSLEDDL  576 (830)
T ss_pred             hcccccCCCCCceeEEEEcCcHH
Confidence            99999998 67777777665543

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.31  E-value=1.3e-11  Score=133.03  Aligned_cols=131  Identities=21%  Similarity=0.139  Sum_probs=111.3

Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      ...|.....|+..+.+.+.+...      .+.++||||+|+..++.|+..|.+.|  +++..||+   .+.+.++..+.+
T Consensus       420 d~v~~t~~~k~~av~~~i~~~~~------~g~PVLVgt~Sie~sE~ls~~L~~~g--i~h~vLna---k~~q~Ea~iia~  488 (896)
T PRK13104        420 DLVYLTQADKFQAIIEDVRECGV------RKQPVLVGTVSIEASEFLSQLLKKEN--IKHQVLNA---KFHEKEAQIIAE  488 (896)
T ss_pred             CeEEcCHHHHHHHHHHHHHHHHh------CCCCEEEEeCcHHHHHHHHHHHHHcC--CCeEeecC---CCChHHHHHHHh
Confidence            34566667788888877766543      47899999999999999999999999  99999999   999999999999


Q ss_pred             HHhcCCccEEEEcCccccCCCCCC--------------------------------------CCEEEEcCCCCChhhHhh
Q psy4150         170 KFRAGEFNTLIATSVGEEGLDIGE--------------------------------------IDLVICFDAQKSPIKMVQ  211 (395)
Q Consensus       170 ~Fk~g~~~vLVaT~v~~~GlDip~--------------------------------------v~~VI~~d~p~s~~~yiQ  211 (395)
                      .|+.|.  |+||||+++||+||-=                                      -=+||--..+.|..---|
T Consensus       489 Ag~~G~--VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~Q  566 (896)
T PRK13104        489 AGRPGA--VTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQ  566 (896)
T ss_pred             CCCCCc--EEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHH
Confidence            999994  9999999999999861                                      127788888889999999


Q ss_pred             hcccccccc-CceEEEEEeCCch
Q psy4150         212 RLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       212 r~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      -.||+||.| +|.+-+|++-+++
T Consensus       567 LrGRaGRQGDPGss~f~lSleD~  589 (896)
T PRK13104        567 LRGRAGRQGDPGSSRFYLSLEDN  589 (896)
T ss_pred             hccccccCCCCCceEEEEEcCcH
Confidence            999999998 6777776665544

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.27  E-value=3e-11  Score=130.02  Aligned_cols=130  Identities=15%  Similarity=0.121  Sum_probs=111.7

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..|.....|+.++.+-+.+...      .+.++||||+|...++.|+.+|...+  +++.+||+   .+++.++..+.+.
T Consensus       426 ~iy~t~~~K~~Aii~ei~~~~~------~GrpVLV~t~sv~~se~ls~~L~~~g--i~~~vLna---k~~~~Ea~ii~~A  494 (908)
T PRK13107        426 LVYLTADEKYQAIIKDIKDCRE------RGQPVLVGTVSIEQSELLARLMVKEK--IPHEVLNA---KFHEREAEIVAQA  494 (908)
T ss_pred             cEEeCHHHHHHHHHHHHHHHHH------cCCCEEEEeCcHHHHHHHHHHHHHCC--CCeEeccC---cccHHHHHHHHhC
Confidence            4456667788888877766544      37899999999999999999999999  99999999   9999999999999


Q ss_pred             HhcCCccEEEEcCccccCCCCCC-------------------------------------CCEEEEcCCCCChhhHhhhc
Q psy4150         171 FRAGEFNTLIATSVGEEGLDIGE-------------------------------------IDLVICFDAQKSPIKMVQRL  213 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDip~-------------------------------------v~~VI~~d~p~s~~~yiQr~  213 (395)
                      |+.|.  |+||||+++||+||.=                                     -=+||--..+.|..-=-|-.
T Consensus       495 g~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLr  572 (908)
T PRK13107        495 GRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLR  572 (908)
T ss_pred             CCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhh
Confidence            99999  9999999999999861                                     22788888999999999999


Q ss_pred             ccccccc-CceEEEEEeCCch
Q psy4150         214 GRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       214 GRagR~~-~g~~i~l~~~~~e  233 (395)
                      ||+||.| +|...+|++-+++
T Consensus       573 GRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        573 GRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             cccccCCCCCceeEEEEeCcH
Confidence            9999998 6777777666554

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

Probab=99.27  E-value=5.7e-11  Score=129.79  Aligned_cols=109  Identities=25%  Similarity=0.379  Sum_probs=101.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      ++++-.-+|..++.+.++..|++.-|..++.+.||   .|+..+-..++.+|-+|+++|||||.+.+-|||||++|.+|.
T Consensus       803 gGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHG---QM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiII  879 (1139)
T COG1197         803 GGQVFYVHNRVESIEKKAERLRELVPEARIAVAHG---QMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIII  879 (1139)
T ss_pred             CCEEEEEecchhhHHHHHHHHHHhCCceEEEEeec---CCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEE
Confidence            69999999999999999999999999999999999   999999999999999999999999999999999999999999


Q ss_pred             cCCCC-ChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         200 FDAQK-SPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       200 ~d~p~-s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      -++.. ..+++.|-.||+||.. .+.+|+++-+.
T Consensus       880 e~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~  913 (1139)
T COG1197         880 ERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQ  913 (1139)
T ss_pred             eccccccHHHHHHhccccCCccceEEEEEeecCc
Confidence            99887 6889999999999995 66677665543

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.26  E-value=1.4e-11  Score=133.04  Aligned_cols=131  Identities=19%  Similarity=0.312  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcc----cC-----C-------CCc-------------ee
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKP----LE-----P-------MVK-------------AS  150 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~----~~-----~-------~~~-------------~~  150 (395)
                      ......++......      ++++||||++++.+...+..|..    ..     +       .+.             -.
T Consensus       239 ~~~~~~~v~~~~~~------~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~  312 (766)
T COG1204         239 DNLALELVLESLAE------GGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAEL  312 (766)
T ss_pred             hHHHHHHHHHHHhc------CCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHH
Confidence            34555555555543      78999999999999999998872    10     0       011             01


Q ss_pred             EEec---cCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE----EcC-----CCCChhhHhhhcccccc
Q psy4150         151 MFVG---QSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI----CFD-----AQKSPIKMVQRLGRTGR  218 (395)
Q Consensus       151 ~lhg---~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI----~~d-----~p~s~~~yiQr~GRagR  218 (395)
                      +.+|   ||.+++...|..+.+.|+.|.++|||||+.+++|+|+|.-.+||    -||     .+-++.+++|+.|||||
T Consensus       313 v~~GvafHhAGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGR  392 (766)
T COG1204         313 VLRGVAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGR  392 (766)
T ss_pred             HHhCccccccCCCHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCC
Confidence            1112   45599999999999999999999999999999999999766666    466     45578999999999999


Q ss_pred             cc---CceEEEEEeCCchhhH
Q psy4150         219 KR---NGRCVILLTQGREAHN  236 (395)
Q Consensus       219 ~~---~g~~i~l~~~~~e~~~  236 (395)
                      .|   -|..+++.+...+...
T Consensus       393 Pg~d~~G~~~i~~~~~~~~~~  413 (766)
T COG1204         393 PGYDDYGEAIILATSHDELEY  413 (766)
T ss_pred             CCcCCCCcEEEEecCccchhH
Confidence            96   4666666645444433

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

Probab=99.26  E-value=1.9e-11  Score=133.61  Aligned_cols=130  Identities=25%  Similarity=0.376  Sum_probs=103.2

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHH----HHHcccCCC--CceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIF----DVLKPLEPM--VKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~----~~L~~~~~~--~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .+...+..++.....+      +-++|+|+.++..++.++    ..+...++.  ..+...+|   ++...+|..+...|
T Consensus       290 s~~~~~~~~~~~~~~~------~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~---~~~~~er~~ie~~~  360 (851)
T COG1205         290 SALAELATLAALLVRN------GIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRA---GLHREERRRIEAEF  360 (851)
T ss_pred             chHHHHHHHHHHHHHc------CceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccc---cCCHHHHHHHHHHH
Confidence            5666677777666554      789999999999999997    333333311  23344445   99999999999999


Q ss_pred             hcCCccEEEEcCccccCCCCCCCCEEEEcCCCC-ChhhHhhhccccccccCceEEEEEeCCchhhH
Q psy4150         172 RAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-SPIKMVQRLGRTGRKRNGRCVILLTQGREAHN  236 (395)
Q Consensus       172 k~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~-s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~  236 (395)
                      +.|++.++++|+.++-||||++++.||.+..|. +..+++||.||+||.+.+...+++...+..+.
T Consensus       361 ~~g~~~~~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~d~  426 (851)
T COG1205         361 KEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPLDS  426 (851)
T ss_pred             hcCCccEEecchhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCccch
Confidence            999999999999999999999999999999999 89999999999999985555444444444333

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

Probab=99.25  E-value=4.1e-11  Score=134.19  Aligned_cols=106  Identities=19%  Similarity=0.294  Sum_probs=87.3

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccC----CC---CceeEEeccCCCCCHHHHHHHHHHHhcCCc-cEEEEcCccccCCC
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLE----PM---VKASMFVGQSSGVTQQEQKEIMKKFRAGEF-NTLIATSVGEEGLD  190 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~----~~---~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~-~vLVaT~v~~~GlD  190 (395)
                      ..+++||||.++.+|+.+++.|.+..    +.   ..+..+||   +.+  ++..++++|+++.. .|||+++++.+|+|
T Consensus       697 ~~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg---~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~D  771 (1123)
T PRK11448        697 GEGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITG---SID--KPDQLIRRFKNERLPNIVVTVDLLTTGID  771 (1123)
T ss_pred             CCCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeC---Ccc--chHHHHHHHhCCCCCeEEEEecccccCCC
Confidence            45899999999999999999877531    11   24556888   654  46789999999987 68999999999999


Q ss_pred             CCCCCEEEEcCCCCChhhHhhhccccccccC--ceEEEEEe
Q psy4150         191 IGEIDLVICFDAQKSPIKMVQRLGRTGRKRN--GRCVILLT  229 (395)
Q Consensus       191 ip~v~~VI~~d~p~s~~~yiQr~GRagR~~~--g~~i~l~~  229 (395)
                      +|.|.+||.++++.|...|+|++||+.|...  |+-..++.
T Consensus       772 vP~v~~vVf~rpvkS~~lf~QmIGRgtR~~~~~~K~~f~I~  812 (1123)
T PRK11448        772 VPSICNLVFLRRVRSRILYEQMLGRATRLCPEIGKTHFRIF  812 (1123)
T ss_pred             cccccEEEEecCCCCHHHHHHHHhhhccCCccCCCceEEEE
Confidence            9999999999999999999999999999843  45444443

>KOG4150|consensus

Probab=99.22  E-value=2.4e-11  Score=122.82  Aligned_cols=172  Identities=19%  Similarity=0.288  Sum_probs=125.2

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHH----HcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDV----LKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~----L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      +......++.+...+      +-|+|.||.+++.|+.+-..    |.+.+|+ -+..+.++.|+...++|.++..++-.|
T Consensus       510 ~i~E~s~~~~~~i~~------~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~-LV~~i~SYRGGY~A~DRRKIE~~~F~G  582 (1034)
T KOG4150|consen  510 KVVEVSHLFAEMVQH------GLRCIAFCPSRKLCELVLCLTREILAETAPH-LVEAITSYRGGYIAEDRRKIESDLFGG  582 (1034)
T ss_pred             HHHHHHHHHHHHHHc------CCcEEEeccHHHHHHHHHHHHHHHHHHhhHH-HHHHHHhhcCccchhhHHHHHHHhhCC
Confidence            555556677776665      68999999999999977654    4455652 334445555699999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhHHHHHHHHc
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCKSYVEKIIN  253 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~  253 (395)
                      ...-+|+|+.++-||||++.+.|+.+++|.|...+.|..|||||.. +.-+++++.....+..|       ......+++
T Consensus       583 ~L~giIaTNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y-------~~HP~~l~~  655 (1034)
T KOG4150|consen  583 KLCGIIATNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYY-------MSHPDKLFG  655 (1034)
T ss_pred             eeeEEEecchhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHh-------hcCcHHHhC
Confidence            9999999999999999999999999999999999999999999985 44455555555444444       244455554


Q ss_pred             ccchhhhhcccCCCCCCCCcchhhhhhcccc
Q psy4150         254 NKSIYANLAKNGPRMIPAHVTPRIKCLHIVV  284 (395)
Q Consensus       254 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  284 (395)
                      .+..-..+...+.-.+..|+.+...++.+..
T Consensus       656 ~pN~EL~LD~~N~~iL~~HlQCAA~ELPIN~  686 (1034)
T KOG4150|consen  656 SPNEELHLDSQNKHVLMQHLQCAALELPINL  686 (1034)
T ss_pred             CCcceeEEecccHHHHHHHHhHHhhcCcccc
Confidence            4433223333444445566666666666654

>KOG0353|consensus

Probab=99.15  E-value=7.3e-11  Score=114.52  Aligned_cols=88  Identities=19%  Similarity=0.248  Sum_probs=84.8

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      .+...||||-+++.++.++..|+.+|  +.+..+|.   .|.+.++.-+-+.+-.|+++|+|+|-..+.|||-|+|.+||
T Consensus       316 ~gqsgiiyc~sq~d~ekva~alkn~g--i~a~~yha---~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvi  390 (695)
T KOG0353|consen  316 AGQSGIIYCFSQKDCEKVAKALKNHG--IHAGAYHA---NLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVI  390 (695)
T ss_pred             CCCcceEEEeccccHHHHHHHHHhcC--cccccccc---ccCccccccccccccccceEEEEEEeeecccCCCCCeeEEE
Confidence            35678999999999999999999999  99999999   99999999999999999999999999999999999999999


Q ss_pred             EcCCCCChhhHhh
Q psy4150         199 CFDAQKSPIKMVQ  211 (395)
Q Consensus       199 ~~d~p~s~~~yiQ  211 (395)
                      +..+|+|.+.|.|
T Consensus       391 hhsl~ksienyyq  403 (695)
T KOG0353|consen  391 HHSLPKSIENYYQ  403 (695)
T ss_pred             ecccchhHHHHHH
Confidence            9999999999999

>KOG0387|consensus

Probab=99.09  E-value=1.2e-09  Score=114.59  Aligned_cols=135  Identities=20%  Similarity=0.237  Sum_probs=114.0

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHc-ccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK-PLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~-~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      .+.|++.+..+|...+..      +.++|+|..++.+.+.|-.+|. ..+  +....+.|   ..+...|..++++|.++
T Consensus       528 ~sGKm~vl~~ll~~W~kq------g~rvllFsqs~~mLdilE~fL~~~~~--ysylRmDG---tT~~~~R~~lVd~Fne~  596 (923)
T KOG0387|consen  528 RSGKMKVLAKLLKDWKKQ------GDRVLLFSQSRQMLDILESFLRRAKG--YSYLRMDG---TTPAALRQKLVDRFNED  596 (923)
T ss_pred             hcchHHHHHHHHHHHhhC------CCEEEEehhHHHHHHHHHHHHHhcCC--ceEEEecC---CCccchhhHHHHhhcCC
Confidence            344777777777765543      6799999999999999999998 466  89999999   89999999999999987


Q ss_pred             C-cc-EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC---ceEEEEEeCCchhhHHHHHH
Q psy4150         175 E-FN-TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN---GRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       175 ~-~~-vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~---g~~i~l~~~~~e~~~~~~~~  241 (395)
                      + +. .|++|.|++-|+++..++-||+||+.|||..-.|..-||.|.|+   -.+|-|++.++.++.+...+
T Consensus       597 ~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~gTIEEkiY~rQ  668 (923)
T KOG0387|consen  597 ESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAGTIEEKIYHRQ  668 (923)
T ss_pred             CceEEEEEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCCcHHHHHHHHH
Confidence            4 33 58999999999999999999999999999999999999999973   34566888888877655433

>KOG0392|consensus

Probab=99.08  E-value=9.3e-10  Score=119.39  Aligned_cols=157  Identities=19%  Similarity=0.288  Sum_probs=123.6

Q ss_pred             ccccHHHHHHHHHHHHHHhhhcc--------CCCccEEEEcCcHHHHHHHHHHHcc-cCCCCceeEEeccCCCCCHHHHH
Q psy4150          95 WSHLKFIRLREILESHFRLHAEK--------GETTKVIIFANYRVVVAEIFDVLKP-LEPMVKASMFVGQSSGVTQQEQK  165 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~--------~~~~r~iVF~~t~~~ae~l~~~L~~-~~~~~~~~~lhg~~~~~~~~~R~  165 (395)
                      ...||+.+|.++|.+.--.....        -.+.|+||||+-+.+++.+.+-|.+ +-|.+....+.|   ..++..|.
T Consensus      1307 ~hspKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDG---SVpp~~R~ 1383 (1549)
T KOG0392|consen 1307 QHSPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDG---SVPPGDRQ 1383 (1549)
T ss_pred             hhchhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecC---CCCcHHHH
Confidence            35689999999998752210000        1468999999999999999886654 554455556778   99999999


Q ss_pred             HHHHHHhcC-CccEE-EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceE---EEEEeCCchhhHHHHH
Q psy4150         166 EIMKKFRAG-EFNTL-IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRC---VILLTQGREAHNFQTS  240 (395)
Q Consensus       166 ~~l~~Fk~g-~~~vL-VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~---i~l~~~~~e~~~~~~~  240 (395)
                      ++.++|.++ .++|| ++|-|++-|+|+.+++.||.++-.|||..-+|.+.||-|-|+.++   +-+++.++-++.++-.
T Consensus      1384 kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlItrGTLEEKVMgL 1463 (1549)
T KOG0392|consen 1384 KIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLITRGTLEEKVMGL 1463 (1549)
T ss_pred             HHHHHhcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCceeeeeeeehhcccHHHHHhhH
Confidence            999999999 89986 788999999999999999999999999999999999999987665   4578899988888766


Q ss_pred             HHHhHHHHHHHHcc
Q psy4150         241 MQTCKSYVEKIINN  254 (395)
Q Consensus       241 ~~~~~~~i~~~i~~  254 (395)
                      ++-...-.+..++.
T Consensus      1464 QkFKmnvAntvInq 1477 (1549)
T KOG0392|consen 1464 QKFKMNVANTVINQ 1477 (1549)
T ss_pred             HHHhhHHHHHHHhc
Confidence            63333333344443

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.05  E-value=6.1e-10  Score=120.89  Aligned_cols=104  Identities=28%  Similarity=0.377  Sum_probs=88.1

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHh----cCCccEEEEcCccccCCCCCC
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFR----AGEFNTLIATSVGEEGLDIGE  193 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk----~g~~~vLVaT~v~~~GlDip~  193 (395)
                      ..+.+++|-|||+..|..++..|+..++  ++..+||   .+....|.+.++.++    .+...|+|||+|.+-|+|+. 
T Consensus       438 ~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~--~v~LlHS---Rf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-  511 (733)
T COG1203         438 KEGKKVLVIVNTVDRAIELYEKLKEKGP--KVLLLHS---RFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-  511 (733)
T ss_pred             ccCCcEEEEEecHHHHHHHHHHHHhcCC--CEEEEec---ccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-
Confidence            3479999999999999999999999985  8999999   999999988888655    46889999999999999995 


Q ss_pred             CCEEEEcCCCCChhhHhhhcccccccc---CceEEEEEe
Q psy4150         194 IDLVICFDAQKSPIKMVQRLGRTGRKR---NGRCVILLT  229 (395)
Q Consensus       194 v~~VI~~d~p~s~~~yiQr~GRagR~~---~g~~i~l~~  229 (395)
                      ++++|-==+|  ..++|||.||++|.|   .|.++++..
T Consensus       512 fd~mITe~aP--idSLIQR~GRv~R~g~~~~~~~~v~~~  548 (733)
T COG1203         512 FDVLITELAP--IDSLIQRAGRVNRHGKKENGKIYVYND  548 (733)
T ss_pred             cCeeeecCCC--HHHHHHHHHHHhhcccccCCceeEeec
Confidence            7877765444  889999999999998   344444433

>KOG0385|consensus

Probab=99.03  E-value=1.4e-09  Score=113.70  Aligned_cols=135  Identities=19%  Similarity=0.257  Sum_probs=117.6

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      +..+.|+..|-.+|..+...      ++|||||.+-..+.+-|.+++.-++  +..+.+.|   .++-++|...++.|..
T Consensus       467 v~nSGKm~vLDkLL~~Lk~~------GhRVLIFSQmt~mLDILeDyc~~R~--y~ycRiDG---St~~eeR~~aI~~fn~  535 (971)
T KOG0385|consen  467 VTNSGKMLVLDKLLPKLKEQ------GHRVLIFSQMTRMLDILEDYCMLRG--YEYCRLDG---STSHEEREDAIEAFNA  535 (971)
T ss_pred             HhcCcceehHHHHHHHHHhC------CCeEEEeHHHHHHHHHHHHHHHhcC--ceeEeecC---CCCcHHHHHHHHhcCC
Confidence            34556999999999887654      8999999999999999999999888  89999999   9999999999999987


Q ss_pred             CC---ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC---ceEEEEEeCCchhhHHHH
Q psy4150         174 GE---FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN---GRCVILLTQGREAHNFQT  239 (395)
Q Consensus       174 g~---~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~---g~~i~l~~~~~e~~~~~~  239 (395)
                      ..   +-.|++|-+++-|||+..+++||.||..|||..-+|.+.||-|.|+   -.++-|+++.+.++.+..
T Consensus       536 ~~s~~FiFlLSTRAGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentVEe~Ive  607 (971)
T KOG0385|consen  536 PPSEKFIFLLSTRAGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTVEEKIVE  607 (971)
T ss_pred             CCcceEEEEEeccccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccchHHHHHHH
Confidence            54   4468999999999999999999999999999999999999999873   445668888887766543

>KOG0384|consensus

Probab=99.00  E-value=7.8e-10  Score=120.22  Aligned_cols=130  Identities=21%  Similarity=0.290  Sum_probs=110.2

Q ss_pred             ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC--
Q psy4150          97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG--  174 (395)
Q Consensus        97 ~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g--  174 (395)
                      +.|+-.|-.||-.+.      ..+.|||||.+-..+.+-|++||...+  +..-.|-|   .+...-|...+..|...  
T Consensus       682 SGKlVLLDKLL~rLk------~~GHrVLIFSQMVRmLDIL~eYL~~r~--ypfQRLDG---svrgelRq~AIDhFnap~S  750 (1373)
T KOG0384|consen  682 SGKLVLLDKLLPRLK------EGGHRVLIFSQMVRMLDILAEYLSLRG--YPFQRLDG---SVRGELRQQAIDHFNAPDS  750 (1373)
T ss_pred             cCcEEeHHHHHHHHh------cCCceEEEhHHHHHHHHHHHHHHHHcC--CcceeccC---CcchHHHHHHHHhccCCCC
Confidence            334444445554443      358999999999999999999999999  88899999   99999999999999873  


Q ss_pred             -CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCc---eEEEEEeCCchhhHH
Q psy4150         175 -EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNG---RCVILLTQGREAHNF  237 (395)
Q Consensus       175 -~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g---~~i~l~~~~~e~~~~  237 (395)
                       .+-.|+||-+++-|||+..++.||+||..|||..-+|.+.||-|.|+.   .+|-|++.++.+..+
T Consensus       751 ddFvFLLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEi  817 (1373)
T KOG0384|consen  751 DDFVFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEI  817 (1373)
T ss_pred             CceEEEEecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHHHH
Confidence             577899999999999999999999999999999999999999999854   456688888766544

>KOG0951|consensus

Probab=98.99  E-value=2e-09  Score=117.22  Aligned_cols=153  Identities=20%  Similarity=0.354  Sum_probs=104.1

Q ss_pred             cccccccceeeeccccH-----HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHccc-------------C
Q psy4150          83 KLDINIMSSEYAWSHLK-----FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPL-------------E  144 (395)
Q Consensus        83 ~~~~~~~~~~~~~~~~K-----~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~-------------~  144 (395)
                      .+...++.|.|+....|     ++...+...+-.   .+..+.++|||||.+|+.+-..+..++..             +
T Consensus       507 syRpvPL~qq~Igi~ek~~~~~~qamNe~~yeKV---m~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~  583 (1674)
T KOG0951|consen  507 SYRPVPLKQQYIGITEKKPLKRFQAMNEACYEKV---LEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMRED  583 (1674)
T ss_pred             ccCcCCccceEeccccCCchHHHHHHHHHHHHHH---HHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcc
Confidence            34444566777654432     222222222211   12244589999999998877777666511             1


Q ss_pred             ----------------CC------CceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE----
Q psy4150         145 ----------------PM------VKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI----  198 (395)
Q Consensus       145 ----------------~~------~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI----  198 (395)
                                      +.      +....   ||+||+..+|..+.+-|+.|.++|||+|-.+++|+++|.-.++|    
T Consensus       584 s~s~eilrtea~~~kn~dLkdLLpygfaI---HhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtq  660 (1674)
T KOG0951|consen  584 SASREILRTEAGQAKNPDLKDLLPYGFAI---HHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQ  660 (1674)
T ss_pred             cchhhhhhhhhhcccChhHHHHhhcccee---eccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCcc
Confidence                            11      22333   33499999999999999999999999999999999999877777    


Q ss_pred             EcCCCC------ChhhHhhhcccccccc--CceEEEEEeCCchhhHHHHHH
Q psy4150         199 CFDAQK------SPIKMVQRLGRTGRKR--NGRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       199 ~~d~p~------s~~~yiQr~GRagR~~--~g~~i~l~~~~~e~~~~~~~~  241 (395)
                      .||+-+      ++.+.+|+.|||||.+  ..+-.++++...+...+...+
T Consensus       661 vy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~~se~qyyls~m  711 (1674)
T KOG0951|consen  661 VYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSELQYYLSLM  711 (1674)
T ss_pred             ccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeeccCchHhhhhHHhh
Confidence            466543      7899999999999995  223345566666666665544

>KOG0952|consensus

Probab=98.91  E-value=6.5e-09  Score=111.81  Aligned_cols=121  Identities=19%  Similarity=0.342  Sum_probs=91.3

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEec----------------cCCCCCHHHHHHHHHHHhcCCccEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVG----------------QSSGVTQQEQKEIMKKFRAGEFNTLIA  181 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg----------------~~~~~~~~~R~~~l~~Fk~g~~~vLVa  181 (395)
                      +.+++|||.++..+-..++.|.+.+-  +....++++                ||++|..++|.-+.+.|+.|.++||+|
T Consensus       349 g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~c  428 (1230)
T KOG0952|consen  349 GHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIKVLCC  428 (1230)
T ss_pred             CCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCceEEEe
Confidence            68999999999999999988875420  012222222                445999999999999999999999999


Q ss_pred             cCccccCCCCCCCCEEEE-----cCCCC------ChhhHhhhcccccccc--CceEEEEEeCCchhhHHHHHH
Q psy4150         182 TSVGEEGLDIGEIDLVIC-----FDAQK------SPIKMVQRLGRTGRKR--NGRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       182 T~v~~~GlDip~v~~VI~-----~d~p~------s~~~yiQr~GRagR~~--~g~~i~l~~~~~e~~~~~~~~  241 (395)
                      |..+++|+++|+ .+||+     ||...      +.-+.+|-.|||||..  +.++.++++..+-.+.|..++
T Consensus       429 TaTLAwGVNLPA-~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~Y~sLl  500 (1230)
T KOG0952|consen  429 TATLAWGVNLPA-YAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDHYESLL  500 (1230)
T ss_pred             cceeeeccCCcc-eEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHHHHHHH
Confidence            999999999995 45554     44433      5677899999999993  445555667766666666555

>KOG0950|consensus

Probab=98.90  E-value=2.1e-09  Score=114.76  Aligned_cols=110  Identities=20%  Similarity=0.343  Sum_probs=87.8

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC------------------------------------CCceeEEeccCCCCCHHH
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP------------------------------------MVKASMFVGQSSGVTQQE  163 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~------------------------------------~~~~~~lhg~~~~~~~~~  163 (395)
                      +.++||||++++.|+.++..+...-|                                    .+.+.+.|.   +++..+
T Consensus       460 ~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHha---GLT~eE  536 (1008)
T KOG0950|consen  460 GSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHA---GLTSEE  536 (1008)
T ss_pred             CCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceeccc---ccccch
Confidence            57799999999999988865432111                                    134455555   999999


Q ss_pred             HHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCC----CChhhHhhhcccccccc---CceEEEEEeCCc
Q psy4150         164 QKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQ----KSPIKMVQRLGRTGRKR---NGRCVILLTQGR  232 (395)
Q Consensus       164 R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p----~s~~~yiQr~GRagR~~---~g~~i~l~~~~~  232 (395)
                      |..+...|+.|.+.|++||+.++.|+++|...++|-.-.-    .+.-.|.|++|||||.|   -|.+++++...+
T Consensus       537 R~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e  612 (1008)
T KOG0950|consen  537 REIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSE  612 (1008)
T ss_pred             HHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccc
Confidence            9999999999999999999999999999999998865432    36789999999999997   466676665544

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

Probab=98.89  E-value=4.6e-09  Score=113.82  Aligned_cols=111  Identities=23%  Similarity=0.312  Sum_probs=97.7

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcc--cCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCC
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKP--LEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEID  195 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~--~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~  195 (395)
                      ...+.+|||.+-...++.+++.|.+  .++.+.+..+||   .++..++.++++--..|.-+|++|||+++.+|.||+|.
T Consensus       257 ~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~---~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr  333 (845)
T COG1643         257 EGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYG---ALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIR  333 (845)
T ss_pred             CCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccc---cCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeE
Confidence            3478899999999999999999987  335588999999   99999999998887777777999999999999999999


Q ss_pred             EEEEcCCC------------------CChhhHhhhccccccccCceEEEEEeCC
Q psy4150         196 LVICFDAQ------------------KSPIKMVQRLGRTGRKRNGRCVILLTQG  231 (395)
Q Consensus       196 ~VI~~d~p------------------~s~~~yiQr~GRagR~~~g~~i~l~~~~  231 (395)
                      +||.-+.-                  -|-.+..||.|||||-+.|.||-+++++
T Consensus       334 ~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~pGicyRLyse~  387 (845)
T COG1643         334 YVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTGPGICYRLYSEE  387 (845)
T ss_pred             EEecCCcccccccccccCceeeeEEEechhhhhhhccccccCCCceEEEecCHH
Confidence            99975543                  2678899999999999999999998863

>KOG0391|consensus

Probab=98.87  E-value=2.5e-08  Score=107.81  Aligned_cols=133  Identities=19%  Similarity=0.316  Sum_probs=111.9

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      +...|+..|.=||.++...      +.|+|||+.-.++.+-|..+|.-+|  +....|.|   ....++|...++.|...
T Consensus      1257 yDcGKLQtLAiLLqQLk~e------ghRvLIfTQMtkmLDVLeqFLnyHg--ylY~RLDg---~t~vEqRQaLmerFNaD 1325 (1958)
T KOG0391|consen 1257 YDCGKLQTLAILLQQLKSE------GHRVLIFTQMTKMLDVLEQFLNYHG--YLYVRLDG---NTSVEQRQALMERFNAD 1325 (1958)
T ss_pred             cccchHHHHHHHHHHHHhc------CceEEehhHHHHHHHHHHHHHhhcc--eEEEEecC---CccHHHHHHHHHHhcCC
Confidence            4556999998887776543      7999999999999999999999999  88888889   88999999999999886


Q ss_pred             C--ccEEEEcCccccCCCCCCCCEEEEcCCCCChh------hHhhhccccccccCceEEEEEeCCchhhHHHHHH
Q psy4150         175 E--FNTLIATSVGEEGLDIGEIDLVICFDAQKSPI------KMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       175 ~--~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~------~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~  241 (395)
                      .  +..+++|-.++.|||+.+++.||.||..||+.      +..||||+|   ++-.+|-|+++.+.+.++.+.-
T Consensus      1326 ~RIfcfILSTrSggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqt---RDVHIYRLISe~TIEeniLkka 1397 (1958)
T KOG0391|consen 1326 RRIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQT---RDVHIYRLISERTIEENILKKA 1397 (1958)
T ss_pred             CceEEEEEeccCCccccccccCceEEEecCCCCchhhhHHHHHHHhhcCc---cceEEEEeeccchHHHHHHhhh
Confidence            3  56789999999999999999999999999874      344455554   6788899999988887775443

>KOG0388|consensus

Probab=98.86  E-value=1.1e-08  Score=106.14  Aligned_cols=148  Identities=20%  Similarity=0.304  Sum_probs=125.5

Q ss_pred             eeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          93 YAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        93 ~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      |...+.|+..|-++|..+-.      .+.|+|+|++-.++.+.+.++|...+  +....+.|   ......|..++++|.
T Consensus      1023 FitdSgKL~~LDeLL~kLka------egHRvL~yfQMTkM~dl~EdYl~yr~--Y~ylRLDG---Ssk~~dRrd~vrDwQ 1091 (1185)
T KOG0388|consen 1023 FITDSGKLVVLDELLPKLKA------EGHRVLMYFQMTKMIDLIEDYLVYRG--YTYLRLDG---SSKASDRRDVVRDWQ 1091 (1185)
T ss_pred             hhccccceeeHHHHHHHhhc------CCceEEehhHHHHHHHHHHHHHHhhc--cceEEecC---cchhhHHHHHHhhcc
Confidence            34566789888888887643      48999999999999999999999998  88899999   888999999999999


Q ss_pred             cCC-ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc---CceEEEEEeCCchhhHHHHHHHHhHHHH
Q psy4150         173 AGE-FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR---NGRCVILLTQGREAHNFQTSMQTCKSYV  248 (395)
Q Consensus       173 ~g~-~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~~e~~~~~~~~~~~~~~i  248 (395)
                      ..+ +-.|++|-.++-||++..++.||.||..|+|..-.|.+.||.|-|   +-.++-+++.++.++.+.... .....+
T Consensus      1092 ~sdiFvFLLSTRAGGLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rgTvEEk~l~rA-~qK~~v 1170 (1185)
T KOG0388|consen 1092 ASDIFVFLLSTRAGGLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRGTVEEKVLERA-NQKDEV 1170 (1185)
T ss_pred             CCceEEEEEecccCcccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeecccccHHHHHHHHh-hhHHHH
Confidence            865 445899999999999999999999999999999999999998886   456777888888887776554 455666


Q ss_pred             HHHH
Q psy4150         249 EKII  252 (395)
Q Consensus       249 ~~~i  252 (395)
                      ++..
T Consensus      1171 Qq~V 1174 (1185)
T KOG0388|consen 1171 QQMV 1174 (1185)
T ss_pred             HHHH
Confidence            6654

>KOG0922|consensus

Probab=98.83  E-value=1e-08  Score=106.19  Aligned_cols=133  Identities=19%  Similarity=0.284  Sum_probs=106.5

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCC------ceeEEeccCCCCCHHHHHHHHH
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMV------KASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~------~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      ..|-.+.+.+.+...++-|.. ++.+-+|||....+.++.+++.|.+.....      .+..+||   .++.+++.+++.
T Consensus       235 ~~p~~dYv~a~~~tv~~Ih~~-E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~---aL~~e~Q~rvF~  310 (674)
T KOG0922|consen  235 KEPTADYVDAALITVIQIHLT-EPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYG---ALPSEEQSRVFD  310 (674)
T ss_pred             cCCchhhHHHHHHHHHHHHcc-CCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecc---cCCHHHhhcccc
Confidence            345555555555554443333 566789999999999999999998753111      3466889   999999999999


Q ss_pred             HHhcCCccEEEEcCccccCCCCCCCCEEEEcCC------------------CCChhhHhhhccccccccCceEEEEEeCC
Q psy4150         170 KFRAGEFNTLIATSVGEEGLDIGEIDLVICFDA------------------QKSPIKMVQRLGRTGRKRNGRCVILLTQG  231 (395)
Q Consensus       170 ~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~------------------p~s~~~yiQr~GRagR~~~g~~i~l~~~~  231 (395)
                      .-..|.-+|+++||+++..|.|+++.+||.-+.                  |-|-.+-.||.|||||.|.|+++-++++.
T Consensus       311 p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~pGkcyRLYte~  390 (674)
T KOG0922|consen  311 PAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRTGPGKCYRLYTES  390 (674)
T ss_pred             CCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCCCCceEEEeeeHH
Confidence            988899999999999999999999999996553                  33778899999999999999999998864


Q ss_pred             c
Q psy4150         232 R  232 (395)
Q Consensus       232 ~  232 (395)
                      .
T Consensus       391 ~  391 (674)
T KOG0922|consen  391 A  391 (674)
T ss_pred             H
Confidence            3

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=98.82  E-value=4.6e-08  Score=106.42  Aligned_cols=217  Identities=21%  Similarity=0.219  Sum_probs=135.4

Q ss_pred             cchHHHHHHHHhCCCcchhhhcccc-Cccc-------cccccccCChhHHHHHHhhcccccc----cccceee-eccccH
Q psy4150          33 HSLASALENLVTYGLRSFYNNLVEV-SKED-------GSCPILGKDNDLQNLLQQLKPKLDI----NIMSSEY-AWSHLK   99 (395)
Q Consensus        33 ~~l~~~~~~L~~~g~r~~~~fsatl-~~~~-------~~~~~l~~~~~~~~~v~~~~~~~~~----~~~~~~~-~~~~~K   99 (395)
                      +.|.+.+..|.+++...++.|+.|. ....       ....+++.++.-. ++..-....-.    ......+ ...+||
T Consensus       193 ~~Lr~ll~~L~t~D~vtF~~yL~~~l~~~~~~~~sk~~~S~Wl~~daa~~-lf~~ak~Rvy~~~~~~~~~~e~~lEe~PK  271 (814)
T TIGR00596       193 KILRHLLQSLVTYDAVSFLGLLDTSLRANKPAVSRKYSESPWLLLDAAQL-IFSYARQRVYYEGEGPNMKNEPVLEENPK  271 (814)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhccccccccccCCcchhhHHHHH-HHHHHHHHHhccccccccccccCcccCCC
Confidence            4567888999999988888888754 2111       0112333332211 11111000000    0001122 248999


Q ss_pred             HHHHHHHHHHHHHhhh---ccCCCccEEEEcCcHHHHHHHHHHHcccCC---CCcee------EEe--cc----------
Q psy4150         100 FIRLREILESHFRLHA---EKGETTKVIIFANYRVVVAEIFDVLKPLEP---MVKAS------MFV--GQ----------  155 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~---~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~---~~~~~------~lh--g~----------  155 (395)
                      ...|.++|.+......   ...+.+++||||+.+++|..|.++|...+-   ..+..      ++.  |+          
T Consensus       272 w~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~~~~~~~~~~fm~~~l~~y~~~~~~~~k~~~~~~~  351 (814)
T TIGR00596       272 WEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTTSNKKRGSRAFLLNKLRWYRKWREETSKLAKEVQS  351 (814)
T ss_pred             HHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHhccccccHHHHHHHHHHHHHhhhhhhhhhhHhhhh
Confidence            9999999988665411   113567899999999999999999955110   00000      000  10          


Q ss_pred             ---------------------------CCCCCHHHHHHHHHHHhcCCcc---------EE--------------------
Q psy4150         156 ---------------------------SSGVTQQEQKEIMKKFRAGEFN---------TL--------------------  179 (395)
Q Consensus       156 ---------------------------~~~~~~~~R~~~l~~Fk~g~~~---------vL--------------------  179 (395)
                                                 ..++++.    .+..|+.|..+         +|                    
T Consensus       352 ~~~~~~~~~~~~~~~~~~~~~~~krrr~rG~s~~----~~~~~r~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  427 (814)
T TIGR00596       352 QDTFPENASSNVNKTFRKEQVPTKRRRVRGGSEV----AVEKLRNANTNDMQHFEEDHELEEEGDDLEDGPAQEINAAND  427 (814)
T ss_pred             ccccccccccccccccccccccccccccccchhH----HHhhhcccccccccccchhhhhhhhhhhhccccccccccccc
Confidence                                       0022222    26677766554         34                    


Q ss_pred             ---EEcCccccCCCCCC----------------------C----------CEEEEcCCCCChhhHhh--hccccccccCc
Q psy4150         180 ---IATSVGEEGLDIGE----------------------I----------DLVICFDAQKSPIKMVQ--RLGRTGRKRNG  222 (395)
Q Consensus       180 ---VaT~v~~~GlDip~----------------------v----------~~VI~~d~p~s~~~yiQ--r~GRagR~~~g  222 (395)
                         |+|++.++|+|++.                      +          ++||.|++..+...-+|  |.||+||.  +
T Consensus       428 ~~~~~~~~~~e~~d~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~L~e~~P~~VImYEP~~sfIR~IEvyra~r~~r~--~  505 (814)
T TIGR00596       428 SKIFEIIDEENDIDIYSGAEFDNLPQHITHFLWGERDEYVLRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLRP--L  505 (814)
T ss_pred             cccccccccccccccchhhccccccceeeeecccccchhhHHHHHhhhCCCEEEEECCChHHHHHHHHHHccCCCCC--c
Confidence               77999999999998                      6          89999999999999999  99999887  6


Q ss_pred             eEEEEEeCC-chhhHHHHHHHHhHHHHHHHHcccc
Q psy4150         223 RCVILLTQG-REAHNFQTSMQTCKSYVEKIINNKS  256 (395)
Q Consensus       223 ~~i~l~~~~-~e~~~~~~~~~~~~~~i~~~i~~~~  256 (395)
                      .+|++++.+ .|+..|....++..+..+++|....
T Consensus       506 rVyfL~y~~S~EEq~yl~sirrEK~AFe~LIreka  540 (814)
T TIGR00596       506 RVYFLYYGGSIEEQRYLTSLRREKDAFTKLIREKA  540 (814)
T ss_pred             EEEEEEECCcHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            777766655 4566777777777777777775544

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

>KOG0389|consensus

Probab=98.81  E-value=5.3e-08  Score=102.34  Aligned_cols=136  Identities=19%  Similarity=0.246  Sum_probs=115.9

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ..+.|...|..+|......      +.|||||.+...+.+-|.-+|.-.+  ++...|-|   ...-..|+.++.+|...
T Consensus       758 mdSgK~r~L~~LLp~~k~~------G~RVLiFSQFTqmLDILE~~L~~l~--~~ylRLDG---sTqV~~RQ~lId~Fn~d  826 (941)
T KOG0389|consen  758 MDSGKCRKLKELLPKIKKK------GDRVLIFSQFTQMLDILEVVLDTLG--YKYLRLDG---STQVNDRQDLIDEFNTD  826 (941)
T ss_pred             hhhhhHhHHHHHHHHHhhc------CCEEEEeeHHHHHHHHHHHHHHhcC--ceEEeecC---CccchHHHHHHHhhccC
Confidence            3456999999999887654      6999999999999999999999999  88999999   88899999999999886


Q ss_pred             C-c-cEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc---CceEEEEEeCCchhhHHHHHH
Q psy4150         175 E-F-NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR---NGRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       175 ~-~-~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~~e~~~~~~~~  241 (395)
                      + + -+|++|-+++-||++..+++||.||...+|-.-.|.-.||.|.|   .-.++-|++.++.++.+..+-
T Consensus       827 ~difVFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~TIEE~I~~lA  898 (941)
T KOG0389|consen  827 KDIFVFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKSTIEEGILRLA  898 (941)
T ss_pred             CceEEEEEeeccCcceecccccceEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEEecCcHHHHHHHHH
Confidence            3 3 35899999999999999999999999999888888666666665   556778999988887665444

>KOG1002|consensus

Probab=98.71  E-value=1.2e-07  Score=95.31  Aligned_cols=150  Identities=19%  Similarity=0.191  Sum_probs=122.7

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC-
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG-  174 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g-  174 (395)
                      .+.|+++|.+-|.-....    ...-+.|||.+...+.+.+.=.|.+.|  +.++-+.|   +|++..|...++.|++. 
T Consensus       618 sSTKIEAL~EEl~~l~~r----d~t~KsIVFSQFTSmLDLi~~rL~kaG--fscVkL~G---sMs~~ardatik~F~nd~  688 (791)
T KOG1002|consen  618 SSTKIEALVEELYFLRER----DRTAKSIVFSQFTSMLDLIEWRLGKAG--FSCVKLVG---SMSPAARDATIKYFKNDI  688 (791)
T ss_pred             chhHHHHHHHHHHHHHHc----ccchhhhhHHHHHHHHHHHHHHhhccC--ceEEEecc---CCChHHHHHHHHHhccCC
Confidence            455777777766554443    445789999999999999999999999  99999999   99999999999999987 


Q ss_pred             CccE-EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccc---cCceEEEEEeCCchhhHHHHHHHHhHHHHHH
Q psy4150         175 EFNT-LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK---RNGRCVILLTQGREAHNFQTSMQTCKSYVEK  250 (395)
Q Consensus       175 ~~~v-LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~---~~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~  250 (395)
                      .+.| ||+-..++..+++..++.|+..|+-|++.--+|...|..|.   ++-+++.|+.+...+..+..++++....+..
T Consensus       689 ~c~vfLvSLkAGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEnsiE~kIieLQeKKa~miha  768 (791)
T KOG1002|consen  689 DCRVFLVSLKAGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIENSIEEKIIELQEKKANMIHA  768 (791)
T ss_pred             CeEEEEEEeccCceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehhccHHHHHHHHHHHHhhhhhh
Confidence            6776 57779999999999999999999999999888855555554   4677888999998888888777555555555


Q ss_pred             HHcc
Q psy4150         251 IINN  254 (395)
Q Consensus       251 ~i~~  254 (395)
                      .++.
T Consensus       769 Ti~q  772 (791)
T KOG1002|consen  769 TIGQ  772 (791)
T ss_pred             hcCC
Confidence            5544

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.69  E-value=1.6e-07  Score=100.93  Aligned_cols=129  Identities=18%  Similarity=0.210  Sum_probs=100.5

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..|.....|+.++.+-+.+...      .+.+|||.|.|...++.|+..|.+.|  ++..+|+.   .  +.++...+=.
T Consensus       403 ~iy~t~~~K~~Aii~ei~~~~~------~gqPVLVgT~SIe~SE~ls~~L~~~g--i~h~vLNA---k--~~e~EA~IIa  469 (925)
T PRK12903        403 SIFGTKHAKWKAVVKEVKRVHK------KGQPILIGTAQVEDSETLHELLLEAN--IPHTVLNA---K--QNAREAEIIA  469 (925)
T ss_pred             cEEEcHHHHHHHHHHHHHHHHh------cCCCEEEEeCcHHHHHHHHHHHHHCC--CCceeecc---c--chhhHHHHHH
Confidence            4556667788888777766543      37899999999999999999999999  88888887   3  2233333322


Q ss_pred             HhcC-CccEEEEcCccccCCCCCCCC--------EEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         171 FRAG-EFNTLIATSVGEEGLDIGEID--------LVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       171 Fk~g-~~~vLVaT~v~~~GlDip~v~--------~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                       ..| .-.|.|||+.++||.||.--.        +||....|.|..---|-.||+||.| +|.+.+|++-+++
T Consensus       470 -~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD~  541 (925)
T PRK12903        470 -KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDDQ  541 (925)
T ss_pred             -hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecchH
Confidence             566 567899999999999996332        8999999999998999999999998 6776666665544

>KOG0923|consensus

Probab=98.68  E-value=3.9e-08  Score=101.58  Aligned_cols=138  Identities=20%  Similarity=0.214  Sum_probs=105.6

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcc-------cCCCCceeEEeccCCCCCHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKP-------LEPMVKASMFVGQSSGVTQQE  163 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~-------~~~~~~~~~lhg~~~~~~~~~  163 (395)
                      ..|+...|-.+.|...+...++-|.. .+.+-+|||..-.+..+...+.|.+       .++.+-+..+|+   ++++..
T Consensus       445 di~Yt~~PEAdYldAai~tVlqIH~t-qp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYa---NLPsel  520 (902)
T KOG0923|consen  445 DIFYTKAPEADYLDAAIVTVLQIHLT-QPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYA---NLPSEL  520 (902)
T ss_pred             eeecccCCchhHHHHHHhhheeeEec-cCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccc---cCChHH
Confidence            34444555555555555444333222 4568899999887776665555543       344566777888   999999


Q ss_pred             HHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCC------------------CChhhHhhhccccccccCceEE
Q psy4150         164 QKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQ------------------KSPIKMVQRLGRTGRKRNGRCV  225 (395)
Q Consensus       164 R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p------------------~s~~~yiQr~GRagR~~~g~~i  225 (395)
                      +..+++.--.|.-+|++|||+++..|.|++|.+||.-++.                  -|..+-.||.|||||-|.|+|+
T Consensus       521 QakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtgPGKCf  600 (902)
T KOG0923|consen  521 QAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTGPGKCF  600 (902)
T ss_pred             HHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCCCCceE
Confidence            9999999999999999999999999999999999976543                  3677889999999999999999


Q ss_pred             EEEeCCc
Q psy4150         226 ILLTQGR  232 (395)
Q Consensus       226 ~l~~~~~  232 (395)
                      -+++...
T Consensus       601 RLYt~~a  607 (902)
T KOG0923|consen  601 RLYTAWA  607 (902)
T ss_pred             Eeechhh
Confidence            9988543

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

Probab=98.68  E-value=2.8e-07  Score=101.58  Aligned_cols=145  Identities=25%  Similarity=0.363  Sum_probs=119.2

Q ss_pred             cHHHHHHHHH-HHHHHhhhccCCCc--cEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          98 LKFIRLREIL-ESHFRLHAEKGETT--KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        98 ~K~~~L~~lL-~~~~~~~~~~~~~~--r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      .|+..+.++| ......      +.  ++|||++...+.+-+..+|...+  +....++|   .++...|...+..|.++
T Consensus       692 ~k~~~l~~ll~~~~~~~------~~~~kvlifsq~t~~l~il~~~l~~~~--~~~~~ldG---~~~~~~r~~~i~~f~~~  760 (866)
T COG0553         692 GKLQALDELLLDKLLEE------GHYHKVLIFSQFTPVLDLLEDYLKALG--IKYVRLDG---STPAKRRQELIDRFNAD  760 (866)
T ss_pred             hHHHHHHHHHHHHHHhh------cccccEEEEeCcHHHHHHHHHHHHhcC--CcEEEEeC---CCChhhHHHHHHHhhcC
Confidence            6888888888 455443      45  99999999999999999999998  88999999   89999999999999996


Q ss_pred             --CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc---CceEEEEEeCCchhhHHHHHHHHhHHHHH
Q psy4150         175 --EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR---NGRCVILLTQGREAHNFQTSMQTCKSYVE  249 (395)
Q Consensus       175 --~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~~e~~~~~~~~~~~~~~i~  249 (395)
                        ..-+|++|.+++.|+++...++||.||+.|++....|.+.|+.|.|   .-.++-+++.++-+..+............
T Consensus       761 ~~~~v~lls~kagg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~tiEe~i~~~~~~K~~l~~  840 (866)
T COG0553         761 EEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGTIEEKILELQEKKQELLD  840 (866)
T ss_pred             CCCceEEEEecccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEEeecCCcHHHHHHHHHHHHHHHHH
Confidence              4445788889999999999999999999999999999999888875   45566788888877666665534433444


Q ss_pred             HHHc
Q psy4150         250 KIIN  253 (395)
Q Consensus       250 ~~i~  253 (395)
                      .++.
T Consensus       841 ~~~~  844 (866)
T COG0553         841 SLID  844 (866)
T ss_pred             HHhh
Confidence            4443

>KOG0390|consensus

Probab=98.65  E-value=3.1e-07  Score=98.17  Aligned_cols=130  Identities=20%  Similarity=0.259  Sum_probs=98.8

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC--
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE--  175 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~--  175 (395)
                      .|+..|..++.....     .....+.+-.|.+.+.+.+....+-.|  ..+..+||   .|+..+|..+++.|.+..  
T Consensus       578 ~kl~~L~~ll~~~~e-----k~~~~~v~Isny~~tldl~e~~~~~~g--~~~~rLdG---~~~~~qRq~~vd~FN~p~~~  647 (776)
T KOG0390|consen  578 GKLLVLVFLLEVIRE-----KLLVKSVLISNYTQTLDLFEQLCRWRG--YEVLRLDG---KTSIKQRQKLVDTFNDPESP  647 (776)
T ss_pred             hHHHHHHHHHHHHhh-----hcceEEEEeccHHHHHHHHHHHHhhcC--ceEEEEcC---CCchHHHHHHHHhccCCCCC
Confidence            355555555533322     123344455566666666666666667  99999999   999999999999998853  


Q ss_pred             -ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCce---EEEEEeCCchhhHH
Q psy4150         176 -FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGR---CVILLTQGREAHNF  237 (395)
Q Consensus       176 -~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~---~i~l~~~~~e~~~~  237 (395)
                       .-.|.+|-++++||++-+++.||.||++|||+.-.|.++|+.|.|+-+   +|-|++.++-++.+
T Consensus       648 ~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iYrLlatGtiEEk~  713 (776)
T KOG0390|consen  648 SFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIYRLLATGTIEEKI  713 (776)
T ss_pred             ceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEEEeecCCCchHHH
Confidence             335788899999999999999999999999999999999999998544   34567777766543

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

Probab=98.63  E-value=2.6e-07  Score=98.95  Aligned_cols=121  Identities=22%  Similarity=0.313  Sum_probs=85.0

Q ss_pred             HHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC--------
Q psy4150         133 VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK--------  204 (395)
Q Consensus       133 ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~--------  204 (395)
                      ++.+.+.|....|..++..+.+.+ ..+...-...+..|..|+++|||+|.+++.|.|+|+|.+|...|...        
T Consensus       493 terieeeL~~~FP~~rv~r~d~Dt-t~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfR  571 (730)
T COG1198         493 TERIEEELKRLFPGARIIRIDSDT-TRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFR  571 (730)
T ss_pred             HHHHHHHHHHHCCCCcEEEEcccc-ccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcc
Confidence            677777777777777777777722 12233456789999999999999999999999999999998887664        


Q ss_pred             ----ChhhHhhhccccccc-cCceEEEEEeCCchhhHHHHHHHH-hHHHHHHHHccc
Q psy4150         205 ----SPIKMVQRLGRTGRK-RNGRCVILLTQGREAHNFQTSMQT-CKSYVEKIINNK  255 (395)
Q Consensus       205 ----s~~~yiQr~GRagR~-~~g~~i~l~~~~~e~~~~~~~~~~-~~~~i~~~i~~~  255 (395)
                          ....+.|-.|||||. ..|.+++-...++ ...+...... .....++.+..+
T Consensus       572 A~Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~-hp~i~~~~~~dy~~F~~~El~~R  627 (730)
T COG1198         572 ASERTFQLLMQVAGRAGRAGKPGEVVIQTYNPD-HPAIQALKRGDYEAFYEQELAER  627 (730)
T ss_pred             hHHHHHHHHHHHHhhhccCCCCCeEEEEeCCCC-cHHHHHHHhcCHHHHHHHHHHHH
Confidence                344588999999999 4777765544444 3334333333 333445555443

>KOG0953|consensus

Probab=98.57  E-value=5.7e-07  Score=91.67  Aligned_cols=143  Identities=17%  Similarity=0.211  Sum_probs=99.8

Q ss_pred             cccCChhHHHHHHhhcccccccccceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC
Q psy4150          66 ILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP  145 (395)
Q Consensus        66 ~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~  145 (395)
                      ++..+|..+.++..+-........+..|.--. .+.....++..+ .+   -.++.-++.|  +++.+-.+...+.+.|.
T Consensus       309 HLCGepsvldlV~~i~k~TGd~vev~~YeRl~-pL~v~~~~~~sl-~n---lk~GDCvV~F--Skk~I~~~k~kIE~~g~  381 (700)
T KOG0953|consen  309 HLCGEPSVLDLVRKILKMTGDDVEVREYERLS-PLVVEETALGSL-SN---LKPGDCVVAF--SKKDIFTVKKKIEKAGN  381 (700)
T ss_pred             hccCCchHHHHHHHHHhhcCCeeEEEeecccC-cceehhhhhhhh-cc---CCCCCeEEEe--ehhhHHHHHHHHHHhcC
Confidence            56677888888876654443333233332111 111111222221 11   1234444444  66778888888888773


Q ss_pred             CCceeEEeccCCCCCHHHHHHHHHHHhc--CCccEEEEcCccccCCCCCCCCEEEEcCCCC---------ChhhHhhhcc
Q psy4150         146 MVKASMFVGQSSGVTQQEQKEIMKKFRA--GEFNTLIATSVGEEGLDIGEIDLVICFDAQK---------SPIKMVQRLG  214 (395)
Q Consensus       146 ~~~~~~lhg~~~~~~~~~R~~~l~~Fk~--g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~---------s~~~yiQr~G  214 (395)
                       .++.++.|   +++++.|.+--..|.+  ++++||||||+.+.|+|+ +++.||.|++-+         +..+-.|-.|
T Consensus       382 -~k~aVIYG---sLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAG  456 (700)
T KOG0953|consen  382 -HKCAVIYG---SLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAG  456 (700)
T ss_pred             -cceEEEec---CCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhh
Confidence             45999999   9999999999999988  899999999999999999 699999988753         6778899999


Q ss_pred             cccccc
Q psy4150         215 RTGRKR  220 (395)
Q Consensus       215 RagR~~  220 (395)
                      ||||.|
T Consensus       457 RAGRf~  462 (700)
T KOG0953|consen  457 RAGRFG  462 (700)
T ss_pred             cccccc
Confidence            999996

>KOG0920|consensus

Probab=98.55  E-value=1.3e-07  Score=102.57  Aligned_cols=128  Identities=22%  Similarity=0.322  Sum_probs=102.1

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC-----CCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP-----MVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~-----~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      ..+.+.+++......    ...+.+|||-+....+..+.+.|....+     .+-+..+|+   .|+..++..++..--.
T Consensus       396 d~~Li~~li~~I~~~----~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs---~~~s~eQ~~VF~~pp~  468 (924)
T KOG0920|consen  396 DYDLIEDLIEYIDER----EFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHS---SIPSEEQQAVFKRPPK  468 (924)
T ss_pred             cHHHHHHHHHhcccC----CCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccc---cCChHHHHHhcCCCCC
Confidence            344445555444332    5678999999999999999999976443     244566677   9999999999999999


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEc--------CCCC----------ChhhHhhhccccccccCceEEEEEeCCch
Q psy4150         174 GEFNTLIATSVGEEGLDIGEIDLVICF--------DAQK----------SPIKMVQRLGRTGRKRNGRCVILLTQGRE  233 (395)
Q Consensus       174 g~~~vLVaT~v~~~GlDip~v~~VI~~--------d~p~----------s~~~yiQr~GRagR~~~g~~i~l~~~~~e  233 (395)
                      |.-+|+++|++++.+|.|++|-+||..        |+-.          |-..-.||.|||||...|.||-+++....
T Consensus       469 g~RKIIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv~~G~cy~L~~~~~~  546 (924)
T KOG0920|consen  469 GTRKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRVRPGICYHLYTRSRY  546 (924)
T ss_pred             CcchhhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCccCCeeEEeechhhh
Confidence            999999999999999999999999964        4333          44567899999999999999998886543

>KOG0924|consensus

Probab=98.52  E-value=1.4e-07  Score=97.71  Aligned_cols=135  Identities=23%  Similarity=0.282  Sum_probs=101.6

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHH----Hccc--CC--CCceeEEeccCCCCCHHHHHHH
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDV----LKPL--EP--MVKASMFVGQSSGVTQQEQKEI  167 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~----L~~~--~~--~~~~~~lhg~~~~~~~~~R~~~  167 (395)
                      ..|--+.+...+.+...-|. ....+-+|||..-.+.++..+..    |.+.  .|  .+.+..|.+   .|++.-+.++
T Consensus       540 k~p~eDYVeaavkq~v~Ihl-~~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYS---QLp~dlQ~ki  615 (1042)
T KOG0924|consen  540 KTPVEDYVEAAVKQAVQIHL-SGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYS---QLPADLQAKI  615 (1042)
T ss_pred             cCchHHHHHHHHhhheEeec-cCCCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehh---hCchhhhhhh
Confidence            34444444444444333222 23567899999877665554444    4332  23  478888888   9999999999


