Citrus Sinensis ID: 042003

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------25
Protein Sequence
LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI
Secondary Structure (PSIPRED)
cccHHHHHHHHHHcccccEEEEEEcccccccccccccccEEEccccHHHHHHHcccccccccEEEEEEcccccccccccHHHHHHHHHHcccccccEEEEEccccHHHHHHHHHHccccEEEEEEccccccccEEEEEEEccccccHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHcccccEEEHHHHHHHcccccccccEEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHccccEEEEEEccccHHHHHHHccccEEEEcccHHHHHHHcccccHHHEEEEEEcHHHHHHHccccHHHHHHHHHccccccccEEEEEccccHHHHHHHHHHHcccEEEEEEccccccccEEEEEEEEccHHHHHHHHHHHHHcccccEEEEEEEccccHHHHHHHHHHcccccEEEcccccHHHHHHHHHHHHcccccEEEEHHHHHccccccccEEEEEEcccccHHHHEEcc
Coil and Loop (DISEMBL)
LATQTTRECKKLAKGNKFQIKLMKKELVrstdlskfscdilisTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDpvvkacsnpsivRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFaeslnppvliFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIargmdfkgvncvinydfpdsgaayihri
Flexible Loop (DISEMBL)
latqttreckklakgnkfqiklMKKElvrstdlskfscdilistplrlrlairrkkidlsrveyLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGrkntasesiKQKLVFAGSEEGKLLALRQSfaeslnppVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQREnavddfragkTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI
Low Complexity Region (SEG)
LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPlrlrlairrkkidlSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI
Disordered region (IsUnstruct)
****************KFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYI***
Disordered Region (DISOPRED)
LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI
Disordered Region (DISEMBL)
LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI
Disordered Region (DISPRO)
LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI
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	248	2.2.26 [Sep-21-2011]
Q84TG1	541	DEAD-box ATP-dependent RN	yes	no	0.995	0.456	0.802	1e-112
Q5K5B6	540	DEAD-box ATP-dependent RN	yes	no	0.995	0.457	0.770	1e-108
Q86IZ9	668	Probable ATP-dependent RN	yes	no	0.995	0.369	0.516	3e-67
A3GHW9	558	ATP-dependent RNA helicas	yes	no	0.995	0.442	0.503	7e-66
Q6BP45	550	ATP-dependent RNA helicas	yes	no	0.995	0.449	0.488	4e-65
Q75AE1	569	ATP-dependent RNA helicas	yes	no	0.987	0.430	0.492	7e-63
A5DIX5	537	ATP-dependent RNA helicas	N/A	no	0.987	0.456	0.476	5e-62
A5E1N2	553	ATP-dependent RNA helicas	N/A	no	0.987	0.443	0.492	6e-62
Q6FN65	565	ATP-dependent RNA helicas	yes	no	0.987	0.433	0.464	8e-62
A7TT88	570	ATP-dependent RNA helicas	N/A	no	0.987	0.429	0.468	3e-61

>sp|Q84TG1|RH57_ARATH DEAD-box ATP-dependent RNA helicase 57 OS=Arabidopsis thaliana GN=RH57 PE=2 SV=1

 Score =  404 bits (1037), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 199/248 (80%), Positives = 219/248 (88%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA QT RE KKL KG+ F I+LM K LV++ D SK  CD+LISTP+RL+ AI+ KKIDLS
Sbjct: 222 LAAQTAREGKKLIKGSNFHIRLMTKPLVKTADFSKLWCDVLISTPMRLKRAIKAKKIDLS 281

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           +VEYLVLDE+DKLFE  +LLK ID VVKACSNPSI+RSLFSATLPD VEELARSIMHDAV
Sbjct: 282 KVEYLVLDESDKLFE-QSLLKQIDCVVKACSNPSIIRSLFSATLPDSVEELARSIMHDAV 340

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVI+GRKNTASE++KQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELY EL
Sbjct: 341 RVIIGRKNTASETVKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYDEL 400

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
             + IRAGVIHSDL   +RENAVD FRAG+ WVLIATDVIARGMDFKG+NCVINYDFPDS
Sbjct: 401 KCENIRAGVIHSDLPPGERENAVDQFRAGEKWVLIATDVIARGMDFKGINCVINYDFPDS 460

Query: 241 GAAYIHRI 248
            +AYIHRI
Sbjct: 461 ASAYIHRI 468

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

>sp|Q5K5B6|RH57_ORYSJ DEAD-box ATP-dependent RNA helicase 57 OS=Oryza sativa subsp. japonica GN=Os07g0647900 PE=2 SV=2

 Score =  391 bits (1005), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 191/248 (77%), Positives = 219/248 (88%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA QTTRECKKLAKG KF IKLM K+L +S +     CDILISTPLRL  A++++ +DLS
Sbjct: 227 LAAQTTRECKKLAKGRKFYIKLMTKDLSKSGNFKDMHCDILISTPLRLDHAVQKRDLDLS 286

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           RVEYLVLDE+DKLFE+G  ++ ID VVKACSNPSI+RSLFSATLPD +E LAR+IMHDAV
Sbjct: 287 RVEYLVLDESDKLFELG-FVEVIDSVVKACSNPSIIRSLFSATLPDSIETLARTIMHDAV 345

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVIVGRKN+AS  IKQKL+FAG+E+GKLLALRQSFAESLNPPVLIFVQSKERAKELY EL
Sbjct: 346 RVIVGRKNSASSLIKQKLIFAGTEKGKLLALRQSFAESLNPPVLIFVQSKERAKELYKEL 405

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
           AFD +RA VIH+DL + QR++AVD+ RAGKTWVLIAT+VIARGMDFKGVNCVINYDFP+S
Sbjct: 406 AFDDVRADVIHADLDEEQRQDAVDNLRAGKTWVLIATEVIARGMDFKGVNCVINYDFPES 465

Query: 241 GAAYIHRI 248
            +AYIHRI
Sbjct: 466 ASAYIHRI 473

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q86IZ9|DDX52_DICDI Probable ATP-dependent RNA helicase ddx52 OS=Dictyostelium discoideum GN=ddx52 PE=3 SV=1

 Score =  255 bits (651), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 129/250 (51%), Positives = 171/250 (68%), Gaps = 3/250 (1%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKF--SCDILISTPLRLRLAIRRKKID 58
           LA Q  R  + L+KG  F+I ++ K L   +       + DILI+TPLRL   I+   + 
Sbjct: 280 LAQQIYRNFRLLSKGKPFRICVLSKNLHNQSTNENLIKNYDILITTPLRLVYLIKENLLS 339

Query: 59  LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHD 118
           L++VEYLV DEADKLF+  N  + +D VV AC NP +   LFSAT+   VEEL  SIM +
Sbjct: 340 LNKVEYLVFDEADKLFD-KNFQEQVDIVVTACQNPKLKICLFSATMNQQVEELGHSIMKN 398

Query: 119 AVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYG 178
            +++I+G +N A+ ++ QKL++ G EEGKLLA+RQ   + L PP+LIF QSKERA +L+ 
Sbjct: 399 PIKIIIGEQNAAAITVDQKLIYVGKEEGKLLAVRQLIQKGLEPPILIFTQSKERAHDLFQ 458

Query: 179 ELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP 238
           EL FDGI   VIHS+ +Q QR+  V  FR GK WVLI T+++ARGMDFKGVN VIN+DFP
Sbjct: 459 ELIFDGINVDVIHSERTQFQRDTIVKKFRMGKIWVLICTELMARGMDFKGVNFVINFDFP 518

Query: 239 DSGAAYIHRI 248
            + A+YIHRI
Sbjct: 519 HTLASYIHRI 528

ATP-binding RNA helicase which may be involved in the ribosome biogenesis.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A3GHW9|ROK1_PICST ATP-dependent RNA helicase ROK1 OS=Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) GN=ROK1 PE=3 SV=1

 Score =  250 bits (638), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 127/252 (50%), Positives = 173/252 (68%), Gaps = 5/252 (1%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVR--STDLSKFS-CDILISTPLRLRLAIRRKKI 57
           LA Q  +E + L +G K  + ++ K+L    + D+ K S  DI++STPLRL   ++ +K+
Sbjct: 206 LAIQIFQELQILTRGKKLNVAILSKQLANKLNNDIVKASKYDIIVSTPLRLIDIVKNEKV 265

Query: 58  DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH 117
           DLS+VE LV+DEADKLF+ G  ++  D ++  C+   I +S+FSAT+P  VEE+A SIM 
Sbjct: 266 DLSKVEQLVIDEADKLFDQG-FVEQTDDILSHCTYTKIRKSMFSATIPSGVEEMAHSIMR 324

Query: 118 DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKERAKEL 176
           D +RVI+GRK  AS +I QKLVF GSEEGKLLA+RQ   E    PP++IF+QS  RAK L
Sbjct: 325 DPIRVIIGRKEAASNTIDQKLVFTGSEEGKLLAIRQMIQEGEFKPPIIIFLQSIHRAKAL 384

Query: 177 YGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD 236
           + EL +D +   VIH++ +  QRE  +  F+ G  WVLI TDV+ARG+DFKGVN VINYD
Sbjct: 385 FHELLYDKLNVDVIHAERTPKQREEVIKRFKNGDIWVLITTDVLARGVDFKGVNMVINYD 444

Query: 237 FPDSGAAYIHRI 248
            P +  AY+HRI
Sbjct: 445 VPQTAQAYVHRI 456

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (taxid: 322104)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6BP45|ROK1_DEBHA ATP-dependent RNA helicase ROK1 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=ROK1 PE=3 SV=2

 Score =  248 bits (632), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 123/252 (48%), Positives = 172/252 (68%), Gaps = 5/252 (1%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTD---LSKFSCDILISTPLRLRLAIRRKKI 57
           LA Q  +E   + KG K +I ++ K+L    +   ++    DIL+STPLRL  +I+ + I
Sbjct: 199 LAVQIFQELNTMTKGKKMKIGILSKQLANKINNKIINSSKYDILVSTPLRLIDSIKNETI 258

Query: 58  DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH 117
            LS+VE LV+DE DKLF+ G  ++  D ++  C+N  + +S+FSAT+P  VEE+A+SIM 
Sbjct: 259 SLSKVEQLVIDETDKLFDQG-FVEQTDEILSNCTNTKLRKSMFSATIPSGVEEMAQSIMK 317

Query: 118 DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKERAKEL 176
           D +RVI+G K  AS +I+QKLVF G+EEGKLLA+RQ   +    PP++IF+QS  RAK L
Sbjct: 318 DPIRVIIGHKEAASNTIEQKLVFTGNEEGKLLAIRQMIQQGEFKPPIIIFLQSITRAKAL 377

Query: 177 YGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD 236
           + EL +D +   VIH++ +  QR+  +  F++G  WVLI TDVIARG+DFKGVN VINYD
Sbjct: 378 FHELLYDRLNVDVIHAERTPKQRDEVIKRFKSGDIWVLITTDVIARGVDFKGVNLVINYD 437

Query: 237 FPDSGAAYIHRI 248
            P S  AY+HRI
Sbjct: 438 VPQSAQAYVHRI 449

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q75AE1|ROK1_ASHGO ATP-dependent RNA helicase ROK1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=ROK1 PE=3 SV=1

 Score =  240 bits (612), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 126/256 (49%), Positives = 173/256 (67%), Gaps = 11/256 (4%)

Query: 1   LATQTTRECKKLA------KGNKFQIKLMKKEL---VRSTDLSKFSCDILISTPLRLRLA 51
           LA Q   EC KLA      K     + L+ K L   +++  +S    DI+ISTPLRL   
Sbjct: 206 LANQIFDECSKLAQRIFLEKKRPLSVALLSKSLAAKLKNQIVSDKKYDIIISTPLRLIDI 265

Query: 52  IRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL 111
           ++ + +DLS V+YL+ DEADKLF+    ++  D ++ ACS+P+I + LFSATLP  VEEL
Sbjct: 266 VKSESLDLSAVKYLIFDEADKLFD-KTFVEQTDDILSACSHPNISKVLFSATLPSSVEEL 324

Query: 112 ARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL-NPPVLIFVQSK 170
           A+SIM D VRVI+G K  A+ +I+QKLVF G+EEGKL+A+RQ   E +  PPV+IF++S 
Sbjct: 325 AQSIMTDPVRVIIGHKEAANTNIEQKLVFCGNEEGKLVAIRQLIQEGMFRPPVIIFLESI 384

Query: 171 ERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVN 230
            RAK L+ EL +D +   VIH++ +Q QRE  ++ F++G  W LI TDV+ARG+DFKG+N
Sbjct: 385 TRAKALFHELLYDKLNVDVIHAERTQVQREKIIERFKSGDLWCLICTDVLARGIDFKGIN 444

Query: 231 CVINYDFPDSGAAYIH 246
            VINYD P S  AY+H
Sbjct: 445 LVINYDVPRSAQAYVH 460

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DIX5|ROK1_PICGU ATP-dependent RNA helicase ROK1 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=ROK1 PE=3 SV=2

 Score =  237 bits (605), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 121/254 (47%), Positives = 170/254 (66%), Gaps = 9/254 (3%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDL-----SKFSCDILISTPLRLRLAIRRK 55
           LA Q  +    + +G+   + L+ K++           +KF  D+LI TPLRL   ++++
Sbjct: 190 LAIQIYQTLAPMCRGSNLNVTLLSKQVASKISSSIISANKF--DVLICTPLRLIDLVKKE 247

Query: 56  KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 115
           ++DLS+VE+LV+DEADKLF+ G  ++  D ++  C+ P+   S+FSAT+P  VEE+A SI
Sbjct: 248 QVDLSKVEHLVIDEADKLFDHG-FVEQTDEILSHCTLPTRRTSMFSATIPSGVEEMANSI 306

Query: 116 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKERAK 174
           M D +R+IVG K  AS SI QKLVF G+EEGKLLA+RQ   +    PP++IF+QS  RAK
Sbjct: 307 MKDQIRIIVGHKEGASTSIDQKLVFTGNEEGKLLAIRQMVQQGEFKPPIIIFLQSIPRAK 366

Query: 175 ELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN 234
            L+ EL +D +   VIH++ +  QRE A+  F+ G  WVLI TDV+ARG+DFKGVN VIN
Sbjct: 367 ALFHELIYDKLNVEVIHAERTPKQREEAIRRFKNGDAWVLITTDVLARGVDFKGVNLVIN 426

Query: 235 YDFPDSGAAYIHRI 248
           YD P +  AY+HRI
Sbjct: 427 YDVPQTSQAYVHRI 440

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (taxid: 294746)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5E1N2|ROK1_LODEL ATP-dependent RNA helicase ROK1 OS=Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) GN=ROK1 PE=3 SV=1

 Score =  237 bits (604), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 123/250 (49%), Positives = 168/250 (67%), Gaps = 5/250 (2%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVR--STDLSKFS-CDILISTPLRLRLAIRRKKI 57
           LA Q  ++ + ++KG    I ++ K+L    S D+ K S  DIL+STPLRL   ++  K+
Sbjct: 204 LAVQIFQQLEIISKGKGLNIAILSKQLAGKISNDVVKASKYDILVSTPLRLIDVVKLGKV 263

Query: 58  DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH 117
           DLS+V  LV+DEADKLF+ G   +  D ++  C+N  I +S+FSAT+P  VEE+A SIM 
Sbjct: 264 DLSKVTQLVIDEADKLFDHG-FAEQTDELLSHCTNVKIRKSMFSATIPSGVEEMAHSIMK 322

Query: 118 DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKERAKEL 176
           D +RVI+G K  AS +I+QKLVF G+EEGKLLA+RQ        PP++IF+QS  RAK L
Sbjct: 323 DPIRVIIGHKEAASNTIEQKLVFTGNEEGKLLAIRQMIQNGEFKPPIIIFLQSITRAKAL 382

Query: 177 YGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD 236
           + EL +D +   VIH++ +  QR+  +  F+ G  WVLI TDV+ARG+DFKGVN VINYD
Sbjct: 383 FHELVYDKLNVDVIHAERTPKQRDEVIKRFKNGDIWVLITTDVLARGVDFKGVNMVINYD 442

Query: 237 FPDSGAAYIH 246
            P S  AY+H
Sbjct: 443 VPQSAQAYVH 452

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (taxid: 379508)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6FN65|ROK1_CANGA ATP-dependent RNA helicase ROK1 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=ROK1 PE=3 SV=1

 Score =  236 bits (603), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 119/256 (46%), Positives = 173/256 (67%), Gaps = 11/256 (4%)

Query: 1   LATQTTRECKKLAK------GNKFQIKLMKKEL---VRSTDLSKFSCDILISTPLRLRLA 51
           LATQ   EC KL+K          Q+ ++ K L   +R+  +S    D++ISTPLRL   
Sbjct: 206 LATQIFNECVKLSKRIYLDKKRPLQVAILSKSLGAKLRNKVISDKKYDLIISTPLRLIDV 265

Query: 52  IRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL 111
           ++ + +DLS V++L+ DEADKLF+    ++  D ++ +C++PS+ +S+FSAT+P  VEE 
Sbjct: 266 VKNEALDLSNVKHLIFDEADKLFD-KTFIEQTDDILNSCTDPSMRKSMFSATIPSSVEET 324

Query: 112 ARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSK 170
           A SIM+D VRVI+G K  A+ +I+QKL+F G+EEGKL+A+RQ   +    PP++IF++S 
Sbjct: 325 ANSIMNDPVRVIIGHKEAANTNIEQKLIFCGNEEGKLIAIRQLVQQGEFKPPIIIFLESI 384

Query: 171 ERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVN 230
            RAK LY EL +D I   VIH++ +  QRE  ++ F+ G+ W LI TDV+ARG+DFKGVN
Sbjct: 385 ARAKALYHELMYDRINVDVIHAERTAIQREKIIERFKTGELWCLICTDVLARGIDFKGVN 444

Query: 231 CVINYDFPDSGAAYIH 246
            VINYD P +  AY+H
Sbjct: 445 LVINYDVPTTAQAYVH 460

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A7TT88|ROK1_VANPO ATP-dependent RNA helicase ROK1 OS=Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294) GN=ROK1 PE=3 SV=1

 Score =  234 bits (598), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 120/256 (46%), Positives = 173/256 (67%), Gaps = 11/256 (4%)

Query: 1   LATQTTRECKKLA------KGNKFQIKLMKKEL---VRSTDLSKFSCDILISTPLRLRLA 51
           LA Q   EC KL+      K    Q+ L+ K L   +R+  +S    DI++STPLRL   
Sbjct: 213 LANQIFLECIKLSNRIFLDKKRPLQVALLSKSLSAKLRNKVISDKKYDIIVSTPLRLIDV 272

Query: 52  IRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL 111
           ++ + +DLS+V++L+ DEADKLF+    ++  D ++ +CS+ S+ +S+FSAT+P  VEE+
Sbjct: 273 VKNEALDLSQVKHLIFDEADKLFD-KTFVEQSDDILSSCSHSSLRKSMFSATIPSNVEEI 331

Query: 112 ARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE-SLNPPVLIFVQSK 170
           A+SIM D VRVI+G K  A+ SI+QKLVF G+EEGKL+A++Q   E    PPV+IF++S 
Sbjct: 332 AKSIMMDPVRVIIGHKEAANTSIEQKLVFCGNEEGKLIAIKQLVQEGEFKPPVIIFLESI 391

Query: 171 ERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVN 230
            RAK LY E+ +D +   VIH++ +Q QR   ++ F++G  W LI TDV+ARG+DFKGVN
Sbjct: 392 TRAKALYHEMMYDSLNVDVIHAERTQVQRNKIIERFKSGDLWCLITTDVLARGVDFKGVN 451

Query: 231 CVINYDFPDSGAAYIH 246
            VINYD P +  AY+H
Sbjct: 452 LVINYDVPRTAQAYVH 467

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294) (taxid: 436907)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	248
449440077	616	PREDICTED: DEAD-box ATP-dependent RNA he	0.995	0.400	0.866	1e-122
297741568	523	unnamed protein product [Vitis vinifera]	0.995	0.472	0.854	1e-119
225439904	524	PREDICTED: DEAD-box ATP-dependent RNA he	0.995	0.471	0.854	1e-119
147784525	554	hypothetical protein VITISV_032421 [Viti	0.995	0.445	0.850	1e-118
255559765	535	dead box ATP-dependent RNA helicase, put	0.995	0.461	0.834	1e-117
356572415	536	PREDICTED: DEAD-box ATP-dependent RNA he	0.995	0.460	0.822	1e-116
357510607	619	DEAD-box ATP-dependent RNA helicase [Med	0.995	0.399	0.810	1e-115
356505198	537	PREDICTED: DEAD-box ATP-dependent RNA he	0.995	0.459	0.818	1e-115
22330935	541	DEAD-box ATP-dependent RNA helicase 57 [	0.995	0.456	0.802	1e-110
6682259	545	putative RNA helicase [Arabidopsis thali	0.995	0.453	0.802	1e-110

>gi|449440077|ref|XP_004137811.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57-like [Cucumis sativus]

 Score =  442 bits (1136), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 215/248 (86%), Positives = 232/248 (93%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA+QT RECKKLAKG KF IKL+ KE++R  D SKFSCD+LISTPLRLRLAIR+KKIDLS
Sbjct: 219 LASQTIRECKKLAKGKKFHIKLVTKEVLRHADFSKFSCDVLISTPLRLRLAIRKKKIDLS 278

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           RVEYLVLDE+DKLFE+G L+K ID VVKACSNPSIVRSLFSATLPDFVE+LARS+MHDAV
Sbjct: 279 RVEYLVLDESDKLFELG-LIKQIDAVVKACSNPSIVRSLFSATLPDFVEDLARSVMHDAV 337

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVIVGRKNTASE++KQKLVFAGSEEGKLLALRQSF+ESLNPPVLIFVQSKERAKELYGEL
Sbjct: 338 RVIVGRKNTASETVKQKLVFAGSEEGKLLALRQSFSESLNPPVLIFVQSKERAKELYGEL 397

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
           AF+ IR  VIHSDLSQ +REN VDDFRAGKTWVLIATDVI+RGMDFKGVNCVINYDFPDS
Sbjct: 398 AFENIRVSVIHSDLSQLERENVVDDFRAGKTWVLIATDVISRGMDFKGVNCVINYDFPDS 457

Query: 241 GAAYIHRI 248
            AAYIHRI
Sbjct: 458 AAAYIHRI 465

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741568|emb|CBI32700.3| unnamed protein product [Vitis vinifera]

 Score =  432 bits (1110), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 212/248 (85%), Positives = 229/248 (92%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA QT RE KKLAKG KF IKL+ KEL+RS D+SK  CDILISTPLRLR AIR+KK+DLS
Sbjct: 208 LAAQTARESKKLAKGKKFYIKLLTKELLRSGDISKLPCDILISTPLRLRSAIRKKKLDLS 267

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           RVEYLVLDE+DKLFE+G L+K ID VVKACSNPSI+RSLFSATLPDFVEELAR+IMHDAV
Sbjct: 268 RVEYLVLDESDKLFELG-LVKQIDAVVKACSNPSIIRSLFSATLPDFVEELARTIMHDAV 326

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVI+GRKN+ASE IKQKLVFAGSEEGKLLALRQSFAESLNPP+L+FVQSKERAKELY EL
Sbjct: 327 RVIIGRKNSASELIKQKLVFAGSEEGKLLALRQSFAESLNPPILLFVQSKERAKELYTEL 386

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
           AFD IR  VIH+DLSQ+QRENAVDDFRAGKTWVLIATDVIARGMDFKG+NCVINYDFPDS
Sbjct: 387 AFDDIRVDVIHADLSQSQRENAVDDFRAGKTWVLIATDVIARGMDFKGINCVINYDFPDS 446

Query: 241 GAAYIHRI 248
            AAYIHRI
Sbjct: 447 PAAYIHRI 454

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225439904|ref|XP_002279705.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57 [Vitis vinifera]

 Score =  432 bits (1110), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 212/248 (85%), Positives = 229/248 (92%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA QT RE KKLAKG KF IKL+ KEL+RS D+SK  CDILISTPLRLR AIR+KK+DLS
Sbjct: 209 LAAQTARESKKLAKGKKFYIKLLTKELLRSGDISKLPCDILISTPLRLRSAIRKKKLDLS 268

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           RVEYLVLDE+DKLFE+G L+K ID VVKACSNPSI+RSLFSATLPDFVEELAR+IMHDAV
Sbjct: 269 RVEYLVLDESDKLFELG-LVKQIDAVVKACSNPSIIRSLFSATLPDFVEELARTIMHDAV 327

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVI+GRKN+ASE IKQKLVFAGSEEGKLLALRQSFAESLNPP+L+FVQSKERAKELY EL
Sbjct: 328 RVIIGRKNSASELIKQKLVFAGSEEGKLLALRQSFAESLNPPILLFVQSKERAKELYTEL 387

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
           AFD IR  VIH+DLSQ+QRENAVDDFRAGKTWVLIATDVIARGMDFKG+NCVINYDFPDS
Sbjct: 388 AFDDIRVDVIHADLSQSQRENAVDDFRAGKTWVLIATDVIARGMDFKGINCVINYDFPDS 447

Query: 241 GAAYIHRI 248
            AAYIHRI
Sbjct: 448 PAAYIHRI 455

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147784525|emb|CAN61726.1| hypothetical protein VITISV_032421 [Vitis vinifera]

 Score =  431 bits (1107), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 211/248 (85%), Positives = 229/248 (92%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA QT RE KKLAKG KF IKL+ KEL+RS D+SK  CDILISTPLRLR AIR+KK+DLS
Sbjct: 205 LAAQTARESKKLAKGKKFYIKLLTKELLRSGDISKLPCDILISTPLRLRSAIRKKKLDLS 264

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           RVEYLVLDE+DKLFE+G L+K ID VVKACSNPSI+RSLFSATLPDFVEELAR+IMHDAV
Sbjct: 265 RVEYLVLDESDKLFELG-LVKQIDAVVKACSNPSIIRSLFSATLPDFVEELARTIMHDAV 323

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVI+GRKN+ASE IKQKLVFAG+EEGKLLALRQSFAESLNPP+L+FVQSKERAKELY EL
Sbjct: 324 RVIIGRKNSASELIKQKLVFAGNEEGKLLALRQSFAESLNPPILLFVQSKERAKELYTEL 383

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
           AFD IR  VIH+DLSQ+QRENAVDDFRAGKTWVLIATDVIARGMDFKG+NCVINYDFPDS
Sbjct: 384 AFDDIRVDVIHADLSQSQRENAVDDFRAGKTWVLIATDVIARGMDFKGINCVINYDFPDS 443

Query: 241 GAAYIHRI 248
            AAYIHRI
Sbjct: 444 PAAYIHRI 451

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559765|ref|XP_002520902.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223540033|gb|EEF41611.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  427 bits (1098), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 207/248 (83%), Positives = 228/248 (91%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA+QTTRECKK+AKGNKF+IKLM KELVR+ DLS+  CDIL+STPLRL+LAIR+KK+DLS
Sbjct: 220 LASQTTRECKKMAKGNKFRIKLMTKELVRTKDLSRLPCDILVSTPLRLQLAIRKKKVDLS 279

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           RVEYLVLDE+DKLFE+G LLK ID V KACSNPS++RSLFSATLP+ VEELAR+IMHDAV
Sbjct: 280 RVEYLVLDESDKLFELG-LLKQIDSVFKACSNPSVIRSLFSATLPESVEELARTIMHDAV 338

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVIVGRKN ASE+IKQKLVF GSEEGKL+ALRQSFAESLNPPVLIFVQ+KERA ELY EL
Sbjct: 339 RVIVGRKNAASETIKQKLVFTGSEEGKLIALRQSFAESLNPPVLIFVQNKERANELYEEL 398

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
            FD IR GVIHSDL QTQRE AVDDFRAG +WVLIATDV+ARGMDFKGVNCVINYDFP+S
Sbjct: 399 KFDSIRVGVIHSDLLQTQREIAVDDFRAGNSWVLIATDVVARGMDFKGVNCVINYDFPNS 458

Query: 241 GAAYIHRI 248
            AAYIHRI
Sbjct: 459 AAAYIHRI 466

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572415|ref|XP_003554364.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57-like [Glycine max]