Q ss_pred             HHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCC------------------CChhhHhhhccccccccCceEEEEEe
Q psy4150         168 MKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQ------------------KSPIKMVQRLGRTGRKRNGRCVILLT  229 (395)
Q Consensus       168 l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p------------------~s~~~yiQr~GRagR~~~g~~i~l~~  229 (395)
                      ++.--.|.-+|+|||++++..|.||++.+||..+..                  -|-..-.||.|||||.|.|.|+-+++
T Consensus       616 Fq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~pG~cYRlYT  695 (1042)
T KOG0924|consen  616 FQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTGPGTCYRLYT  695 (1042)
T ss_pred             cccCCCCceeEEEeccchhhceeecceEEEEecCceeeeecccccccceeEEEechhccchhhccccCCCCCcceeeehh
Confidence            998888999999999999999999999999976653                  36677899999999999999999988


Q ss_pred             CCchh
Q psy4150         230 QGREA  234 (395)
Q Consensus       230 ~~~e~  234 (395)
                      .....
T Consensus       696 e~ay~  700 (1042)
T KOG0924|consen  696 EDAYK  700 (1042)
T ss_pred             hhHHH
Confidence            75433

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.52  E-value=9.7e-07  Score=93.76  Aligned_cols=130  Identities=21%  Similarity=0.172  Sum_probs=100.0

Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      ...|.....|+.++.+-+.....      .+.+|||.|.|....+.|+..|.+.|  ++..+|+.   .-...+ .+++.
T Consensus       403 d~iy~t~~~k~~Aii~ei~~~~~------~GrPVLVgt~sI~~SE~ls~~L~~~g--I~h~vLNA---k~~~~E-A~IIa  470 (764)
T PRK12326        403 DRVYATAAEKNDAIVEHIAEVHE------TGQPVLVGTHDVAESEELAERLRAAG--VPAVVLNA---KNDAEE-ARIIA  470 (764)
T ss_pred             CceEeCHHHHHHHHHHHHHHHHH------cCCCEEEEeCCHHHHHHHHHHHHhCC--Ccceeecc---CchHhH-HHHHH
Confidence            34566667788888777766543      37899999999999999999999999  88888887   423222 33333


Q ss_pred             HHhcC-CccEEEEcCccccCCCCCC---------------CCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         170 KFRAG-EFNTLIATSVGEEGLDIGE---------------IDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       170 ~Fk~g-~~~vLVaT~v~~~GlDip~---------------v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                        ..| .-.|.|||+.++||.||.=               -=+||-...|.|..--.|-.||+||.| +|.+.+|++-++
T Consensus       471 --~AG~~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleD  548 (764)
T PRK12326        471 --EAGKYGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLED  548 (764)
T ss_pred             --hcCCCCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence              345 4568899999999999862               238898999999999999999999998 677776666544


Q ss_pred             h
Q psy4150         233 E  233 (395)
Q Consensus       233 e  233 (395)
                      +
T Consensus       549 d  549 (764)
T PRK12326        549 D  549 (764)
T ss_pred             h
Confidence            3

>KOG0947|consensus

Probab=98.51  E-value=3.2e-07  Score=98.23  Aligned_cols=108  Identities=22%  Similarity=0.327  Sum_probs=84.2

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccC----------------------------CC---------CceeEEeccCCCCCHH
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLE----------------------------PM---------VKASMFVGQSSGVTQQ  162 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~----------------------------~~---------~~~~~lhg~~~~~~~~  162 (395)
                      --++||||-+++.|++.+++|....                            |.         -...+   ||+++-+-
T Consensus       567 lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaV---HH~GlLPi  643 (1248)
T KOG0947|consen  567 LLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAV---HHGGLLPI  643 (1248)
T ss_pred             cCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchh---hcccchHH
Confidence            4689999999999999999997432                            00         01223   34488888


Q ss_pred             HHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC---------ChhhHhhhcccccccc---CceEEEEEeC
Q psy4150         163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK---------SPIKMVQRLGRTGRKR---NGRCVILLTQ  230 (395)
Q Consensus       163 ~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~---------s~~~yiQr~GRagR~~---~g~~i~l~~~  230 (395)
                      -..-+.--|..|-++||+||..++.|+|.|.-.+|+. .+-+         .|-.|.|+.|||||.|   .|.+++++..
T Consensus       644 vKE~VE~LFqrGlVKVLFATETFAMGVNMPARtvVF~-Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~  722 (1248)
T KOG0947|consen  644 VKEVVELLFQRGLVKVLFATETFAMGVNMPARTVVFS-SLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKD  722 (1248)
T ss_pred             HHHHHHHHHhcCceEEEeehhhhhhhcCCCceeEEee-ehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecC
Confidence            8888888899999999999999999999997666653 2222         5789999999999997   6777777665


Q ss_pred             C
Q psy4150         231 G  231 (395)
Q Consensus       231 ~  231 (395)
                      .
T Consensus       723 ~  723 (1248)
T KOG0947|consen  723 S  723 (1248)
T ss_pred             C
Confidence            4

>KOG1123|consensus

Probab=98.48  E-value=1.9e-06  Score=86.99  Aligned_cols=129  Identities=23%  Similarity=0.373  Sum_probs=99.8

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      .-.+.|+..-.-||.-|-.      .+.++|||....-.....+-.|.+       -++.|   ..+|.+|..+++.|+.
T Consensus       523 vMNP~KFraCqfLI~~HE~------RgDKiIVFsDnvfALk~YAikl~K-------pfIYG---~Tsq~ERm~ILqnFq~  586 (776)
T KOG1123|consen  523 VMNPNKFRACQFLIKFHER------RGDKIIVFSDNVFALKEYAIKLGK-------PFIYG---PTSQNERMKILQNFQT  586 (776)
T ss_pred             ecCcchhHHHHHHHHHHHh------cCCeEEEEeccHHHHHHHHHHcCC-------ceEEC---CCchhHHHHHHHhccc
Confidence            4455577665555554433      478999999987766666655543       24778   8999999999999998


Q ss_pred             C-CccEEEEcCccccCCCCCCCCEEEEcCCCC-ChhhHhhhcccccccc-------CceEEEEEeCCchhhHHH
Q psy4150         174 G-EFNTLIATSVGEEGLDIGEIDLVICFDAQK-SPIKMVQRLGRTGRKR-------NGRCVILLTQGREAHNFQ  238 (395)
Q Consensus       174 g-~~~vLVaT~v~~~GlDip~v~~VI~~d~p~-s~~~yiQr~GRagR~~-------~g~~i~l~~~~~e~~~~~  238 (395)
                      + .++.++-+.|+...+|+|+++++|+..... |..+--||.||..|+.       +.-.+.+++.++.++.|.
T Consensus       587 n~~vNTIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~DTqEM~YS  660 (776)
T KOG1123|consen  587 NPKVNTIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKDTQEMYYS  660 (776)
T ss_pred             CCccceEEEeeccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCccccceeeeeeeecchHHHHhh
Confidence            6 789999999999999999999999998765 7788899999999983       233567788877776664

>KOG0948|consensus

Probab=98.39  E-value=8.2e-07  Score=93.10  Aligned_cols=113  Identities=24%  Similarity=0.345  Sum_probs=85.6

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccC----------------------------CC---C------ceeEEeccCCCCCH
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLE----------------------------PM---V------KASMFVGQSSGVTQ  161 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~----------------------------~~---~------~~~~lhg~~~~~~~  161 (395)
                      ...+||||+-+++.|+.++-.+.+..                            |.   +      ...+.|   +|+-+
T Consensus       382 ~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHH---sGLLP  458 (1041)
T KOG0948|consen  382 NYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHH---SGLLP  458 (1041)
T ss_pred             cCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHhcccccc---ccchH
Confidence            46789999999999999998876532                            00   0      123333   48888


Q ss_pred             HHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE----cCCCC----ChhhHhhhcccccccc---CceEEEEEeC
Q psy4150         162 QEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC----FDAQK----SPIKMVQRLGRTGRKR---NGRCVILLTQ  230 (395)
Q Consensus       162 ~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~----~d~p~----s~~~yiQr~GRagR~~---~g~~i~l~~~  230 (395)
                      --..-+.=-|..|=+++|+||...+.|||.|.-++|+-    ||-..    |.-.|||+.|||||.|   .|.+++++.+
T Consensus       459 IlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDe  538 (1041)
T KOG0948|consen  459 ILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDE  538 (1041)
T ss_pred             HHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccCCcceeeecccceEEecccccccCCCCCceEEEEecC
Confidence            87777777899999999999999999999998777763    33222    5668999999999997   5777877766


Q ss_pred             Cchh
Q psy4150         231 GREA  234 (395)
Q Consensus       231 ~~e~  234 (395)
                      .=+.
T Consensus       539 km~~  542 (1041)
T KOG0948|consen  539 KMEP  542 (1041)
T ss_pred             cCCH
Confidence            4433

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

Probab=98.37  E-value=3.3e-06  Score=93.54  Aligned_cols=118  Identities=19%  Similarity=0.311  Sum_probs=82.8

Q ss_pred             HHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEE
Q psy4150         102 RLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIA  181 (395)
Q Consensus       102 ~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVa  181 (395)
                      .+.+.|......     ..+++|||+++....+.+++.|...........+..   +.. ..|..+++.|+.|+..||+|
T Consensus       661 ~ia~~i~~l~~~-----~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~q---~~~-~~r~~ll~~F~~~~~~iLlg  731 (850)
T TIGR01407       661 EIASYIIEITAI-----TSPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQ---GIN-GSRAKIKKRFNNGEKAILLG  731 (850)
T ss_pred             HHHHHHHHHHHh-----cCCCEEEEeCCHHHHHHHHHHHhhhccccCceEEec---CCC-ccHHHHHHHHHhCCCeEEEE
Confidence            455555555442     357999999999999999999976321111223333   333 47889999999999999999


Q ss_pred             cCccccCCCCCCCC--EEEEcCCCCC------------------------------hhhHhhhcccccccc-CceEEEEE
Q psy4150         182 TSVGEEGLDIGEID--LVICFDAQKS------------------------------PIKMVQRLGRTGRKR-NGRCVILL  228 (395)
Q Consensus       182 T~v~~~GlDip~v~--~VI~~d~p~s------------------------------~~~yiQr~GRagR~~-~g~~i~l~  228 (395)
                      |+.+.||||+|+..  +||+..+|..                              ...+.|.+||.-|.. +.++++++
T Consensus       732 t~sf~EGVD~~g~~l~~viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~il  811 (850)
T TIGR01407       732 TSSFWEGVDFPGNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVIL  811 (850)
T ss_pred             cceeecccccCCCceEEEEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEE
Confidence            99999999999866  6666666631                              134678889998885 33333333

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.

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.34  E-value=4e-06  Score=91.70  Aligned_cols=131  Identities=20%  Similarity=0.178  Sum_probs=100.6

Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      ...|.....|+.++.+-+.....      .+.+|||-|.|....+.|+..|...|  ++..+|..   .....+- +++.
T Consensus       604 D~vy~t~~eK~~Aii~ei~~~~~------~GrPVLVGT~SVe~SE~lS~~L~~~g--I~H~VLNA---K~h~~EA-eIVA  671 (1112)
T PRK12901        604 DLVYKTKREKYNAVIEEITELSE------AGRPVLVGTTSVEISELLSRMLKMRK--IPHNVLNA---KLHQKEA-EIVA  671 (1112)
T ss_pred             CeEecCHHHHHHHHHHHHHHHHH------CCCCEEEEeCcHHHHHHHHHHHHHcC--CcHHHhhc---cchhhHH-HHHH
Confidence            34456667788888877777544      37899999999999999999999999  88888876   4333332 2222


Q ss_pred             HHhcC-CccEEEEcCccccCCCCC--------CCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         170 KFRAG-EFNTLIATSVGEEGLDIG--------EIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       170 ~Fk~g-~~~vLVaT~v~~~GlDip--------~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                        ..| .-.|-|||+.++||.||-        +-=+||--..+.|..---|-.||+||.| +|..-+|++-.++.
T Consensus       672 --~AG~~GaVTIATNMAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDdL  744 (1112)
T PRK12901        672 --EAGQPGTVTIATNMAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDNL  744 (1112)
T ss_pred             --hcCCCCcEEEeccCcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccHH
Confidence              245 456889999999999996        3348888889999999999999999998 67766666655443

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.33  E-value=4.7e-06  Score=90.78  Aligned_cols=129  Identities=20%  Similarity=0.188  Sum_probs=98.3

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHH-HHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQK-EIMK  169 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~-~~l~  169 (395)
                      ..|.....|..++.+-+.+...      .+.+|||-|.|....+.|+..|.+.|  ++..+|+.   .  +.+++ +++.
T Consensus       545 ~iy~t~~~k~~ai~~ei~~~~~------~grPvLigt~si~~se~ls~~L~~~g--i~h~vLNa---k--~~~~Ea~iia  611 (970)
T PRK12899        545 EFYMTEREKYHAIVAEIASIHR------KGNPILIGTESVEVSEKLSRILRQNR--IEHTVLNA---K--NHAQEAEIIA  611 (970)
T ss_pred             cEecCHHHHHHHHHHHHHHHHh------CCCCEEEEeCcHHHHHHHHHHHHHcC--Ccceeccc---c--hhhhHHHHHH
Confidence            3455556788887776666543      36889999999999999999999999  88888877   3  22333 2332


Q ss_pred             HHhcC-CccEEEEcCccccCCCCCC---C-----CEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         170 KFRAG-EFNTLIATSVGEEGLDIGE---I-----DLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       170 ~Fk~g-~~~vLVaT~v~~~GlDip~---v-----~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                        ..| .-.|.|||+.++||.||.-   |     =+||.-..|.|..--.|-.||+||.| +|.+.+|++-+++.
T Consensus       612 --~AG~~g~VTIATNmAGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlEDdL  684 (970)
T PRK12899        612 --GAGKLGAVTVATNMAGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFEDRL  684 (970)
T ss_pred             --hcCCCCcEEEeeccccCCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcchHH
Confidence              346 4678999999999999842   2     27888889999999999999999998 67777777665443

>KOG1000|consensus

Probab=98.29  E-value=4.5e-06  Score=84.21  Aligned_cols=146  Identities=15%  Similarity=0.209  Sum_probs=116.4

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC-
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG-  174 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g-  174 (395)
                      .-.|....++.|..+.--  -..++.+++||+.-....+.+...+.+.+  +....+.|   ..+..+|....+.|... 
T Consensus       470 giaK~~av~eyi~~~~~l--~d~~~~KflVFaHH~~vLd~Iq~~~~~r~--vg~IRIDG---st~s~~R~ll~qsFQ~se  542 (689)
T KOG1000|consen  470 GIAKAAAVCEYILENYFL--PDAPPRKFLVFAHHQIVLDTIQVEVNKRK--VGSIRIDG---STPSHRRTLLCQSFQTSE  542 (689)
T ss_pred             cccccHHHHHHHHhCccc--ccCCCceEEEEehhHHHHHHHHHHHHHcC--CCeEEecC---CCCchhHHHHHHHhcccc
Confidence            345777777777663211  11467899999999999999999999998  88899999   89999999999999876 


Q ss_pred             CccE-EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC---ceEEEEEeCCchhhHHHHHHHHhHHHH
Q psy4150         175 EFNT-LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN---GRCVILLTQGREAHNFQTSMQTCKSYV  248 (395)
Q Consensus       175 ~~~v-LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~---g~~i~l~~~~~e~~~~~~~~~~~~~~i  248 (395)
                      +..| +++...++.||++...+.|+...++|||--++|.-.|+.|.|+   -.+++|+..++.++.+...+++...-+
T Consensus       543 ev~VAvlsItA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQkssV~v~ylvAKgT~Ddy~Wp~l~~KL~vl  620 (689)
T KOG1000|consen  543 EVRVAVLSITAAGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSSVFVQYLVAKGTADDYMWPMLQQKLDVL  620 (689)
T ss_pred             ceEEEEEEEeecccceeeeccceEEEEEecCCCceEEechhhhhhccccceeeEEEEEecCchHHHHHHHHHHHHHHH
Confidence            5555 6777899999999999999999999999999998777777763   445678888888877766664444333

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

Probab=98.27  E-value=5.7e-06  Score=89.28  Aligned_cols=119  Identities=17%  Similarity=0.151  Sum_probs=85.5

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCC---CceeEEeccCCCC--------------C-
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPM---VKASMFVGQSSGV--------------T-  160 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~---~~~~~lhg~~~~~--------------~-  160 (395)
                      .+..+...+.+|+..... ..+.+++|||.++..|..+.+.|.+..+.   ..+..+++..++-              + 
T Consensus       494 ~~~~ia~~i~~h~~~~~~-~~~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~  572 (667)
T TIGR00348       494 RLESIAKDIAEHYAKFKE-LFKFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDK  572 (667)
T ss_pred             HHHHHHHHHHHHHHHhhh-cccCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhcccccc
Confidence            344555555556544222 23589999999999999999998776543   2455566522110              0 


Q ss_pred             ---HHHHHHHHHHHhc-CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccc
Q psy4150         161 ---QQEQKEIMKKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK  219 (395)
Q Consensus       161 ---~~~R~~~l~~Fk~-g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~  219 (395)
                         ......++++|+. +.++|||++|.+..|.|.|.+++++..-+-.+. .++|.+||+.|.
T Consensus       573 ~~~~~~~~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk~h-~LlQai~R~nR~  634 (667)
T TIGR00348       573 SDGFEIYYKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYH-GLLQAIARTNRI  634 (667)
T ss_pred             chhhhHHHHHHHHhcCCCCceEEEEEcccccccCCCccceEEEecccccc-HHHHHHHHhccc
Confidence               0123478999987 689999999999999999999999887766654 689999999994

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

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.25  E-value=6.4e-06  Score=89.57  Aligned_cols=131  Identities=20%  Similarity=0.169  Sum_probs=99.8

Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      ...|.....|+.++.+-+.....      .+.+|||-|.|....+.|+..|.+.+  ++..+|..   .....+ .+++.
T Consensus       425 d~vy~t~~eK~~Ai~~ei~~~~~------~GrPVLVGT~SVe~SE~ls~~L~~~g--i~h~VLNA---k~~~~E-A~IIa  492 (913)
T PRK13103        425 DLVYLTAEEKYAAIITDIKECMA------LGRPVLVGTATIETSEHMSNLLKKEG--IEHKVLNA---KYHEKE-AEIIA  492 (913)
T ss_pred             CeEEcCHHHHHHHHHHHHHHHHh------CCCCEEEEeCCHHHHHHHHHHHHHcC--CcHHHhcc---ccchhH-HHHHH
Confidence            34566677788888877776544      47899999999999999999999999  87777776   333222 22333


Q ss_pred             HHhcC-CccEEEEcCccccCCCCC-------------------------------------CCCEEEEcCCCCChhhHhh
Q psy4150         170 KFRAG-EFNTLIATSVGEEGLDIG-------------------------------------EIDLVICFDAQKSPIKMVQ  211 (395)
Q Consensus       170 ~Fk~g-~~~vLVaT~v~~~GlDip-------------------------------------~v~~VI~~d~p~s~~~yiQ  211 (395)
                        ..| .-.|.|||+.++||.||-                                     +-=+||--..|.|..---|
T Consensus       493 --~AG~~GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~Q  570 (913)
T PRK13103        493 --QAGRPGALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQ  570 (913)
T ss_pred             --cCCCCCcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHH
Confidence              456 567899999999999994                                     1227888889999999999


Q ss_pred             hcccccccc-CceEEEEEeCCchh
Q psy4150         212 RLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       212 r~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      -.||+||.| +|.+-+|++-+++.
T Consensus       571 LrGRaGRQGDPGsS~f~lSlED~L  594 (913)
T PRK13103        571 LRGRAGRQGDPGSSRFYLSLEDSL  594 (913)
T ss_pred             hccccccCCCCCceEEEEEcCcHH
Confidence            999999998 67777777665443

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

Probab=98.22  E-value=4.6e-06  Score=74.43  Aligned_cols=108  Identities=23%  Similarity=0.309  Sum_probs=73.7

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC--ccccCCCCCC--C
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS--VGEEGLDIGE--I  194 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~--v~~~GlDip~--v  194 (395)
                      .++++|||+++....+.+.+.+...+..-...++.-     +...+..+++.|+.++-.||+|+.  .+.+|||+++  +
T Consensus         8 ~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q-----~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~   82 (167)
T PF13307_consen    8 VPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ-----GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLL   82 (167)
T ss_dssp             CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES-----TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec-----CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchh
Confidence            358999999999999999999987652111223332     245678899999999999999998  9999999995  8


Q ss_pred             CEEEEcCCCC----C--------------------------hhhHhhhccccccccCceEEEEEeCC
Q psy4150         195 DLVICFDAQK----S--------------------------PIKMVQRLGRTGRKRNGRCVILLTQG  231 (395)
Q Consensus       195 ~~VI~~d~p~----s--------------------------~~~yiQr~GRagR~~~g~~i~l~~~~  231 (395)
                      ..||...+|.    +                          .....|-+||+-|..+...++++.+.
T Consensus        83 r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~  149 (167)
T PF13307_consen   83 RAVIIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDS  149 (167)
T ss_dssp             EEEEEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESG
T ss_pred             heeeecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcC
Confidence            8999998884    1                          12346789999999755555555543

>KOG1015|consensus

Probab=98.19  E-value=5.1e-06  Score=89.05  Aligned_cols=135  Identities=24%  Similarity=0.222  Sum_probs=105.7

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHccc---CC-----------------CCceeEEecc
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPL---EP-----------------MVKASMFVGQ  155 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~---~~-----------------~~~~~~lhg~  155 (395)
                      -++|+-.|++||...-.      -+.++|||.++-.+.+.|-.+|..-   |.                 +.....|.| 
T Consensus      1124 ~SgKmiLLleIL~mcee------IGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDG- 1196 (1567)
T KOG1015|consen 1124 HSGKMILLLEILRMCEE------IGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDG- 1196 (1567)
T ss_pred             cCcceehHHHHHHHHHH------hcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecC-
Confidence            45699999999877533      3789999999999988888888531   11                 123344555 


Q ss_pred             CCCCCHHHHHHHHHHHhcCC-c---cEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC---ceEEEEE
Q psy4150         156 SSGVTQQEQKEIMKKFRAGE-F---NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN---GRCVILL  228 (395)
Q Consensus       156 ~~~~~~~~R~~~l~~Fk~g~-~---~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~---g~~i~l~  228 (395)
                        ..+..+|..+...|.+-. .   -.||+|-+++-|||+-.++.||+||..|+|.--+|-+=|+.|.|+   ..+|-|+
T Consensus      1197 --st~s~~R~k~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYRfi 1274 (1567)
T KOG1015|consen 1197 --STTSQSRKKWAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYRFI 1274 (1567)
T ss_pred             --cccHHHHHHHHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehhhh
Confidence              788999999999998742 2   269999999999999999999999999999999999999999984   3344467


Q ss_pred             eCCchhhHHHH
Q psy4150         229 TQGREAHNFQT  239 (395)
Q Consensus       229 ~~~~e~~~~~~  239 (395)
                      ..++-++.+.+
T Consensus      1275 AqGTmEeKIYk 1285 (1567)
T KOG1015|consen 1275 AQGTMEEKIYK 1285 (1567)
T ss_pred             hcccHHHHHHH
Confidence            77777666543

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

Probab=98.08  E-value=1.4e-05  Score=85.35  Aligned_cols=115  Identities=20%  Similarity=0.205  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCc---eeEEeccCCCCCHHHHHHHHHHHhcC--
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVK---ASMFVGQSSGVTQQEQKEIMKKFRAG--  174 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~---~~~lhg~~~~~~~~~R~~~l~~Fk~g--  174 (395)
                      .+.+...|.+++..........++||||.+..+|+.+...|....|...   +..+.|   +  ..+-...+..|...  
T Consensus       406 ~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~---d--~~~~q~~Id~f~~ke~  480 (875)
T COG4096         406 TETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITG---D--AEQAQALIDNFIDKEK  480 (875)
T ss_pred             HHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEec---c--chhhHHHHHHHHhcCC
Confidence            3444455555544311112267999999999999999999998876544   456666   3  33334556777663  


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccc
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK  219 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~  219 (395)
                      --+|.|+.+++..|||+|.|-.++.+-.-.|..-|.|++||+-|.
T Consensus       481 ~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         481 YPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             CCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCcccc
Confidence            346888889999999999999999999999999999999999996

>KOG0949|consensus

Probab=98.07  E-value=8.4e-06  Score=87.82  Aligned_cols=74  Identities=26%  Similarity=0.389  Sum_probs=63.7

Q ss_pred             CCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCC-CCChhhHhhhcccccccc---CceEEEEEeC
Q psy4150         157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDA-QKSPIKMVQRLGRTGRKR---NGRCVILLTQ  230 (395)
Q Consensus       157 ~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~-p~s~~~yiQr~GRagR~~---~g~~i~l~~~  230 (395)
                      ++|+...|..+.=-||.|...||+||..++-|||.|.-.+|.--|. --++-.|-|+.|||||.|   .|.++++-.+
T Consensus       970 aglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~FmgiP 1047 (1330)
T KOG0949|consen  970 AGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVFMGIP 1047 (1330)
T ss_pred             cccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEEEeCc
Confidence            3999999999999999999999999999999999997777766653 348899999999999997   5777766443

>KOG0386|consensus

Probab=98.04  E-value=1.6e-05  Score=85.91  Aligned_cols=133  Identities=25%  Similarity=0.302  Sum_probs=111.8

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ....|++.|-.+|-.+...      ++|||.||.-....+.+.++|.-.+  ++...+-|   .....+|-..++.|..-
T Consensus       707 R~sGKfELLDRiLPKLkat------gHRVLlF~qMTrlmdimEdyL~~~~--~kYlRLDG---~TK~~eRg~ll~~FN~P  775 (1157)
T KOG0386|consen  707 RVSGKFELLDRILPKLKAT------GHRVLLFSQMTRLMDILEDYLQIRE--YKYLRLDG---QTKVEERGDLLEIFNAP  775 (1157)
T ss_pred             HhccHHHHHHhhhHHHHhc------CcchhhHHHHHHHHHHHHHHHhhhh--hheeeecC---CcchhhHHHHHHHhcCC
Confidence            3566999888888776553      8999999999999999999998887  88888999   78899999999999885


Q ss_pred             C---ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc---CceEEEEEeCCchhhHHH
Q psy4150         175 E---FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR---NGRCVILLTQGREAHNFQ  238 (395)
Q Consensus       175 ~---~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~~e~~~~~  238 (395)
                      .   +.+|.+|-.++.|+|+..++.||+||..|++....|+..||-|.|   ...++.+++-...++.+.
T Consensus       776 ds~yf~FllstragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~tv~sveE~il  845 (1157)
T KOG0386|consen  776 DSPYFIFLLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLITVNSVEEKIL  845 (1157)
T ss_pred             CCceeeeeeeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeeehhhHHHHHHH
Confidence            4   346899999999999999999999999999999999999999987   345555666555544443

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.03  E-value=1.6e-05  Score=86.33  Aligned_cols=96  Identities=21%  Similarity=0.365  Sum_probs=79.8

Q ss_pred             cceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCc---HHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHH
Q psy4150          89 MSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANY---RVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQK  165 (395)
Q Consensus        89 ~~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t---~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~  165 (395)
                      +...|... +-..++.+++..+         +.-.|||++.   ++.++.|+++|+.+|  +++..+|+   .     ..
T Consensus       314 IvD~y~~~-~~~e~~~elvk~l---------G~GgLIfV~~d~G~e~aeel~e~Lr~~G--i~a~~~~a---~-----~~  373 (1187)
T COG1110         314 IVDIYVES-ESLEKVVELVKKL---------GDGGLIFVPIDYGREKAEELAEYLRSHG--INAELIHA---E-----KE  373 (1187)
T ss_pred             eeeeeccC-ccHHHHHHHHHHh---------CCCeEEEEEcHHhHHHHHHHHHHHHhcC--ceEEEeec---c-----ch
Confidence            33444444 6667777777765         4568999999   999999999999999  99999987   2     26


Q ss_pred             HHHHHHhcCCccEEEEc----CccccCCCCCC-CCEEEEcCCCC
Q psy4150         166 EIMKKFRAGEFNTLIAT----SVGEEGLDIGE-IDLVICFDAQK  204 (395)
Q Consensus       166 ~~l~~Fk~g~~~vLVaT----~v~~~GlDip~-v~~VI~~d~p~  204 (395)
                      +.++.|..|++++||++    .++-||||+|+ +.++|.|+.|+
T Consensus       374 ~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         374 EALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             hhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCCc
Confidence            78999999999999886    57999999997 78999999995

>KOG0926|consensus

Probab=98.03  E-value=2.6e-06  Score=90.04  Aligned_cols=82  Identities=27%  Similarity=0.357  Sum_probs=69.9

Q ss_pred             CceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC------------------Chhh
Q psy4150         147 VKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK------------------SPIK  208 (395)
Q Consensus       147 ~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~------------------s~~~  208 (395)
                      +.|..|.+   -++...+.+++...-.|.--++|+|+|++..|.||+|.+||..+.-+                  |-.+
T Consensus       605 LyvLPLYS---LLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkAS  681 (1172)
T KOG0926|consen  605 LYVLPLYS---LLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKAS  681 (1172)
T ss_pred             eEEeehhh---hcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccc
Confidence            45666666   78999999999999999999999999999999999999999655432                  4556


Q ss_pred             HhhhccccccccCceEEEEEeCC
Q psy4150         209 MVQRLGRTGRKRNGRCVILLTQG  231 (395)
Q Consensus       209 yiQr~GRagR~~~g~~i~l~~~~  231 (395)
                      --||.|||||.|.|.||-+++..
T Consensus       682 adQRAGRAGRtgpGHcYRLYSSA  704 (1172)
T KOG0926|consen  682 ADQRAGRAGRTGPGHCYRLYSSA  704 (1172)
T ss_pred             cchhccccCCCCCCceeehhhhH
Confidence            68999999999999999887653

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.02  E-value=5.8e-05  Score=81.92  Aligned_cols=89  Identities=17%  Similarity=0.144  Sum_probs=65.5

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCH-HHHHHHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQ-QEQKEIMK  169 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~-~~R~~~l~  169 (395)
                      ..|.....|..++.+-+.....      .+.+|||-|.|....+.|+..|.+.|  ++..+++.   .-.. ..=.+++.
T Consensus       401 ~v~~t~~~K~~AI~~ei~~~~~------~grPVLIgT~SIe~SE~ls~~L~~~g--i~h~vLNA---k~~~~~~EA~IIA  469 (870)
T CHL00122        401 LIYKDELSKWRAIADECLQMHQ------TGRPILIGTTTIEKSELLSQLLKEYR--LPHQLLNA---KPENVRRESEIVA  469 (870)
T ss_pred             eEEeCHHHHHHHHHHHHHHHHh------cCCCEEEeeCCHHHHHHHHHHHHHcC--CccceeeC---CCccchhHHHHHH
Confidence            4455666788877766555433      47899999999999999999999999  88888887   3211 22233443


Q ss_pred             HHhcC-CccEEEEcCccccCCCCC
Q psy4150         170 KFRAG-EFNTLIATSVGEEGLDIG  192 (395)
Q Consensus       170 ~Fk~g-~~~vLVaT~v~~~GlDip  192 (395)
                      +  .| .-.|-|||+.++||.||-
T Consensus       470 ~--AG~~G~VTIATNMAGRGTDI~  491 (870)
T CHL00122        470 Q--AGRKGSITIATNMAGRGTDII  491 (870)
T ss_pred             h--cCCCCcEEEeccccCCCcCee
Confidence            2  55 466889999999999984

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

Probab=97.86  E-value=0.00013  Score=81.70  Aligned_cols=96  Identities=15%  Similarity=0.193  Sum_probs=70.9

Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEE
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI  180 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLV  180 (395)
                      ..+.+.|......     ..+++|||+++.+..+.+++.|......-....+.-   +++...|..+++.|+.++-.||+
T Consensus       738 ~~la~~i~~l~~~-----~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Q---g~~~~~r~~l~~~F~~~~~~iLl  809 (928)
T PRK08074        738 EEVAAYIAKIAKA-----TKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQ---GVSSGSRARLTKQFQQFDKAILL  809 (928)
T ss_pred             HHHHHHHHHHHHh-----CCCCEEEEECCHHHHHHHHHHHhhcccccCceEEec---CCCCCCHHHHHHHHHhcCCeEEE
Confidence            4555556555432     357999999999999999999976542111222322   34445678899999999889999


Q ss_pred             EcCccccCCCCCC--CCEEEEcCCCC
Q psy4150         181 ATSVGEEGLDIGE--IDLVICFDAQK  204 (395)
Q Consensus       181 aT~v~~~GlDip~--v~~VI~~d~p~  204 (395)
                      +|....+|||+|+  +.+||+..+|.
T Consensus       810 G~~sFwEGVD~pg~~l~~viI~kLPF  835 (928)
T PRK08074        810 GTSSFWEGIDIPGDELSCLVIVRLPF  835 (928)
T ss_pred             ecCcccCccccCCCceEEEEEecCCC
Confidence            9999999999996  57888877664

>KOG4439|consensus

Probab=97.83  E-value=0.00023  Score=74.75  Aligned_cols=136  Identities=20%  Similarity=0.266  Sum_probs=114.2

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc--
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA--  173 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~--  173 (395)
                      .+-|+..++++++..+.     ....+++|...-.....-+...|.+.|  +....+||   .....+|..+++.|..  
T Consensus       727 ~S~Ki~~~l~~le~i~~-----~skeK~viVSQwtsvLniv~~hi~~~g--~~y~si~G---qv~vK~Rq~iv~~FN~~k  796 (901)
T KOG4439|consen  727 PSCKIAMVLEILETILT-----SSKEKVVIVSQWTSVLNIVRKHIQKGG--HIYTSITG---QVLVKDRQEIVDEFNQEK  796 (901)
T ss_pred             chhHHHHHHHHHHHHhh-----cccceeeehhHHHHHHHHHHHHHhhCC--eeeeeecC---ccchhHHHHHHHHHHhcc
Confidence            45589999999988743     456788888888888888889999988  88899999   9999999999999976  


Q ss_pred             CCccE-EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCce---EEEEEeCCchhhHHHHHH
Q psy4150         174 GEFNT-LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGR---CVILLTQGREAHNFQTSM  241 (395)
Q Consensus       174 g~~~v-LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~---~i~l~~~~~e~~~~~~~~  241 (395)
                      |..+| |++-..++.|||+-+.+++|..|+.|++.---|.+.|.-|.|+.+   ++-|++.++.++.+...+
T Consensus       797 ~~~rVmLlSLtAGGVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V~IhR~~~~gTvEqrV~~LQ  868 (901)
T KOG4439|consen  797 GGARVMLLSLTAGGVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDVFIHRLMCKGTVEQRVKSLQ  868 (901)
T ss_pred             CCceEEEEEEccCcceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCceEEEEEEecCcHHHHHHHHH
Confidence            44555 567789999999999999999999999998889889999987433   345788999888887766

>KOG0925|consensus

Probab=97.81  E-value=6.3e-05  Score=76.04  Aligned_cols=131  Identities=21%  Similarity=0.295  Sum_probs=89.0

Q ss_pred             eeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHccc----CC---CCceeEEeccCCCCCHHHHH
Q psy4150          93 YAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPL----EP---MVKASMFVGQSSGVTQQEQK  165 (395)
Q Consensus        93 ~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~----~~---~~~~~~lhg~~~~~~~~~R~  165 (395)
                      |+...+-.+.|...+...++-|.. +..+-+|||...-+.++..++.+...    ++   .+++..+|.       .++.
T Consensus       227 ~Yt~e~erDylEaairtV~qih~~-ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLyP-------~~qq  298 (699)
T KOG0925|consen  227 FYTPEPERDYLEAAIRTVLQIHMC-EEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLYP-------AQQQ  298 (699)
T ss_pred             EecCCCChhHHHHHHHHHHHHHhc-cCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecCc-------hhhc
Confidence            444444444444444333333332 34678999999988888777766532    21   266776664       3333


Q ss_pred             HHHHHHh---cC--CccEEEEcCccccCCCCCCCCEEEEcCC------------------CCChhhHhhhccccccccCc
Q psy4150         166 EIMKKFR---AG--EFNTLIATSVGEEGLDIGEIDLVICFDA------------------QKSPIKMVQRLGRTGRKRNG  222 (395)
Q Consensus       166 ~~l~~Fk---~g--~~~vLVaT~v~~~GlDip~v~~VI~~d~------------------p~s~~~yiQr~GRagR~~~g  222 (395)
                      .+++-..   .|  .-+|+|+|++++..+.+++|-+||.-++                  |.|..+-.||.||+||.+.|
T Consensus       299 ~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt~pG  378 (699)
T KOG0925|consen  299 RIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPG  378 (699)
T ss_pred             cccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCCCCC
Confidence            3433322   23  3469999999999999999999997654                  44778889999999999999


Q ss_pred             eEEEEEeCC
Q psy4150         223 RCVILLTQG  231 (395)
Q Consensus       223 ~~i~l~~~~  231 (395)
                      +++.++++.
T Consensus       379 kcfrLYte~  387 (699)
T KOG0925|consen  379 KCFRLYTEE  387 (699)
T ss_pred             ceEEeecHH
Confidence            999988764

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

Probab=97.78  E-value=0.00016  Score=77.97  Aligned_cols=118  Identities=21%  Similarity=0.290  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCc-c
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEF-N  177 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~-~  177 (395)
                      =...+...|......     ..+++|||+++....+.+++.|...... .....+|      ...+...++.|+.+.- -
T Consensus       463 ~~~~~~~~i~~~~~~-----~~~~~lvlF~Sy~~l~~~~~~~~~~~~~-~~v~~q~------~~~~~~~l~~f~~~~~~~  530 (654)
T COG1199         463 LLAKLAAYLREILKA-----SPGGVLVLFPSYEYLKRVAERLKDERST-LPVLTQG------EDEREELLEKFKASGEGL  530 (654)
T ss_pred             HHHHHHHHHHHHHhh-----cCCCEEEEeccHHHHHHHHHHHhhcCcc-ceeeecC------CCcHHHHHHHHHHhcCCe
Confidence            444555555555543     3459999999999999999999876621 2344455      3344588999988655 8


Q ss_pred             EEEEcCccccCCCCCC--CCEEEEcCCCC------------------------------ChhhHhhhcccccccc-CceE
Q psy4150         178 TLIATSVGEEGLDIGE--IDLVICFDAQK------------------------------SPIKMVQRLGRTGRKR-NGRC  224 (395)
Q Consensus       178 vLVaT~v~~~GlDip~--v~~VI~~d~p~------------------------------s~~~yiQr~GRagR~~-~g~~  224 (395)
                      ++|+|..+.+|||+|+  +.+||...+|.                              ....+.|-+||.-|.. +.++
T Consensus       531 ~lv~~gsf~EGVD~~g~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~  610 (654)
T COG1199         531 ILVGGGSFWEGVDFPGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGV  610 (654)
T ss_pred             EEEeeccccCcccCCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceE
Confidence            9999999999999996  57888888774                              2456789999999984 4444


Q ss_pred             EEEE
Q psy4150         225 VILL  228 (395)
Q Consensus       225 i~l~  228 (395)
                      ++++
T Consensus       611 ivll  614 (654)
T COG1199         611 IVLL  614 (654)
T ss_pred             EEEe
Confidence            4444

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.71  E-value=0.00051  Score=74.87  Aligned_cols=89  Identities=16%  Similarity=0.152  Sum_probs=66.5

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCC-CCHHHHHHHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMK  169 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~-~~~~~R~~~l~  169 (395)
                      ..|.....|..++.+-+.+...      .+.+|||-|.|....+.|+..|.+.|  ++..+++.   . .....=.+++.
T Consensus       416 ~vy~t~~~K~~Ai~~ei~~~~~------~GrPVLIgT~SVe~SE~ls~~L~~~g--i~h~vLNA---k~~~~~~EA~IIa  484 (939)
T PRK12902        416 QVYKTEIAKWRAVANETAEMHK------QGRPVLVGTTSVEKSELLSALLQEQG--IPHNLLNA---KPENVEREAEIVA  484 (939)
T ss_pred             eEEcCHHHHHHHHHHHHHHHHh------CCCCEEEeeCCHHHHHHHHHHHHHcC--CchheeeC---CCcchHhHHHHHH
Confidence            3455567788888776666433      47899999999999999999999999  88888887   3 22222233443


Q ss_pred             HHhcC-CccEEEEcCccccCCCCC
Q psy4150         170 KFRAG-EFNTLIATSVGEEGLDIG  192 (395)
Q Consensus       170 ~Fk~g-~~~vLVaT~v~~~GlDip  192 (395)
                      +  .| .-.|-|||+.++||.||.
T Consensus       485 ~--AG~~GaVTIATNMAGRGTDIk  506 (939)
T PRK12902        485 Q--AGRKGAVTIATNMAGRGTDII  506 (939)
T ss_pred             h--cCCCCcEEEeccCCCCCcCEe
Confidence            2  56 456889999999999984

>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []

Probab=97.68  E-value=2e-05  Score=51.93  Aligned_cols=35  Identities=14%  Similarity=0.175  Sum_probs=31.5

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhh
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQ  364 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~  364 (395)
                      +.+.+++..|..|++.++  ||.|+.+||+|..|+.|
T Consensus         2 ~~i~~l~~~m~~a~~~~d--fE~Aa~~Rd~i~~l~~q   36 (36)
T PF02151_consen    2 KLIKELEEKMEEAVENED--FEKAARLRDQIKALKKQ   36 (36)
T ss_dssp             HHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcC--HHHHHHHHHHHHHHHcC
Confidence            468889999999999999  99999999999999875

UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.

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

Probab=97.68  E-value=8.3e-05  Score=82.20  Aligned_cols=115  Identities=22%  Similarity=0.307  Sum_probs=85.5

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccC-----C---------------------CCc-------eeEEec---cCCCCCHH
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLE-----P---------------------MVK-------ASMFVG---QSSGVTQQ  162 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~-----~---------------------~~~-------~~~lhg---~~~~~~~~  162 (395)
                      ...++|+|+-++..|+..+..+....     +                     .+.       ...+-|   ||++|=+.
T Consensus       378 ~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~  457 (1041)
T COG4581         378 NLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPA  457 (1041)
T ss_pred             cCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchH
Confidence            35689999999999999998876221     0                     011       000001   45599999


Q ss_pred             HHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE----EcC----CCCChhhHhhhcccccccc---CceEEEEEeCC
Q psy4150         163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI----CFD----AQKSPIKMVQRLGRTGRKR---NGRCVILLTQG  231 (395)
Q Consensus       163 ~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI----~~d----~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~  231 (395)
                      .+..+..-|..|-++||++|.+++.|+|.|.=++|+    -+|    .+-++..|+|..|||||.|   .|.++++-.+.
T Consensus       458 ~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~~  537 (1041)
T COG4581         458 IKELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPPF  537 (1041)
T ss_pred             HHHHHHHHHhccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCCC
Confidence            999999999999999999999999999999766655    222    1227889999999999997   57777664444


Q ss_pred             ch
Q psy4150         232 RE  233 (395)
Q Consensus       232 ~e  233 (395)
                      ..
T Consensus       538 ~~  539 (1041)
T COG4581         538 ES  539 (1041)
T ss_pred             CC
Confidence            33

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.65  E-value=0.00041  Score=75.36  Aligned_cols=91  Identities=19%  Similarity=0.215  Sum_probs=65.9

Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc----CC
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA----GE  175 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~----g~  175 (395)
                      ...+.+.|......      .+++|||+++....+.+++.|....  -.....+|   .   ..+..+++.|+.    |+
T Consensus       520 ~~~~~~~i~~l~~~------~gg~LVlFtSy~~l~~v~~~l~~~~--~~~ll~Q~---~---~~~~~ll~~f~~~~~~~~  585 (697)
T PRK11747        520 TAEMAEFLPELLEK------HKGSLVLFASRRQMQKVADLLPRDL--RLMLLVQG---D---QPRQRLLEKHKKRVDEGE  585 (697)
T ss_pred             HHHHHHHHHHHHhc------CCCEEEEeCcHHHHHHHHHHHHHhc--CCcEEEeC---C---chHHHHHHHHHHHhccCC
Confidence            34455555554432      3568999999999999999987532  12344555   3   246778877774    67


Q ss_pred             ccEEEEcCccccCCCCCC--CCEEEEcCCCC
Q psy4150         176 FNTLIATSVGEEGLDIGE--IDLVICFDAQK  204 (395)
Q Consensus       176 ~~vLVaT~v~~~GlDip~--v~~VI~~d~p~  204 (395)
                      -.||++|..+.+|||+|+  +++||+..+|.
T Consensus       586 ~~VL~g~~sf~EGVD~pGd~l~~vII~kLPF  616 (697)
T PRK11747        586 GSVLFGLQSFAEGLDLPGDYLTQVIITKIPF  616 (697)
T ss_pred             CeEEEEeccccccccCCCCceEEEEEEcCCC
Confidence            789999999999999986  78999888763

>COG4889 Predicted helicase [General function prediction only]

Probab=97.54  E-value=4.7e-05  Score=81.50  Aligned_cols=100  Identities=27%  Similarity=0.338  Sum_probs=76.1

Q ss_pred             CccEEEEcCcHHHHHHHHH-----------HHcccCCCCceeEEeccCCCCCHHHHHHHHH---HHhcCCccEEEEcCcc
Q psy4150         120 TTKVIIFANYRVVVAEIFD-----------VLKPLEPMVKASMFVGQSSGVTQQEQKEIMK---KFRAGEFNTLIATSVG  185 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~-----------~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~---~Fk~g~~~vLVaT~v~  185 (395)
                      -.|+|-||.+.++...+++           .|.+.++.+++.+=|-.+ .|+..+|...+.   .|...+++||-.--++
T Consensus       460 ~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDG-tmNal~R~~l~~l~~~~~~neckIlSNaRcL  538 (1518)
T COG4889         460 MQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDG-TMNALERLDLLELKNTFEPNECKILSNARCL  538 (1518)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccc-cccHHHHHHHHhccCCCCcchheeeccchhh
Confidence            3466777777666544443           344445556666666322 899999855544   3455789999989999


Q ss_pred             ccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc
Q psy4150         186 EEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR  220 (395)
Q Consensus       186 ~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~  220 (395)
                      ++|+|+|..+.||.||+-.+..+.+|.+||+-|..
T Consensus       539 SEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa  573 (1518)
T COG4889         539 SEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKA  573 (1518)
T ss_pred             hcCCCccccceEEEecCchhHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999983

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=97.47  E-value=0.0013  Score=72.81  Aligned_cols=88  Identities=17%  Similarity=0.196  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEE
Q psy4150         102 RLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIA  181 (395)
Q Consensus       102 ~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVa  181 (395)
                      .+.+.|.....      .+++++|+++|.+..+.+++.|....  +.+ ...|.  +.   .+..+++.|+.++-.||++
T Consensus       635 ~~~~~i~~~~~------~~g~~LVLFtS~~~l~~v~~~l~~~~--~~~-l~Qg~--~~---~~~~l~~~F~~~~~~vLlG  700 (820)
T PRK07246        635 EIAKRLEELKQ------LQQPILVLFNSKKHLLAVSDLLDQWQ--VSH-LAQEK--NG---TAYNIKKRFDRGEQQILLG  700 (820)
T ss_pred             HHHHHHHHHHh------cCCCEEEEECcHHHHHHHHHHHhhcC--CcE-EEeCC--Cc---cHHHHHHHHHcCCCeEEEe
Confidence            45555544432      35899999999999999999997543  333 44441  22   2456899999998899999


Q ss_pred             cCccccCCCCC--CCCEEEEcCCC
Q psy4150         182 TSVGEEGLDIG--EIDLVICFDAQ  203 (395)
Q Consensus       182 T~v~~~GlDip--~v~~VI~~d~p  203 (395)
                      |+...+|||+|  +...||...+|
T Consensus       701 ~~sFwEGVD~p~~~~~~viI~kLP  724 (820)
T PRK07246        701 LGSFWEGVDFVQADRMIEVITRLP  724 (820)
T ss_pred             cchhhCCCCCCCCCeEEEEEecCC
Confidence            99999999997  35566666655

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.22  E-value=0.0036  Score=68.28  Aligned_cols=96  Identities=17%  Similarity=0.235  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCC-----CceeEEeccCCCCCHHHHHHHHHHHhc-
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPM-----VKASMFVGQSSGVTQQEQKEIMKKFRA-  173 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~-----~~~~~lhg~~~~~~~~~R~~~l~~Fk~-  173 (395)
                      ...+.++|.+....     .++.+|||+++-...+.+.+.+...+..     .+..+.-+    -...++..+++.|+. 
T Consensus       507 ~~~l~~~i~~~~~~-----~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~----~~~~~~~~~l~~f~~~  577 (705)
T TIGR00604       507 VRNLGELLVEFSKI-----IPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVET----KDAQETSDALERYKQA  577 (705)
T ss_pred             HHHHHHHHHHHhhc-----CCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeC----CCcchHHHHHHHHHHH
Confidence            45566666665542     3578999999999999999988765410     12233323    112577889999975 


Q ss_pred             ---CCccEEEEc--CccccCCCCCC--CCEEEEcCCCC
Q psy4150         174 ---GEFNTLIAT--SVGEEGLDIGE--IDLVICFDAQK  204 (395)
Q Consensus       174 ---g~~~vLVaT--~v~~~GlDip~--v~~VI~~d~p~  204 (395)
                         |.-.||+|+  ..++||||+++  +..||..++|-
T Consensus       578 ~~~~~gavL~av~gGk~sEGIDf~~~~~r~ViivGlPf  615 (705)
T TIGR00604       578 VSEGRGAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPY  615 (705)
T ss_pred             HhcCCceEEEEecCCcccCccccCCCCCcEEEEEccCC
Confidence               455699999  88999999996  78999999885

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).

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=97.14  E-value=0.0081  Score=64.31  Aligned_cols=90  Identities=14%  Similarity=0.091  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc----CCccE
Q psy4150         103 LREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA----GEFNT  178 (395)
Q Consensus       103 L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~----g~~~v  178 (395)
                      +.+.+..++..     .+++++|.+.+....+.+++.|....+  -..++.|   +.+  .+...++.|+.    |.-.|
T Consensus       458 ~~~~~~~~~~~-----~~G~~lvLfTS~~~~~~~~~~l~~~l~--~~~l~qg---~~~--~~~~l~~~f~~~~~~~~~~v  525 (636)
T TIGR03117       458 VSLSTAAILRK-----AQGGTLVLTTAFSHISAIGQLVELGIP--AEIVIQS---EKN--RLASAEQQFLALYANGIQPV  525 (636)
T ss_pred             HHHHHHHHHHH-----cCCCEEEEechHHHHHHHHHHHHhhcC--CCEEEeC---CCc--cHHHHHHHHHHhhcCCCCcE
Confidence            44555554442     357999999999999999999976542  3345556   332  34668888987    47899


Q ss_pred             EEEcCccccCCCC----------CCCCEEEEcCCCC
Q psy4150         179 LIATSVGEEGLDI----------GEIDLVICFDAQK  204 (395)
Q Consensus       179 LVaT~v~~~GlDi----------p~v~~VI~~d~p~  204 (395)
                      |++|+.+-+|||+          ..+++||+.-+|.
T Consensus       526 L~gt~sfweGvDv~~~~~~p~~G~~Ls~ViI~kLPF  561 (636)
T TIGR03117       526 LIAAGGAWTGIDLTHKPVSPDKDNLLTDLIITCAPF  561 (636)
T ss_pred             EEeCCccccccccCCccCCCCCCCcccEEEEEeCCC
Confidence            9999999999999          2489999888873

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.

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=97.07  E-value=0.0043  Score=53.85  Aligned_cols=47  Identities=23%  Similarity=0.251  Sum_probs=37.6

Q ss_pred             CCCHHHHHHHHHHHhcCC-ccEEEEcCccccCCCCCC--CCEEEEcCCCC
Q psy4150         158 GVTQQEQKEIMKKFRAGE-FNTLIATSVGEEGLDIGE--IDLVICFDAQK  204 (395)
Q Consensus       158 ~~~~~~R~~~l~~Fk~g~-~~vLVaT~v~~~GlDip~--v~~VI~~d~p~  204 (395)
                      +.+..+...+++.|+... ..||++|.-+.+|||+|+  +..||...+|.
T Consensus        30 ~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492       30 GEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             CCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCC
Confidence            345556788999998754 379999988999999996  67888888774

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=96.91  E-value=0.005  Score=53.50  Aligned_cols=42  Identities=26%  Similarity=0.310  Sum_probs=33.8

Q ss_pred             HHHHHHHHHhcCCc---cEEEEcCc--cccCCCCCC--CCEEEEcCCCC
Q psy4150         163 EQKEIMKKFRAGEF---NTLIATSV--GEEGLDIGE--IDLVICFDAQK  204 (395)
Q Consensus       163 ~R~~~l~~Fk~g~~---~vLVaT~v--~~~GlDip~--v~~VI~~d~p~  204 (395)
                      +...+++.|+...-   .||+|+.-  +.+|||+|+  +..||...+|-
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            44788999987543   58888877  999999996  67999888773

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=96.90  E-value=0.0036  Score=69.49  Aligned_cols=92  Identities=20%  Similarity=0.181  Sum_probs=64.3

Q ss_pred             EEEcCcHHHHHHHHHHHcccC----CCCceeEEeccCCCCCHHHHHHHHHHH----------------------hc----
Q psy4150         124 IIFANYRVVVAEIFDVLKPLE----PMVKASMFVGQSSGVTQQEQKEIMKKF----------------------RA----  173 (395)
Q Consensus       124 iVF~~t~~~ae~l~~~L~~~~----~~~~~~~lhg~~~~~~~~~R~~~l~~F----------------------k~----  173 (395)
                      +|=+++.+.+-.++..|....    ..+...++|+   ......|..+.+.+                      +.    
T Consensus       760 liR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHS---r~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~  836 (1110)
T TIGR02562       760 LIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHA---QDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPAL  836 (1110)
T ss_pred             EEEEcCchHHHHHHHHHHhhccccCCceeEEEecc---cChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhccccc
Confidence            566777777777777766543    2355788898   55444444433322                      12    


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC
Q psy4150         174 GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN  221 (395)
Q Consensus       174 g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~  221 (395)
                      +..-|+|+|+|.+-|+|+ +.+++|--  |.+..+.|||+||+.|.|.
T Consensus       837 ~~~~i~v~Tqv~E~g~D~-dfd~~~~~--~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       837 NHLFIVLATPVEEVGRDH-DYDWAIAD--PSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             CCCeEEEEeeeEEEEecc-cCCeeeec--cCcHHHHHHHhhccccccc
Confidence            356799999999999998 46666543  5669999999999999863

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.