 Score =  422 bits (1086), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 204/248 (82%), Positives = 223/248 (89%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           L+ QT RECKKLAK  KF+IKLM K L+R+ D SKF CD+LISTPLRLRLAI+RKKIDLS
Sbjct: 224 LSVQTYRECKKLAKRKKFRIKLMTKNLLRNADFSKFPCDVLISTPLRLRLAIKRKKIDLS 283

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           RVEYLVLDE+DKLFE   L K ID V+KACSNPSI+RSLFSATLPDFVE+ AR +MHDAV
Sbjct: 284 RVEYLVLDESDKLFE-PELFKQIDSVIKACSNPSIIRSLFSATLPDFVEDQARELMHDAV 342

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVIVGRKN ASE+IKQKLVF GSEEGKLLA+RQSFAESLNPPVL+F+QSKERAKELY EL
Sbjct: 343 RVIVGRKNMASETIKQKLVFTGSEEGKLLAIRQSFAESLNPPVLVFLQSKERAKELYSEL 402

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
           AFD IR  VIHSDLSQ +RENAVD+FRAGKTWVLIATDV+ARGMDFKGVNCVINYDFPDS
Sbjct: 403 AFDNIRVDVIHSDLSQAERENAVDNFRAGKTWVLIATDVVARGMDFKGVNCVINYDFPDS 462

Query: 241 GAAYIHRI 248
            AAY+HRI
Sbjct: 463 AAAYVHRI 470

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357510607|ref|XP_003625592.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula] gi|355500607|gb|AES81810.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula]

 Score =  420 bits (1080), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 201/248 (81%), Positives = 225/248 (90%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           L+ QT RECKKLAKG KF+IKLM K L+R+ D SKFSCDILISTPLRL LAI++KK+DLS
Sbjct: 214 LSGQTYRECKKLAKGEKFRIKLMTKNLLRNADFSKFSCDILISTPLRLCLAIKKKKVDLS 273

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           RVEYLVLDE+DKLFE   L K ID ++KAC+NPSI+RSLFSATLPDFVE+ AR +MHDAV
Sbjct: 274 RVEYLVLDESDKLFE-PQLFKQIDSIIKACTNPSIIRSLFSATLPDFVEDRARELMHDAV 332

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVIVGRKN AS++IKQKLVF GSEEGKLLA+RQSFAESLNPPVL+F+QSKERAKELYGEL
Sbjct: 333 RVIVGRKNMASDTIKQKLVFTGSEEGKLLAIRQSFAESLNPPVLVFLQSKERAKELYGEL 392

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
           AFD IR  VIHSDLSQ +RENAVD+FRAGKTWVLIATDV+ARGMDFKG+NCVINYDFPDS
Sbjct: 393 AFDNIRVDVIHSDLSQEERENAVDNFRAGKTWVLIATDVVARGMDFKGINCVINYDFPDS 452

Query: 241 GAAYIHRI 248
            +AYIHRI
Sbjct: 453 ASAYIHRI 460

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505198|ref|XP_003521379.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 57-like [Glycine max]

 Score =  419 bits (1076), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 203/248 (81%), Positives = 222/248 (89%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           L+ QT RECKKLAK  KF+IKLM K L+R+ D SKF CD+LISTPLRLRLAI+RKKIDLS
Sbjct: 225 LSVQTYRECKKLAKRKKFRIKLMTKNLLRNADFSKFPCDVLISTPLRLRLAIKRKKIDLS 284

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           RVEYLVLDE+DKLFE   L K ID V+KACSNPSI+RSLFSATLPDFVE+ AR +MHDAV
Sbjct: 285 RVEYLVLDESDKLFE-PELFKQIDSVIKACSNPSIIRSLFSATLPDFVEDRARELMHDAV 343

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVIVGRKN ASE+IKQKLVF GSEEGKLLA+RQSFAESLNPPVL+F+QSKERAKEL  EL
Sbjct: 344 RVIVGRKNMASETIKQKLVFTGSEEGKLLAIRQSFAESLNPPVLVFLQSKERAKELCSEL 403

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
           AFD IR  VIHSDLSQ +RENAVD+FRAGKTWVLIATDV+ARGMDFKGVNCVINYDFPDS
Sbjct: 404 AFDSIRVDVIHSDLSQAERENAVDNFRAGKTWVLIATDVVARGMDFKGVNCVINYDFPDS 463

Query: 241 GAAYIHRI 248
            AAY+HRI
Sbjct: 464 AAAYVHRI 471

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330935|ref|NP_187583.2| DEAD-box ATP-dependent RNA helicase 57 [Arabidopsis thaliana] gi|75328099|sp|Q84TG1.1|RH57_ARATH RecName: Full=DEAD-box ATP-dependent RNA helicase 57 gi|29028778|gb|AAO64768.1| At3g09720 [Arabidopsis thaliana] gi|110742885|dbj|BAE99340.1| RNA helicase like protein [Arabidopsis thaliana] gi|332641282|gb|AEE74803.1| DEAD-box ATP-dependent RNA helicase 57 [Arabidopsis thaliana]

 Score =  404 bits (1037), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 199/248 (80%), Positives = 219/248 (88%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA QT RE KKL KG+ F I+LM K LV++ D SK  CD+LISTP+RL+ AI+ KKIDLS
Sbjct: 222 LAAQTAREGKKLIKGSNFHIRLMTKPLVKTADFSKLWCDVLISTPMRLKRAIKAKKIDLS 281

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           +VEYLVLDE+DKLFE  +LLK ID VVKACSNPSI+RSLFSATLPD VEELARSIMHDAV
Sbjct: 282 KVEYLVLDESDKLFE-QSLLKQIDCVVKACSNPSIIRSLFSATLPDSVEELARSIMHDAV 340

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVI+GRKNTASE++KQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELY EL
Sbjct: 341 RVIIGRKNTASETVKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYDEL 400

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
             + IRAGVIHSDL   +RENAVD FRAG+ WVLIATDVIARGMDFKG+NCVINYDFPDS
Sbjct: 401 KCENIRAGVIHSDLPPGERENAVDQFRAGEKWVLIATDVIARGMDFKGINCVINYDFPDS 460

Query: 241 GAAYIHRI 248
            +AYIHRI
Sbjct: 461 ASAYIHRI 468

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6682259|gb|AAF23311.1|AC016661_36 putative RNA helicase [Arabidopsis thaliana]

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 199/248 (80%), Positives = 219/248 (88%), Gaps = 1/248 (0%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA QT RE KKL KG+ F I+LM K LV++ D SK  CD+LISTP+RL+ AI+ KKIDLS
Sbjct: 226 LAAQTAREGKKLIKGSNFHIRLMTKPLVKTADFSKLWCDVLISTPMRLKRAIKAKKIDLS 285

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           +VEYLVLDE+DKLFE  +LLK ID VVKACSNPSI+RSLFSATLPD VEELARSIMHDAV
Sbjct: 286 KVEYLVLDESDKLFE-QSLLKQIDCVVKACSNPSIIRSLFSATLPDSVEELARSIMHDAV 344

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
           RVI+GRKNTASE++KQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELY EL
Sbjct: 345 RVIIGRKNTASETVKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYDEL 404

Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
             + IRAGVIHSDL   +RENAVD FRAG+ WVLIATDVIARGMDFKG+NCVINYDFPDS
Sbjct: 405 KCENIRAGVIHSDLPPGERENAVDQFRAGEKWVLIATDVIARGMDFKGINCVINYDFPDS 464

Query: 241 GAAYIHRI 248
            +AYIHRI
Sbjct: 465 ASAYIHRI 472

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	248
TAIR|locus:2075034	541	AT3G09720 [Arabidopsis thalian	0.995	0.456	0.766	6.1e-94
DICTYBASE|DDB_G0274325	668	ddx52 "DEAD/DEAH box helicase"	0.995	0.369	0.504	3.2e-58
SGD|S000003139	564	ROK1 "RNA-dependent ATPase" [S	0.995	0.437	0.453	1.5e-53
ZFIN|ZDB-GENE-060623-1	606	ddx52 "DEAD (Asp-Glu-Ala-Asp)	0.991	0.405	0.463	3.8e-53
UNIPROTKB|A5D7C1	596	DDX52 "Probable ATP-dependent	1.0	0.416	0.462	2.7e-52
RGD|621743	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	1.0	0.414	0.450	5.6e-52
UNIPROTKB|I3LJA0	507	DDX52 "Uncharacterized protein	1.0	0.489	0.450	9.2e-52
MGI|MGI:1925644	598	Ddx52 "DEAD (Asp-Glu-Ala-Asp)	1.0	0.414	0.447	9.2e-52
UNIPROTKB|E2RB54	601	DDX52 "Uncharacterized protein	1.0	0.412	0.450	1.5e-51
UNIPROTKB|A8MTP9	491	DDX52 "Probable ATP-dependent	1.0	0.505	0.447	4e-51

TAIR|locus:2075034 AT3G09720 [Arabidopsis thaliana (taxid:3702)]

 Score = 935 (334.2 bits), Expect = 6.1e-94, P = 6.1e-94
 Identities = 190/248 (76%), Positives = 207/248 (83%)

Query:     1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPXXXXXXXXXXXXXXS 60
             LA QT RE KKL KG+ F I+LM K LV++ D SK  CD+LISTP              S
Sbjct:   222 LAAQTAREGKKLIKGSNFHIRLMTKPLVKTADFSKLWCDVLISTPMRLKRAIKAKKIDLS 281

Query:    61 RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
             +VEYLVLDE+DKLFE  +LLK ID VVKACSNPSI+RSLFSATLPD VEELARSIMHDAV
Sbjct:   282 KVEYLVLDESDKLFEQ-SLLKQIDCVVKACSNPSIIRSLFSATLPDSVEELARSIMHDAV 340

Query:   121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
             RVI+GRKNTASE++KQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELY EL
Sbjct:   341 RVIIGRKNTASETVKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYDEL 400

Query:   181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
               + IRAGVIHSDL   +RENAVD FRAG+ WVLIATDVIARGMDFKG+NCVINYDFPDS
Sbjct:   401 KCENIRAGVIHSDLPPGERENAVDQFRAGEKWVLIATDVIARGMDFKGINCVINYDFPDS 460

Query:   241 GAAYIHRI 248
              +AYIHRI
Sbjct:   461 ASAYIHRI 468

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

DICTYBASE|DDB_G0274325 ddx52 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 598 (215.6 bits), Expect = 3.2e-58, P = 3.2e-58
 Identities = 126/250 (50%), Positives = 168/250 (67%)

Query:     1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKF-SCDILISTPXXXXXXXXXXXXX 58
             LA Q  R  + L+KG  F+I ++ K L  +ST+ +   + DILI+TP             
Sbjct:   280 LAQQIYRNFRLLSKGKPFRICVLSKNLHNQSTNENLIKNYDILITTPLRLVYLIKENLLS 339

Query:    59 XSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHD 118
              ++VEYLV DEADKLF+  N  + +D VV AC NP +   LFSAT+   VEEL  SIM +
Sbjct:   340 LNKVEYLVFDEADKLFDK-NFQEQVDIVVTACQNPKLKICLFSATMNQQVEELGHSIMKN 398

Query:   119 AVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYG 178
              +++I+G +N A+ ++ QKL++ G EEGKLLA+RQ   + L PP+LIF QSKERA +L+ 
Sbjct:   399 PIKIIIGEQNAAAITVDQKLIYVGKEEGKLLAVRQLIQKGLEPPILIFTQSKERAHDLFQ 458

Query:   179 ELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP 238
             EL FDGI   VIHS+ +Q QR+  V  FR GK WVLI T+++ARGMDFKGVN VIN+DFP
Sbjct:   459 ELIFDGINVDVIHSERTQFQRDTIVKKFRMGKIWVLICTELMARGMDFKGVNFVINFDFP 518

Query:   239 DSGAAYIHRI 248
              + A+YIHRI
Sbjct:   519 HTLASYIHRI 528

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

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0016887 "ATPase activity" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

SGD|S000003139 ROK1 "RNA-dependent ATPase" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 554 (200.1 bits), Expect = 1.5e-53, P = 1.5e-53
 Identities = 117/258 (45%), Positives = 165/258 (63%)

Query:     1 LATQTTRECKKLA------KGNKFQIKLMKKEL---VRSTDLSKFSCDILISTPXXXXXX 51
             LA Q   EC KL+      K    Q+ L+ K L   +++  +S    DI+ISTP      
Sbjct:   204 LANQIFIECFKLSYKIFLEKKRPLQVALLSKSLGAKLKNKVVSDKKYDIIISTPLRLIDV 263

Query:    52 XXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL 111
                     S+V++L+ DEADKLF+    ++  D ++ AC  PS+ +++FSAT+P  VEE+
Sbjct:   264 VKNEALDLSKVKHLIFDEADKLFDK-TFVEQSDDILSACREPSLRKAMFSATIPSNVEEI 322

Query:   112 ARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSK 170
             A+SIM D VRVI+G K  A+ +I+QKL+F G+EEGKL+A+RQ   E    PP++IF++S 
Sbjct:   323 AQSIMMDPVRVIIGHKEAANTNIEQKLIFCGNEEGKLIAIRQLVQEGEFKPPIIIFLESI 382

Query:   171 ERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVN 230
              RAK LY EL +D I   VIH++ +  QR+  ++ F+ G+ W LI TDV+ARG+DFKGVN
Sbjct:   383 TRAKALYHELMYDRINVDVIHAERTALQRDRIIERFKTGELWCLICTDVLARGIDFKGVN 442

Query:   231 CVINYDFPDSGAAYIHRI 248
              VINYD P S  AY+HRI
Sbjct:   443 LVINYDVPGSSQAYVHRI 460

GO:0000447 "endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IMP

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

GO:0000480 "endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IMP

GO:0005730 "nucleolus" evidence=IEA;IDA

GO:0004004 "ATP-dependent RNA helicase activity" evidence=IDA

GO:0030686 "90S preribosome" evidence=IDA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0008186 "RNA-dependent ATPase activity" evidence=IDA

GO:0048254 "snoRNA localization" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000472 "endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IMP

ZFIN|ZDB-GENE-060623-1 ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Danio rerio (taxid:7955)]

 Score = 550 (198.7 bits), Expect = 3.8e-53, P = 3.8e-53
 Identities = 119/257 (46%), Positives = 165/257 (64%)

Query:     1 LATQTTRECKKLAKGNKFQIKLMKK--ELVRS---TDLSKFSCDILISTPXXXXXXXXXX 55
             LATQT RE  KL++G  F++ ++ K  E V+        KF  DIL++TP          
Sbjct:   248 LATQTHRELLKLSEGVGFRVHMINKGVEAVKKYGPKSAKKF--DILVTTPNRLIYLLNQD 305

Query:    56 --XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL 111
                   S VE+LV+DE+DKLFE G     + +  +  ACS+P++ R LFSAT    VE  
Sbjct:   306 PPAINLSSVEWLVVDESDKLFEDGKTGFREQLATIFLACSSPNVRRVLFSATFATDVERW 365

Query:   112 ARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKE 171
              +  + + V V +G +N+A+E+++Q+L+F GSE GK+LA+R    +   PPVL+FVQS +
Sbjct:   366 CKLNLDNLVSVSIGARNSAAETVEQQLLFVGSENGKILAMRNLIKQGFLPPVLVFVQSID 425

Query:   172 RAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC 231
             RA+ELY EL ++GI   VIH+D +Q QR+N V  FR+GK WVLI T ++ARG+DFKG+N 
Sbjct:   426 RARELYHELVYEGINVDVIHADRTQQQRDNVVSSFRSGKIWVLICTALLARGIDFKGINL 485

Query:   232 VINYDFPDSGAAYIHRI 248
             VINYDFP S   YIHRI
Sbjct:   486 VINYDFPTSAVEYIHRI 502

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|A5D7C1 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Bos taurus (taxid:9913)]

 Score = 542 (195.9 bits), Expect = 2.7e-52, P = 2.7e-52
 Identities = 118/255 (46%), Positives = 161/255 (63%)

Query:     1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSC---DILISTPXXXXXXXXXX-- 55
             LA+Q  RE  KL++G  F+I ++ K  V +      S    DIL++TP            
Sbjct:   244 LASQIHRELVKLSEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPP 303

Query:    56 XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR 113
                 + VE+LV+DE+DKLFE G       +  +  AC++  + R++FSAT    VE+  R
Sbjct:   304 GIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVKRAMFSATFAYDVEQWCR 363

Query:   114 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERA 173
               +   + V VG +N+A E+++Q+L+F GSE GKLLA+R+   +  NPPVL+FVQS ERA
Sbjct:   364 LNLDSVITVSVGARNSAVETVEQELLFVGSETGKLLAMRELVKKGFNPPVLVFVQSIERA 423

Query:   174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI 233
             KEL+ EL ++GI   VIH+D +Q QR+N V  FRAGK WVLI T ++ARG+DFKGVN VI
Sbjct:   424 KELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAGKIWVLICTALLARGIDFKGVNLVI 483

Query:   234 NYDFPDSGAAYIHRI 248
             NYDFP S   YIHRI
Sbjct:   484 NYDFPTSSVEYIHRI 498

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

RGD|621743 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Rattus norvegicus (taxid:10116)]

 Score = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 115/255 (45%), Positives = 163/255 (63%)

Query:     1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSC---DILISTPXXXXXXXXXX-- 55
             LA+Q  RE  K+++G  F+I ++ K  + +      S    DIL++TP            
Sbjct:   247 LASQIHRELIKISEGTGFRIHMIHKAAIAAKKFGPKSSKKFDILVTTPNRLIYLLKQEPP 306

Query:    56 XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR 113
                 + VE+LV+DE+DKLFE G       +  +  AC++P + R++FSAT    VE+  +
Sbjct:   307 GIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSPKVRRAMFSATFAYDVEQWCK 366

Query:   114 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERA 173
               + + V V +G +N+A E+++Q+L+F GSE GKLLA+R+   +  NPPVL+FVQS ERA
Sbjct:   367 LNLDNIVSVSIGARNSAVETVEQELLFVGSETGKLLAMRELVKKGFNPPVLVFVQSIERA 426

Query:   174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI 233
             KEL+ EL ++GI   VIH++ +Q QR+N V  FRAGK WVLI T ++ARG+DFKGVN VI
Sbjct:   427 KELFHELIYEGINVDVIHAERTQQQRDNTVHSFRAGKIWVLICTALLARGIDFKGVNLVI 486

Query:   234 NYDFPDSGAAYIHRI 248
             NYDFP S   YIHRI
Sbjct:   487 NYDFPTSSVEYIHRI 501

GO:0003723 "RNA binding" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=NAS

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005730 "nucleolus" evidence=IEA

GO:0006364 "rRNA processing" evidence=TAS

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

UNIPROTKB|I3LJA0 DDX52 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 537 (194.1 bits), Expect = 9.2e-52, P = 9.2e-52
 Identities = 115/255 (45%), Positives = 162/255 (63%)

Query:     1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSC---DILISTPXXXXXXXXXX-- 55
             LA+Q  RE  K+++G  F+I ++ K  V +      S    DIL++TP            
Sbjct:   154 LASQIHRELVKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPP 213

Query:    56 XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR 113
                 + VE+LV+DE+DKLFE G       +  +  AC++  + R++FSAT    VE+  +
Sbjct:   214 GIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVKRAMFSATFAYDVEQWCK 273

Query:   114 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERA 173
               + + + V +G +N+A E+++Q+L+F GSE GKLLA+R+   +  NPPVL+FVQS ERA
Sbjct:   274 LNLDNVITVSIGARNSAVETVEQELLFVGSETGKLLAMRELVKKGFNPPVLVFVQSIERA 333

Query:   174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI 233
             KEL+ EL ++GI   VIH+D +Q QR+N V  FRAGK WVLI T ++ARG+DFKGVN VI
Sbjct:   334 KELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAGKIWVLICTALLARGIDFKGVNLVI 393

Query:   234 NYDFPDSGAAYIHRI 248
             NYDFP S   YIHRI
Sbjct:   394 NYDFPTSSVEYIHRI 408

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1925644 Ddx52 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 52" [Mus musculus (taxid:10090)]

 Score = 537 (194.1 bits), Expect = 9.2e-52, P = 9.2e-52
 Identities = 114/255 (44%), Positives = 163/255 (63%)

Query:     1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSC---DILISTPXXXXXXXXXX-- 55
             LA+Q  RE  K+++G  F+I ++ K  + +      S    DIL++TP            
Sbjct:   247 LASQIHRELIKISEGTGFRIHMIHKAAIAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPP 306

Query:    56 XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR 113
                 + VE+LV+DE+DKLFE G     + +  +  AC++P + R++FSAT    VE+  +
Sbjct:   307 GIDLTNVEWLVVDESDKLFEDGKTGFREQLASIFLACTSPKVRRAMFSATFAYDVEQWCK 366

Query:   114 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERA 173
               + + V V +G +N+A E+++Q+L+F GSE GKLLA+R+   +   PPVL+FVQS ERA
Sbjct:   367 LNLDNVVSVSIGARNSAVETVEQELLFVGSETGKLLAMRELVKKGFKPPVLVFVQSIERA 426

Query:   174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI 233
             KEL+ EL ++GI   VIH++ +Q QR+N V  FRAGK WVLI T ++ARG+DFKGVN VI
Sbjct:   427 KELFHELIYEGINVDVIHAERTQQQRDNTVHSFRAGKIWVLICTALLARGIDFKGVNLVI 486

Query:   234 NYDFPDSGAAYIHRI 248
             NYDFP S   YIHRI
Sbjct:   487 NYDFPTSSVEYIHRI 501

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|E2RB54 DDX52 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 535 (193.4 bits), Expect = 1.5e-51, P = 1.5e-51
 Identities = 115/255 (45%), Positives = 161/255 (63%)

Query:     1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSC---DILISTPXXXXXXXXXX-- 55
             LA Q  RE  K+++G  F+I ++ K  V +      S    DIL++TP            
Sbjct:   248 LANQIHRELVKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPP 307

Query:    56 XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR 113
                 + VE+LV+DE+DKLFE G       +  +  AC++  + R++FSAT    VE+  +
Sbjct:   308 GIDLTSVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCK 367

Query:   114 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERA 173
               + + + V +G +N+A E+++Q+L+F GSE GKLLA+R+   +  NPPVL+FVQS ERA
Sbjct:   368 LNLDNVITVSIGARNSAVETVEQELLFVGSETGKLLAMRELVKKGFNPPVLVFVQSIERA 427

Query:   174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI 233
             KEL+ EL ++GI   VIH+D +Q QR+N V  FRAGK WVLI T ++ARG+DFKGVN VI
Sbjct:   428 KELFHELIYEGINVDVIHADRTQQQRDNTVHSFRAGKIWVLICTALLARGIDFKGVNLVI 487

Query:   234 NYDFPDSGAAYIHRI 248
             NYDFP S   YIHRI
Sbjct:   488 NYDFPTSSVEYIHRI 502

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|A8MTP9 DDX52 "Probable ATP-dependent RNA helicase DDX52" [Homo sapiens (taxid:9606)]

 Score = 531 (192.0 bits), Expect = 4.0e-51, P = 4.0e-51
 Identities = 114/255 (44%), Positives = 162/255 (63%)

Query:     1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSC---DILISTPXXXXXXXXXX-- 55
             LA+Q  RE  K+++G  F+I ++ K  V +      S    DIL++TP            
Sbjct:   138 LASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPP 197

Query:    56 XXXXSRVEYLVLDEADKLFEVGN--LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR 113
                 + VE+LV+DE+DKLFE G       +  +  AC++  + R++FSAT    VE+  +
Sbjct:   198 GIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCK 257

Query:   114 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERA 173
               + + + V +G +N+A E+++Q+L+F GSE GKLLA+R+   +  NPPVL+FVQS ERA
Sbjct:   258 LNLDNVISVSIGARNSAVETVEQELLFVGSETGKLLAMRELVKKGFNPPVLVFVQSIERA 317

Query:   174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI 233
             KEL+ EL ++GI   VIH++ +Q QR+N V  FRAGK WVLI T ++ARG+DFKGVN VI
Sbjct:   318 KELFHELIYEGINVDVIHAERTQQQRDNTVHSFRAGKIWVLICTALLARGIDFKGVNLVI 377

Query:   234 NYDFPDSGAAYIHRI 248
             NYDFP S   YIHRI
Sbjct:   378 NYDFPTSSVEYIHRI 392

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5K5B6	RH57_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.7701	0.9959	0.4574	yes	no
Q84TG1	RH57_ARATH	3, ., 6, ., 4, ., 1, 3	0.8024	0.9959	0.4565	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	248
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	6e-66
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	6e-39
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	3e-37
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	2e-34
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	7e-34
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-33
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-32
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	1e-29
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	4e-29
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-27
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	2e-26
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	5e-24
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	3e-23
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-23
cd00268	203	cd00268, DEADc, DEAD-box helicases	2e-22
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-15
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	5e-14
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	4e-12
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	5e-09
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	2e-07
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	1e-06
PRK09401	1176	PRK09401, PRK09401, reverse gyrase; Reviewed	5e-06
COG1205	851	COG1205, COG1205, Distinct helicase family with a	1e-05
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	3e-05
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	1e-04
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	2e-04
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	2e-04
COG1110	1187	COG1110, COG1110, Reverse gyrase [DNA replication,	4e-04
pfam13307	165	pfam13307, Helicase_C_2, Helicase C-terminal domai	5e-04
TIGR01587	358	TIGR01587, cas3_core, CRISPR-associated helicase C	6e-04
cd09639	353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	0.001
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	0.001
TIGR01054	1171	TIGR01054, rgy, reverse gyrase	0.003
COG4098	441	COG4098, comFA, Superfamily II DNA/RNA helicase re	0.003
pfam06862	436	pfam06862, DUF1253, Protein of unknown function (D	0.003
TIGR00595	505	TIGR00595, priA, primosomal protein N'	0.003
PRK10917	681	PRK10917, PRK10917, ATP-dependent DNA helicase Rec	0.004

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

 Score =  212 bits (541), Expect = 6e-66
 Identities = 95/257 (36%), Positives = 139/257 (54%), Gaps = 15/257 (5%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELV-------RSTDLSKFSCDILISTPLRLRLAIR 53
           LA Q   E +KL K       L    +        +   L +   DI+++TP RL   I+
Sbjct: 111 LAVQIAEELRKLGK---NLGGLRVAVVYGGVSIRKQIEALKR-GVDIVVATPGRLLDLIK 166

Query: 54  RKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR 113
           R K+DLS VE LVLDEAD++ ++G  +  I+ ++KA   P     LFSAT+PD + ELAR
Sbjct: 167 RGKLDLSGVETLVLDEADRMLDMG-FIDDIEKILKAL-PPDRQTLLFSATMPDDIRELAR 224

Query: 114 SIMHDAVRVIVGRKNT--ASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKE 171
             ++D V + V  +      + IKQ  +   SEE KL  L +   +     V++FV++K 
Sbjct: 225 RYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKR 284

Query: 172 RAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC 231
             +EL   L   G +   +H DL Q +R+ A++ F+ G+  VL+ATDV ARG+D   V+ 
Sbjct: 285 LVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSH 344

Query: 232 VINYDFPDSGAAYIHRI 248
           VINYD P     Y+HRI
Sbjct: 345 VINYDLPLDPEDYVHRI 361

Length = 513

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

 Score =  139 bits (353), Expect = 6e-39
 Identities = 78/210 (37%), Positives = 120/210 (57%), Gaps = 3/210 (1%)

Query: 39  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 98
           D+L++TP RL     +  + L +VE LVLDEAD++ ++G +  H    V A         
Sbjct: 127 DVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFI--HDIRRVLAKLPAKRQNL 184

Query: 99  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 158
           LFSAT  D ++ LA  ++H+ + + V R+NTASE + Q + F   +  + L L Q   + 
Sbjct: 185 LFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKREL-LSQMIGKG 243

Query: 159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD 218
               VL+F ++K  A  L  +L  DGIR+  IH + SQ  R  A+ DF++G   VL+ATD
Sbjct: 244 NWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATD 303

Query: 219 VIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           + ARG+D + +  V+NY+ P+    Y+HRI
Sbjct: 304 IAARGLDIEELPHVVNYELPNVPEDYVHRI 333

Length = 456

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

 Score =  136 bits (345), Expect = 3e-37
 Identities = 83/214 (38%), Positives = 119/214 (55%), Gaps = 7/214 (3%)

Query: 39  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS 98
           +ILI+ P RL   +     +L RV YLVLDEAD++ ++G     I  +V     P     
Sbjct: 255 EILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMG-FEPQIRKIVSQI-RPDRQTL 312

Query: 99  LFSATLPDFVEELARSIM-HDAVRVIVGRKN-TASESIKQKLVFAGSEEGKLLALRQSFA 156
           ++SAT P  V+ LAR +   + V V VG  + TA  +IKQ+ VF   E  K   L+    
Sbjct: 313 MWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQE-VFVVEEHEKRGKLKMLLQ 371

Query: 157 ESL--NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVL 214
             +     +LIFV++K+ A  L  EL  DG  A  IH D  Q +R   +++F+ GK+ ++
Sbjct: 372 RIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIM 431

Query: 215 IATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           IATDV +RG+D K V  VIN+DFP+    Y+HRI
Sbjct: 432 IATDVASRGLDVKDVKYVINFDFPNQIEDYVHRI 465

Length = 545

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

 Score =  127 bits (322), Expect = 2e-34
 Identities = 79/212 (37%), Positives = 117/212 (55%), Gaps = 5/212 (2%)

Query: 39  DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNP-SIVR 97
           DILI T  RL    ++  I+L  ++ +VLDEAD++F++G  +K I  + +        + 
Sbjct: 135 DILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLG-FIKDIRWLFRRMPPANQRLN 193

Query: 98  SLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE 157
            LFSATL   V ELA   M++   V V  +      IK++L F  S E K+  L Q+  E
Sbjct: 194 MLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEEL-FYPSNEEKM-RLLQTLIE 251

Query: 158 SLNPP-VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIA 216
              P   +IF  +K R +E++G LA DG R G++  D++Q +R   +++F  G   +L+A
Sbjct: 252 EEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVA 311

Query: 217 TDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           TDV ARG+    V  V NYD PD    Y+HRI
Sbjct: 312 TDVAARGLHIPAVTHVFNYDLPDDCEDYVHRI 343

Length = 423

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

 Score =  126 bits (319), Expect = 7e-34
 Identities = 78/224 (34%), Positives = 120/224 (53%), Gaps = 27/224 (12%)

Query: 38  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 97
           CDIL++TP RL    +R ++ L  VE +VLDEAD++ ++G +     P V+      I+R
Sbjct: 214 CDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFI-----PQVR-----QIIR 263

Query: 98  S----------LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL-VFAGSEEG 146
                      LFSAT  D V  LA+    D   V +  +N AS++++Q +   AGS++ 
Sbjct: 264 QTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKY 323

Query: 147 KLL--ALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVD 204
           KLL   + Q+  E     V++F   K+  + +   L  DGI A  +  D+ Q +R   ++
Sbjct: 324 KLLYNLVTQNPWER----VMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLE 379

Query: 205 DFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            FR GK  VL+ATDV  RG+   G++ VIN+  P+    Y+HRI
Sbjct: 380 GFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRI 423

Length = 475

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

 Score =  126 bits (318), Expect = 1e-33
 Identities = 65/212 (30%), Positives = 111/212 (52%), Gaps = 10/212 (4%)

Query: 40  ILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS- 98
           I++ TP R+   +R+  +DL  +  LVLDEAD++ ++G     ID +++    P+  ++ 
Sbjct: 126 IIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMG-FQDAIDAIIRQA--PARRQTL 182

Query: 99  LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES 158
           LFSAT P+ +  +++    D V V V   +    +I+Q   +  S + +L AL++     
Sbjct: 183 LFSATYPEGIAAISQRFQRDPVEVKVESTHDLP-AIEQ-RFYEVSPDERLPALQRLLLH- 239

Query: 159 LNPPV--LIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIA 216
            + P   ++F  +K+  +E+   L   G  A  +H DL Q  R+  +  F      VL+A
Sbjct: 240 -HQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVA 298

Query: 217 TDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           TDV ARG+D K +  VINY+       ++HRI
Sbjct: 299 TDVAARGLDIKALEAVINYELARDPEVHVHRI 330

Length = 460

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

 Score =  121 bits (306), Expect = 4e-32
 Identities = 84/263 (31%), Positives = 125/263 (47%), Gaps = 29/263 (11%)

Query: 1   LATQTTRECKKLAKGNKFQIKL-------MKKELVRSTDLSKFSCDILISTPLRLRLAIR 53
           LA Q   + ++LAK     I         M    V S +      DI+++TP RL   I+
Sbjct: 85  LAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQ-----DIVVATPGRLLQYIK 139

Query: 54  RKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS---LFSATLP-DFVE 109
            +  D   VE L+LDEAD++ ++G         ++  +  +  R    LFSATL  D V+
Sbjct: 140 EENFDCRAVETLILDEADRMLDMG-----FAQDIETIAAETRWRKQTLLFSATLEGDAVQ 194

Query: 110 ELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGK--LLA--LRQSFAESLNPPVLI 165
           + A  +++D V V         + I Q    A   E K  LL   L+Q          ++
Sbjct: 195 DFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQPEVTR----SIV 250

Query: 166 FVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMD 225
           FV+++ER  EL G L   GI    +  ++ Q +R  A+     G+  VL+ATDV ARG+D
Sbjct: 251 FVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGID 310

Query: 226 FKGVNCVINYDFPDSGAAYIHRI 248
              V+ VIN+D P S   Y+HRI
Sbjct: 311 IDDVSHVINFDMPRSADTYLHRI 333

Length = 434

>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 =  107 bits (270), Expect = 1e-29
 Identities = 53/117 (45%), Positives = 69/117 (58%), Gaps = 4/117 (3%)

Query: 134 IKQKLVFAGSEEGKLLALRQSFAESLNPP--VLIFVQSKERAKELYGELAFDGIRAGVIH 191
           IKQ ++    E+ KL AL +   E L     VLIF  SK+   EL   L   GI+   +H
Sbjct: 2   IKQYVLP--VEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALH 59

Query: 192 SDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            D SQ +RE  + DFR G+  VL+ATDVIARG+D   V+ VINYD P S ++Y+ RI
Sbjct: 60  GDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRI 116

Length = 131

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

 Score =  112 bits (282), Expect = 4e-29
 Identities = 66/209 (31%), Positives = 107/209 (51%), Gaps = 2/209 (0%)

Query: 40  ILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 99
           +++ TP R+   I ++ + +  ++  +LDEAD++   G     I  V K    P +  +L
Sbjct: 149 MVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRG-FKGQIYDVFKKLP-PDVQVAL 206

Query: 100 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 159
           FSAT+P+ + EL    M D  R++V +     E I+Q  V    EE K   L   +    
Sbjct: 207 FSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLT 266

Query: 160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV 219
               +I+  ++ +   L  ++         +H D+ Q  R+  + +FR+G T VLI TD+
Sbjct: 267 ITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDL 326

Query: 220 IARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           +ARG+D + V+ VINYD P S   YIHRI
Sbjct: 327 LARGIDVQQVSLVINYDLPASPENYIHRI 355

Length = 401

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

 Score =  110 bits (276), Expect = 1e-27
 Identities = 71/215 (33%), Positives = 118/215 (54%), Gaps = 10/215 (4%)

Query: 39  DILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKA----CSNP 93
           D++I+TP RL   +++ K+  L   E  VLDEAD++F++G  +K I  +++      +  
Sbjct: 136 DVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLG-FIKDIRFLLRRMPERGTRQ 194

Query: 94  SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ 153
           ++   LFSATL   V ELA   M++  +++V  +   +  ++Q++ F   EE K   L  
Sbjct: 195 TL---LFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEE-KQTLLLG 250

Query: 154 SFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWV 213
             + S     ++FV +K   + +   L   G R GV+  D+ Q +RE+ ++ F+ G+  +
Sbjct: 251 LLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEI 310

Query: 214 LIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           L+ATDV ARG+   GV  V NYD P     Y+HRI
Sbjct: 311 LVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRI 345

Length = 572

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

 Score =  106 bits (267), Expect = 2e-26
 Identities = 78/261 (29%), Positives = 131/261 (50%), Gaps = 25/261 (9%)

Query: 1   LATQTTRECKKLAKGNKFQIKL------MKKELVRSTDLSKFSCDILISTPLRLRLAIRR 54
           L  Q   + K L KG  F+  L      M ++L R     +   ++++ TP RL   + +
Sbjct: 208 LCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRI----QQGVELIVGTPGRLIDLLSK 263

Query: 55  KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS 114
             I+L  V  LVLDE D + E G     +  + +A S P ++  LFSAT+   VE+ A S
Sbjct: 264 HDIELDNVSVLVLDEVDCMLERG-FRDQVMQIFQALSQPQVL--LFSATVSPEVEKFASS 320

Query: 115 IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGK-----LLALRQSFAESLNPPVLIFVQS 169
           +  D + + +G  N  ++++KQ  ++  +++ K     +L  +Q F     PP ++FV S
Sbjct: 321 LAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHF----KPPAVVFVSS 376

Query: 170 KERAKELYGEL--AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK 227
           +  A +L         G++A  IH + S  +R   +  F  G+  V++AT V+ RG+D  
Sbjct: 377 RLGA-DLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLL 435

Query: 228 GVNCVINYDFPDSGAAYIHRI 248
            V  VI +D P++   YIH+I
Sbjct: 436 RVRQVIIFDMPNTIKEYIHQI 456

Length = 518

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

 Score = 91.4 bits (228), Expect = 5e-24
 Identities = 36/70 (51%), Positives = 46/70 (65%)

Query: 179 ELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP 238
            L   GI+   +H  LSQ +RE  ++DFR GK+ VL+ATDV  RG+D   VN VINYD P
Sbjct: 2   LLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLP 61

Query: 239 DSGAAYIHRI 248
            + A+YI RI
Sbjct: 62  WNPASYIQRI 71

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 = 89.6 bits (223), Expect = 3e-23
 Identities = 37/75 (49%), Positives = 46/75 (61%)

Query: 174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI 233
           +EL   L   GI+   +H  LSQ +RE  +D F  GK  VL+ATDV  RG+D  GV+ VI
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 234 NYDFPDSGAAYIHRI 248
            YD P S A+YI RI
Sbjct: 61  IYDLPWSPASYIQRI 75

Length = 82

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

 Score = 97.6 bits (243), Expect = 3e-23
 Identities = 64/215 (29%), Positives = 108/215 (50%), Gaps = 15/215 (6%)

Query: 40  ILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNP 93
           I++ TP RL   ++R  +DLS++  LVLDEAD++  +G       ++  I    +     
Sbjct: 128 IVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQT---- 183

Query: 94  SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ 153
               +LFSAT+P+ +  + R  M +   V +    T    I Q              +R 
Sbjct: 184 ----ALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRF 239

Query: 154 SFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWV 213
             AE  +  + IFV++K    E+   L  +G  +  ++ D++Q  RE  ++  + G+  +
Sbjct: 240 LEAEDFDAAI-IFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDI 298

Query: 214 LIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           LIATDV ARG+D + ++ V+NYD P    +Y+HRI
Sbjct: 299 LIATDVAARGLDVERISLVVNYDIPMDSESYVHRI 333

Length = 629

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

 Score = 90.6 bits (226), Expect = 2e-22
 Identities = 42/128 (32%), Positives = 66/128 (51%), Gaps = 12/128 (9%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLS------KFSCDILISTPLRLRLAIRR 54
           LA Q     +KL K    ++ +    +   T +       K    I+++TP RL   + R
Sbjct: 81  LALQIAEVARKLGKHTNLKVVV----IYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLER 136

Query: 55  KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS 114
            K+DLS+V+YLVLDEAD++ ++G     I  ++K          LFSAT+P  V +LAR 
Sbjct: 137 GKLDLSKVKYLVLDEADRMLDMG-FEDQIREILKLL-PKDRQTLLFSATMPKEVRDLARK 194

Query: 115 IMHDAVRV 122
            + + VR+
Sbjct: 195 FLRNPVRI 202

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

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

 Score = 72.5 bits (178), Expect = 1e-15
 Identities = 41/140 (29%), Positives = 67/140 (47%), Gaps = 7/140 (5%)

Query: 1   LATQTTRECKKLAKGNKFQIKLM---KKELVRSTDLSKFSCDILISTPLRLRLAIRRKKI 57
           LA Q   E KKL      ++  +     +  +   L     DIL++TP RL   +   K+
Sbjct: 66  LAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKL 125

Query: 58  DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH 117
            LS V+ ++LDEA +L + G     ++ ++K     ++   L SAT P+ +E L    ++
Sbjct: 126 SLSNVDLVILDEAHRLLDGGF-GDQLEKLLKLL-PKNVQLLLLSATPPEEIENLLELFLN 183

Query: 118 DAVRVIVGRKNTASESIKQK 137
           D V + VG   T  E I+Q 
Sbjct: 184 DPVFIDVGF--TPLEPIEQF 201

Length = 201

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

 Score = 67.7 bits (166), Expect = 5e-14
 Identities = 39/115 (33%), Positives = 59/115 (51%), Gaps = 6/115 (5%)

Query: 1   LATQTTRECKKLAKGNKFQIKLM---KKELVRSTDLSKFSCDILISTPLRLRLAIRRKKI 57
           LA Q   E KKL K    ++ L+        ++  L K   DIL+ TP RL   +RR K+
Sbjct: 57  LAEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKL 116

Query: 58  DLSR-VEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL 111
            L + ++ LVLDEA +L ++G     ++ ++     P     L SATLP  +E+L
Sbjct: 117 KLLKNLKLLVLDEAHRLLDMG-FGDDLEEILSRL-PPDRQILLLSATLPRNLEDL 169

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

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

 Score = 65.0 bits (159), Expect = 4e-12
 Identities = 49/211 (23%), Positives = 86/211 (40%), Gaps = 8/211 (3%)

Query: 38  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLK--HIDPVVKACSNPSI 95
             +L  +P RL      + +    +  + +DEA  + + G+  +  +          P+ 
Sbjct: 108 LKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNP 167

Query: 96  VRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSF 155
                +AT    V +  R  +      I  R +    ++  K+V  G    +L  L    
Sbjct: 168 PVLALTATATPRVRDDIREQLGLQDANIF-RGSFDRPNLALKVVEKGEPSDQLAFLATVL 226

Query: 156 AESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLI 215
            +      +I+  ++++ +EL   L  +GI AG  H+ LS  +RE     F   +  V++
Sbjct: 227 PQLSKS-GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMV 285

Query: 216 ATDVIARGM--DFKGVNCVINYDFPDSGAAY 244
           AT   A GM  D   V  VI+YD P S  +Y
Sbjct: 286 AT--NAFGMGIDKPDVRFVIHYDLPGSIESY 314

Length = 590

>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily

 Score = 53.1 bits (128), Expect = 5e-09
 Identities = 26/106 (24%), Positives = 41/106 (38%), Gaps = 5/106 (4%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFS--CDILISTPLRLRLAIRRKKID 58
           LA Q     K+L      ++  +             S   DI++ TP RL   + R K+ 
Sbjct: 42  LANQVAERLKELFGEGI-KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLS 100

Query: 59  LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL 104
           L +++ L+LDEA +L   G     +   +           L SAT 
Sbjct: 101 LKKLDLLILDEAHRLLNQG--FGLLGLKILLKLPKDRQVLLLSATP 144

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Length = 144

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

 Score = 50.9 bits (122), Expect = 2e-07
 Identities = 24/91 (26%), Positives = 38/91 (41%), Gaps = 2/91 (2%)

Query: 144 EEGKLLALRQSFAESLNP-PVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENA 202
            E K+ A+R    +       LIF    E A E+       GI    I  +  + +RE  
Sbjct: 266 SERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGIVE-AITGETPKEEREAI 324

Query: 203 VDDFRAGKTWVLIATDVIARGMDFKGVNCVI 233
           ++ FR G   VL+   V+  G+D    + +I
Sbjct: 325 LERFRTGGIKVLVTVKVLDEGVDIPDADVLI 355

Length = 442

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

 Score = 48.9 bits (117), Expect = 1e-06
 Identities = 43/151 (28%), Positives = 68/151 (45%), Gaps = 22/151 (14%)

Query: 112 ARSIMHD-AVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL----NPPVLIF 166
           A+S++ D   +  +     A ES        G E  KL  LR+   E L    +  V++F
Sbjct: 321 AKSLLADPYFKRALRLLIRADES--------GVEHPKLEKLREILKEQLEKNGDSRVIVF 372

Query: 167 VQSKERAKELYGELAFDGIRAGVI--------HSD-LSQTQRENAVDDFRAGKTWVLIAT 217
            + ++ A+E+   L   GI+A V             +SQ +++  +D FR G+  VL+AT
Sbjct: 373 TEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVAT 432

Query: 218 DVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            V   G+D   V+ VI Y+   S    I R 
Sbjct: 433 SVGEEGLDIPEVDLVIFYEPVPSEIRSIQRK 463

Length = 542

>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed

 Score = 46.8 bits (112), Expect = 5e-06
 Identities = 26/74 (35%), Positives = 34/74 (45%), Gaps = 12/74 (16%)

Query: 159 LNPPVLIFVQS---KERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLI 215
           L    LIFV S   KE A+EL   L   GI A +  S       E   + F  G+  VL+
Sbjct: 327 LGDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDVLV 381

Query: 216 --AT--DVIARGMD 225
             A+   V+ RG+D
Sbjct: 382 GVASYYGVLVRGID 395

Length = 1176

>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 = 45.5 bits (108), Expect = 1e-05
 Identities = 48/238 (20%), Positives = 88/238 (36%), Gaps = 40/238 (16%)

Query: 38  CDILISTPLRLRLAIRRKK----IDLSRVEYLVLDEA---DKLF--EVGNLLKHIDPVVK 88
            DIL++ P  L   + R        L  ++YLV+DE      +   EV  LL+ +   ++
Sbjct: 168 PDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRRLR 227

Query: 89  ACSNPSIVRSLFSATLPD---FVEELARSIM----------HDAVRVIVGRKNTASESIK 135
              +P  +    SATL +   F EEL                     +          + 
Sbjct: 228 RYGSPLQIICT-SATLANPGEFAEELFGRDFEVPVDEDGSPRGLRYFVRR--EPPIRELA 284

Query: 136 QKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELY----------GELAFDGI 185
           + +  +   E   LA   +         L+F +S+++ + LY          G    D +
Sbjct: 285 ESIRRSALAELATLA---ALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAV 341

Query: 186 RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAA 243
                 + L + +R     +F+ G+   +IAT+ +  G+D   ++ VI Y +P     
Sbjct: 342 STY--RAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVL 397

Length = 851

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

 Score = 44.5 bits (106), Expect = 3e-05
 Identities = 25/81 (30%), Positives = 45/81 (55%), Gaps = 8/81 (9%)

Query: 163 VLIFVQSKERAKELYGELAFDGIRAG--VIHSD------LSQTQRENAVDDFRAGKTWVL 214
           +++F Q ++ A+++   L  +GI+A   V  +       +SQ ++   +D FRAG+  VL
Sbjct: 368 IIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVL 427

Query: 215 IATDVIARGMDFKGVNCVINY 235
           ++T V   G+D   V+ VI Y
Sbjct: 428 VSTSVAEEGLDIPSVDLVIFY 448

Length = 773

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

 Score = 42.8 bits (101), Expect = 1e-04
 Identities = 18/63 (28%), Positives = 32/63 (50%)

Query: 164 LIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG 223
           ++F  S+ R  EL   L   G++A   H+ L   +R++    F A +   ++ T  +A G
Sbjct: 444 IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAG 503

Query: 224 MDF 226
           +DF
Sbjct: 504 VDF 506

Length = 830

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

 Score = 42.2 bits (100), Expect = 2e-04
 Identities = 47/227 (20%), Positives = 86/227 (37%), Gaps = 26/227 (11%)

Query: 39  DILISTP--LRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN--------LLKHIDPVVK 88
            ILI+TP  L + L   + +  L  V Y+++DE   L    +         L+ +  +  
Sbjct: 125 HILITTPESLAILLNSPKFRELLRDVRYVIVDEIHAL--AESKRGVQLALSLERLRELA- 181

Query: 89  ACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASE------SIKQKLVFAG 142
                   R   SAT+    EE+A+ ++       +   + A +      S  + L++  
Sbjct: 182 ----GDFQRIGLSATVGP-PEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDE 236

Query: 143 SEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELA-FDGIRAGVIHSDLSQTQREN 201
                L        +  +   LIF  ++  A+ L   L         V H  LS+  R  
Sbjct: 237 ELWAALYERIAELVKK-HRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLE 295

Query: 202 AVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
             +  + G+   ++AT  +  G+D   ++ VI    P S   ++ RI
Sbjct: 296 VEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRI 342

Length = 814

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

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 26/81 (32%), Positives = 41/81 (50%)

Query: 164 LIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG 223
           +I+  S+++ +EL   L   GI A   H+ LS   R    +DF      V++AT+    G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287

Query: 224 MDFKGVNCVINYDFPDSGAAY 244
           +D   V  VI+YD P +  +Y
Sbjct: 288 IDKPNVRFVIHYDMPGNLESY 308

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and repair]

 Score = 41.2 bits (97), Expect = 4e-04
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 12/76 (15%)

Query: 157 ESLNPPVLIFVQS---KERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWV 213
           + L    LIFV     +E+A+EL   L   GI A +IH+     ++E A++DF  G+  V
Sbjct: 332 KKLGDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHA-----EKEEALEDFEEGEVDV 386

Query: 214 LIAT----DVIARGMD 225
           L+       V+ RG+D
Sbjct: 387 LVGVASYYGVLVRGLD 402

Length = 1187

>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 16/69 (23%), Positives = 29/69 (42%)

Query: 163 VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR 222
           VL+   S    +++   LA + +  G+      +  RE  ++ F+ GK  +L        
Sbjct: 12  VLVLFPSYSLLEQVAELLASELLEKGIELLVQGEGSREKLLERFKKGKGAILFGVGSFWE 71

Query: 223 GMDFKGVNC 231
           G+DF G   
Sbjct: 72  GIDFPGDAL 80

This domain is the second of two tandem AAA domains found in a wide variety of helicase enzymes. Length = 165

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

 Score = 40.1 bits (94), Expect = 6e-04
 Identities = 36/171 (21%), Positives = 74/171 (43%), Gaps = 13/171 (7%)

Query: 65  LVLDEADKL--FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRV 122
           L+ DE      + +  +L  ++ V+K    P +   L SATLP F++E A  I +     
Sbjct: 128 LIFDEVHFYDEYTLALILAVLE-VLKDNDVPIL---LMSATLPKFLKEYAEKIGYVEFNE 183

Query: 123 IVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNP-PVLIFVQSKERAKELYGELA 181
            +  K        + +     + G++ +L +          + I V + +RA+E Y +L 
Sbjct: 184 PLDLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLK 243

Query: 182 FDGIRAGVI--HSDLSQTQRENA----VDDFRAGKTWVLIATDVIARGMDF 226
            +     ++  HS  ++  R       +++ +  + +V++AT VI   +D 
Sbjct: 244 ENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDI 294

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

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 41/170 (24%), Positives = 71/170 (41%), Gaps = 14/170 (8%)

Query: 65  LVLDEADKL--FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRV 122
           L+ DE      + +  +L  ++ V+K    P +   L SATLP F++E A  I +     
Sbjct: 127 LIFDEVHFYDEYTLALILAVLE-VLKDNDVPIL---LMSATLPKFLKEYAEKIGYVEENE 182

Query: 123 IVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAF 182
            +  K        +       E   L  L +   +     V I V + +RA+E Y +L  
Sbjct: 183 PLDLKPNERAPFIKIESDKVGEISSLERLLEFIKKGG--SVAIIVNTVDRAQEFYQQLKE 240

Query: 183 DGIRAGV--IHSDLSQTQRENA----VDDFRAGKTWVLIATDVIARGMDF 226
            G    +  IHS  ++  R       + +F+  + +V++AT VI   +D 
Sbjct: 241 KGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKSEKFVIVATQVIEASLDI 290

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

 Score = 39.4 bits (92), Expect = 0.001
 Identities = 31/137 (22%), Positives = 55/137 (40%), Gaps = 14/137 (10%)

Query: 101 SATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLN 160
           SATLP F++E    +     +     +N      + +      E   +    Q     L 
Sbjct: 377 SATLPPFLKEK---LKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELI 433

Query: 161 P-------PVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRA----G 209
                    VL+ V + +RA ELY +L   G +  ++HS  +   RE    + +      
Sbjct: 434 SEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQN 493

Query: 210 KTWVLIATDVIARGMDF 226
           + ++++AT VI  G+D 
Sbjct: 494 EGFIVVATQVIEAGVDI 510

Length = 733

>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase

 Score = 38.7 bits (90), Expect = 0.003
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 11/70 (15%)

Query: 163 VLIFVQS---KERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIAT-- 217
            +++V     KE+A+E+   L   G++A   H+    T+ +   + F  G+  VLI    
Sbjct: 329 GIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHA----TKPKEDYEKFAEGEIDVLIGVAS 384

Query: 218 --DVIARGMD 225
               + RG+D
Sbjct: 385 YYGTLVRGLD 394

This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 1171

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

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 162 PVLIFVQSKERAKELYGELA--FDGIRAGVIHSDLSQTQ-RENAVDDFRAGKTWVLIATD 218
           PVLIF    E  +++   L           +HS   + Q R+  V+ FR GK  +LI T 
Sbjct: 307 PVLIFFPEIETMEQVAAALKKKLPKETIASVHS---EDQHRKEKVEAFRDGKITLLITTT 363

Query: 219 VIARGMDFKGVNCVI 233
           ++ RG+ F  V+  +
Sbjct: 364 ILERGVTFPNVDVFV 378

Length = 441

>gnl|CDD|219205 pfam06862, DUF1253, Protein of unknown function (DUF1253)

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 11/59 (18%)

Query: 36  FSCDILISTPLRLRLAIRR---KKID---LSRVEYLVLDEADKLF-----EVGNLLKHI 83
           +S DI+I++PL LR+ I     KK D   LS +E L++D+AD +       V  + KH+
Sbjct: 125 YSSDIIIASPLGLRMIIENEDKKKRDYDFLSSIEVLIVDQADVILMQNWEHVLTVFKHL 183

This family represents the C-terminal portion (approximately 500 residues) of several hypothetical eukaryotic proteins of unknown function. Length = 436

>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 182 FDGIRAGVIHSDLSQTQR--ENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV 232
           F G R   I SD +  +   E  ++ F  GK  +LI T +IA+G  F  V  V
Sbjct: 282 FPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLV 334

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) [DNA metabolism, DNA replication, recombination, and repair]. Length = 505

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

 Score = 37.8 bits (89), Expect = 0.004
 Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 2/50 (4%)

Query: 173 AKELYGEL--AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI 220
           A+E Y EL  AF  +R G++H  +   +++  +  F+AG+  +L+AT VI
Sbjct: 492 AEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVI 541