>PF13871 Helicase_C_4: Helicase_C-like

Probab=96.74  E-value=0.0067  Score=58.40  Aligned_cols=82  Identities=21%  Similarity=0.283  Sum_probs=61.4

Q ss_pred             HHHHHHhcCCccEEEEcCccccCCCCCCC--------CEEEEcCCCCChhhHhhhccccccccC--c-eEEEEEeCCchh
Q psy4150         166 EIMKKFRAGEFNTLIATSVGEEGLDIGEI--------DLVICFDAQKSPIKMVQRLGRTGRKRN--G-RCVILLTQGREA  234 (395)
Q Consensus       166 ~~l~~Fk~g~~~vLVaT~v~~~GlDip~v--------~~VI~~d~p~s~~~yiQr~GRagR~~~--g-~~i~l~~~~~e~  234 (395)
                      ...+.|.+|+..|+|.|+.++.||-+..-        .+-|.+.+||+....+|..||+.|.++  . .+.+++++-..+
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            55678999999999999999999988632        255788999999999999999999963  3 344455555556


Q ss_pred             hHHHHHHHHhHHH
Q psy4150         235 HNFQTSMQTCKSY  247 (395)
Q Consensus       235 ~~~~~~~~~~~~~  247 (395)
                      ..+.....+..+.
T Consensus       132 ~Rfas~va~rL~s  144 (278)
T PF13871_consen  132 RRFASTVARRLES  144 (278)
T ss_pred             HHHHHHHHHHHhh
Confidence            6665555333333

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=96.60  E-value=0.0048  Score=67.03  Aligned_cols=125  Identities=19%  Similarity=0.161  Sum_probs=84.0

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..|.....|+....+-+.....      .+.++||-+.+....+.+++.|.+.|  ++..++..   .-.  +|..-+-.
T Consensus       406 ~vy~t~~~K~~Aiv~~I~~~~~------~gqPvLvgT~sie~SE~ls~~L~~~~--i~h~VLNA---k~h--~~EA~Iia  472 (822)
T COG0653         406 LVYKTEEEKFKAIVEDIKERHE------KGQPVLVGTVSIEKSELLSKLLRKAG--IPHNVLNA---KNH--AREAEIIA  472 (822)
T ss_pred             ccccchHHHHHHHHHHHHHHHh------cCCCEEEcCcceecchhHHHHHHhcC--CCceeecc---ccH--HHHHHHHh
Confidence            3455566688887777766544      47999999999999999999999999  87777766   333  33333333


Q ss_pred             HhcCC-ccEEEEcCccccCCCCCCCC-----------EEEEcCCCCChhhHhhhccccccccC-ceEEEEEe
Q psy4150         171 FRAGE-FNTLIATSVGEEGLDIGEID-----------LVICFDAQKSPIKMVQRLGRTGRKRN-GRCVILLT  229 (395)
Q Consensus       171 Fk~g~-~~vLVaT~v~~~GlDip~v~-----------~VI~~d~p~s~~~yiQr~GRagR~~~-g~~i~l~~  229 (395)
                      + .|. --|-|||+.++||.||.--.           +||--.-..|..---|-.||+||.|+ |....|++
T Consensus       473 ~-AG~~gaVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lS  543 (822)
T COG0653         473 Q-AGQPGAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLS  543 (822)
T ss_pred             h-cCCCCccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhh
Confidence            3 343 35779999999999985222           23333333333333478899999985 44444443

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.38  E-value=0.014  Score=63.06  Aligned_cols=79  Identities=15%  Similarity=0.152  Sum_probs=57.8

Q ss_pred             HHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC----ccccCCCCCCCCEEEEcCCCC----
Q psy4150         133 VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS----VGEEGLDIGEIDLVICFDAQK----  204 (395)
Q Consensus       133 ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~----v~~~GlDip~v~~VI~~d~p~----  204 (395)
                      ++.+.+.|.+..|..++..+.+          ..++..|. ++.+|||+|.    +++     +++.+|+.+|...    
T Consensus       440 ter~eeeL~~~FP~~~V~r~d~----------d~~l~~~~-~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~  503 (665)
T PRK14873        440 ARRTAEELGRAFPGVPVVTSGG----------DQVVDTVD-AGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGR  503 (665)
T ss_pred             HHHHHHHHHHHCCCCCEEEECh----------HHHHHhhc-cCCCEEEECCCCccccc-----CCceEEEEEcchhhhcC
Confidence            7788888888777666665443          24789996 5999999998    555     4788888887653    


Q ss_pred             --------ChhhHhhhcccccccc-CceEEEE
Q psy4150         205 --------SPIKMVQRLGRTGRKR-NGRCVIL  227 (395)
Q Consensus       205 --------s~~~yiQr~GRagR~~-~g~~i~l  227 (395)
                              ....+.|-.||+||.+ .|.+++.
T Consensus       504 pDfRA~Er~~qll~qvagragr~~~~G~V~iq  535 (665)
T PRK14873        504 QDLRAAEDTLRRWMAAAALVRPRADGGQVVVV  535 (665)
T ss_pred             CCcChHHHHHHHHHHHHHhhcCCCCCCEEEEE
Confidence                    3445688899999986 4555554

>KOG1001|consensus

Probab=96.36  E-value=0.0017  Score=69.77  Aligned_cols=135  Identities=15%  Similarity=0.155  Sum_probs=105.6

Q ss_pred             ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC-C
Q psy4150          97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG-E  175 (395)
Q Consensus        97 ~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g-~  175 (395)
                      +.|+..+..+|..   . ..+.. .++|||++....++-+.-.|...+  +....+.|   .|+...|...+..|..+ .
T Consensus       521 s~ki~~~~~~l~~---~-~~s~~-~kiiifsq~~~~l~l~~~~l~~~~--~~~~~~~g---~~~~~~r~~s~~~~~~~~~  590 (674)
T KOG1001|consen  521 SSKIYAFLKILQA---K-EMSEQ-PKIVIFSQLIWGLALVCLRLFFKG--FVFLRYDG---EMLMKIRTKSFTDFPCDPL  590 (674)
T ss_pred             hhhhHHHHHHHhh---c-cCCCC-CceeeehhHHHHHHHhhhhhhhcc--cccchhhh---hhHHHHHHhhhcccccCcc
Confidence            4466666666652   1 11222 499999999999999999998777  77777888   99999999999999965 3


Q ss_pred             ccE-EEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC---ceEEEEEeCCchhhHHHHHH
Q psy4150         176 FNT-LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN---GRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       176 ~~v-LVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~---g~~i~l~~~~~e~~~~~~~~  241 (395)
                      ..| |++..++.-|+++..+++|+..|+-|++..--|.+-|+-|-|+   -.+.-++..+..++.+.+.+
T Consensus       591 ~~vll~Slkag~~glnlt~a~~v~~~d~~wnp~~eeQaidR~hrigq~k~v~v~r~~i~dtveer~l~iq  660 (674)
T KOG1001|consen  591 VTALLMSLKAGKVGLNLTAASHVLLMDPWWNPAVEEQAIDRAHRIGQTKPVKVSRFIIKDTVEERILKIQ  660 (674)
T ss_pred             HHHHHHHHHHhhhhhchhhhhHHHhhchhcChHHHHHHHHHHHHhcccceeeeeeehhhhccHHHHHHHH
Confidence            344 5788999999999999999999999999999999888888874   33444666666676666666

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.35  E-value=0.019  Score=62.48  Aligned_cols=100  Identities=16%  Similarity=0.277  Sum_probs=76.9

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .++.|.....-.+.....      .+.+++|.++|+..|...++.+.+..+  ++++..+||   +++..+|..++..+.
T Consensus       291 TGSGKT~va~~~il~~~~------~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G---~~~~~~r~~~~~~l~  361 (681)
T PRK10917        291 VGSGKTVVAALAALAAIE------AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTG---SLKGKERREILEAIA  361 (681)
T ss_pred             CCCcHHHHHHHHHHHHHH------cCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcC---CCCHHHHHHHHHHHh
Confidence            345566554433333332      257999999999999988887776532  288999999   999999999999999


Q ss_pred             cCCccEEEEcC-ccccCCCCCCCCEEEEcCCC
Q psy4150         173 AGEFNTLIATS-VGEEGLDIGEIDLVICFDAQ  203 (395)
Q Consensus       173 ~g~~~vLVaT~-v~~~GlDip~v~~VI~~d~p  203 (395)
                      +|.++|+|+|. .+..++.+..+.+||.=...
T Consensus       362 ~g~~~IvVgT~~ll~~~v~~~~l~lvVIDE~H  393 (681)
T PRK10917        362 SGEADIVIGTHALIQDDVEFHNLGLVIIDEQH  393 (681)
T ss_pred             CCCCCEEEchHHHhcccchhcccceEEEechh
Confidence            99999999996 45667888899988865443

>KOG0701|consensus

Probab=96.35  E-value=0.0015  Score=75.25  Aligned_cols=97  Identities=32%  Similarity=0.452  Sum_probs=78.6

Q ss_pred             cEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCC--------CCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCC
Q psy4150         122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSS--------GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGE  193 (395)
Q Consensus       122 r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~--------~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~  193 (395)
                      ..|+||+.+..+..+.+.+.+.+. ..+..+.|-.+        ......+.+++..|....+++|++|.++.+|+|++.
T Consensus       294 ~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~  372 (1606)
T KOG0701|consen  294 SGIIFVDQRYTAYVLLELLREIFS-NDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPK  372 (1606)
T ss_pred             hheeecccchHHHHHHHHHHHhhc-cCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhh
Confidence            469999999999999988877542 33333555221        112334778999999999999999999999999999


Q ss_pred             CCEEEEcCCCCChhhHhhhccccccc
Q psy4150         194 IDLVICFDAQKSPIKMVQRLGRTGRK  219 (395)
Q Consensus       194 v~~VI~~d~p~s~~~yiQr~GRagR~  219 (395)
                      |+.|+.++.|....+|+|+.||+-+.
T Consensus       373 ~~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  373 CNLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhhheeccCcchHHHHHHhhcccccc
Confidence            99999999999999999999998554

>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=96.28  E-value=0.056  Score=55.40  Aligned_cols=124  Identities=13%  Similarity=0.149  Sum_probs=93.3

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      +++.+.+-+.-.+..   .....++|||+++--.--.|.++|++.+  +....+|-   ..++.+-..+-..|..|+..|
T Consensus       282 Rf~yF~~~iLP~l~~---~~~~~~~LIfIPSYfDfVRlRN~lk~~~--~sF~~i~E---Yts~~~isRAR~~F~~G~~~i  353 (442)
T PF06862_consen  282 RFKYFTKKILPQLKR---DSKMSGTLIFIPSYFDFVRLRNYLKKEN--ISFVQISE---YTSNSDISRARSQFFHGRKPI  353 (442)
T ss_pred             HHHHHHHHHHHHhhh---ccCCCcEEEEecchhhhHHHHHHHHhcC--CeEEEecc---cCCHHHHHHHHHHHHcCCceE
Confidence            555555533333331   2457899999999999999999999877  88888888   678888888999999999999


Q ss_pred             EEEcCcc--ccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-------CceEEEEEeC
Q psy4150         179 LIATSVG--EEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-------NGRCVILLTQ  230 (395)
Q Consensus       179 LVaT~v~--~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-------~g~~i~l~~~  230 (395)
                      |+.|-=+  =+=..|-+|..||.|.+|..+.-|-.-++-.+...       ...+.++++.
T Consensus       354 LL~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk  414 (442)
T PF06862_consen  354 LLYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSK  414 (442)
T ss_pred             EEEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecH
Confidence            9999421  12345678999999999999988877665444432       4667777765

; GO: 0005634 nucleus

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.05  E-value=0.049  Score=59.25  Aligned_cols=98  Identities=10%  Similarity=0.134  Sum_probs=79.4

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      .++.|......++...+..      +.++||.++++..+..+.+.|.+..+ ..+..+||   +++..+|...+.++..|
T Consensus       171 TGSGKT~v~l~~i~~~l~~------g~~vLvLvPt~~L~~Q~~~~l~~~fg-~~v~~~~s---~~s~~~r~~~~~~~~~g  240 (679)
T PRK05580        171 TGSGKTEVYLQAIAEVLAQ------GKQALVLVPEIALTPQMLARFRARFG-APVAVLHS---GLSDGERLDEWRKAKRG  240 (679)
T ss_pred             CCChHHHHHHHHHHHHHHc------CCeEEEEeCcHHHHHHHHHHHHHHhC-CCEEEEEC---CCCHHHHHHHHHHHHcC
Confidence            3566888877777665543      57899999999999999999987532 78899999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCC
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQ  203 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p  203 (395)
                      ..+|+|+|..+. -+.+.++.+||.-+..
T Consensus       241 ~~~IVVgTrsal-~~p~~~l~liVvDEeh  268 (679)
T PRK05580        241 EAKVVIGARSAL-FLPFKNLGLIIVDEEH  268 (679)
T ss_pred             CCCEEEeccHHh-cccccCCCEEEEECCC
Confidence            999999996432 2567788888877654

>TIGR00595 priA primosomal protein N'

Probab=96.05  E-value=0.044  Score=57.46  Aligned_cols=97  Identities=15%  Similarity=0.188  Sum_probs=77.4

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      .++.|......++...+..      +.++||.+++...+..+++.|++..+ ..+..+||   +++..+|..++.+...|
T Consensus         6 TGsGKT~v~l~~i~~~l~~------g~~vLvlvP~i~L~~Q~~~~l~~~f~-~~v~vlhs---~~~~~er~~~~~~~~~g   75 (505)
T TIGR00595         6 TGSGKTEVYLQAIEKVLAL------GKSVLVLVPEIALTPQMIQRFKYRFG-SQVAVLHS---GLSDSEKLQAWRKVKNG   75 (505)
T ss_pred             CCCCHHHHHHHHHHHHHHc------CCeEEEEeCcHHHHHHHHHHHHHHhC-CcEEEEEC---CCCHHHHHHHHHHHHcC
Confidence            3556887777777665543      57899999999999999999987532 67889999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCC
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDA  202 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~  202 (395)
                      +.+|+|+|..+-- +.+.++.+||.-+.
T Consensus        76 ~~~IVVGTrsalf-~p~~~l~lIIVDEe  102 (505)
T TIGR00595        76 EILVVIGTRSALF-LPFKNLGLIIVDEE  102 (505)
T ss_pred             CCCEEECChHHHc-CcccCCCEEEEECC
Confidence            9999999965432 45678888886654

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).

>KOG1016|consensus

Probab=96.04  E-value=0.0048  Score=65.79  Aligned_cols=115  Identities=21%  Similarity=0.273  Sum_probs=88.6

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC----------------CCceeEEeccCCCCCH
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP----------------MVKASMFVGQSSGVTQ  161 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~----------------~~~~~~lhg~~~~~~~  161 (395)
                      +|.-.+++++.+..      .-+.++|||...-...+.|.++|.+..-                ...-..+.|   ..+.
T Consensus       703 pk~V~~~~~~des~------~~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG---~t~a  773 (1387)
T KOG1016|consen  703 PKIVISLEILDEST------QIGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDG---TTSA  773 (1387)
T ss_pred             CceEEEEeeecccc------ccCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccC---Cccc
Confidence            44444444444432      2378999999999999999999987530                011223444   6778


Q ss_pred             HHHHHHHHHHhcC---CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC
Q psy4150         162 QEQKEIMKKFRAG---EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN  221 (395)
Q Consensus       162 ~~R~~~l~~Fk~g---~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~  221 (395)
                      .+|++.+++|.+.   ..-+|++|-.+.-||++-..+.+|.||+.|++.--.|.+-|+-|.|+
T Consensus       774 ~~rekLinqfN~e~~lsWlfllstrag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ  836 (1387)
T KOG1016|consen  774 ADREKLINQFNSEPGLSWLFLLSTRAGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQ  836 (1387)
T ss_pred             chHHHHHHhccCCCCceeeeeehhccccccceeeccceEEEEEeecCccccchhhhhhhhhcC
Confidence            8999999999874   33578999999999999999999999999999999999999988874

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=95.85  E-value=0.048  Score=58.82  Aligned_cols=81  Identities=16%  Similarity=0.380  Sum_probs=67.8

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-ccccCCCCCCCCE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-VGEEGLDIGEIDL  196 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-v~~~GlDip~v~~  196 (395)
                      +.+++|-++|+.-|..+++.+.+..+  ++++..+||   +++..+|..+++.+.+|+++|+|+|. .+..++++..+.+
T Consensus       284 g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg---~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~l  360 (630)
T TIGR00643       284 GYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTG---SLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLAL  360 (630)
T ss_pred             CCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEec---CCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccce
Confidence            57999999999999988887766432  389999999   99999999999999999999999995 4555678888888


Q ss_pred             EEEcCCC
Q psy4150         197 VICFDAQ  203 (395)
Q Consensus       197 VI~~d~p  203 (395)
                      ||.=...
T Consensus       361 vVIDEaH  367 (630)
T TIGR00643       361 VIIDEQH  367 (630)
T ss_pred             EEEechh
Confidence            8865543

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.40  E-value=0.078  Score=57.35  Aligned_cols=97  Identities=12%  Similarity=0.119  Sum_probs=80.6

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      ++.|.+.+++++...+..      +.++||.++....+..+.+.|....+...+..+|+   +++..+|.+.+...++|+
T Consensus       170 GSGKTevyl~~i~~~l~~------Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS---~l~~~~R~~~w~~~~~G~  240 (665)
T PRK14873        170 GEDWARRLAAAAAATLRA------GRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSA---GLGPADRYRRWLAVLRGQ  240 (665)
T ss_pred             CCcHHHHHHHHHHHHHHc------CCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECC---CCCHHHHHHHHHHHhCCC
Confidence            568999999999887764      67899999999999999999998765456888999   999999999999999999


Q ss_pred             ccEEEEcCccccCCCCCCCCEEEEcCC
Q psy4150         176 FNTLIATSVGEEGLDIGEIDLVICFDA  202 (395)
Q Consensus       176 ~~vLVaT~v~~~GlDip~v~~VI~~d~  202 (395)
                      .+|+|+|-.+- =+-+++..+||..+=
T Consensus       241 ~~IViGtRSAv-FaP~~~LgLIIvdEE  266 (665)
T PRK14873        241 ARVVVGTRSAV-FAPVEDLGLVAIWDD  266 (665)
T ss_pred             CcEEEEcceeE-EeccCCCCEEEEEcC
Confidence            99999996532 244556777776553

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=95.27  E-value=0.1  Score=58.48  Aligned_cols=99  Identities=16%  Similarity=0.196  Sum_probs=75.4

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .+..|.......+.....      .+.+++|.|+|+..|...++.+.+...  .+++..++|   ..+..++..+++.++
T Consensus       481 TGsGKT~val~a~l~al~------~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg---~~~~~e~~~~~~~l~  551 (926)
T TIGR00580       481 VGFGKTEVAMRAAFKAVL------DGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSR---FRSAKEQNEILKELA  551 (926)
T ss_pred             CCccHHHHHHHHHHHHHH------hCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEec---cccHHHHHHHHHHHH
Confidence            355577654433333322      247999999999999999988776432  267788998   889999999999999


Q ss_pred             cCCccEEEEcC-ccccCCCCCCCCEEEEcCC
Q psy4150         173 AGEFNTLIATS-VGEEGLDIGEIDLVICFDA  202 (395)
Q Consensus       173 ~g~~~vLVaT~-v~~~GlDip~v~~VI~~d~  202 (395)
                      .|.++|+|+|. ++...+.+.++.+||.-..
T Consensus       552 ~g~~dIVIGTp~ll~~~v~f~~L~llVIDEa  582 (926)
T TIGR00580       552 SGKIDILIGTHKLLQKDVKFKDLGLLIIDEE  582 (926)
T ss_pred             cCCceEEEchHHHhhCCCCcccCCEEEeecc
Confidence            99999999995 5666788888988886443

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=94.47  E-value=0.22  Score=57.17  Aligned_cols=97  Identities=14%  Similarity=0.144  Sum_probs=72.6

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .+..|.......+.....      .+.+++|.|+|+..|..+++.+.+...  .+++..++|   ..+..++..+++.++
T Consensus       630 TGsGKT~val~aa~~~~~------~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g---~~s~~e~~~il~~l~  700 (1147)
T PRK10689        630 VGFGKTEVAMRAAFLAVE------NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSR---FRSAKEQTQILAEAA  700 (1147)
T ss_pred             CCcCHHHHHHHHHHHHHH------cCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEEC---CCCHHHHHHHHHHHH
Confidence            455677644322222222      258999999999999999988876432  267778888   889999999999999


Q ss_pred             cCCccEEEEcC-ccccCCCCCCCCEEEEc
Q psy4150         173 AGEFNTLIATS-VGEEGLDIGEIDLVICF  200 (395)
Q Consensus       173 ~g~~~vLVaT~-v~~~GlDip~v~~VI~~  200 (395)
                      .|.++|+|+|. ++..++.+..+.+||.=
T Consensus       701 ~g~~dIVVgTp~lL~~~v~~~~L~lLVID  729 (1147)
T PRK10689        701 EGKIDILIGTHKLLQSDVKWKDLGLLIVD  729 (1147)
T ss_pred             hCCCCEEEECHHHHhCCCCHhhCCEEEEe
Confidence            99999999995 55566777788888753

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

Probab=94.28  E-value=0.34  Score=51.74  Aligned_cols=87  Identities=20%  Similarity=0.408  Sum_probs=69.8

Q ss_pred             CCccEEEEcCcHHHHHHH----HHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-ccccCCCCCC
Q psy4150         119 ETTKVIIFANYRVVVAEI----FDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-VGEEGLDIGE  193 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l----~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-v~~~GlDip~  193 (395)
                      .+.++.+-++|---|+..    .++|...|  +++..+.|   .+...+|.+++....+|+++++|+|- +....+++.+
T Consensus       310 ~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~--i~V~lLtG---~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~  384 (677)
T COG1200         310 AGYQAALMAPTEILAEQHYESLRKWLEPLG--IRVALLTG---SLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHN  384 (677)
T ss_pred             cCCeeEEeccHHHHHHHHHHHHHHHhhhcC--CeEEEeec---ccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecc
Confidence            478999999996655554    45555556  99999999   99999999999999999999999994 5688999998


Q ss_pred             CCEEEEcCCCCChhhHhhhcccccc
Q psy4150         194 IDLVICFDAQKSPIKMVQRLGRTGR  218 (395)
Q Consensus       194 v~~VI~~d~p~s~~~yiQr~GRagR  218 (395)
                      .-+||.-        =.||.|=.-|
T Consensus       385 LgLVIiD--------EQHRFGV~QR  401 (677)
T COG1200         385 LGLVIID--------EQHRFGVHQR  401 (677)
T ss_pred             eeEEEEe--------ccccccHHHH
Confidence            8888863        3455554444

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

Probab=94.27  E-value=0.11  Score=56.59  Aligned_cols=94  Identities=16%  Similarity=0.195  Sum_probs=77.8

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      ..++.|.+.+++++...+..      +.++||-++.......+.+.|+.+.. .++..+|+   ++++.+|...+.+.++
T Consensus       225 vTGSGKTEvYl~~i~~~L~~------GkqvLvLVPEI~Ltpq~~~rf~~rFg-~~v~vlHS---~Ls~~er~~~W~~~~~  294 (730)
T COG1198         225 VTGSGKTEVYLEAIAKVLAQ------GKQVLVLVPEIALTPQLLARFKARFG-AKVAVLHS---GLSPGERYRVWRRARR  294 (730)
T ss_pred             CCCCcHHHHHHHHHHHHHHc------CCEEEEEeccccchHHHHHHHHHHhC-CChhhhcc---cCChHHHHHHHHHHhc
Confidence            35678999999999998875      68999999999988888888887654 78999999   9999999999999999


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEE
Q psy4150         174 GEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       174 g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      |+.+|+|+|-.+- =.=+++..+||
T Consensus       295 G~~~vVIGtRSAl-F~Pf~~LGLII  318 (730)
T COG1198         295 GEARVVIGTRSAL-FLPFKNLGLII  318 (730)
T ss_pred             CCceEEEEechhh-cCchhhccEEE
Confidence            9999999995431 23344555555

>KOG0921|consensus

Probab=94.13  E-value=0.053  Score=59.07  Aligned_cols=109  Identities=22%  Similarity=0.307  Sum_probs=86.5

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccC-----CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCC
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLE-----PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIG  192 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~-----~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip  192 (395)
                      .-.+-++||-.-....-.|..+|..+.     .......+|+   .....+..++.+....|..++++.|++++.-+.+.
T Consensus       641 ~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hs---q~~~~eqrkvf~~~p~gv~kii~stniaetsiTid  717 (1282)
T KOG0921|consen  641 NIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHS---QLTSQEQRKVFEPVPEGVTKIILSTNIAETSITID  717 (1282)
T ss_pred             CCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchh---hcccHhhhhccCcccccccccccccceeeEeeeec
Confidence            346778999999999999988887653     1234455566   78888888899988899999999999999999999


Q ss_pred             CCCEEEEcCCC------------------CChhhHhhhccccccccCceEEEEEe
Q psy4150         193 EIDLVICFDAQ------------------KSPIKMVQRLGRTGRKRNGRCVILLT  229 (395)
Q Consensus       193 ~v~~VI~~d~p------------------~s~~~yiQr~GRagR~~~g~~i~l~~  229 (395)
                      ++..||..+.-                  .+....+||.||+||.+.|.+..++.
T Consensus       718 d~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grvR~G~~f~lcs  772 (1282)
T KOG0921|consen  718 DVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRVRPGFCFHLCS  772 (1282)
T ss_pred             ceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCceecccccccccH
Confidence            88777754432                  15678899999999999998887654

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=93.47  E-value=0.35  Score=52.82  Aligned_cols=100  Identities=13%  Similarity=0.198  Sum_probs=72.6

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCC--CEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEI--DLV  197 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v--~~V  197 (395)
                      +.++-||+.|...++.+++......  -++..++|   .-+..+   + +.  =++++|++=|+++.-|+++.+.  +-|
T Consensus       282 gknIcvfsSt~~~~~~v~~~~~~~~--~~Vl~l~s---~~~~~d---v-~~--W~~~~VviYT~~itvG~Sf~~~HF~~~  350 (824)
T PF02399_consen  282 GKNICVFSSTVSFAEIVARFCARFT--KKVLVLNS---TDKLED---V-ES--WKKYDVVIYTPVITVGLSFEEKHFDSM  350 (824)
T ss_pred             CCcEEEEeChHHHHHHHHHHHHhcC--CeEEEEcC---CCCccc---c-cc--ccceeEEEEeceEEEEeccchhhceEE
Confidence            6888899999999999999998876  67777777   333331   1 11  2579999999999999999753  445


Q ss_pred             EEc--CCC--CChhhHhhhccccccccCceEEEEEeC
Q psy4150         198 ICF--DAQ--KSPIKMVQRLGRTGRKRNGRCVILLTQ  230 (395)
Q Consensus       198 I~~--d~p--~s~~~yiQr~GRagR~~~g~~i~l~~~  230 (395)
                      ..|  ...  .+..+..|.+||+-.-....+++++..
T Consensus       351 f~yvk~~~~gpd~~s~~Q~lgRvR~l~~~ei~v~~d~  387 (824)
T PF02399_consen  351 FAYVKPMSYGPDMVSVYQMLGRVRSLLDNEIYVYIDA  387 (824)
T ss_pred             EEEecCCCCCCcHHHHHHHHHHHHhhccCeEEEEEec
Confidence            544  222  356679999999933367777766544

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

>PRK07883 hypothetical protein; Validated

Probab=93.32  E-value=0.067  Score=56.80  Aligned_cols=38  Identities=11%  Similarity=0.151  Sum_probs=34.7

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhcC
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSG  367 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~~  367 (395)
                      +.+.+|+++|..||+.|+  ||.||++||+|..|+.....
T Consensus       406 ~~~~~l~~~M~~aa~~l~--FE~Aa~~Rd~i~~l~~~~~~  443 (557)
T PRK07883        406 AVLAALRARIDRLAAAER--FEEAARLRDRLAALLRALAR  443 (557)
T ss_pred             HHHHHHHHHHHHHHHhcC--HHHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999  99999999999999976544

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

Probab=92.97  E-value=0.21  Score=52.53  Aligned_cols=70  Identities=24%  Similarity=0.473  Sum_probs=57.0

Q ss_pred             EEEEcCcHHHHHHHHHHHcccCC---CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-----ccccC-CCCCC
Q psy4150         123 VIIFANYRVVVAEIFDVLKPLEP---MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-----VGEEG-LDIGE  193 (395)
Q Consensus       123 ~iVF~~t~~~ae~l~~~L~~~~~---~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-----v~~~G-lDip~  193 (395)
                      +||+++||+.|..+++.+...+.   .+++..++|   +++...+...+   +.| .+|||||+     .+.+| +|+..
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~G---G~~~~~q~~~l---~~~-~~ivVaTPGRllD~i~~~~l~l~~  174 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYG---GVSIRKQIEAL---KRG-VDIVVATPGRLLDLIKRGKLDLSG  174 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEEC---CCCHHHHHHHH---hcC-CCEEEECccHHHHHHHcCCcchhh
Confidence            99999999999999998876542   477899999   88887776444   446 99999997     56676 88889


Q ss_pred             CCEEEE
Q psy4150         194 IDLVIC  199 (395)
Q Consensus       194 v~~VI~  199 (395)
                      |.++|.
T Consensus       175 v~~lVl  180 (513)
T COG0513         175 VETLVL  180 (513)
T ss_pred             cCEEEe
Confidence            988884

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=92.95  E-value=0.074  Score=56.89  Aligned_cols=38  Identities=13%  Similarity=0.207  Sum_probs=35.3

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhcC
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSG  367 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~~  367 (395)
                      +.+..++++|..||++|+  ||.||.+||+|..|+.....
T Consensus       202 ~~i~~L~~~M~~aa~~l~--FE~Aa~~RD~i~aL~~~~~~  239 (598)
T PRK00558        202 EVLKELEEKMEEASENLE--FERAARYRDQIQALRRVQEK  239 (598)
T ss_pred             HHHHHHHHHHHHHHHhhC--HHHHHHHHHHHHHHHHHHhc
Confidence            688999999999999999  99999999999999987654

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=92.90  E-value=0.28  Score=54.53  Aligned_cols=62  Identities=23%  Similarity=0.442  Sum_probs=51.0

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccC-----CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCc
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLE-----PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSV  184 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~-----~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v  184 (395)
                      .+.|+++-++|..-+...++.|.+..     ..+... +||   .|+..++.+++++|.+|.++|||+|+.
T Consensus       124 kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~-yh~---~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         124 KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVV-YHS---ALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             cCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeee-ecc---ccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            46899999999988888888776543     223333 777   999999999999999999999999974

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

Probab=92.09  E-value=0.47  Score=53.60  Aligned_cols=79  Identities=18%  Similarity=0.298  Sum_probs=68.0

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccCCC--CceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEc-CccccCCCCCCC
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLEPM--VKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIAT-SVGEEGLDIGEI  194 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~~~--~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT-~v~~~GlDip~v  194 (395)
                      ..+.+|.|.|+|.--|+.-++.+.++..+  +++..+..   =.+..+..++++.+++|+++|+|+| .+++.+|-+.++
T Consensus       641 ~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSR---F~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdL  717 (1139)
T COG1197         641 MDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSR---FRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDL  717 (1139)
T ss_pred             cCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecc---cCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecC
Confidence            34799999999999999999988886533  56666666   6789999999999999999999999 789999999999


Q ss_pred             CEEEE
Q psy4150         195 DLVIC  199 (395)
Q Consensus       195 ~~VI~  199 (395)
                      -+||.
T Consensus       718 GLlII  722 (1139)
T COG1197         718 GLLII  722 (1139)
T ss_pred             CeEEE
Confidence            98884

>PRK12306 uvrC excinuclease ABC subunit C; Reviewed

Probab=91.53  E-value=0.11  Score=54.38  Aligned_cols=37  Identities=8%  Similarity=0.105  Sum_probs=34.1

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhc
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSS  366 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~  366 (395)
                      +.+..++++|..||+.|+  ||.||++||++..|+....
T Consensus       192 ~~~~~L~~~M~~aa~~l~--FE~Aa~~RD~l~~l~~~~~  228 (519)
T PRK12306        192 ELIEKLEEEMAEKAKNQQ--FERALVIRDEINAIENLQE  228 (519)
T ss_pred             HHHHHHHHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHh
Confidence            688899999999999999  9999999999999997554

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=91.43  E-value=0.12  Score=54.94  Aligned_cols=38  Identities=16%  Similarity=0.222  Sum_probs=34.7

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhcC
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSG  367 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~~  367 (395)
                      +.+..++.+|..||+.|+  ||.||++||+|..|+.....
T Consensus       194 ~~~~~L~~~M~~aa~~l~--FE~Aa~~Rd~i~~l~~~~~~  231 (574)
T TIGR00194       194 EVIKELEQKMEKASENLE--FEEAARIRDQIAAVRELNEK  231 (574)
T ss_pred             HHHHHHHHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHhc
Confidence            688899999999999999  99999999999999976553

This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=91.34  E-value=0.11  Score=55.85  Aligned_cols=37  Identities=11%  Similarity=0.217  Sum_probs=34.0

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhc
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSS  366 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~  366 (395)
                      +.+..++++|..||+.|+  ||.||++||+|..|+....
T Consensus       215 ~l~~~L~~~M~~as~~l~--FE~Aa~~RD~i~~l~~~~~  251 (621)
T PRK14671        215 ALIRSLTEEMQRAAAELK--FEEAAELKDQIESLKRYAE  251 (621)
T ss_pred             HHHHHHHHHHHHHHHhcc--HHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999  9999999999999986544

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=91.19  E-value=0.11  Score=55.19  Aligned_cols=37  Identities=19%  Similarity=0.093  Sum_probs=34.5

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhc
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSS  366 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~  366 (395)
                      +.+..|+++|..||++|+  ||.||++||++..|+....
T Consensus       177 ~~~~~L~~~M~~aa~~l~--FE~Aa~~RD~i~al~~~~~  213 (574)
T PRK14670        177 KLLSQIEIKMKEAIQKED--FEAAIKLKETKRSLIEISQ  213 (574)
T ss_pred             HHHHHHHHHHHHHHHhcC--HHHHHHHHHHHHHHHHHHh
Confidence            688899999999999999  9999999999999998665

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=91.16  E-value=1.4  Score=45.13  Aligned_cols=77  Identities=19%  Similarity=0.377  Sum_probs=56.0

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC------ccccCCC
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS------VGEEGLD  190 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~------v~~~GlD  190 (395)
                      ...++||.++|+..+..+++.+....  ..+.+..++|   +.+...+...+    .+..+|||||.      +....++
T Consensus        72 ~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~g---g~~~~~~~~~l----~~~~~IlV~Tp~rl~~~~~~~~~~  144 (434)
T PRK11192         72 GPPRILILTPTRELAMQVADQARELAKHTHLDIATITG---GVAYMNHAEVF----SENQDIVVATPGRLLQYIKEENFD  144 (434)
T ss_pred             CCceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEEC---CCCHHHHHHHh----cCCCCEEEEChHHHHHHHHcCCcC
Confidence            34689999999999988877655432  1278899999   88777665444    35688999996      2235678


Q ss_pred             CCCCCEEEEcCC
Q psy4150         191 IGEIDLVICFDA  202 (395)
Q Consensus       191 ip~v~~VI~~d~  202 (395)
                      +..+++||.=++
T Consensus       145 ~~~v~~lViDEa  156 (434)
T PRK11192        145 CRAVETLILDEA  156 (434)
T ss_pred             cccCCEEEEECH
Confidence            888888886544

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=91.15  E-value=0.11  Score=55.56  Aligned_cols=38  Identities=11%  Similarity=0.156  Sum_probs=34.8

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhcC
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSG  367 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~~  367 (395)
                      +.+..|+++|..||++|+  ||.||++||+|..|+.....
T Consensus       203 ~l~~~L~~~M~~aa~~l~--FE~Aa~~RD~i~~l~~~~~~  240 (624)
T PRK14669        203 DLARSLRARMEAAALEMQ--FELAAKYRDLITTVEELEEK  240 (624)
T ss_pred             HHHHHHHHHHHHHHHhcC--HHHHHHHHHHHHHHHHHHhc
Confidence            688899999999999999  99999999999999876553

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=91.10  E-value=0.11  Score=54.97  Aligned_cols=38  Identities=11%  Similarity=0.130  Sum_probs=34.6

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhcC
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSG  367 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~~  367 (395)
                      +.+..|+++|..||++|+  ||.||.+||++..|+.....
T Consensus       199 ~l~~~L~~~M~~aa~~l~--FE~Aa~~RD~i~~l~~~~~~  236 (567)
T PRK14667        199 EVLPELYDKIEEYSQKLM--FEKAAVIRDQILALENLIKG  236 (567)
T ss_pred             HHHHHHHHHHHHHHHhcC--HHHHHHHHHHHHHHHHHHhc
Confidence            688999999999999999  99999999999999876553

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=91.06  E-value=0.13  Score=55.48  Aligned_cols=37  Identities=11%  Similarity=0.116  Sum_probs=34.5

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhc
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSS  366 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~  366 (395)
                      +.+..|+++|..||+.|+  ||.||++||+|..|+....
T Consensus       201 ~l~~~L~~~M~~AAe~l~--FE~AA~lRD~i~aL~~~~~  237 (694)
T PRK14666        201 ELVDALRTEMEAASEALE--FERAAVLRDQIRAVERTVE  237 (694)
T ss_pred             HHHHHHHHHHHHHHHhcc--HHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999  9999999999999997655

>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]

Probab=90.89  E-value=0.22  Score=43.94  Aligned_cols=38  Identities=11%  Similarity=0.134  Sum_probs=32.7

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhcC
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSG  367 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~~  367 (395)
                      ..|..|.+.+.+.-..-+  ||+||-+||||..|+++.-+
T Consensus       136 ~~I~~L~e~Lq~~i~~Ee--fEeAA~iRDqIr~Lk~k~~~  173 (176)
T COG3880         136 RKIIALKEALQDLIEREE--FEEAAVIRDQIRALKAKNGG  173 (176)
T ss_pred             HHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHhhcCC
Confidence            467778888888888889  99999999999999988533

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=90.79  E-value=0.17  Score=53.65  Aligned_cols=42  Identities=14%  Similarity=0.215  Sum_probs=37.2

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhcCCCCC
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSGEPVS  371 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~~~~~~  371 (395)
                      +.+..|++.|..||..|+  ||.||++||+|.-|.........+
T Consensus       202 ~v~~~L~~~M~~As~~l~--FE~Aa~~RD~i~al~~l~~~q~v~  243 (581)
T COG0322         202 AVLQELEEKMEEASENLD--FERAARLRDQIKALEKLQEKQAVS  243 (581)
T ss_pred             HHHHHHHHHHHHHHHhhc--hHHHHHHHHHHHHHHHHHhccccc
Confidence            688899999999999999  999999999999999877654443

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=90.57  E-value=0.14  Score=55.04  Aligned_cols=37  Identities=8%  Similarity=0.070  Sum_probs=33.8

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhc
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSS  366 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~  366 (395)
                      +.+..++++|..||+.|+  ||.||++||+|..|+....
T Consensus       205 ~ll~~L~~~M~~AA~~l~--FE~AA~lRD~i~aL~~~~~  241 (691)
T PRK14672        205 ATVARLEKRMKRAVRQEA--FEAAARIRDDIQAIRCITH  241 (691)
T ss_pred             HHHHHHHHHHHHHHHhcC--HHHHHHHHHHHHHHHHHHh
Confidence            688999999999999999  9999999999999986544

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=90.16  E-value=0.19  Score=53.54  Aligned_cols=37  Identities=8%  Similarity=0.074  Sum_probs=34.0

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhc
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSS  366 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~  366 (395)
                      ..+..++.+|..||+.|+  ||.||++||+|..|+....
T Consensus       199 ~~~~~l~~~m~~aa~~l~--FE~Aa~~Rd~i~~l~~~~~  235 (577)
T PRK14668        199 VLADPLRREMEAAAQAQE--FERAANLRDRLEAVEAFHG  235 (577)
T ss_pred             HHHHHHHHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHH
Confidence            588899999999999999  9999999999999997654

>PRK14701 reverse gyrase; Provisional

Probab=90.07  E-value=0.76  Score=54.63  Aligned_cols=62  Identities=16%  Similarity=0.366  Sum_probs=53.9

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccC----CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCc
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLE----PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSV  184 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~----~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v  184 (395)
                      +.++||.++|+..+..+++.|...+    ..+.+.++||   +++..++.++++.++.|..+|||+|+-
T Consensus       122 g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g---~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        122 GKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHS---NLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             CCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeC---CCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            5689999999999999998887643    1367788999   999999999999999999999999974

>cd00268 DEADc DEAD-box helicases

Probab=89.96  E-value=3.3  Score=37.19  Aligned_cols=100  Identities=23%  Similarity=0.236  Sum_probs=61.9

Q ss_pred             ccccHHHH-HHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          95 WSHLKFIR-LREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        95 ~~~~K~~~-L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .+..|... +..++......  ....+.++||.|+++..+......+...+.  .+.+..++|   +.+..+....+.  
T Consensus        45 TG~GKT~~~~~~~l~~~~~~--~~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~--  117 (203)
T cd00268          45 TGSGKTAAFLIPILEKLDPS--PKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYG---GTSIDKQIRKLK--  117 (203)
T ss_pred             CCCcHHHHHHHHHHHHHHhh--cccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEEC---CCCHHHHHHHhc--
Confidence            45556544 33444332221  002456899999999999888776655421  377888888   777665543332  


Q ss_pred             hcCCccEEEEcCc-----ccc-CCCCCCCCEEEEcCCC
Q psy4150         172 RAGEFNTLIATSV-----GEE-GLDIGEIDLVICFDAQ  203 (395)
Q Consensus       172 k~g~~~vLVaT~v-----~~~-GlDip~v~~VI~~d~p  203 (395)
                        +.+.|+|||.-     +.. -.+++.++++|.=++.
T Consensus       118 --~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h  153 (203)
T cd00268         118 --RGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEAD  153 (203)
T ss_pred             --CCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChH
Confidence              67899999952     222 2566778877754443

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.

>KOG0331|consensus

Probab=89.94  E-value=2  Score=44.93  Aligned_cols=94  Identities=19%  Similarity=0.359  Sum_probs=71.9

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccCCC--CceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-----ccccC-C
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLEPM--VKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-----VGEEG-L  189 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~~~--~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-----v~~~G-l  189 (395)
                      ..+.++||-++||+.|..+...+.+.+..  +++.++.|   +.+...+..-++.    .++|+|||+     .++.| +
T Consensus       163 ~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyG---G~~~~~Q~~~l~~----gvdiviaTPGRl~d~le~g~~  235 (519)
T KOG0331|consen  163 GDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYG---GAPKGPQLRDLER----GVDVVIATPGRLIDLLEEGSL  235 (519)
T ss_pred             CCCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeC---CCCccHHHHHHhc----CCcEEEeCChHHHHHHHcCCc
Confidence            34677999999999999999998887643  55899999   8877766555542    478999995     56676 7


Q ss_pred             CCCCCCEEEEcCCC--------CChhhHhhhcccccc
Q psy4150         190 DIGEIDLVICFDAQ--------KSPIKMVQRLGRTGR  218 (395)
Q Consensus       190 Dip~v~~VI~~d~p--------~s~~~yiQr~GRagR  218 (395)
                      |+..|.++|.=.+.        ......+++++|.-|
T Consensus       236 ~l~~v~ylVLDEADrMldmGFe~qI~~Il~~i~~~~r  272 (519)
T KOG0331|consen  236 NLSRVTYLVLDEADRMLDMGFEPQIRKILSQIPRPDR  272 (519)
T ss_pred             cccceeEEEeccHHhhhccccHHHHHHHHHhcCCCcc
Confidence            88889988854333        356778888888866

>KOG1513|consensus

Probab=89.60  E-value=0.48  Score=51.39  Aligned_cols=78  Identities=21%  Similarity=0.296  Sum_probs=60.9

Q ss_pred             HHHhcCCccEEEEcCccccCCCCCCCCEE--------EEcCCCCChhhHhhhcccccccc---CceEEEEEeCCchhhHH
Q psy4150         169 KKFRAGEFNTLIATSVGEEGLDIGEIDLV--------ICFDAQKSPIKMVQRLGRTGRKR---NGRCVILLTQGREAHNF  237 (395)
Q Consensus       169 ~~Fk~g~~~vLVaT~v~~~GlDip~v~~V--------I~~d~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~~e~~~~  237 (395)
                      ++|-+|+-.|-|-+..++-||-+..-..|        |-+.+|||...-||..|||-|..   ...+++++++-..+..|
T Consensus       851 qrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFlIseLAGErRF  930 (1300)
T KOG1513|consen  851 QRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFLISELAGERRF  930 (1300)
T ss_pred             hhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEEehhhccchHH
Confidence            46889999998889999999999865555        56889999999999999999983   34556677776667777


Q ss_pred             HHHHHHhHH
Q psy4150         238 QTSMQTCKS  246 (395)
Q Consensus       238 ~~~~~~~~~  246 (395)
                      .....+..+
T Consensus       931 AS~VAKRLE  939 (1300)
T KOG1513|consen  931 ASIVAKRLE  939 (1300)
T ss_pred             HHHHHHHHH
Confidence            666544333

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=89.47  E-value=1.7  Score=44.85  Aligned_cols=99  Identities=15%  Similarity=0.196  Sum_probs=66.0

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC---CCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE---PMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~---~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..+..|.....--+...+..   .....++||.|+|+..|..+++.++..+   +.+++..++|   +.+...+...++ 
T Consensus        49 ~TGsGKT~a~~lpil~~l~~---~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~G---g~~~~~~~~~l~-  121 (460)
T PRK11776         49 KTGSGKTAAFGLGLLQKLDV---KRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCG---GVPMGPQIDSLE-  121 (460)
T ss_pred             CCCCcHHHHHHHHHHHHhhh---ccCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEEC---CCChHHHHHHhc-
Confidence            34556775533333333321   1223479999999999999988777542   3478888999   888776654443 


Q ss_pred             HhcCCccEEEEcC-----ccc-cCCCCCCCCEEEEcCC
Q psy4150         171 FRAGEFNTLIATS-----VGE-EGLDIGEIDLVICFDA  202 (395)
Q Consensus       171 Fk~g~~~vLVaT~-----v~~-~GlDip~v~~VI~~d~  202 (395)
                         +..+|+|||+     .+. ..+++.++.+||.-++
T Consensus       122 ---~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEa  156 (460)
T PRK11776        122 ---HGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEA  156 (460)
T ss_pred             ---CCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECH
Confidence               5689999994     333 4578888998885444

>KOG0298|consensus

Probab=89.40  E-value=0.56  Score=53.15  Aligned_cols=114  Identities=19%  Similarity=0.223  Sum_probs=85.1

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE-EEEcCccccCCCCCCCCE
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT-LIATSVGEEGLDIGEIDL  196 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v-LVaT~v~~~GlDip~v~~  196 (395)
                      +...++|||+.--...+-+...+.-++  +.....-+      .+.-...+..|++  +++ |+-+...+-|+++-+..+
T Consensus      1219 ~~qekvIvfsqws~~ldV~e~~~~~N~--I~~~~~~~------t~d~~dc~~~fk~--I~clll~~~~~~~GLNL~eA~H 1288 (1394)
T KOG0298|consen 1219 NEQEKVIVFSQWSVVLDVKELRYLMNL--IKKQLDGE------TEDFDDCIICFKS--IDCLLLFVSKGSKGLNLIEATH 1288 (1394)
T ss_pred             CcCceEEEEEehHHHHHHHHHHHHhhh--hHhhhccC------Ccchhhhhhhccc--ceEEEEEeccCcccccHHhhhh
Confidence            346899999999888888887776666  55443322      3334557777777  555 477888999999999999


Q ss_pred             EEEcCCCCChhhHhhhccccccccC---ceEEEEEeCCchhhHHHHHH
Q psy4150         197 VICFDAQKSPIKMVQRLGRTGRKRN---GRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       197 VI~~d~p~s~~~yiQr~GRagR~~~---g~~i~l~~~~~e~~~~~~~~  241 (395)
                      |+..++--++..-.|.+||..|.|+   ..+.-++..++.+..+..+.
T Consensus      1289 vfl~ePiLN~~~E~QAigRvhRiGQ~~pT~V~~fiv~~TvEe~Il~l~ 1336 (1394)
T KOG0298|consen 1289 VFLVEPILNPGDEAQAIGRVHRIGQKRPTFVHRFIVNETVEENILSLI 1336 (1394)
T ss_pred             hheeccccCchHHHhhhhhhhhcccccchhhhhhhhccchHHHHHHHh
Confidence            9999999999999999999999974   33455666666666554433

>KOG0347|consensus

Probab=89.07  E-value=0.74  Score=48.09  Aligned_cols=54  Identities=17%  Similarity=0.391  Sum_probs=47.9

Q ss_pred             EEEEcCcHHHHHHHHHHHcccC--CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC
Q psy4150         123 VIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS  183 (395)
Q Consensus       123 ~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~  183 (395)
                      .|||++||+.|..+.++|....  +.+++..+.|   ||+...++++++.    .-+|+|||+
T Consensus       266 ~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~G---GLavqKQqRlL~~----~p~IVVATP  321 (731)
T KOG0347|consen  266 ALVVTPTRELAHQVKQHLKAIAEKTQIRVASITG---GLAVQKQQRLLNQ----RPDIVVATP  321 (731)
T ss_pred             eEEecChHHHHHHHHHHHHHhccccCeEEEEeec---hhHHHHHHHHHhc----CCCEEEecc
Confidence            8999999999999999997643  3599999999   9999999999987    578999997

>KOG0951|consensus

Probab=88.66  E-value=1.9  Score=49.26  Aligned_cols=110  Identities=19%  Similarity=0.336  Sum_probs=75.0

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccC----------------CCCceeEEecc-CCCCCHHHHHHHHHHHhcCCccEEEE
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLE----------------PMVKASMFVGQ-SSGVTQQEQKEIMKKFRAGEFNTLIA  181 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~----------------~~~~~~~lhg~-~~~~~~~~R~~~l~~Fk~g~~~vLVa  181 (395)
                      ...+.+||+++++.|..++.-|-...                ...+...-||- |.+++.....-+-.-|..|.+.|+|.
T Consensus      1358 ~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~ 1437 (1674)
T KOG0951|consen 1358 NRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVM 1437 (1674)
T ss_pred             CCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEE
Confidence            36899999999999988776543211                01122222221 22888888888888899999999988


Q ss_pred             cCccccCCCCCCCCEEEE-----cCC------CCChhhHhhhccccccccCceEEEEEeCCc
Q psy4150         182 TSVGEEGLDIGEIDLVIC-----FDA------QKSPIKMVQRLGRTGRKRNGRCVILLTQGR  232 (395)
Q Consensus       182 T~v~~~GlDip~v~~VI~-----~d~------p~s~~~yiQr~GRagR~~~g~~i~l~~~~~  232 (395)
                      ..- ..|+-.. .++||.     ||.      +-+...+.|++|+|.|  .|++++++....
T Consensus      1438 s~~-~~~~~~~-~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~--~~k~vi~~~~~~ 1495 (1674)
T KOG0951|consen 1438 SRD-CYGTKLK-AHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG--AGKCVIMCHTPK 1495 (1674)
T ss_pred             Ecc-ccccccc-ceEEEEecceeecccccccccCchhHHHHHhhhhcC--CccEEEEecCch
Confidence            765 7777764 344442     443      2357889999999987  577887766554

>TIGR01054 rgy reverse gyrase

Probab=88.50  E-value=1.5  Score=50.69  Aligned_cols=61  Identities=21%  Similarity=0.428  Sum_probs=51.2

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCC--Cce---eEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPM--VKA---SMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS  183 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~--~~~---~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~  183 (395)
                      +.++||.++|+..|..+++.+......  +.+   .++||   +++..++...++.+++|..+|||+|+
T Consensus       121 g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~G---g~~~~e~~~~~~~l~~~~~dIlV~Tp  186 (1171)
T TIGR01054       121 GKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHS---RLPTKEKKEFMERIENGDFDILITTT  186 (1171)
T ss_pred             CCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecC---CCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            578999999999999999888765421  332   35788   99999999999999999999999996

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=88.21  E-value=1.5  Score=45.61  Aligned_cols=78  Identities=15%  Similarity=0.254  Sum_probs=62.5

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCcc-cc------CC-CC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVG-EE------GL-DI  191 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~-~~------Gl-Di  191 (395)
                      ...+||.++++..+......|...|  +.+..++|   +.+..++..++..++.|.+++|++|+-. ..      .+ ..
T Consensus        51 ~~~~lVi~P~~~L~~dq~~~l~~~g--i~~~~l~~---~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~  125 (470)
T TIGR00614        51 DGITLVISPLISLMEDQVLQLKASG--IPATFLNS---SQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEER  125 (470)
T ss_pred             CCcEEEEecHHHHHHHHHHHHHHcC--CcEEEEeC---CCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhc
Confidence            4689999999999999999998888  88999999   8899999999999999999999999632 11      12 44


Q ss_pred             CCCCEEEEcCC
Q psy4150         192 GEIDLVICFDA  202 (395)
Q Consensus       192 p~v~~VI~~d~  202 (395)
                      ..+.+||.-.+
T Consensus       126 ~~i~~iViDEa  136 (470)
T TIGR00614       126 KGITLIAVDEA  136 (470)
T ss_pred             CCcCEEEEeCC
Confidence            56666665443

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

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=87.41  E-value=1.3  Score=47.29  Aligned_cols=76  Identities=17%  Similarity=0.305  Sum_probs=55.6

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-----cccc--CCC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-----VGEE--GLD  190 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-----v~~~--GlD  190 (395)
                      ..++||.++|+..|..+++.+...+.  .+++..+||   +.+...+...+.    +..+|||+|.     .+..  .++
T Consensus        84 ~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~G---g~~~~~q~~~l~----~~~dIiV~TP~rL~~~l~~~~~~~  156 (572)
T PRK04537         84 DPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYG---GVDYDKQRELLQ----QGVDVIIATPGRLIDYVKQHKVVS  156 (572)
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEEC---CCCHHHHHHHHh----CCCCEEEECHHHHHHHHHhccccc
Confidence            46899999999999998887766432  377889999   888776655543    4689999995     3333  367


Q ss_pred             CCCCCEEEEcCC
Q psy4150         191 IGEIDLVICFDA  202 (395)
Q Consensus       191 ip~v~~VI~~d~  202 (395)
                      +..+.+||.-.+
T Consensus       157 l~~v~~lViDEA  168 (572)
T PRK04537        157 LHACEICVLDEA  168 (572)
T ss_pred             hhheeeeEecCH
Confidence            777887775443

>KOG2340|consensus

Probab=87.27  E-value=2.6  Score=43.94  Aligned_cols=124  Identities=14%  Similarity=0.155  Sum_probs=84.6

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      ..+..+..-|.-.+..    ....-+||+.++--.--.+.+++++..  +..+.+|-   --+...-.++-.-|-.|...
T Consensus       534 ~RFkyFv~~ImPq~~k----~t~s~~LiyIPSYfDFVRvRNy~K~e~--i~F~~i~E---Yssk~~vsRAR~lF~qgr~~  604 (698)
T KOG2340|consen  534 ARFKYFVDKIMPQLIK----RTESGILIYIPSYFDFVRVRNYMKKEE--ISFVMINE---YSSKSKVSRARELFFQGRKS  604 (698)
T ss_pred             HHHHHHHHhhchhhcc----cccCceEEEecchhhHHHHHHHhhhhh--cchHHHhh---hhhHhhhhHHHHHHHhcCce
Confidence            3555555444333322    335678999999999999999999887  66666665   23344444555668899999


Q ss_pred             EEEEcCcc--ccCCCCCCCCEEEEcCCCCChhhH---hhhccccccccC-----ceEEEEEeC
Q psy4150         178 TLIATSVG--EEGLDIGEIDLVICFDAQKSPIKM---VQRLGRTGRKRN-----GRCVILLTQ  230 (395)
Q Consensus       178 vLVaT~v~--~~GlDip~v~~VI~~d~p~s~~~y---iQr~GRagR~~~-----g~~i~l~~~  230 (395)
                      ||+-|.-+  =+--+|.+|.-||.|.+|.+|.-|   +-.+||+.-.|.     -.|.++++.
T Consensus       605 vlLyTER~hffrR~~ikGVk~vVfYqpP~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytK  667 (698)
T KOG2340|consen  605 VLLYTERAHFFRRYHIKGVKNVVFYQPPNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTK  667 (698)
T ss_pred             EEEEehhhhhhhhheecceeeEEEecCCCCcHHHHHHHhhhhhhhccCCccccceEEEEEeec
Confidence            99999533  355788999999999999998666   446666654441     234556554

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=87.17  E-value=3.4  Score=44.64  Aligned_cols=96  Identities=14%  Similarity=0.170  Sum_probs=61.9

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHccc---CCCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPL---EPMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~---~~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      .....|...+.--+.+.+..   .....++||.|+|+..|..+++.+...   .+.+.+..+||   +.+...+...+  
T Consensus        51 pTGsGKT~af~lpll~~l~~---~~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~g---G~~~~~q~~~l--  122 (629)
T PRK11634         51 QTGSGKTAAFSLPLLHNLDP---ELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYG---GQRYDVQLRAL--  122 (629)
T ss_pred             CCCCcHHHHHHHHHHHHhhh---ccCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEEC---CcCHHHHHHHh--
Confidence            34556766543222222221   123468999999999999988876653   23478888898   77766554433  


Q ss_pred             HhcCCccEEEEcC-----ccccC-CCCCCCCEEEE
Q psy4150         171 FRAGEFNTLIATS-----VGEEG-LDIGEIDLVIC  199 (395)
Q Consensus       171 Fk~g~~~vLVaT~-----v~~~G-lDip~v~~VI~  199 (395)
                       + +..+|+|+|+     .+.++ +++..+.+||.
T Consensus       123 -~-~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVl  155 (629)
T PRK11634        123 -R-QGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVL  155 (629)
T ss_pred             -c-CCCCEEEECHHHHHHHHHcCCcchhhceEEEe
Confidence             2 4578999994     34444 77888887774

>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=86.58  E-value=2.3  Score=40.17  Aligned_cols=98  Identities=11%  Similarity=0.105  Sum_probs=63.7

Q ss_pred             HHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC----ccEEEEcCccccCCCCCCCCEEEEcCCCCChhh
Q psy4150         133 VAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE----FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIK  208 (395)
Q Consensus       133 ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~----~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~  208 (395)
                      ...|...+.. +  +.+..+.|   +.+...     -++..+.    ..|+|+=+.++||+.+++..+......+.+..+
T Consensus       100 ~~~l~~~~~~-~--~~v~~vNS---~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DT  168 (239)
T PF10593_consen  100 KPELPKAISD-G--IEVVVVNS---GSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDT  168 (239)
T ss_pred             HHHHHHHHhc-C--ceEEEEeC---CCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHH
Confidence            3444444444 4  88888887   332222     3445543    889999999999999999999999999998888


Q ss_pred             Hhhhccccc-cccCceEEEEEeCCchhhHHHHHH
Q psy4150         209 MVQRLGRTG-RKRNGRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       209 yiQr~GRag-R~~~g~~i~l~~~~~e~~~~~~~~  241 (395)
                      ++||.-.-| |.|=...+-++.+.+-.+.|....
T Consensus       169 L~QmgRwFGYR~gY~dl~Ri~~~~~l~~~f~~i~  202 (239)
T PF10593_consen  169 LMQMGRWFGYRPGYEDLCRIYMPEELYDWFRHIA  202 (239)
T ss_pred             HHHHhhcccCCcccccceEEecCHHHHHHHHHHH
Confidence            888754443 224233444555555455554333

This domain is found associated with a helicase domain of superfamily type II [].

>PF04364 DNA_pol3_chi: DNA polymerase III chi subunit, HolC; InterPro: IPR007459 The DNA polymerase III holoenzyme (2

Probab=85.91  E-value=6.9  Score=33.60  Aligned_cols=92  Identities=14%  Similarity=0.134  Sum_probs=47.9

Q ss_pred             eeeeccccHH-HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          91 SEYAWSHLKF-IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        91 ~~~~~~~~K~-~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      ..|.....+. ..++.|+...+..      +.|++|+|.....++.|-+.|=...+  ...+=|+..++-          
T Consensus         5 ~Fy~l~~~~~~~~~c~L~~k~~~~------g~rv~V~~~d~~~a~~lD~~LW~~~~--~sFlPH~~~~~~----------   66 (137)
T PF04364_consen    5 DFYHLSSDDLERFACRLAEKAYRQ------GQRVLVLCPDEEQAEALDELLWTFSP--DSFLPHGLAGEP----------   66 (137)
T ss_dssp             EEEE-S----HHHHHHHHHHHHHT------T--EEEE-SSHHHHHHHHHHTTTSST--T----EEETT-S----------
T ss_pred             EEEEcCCCcHHHHHHHHHHHHHHc------CCeEEEEeCCHHHHHHHHHHHHCCCC--CCCCCCcccCCC----------
Confidence            3455555565 7888999888775      78999999999999999999966542  233345521111          


Q ss_pred             HHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC
Q psy4150         170 KFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK  204 (395)
Q Consensus       170 ~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~  204 (395)
                        -.....|+|+++...  -..+..+++||++...
T Consensus        67 --~~~~~PV~i~~~~~~--~~~~~~~vLinL~~~~   97 (137)
T PF04364_consen   67 --PAARQPVLITWDQEA--NPNNHADVLINLSGEV   97 (137)
T ss_dssp             --STT--SEEEE-TTS------S--SEEEE--SS-
T ss_pred             --CCCCCeEEEecCccc--CCCCCCCEEEECCCCC
Confidence              111247999886532  2334478999997653

7.7.7 from EC) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either the tau or gamma product of gene dnax, complexed to delta.delta and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3SXU_A 1EM8_C.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=85.88  E-value=3.8  Score=43.82  Aligned_cols=59  Identities=19%  Similarity=0.307  Sum_probs=54.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS  183 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~  183 (395)
                      .+.+||.++++..+....+.|...|  +.+..+||   +++..++..++..+..|.+++|++|+
T Consensus        53 ~g~~lVisPl~sL~~dq~~~l~~~g--i~~~~~~s---~~~~~~~~~~~~~l~~~~~~il~~tp  111 (591)
T TIGR01389        53 KGLTVVISPLISLMKDQVDQLRAAG--VAAAYLNS---TLSAKEQQDIEKALVNGELKLLYVAP  111 (591)
T ss_pred             CCcEEEEcCCHHHHHHHHHHHHHcC--CcEEEEeC---CCCHHHHHHHHHHHhCCCCCEEEECh
Confidence            3678999999999999999999888  89999999   99999999999999999999999885

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.

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=85.61  E-value=2.6  Score=43.60  Aligned_cols=76  Identities=17%  Similarity=0.360  Sum_probs=55.1

Q ss_pred             ccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC------ccccCCCCC
Q psy4150         121 TKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS------VGEEGLDIG  192 (395)
Q Consensus       121 ~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~------v~~~GlDip  192 (395)
                      .++||.|+|+..|..+.+.+.....  .+.+..++|   +.+...+...+    .+..+|||||.      +....+++.
T Consensus        76 ~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~g---g~~~~~~~~~l----~~~~~IiV~TP~rL~~~~~~~~~~l~  148 (456)
T PRK10590         76 VRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFG---GVSINPQMMKL----RGGVDVLVATPGRLLDLEHQNAVKLD  148 (456)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEEC---CcCHHHHHHHH----cCCCcEEEEChHHHHHHHHcCCcccc
Confidence            4799999999999988887765421  267778888   77766543322    36789999995      234567888


Q ss_pred             CCCEEEEcCCC
Q psy4150         193 EIDLVICFDAQ  203 (395)
Q Consensus       193 ~v~~VI~~d~p  203 (395)
                      .+++||.=.+.
T Consensus       149 ~v~~lViDEah  159 (456)
T PRK10590        149 QVEILVLDEAD  159 (456)
T ss_pred             cceEEEeecHH
Confidence            89988865443

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=84.08  E-value=9.4  Score=32.78  Aligned_cols=79  Identities=18%  Similarity=0.308  Sum_probs=55.5

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHH-HHHHHHHH
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQ-EQKEIMKK  170 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~-~R~~~l~~  170 (395)
                      ..+..|-....-.+......    ....++||.++++..++.+.+.+...+.  .+.+..+||   +.+.. +....+  
T Consensus        22 ptGsGKT~~~~~~~l~~~~~----~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~--   92 (169)
T PF00270_consen   22 PTGSGKTLAYILPALNRLQE----GKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHG---GQSISEDQREVL--   92 (169)
T ss_dssp             STTSSHHHHHHHHHHHHHHT----TSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEEST---TSCHHHHHHHHH--
T ss_pred             CCCCccHHHHHHHHHhhhcc----CCCceEEEEeecccccccccccccccccccccccccccc---cccccccccccc--
Confidence            34556777766555554443    2345999999999999999988877653  367888888   77644 333333  


Q ss_pred             HhcCCccEEEEcC
Q psy4150         171 FRAGEFNTLIATS  183 (395)
Q Consensus       171 Fk~g~~~vLVaT~  183 (395)
                        .+..+|+|+|.
T Consensus        93 --~~~~~ilv~T~  103 (169)
T PF00270_consen   93 --SNQADILVTTP  103 (169)
T ss_dssp             --HTTSSEEEEEH
T ss_pred             --cccccccccCc
Confidence              77899999994

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 ....