Length = 681

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	248
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.98
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.97
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.97
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.97
PRK00254	720	ski2-like helicase; Provisional	99.97
PRK09401	1176	reverse gyrase; Reviewed	99.97
PRK10689	1147	transcription-repair coupling factor; Provisional	99.97
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.97
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.97
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.97
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.97
PRK01172	674	ski2-like helicase; Provisional	99.97
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.97
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.96
PHA02653	675	RNA helicase NPH-II; Provisional	99.96
PHA02558	501	uvsW UvsW helicase; Provisional	99.96
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.96
PRK14701	1638	reverse gyrase; Provisional	99.95
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.95
COG1202	830	Superfamily II helicase, archaea-specific [General	99.95
COG1204	766	Superfamily II helicase [General function predicti	99.95
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.95
PRK13766	773	Hef nuclease; Provisional	99.95
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.95
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.95
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.94
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.93
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.93
PRK04914	956	ATP-dependent helicase HepA; Validated	99.92
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.92
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.92
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.91
KOG0354	746	consensus DEAD-box like helicase [General function	99.91
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.91
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.9
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.9
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.9
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.89
COG1205	851	Distinct helicase family with a unique C-terminal	99.87
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.87
PRK09694	878	helicase Cas3; Provisional	99.86
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.85
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.84
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.83
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.82
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.82
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.81
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.8
PRK05580	679	primosome assembly protein PriA; Validated	99.8
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.79
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.79
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.78
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.78
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.77
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.76
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.76
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.75
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.74
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.71
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.7
PRK05298	652	excinuclease ABC subunit B; Provisional	99.69
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.67
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.63
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.63
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.6
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	99.6
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.59
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.58
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.58
KOG1123	776	consensus RNA polymerase II transcription initiati	99.57
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.56
COG4096	875	HsdR Type I site-specific restriction-modification	99.55
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.53
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.49
KOG0387	923	consensus Transcription-coupled repair protein CSB	99.47
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.46
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	99.45
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.45
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.43
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.41
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.34
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.32
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.31
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.16
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.15
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	99.14
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	99.13
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.12
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.1
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	99.1
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	99.07
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.07
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.99
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	98.97
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.95
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.94
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.91
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.87
COG4889	1518	Predicted helicase [General function prediction on	98.81
KOG2340	698	consensus Uncharacterized conserved protein [Funct	98.76
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	98.75
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.73
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.72
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.72
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.54
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.53
KOG4439	901	consensus RNA polymerase II transcription terminat	98.49
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	98.48
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.46
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.44
PRK14873	665	primosome assembly protein PriA; Provisional	98.43
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.39
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.31
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	98.3
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.19
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.17
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.15
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.0
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.95
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	97.86
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	97.83
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	97.71
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	97.56
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.46
COG0610	962	Type I site-specific restriction-modification syst	97.37
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	97.33
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	97.24
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	97.24
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.1
PRK05580	679	primosome assembly protein PriA; Validated	97.07
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	97.02
TIGR00595	505	priA primosomal protein N'. All proteins in this f	97.01
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.84
PRK14873	665	primosome assembly protein PriA; Provisional	96.81
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	96.71
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	96.52
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	96.49
PRK10689	1147	transcription-repair coupling factor; Provisional	96.41
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	96.3
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	96.15
COG1198	730	PriA Primosomal protein N' (replication factor Y)	96.02
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	95.87
PRK14701	1638	reverse gyrase; Provisional	95.69
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	95.48
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	95.43
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	95.33
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	95.12
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	95.11
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	95.06
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	94.98
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	94.59
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	94.41
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	94.28
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	94.2
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	94.18
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	94.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	93.76
KOG0347	731	consensus RNA helicase [RNA processing and modific	93.73
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	93.57
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	93.29
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	92.97
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	92.97
KOG1002	791	consensus Nucleotide excision repair protein RAD16	92.81
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	92.71
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	92.7
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	92.66
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	92.45
KOG1001	674	consensus Helicase-like transcription factor HLTF/	92.37
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	92.32
PRK09401	1176	reverse gyrase; Reviewed	92.05
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	91.92
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	91.47
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	91.01
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	91.0
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	90.82
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	90.7
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	90.49
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	90.28
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	90.21
PRK08727	233	hypothetical protein; Validated	90.14
PTZ00110	545	helicase; Provisional	90.1
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	90.05
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	90.0
PRK06893	229	DNA replication initiation factor; Validated	89.68
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	89.43
PF13871	278	Helicase_C_4: Helicase_C-like	88.99
PRK08084	235	DNA replication initiation factor; Provisional	88.63
PRK05642	234	DNA replication initiation factor; Validated	88.49
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	88.47
KOG1001	674	consensus Helicase-like transcription factor HLTF/	88.45
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	88.45
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	88.35
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	88.31
COG3973	747	Superfamily I DNA and RNA helicases [General funct	87.69
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	87.59
PRK12422	445	chromosomal replication initiation protein; Provis	87.27
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	87.27
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	86.98
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	86.86
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	86.74
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	86.52
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	86.26
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	85.75
KOG3089	271	consensus Predicted DEAD-box-containing helicase [	85.65
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	85.57
PRK13766	773	Hef nuclease; Provisional	85.54
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	85.35
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	85.33
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	85.24
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	85.11
PRK14087	450	dnaA chromosomal replication initiation protein; P	84.8
PF13173	128	AAA_14: AAA domain	84.73
cd01518	101	RHOD_YceA Member of the Rhodanese Homology Domain	84.33
cd01534	95	4RHOD_Repeat_3 Member of the Rhodanese Homology Do	83.88
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	83.82
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	83.7
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	83.69
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	83.64
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	83.6
COG2519	256	GCD14 tRNA(1-methyladenosine) methyltransferase an	83.5
KOG0343	758	consensus RNA Helicase [RNA processing and modific	83.32
PRK14088	440	dnaA chromosomal replication initiation protein; P	83.21
cd06533	171	Glyco_transf_WecG_TagA The glycosyltransferase Wec	82.0
cd01527	99	RHOD_YgaP Member of the Rhodanese Homology Domain	81.93
cd01449	118	TST_Repeat_2 Thiosulfate sulfurtransferase (TST),	81.88
TIGR00696	177	wecB_tagA_cpsF bacterial polymer biosynthesis prot	81.65
PRK05728	142	DNA polymerase III subunit chi; Validated	81.54
PF03808	172	Glyco_tran_WecB: Glycosyl transferase WecB/TagA/Cp	81.27
cd01521	110	RHOD_PspE2 Member of the Rhodanese Homology Domain	81.14
cd01533	109	4RHOD_Repeat_2 Member of the Rhodanese Homology Do	81.0
cd01526	122	RHOD_ThiF Member of the Rhodanese Homology Domain	80.95
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	80.72
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	80.7
PRK09200	790	preprotein translocase subunit SecA; Reviewed	80.57
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	80.02

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

Probab=100.00  E-value=5e-48  Score=316.73  Aligned_cols=245  Identities=35%  Similarity=0.512  Sum_probs=220.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+.+.+..++...+ .+..+++||.   .|...+.++.+|+|+||+++.++++.+.+.++++.++|+||||.|++.|
T Consensus       177 LA~QV~~~~~~~~~~~~-~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmG  255 (519)
T KOG0331|consen  177 LAVQVQAEAREFGKSLR-LRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMG  255 (519)
T ss_pred             HHHHHHHHHHHHcCCCC-ccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhhhccc
Confidence            79999999999999999 6666666666   6667788899999999999999999999999999999999999999999


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccc--cccccceeEEEEcCCchhHHHHHHHHH
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKN--TASESIKQKLVFAGSEEGKLLALRQSF  155 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~  155 (248)
                       |...+..++.....+..|+++.|||+|...+.+...++.++..+.+....  ....++.+....+. ...|...+..++
T Consensus       256 -Fe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~-~~~K~~~l~~lL  333 (519)
T KOG0331|consen  256 -FEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCD-ETAKLRKLGKLL  333 (519)
T ss_pred             -cHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcC-HHHHHHHHHHHH
Confidence             99999999999767777999999999999999999999999888877543  44556666666555 556777777766


Q ss_pred             hcc---CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEE
Q 042003          156 AES---LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV  232 (248)
Q Consensus       156 ~~~---~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~V  232 (248)
                      ...   .++|+||||++++.|+++...|+..++++..+||+.++.+|..+++.|++|+..|||||+++++|+|+|++++|
T Consensus       334 ~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lV  413 (519)
T KOG0331|consen  334 EDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLV  413 (519)
T ss_pred             HHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccccEE
Confidence            654   36799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccCCCCcccceecC
Q 042003          233 INYDFPDSGAAYIHRI  248 (248)
Q Consensus       233 i~~~~p~~~~~~~qri  248 (248)
                      ||||+|.++++|+||+
T Consensus       414 InydfP~~vEdYVHRi  429 (519)
T KOG0331|consen  414 INYDFPNNVEDYVHRI  429 (519)
T ss_pred             EeCCCCCCHHHHHhhc
Confidence            9999999999999996

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

Probab=100.00  E-value=1.1e-47  Score=287.26  Aligned_cols=245  Identities=31%  Similarity=0.429  Sum_probs=232.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+.+.+..++...+ ..++.+.||.   +.-..+..+.+++.+||+++.++++++.+..+.++++|+|||+.+++.|
T Consensus       107 La~Qi~~vi~alg~~mn-vq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~kg  185 (400)
T KOG0328|consen  107 LAVQIQKVILALGDYMN-VQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNKG  185 (400)
T ss_pred             HHHHHHHHHHHhccccc-ceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHHHHHhh
Confidence            68899999999999999 6777766666   4445566899999999999999999999999999999999999999998


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                       |..++..+.++ .++..|++++|||+|.+..+..+.++.+|+.+.+.+.+.+..+++++++.++.+++|.+.|.++...
T Consensus       186 -fk~Qiydiyr~-lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtLcdLYd~  263 (400)
T KOG0328|consen  186 -FKEQIYDIYRY-LPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDT  263 (400)
T ss_pred             -HHHHHHHHHHh-CCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhHhHHHHHhhh
Confidence             99999999999 7889999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      ..-.+++|||||+..+..+.+.+++.++.|.-.||+|++++|..+++.|++|+.+||++|++.++|+|+|.+++|||||.
T Consensus       264 LtItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDL  343 (400)
T KOG0328|consen  264 LTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYDL  343 (400)
T ss_pred             hehheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEecCC
Confidence            87889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      |.+...|+|||
T Consensus       344 P~nre~YIHRI  354 (400)
T KOG0328|consen  344 PNNRELYIHRI  354 (400)
T ss_pred             CccHHHHhhhh
Confidence            99999999997

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

Probab=100.00  E-value=1.5e-47  Score=297.57  Aligned_cols=245  Identities=29%  Similarity=0.448  Sum_probs=228.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhc-CCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~-~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+.+.++.++.+.|+..+.+++|..  .+...+.+.|+|+|+||++|++.+.+ +.+++..++++|+||||.+++..
T Consensus       141 LA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~d  220 (476)
T KOG0330|consen  141 LAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMD  220 (476)
T ss_pred             HHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhhhhh
Confidence            7899999999999999955555555555  66777888999999999999999996 67889999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                       |...+..+++. .+...|++++|||++.....+.+.-..+|..+.........+.+++.++.++..+ |...|..+++.
T Consensus       221 -F~~~ld~ILk~-ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~-K~~yLV~ll~e  297 (476)
T KOG0330|consen  221 -FEEELDYILKV-IPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKD-KDTYLVYLLNE  297 (476)
T ss_pred             -hHHHHHHHHHh-cCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccc-cchhHHHHHHh
Confidence             99999999999 5688999999999999999999999999999999999999999999998887765 88889999998


Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      ..++.+||||++...++.++-.|+..|+.+..+||.|++..|...++.|++|..+||+||+++++|+|+|.+++|||||.
T Consensus       298 ~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDi  377 (476)
T KOG0330|consen  298 LAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNYDI  377 (476)
T ss_pred             hcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEecCC
Confidence            88999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      |.+..+|+||+
T Consensus       378 P~~skDYIHRv  388 (476)
T KOG0330|consen  378 PTHSKDYIHRV  388 (476)
T ss_pred             CCcHHHHHHHc
Confidence            99999999996

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

Probab=100.00  E-value=6.5e-46  Score=314.45  Aligned_cols=245  Identities=39%  Similarity=0.552  Sum_probs=225.3

Q ss_pred             CcchHHHHHHHhhcCC-CcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGN-KFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~-~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      ||.|+++.++++++.. + ..+..++||.   .+...+..+++|+|+||+++++++.++.+.+++++++|+||||.+++.
T Consensus       111 LA~Qi~~~~~~~~~~~~~-~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd~  189 (513)
T COG0513         111 LAVQIAEELRKLGKNLGG-LRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDM  189 (513)
T ss_pred             HHHHHHHHHHHHHhhcCC-ccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhcC
Confidence            7899999999999998 6 4466666665   444556667999999999999999999999999999999999999999


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccccc--ccccceeEEEEcCCchhHHHHHHHH
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNT--ASESIKQKLVFAGSEEGKLLALRQS  154 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~  154 (248)
                      | |...+..+++.+. .+.|++++|||+|.....+.+.++.+|..+.+.....  ....+.+.++.+...++|...|..+
T Consensus       190 G-f~~~i~~I~~~~p-~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~l  267 (513)
T COG0513         190 G-FIDDIEKILKALP-PDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKL  267 (513)
T ss_pred             C-CHHHHHHHHHhCC-cccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHH
Confidence            8 9999999999954 4899999999999999999999999998888775555  7888999999888877899999999


Q ss_pred             HhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe
Q 042003          155 FAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN  234 (248)
Q Consensus       155 ~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~  234 (248)
                      ++.....++||||+++..++.++..|+..|+++..+||+|++++|.++++.|++|+.+|||||+++++|||+|++++|||
T Consensus       268 l~~~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~Vin  347 (513)
T COG0513         268 LKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVIN  347 (513)
T ss_pred             HhcCCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeEE
Confidence            99887778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCcccceecC
Q 042003          235 YDFPDSGAAYIHRI  248 (248)
Q Consensus       235 ~~~p~~~~~~~qri  248 (248)
                      ||+|.++..|+|||
T Consensus       348 yD~p~~~e~yvHRi  361 (513)
T COG0513         348 YDLPLDPEDYVHRI  361 (513)
T ss_pred             ccCCCCHHHheecc
Confidence            99999999999997

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

Probab=100.00  E-value=2.4e-45  Score=294.89  Aligned_cols=246  Identities=33%  Similarity=0.520  Sum_probs=228.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      ||+|+++.-.+|++.+++.++.+++|..  ++.-.+..+|+|+|+||++|.+.+.+..+.++.+.++|+|||+.+.+.| 
T Consensus       334 LaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~lvl~qctyvvldeadrmiDmg-  412 (673)
T KOG0333|consen  334 LAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMG-  412 (673)
T ss_pred             HHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHHHHhccCceEeccchhhhhccc-
Confidence            6899999999999999977777777776  5555788999999999999999999999999999999999999999998 


Q ss_pred             ccccchhHhhhCCCcc------------------------ceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccc
Q 042003           79 LLKHIDPVVKACSNPS------------------------IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESI  134 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~------------------------~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (248)
                      |...+..++.++.+.+                        .|.+++|||+|+....+++.|+.+|+.+.++....+.+.+
T Consensus       413 fE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~gk~~~rv  492 (673)
T KOG0333|consen  413 FEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTPRV  492 (673)
T ss_pred             ccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCccch
Confidence            9888888888765422                        6899999999999999999999999999999999999999


Q ss_pred             eeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEE
Q 042003          135 KQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVL  214 (248)
Q Consensus       135 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~il  214 (248)
                      .+.++.+...+ +...|.++++.....++|||+|+++.|+.+++.|.+.++++..+||+-++++|+..++.|++|..+|+
T Consensus       493 eQ~v~m~~ed~-k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIl  571 (673)
T KOG0333|consen  493 EQKVEMVSEDE-KRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDIL  571 (673)
T ss_pred             heEEEEecchH-HHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEE
Confidence            88887777665 69999999999878899999999999999999999999999999999999999999999999999999


Q ss_pred             EEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          215 IATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       215 v~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |||+++++|||+|++++|||||++.|+.+|+|||
T Consensus       572 VaTDvAgRGIDIpnVSlVinydmaksieDYtHRI  605 (673)
T KOG0333|consen  572 VATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRI  605 (673)
T ss_pred             EEecccccCCCCCccceeeecchhhhHHHHHHHh
Confidence            9999999999999999999999999999999997

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=3.9e-43  Score=293.74  Aligned_cols=245  Identities=33%  Similarity=0.492  Sum_probs=212.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++.+.+..+ ..+..++|+.   .+...+..+++|+|+||+++.+++..+.+.+++++++|+||||++++++
T Consensus        95 La~Qi~~~~~~l~~~~~-~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad~l~~~~  173 (423)
T PRK04837         95 LAVQIHADAEPLAQATG-LKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLG  173 (423)
T ss_pred             HHHHHHHHHHHHhccCC-ceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHHHHhhcc
Confidence            68999999999999988 4555555554   3344556789999999999999999888899999999999999999988


Q ss_pred             cccccchhHhhhCCC-ccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHh
Q 042003           78 NLLKHIDPVVKACSN-PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA  156 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  156 (248)
                       |...+..++..+.. ...+.+++|||++.....+....+.++..+...........+.+.+.+. ....+...+..++.
T Consensus       174 -f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~-~~~~k~~~l~~ll~  251 (423)
T PRK04837        174 -FIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYP-SNEEKMRLLQTLIE  251 (423)
T ss_pred             -cHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeC-CHHHHHHHHHHHHH
Confidence             88888888887544 3567789999999989888888888888877766655555666655544 44568888888888


Q ss_pred             ccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          157 ESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       157 ~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      .....++||||+++..|+.+++.|+..++++..+||+|++++|..+++.|++|+.+|||||+++++|+|+|++++||+||
T Consensus       252 ~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~VI~~d  331 (423)
T PRK04837        252 EEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYD  331 (423)
T ss_pred             hcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCEEEEeC
Confidence            77678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccceecC
Q 042003          237 FPDSGAAYIHRI  248 (248)
Q Consensus       237 ~p~~~~~~~qri  248 (248)
                      +|.|+..|+||+
T Consensus       332 ~P~s~~~yiqR~  343 (423)
T PRK04837        332 LPDDCEDYVHRI  343 (423)
T ss_pred             CCCchhheEecc
Confidence            999999999996

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=1.1e-42  Score=293.99  Aligned_cols=244  Identities=29%  Similarity=0.441  Sum_probs=214.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+.+.++.+++......+..++|+.   .+...+..+++|+|+||+++.+++.++.+.+++++++|+||||++++.+
T Consensus        84 La~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g  163 (460)
T PRK11776         84 LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMG  163 (460)
T ss_pred             HHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcC
Confidence            6899999999998765335666667665   3334456789999999999999999988889999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                       |...+..++.. .+...|++++|||+++....+...++.++..+...... ....+.+.++.+... .+...+..++..
T Consensus       164 -~~~~l~~i~~~-~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~~~-~k~~~l~~ll~~  239 (460)
T PRK11776        164 -FQDAIDAIIRQ-APARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVSPD-ERLPALQRLLLH  239 (460)
T ss_pred             -cHHHHHHHHHh-CCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeCcH-HHHHHHHHHHHh
Confidence             88889988888 56678999999999999999999999998887765544 344466666655554 488899999988


Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      ..+.++||||++++.++.+++.|...++.+..+||+|++.+|+.+++.|++|+.++||||+++++|+|+|++++||+||+
T Consensus       240 ~~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~  319 (460)
T PRK11776        240 HQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYEL  319 (460)
T ss_pred             cCCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecC
Confidence            77789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      |.++..|+||+
T Consensus       320 p~~~~~yiqR~  330 (460)
T PRK11776        320 ARDPEVHVHRI  330 (460)
T ss_pred             CCCHhHhhhhc
Confidence            99999999996

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

Probab=100.00  E-value=6.3e-44  Score=271.33  Aligned_cols=243  Identities=28%  Similarity=0.399  Sum_probs=221.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+.+.|..+++..+ ..+....||.   +....+....+++|+||++++++...+--.++++.++|+||||.+++..
T Consensus       165 lALQtSqvc~~lskh~~-i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~  243 (459)
T KOG0326|consen  165 LALQTSQVCKELSKHLG-IKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVD  243 (459)
T ss_pred             hhHHHHHHHHHHhcccC-eEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchh
Confidence            78999999999999999 7777777777   3333355678999999999999999998889999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                       |...+..++.. .+.+.|+++.|||+|-........++.+|+.+... ++....++.+++.++... +|...|..++.+
T Consensus       244 -F~~~~e~li~~-lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM-~eLtl~GvtQyYafV~e~-qKvhCLntLfsk  319 (459)
T KOG0326|consen  244 -FQPIVEKLISF-LPKERQILLYSATFPLTVKGFMDRHLKKPYEINLM-EELTLKGVTQYYAFVEER-QKVHCLNTLFSK  319 (459)
T ss_pred             -hhhHHHHHHHh-CCccceeeEEecccchhHHHHHHHhccCcceeehh-hhhhhcchhhheeeechh-hhhhhHHHHHHH
Confidence             99999999998 78899999999999999999999999999887554 455667888888777654 588999999998


Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      ..-++.+|||||...++.+++.+.+.|++|.++|+.|.+++|..+++.|++|.++.||||+.+.+|||++.+++||+||+
T Consensus       320 LqINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDf  399 (459)
T KOG0326|consen  320 LQINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDF  399 (459)
T ss_pred             hcccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCC
Confidence            88889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      |++..+|+|||
T Consensus       400 pk~aEtYLHRI  410 (459)
T KOG0326|consen  400 PKNAETYLHRI  410 (459)
T ss_pred             CCCHHHHHHHc
Confidence            99999999997

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=2.2e-42  Score=290.44  Aligned_cols=245  Identities=31%  Similarity=0.449  Sum_probs=216.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++.+++..+ ..+..+.|+.   .+.....++++|+|+||++|.+.+..+.+.++++++||+||||++++++
T Consensus        85 La~Q~~~~~~~l~~~~~-~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~~~  163 (434)
T PRK11192         85 LAMQVADQARELAKHTH-LDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMG  163 (434)
T ss_pred             HHHHHHHHHHHHHccCC-cEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhCCC
Confidence            68999999999999988 5566666655   3444566789999999999999999988889999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCc-hHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHh
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPD-FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA  156 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  156 (248)
                       |...+..+... .+...|++++|||++. ....+...++.++..+...........+.+.+......+.+...+..+++
T Consensus       164 -~~~~~~~i~~~-~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~  241 (434)
T PRK11192        164 -FAQDIETIAAE-TRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLK  241 (434)
T ss_pred             -cHHHHHHHHHh-CccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHh
Confidence             88888888776 4567899999999985 47777888888888887776666666777777777777889999999998


Q ss_pred             ccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          157 ESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       157 ~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      .....++||||++++.++.+++.|+..++.+..+||+|++++|..+++.|++|+.+|||||+++++|+|+|++++||+||
T Consensus       242 ~~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d  321 (434)
T PRK11192        242 QPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFD  321 (434)
T ss_pred             cCCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEEC
Confidence            76678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccceecC
Q 042003          237 FPDSGAAYIHRI  248 (248)
Q Consensus       237 ~p~~~~~~~qri  248 (248)
                      +|.|...|+||+
T Consensus       322 ~p~s~~~yiqr~  333 (434)
T PRK11192        322 MPRSADTYLHRI  333 (434)
T ss_pred             CCCCHHHHhhcc
Confidence            999999999996

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=2.1e-42  Score=291.33  Aligned_cols=245  Identities=33%  Similarity=0.502  Sum_probs=210.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      ||.|+.+.++.+.+..++....+++|..  .+...+.++++|+|+||++|++++....+.+++++++|+||||++++++ 
T Consensus        87 La~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~ll~~~-  165 (456)
T PRK10590         87 LAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMG-  165 (456)
T ss_pred             HHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHHhccc-
Confidence            6899999999999988844444444433  3334456789999999999999999888889999999999999999988 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES  158 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  158 (248)
                      |...+..++.. .+...|++++|||+++....+..+++.++..+...........+.+.+.... ...+...+..++...
T Consensus       166 ~~~~i~~il~~-l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~l~~~~  243 (456)
T PRK10590        166 FIHDIRRVLAK-LPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVD-KKRKRELLSQMIGKG  243 (456)
T ss_pred             cHHHHHHHHHh-CCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcC-HHHHHHHHHHHHHcC
Confidence            88888888877 4567899999999999889999999889888777666655566666665444 445667777777776


Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                      ...++||||+++..++.+++.|++.++.+..+||+|++++|..+++.|++|+.+|||||+++++|+|+|++++||+|++|
T Consensus       244 ~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P  323 (456)
T PRK10590        244 NWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELP  323 (456)
T ss_pred             CCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEEEeCCC
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccceecC
Q 042003          239 DSGAAYIHRI  248 (248)
Q Consensus       239 ~~~~~~~qri  248 (248)
                      .++.+|+||+
T Consensus       324 ~~~~~yvqR~  333 (456)
T PRK10590        324 NVPEDYVHRI  333 (456)
T ss_pred             CCHHHhhhhc
Confidence            9999999996

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=1.3e-42  Score=296.86  Aligned_cols=244  Identities=36%  Similarity=0.518  Sum_probs=207.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.+++++...+ ..+.+++|+.   .+...+..+++|+|+||++|.+++..+...+++++++|+||||++++++
T Consensus       215 La~Qi~~~~~~~~~~~~-i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~g  293 (545)
T PTZ00110        215 LAEQIREQCNKFGASSK-IRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMG  293 (545)
T ss_pred             HHHHHHHHHHHHhcccC-ccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhcc
Confidence            78999999999999888 4455555554   3334456789999999999999999888889999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcC-CcEEEEEcccc-cccccceeEEEEcCCchhHHHHHHHHH
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH-DAVRVIVGRKN-TASESIKQKLVFAGSEEGKLLALRQSF  155 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~  155 (248)
                       |...+..++.. ..+..|++++|||+|.....+...++. ++..+...... .....+.+.+..+. ...|...+..++
T Consensus       294 -f~~~i~~il~~-~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~-~~~k~~~L~~ll  370 (545)
T PTZ00110        294 -FEPQIRKIVSQ-IRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVE-EHEKRGKLKMLL  370 (545)
T ss_pred             -hHHHHHHHHHh-CCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEe-chhHHHHHHHHH
Confidence             88889999887 456789999999999999999888775 46666555433 23345556655444 345677777777


Q ss_pred             hcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEE
Q 042003          156 AES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI  233 (248)
Q Consensus       156 ~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi  233 (248)
                      ...  .+.++||||++++.|+.+++.|+..++.+..+||++++++|..+++.|++|+.+|||||+++++|+|+|++++||
T Consensus       371 ~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI  450 (545)
T PTZ00110        371 QRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVI  450 (545)
T ss_pred             HHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEE
Confidence            654  367999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCcccceecC
Q 042003          234 NYDFPDSGAAYIHRI  248 (248)
Q Consensus       234 ~~~~p~~~~~~~qri  248 (248)
                      +||+|.++.+|+||+
T Consensus       451 ~~d~P~s~~~yvqRi  465 (545)
T PTZ00110        451 NFDFPNQIEDYVHRI  465 (545)
T ss_pred             EeCCCCCHHHHHHHh
Confidence            999999999999996

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.8e-42  Score=295.76  Aligned_cols=245  Identities=31%  Similarity=0.478  Sum_probs=211.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcC-CcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~-~~~~~~~~~lIiDEah~~~~~   76 (248)
                      ||.|+++.+++++...+ ..+..++|+.   .+...+..+++|+|+||++|++++.+. .+.+++++++|+||||+++++
T Consensus        96 La~Qi~~~~~~l~~~~~-i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~lld~  174 (572)
T PRK04537         96 LAIQIHKDAVKFGADLG-LRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDL  174 (572)
T ss_pred             HHHHHHHHHHHHhccCC-ceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHHHHhhc
Confidence            68999999999999988 5566666655   334456668999999999999999775 467899999999999999998


Q ss_pred             CcccccchhHhhhCCC-ccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHH
Q 042003           77 GNLLKHIDPVVKACSN-PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSF  155 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  155 (248)
                      + |...+..+++.+.. ...|++++|||++.....+...++.++..+...........+.+.+... ....+...+..++
T Consensus       175 g-f~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~-~~~~k~~~L~~ll  252 (572)
T PRK04537        175 G-FIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFP-ADEEKQTLLLGLL  252 (572)
T ss_pred             c-hHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEec-CHHHHHHHHHHHH
Confidence            8 88888888887543 3679999999999988898888888887776655555555566665544 4556888888888