>PRK09401 reverse gyrase; Reviewed

Probab=83.55  E-value=6  Score=45.89  Aligned_cols=82  Identities=21%  Similarity=0.363  Sum_probs=59.6

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-----ccccCCCC
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-----VGEEGLDI  191 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-----v~~~GlDi  191 (395)
                      .+.++||.++|+.-+..+++.+...+.  .+.+..+.|++ +++..++....+.++.|..+|+|||.     .+. .+..
T Consensus       122 ~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~-~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~-~l~~  199 (1176)
T PRK09401        122 KGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHS-SLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD-ELPK  199 (1176)
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccC-CcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH-hccc
Confidence            368999999999999999999887653  24444454422 56678888888999999999999995     222 4444


Q ss_pred             CCCCEEEEcCC
Q psy4150         192 GEIDLVICFDA  202 (395)
Q Consensus       192 p~v~~VI~~d~  202 (395)
                      ..+++||.=++
T Consensus       200 ~~~~~lVvDEa  210 (1176)
T PRK09401        200 KKFDFVFVDDV  210 (1176)
T ss_pred             cccCEEEEECh
Confidence            45777775444

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=83.35  E-value=4.1  Score=41.52  Aligned_cols=77  Identities=22%  Similarity=0.387  Sum_probs=54.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-----cc-ccCCCC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-----VG-EEGLDI  191 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-----v~-~~GlDi  191 (395)
                      +.++||.++|+..|..+++.+....  ..+++..++|   +.+...+...+    .+..+|||||.     .+ ...+++
T Consensus        83 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~g---g~~~~~~~~~l----~~~~~IlV~TP~~l~~~l~~~~~~l  155 (423)
T PRK04837         83 QPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYG---GDGYDKQLKVL----ESGVDILIGTTGRLIDYAKQNHINL  155 (423)
T ss_pred             CceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEEC---CCCHHHHHHHh----cCCCCEEEECHHHHHHHHHcCCccc
Confidence            4689999999999998877655432  1278888998   76655544333    24579999996     22 345788


Q ss_pred             CCCCEEEEcCCC
Q psy4150         192 GEIDLVICFDAQ  203 (395)
Q Consensus       192 p~v~~VI~~d~p  203 (395)
                      ..+.+||.-.+.
T Consensus       156 ~~v~~lViDEad  167 (423)
T PRK04837        156 GAIQVVVLDEAD  167 (423)
T ss_pred             ccccEEEEecHH
Confidence            888888865443

>PTZ00110 helicase; Provisional

Probab=82.20  E-value=3.9  Score=43.38  Aligned_cols=77  Identities=18%  Similarity=0.279  Sum_probs=55.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-----ccccC-CCC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-----VGEEG-LDI  191 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-----v~~~G-lDi  191 (395)
                      +..+||.++|++.|..+.+.+...+.  .+++..++|   +.+...+...+   +. .++|||+|+     .+..+ +++
T Consensus       203 gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~g---g~~~~~q~~~l---~~-~~~IlVaTPgrL~d~l~~~~~~l  275 (545)
T PTZ00110        203 GPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYG---GVPKRGQIYAL---RR-GVEILIACPGRLIDFLESNVTNL  275 (545)
T ss_pred             CcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeC---CCCHHHHHHHH---Hc-CCCEEEECHHHHHHHHHcCCCCh
Confidence            45799999999999999888877543  367778888   77665544333   33 479999995     44444 677


Q ss_pred             CCCCEEEEcCCC
Q psy4150         192 GEIDLVICFDAQ  203 (395)
Q Consensus       192 p~v~~VI~~d~p  203 (395)
                      ..+.+||.=.+.
T Consensus       276 ~~v~~lViDEAd  287 (545)
T PTZ00110        276 RRVTYLVLDEAD  287 (545)
T ss_pred             hhCcEEEeehHH
Confidence            788888765443

>KOG0343|consensus

Probab=81.66  E-value=4.5  Score=42.56  Aligned_cols=75  Identities=23%  Similarity=0.384  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHHHh-hhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCc
Q psy4150         100 FIRLREILESHFRL-HAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus       100 ~~~L~~lL~~~~~~-~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      +.-|.-+|+.++.. |.. ..+--+||.++||+.|-.+.+.|.+.|.  .+.+..+.|   |.+-.     .+.-+-..+
T Consensus       121 LAFlvPvlE~L~r~kWs~-~DGlGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiG---G~~~k-----~E~eRi~~m  191 (758)
T KOG0343|consen  121 LAFLVPVLEALYRLKWSP-TDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIG---GKDVK-----FELERISQM  191 (758)
T ss_pred             eeehHHHHHHHHHcCCCC-CCCceeEEecchHHHHHHHHHHHHHHhhccccccceeec---CchhH-----HHHHhhhcC
Confidence            34455666665544 543 4456799999999999999999988653  478888888   66533     334455679


Q ss_pred             cEEEEcC
Q psy4150         177 NTLIATS  183 (395)
Q Consensus       177 ~vLVaT~  183 (395)
                      +|||||+
T Consensus       192 NILVCTP  198 (758)
T KOG0343|consen  192 NILVCTP  198 (758)
T ss_pred             CeEEech
Confidence            9999997

>KOG1133|consensus

Probab=81.33  E-value=12  Score=40.34  Aligned_cols=95  Identities=12%  Similarity=0.093  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC-----CCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP-----MVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~-----~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      -+..|..++.++...     -.+-+++|+++-.-...+.+.+...|-     .-+.++.-.   .-+   -..+++.+..
T Consensus       613 ~l~~l~~~~~nL~~~-----VPgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~---k~~---~~dvl~~Ya~  681 (821)
T KOG1133|consen  613 MIKDLGSSISNLSNA-----VPGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEP---KDT---VEDVLEGYAE  681 (821)
T ss_pred             HHHHHHHHHHHHHhh-----CCCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccC---ccc---HHHHHHHHHH
Confidence            445555666655443     247799999999988888888876651     112222222   111   3456666654


Q ss_pred             ----CCccEEEEc--CccccCCCCCC--CCEEEEcCCCC
Q psy4150         174 ----GEFNTLIAT--SVGEEGLDIGE--IDLVICFDAQK  204 (395)
Q Consensus       174 ----g~~~vLVaT--~v~~~GlDip~--v~~VI~~d~p~  204 (395)
                          |.-.+|+|.  -=+++|||+.+  +.+||..++|-
T Consensus       682 a~~~g~GaiLlaVVGGKlSEGINF~D~LgRaVvvVGlPy  720 (821)
T KOG1133|consen  682 AAERGRGAILLAVVGGKLSEGINFSDDLGRAVVVVGLPY  720 (821)
T ss_pred             HhhcCCCeEEEEEeccccccccccccccccEEEEeecCC
Confidence                444566554  45789999986  78888888874

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=80.74  E-value=6.4  Score=40.82  Aligned_cols=78  Identities=22%  Similarity=0.328  Sum_probs=56.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCc------cccCCCC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSV------GEEGLDI  191 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v------~~~GlDi  191 (395)
                      ..++||.++|+..+..+.+.+.....  .+.+..++|   +.+...+   .+.+..+..+|||+|.-      -...+.+
T Consensus       162 ~~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~g---g~~~~~~---~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l  235 (475)
T PRK01297        162 EPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVG---GMDFDKQ---LKQLEARFCDILVATPGRLLDFNQRGEVHL  235 (475)
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEc---cCChHHH---HHHHhCCCCCEEEECHHHHHHHHHcCCccc
Confidence            46899999999999998887765432  277888888   7665543   34556778999999962      2335677


Q ss_pred             CCCCEEEEcCCC
Q psy4150         192 GEIDLVICFDAQ  203 (395)
Q Consensus       192 p~v~~VI~~d~p  203 (395)
                      ..+++||.=.+.
T Consensus       236 ~~l~~lViDEah  247 (475)
T PRK01297        236 DMVEVMVLDEAD  247 (475)
T ss_pred             ccCceEEechHH
Confidence            788888765443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	395
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		1e-26
3tmi_A	695	Structural Basis For Rna Recognition And Activation		5e-13
2ykg_A	696	Structural Insights Into Rna Recognition By Rig-I L		6e-13
4ay2_A	687	Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I		6e-13
3tbk_A	555	Mouse Rig-I Atpase Domain Length = 555		4e-12
4a2w_A	936	Structure Of Full-Length Duck Rig-I Length = 936		3e-11
4a2q_A	797	Structure Of Duck Rig-I Tandem Cards And Helicase D		3e-11
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		4e-11
4a2p_A	556	Structure Of Duck Rig-I Helicase Domain Length = 55		4e-11
4i1s_A	243	Melanoma Differentiation Associated Protein-5 Helic		7e-10
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		6e-08
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		8e-08
2fwr_A	472	Structure Of Archaeoglobus Fulgidis Xpb Length = 47		2e-07
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-07
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-07
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-07
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-07
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-07
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-07
2fzl_A	219	Structure Of C-Terminal Domain Of Archaeoglobus Ful		2e-07
2jgn_A	185	Ddx3 Helicase Domain Length = 185		7e-07
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-06
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		2e-06
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		3e-06
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		3e-06
3v4r_A	667	Crystal Structure Of A Uvrb Dimer-Dna Complex Lengt		7e-06
2d7d_A	661	Structural Insights Into The Cryptic Dna Dependent		7e-06
2fdc_A	658	Structural Basis Of Dna Damage Recognition And Proc		7e-06
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		8e-06
1d9z_A	657	Crystal Structure Of The Dna Repair Protein Uvrb In		8e-06
1t5l_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Po		8e-06
1d9x_A	658	Crystal Structure Of The Dna Repair Protein Uvrb Le		8e-06
3uwx_B	683	Crystal Structure Of Uvra-Uvrb Complex Length = 683		8e-06
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		2e-05
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		3e-05
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		3e-05
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		4e-05
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		6e-05
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		6e-05
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		8e-05
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		1e-04
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		1e-04
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		2e-04
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		4e-04
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		5e-04
1d2m_A	665	Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleot		6e-04
1c4o_A	664	Crystal Structure Of The Dna Nucleotide Excision Re		6e-04
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		8e-04

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score =  117 bits (293), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 66/164 (40%), Positives = 102/164 (62%), Gaps = 12/164 (7%)
Query: 88  IMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMV 147
           + + E    H K  +L+EI+    R   ++ + +K+I+F NYR    +I + L  ++  +
Sbjct: 333 VQAKEIGLDHPKMDKLKEII----REQLQRKQNSKIIVFTNYRETAKKIVNEL--VKDGI 386
Query: 148 KASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDA 202
           KA  FVGQ+S     G++Q+EQK I+ +F  GEFN L+ATSVGEEGLD+ E+DLV+ ++ 
Sbjct: 387 KAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEP 446
Query: 203 QKSPIKMVQRLGRTGRKRNGRCVILLTQG-REAHNFQTSMQTCK 245
             S I+ +QR GRTGR   GR +IL+ +G R+   + +S Q  K
Sbjct: 447 VPSAIRSIQRRGRTGRHMPGRVIILMAKGTRDEAYYWSSRQKEK 490

>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of Rig-I Length = 695

Iteration: 1
 Score = 72.0 bits (175), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 84/157 (53%), Gaps = 18/157 (11%)
Query: 106 ILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK--PLEPMVKASMFVG-----QSSG 158
           IL+  + L+ E    T  I+F   R +V  + + ++  P    +K  +  G     Q++G
Sbjct: 387 ILQEEYHLNPE----TITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTG 442
Query: 159 VTQQEQKEIMKKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTG 217
           +T   QK I+  F+A G+ N LIATSV +EG+DI + +LVI ++   + IKM+Q  GR G
Sbjct: 443 MTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-G 501
Query: 218 RKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINN 254
           R R  +C +L +        Q +M     Y EK++N+
Sbjct: 502 RARGSKCFLLTSNAGVIEKEQINM-----YKEKMMND 533

>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I Length = 696

Iteration: 1
 Score = 72.0 bits (175), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 84/157 (53%), Gaps = 18/157 (11%)
Query: 106 ILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK--PLEPMVKASMFVG-----QSSG 158
           IL+  + L+ E    T  I+F   R +V  + + ++  P    +K  +  G     Q++G
Sbjct: 388 ILQEEYHLNPE----TITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTG 443
Query: 159 VTQQEQKEIMKKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTG 217
           +T   QK I+  F+A G+ N LIATSV +EG+DI + +LVI ++   + IKM+Q  GR G
Sbjct: 444 MTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-G 502
Query: 218 RKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINN 254
           R R  +C +L +        Q +M     Y EK++N+
Sbjct: 503 RARGSKCFLLTSNAGVIEKEQINM-----YKEKMMND 534

>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I Length = 687

Iteration: 1
 Score = 72.0 bits (175), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 52/157 (33%), Positives = 84/157 (53%), Gaps = 18/157 (11%)
Query: 106 ILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK--PLEPMVKASMFVG-----QSSG 158
           IL+  + L+ E    T  I+F   R +V  + + ++  P    +K  +  G     Q++G
Sbjct: 379 ILQEEYHLNPE----TITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTG 434
Query: 159 VTQQEQKEIMKKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTG 217
           +T   QK I+  F+A G+ N LIATSV +EG+DI + +LVI ++   + IKM+Q  GR G
Sbjct: 435 MTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-G 493
Query: 218 RKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINN 254
           R R  +C +L +        Q +M     Y EK++N+
Sbjct: 494 RARGSKCFLLTSNAGVIEKEQINM-----YKEKMMND 525

>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain Length = 555

Iteration: 1
 Score = 69.3 bits (168), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 48/138 (34%), Positives = 73/138 (52%), Gaps = 21/138 (15%)
Query: 106 ILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK------PLEPMVKASMFVGQ---- 155
           +L+  + L  E    TK I+F   R +V    D LK      P    +K  +  G+    
Sbjct: 379 VLQEEYHLKPE----TKTILFVKTRALV----DALKKWIEENPALSFLKPGILTGRGRTN 430
Query: 156 -SSGVTQQEQKEIMKKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRL 213
            ++G T   QK +++ FRA G+ N LIATSV +EG+DI E +LVI ++   + IK +Q  
Sbjct: 431 RATGXTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKXIQTR 490
Query: 214 GRTGRKRNGRCVILLTQG 231
           GR GR R+ +C +L +  
Sbjct: 491 GR-GRARDSKCFLLTSSA 507

>pdb|4A2W|A Chain A, Structure Of Full-Length Duck Rig-I Length = 936

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/156 (27%), Positives = 85/156 (54%), Gaps = 18/156 (11%)
Query: 106 ILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK--PLEPMVKASMFVG-----QSSG 158
           IL+  +R + +    T+ ++FA  R +V+ +   ++  P+   +K  + +G     Q++G
Sbjct: 621 ILDDAYRYNPQ----TRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTG 676
Query: 159 VTQQEQKEIMKKFRAGEFN-TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTG 217
           +T   QK ++  F+  + N  LIATSV +EG+DI + +LV+ ++   +  KM+Q  GR G
Sbjct: 677 MTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-G 735
Query: 218 RKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIIN 253
           R    +C+++ ++     N     + C  Y E+++N
Sbjct: 736 RAAGSKCILVTSKTEVVEN-----EKCNRYKEEMMN 766

>pdb|4A2Q|A Chain A, Structure Of Duck Rig-I Tandem Cards And Helicase Domain Length = 797

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/156 (27%), Positives = 85/156 (54%), Gaps = 18/156 (11%)
Query: 106 ILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK--PLEPMVKASMFVG-----QSSG 158
           IL+  +R + +    T+ ++FA  R +V+ +   ++  P+   +K  + +G     Q++G
Sbjct: 621 ILDDAYRYNPQ----TRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTG 676
Query: 159 VTQQEQKEIMKKFRAGEFN-TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTG 217
           +T   QK ++  F+  + N  LIATSV +EG+DI + +LV+ ++   +  KM+Q  GR G
Sbjct: 677 MTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-G 735
Query: 218 RKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIIN 253
           R    +C+++ ++     N     + C  Y E+++N
Sbjct: 736 RAAGSKCILVTSKTEVVEN-----EKCNRYKEEMMN 766

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 65.9 bits (159), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 49/132 (37%), Positives = 68/132 (51%), Gaps = 14/132 (10%)
Query: 95  WSHLKFIRLRE-ILESHFRLHAEKGETTKVIIFANYR----VVVAEIFDVLKPLEPMVKA 149
           + + K  +LR  I+E + R      E+ + IIF   R     +   I +  K  E  VKA
Sbjct: 378 YENEKLTKLRNTIMEQYTRTE----ESARGIIFTKTRQSAYALSQWITENEKFAEVGVKA 433
Query: 150 SMFVGQSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK 204
              +G         +TQ EQKE++ KFR G+ N LIAT+V EEGLDI E ++VI +    
Sbjct: 434 HHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVT 493
Query: 205 SPIKMVQRLGRT 216
           + I MVQ  GR 
Sbjct: 494 NEIAMVQARGRA 505

>pdb|4A2P|A Chain A, Structure Of Duck Rig-I Helicase Domain Length = 556

Iteration: 1
 Score = 65.9 bits (159), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 43/156 (27%), Positives = 85/156 (54%), Gaps = 18/156 (11%)
Query: 106 ILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK--PLEPMVKASMFVG-----QSSG 158
           IL+  +R + +    T+ ++FA  R +V+ +   ++  P+   +K  + +G     Q++G
Sbjct: 380 ILDDAYRYNPQ----TRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTG 435
Query: 159 VTQQEQKEIMKKFRAGEFN-TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTG 217
           +T   QK ++  F+  + N  LIATSV +EG+DI + +LV+ ++   +  KM+Q  GR G
Sbjct: 436 MTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-G 494
Query: 218 RKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIIN 253
           R    +C+++ ++     N     + C  Y E+++N
Sbjct: 495 RAAGSKCILVTSKTEVVEN-----EKCNRYKEEMMN 525

>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase Domain Complex With Inhibitor Non-structural Protein V Length = 243

Iteration: 1
 Score = 61.6 bits (148), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 42/111 (37%), Positives = 56/111 (50%), Gaps = 12/111 (10%)
Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYR----VVVAEIFDVLKPLEPMVKASMFVG 154
           K  +LR  +  HF       E+ + IIF   R     +   I D  K  E  VKA   +G
Sbjct: 132 KLTKLRNTIXEHF---TRTEESARGIIFTKTRQSAYALSQWITDNKKFAEVGVKAHHLIG 188
Query: 155 QSSG-----VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICF 200
                     TQ EQ+E++ KFR G+ N LIAT+V EEGLDI E ++VI +
Sbjct: 189 AGHSSEFKPXTQNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVIRY 239

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
            G+ Q+++ ++M +F+ GE+  L+AT V   G+DI  I LVI +D        V R GRT
Sbjct: 67  GGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRT 126
Query: 217 GRKRN-GRCVILLT 229
           GR  N G+ +  +T
Sbjct: 127 GRAGNKGKAISFVT 140

>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 = 54.7 bits (130), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 41/140 (29%), Positives = 67/140 (47%), Gaps = 11/140 (7%)
Query: 119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT 178
           E T+ I+F   R  V E+ + L+  E  +      G+   + Q ++ E +K+   G  N 
Sbjct: 29  EATRSIVFVRKRERVHELANWLR--EAGINNCYLEGE---MVQGKRNEAIKRLTEGRVNV 83
Query: 179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQGREAHNF 237
           L+AT V   G+DI ++  V  FD  +S    + R+GRT R  R G  + L+    EAH+ 
Sbjct: 84  LVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLV----EAHD- 138
Query: 238 QTSMQTCKSYVEKIINNKSI 257
              +     Y+E+ I  + I
Sbjct: 139 HLLLGKVGRYIEEPIKARVI 158

>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb Length = 472

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 66/132 (50%), Gaps = 18/132 (13%)
Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K  +LREILE H           K+IIF  +  +V  I  V   L P +        +  
Sbjct: 336 KIRKLREILERH--------RKDKIIIFTRHNELVYRISKVF--LIPAI--------THR 377
Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
            +++E++EI++ FR G F  ++++ V +EG+D+ + ++ +      S  + +QRLGR  R
Sbjct: 378 TSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILR 437
Query: 219 KRNGRCVILLTQ 230
              G+   +L +
Sbjct: 438 PSKGKKEAVLYE 449

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 56/99 (56%), Gaps = 7/99 (7%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
           T+ +IF N +  V    D L   E M +A+  V    G + Q+E++ IMK+FR+G    L
Sbjct: 277 TQAVIFCNTKRKV----DWLT--EKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 330
Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           I+T V   GLD+ ++ L+I +D   +    + R+GR+GR
Sbjct: 331 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 369

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 56/99 (56%), Gaps = 7/99 (7%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
           T+ +IF N +  V    D L   E M +A+  V    G + Q+E++ IMK+FR+G    L
Sbjct: 278 TQAVIFCNTKRKV----DWLT--EKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 331
Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           I+T V   GLD+ ++ L+I +D   +    + R+GR+GR
Sbjct: 332 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 370

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 38/107 (35%), Positives = 59/107 (55%), Gaps = 8/107 (7%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
           T+ +IF N +  V    D L   E M +A+  V    G + Q+E++ IMK+FR+G    L
Sbjct: 241 TQAVIFCNTKRKV----DWLT--EKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 294
Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR-KRNGRCV 225
           I+T V   GLD+ ++ L+I +D   +    + R+GR+GR  R G  V
Sbjct: 295 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAV 341

>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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 56/99 (56%), Gaps = 7/99 (7%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
           T+ +IF N +  V    D L   E M +A+  V    G + Q+E++ IMK+FR+G    L
Sbjct: 278 TQAVIFCNTKRKV----DWLT--EKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 331
Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           I+T V   GLD+ ++ L+I +D   +    + R+GR+GR
Sbjct: 332 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 370

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 56/99 (56%), Gaps = 7/99 (7%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
           T+ +IF N +  V    D L   E M +A+  V    G + Q+E++ IMK+FR+G    L
Sbjct: 241 TQAVIFCNTKRKV----DWLT--EKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 294
Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           I+T V   GLD+ ++ L+I +D   +    + R+GR+GR
Sbjct: 295 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 333

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 56/99 (56%), Gaps = 7/99 (7%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
           T+ +IF N +  V    D L   E M +A+  V    G + Q+E++ IMK+FR+G    L
Sbjct: 256 TQAVIFCNTKRKV----DWLT--EKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL 309
Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           I+T V   GLD+ ++ L+I +D   +    + R+GR+GR
Sbjct: 310 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 348

>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus Xpb Length = 219

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 66/132 (50%), Gaps = 18/132 (13%)
Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K  +LREILE H           K+IIF  +  +V  I  V   L P +        +  
Sbjct: 101 KIRKLREILERH--------RKDKIIIFTRHNELVYRISKVF--LIPAI--------THR 142
Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
            +++E++EI++ FR G F  ++++ V +EG+D+ + ++ +      S  + +QRLGR  R
Sbjct: 143 TSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILR 202
Query: 219 KRNGRCVILLTQ 230
              G+   +L +
Sbjct: 203 PSKGKKEAVLYE 214

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 39/62 (62%)
Query: 160 TQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK 219
           +Q++++E + +FR+G+   L+AT+V   GLDI  +  VI FD      + V R+GRTGR 
Sbjct: 81  SQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV 140
Query: 220 RN 221
            N
Sbjct: 141 GN 142

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 39/62 (62%)
Query: 160 TQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK 219
           +Q++++E + +FR+G+   L+AT+V   GLDI  +  VI FD      + V R+GRTGR 
Sbjct: 311 SQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV 370
Query: 220 RN 221
            N
Sbjct: 371 GN 372

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 59/134 (44%), Gaps = 14/134 (10%)
Query: 88  IMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMV 147
           I   EY     K + L E L+              V+IFA  +  V  I + L     ++
Sbjct: 31  IQEVEYVKEEAKMVYLLECLQK---------TPPPVLIFAEKKADVDAIHEYL-----LL 76
Query: 148 KASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPI 207
           K    V    G  Q+E+ + ++ FR G+ + L+AT V  +GLD   I  VI +D  +   
Sbjct: 77  KGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIE 136
Query: 208 KMVQRLGRTGRKRN 221
             V R+GRTG   N
Sbjct: 137 NYVHRIGRTGCSGN 150

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 171 FRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR-KRNGRCVILL 228
           FR GE++ LI T V   GLDI  ++ VI FDA +     + R+GRTGR  R G  +  +
Sbjct: 262 FREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFI 320

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR-K 219
           Q ++++ ++ F+ G    LIATSV   GLDI  I  VI +D        V R+GRTGR  
Sbjct: 336 QSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395
Query: 220 RNGRC 224
            NGR 
Sbjct: 396 NNGRA 400

>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex Length = 667

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQ 211
           S +   E+ EI++  R G+++ L+  ++  EGLDI E+ LV   DA K     S   ++Q
Sbjct: 483 SEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQ 542
Query: 212 RLGRTGRKRNGRCVI 226
            +GR  R   GR ++
Sbjct: 543 TIGRAARNAEGRVIM 557

>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase Activity Of Uvrb Length = 661

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQ 211
           S +   E+ EI++  R G+++ L+  ++  EGLDI E+ LV   DA K     S   ++Q
Sbjct: 477 SEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQ 536
Query: 212 RLGRTGRKRNGRCVI 226
            +GR  R   GR ++
Sbjct: 537 TIGRAARNAEGRVIM 551

>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX Length = 658

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQ 211
           S +   E+ EI++  R G+++ L+  ++  EGLDI E+ LV   DA K     S   ++Q
Sbjct: 477 SEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQ 536
Query: 212 RLGRTGRKRNGRCVI 226
            +GR  R  NG  ++
Sbjct: 537 TIGRAARNANGHVIM 551

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 37/58 (63%)
Query: 161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           QQE+ ++  +FR G+  TL+ + +   G+DI  +++VI FD  K+    + R+GR+GR
Sbjct: 294 QQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGR 351

>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In Complex With Atp Length = 657

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQ 211
           S +   E+ EI++  R G+++ L+  ++  EGLDI E+ LV   DA K     S   ++Q
Sbjct: 476 SEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQ 535
Query: 212 RLGRTGRKRNGRCVI 226
            +GR  R  NG  ++
Sbjct: 536 TIGRAARNANGHVIM 550

>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 = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQ 211
           S +   E+ EI++  R G+++ L+  ++  EGLDI E+ LV   DA K     S   ++Q
Sbjct: 477 SEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQ 536
Query: 212 RLGRTGRKRNGRCVI 226
            +GR  R  NG  ++
Sbjct: 537 TIGRAARNANGHVIM 551

>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Length = 658

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQ 211
           S +   E+ EI++  R G+++ L+  ++  EGLDI E+ LV   DA K     S   ++Q
Sbjct: 477 SEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQ 536
Query: 212 RLGRTGRKRNGRCVI 226
            +GR  R  NG  ++
Sbjct: 537 TIGRAARNANGHVIM 551

>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex Length = 683

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQ 211
           S +   E+ EI++  R G+++ L+  ++  EGLDI E+ LV   DA K     S   ++Q
Sbjct: 502 SEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQ 561
Query: 212 RLGRTGRKRNGRCVI 226
            +GR  R  NG  ++
Sbjct: 562 TIGRAARNANGHVIM 576

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 162 QEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFD------AQKSPIKMVQRLGR 215
           QE+  ++  FR G    LI T+V   G+DI  + +V+ +D       Q  P   + R+GR
Sbjct: 72  QERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGR 131
Query: 216 TGRKRNGRCVILLTQGREAHNFQTSMQ 242
           TGR       I     + + N  +++Q
Sbjct: 132 TGRFGRKGVAISFVHDKNSFNILSAIQ 158

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 162 QEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFD------AQKSPIKMVQRLGR 215
           QE+  ++  FR G    LI T+V   G+DI  + +V+ +D       Q  P   + R+GR
Sbjct: 280 QERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGR 339
Query: 216 TGRKRNGRCVILLTQGREAHNFQTSMQ 242
           TGR       I     + + N  +++Q
Sbjct: 340 TGRFGRKGVAISFVHDKNSFNILSAIQ 366

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 162 QEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFD------AQKSPIKMVQRLGR 215
           QE+  ++  FR G    LI T+V   G+DI  + +V+ +D       Q  P   + R+GR
Sbjct: 280 QERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGR 339
Query: 216 TGRKRNGRCVILLTQGREAHNFQTSMQ 242
           TGR       I     + + N  +++Q
Sbjct: 340 TGRFGRKGVAISFVHDKNSFNILSAIQ 366

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 5/81 (6%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI 180
           T+ +IF N R  V E+   L+  +  V A       S + QQE+  IMK+FR+G    LI
Sbjct: 31  TQAVIFCNTRRKVEELTTKLRNDKFTVSAIY-----SDLPQQERDTIMKEFRSGSSRILI 85
Query: 181 ATSVGEEGLDIGEIDLVICFD 201
           +T +   G+D+ ++ LVI +D
Sbjct: 86  STDLLARGIDVQQVSLVINYD 106

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 162 QEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFD------AQKSPIKMVQRLGR 215
           QE+  ++  FR G    LI T+V   G+DI  +  V+ +D       Q  P   + R+GR
Sbjct: 74  QERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGR 133
Query: 216 TGRKRNGRCVILLTQGREAHNFQTSMQ 242
           TGR       I     + + N  +++Q
Sbjct: 134 TGRFGRKGVAISFVHDKNSFNILSAIQ 160

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 162 QEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFD------AQKSPIKMVQRLGR 215
           QE+  ++  FR G    LI T+V   G+DI  +  V+ +D       Q  P   + R+GR
Sbjct: 73  QERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGR 132
Query: 216 TGRKRNGRCVILLTQGREAHNFQTSMQ 242
           TGR       I     + + N  +++Q
Sbjct: 133 TGRFGRKGVAISFVHDKNSFNILSAIQ 159

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 5/81 (6%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI 180
           T+ +IF N R  V E+   L+  +  V A       S + QQE+  IMK+FR+G    LI
Sbjct: 261 TQAVIFCNTRRKVEELTTKLRNDKFTVSAIY-----SDLPQQERDTIMKEFRSGSSRILI 315
Query: 181 ATSVGEEGLDIGEIDLVICFD 201
           +T +   G+D+ ++ LVI +D
Sbjct: 316 STDLLARGIDVQQVSLVINYD 336

>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 = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 28/42 (66%)
Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICF 200
           ++Q E++ +M  FR GE   L+AT V   GLDI ++DLV+ +
Sbjct: 62  MSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHY 103

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/73 (26%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           ++Q +++++++ F+  +   LIAT V   G+D+ +++ VI +   ++P     R+GRTGR
Sbjct: 272 LSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGR 331
Query: 219 K-RNGRCVILLTQ 230
             + G+ + ++ +
Sbjct: 332 AGKKGKAISIINR 344

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 28/42 (66%)
Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICF 200
           ++Q E++ ++  FR GE   L+AT V   GLDI ++DLV+ +
Sbjct: 65  LSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHY 106

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 5/81 (6%)
Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI 180
           T+ +IF N R  V E+   L+  +  V A       S + QQE+  I K+FR+G    LI
Sbjct: 260 TQAVIFCNTRRKVEELTTKLRNDKFTVSAIY-----SDLPQQERDTIXKEFRSGSSRILI 314
Query: 181 ATSVGEEGLDIGEIDLVICFD 201
           +T +   G+D+ ++ LVI +D
Sbjct: 315 STDLLARGIDVQQVSLVINYD 335

>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide Excision Repair Enzyme Length = 665

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 164 QKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTGR 218
           ++ +++  R G ++ L+  ++  EGLDI E+ LV   DA K     S   ++Q +GR   
Sbjct: 479 RQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAA- 537
Query: 219 KRNGRCVILLTQGREAHNFQTSMQ 242
            RN R  + L   R +   Q +++
Sbjct: 538 -RNARGEVWLYADRVSEAMQRAIE 560

>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair Enzyme Uvrb From Thermus Thermophilus Length = 664

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 164 QKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTGR 218
           ++ +++  R G ++ L+  ++  EGLDI E+ LV   DA K     S   ++Q +GR   
Sbjct: 478 RQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAA- 536
Query: 219 KRNGRCVILLTQGREAHNFQTSMQ 242
            RN R  + L   R +   Q +++
Sbjct: 537 -RNARGEVWLYADRVSEAMQRAIE 559

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 12/72 (16%)
Query: 156 SSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIK------- 208
           S  +T +++  I+++FR G+   LI T+V   G+D+ ++ +V+ FD    P+K       
Sbjct: 65  SGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDL---PVKQGEEPDY 121
Query: 209 --MVQRLGRTGR 218
              + R+GRTGR
Sbjct: 122 ETYLHRIGRTGR 133

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	395
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-41
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	3e-37
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	4e-36
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	3e-35
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	6e-34
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	6e-33
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	1e-13
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	1e-13
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	3e-13
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	4e-13
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	1e-12
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-12
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	2e-12
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	2e-12
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	3e-12
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	4e-12
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	4e-12
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	5e-12
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	7e-12
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-11
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	2e-11
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	4e-11
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	4e-11
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	7e-11
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-10
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-10
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	3e-10
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	3e-10
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	6e-10
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	7e-10
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	2e-09
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	7e-09
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	8e-06
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	1e-05
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	1e-05
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	1e-04
3h1t_A	590	Type I site-specific restriction-modification syst	4e-04
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	7e-04

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Length = 494

 Score =  151 bits (382), Expect = 2e-41
 Identities = 72/225 (32%), Positives = 121/225 (53%), Gaps = 13/225 (5%)

Query: 23  RMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKP 82
           R +     +   L  A+E L T GL +    + ++ +E  +           +  +++K 
Sbjct: 270 RGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSD--KRMKK 327

Query: 83  KLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKP 142
            + + + + E    H K  +L+EI+        ++ + +K+I+F NYR    +I + L  
Sbjct: 328 AISLLVQAKEIGLDHPKMDKLKEIIREQL----QRKQNSKIIVFTNYRETAKKIVNELV- 382

Query: 143 LEPMVKASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLV 197
            +  +KA  FVGQ+S     G++Q+EQK I+ +F  GEFN L+ATSVGEEGLD+ E+DLV
Sbjct: 383 -KDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLV 441

Query: 198 ICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQ 242
           + ++   S I+ +QR GRTGR   GR +IL+ +G     +  S +
Sbjct: 442 VFYEPVPSAIRSIQRRGRTGRHMPGRVIILMAKGTRDEAYYWSSR 486

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

 Score =  140 bits (354), Expect = 3e-37
 Identities = 53/237 (22%), Positives = 105/237 (44%), Gaps = 18/237 (7%)

Query: 16  HINRDLDRMIQRDFHVTHSL---ASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDND 72
               +  R+ +  F  T  L     AL       +    + L E      + P    +  
Sbjct: 289 EDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQH 348

Query: 73  LQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVV 132
           L    Q+ +P+L    +S +    + K   L  IL+  +R + +    T+ ++FA  R +
Sbjct: 349 LTAKFQEKEPEL--IALSKDETNENPKLEELVCILDDAYRYNPQ----TRTLLFAKTRAL 402

Query: 133 VAEIFDVLKPLEPM--VKASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNT-LIATSV 184
           V+ +   ++    +  +K  + +G+       G+T   QK ++  F+  + N  LIATSV
Sbjct: 403 VSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSV 462

Query: 185 GEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSM 241
            +EG+DI + +LV+ ++   +  KM+Q  GR GR    +C+++ ++     N + + 
Sbjct: 463 ADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSKCILVTSKTEVVENEKCNR 518

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

 Score =  137 bits (346), Expect = 4e-36
 Identities = 60/248 (24%), Positives = 102/248 (41%), Gaps = 18/248 (7%)

Query: 17  INRDLDRMIQRDFHVTHSL---ASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDL 73
              +  R+ +  F  T  L     AL       +    N L     +         + +L
Sbjct: 289 DKEEESRVCKALFLYTSHLRKYNDALIISEDAQMTDALNYLKAFFHDVREAAFDETEREL 348

Query: 74  QNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVV 133
               ++   +L+           + K   L  +L+  +         TK I+F   R +V
Sbjct: 349 TRRFEEKLEELEKVSRDPS--NENPKLRDLYLVLQEEYH----LKPETKTILFVKTRALV 402

Query: 134 AEIFDVLK--PLEPMVKASMFVGQSS-----GVTQQEQKEIMKKFRA-GEFNTLIATSVG 185
             +   ++  P    +K  +  G+       G+T   QK +++ FRA G+ N LIATSV 
Sbjct: 403 DALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVA 462

Query: 186 EEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCK 245
           +EG+DI E +LVI ++   + IKM+Q  GR GR R+ +C +L +        + +M   K
Sbjct: 463 DEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRARDSKCFLLTSSADVIEKEKANMIKEK 521

Query: 246 SYVEKIIN 253
              E I+ 
Sbjct: 522 IMNESILR 529

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Length = 936

 Score =  137 bits (344), Expect = 3e-35
 Identities = 66/355 (18%), Positives = 136/355 (38%), Gaps = 32/355 (9%)

Query: 16  HINRDLDRMIQRDFHVTHSL---ASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDND 72
               +  R+ +  F  T  L     AL       +    + L E      + P    +  
Sbjct: 530 EDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQH 589

Query: 73  LQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVV 132
           L    Q+ +P  ++  +S +    + K   L  IL+  +R        T+ ++FA  R +
Sbjct: 590 LTAKFQEKEP--ELIALSKDETNENPKLEELVCILDDAYR----YNPQTRTLLFAKTRAL 643

Query: 133 VAEIFDVLKPLEPM--VKASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNT-LIATSV 184
           V+ +   ++    +  +K  + +G+       G+T   QK ++  F+  + N  LIATSV
Sbjct: 644 VSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSV 703

Query: 185 GEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTC 244
            +EG+DI + +LV+ ++   +  KM+Q  GR GR    +C+++ ++     N + +    
Sbjct: 704 ADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSKCILVTSKTEVVENEKCNR--- 759

Query: 245 KSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKA 304
             Y E+++N         +   +        +I  L +  +      +   K      + 
Sbjct: 760 --YKEEMMNKAV------EKIQKWDEETFAKKIHNLQMKERVLRDSRRKEIKPKVVEGQK 811

Query: 305 NKKSKKKLETDGNSE---PAGKQNKTNAKKTKKQPMMTQSNDIRTCFENITKKKK 356
           N    K      +++        +     +  K+   T+ +     F+   KK K
Sbjct: 812 NLLCGKCKAYACSTDDIRIIKDSHHIVLGEAFKERYTTKPHKKPMQFDGFEKKSK 866

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score =  132 bits (333), Expect = 6e-34
 Identities = 52/237 (21%), Positives = 100/237 (42%), Gaps = 18/237 (7%)

Query: 16  HINRDLDRMIQRDFHVTHSL---ASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDND 72
               +  R+ +  F  T  L     AL       +    + L E      + P    +  
Sbjct: 530 EDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQH 589

Query: 73  LQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVV 132
           L    Q+ +P+L            + K   L  IL+  +R        T+ ++FA  R +
Sbjct: 590 LTAKFQEKEPELIALSKDETN--ENPKLEELVCILDDAYR----YNPQTRTLLFAKTRAL 643

Query: 133 VAEIFDVLKPLEPM--VKASMFVGQSS-----GVTQQEQKEIMKKFRAGEFNT-LIATSV 184
           V+ +   ++    +  +K  + +G+       G+T   QK ++  F+  + N  LIATSV
Sbjct: 644 VSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSV 703

Query: 185 GEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSM 241
            +EG+DI + +LV+ ++   +  KM+Q  GR GR    +C+++ ++     N + + 
Sbjct: 704 ADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSKCILVTSKTEVVENEKCNR 759

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

 Score =  129 bits (325), Expect = 6e-33
 Identities = 73/323 (22%), Positives = 128/323 (39%), Gaps = 31/323 (9%)

Query: 9   KSKAQFPHINRDLDRMIQRDFHVTHS----LASALENLVTYGLRSFYNNLVEVSKEDGSC 64
           K+   F   ++D +  I +   +  S       AL       ++   + L +      + 
Sbjct: 289 KACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAA 348

Query: 65  PILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVI 124
                + DL    ++   +L    +S + +  + K   L  IL+  + L+ E    T  I
Sbjct: 349 GFDEIEQDLTQRFEEKLQEL--ESVSRDPSNENPKLEDLCFILQEEYHLNPE----TITI 402

Query: 125 IFANYRVVVAEIFDVLKPLEPM--VKASMFVGQSS-----GVTQQEQKEIMKKFRA-GEF 176
           +F   R +V  + + ++    +  +K  +  G+       G+T   QK I+  F+A G+ 
Sbjct: 403 LFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDH 462

Query: 177 NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHN 236
           N LIATSV +EG+DI + +LVI ++   + IKM+Q  GR GR R  +C +L +       
Sbjct: 463 NILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFLLTSNAGVIEK 521

Query: 237 FQTSMQTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKK 296
            Q +M     Y EK++N+                A    +I  +    K      +  K 
Sbjct: 522 EQINM-----YKEKMMNDS------ILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKP 570

Query: 297 KPKENEKANKKSK-KKLETDGNS 318
            P +  K     K K L      
Sbjct: 571 VPDKENKKLLCRKCKALACYTAD 593

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score = 67.6 bits (166), Expect = 1e-13
 Identities = 33/127 (25%), Positives = 58/127 (45%), Gaps = 12/127 (9%)

Query: 92  EYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASM 151
            +     K   L ++L +        G+ +  ++F   +     + D L   E     S+
Sbjct: 25  VWVEESDKRSFLLDLLNAT-------GKDSLTLVFVETKKGADSLEDFLY-HEGYACTSI 76

Query: 152 FVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQ 211
                   +Q++++E + +FR+G+   L+AT+V   GLDI  +  VI FD      + V 
Sbjct: 77  H----GDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVH 132

Query: 212 RLGRTGR 218
           R+GRTGR
Sbjct: 133 RIGRTGR 139

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Length = 472

 Score = 71.0 bits (174), Expect = 1e-13
 Identities = 35/132 (26%), Positives = 63/132 (47%), Gaps = 19/132 (14%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K  +LREILE H           K+IIF  +  +V  I  V               ++S 
Sbjct: 336 KIRKLREILERH--------RKDKIIIFTRHNELVYRISKVFL-------IPAITHRTS- 379

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
             ++E++EI++ FR G F  ++++ V +EG+D+ + ++ +      S  + +QRLGR  R
Sbjct: 380 --REEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILR 437

Query: 219 -KRNGRCVILLT 229
             +  +  +L  
Sbjct: 438 PSKGKKEAVLYE 449

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A Length = 212

 Score = 67.3 bits (165), Expect = 3e-13
 Identities = 36/139 (25%), Positives = 59/139 (42%), Gaps = 17/139 (12%)

Query: 119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSS-----GVTQQEQKEIMKKFRA 173
              + ++F   +    EI   L  L          G  +      ++Q E++ ++  FR 
Sbjct: 30  SPDRAMVFTRTKAETEEIAQGLLRL----------GHPAQALHGDLSQGERERVLGAFRQ 79

Query: 174 GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQGR 232
           GE   L+AT V   GLDI ++DLV+ +           R GRTGR  R GR  +LL   R
Sbjct: 80  GEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRV-VLLYGPR 138

Query: 233 EAHNFQTSMQTCKSYVEKI 251
           E  + +   +      +++
Sbjct: 139 ERRDVEALERAVGRRFKRV 157

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score = 66.1 bits (162), Expect = 4e-13
 Identities = 26/154 (16%), Positives = 60/154 (38%), Gaps = 14/154 (9%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K  +L ++L+          E  +V+IF         +  +L        A        G
Sbjct: 18  KNRKLFDLLDVL--------EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI-----HRG 64

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           + Q+E+    ++F+  +   L+AT++   G+DI  +++   +D  +     + R+ R GR
Sbjct: 65  MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 124

Query: 219 -KRNGRCVILLTQGREAHNFQTSMQTCKSYVEKI 251
               G  +  ++   +A          +  + ++
Sbjct: 125 FGTKGLAITFVSDENDAKILNDVQDRFEVNISEL 158

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score = 66.7 bits (163), Expect = 1e-12
 Identities = 37/136 (27%), Positives = 59/136 (43%), Gaps = 17/136 (12%)

Query: 122 KVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSS-----GVTQQEQKEIMKKFRAGEF 176
           + ++F   +    EI   L  L          G  +      ++Q E++ +M  FR GE 
Sbjct: 30  RAMVFTRTKAETEEIAQGLLRL----------GHPAQALHGDMSQGERERVMGAFRQGEV 79

Query: 177 NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQGREAH 235
             L+AT V   GLDI ++DLV+ +           R GRTGR  R GR  +LL   RE  
Sbjct: 80  RVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRV-VLLYGPRERR 138

Query: 236 NFQTSMQTCKSYVEKI 251
           + +   +      +++
Sbjct: 139 DVEALERAVGRRFKRV 154

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score = 66.8 bits (164), Expect = 2e-12
 Identities = 33/137 (24%), Positives = 66/137 (48%), Gaps = 7/137 (5%)

Query: 116 EKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE 175
           +    T+ +IF N +  V  + + ++     V +         + Q+E++ IMK+FR+G 
Sbjct: 272 DTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSM-----HGDMPQKERESIMKEFRSGA 326

Query: 176 FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQGREA 234
              LI+T V   GLD+ ++ L+I +D   +    + R+GR+GR  R G   I   +  + 
Sbjct: 327 SRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGV-AINFVKNDDI 385

Query: 235 HNFQTSMQTCKSYVEKI 251
              +   Q   + ++++
Sbjct: 386 RILRDIEQYYSTQIDEM 402

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

 Score = 64.2 bits (157), Expect = 2e-12
 Identities = 40/127 (31%), Positives = 58/127 (45%), Gaps = 14/127 (11%)

Query: 92  EYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASM 151
           EY     K + L E L+              V+IFA  +  V  I + L  L   V+A  
Sbjct: 35  EYVKEEAKMVYLLECLQKT---------PPPVLIFAEKKADVDAIHEYL--LLKGVEAVA 83

Query: 152 FVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQ 211
             G   G  Q+E+ + ++ FR G+ + L+AT V  +GLD   I  VI +D  +     V 
Sbjct: 84  IHG---GKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVH 140

Query: 212 RLGRTGR 218
           R+GRTG 
Sbjct: 141 RIGRTGC 147

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

 Score = 63.3 bits (155), Expect = 3e-12
 Identities = 36/120 (30%), Positives = 55/120 (45%), Gaps = 13/120 (10%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           KF  L+++L +              IIF   +  V ++ D L  L              G
Sbjct: 22  KFSLLKDVLMTE--------NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIH-----GG 68

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           + Q+++ ++M +F+ GE+  L+AT V   G+DI  I LVI +D        V R GRTGR
Sbjct: 69  MIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGR 128

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score = 66.0 bits (162), Expect = 4e-12
 Identities = 41/154 (26%), Positives = 71/154 (46%), Gaps = 15/154 (9%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K+  L ++ +S           T+ +IF N R  V E+   L+  +  V A       S 
Sbjct: 246 KYECLTDLYDSI--------SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI-----YSD 292

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           + QQE+  IMK+FR+G    LI+T +   G+D+ ++ LVI +D   +    + R+GR GR
Sbjct: 293 LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR 352

Query: 219 K-RNGRCVILLTQGREAHNFQTSMQTCKSYVEKI 251
             R G   I      +    +   +   + +E++
Sbjct: 353 FGRKGV-AINFVTNEDVGAMRELEKFYSTQIEEL 385

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score = 66.1 bits (162), Expect = 4e-12
 Identities = 26/154 (16%), Positives = 60/154 (38%), Gaps = 14/154 (9%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K  +L ++L+          E  +V+IF         +  +L        A        G
Sbjct: 237 KNRKLFDLLDVL--------EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI-----HRG 283

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           + Q+E+    ++F+  +   L+AT++   G+DI  +++   +D  +     + R+ R GR
Sbjct: 284 MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 343

Query: 219 K-RNGRCVILLTQGREAHNFQTSMQTCKSYVEKI 251
               G  +  ++   +A          +  + ++
Sbjct: 344 FGTKGLAITFVSDENDAKILNDVQDRFEVNISEL 377

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

 Score = 63.0 bits (154), Expect = 5e-12
 Identities = 34/100 (34%), Positives = 53/100 (53%), Gaps = 5/100 (5%)

Query: 119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT 178
             T+ +IF N R  V E+   L+  +  V A       S + QQE+  IMK+FR+G    
Sbjct: 29  SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI-----YSDLPQQERDTIMKEFRSGSSRI 83

Query: 179 LIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           LI+T +   G+D+ ++ LVI +D   +    + R+GR GR
Sbjct: 84  LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR 123

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

 Score = 65.3 bits (160), Expect = 7e-12
 Identities = 32/129 (24%), Positives = 57/129 (44%), Gaps = 16/129 (12%)

Query: 92  EYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASM 151
            +     K   L ++L +        G+ +  ++F   +     + D L           
Sbjct: 255 VWVEESDKRSFLLDLLNAT-------GKDSLTLVFVETKKGADSLEDFLYHEG------- 300

Query: 152 FVGQS--SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKM 209
           +   S     +Q++++E + +FR+G+   L+AT+V   GLDI  +  VI FD      + 
Sbjct: 301 YACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEY 360

Query: 210 VQRLGRTGR 218
           V R+GRTGR
Sbjct: 361 VHRIGRTGR 369

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score = 64.9 bits (159), Expect = 1e-11
 Identities = 34/137 (24%), Positives = 62/137 (45%), Gaps = 7/137 (5%)

Query: 116 EKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE 175
           E    T+ +IF N R  V  + + +   +  V A         + Q+E+  IM++FR+G 
Sbjct: 276 ETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAM-----HGDMDQKERDVIMREFRSGS 330

Query: 176 FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQGREA 234
              LI T +   G+D+ ++ LVI +D   +    + R+GR GR  R G   I +    + 
Sbjct: 331 SRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGV-AINMVTEEDK 389

Query: 235 HNFQTSMQTCKSYVEKI 251
              +       + +E++
Sbjct: 390 RTLRDIETFYNTSIEEM 406

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score = 64.4 bits (157), Expect = 2e-11
 Identities = 28/119 (23%), Positives = 52/119 (43%), Gaps = 5/119 (4%)

Query: 114 HAEKGETTKVIIFANYRVVVAEIFDVLK-PLEPMVKASMFVGQSSGVTQQEQKEIMKKFR 172
             E+    K IIFA      + +  +LK   +  +    F G+ +   Q ++  ++K+F+
Sbjct: 333 IKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKIT---QNKRTSLVKRFK 389

Query: 173 AGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQ 230
             E   L+ T VG  G+D   +  V+           + R+GRT R  + G  V+ + +
Sbjct: 390 KDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICK 448

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score = 63.0 bits (154), Expect = 4e-11
 Identities = 36/150 (24%), Positives = 65/150 (43%), Gaps = 7/150 (4%)

Query: 116 EKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE 175
            K +  + IIF N    V  +   +  L      S      + + QQE+ ++  +FR G+
Sbjct: 254 SKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYS-----HARMKQQERNKVFHEFRQGK 308

Query: 176 FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLTQGREA 234
             TL+ + +   G+DI  +++VI FD  K+    + R+GR+GR    G  + L+    + 
Sbjct: 309 VRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLIN-WNDR 367

Query: 235 HNFQTSMQTCKSYVEKIINNKSIYANLAKN 264
            N     Q   + +  I         +A+N
Sbjct: 368 FNLYKIEQELGTEIAAIPATIDKSLYVAEN 397

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score = 60.3 bits (147), Expect = 4e-11
 Identities = 26/104 (25%), Positives = 47/104 (45%), Gaps = 11/104 (10%)

Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI 180
            + IIF   R     +   +      V        S  +T +++  I+++FR G+   LI
Sbjct: 35  GQAIIFCQTRRNAKWLTVEMIQDGHQVSLL-----SGELTVEQRASIIQRFRDGKEKVLI 89

Query: 181 ATSVGEEGLDIGEIDLVICFD------AQKSPIKMVQRLGRTGR 218
            T+V   G+D+ ++ +V+ FD       +      + R+GRTGR
Sbjct: 90  TTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGR 133

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 62.5 bits (152), Expect = 7e-11
 Identities = 29/118 (24%), Positives = 52/118 (44%), Gaps = 5/118 (4%)

Query: 114 HAEKGETTKVIIFANYRVVVAEIFDVLK-PLEPMVKASMFVGQSSGVTQQEQKEIMKKFR 172
             E+    K IIFA      + +  +LK   +  +    F G+   +TQ ++  ++K+F+
Sbjct: 282 IKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGK---ITQNKRTSLVKRFK 338

Query: 173 AGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLT 229
             E   L+ T VG  G+D   +  V+           + R+GRT R  + G  V+ + 
Sbjct: 339 KDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFIC 396

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score = 61.4 bits (150), Expect = 1e-10
 Identities = 32/155 (20%), Positives = 72/155 (46%), Gaps = 18/155 (11%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           +F  L  +L++         +    ++F   +    E+  +L+            G   G
Sbjct: 226 RFEALCRLLKN---------KEFYGLVFCKTKRDTKELASMLR------DIGFKAGAIHG 270

Query: 159 -VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTG 217
            ++Q +++++++ F+  +   LIAT V   G+D+ +++ VI +   ++P   + R+GRTG
Sbjct: 271 DLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTG 330

Query: 218 RK-RNGRCVILLTQGREAHNFQTSMQTCKSYVEKI 251
           R  + G+  I +   RE    +   +  K  ++K+
Sbjct: 331 RAGKKGKA-ISIINRREYKKLRYIERAMKLKIKKL 364

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score = 61.4 bits (150), Expect = 1e-10
 Identities = 38/140 (27%), Positives = 54/140 (38%), Gaps = 19/140 (13%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQS-- 156
           K  +L EIL           +    I+F   +     +   L   E       F   S  
Sbjct: 288 KRSKLIEILSE---------QADGTIVFVETKRGADFLASFLSEKE-------FPTTSIH 331

Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRT 216
               Q ++++ ++ F+ G    LIATSV   GLDI  I  VI +D        V R+GRT
Sbjct: 332 GDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRT 391

Query: 217 GRKRN-GRCVILLTQGREAH 235
           GR  N GR        ++  
Sbjct: 392 GRVGNNGRATSFFDPEKDRA 411

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 60.9 bits (147), Expect = 3e-10
 Identities = 32/203 (15%), Positives = 77/203 (37%), Gaps = 19/203 (9%)

Query: 34  SLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDINIMSSEY 93
                  + +   L + Y   ++VS   G+      ++  +++L   +   +    ++ +
Sbjct: 427 GFPKRELHTIKLPLPTQYQTAIKVSGIMGA--RKSAEDRARDMLYPERIYQEFEGDNATW 484

Query: 94  AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFV 153
                +   L   L SH         + KV++         ++  VL+  E + +A++F 
Sbjct: 485 WNFDPRVEWLMGYLTSH--------RSQKVLVICAKAATALQLEQVLREREGI-RAAVFH 535

Query: 154 GQSSGVTQQEQKEIMKKFRAGE--FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQ 211
               G++  E+      F   +     L+ + +G EG +      ++ FD   +P  + Q
Sbjct: 536 E---GMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQ 592

Query: 212 RLGRT---GRKRNGRCVILLTQG 231
           R+GR    G+  + +  +   + 
Sbjct: 593 RIGRLDRIGQAHDIQIHVPYLEK 615

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score = 60.3 bits (147), Expect = 3e-10
 Identities = 25/105 (23%), Positives = 49/105 (46%), Gaps = 13/105 (12%)

Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
            + +IF + R   + +         + K    V   SG +  +++  ++++FR G+   L
Sbjct: 267 AQAMIFCHTRKTASWLA------AELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 320

Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKM------VQRLGRTGR 218
           + T+V   G+D+ ++ +VI FD              + R+GRTGR
Sbjct: 321 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGR 365

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score = 59.6 bits (145), Expect = 6e-10
 Identities = 25/105 (23%), Positives = 49/105 (46%), Gaps = 13/105 (12%)

Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
            + +IF + R   + +         + K    V   SG +  +++  ++++FR G+   L
Sbjct: 334 AQAMIFCHTRKTASWLA------AELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVL 387

Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKM------VQRLGRTGR 218
           + T+V   G+D+ ++ +VI FD              + R+GRTGR
Sbjct: 388 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGR 432

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score = 59.1 bits (144), Expect = 7e-10
 Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 13/105 (12%)

Query: 121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAGEFNTL 179
              IIF   +     +         +      V    G +  QE+  ++  FR G    L
Sbjct: 244 GSSIIFVATKKTANVL------YGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVL 297

Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIKM------VQRLGRTGR 218
           I T+V   G+DI  + +V+ +D              + R+GRTGR
Sbjct: 298 ITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGR 342

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score = 55.3 bits (134), Expect = 2e-09
 Identities = 21/59 (35%), Positives = 32/59 (54%)

Query: 160 TQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
            Q ++ E +K+   G  N L+AT V   G+DI ++  V  FD  +S    + R+GRT R
Sbjct: 65  VQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTAR 123

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

 Score = 56.3 bits (136), Expect = 7e-09
 Identities = 31/138 (22%), Positives = 50/138 (36%), Gaps = 29/138 (21%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K + L EI                ++IFA       E+++ LK              + G
Sbjct: 243 KLVELLEIFRD------------GILIFAQTEEEGKELYEYLK----------RFKFNVG 280

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEE----GLDIGE-IDLVICFDA--QKSPIKMVQ 211
            T  E ++  + F+ G+ N LI           G+D+ E I  VI +           +Q
Sbjct: 281 ETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQ 340

Query: 212 RLGRTGRKRNGRCVILLT 229
             GR+ R  NG  V  ++
Sbjct: 341 ASGRSSRILNGVLVKGVS 358

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

 Score = 55.2 bits (134), Expect = 1e-08
 Identities = 33/116 (28%), Positives = 52/116 (44%), Gaps = 12/116 (10%)

Query: 116 EKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG-VTQQEQKEIMKKFRAG 174
            + +   VI+F   R  VA++  +      +           G + Q  +   +  FR G
Sbjct: 216 RENKDKGVIVFVRTRNRVAKLVRLFDNAIEL----------RGDLPQSVRNRNIDAFREG 265

Query: 175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRK-RNGRCVILLT 229
           E++ LI T V   GLDI  ++ VI FDA +     + R+GRTGR  R G  +  + 
Sbjct: 266 EYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL 321

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

 Score = 51.4 bits (122), Expect = 3e-07
 Identities = 45/280 (16%), Positives = 84/280 (30%), Gaps = 72/280 (25%)

Query: 13  QFPHINRD-LDRMIQRDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCP-----I 66
            + H+N D L  +I+          S+L  L     R  ++ L  V       P     +
Sbjct: 346 NWKHVNCDKLTTIIE----------SSLNVLEPAEYRKMFDRLS-VFPPSAHIPTILLSL 394

Query: 67  L---GKDNDLQNLLQQLKPKLDINIMSSEYAWS-HLKFIRLREILESHFRLHAEKGETTK 122
           +      +D+  ++ +L     +     E   S    ++ L+  LE+ + LH       +
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALH-------R 447

Query: 123 VIIFANYRVVVA-EIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIA 181
            I+  +Y +    +  D++ P       S  +G      +  ++          F  +  
Sbjct: 448 SIV-DHYNIPKTFDSDDLIPPYLDQYFYS-HIGHHLKNIEHPER-------MTLFRMVF- 497

Query: 182 TSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSM 241
                  LD         F        + Q++       N    IL T           +
Sbjct: 498 -------LDFR-------F--------LEQKIRHDSTAWNASGSILNT-----------L 524

Query: 242 QTCKSYVEKIINNKSIYANLAKNGPRMIPAHVTPRIKCLH 281
           Q  K Y   I +N   Y  L       +P      I   +
Sbjct: 525 QQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKY 564

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

 Score = 44.1 bits (103), Expect = 6e-05
 Identities = 57/361 (15%), Positives = 113/361 (31%), Gaps = 85/361 (23%)

Query: 6   KYVKSKAQFPHINRDLDRMIQRDFHVTHSLASALENLVTY----GLRSFYNNLVEVSKED 61
           K + SK +  HI    D  +     +  +L S  E +V       LR  Y  L+   K +
Sbjct: 43  KSILSKEEIDHIIMSKDA-VSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTE 101

Query: 62  GSCPILGKD------NDLQNLLQQLKPKLDINIMSSEYAWSHLKFIRLREILESHFRLHA 115
              P +         + L N  Q    K +++ +          +++LR+ L     L  
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVF-AKYNVSRLQ--------PYLKLRQALL---ELRP 149

Query: 116 EK----------GETTKVI-IFANYRVVVA---EIF-----------DVLKPLEPM---V 147
            K          G+T   + +  +Y+V      +IF            VL+ L+ +   +
Sbjct: 150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209

Query: 148 KASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPI 207
             +           + +   ++     E   L+ +   E  L +  +  V      ++  
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQA----ELRRLLKSKPYENCLLV--LLNV------QNA- 256