Q ss_pred             hccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEec
Q 042003          156 AESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY  235 (248)
Q Consensus       156 ~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~  235 (248)
                      ....+.++||||+++..++.+++.|.+.++.+..+||+|++.+|+.+++.|++|+.+|||||+++++|||+|++++||+|
T Consensus       253 ~~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~VIny  332 (572)
T PRK04537        253 SRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNY  332 (572)
T ss_pred             hcccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEc
Confidence            88778899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcccceecC
Q 042003          236 DFPDSGAAYIHRI  248 (248)
Q Consensus       236 ~~p~~~~~~~qri  248 (248)
                      |+|.+..+|+||+
T Consensus       333 d~P~s~~~yvqRi  345 (572)
T PRK04537        333 DLPFDAEDYVHRI  345 (572)
T ss_pred             CCCCCHHHHhhhh
Confidence            9999999999996

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

Probab=100.00  E-value=1.4e-41  Score=289.57  Aligned_cols=244  Identities=29%  Similarity=0.443  Sum_probs=208.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      ||.|+++.++.+++..++..+..++|..  .+...+..+++|+|+||++|.+++.++...+++++++|+||||++++++ 
T Consensus       208 La~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~g-  286 (518)
T PLN00206        208 LCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERG-  286 (518)
T ss_pred             HHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHHHhhcc-
Confidence            6889999999999998854444444443  3333456689999999999999999988889999999999999999988 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES  158 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  158 (248)
                      |...+..++..+  +..|++++|||+++....+...+..++..+...........+.+...++... .+...+.+++...
T Consensus       287 f~~~i~~i~~~l--~~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~-~k~~~l~~~l~~~  363 (518)
T PLN00206        287 FRDQVMQIFQAL--SQPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETK-QKKQKLFDILKSK  363 (518)
T ss_pred             hHHHHHHHHHhC--CCCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccch-hHHHHHHHHHHhh
Confidence            888888887764  3579999999999999999999988888888777666666677777666554 4566677776643


Q ss_pred             C--CCCEEEEecchHHHHHHHHHhhc-CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEec
Q 042003          159 L--NPPVLIFVQSKERAKELYGELAF-DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY  235 (248)
Q Consensus       159 ~--~~~~liF~~~~~~~~~l~~~L~~-~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~  235 (248)
                      .  ..++||||+++..++.+++.|.. .++++..+||+|++++|..+++.|++|+.+|||||+++++|+|+|++++||+|
T Consensus       364 ~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~  443 (518)
T PLN00206        364 QHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIF  443 (518)
T ss_pred             cccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEe
Confidence            2  46899999999999999999975 58899999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcccceecC
Q 042003          236 DFPDSGAAYIHRI  248 (248)
Q Consensus       236 ~~p~~~~~~~qri  248 (248)
                      |+|.++.+|+||+
T Consensus       444 d~P~s~~~yihRi  456 (518)
T PLN00206        444 DMPNTIKEYIHQI  456 (518)
T ss_pred             CCCCCHHHHHHhc
Confidence            9999999999996

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=1.4e-41  Score=293.23  Aligned_cols=245  Identities=27%  Similarity=0.402  Sum_probs=212.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.+.++.+...-..+..++|+.   .+...+..+++|+|+||+++.+++.++.+.+++++++|+||||.+++.+
T Consensus        86 La~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~g  165 (629)
T PRK11634         86 LAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMG  165 (629)
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcc
Confidence            6899999999998776324455555554   3334456789999999999999999988899999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                       |...+..++.. .+...|++++|||+|+....+...++.++..+.+.......+.+.+.++.+. ...|...+..++..
T Consensus       166 -f~~di~~Il~~-lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~-~~~k~~~L~~~L~~  242 (629)
T PRK11634        166 -FIEDVETIMAQ-IPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVW-GMRKNEALVRFLEA  242 (629)
T ss_pred             -cHHHHHHHHHh-CCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEec-hhhHHHHHHHHHHh
Confidence             88888888887 5667899999999999999999999999988877666655566666665444 34578888888887


Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      ....++||||+++..++.+++.|...++.+..+||+|++.+|+.+++.|++|+.+|||||+++++|+|+|++++||+||+
T Consensus       243 ~~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~  322 (629)
T PRK11634        243 EDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDI  322 (629)
T ss_pred             cCCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCC
Confidence            76789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      |.+..+|+||+
T Consensus       323 P~~~e~yvqRi  333 (629)
T PRK11634        323 PMDSESYVHRI  333 (629)
T ss_pred             CCCHHHHHHHh
Confidence            99999999995

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

Probab=100.00  E-value=5.1e-43  Score=280.76  Aligned_cols=245  Identities=31%  Similarity=0.482  Sum_probs=222.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcC-CcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~-~~~~~~~~~lIiDEah~~~~~   76 (248)
                      ||.|++...++++.... +.++++.||.   .|+..+..+|||+|+||++|.+++.+. .+.++++.++|+|||+++++.
T Consensus       264 LaiQv~sV~~qlaqFt~-I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRMLee  342 (691)
T KOG0338|consen  264 LAIQVHSVTKQLAQFTD-ITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEE  342 (691)
T ss_pred             HHHHHHHHHHHHHhhcc-ceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHHHHH
Confidence            68999999999999999 6666666666   777889999999999999999999985 678999999999999999999


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCC--chhHHHHHHHH
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS--EEGKLLALRQS  154 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~  154 (248)
                      + |...+.++.+.| +.+.|.+++|||++....+++.--+.+|+.+.+.......+.+.+.++....  .-.+-..+..+
T Consensus       343 g-FademnEii~lc-pk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l  420 (691)
T KOG0338|consen  343 G-FADEMNEIIRLC-PKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASL  420 (691)
T ss_pred             H-HHHHHHHHHHhc-cccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHHH
Confidence            9 999999999995 5688999999999999999999999999999999988888888777765543  33456677777


Q ss_pred             HhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe
Q 042003          155 FAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN  234 (248)
Q Consensus       155 ~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~  234 (248)
                      +......+++||+.|+++|.++.-.|.-.|.+++.+||.+++++|.+.++.|+++++++||||+++++|+||+++..|||
T Consensus       421 ~~rtf~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVIN  500 (691)
T KOG0338|consen  421 ITRTFQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVIN  500 (691)
T ss_pred             HHHhcccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEe
Confidence            77776789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCcccceecC
Q 042003          235 YDFPDSGAAYIHRI  248 (248)
Q Consensus       235 ~~~p~~~~~~~qri  248 (248)
                      |.+|.+...|+|||
T Consensus       501 y~mP~t~e~Y~HRV  514 (691)
T KOG0338|consen  501 YAMPKTIEHYLHRV  514 (691)
T ss_pred             ccCchhHHHHHHHh
Confidence            99999999999997

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.3e-40  Score=282.06  Aligned_cols=246  Identities=30%  Similarity=0.482  Sum_probs=209.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||+|+++.++.+.+..++......+|..   .........++|+|+||++|..+..+....+++++++||||||.+.+.+
T Consensus       174 La~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDEah~l~~~~  253 (475)
T PRK01297        174 LVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMG  253 (475)
T ss_pred             HHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEechHHHHHhcc
Confidence            6899999999999988844444444433   2223345578999999999999988888889999999999999999887


Q ss_pred             cccccchhHhhhCCC-ccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHh
Q 042003           78 NLLKHIDPVVKACSN-PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA  156 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  156 (248)
                       |...+..+++.+.. ...|++++|||++.....+...+..++..+...........+.+.+.... ..++...+..++.
T Consensus       254 -~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~k~~~l~~ll~  331 (475)
T PRK01297        254 -FIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVA-GSDKYKLLYNLVT  331 (475)
T ss_pred             -cHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEec-chhHHHHHHHHHH
Confidence             88888888887543 35799999999999889999988888887776666555555666655444 3457788888888


Q ss_pred             ccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          157 ESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       157 ~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      .....++||||+++++++.+++.|...++.+..+||+++.++|.++++.|++|+.++||||+++++|+|+|++++||+||
T Consensus       332 ~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI~~~  411 (475)
T PRK01297        332 QNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFT  411 (475)
T ss_pred             hcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCCEEEEeC
Confidence            77678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccceecC
Q 042003          237 FPDSGAAYIHRI  248 (248)
Q Consensus       237 ~p~~~~~~~qri  248 (248)
                      +|.|..+|+||+
T Consensus       412 ~P~s~~~y~Qr~  423 (475)
T PRK01297        412 LPEDPDDYVHRI  423 (475)
T ss_pred             CCCCHHHHHHhh
Confidence            999999999995

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=2.8e-40  Score=275.52  Aligned_cols=246  Identities=30%  Similarity=0.452  Sum_probs=210.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      ||.|+++.++.++...+.....+.+|..  ........+++|+|+||+++.+++.++...+++++++|+||||++.+++ 
T Consensus       108 L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~~-  186 (401)
T PTZ00424        108 LAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRG-  186 (401)
T ss_pred             HHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHhcc-
Confidence            6889999999998877744333333333  3333455678999999999999999888889999999999999999887 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES  158 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  158 (248)
                      +...+..+++. .+...|++++|||+++....+...++.++..+..........++.+.+......+.+...+..+++..
T Consensus       187 ~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  265 (401)
T PTZ00424        187 FKGQIYDVFKK-LPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETL  265 (401)
T ss_pred             hHHHHHHHHhh-CCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHHhc
Confidence            77777777776 45678999999999998888888888888777666655556667777777766667778888888776


Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                      ...+++|||++++.++.+++.|+..++++..+||+|++++|+.+++.|++|+.+|||||+++++|+|+|++++||++|+|
T Consensus       266 ~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p  345 (401)
T PTZ00424        266 TITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLP  345 (401)
T ss_pred             CCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCC
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccceecC
Q 042003          239 DSGAAYIHRI  248 (248)
Q Consensus       239 ~~~~~~~qri  248 (248)
                      .|...|+||+
T Consensus       346 ~s~~~y~qr~  355 (401)
T PTZ00424        346 ASPENYIHRI  355 (401)
T ss_pred             CCHHHEeecc
Confidence            9999999996

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

Probab=100.00  E-value=7e-41  Score=270.59  Aligned_cols=246  Identities=37%  Similarity=0.517  Sum_probs=217.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++++.-... ......||+.   .+......+|+|+|+||++|.+++..+.+.+++++++|+|||+++++.-
T Consensus       164 L~~Qi~nea~k~~~~s~-~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~m  242 (482)
T KOG0335|consen  164 LVDQIYNEARKFSYLSG-MKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEM  242 (482)
T ss_pred             HhhHHHHHHHhhccccc-ceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEecchHHhhhhc
Confidence            78999999999999988 5555566665   5556677899999999999999999999999999999999999999943


Q ss_pred             cccccchhHhhhCCC---ccceeEEEEeecCchHHHHHHHhcCC-cEEEEEcccccccccceeEEEEcCCchhHHHHHHH
Q 042003           78 NLLKHIDPVVKACSN---PSIVRSLFSATLPDFVEELARSIMHD-AVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~---~~~~~i~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  153 (248)
                      .|...+.++......   ...|.+++|||+|.....+...+..+ -..+.+.+-.....++.+.+.++...+ |.+.|.+
T Consensus       243 gF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~-kr~~Lld  321 (482)
T KOG0335|consen  243 GFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNEME-KRSKLLD  321 (482)
T ss_pred             cccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecchh-hHHHHHH
Confidence            499999999887544   47899999999999999988887776 456777888888899999998888876 6666666


Q ss_pred             HHhccC----CC-----CEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCC
Q 042003          154 SFAESL----NP-----PVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGM  224 (248)
Q Consensus       154 ~~~~~~----~~-----~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gi  224 (248)
                      ++....    ..     +++|||++++.|..++..|...++++..+||..++.+|.+.++.|++|+..+||||+++++|+
T Consensus       322 ll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGl  401 (482)
T KOG0335|consen  322 LLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGL  401 (482)
T ss_pred             HhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCC
Confidence            665332    22     899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEeccCCCCcccceecC
Q 042003          225 DFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       225 dip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+|+++|||+||+|.+..+|+|||
T Consensus       402 Di~~V~hVInyDmP~d~d~YvHRI  425 (482)
T KOG0335|consen  402 DIPNVKHVINYDMPADIDDYVHRI  425 (482)
T ss_pred             CCCCCceeEEeecCcchhhHHHhc
Confidence            999999999999999999999997

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

Probab=100.00  E-value=1.3e-40  Score=265.95  Aligned_cols=244  Identities=30%  Similarity=0.405  Sum_probs=212.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh----hhcccccCCCcEEEeChHHHHHHHhcC-CcccCceeEEEEeccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV----RSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~i~v~Tp~~l~~~~~~~-~~~~~~~~~lIiDEah~~~~   75 (248)
                      ||.|++..++.+.+....+.+..+.||.    .+..+.+ +++|+|+||++|.+.+.+. .+.+++++++|+||||++++
T Consensus       166 LA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k-~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEADrlLd  244 (543)
T KOG0342|consen  166 LAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVK-GCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLD  244 (543)
T ss_pred             HHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhc-cccEEEeCCchHHhHhhcCCcchhhccceeEeecchhhhh
Confidence            7899999999999999448888888877    3344444 9999999999999999984 45678889999999999999


Q ss_pred             cCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcC-CcEEEEEccc--ccccccceeEEEEcCCchhHHHHHH
Q 042003           76 VGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH-DAVRVIVGRK--NTASESIKQKLVFAGSEEGKLLALR  152 (248)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~  152 (248)
                      .| |...+..+.+. .+...|..++|||.++..+++.+-.+. ++..+.+...  ......+.+.++-++... ++..+.
T Consensus       245 ~G-F~~di~~Ii~~-lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~-~f~ll~  321 (543)
T KOG0342|consen  245 IG-FEEDVEQIIKI-LPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDS-RFSLLY  321 (543)
T ss_pred             cc-cHHHHHHHHHh-ccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccc-hHHHHH
Confidence            99 99999999999 568899999999999999999987554 4666654433  344456777676555554 588888


Q ss_pred             HHHhccCC-CCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcE
Q 042003          153 QSFAESLN-PPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC  231 (248)
Q Consensus       153 ~~~~~~~~-~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~  231 (248)
                      .+++++.. .|++|||+|-.....+++.|+..+.+|..+||+.++..|..+...|.+.+..||+||+++++|+|+|+++.
T Consensus       322 ~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~  401 (543)
T KOG0342|consen  322 TFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDW  401 (543)
T ss_pred             HHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceE
Confidence            88888876 89999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccCCCCcccceecC
Q 042003          232 VINYDFPDSGAAYIHRI  248 (248)
Q Consensus       232 Vi~~~~p~~~~~~~qri  248 (248)
                      ||+||+|.++.+|+|||
T Consensus       402 VvQ~~~P~d~~~YIHRv  418 (543)
T KOG0342|consen  402 VVQYDPPSDPEQYIHRV  418 (543)
T ss_pred             EEEeCCCCCHHHHHHHh
Confidence            99999999999999997

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=2.3e-40  Score=267.81  Aligned_cols=244  Identities=30%  Similarity=0.398  Sum_probs=215.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcC-CcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~-~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.+++.++...+. ..++.||.  ..+....++.+|+||||++|+.++... .+.-+++.++|+|||+++++-|
T Consensus       153 LA~QtFevL~kvgk~h~fS-aGLiiGG~~~k~E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMG  231 (758)
T KOG0343|consen  153 LALQTFEVLNKVGKHHDFS-AGLIIGGKDVKFELERISQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMG  231 (758)
T ss_pred             HHHHHHHHHHHHhhccccc-cceeecCchhHHHHHhhhcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHHHh
Confidence            7899999999999999954 44555555  333344567999999999999999775 5678999999999999999999


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccc--ccccccceeEEEEcCCchhHHHHHHHHH
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK--NTASESIKQKLVFAGSEEGKLLALRQSF  155 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~~  155 (248)
                       |...+..++.. .+...|++++|||.+.....+++--+.+|..+.+...  ...+.++.++++.+.. .+|++.|..++
T Consensus       232 -Fk~tL~~Ii~~-lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l-~~Ki~~L~sFI  308 (758)
T KOG0343|consen  232 -FKKTLNAIIEN-LPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPL-EDKIDMLWSFI  308 (758)
T ss_pred             -HHHHHHHHHHh-CChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEeh-hhHHHHHHHHH
Confidence             99999999999 6788999999999999999999988899988877633  4556677777765554 46999999999


Q ss_pred             hccCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEE
Q 042003          156 AESLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI  233 (248)
Q Consensus       156 ~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi  233 (248)
                      ..+...+.|||++|-+++..+|+.+.+.  |+++..+||+|++..|.+++..|-+.+-.||+||+++++|+|+|.+++||
T Consensus       309 ~shlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwVi  388 (758)
T KOG0343|consen  309 KSHLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVI  388 (758)
T ss_pred             HhccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceEE
Confidence            9998899999999999999999999875  78899999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCcccceecC
Q 042003          234 NYDFPDSGAAYIHRI  248 (248)
Q Consensus       234 ~~~~p~~~~~~~qri  248 (248)
                      ++|.|.++++|+||+
T Consensus       389 Q~DCPedv~tYIHRv  403 (758)
T KOG0343|consen  389 QVDCPEDVDTYIHRV  403 (758)
T ss_pred             EecCchhHHHHHHHh
Confidence            999999999999996

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

Probab=100.00  E-value=8.7e-40  Score=262.19  Aligned_cols=246  Identities=36%  Similarity=0.520  Sum_probs=228.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      ||.|++..+++|++..++.++.+++|+.  .|...+..++.|+||||++|.+++.....++.+..++|+|||+.+++-| 
T Consensus       308 la~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmG-  386 (731)
T KOG0339|consen  308 LASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMG-  386 (731)
T ss_pred             HHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhhhhccc-
Confidence            6899999999999999977777777777  6667777999999999999999999999999999999999999999999 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES  158 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  158 (248)
                      |...+..|... -++..|.+++|||++.....+++..+.+|+.+..+.-......+.+.+.-+.+.+.|+++|..-+-..
T Consensus       387 fe~qVrSI~~h-irpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f  465 (731)
T KOG0339|consen  387 FEPQVRSIKQH-IRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEF  465 (731)
T ss_pred             cHHHHHHHHhh-cCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhh
Confidence            99999999998 67899999999999999999999999999999888777777778888888999999999988766544


Q ss_pred             -CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          159 -LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       159 -~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                       ..+++|+|+.-+..++.++..|.-++++|..+||+|.+.+|.+++..|+.+...|+|+|+++.+|+|+|+++.||+||+
T Consensus       466 ~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~  545 (731)
T KOG0339|consen  466 SSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDF  545 (731)
T ss_pred             ccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccc
Confidence             3689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      .++++.|.|||
T Consensus       546 ardIdththri  556 (731)
T KOG0339|consen  546 ARDIDTHTHRI  556 (731)
T ss_pred             cchhHHHHHHh
Confidence            99999999996

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

Probab=100.00  E-value=1.4e-39  Score=255.29  Aligned_cols=244  Identities=32%  Similarity=0.477  Sum_probs=215.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      ||.|++-.+.+..-. ++..+++++|+.  .+...++.+.+|+++||++|.++...+.++++++.++|+|||+++++-| 
T Consensus       306 Lalqie~e~~kysyn-g~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMg-  383 (629)
T KOG0336|consen  306 LALQIEGEVKKYSYN-GLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMG-  383 (629)
T ss_pred             HHHHHHhHHhHhhhc-CcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhccc-
Confidence            677888887775443 435566666666  6777788999999999999999999999999999999999999999999 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccc-cccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTA-SESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                      |...+.+++-. -.+..|+++.|||+|+..+.+...|+++|..+.++..+.. ...+++.+ .+....+|.+....+++.
T Consensus       384 FEpqIrkilld-iRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i-~v~~d~~k~~~~~~f~~~  461 (629)
T KOG0336|consen  384 FEPQIRKILLD-IRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNI-IVTTDSEKLEIVQFFVAN  461 (629)
T ss_pred             ccHHHHHHhhh-cCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeE-EecccHHHHHHHHHHHHh
Confidence            99999888777 6788999999999999999999999999998888766544 44566666 677777899988888876


Q ss_pred             cC-CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          158 SL-NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       158 ~~-~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      .. ..|+||||.++..|..+..-|--.|+...-+||...+.+|+..++.|++|+.+|||+|+.+++|+|+|+++||++||
T Consensus       462 ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyD  541 (629)
T KOG0336|consen  462 MSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYD  541 (629)
T ss_pred             cCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccC
Confidence            54 57999999999999888888888899999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccceecC
Q 042003          237 FPDSGAAYIHRI  248 (248)
Q Consensus       237 ~p~~~~~~~qri  248 (248)
                      +|.++..|.|||
T Consensus       542 FP~nIeeYVHRv  553 (629)
T KOG0336|consen  542 FPRNIEEYVHRV  553 (629)
T ss_pred             CCccHHHHHHHh
Confidence            999999999996

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

Probab=100.00  E-value=4.4e-39  Score=255.87  Aligned_cols=245  Identities=26%  Similarity=0.341  Sum_probs=212.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh----hhcccccCCCcEEEeChHHHHHHHhcC--CcccCceeEEEEecccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV----RSTDLSKFSCDILISTPLRLRLAIRRK--KIDLSRVEYLVLDEADKLF   74 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~i~v~Tp~~l~~~~~~~--~~~~~~~~~lIiDEah~~~   74 (248)
                      ||.|+.+.+..|...+....+.++.||.    +......++++|+||||++|.+++.+.  .+++++++++|+||||+++
T Consensus        91 La~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLl  170 (567)
T KOG0345|consen   91 LARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLL  170 (567)
T ss_pred             HHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEecchHhHh
Confidence            6899999999998885445566666655    334446678999999999999999984  4556799999999999999


Q ss_pred             ccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccccc--ccccceeEEEEcCCchhHHHHHH
Q 042003           75 EVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNT--ASESIKQKLVFAGSEEGKLLALR  152 (248)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~  152 (248)
                      +-| |...+..|++. .+...++=++|||......++.+..+.+|+.+.+.....  .+..+..++. ....+.|...+.
T Consensus       171 dmg-Fe~~~n~ILs~-LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~-v~~a~eK~~~lv  247 (567)
T KOG0345|consen  171 DMG-FEASVNTILSF-LPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYL-VCEADEKLSQLV  247 (567)
T ss_pred             ccc-HHHHHHHHHHh-cccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceee-EecHHHHHHHHH
Confidence            999 99999999999 677778889999999999999999999999998877664  4455555554 444556999999


Q ss_pred             HHHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCc
Q 042003          153 QSFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVN  230 (248)
Q Consensus       153 ~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~  230 (248)
                      +++.....+|++||++|=..++..+..+...  ...+..+||.|.+.+|..+++.|.+....+|+||+++++|+|+|+++
T Consensus       248 ~~L~~~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD  327 (567)
T KOG0345|consen  248 HLLNNNKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGID  327 (567)
T ss_pred             HHHhccccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCce
Confidence            9999988899999999999999988888764  66899999999999999999999998889999999999999999999


Q ss_pred             EEEeccCCCCcccceecC
Q 042003          231 CVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       231 ~Vi~~~~p~~~~~~~qri  248 (248)
                      +||+||+|.+++.|.||.
T Consensus       328 ~VvQ~DpP~~~~~FvHR~  345 (567)
T KOG0345|consen  328 LVVQFDPPKDPSSFVHRC  345 (567)
T ss_pred             EEEecCCCCChhHHHhhc
Confidence            999999999999999994

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

Probab=100.00  E-value=1.5e-38  Score=246.47  Aligned_cols=246  Identities=31%  Similarity=0.420  Sum_probs=221.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhc-CCcccCceeEEEEeccccccccCcc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNL   79 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~-~~~~~~~~~~lIiDEah~~~~~~~~   79 (248)
                      ||.|+-+.+.++++..+ ++...+..+....+-..-..+|+|+||+.+.+++.. ..+.+..++.+|+|||+.+.+...|
T Consensus       172 LA~Q~~eVv~eMGKf~~-ita~yair~sk~~rG~~i~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~  250 (477)
T KOG0332|consen  172 LAPQTGEVVEEMGKFTE-LTASYAIRGSKAKRGNKLTEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGF  250 (477)
T ss_pred             HHHHHHHHHHHhcCcee-eeEEEEecCcccccCCcchhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhcccc
Confidence            68899999999999997 555544444333333333578999999999999988 8888999999999999998876558


Q ss_pred             cccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccC
Q 042003           80 LKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL  159 (248)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  159 (248)
                      ......+.+. .+.++|++++|||+.......+....+++..+...+++....+++++++.|...++|++.+.+++....
T Consensus       251 ~D~S~rI~~~-lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~t  329 (477)
T KOG0332|consen  251 QDQSIRIMRS-LPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLT  329 (477)
T ss_pred             cccchhhhhh-cCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhhh
Confidence            8888888887 568999999999999999999999999999999999999999999999999999999999999998877


Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD  239 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~  239 (248)
                      -++.+|||.+++.|+.+++.+.+.|+.|..+||.|..++|..+++.|++|..+|||+|+++++|||++.+++|||||+|.
T Consensus       330 igqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~  409 (477)
T KOG0332|consen  330 IGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPV  409 (477)
T ss_pred             hhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCcc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999996


Q ss_pred             ------CcccceecC
Q 042003          240 ------SGAAYIHRI  248 (248)
Q Consensus       240 ------~~~~~~qri  248 (248)
                            +..+|+|||
T Consensus       410 ~~~~~pD~etYlHRi  424 (477)
T KOG0332|consen  410 KYTGEPDYETYLHRI  424 (477)
T ss_pred             ccCCCCCHHHHHHHh
Confidence                  567999997

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

Probab=100.00  E-value=1.3e-38  Score=245.21  Aligned_cols=244  Identities=25%  Similarity=0.308  Sum_probs=204.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcC----CcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRK----KIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~----~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+.+.|..+++..+ .++..++||.   .+...+..++|++|+||+++...+..+    ...+++++++|+|||+.+
T Consensus        87 LA~QiaEQF~alGk~l~-lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrv  165 (442)
T KOG0340|consen   87 LALQIAEQFIALGKLLN-LKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRV  165 (442)
T ss_pred             HHHHHHHHHHHhccccc-ceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhh
Confidence            68999999999999999 7777777776   666778889999999999999999875    235899999999999999


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCC--cEEEEEcccccccccceeEEEEcCCchhHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHD--AVRVIVGRKNTASESIKQKLVFAGSEEGKLLAL  151 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  151 (248)
                      .+.. |-..+..+.+. .+...|.+++|||+++...++...-..+  ...+...........+.+.++.++.. .+...+
T Consensus       166 L~~~-f~d~L~~i~e~-lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~-vkdaYL  242 (442)
T KOG0340|consen  166 LAGC-FPDILEGIEEC-LPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSID-VKDAYL  242 (442)
T ss_pred             hccc-hhhHHhhhhcc-CCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchh-hhHHHH
Confidence            9877 88888888777 5666899999999988666665443333  33344445555566677777665554 355555


Q ss_pred             HHHHhcc---CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCC
Q 042003          152 RQSFAES---LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKG  228 (248)
Q Consensus       152 ~~~~~~~---~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~  228 (248)
                      ...+...   +.+.++||+++-.+|+.++..|+..++.+..+||.|++.+|...+..|+++..+|||||+++++|+|||.
T Consensus       243 v~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~  322 (442)
T KOG0340|consen  243 VHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPT  322 (442)
T ss_pred             HHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCc
Confidence            5555543   3568999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcEEEeccCCCCcccceecC
Q 042003          229 VNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       229 ~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++.|||||.|.++.+|+||+
T Consensus       323 V~LVvN~diPr~P~~yiHRv  342 (442)
T KOG0340|consen  323 VELVVNHDIPRDPKDYIHRV  342 (442)
T ss_pred             eeEEEecCCCCCHHHHHHhh
Confidence            99999999999999999996

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

Probab=100.00  E-value=5.3e-40  Score=256.05  Aligned_cols=244  Identities=33%  Similarity=0.513  Sum_probs=219.2

Q ss_pred             CcchHHHHHHHhhcC-----CCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKG-----NKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~-----~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~   72 (248)
                      ||.|++..+..+...     .+..+..++.||.   ++-+..+.+.+|+|+||++|.+++....++++-++++.+|||++
T Consensus       258 LArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADR  337 (610)
T KOG0341|consen  258 LARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADR  337 (610)
T ss_pred             HHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHhhhhhHHH
Confidence            678888888876443     3345666666666   55666788999999999999999999999999999999999999


Q ss_pred             ccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHH
Q 042003           73 LFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALR  152 (248)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  152 (248)
                      +.+-| |...+..++..+ ....|++++|||+|...+.+.+.-+-+|+++.+++.....-++.+..-|+.... |+..++
T Consensus       338 miDmG-FEddir~iF~~F-K~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyVkqEa-KiVylL  414 (610)
T KOG0341|consen  338 MIDMG-FEDDIRTIFSFF-KGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYVKQEA-KIVYLL  414 (610)
T ss_pred             Hhhcc-chhhHHHHHHHH-hhhhheeeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHHHHhhh-hhhhHH
Confidence            99999 999999999985 456899999999999999999999999999999999888888877776666654 888888


Q ss_pred             HHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEE
Q 042003          153 QSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV  232 (248)
Q Consensus       153 ~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~V  232 (248)
                      +.+.+. ..+++|||..+.++..++++|.-+|..+..+|||-++++|...++.|+.|+.+|||+|++++.|+|+|++.||
T Consensus       415 eCLQKT-~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHV  493 (610)
T KOG0341|consen  415 ECLQKT-SPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHV  493 (610)
T ss_pred             HHhccC-CCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhh
Confidence            888887 5799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccCCCCcccceecC
Q 042003          233 INYDFPDSGAAYIHRI  248 (248)
Q Consensus       233 i~~~~p~~~~~~~qri  248 (248)
                      ||||+|..+..|.|||
T Consensus       494 INyDMP~eIENYVHRI  509 (610)
T KOG0341|consen  494 INYDMPEEIENYVHRI  509 (610)
T ss_pred             ccCCChHHHHHHHHHh
Confidence            9999999999999997

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=2.1e-37  Score=254.75  Aligned_cols=247  Identities=28%  Similarity=0.342  Sum_probs=226.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      ||.|+.++++++++.+.-..+..+.||.  .......+.++|+|+||+++..++..+-++.++++++|+||||.+.+.++
T Consensus       105 iaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~s  184 (980)
T KOG4284|consen  105 IAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTES  184 (980)
T ss_pred             hhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhhceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhchhh
Confidence            5789999999999987557777777777  33344456799999999999999999999999999999999999999888


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCc-------hhHHHHH
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSE-------EGKLLAL  151 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~l  151 (248)
                      |...+..+... .+...|++++|||.|..+.+....++.+|..+.........-+++++++.....       ..|+..|
T Consensus       185 fq~~In~ii~s-lP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L  263 (980)
T KOG4284|consen  185 FQDDINIIINS-LPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKL  263 (980)
T ss_pred             HHHHHHHHHHh-cchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHH
Confidence            99999999998 678899999999999999999999999999999988888888999988766654       3577888


Q ss_pred             HHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcE
Q 042003          152 RQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC  231 (248)
Q Consensus       152 ~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~  231 (248)
                      ..+++..+..++||||+....|+-++..|...|+.|-.++|.|++.+|..+++.++.-..+|||+|+..++|||-|.++.
T Consensus       264 ~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNL  343 (980)
T KOG4284|consen  264 THVFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNL  343 (980)
T ss_pred             HHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccce
Confidence            88888888889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccCCCCcccceecC
Q 042003          232 VINYDFPDSGAAYIHRI  248 (248)
Q Consensus       232 Vi~~~~p~~~~~~~qri  248 (248)
                      |||.|+|.+..+|+|||
T Consensus       344 VVNiD~p~d~eTY~HRI  360 (980)
T KOG4284|consen  344 VVNIDAPADEETYFHRI  360 (980)
T ss_pred             EEecCCCcchHHHHHHh
Confidence            99999999999999997

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

Probab=100.00  E-value=3.3e-37  Score=248.69  Aligned_cols=246  Identities=29%  Similarity=0.405  Sum_probs=201.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhc-CCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~-~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      ||.|+|+.++++.+.+-|++.+.+.||.   ...-.+..+++|+|+||++|.+.+.+ ..+.+++++++|+||+|++++-
T Consensus       223 L~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrlleL  302 (708)
T KOG0348|consen  223 LALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLEL  302 (708)
T ss_pred             HHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEecchhHHHhc
Confidence            7899999999999999999888877776   44445778999999999999999998 4677899999999999999999


Q ss_pred             CcccccchhHhhhCCC------------ccceeEEEEeecCchHHHHHHHhcCCcEEEEEccc-----------------
Q 042003           77 GNLLKHIDPVVKACSN------------PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK-----------------  127 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~------------~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-----------------  127 (248)
                      | |...+..|++...+            ...|.+++|||++....++...-+.||..+..+..                 
T Consensus       303 G-fekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~~  381 (708)
T KOG0348|consen  303 G-FEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDDG  381 (708)
T ss_pred             c-chhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhcCCc
Confidence            9 99999888877522            13677899999999999999888888887762110                 


Q ss_pred             --------ccccccceeEEEEcCCchhHHHHHHHHH----hccCCCCEEEEecchHHHHHHHHHhhc-------------
Q 042003          128 --------NTASESIKQKLVFAGSEEGKLLALRQSF----AESLNPPVLIFVQSKERAKELYGELAF-------------  182 (248)
Q Consensus       128 --------~~~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~~~~~~liF~~~~~~~~~l~~~L~~-------------  182 (248)
                              ...+.++.+.+.-++..- ++-.|..++    +.....|+|||+++.+.++.-|..|..             
T Consensus       382 ~~~~~l~~~~iPeqL~qry~vVPpKL-RLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~  460 (708)
T KOG0348|consen  382 PAGDKLDSFAIPEQLLQRYTVVPPKL-RLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAP  460 (708)
T ss_pred             ccccccccccCcHHhhhceEecCCch-hHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCc
Confidence                    112233445555454443 444444433    444467999999999999988888753             


Q ss_pred             ---------CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          183 ---------DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       183 ---------~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                               .+.++..+||+|++++|..+++.|...+-.||+||+++++|+|+|++++||+||+|.+..+|+|||
T Consensus       461 ~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRv  535 (708)
T KOG0348|consen  461 DSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRV  535 (708)
T ss_pred             ccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHh
Confidence                     135789999999999999999999999999999999999999999999999999999999999997

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.2e-37  Score=252.03  Aligned_cols=243  Identities=28%  Similarity=0.358  Sum_probs=192.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCc---ccCceeEEEEecccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKI---DLSRVEYLVLDEADKLF   74 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~---~~~~~~~lIiDEah~~~   74 (248)
                      ||.|+.+-+..+.+..+ +++..+.||.   .|..++...++|+|+||++||.++..+..   .++++.++|+||||++.
T Consensus       275 La~QV~~Hl~ai~~~t~-i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~k~vkcLVlDEaDRmv  353 (731)
T KOG0347|consen  275 LAHQVKQHLKAIAEKTQ-IRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRMV  353 (731)
T ss_pred             HHHHHHHHHHHhccccC-eEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhhhhceEEEEccHHHHh
Confidence            68999999999999999 6666666665   56677888999999999999999988654   57889999999999999


Q ss_pred             ccCcccccchhHhhhCC----CccceeEEEEeecCc---------------------hHHHHHHH--hcCCcEEEEEccc
Q 042003           75 EVGNLLKHIDPVVKACS----NPSIVRSLFSATLPD---------------------FVEELARS--IMHDAVRVIVGRK  127 (248)
Q Consensus        75 ~~~~~~~~~~~~~~~~~----~~~~~~i~~SAT~~~---------------------~~~~~~~~--~~~~~~~~~~~~~  127 (248)
                      +.| .+..+..+++.+.    ....|.+.+|||++-                     .++.+...  +.++|..+...+.
T Consensus       354 ekg-hF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpkiiD~t~q  432 (731)
T KOG0347|consen  354 EKG-HFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGKPKIIDLTPQ  432 (731)
T ss_pred             hhc-cHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccCCCeeEecCcc
Confidence            999 7777777776644    345799999999852                     12222222  2234555555444


Q ss_pred             ccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhh
Q 042003          128 NTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFR  207 (248)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~  207 (248)
                      ......+....+.| ...+|--.|..++..+ +++++||||+++.+.+++-.|+..++....+|+.|.+..|...++.|+
T Consensus       433 ~~ta~~l~Es~I~C-~~~eKD~ylyYfl~ry-PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~  510 (731)
T KOG0347|consen  433 SATASTLTESLIEC-PPLEKDLYLYYFLTRY-PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFK  510 (731)
T ss_pred             hhHHHHHHHHhhcC-CccccceeEEEEEeec-CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHh
Confidence            44444443333333 2222333333344444 789999999999999999999999999999999999999999999999


Q ss_pred             cCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceec
Q 042003          208 AGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHR  247 (248)
Q Consensus       208 ~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qr  247 (248)
                      +....|||||+++++|+|||++.|||||-.|.+..-|+||
T Consensus       511 ~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHR  550 (731)
T KOG0347|consen  511 QSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHR  550 (731)
T ss_pred             cCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEec
Confidence            9999999999999999999999999999999999999998

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

Probab=100.00  E-value=5.5e-36  Score=233.22  Aligned_cols=242  Identities=30%  Similarity=0.455  Sum_probs=221.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh----hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV----RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      ||.|+.+....++...+ ..+..+.|+.    ....+....++|+++||+++..++....+..+.++++++|||+.++..
T Consensus       106 La~qi~~v~~~lg~~~~-~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~  184 (397)
T KOG0327|consen  106 LAQQIQKVVRALGDHMD-VSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSR  184 (397)
T ss_pred             HHHHHHHHHHhhhcccc-eeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHhhhcc
Confidence            68899999999999998 5566554444    223345557999999999999999999888899999999999999999


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHh
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA  156 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  156 (248)
                      | |...+..+... .+++.|++++|||.|.+..+..+.++.+|..+.....+.....+++++......+ |+..+..+..
T Consensus       185 g-fkdqI~~if~~-lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~-k~~~l~dl~~  261 (397)
T KOG0327|consen  185 G-FKDQIYDIFQE-LPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEE-KLDTLCDLYR  261 (397)
T ss_pred             c-hHHHHHHHHHH-cCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccc-cccHHHHHHH
Confidence            9 99999999999 6778899999999999999999999999999999999988899999998887776 9999999998


Q ss_pred             ccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          157 ESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       157 ~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                        .-...+||||+++.+..+...|...+..+..+||.|.+.+|..+.+.|+.|..++||+|+.+++|+|+.+++.||+|+
T Consensus       262 --~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinyd  339 (397)
T KOG0327|consen  262 --RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYD  339 (397)
T ss_pred             --hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeec
Confidence              368999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccceecC
Q 042003          237 FPDSGAAYIHRI  248 (248)
Q Consensus       237 ~p~~~~~~~qri  248 (248)
                      .|.+...|+||+
T Consensus       340 lP~~~~~yihR~  351 (397)
T KOG0327|consen  340 LPARKENYIHRI  351 (397)
T ss_pred             cccchhhhhhhc
Confidence            999999999996

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

Probab=100.00  E-value=7.9e-35  Score=255.87  Aligned_cols=239  Identities=19%  Similarity=0.219  Sum_probs=177.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcCC----cccCceeEEEEecccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRKK----IDLSRVEYLVLDEADKLF   74 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~~----~~~~~~~~lIiDEah~~~   74 (248)
                      ||.|+.+.+++++ ..+ ..+..+.|+.  .+......+++|+|+||+++...+....    ..+++++++|+||||.+.
T Consensus        93 La~q~~~~l~~l~-~~~-i~v~~~~Gdt~~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~  170 (742)
T TIGR03817        93 LAADQLRAVRELT-LRG-VRPATYDGDTPTEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYR  170 (742)
T ss_pred             HHHHHHHHHHHhc-cCC-eEEEEEeCCCCHHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhcc
Confidence            6899999999987 334 5566666665  3334456679999999999875443221    237899999999999986


Q ss_pred             ccCcccccchhHhhh----C--CCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCC-----
Q 042003           75 EVGNLLKHIDPVVKA----C--SNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS-----  143 (248)
Q Consensus        75 ~~~~~~~~~~~~~~~----~--~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----  143 (248)
                      + . |...+..+++.    +  ...++|++++|||+++.. +...++++.+..+. .....+... .+...+...     
T Consensus       171 g-~-fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~-~~~~~l~g~~~~~i-~~~~~~~~~-~~~~~~~p~~~~~~  245 (742)
T TIGR03817       171 G-V-FGSHVALVLRRLRRLCARYGASPVFVLASATTADPA-AAASRLIGAPVVAV-TEDGSPRGA-RTVALWEPPLTELT  245 (742)
T ss_pred             C-c-cHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHH-HHHHHHcCCCeEEE-CCCCCCcCc-eEEEEecCCccccc
Confidence            5 2 44443333222    1  235689999999999864 46677777775543 222222221 222222111     


Q ss_pred             -----------chhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC--------CCeeEEEecCCCHHHHHHHHH
Q 042003          144 -----------EEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD--------GIRAGVIHSDLSQTQRENAVD  204 (248)
Q Consensus       144 -----------~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--------~~~v~~~~~~~~~~~r~~~~~  204 (248)
                                 ...+...+..+++.  +.++||||+|++.++.+++.|++.        +.++..+||++++++|.++++
T Consensus       246 ~~~~~~~r~~~~~~~~~~l~~l~~~--~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~  323 (742)
T TIGR03817       246 GENGAPVRRSASAEAADLLADLVAE--GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELER  323 (742)
T ss_pred             cccccccccchHHHHHHHHHHHHHC--CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHH
Confidence                       12455566666664  579999999999999999988653        567899999999999999999


Q ss_pred             HhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          205 DFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       205 ~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      .|++|+.++||||+++++|||+|++++||++|.|.+..+|+||+
T Consensus       324 ~f~~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRi  367 (742)
T TIGR03817       324 ALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQA  367 (742)
T ss_pred             HHHcCCceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhc
Confidence            99999999999999999999999999999999999999999996

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=5.7e-34  Score=240.87  Aligned_cols=208  Identities=18%  Similarity=0.233  Sum_probs=156.4

Q ss_pred             ccCCCcEEEeChHHHHHHH-hcCCc-ccCceeEEEEeccccccccC-cccccchhH---hhhCCCccceeEEEEeecCch
Q 042003           34 SKFSCDILISTPLRLRLAI-RRKKI-DLSRVEYLVLDEADKLFEVG-NLLKHIDPV---VKACSNPSIVRSLFSATLPDF  107 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~-~~~~~-~~~~~~~lIiDEah~~~~~~-~~~~~~~~~---~~~~~~~~~~~i~~SAT~~~~  107 (248)
                      ..+.++++++||+++.... ....+ ...+++++||||||++.+|| .|+..+..+   ...  .+..+++++|||+++.
T Consensus        98 ~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~~l~~~--~~~~~~l~lTAT~~~~  175 (470)
T TIGR00614        98 KDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQK--FPNVPIMALTATASPS  175 (470)
T ss_pred             hcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHHHHHHH--cCCCceEEEecCCCHH
Confidence            3456899999999875432 11122 46789999999999999987 355554443   333  2467899999999987


Q ss_pred             HHHHHHHhc--CCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHh-ccCCCCEEEEecchHHHHHHHHHhhcCC
Q 042003          108 VEELARSIM--HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA-ESLNPPVLIFVQSKERAKELYGELAFDG  184 (248)
Q Consensus       108 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~liF~~~~~~~~~l~~~L~~~~  184 (248)
                      ........+  .++..+....   ..+++.....  .........+..++. ...++++||||+++++++.+++.|++.+
T Consensus       176 ~~~di~~~l~l~~~~~~~~s~---~r~nl~~~v~--~~~~~~~~~l~~~l~~~~~~~~~IIF~~s~~~~e~la~~L~~~g  250 (470)
T TIGR00614       176 VREDILRQLNLKNPQIFCTSF---DRPNLYYEVR--RKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLG  250 (470)
T ss_pred             HHHHHHHHcCCCCCcEEeCCC---CCCCcEEEEE--eCCccHHHHHHHHHHHhcCCCceEEEECcHHHHHHHHHHHHhcC
Confidence            765554433  2333332211   1222222221  122235556666665 3445667999999999999999999999


Q ss_pred             CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          185 IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       185 ~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +++..+||+|++++|+.+++.|++|+.+|||||+++++|+|+|++++||++++|.|+..|+||+
T Consensus       251 ~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~  314 (470)
T TIGR00614       251 IAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQES  314 (470)
T ss_pred             CCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHHhhh
Confidence            9999999999999999999999999999999999999999999999999999999999999996

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

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.3e-34  Score=228.82  Aligned_cols=245  Identities=28%  Similarity=0.358  Sum_probs=209.3

Q ss_pred             CcchHHHHHHHhhcCCC-cEEEEccc-ch--hhhcccccCCCcEEEeChHHHHHHHhcCC-cccCceeEEEEeccccccc
Q 042003            1 LATQTTRECKKLAKGNK-FQIKLMKK-EL--VRSTDLSKFSCDILISTPLRLRLAIRRKK-IDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~-~~~~~~~~-~~--~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~-~~~~~~~~lIiDEah~~~~   75 (248)
                      ||+|++..+.++....+ .+.+.-+. ..  ......+...|+|+|+||+.+++++..+. ..++.+.++|+||||.+++
T Consensus       105 L~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDEADLlls  184 (569)
T KOG0346|consen  105 LAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDEADLLLS  184 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEechhhhhhh
Confidence            68999999999877664 22222222 11  23445677789999999999999999877 6789999999999999999


Q ss_pred             cCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccc-cccceeEEEEcCCchhHHHHHHHH
Q 042003           76 VGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTA-SESIKQKLVFAGSEEGKLLALRQS  154 (248)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~  154 (248)
                      -| |...+..+.+. .++..|-++||||++..+..+...++.+|..+.....+.+ ..++.++.+.|+ ..+|...+..+
T Consensus       185 fG-Yeedlk~l~~~-LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cs-e~DKflllyal  261 (569)
T KOG0346|consen  185 FG-YEEDLKKLRSH-LPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCS-EEDKFLLLYAL  261 (569)
T ss_pred             cc-cHHHHHHHHHh-CCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEec-cchhHHHHHHH
Confidence            99 99999999999 6788999999999999999999999999998877665554 456778888787 55577766666


Q ss_pred             Hhc-cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec---------------
Q 042003          155 FAE-SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD---------------  218 (248)
Q Consensus       155 ~~~-~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~---------------  218 (248)
                      ++- ...+|++||+|+.+.|.++.-.|+..|++..+++|.||..-|..++++|..|-.+++|||+               
T Consensus       262 lKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk  341 (569)
T KOG0346|consen  262 LKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGK  341 (569)
T ss_pred             HHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhcccccc
Confidence            653 3478999999999999999999999999999999999999999999999999999999999               


Q ss_pred             --------------------ccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          219 --------------------VIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       219 --------------------~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                                          ..++|||+..+..|+|||+|.+...|+|||
T Consensus       342 ~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRv  391 (569)
T KOG0346|consen  342 SDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRV  391 (569)
T ss_pred             ccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhc
Confidence                                235899999999999999999999999996

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

Probab=100.00  E-value=2e-34  Score=226.67  Aligned_cols=244  Identities=33%  Similarity=0.410  Sum_probs=217.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+.+.++.++++.+ ..+.+.+|+.   ++...+..++||+++||+++..+...-.+.++.+.++|+||++.++..|
T Consensus       102 La~qtlkvvkdlgrgt~-lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfemg  180 (529)
T KOG0337|consen  102 LALQTLKVVKDLGRGTK-LRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMG  180 (529)
T ss_pred             HHHHHHHHHHHhccccc-hhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhhh
Confidence            68999999999999999 5555555544   6777788899999999999998888777889999999999999999998


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                       |...+.+++.. .+...|.++||||+|..+-...++.+.+|..+..+.+......++..+..+ ..++|...|+.++..
T Consensus       181 -fqeql~e~l~r-l~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~-~~a~K~aaLl~il~~  257 (529)
T KOG0337|consen  181 -FQEQLHEILSR-LPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRV-RKAEKEAALLSILGG  257 (529)
T ss_pred             -hHHHHHHHHHh-CCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeee-ccHHHHHHHHHHHhc
Confidence             99999999999 555669999999999999999999989998888777666666666666544 455699999998887


Q ss_pred             cC-CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          158 SL-NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       158 ~~-~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      .. +++++||+.+..+++.+.+.|++.|+.+..+.|+|+++.|..-...|+.++..++|.|+.+++|+|+|-.+.||+||
T Consensus       258 ~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd  337 (529)
T KOG0337|consen  258 RIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYD  337 (529)
T ss_pred             cccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCcccccccccc
Confidence            64 35899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccceecC
Q 042003          237 FPDSGAAYIHRI  248 (248)
Q Consensus       237 ~p~~~~~~~qri  248 (248)
                      .|.+..-|+||+
T Consensus       338 ~p~~~klFvhRV  349 (529)
T KOG0337|consen  338 FPPDDKLFVHRV  349 (529)
T ss_pred             CCCCCceEEEEe
Confidence            999999999996

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=100.00  E-value=1.8e-33  Score=256.67  Aligned_cols=241  Identities=22%  Similarity=0.235  Sum_probs=172.5

Q ss_pred             CcchHHHHHHHhhc------------CCCcEEEEcccchhhhc---ccccCCCcEEEeChHHHHHHHhcC-CcccCceeE
Q 042003            1 LATQTTRECKKLAK------------GNKFQIKLMKKELVRST---DLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEY   64 (248)
Q Consensus         1 L~~Q~~~~~~~~~~------------~~~~~~~~~~~~~~~~~---~~~~~~~~i~v~Tp~~l~~~~~~~-~~~~~~~~~   64 (248)
                      |+.|+++.++....            ..+ +++....|+....   .+..+.++|+|+||+++..++.+. ...++++++
T Consensus        49 La~Dv~~~L~~pl~~i~~~~~~~g~~~~~-i~V~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~  127 (1490)
T PRK09751         49 LGTDVQRNLQIPLKGIADERRRRGETEVN-LRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVET  127 (1490)
T ss_pred             HHHHHHHHHHHHHHhhhhhhhhcccccCc-eEEEEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCE
Confidence            57788887764221            234 6777777776332   345668999999999999887653 346899999


Q ss_pred             EEEeccccccccC--c-ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCC-cEEEEEcccccccccceeEEEE
Q 042003           65 LVLDEADKLFEVG--N-LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHD-AVRVIVGRKNTASESIKQKLVF  140 (248)
Q Consensus        65 lIiDEah~~~~~~--~-~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  140 (248)
                      |||||+|.+.+..  . +...+.++... ...+.|+|++|||+++ .+++..++.++ +..+.. ........+. ....
T Consensus       128 VIVDE~H~L~g~kRG~~Lel~LeRL~~l-~~~~~QrIgLSATI~n-~eevA~~L~g~~pv~Iv~-~~~~r~~~l~-v~vp  203 (1490)
T PRK09751        128 VIIDEVHAVAGSKRGAHLALSLERLDAL-LHTSAQRIGLSATVRS-ASDVAAFLGGDRPVTVVN-PPAMRHPQIR-IVVP  203 (1490)
T ss_pred             EEEecHHHhcccccccHHHHHHHHHHHh-CCCCCeEEEEEeeCCC-HHHHHHHhcCCCCEEEEC-CCCCcccceE-EEEe
Confidence            9999999998643  1 22244444444 4567899999999988 56777766543 444432 2222222222 1222


Q ss_pred             cCCch-------------------h----HHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCC-------------
Q 042003          141 AGSEE-------------------G----KLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDG-------------  184 (248)
Q Consensus       141 ~~~~~-------------------~----~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~-------------  184 (248)
                      ..+..                   .    ....+...+.  .++++||||||++.|+.++..|++..             
T Consensus       204 ~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~il~~i~--~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~  281 (1490)
T PRK09751        204 VANMDDVSSVASGTGEDSHAGREGSIWPYIETGILDEVL--RHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVD  281 (1490)
T ss_pred             cCchhhccccccccccccchhhhhhhhHHHHHHHHHHHh--cCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccch
Confidence            21110                   0    0011222222  25799999999999999999987531             


Q ss_pred             --------------------CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccc
Q 042003          185 --------------------IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAY  244 (248)
Q Consensus       185 --------------------~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~  244 (248)
                                          ..+..+||+|++++|..+++.|++|++++||||++++.|||+|++++||+++.|.|+.+|
T Consensus       282 ~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~  361 (1490)
T PRK09751        282 AAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASG  361 (1490)
T ss_pred             hhhhhhccccchhccccccceeeeeccccCCHHHHHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHH
Confidence                                126789999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC
Q 042003          245 IHRI  248 (248)
Q Consensus       245 ~qri  248 (248)
                      +||+
T Consensus       362 LQRi  365 (1490)
T PRK09751        362 LQRI  365 (1490)
T ss_pred             HHHh
Confidence            9996

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=6.5e-34  Score=245.59  Aligned_cols=245  Identities=32%  Similarity=0.510  Sum_probs=221.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcc---cCceeEEEEecccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKID---LSRVEYLVLDEADKLF   74 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~---~~~~~~lIiDEah~~~   74 (248)
                      ||.|+.+++++|.+.++ +.+.++||+.   .+...++.++.|+||||+++.+++..+.-.   +++..++|+||||+++
T Consensus       450 la~QI~r~~~kf~k~l~-ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmf  528 (997)
T KOG0334|consen  450 LAMQIHREVRKFLKLLG-IRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMF  528 (997)
T ss_pred             HHHHHHHHHHHHHhhcC-ceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhhh
Confidence            68999999999999999 6777777776   445557778999999999999999876554   4455599999999999


Q ss_pred             ccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHH
Q 042003           75 EVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS  154 (248)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  154 (248)
                      +-+ |.+....++.. ..+..|++++|||+|..++.+.+..+..|..+.++........+.+.+.-+...++|+..|.++
T Consensus       529 dmg-fePq~~~Ii~n-lrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~eL  606 (997)
T KOG0334|consen  529 DMG-FEPQITRILQN-LRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLEL  606 (997)
T ss_pred             eec-cCcccchHHhh-cchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHHH
Confidence            777 99988888888 5888999999999999999999998889999999988888888988888888788899999988


Q ss_pred             HhccC-CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEE
Q 042003          155 FAESL-NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI  233 (248)
Q Consensus       155 ~~~~~-~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi  233 (248)
                      +.... ..+++|||.+.+.|..+.+.|.+.++.|..+||+.++.+|..++++|++|..++||+|+.+++|+|++++..||
T Consensus       607 l~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvv  686 (997)
T KOG0334|consen  607 LGERYEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVV  686 (997)
T ss_pred             HHHHhhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEE
Confidence            87544 67999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCcccceecC
Q 042003          234 NYDFPDSGAAYIHRI  248 (248)
Q Consensus       234 ~~~~p~~~~~~~qri  248 (248)
                      ||++|....+|.||+
T Consensus       687 nyd~pnh~edyvhR~  701 (997)
T KOG0334|consen  687 NYDFPNHYEDYVHRV  701 (997)
T ss_pred             EcccchhHHHHHHHh
Confidence            999999999999985

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

Probab=100.00  E-value=3e-34  Score=234.19  Aligned_cols=248  Identities=53%  Similarity=0.810  Sum_probs=221.4

Q ss_pred             CcchHHHHHHHhh--cCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCC--cccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLA--KGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKK--IDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~--~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~--~~~~~~~~lIiDEah~~   73 (248)
                      ||.|++..++++.  ++.++.....-+...   .........++++|+||.++...+..+.  ++++++.++|+||++++
T Consensus       221 La~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~l  300 (593)
T KOG0344|consen  221 LAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLL  300 (593)
T ss_pred             HHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhh
Confidence            6889999999998  666633333322222   1122233468999999999999998875  68999999999999999