Query: 208 KMVQRLGRTGRKRNGRCVILL-TQGREAHNFQTSMQTCKSYVEKII------NNKSIYAN 260
           K            N  C ILL T+ ++  +F ++  T    ++           KS+   
Sbjct: 257 KAWNAF-------NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK 309

Query: 261 LAKNGPRMIPAHVTPRIKCLHI-----VVKDRVTPAKPSKKKPKEN-EKANKKSKKKLET 314
                P+ +P           +      ++D +      K    +      + S   LE 
Sbjct: 310 YLDCRPQDLP-REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP 368

Query: 315 D 315
            
Sbjct: 369 A 369

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B* Length = 661

 Score = 46.8 bits (112), Expect = 8e-06
 Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 6/70 (8%)

Query: 163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTG 217
           E+ EI++  R G+++ L+  ++  EGLDI E+ LV   DA K     S   ++Q +GR  
Sbjct: 483 ERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAA 542

Query: 218 RKRNGRCVIL 227
           R   GR VI+
Sbjct: 543 RNAEGR-VIM 551

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A* Length = 664

 Score = 46.4 bits (111), Expect = 1e-05
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 6/70 (8%)

Query: 163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTG 217
           +++ +++  R G ++ L+  ++  EGLDI E+ LV   DA K     S   ++Q +GR  
Sbjct: 477 KRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAA 536

Query: 218 RKRNGRCVIL 227
           R   G  V L
Sbjct: 537 RNARGE-VWL 545

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

 Score = 46.2 bits (109), Expect = 1e-05
 Identities = 22/108 (20%), Positives = 30/108 (27%), Gaps = 29/108 (26%)

Query: 157 SGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI--------CFDAQKSPIK 208
            G+       I           ++AT     G      D VI          D    P  
Sbjct: 428 RGLDVSVIPTIGDVV-------VVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTF 479

Query: 209 MV-------------QRLGRTGRKRNGRCVILLTQGREAHNFQTSMQT 243
            +             QR GRTGR R G    +    R +  F +S+  
Sbjct: 480 TIETTTVPQDAVSRSQRRGRTGRGRRGIYRFVTPGERPSGMFDSSVLC 527

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 43.0 bits (100), Expect = 1e-04
 Identities = 25/135 (18%), Positives = 48/135 (35%), Gaps = 9/135 (6%)

Query: 89  MSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVK 148
              E         R + I +   +L  +        +   +      IFD++K     V 
Sbjct: 319 YQEEIKIITGLSKRNKWIAKLAIKLAQKDE---NAFVMFKHVSHGKAIFDLIKNEYDKV- 374

Query: 149 ASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIAT-SVGEEGLDIGEIDLVICFDAQKSPI 207
              +V  S  V  + +  +      G+   ++A+  V   G+ +  +  V+     KS I
Sbjct: 375 --YYV--SGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSKI 430

Query: 208 KMVQRLGRTGRKRNG 222
            ++Q +GR  RK   
Sbjct: 431 IVLQTIGRVLRKHGS 445

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus} Length = 590

 Score = 41.7 bits (98), Expect = 4e-04
 Identities = 21/123 (17%), Positives = 40/123 (32%), Gaps = 13/123 (10%)

Query: 102 RLREILESHFRLHAEKGETTKVIIF------ANYRVVVAEIFDVLKPLEPMVKASMFVGQ 155
           R     +             K I+F      A+    +    + L   +   K   +V +
Sbjct: 421 RTDAFAKHLTDFMKRTDRFAKTIVFCVDQEHADE---MRRALNNLNS-DLSRKHPDYVAR 476

Query: 156 SSGVTQQEQKEIMKKFRAGEFNTL-IATSVG--EEGLDIGEIDLVICFDAQKSPIKMVQR 212
            +    +  K  + +F+  E +T  I T+      G+D      V+      S  +  Q 
Sbjct: 477 VTSEEGKIGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQI 536

Query: 213 LGR 215
           +GR
Sbjct: 537 VGR 539

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

 Score = 40.7 bits (95), Expect = 7e-04
 Identities = 14/79 (17%), Positives = 20/79 (25%), Gaps = 21/79 (26%)

Query: 180 IATSVGEEGLDIGEIDLVICFDAQKSPIK--------------------MVQRLGRTGRK 219
           + T + E G +      VI       P+                       QR GR GR 
Sbjct: 406 VTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRN 464

Query: 220 RNGRCVILLTQGREAHNFQ 238
                   +  G    N +
Sbjct: 465 PAQEDDQYVFSGDPLKNDE 483

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	395
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.96
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.96
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.95
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.94
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.94
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.93
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.93
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.93
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.93
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.93
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.92
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.91
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.91
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.91
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.91
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.91
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.84
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.9
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.9
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.9
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.89
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.89
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.88
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.88
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.88
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.88
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.87
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.87
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.87
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.87
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.86
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.86
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.86
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.86
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.85
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.84
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.84
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.82
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.81
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.8
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.79
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.79
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.79
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.78
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.78
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.77
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.77
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.76
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.76
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.75
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.75
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.75
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.73
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.73
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.72
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.72
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.72
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.71
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.71
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.7
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.7
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.7
3h1t_A	590	Type I site-specific restriction-modification syst	99.69
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.69
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.68
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.66
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.66
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.53
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.46
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.31
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.44
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.43
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.15
1e52_A	63	Excinuclease ABC subunit; DNA excision repair, UVR	98.1
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	97.55
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	96.55
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	95.98
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	93.84
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	93.24
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	93.11
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	92.97
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	90.87
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	90.12
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	90.11
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	89.88
3bor_A	237	Human initiation factor 4A-II; translation initiat	89.72
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	88.41
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	88.03
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	87.8
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	86.6
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	86.43
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	86.2
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	85.47
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	84.57
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	83.43
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	83.22
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	82.12
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	80.64

>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=99.96  E-value=8.9e-29  Score=263.45  Aligned_cols=221  Identities=16%  Similarity=0.228  Sum_probs=124.6

Q ss_pred             ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCc
Q psy4150          97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus        97 ~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      ..+...|...|......      +.++||||+|+..++.|++.|.+.|  +++.++||   ++++.+|..++++|+.|++
T Consensus       422 ~~~~~~Ll~~l~~~~~~------~~~vlVf~~t~~~ae~L~~~L~~~g--i~~~~lh~---~~~~~~R~~~~~~f~~g~~  490 (664)
T 1c4o_A          422 ENQILDLMEGIRERAAR------GERTLVTVLTVRMAEELTSFLVEHG--IRARYLHH---ELDAFKRQALIRDLRLGHY  490 (664)
T ss_dssp             TTHHHHHHHHHHHHHHT------TCEEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TCCHHHHHHHHHHHHTTSC
T ss_pred             cchHHHHHHHHHHHHhc------CCEEEEEECCHHHHHHHHHHHHhcC--CCceeecC---CCCHHHHHHHHHHhhcCCc
Confidence            34666666666554432      5799999999999999999999998  89999999   9999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEcCC-----CCChhhHhhhccccccccCceEEEEEeCCchhhHHHHHHHHhHHHHHHH
Q psy4150         177 NTLIATSVGEEGLDIGEIDLVICFDA-----QKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKI  251 (395)
Q Consensus       177 ~vLVaT~v~~~GlDip~v~~VI~~d~-----p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~  251 (395)
                      +|||||+++++|+|+|+|++||++|.     |++..+|+||+|||||.+.|.+++++...+....      .........
T Consensus       491 ~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~~G~~i~~~~~~~~~~~------~~i~~~~~~  564 (664)
T 1c4o_A          491 DCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQ------RAIEETNRR  564 (664)
T ss_dssp             SEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHH------HHHHHHHHH
T ss_pred             eEEEccChhhcCccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCCCCEEEEEEcCCCHHHH------HHHHHHHHH
Confidence            99999999999999999999999998     8999999999999999999999988876544322      112222222


Q ss_pred             HcccchhhhhcccCCCCCCCCcchhhhhhcccccccCCCCCCCCCCchhhHHhhhcchhhhccCCCCCcccccccchhhh
Q psy4150         252 INNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKK  331 (395)
Q Consensus       252 i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~  331 (395)
                      ......++..+...|..+...+...+.    .  ...  . . .    .  -....+.+++.              ..+.
T Consensus       565 r~~~~~~~~~~~~~p~~~~~~i~~~~~----~--~~~--~-~-~----~--~~~~~~~~~~~--------------~~i~  614 (664)
T 1c4o_A          565 RALQEAYNLEHGITPETVRKEVRAVIR----P--EGY--E-E-A----P--LEADLSGEDLR--------------ERIA  614 (664)
T ss_dssp             HHHHHHHHHHHTCCCCCC--------------------------------------------------------------
T ss_pred             HHHHHHHHHhcCCCCcchhHHHHHHhh----h--hhc--c-h-h----h--hhhhcCHHHHH--------------HHHH
Confidence            222334444555566666555544332    0  000  0 0 0    0  01122334444              6899


Q ss_pred             hhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhc
Q psy4150         332 TKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSS  366 (395)
Q Consensus       332 ~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~  366 (395)
                      +++++|.+||++|+  ||.||++||+|..|++++.
T Consensus       615 ~l~~~m~~aa~~l~--fe~Aa~lRd~i~~l~~~~~  647 (664)
T 1c4o_A          615 ELELAMWQAAEALD--FERAARLRDEIRALEARLQ  647 (664)
T ss_dssp             -----------------------------------
T ss_pred             HHHHHHHHHHHhcC--hHHHHHHHHHHHHHHHHHH
Confidence            99999999999999  9999999999999998863

>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=99.96  E-value=1.6e-28  Score=261.30  Aligned_cols=228  Identities=18%  Similarity=0.338  Sum_probs=156.0

Q ss_pred             ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCc
Q psy4150          97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus        97 ~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      ..+...|...|.....      .+.++||||+|+..++.|++.|.+.|  +++.++||   ++++.+|..++++|+.|++
T Consensus       428 ~~~~~~Ll~~l~~~~~------~~~~vlVf~~t~~~ae~L~~~L~~~g--i~~~~lh~---~~~~~~R~~~l~~f~~g~~  496 (661)
T 2d7d_A          428 EGQIDDLIGEIQARIE------RNERVLVTTLTKKMSEDLTDYLKEIG--IKVNYLHS---EIKTLERIEIIRDLRLGKY  496 (661)
T ss_dssp             TTHHHHHHHHHHHHHT------TTCEEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TCCHHHHHHHHHHHHHTSC
T ss_pred             cchHHHHHHHHHHHHh------cCCeEEEEECCHHHHHHHHHHHHhcC--CCeEEEeC---CCCHHHHHHHHHHHhcCCe
Confidence            3456666665555432      35799999999999999999999998  89999999   9999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEcCC-----CCChhhHhhhccccccccCceEEEEEeCCchhhHHHHHHHHhHHHHHHH
Q psy4150         177 NTLIATSVGEEGLDIGEIDLVICFDA-----QKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKI  251 (395)
Q Consensus       177 ~vLVaT~v~~~GlDip~v~~VI~~d~-----p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~  251 (395)
                      +|||||+++++|+|+|+|++||++|.     |.+..+|+||+|||||.+.|.+++++++.+.....      ....+...
T Consensus       497 ~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~~~G~~i~~~~~~~~~~~~------~i~~~~~~  570 (661)
T 2d7d_A          497 DVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEI------AINETKRR  570 (661)
T ss_dssp             SEEEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTSTTCEEEEECSSCCHHHHH------HHHHHHHH
T ss_pred             EEEEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCCCCCEEEEEEeCCCHHHHH------HHHHHHHH
Confidence            99999999999999999999999998     99999999999999999899999888776543221      11222222


Q ss_pred             HcccchhhhhcccCCCCCCCCcchhhhhhcccccccCCCCCCCCCCchhhHHhhhcchhhhccCCCCCcccccccchhhh
Q psy4150         252 INNKSIYANLAKNGPRMIPAHVTPRIKCLHIVVKDRVTPAKPSKKKPKENEKANKKSKKKLETDGNSEPAGKQNKTNAKK  331 (395)
Q Consensus       252 i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~  331 (395)
                      ......++..+...|..+...+...+.. ...    . ... ..............+++++.              +.+.
T Consensus       571 r~i~~~~~~~~~~~p~~~~~~i~~~~~~-~~~----~-~~~-~~~~~~~~~~~~~~~~~~~~--------------~~i~  629 (661)
T 2d7d_A          571 REQQERFNEEHGITPKTINKEIRDVIRA-TVA----A-EDK-AEYKTKAAPKLSKMTKKERQ--------------KVVE  629 (661)
T ss_dssp             HHHHHHHHHHHTCCCCCCCC--------------------------------------HHHH--------------HHHH
T ss_pred             HHHHHHhhhhcCCCCCchhhHHHHHHhh-ccc----c-ccc-cccchhhhhhhhhCCHHHHH--------------HHHH
Confidence            2222334444566666666665544320 000    0 000 00000000011123444444              7899


Q ss_pred             hhccchhhhhHHHHHHHHhhhhchhhHHHHHhh
Q psy4150         332 TKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQ  364 (395)
Q Consensus       332 ~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~  364 (395)
                      +++++|.+||++|+  ||.||++||+|..|+++
T Consensus       630 ~l~~~m~~aa~~~~--fe~Aa~~Rd~i~~l~~~  660 (661)
T 2d7d_A          630 QMEHEMKEAAKALD--FERAAELRDLLLELKAE  660 (661)
T ss_dssp             HHHHHHHHHHHTTC--HHHHHHHHHHC------
T ss_pred             HHHHHHHHHHHccC--HHHHHHHHHHHHHHHhc
Confidence            99999999999999  99999999999999753

>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=99.95  E-value=1.3e-27  Score=242.27  Aligned_cols=193  Identities=21%  Similarity=0.247  Sum_probs=151.2

Q ss_pred             HHHHHHHhcchHHHHHHHHhC----CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceee--eccc
Q psy4150          25 IQRDFHVTHSLASALENLVTY----GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEY--AWSH   97 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~----g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~--~~~~   97 (395)
                      .|+|.++++||...+..+..+    ..++++.||||++.... .+..++.++.+..+... ..  ....+.+.+  ....
T Consensus       210 DEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~-~~--~~~~i~~~~~~~~~~  286 (434)
T 2db3_A          210 DEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIV-GG--ACSDVKQTIYEVNKY  286 (434)
T ss_dssp             ETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESST-TC--CCTTEEEEEEECCGG
T ss_pred             ccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccc-cc--cccccceEEEEeCcH
Confidence            399999999999998888764    46789999999987652 22233333322111000 00  001122222  3345


Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .|...|.++|...         ..++||||+|+..|+.+++.|.+.+  +.+..+||   ++++.+|..++++|++|+++
T Consensus       287 ~k~~~l~~~l~~~---------~~~~lVF~~t~~~a~~l~~~L~~~~--~~~~~lhg---~~~~~~R~~~l~~F~~g~~~  352 (434)
T 2db3_A          287 AKRSKLIEILSEQ---------ADGTIVFVETKRGADFLASFLSEKE--FPTTSIHG---DRLQSQREQALRDFKNGSMK  352 (434)
T ss_dssp             GHHHHHHHHHHHC---------CTTEEEECSSHHHHHHHHHHHHHTT--CCEEEEST---TSCHHHHHHHHHHHHTSSCS
T ss_pred             HHHHHHHHHHHhC---------CCCEEEEEeCcHHHHHHHHHHHhCC--CCEEEEeC---CCCHHHHHHHHHHHHcCCCc
Confidence            6888888777652         2459999999999999999999998  99999999   99999999999999999999


Q ss_pred             EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         178 TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       178 vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      |||||+++++|||+|+|++||+||+|++..+|+||+|||||.| .|.+++|+++.++.
T Consensus       353 vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~  410 (434)
T 2db3_A          353 VLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDR  410 (434)
T ss_dssp             EEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCG
T ss_pred             EEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccH
Confidence            9999999999999999999999999999999999999999997 68888888765544

>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=99.94  E-value=2.7e-26  Score=204.22  Aligned_cols=125  Identities=20%  Similarity=0.315  Sum_probs=114.3

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ....|+..|.++|...        .+.++||||+++..++.+++.|...+  +.+..+||   +|++.+|..+++.|++|
T Consensus        14 ~~~~K~~~L~~ll~~~--------~~~~~lVF~~~~~~~~~l~~~L~~~~--~~~~~~hg---~~~~~~r~~~~~~f~~g   80 (172)
T 1t5i_A           14 KDNEKNRKLFDLLDVL--------EFNQVVIFVKSVQRCIALAQLLVEQN--FPAIAIHR---GMPQEERLSRYQQFKDF   80 (172)
T ss_dssp             CGGGHHHHHHHHHHHS--------CCSSEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHTT
T ss_pred             ChHHHHHHHHHHHHhC--------CCCcEEEEECCHHHHHHHHHHHHhcC--CCEEEEEC---CCCHHHHHHHHHHHHCC
Confidence            3567999988888752        45799999999999999999999988  89999999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      +++|||||+++++|+|+|++++||+||+|+++..|+||+||+||.| .|.+++++++.+
T Consensus        81 ~~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~  139 (172)
T 1t5i_A           81 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  139 (172)
T ss_dssp             SCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHH
T ss_pred             CCcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChh
Confidence            9999999999999999999999999999999999999999999997 677777776543

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

Probab=99.94  E-value=1.1e-25  Score=198.25  Aligned_cols=124  Identities=31%  Similarity=0.527  Sum_probs=113.5

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ..+.|+..|.++|...        .+.++||||+++..++.+++.|...+  +.+..+||   +|++.+|..+++.|++|
T Consensus        18 ~~~~K~~~L~~ll~~~--------~~~~~lVF~~~~~~~~~l~~~L~~~~--~~~~~~hg---~~~~~~r~~~~~~f~~g   84 (163)
T 2hjv_A           18 REENKFSLLKDVLMTE--------NPDSCIIFCRTKEHVNQLTDELDDLG--YPCDKIHG---GMIQEDRFDVMNEFKRG   84 (163)
T ss_dssp             CGGGHHHHHHHHHHHH--------CCSSEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHTT
T ss_pred             ChHHHHHHHHHHHHhc--------CCCcEEEEECCHHHHHHHHHHHHHcC--CcEEEEeC---CCCHHHHHHHHHHHHcC
Confidence            3567999999888763        35799999999999999999999988  89999999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      +++|||||+++++|+|+|++++||+||+|+++..|+||+||+||.| .|.++++++..
T Consensus        85 ~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~  142 (163)
T 2hjv_A           85 EYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAF  142 (163)
T ss_dssp             SCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGG
T ss_pred             CCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHH
Confidence            9999999999999999999999999999999999999999999997 67777777643

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

Probab=99.93  E-value=2.1e-25  Score=196.73  Aligned_cols=124  Identities=30%  Similarity=0.475  Sum_probs=110.4

Q ss_pred             ccc-HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          96 SHL-KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        96 ~~~-K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ... |+..|.+++..+        .+.++||||+++..++.++..|...+  +.+..+||   +|++.+|..+++.|++|
T Consensus        13 ~~~~K~~~l~~ll~~~--------~~~~~lVF~~~~~~~~~l~~~L~~~~--~~~~~~~~---~~~~~~r~~~~~~f~~g   79 (165)
T 1fuk_A           13 EEEYKYECLTDLYDSI--------SVTQAVIFCNTRRKVEELTTKLRNDK--FTVSAIYS---DLPQQERDTIMKEFRSG   79 (165)
T ss_dssp             SGGGHHHHHHHHHHHT--------TCSCEEEEESSHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHTT
T ss_pred             cchhHHHHHHHHHHhC--------CCCCEEEEECCHHHHHHHHHHHHHcC--CCEEEEEC---CCCHHHHHHHHHHHHcC
Confidence            344 999988888763        35899999999999999999999988  89999999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      +++|||||+++++|+|+|++++||+||+|+++..|+||+||+||.| .|.+++++++.+
T Consensus        80 ~~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~  138 (165)
T 1fuk_A           80 SSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNED  138 (165)
T ss_dssp             SCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTT
T ss_pred             CCEEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchH
Confidence            9999999999999999999999999999999999999999999996 688888877554

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

Probab=99.93  E-value=8.5e-26  Score=204.66  Aligned_cols=126  Identities=30%  Similarity=0.454  Sum_probs=112.3

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ....|+..|.++|..         .+.++||||+++..++.+++.|...+  +.+..+||   +|++.+|..+++.|++|
T Consensus        38 ~~~~K~~~L~~~l~~---------~~~~~lVF~~~~~~~~~l~~~L~~~g--~~~~~lhg---~~~~~~R~~~l~~F~~g  103 (191)
T 2p6n_A           38 KEEAKMVYLLECLQK---------TPPPVLIFAEKKADVDAIHEYLLLKG--VEAVAIHG---GKDQEERTKAIEAFREG  103 (191)
T ss_dssp             CGGGHHHHHHHHHTT---------SCSCEEEECSCHHHHHHHHHHHHHHT--CCEEEECT---TSCHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHh---------CCCCEEEEECCHHHHHHHHHHHHHcC--CcEEEEeC---CCCHHHHHHHHHHHhcC
Confidence            456688888777653         24689999999999999999999988  99999999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      +++|||||+++++|+|+|++++||+||+|+++..|+||+||+||.| .|.+++|++..++.
T Consensus       104 ~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~  164 (191)
T 2p6n_A          104 KKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDE  164 (191)
T ss_dssp             SCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCH
T ss_pred             CCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhH
Confidence            9999999999999999999999999999999999999999999997 78888888766444

>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=99.93  E-value=2.8e-25  Score=197.73  Aligned_cols=131  Identities=24%  Similarity=0.371  Sum_probs=110.2

Q ss_pred             cceeeeccc---cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHH
Q psy4150          89 MSSEYAWSH---LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQK  165 (395)
Q Consensus        89 ~~~~~~~~~---~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~  165 (395)
                      +.+.|....   .|+..|.+++..        ....++||||+++..++.++..|...+  +.+..+||   +|++.+|.
T Consensus         8 i~q~~~~~~~~~~K~~~L~~ll~~--------~~~~~~lVF~~~~~~~~~l~~~L~~~~--~~~~~~~g---~~~~~~R~   74 (175)
T 2rb4_A            8 IRQYYVLCEHRKDKYQALCNIYGS--------ITIGQAIIFCQTRRNAKWLTVEMIQDG--HQVSLLSG---ELTVEQRA   74 (175)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHHTT--------SCCSEEEEECSCHHHHHHHHHHHHTTT--CCEEEECS---SCCHHHHH
T ss_pred             ceEEEEEcCChHhHHHHHHHHHHh--------CCCCCEEEEECCHHHHHHHHHHHHHcC--CcEEEEeC---CCCHHHHH
Confidence            344555433   277777776654        245799999999999999999999998  89999999   99999999


Q ss_pred             HHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCC------CChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         166 EIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQ------KSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       166 ~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p------~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      .+++.|++|.++|||||+++++|+|+|++++||+||+|      .+..+|+||+||+||.| .|.+++++...+
T Consensus        75 ~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~  148 (175)
T 2rb4_A           75 SIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDE  148 (175)
T ss_dssp             HHHHHHHTTSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGG
T ss_pred             HHHHHHHcCCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccch
Confidence            99999999999999999999999999999999999999      89999999999999996 677777776543

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=99.93  E-value=2.3e-25  Score=204.81  Aligned_cols=125  Identities=30%  Similarity=0.448  Sum_probs=114.1

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      .....|+..|.+++...        .+.++||||+++..++.+++.|...+  +.+..+||   +|++.+|..+++.|++
T Consensus        13 ~~~~~k~~~l~~ll~~~--------~~~~~lVF~~~~~~~~~l~~~L~~~~--~~~~~lhg---~~~~~~r~~~~~~f~~   79 (212)
T 3eaq_A           13 APVRGRLEVLSDLLYVA--------SPDRAMVFTRTKAETEEIAQGLLRLG--HPAQALHG---DLSQGERERVLGAFRQ   79 (212)
T ss_dssp             CCTTSHHHHHHHHHHHH--------CCSCEEEECSSHHHHHHHHHHHHHHT--CCEEEECS---SSCHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHHHhC--------CCCeEEEEeCCHHHHHHHHHHHHHcC--CCEEEEEC---CCCHHHHHHHHHHHHC
Confidence            34567999999988753        35799999999999999999999988  89999999   9999999999999999


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         174 GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       174 g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      |.++|||||+++++|||+|+|++||+||+|+++.+|+||+|||||.| .|.++++++..
T Consensus        80 g~~~vlvaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~  138 (212)
T 3eaq_A           80 GEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPR  138 (212)
T ss_dssp             SSCCEEEECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGG
T ss_pred             CCCeEEEecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchh
Confidence            99999999999999999999999999999999999999999999997 77777777653

>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=99.93  E-value=3.5e-25  Score=199.47  Aligned_cols=125  Identities=26%  Similarity=0.394  Sum_probs=100.1

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ....|+..|.++|...       ..+.++||||+++..++.++..|...|  +.+..+||   +|++.+|..+++.|++|
T Consensus        28 ~~~~K~~~L~~ll~~~-------~~~~k~lVF~~~~~~~~~l~~~L~~~g--~~~~~lhg---~~~~~~r~~~~~~f~~g   95 (185)
T 2jgn_A           28 EESDKRSFLLDLLNAT-------GKDSLTLVFVETKKGADSLEDFLYHEG--YACTSIHG---DRSQRDREEALHQFRSG   95 (185)
T ss_dssp             CGGGHHHHHHHHHHHC--------CCSCEEEEESCHHHHHHHHHHHHHTT--CCEEEEC-----------CHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHhc-------CCCCeEEEEECCHHHHHHHHHHHHHcC--CceEEEeC---CCCHHHHHHHHHHHHcC
Confidence            4567999999888763       246899999999999999999999988  89999999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      +++|||||+++++|+|+|++++||+||+|+++.+|+||+||+||.| .|.+++++++.
T Consensus        96 ~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~  153 (185)
T 2jgn_A           96 KSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNER  153 (185)
T ss_dssp             SSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGG
T ss_pred             CCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchh
Confidence            9999999999999999999999999999999999999999999997 67777777653

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

Probab=99.92  E-value=2e-24  Score=208.94  Aligned_cols=126  Identities=30%  Similarity=0.451  Sum_probs=112.2

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      +....|+..|.+++..+        .+.++||||+|+..++.|++.|...+  +.+..+||   +|++.+|..+++.|+.
T Consensus        10 ~~~~~K~~~L~~ll~~~--------~~~~~LVF~~t~~~~~~l~~~L~~~g--~~~~~lhg---~l~~~~r~~~~~~f~~   76 (300)
T 3i32_A           10 APVRGRLEVLSDLLYVA--------SPDRAMVFTRTKAETEEIAQGLLRLG--HPAQALHG---DMSQGERERVMGAFRQ   76 (300)
T ss_dssp             CCSSSHHHHHHHHHHHH--------CCSSEEEECSSHHHHHHHHHHHHTTT--CCEEEECS---CCCTHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhc--------CCCCEEEEECCHHHHHHHHHHHHhCC--CCEEEEeC---CCCHHHHHHHHHHhhc
Confidence            34567999999988764        25899999999999999999999988  99999999   9999999999999999


Q ss_pred             CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         174 GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       174 g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      |.++|||||+++++|||+|+|++||+||+|++..+|+||+|||||.| .|.+++|++..+
T Consensus        77 g~~~vLVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e  136 (300)
T 3i32_A           77 GEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRE  136 (300)
T ss_dssp             TSCCEEEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSST
T ss_pred             CCceEEEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHH
Confidence            99999999999999999999999999999999999999999999997 788888776543

>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=99.91  E-value=2.4e-24  Score=214.85  Aligned_cols=190  Identities=21%  Similarity=0.311  Sum_probs=147.0

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeec---cccH
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAW---SHLK   99 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~---~~~K   99 (395)
                      |+|.+...++...+..+...  ...+.+.+|||++.... ....++.++....+...   ......+.+.+..   ...|
T Consensus       187 Eah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~k  263 (410)
T 2j0s_A          187 EADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRD---ELTLEGIKQFFVAVEREEWK  263 (410)
T ss_dssp             THHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGG---GCSCTTEEEEEEEESSTTHH
T ss_pred             cHHHHHhhhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCc---cccCCCceEEEEEeCcHHhH
Confidence            99999999988887776664  34688999999987542 22333333321111000   0111112222222   2337


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ...|.+++...        ...++||||+++..++.+++.|.+.+  +.+..+||   ++++.+|..+++.|++|+++||
T Consensus       264 ~~~l~~~~~~~--------~~~~~lVf~~~~~~~~~l~~~L~~~~--~~~~~~h~---~~~~~~r~~~~~~f~~g~~~vl  330 (410)
T 2j0s_A          264 FDTLCDLYDTL--------TITQAVIFCNTKRKVDWLTEKMREAN--FTVSSMHG---DMPQKERESIMKEFRSGASRVL  330 (410)
T ss_dssp             HHHHHHHHHHH--------TSSEEEEECSSHHHHHHHHHHHHHTT--CCCEEECT---TSCHHHHHHHHHHHHHTSSCEE
T ss_pred             HHHHHHHHHhc--------CCCcEEEEEcCHHHHHHHHHHHHhCC--CceEEeeC---CCCHHHHHHHHHHHHCCCCCEE
Confidence            88887777654        24699999999999999999999998  89999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      |||+++++|+|+|++++||+||+|+++..|+||+||+||.| .|.+++++++.
T Consensus       331 v~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~  383 (410)
T 2j0s_A          331 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND  383 (410)
T ss_dssp             EECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGG
T ss_pred             EECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHH
Confidence            99999999999999999999999999999999999999997 67777777653

>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=1.2e-24  Score=217.02  Aligned_cols=192  Identities=20%  Similarity=0.261  Sum_probs=144.9

Q ss_pred             HHHHHHhcchHHHHHHHHhC------CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceee--ecc
Q psy4150          26 QRDFHVTHSLASALENLVTY------GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEY--AWS   96 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~------g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~--~~~   96 (395)
                      |+|.+...+|...+..+...      +..+.+.+|||++.... ....++.++.+..+...   ......+.+.+  ...
T Consensus       183 Eah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~i~~~~~~~~~  259 (417)
T 2i4i_A          183 EADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRV---GSTSENITQKVVWVEE  259 (417)
T ss_dssp             SHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC-------CCSSEEEEEEECCG
T ss_pred             ChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCC---CCCccCceEEEEEecc
Confidence            99999999999888887763      24678899999987542 11222222211100000   00001122222  334


Q ss_pred             ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCc
Q psy4150          97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus        97 ~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      ..|...|.+++...       ..+.++||||+++..++.+++.|.+.+  +.+..+||   ++++.+|..+++.|++|++
T Consensus       260 ~~~~~~l~~~l~~~-------~~~~~~lVf~~~~~~~~~l~~~L~~~~--~~~~~~h~---~~~~~~r~~~~~~f~~g~~  327 (417)
T 2i4i_A          260 SDKRSFLLDLLNAT-------GKDSLTLVFVETKKGADSLEDFLYHEG--YACTSIHG---DRSQRDREEALHQFRSGKS  327 (417)
T ss_dssp             GGHHHHHHHHHHTC-------CTTCEEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHHTSS
T ss_pred             HhHHHHHHHHHHhc-------CCCCeEEEEECCHHHHHHHHHHHHHCC--CCeeEecC---CCCHHHHHHHHHHHHcCCC
Confidence            56777777777653       346899999999999999999999988  89999999   9999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         177 NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       177 ~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      +|||||+++++|+|+|++++||+||+|++..+|+||+||+||.| .|.+++++.+.+
T Consensus       328 ~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  384 (417)
T 2i4i_A          328 PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERN  384 (417)
T ss_dssp             CEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGG
T ss_pred             CEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEcccc
Confidence            99999999999999999999999999999999999999999997 577777776433

>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=99.91  E-value=2e-24  Score=224.86  Aligned_cols=200  Identities=18%  Similarity=0.212  Sum_probs=143.3

Q ss_pred             HHHHHHhcchHHHHHHHHhC---------CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccc-cccccceeee
Q psy4150          26 QRDFHVTHSLASALENLVTY---------GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKL-DINIMSSEYA   94 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~---------g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~-~~~~~~~~~~   94 (395)
                      |+|.+++++|...++.|...         ...+.+.+|||++..+. ....++.++....+........ ....+.+.+.
T Consensus       234 Eah~l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  313 (563)
T 3i5x_A          234 EADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVV  313 (563)
T ss_dssp             THHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEE
T ss_pred             CHHHHhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEE
Confidence            99999999998887776543         14578999999987642 2233333321110000000000 0011222222


Q ss_pred             cc---ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC-CCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          95 WS---HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP-MVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        95 ~~---~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~-~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..   ..+...+...+...+..   ...+.++||||+|+..|+.+++.|....+ .+.+..+||   +|++.+|..+++.
T Consensus       314 ~~~~~~~~~~~~~~~l~~~~~~---~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~---~~~~~~R~~~~~~  387 (563)
T 3i5x_A          314 ISEKFANSIFAAVEHIKKQIKE---RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHG---KITQNKRTSLVKR  387 (563)
T ss_dssp             EESSTTHHHHHHHHHHHHHHHH---TTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEEST---TSCHHHHHHHHHH
T ss_pred             ECchhHhhHHHHHHHHHHHHhh---cCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecC---CCCHHHHHHHHHH
Confidence            22   22333333333333322   24568999999999999999999988622 288999999   9999999999999


Q ss_pred             HhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         171 FRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      |++|+++|||||+++++|||+|+|++||+||+|+++.+|+||+|||||.| .|.+++++++.
T Consensus       388 f~~g~~~vLvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~  449 (563)
T 3i5x_A          388 FKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKD  449 (563)
T ss_dssp             HHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGG
T ss_pred             HhcCCCCEEEEcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchh
Confidence            99999999999999999999999999999999999999999999999997 67778777753

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

Probab=99.91  E-value=2.1e-24  Score=226.19  Aligned_cols=200  Identities=18%  Similarity=0.212  Sum_probs=144.0

Q ss_pred             HHHHHHhcchHHHHHHHHhC---------CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccc-cccccceeee
Q psy4150          26 QRDFHVTHSLASALENLVTY---------GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKL-DINIMSSEYA   94 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~---------g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~-~~~~~~~~~~   94 (395)
                      |+|.++.+||...++.|...         ...+++.||||++..+. .+..++.++....+........ ....+.+.+.
T Consensus       183 Eah~l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~  262 (579)
T 3sqw_A          183 EADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVV  262 (579)
T ss_dssp             THHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEE
T ss_pred             ChHHhhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEE
Confidence            99999999999887776553         14578999999987652 2333443332111100000000 0011222222


Q ss_pred             cc---ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC-CCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          95 WS---HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP-MVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        95 ~~---~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~-~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..   ..+...+...+...+..   ...+.++||||+|+..|+.+++.|....+ .+.+..+||   +|++.+|..+++.
T Consensus       263 ~~~~~~~~~~~~~~~l~~~~~~---~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg---~~~~~~R~~~~~~  336 (579)
T 3sqw_A          263 ISEKFANSIFAAVEHIKKQIKE---RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHG---KITQNKRTSLVKR  336 (579)
T ss_dssp             EESSTTHHHHHHHHHHHHHHHH---TTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEEST---TSCHHHHHHHHHH
T ss_pred             EecchhhhHHHHHHHHHHHHhh---cCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecC---CCCHHHHHHHHHH
Confidence            22   22333333333333322   24568999999999999999999988621 288999999   9999999999999


Q ss_pred             HhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         171 FRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       171 Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      |+.|+++|||||+++++|||+|+|++||+||+|+++..|+||+|||||.| .|.+++++++.
T Consensus       337 F~~g~~~vLVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~  398 (579)
T 3sqw_A          337 FKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKD  398 (579)
T ss_dssp             HHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGG
T ss_pred             hhcCCCeEEEEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEccc
Confidence            99999999999999999999999999999999999999999999999997 67777777753

>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=99.91  E-value=5.7e-24  Score=210.14  Aligned_cols=193  Identities=18%  Similarity=0.242  Sum_probs=143.2

Q ss_pred             HHHHHHh-cchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeee--ccccH
Q psy4150          26 QRDFHVT-HSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYA--WSHLK   99 (395)
Q Consensus        26 ead~~~~-~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~--~~~~K   99 (395)
                      |++.+.. .++...+..+...  ...+.+.+|||++.... .+..++.++....+..  ........+.+.+.  ....|
T Consensus       160 EaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~  237 (391)
T 1xti_A          160 ECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDD--ETKLTLHGLQQYYVKLKDNEK  237 (391)
T ss_dssp             SHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCC--CCCCCCTTCEEEEEECCGGGH
T ss_pred             CHHHHhhccchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecC--ccccCcccceEEEEEcCchhH
Confidence            7887766 4666666655543  35678899999987542 1122222221110000  00011111222222  34567


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ...|.+++..        ..+.++||||+++..++.+++.|...+  +.+..+||   ++++.+|..+++.|++|+.+||
T Consensus       238 ~~~l~~~l~~--------~~~~~~lvf~~~~~~~~~l~~~L~~~~--~~~~~~~~---~~~~~~r~~~~~~f~~~~~~vl  304 (391)
T 1xti_A          238 NRKLFDLLDV--------LEFNQVVIFVKSVQRCIALAQLLVEQN--FPAIAIHR---GMPQEERLSRYQQFKDFQRRIL  304 (391)
T ss_dssp             HHHHHHHHHH--------SCCSEEEEECSCHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHTTCCSEE
T ss_pred             HHHHHHHHHh--------cCCCcEEEEeCcHHHHHHHHHHHHhCC--CcEEEEeC---CCCHHHHHHHHHHHhcCCCcEE
Confidence            7777777765        246899999999999999999999998  89999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      |||+++++|+|+|++++||+||+|+++..|+||+||+||.| .|.+++++++.++
T Consensus       305 v~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  359 (391)
T 1xti_A          305 VATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEND  359 (391)
T ss_dssp             EESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHH
T ss_pred             EECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccch
Confidence            99999999999999999999999999999999999999997 6777777765443

>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=99.84  E-value=6.6e-26  Score=201.05  Aligned_cols=122  Identities=29%  Similarity=0.465  Sum_probs=111.0

Q ss_pred             ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCc
Q psy4150          97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus        97 ~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      ..|+..|.+++...        .+.++||||+++..++.+++.|...+  +.+..+||   +|++.+|..+++.|++|++
T Consensus        15 ~~k~~~l~~ll~~~--------~~~~~iVF~~~~~~~~~l~~~L~~~~--~~~~~~~g---~~~~~~r~~~~~~f~~g~~   81 (170)
T 2yjt_D           15 EHKTALLVHLLKQP--------EATRSIVFVRKRERVHELANWLREAG--INNCYLEG---EMVQGKRNEAIKRLTEGRV   81 (170)
Confidence            55888888877652        35799999999999999999999988  89999999   9999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         177 NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       177 ~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      +|||||+++++|+|+|++++||+||+|+++..|+||+||+||.| .|.+++++...
T Consensus        82 ~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~  137 (170)
T 2yjt_D           82 NVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAH  137 (170)
Confidence            99999999999999999999999999999999999999999997 67777776554

>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=4.8e-24  Score=210.22  Aligned_cols=192  Identities=19%  Similarity=0.302  Sum_probs=139.3

Q ss_pred             HHHHHHh-cchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeecc---cc
Q psy4150          26 QRDFHVT-HSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWS---HL   98 (395)
Q Consensus        26 ead~~~~-~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~---~~   98 (395)
                      |++.+.. .++......+...  ...+.+.+|||++.... ....++.++....+...   ......+.+.+...   ..
T Consensus       153 Eah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~  229 (395)
T 3pey_A          153 EADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTN---EVNVDAIKQLYMDCKNEAD  229 (395)
T ss_dssp             THHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGG---GCSCTTEEEEEEECSSHHH
T ss_pred             ChhhhcCccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEcccc---ccccccccEEEEEcCchHH
Confidence            8887777 6777776666554  34678899999886541 11112211111100000   00111122223322   23


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      |...+..++..        ..+.++||||+++..++.+++.|...+  +.+..+||   ++++.+|..+++.|++|+++|
T Consensus       230 ~~~~l~~~~~~--------~~~~~~lvf~~~~~~~~~l~~~l~~~~--~~~~~~~~---~~~~~~r~~~~~~f~~g~~~v  296 (395)
T 3pey_A          230 KFDVLTELYGL--------MTIGSSIIFVATKKTANVLYGKLKSEG--HEVSILHG---DLQTQERDRLIDDFREGRSKV  296 (395)
T ss_dssp             HHHHHHHHHTT--------TTSSEEEEECSCHHHHHHHHHHHHHTT--CCCEEECT---TSCHHHHHHHHHHHHTTSCCE
T ss_pred             HHHHHHHHHHh--------ccCCCEEEEeCCHHHHHHHHHHHHhcC--CcEEEeCC---CCCHHHHHHHHHHHHCCCCCE
Confidence            44444443322        346899999999999999999999998  89999999   999999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCC------ChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQK------SPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~------s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      ||||+++++|+|+|++++||+||+|+      ++.+|+||+||+||.| .|.+++++.+.++
T Consensus       297 lv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~  358 (395)
T 3pey_A          297 LITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNS  358 (395)
T ss_dssp             EEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHH
T ss_pred             EEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHH
Confidence            99999999999999999999999999      9999999999999997 5777777765443

>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=99.90  E-value=3e-24  Score=213.72  Aligned_cols=191  Identities=20%  Similarity=0.292  Sum_probs=131.9

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeee---ccccH
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYA---WSHLK   99 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~---~~~~K   99 (395)
                      |++.+...++...+..+...  ...+.+.+|||++.... ....++.++......   ........+.+.+.   ....|
T Consensus       191 Eah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~  267 (414)
T 3eiq_A          191 EADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK---KEELTLEGIRQFYINVEREEWK  267 (414)
T ss_dssp             SHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCC---CCCCCTTSCCEEEEECSSSTTH
T ss_pred             CHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEec---CCccCCCCceEEEEEeChHHhH
Confidence            88888888888776666554  45678899999876542 122222222111000   00011111222222   23347


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      +..+.+++..        ....++||||+++..++.+++.|...+  +.+..+||   ++++.+|..+++.|++|+++||
T Consensus       268 ~~~l~~~~~~--------~~~~~~lvf~~~~~~~~~l~~~l~~~~--~~~~~~h~---~~~~~~r~~~~~~f~~g~~~vl  334 (414)
T 3eiq_A          268 LDTLCDLYET--------LTITQAVIFINTRRKVDWLTEKMHARD--FTVSAMHG---DMDQKERDVIMREFRSGSSRVL  334 (414)
T ss_dssp             HHHHHHHHHS--------SCCSSCEEECSCHHHHHHHHHHHHTTT--CCCEEC------CHHHHHHHHHHHHSCC---CE
T ss_pred             HHHHHHHHHh--------CCCCcEEEEeCCHHHHHHHHHHHHhcC--CeEEEecC---CCCHHHHHHHHHHHHcCCCcEE
Confidence            7777766654        345799999999999999999999988  89999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      |||+++++|+|+|++++||+||+|++..+|+||+||+||.| .|.+++++++.+
T Consensus       335 v~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  388 (414)
T 3eiq_A          335 ITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEED  388 (414)
T ss_dssp             EECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTH
T ss_pred             EECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHH
Confidence            99999999999999999999999999999999999999997 688888877643

>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=99.90  E-value=8.6e-24  Score=210.04  Aligned_cols=191  Identities=17%  Similarity=0.267  Sum_probs=140.2

Q ss_pred             HHHHHHh-cchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeecc---cc
Q psy4150          26 QRDFHVT-HSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWS---HL   98 (395)
Q Consensus        26 ead~~~~-~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~---~~   98 (395)
                      |++.+.. .++......+...  ...+.+.+|||++.... .....+.++....+.....   ....+.+.+...   ..
T Consensus       176 Eah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~  252 (412)
T 3fht_A          176 EADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE---TLDTIKQYYVLCSSRDE  252 (412)
T ss_dssp             THHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGS---SCTTEEEEEEECSSHHH
T ss_pred             CHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccc---cccCceEEEEEcCChHH
Confidence            8888776 6777666666554  34678899999987541 1122222222111111000   011122333322   34


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      |...|.+++...        ...++||||+++..++.+++.|...+  +.+..+||   +|++.+|..+++.|++|+++|
T Consensus       253 ~~~~l~~~~~~~--------~~~~~lvf~~~~~~~~~l~~~L~~~~--~~~~~~~~---~~~~~~r~~~~~~f~~g~~~v  319 (412)
T 3fht_A          253 KFQALCNLYGAI--------TIAQAMIFCHTRKTASWLAAELSKEG--HQVALLSG---EMMVEQRAAVIERFREGKEKV  319 (412)
T ss_dssp             HHHHHHHHHHHH--------SSSEEEEECSSHHHHHHHHHHHHHTT--CCCEEECT---TSCHHHHHHHHHHHHTTSCSE
T ss_pred             HHHHHHHHHhhc--------CCCCEEEEeCCHHHHHHHHHHHHhCC--CeEEEecC---CCCHHHHHHHHHHHHCCCCcE
Confidence            666666655542        35799999999999999999999998  89999999   999999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCC------ChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQK------SPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~------s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      ||||+++++|+|+|++++||+||+|+      +..+|+||+||+||.| .|.+++++...+
T Consensus       320 lv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  380 (412)
T 3fht_A          320 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  380 (412)
T ss_dssp             EEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             EEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChh
Confidence            99999999999999999999999995      6689999999999997 567777765533

>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=99.89  E-value=2.8e-23  Score=206.17  Aligned_cols=190  Identities=19%  Similarity=0.270  Sum_probs=143.3

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceee--eccccHH
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEY--AWSHLKF  100 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~--~~~~~K~  100 (395)
                      |++.+...++...+..+...  ...+.+.++||++.... .....+..+....+.    .......+.+.+  .....|.
T Consensus       171 EaH~~~~~~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~k~  246 (400)
T 1s2m_A          171 EADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM----EELTLKGITQYYAFVEERQKL  246 (400)
T ss_dssp             SHHHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCC----SSCBCTTEEEEEEECCGGGHH
T ss_pred             CchHhhhhchHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEec----cccccCCceeEEEEechhhHH
Confidence            88888877777777777664  34678889999876541 111111111100000    001111122222  2345677


Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEE
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI  180 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLV  180 (395)
                      ..+..++..        ....++||||+++..++.+++.|...+  +.+..+||   ++++.+|..+++.|++|+++|||
T Consensus       247 ~~l~~~~~~--------~~~~~~lVf~~~~~~~~~l~~~L~~~~--~~~~~~~~---~~~~~~r~~~~~~f~~g~~~vLv  313 (400)
T 1s2m_A          247 HCLNTLFSK--------LQINQAIIFCNSTNRVELLAKKITDLG--YSCYYSHA---RMKQQERNKVFHEFRQGKVRTLV  313 (400)
T ss_dssp             HHHHHHHHH--------SCCSEEEEECSSHHHHHHHHHHHHHHT--CCEEEECT---TSCHHHHHHHHHHHHTTSSSEEE
T ss_pred             HHHHHHHhh--------cCCCcEEEEEecHHHHHHHHHHHHhcC--CCeEEecC---CCCHHHHHHHHHHHhcCCCcEEE
Confidence            777776654        345799999999999999999999988  89999999   99999999999999999999999


Q ss_pred             EcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         181 ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       181 aT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      ||+++++|+|+|++++||+||+|+++.+|+||+||+||.| .|.+++++...+
T Consensus       314 ~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~  366 (400)
T 1s2m_A          314 CSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWND  366 (400)
T ss_dssp             ESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGG
T ss_pred             EcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccch
Confidence            9999999999999999999999999999999999999997 677777776543

>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=99.89  E-value=3.5e-23  Score=213.77  Aligned_cols=136  Identities=28%  Similarity=0.524  Sum_probs=80.4

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEecc-----CCCCCHHHHHHHH
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQ-----SSGVTQQEQKEIM  168 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~-----~~~~~~~~R~~~l  168 (395)
                      .++|+..|.++|.+++..    ..+.++||||+++.+++.|++.|....  +.+++..+||+     |++|++.+|..++
T Consensus       370 ~~~K~~~L~~~l~~~~~~----~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~  445 (556)
T 4a2p_A          370 ENPKLEELVCILDDAYRY----NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVL  445 (556)
T ss_dssp             CCHHHHHHHHHHHHHHHH----CTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC----------------------
T ss_pred             CChHHHHHHHHHHHHhcC----CCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHH
Confidence            478999999999887754    457899999999999999999998861  12566666653     3389999999999


Q ss_pred             HHHhc-CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchhhH
Q psy4150         169 KKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHN  236 (395)
Q Consensus       169 ~~Fk~-g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~  236 (395)
                      ++|++ |+++|||||+++++|||+|+|++||+||+|+|+..|+||+|| ||.+.|.++++++.++..+.
T Consensus       446 ~~F~~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~~~g~~~~l~~~~~~~~~  513 (556)
T 4a2p_A          446 DAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSKCILVTSKTEVVEN  513 (556)
T ss_dssp             --------CCEEEEEC-----------CEEEEETCCSCHHHHHHC---------CCEEEEESCHHHHHH
T ss_pred             HHhcccCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCCCCceEEEEEeCcchHHH
Confidence            99999 999999999999999999999999999999999999999999 99999999999888766554

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.88  E-value=5.4e-23  Score=206.58  Aligned_cols=141  Identities=43%  Similarity=0.711  Sum_probs=124.6

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccC-----CCCCHHHHHHHHH
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQS-----SGVTQQEQKEIMK  169 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~-----~~~~~~~R~~~l~  169 (395)
                      ..++|+..|.++|..++..    ..+.++||||+++..++.+++.|...|  +.+..+||+.     +++++.+|.++++
T Consensus       340 ~~~~k~~~l~~~l~~~~~~----~~~~k~lVF~~~~~~~~~l~~~L~~~~--~~~~~~~g~~~~~~~~~~~~~~r~~~~~  413 (494)
T 1wp9_A          340 LDHPKMDKLKEIIREQLQR----KQNSKIIVFTNYRETAKKIVNELVKDG--IKAKRFVGQASKENDRGLSQREQKLILD  413 (494)
T ss_dssp             CSCHHHHHHHHHHHHHHHH----CTTCCEEEECSCHHHHHHHHHHHHHTT--CCEEEECCSSCC-------CCHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHhcc----CCCCeEEEEEccHHHHHHHHHHHHHcC--CCcEEEeccccccccccCCHHHHHHHHH
Confidence            4678999999999987653    457899999999999999999999998  8999999943     2789999999999


Q ss_pred             HHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchhhHHHHHH
Q psy4150         170 KFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       170 ~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~  241 (395)
                      .|++|+++|||||+++++|||+|++++||+||+||++..|+||+||+||.|+|.++.+++.++.++.+....
T Consensus       414 ~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~g~~~~l~~~~t~ee~~~~~~  485 (494)
T 1wp9_A          414 EFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILMAKGTRDEAYYWSS  485 (494)
T ss_dssp             HHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCCSEEEEEEETTSHHHHHHHHC
T ss_pred             HHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCCceEEEEEecCCHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999988776654433

>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=99.88  E-value=5.6e-25  Score=224.83  Aligned_cols=193  Identities=17%  Similarity=0.263  Sum_probs=29.7

Q ss_pred             HHHHHHh-cchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeec---ccc
Q psy4150          26 QRDFHVT-HSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAW---SHL   98 (395)
Q Consensus        26 ead~~~~-~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~---~~~   98 (395)
                      |+|.+.. .++......+...  ...+.+.+|||++.... ....++.++.++.+.....   ....+.+.+..   ...
T Consensus       243 Eah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~---~~~~~~~~~~~~~~~~~  319 (479)
T 3fmp_B          243 EADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE---TLDTIKQYYVLCSSRDE  319 (479)
T ss_dssp             CHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC------------------------
T ss_pred             CHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEecccccc---CcCCceEEEEEeCCHHH
Confidence            8888887 5777666666554  34688999999987652 1122222221111000000   00011222222   234


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      |...|..++...        ...++||||+++..|+.+++.|...+  +.+..+||   ++++.+|..+++.|++|+++|
T Consensus       320 ~~~~l~~~~~~~--------~~~~~lvF~~s~~~~~~l~~~L~~~~--~~v~~lh~---~~~~~~R~~~~~~f~~g~~~i  386 (479)
T 3fmp_B          320 KFQALCNLYGAI--------TIAQAMIFCHTRKTASWLAAELSKEG--HQVALLSG---EMMVEQRAAVIERFREGKEKV  386 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHhhc--------cCCceEEEeCcHHHHHHHHHHHHhCC--ccEEEecC---CCCHHHHHHHHHHHHcCCCcE
Confidence            666666655442        34789999999999999999999988  89999999   999999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCC------ChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQK------SPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~------s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      ||||+++++|||+|+|++||+||+|+      +...|+||+|||||.| .|.+++++....+.
T Consensus       387 Lv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~  449 (479)
T 3fmp_B          387 LVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSM  449 (479)
T ss_dssp             ---------------------------------------------------------------
T ss_pred             EEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchH
Confidence            99999999999999999999999995      5689999999999997 68888887765544

>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=99.88  E-value=4e-22  Score=194.48  Aligned_cols=186  Identities=18%  Similarity=0.327  Sum_probs=142.7

Q ss_pred             HHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceee--eccccH
Q psy4150          25 IQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEY--AWSHLK   99 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~--~~~~~K   99 (395)
                      .|++.+...++...+..+...  ...+.+.++||++.... ....++.+..+..      ... ...+.+.+  .....|
T Consensus       154 DEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~------~~~-~~~~~~~~~~~~~~~~  226 (367)
T 1hv8_A          154 DEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIK------AKI-NANIEQSYVEVNENER  226 (367)
T ss_dssp             ETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEE------CCS-SSSSEEEEEECCGGGH
T ss_pred             eCchHhhhhchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEE------ecC-CCCceEEEEEeChHHH
Confidence            389988888888776666554  44677888999876541 1111222211110      000 00122222  234567


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      +..+.+++.         ..+.++||||+++..++.+++.|.+.+  +.+..+||   ++++.+|..+++.|++|+.+||
T Consensus       227 ~~~l~~~l~---------~~~~~~lvf~~~~~~~~~l~~~L~~~~--~~~~~~~~---~~~~~~r~~~~~~f~~~~~~vl  292 (367)
T 1hv8_A          227 FEALCRLLK---------NKEFYGLVFCKTKRDTKELASMLRDIG--FKAGAIHG---DLSQSQREKVIRLFKQKKIRIL  292 (367)
T ss_dssp             HHHHHHHHC---------STTCCEEEECSSHHHHHHHHHHHHHTT--CCEEEECS---SSCHHHHHHHHHHHHTTSSSEE
T ss_pred             HHHHHHHHh---------cCCCcEEEEECCHHHHHHHHHHHHhcC--CCeEEeeC---CCCHHHHHHHHHHHHcCCCeEE
Confidence            777766654         236799999999999999999999998  89999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      |||+++++|+|+|++++||+||+|+++.+|+||+||+||.| .|.+++++.+.
T Consensus       293 v~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  345 (367)
T 1hv8_A          293 IATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRR  345 (367)
T ss_dssp             EECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTT
T ss_pred             EECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHH
Confidence            99999999999999999999999999999999999999997 78888887654

>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=99.88  E-value=4e-22  Score=206.79  Aligned_cols=123  Identities=18%  Similarity=0.320  Sum_probs=110.1

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ....+...|.++|..+        .+.++||||+|++.++.+++.|...|  +.+..+||   +|++.+|..+++.|++|
T Consensus       219 ~~~~~~~~l~~~l~~~--------~~~~~IVf~~sr~~~e~l~~~L~~~g--~~~~~~h~---~l~~~~R~~~~~~f~~g  285 (523)
T 1oyw_A          219 EKFKPLDQLMRYVQEQ--------RGKSGIIYCNSRAKVEDTAARLQSKG--ISAAAYHA---GLENNVRADVQEKFQRD  285 (523)
T ss_dssp             ECSSHHHHHHHHHHHT--------TTCCEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHTT
T ss_pred             eCCCHHHHHHHHHHhc--------CCCcEEEEeCCHHHHHHHHHHHHHCC--CCEEEecC---CCCHHHHHHHHHHHHcC
Confidence            3455777777766542        45799999999999999999999998  89999999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      +++|||||+++++|||+|+|++||+||+|+|..+|+||+||+||.| .|.+++++..
T Consensus       286 ~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~  342 (523)
T 1oyw_A          286 DLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP  342 (523)
T ss_dssp             SCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECH
T ss_pred             CCeEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCH
Confidence            9999999999999999999999999999999999999999999997 5666666654

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

Probab=99.87  E-value=1.8e-22  Score=207.84  Aligned_cols=136  Identities=34%  Similarity=0.574  Sum_probs=100.2

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEec-----cCCCCCHHHHHHHH
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVG-----QSSGVTQQEQKEIM  168 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg-----~~~~~~~~~R~~~l  168 (395)
                      .++|+..|.++|..++..    ..+.++||||+++.+++.|++.|...+  ..+.+..+||     +|++|++.+|..++
T Consensus       369 ~~~k~~~l~~~l~~~~~~----~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~  444 (555)
T 3tbk_A          369 ENPKLRDLYLVLQEEYHL----KPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVL  444 (555)
T ss_dssp             CCHHHHHHHHHHHHHHHH----CTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-------------------
T ss_pred             CCHHHHHHHHHHHHHhcc----CCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHH
Confidence            478999999999988765    557899999999999999999998764  1245555554     22389999999999


Q ss_pred             HHHhc-CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchhhH
Q psy4150         169 KKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHN  236 (395)
Q Consensus       169 ~~Fk~-g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~  236 (395)
                      ++|++ |+++|||||+++++|||+|+|++||+||+|+|+.+|+||+|| ||...|.+++++++++....
T Consensus       445 ~~F~~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~~~g~~~~l~~~~~~~~~  512 (555)
T 3tbk_A          445 EAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRARDSKCFLLTSSADVIEK  512 (555)
T ss_dssp             -------CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTTTSCEEEEEESCHHHHHH
T ss_pred             HHHhcCCCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcCCCceEEEEEcCCCHHHH
Confidence            99999 999999999999999999999999999999999999999999 99988999988877655443

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

Probab=99.87  E-value=7e-22  Score=197.89  Aligned_cols=173  Identities=19%  Similarity=0.228  Sum_probs=128.6

Q ss_pred             HHHHh-cchHHH-HHHHHhC-------------CCcchhhhccc-cCccccccccccCChhHHHHHH-hhccc-cccccc
Q psy4150          28 DFHVT-HSLASA-LENLVTY-------------GLRSFYNNLVE-VSKEDGSCPILGKDNDLQNLLQ-QLKPK-LDINIM   89 (395)
Q Consensus        28 d~~~~-~~l~~~-~~~L~~~-------------g~r~~~~fsat-l~~~~~~~~~l~~~~~~~~~v~-~~~~~-~~~~~~   89 (395)
                      |.++. +||... +..+...             ...+.+.+||| .+....   .    ..+..... ..... .....+
T Consensus       159 d~~l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~---~----~~~~~~~~~~~~~~~~~~~~i  231 (414)
T 3oiy_A          159 DTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIR---P----LLFRDLLNFTVGRLVSVARNI  231 (414)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSST---T----HHHHHHHSCCSSCCCCCCCSE
T ss_pred             hhHHhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhH---H----HHHHHhhccCcCccccccccc
Confidence            77777 888776 5555542             45788999999 454431   0    00111111 01111 111113


Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCcee-EEeccCCCCCHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKAS-MFVGQSSGVTQQEQKEIM  168 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~-~lhg~~~~~~~~~R~~~l  168 (395)
                      .+.+ ...+|...|.++|...         +.++||||+++..|+.+++.|...|  +.+. .+||   .    +|.  +
T Consensus       232 ~~~~-~~~~~~~~l~~~l~~~---------~~~~lVF~~~~~~~~~l~~~L~~~~--~~~~~~~h~---~----~r~--~  290 (414)
T 3oiy_A          232 THVR-ISSRSKEKLVELLEIF---------RDGILIFAQTEEEGKELYEYLKRFK--FNVGETWSE---F----EKN--F  290 (414)
T ss_dssp             EEEE-ESSCCHHHHHHHHHHH---------CSSEEEEESSHHHHHHHHHHHHHTT--CCEEESSSC---H----HHH--H
T ss_pred             hhee-eccCHHHHHHHHHHHc---------CCCEEEEECCHHHHHHHHHHHHHcC--CceehhhcC---c----chH--H
Confidence            3333 3347888888888772         3799999999999999999999998  8887 8888   3    344  9


Q ss_pred             HHHhcCCccEEEE----cCccccCCCCCC-CCEEEEcCCC--CChhhHhhhcccccccc-----CceEEEEE
Q psy4150         169 KKFRAGEFNTLIA----TSVGEEGLDIGE-IDLVICFDAQ--KSPIKMVQRLGRTGRKR-----NGRCVILL  228 (395)
Q Consensus       169 ~~Fk~g~~~vLVa----T~v~~~GlDip~-v~~VI~~d~p--~s~~~yiQr~GRagR~~-----~g~~i~l~  228 (395)
                      +.|++|+++||||    |+++++|||+|+ |++||+||+|  .++.+|+||+|||||.|     .|.+++++
T Consensus       291 ~~f~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~  362 (414)
T 3oiy_A          291 EDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE  362 (414)
T ss_dssp             HHHHTTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC
T ss_pred             HHHhCCCCeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE
Confidence            9999999999999    999999999999 9999999999  99999999999999986     56677776

>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=99.87  E-value=3.7e-22  Score=212.84  Aligned_cols=129  Identities=35%  Similarity=0.523  Sum_probs=105.5

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCC-CccEEEEcCcHHHHHHHHHHHccc------CCCCceeEEeccCCC--------CC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGE-TTKVIIFANYRVVVAEIFDVLKPL------EPMVKASMFVGQSSG--------VT  160 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~-~~r~iVF~~t~~~ae~l~~~L~~~------~~~~~~~~lhg~~~~--------~~  160 (395)
                      .++|+..|.++|..++..    .+ +.++||||+++.+++.|++.|...      |  +++..+||   +        |+
T Consensus       379 ~~~k~~~L~~~L~~~~~~----~~~~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g--~~~~~lhg---~~~~~~~~~~~  449 (699)
T 4gl2_A          379 ENEKLTKLRNTIMEQYTR----TEESARGIIFTKTRQSAYALSQWITENEKFAEVG--VKAHHLIG---AGHSSEFKPMT  449 (699)
T ss_dssp             ---CSSCSHHHHHHHHHH----SSSCCCEEEECSCHHHHHHHHHHHHSSCSCC-------CEECCC---SCCCTTCCCCC
T ss_pred             CCHHHHHHHHHHHHHHhc----CCCCCcEEEEECcHHHHHHHHHHHHhCccccccC--cceEEEEC---CCCccCCCCCC
Confidence            457888888888887664    34 689999999999999999999987      6  89999999   6        99


Q ss_pred             HHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchh
Q psy4150         161 QQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREA  234 (395)
Q Consensus       161 ~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~  234 (395)
                      +.+|.++++.|++|+++|||||+++++|||+|+|++||+||+|+|+.+|+||+||+||.| +.++++...+...
T Consensus       450 ~~eR~~~~~~F~~g~~~VLVaT~~~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRArr~g-~~~~l~~~~~~~~  522 (699)
T 4gl2_A          450 QNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADE-STYVLVAHSGSGV  522 (699)
T ss_dssp             HHHHHHHHHHHCC---CCSEEECSCCTTSCCCSCCCCEEESCCCCHHHHHHHHTTSCSSS-CEEEEEEESSSCS
T ss_pred             HHHHHHHHHHHhcCCCcEEEEccccccCCccccCCEEEEeCCCCCHHHHHHHcCCCCCCC-ceEEEEEeCCchH
Confidence            999999999999999999999999999999999999999999999999999999976655 5555555544433

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

Probab=99.87  E-value=1.9e-21  Score=185.53  Aligned_cols=149  Identities=20%  Similarity=0.295  Sum_probs=116.4

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHccc-CCCCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPL-EPMVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~-~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      ...++|+..|.++|..+...      +.++||||+++.+++.|...|... |  +.+..+||   ++++.+|..+++.|+
T Consensus        92 ~~~s~K~~~L~~ll~~~~~~------~~kvlIFs~~~~~~~~l~~~L~~~~g--~~~~~l~G---~~~~~~R~~~i~~F~  160 (271)
T 1z5z_A           92 VRRSGKMIRTMEIIEEALDE------GDKIAIFTQFVDMGKIIRNIIEKELN--TEVPFLYG---ELSKKERDDIISKFQ  160 (271)
T ss_dssp             STTCHHHHHHHHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHHC--SCCCEECT---TSCHHHHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHHHHhC------CCeEEEEeccHHHHHHHHHHHHHhcC--CcEEEEEC---CCCHHHHHHHHHHhc
Confidence            44678999999999887543      689999999999999999999885 7  88999999   999999999999999


Q ss_pred             cC-Ccc-EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC---ceEEEEEeCCchhhHHHHHHHHhHHH
Q psy4150         173 AG-EFN-TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN---GRCVILLTQGREAHNFQTSMQTCKSY  247 (395)
Q Consensus       173 ~g-~~~-vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~---g~~i~l~~~~~e~~~~~~~~~~~~~~  247 (395)
                      +| .++ +|++|+++++|||++.+++||+||+|||+..|+||+||++|.|+   ..++.+++.++-++.+...+......
T Consensus       161 ~~~~~~v~L~st~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~TiEe~i~~~~~~K~~l  240 (271)
T 1z5z_A          161 NNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSL  240 (271)
T ss_dssp             HCTTCCEEEEECCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSHHHHHHHHHHHCHHH
T ss_pred             CCCCCCEEEEehhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCCCHHHHHHHHHHHHHHH
Confidence            99 777 78999999999999999999999999999999999999999973   34567888888777766655444444


Q ss_pred             HHHHHc
Q psy4150         248 VEKIIN  253 (395)
Q Consensus       248 i~~~i~  253 (395)
                      .+..++
T Consensus       241 ~~~~~~  246 (271)
T 1z5z_A          241 FKDIIS  246 (271)
T ss_dssp             HTTGGG
T ss_pred             HHHHHc
Confidence            444443

>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=99.86  E-value=6.5e-22  Score=214.76  Aligned_cols=136  Identities=28%  Similarity=0.524  Sum_probs=86.1

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEecc-----CCCCCHHHHHHHH
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQ-----SSGVTQQEQKEIM  168 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~-----~~~~~~~~R~~~l  168 (395)
                      .++|+..|.++|..++..    ..+.++||||+++.+++.|+++|....  +.+++..++|+     |++|++.+|..++
T Consensus       611 ~~~K~~~L~~lL~~~~~~----~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l  686 (797)
T 4a2q_A          611 ENPKLEELVCILDDAYRY----NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVL  686 (797)
T ss_dssp             CCHHHHHHHHHHHHHHHH----CSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC---------------------
T ss_pred             CChHHHHHHHHHHHHhcc----CCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHH
Confidence            578999999999987765    557899999999999999999998741  12445555442     2389999999999


Q ss_pred             HHHhc-CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchhhH
Q psy4150         169 KKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHN  236 (395)
Q Consensus       169 ~~Fk~-g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~  236 (395)
                      ++|++ |+++|||||+++++|||+|+|++||+||+|+|+..|+||+|| ||.+.|.++++++.++....
T Consensus       687 ~~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~~~g~~i~l~~~~~~ee~  754 (797)
T 4a2q_A          687 DAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSKCILVTSKTEVVEN  754 (797)
T ss_dssp             -------CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC--------CCCEEEEECCHHHHHH
T ss_pred             HHhhccCCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCCCCceEEEEEeCCcHHHH
Confidence            99999 999999999999999999999999999999999999999999 99999999999987766554

>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=99.86  E-value=9.6e-22  Score=189.80  Aligned_cols=182  Identities=20%  Similarity=0.304  Sum_probs=131.8

Q ss_pred             HHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeeeccccHHH
Q psy4150          25 IQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFI  101 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~K~~  101 (395)
                      .|++.+...++...+..+...  ...+...++||++.... ....++.++...      ..........+.+........
T Consensus       136 DEah~~~~~~~~~~~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~  209 (337)
T 2z0m_A          136 DEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEI------EACIGLANVEHKFVHVKDDWR  209 (337)
T ss_dssp             ESHHHHHHTTCHHHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEE------ECSGGGGGEEEEEEECSSSSH
T ss_pred             EChHHhhccccHHHHHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceee------ecccccCCceEEEEEeChHHH
Confidence            388888888887776665543  34556678999876541 111122211110      001111112233333333333


Q ss_pred             HHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEE
Q psy4150         102 RLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIA  181 (395)
Q Consensus       102 ~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVa  181 (395)
                      .....+..        ..+.++||||++++.++.+++.|.      .+..+||   ++++.+|.+++++|++|+++||||
T Consensus       210 ~~~~~~~~--------~~~~~~lvf~~~~~~~~~l~~~l~------~~~~~~~---~~~~~~r~~~~~~f~~~~~~vlv~  272 (337)
T 2z0m_A          210 SKVQALRE--------NKDKGVIVFVRTRNRVAKLVRLFD------NAIELRG---DLPQSVRNRNIDAFREGEYDMLIT  272 (337)
T ss_dssp             HHHHHHHT--------CCCSSEEEECSCHHHHHHHHTTCT------TEEEECT---TSCHHHHHHHHHHHHTTSCSEEEE
T ss_pred             HHHHHHHh--------CCCCcEEEEEcCHHHHHHHHHHhh------hhhhhcC---CCCHHHHHHHHHHHHcCCCcEEEE
Confidence            33333322        457899999999999999999885      4678899   999999999999999999999999


Q ss_pred             cCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEe
Q psy4150         182 TSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLT  229 (395)
Q Consensus       182 T~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~  229 (395)
                      |+++++|+|+|++++||+||+|+++.+|+||+||+||.| .|.+++++.
T Consensus       273 T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~  321 (337)
T 2z0m_A          273 TDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL  321 (337)
T ss_dssp             CHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES
T ss_pred             cCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe
Confidence            999999999999999999999999999999999999997 677777776

>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=1.1e-21  Score=206.39  Aligned_cols=107  Identities=21%  Similarity=0.338  Sum_probs=101.0

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      .+.++||||+|++.++.+++.|...|  +.+..+||   +|++.+|..+++.|+.|+++|||||+++++|||+|+|++||
T Consensus       266 ~~~~~IVf~~sr~~~e~la~~L~~~g--~~~~~~h~---~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI  340 (591)
T 2v1x_A          266 KGQSGIIYCFSQKDSEQVTVSLQNLG--IHAGAYHA---NLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVI  340 (591)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEE
T ss_pred             cCCCeEEEeCcHHHHHHHHHHHHHCC--CCEEEecC---CCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEE
Confidence            46899999999999999999999998  99999999   99999999999999999999999999999999999999999


Q ss_pred             EcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         199 CFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       199 ~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      +||+|+|..+|+||+|||||.| .|.+++++..
T Consensus       341 ~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~  373 (591)
T 2v1x_A          341 HHSMSKSMENYYQESGRAGRDDMKADCILYYGF  373 (591)
T ss_dssp             ESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECH
T ss_pred             EeCCCCCHHHHHHHhccCCcCCCCceEEEEECh
Confidence            9999999999999999999997 6667766654

>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=99.86  E-value=7.1e-22  Score=217.79  Aligned_cols=151  Identities=26%  Similarity=0.475  Sum_probs=92.9

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEecc-----CCCCCHHHHHHHH
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQ-----SSGVTQQEQKEIM  168 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~-----~~~~~~~~R~~~l  168 (395)
                      .++|+..|.++|.+++..    ..+.++||||+++.+++.|+++|....  +.+++.+++|.     |++|++.+|.+++
T Consensus       611 ~~~K~~~L~~lL~~~~~~----~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il  686 (936)
T 4a2w_A          611 ENPKLEELVCILDDAYRY----NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVL  686 (936)
T ss_dssp             CCHHHHHHHHHHHHTTTS----CTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC---------------------
T ss_pred             CCHHHHHHHHHHHHHhcc----CCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHH
Confidence            578999999999886643    457899999999999999999998761  12566666553     3489999999999


Q ss_pred             HHHhc-CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchhhHHHHHHHHhHHH
Q psy4150         169 KKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSY  247 (395)
Q Consensus       169 ~~Fk~-g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~~~~~~~  247 (395)
                      ++|+. |+++|||||+++++|||+|+|++||+||+|+|+.+|+||+|| ||.+.|.++++++.++.+..+. ........
T Consensus       687 ~~Fr~~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~~~g~vi~Li~~~t~ee~~~-~~~~ke~~  764 (936)
T 4a2w_A          687 DAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRAAGSKCILVTSKTEVVENEK-CNRYKEEM  764 (936)
T ss_dssp             -------CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC--------CCCEEEEESCHHHHHHHH-HHHHHHHH
T ss_pred             HHhhccCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCCCCCEEEEEEeCCCHHHHHH-HHHHHHHH
Confidence            99999 999999999999999999999999999999999999999999 9999999999988876655433 22233334


Q ss_pred             HHHHH
Q psy4150         248 VEKII  252 (395)
Q Consensus       248 i~~~i  252 (395)
                      +.+.+
T Consensus       765 ~~~~i  769 (936)
T 4a2w_A          765 MNKAV  769 (936)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44444

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

Probab=99.85  E-value=1.4e-21  Score=208.23  Aligned_cols=133  Identities=34%  Similarity=0.569  Sum_probs=83.1

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEecc-----CCCCCHHHHHHHH
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQ-----SSGVTQQEQKEIM  168 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~-----~~~~~~~~R~~~l  168 (395)
                      .++|+..|.++|..++..    ..+.++||||+++..++.|++.|...+  +.+++..+||+     |++|++.+|.+++
T Consensus       378 ~~~k~~~L~~ll~~~~~~----~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~  453 (696)
T 2ykg_A          378 ENPKLEDLCFILQEEYHL----NPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCIL  453 (696)
T ss_dssp             CCHHHHHHHHHHHHHHTT----CTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC----------------------
T ss_pred             CCHHHHHHHHHHHHHhcc----CCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHH
Confidence            567999999999887643    456899999999999999999998875  23678888662     3489999999999


Q ss_pred             HHHhc-CCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCch
Q psy4150         169 KKFRA-GEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGRE  233 (395)
Q Consensus       169 ~~Fk~-g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e  233 (395)
                      ++|++ |+++|||||+++++|||+|+|++||+||+|+|+.+|+||+|| ||.+.|.++++++.++.
T Consensus       454 ~~F~~~g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~~~g~~~~l~~~~~~  518 (696)
T 2ykg_A          454 DAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFLLTSNAGV  518 (696)
T ss_dssp             -------CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC----------CCCEEEEEESCHHH
T ss_pred             HHHHhcCCccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcCCCceEEEEecCCCH
Confidence            99998 999999999999999999999999999999999999999999 99988888877765443

>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=99.84  E-value=2.6e-23  Score=205.37  Aligned_cols=190  Identities=22%  Similarity=0.310  Sum_probs=28.1

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChhHHHHHHhhcccccccccceeee---ccccH
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDNDLQNLLQQLKPKLDINIMSSEYA---WSHLK   99 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~---~~~~K   99 (395)
                      |++.+...++...+..+...  ...+.+.++||++.... ....++.++......   ........+.+.+.   ....|
T Consensus       170 Eah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~  246 (394)
T 1fuu_A          170 EADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVK---KDELTLEGIKQFYVNVEEEEYK  246 (394)
T ss_dssp             THHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEEC---C---------------------
T ss_pred             ChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEec---CccccCCCceEEEEEcCchhhH
Confidence            88888888887776665543  34678889999876431 111111111100000   00000000111111   11225


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ...+.+++...        ...++||||+++..++.+++.|...+  +.+..+||   ++++.+|..+++.|++|+.+||
T Consensus       247 ~~~l~~~~~~~--------~~~~~lVf~~~~~~~~~l~~~L~~~~--~~~~~~~~---~~~~~~r~~~~~~f~~~~~~vl  313 (394)
T 1fuu_A          247 YECLTDLYDSI--------SVTQAVIFCNTRRKVEELTTKLRNDK--FTVSAIYS---DLPQQERDTIMKEFRSGSSRIL  313 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHhcC--------CCCcEEEEECCHHHHHHHHHHHHHcC--CeEEEeeC---CCCHHHHHHHHHHHHCCCCcEE
Confidence            55555555432        34799999999999999999999988  89999999   9999999999999999999999


Q ss_pred             EEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         180 IATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       180 VaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      |||+++++|+|+|++++||+||+|+++.+|+||+||+||.| .|.+++++++.
T Consensus       314 v~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~  366 (394)
T 1fuu_A          314 ISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE  366 (394)
T ss_dssp             -----------------------------------------------------
T ss_pred             EECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchh
Confidence            99999999999999999999999999999999999999996 67777777654

>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=99.82  E-value=3.3e-20  Score=198.34  Aligned_cols=129  Identities=21%  Similarity=0.158  Sum_probs=111.7

Q ss_pred             eeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          92 EYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        92 ~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .|.....|+..|.++|......      +.++||||+|+..++.|+..|...|  +++..|||   ++++.+|..+.+.|
T Consensus       410 v~~~~~~K~~al~~~i~~~~~~------~~pvLVft~s~~~se~Ls~~L~~~g--i~~~vLhg---~~~~rEr~ii~~ag  478 (844)
T 1tf5_A          410 IYRTMEGKFKAVAEDVAQRYMT------GQPVLVGTVAVETSELISKLLKNKG--IPHQVLNA---KNHEREAQIIEEAG  478 (844)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHH------TCCEEEEESCHHHHHHHHHHHHTTT--CCCEEECS---SCHHHHHHHHTTTT
T ss_pred             EEeCHHHHHHHHHHHHHHHHhc------CCcEEEEECCHHHHHHHHHHHHHCC--CCEEEeeC---CccHHHHHHHHHcC
Confidence            3445567898888888764332      4689999999999999999999999  99999999   88888887676666


Q ss_pred             hcCCccEEEEcCccccCCCCC--------CCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         172 RAGEFNTLIATSVGEEGLDIG--------EIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       172 k~g~~~vLVaT~v~~~GlDip--------~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      +.|  .||||||+++||+||+        ++.+||+||.|.|...|+||+|||||.| .|.+++|++..+.
T Consensus       479 ~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          479 QKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             STT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             CCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            665  6999999999999999        7889999999999999999999999998 7888888887654

>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=99.81  E-value=1.5e-20  Score=198.36  Aligned_cols=166  Identities=14%  Similarity=0.143  Sum_probs=123.2

Q ss_pred             HHHHHHhcchHHHHHHHHhC---CCcchhhhccccCccccccccccC-ChhHHHHHHhhcccccccccceeeeccccHHH
Q psy4150          26 QRDFHVTHSLASALENLVTY---GLRSFYNNLVEVSKEDGSCPILGK-DNDLQNLLQQLKPKLDINIMSSEYAWSHLKFI  101 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~---g~r~~~~fsatl~~~~~~~~~l~~-~~~~~~~v~~~~~~~~~~~~~~~~~~~~~K~~  101 (395)
                      |+|.+ ++++...+..|...   ..++++.||||++....   .+.. ++...          ...   ..+  ...++.
T Consensus       285 Eah~~-~~~~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~---~~~~~~~~~~----------~v~---~~~--~~~~~~  345 (618)
T 2whx_A          285 EAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTD---PFPQSNSPIE----------DIE---REI--PERSWN  345 (618)
T ss_dssp             STTCC-SHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCC---SSCCCSSCEE----------EEE---CCC--CSSCCS
T ss_pred             CCCCC-CccHHHHHHHHHHHhcccCccEEEEECCCchhhh---hhhccCCcee----------eec---ccC--CHHHHH
Confidence            66665 66666666655543   45789999999987652   2221 11100          000   000  111222


Q ss_pred             HHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEE
Q psy4150         102 RLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIA  181 (395)
Q Consensus       102 ~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVa  181 (395)
                      .+...|.+         ...++||||+|+..|+.+++.|.+.+  +.+..+||   +    +|.+++++|++|+++||||
T Consensus       346 ~ll~~l~~---------~~~~~LVF~~s~~~a~~l~~~L~~~g--~~v~~lhg---~----~R~~~l~~F~~g~~~VLVa  407 (618)
T 2whx_A          346 TGFDWITD---------YQGKTVWFVPSIKAGNDIANCLRKSG--KRVIQLSR---K----TFDTEYPKTKLTDWDFVVT  407 (618)
T ss_dssp             SSCHHHHH---------CCSCEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---T----THHHHTTHHHHSCCSEEEE
T ss_pred             HHHHHHHh---------CCCCEEEEECChhHHHHHHHHHHHcC--CcEEEECh---H----HHHHHHHhhcCCCcEEEEE
Confidence            23333322         14799999999999999999999998  89999998   4    6888999999999999999


Q ss_pred             cCccccCCCCCCCCEE--------------------EEcCCCCChhhHhhhcccccccc--CceEEEEEe
Q psy4150         182 TSVGEEGLDIGEIDLV--------------------ICFDAQKSPIKMVQRLGRTGRKR--NGRCVILLT  229 (395)
Q Consensus       182 T~v~~~GlDip~v~~V--------------------I~~d~p~s~~~yiQr~GRagR~~--~g~~i~l~~  229 (395)
                      ||++++|||+| |++|                    |+||.|.+..+|+||+|||||.|  .|.+++|++
T Consensus       408 Tdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~  476 (618)
T 2whx_A          408 TDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSG  476 (618)
T ss_dssp             CGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             CcHHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEcc
Confidence            99999999998 9988                    78888999999999999999995  788888876

>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=99.80  E-value=2.9e-19  Score=187.77  Aligned_cols=130  Identities=18%  Similarity=0.205  Sum_probs=110.4

Q ss_pred             eeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          92 EYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        92 ~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .|.....|+..+.+.+......      +.++||||+|+..++.|+..|.+.|  +++..+||   +..+.++..+...|
T Consensus       452 vy~t~~eK~~al~~~I~~~~~~------gqpVLVFt~S~e~sE~Ls~~L~~~G--i~~~vLhg---kq~~rE~~ii~~ag  520 (822)
T 3jux_A          452 VFRTQKEKYEKIVEEIEKRYKK------GQPVLVGTTSIEKSELLSSMLKKKG--IPHQVLNA---KYHEKEAEIVAKAG  520 (822)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHH------TCCEEEEESSHHHHHHHHHHHHTTT--CCCEEECS---CHHHHHHHHHHHHH
T ss_pred             EEecHHHHHHHHHHHHHHHhhC------CCCEEEEECCHHHHHHHHHHHHHCC--CCEEEeeC---CchHHHHHHHHhCC
Confidence            4555667999998888775433      5789999999999999999999999  99999999   76566665555666


Q ss_pred             hcCCccEEEEcCccccCCCCC--------CCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         172 RAGEFNTLIATSVGEEGLDIG--------EIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       172 k~g~~~vLVaT~v~~~GlDip--------~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      +.|  .|+||||+++||+||+        ++.+||+|+.|.+...|+||+|||||.| +|.+++|++..++.
T Consensus       521 ~~g--~VtVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~l  590 (822)
T 3jux_A          521 QKG--MVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDL  590 (822)
T ss_dssp             STT--CEEEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSHH
T ss_pred             CCC--eEEEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHHH
Confidence            655  6999999999999998        6679999999999999999999999998 78888888876643

>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=99.79  E-value=3.2e-20  Score=189.46  Aligned_cols=102  Identities=22%  Similarity=0.212  Sum_probs=92.1

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      .+++||||+++..++.+++.|...+  +.+..+||   .    +|..+++.|++|+++|||||+++++|||+|+ ++||+
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~g--~~v~~lh~---~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~  259 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRAG--KKVIQLNR---K----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVID  259 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT--CCEEEEST---T----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEE
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhcC--CcEEecCH---H----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEE
Confidence            5799999999999999999999998  89999998   4    5778999999999999999999999999999 99999


Q ss_pred             --------------------cCCCCChhhHhhhcccccccc--CceEEEEEeCC
Q psy4150         200 --------------------FDAQKSPIKMVQRLGRTGRKR--NGRCVILLTQG  231 (395)
Q Consensus       200 --------------------~d~p~s~~~yiQr~GRagR~~--~g~~i~l~~~~  231 (395)
                                          ||.|.+..+|+||+|||||.|  .|.+++|+...
T Consensus       260 ~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          260 CRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             CCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             CCcccccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence                                789999999999999999996  78888888775

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

Probab=99.79  E-value=7.1e-20  Score=204.34  Aligned_cols=149  Identities=17%  Similarity=0.231  Sum_probs=109.0

Q ss_pred             HHHHh-cchHHH-HHHHHhC-------------CCcchhhhccc-cCccccccccccCChhHHHHHH-hhc-cccccccc
Q psy4150          28 DFHVT-HSLASA-LENLVTY-------------GLRSFYNNLVE-VSKEDGSCPILGKDNDLQNLLQ-QLK-PKLDINIM   89 (395)
Q Consensus        28 d~~~~-~~l~~~-~~~L~~~-------------g~r~~~~fsat-l~~~~~~~~~l~~~~~~~~~v~-~~~-~~~~~~~~   89 (395)
                      |.+++ +||... +..+..+             ...+++.|||| .+.....  .+     +...+. ... .......+
T Consensus       216 Dr~L~~~gf~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~--~~-----~~~~l~i~v~~~~~~~~~i  288 (1104)
T 4ddu_A          216 DTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRP--LL-----FRDLLNFTVGRLVSVARNI  288 (1104)
T ss_dssp             HHHHHTSSCCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTT--HH-----HHHHTCCCCCBCCCCCCCE
T ss_pred             hhhhHhcCCCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHH--HH-----hhcceeEEeccCCCCcCCc
Confidence            88888 998876 5555542             45789999999 4554410  00     111110 000 01111113


Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCcee-EEeccCCCCCHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKAS-MFVGQSSGVTQQEQKEIM  168 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~-~lhg~~~~~~~~~R~~~l  168 (395)
                      .+.+.. .+|...|.++|...         +.++||||+++..++.++..|...|  +.+. .+||   .     |.+ +
T Consensus       289 ~~~~~~-~~k~~~L~~ll~~~---------~~~~LVF~~s~~~a~~l~~~L~~~g--~~~~~~lhg---~-----rr~-l  347 (1104)
T 4ddu_A          289 THVRIS-SRSKEKLVELLEIF---------RDGILIFAQTEEEGKELYEYLKRFK--FNVGETWSE---F-----EKN-F  347 (1104)
T ss_dssp             EEEEES-CCCHHHHHHHHHHH---------CSSEEEEESSSHHHHHHHHHHHHTT--CCEEESSSS---H-----HHH-H
T ss_pred             eeEEEe-cCHHHHHHHHHHhc---------CCCEEEEECcHHHHHHHHHHHHhCC--CCeeeEecC---c-----HHH-H
Confidence            334433 37888888888772         3899999999999999999999998  8887 8888   2     455 9


Q ss_pred             HHHhcCCccEEEE----cCccccCCCCCC-CCEEEEcCCCC
Q psy4150         169 KKFRAGEFNTLIA----TSVGEEGLDIGE-IDLVICFDAQK  204 (395)
Q Consensus       169 ~~Fk~g~~~vLVa----T~v~~~GlDip~-v~~VI~~d~p~  204 (395)
                      ++|++|+++||||    |+++++|||+|+ |++||+||+|.
T Consensus       348 ~~F~~G~~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          348 EDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             HHHHHTSCSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             HHHHCCCCCEEEEecCCCCeeEecCcCCCCCCEEEEECCCC
Confidence            9999999999999    999999999999 99999999998

>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=99.79  E-value=9e-20  Score=185.23  Aligned_cols=99  Identities=15%  Similarity=0.154  Sum_probs=84.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      +.++||||+++..++.+++.|...+  +++..+||   +    +|..+++.|++|+++|||||+++++|||+| +++||+
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~~--~~v~~lhg---~----~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~  246 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKAG--KSVVVLNR---K----TFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLD  246 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT--CCEEECCS---S----SCC--------CCCSEEEESSSTTCCTTCC-CSEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcC--CCEEEecc---h----hHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEe
Confidence            5799999999999999999999988  89999998   3    478899999999999999999999999999 999996


Q ss_pred             -------------------cCCCCChhhHhhhccccccc-c-CceEEEEE
Q psy4150         200 -------------------FDAQKSPIKMVQRLGRTGRK-R-NGRCVILL  228 (395)
Q Consensus       200 -------------------~d~p~s~~~yiQr~GRagR~-~-~g~~i~l~  228 (395)
                                         |+.|.+..+|+||+||+||. + .|.+++++
T Consensus       247 ~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~  296 (440)
T 1yks_A          247 CRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  296 (440)
T ss_dssp             CCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             CCccceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEe
Confidence                               89999999999999999997 4 78888886

>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=99.78  E-value=5.7e-19  Score=195.19  Aligned_cols=129  Identities=19%  Similarity=0.257  Sum_probs=113.5

Q ss_pred             eeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcc-cCCCCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          93 YAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKP-LEPMVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        93 ~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~-~~~~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      +...++|...|.+++..        ..+.++||||+++..++.|+..|.. .|  +++..+||   +|++.+|..++++|
T Consensus       484 ~~~~~~K~~~L~~ll~~--------~~~~k~iVF~~~~~~~~~l~~~L~~~~g--~~~~~lhG---~~~~~~R~~~l~~F  550 (968)
T 3dmq_A          484 WWNFDPRVEWLMGYLTS--------HRSQKVLVICAKAATALQLEQVLREREG--IRAAVFHE---GMSIIERDRAAAWF  550 (968)
T ss_dssp             TTTTSHHHHHHHHHHHH--------TSSSCCCEECSSTHHHHHHHHHHHTTTC--CCEEEECT---TSCTTHHHHHHHHH
T ss_pred             ccCccHHHHHHHHHHHh--------CCCCCEEEEeCcHHHHHHHHHHHHHHcC--CcEEEEeC---CCCHHHHHHHHHHH
Confidence            34567799999998876        3468999999999999999999985 57  89999999   99999999999999


Q ss_pred             hcCC--ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC-ce--EEEEEeCCchh
Q psy4150         172 RAGE--FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN-GR--CVILLTQGREA  234 (395)
Q Consensus       172 k~g~--~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~-g~--~i~l~~~~~e~  234 (395)
                      ++|+  ++|||||+++++|||+|.+++||+||+|+++..|+||+||+||.|. |.  ++.++..++.+
T Consensus       551 ~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~e  618 (968)
T 3dmq_A          551 AEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQ  618 (968)
T ss_dssp             HSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSHH
T ss_pred             hCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEecCCChHH
Confidence            9998  9999999999999999999999999999999999999999999974 33  34455555544

>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=99.78  E-value=6.8e-19  Score=187.91  Aligned_cols=129  Identities=17%  Similarity=0.098  Sum_probs=113.1

Q ss_pred             eeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          92 EYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        92 ~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .|.....|+..|.+++.....      .+.++||||+|+..++.|+..|.+.|  +++.+|||   ++.+.++..+.+.|
T Consensus       419 v~~~~~~K~~al~~~i~~~~~------~gqpvLVft~sie~se~Ls~~L~~~g--i~~~vLna---k~~~rEa~iia~ag  487 (853)
T 2fsf_A          419 VYMTEAEKIQAIIEDIKERTA------KGQPVLVGTISIEKSELVSNELTKAG--IKHNVLNA---KFHANEAAIVAQAG  487 (853)
T ss_dssp             EESSHHHHHHHHHHHHHHHHT------TTCCEEEEESSHHHHHHHHHHHHHTT--CCCEECCT---TCHHHHHHHHHTTT
T ss_pred             EEeCHHHHHHHHHHHHHHHhc------CCCCEEEEECcHHHHHHHHHHHHHCC--CCEEEecC---ChhHHHHHHHHhcC
Confidence            455567799998888866432      35789999999999999999999999  99999999   88899998888999


Q ss_pred             hcCCccEEEEcCccccCCCCCCC-------------------------------------CEEEEcCCCCChhhHhhhcc
Q psy4150         172 RAGEFNTLIATSVGEEGLDIGEI-------------------------------------DLVICFDAQKSPIKMVQRLG  214 (395)
Q Consensus       172 k~g~~~vLVaT~v~~~GlDip~v-------------------------------------~~VI~~d~p~s~~~yiQr~G  214 (395)
                      +.|  .|+||||+++||+||+..                                     .+||+|+.|.|...|+||+|
T Consensus       488 r~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~G  565 (853)
T 2fsf_A          488 YPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRG  565 (853)
T ss_dssp             STT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHT
T ss_pred             CCC--eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhcc
Confidence            988  699999999999999973                                     69999999999999999999


Q ss_pred             cccccc-CceEEEEEeCCch
Q psy4150         215 RTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       215 RagR~~-~g~~i~l~~~~~e  233 (395)
                      ||||.| +|.+++|++..++
T Consensus       566 RTGRqGd~G~s~~fls~eD~  585 (853)
T 2fsf_A          566 RSGRQGDAGSSRFYLSMEDA  585 (853)
T ss_dssp             TSSGGGCCEEEEEEEETTSG
T ss_pred             ccccCCCCeeEEEEecccHH
Confidence            999998 6888888876654

>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=99.77  E-value=5e-19  Score=197.63  Aligned_cols=111  Identities=21%  Similarity=0.266  Sum_probs=94.8

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCCCCc---------------------------------------eeEEeccCCCC
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVK---------------------------------------ASMFVGQSSGV  159 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~---------------------------------------~~~lhg~~~~~  159 (395)
                      ...++||||+++..|+.++..|...+  +.                                       +.++||   +|
T Consensus       440 ~~~~vIVF~~sr~~~e~la~~L~~~~--~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg---~l  514 (1108)
T 3l9o_A          440 KYNPVIVFSFSKRDCEELALKMSKLD--FNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHS---GL  514 (1108)
T ss_dssp             TCCCEEEEESCHHHHHHHHHHTCSHH--HHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECS---CS
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecC---CC
Confidence            46799999999999999999997643  22                                       677888   99


Q ss_pred             CHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC--------ChhhHhhhcccccccc---CceEEEEE
Q psy4150         160 TQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK--------SPIKMVQRLGRTGRKR---NGRCVILL  228 (395)
Q Consensus       160 ~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~--------s~~~yiQr~GRagR~~---~g~~i~l~  228 (395)
                      ++.+|..+++.|+.|.++|||||+++++|||+|++++||+++.|+        |+.+|+||+|||||.|   .|.+++++
T Consensus       515 ~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~  594 (1108)
T 3l9o_A          515 LPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMI  594 (1108)
T ss_dssp             CHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEE
T ss_pred             CHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEe
Confidence            999999999999999999999999999999999999999887644        6677999999999997   67788777


Q ss_pred             eCCchh
Q psy4150         229 TQGREA  234 (395)
Q Consensus       229 ~~~~e~  234 (395)
                      .+..+.
T Consensus       595 ~~~~~~  600 (1108)
T 3l9o_A          595 DEKMEP  600 (1108)
T ss_dssp             CCCCCH
T ss_pred             cCCcCH
Confidence            766443

>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=99.77  E-value=3.5e-19  Score=181.39  Aligned_cols=125  Identities=30%  Similarity=0.478  Sum_probs=105.6

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      ...|...|.++|..        ..+.++||||+++..++.+++.|.       +..+||   ++++.+|.++++.|++|+
T Consensus       333 ~~~k~~~l~~~l~~--------~~~~k~lvF~~~~~~~~~l~~~l~-------~~~~~g---~~~~~~R~~~~~~F~~g~  394 (472)
T 2fwr_A          333 SKNKIRKLREILER--------HRKDKIIIFTRHNELVYRISKVFL-------IPAITH---RTSREEREEILEGFRTGR  394 (472)
T ss_dssp             CSHHHHHHHHHHHH--------TSSSCBCCBCSCHHHHHHHHHHTT-------CCBCCS---SSCSHHHHTHHHHHHHSS
T ss_pred             ChHHHHHHHHHHHh--------CCCCcEEEEECCHHHHHHHHHHhC-------cceeeC---CCCHHHHHHHHHHHhCCC
Confidence            45678888887766        236899999999999999999884       456888   999999999999999999


Q ss_pred             ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCc--e--EEEEEeCCchhhHHH
Q psy4150         176 FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNG--R--CVILLTQGREAHNFQ  238 (395)
Q Consensus       176 ~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g--~--~i~l~~~~~e~~~~~  238 (395)
                      ++|||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+|  .  ++.+++.++.++.+.
T Consensus       395 ~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~t~ee~~~  461 (472)
T 2fwr_A          395 FRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGTGEVNTA  461 (472)
T ss_dssp             CSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECSCC-----
T ss_pred             CCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCCCchHHHH
Confidence            99999999999999999999999999999999999999999999866  3  445677776665543

>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=99.76  E-value=9.9e-19  Score=179.32  Aligned_cols=132  Identities=21%  Similarity=0.323  Sum_probs=111.3

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHccc-CCCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPL-EPMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~-~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      ..++|+..+.++|.++..      .+.++||||+++..++.+.+.|... +  +.+..+||   ++++.+|.++++.|++
T Consensus       322 ~~s~K~~~l~~~l~~~~~------~~~k~lvF~~~~~~~~~l~~~l~~~~~--~~~~~~~g---~~~~~~R~~~~~~F~~  390 (500)
T 1z63_A          322 RRSGKMIRTMEIIEEALD------EGDKIAIFTQFVDMGKIIRNIIEKELN--TEVPFLYG---ELSKKERDDIISKFQN  390 (500)
T ss_dssp             TTCHHHHHHHHHHHHHHT------TTCCEEEECSCHHHHHHHHHHHHHHHT--CCCCEEET---TSCHHHHHHHHHHHHH
T ss_pred             hcchhHHHHHHHHHHHHc------cCCcEEEEEehHHHHHHHHHHHHHhhC--CCeEEEEC---CCCHHHHHHHHHHhcC
Confidence            356799999999988754      3689999999999999999999875 7  88999999   9999999999999999


Q ss_pred             C-Ccc-EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCc---eEEEEEeCCchhhHH
Q psy4150         174 G-EFN-TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNG---RCVILLTQGREAHNF  237 (395)
Q Consensus       174 g-~~~-vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g---~~i~l~~~~~e~~~~  237 (395)
                      | .+. +||||+++++|+|++.+++||+||+|||+..|+||+||++|.|+.   .++.+++.++.++.+
T Consensus       391 ~~~~~vil~st~~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~tiee~i  459 (500)
T 1z63_A          391 NPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKI  459 (500)
T ss_dssp             CTTCCCCEEECCCC-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETTSHHHHT
T ss_pred             CCCCCEEEEecccccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCCCHHHHH
Confidence            8 565 799999999999999999999999999999999999999999743   345677777655433

>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=99.76  E-value=3e-18  Score=183.34  Aligned_cols=129  Identities=20%  Similarity=0.191  Sum_probs=112.1

Q ss_pred             eeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          92 EYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        92 ~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .|.....|+..+.+.+.....      .+.++||||+|+..++.|+..|.+.|  +++.+|||   ++.+.++..+.+.|
T Consensus       438 v~~t~~~K~~al~~~i~~~~~------~gqpvLVft~Sie~sE~Ls~~L~~~G--i~~~vLna---k~~~rEa~iia~ag  506 (922)
T 1nkt_A          438 IYKTEEAKYIAVVDDVAERYA------KGQPVLIGTTSVERSEYLSRQFTKRR--IPHNVLNA---KYHEQEATIIAVAG  506 (922)
T ss_dssp             EESCHHHHHHHHHHHHHHHHH------TTCCEEEEESCHHHHHHHHHHHHHTT--CCCEEECS---SCHHHHHHHHHTTT
T ss_pred             EEeCHHHHHHHHHHHHHHHHh------cCCcEEEEECCHHHHHHHHHHHHHCC--CCEEEecC---ChhHHHHHHHHhcC
Confidence            445556788888888876433      25689999999999999999999999  99999999   88888888888888


Q ss_pred             hcCCccEEEEcCccccCCCCCCC----------------------------------------------------CEEEE
Q psy4150         172 RAGEFNTLIATSVGEEGLDIGEI----------------------------------------------------DLVIC  199 (395)
Q Consensus       172 k~g~~~vLVaT~v~~~GlDip~v----------------------------------------------------~~VI~  199 (395)
                      +.|  .|+||||+++||+||+.+                                                    .+||+
T Consensus       507 r~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~  584 (922)
T 1nkt_A          507 RRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLG  584 (922)
T ss_dssp             STT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEE
T ss_pred             CCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEe
Confidence            887  699999999999999975                                                    59999


Q ss_pred             cCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         200 FDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       200 ~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                      |+.|.|...|+||+|||||.| .|.+++|++..++
T Consensus       585 te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          585 TERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             CSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             ccCCCCHHHHHHHhcccccCCCCeeEEEEechhHH
Confidence            999999999999999999998 6888888877654

>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=99.75  E-value=1.6e-19  Score=201.12  Aligned_cols=88  Identities=26%  Similarity=0.317  Sum_probs=73.0

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      ...|...|.+++..+         +.++||||+|+..|+.+++.|...   +++..+||   ++     ..++++|++|+
T Consensus       260 ~~~k~~~L~~ll~~~---------~~~~LVF~~t~~~a~~l~~~L~~~---~~v~~lhg---~~-----~~~l~~F~~G~  319 (1054)
T 1gku_B          260 NDESISTLSSILEKL---------GTGGIIYARTGEEAEEIYESLKNK---FRIGIVTA---TK-----KGDYEKFVEGE  319 (1054)
T ss_dssp             SCCCTTTTHHHHTTS---------CSCEEEEESSHHHHHHHHHTTTTS---SCEEECTT---SS-----SHHHHHHHHTS
T ss_pred             chhHHHHHHHHHhhc---------CCCEEEEEcCHHHHHHHHHHHhhc---cCeeEEec---cH-----HHHHHHHHcCC
Confidence            566777777776542         478999999999999999999876   78999999   77     37899999999


Q ss_pred             ccEEEE----cCccccCCCCCCC-CEEEEcCCC
Q psy4150         176 FNTLIA----TSVGEEGLDIGEI-DLVICFDAQ  203 (395)
Q Consensus       176 ~~vLVa----T~v~~~GlDip~v-~~VI~~d~p  203 (395)
                      ++||||    |+++++|||+|+| ++||+||+|
T Consensus       320 ~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P  352 (1054)
T 1gku_B          320 IDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP  352 (1054)
T ss_dssp             CSEEEEECC------CCSCCTTTCCEEEEESCC
T ss_pred             CcEEEEecCCCCeeEeccccCCcccEEEEeCCC
Confidence            999999    9999999999996 999999999

>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=99.75  E-value=1.8e-18  Score=176.17  Aligned_cols=101  Identities=17%  Similarity=0.203  Sum_probs=91.6

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      .+++||||+|+..|+.+++.|.+.+  +.+..+||   ++.    ..+++.|++|+++|||||+++++|||+|+ ++||+
T Consensus       188 ~~~~lVF~~s~~~a~~l~~~L~~~g--~~~~~lh~---~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~  257 (451)
T 2jlq_A          188 QGKTVWFVPSIKAGNDIANCLRKSG--KRVIQLSR---KTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVID  257 (451)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTTT--CCEEEECT---TTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEE
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHcC--CeEEECCH---HHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEE
Confidence            4699999999999999999999988  89999999   653    57999999999999999999999999999 99999


Q ss_pred             cC--------------------CCCChhhHhhhcccccccc--CceEEEEEeC
Q psy4150         200 FD--------------------AQKSPIKMVQRLGRTGRKR--NGRCVILLTQ  230 (395)
Q Consensus       200 ~d--------------------~p~s~~~yiQr~GRagR~~--~g~~i~l~~~  230 (395)
                      ||                    .|.+..+|+||+|||||.|  .|.++++...
T Consensus       258 ~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          258 PRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             CCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             CCCcccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence            99                    9999999999999999997  5677666543

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

Probab=99.75  E-value=3e-18  Score=189.67  Aligned_cols=122  Identities=21%  Similarity=0.283  Sum_probs=98.9

Q ss_pred             ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCC------------------------------
Q psy4150          97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPM------------------------------  146 (395)
Q Consensus        97 ~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~------------------------------  146 (395)
                      ..++..+...|..        ....++||||+|+..|+.++..|...+-.                              
T Consensus       321 ~~~~~~li~~l~~--------~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~  392 (997)
T 4a4z_A          321 KKTWPEIVNYLRK--------RELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQIL  392 (997)
T ss_dssp             TTHHHHHHHHHHH--------TTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHH
T ss_pred             hhHHHHHHHHHHh--------CCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHH
Confidence            3455555555544        34579999999999999999999876510                              


Q ss_pred             -------CceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC---------ChhhHh
Q psy4150         147 -------VKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK---------SPIKMV  210 (395)
Q Consensus       147 -------~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~---------s~~~yi  210 (395)
                             ..+.++||   +|++.+|..+++.|+.|.++|||||+++++|||+|+ ..||+++.|+         |+.+|+
T Consensus       393 ~l~~~l~~gi~~~H~---gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~  468 (997)
T 4a4z_A          393 KTRSLLERGIAVHHG---GLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFT  468 (997)
T ss_dssp             HHHHHHTTTEEEECT---TSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHH
T ss_pred             HHHHHhhcCeeeecC---CCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHh
Confidence                   14678888   999999999999999999999999999999999999 4555555554         999999


Q ss_pred             hhcccccccc---CceEEEEEeC
Q psy4150         211 QRLGRTGRKR---NGRCVILLTQ  230 (395)
Q Consensus       211 Qr~GRagR~~---~g~~i~l~~~  230 (395)
                      ||+|||||.|   .|.+++++..
T Consensus       469 Qr~GRAGR~G~~~~G~vi~l~~~  491 (997)
T 4a4z_A          469 QMAGRAGRRGLDSTGTVIVMAYN  491 (997)
T ss_dssp             HHHGGGCCTTTCSSEEEEEECCS
T ss_pred             HHhcccccCCCCcceEEEEecCC
Confidence            9999999986   6777766643

>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=99.73  E-value=1.6e-18  Score=187.26  Aligned_cols=125  Identities=19%  Similarity=0.218  Sum_probs=106.8

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcc---------cCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKP---------LEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~---------~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      +.......+......    ...+++||||+++..++.+++.|.+         ....+.+..+||   +|++.+|..+++
T Consensus       286 ~~~~~l~~l~~~~~~----~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg---~l~~~eR~~v~~  358 (773)
T 2xau_A          286 YLDSAIRTVLQIHAT----EEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYG---SLPPHQQQRIFE  358 (773)
T ss_dssp             HHHHHHHHHHHHHHH----SCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECT---TCCHHHHGGGGS
T ss_pred             HHHHHHHHHHHHHHh----cCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCC---CCCHHHHHHHHh
Confidence            444444444443332    3468999999999999999999975         112388999999   999999999999


Q ss_pred             HHh-----cCCccEEEEcCccccCCCCCCCCEEEEcCC------------------CCChhhHhhhccccccccCceEEE
Q psy4150         170 KFR-----AGEFNTLIATSVGEEGLDIGEIDLVICFDA------------------QKSPIKMVQRLGRTGRKRNGRCVI  226 (395)
Q Consensus       170 ~Fk-----~g~~~vLVaT~v~~~GlDip~v~~VI~~d~------------------p~s~~~yiQr~GRagR~~~g~~i~  226 (395)
                      .|+     .|..+|||||+++++|||||+|++||++++                  |.|..+|+||+|||||.+.|.++.
T Consensus       359 ~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~~~G~~~~  438 (773)
T 2xau_A          359 PAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFR  438 (773)
T ss_dssp             CCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSSSSEEEEE
T ss_pred             hcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCCCCCEEEE
Confidence            999     999999999999999999999999999888                  889999999999999998899988


Q ss_pred             EEeC
Q psy4150         227 LLTQ  230 (395)
Q Consensus       227 l~~~  230 (395)
                      ++++
T Consensus       439 l~~~  442 (773)
T 2xau_A          439 LYTE  442 (773)
T ss_dssp             SSCH
T ss_pred             EecH
Confidence            8764

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

Probab=99.73  E-value=1.4e-17  Score=178.38  Aligned_cols=110  Identities=17%  Similarity=0.306  Sum_probs=94.4

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCC----------------------------------CceeEEeccCCCCCHHHHH
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPM----------------------------------VKASMFVGQSSGVTQQEQK  165 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~----------------------------------~~~~~lhg~~~~~~~~~R~  165 (395)
                      ++++||||++++.++.++..|.+....                                  ..+.++||   +|++.+|.
T Consensus       252 ~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~---~l~~~~r~  328 (715)
T 2va8_A          252 NGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHA---GLSKALRD  328 (715)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECT---TSCHHHHH
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECC---CCCHHHHH
Confidence            589999999999999999999865321                                  24778888   99999999


Q ss_pred             HHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE----cC-------CCCChhhHhhhcccccccc---CceEEEEEeCC
Q psy4150         166 EIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC----FD-------AQKSPIKMVQRLGRTGRKR---NGRCVILLTQG  231 (395)
Q Consensus       166 ~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~----~d-------~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~  231 (395)
                      .+++.|++|.++|||||+++++|||+|++++||+    ||       .|.|..+|+||+|||||.|   .|.+++++++.
T Consensus       329 ~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~  408 (715)
T 2va8_A          329 LIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDK  408 (715)
T ss_dssp             HHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEECSCG
T ss_pred             HHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCCc
Confidence            9999999999999999999999999999999999    99       8999999999999999997   78888887665


Q ss_pred             c
Q psy4150         232 R  232 (395)
Q Consensus       232 ~  232 (395)
                      +
T Consensus       409 ~  409 (715)
T 2va8_A          409 E  409 (715)
T ss_dssp             G
T ss_pred             h
Confidence            4

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

Probab=99.72  E-value=2e-17  Score=183.12  Aligned_cols=112  Identities=21%  Similarity=0.268  Sum_probs=99.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCC-------------------------------------CceeEEeccCCCCCHH
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPM-------------------------------------VKASMFVGQSSGVTQQ  162 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~-------------------------------------~~~~~lhg~~~~~~~~  162 (395)
                      ..++||||+++..|+.++..|...+-.                                     ..+.++||   +|++.
T Consensus       343 ~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hg---gl~~~  419 (1010)
T 2xgj_A          343 YNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHS---GLLPI  419 (1010)
T ss_dssp             CCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEEST---TSCHH
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECC---CCCHH
Confidence            468999999999999999999875410                                     01567788   99999


Q ss_pred             HHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE----cCC----CCChhhHhhhcccccccc---CceEEEEEeCC
Q psy4150         163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC----FDA----QKSPIKMVQRLGRTGRKR---NGRCVILLTQG  231 (395)
Q Consensus       163 ~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~----~d~----p~s~~~yiQr~GRagR~~---~g~~i~l~~~~  231 (395)
                      +|..+++.|++|.++|||||+++++|||+|++++||+    ||.    |.++.+|+||+|||||.|   .|.+++++.+.
T Consensus       420 eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~  499 (1010)
T 2xgj_A          420 LKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEK  499 (1010)
T ss_dssp             HHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSC
T ss_pred             HHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCC
Confidence            9999999999999999999999999999999999999    999    899999999999999997   38888888766


Q ss_pred             chh
Q psy4150         232 REA  234 (395)
Q Consensus       232 ~e~  234 (395)
                      .+.
T Consensus       500 ~e~  502 (1010)
T 2xgj_A          500 MEP  502 (1010)
T ss_dssp             CCH
T ss_pred             CCH
Confidence            443

>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=99.72  E-value=6.4e-17  Score=171.66  Aligned_cols=136  Identities=17%  Similarity=0.220  Sum_probs=117.8

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      .+.|+..|..++.....     ..+.++||||+++.+++.|...|...|  +.+..+||   ++++.+|.++++.|++|.
T Consensus       397 ~s~K~~~l~~ll~~~~~-----~~~~k~lIFs~~~~~~~~l~~~l~~~g--~~~~~l~G---~~~~~~R~~~i~~F~~~~  466 (644)
T 1z3i_X          397 LSGKMLVLDYILAMTRT-----TTSDKVVLVSNYTQTLDLFEKLCRNRR--YLYVRLDG---TMSIKKRAKIVERFNNPS  466 (644)
T ss_dssp             GSHHHHHHHHHHHHHHH-----HCCCEEEEEESCHHHHHHHHHHHHHHT--CCEEEECS---SCCHHHHHHHHHHHHSTT
T ss_pred             cChHHHHHHHHHHHHhh-----cCCCEEEEEEccHHHHHHHHHHHHHCC--CCEEEEeC---CCCHHHHHHHHHHhcCCC
Confidence            35688888887776543     246899999999999999999999998  99999999   999999999999999987


Q ss_pred             cc---EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCc---eEEEEEeCCchhhHHHHHH
Q psy4150         176 FN---TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNG---RCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       176 ~~---vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g---~~i~l~~~~~e~~~~~~~~  241 (395)
                      ..   +||+|+++++|||++.+++||+||+|||+..|.|++||++|.|+.   .++.+++.++.++.+...+
T Consensus       467 ~~~~v~L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~tiEe~i~~~~  538 (644)
T 1z3i_X          467 SPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQRQ  538 (644)
T ss_dssp             CCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHHHHHHH
T ss_pred             CCcEEEEEecccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEEECCCHHHHHHHHH
Confidence            64   899999999999999999999999999999999999999999743   4566888887766654433

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

Probab=99.72  E-value=1.2e-17  Score=171.57  Aligned_cols=120  Identities=18%  Similarity=0.222  Sum_probs=102.5

Q ss_pred             cHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCcc
Q psy4150          98 LKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFN  177 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~  177 (395)
                      .+...+.+++.....     ..+.++|||++ ...++.|++.|.+.+  .++..+||   ++++.+|.++++.|++|+++
T Consensus       331 ~~~~~l~~~l~~~~~-----~~~~~~ivf~~-~~~~~~l~~~L~~~~--~~v~~~~g---~~~~~~r~~i~~~f~~g~~~  399 (510)
T 2oca_A          331 KRNKWIAKLAIKLAQ-----KDENAFVMFKH-VSHGKAIFDLIKNEY--DKVYYVSG---EVDTETRNIMKTLAENGKGI  399 (510)
T ss_dssp             HHHHHHHHHHHHHHT-----TTCEEEEEESS-HHHHHHHHHHHHTTC--SSEEEESS---STTHHHHHHHHHHHHHCCSC
T ss_pred             HHHHHHHHHHHHHHh-----cCCCeEEEEec-HHHHHHHHHHHHHcC--CCeEEEEC---CCCHHHHHHHHHHHhCCCCC
Confidence            455556666655443     23566777777 888889999999988  68999999   99999999999999999999


Q ss_pred             EEEEc-CccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCce-EEEEE
Q psy4150         178 TLIAT-SVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGR-CVILL  228 (395)
Q Consensus       178 vLVaT-~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~-~i~l~  228 (395)
                      ||||| +++++|+|+|+|++||++++|+++..|+||+||+||.|.++ .++++
T Consensus       400 vLv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~  452 (510)
T 2oca_A          400 IIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVW  452 (510)
T ss_dssp             EEEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEE
T ss_pred             EEEEEcChhhcccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEE
Confidence            99999 99999999999999999999999999999999999998654 44333

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

Probab=99.71  E-value=1.3e-17  Score=177.53  Aligned_cols=100  Identities=21%  Similarity=0.247  Sum_probs=92.5

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      +.++||||+++..++.+++.|...+  +++..+||   +    +|..+++.|++|+++|||||+++++|||+| +++||+
T Consensus       410 ~~~~lVF~~s~~~~e~la~~L~~~g--~~v~~lHg---~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~  479 (673)
T 2wv9_A          410 AGKTVWFVASVKMSNEIAQCLQRAG--KRVIQLNR---K----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVID  479 (673)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTTT--CCEEEECS---S----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhCC--CeEEEeCh---H----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEE
Confidence            5899999999999999999999988  99999999   4    688999999999999999999999999999 999998


Q ss_pred             --------------------cCCCCChhhHhhhccccccc-c-CceEEEEEe
Q psy4150         200 --------------------FDAQKSPIKMVQRLGRTGRK-R-NGRCVILLT  229 (395)
Q Consensus       200 --------------------~d~p~s~~~yiQr~GRagR~-~-~g~~i~l~~  229 (395)
                                          ||.|.+..+|+||+||+||. + .|.+++|+.
T Consensus       480 ~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~  531 (673)
T 2wv9_A          480 CRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGG  531 (673)
T ss_dssp             CCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECS
T ss_pred             CCCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEe
Confidence                                67899999999999999999 4 677777763

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

Probab=99.71  E-value=4.6e-17  Score=176.79  Aligned_cols=135  Identities=19%  Similarity=0.256  Sum_probs=119.7

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      .+.|+..|.++|..+..      .+.++||||+++.+++.|.++|...|  +.+..+||   +++..+|..+++.|+.|.
T Consensus       554 ~s~K~~~L~~lL~~~~~------~g~kvLIFsq~~~~ld~L~~~L~~~g--~~~~~i~G---~~~~~eR~~~i~~F~~~~  622 (800)
T 3mwy_W          554 SSGKMVLLDQLLTRLKK------DGHRVLIFSQMVRMLDILGDYLSIKG--INFQRLDG---TVPSAQRRISIDHFNSPD  622 (800)
T ss_dssp             TCHHHHHHHHHHHHHTT------TTCCEEEEESCHHHHHHHHHHHHHHT--CCCEEEST---TSCHHHHHHHHHTTSSTT
T ss_pred             cChHHHHHHHHHHHHhh------CCCeEEEEechHHHHHHHHHHHHhCC--CCEEEEeC---CCCHHHHHHHHHHhhCCC
Confidence            57799999999988754      36899999999999999999999988  99999999   999999999999999965


Q ss_pred             c---cEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC---ceEEEEEeCCchhhHHHHHH
Q psy4150         176 F---NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN---GRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       176 ~---~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~---g~~i~l~~~~~e~~~~~~~~  241 (395)
                      .   .+|++|.++++|||++.+++||+||+|||+..++||+||++|.|+   ..++.|++.++.+..+....
T Consensus       623 ~~~~v~LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe~i~~~~  694 (800)
T 3mwy_W          623 SNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERA  694 (800)
T ss_dssp             CSCCCEEEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHHHHHHHH
T ss_pred             CCceEEEEecccccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHHHHHHHH
Confidence            5   489999999999999999999999999999999999999999973   45667888888776654433

>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=99.70  E-value=2.9e-17  Score=176.24  Aligned_cols=110  Identities=22%  Similarity=0.338  Sum_probs=97.2

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCC-------------------------------CceeEEeccCCCCCHHHHHHHH
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPM-------------------------------VKASMFVGQSSGVTQQEQKEIM  168 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~-------------------------------~~~~~lhg~~~~~~~~~R~~~l  168 (395)
                      ++++||||++++.++.++..|.+....                               ..+.++||   +|++.+|..++
T Consensus       237 ~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~---~l~~~~R~~v~  313 (720)
T 2zj8_A          237 KKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHA---GLGRDERVLVE  313 (720)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECT---TSCHHHHHHHH
T ss_pred             CCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecC---CCCHHHHHHHH
Confidence            589999999999999999998753210                               23778888   99999999999


Q ss_pred             HHHhcCCccEEEEcCccccCCCCCCCCEEEE----cC----CCCChhhHhhhcccccccc---CceEEEEEeCCc
Q psy4150         169 KKFRAGEFNTLIATSVGEEGLDIGEIDLVIC----FD----AQKSPIKMVQRLGRTGRKR---NGRCVILLTQGR  232 (395)
Q Consensus       169 ~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~----~d----~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~~  232 (395)
                      +.|++|.++|||||+++++|||+|++++||+    ||    .|.+..+|+||+|||||.|   .|.+++++++.+
T Consensus       314 ~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  388 (720)
T 2zj8_A          314 ENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDD  388 (720)
T ss_dssp             HHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSC
T ss_pred             HHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCcc
Confidence            9999999999999999999999999999999    77    5889999999999999987   577888777655

>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=99.70  E-value=3e-17  Score=175.66  Aligned_cols=110  Identities=19%  Similarity=0.343  Sum_probs=97.2

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC----------------------------CCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP----------------------------MVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~----------------------------~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      ++++||||++++.++.++..|.+..+                            ...+.++||   +|++.+|..+++.|
T Consensus       242 ~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~---~l~~~~R~~v~~~f  318 (702)
T 2p6r_A          242 NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHA---GLLNGQRRVVEDAF  318 (702)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECT---TSCHHHHHHHHHHH
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecC---CCCHHHHHHHHHHH
Confidence            58999999999999999998875310                            024778888   99999999999999