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  153 (248)
                      +++..|..++..+...|.++...+-++|||.+...+++......++..+.++..+.....+.+..+++.....|+-.+.+
T Consensus       301 fe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq  380 (593)
T KOG0344|consen  301 FEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALRQ  380 (593)
T ss_pred             hChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecchhHhhhhhhhheeeecchhHHHHHHH
Confidence            99833999999999999888888889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccCCCCEEEEecchHHHHHHHHHh-hcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEE
Q 042003          154 SFAESLNPPVLIFVQSKERAKELYGEL-AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV  232 (248)
Q Consensus       154 ~~~~~~~~~~liF~~~~~~~~~l~~~L-~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~V  232 (248)
                      ++......+++||+.+.+.|.++++.| ...++.+.++||+.++.+|.+.+++|+.|++++|+||+++++|+|+.+++.|
T Consensus       381 ~v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~V  460 (593)
T KOG0344|consen  381 LVASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLV  460 (593)
T ss_pred             HHhccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceE
Confidence            999988899999999999999999999 6778999999999999999999999999999999999999999999999999


Q ss_pred             EeccCCCCcccceecC
Q 042003          233 INYDFPDSGAAYIHRI  248 (248)
Q Consensus       233 i~~~~p~~~~~~~qri  248 (248)
                      |+||.|.+..+|+|||
T Consensus       461 InyD~p~s~~syihrI  476 (593)
T KOG0344|consen  461 INYDFPQSDLSYIHRI  476 (593)
T ss_pred             EecCCCchhHHHHHHh
Confidence            9999999999999997

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=3.4e-33  Score=242.03  Aligned_cols=207  Identities=18%  Similarity=0.247  Sum_probs=158.0

Q ss_pred             ccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC-cccccchhH---hhhCCCccceeEEEEeecCchHH
Q 042003           34 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPV---VKACSNPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~-~~~~~~~~~---~~~~~~~~~~~i~~SAT~~~~~~  109 (248)
                      ..+..+++++||+++........+...+++++||||||++.+|| +|+..+..+   ...  .+..+++++|||+++...
T Consensus       112 ~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~y~~L~~l~~~--~p~~~~v~lTAT~~~~~~  189 (607)
T PRK11057        112 RTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFRPEYAALGQLRQR--FPTLPFMALTATADDTTR  189 (607)
T ss_pred             hCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcccHHHHHHHHHHHh--CCCCcEEEEecCCChhHH
Confidence            34568999999999874333333445678999999999999987 355444433   333  246789999999998765


Q ss_pred             HHHHHhc--CCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCee
Q 042003          110 ELARSIM--HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRA  187 (248)
Q Consensus       110 ~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v  187 (248)
                      ......+  .++.... ...  ..+++....   .....+...+..++....++++||||+|+++|+.+++.|++.++++
T Consensus       190 ~di~~~l~l~~~~~~~-~~~--~r~nl~~~v---~~~~~~~~~l~~~l~~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v  263 (607)
T PRK11057        190 QDIVRLLGLNDPLIQI-SSF--DRPNIRYTL---VEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSRGISA  263 (607)
T ss_pred             HHHHHHhCCCCeEEEE-CCC--CCCcceeee---eeccchHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCE
Confidence            5443332  3333222 211  122222221   1222345666777776667899999999999999999999999999


Q ss_pred             EEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          188 GVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       188 ~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ..+||+|++++|..+++.|++|+.+|||||+++++|||+|++++||+||+|.|...|+||+
T Consensus       264 ~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~  324 (607)
T PRK11057        264 AAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQET  324 (607)
T ss_pred             EEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999999999985

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=3e-33  Score=242.75  Aligned_cols=209  Identities=21%  Similarity=0.277  Sum_probs=162.3

Q ss_pred             ccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC-cccccchhHhhhCC-CccceeEEEEeecCchHHHH
Q 042003           34 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKACS-NPSIVRSLFSATLPDFVEEL  111 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~-~~~~~~~~~~~~~~-~~~~~~i~~SAT~~~~~~~~  111 (248)
                      ..+..+++++||+++.+....+.+...+++++|+||||++.+|| .|+..+..+..... -+..+++++|||+++.....
T Consensus       100 ~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l~~l~~~~~~~~vi~lTAT~~~~~~~~  179 (591)
T TIGR01389       100 VNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQVPRIALTATADAETRQD  179 (591)
T ss_pred             hCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHHHHHHHhCCCCCEEEEEeCCCHHHHHH
Confidence            44578999999999876554445556789999999999999887 35555544433211 12345899999999877765


Q ss_pred             HHHhcC--CcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEE
Q 042003          112 ARSIMH--DAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGV  189 (248)
Q Consensus       112 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~  189 (248)
                      ....++  ++..+. ..  ...+++....   .....+...+.+++....+.++||||++++.++.+++.|...++++..
T Consensus       180 i~~~l~~~~~~~~~-~~--~~r~nl~~~v---~~~~~~~~~l~~~l~~~~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~  253 (591)
T TIGR01389       180 IRELLRLADANEFI-TS--FDRPNLRFSV---VKKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALA  253 (591)
T ss_pred             HHHHcCCCCCCeEe-cC--CCCCCcEEEE---EeCCCHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEE
Confidence            555443  332222 11  1122222222   223346677777777766789999999999999999999999999999


Q ss_pred             EecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          190 IHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       190 ~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +||+|+.++|+.+++.|.+|+++|||||+++++|||+|++++||+|++|.|...|.||+
T Consensus       254 ~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~  312 (591)
T TIGR01389       254 YHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEA  312 (591)
T ss_pred             EECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhh
Confidence            99999999999999999999999999999999999999999999999999999999985

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.

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

Probab=100.00  E-value=9.7e-33  Score=243.66  Aligned_cols=208  Identities=17%  Similarity=0.187  Sum_probs=155.5

Q ss_pred             CCCcEEEeChHHHHH--HHhc---CCcccCceeEEEEeccccccccC-cccccchhH--hhhCCCccceeEEEEeecCch
Q 042003           36 FSCDILISTPLRLRL--AIRR---KKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPV--VKACSNPSIVRSLFSATLPDF  107 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~--~~~~---~~~~~~~~~~lIiDEah~~~~~~-~~~~~~~~~--~~~~~~~~~~~i~~SAT~~~~  107 (248)
                      +.++|+++||+++..  .+.+   .......+.++||||||++.+|| +|+..+..+  +.. ..+..+++++|||+++.
T Consensus       551 g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~-~fp~vPilALTATAT~~  629 (1195)
T PLN03137        551 SKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQ-KFPNIPVLALTATATAS  629 (1195)
T ss_pred             CCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhcccchHHHHHHHHHHHH-hCCCCCeEEEEecCCHH
Confidence            568999999999853  1221   11123558899999999999997 566655543  222 22467889999999988


Q ss_pred             HHHHHHHhcCCc-EEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc-CCCCEEEEecchHHHHHHHHHhhcCCC
Q 042003          108 VEELARSIMHDA-VRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKERAKELYGELAFDGI  185 (248)
Q Consensus       108 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~liF~~~~~~~~~l~~~L~~~~~  185 (248)
                      ....+...++-. ..+...  ....+++...+  ..........+..++... .+.+.||||+++++++.+++.|++.|+
T Consensus       630 V~eDI~~~L~l~~~~vfr~--Sf~RpNL~y~V--v~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gi  705 (1195)
T PLN03137        630 VKEDVVQALGLVNCVVFRQ--SFNRPNLWYSV--VPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGH  705 (1195)
T ss_pred             HHHHHHHHcCCCCcEEeec--ccCccceEEEE--eccchhHHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCC
Confidence            777555443322 222221  12223332222  222222345566666543 356899999999999999999999999


Q ss_pred             eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          186 RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       186 ~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++..+||+|++++|..+++.|.+|+.+|||||+++++|||+|++++||||++|.|+..|+||+
T Consensus       706 ka~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQri  768 (1195)
T PLN03137        706 KAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQEC  768 (1195)
T ss_pred             CeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhh
Confidence            999999999999999999999999999999999999999999999999999999999999995

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=1.2e-32  Score=246.53  Aligned_cols=224  Identities=22%  Similarity=0.288  Sum_probs=160.4

Q ss_pred             EEEEcccchhhh---cccccCCCcEEEeChHHHHHHHhcCCc--ccCceeEEEEeccccccccCcccc----cchhHhhh
Q 042003           19 QIKLMKKELVRS---TDLSKFSCDILISTPLRLRLAIRRKKI--DLSRVEYLVLDEADKLFEVGNLLK----HIDPVVKA   89 (248)
Q Consensus        19 ~~~~~~~~~~~~---~~~~~~~~~i~v~Tp~~l~~~~~~~~~--~~~~~~~lIiDEah~~~~~~~~~~----~~~~~~~~   89 (248)
                      ..+....|+...   .....+.++|+|+||+++..++.....  .+++++++|+||+|.+.+.. +..    .+.++...
T Consensus       125 i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~VVIDE~H~l~~~~-RG~~l~~~L~rL~~l  203 (876)
T PRK13767        125 IRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWVIVDEIHSLAENK-RGVHLSLSLERLEEL  203 (876)
T ss_pred             eeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEEEEechhhhccCc-cHHHHHHHHHHHHHh
Confidence            567777776632   234566899999999999877765433  47899999999999988653 333    23333333


Q ss_pred             CCCccceeEEEEeecCchHHHHHHHhcCC-------cEEEEEcccccccccceeE-----EEEcCC---chhHHHHHHHH
Q 042003           90 CSNPSIVRSLFSATLPDFVEELARSIMHD-------AVRVIVGRKNTASESIKQK-----LVFAGS---EEGKLLALRQS  154 (248)
Q Consensus        90 ~~~~~~~~i~~SAT~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~-----~~~~~~---~~~~~~~l~~~  154 (248)
                       .....|++++|||+++ ......++.+.       +..+..... .....+...     ......   .......+.++
T Consensus       204 -~~~~~q~IglSATl~~-~~~va~~L~~~~~~~~~r~~~iv~~~~-~k~~~i~v~~p~~~l~~~~~~~~~~~l~~~L~~~  280 (876)
T PRK13767        204 -AGGEFVRIGLSATIEP-LEEVAKFLVGYEDDGEPRDCEIVDARF-VKPFDIKVISPVDDLIHTPAEEISEALYETLHEL  280 (876)
T ss_pred             -cCCCCeEEEEecccCC-HHHHHHHhcCccccCCCCceEEEccCC-CccceEEEeccCccccccccchhHHHHHHHHHHH
Confidence             3457899999999987 45555555432       122211111 000000000     000011   11223444444


Q ss_pred             HhccCCCCEEEEecchHHHHHHHHHhhcC------CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCC
Q 042003          155 FAESLNPPVLIFVQSKERAKELYGELAFD------GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKG  228 (248)
Q Consensus       155 ~~~~~~~~~liF~~~~~~~~~l~~~L~~~------~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~  228 (248)
                      ++.  ++++||||||++.|+.++..|++.      +..+..+||++++++|..+++.|++|+.++||||+++++|||+|+
T Consensus       281 i~~--~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~  358 (876)
T PRK13767        281 IKE--HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGY  358 (876)
T ss_pred             Hhc--CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCC
Confidence            444  579999999999999999999863      468999999999999999999999999999999999999999999


Q ss_pred             CcEEEeccCCCCcccceecC
Q 042003          229 VNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       229 ~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +++||+++.|.|+.+|+||+
T Consensus       359 Vd~VI~~~~P~sv~~ylQRi  378 (876)
T PRK13767        359 IDLVVLLGSPKSVSRLLQRI  378 (876)
T ss_pred             CcEEEEeCCCCCHHHHHHhc
Confidence            99999999999999999996

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

Probab=100.00  E-value=4.9e-33  Score=223.02  Aligned_cols=245  Identities=30%  Similarity=0.422  Sum_probs=186.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh----hhcccccCCC----cEEEeChHHHHHHHhc-CCcccCceeEEEEeccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV----RSTDLSKFSC----DILISTPLRLRLAIRR-KKIDLSRVEYLVLDEAD   71 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~----~i~v~Tp~~l~~~~~~-~~~~~~~~~~lIiDEah   71 (248)
                      |+.|++..+.++..+.++. |+...|..    +...+....+    ||+|+||++|.+++.+ ..+.+++++++||||||
T Consensus       227 L~~QV~~~f~~~~~~tgL~-V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEAD  305 (620)
T KOG0350|consen  227 LALQVYDTFKRLNSGTGLA-VCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEAD  305 (620)
T ss_pred             HHHHHHHHHHHhccCCceE-EEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEechHH
Confidence            6889999999999999955 66666655    3333333334    9999999999999996 67899999999999999


Q ss_pred             cccccCcccccchhHhhhCCC---------------------------------ccceeEEEEeecCchHHHHHHHhcCC
Q 042003           72 KLFEVGNLLKHIDPVVKACSN---------------------------------PSIVRSLFSATLPDFVEELARSIMHD  118 (248)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~~---------------------------------~~~~~i~~SAT~~~~~~~~~~~~~~~  118 (248)
                      ++++.. |..|+..+...+..                                 ++.+.+.+|||+......+...-...
T Consensus       306 Rll~qs-fQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~  384 (620)
T KOG0350|consen  306 RLLDQS-FQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHI  384 (620)
T ss_pred             HHHHHH-HHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHHHhhhhcCC
Confidence            998765 55555555444332                                 22345677777776555555554555


Q ss_pred             cEEEEEc----ccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhh----cCCCeeEEE
Q 042003          119 AVRVIVG----RKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELA----FDGIRAGVI  190 (248)
Q Consensus       119 ~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~----~~~~~v~~~  190 (248)
                      |....+.    .....+..+.+....++. ..+-..+..++......++|+|+++.+.+.+++..|+    +.+.++-.+
T Consensus       385 Prl~~v~~~~~~ryslp~~l~~~~vv~~~-~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~  463 (620)
T KOG0350|consen  385 PRLFHVSKPLIGRYSLPSSLSHRLVVTEP-KFKPLAVYALITSNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEF  463 (620)
T ss_pred             CceEEeecccceeeecChhhhhceeeccc-ccchHhHHHHHHHhhcceEEEEecchHHHHHHHHHHHHHhccccchhhhh
Confidence            5333333    122233334444433333 3455666677777778899999999999999999887    346677789


Q ss_pred             ecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       191 ~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      .|+++...|...++.|..|++.+||||+++++|+|+-+++.||+||+|.+..+|+||+
T Consensus       464 t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~  521 (620)
T KOG0350|consen  464 TGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRA  521 (620)
T ss_pred             hhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhh
Confidence            9999999999999999999999999999999999999999999999999999999996

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=5.5e-32  Score=239.77  Aligned_cols=242  Identities=21%  Similarity=0.208  Sum_probs=172.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      ||.|.++.++++.+ .+ .++...+|+..........++|+|+||+++..++.++...+++++++|+||+|.+.+.+ +.
T Consensus        79 La~q~~~~~~~~~~-~g-~~v~~~tGd~~~~~~~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~-rg  155 (737)
T PRK02362         79 LASEKFEEFERFEE-LG-VRVGISTGDYDSRDEWLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSAN-RG  155 (737)
T ss_pred             HHHHHHHHHHHhhc-CC-CEEEEEeCCcCccccccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCc-ch
Confidence            67899999988764 35 55666677664444344568999999999999988766678999999999999998765 66


Q ss_pred             ccchhHhhhC--CCccceeEEEEeecCchHHHHHHHhcCCc-------EEEEEcc--cccccccceeEEEEcCCchhHHH
Q 042003           81 KHIDPVVKAC--SNPSIVRSLFSATLPDFVEELARSIMHDA-------VRVIVGR--KNTASESIKQKLVFAGSEEGKLL  149 (248)
Q Consensus        81 ~~~~~~~~~~--~~~~~~~i~~SAT~~~~~~~~~~~~~~~~-------~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~  149 (248)
                      ..+..++..+  .....|++++|||+++ ..++..|+....       .......  .......-.+............+
T Consensus       156 ~~le~il~rl~~~~~~~qii~lSATl~n-~~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~~~  234 (737)
T PRK02362        156 PTLEVTLAKLRRLNPDLQVVALSATIGN-ADELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDTLN  234 (737)
T ss_pred             HHHHHHHHHHHhcCCCCcEEEEcccCCC-HHHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccchHHHH
Confidence            6665554432  2456899999999986 556666653221       1100000  00000000001111111123444


Q ss_pred             HHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC------------------------------------CCeeEEEecC
Q 042003          150 ALRQSFAESLNPPVLIFVQSKERAKELYGELAFD------------------------------------GIRAGVIHSD  193 (248)
Q Consensus       150 ~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~------------------------------------~~~v~~~~~~  193 (248)
                      .+.+.+.  .++++||||++++.|+.+++.|...                                    ..+++++||+
T Consensus       235 ~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHag  312 (737)
T PRK02362        235 LVLDTLE--EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAG  312 (737)
T ss_pred             HHHHHHH--cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCC
Confidence            4544444  3689999999999999988877532                                    1378999999


Q ss_pred             CCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe----cc-----CCCCcccceecC
Q 042003          194 LSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN----YD-----FPDSGAAYIHRI  248 (248)
Q Consensus       194 ~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~----~~-----~p~~~~~~~qri  248 (248)
                      |++++|+.+++.|++|.++|||||+++++|+|+|+.++||+    |+     .|.+..+|+||+
T Consensus       313 l~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~  376 (737)
T PRK02362        313 LSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMA  376 (737)
T ss_pred             CCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHh
Confidence            99999999999999999999999999999999999999997    66     588999999985

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

Probab=99.98  E-value=1.9e-31  Score=230.58  Aligned_cols=242  Identities=21%  Similarity=0.215  Sum_probs=185.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhh---cccccCCCcEEEeChHHHHHHHhcCCc--ccCceeEEEEeccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRS---TDLSKFSCDILISTPLRLRLAIRRKKI--DLSRVEYLVLDEADKLFE   75 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~v~Tp~~l~~~~~~~~~--~~~~~~~lIiDEah~~~~   75 (248)
                      |+..+...++.+++..| ..+....|...+   ..+.++-|||+|+|||+|.-++.....  .+++++++||||.|.+.+
T Consensus        85 Ln~Di~~rL~~~~~~~G-~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~  163 (814)
T COG1201          85 LNNDIRRRLEEPLRELG-IEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAE  163 (814)
T ss_pred             HHHHHHHHHHHHHHHcC-CccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhc
Confidence            45667788888888888 555677776633   355667799999999999988877533  589999999999999876


Q ss_pred             cC--cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCc--EEEEEcccccccccceeEEEE------cCCch
Q 042003           76 VG--NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDA--VRVIVGRKNTASESIKQKLVF------AGSEE  145 (248)
Q Consensus        76 ~~--~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~------~~~~~  145 (248)
                      ..  ......-+.+..+.. +.|.|++|||..+ .....+++.+..  ..+. .........++-....      -....
T Consensus       164 sKRG~~Lsl~LeRL~~l~~-~~qRIGLSATV~~-~~~varfL~g~~~~~~Iv-~~~~~k~~~i~v~~p~~~~~~~~~~~~  240 (814)
T COG1201         164 SKRGVQLALSLERLRELAG-DFQRIGLSATVGP-PEEVAKFLVGFGDPCEIV-DVSAAKKLEIKVISPVEDLIYDEELWA  240 (814)
T ss_pred             cccchhhhhhHHHHHhhCc-ccEEEeehhccCC-HHHHHHHhcCCCCceEEE-EcccCCcceEEEEecCCccccccchhH
Confidence            53  222222233333333 8999999999986 777777777664  3332 2222121211111100      11113


Q ss_pred             hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCC-CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCC
Q 042003          146 GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDG-IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGM  224 (248)
Q Consensus       146 ~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~-~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gi  224 (248)
                      .....+.++++++  +.++||+||+..++.++..|++.+ ..+..+||+++.+.|..+.+.|++|+.+.+|||+.++.||
T Consensus       241 ~~~~~i~~~v~~~--~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGI  318 (814)
T COG1201         241 ALYERIAELVKKH--RTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGI  318 (814)
T ss_pred             HHHHHHHHHHhhc--CcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhcc
Confidence            4567777777775  599999999999999999999886 7999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEeccCCCCcccceecC
Q 042003          225 DFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       225 dip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+.+++.||+++.|.+++.++|||
T Consensus       319 DiG~vdlVIq~~SP~sV~r~lQRi  342 (814)
T COG1201         319 DIGDIDLVIQLGSPKSVNRFLQRI  342 (814)
T ss_pred             ccCCceEEEEeCCcHHHHHHhHhc
Confidence            999999999999999999999997

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

Probab=99.97  E-value=1.3e-30  Score=226.63  Aligned_cols=237  Identities=15%  Similarity=0.169  Sum_probs=174.4

Q ss_pred             CcchHHHHHHHhhcCCC----------------------cEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcC
Q 042003            1 LATQTTRECKKLAKGNK----------------------FQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRK   55 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~----------------------~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~   55 (248)
                      ||.|+++.++++++..+                      -.++..++||.   .+......+++|+|+|++.+.+.....
T Consensus        74 La~Qi~~~~~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~sr~L~~  153 (844)
T TIGR02621        74 VVDQVTEEAEKIGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIGSRLLFS  153 (844)
T ss_pred             HHHHHHHHHHHHHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHcCCcccc
Confidence            68899999999988652                      15566667775   555667778999999975553322210


Q ss_pred             ---------Cc---ccCceeEEEEeccccccccCcccccchhHhhhC-CCc---cceeEEEEeecCchHHHHHHHhcCCc
Q 042003           56 ---------KI---DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC-SNP---SIVRSLFSATLPDFVEELARSIMHDA  119 (248)
Q Consensus        56 ---------~~---~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~-~~~---~~~~i~~SAT~~~~~~~~~~~~~~~~  119 (248)
                               .+   .++++.++|+||||  ++.+ |...+..+.+.. .+.   +.|+++||||++.........++.++
T Consensus       154 gYg~~~~~~pi~ag~L~~v~~LVLDEAD--Ld~g-F~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p  230 (844)
T TIGR02621       154 GYGCGFKSRPLHAGFLGQDALIVHDEAH--LEPA-FQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAED  230 (844)
T ss_pred             ccccccccccchhhhhccceEEEEehhh--hccc-cHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCC
Confidence                     01   26889999999999  4555 889999998863 122   36999999999988877777777677


Q ss_pred             EEEEEcccccccccceeEEEEcCCchhHHHH----HHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          120 VRVIVGRKNTASESIKQKLVFAGSEEGKLLA----LRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      ....+........++.++ +.... +.+...    +..... ..++++||||||++.|+.+++.|++.++  ..+||+|+
T Consensus       231 ~~i~V~~~~l~a~ki~q~-v~v~~-e~Kl~~lv~~L~~ll~-e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~  305 (844)
T TIGR02621       231 YKHPVLKKRLAAKKIVKL-VPPSD-EKFLSTMVKELNLLMK-DSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLR  305 (844)
T ss_pred             ceeecccccccccceEEE-EecCh-HHHHHHHHHHHHHHHh-hCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCC
Confidence            665555444444444443 22222 233332    222232 2367999999999999999999998876  89999999


Q ss_pred             HHHHH-----HHHHHhhc----CC-------ceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          196 QTQRE-----NAVDDFRA----GK-------TWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       196 ~~~r~-----~~~~~f~~----g~-------~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +.+|.     .+++.|++    |+       ..|||||+++++|+|++. ++||++..|  .+.|+||+
T Consensus       306 q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRi  371 (844)
T TIGR02621       306 GAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRF  371 (844)
T ss_pred             HHHHhhHHHHHHHHHHhccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHh
Confidence            99999     78899987    44       679999999999999986 888887766  58999996

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.

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

Probab=99.97  E-value=1.4e-31  Score=223.95  Aligned_cols=212  Identities=22%  Similarity=0.284  Sum_probs=164.8

Q ss_pred             ccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC-cccccchhHhhhCCC-ccceeEEEEeecCchHHHH
Q 042003           34 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKACSN-PSIVRSLFSATLPDFVEEL  111 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~-~~~~~~~~~~~~~~~-~~~~~i~~SAT~~~~~~~~  111 (248)
                      ..+..+++.-+||++..-...+.+..-.+.+++|||||++.+|| +|++.+..+...... +++.++++|||.++.+..-
T Consensus       104 ~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~~~~~~p~~AlTATA~~~v~~D  183 (590)
T COG0514         104 KSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTATATPRVRDD  183 (590)
T ss_pred             hcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHHHHHhhCCCCCEEEEeCCCChHHHHH
Confidence            34458999999999876655555556778899999999999998 788888777554322 4778899999999988887


Q ss_pred             HHHhcCCcE-EEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEE
Q 042003          112 ARSIMHDAV-RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVI  190 (248)
Q Consensus       112 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~  190 (248)
                      +...+.-.. .+...  ....+++........+...+...+.+ ......+..||||.|++.++.+++.|+..|+++..+
T Consensus       184 I~~~L~l~~~~~~~~--sfdRpNi~~~v~~~~~~~~q~~fi~~-~~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~Y  260 (590)
T COG0514         184 IREQLGLQDANIFRG--SFDRPNLALKVVEKGEPSDQLAFLAT-VLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAY  260 (590)
T ss_pred             HHHHhcCCCcceEEe--cCCCchhhhhhhhcccHHHHHHHHHh-hccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEe
Confidence            766443222 22222  22233343333333333344444443 123336789999999999999999999999999999


Q ss_pred             ecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       191 ~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+||+.++|+.+.++|..++.+|+|||.++++|||-|+++.||||++|.|++.|.|.+
T Consensus       261 HaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~  318 (590)
T COG0514         261 HAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQET  318 (590)
T ss_pred             cCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999964

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.97  E-value=2e-30  Score=230.70  Aligned_cols=230  Identities=19%  Similarity=0.167  Sum_probs=168.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh---hc----ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR---ST----DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~---~~----~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.++++.+..+ ..+..+.|+..   ..    .+..+.++|+|+||..+     .....+++++++|+||+|++
T Consensus       512 LA~Q~~~~f~~~~~~~~-i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll-----~~~v~f~~L~llVIDEahrf  585 (926)
T TIGR00580       512 LAQQHFETFKERFANFP-VTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLL-----QKDVKFKDLGLLIIDEEQRF  585 (926)
T ss_pred             HHHHHHHHHHHHhccCC-cEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHh-----hCCCCcccCCEEEeeccccc
Confidence            78999999999888887 55555555431   11    12234699999999432     34567899999999999995


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  153 (248)
                      ..      .....++. .....++++||||+.++...+......++..+...+...  ..+..++.... .......+..
T Consensus       586 gv------~~~~~L~~-~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~R--~~V~t~v~~~~-~~~i~~~i~~  655 (926)
T TIGR00580       586 GV------KQKEKLKE-LRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDR--LPVRTFVMEYD-PELVREAIRR  655 (926)
T ss_pred             ch------hHHHHHHh-cCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCCc--cceEEEEEecC-HHHHHHHHHH
Confidence            32      22333443 345689999999988877666555555555554433221  23444433222 1111233333


Q ss_pred             HHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcE
Q 042003          154 SFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC  231 (248)
Q Consensus       154 ~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~  231 (248)
                      .+.+  +++++||||+++.++.+++.|++.  +.++..+||+|++++|+++++.|++|+.+|||||+++++|+|+|++++
T Consensus       656 el~~--g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~  733 (926)
T TIGR00580       656 ELLR--GGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANT  733 (926)
T ss_pred             HHHc--CCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCE
Confidence            3333  679999999999999999999874  789999999999999999999999999999999999999999999999


Q ss_pred             EEeccCCC-CcccceecC
Q 042003          232 VINYDFPD-SGAAYIHRI  248 (248)
Q Consensus       232 Vi~~~~p~-~~~~~~qri  248 (248)
                      ||++++|. +..+|.||+
T Consensus       734 VIi~~a~~~gls~l~Qr~  751 (926)
T TIGR00580       734 IIIERADKFGLAQLYQLR  751 (926)
T ss_pred             EEEecCCCCCHHHHHHHh
Confidence            99999975 567888874

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.