Q ss_pred             hcCCccEEEEcCccccCCCCCCCCEEEE----cC---CCCChhhHhhhcccccccc---CceEEEEEeCCc
Q psy4150         172 RAGEFNTLIATSVGEEGLDIGEIDLVIC----FD---AQKSPIKMVQRLGRTGRKR---NGRCVILLTQGR  232 (395)
Q Consensus       172 k~g~~~vLVaT~v~~~GlDip~v~~VI~----~d---~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~~  232 (395)
                      ++|.++|||||+++++|||+|++++||+    ||   .|.+..+|+||+|||||.|   .|.++++++..+
T Consensus       319 ~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  389 (702)
T 2p6r_A          319 RRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  389 (702)
T ss_dssp             HTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             HCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCcc
Confidence            9999999999999999999999999999    77   7889999999999999997   678888776654

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

Probab=99.70  E-value=1.5e-17  Score=168.41  Aligned_cols=100  Identities=19%  Similarity=0.182  Sum_probs=88.2

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCE---
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDL---  196 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~---  196 (395)
                      ++++||||+++..++.+++.|.+.+  +++..+||   +    +|.+++++|++|+++|||||+++++|||+| +..   
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~~--~~v~~lhg---~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~  240 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKAG--KKVLYLNR---K----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVID  240 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHTT--CCEEEEST---T----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcC--CeEEEeCC---c----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEe
Confidence            4689999999999999999999987  89999999   5    578899999999999999999999999999 654   


Q ss_pred             --------------EEEcCCCCChhhHhhhcccccccc-CceEEEEEe
Q psy4150         197 --------------VICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLT  229 (395)
Q Consensus       197 --------------VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~  229 (395)
                                    ||+++.|.+..+|+||+||+||.| .+.+++++.
T Consensus       241 ~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          241 PRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             CCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             cCccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence                          688899999999999999999997 333444443

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

Probab=99.69  E-value=2.6e-17  Score=172.55  Aligned_cols=116  Identities=17%  Similarity=0.151  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCC------CceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPM------VKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~------~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      +...+.+.|.+++..   .....++||||+++..|+.+++.|.+.++.      -.+..+||   +++ .+|..++++|+
T Consensus       421 r~~~i~~~l~~~l~~---~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g---~~~-~~r~~~l~~F~  493 (590)
T 3h1t_A          421 RTDAFAKHLTDFMKR---TDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTS---EEG-KIGKGHLSRFQ  493 (590)
T ss_dssp             THHHHHHHHHHHHHH---HCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSS---TTH-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh---cCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeC---CCh-HHHHHHHHHHh
Confidence            444555555555443   144689999999999999999999876531      12567788   664 47999999999


Q ss_pred             cCCcc---EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC
Q psy4150         173 AGEFN---TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN  221 (395)
Q Consensus       173 ~g~~~---vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~  221 (395)
                      +|+.+   |||||+++++|||+|.|++||++++|+|+..|+||+||+||.+.
T Consensus       494 ~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          494 ELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             CTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             CCCCCCCEEEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            98876   89999999999999999999999999999999999999999864

>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=99.69  E-value=7.6e-17  Score=180.83  Aligned_cols=108  Identities=23%  Similarity=0.322  Sum_probs=100.2

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      +++++|||+++..++.+++.|.+..|.+++..+||   +|++.+|..++++|++|+++|||||+++++|||+|++++||+
T Consensus       812 g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg---~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi  888 (1151)
T 2eyq_A          812 GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHG---QMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIII  888 (1151)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCS---SCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEE
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeC---CCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEE
Confidence            68999999999999999999999866689999999   999999999999999999999999999999999999999999


Q ss_pred             cCC-CCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         200 FDA-QKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       200 ~d~-p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      +++ +++..+|+||+||+||.| .|.+++++.+
T Consensus       889 ~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~  921 (1151)
T 2eyq_A          889 ERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPH  921 (1151)
T ss_dssp             TTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECC
T ss_pred             eCCCCCCHHHHHHHHhccCcCCCceEEEEEECC
Confidence            998 569999999999999997 6777766654

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

Probab=99.68  E-value=2e-16  Score=168.19  Aligned_cols=94  Identities=18%  Similarity=0.235  Sum_probs=89.6

Q ss_pred             ccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhc--CCccEEEEcCccccCCCCCCCCEEE
Q psy4150         121 TKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRA--GEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       121 ~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~--g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      ...||||+|+..++.+++.|.+.+  +.+..+||   +|++.+|..+++.|+.  |.++|||||+++++|||+ .|++||
T Consensus       321 ~g~iIf~~s~~~ie~la~~L~~~g--~~v~~lHG---~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI  394 (677)
T 3rc3_A          321 PGDCIVCFSKNDIYSVSRQIEIRG--LESAVIYG---SLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRII  394 (677)
T ss_dssp             TTEEEECSSHHHHHHHHHHHHHTT--CCCEEECT---TSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEE
T ss_pred             CCCEEEEcCHHHHHHHHHHHHhcC--CCeeeeec---cCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEE
Confidence            445899999999999999999988  89999999   9999999999999999  889999999999999999 899999


Q ss_pred             EcCC--------------CCChhhHhhhcccccccc
Q psy4150         199 CFDA--------------QKSPIKMVQRLGRTGRKR  220 (395)
Q Consensus       199 ~~d~--------------p~s~~~yiQr~GRagR~~  220 (395)
                      ++|+              |.+..+|+||+|||||.|
T Consensus       395 ~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g  430 (677)
T 3rc3_A          395 FYSLIKPSINEKGERELEPITTSQALQIAGRAGRFS  430 (677)
T ss_dssp             ESCSBC-----------CBCCHHHHHHHHTTBTCTT
T ss_pred             ECCccccccccCCccccccCCHHHHHHHhcCCCCCC
Confidence            9999              779999999999999997

>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=99.66  E-value=4.5e-17  Score=172.01  Aligned_cols=102  Identities=25%  Similarity=0.307  Sum_probs=89.9

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      .++++||||+|++.++.+++.|.+.+  +.+..+||   +|++.+       |+.+..+||||||++++|||+| |++||
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~g--~~v~~lHG---~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI  461 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGLG--INAVAYYR---GLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVI  461 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTTT--CCEEEECT---TSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEE
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhCC--CcEEEecC---CCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEE
Confidence            36899999999999999999999998  99999999   999875       5567779999999999999997 99988


Q ss_pred             ----------EcC-----------CCCChhhHhhhccccccccCceEEEEEeCCchh
Q psy4150         199 ----------CFD-----------AQKSPIKMVQRLGRTGRKRNGRCVILLTQGREA  234 (395)
Q Consensus       199 ----------~~d-----------~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~  234 (395)
                                |||           .|.+..+|+||+|||||.+.|. +.|+++.+..
T Consensus       462 ~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGRg~~G~-i~lvt~~e~~  517 (666)
T 3o8b_A          462 DCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGRRGI-YRFVTPGERP  517 (666)
T ss_dssp             ECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCSSSCEE-EEESCCCCBC
T ss_pred             ecCcccccccccccccccccccccCcCCHHHHHHHhccCCCCCCCE-EEEEecchhh
Confidence                      788           8999999999999999955777 7777765543

>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=99.66  E-value=2.9e-17  Score=177.09  Aligned_cols=126  Identities=19%  Similarity=0.371  Sum_probs=104.7

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcH--------HHHHHHHHHHcc-cCCCCceeEEeccCCCCCHHHHH
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYR--------VVVAEIFDVLKP-LEPMVKASMFVGQSSGVTQQEQK  165 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~--------~~ae~l~~~L~~-~~~~~~~~~lhg~~~~~~~~~R~  165 (395)
                      ....+...+.+.+.....      .+.+++|||++.        ..++.+++.|.+ ..+.+.+..+||   +|++.+|.
T Consensus       559 ~~~~~~~~l~~~i~~~l~------~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG---~m~~~eR~  629 (780)
T 1gm5_A          559 VPMDRVNEVYEFVRQEVM------RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHG---RLSQEEKD  629 (780)
T ss_dssp             CCSSTHHHHHHHHHHHTT------TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCS---SSCCSCSH
T ss_pred             eccchHHHHHHHHHHHHh------cCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeC---CCCHHHHH
Confidence            344566666666665443      368999999965        458889999988 545589999999   99999999


Q ss_pred             HHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC-ChhhHhhhcccccccc-CceEEEEEe
Q psy4150         166 EIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-SPIKMVQRLGRTGRKR-NGRCVILLT  229 (395)
Q Consensus       166 ~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~-s~~~yiQr~GRagR~~-~g~~i~l~~  229 (395)
                      .++++|++|+++|||||+++++|||+|+|++||++|+|. +...|.||+||+||.| .|.+++++.
T Consensus       630 ~v~~~F~~G~~~ILVaT~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~  695 (780)
T 1gm5_A          630 RVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVG  695 (780)
T ss_dssp             HHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCC
T ss_pred             HHHHHHHCCCCeEEEECCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEEC
Confidence            999999999999999999999999999999999999996 6888999999999997 677776665

>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=99.53  E-value=7.5e-15  Score=169.75  Aligned_cols=112  Identities=16%  Similarity=0.360  Sum_probs=91.8

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccC----C-------------------------------CCceeEEeccCCCCCHH
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLE----P-------------------------------MVKASMFVGQSSGVTQQ  162 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~----~-------------------------------~~~~~~lhg~~~~~~~~  162 (395)
                      ..++++||||+||+.|+.++..|.+..    .                               ...+.+.||   +|++.
T Consensus       315 ~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHa---gL~~~  391 (1724)
T 4f92_B          315 AGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHA---GMTRV  391 (1724)
T ss_dssp             CSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECS---SSCTH
T ss_pred             hcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcC---CCCHH
Confidence            346789999999999998888775320    0                               023566677   99999


Q ss_pred             HHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE----cCC------CCChhhHhhhcccccccc---CceEEEEEe
Q psy4150         163 EQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC----FDA------QKSPIKMVQRLGRTGRKR---NGRCVILLT  229 (395)
Q Consensus       163 ~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~----~d~------p~s~~~yiQr~GRagR~~---~g~~i~l~~  229 (395)
                      +|..+.+.|++|.++|||||+++++|||+|.+++||.    ||.      |-++.+|+||+|||||.|   .|.+++++.
T Consensus       392 ~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~  471 (1724)
T 4f92_B          392 DRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITS  471 (1724)
T ss_dssp             HHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEE
T ss_pred             HHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEec
Confidence            9999999999999999999999999999999999995    554      458999999999999996   577776665


Q ss_pred             CCc
Q psy4150         230 QGR  232 (395)
Q Consensus       230 ~~~  232 (395)
                      ..+
T Consensus       472 ~~~  474 (1724)
T 4f92_B          472 HGE  474 (1724)
T ss_dssp             STT
T ss_pred             chh
Confidence            544

>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=99.46  E-value=1.3e-13  Score=159.54  Aligned_cols=111  Identities=17%  Similarity=0.280  Sum_probs=91.4

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccC-----C---------------------------CCceeEEeccCCCCCHHHHH
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLE-----P---------------------------MVKASMFVGQSSGVTQQEQK  165 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~-----~---------------------------~~~~~~lhg~~~~~~~~~R~  165 (395)
                      ..+.++||||+|+..|+.++..|....     +                           ...+.++||   +|++.+|.
T Consensus      1153 ~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHa---gL~~~~R~ 1229 (1724)
T 4f92_B         1153 SPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHE---GLSPMERR 1229 (1724)
T ss_dssp             CSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECT---TSCHHHHH
T ss_pred             cCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECC---CCCHHHHH
Confidence            456899999999999998887663210     0                           123667788   99999999


Q ss_pred             HHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE----cC------CCCChhhHhhhcccccccc---CceEEEEEeCC
Q psy4150         166 EIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC----FD------AQKSPIKMVQRLGRTGRKR---NGRCVILLTQG  231 (395)
Q Consensus       166 ~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~----~d------~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~  231 (395)
                      .+.+.|++|.++|||||+++++|||+|.+.+||.    ||      .|-++.+|+||+|||||+|   .|.+++++.+.
T Consensus      1230 ~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~ 1308 (1724)
T 4f92_B         1230 LVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGS 1308 (1724)
T ss_dssp             HHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGG
T ss_pred             HHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecch
Confidence            9999999999999999999999999999999983    33      3568999999999999997   57777776643

>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=99.31  E-value=1.1e-11  Score=137.11  Aligned_cols=123  Identities=11%  Similarity=0.231  Sum_probs=92.1

Q ss_pred             cHHHHHHHHHHHHHHhhhc----cCCCccEEEEcCcHHHHHHHHHHHcccCC----------CCce-eEEeccCC-----
Q psy4150          98 LKFIRLREILESHFRLHAE----KGETTKVIIFANYRVVVAEIFDVLKPLEP----------MVKA-SMFVGQSS-----  157 (395)
Q Consensus        98 ~K~~~L~~lL~~~~~~~~~----~~~~~r~iVF~~t~~~ae~l~~~L~~~~~----------~~~~-~~lhg~~~-----  157 (395)
                      .++..+...+..++.....    ...+.++||||+++..|..+++.|.+.++          .+++ .++||..+     
T Consensus       511 ~ri~~I~~~Il~~~~~~~~~~~~~~~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~  590 (1038)
T 2w00_A          511 MRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNA  590 (1038)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSSSSCCCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------
T ss_pred             HHHHHHHHHHHHHHHHhhhhhcccCCCCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCcccccc
Confidence            3455555555555533110    01346899999999999999999987641          2455 44554210     


Q ss_pred             --C----------CCH-----------------------------HHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCE
Q psy4150         158 --G----------VTQ-----------------------------QEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDL  196 (395)
Q Consensus       158 --~----------~~~-----------------------------~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~  196 (395)
                        .          |++                             .+|..++++|++|+++|||+|+++.+|+|+|.+ .
T Consensus       591 ~G~~~~e~~~~~~~~~~~r~~l~~~I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~  669 (1038)
T 2w00_A          591 IGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-N  669 (1038)
T ss_dssp             CCCCCCCCSCGGGSCHHHHHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-E
T ss_pred             ccccccccccccccchhHHHHHHHHHHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-c
Confidence              1          232                             248899999999999999999999999999999 7


Q ss_pred             EEEcCCCCChhhHhhhccccccccC
Q psy4150         197 VICFDAQKSPIKMVQRLGRTGRKRN  221 (395)
Q Consensus       197 VI~~d~p~s~~~yiQr~GRagR~~~  221 (395)
                      |+++|.|.+...|+||+||++|.+.
T Consensus       670 tlylDkpl~~~~liQaIGRtnR~~~  694 (1038)
T 2w00_A          670 TLFVDKNLRYHGLMQAFSRTNRIYD  694 (1038)
T ss_dssp             EEEEESCCCHHHHHHHHHTTCCCCC
T ss_pred             EEEEccCCCccceeehhhccCcCCC
Confidence            8899999999999999999999854

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.44  E-value=4e-07  Score=94.41  Aligned_cols=88  Identities=10%  Similarity=0.194  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEE
Q psy4150         101 IRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLI  180 (395)
Q Consensus       101 ~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLV  180 (395)
                      ..+.+.|.....     ...+++|||++|....+.+++.|...     ..+.+|   ..  ..|..+++.|+.|. .||+
T Consensus       370 ~~~~~~l~~~~~-----~~~g~~lvff~S~~~~~~v~~~l~~~-----~~~~q~---~~--~~~~~~l~~f~~~~-~il~  433 (540)
T 2vl7_A          370 PIYSILLKRIYE-----NSSKSVLVFFPSYEMLESVRIHLSGI-----PVIEEN---KK--TRHEEVLELMKTGK-YLVM  433 (540)
T ss_dssp             HHHHHHHHHHHH-----TCSSEEEEEESCHHHHHHHHTTCTTS-----CEEEST---TT--CCHHHHHHHHHTSC-CEEE
T ss_pred             HHHHHHHHHHHH-----hCCCCEEEEeCCHHHHHHHHHHhccC-----ceEecC---CC--CcHHHHHHHHhcCC-eEEE
Confidence            556666666544     24578999999999999999888642     245565   32  45888999999865 5666


Q ss_pred             --EcCccccCCCCCC----CCEEEEcCCCC
Q psy4150         181 --ATSVGEEGLDIGE----IDLVICFDAQK  204 (395)
Q Consensus       181 --aT~v~~~GlDip~----v~~VI~~d~p~  204 (395)
                        ||+.+.+|||+|+    +++||++++|.
T Consensus       434 ~V~~~~~~EGiD~~~~~~~~~~Vii~~lPf  463 (540)
T 2vl7_A          434 LVMRAKESEGVEFREKENLFESLVLAGLPY  463 (540)
T ss_dssp             EEC---------------CEEEEEEESCCC
T ss_pred             EEecCceecceecCCCcccccEEEEECCCC
Confidence              8999999999997    89999999985

>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=98.43  E-value=1.9e-06  Score=83.30  Aligned_cols=130  Identities=17%  Similarity=0.111  Sum_probs=95.1

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ..+.|+..|..+|.....      .+.++|||++...+.+-|.++|...+  +....+.|   .....++.     -.++
T Consensus       106 ~~SGKf~~L~~LL~~l~~------~~~kVLIfsq~t~~LDilE~~l~~~~--~~y~RlDG---~~~~~~~k-----~~~~  169 (328)
T 3hgt_A          106 ENSGKFSVLRDLINLVQE------YETETAIVCRPGRTMDLLEALLLGNK--VHIKRYDG---HSIKSAAA-----ANDF  169 (328)
T ss_dssp             HTCHHHHHHHHHHHHHTT------SCEEEEEEECSTHHHHHHHHHHTTSS--CEEEESSS---CCC------------CC
T ss_pred             HcCccHHHHHHHHHHHHh------CCCEEEEEECChhHHHHHHHHHhcCC--CceEeCCC---Cchhhhhh-----cccC
Confidence            356799999999987643      47899999999999999999999888  88888888   42222211     1245


Q ss_pred             CccEEEEcCccccCCC-----CCCCCEEEEcCCCCChhhH-hhhcccccccc-----CceEEEEEeCCchhhHHHHH
Q psy4150         175 EFNTLIATSVGEEGLD-----IGEIDLVICFDAQKSPIKM-VQRLGRTGRKR-----NGRCVILLTQGREAHNFQTS  240 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlD-----ip~v~~VI~~d~p~s~~~y-iQr~GRagR~~-----~g~~i~l~~~~~e~~~~~~~  240 (395)
                      .+.+.+.|..+.-|++     +...+.||.||..|++..= +|.+-|+.|.|     .-.++-+++.++-++.....
T Consensus       170 ~~~i~Lltsag~~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiEh~~l~~  246 (328)
T 3hgt_A          170 SCTVHLFSSEGINFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFF  246 (328)
T ss_dssp             SEEEEEEESSCCCTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHHHHHHHH
T ss_pred             CceEEEEECCCCCCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHHHHHHHc
Confidence            5566555777777776     6789999999999999874 88887777763     34577889998887765544

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.15  E-value=1.9e-05  Score=85.07  Aligned_cols=129  Identities=20%  Similarity=0.213  Sum_probs=93.8

Q ss_pred             eeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHc-----------------------------
Q psy4150          91 SEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLK-----------------------------  141 (395)
Q Consensus        91 ~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~-----------------------------  141 (395)
                      ..|.....|+..+.+-+.+....      +.+|||+|.|....+.|+..|.                             
T Consensus       420 ~vy~t~~~K~~AIv~eI~~~~~~------GqPVLVgT~SIe~SE~LS~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  493 (997)
T 2ipc_A          420 VVYRTEKGKFYAVVEEIAEKYER------GQPVLVGTISIEKSERLSQMLKEPRLYLPRLEMRLELFKKASQKQQGPEWE  493 (997)
T ss_dssp             EEESSHHHHHHHHHHHHHHHHHH------TCCEEEECSSHHHHHHHHHHHHCGGGGHHHHHHHHHHHHHHHTTCCSHHHH
T ss_pred             eEEcCHHHHHHHHHHHHHHHHHC------CCCEEEEeCCHHHHHHHHHHHhhccccchhhhhhhhhhhhhhhhccccchh
Confidence            44556677888887767665543      6899999999999999999998                             


Q ss_pred             -----------------------------------------------ccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150         142 -----------------------------------------------PLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus       142 -----------------------------------------------~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                                                                     +.|  ++..+|..   .-...+ .+++.  ..|
T Consensus       494 ~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g--I~H~VLNA---K~he~E-AeIIA--qAG  565 (997)
T 2ipc_A          494 RLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVLRQG--IPHQVLNA---KHHARE-AEIVA--QAG  565 (997)
T ss_dssp             HHHHHTSSSTTCSHHHHSGGGGGCCSSHHHHHHHHHHHHHHHHHHHHHHC--CCCCEECS---SSHHHH-HHHHH--TTT
T ss_pred             hhhhhhhccccccccccccccccccccccccccccccchhhhhhHHHHcC--CCeeeccc---cchHHH-HHHHH--hcC
Confidence                                                           233  55555555   222222 22332  345


Q ss_pred             -CccEEEEcCccccCCCCCCC-------------------C---------------------------------------
Q psy4150         175 -EFNTLIATSVGEEGLDIGEI-------------------D---------------------------------------  195 (395)
Q Consensus       175 -~~~vLVaT~v~~~GlDip~v-------------------~---------------------------------------  195 (395)
                       .-.|-|||+.++||.||-=-                   +                                       
T Consensus       566 ~~GaVTIATNMAGRGTDIkLggn~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  645 (997)
T 2ipc_A          566 RSKTVTIATNMAGRGTDIKLGGNPEYLAAALLEKEGFDRYEWKVELFIKKMVAGKEEEARALAQELGIREELLERIREIR  645 (997)
T ss_dssp             STTCEEEECSSTTTTSCCCSSCCHHHHHHHTTSSSCSSTTHHHHHHHHHHHHHTCHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCeEEEEecccCCCcCeecCCCHHHHHHHHHHhhcccccccccccccccccccchhhccccchhhhhhhhHHHHHHHhh
Confidence             45688999999999999522                   1                                       


Q ss_pred             ----------------EEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCch
Q psy4150         196 ----------------LVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGRE  233 (395)
Q Consensus       196 ----------------~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e  233 (395)
                                      +||--..+.|..--.|-.||+||.| +|...+|++-.++
T Consensus       646 ~~~~~e~~~V~e~GGLhVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeDd  700 (997)
T 2ipc_A          646 EECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDDD  700 (997)
T ss_dssp             HHHHHHHHHHTTTCCCCEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSSH
T ss_pred             hhhhhhhhHHHhcCCeEEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECChH
Confidence                            7888889999999999999999998 6777677665543

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=97.55  E-value=0.00019  Score=75.52  Aligned_cols=91  Identities=19%  Similarity=0.277  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ...+.+.|......     .+++++||++|....+.+++.|....  .+   ...   +++..++..+++.|+ ++-.||
T Consensus       433 ~~~~~~~i~~l~~~-----~~g~~lvlF~Sy~~l~~v~~~l~~~~--~~---~~q---~~~~~~~~~ll~~f~-~~~~vL  498 (620)
T 4a15_A          433 LDRMATVIEDIILK-----VKKNTIVYFPSYSLMDRVENRVSFEH--MK---EYR---GIDQKELYSMLKKFR-RDHGTI  498 (620)
T ss_dssp             HHHHHHHHHHHHHH-----HCSCEEEEESCHHHHHHHTSSCCSCC--EE---CCT---TCCSHHHHHHHHHHT-TSCCEE
T ss_pred             HHHHHHHHHHHHHh-----CCCCEEEEeCCHHHHHHHHHHHHhcc--hh---ccC---CCChhHHHHHHHHhc-cCCcEE
Confidence            34555666665543     25779999999999999999887222  22   333   677778999999999 888999


Q ss_pred             EEcC--ccccCCCCCC--CCEEEEcCCCC
Q psy4150         180 IATS--VGEEGLDIGE--IDLVICFDAQK  204 (395)
Q Consensus       180 VaT~--v~~~GlDip~--v~~VI~~d~p~  204 (395)
                      +||.  .+.+|||+|+  +.+||+..+|.
T Consensus       499 ~~v~~gsf~EGiD~~g~~l~~viI~~lPf  527 (620)
T 4a15_A          499 FAVSGGRLSEGINFPGNELEMIILAGLPF  527 (620)
T ss_dssp             EEETTSCC--------CCCCEEEESSCCC
T ss_pred             EEEecCceeccccCCCCceEEEEEEcCCC
Confidence            9985  8999999996  78999998884

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=96.55  E-value=0.016  Score=59.73  Aligned_cols=89  Identities=9%  Similarity=0.140  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEE
Q psy4150         100 FIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTL  179 (395)
Q Consensus       100 ~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vL  179 (395)
                      ...+.+.|......     .++++|||+++....+.+++.   .+  . ..+..+.  +++   +..+++.|+.+.-.||
T Consensus       378 ~~~l~~~i~~l~~~-----~~g~~lvlF~Sy~~l~~v~~~---~~--~-~v~~q~~--~~~---~~~~~~~~~~~~~~vl  441 (551)
T 3crv_A          378 WKRYADYLLKIYFQ-----AKANVLVVFPSYEIMDRVMSR---IS--L-PKYVESE--DSS---VEDLYSAISANNKVLI  441 (551)
T ss_dssp             HHHHHHHHHHHHHH-----CSSEEEEEESCHHHHHHHHTT---CC--S-SEEECCS--SCC---HHHHHHHTTSSSSCEE
T ss_pred             HHHHHHHHHHHHHh-----CCCCEEEEecCHHHHHHHHHh---cC--C-cEEEcCC--CCC---HHHHHHHHHhcCCeEE
Confidence            45667777666553     356999999999999998872   22  2 2333331  344   3457778854444899


Q ss_pred             EEc--CccccCCCCC-----CCCEEEEcCCCC
Q psy4150         180 IAT--SVGEEGLDIG-----EIDLVICFDAQK  204 (395)
Q Consensus       180 VaT--~v~~~GlDip-----~v~~VI~~d~p~  204 (395)
                      +||  ..+.+|||+|     .+.+||...+|.
T Consensus       442 ~~v~gg~~~EGiD~~d~~g~~l~~viI~~lPf  473 (551)
T 3crv_A          442 GSVGKGKLAEGIELRNNDRSLISDVVIVGIPY  473 (551)
T ss_dssp             EEESSCCSCCSSCCEETTEESEEEEEEESCCC
T ss_pred             EEEecceecccccccccCCcceeEEEEEcCCC
Confidence            998  6999999999     488999888774

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=95.98  E-value=0.027  Score=60.60  Aligned_cols=101  Identities=13%  Similarity=0.230  Sum_probs=78.5

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .+..|.....-.+...+..      +.+++|.++|+.-+..+++.+.+..+  ++++..+||   +++..+|...+..+.
T Consensus       398 TGSGKTlvall~il~~l~~------g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G---~~~~~~r~~~~~~l~  468 (780)
T 1gm5_A          398 VGSGKTVVAQLAILDNYEA------GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIG---ATTPSEKEKIKSGLR  468 (780)
T ss_dssp             SSSSHHHHHHHHHHHHHHH------TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCS---SSCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHc------CCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeC---CCCHHHHHHHHHHHh
Confidence            4556766655444444433      57999999999998888877665421  288999999   999999999999999


Q ss_pred             cCCccEEEEcC-ccccCCCCCCCCEEEEcCCCC
Q psy4150         173 AGEFNTLIATS-VGEEGLDIGEIDLVICFDAQK  204 (395)
Q Consensus       173 ~g~~~vLVaT~-v~~~GlDip~v~~VI~~d~p~  204 (395)
                      +|.++|+|+|. .+...+++..+.+||.=....
T Consensus       469 ~g~~~IvVgT~~ll~~~~~~~~l~lVVIDEaHr  501 (780)
T 1gm5_A          469 NGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHR  501 (780)
T ss_dssp             SSCCCEEEECTTHHHHCCCCSCCCEEEEESCCC
T ss_pred             cCCCCEEEECHHHHhhhhhccCCceEEecccch
Confidence            99999999995 456678899999998766553

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

Probab=93.84  E-value=0.21  Score=48.75  Aligned_cols=98  Identities=17%  Similarity=0.140  Sum_probs=71.5

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC-CCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP-MVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~-~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      .+..|.-...-.+....      ..+.++||.++|+..+..+++.+...++ .+++..+||   +.+..++...++.+..
T Consensus        45 TGsGKT~~~l~~~~~~~------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g---~~~~~~~~~~~~~l~~  115 (414)
T 3oiy_A           45 TGVGKTTFGMMTALWLA------RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYS---SMKKEEKEKFEKSFEE  115 (414)
T ss_dssp             SSSSHHHHHHHHHHHHH------TTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCT---TSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHh------cCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEEC---CCChhhHHHHHHHhhc
Confidence            45557663333322222      2368999999999999999999988542 389999999   9999999999999999


Q ss_pred             CCccEEEEcCc-----cccCCCCCCCCEEEEcCC
Q psy4150         174 GEFNTLIATSV-----GEEGLDIGEIDLVICFDA  202 (395)
Q Consensus       174 g~~~vLVaT~v-----~~~GlDip~v~~VI~~d~  202 (395)
                      |..+|+|||.-     +.. +++..+++||.=.+
T Consensus       116 ~~~~Iiv~Tp~~l~~~l~~-~~~~~~~~iViDEa  148 (414)
T 3oiy_A          116 DDYHILVFSTQFVSKNREK-LSQKRFDFVFVDDV  148 (414)
T ss_dssp             TCCSEEEEEHHHHHHCHHH-HTTCCCSEEEESCH
T ss_pred             CCCCEEEECHHHHHHHHHH-hccccccEEEEeCh
Confidence            99999999953     122 44556676665444

>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=93.24  E-value=0.39  Score=41.74  Aligned_cols=101  Identities=17%  Similarity=0.256  Sum_probs=64.7

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      .+..|.-...-.+...+........+.++||.|+++..+..+++.+....+.+++..++|   +.+.......+.    .
T Consensus        47 TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~----~  119 (207)
T 2gxq_A           47 TGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYG---GTGYGKQKEALL----R  119 (207)
T ss_dssp             TTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECS---SSCSHHHHHHHH----H
T ss_pred             CCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEEC---CCChHHHHHHhh----C
Confidence            455677654333333322111113467899999999999999999998876688888888   665544433332    2


Q ss_pred             CccEEEEcC-----ccc-cCCCCCCCCEEEEcCC
Q psy4150         175 EFNTLIATS-----VGE-EGLDIGEIDLVICFDA  202 (395)
Q Consensus       175 ~~~vLVaT~-----v~~-~GlDip~v~~VI~~d~  202 (395)
                      ..+|+|+|.     .+. ..+++..+++||.=.+
T Consensus       120 ~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEa  153 (207)
T 2gxq_A          120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEA  153 (207)
T ss_dssp             CCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESH
T ss_pred             CCCEEEECHHHHHHHHHcCCcchhhceEEEEECh
Confidence            588999995     222 3456777777775443

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=93.11  E-value=0.32  Score=54.60  Aligned_cols=96  Identities=15%  Similarity=0.174  Sum_probs=72.8

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .+..|.......+.....      .+.+++|.|+|+..+...++.+.+..+  .+.+..++|   ..+..++..+++.+.
T Consensus       633 TGsGKT~val~aa~~~~~------~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~---~~~~~~~~~~~~~l~  703 (1151)
T 2eyq_A          633 VGFGKTEVAMRAAFLAVD------NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISR---FRSAKEQTQILAEVA  703 (1151)
T ss_dssp             CCTTTHHHHHHHHHHHHT------TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEEST---TSCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHH------hCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeC---CCCHHHHHHHHHHHh
Confidence            445576554333322222      357999999999999988888775432  267888998   888999999999999


Q ss_pred             cCCccEEEEc-CccccCCCCCCCCEEEE
Q psy4150         173 AGEFNTLIAT-SVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       173 ~g~~~vLVaT-~v~~~GlDip~v~~VI~  199 (395)
                      .|.++|+|+| .++...+.+.++.+||.
T Consensus       704 ~g~~dIvV~T~~ll~~~~~~~~l~lvIi  731 (1151)
T 2eyq_A          704 EGKIDILIGTHKLLQSDVKFKDLGLLIV  731 (1151)
T ss_dssp             TTCCSEEEECTHHHHSCCCCSSEEEEEE
T ss_pred             cCCCCEEEECHHHHhCCccccccceEEE
Confidence            9999999999 56666788888888874

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

Probab=92.97  E-value=0.23  Score=55.48  Aligned_cols=99  Identities=17%  Similarity=0.140  Sum_probs=75.0

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC-CCCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE-PMVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~-~~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      ..+..|-...+-.+....      ..+.++||.++|+..|..+++.|...+ ..+++..+||   +++..+|...++.+.
T Consensus       101 pTGSGKTl~~l~~il~~~------~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~G---g~~~~er~~~~~~l~  171 (1104)
T 4ddu_A          101 PTGVGKTTFGMMTALWLA------RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYS---SMKKEEKEKFEKSFE  171 (1104)
T ss_dssp             STTCCHHHHHHHHHHHHH------TTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECT---TCCTTHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHH------hcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeC---CCCHHHHHHHHHHHh
Confidence            345667775444443333      236899999999999999999998843 2379999999   999988899999999


Q ss_pred             cCCccEEEEcCc-----cccCCCCCCCCEEEEcCC
Q psy4150         173 AGEFNTLIATSV-----GEEGLDIGEIDLVICFDA  202 (395)
Q Consensus       173 ~g~~~vLVaT~v-----~~~GlDip~v~~VI~~d~  202 (395)
                      .|..+|||||.-     +.. +++..+++||.=.+
T Consensus       172 ~g~~~IlV~Tp~rL~~~l~~-l~~~~l~~lViDEa  205 (1104)
T 4ddu_A          172 EDDYHILVFSTQFVSKNREK-LSQKRFDFVFVDDV  205 (1104)
T ss_dssp             TSCCSEEEEEHHHHHHSHHH-HHTSCCSEEEESCH
T ss_pred             CCCCCEEEECHHHHHHHHHh-hcccCcCEEEEeCC
Confidence            999999999952     222 55667888886554

>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=90.87  E-value=1.4  Score=38.64  Aligned_cols=98  Identities=15%  Similarity=0.200  Sum_probs=62.9

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC---CCCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE---PMVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~---~~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .+..|.-...-.+...+..   .....++||.|+|+..+..+++.+.+..   +.+++..++|   +.+...+..   .+
T Consensus        60 TGsGKT~~~~~~~~~~~~~---~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g---~~~~~~~~~---~~  130 (220)
T 1t6n_A           60 SGMGKTAVFVLATLQQLEP---VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFG---GLSIKKDEE---VL  130 (220)
T ss_dssp             TTSCHHHHHHHHHHHHCCC---CTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESC---CSCHHHHHH---HH
T ss_pred             CCCchhhhhhHHHHHhhhc---cCCCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeC---CCChHHHHH---HH
Confidence            4555765544333333221   1234589999999999999888776653   2478889999   777665543   44


Q ss_pred             hcCCccEEEEcCc-----c-ccCCCCCCCCEEEEcC
Q psy4150         172 RAGEFNTLIATSV-----G-EEGLDIGEIDLVICFD  201 (395)
Q Consensus       172 k~g~~~vLVaT~v-----~-~~GlDip~v~~VI~~d  201 (395)
                      ..+..+|+|+|.-     + ...+++..+++||.=.
T Consensus       131 ~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDE  166 (220)
T 1t6n_A          131 KKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE  166 (220)
T ss_dssp             HHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEES
T ss_pred             hcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcC
Confidence            5677899999952     1 2335566666666433

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=90.12  E-value=1.1  Score=39.90  Aligned_cols=75  Identities=19%  Similarity=0.369  Sum_probs=50.6

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCc-----ccc--CC
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSV-----GEE--GL  189 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v-----~~~--Gl  189 (395)
                      .+.++||.|+|+..+..+++.+...+.  .+.+..++|   +.+.......+     +..+|+|+|.-     +.+  .+
T Consensus        96 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~  167 (236)
T 2pl3_A           96 DGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIG---GKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSF  167 (236)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECC---C--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSC
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEEC---CCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCc
Confidence            357899999999999999988877653  277888888   66544433332     46899999952     222  35


Q ss_pred             CCCCCCEEEEcC
Q psy4150         190 DIGEIDLVICFD  201 (395)
Q Consensus       190 Dip~v~~VI~~d  201 (395)
                      ++..+++||.=.
T Consensus       168 ~~~~~~~lViDE  179 (236)
T 2pl3_A          168 HATDLQMLVLDE  179 (236)
T ss_dssp             CCTTCCEEEETT
T ss_pred             ccccccEEEEeC
Confidence            666677666543

>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=90.11  E-value=1  Score=40.43  Aligned_cols=77  Identities=16%  Similarity=0.190  Sum_probs=55.5

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-----ccc-cCCC
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-----VGE-EGLD  190 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-----v~~-~GlD  190 (395)
                      .+.++||.++|+..+..+.+.+...+  ..+.+..++|   +.+...+...+..    ..+|+|||.     .+. ..++
T Consensus       101 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~  173 (242)
T 3fe2_A          101 DGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYG---GAPKGPQIRDLER----GVEICIATPGRLIDFLECGKTN  173 (242)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECT---TSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHTSCC
T ss_pred             CCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEEC---CCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCC
Confidence            46789999999999998888776642  1278888999   8887766555443    489999995     232 3457


Q ss_pred             CCCCCEEEEcCC
Q psy4150         191 IGEIDLVICFDA  202 (395)
Q Consensus       191 ip~v~~VI~~d~  202 (395)
                      +..+.+||.=.+
T Consensus       174 ~~~~~~lViDEa  185 (242)
T 3fe2_A          174 LRRTTYLVLDEA  185 (242)
T ss_dssp             CTTCCEEEETTH
T ss_pred             cccccEEEEeCH
Confidence            778888775443

>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=89.88  E-value=2  Score=38.90  Aligned_cols=98  Identities=16%  Similarity=0.180  Sum_probs=63.7

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .+..|.-...-.+...+..   ...+.++||.++|+..+..+++.+...+.  .+.+..++|   +.+...+...+    
T Consensus        89 TGsGKT~~~~~~il~~l~~---~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~~~----  158 (249)
T 3ber_A           89 TGSGKTGAFALPILNALLE---TPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVG---GIDSMSQSLAL----  158 (249)
T ss_dssp             TTSCHHHHHHHHHHHHHHH---SCCSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECT---TSCHHHHHHHH----
T ss_pred             CCCCchhHhHHHHHHHHhc---CCCCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEEC---CCChHHHHHHh----
Confidence            4556776543333333222   13356899999999999988887766421  278888898   77766544333    


Q ss_pred             cCCccEEEEcCc-----cc--cCCCCCCCCEEEEcCC
Q psy4150         173 AGEFNTLIATSV-----GE--EGLDIGEIDLVICFDA  202 (395)
Q Consensus       173 ~g~~~vLVaT~v-----~~--~GlDip~v~~VI~~d~  202 (395)
                      .+..+|+|||.-     +.  .++++..+++||.=.+
T Consensus       159 ~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEa  195 (249)
T 3ber_A          159 AKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEA  195 (249)
T ss_dssp             HTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSH
T ss_pred             cCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcCh
Confidence            256899999942     22  4577788888776444

>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=89.72  E-value=0.9  Score=40.71  Aligned_cols=77  Identities=18%  Similarity=0.242  Sum_probs=47.6

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-----cccc-CCC
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-----VGEE-GLD  190 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-----v~~~-GlD  190 (395)
                      .+.++||.++|+..+..+++.+...+.  .+.+..++|   +.+..   .....+..+..+|+|+|.     .+.+ .++
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g---~~~~~---~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~  170 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIG---GTNVR---NEMQKLQAEAPHIVVGTPGRVFDMLNRRYLS  170 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------------CCCSEEEECHHHHHHHHHTTSSC
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEEC---CCchH---HHHHHHhcCCCCEEEECHHHHHHHHHhCCcC
Confidence            457999999999999999998877543  256677777   54433   234456677899999993     3333 356


Q ss_pred             CCCCCEEEEcC
Q psy4150         191 IGEIDLVICFD  201 (395)
Q Consensus       191 ip~v~~VI~~d  201 (395)
                      +..+++||.=.
T Consensus       171 ~~~~~~lViDE  181 (237)
T 3bor_A          171 PKWIKMFVLDE  181 (237)
T ss_dssp             STTCCEEEEES
T ss_pred             cccCcEEEECC
Confidence            67777777543

>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=88.41  E-value=1.4  Score=39.19  Aligned_cols=94  Identities=19%  Similarity=0.227  Sum_probs=61.3

Q ss_pred             ccccHHHH-HHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC---CCCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          95 WSHLKFIR-LREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE---PMVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        95 ~~~~K~~~-L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~---~~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      .+..|.-. +.-++.....    ...+.++||.|+|+..+..+++.+...+   +.+++..++|   +.+..++...+  
T Consensus        70 TGsGKT~~~~l~~l~~l~~----~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~~~--  140 (230)
T 2oxc_A           70 SGTGKTCVFSTIALDSLVL----ENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIG---GTPLSQDKTRL--  140 (230)
T ss_dssp             TTSSHHHHHHHHHHHHCCT----TSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECT---TSCHHHHHHHT--
T ss_pred             CCCcHHHHHHHHHHHHHHh----cCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeC---CCCHHHHHHhc--
Confidence            45567655 3333333222    1345799999999999999998887653   2478888999   88776655443  


Q ss_pred             HhcCCccEEEEcCc-----c-ccCCCCCCCCEEEEc
Q psy4150         171 FRAGEFNTLIATSV-----G-EEGLDIGEIDLVICF  200 (395)
Q Consensus       171 Fk~g~~~vLVaT~v-----~-~~GlDip~v~~VI~~  200 (395)
                         ...+|+|+|.-     + ...+++..+++||.=
T Consensus       141 ---~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViD  173 (230)
T 2oxc_A          141 ---KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILD  173 (230)
T ss_dssp             ---TSCSEEEECHHHHHHHHHTTSSCGGGCCEEEES
T ss_pred             ---cCCCEEEECHHHHHHHHhcCCcccccCCEEEeC
Confidence               35899999952     1 234556666666643

>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=88.03  E-value=1  Score=45.92  Aligned_cols=59  Identities=19%  Similarity=0.267  Sum_probs=54.6

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS  183 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~  183 (395)
                      .+++||.++++..+....+.|...|  +.+..++|   +.+..++..++..+..|..+||++|.
T Consensus        65 ~g~~lvi~P~~aL~~q~~~~l~~~g--i~~~~l~~---~~~~~~~~~~~~~~~~~~~~ilv~Tp  123 (523)
T 1oyw_A           65 NGLTVVVSPLISLMKDQVDQLQANG--VAAACLNS---TQTREQQLEVMTGCRTGQIRLLYIAP  123 (523)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHHTCCSEEEECH
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcC--CcEEEEeC---CCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            3789999999999999999999988  89999999   89999999999999999999999995

>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=87.80  E-value=1.7  Score=37.51  Aligned_cols=97  Identities=11%  Similarity=0.117  Sum_probs=60.3

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC---CCCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE---PMVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~---~~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .+..|--...-.+......   ...+.++||.|+|+..+..+++.+....   +.+.+..++|   +.+..+....   +
T Consensus        49 TGsGKT~~~~~~~~~~~~~---~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~~---~  119 (206)
T 1vec_A           49 NGTGKSGAYLIPLLERLDL---KKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTG---GTNLRDDIMR---L  119 (206)
T ss_dssp             SSSTTHHHHHHHHHHHCCT---TSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECS---SSCHHHHHHH---T
T ss_pred             CCCchHHHHHHHHHHHhcc---cCCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeC---CccHHHHHHh---c
Confidence            4555665433323232211   1345689999999999999888876543   2377888888   7766544322   2


Q ss_pred             hcCCccEEEEcC-----cccc-CCCCCCCCEEEEcC
Q psy4150         172 RAGEFNTLIATS-----VGEE-GLDIGEIDLVICFD  201 (395)
Q Consensus       172 k~g~~~vLVaT~-----v~~~-GlDip~v~~VI~~d  201 (395)
                       .+..+|+|+|.     .+.. .+++..+++||.=.
T Consensus       120 -~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDE  154 (206)
T 1vec_A          120 -DDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDE  154 (206)
T ss_dssp             -TSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEET
T ss_pred             -CCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEC
Confidence             35789999996     2223 34666777777533

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=86.60  E-value=1.1  Score=46.46  Aligned_cols=59  Identities=15%  Similarity=0.263  Sum_probs=54.1

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHH--hcCCccEEEEcC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKF--RAGEFNTLIATS  183 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~F--k~g~~~vLVaT~  183 (395)
                      .+++||.++++..+....+.|...|  +.+..++|   +++..++..++..+  ..+..+|||+|+
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~g--i~~~~l~~---~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLG--ISATMLNA---SSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHT--CCEEECCS---SCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcC--CcEEEEeC---CCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            4799999999999999999999988  99999999   99999999999988  578999999997

>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=86.43  E-value=4.1  Score=37.02  Aligned_cols=101  Identities=20%  Similarity=0.268  Sum_probs=62.1

Q ss_pred             ccccHHHHH-HHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          95 WSHLKFIRL-REILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        95 ~~~~K~~~L-~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .+..|.-.. .-++............+.++||.++|+..+..+++.+.+.+.  .+.+..++|   +.........   +
T Consensus       100 TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~~---~  173 (262)
T 3ly5_A          100 TGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMG---GSNRSAEAQK---L  173 (262)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECS---SSCHHHHHHH---H
T ss_pred             CCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEEC---CCCHHHHHHH---h
Confidence            455576553 333333322100112367899999999999999888877542  266777888   6665554333   3


Q ss_pred             hcCCccEEEEcC-----ccc--cCCCCCCCCEEEEcCC
Q psy4150         172 RAGEFNTLIATS-----VGE--EGLDIGEIDLVICFDA  202 (395)
Q Consensus       172 k~g~~~vLVaT~-----v~~--~GlDip~v~~VI~~d~  202 (395)
                      ..| .+|+|||.     .+.  .++++..+.+||.=.+
T Consensus       174 ~~~-~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEa  210 (262)
T 3ly5_A          174 GNG-INIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEA  210 (262)
T ss_dssp             HHC-CSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSH
T ss_pred             cCC-CCEEEEcHHHHHHHHHccCCcccccCCEEEEcCh
Confidence            344 89999994     222  2467778888775443

>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=86.20  E-value=1.2  Score=39.49  Aligned_cols=77  Identities=14%  Similarity=0.199  Sum_probs=49.9

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccC-CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC-----c-cccCCCC
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLE-PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS-----V-GEEGLDI  191 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~-~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~-----v-~~~GlDi  191 (395)
                      .+.++||.++|+..+..+++.+.... ..+.+..++|   +.+...+...   +. ...+|+|||.     . ....+++
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~---~~-~~~~iiv~Tp~~l~~~~~~~~~~~  165 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYG---GRNRNGQIED---IS-KGVDIIIATPGRLNDLQMNNSVNL  165 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC---------CHHH---HH-SCCSEEEECHHHHHHHHHTTCCCC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEEC---CCChHHHHHH---hc-CCCCEEEECHHHHHHHHHcCCcCc
Confidence            46789999999999999998887753 3478888888   6554443332   22 3489999994     1 2234567


Q ss_pred             CCCCEEEEcCC
Q psy4150         192 GEIDLVICFDA  202 (395)
Q Consensus       192 p~v~~VI~~d~  202 (395)
                      ..+++||.=.+
T Consensus       166 ~~~~~lViDEa  176 (228)
T 3iuy_A          166 RSITYLVIDEA  176 (228)
T ss_dssp             TTCCEEEECCH
T ss_pred             ccceEEEEECH
Confidence            77777775443

>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=85.47  E-value=4.2  Score=38.58  Aligned_cols=99  Identities=15%  Similarity=0.183  Sum_probs=65.5

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC---CCCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE---PMVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~---~~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .+..|.-...-.+...+..   .....++||.|+++..+..+++.+.+..   +.+++..++|   +.+......   .+
T Consensus        54 TGsGKT~~~~~~~~~~l~~---~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~---~~  124 (391)
T 1xti_A           54 SGMGKTAVFVLATLQQLEP---VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFG---GLSIKKDEE---VL  124 (391)
T ss_dssp             SCSSHHHHHHHHHHHHCCC---CTTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECT---TSCHHHHHH---HH
T ss_pred             CCCcHHHHHHHHHHHhhcc---cCCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeC---CCCHHHHHH---HH
Confidence            3455765443333333221   1235699999999999999888776642   3488999999   777665544   34


Q ss_pred             hcCCccEEEEcCc-c-----ccCCCCCCCCEEEEcCC
Q psy4150         172 RAGEFNTLIATSV-G-----EEGLDIGEIDLVICFDA  202 (395)
Q Consensus       172 k~g~~~vLVaT~v-~-----~~GlDip~v~~VI~~d~  202 (395)
                      ..+..+|+|+|.- +     ...+++..+++||.=.+
T Consensus       125 ~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEa  161 (391)
T 1xti_A          125 KKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEC  161 (391)
T ss_dssp             HHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSH
T ss_pred             hcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCH
Confidence            5677899999942 1     23467788888886443

>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=84.57  E-value=3.5  Score=39.84  Aligned_cols=96  Identities=17%  Similarity=0.186  Sum_probs=67.1

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .+..|.-....++..++.     ..+.++||.|+++..+..+.+.+.+..  +...+..+||   +....++.....   
T Consensus        32 tG~GKT~~~~~~~~~~~~-----~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g---~~~~~~~~~~~~---  100 (494)
T 1wp9_A           32 TGLGKTLIAMMIAEYRLT-----KYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTG---EKSPEERSKAWA---  100 (494)
T ss_dssp             TTSCHHHHHHHHHHHHHH-----HSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECS---CSCHHHHHHHHH---
T ss_pred             CCCCHHHHHHHHHHHHHh-----cCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeC---Ccchhhhhhhcc---
Confidence            355577766666655543     135799999999999999988888763  3348899999   888776655443   


Q ss_pred             cCCccEEEEcC-cc-----ccCCCCCCCCEEEEcCCC
Q psy4150         173 AGEFNTLIATS-VG-----EEGLDIGEIDLVICFDAQ  203 (395)
Q Consensus       173 ~g~~~vLVaT~-v~-----~~GlDip~v~~VI~~d~p  203 (395)
                        ..+|+|+|. .+     ...+....+++||.=.+.
T Consensus       101 --~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH  135 (494)
T 1wp9_A          101 --RAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAH  135 (494)
T ss_dssp             --HCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGG
T ss_pred             --CCCEEEecHHHHHHHHhcCCcchhhceEEEEECCc
Confidence              478999994 22     224667788888864443

>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=83.43  E-value=2.3  Score=38.28  Aligned_cols=75  Identities=15%  Similarity=0.185  Sum_probs=51.0

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCc-----c-ccCCCC
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSV-----G-EEGLDI  191 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v-----~-~~GlDi  191 (395)
                      +.++||.|+|+..+..+++.+...+.  .+.+..++|   +.+.......+    ....+|+|||.-     + ...+++
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~  172 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYG---GADTHSQIREV----QMGCHLLVATPGRLVDFIEKNKISL  172 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECS---SSCSHHHHHHH----SSCCSEEEECHHHHHHHHHTTSBCC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEEC---CCCHHHHHHHh----CCCCCEEEECHHHHHHHHHcCCCCh
Confidence            46899999999999998888766432  267778888   66554433322    346899999952     1 223567


Q ss_pred             CCCCEEEEcC
Q psy4150         192 GEIDLVICFD  201 (395)
Q Consensus       192 p~v~~VI~~d  201 (395)
                      ..+++||.=.
T Consensus       173 ~~~~~lViDE  182 (253)
T 1wrb_A          173 EFCKYIVLDE  182 (253)
T ss_dssp             TTCCEEEEET
T ss_pred             hhCCEEEEeC
Confidence            7777777543

>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=83.22  E-value=2  Score=37.73  Aligned_cols=95  Identities=17%  Similarity=0.145  Sum_probs=55.3

Q ss_pred             ccccHHHH-HHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150          95 WSHLKFIR-LREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus        95 ~~~~K~~~-L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      .+..|--. +.-++.....    ...+.++||.++++..+..+++.+...+.  .+.+..++|   +.+..++...   +
T Consensus        60 TGsGKT~~~~~~~l~~l~~----~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~~---~  129 (224)
T 1qde_A           60 SGTGKTGTFSIAALQRIDT----SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIG---GTSFVEDAEG---L  129 (224)
T ss_dssp             TTSSHHHHHHHHHHHHCCT----TCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------------C
T ss_pred             CCCcHHHHHHHHHHHHHhc----cCCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeC---CcchHHHHhc---C
Confidence            45567755 3333333211    13457999999999999988887776432  377888888   6554443322   2


Q ss_pred             hcCCccEEEEcCc------cccCCCCCCCCEEEEcC
Q psy4150         172 RAGEFNTLIATSV------GEEGLDIGEIDLVICFD  201 (395)
Q Consensus       172 k~g~~~vLVaT~v------~~~GlDip~v~~VI~~d  201 (395)
                      .  ..+|+|+|.-      ....+++..+++||.=.
T Consensus       130 ~--~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDE  163 (224)
T 1qde_A          130 R--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDE  163 (224)
T ss_dssp             T--TCSEEEECHHHHHHHHHTTSSCCTTCCEEEEET
T ss_pred             C--CCCEEEECHHHHHHHHHhCCcchhhCcEEEEcC
Confidence            2  3889999952      13456667777777543

>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=82.12  E-value=1.2  Score=39.94  Aligned_cols=100  Identities=13%  Similarity=0.212  Sum_probs=59.4

Q ss_pred             eccccHHHHH-HHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHH
Q psy4150          94 AWSHLKFIRL-REILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKK  170 (395)
Q Consensus        94 ~~~~~K~~~L-~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~  170 (395)
                      ..+..|.-.. .-++... ..  ....+.++||.++|+..+..+++.+.+.+.  .+.+..++|   +...   ......
T Consensus        74 ~TGsGKT~~~~l~~l~~l-~~--~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~---~~~~---~~~~~~  144 (245)
T 3dkp_A           74 PTGSGKTLAFSIPILMQL-KQ--PANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHK---AAVA---AKKFGP  144 (245)
T ss_dssp             CTTSCHHHHHHHHHHHHH-CS--CCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCH---HHHH---HTTTST
T ss_pred             CCCCcHHHHHHHHHHHHH-hh--cccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEec---CccH---HHHhhh
Confidence            3455676553 3333332 21  112456899999999999999988877532  266666666   2211   111122


Q ss_pred             HhcCCccEEEEcC-----cccc---CCCCCCCCEEEEcCC
Q psy4150         171 FRAGEFNTLIATS-----VGEE---GLDIGEIDLVICFDA  202 (395)
Q Consensus       171 Fk~g~~~vLVaT~-----v~~~---GlDip~v~~VI~~d~  202 (395)
                      ...+..+|+|||.     .+..   ++++..+.+||.=.+
T Consensus       145 ~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEa  184 (245)
T 3dkp_A          145 KSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDES  184 (245)
T ss_dssp             TSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSH
T ss_pred             hhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeCh
Confidence            2356789999994     2222   477888888776444

>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=80.64  E-value=2.7  Score=46.66  Aligned_cols=96  Identities=14%  Similarity=0.160  Sum_probs=65.6

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CC----ceeEEeccCCCCCHHHHHHHH
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MV----KASMFVGQSSGVTQQEQKEIM  168 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~----~~~~lhg~~~~~~~~~R~~~l  168 (395)
                      .+..|--.++-++....      ..+.++||.++|+..+..+++.+...+.  .+    .+..+||   +.+..++...+
T Consensus        80 TGSGKTl~~lp~l~~~~------~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~G---g~~~~~~~~~~  150 (1054)
T 1gku_B           80 TGVGKTSFGLAMSLFLA------LKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHG---RIPKREKENFM  150 (1054)
T ss_dssp             BTSCSHHHHHHHHHHHH------TTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCS---SCCSHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHh------hcCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeC---CCChhhHHHHH
Confidence            45557653333333332      2357999999999999998888876432  25    7888999   88888888888


Q ss_pred             HHHhcCCccEEEEcCc-cccCCC-CCCCCEEEEcC
Q psy4150         169 KKFRAGEFNTLIATSV-GEEGLD-IGEIDLVICFD  201 (395)
Q Consensus       169 ~~Fk~g~~~vLVaT~v-~~~GlD-ip~v~~VI~~d  201 (395)
                      +.++.  .+|+|||+- +..-+. +..+++||.=.
T Consensus       151 ~~l~~--~~IlV~TP~~L~~~l~~L~~l~~lViDE  183 (1054)
T 1gku_B          151 QNLRN--FKIVITTTQFLSKHYRELGHFDFIFVDD  183 (1054)
T ss_dssp             HSGGG--CSEEEEEHHHHHHCSTTSCCCSEEEESC
T ss_pred             hhccC--CCEEEEcHHHHHHHHHHhccCCEEEEeC
Confidence            88877  999999951 111111 55777777533

---

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	395
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	8e-27
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	8e-17
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	5e-10
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	1e-08
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-08
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	5e-08
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	2e-07
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	3e-07
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	4e-07
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-06
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	7e-05

>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 =  106 bits (264), Expect = 8e-27
 Identities = 71/220 (32%), Positives = 119/220 (54%), Gaps = 15/220 (6%)

Query: 27  RDFHVTHSLASALENLVTYGLRSFYNNLVEVSKEDGSCPILGKDNDLQNLLQQLKPKLDI 86
               +   L  A+E L T GL +    + ++ +E  +           +  +++K  + +
Sbjct: 74  LYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSD--KRMKKAISL 131

Query: 87  NIMSSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPM 146
            + + E    H K  +L+EI+        ++ + +K+I+F NYR    +I + L   +  
Sbjct: 132 LVQAKEIGLDHPKMDKLKEIIREQL----QRKQNSKIIVFTNYRETAKKIVNELV--KDG 185

Query: 147 VKASMFVGQSSGV-----TQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFD 201
           +KA  FVGQ+S       +Q+EQK I+ +F  GEFN L+ATSVGEEGLD+ E+DLV+ ++
Sbjct: 186 IKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYE 245

Query: 202 AQKSPIKMVQRLGRTGRKRNGRCVILLTQGR--EAHNFQT 239
              S I+ +QR GRTGR   GR +IL+ +G   EA+ + +
Sbjct: 246 PVPSAIRSIQRRGRTGRHMPGRVIILMAKGTRDEAYYWSS 285

>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 = 78.0 bits (192), Expect = 8e-17
 Identities = 25/135 (18%), Positives = 47/135 (34%), Gaps = 10/135 (7%)

Query: 113 LHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKA-----SMFVGQSSGVTQQEQKEI 167
           L   KG   + +IF + +    E+   L  L     A      + V  +SG       + 
Sbjct: 31  LEVIKGG--RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDA 88

Query: 168 MKKFRAGEFNTLIATSV---GEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRC 224
           +     G+F+++I  +          +     +      +  +   QR GRTGR + G  
Sbjct: 89  LMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIY 148

Query: 225 VILLTQGREAHNFQT 239
             +    R +  F +
Sbjct: 149 RFVAPGERPSGMFDS 163

>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 = 56.4 bits (135), Expect = 5e-10
 Identities = 32/132 (24%), Positives = 64/132 (48%), Gaps = 19/132 (14%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K  +LREILE H           K+IIF  +        +++  +  +        ++S 
Sbjct: 80  KIRKLREILERH--------RKDKIIIFTRH-------NELVYRISKVFLIPAITHRTS- 123

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
             ++E++EI++ FR G F  ++++ V +EG+D+ + ++ +      S  + +QRLGR  R
Sbjct: 124 --REEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILR 181

Query: 219 K-RNGRCVILLT 229
             +  +  +L  
Sbjct: 182 PSKGKKEAVLYE 193

>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 = 52.1 bits (124), Expect = 1e-08
 Identities = 27/110 (24%), Positives = 49/110 (44%), Gaps = 5/110 (4%)

Query: 151 MFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-----S 205
                 S +   E+ EI++  R G+++ L+  ++  EGLDI E+ LV   DA K     S
Sbjct: 57  KVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRS 116

Query: 206 PIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNK 255
              ++Q +GR  R  NG  ++      ++          +  +++  N K
Sbjct: 117 ERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRK 166

>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 = 50.7 bits (120), Expect = 3e-08
 Identities = 41/162 (25%), Positives = 71/162 (43%), Gaps = 20/162 (12%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           K+  L ++ +S           T+ +IF N R  V E+   L+  +  V A       S 
Sbjct: 14  KYECLTDLYDSI--------SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIY-----SD 60

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
           + QQE+  IMK+FR+G    LI+T +   G+D+ ++ LVI +D   +    + R+GR GR
Sbjct: 61  LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR 120

Query: 219 KRNGRCVILLTQGREAHN-------FQTSMQTCKSYVEKIIN 253
                  I      +          + T ++   S +  ++N
Sbjct: 121 FGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLLN 162

>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 = 49.6 bits (117), Expect = 5e-08
 Identities = 30/153 (19%), Positives = 66/153 (43%), Gaps = 14/153 (9%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           +F  L  +L++              ++F   +    E+  +L+ +     A         
Sbjct: 16  RFEALCRLLKNK---------EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLS--- 63

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
             Q +++++++ F+  +   LIAT V   G+D+ +++ VI +   ++P   + R+GRTGR
Sbjct: 64  --QSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGR 121

Query: 219 KRNGRCVILLTQGREAHNFQTSMQTCKSYVEKI 251
                  I +   RE    +   +  K  ++K+
Sbjct: 122 AGKKGKAISIINRREYKKLRYIERAMKLKIKKL 154

>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 = 49.4 bits (117), Expect = 2e-07
 Identities = 25/158 (15%), Positives = 44/158 (27%), Gaps = 29/158 (18%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
               L  ILE               II+A       EI++ LK                G
Sbjct: 13  SISTLSSILEKLGT---------GGIIYARTGEEAEEIYESLK-----------NKFRIG 52

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIG-----EIDLVICFDAQKSPIKMVQRL 213
           +    +K   +KF  GE + LI T+     L  G      I   +              +
Sbjct: 53  IVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTI 108

Query: 214 GRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKI 251
                       +L    R     +  +   + +++++
Sbjct: 109 EDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEV 146

>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 = 48.0 bits (113), Expect = 3e-07
 Identities = 34/153 (22%), Positives = 69/153 (45%), Gaps = 13/153 (8%)

Query: 99  KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSG 158
           KF  L ++ ++           T+ +IF N +  V  + + ++     V +         
Sbjct: 21  KFDTLCDLYDTL--------TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMP--- 69

Query: 159 VTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGR 218
             Q+E++ IMK+FR+G    LI+T V   GLD+ ++ L+I +D   +    + R+GR+GR
Sbjct: 70  --QKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 127

Query: 219 KRNGRCVILLTQGREAHNFQTSMQTCKSYVEKI 251
                  I   +  +    +   Q   + ++++
Sbjct: 128 YGRKGVAINFVKNDDIRILRDIEQYYSTQIDEM 160

>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 = 46.6 bits (110), Expect = 4e-07
 Identities = 22/124 (17%), Positives = 35/124 (28%), Gaps = 17/124 (13%)

Query: 112 RLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKF 171
            L   KG   + +IF + +    E+   L  L                    +   +   
Sbjct: 29  PLEVIKGG--RHLIFCHSKKKCDELAAKLVALGINA------------VAYYRGLDVSVI 74

Query: 172 RAGEFNTLIATSVGEEGLDIGE---IDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILL 228
                  ++AT     G        ID        +  +   QR GRTGR + G    + 
Sbjct: 75  PTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGRGKPGIYRFVA 134

Query: 229 TQGR 232
              R
Sbjct: 135 PGER 138

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 46.1 bits (108), Expect = 3e-06
 Identities = 26/162 (16%), Positives = 45/162 (27%), Gaps = 33/162 (20%)

Query: 95  WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVG 154
               + I  R     H  +   KG   K + F        +I   L+     V       
Sbjct: 156 MDEEREIPERSWNSGHEWVTDFKG---KTVWFVPSIKAGNDIAACLRKNGKKVIQ----- 207

Query: 155 QSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIK------ 208
               ++++       K R  +++ ++ T + E G +    + VI       P+       
Sbjct: 208 ----LSRKTFDSEYIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPVILTDGEE 262

Query: 209 --------------MVQRLGRTGRKRNGRCVILLTQGREAHN 236
                           QR GR GR         +  G    N
Sbjct: 263 RVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGEPLEN 304

>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 = 41.3 bits (96), Expect = 7e-05
 Identities = 19/105 (18%), Positives = 41/105 (39%), Gaps = 1/105 (0%)

Query: 141 KPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDL-VIC 199
              + +            ++Q+E+  +M +F  G ++ L++T+V E G+D+   ++ VI 
Sbjct: 56  YLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIE 115

Query: 200 FDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTC 244
              +    ++ Q  GR GR        L+         +      
Sbjct: 116 NPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERLRFFT 160

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	395
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.96
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.96
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.96
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.96
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.96
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.96
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.96
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.95
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.95
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.95
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.88
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.83
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.82
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.81
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.78
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.77
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.7
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.7
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.67
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.52
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.41
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.3
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.78
d1e52a_	56	C-terminal UvrC-binding domain of UvrB {Escherichi	98.51
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.41
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	91.45
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	88.79
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	87.67
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	87.19
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	84.45
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	82.72
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	81.15

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.96  E-value=1.4e-29  Score=221.75  Aligned_cols=137  Identities=28%  Similarity=0.446  Sum_probs=117.4

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      .+.|++.|.+++..+        ...++||||+|+..++.+++.|...+  +.+..+||   ++++.+|..+++.|+.|+
T Consensus        11 ~e~K~~~L~~ll~~~--------~~~k~iIF~~s~~~~~~l~~~L~~~~--~~~~~~~~---~~~~~~r~~~l~~f~~~~   77 (162)
T d1fuka_          11 EEYKYECLTDLYDSI--------SVTQAVIFCNTRRKVEELTTKLRNDK--FTVSAIYS---DLPQQERDTIMKEFRSGS   77 (162)
T ss_dssp             GGGHHHHHHHHHHHT--------TCSCEEEEESSHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHTTS
T ss_pred             cHHHHHHHHHHHHhC--------CCCcEEEEEEEEchHHHHHHHHhhcC--ceEEEecc---CCchhhHHHHHHHHhhcc
Confidence            345999999988763        45899999999999999999999999  99999999   999999999999999999


Q ss_pred             ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhHHHHHHHHcc
Q psy4150         176 FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCKSYVEKIINN  254 (395)
Q Consensus       176 ~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~~  254 (395)
                      ++||||||+++||+|+|+|++|||||+|+++..|+||+|||||.| .|.+++++++.+.         .....+++.++.
T Consensus        78 ~~iLv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~---------~~~~~i~~~~~~  148 (162)
T d1fuka_          78 SRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDV---------GAMRELEKFYST  148 (162)
T ss_dssp             CSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTH---------HHHHHHHHHSSC
T ss_pred             cceeeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHH---------HHHHHHHHHHcC
Confidence            999999999999999999999999999999999999999999997 6888888876432         223456666554

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.96  E-value=5.6e-29  Score=219.67  Aligned_cols=144  Identities=24%  Similarity=0.355  Sum_probs=123.6

Q ss_pred             cceeee--ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHH
Q psy4150          89 MSSEYA--WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKE  166 (395)
Q Consensus        89 ~~~~~~--~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~  166 (395)
                      +.|.|.  ....|+..|.++|..        .+..++||||+|+.+++.|+..|...|  +.+..+||   ++++.+|..
T Consensus         7 i~q~yi~v~~~~K~~~L~~ll~~--------~~~~k~iVF~~~~~~~~~l~~~L~~~g--~~~~~~h~---~~~~~~r~~   73 (171)
T d1s2ma2           7 ITQYYAFVEERQKLHCLNTLFSK--------LQINQAIIFCNSTNRVELLAKKITDLG--YSCYYSHA---RMKQQERNK   73 (171)
T ss_dssp             EEEEEEECCGGGHHHHHHHHHHH--------SCCSEEEEECSSHHHHHHHHHHHHHHT--CCEEEECT---TSCHHHHHH
T ss_pred             eEEEEEEcCHHHHHHHHHHHHHh--------CCCCceEEEEeeeehhhHhHHhhhccc--cccccccc---ccchhhhhh
Confidence            334444  445689999998876        346899999999999999999999999  99999999   999999999


Q ss_pred             HHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchhhHHHHHHHHhH
Q psy4150         167 IMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREAHNFQTSMQTCK  245 (395)
Q Consensus       167 ~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~~~~~~~~~~~~  245 (395)
                      ++++|+.|.+++||||+++++|+|+|+|++|||||+|+++.+|+||+||+||.| .|.+++|+++.+ .        ...
T Consensus        74 ~~~~f~~~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e-~--------~~~  144 (171)
T d1s2ma2          74 VFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWND-R--------FNL  144 (171)
T ss_dssp             HHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGG-H--------HHH
T ss_pred             hhhhcccCccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHH-H--------HHH
Confidence            999999999999999999999999999999999999999999999999999997 677777776543 2        223


Q ss_pred             HHHHHHHcc
Q psy4150         246 SYVEKIINN  254 (395)
Q Consensus       246 ~~i~~~i~~  254 (395)
                      ..+++.++.
T Consensus       145 ~~i~~~l~~  153 (171)
T d1s2ma2         145 YKIEQELGT  153 (171)
T ss_dssp             HHHHHHHTC
T ss_pred             HHHHHHHCC
Confidence            556666654

>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=99.96  E-value=2.5e-28  Score=217.30  Aligned_cols=125  Identities=23%  Similarity=0.421  Sum_probs=108.9

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccE
Q psy4150          99 KFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNT  178 (395)
Q Consensus        99 K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~v  178 (395)
                      +.+.|+..+.+...      .+.++||||+++..++.++..|.+.|  +++.++||   +|++.+|.+++++|++|+++|
T Consensus        16 qvd~ll~~i~~~~~------~~~~~iif~~~~~~~~~~~~~l~~~g--~~~~~~hg---~~~~~eR~~~l~~Fr~g~~~v   84 (181)
T d1t5la2          16 QIDDLIGEIRERVE------RNERTLVTTLTKKMAEDLTDYLKEAG--IKVAYLHS---EIKTLERIEIIRDLRLGKYDV   84 (181)
T ss_dssp             HHHHHHHHHHHHHH------TTCEEEEECSSHHHHHHHHHHHHTTT--CCEEEECS---SCCHHHHHHHHHHHHHTSCSE
T ss_pred             cHHHHHHHHHHHHh------cCCeEEEEeehhhhhHHHHHHHHhCC--cceeEecC---CccHHHHHHHHHHHHCCCCCE
Confidence            44445544444333      25799999999999999999999999  99999999   999999999999999999999


Q ss_pred             EEEcCccccCCCCCCCCEEEEcCCCC-----ChhhHhhhccccccccCceEEEEEeCCchh
Q psy4150         179 LIATSVGEEGLDIGEIDLVICFDAQK-----SPIKMVQRLGRTGRKRNGRCVILLTQGREA  234 (395)
Q Consensus       179 LVaT~v~~~GlDip~v~~VI~~d~p~-----s~~~yiQr~GRagR~~~g~~i~l~~~~~e~  234 (395)
                      ||||++++||||+|+|++|||||+|.     +..+|+||+|||||.|.|.+++++......
T Consensus        85 LVaTdv~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~~~~~~~~~~~  145 (181)
T d1t5la2          85 LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKS  145 (181)
T ss_dssp             EEESCCCSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHH
T ss_pred             EEehhHHHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccCceeEeecchhhHH
Confidence            99999999999999999999999996     689999999999999988877766554433

>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=99.96  E-value=3e-28  Score=214.52  Aligned_cols=138  Identities=20%  Similarity=0.314  Sum_probs=115.7

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      +.++||||+|+++|+.|+.+|.+.|  +++.++||   +|++.+|.+++++|++|+++|||||++++||||+|+|++||+
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~G--i~a~~~Hg---~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~  105 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEHG--IRARYLHH---ELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAI  105 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEE
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhcC--CceEEEec---ccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEE
Confidence            6899999999999999999999999  99999999   999999999999999999999999999999999999999999


Q ss_pred             cCCCC-----ChhhHhhhccccccccCceEEEEEeCCchhhHHHHHHHHhHHHHHHHHcccchhhhhcccCCCC
Q psy4150         200 FDAQK-----SPIKMVQRLGRTGRKRNGRCVILLTQGREAHNFQTSMQTCKSYVEKIINNKSIYANLAKNGPRM  268 (395)
Q Consensus       200 ~d~p~-----s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~  268 (395)
                      ||+|.     +..+|+||+||+||.+.|.++++.....+.  +.    +..++..+....+..++..++..|..
T Consensus       106 ~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~--~~----~~i~et~rRr~iq~~~N~~h~i~p~~  173 (174)
T d1c4oa2         106 LDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEA--MQ----RAIEETNRRRALQEAYNLEHGITPET  173 (174)
T ss_dssp             TTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHH--HH----HHHHHHHHHHHHHHHHHHHHTCCCCC
T ss_pred             eccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHH--HH----HHHHHHHHHHHHHHHHHHhCCCCCCc
Confidence            99876     457899999999999999888876554432  22    23344444444455566656666553

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.8e-28  Score=215.93  Aligned_cols=122  Identities=28%  Similarity=0.493  Sum_probs=113.2

Q ss_pred             ccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCc
Q psy4150          97 HLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus        97 ~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      .+|++.|.++|..+        ...++||||+++..++.++..|...+  +.+..+||   ++++.+|..+++.|++|++
T Consensus        19 ~~K~~~L~~ll~~~--------~~~k~iiF~~~~~~~~~~~~~l~~~~--~~~~~~~~---~~~~~~r~~~~~~fk~g~~   85 (168)
T d2j0sa2          19 EWKFDTLCDLYDTL--------TITQAVIFCNTKRKVDWLTEKMREAN--FTVSSMHG---DMPQKERESIMKEFRSGAS   85 (168)
T ss_dssp             THHHHHHHHHHHHH--------TSSEEEEECSSHHHHHHHHHHHHHTT--CCCEEECT---TSCHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHHHhC--------CCCceEEEeeeHHHHHHHHHHhhhcc--cchhhhhh---hhhHHHHHHHHHHHhcCCc
Confidence            45999999998764        24799999999999999999999999  89999999   9999999999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         177 NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       177 ~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      ++|||||+++||||+|+|++|||||+|+++.+|+||+||+||.| .|.+++++++.
T Consensus        86 ~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~  141 (168)
T d2j0sa2          86 RVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND  141 (168)
T ss_dssp             CEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGG
T ss_pred             cEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHH
Confidence            99999999999999999999999999999999999999999997 57777777664

>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=99.96  E-value=1.3e-28  Score=213.73  Aligned_cols=123  Identities=23%  Similarity=0.479  Sum_probs=112.4

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ...+|++.|.++|..         .+.++||||+|+++|+.|+..|...|  +.+..+||   ++++.+|..++++|+.|
T Consensus        12 ~~~~K~~~L~~ll~~---------~~~k~IIF~~s~~~~~~l~~~L~~~g--~~~~~~~~---~~~~~~r~~~~~~f~~~   77 (155)
T d1hv8a2          12 NENERFEALCRLLKN---------KEFYGLVFCKTKRDTKELASMLRDIG--FKAGAIHG---DLSQSQREKVIRLFKQK   77 (155)
T ss_dssp             CGGGHHHHHHHHHCS---------TTCCEEEECSSHHHHHHHHHHHHHTT--CCEEEECS---SSCHHHHHHHHHHHHTT
T ss_pred             ChHHHHHHHHHHHcc---------CCCCEEEEECchHHHHHHHhhhcccc--cccccccc---cchhhhhhhhhhhhhcc
Confidence            456799988887743         24689999999999999999999999  89999999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCC
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQG  231 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~  231 (395)
                      +.+|||||+++++|||+|+|++||+||+|+|+.+|+||+||+||.| .|.+++++.+.
T Consensus        78 ~~~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  135 (155)
T d1hv8a2          78 KIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRR  135 (155)
T ss_dssp             SSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTT
T ss_pred             cceeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchH
Confidence            9999999999999999999999999999999999999999999997 67777777654

>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=99.96  E-value=3.8e-29  Score=237.66  Aligned_cols=198  Identities=35%  Similarity=0.569  Sum_probs=156.2

Q ss_pred             HHHHHhcchHHHHHHHHhCCCcchhhhccccCccc-----cccccccCChhHHHHHHhhcccccccccceeeeccccHHH
Q psy4150          27 RDFHVTHSLASALENLVTYGLRSFYNNLVEVSKED-----GSCPILGKDNDLQNLLQQLKPKLDINIMSSEYAWSHLKFI  101 (395)
Q Consensus        27 ad~~~~~~l~~~~~~L~~~g~r~~~~fsatl~~~~-----~~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~K~~  101 (395)
                      ......+.+.+++++|..+|+..+..|...+....     .....++.++.+..........       ......+||++
T Consensus        74 ~~~~~~~~l~~~~e~L~~~gi~~~~~~l~~~~~~~~~~~~~~~~~l~~d~~~~~~~~~~~~~-------~~~~~~~pK~~  146 (286)
T d1wp9a2          74 LYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQA-------KEIGLDHPKMD  146 (286)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTCCHHHHHHHTSHHHHHHHHHHHHH-------HHHTCSCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhhhhccchHHHHHhcCHHHHHHHHHHHhh-------HhccCCCcHHH
Confidence            34556777889999999998877766655332221     1123445555555544333221       11234689999


Q ss_pred             HHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEecc-----CCCCCHHHHHHHHHHHhcCCc
Q psy4150         102 RLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQ-----SSGVTQQEQKEIMKKFRAGEF  176 (395)
Q Consensus       102 ~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~-----~~~~~~~~R~~~l~~Fk~g~~  176 (395)
                      .|.++|..++..    ..+.++||||+++.+++.+++.|.+.+  +++..+||.     ++++++.+|..+++.|++|++
T Consensus       147 ~l~~~l~~~~~~----~~~~k~iiF~~~~~~~~~~~~~L~~~~--~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~  220 (286)
T d1wp9a2         147 KLKEIIREQLQR----KQNSKIIVFTNYRETAKKIVNELVKDG--IKAKRFVGQASKENDRGLSQREQKLILDEFARGEF  220 (286)
T ss_dssp             HHHHHHHHHHHH----CTTCCEEEECSCHHHHHHHHHHHHHTT--CCEEEECCSSCC-------CCHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHh----CCCCcEEEEeCcHHhHHHHHHHHHHcC--CceEEeeccccccccchhchHHHHHHHHHHHcCCC
Confidence            999999988765    567899999999999999999999988  899999884     336788899999999999999


Q ss_pred             cEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCCchhhHH
Q psy4150         177 NTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQGREAHNF  237 (395)
Q Consensus       177 ~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~e~~~~  237 (395)
                      +|||||+++++|||+|+|++||+||+|||+..|+||+||+||.++|.+++|++.++.++.+
T Consensus       221 ~vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~~~~~~~l~~~~~~ee~~  281 (286)
T d1wp9a2         221 NVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILMAKGTRDEAY  281 (286)
T ss_dssp             SEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCCSEEEEEEETTSHHHHH
T ss_pred             cEEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCCCCEEEEEEeCCCHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999876554

>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=99.95  E-value=5.1e-28  Score=212.97  Aligned_cols=125  Identities=20%  Similarity=0.315  Sum_probs=114.9

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcC
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAG  174 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g  174 (395)
                      ..+.|+..|.++|..+        ...++||||+++..++.|++.|.+.|  +.+..+||   +|++.+|..++++|++|
T Consensus        10 ~~~~K~~~L~~ll~~~--------~~~k~iIF~~~~~~~~~l~~~L~~~~--~~~~~ihg---~~~~~~r~~~l~~F~~g   76 (168)
T d1t5ia_          10 KDNEKNRKLFDLLDVL--------EFNQVVIFVKSVQRCIALAQLLVEQN--FPAIAIHR---GMPQEERLSRYQQFKDF   76 (168)
T ss_dssp             CGGGHHHHHHHHHHHS--------CCSSEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHHTT
T ss_pred             ChHHHHHHHHHHHHhC--------CCCeEEEEEeeeecchhhhhhhcccc--cccccccc---ccchhhhhhhhhhhccc
Confidence            4567999999988763        35799999999999999999999999  89999999   99999999999999999


Q ss_pred             CccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCc
Q psy4150         175 EFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGR  232 (395)
Q Consensus       175 ~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~  232 (395)
                      +++|||||+++++|+|+|.+++||+||+|+++.+|+||+||+||.| .|.+++++++..
T Consensus        77 ~~~iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~  135 (168)
T d1t5ia_          77 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  135 (168)
T ss_dssp             SCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHH
T ss_pred             cceeeeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchH
Confidence            9999999999999999999999999999999999999999999997 677777776533

>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=99.95  E-value=1.9e-27  Score=214.93  Aligned_cols=125  Identities=18%  Similarity=0.313  Sum_probs=113.7

Q ss_pred             eeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          93 YAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        93 ~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      ......|++.|..+|..+        .+.++||||+|+..++.|+..|...+  +.+..+||   ++++.+|..+++.|+
T Consensus        11 v~~~~~k~~~L~~~l~~~--------~~~~~IIF~~t~~~~~~l~~~l~~~~--~~~~~~h~---~~~~~~r~~~~~~f~   77 (200)
T d1oywa3          11 LMEKFKPLDQLMRYVQEQ--------RGKSGIIYCNSRAKVEDTAARLQSKG--ISAAAYHA---GLENNVRADVQEKFQ   77 (200)
T ss_dssp             EEECSSHHHHHHHHHHHT--------TTCCEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TSCHHHHHHHHHHHH
T ss_pred             EEcCCcHHHHHHHHHHhc--------CCCCEEEEEeeehhhHHhhhhhccCC--ceeEEecC---CCcHHHHHHHHHHHh
Confidence            344567888888887663        45789999999999999999999999  99999999   999999999999999


Q ss_pred             cCCccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         173 AGEFNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       173 ~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      +|+++|||||+++++|||+|+|++||+||+|+++.+|+||+|||||.| .|.+++|+++
T Consensus        78 ~g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~  136 (200)
T d1oywa3          78 RDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP  136 (200)
T ss_dssp             TTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECH
T ss_pred             cccceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCH
Confidence            999999999999999999999999999999999999999999999997 6777777654

>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=99.88  E-value=2e-23  Score=177.34  Aligned_cols=99  Identities=22%  Similarity=0.318  Sum_probs=88.4

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      ++++||||+|+..|+.|++.|...|  +.+..+||   +|++.       +|++|+.+||||||++++||| |++++||+
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~G--~~~~~~H~---~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~  101 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVALG--INAVAYYR---GLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVID  101 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHT--CEEEEECT---TCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEE
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhccc--cchhhhhc---cchhh-------hhhhhhcceeehhHHHHhccc-cccceEEE
Confidence            5799999999999999999999999  99999999   88854       478999999999999999999 99999998


Q ss_pred             cC----CCCChhhHhhhccccccccCceEEEEEeCCc
Q psy4150         200 FD----AQKSPIKMVQRLGRTGRKRNGRCVILLTQGR  232 (395)
Q Consensus       200 ~d----~p~s~~~yiQr~GRagR~~~g~~i~l~~~~~  232 (395)
                      ||    +|.+..+|+||+||||| |..+++.|+++++
T Consensus       102 ~~~~~~~P~~~~~y~qr~GR~gR-g~~G~~~~i~~~e  137 (138)
T d1jr6a_         102 CNTSDGKPQDAVSRTQRRGRTGR-GKPGIYRFVAPGE  137 (138)
T ss_dssp             CSEETTEECCHHHHHHHHTTBCS-SSCEEEEECCSSC
T ss_pred             EEecCCCCCCHHHHHhHhccccC-CCCcEEEEEcCCC
Confidence            65    69999999999999999 6544677777653

>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=99.83  E-value=3.5e-21  Score=172.96  Aligned_cols=119  Identities=31%  Similarity=0.533  Sum_probs=103.2

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      .+.|++.|.++|..+        .+.++||||++...++.|++.|.       +..+||   ++++.+|..++++|++|+
T Consensus        77 ~~~K~~~l~~ll~~~--------~~~k~lvf~~~~~~~~~l~~~l~-------~~~i~g---~~~~~~R~~~l~~F~~~~  138 (200)
T d2fwra1          77 SKNKIRKLREILERH--------RKDKIIIFTRHNELVYRISKVFL-------IPAITH---RTSREEREEILEGFRTGR  138 (200)
T ss_dssp             CSHHHHHHHHHHHHT--------SSSCBCCBCSCHHHHHHHHHHTT-------CCBCCS---SSCSHHHHTHHHHHHHSS
T ss_pred             cHHHHHHHHHHHHhC--------CCCcEEEEeCcHHHHHHHHhhcC-------cceeeC---CCCHHHHHHHHHHhhcCC
Confidence            456999998888763        35799999999999999998773       334688   999999999999999999


Q ss_pred             ccEEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccCce----EEEEEeCCc
Q psy4150         176 FNTLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGR----CVILLTQGR  232 (395)
Q Consensus       176 ~~vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~----~i~l~~~~~  232 (395)
                      ++|||||+++++|||+|.+++||+||+|||+..|+||+||++|.|+|+    ++.|++.++
T Consensus       139 ~~vLv~~~~~~~Gidl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k~~~~i~~~v~~~T  199 (200)
T d2fwra1         139 FRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGT  199 (200)
T ss_dssp             CSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECSC
T ss_pred             eeeeeecchhhcccCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCCcEEEEEEEecCCC
Confidence            999999999999999999999999999999999999999999997542    344666543

>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=1.4e-20  Score=169.50  Aligned_cols=108  Identities=18%  Similarity=0.335  Sum_probs=91.6

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCC----------------------------CCceeEEeccCCCCCHHHHHHHHHHH
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEP----------------------------MVKASMFVGQSSGVTQQEQKEIMKKF  171 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~----------------------------~~~~~~lhg~~~~~~~~~R~~~l~~F  171 (395)
                      +.++||||+|++.|+.++..|.....                            ...+.++||   +|++.+|..+.+.|
T Consensus        40 ~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~---~l~~~~r~~ie~~f  116 (201)
T d2p6ra4          40 NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHA---GLLNGQRRVVEDAF  116 (201)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECT---TSCHHHHHHHHHHH
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHH---HhhhhhHHHHHHHH
Confidence            57999999999999988887764210                            012567778   99999999999999


Q ss_pred             hcCCccEEEEcCccccCCCCCCCCEEEE-------cCCCCChhhHhhhcccccccc---CceEEEEEeC
Q psy4150         172 RAGEFNTLIATSVGEEGLDIGEIDLVIC-------FDAQKSPIKMVQRLGRTGRKR---NGRCVILLTQ  230 (395)
Q Consensus       172 k~g~~~vLVaT~v~~~GlDip~v~~VI~-------~d~p~s~~~yiQr~GRagR~~---~g~~i~l~~~  230 (395)
                      ++|.++|||||+.+++|||+|.+++||.       ++.|.+..+|+||+|||||.|   .|.+++++..
T Consensus       117 ~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~  185 (201)
T d2p6ra4         117 RRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGK  185 (201)
T ss_dssp             HTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCG
T ss_pred             hCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCC
Confidence            9999999999999999999999999996       678889999999999999986   5667665444

>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=1.4e-21  Score=181.52  Aligned_cols=113  Identities=25%  Similarity=0.275  Sum_probs=93.9

Q ss_pred             eeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          93 YAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        93 ~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      ++....|+..|.++|..+         +.++||||+|+++|+.|+++|...        +||   ++++.+|.+++++|+
T Consensus         7 ~~~~~~~~~~l~~~l~~~---------~~~~iif~~~~~~~~~l~~~l~~~--------~hg---~~~~~~R~~~~~~f~   66 (248)
T d1gkub2           7 VAVNDESISTLSSILEKL---------GTGGIIYARTGEEAEEIYESLKNK--------FRI---GIVTATKKGDYEKFV   66 (248)
T ss_dssp             EEESCCCTTTTHHHHTTS---------CSCEEEEESSHHHHHHHHHTTTTS--------SCE---EECTTSSSHHHHHHH
T ss_pred             EecCchHHHHHHHHHHHh---------CCCEEEEECCHHHHHHHHHHHHHh--------ccC---CCCHHHHHHHHHHHH
Confidence            345677899888888642         468999999999999999999753        688   999999999999999


Q ss_pred             cCCccEEEEc----CccccCCCCCC-CCEEEEcCCCCChhhHhhhcccccccc-CceEEEEEe
Q psy4150         173 AGEFNTLIAT----SVGEEGLDIGE-IDLVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLT  229 (395)
Q Consensus       173 ~g~~~vLVaT----~v~~~GlDip~-v~~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~  229 (395)
                      +|+++|||||    ++++||||+|+ |++|||||+|+    |+||+||+||.| .|.+++++.
T Consensus        67 ~g~~~vLVaT~a~~~v~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~  125 (248)
T d1gkub2          67 EGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYL  125 (248)
T ss_dssp             HTSCSEEEEECC------CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTT
T ss_pred             hCCCeEEEEeccccchhhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeecc
Confidence            9999999999    88999999996 99999999995    999999999996 455554443

>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=99.78  E-value=3.3e-20  Score=173.80  Aligned_cols=106  Identities=18%  Similarity=0.284  Sum_probs=91.2

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHH----------HHHHHHHhcCCccEEEEcCcccc--
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQ----------KEIMKKFRAGEFNTLIATSVGEE--  187 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R----------~~~l~~Fk~g~~~vLVaT~v~~~--  187 (395)
                      ++++||||+|+..|+.|+..|.+.|  +++..+||   ++++..|          ..+++.|+.|++++||+|+++++  
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~G--i~a~~~Hg---glsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~  110 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALG--INAVAYYR---GLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQT  110 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTT--CCEEEECT---TSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEE
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCC--CCEEEEeC---CchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccC
Confidence            4899999999999999999999999  99999999   9999876          56889999999999999999998  


Q ss_pred             -CCCCCCCCEEEEcCCCCChhhHhhhccccccccCceEEEEEeCC
Q psy4150         188 -GLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRNGRCVILLTQG  231 (395)
Q Consensus       188 -GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~g~~i~l~~~~  231 (395)
                       |+|++.|.+||+||+|.|..+|+||+|||||.+.|.+. ++...
T Consensus       111 ~giDid~V~~VI~~d~P~SvesyIQRiGRTGRGr~G~~~-~l~~~  154 (299)
T d1a1va2         111 VDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYR-FVAPG  154 (299)
T ss_dssp             EECCCSSSCEEEEEEEECBHHHHHHHHTTBCSSSCEEEE-ESCSC
T ss_pred             CCCCCCcceEEEeCCCCCCHHHHHhhccccCCCCCceEE-EEecC
Confidence             78888899999999999999999999999994355444 44443

>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=99.77  E-value=6.3e-20  Score=165.43  Aligned_cols=128  Identities=19%  Similarity=0.355  Sum_probs=99.8

Q ss_pred             eccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHH--------HHHHHHHHc-ccCCCCceeEEeccCCCCCHHHH
Q psy4150          94 AWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVV--------VAEIFDVLK-PLEPMVKASMFVGQSSGVTQQEQ  164 (395)
Q Consensus        94 ~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~--------ae~l~~~L~-~~~~~~~~~~lhg~~~~~~~~~R  164 (395)
                      .....+.+.+.+.|...+..      +.++.+.|+..+.        +....+.|. ...|.+++.++||   .|++.+|
T Consensus         9 vv~~~~~~~v~~~I~~el~~------g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG---~m~~~ek   79 (206)
T d1gm5a4           9 LVPMDRVNEVYEFVRQEVMR------GGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHG---RLSQEEK   79 (206)
T ss_dssp             CCCSSTHHHHHHHHHHHTTT------SCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCS---SSCCSCS
T ss_pred             EECcccHHHHHHHHHHHHHc------CCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEee---cccHHHH
Confidence            44556788888888876543      6788888876543        333445543 4556789999999   9999999


Q ss_pred             HHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEEcCCCC-ChhhHhhhcccccccc-CceEEEEEeC
Q psy4150         165 KEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVICFDAQK-SPIKMVQRLGRTGRKR-NGRCVILLTQ  230 (395)
Q Consensus       165 ~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~~d~p~-s~~~yiQr~GRagR~~-~g~~i~l~~~  230 (395)
                      ..++.+|++|+++|||||+++++|||+|++++||++++|. ..+.|.|..||+||.+ .|.|++++.+
T Consensus        80 e~~m~~F~~g~~~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~  147 (206)
T d1gm5a4          80 DRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD  147 (206)
T ss_dssp             HHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             HHHHHHHHCCCEEEEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeecc
Confidence            9999999999999999999999999999999999999998 5666666789999996 6677666544

>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=99.70  E-value=5.5e-17  Score=145.36  Aligned_cols=120  Identities=24%  Similarity=0.329  Sum_probs=104.8

Q ss_pred             HHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEE
Q psy4150         102 RLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIA  181 (395)
Q Consensus       102 ~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVa  181 (395)
                      .+.+.|...+.      .++++.+.|+..+..+.+.+.|.+..|.+++.++||   .|++.++.+++.+|++|+++||||
T Consensus        19 ~i~~~I~~El~------rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHG---km~~~eke~im~~F~~g~~~ILv~   89 (211)
T d2eyqa5          19 VVREAILREIL------RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHG---QMRERELERVMNDFHHQRFNVLVC   89 (211)
T ss_dssp             HHHHHHHHHHT------TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCS---SCCHHHHHHHHHHHHTTSCCEEEE
T ss_pred             HHHHHHHHHHH------cCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEe---ccCHHHHHHHHHHHHcCCcceEEE
Confidence            35555555443      479999999999999999999999999999999999   999999999999999999999999


Q ss_pred             cCccccCCCCCCCCEEEEcCCCC-ChhhHhhhccccccccCceEEEEEeC
Q psy4150         182 TSVGEEGLDIGEIDLVICFDAQK-SPIKMVQRLGRTGRKRNGRCVILLTQ  230 (395)
Q Consensus       182 T~v~~~GlDip~v~~VI~~d~p~-s~~~yiQr~GRagR~~~g~~i~l~~~  230 (395)
                      |.+.+.|||+|+++++|+++++. ...++-|-.||+||.+...+++|+++
T Consensus        90 TtvIEvGiDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~  139 (211)
T d2eyqa5          90 TTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTP  139 (211)
T ss_dssp             SSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEEC
T ss_pred             ehhhhhccCCCCCcEEEEecchhccccccccccceeeecCccceEEEEec
Confidence            99999999999999999999997 78888888999999974444445544

>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=99.70  E-value=1.2e-16  Score=147.42  Aligned_cols=148  Identities=21%  Similarity=0.303  Sum_probs=112.1

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHccc-CCCCceeEEeccCCCCCHHHHHHHHHHHhc
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPL-EPMVKASMFVGQSSGVTQQEQKEIMKKFRA  173 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~-~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~  173 (395)
                      ..++|+..|.++|.+....      +.++||||+++...+.+..+|... +  +.+..+||   +++..+|..++++|..
T Consensus        66 ~~S~K~~~l~~~l~~~~~~------g~kviIFs~~~~~~~~l~~~l~~~~~--~~~~~i~G---~~~~~~R~~~i~~F~~  134 (244)
T d1z5za1          66 RRSGKMIRTMEIIEEALDE------GDKIAIFTQFVDMGKIIRNIIEKELN--TEVPFLYG---ELSKKERDDIISKFQN  134 (244)
T ss_dssp             TTCHHHHHHHHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHHC--SCCCEECT---TSCHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHhhccc------ccceEEEeeceehHHHHHHHHHhhcc--ceEEEEec---ccchhccchhhhhhhc
Confidence            3568999999999886543      689999999999999999988765 6  78889999   9999999999999988


Q ss_pred             C-CccEEE-EcCccccCCCCCCCCEEEEcCCCCChhhHhhhcccccccc---CceEEEEEeCCchhhHHHHHHHHhHHHH
Q psy4150         174 G-EFNTLI-ATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKR---NGRCVILLTQGREAHNFQTSMQTCKSYV  248 (395)
Q Consensus       174 g-~~~vLV-aT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~---~g~~i~l~~~~~e~~~~~~~~~~~~~~i  248 (395)
                      + ...||| +|.+++.|+|++.+++||+||+|||+..+.|++||+.|.|   +..++.+++.++.+..+..........+
T Consensus       135 ~~~~~vll~~~~~~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~Tiee~i~~~~~~K~~~~  214 (244)
T d1z5za1         135 NPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLF  214 (244)
T ss_dssp             CTTCCEEEEECCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSHHHHHHHHHHHCHHHH
T ss_pred             cccchhccccccccccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCCCHHHHHHHHHHHHHHHH
Confidence            7 467665 4589999999999999999999999999999999999987   3456668888887777766664544444


Q ss_pred             HHHHc
Q psy4150         249 EKIIN  253 (395)
Q Consensus       249 ~~~i~  253 (395)
                      ...++
T Consensus       215 ~~~~~  219 (244)
T d1z5za1         215 KDIIS  219 (244)
T ss_dssp             TTGGG
T ss_pred             HHHHh
Confidence            44443

>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=99.67  E-value=4.8e-16  Score=150.61  Aligned_cols=136  Identities=17%  Similarity=0.217  Sum_probs=117.6

Q ss_pred             cccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCC
Q psy4150          96 SHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGE  175 (395)
Q Consensus        96 ~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~  175 (395)
                      .+.|+..|.++|......     .+.|+|||+++..+.+.|.++|...|  +.+..++|   +++..+|..+++.|+++.
T Consensus        99 ~S~Kl~~L~~ll~~~~~~-----~g~KvlIFs~~~~~ld~l~~~l~~~g--~~~~~l~G---~~~~~~R~~~i~~F~~~~  168 (346)
T d1z3ix1          99 LSGKMLVLDYILAMTRTT-----TSDKVVLVSNYTQTLDLFEKLCRNRR--YLYVRLDG---TMSIKKRAKIVERFNNPS  168 (346)
T ss_dssp             GSHHHHHHHHHHHHHHHH-----CCCEEEEEESCHHHHHHHHHHHHHHT--CCEEEECS---SCCHHHHHHHHHHHHSTT
T ss_pred             cCHHHHHHHHHHHHHHHh-----cCCceeEEeehhhhhHHHHHHHhhhh--cccccccc---chhHHHHHHHHHhhhccc
Confidence            467999999988765432     46799999999999999999999999  99999999   999999999999999875


Q ss_pred             cc---EEEEcCccccCCCCCCCCEEEEcCCCCChhhHhhhccccccccC---ceEEEEEeCCchhhHHHHHH
Q psy4150         176 FN---TLIATSVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGRTGRKRN---GRCVILLTQGREAHNFQTSM  241 (395)
Q Consensus       176 ~~---vLVaT~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GRagR~~~---g~~i~l~~~~~e~~~~~~~~  241 (395)
                      ..   +|++|.+++.|||++.++.||+||++||+..+.|++||+.|.|+   ..++.|++.++.++.+...+
T Consensus       169 ~~~~vlLls~~agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~TiEe~i~~~~  240 (346)
T d1z3ix1         169 SPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQRQ  240 (346)
T ss_dssp             CCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHHHHHHH
T ss_pred             ccceeeeecchhhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCCCHHHHHHHHH
Confidence            43   67899999999999999999999999999999999999999973   34566888888776654333

>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=99.52  E-value=5.3e-15  Score=138.92  Aligned_cols=101  Identities=20%  Similarity=0.210  Sum_probs=83.1

Q ss_pred             CCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEE
Q psy4150         119 ETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVI  198 (395)
Q Consensus       119 ~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI  198 (395)
                      .++++||||++++.++.+++.|.+.+  +.+..+||   ++.+..    ...|++|..+++|||+++++|+|++ ++.||
T Consensus       177 ~~~~~lvf~~~~~~~~~l~~~L~~~~--~~~~~l~~---~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi  246 (305)
T d2bmfa2         177 FKGKTVWFVPSIKAGNDIAACLRKNG--KKVIQLSR---KTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVI  246 (305)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHT--CCCEECCT---TCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEE
T ss_pred             hCCCEEEEeccHHHHHHHHHHHHhCC--CCEEEeCC---cChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEE
Confidence            36899999999999999999999998  88899999   876544    4568999999999999999999995 55554


Q ss_pred             ----------EcCC----------CCChhhHhhhccccccccCceEEEEEe
Q psy4150         199 ----------CFDA----------QKSPIKMVQRLGRTGRKRNGRCVILLT  229 (395)
Q Consensus       199 ----------~~d~----------p~s~~~yiQr~GRagR~~~g~~i~l~~  229 (395)
                                +||.          |.|..+|+||+||+||.|.|....++.
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~  297 (305)
T d2bmfa2         247 DPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIY  297 (305)
T ss_dssp             ECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEE
T ss_pred             EcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEE
Confidence                      4444          457889999999999998666544433

>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=99.41  E-value=1.7e-13  Score=129.54  Aligned_cols=100  Identities=16%  Similarity=0.163  Sum_probs=78.1

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      ++++||||++...++.+++.|.+.|  .++..+||   .+...++.    .|++|+.+||||||+++.|||+ +|.+||.
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g--~~V~~l~~---~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid  105 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAG--KSVVVLNR---KTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLD  105 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT--CCEEECCS---SSCC------------CCCSEEEESSSTTCCTTC-CCSEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcC--CeEEEEcC---cCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEe
Confidence            5899999999999999999999999  88999999   77766654    5789999999999999999999 5999997


Q ss_pred             cCCC-------------------CChhhHhhhccccccccCc-eEEEEEe
Q psy4150         200 FDAQ-------------------KSPIKMVQRLGRTGRKRNG-RCVILLT  229 (395)
Q Consensus       200 ~d~p-------------------~s~~~yiQr~GRagR~~~g-~~i~l~~  229 (395)
                      ++.+                   .|..+..||.||+||.+.+ .++.++.
T Consensus       106 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         106 CRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             CCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             cCceeceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence            6542                   3677889999999998533 3444443

>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=99.30  E-value=2.5e-11  Score=104.93  Aligned_cols=132  Identities=19%  Similarity=0.138  Sum_probs=103.2

Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      +..|.....|+.++.+-+.+....      +.+|||||.|...++.|+.+|.+.+  ++..+++.   ...  +++..+-
T Consensus        10 D~vf~T~~eK~~AIi~eV~~~~~~------grPVLIgT~SIe~SE~ls~~L~~~g--i~h~vLnA---k~~--~~Ea~II   76 (175)
T d1tf5a4          10 DLIYRTMEGKFKAVAEDVAQRYMT------GQPVLVGTVAVETSELISKLLKNKG--IPHQVLNA---KNH--EREAQII   76 (175)
T ss_dssp             CEEESSHHHHHHHHHHHHHHHHHH------TCCEEEEESCHHHHHHHHHHHHTTT--CCCEEECS---SCH--HHHHHHH
T ss_pred             CeEEcCHHHHHHHHHHHHHHHHhc------CCCEEEEeCcHHHHHHHHHHHHHcC--CCceeehh---hhH--HHHHHHH
Confidence            345667778999998888776554      6899999999999999999999999  88889987   433  3333333


Q ss_pred             HHhcCCccEEEEcCccccCCCCCC---CC-----EEEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         170 KFRAGEFNTLIATSVGEEGLDIGE---ID-----LVICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       170 ~Fk~g~~~vLVaT~v~~~GlDip~---v~-----~VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      ...-..-.|.|||++++||.||.-   |.     +||.-..|.|..-..|-.||+||.| .|.+.+|++-+++.
T Consensus        77 ~~Ag~~g~VtIATNmAGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD~l  150 (175)
T d1tf5a4          77 EEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDEL  150 (175)
T ss_dssp             TTTTSTTCEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSSG
T ss_pred             HhccCCCceeehhhHHHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCHHH
Confidence            323335679999999999999842   22     8899999999999999999999998 56666676665543

>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=98.78  E-value=5.1e-08  Score=85.58  Aligned_cols=131  Identities=19%  Similarity=0.165  Sum_probs=102.0

Q ss_pred             ceeeeccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHH
Q psy4150          90 SSEYAWSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMK  169 (395)
Q Consensus        90 ~~~~~~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~  169 (395)
                      +..|.....|+.++.+-+......      +.+|||.|.|....+.|+..|.+.+  ++..+|+.   .-.  +|+.-+=
T Consensus        10 D~Vy~T~~~K~~Avv~ei~~~h~~------GqPVLVGT~SVe~SE~lS~lL~~~g--i~h~vLNA---K~h--erEAeII   76 (219)
T d1nkta4          10 DLIYKTEEAKYIAVVDDVAERYAK------GQPVLIGTTSVERSEYLSRQFTKRR--IPHNVLNA---KYH--EQEATII   76 (219)
T ss_dssp             CEEESCHHHHHHHHHHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHTT--CCCEEECS---SCH--HHHHHHH
T ss_pred             CeEEcCHHHHHHHHHHHHHHHHhc------CCCEEEeeCcHHHHHHHHHHHHHhc--cchhccch---hhH--HHHHHHH
Confidence            456677788999999888876554      7899999999999999999999999  99999988   322  3433332


Q ss_pred             HHhcC-CccEEEEcCccccCCCCCC----------------------------------------------------CCE
Q psy4150         170 KFRAG-EFNTLIATSVGEEGLDIGE----------------------------------------------------IDL  196 (395)
Q Consensus       170 ~Fk~g-~~~vLVaT~v~~~GlDip~----------------------------------------------------v~~  196 (395)
                      . ..| .-.|-|||+.++||.||-=                                                    -=+
T Consensus        77 A-qAG~~GaVTIATNMAGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~  155 (219)
T d1nkta4          77 A-VAGRRGGVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLY  155 (219)
T ss_dssp             H-TTTSTTCEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEE
T ss_pred             H-hcccCCcEEeeccccCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcE
Confidence            2 345 4568899999999999921                                                    127


Q ss_pred             EEEcCCCCChhhHhhhcccccccc-CceEEEEEeCCchh
Q psy4150         197 VICFDAQKSPIKMVQRLGRTGRKR-NGRCVILLTQGREA  234 (395)
Q Consensus       197 VI~~d~p~s~~~yiQr~GRagR~~-~g~~i~l~~~~~e~  234 (395)
                      ||-.....|..---|-.||+||.| +|...+|++-+++.
T Consensus       156 VIGTErHeSrRIDnQLRGRsGRQGDPGsSrFflSLeDdL  194 (219)
T d1nkta4         156 VLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDEL  194 (219)
T ss_dssp             EEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSHH
T ss_pred             EEeccccccccccccccccccccCCCccceeEEeccHHH
Confidence            888888889888999999999998 56666666655443

>d1e52a_ a.2.9.1 (A:) C-terminal UvrC-binding domain of UvrB {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: C-terminal UvrC-binding domain of UvrB
family: C-terminal UvrC-binding domain of UvrB
domain: C-terminal UvrC-binding domain of UvrB
species: Escherichia coli [TaxId: 562]

Probab=98.51  E-value=7e-09  Score=72.13  Aligned_cols=40  Identities=10%  Similarity=0.173  Sum_probs=37.5

Q ss_pred             hhhhhhccchhhhhHHHHHHHHhhhhchhhHHHHHhhhcCCC
Q psy4150         328 NAKKTKKQPMMTQSNDIRTCFENITKKKKTFIDFLTQSSGEP  369 (395)
Q Consensus       328 ~~~~~~~~~m~~a~~~l~~~fe~a~~~rd~~~~~~~~~~~~~  369 (395)
                      +.+++++++|..||+.|+  ||.||++||+|..|+..+.+.+
T Consensus        17 k~i~~Le~~M~~aa~~l~--FE~AA~~RD~I~~l~~~l~~~s   56 (56)
T d1e52a_          17 QKIHELEGLMMQHAQNLE--FEEAAQIRDQLHQLRELFIAAS   56 (56)
T ss_dssp             HHHHHHHHHHHHHHHTTC--HHHHTTHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHhcC
Confidence            789999999999999999  9999999999999999987643

>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=97.41  E-value=0.00038  Score=63.16  Aligned_cols=110  Identities=14%  Similarity=0.212  Sum_probs=82.2

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .++.|.......+...+..      +.++++-++|.--+...+..+.+..+  ++.+..+||   +++..+|.+++.+++
T Consensus       113 vGSGKT~Va~~a~~~~~~~------g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~---~~~~~~r~~~~~~~~  183 (264)
T d1gm5a3         113 VGSGKTVVAQLAILDNYEA------GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIG---ATTPSEKEKIKSGLR  183 (264)
T ss_dssp             SSSSHHHHHHHHHHHHHHH------TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCS---SSCHHHHHHHHHHHH
T ss_pred             ccccccHHHHHHHHHHHhc------ccceeEEeehHhhhHHHHHHHHHhhhhccccceeecc---ccchHHHHHHHHHHH
Confidence            4566877776666665554      68999999998888877766655332  278899999   999999999999999


Q ss_pred             cCCccEEEEc-CccccCCCCCCCCEEEEcCCCCChhhHhhhccc
Q psy4150         173 AGEFNTLIAT-SVGEEGLDIGEIDLVICFDAQKSPIKMVQRLGR  215 (395)
Q Consensus       173 ~g~~~vLVaT-~v~~~GlDip~v~~VI~~d~p~s~~~yiQr~GR  215 (395)
                      +|+++|+|+| .++...+.+.++.+||.=.-.  ...|-||-+-
T Consensus       184 ~g~~~iiIGThsl~~~~~~f~~LglviiDEqH--~fgv~Qr~~l  225 (264)
T d1gm5a3         184 NGQIDVVIGTHALIQEDVHFKNLGLVIIDEQH--RFGVKQREAL  225 (264)
T ss_dssp             SSCCCEEEECTTHHHHCCCCSCCCEEEEESCC--CC-----CCC
T ss_pred             CCCCCEEEeehHHhcCCCCccccceeeecccc--ccchhhHHHH
Confidence            9999999999 566678999899988876543  3356776554

>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=97.00  E-value=0.0017  Score=57.59  Aligned_cols=109  Identities=13%  Similarity=0.135  Sum_probs=86.6

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccCC--CCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLEP--MVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~~--~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .++.|.......+...+..      +.++++.++|.-.+..+++.+++..+  .+.+..+||   .++..+|..++..+.
T Consensus        85 vGsGKT~V~~~a~~~~~~~------g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~---~~~~~~~~~~~~~~~  155 (233)
T d2eyqa3          85 VGFGKTEVAMRAAFLAVDN------HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISR---FRSAKEQTQILAEVA  155 (233)
T ss_dssp             CCTTTHHHHHHHHHHHHTT------TCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEEST---TSCHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHc------CCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccC---cccchhHHHHHHHHh
Confidence            4566888877777666543      78999999999999999998887533  267888999   999999999999999


Q ss_pred             cCCccEEEEcC-ccccCCCCCCCCEEEEcCCCCChhhHhhhcc
Q psy4150         173 AGEFNTLIATS-VGEEGLDIGEIDLVICFDAQKSPIKMVQRLG  214 (395)
Q Consensus       173 ~g~~~vLVaT~-v~~~GlDip~v~~VI~~d~p~s~~~yiQr~G  214 (395)
                      +|+++|+|+|- ++...+.+.++.+||.-.-.  -.+|-||.+
T Consensus       156 ~g~~~iviGths~l~~~~~f~~LgLiIiDEeH--~fg~kQ~~~  196 (233)
T d2eyqa3         156 EGKIDILIGTHKLLQSDVKFKDLGLLIVDEEH--RFGVRHKER  196 (233)
T ss_dssp             TTCCSEEEECTHHHHSCCCCSSEEEEEEESGG--GSCHHHHHH
T ss_pred             CCCCCEEEeehhhhccCCccccccceeeechh--hhhhHHHHH
Confidence            99999999996 55567899899888865543  234566543

>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=91.45  E-value=0.48  Score=39.89  Aligned_cols=97  Identities=18%  Similarity=0.180  Sum_probs=65.0

Q ss_pred             ccccHHHHHHHHHHHHHHhhhccCCCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEeccCCCCCHHHHHHHHHHHh
Q psy4150          95 WSHLKFIRLREILESHFRLHAEKGETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQSSGVTQQEQKEIMKKFR  172 (395)
Q Consensus        95 ~~~~K~~~L~~lL~~~~~~~~~~~~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~~~~~~~~~R~~~l~~Fk  172 (395)
                      .+..|.-...-.+.+...    ...+.++||.|+|+..|..+.+.+....  ...++..++|   +.+..++...++   
T Consensus        51 TGsGKT~~~~l~~~~~~~----~~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g---~~~~~~~~~~l~---  120 (208)
T d1hv8a1          51 TGSGKTASFAIPLIELVN----ENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYG---GKAIYPQIKALK---  120 (208)
T ss_dssp             SSSSHHHHHHHHHHHHSC----SSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECT---TSCHHHHHHHHH---
T ss_pred             hcccccceeecccccccc----cccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeC---CCChHHHHHhcC---
Confidence            455566555443433332    2456789999999999999888776642  2367788888   777776655443   


Q ss_pred             cCCccEEEEcC-----cc-ccCCCCCCCCEEEEcCCC
Q psy4150         173 AGEFNTLIATS-----VG-EEGLDIGEIDLVICFDAQ  203 (395)
Q Consensus       173 ~g~~~vLVaT~-----v~-~~GlDip~v~~VI~~d~p  203 (395)
                        ..+|||||+     .+ ...+++..+.++|.-++.
T Consensus       121 --~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad  155 (208)
T d1hv8a1         121 --NANIVVGTPGRILDHINRGTLNLKNVKYFILDEAD  155 (208)
T ss_dssp             --TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHH
T ss_pred             --CCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChH
Confidence              378999995     23 345688888888765543

>d2eyqa2 c.37.1.19 (A:349-465) 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=88.79  E-value=0.17  Score=39.04  Aligned_cols=65  Identities=8%  Similarity=0.096  Sum_probs=49.5

Q ss_pred             CccEEEEcCcHHHHHHHHHHHcccCCCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcCccccCCCCCCCCEEEE
Q psy4150         120 TTKVIIFANYRVVVAEIFDVLKPLEPMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATSVGEEGLDIGEIDLVIC  199 (395)
Q Consensus       120 ~~r~iVF~~t~~~ae~l~~~L~~~~~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~v~~~GlDip~v~~VI~  199 (395)
                      ..+|||.|.+...++.|.+.|.+.+  +.+..+.+    ++         +|..+.  +.|+...++.|.-+|+..++|.
T Consensus        34 ~~~Vli~a~s~g~~erl~e~L~~~~--i~~~~~~~----~~---------~~~~~~--~~i~~~~l~~GF~~~~~~l~vI   96 (117)
T d2eyqa2          34 DGPVVFSVESEGRREALGELLARIK--IAPQRIMR----LD---------EASDRG--RYLMIGAAEHGFVDTVRNLALI   96 (117)
T ss_dssp             CSCCCEEESSHHHHHHHHHHHGGGT--CCCEECSS----GG---------GCCTTC--CEEEECCCCSCEEETTTTEEEE
T ss_pred             CCeEEEEECCccHHHHHHHHHHHcC--CCceEecC----hh---------hhcCce--EEEEEecCccccccCCCCEEEE
Confidence            5689999999999999999999998  77655443    22         244444  4566677899998898888886


Q ss_pred             cC
Q psy4150         200 FD  201 (395)
Q Consensus       200 ~d  201 (395)
                      -+
T Consensus        97 tE   98 (117)
T d2eyqa2          97 CE   98 (117)
T ss_dssp             EH
T ss_pred             Ec
Confidence            43

>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=87.67  E-value=1  Score=38.37  Aligned_cols=76  Identities=18%  Similarity=0.217  Sum_probs=54.5

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccC--CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC------ccccCC
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLE--PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS------VGEEGL  189 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~--~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~------v~~~Gl  189 (395)
                      ....++||+|+|++.|..+++.+...+  ..+++..++|   +.+..+....++   . ..+|||+|+      +-...+
T Consensus        83 ~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g---~~~~~~~~~~l~---~-~~~Ilv~TPgrl~~~~~~~~~  155 (222)
T d2j0sa1          83 VRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIG---GTNVGEDIRKLD---Y-GQHVVAGTPGRVFDMIRRRSL  155 (222)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECT---TSCHHHHHHHHH---H-CCSEEEECHHHHHHHHHTTSS
T ss_pred             ccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEee---cccchhhHHHhc---c-CCeEEeCCCCcHHhccccccc
Confidence            345689999999999999998887643  3477888888   777666555443   3 368999995      224556


Q ss_pred             CCCCCCEEEEc
Q psy4150         190 DIGEIDLVICF  200 (395)
Q Consensus       190 Dip~v~~VI~~  200 (395)
                      ++..+.++|.=
T Consensus       156 ~~~~l~~lVlD  166 (222)
T d2j0sa1         156 RTRAIKMLVLD  166 (222)
T ss_dssp             CCTTCCEEEEE
T ss_pred             ccccceeeeec
Confidence            77777777643

>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=87.19  E-value=0.097  Score=45.23  Aligned_cols=47  Identities=9%  Similarity=0.002  Sum_probs=38.2

Q ss_pred             HHHHHHHhcchHHHHHHHHhC--CCcchhhhccccCccc-cccccccCCh
Q psy4150          25 IQRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKED-GSCPILGKDN   71 (395)
Q Consensus        25 lead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~-~~~~~l~~~~   71 (395)
                      .|+|.++++||.+.+..+.++  ..+|+++||||+++.+ ..++.++.+|
T Consensus       166 DEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~P  215 (222)
T d2j0sa1         166 DEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDP  215 (222)
T ss_dssp             ETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSC
T ss_pred             cchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCC
Confidence            499999999999998888886  5689999999999876 3455566655

>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=84.45  E-value=0.085  Score=44.90  Aligned_cols=46  Identities=7%  Similarity=-0.023  Sum_probs=36.1

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCCh
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDN   71 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~   71 (395)
                      |+|.+++.||.+.++.|..+  ..+|+++||||++..+. .+..++.+|
T Consensus       154 EaD~ll~~~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P  202 (206)
T d1veca_         154 EADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKP  202 (206)
T ss_dssp             THHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSC
T ss_pred             ccccccccchHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCC
Confidence            99999999999998888775  56899999999988762 334444443

>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=82.72  E-value=2.7  Score=34.89  Aligned_cols=60  Identities=18%  Similarity=0.364  Sum_probs=43.6

Q ss_pred             CCCccEEEEcCcHHHHHHHHHHHcccC---CCCceeEEeccCCCCCHHHHHHHHHHHhcCCccEEEEcC
Q psy4150         118 GETTKVIIFANYRVVVAEIFDVLKPLE---PMVKASMFVGQSSGVTQQEQKEIMKKFRAGEFNTLIATS  183 (395)
Q Consensus       118 ~~~~r~iVF~~t~~~ae~l~~~L~~~~---~~~~~~~lhg~~~~~~~~~R~~~l~~Fk~g~~~vLVaT~  183 (395)
                      ....+++|.|+|+..+..+.+.+...+   +.+.+..++|   +.+......   .+..+..+|||||+
T Consensus        67 ~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g---~~~~~~~~~---~l~~~~~~ilI~TP  129 (207)
T d1t6na_          67 TGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFG---GLSIKKDEE---VLKKNCPHIVVGTP  129 (207)
T ss_dssp             TTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESC---CSCHHHHHH---HHHHSCCSEEEECH
T ss_pred             CCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEec---cccHHHHHH---HHHhcCCCEEEeCc
Confidence            345689999999999999888876654   3356677777   666555433   34456789999995

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=81.15  E-value=0.078  Score=44.82  Aligned_cols=47  Identities=2%  Similarity=-0.022  Sum_probs=36.8

Q ss_pred             HHHHHHhcchHHHHHHHHhC--CCcchhhhccccCcccc-ccccccCChh
Q psy4150          26 QRDFHVTHSLASALENLVTY--GLRSFYNNLVEVSKEDG-SCPILGKDND   72 (395)
Q Consensus        26 ead~~~~~~l~~~~~~L~~~--g~r~~~~fsatl~~~~~-~~~~l~~~~~   72 (395)
                      |+|.+++.+|...++.|..+  ..+|+++||||+++.+. .++.++.+|.
T Consensus       155 Ead~ll~~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~  204 (209)
T d1q0ua_         155 EADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPT  204 (209)
T ss_dssp             SHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCE
T ss_pred             ecccccccccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCE
Confidence            99999999999998888775  56899999999988763 3444555543