>PRK00254 ski2-like helicase; Provisional

Probab=99.97  E-value=7.8e-31  Score=231.95  Aligned_cols=239  Identities=21%  Similarity=0.184  Sum_probs=169.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      ||.|+++.++.+.+ .+ ..+....|+........+.++|+|+||+++..++.++...+++++++|+||+|.+.+.+ +.
T Consensus        80 La~q~~~~~~~~~~-~g-~~v~~~~Gd~~~~~~~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~-rg  156 (720)
T PRK00254         80 LAEEKYREFKDWEK-LG-LRVAMTTGDYDSTDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYD-RG  156 (720)
T ss_pred             HHHHHHHHHHHHhh-cC-CEEEEEeCCCCCchhhhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCcc-ch
Confidence            57888888887643 45 56666666654433344578999999999999888776778999999999999998776 67


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccc-c-ceeEEEEcCCc------hhHHHHHH
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASE-S-IKQKLVFAGSE------EGKLLALR  152 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~------~~~~~~l~  152 (248)
                      ..+..++... ....|++++|||+++ ..++..|+....  +.......+.. . ..+......+.      ......+.
T Consensus       157 ~~le~il~~l-~~~~qiI~lSATl~n-~~~la~wl~~~~--~~~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (720)
T PRK00254        157 ATLEMILTHM-LGRAQILGLSATVGN-AEELAEWLNAEL--VVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVY  232 (720)
T ss_pred             HHHHHHHHhc-CcCCcEEEEEccCCC-HHHHHHHhCCcc--ccCCCCCCcceeeEecCCeeeccCcchhcchHHHHHHHH
Confidence            7777777773 467899999999987 566666653321  11111111110 0 01111111111      11123333


Q ss_pred             HHHhccCCCCEEEEecchHHHHHHHHHhhc---------------------------------CCCeeEEEecCCCHHHH
Q 042003          153 QSFAESLNPPVLIFVQSKERAKELYGELAF---------------------------------DGIRAGVIHSDLSQTQR  199 (248)
Q Consensus       153 ~~~~~~~~~~~liF~~~~~~~~~l~~~L~~---------------------------------~~~~v~~~~~~~~~~~r  199 (248)
                      +.+..  ++++||||+|++.|+.++..|.+                                 ...+++++||+|++++|
T Consensus       233 ~~i~~--~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR  310 (720)
T PRK00254        233 DAVKK--GKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTER  310 (720)
T ss_pred             HHHHh--CCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHH
Confidence            44443  67999999999999887766632                                 12369999999999999


Q ss_pred             HHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe-------ccCCC-CcccceecC
Q 042003          200 ENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN-------YDFPD-SGAAYIHRI  248 (248)
Q Consensus       200 ~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~-------~~~p~-~~~~~~qri  248 (248)
                      ..+++.|++|.++|||||+++++|+|+|+.++||.       ++.|. +..+|+||+
T Consensus       311 ~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~  367 (720)
T PRK00254        311 VLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMM  367 (720)
T ss_pred             HHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhh
Confidence            99999999999999999999999999999999994       56554 456888885

>PRK09401 reverse gyrase; Reviewed

Probab=99.97  E-value=2.4e-30  Score=235.15  Aligned_cols=234  Identities=20%  Similarity=0.242  Sum_probs=172.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh---h----c-ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR---S----T-DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~---~----~-~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~   72 (248)
                      ||.|+++.+++++...+.....+.+++..   +    . .+..++++|+|+||+++.+.+.  .+...+++++|+||||+
T Consensus       135 La~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~  212 (1176)
T PRK09401        135 LVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDA  212 (1176)
T ss_pred             HHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHH
Confidence            78999999999999888444444444321   1    1 1123569999999999998876  45556799999999999


Q ss_pred             ccccC----------ccc-ccchhHhhhCC-----------------------CccceeEEEEeecCchHHHHHHHhcCC
Q 042003           73 LFEVG----------NLL-KHIDPVVKACS-----------------------NPSIVRSLFSATLPDFVEELARSIMHD  118 (248)
Q Consensus        73 ~~~~~----------~~~-~~~~~~~~~~~-----------------------~~~~~~i~~SAT~~~~~~~~~~~~~~~  118 (248)
                      +++++          .|. ..+..++..+.                       ....|++++|||+++.....  .++.+
T Consensus       213 ~L~~~k~id~~l~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~--~l~~~  290 (1176)
T PRK09401        213 VLKSSKNIDKLLYLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV--KLFRE  290 (1176)
T ss_pred             hhhcccchhhHHHhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH--HHhhc
Confidence            98642          142 23444443322                       12679999999998742211  23344


Q ss_pred             cEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHH---HHHHHHHhhcCCCeeEEEecCCC
Q 042003          119 AVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKER---AKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~---~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      +..+.++.......++.+.+....   ++...+.++++.. +.++||||++...   ++.+++.|+..|+++..+||+| 
T Consensus       291 ll~~~v~~~~~~~rnI~~~yi~~~---~k~~~L~~ll~~l-~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-  365 (1176)
T PRK09401        291 LLGFEVGSPVFYLRNIVDSYIVDE---DSVEKLVELVKRL-GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-  365 (1176)
T ss_pred             cceEEecCcccccCCceEEEEEcc---cHHHHHHHHHHhc-CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-
Confidence            555666666666677777776554   4666777877766 4689999999777   9999999999999999999999 


Q ss_pred             HHHHHHHHHHhhcCCceEEEE----ecccccCCCCCC-CcEEEeccCCC------Ccccceec
Q 042003          196 QTQRENAVDDFRAGKTWVLIA----TDVIARGMDFKG-VNCVINYDFPD------SGAAYIHR  247 (248)
Q Consensus       196 ~~~r~~~~~~f~~g~~~ilv~----T~~~~~Gidip~-~~~Vi~~~~p~------~~~~~~qr  247 (248)
                          +..++.|++|+.+||||    |+++++|+|+|+ +++|||||.|.      ....|.||
T Consensus       366 ----~~~l~~F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~  424 (1176)
T PRK09401        366 ----ERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFL  424 (1176)
T ss_pred             ----HHHHHHHHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHH
Confidence                23459999999999999    689999999999 89999999998      44455554

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.97  E-value=7e-30  Score=231.64  Aligned_cols=230  Identities=19%  Similarity=0.130  Sum_probs=167.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhccc----ccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDL----SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~----~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.+++.....+ ..+..+.|+.   .+...    ..+.++|+|+||+.+     .....+++++++|+||+|++
T Consensus       661 LA~Q~~~~f~~~~~~~~-v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL-----~~~v~~~~L~lLVIDEahrf  734 (1147)
T PRK10689        661 LAQQHYDNFRDRFANWP-VRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL-----QSDVKWKDLGLLIVDEEHRF  734 (1147)
T ss_pred             HHHHHHHHHHHhhccCC-ceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH-----hCCCCHhhCCEEEEechhhc
Confidence            68999999998777766 4444444433   22221    235789999999643     23456789999999999996


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  153 (248)
                      ..    .  ....++. .+.+.|++++|||+.+....+....+.++..+.......  ..+.+..........+...+.+
T Consensus       735 G~----~--~~e~lk~-l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~r--~~v~~~~~~~~~~~~k~~il~e  805 (1147)
T PRK10689        735 GV----R--HKERIKA-MRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARR--LAVKTFVREYDSLVVREAILRE  805 (1147)
T ss_pred             ch----h--HHHHHHh-cCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCCC--CCceEEEEecCcHHHHHHHHHH
Confidence            22    1  1233444 346789999999998888887777777777665544322  2344444333222223333333


Q ss_pred             HHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcE
Q 042003          154 SFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC  231 (248)
Q Consensus       154 ~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~  231 (248)
                      +. .  +++++||||+++.++.+++.|++.  +.++..+||+|++++|+++++.|++|+.+|||||+++++|+|+|++++
T Consensus       806 l~-r--~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~  882 (1147)
T PRK10689        806 IL-R--GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT  882 (1147)
T ss_pred             Hh-c--CCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCE
Confidence            33 2  578999999999999999999887  778999999999999999999999999999999999999999999999


Q ss_pred             EEeccCC-CCcccceecC
Q 042003          232 VINYDFP-DSGAAYIHRI  248 (248)
Q Consensus       232 Vi~~~~p-~~~~~~~qri  248 (248)
                      ||+.+.. .+..+|.||+
T Consensus       883 VIi~~ad~fglaq~~Qr~  900 (1147)
T PRK10689        883 IIIERADHFGLAQLHQLR  900 (1147)
T ss_pred             EEEecCCCCCHHHHHHHh
Confidence            9955443 3455688874

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.97  E-value=1.3e-29  Score=222.01  Aligned_cols=230  Identities=16%  Similarity=0.202  Sum_probs=160.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhh-------cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRS-------TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.++++.+..+ ..+.++.|+...       .....+.++|+|+||+.+..     ...+++++++|+||+|++
T Consensus       322 LA~Q~~~~l~~l~~~~~-i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrf  395 (681)
T PRK10917        322 LAEQHYENLKKLLEPLG-IRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRF  395 (681)
T ss_pred             HHHHHHHHHHHHHhhcC-cEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhh
Confidence            78999999999999888 566666666521       12234469999999986633     345789999999999996


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  153 (248)
                      ...  .+.    .+.. ....+++++||||+.+....+..  .++...............+...+......+.....+.+
T Consensus       396 g~~--qr~----~l~~-~~~~~~iL~~SATp~prtl~~~~--~g~~~~s~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~~  466 (681)
T PRK10917        396 GVE--QRL----ALRE-KGENPHVLVMTATPIPRTLAMTA--YGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE  466 (681)
T ss_pred             hHH--HHH----HHHh-cCCCCCEEEEeCCCCHHHHHHHH--cCCCceEEEecCCCCCCCcEEEEeCcccHHHHHHHHHH
Confidence            432  111    2222 23357899999998775544433  33322222221111122344444333322333344444


Q ss_pred             HHhccCCCCEEEEecch--------HHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccC
Q 042003          154 SFAESLNPPVLIFVQSK--------ERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG  223 (248)
Q Consensus       154 ~~~~~~~~~~liF~~~~--------~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G  223 (248)
                      .+.+  +++++|||+.+        ..++.+++.|.+.  ++++..+||+|++++|+++++.|++|+.+|||||+++++|
T Consensus       467 ~~~~--g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~G  544 (681)
T PRK10917        467 EIAK--GRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVG  544 (681)
T ss_pred             HHHc--CCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeC
Confidence            4433  67999999964        3456777888765  5789999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEeccCCCC-cccceec
Q 042003          224 MDFKGVNCVINYDFPDS-GAAYIHR  247 (248)
Q Consensus       224 idip~~~~Vi~~~~p~~-~~~~~qr  247 (248)
                      +|+|++++||++++|.. .+++.||
T Consensus       545 iDip~v~~VIi~~~~r~gls~lhQ~  569 (681)
T PRK10917        545 VDVPNATVMVIENAERFGLAQLHQL  569 (681)
T ss_pred             cccCCCcEEEEeCCCCCCHHHHHHH
Confidence            99999999999999974 5666665

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

Probab=99.97  E-value=1.9e-29  Score=203.52  Aligned_cols=246  Identities=23%  Similarity=0.294  Sum_probs=175.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNL   79 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~   79 (248)
                      |+.|+++.|++.....+..++.+.+... +.+...+...+|+|+||+.+.+-+..+.++++++.++|+||||+-.+..+|
T Consensus        70 LV~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~~w~~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAY  149 (542)
T COG1111          70 LVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELWAKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAY  149 (542)
T ss_pred             HHHHHHHHHHHHhCCChhheeeecCCCChHHHHHHHhhCCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchH
Confidence            6889999999988887644444444444 446778889999999999999999999999999999999999998776545


Q ss_pred             cccchhHhhhCCCccceeEEEEeecCchHHHH---HHHhcCCcEEEEEccccc---------------------------
Q 042003           80 LKHIDPVVKACSNPSIVRSLFSATLPDFVEEL---ARSIMHDAVRVIVGRKNT---------------------------  129 (248)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~---~~~~~~~~~~~~~~~~~~---------------------------  129 (248)
                      .......++.  ..++.++++|||+....+.+   +..+.-....+.......                           
T Consensus       150 v~Va~~y~~~--~k~~~ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~  227 (542)
T COG1111         150 VFVAKEYLRS--AKNPLILGLTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDL  227 (542)
T ss_pred             HHHHHHHHHh--ccCceEEEEecCCCCCHHHHHHHHHhCCcceEEEecCCCccHHHhhccceeEEEeccCcHHHHHHHHH
Confidence            5555555554  34678999999975432222   111111111110000000                           


Q ss_pred             --------------------cc------------------cc-----------------------------ce-------
Q 042003          130 --------------------AS------------------ES-----------------------------IK-------  135 (248)
Q Consensus       130 --------------------~~------------------~~-----------------------------~~-------  135 (248)
                                          ..                  .+                             +.       
T Consensus       228 l~~~l~~~Lk~L~~~g~~~~~~~~~~kdl~~~~~~~~~~a~~~~~~~~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~  307 (542)
T COG1111         228 LRDALKPRLKPLKELGVIESSSPVSKKDLLELRQIRLIMAKNEDSDKFRLLSVLAEAIKLAHALELLETQGIRPFYQYLE  307 (542)
T ss_pred             HHHHHHHHHHHHHHcCceeccCcccHhHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHH
Confidence                                00                  00                             00       


Q ss_pred             ------------------------------eEEEEcCCchhHHHHHHHHH----hccCCCCEEEEecchHHHHHHHHHhh
Q 042003          136 ------------------------------QKLVFAGSEEGKLLALRQSF----AESLNPPVLIFVQSKERAKELYGELA  181 (248)
Q Consensus       136 ------------------------------~~~~~~~~~~~~~~~l~~~~----~~~~~~~~liF~~~~~~~~~l~~~L~  181 (248)
                                                    ...........|+..+.+++    ++..+.++|||++.+++|+.+.+.|.
T Consensus       308 ~l~e~~~~~~sk~a~~l~~d~~~~~al~~~~~~~~~~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~  387 (542)
T COG1111         308 KLEEEATKGGSKAAKSLLADPYFKRALRLLIRADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLK  387 (542)
T ss_pred             HHHHHhcccchHHHHHHhcChhhHHHHHHHHHhccccCCCccHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHH
Confidence                                          00000111112333344433    34446799999999999999999999


Q ss_pred             cCCCeeE-EE--------ecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          182 FDGIRAG-VI--------HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       182 ~~~~~v~-~~--------~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +.+.++. .+        ..||+++++.++++.|++|..++||||++.++|+|+|+++.||.|++..|..+++||.
T Consensus       388 ~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~  463 (542)
T COG1111         388 KIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRK  463 (542)
T ss_pred             hcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhh
Confidence            9887774 33        2579999999999999999999999999999999999999999999999999999994

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

Probab=99.97  E-value=1.2e-31  Score=198.79  Aligned_cols=211  Identities=28%  Similarity=0.417  Sum_probs=183.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+.+...+|.+..+..++...+||.   .....+++-|+|+|+||++++.+.+++.+++++++.+|+|||+.++.+-
T Consensus       122 lafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~l  201 (387)
T KOG0329|consen  122 LAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQL  201 (387)
T ss_pred             HHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHH
Confidence            6889999999999999888899888887   4445566789999999999999999999999999999999999999887


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccc-ccccccceeEEEEcCCchhHHHHHHHHHh
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK-NTASESIKQKLVFAGSEEGKLLALRQSFA  156 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  156 (248)
                      ++++.++++.+. .+...|+.++|||++.+.+...+.++.+|..+.+..+ .....++.++++..+..+ |...+.+++.
T Consensus       202 DMrRDvQEifr~-tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~e-KNrkl~dLLd  279 (387)
T KOG0329|consen  202 DMRRDVQEIFRM-TPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENE-KNRKLNDLLD  279 (387)
T ss_pred             HHHHHHHHHhhc-CcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhh-hhhhhhhhhh
Confidence            799999999998 7788899999999999999999999999987766544 556777888887777664 7778888888


Q ss_pred             ccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          157 ESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       157 ~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      ....++++||+.+.....                               |   +.+ +|+|+.+++|+|+..++.|+|||
T Consensus       280 ~LeFNQVvIFvKsv~Rl~-------------------------------f---~kr-~vat~lfgrgmdiervNi~~NYd  324 (387)
T KOG0329|consen  280 VLEFNQVVIFVKSVQRLS-------------------------------F---QKR-LVATDLFGRGMDIERVNIVFNYD  324 (387)
T ss_pred             hhhhcceeEeeehhhhhh-------------------------------h---hhh-hHHhhhhccccCcccceeeeccC
Confidence            877889999999877610                               2   223 89999999999999999999999


Q ss_pred             CCCCcccceecC
Q 042003          237 FPDSGAAYIHRI  248 (248)
Q Consensus       237 ~p~~~~~~~qri  248 (248)
                      +|.+.++|+||+
T Consensus       325 mp~~~DtYlHrv  336 (387)
T KOG0329|consen  325 MPEDSDTYLHRV  336 (387)
T ss_pred             CCCCchHHHHHh
Confidence            999999999996

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.97  E-value=6.8e-29  Score=216.15  Aligned_cols=232  Identities=16%  Similarity=0.186  Sum_probs=156.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhh-------cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRS-------TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.++++.+..+ ..+.++.|+...       ..+..+.++|+|+||+.+..     ...+.+++++|+||+|++
T Consensus       296 LA~Q~~~~~~~l~~~~g-i~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~f  369 (630)
T TIGR00643       296 LAEQHYNSLRNLLAPLG-IEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRF  369 (630)
T ss_pred             HHHHHHHHHHHHhcccC-cEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhc
Confidence            78999999999999888 556666666521       12334568999999987643     355789999999999996


Q ss_pred             cccCcccccchhHhhhCCC-ccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSN-PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALR  152 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  152 (248)
                      ...  .+.   .+...... ..+++++||||+.+....+.  ..++...............+..........+.....+.
T Consensus       370 g~~--qr~---~l~~~~~~~~~~~~l~~SATp~prtl~l~--~~~~l~~~~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~  442 (630)
T TIGR00643       370 GVE--QRK---KLREKGQGGFTPHVLVMSATPIPRTLALT--VYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIE  442 (630)
T ss_pred             cHH--HHH---HHHHhcccCCCCCEEEEeCCCCcHHHHHH--hcCCcceeeeccCCCCCCceEEEEeCcchHHHHHHHHH
Confidence            432  111   22222111 25789999999877554443  22332211111111111223333322211112222222


Q ss_pred             HHHhccCCCCEEEEecch--------HHHHHHHHHhhc--CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccccc
Q 042003          153 QSFAESLNPPVLIFVQSK--------ERAKELYGELAF--DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR  222 (248)
Q Consensus       153 ~~~~~~~~~~~liF~~~~--------~~~~~l~~~L~~--~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~  222 (248)
                      +.+.  .+++++|||+..        ..++.+++.|.+  .++++..+||+|++++|.++++.|++|+.+|||||+++++
T Consensus       443 ~~l~--~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~  520 (630)
T TIGR00643       443 EEIA--KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEV  520 (630)
T ss_pred             HHHH--hCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeec
Confidence            2222  267999999876        456677777765  3678999999999999999999999999999999999999


Q ss_pred             CCCCCCCcEEEeccCCC-Ccccceec
Q 042003          223 GMDFKGVNCVINYDFPD-SGAAYIHR  247 (248)
Q Consensus       223 Gidip~~~~Vi~~~~p~-~~~~~~qr  247 (248)
                      |+|+|++++||+++.|. +.++|.||
T Consensus       521 GvDiP~v~~VIi~~~~r~gls~lhQ~  546 (630)
T TIGR00643       521 GVDVPNATVMVIEDAERFGLSQLHQL  546 (630)
T ss_pred             CcccCCCcEEEEeCCCcCCHHHHHHH
Confidence            99999999999999997 55666666

>PRK01172 ski2-like helicase; Provisional

Probab=99.97  E-value=9.9e-30  Score=223.93  Aligned_cols=236  Identities=20%  Similarity=0.167  Sum_probs=161.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      ||.|+++.++++. ..+ ..+....|+..........++|+|+||+++..++.+....+.+++++|+||+|.+.+.+ +.
T Consensus        77 La~q~~~~~~~l~-~~g-~~v~~~~G~~~~~~~~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~-rg  153 (674)
T PRK01172         77 LAMEKYEELSRLR-SLG-MRVKISIGDYDDPPDFIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDED-RG  153 (674)
T ss_pred             HHHHHHHHHHHHh-hcC-CeEEEEeCCCCCChhhhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCC-cc
Confidence            6788999888864 345 44555555543333233568999999999998888776678999999999999988765 55


Q ss_pred             ccchhHhhhC--CCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEE-----EcCCch----hHHH
Q 042003           81 KHIDPVVKAC--SNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLV-----FAGSEE----GKLL  149 (248)
Q Consensus        81 ~~~~~~~~~~--~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~----~~~~  149 (248)
                      ..+..++...  ..++.|++++|||+++ ..++..|+....  +.....   +..+.....     +.....    ....
T Consensus       154 ~~le~ll~~~~~~~~~~riI~lSATl~n-~~~la~wl~~~~--~~~~~r---~vpl~~~i~~~~~~~~~~~~~~~~~~~~  227 (674)
T PRK01172        154 PTLETVLSSARYVNPDARILALSATVSN-ANELAQWLNASL--IKSNFR---PVPLKLGILYRKRLILDGYERSQVDINS  227 (674)
T ss_pred             HHHHHHHHHHHhcCcCCcEEEEeCccCC-HHHHHHHhCCCc--cCCCCC---CCCeEEEEEecCeeeecccccccccHHH
Confidence            5555554432  3457899999999986 566666553221  111111   111111111     111111    1122


Q ss_pred             HHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC-------------------------CCeeEEEecCCCHHHHHHHHH
Q 042003          150 ALRQSFAESLNPPVLIFVQSKERAKELYGELAFD-------------------------GIRAGVIHSDLSQTQRENAVD  204 (248)
Q Consensus       150 ~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~-------------------------~~~v~~~~~~~~~~~r~~~~~  204 (248)
                      .+.+...  .+++++|||++++.++.+++.|...                         ..+++++||+|++++|..+++
T Consensus       228 ~i~~~~~--~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~  305 (674)
T PRK01172        228 LIKETVN--DGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEE  305 (674)
T ss_pred             HHHHHHh--CCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHH
Confidence            2222222  2679999999999999999888542                         125889999999999999999


Q ss_pred             HhhcCCceEEEEecccccCCCCCCCcEEEeccC---------CCCcccceecC
Q 042003          205 DFRAGKTWVLIATDVIARGMDFKGVNCVINYDF---------PDSGAAYIHRI  248 (248)
Q Consensus       205 ~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~---------p~~~~~~~qri  248 (248)
                      .|++|.++|||||+++++|+|+|+. .||+.+.         |.++.+|.||+
T Consensus       306 ~f~~g~i~VLvaT~~la~Gvnipa~-~VII~~~~~~~~~~~~~~s~~~~~Qm~  357 (674)
T PRK01172        306 MFRNRYIKVIVATPTLAAGVNLPAR-LVIVRDITRYGNGGIRYLSNMEIKQMI  357 (674)
T ss_pred             HHHcCCCeEEEecchhhccCCCcce-EEEEcCceEeCCCCceeCCHHHHHHHh
Confidence            9999999999999999999999975 5555554         34666778875

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.97  E-value=5.7e-29  Score=219.32  Aligned_cols=226  Identities=17%  Similarity=0.175  Sum_probs=162.4

Q ss_pred             CcchHHHHHH-HhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc-ccccCc
Q 042003            1 LATQTTRECK-KLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK-LFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~-~~~~~~   78 (248)
                      +|.|+++.+. .++...+ ..+....++   ......+.+|+|+||+.|.+++... ..++++++||+||+|. .++.+ 
T Consensus        57 aA~qiA~rva~~~~~~~g-~~VGy~vr~---~~~~s~~t~I~v~T~G~Llr~l~~d-~~L~~v~~VIiDEaHER~L~~D-  130 (819)
T TIGR01970        57 AARSAAQRLASQLGEAVG-QTVGYRVRG---ENKVSRRTRLEVVTEGILTRMIQDD-PELDGVGALIFDEFHERSLDAD-  130 (819)
T ss_pred             HHHHHHHHHHHHhCCCcC-cEEEEEEcc---ccccCCCCcEEEECCcHHHHHHhhC-cccccCCEEEEeccchhhhccc-
Confidence            4677887764 4555555 333332222   2233456899999999999998764 4689999999999995 45433 


Q ss_pred             cc-ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhH----HHHHHH
Q 042003           79 LL-KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGK----LLALRQ  153 (248)
Q Consensus        79 ~~-~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~l~~  153 (248)
                      +. ..+..+... ...+.|+++||||++...   ...+++++..+.....   ...+.+++......+..    ...+..
T Consensus       131 l~L~ll~~i~~~-lr~dlqlIlmSATl~~~~---l~~~l~~~~vI~~~gr---~~pVe~~y~~~~~~~~~~~~v~~~l~~  203 (819)
T TIGR01970       131 LGLALALDVQSS-LREDLKILAMSATLDGER---LSSLLPDAPVVESEGR---SFPVEIRYLPLRGDQRLEDAVSRAVEH  203 (819)
T ss_pred             hHHHHHHHHHHh-cCCCceEEEEeCCCCHHH---HHHHcCCCcEEEecCc---ceeeeeEEeecchhhhHHHHHHHHHHH
Confidence            32 233344443 356789999999998643   3456665554443322   22345555444332211    123444


Q ss_pred             HHhccCCCCEEEEecchHHHHHHHHHhhc---CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCc
Q 042003          154 SFAESLNPPVLIFVQSKERAKELYGELAF---DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVN  230 (248)
Q Consensus       154 ~~~~~~~~~~liF~~~~~~~~~l~~~L~~---~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~  230 (248)
                      .++.. .+++|||+++.++++.+++.|++   .++.+..+||+|++++|.++++.|++|+.+|||||+++++|||+|+++
T Consensus       204 ~l~~~-~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~  282 (819)
T TIGR01970       204 ALASE-TGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIR  282 (819)
T ss_pred             HHHhc-CCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCce
Confidence            44443 67999999999999999999987   478999999999999999999999999999999999999999999999


Q ss_pred             EEEeccCCCC
Q 042003          231 CVINYDFPDS  240 (248)
Q Consensus       231 ~Vi~~~~p~~  240 (248)
                      +||++|.|..
T Consensus       283 ~VID~Gl~r~  292 (819)
T TIGR01970       283 VVIDSGLARV  292 (819)
T ss_pred             EEEEcCcccc
Confidence            9999999863

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.96  E-value=1.3e-28  Score=217.48  Aligned_cols=227  Identities=16%  Similarity=0.174  Sum_probs=162.0

Q ss_pred             CcchHHHHHH-HhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc-cccCc
Q 042003            1 LATQTTRECK-KLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-FEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~-~~~~~   78 (248)
                      +|.|+++.+. .++...+ ..+....++.   .......+|+|+||+.+.+++... ..+++++++|+||+|.. .+.+-
T Consensus        60 aA~qia~rva~~l~~~~g-~~VGy~vr~~---~~~~~~t~I~v~T~G~Llr~l~~d-~~L~~v~~IIlDEaHER~l~~Dl  134 (812)
T PRK11664         60 AARNVAQRLAEQLGEKPG-ETVGYRMRAE---SKVGPNTRLEVVTEGILTRMIQRD-PELSGVGLVILDEFHERSLQADL  134 (812)
T ss_pred             HHHHHHHHHHHHhCcccC-ceEEEEecCc---cccCCCCcEEEEChhHHHHHHhhC-CCcCcCcEEEEcCCCccccccch
Confidence            4678888774 4555555 4444333332   223345789999999999988764 46899999999999973 33221


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHH----HHHHHH
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKL----LALRQS  154 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~l~~~  154 (248)
                      ....+..+.+. ...+.|+++||||++..  . ...+++++..+.....   ...+.+++......+...    ..+...
T Consensus       135 ~L~ll~~i~~~-lr~~lqlilmSATl~~~--~-l~~~~~~~~~I~~~gr---~~pV~~~y~~~~~~~~~~~~v~~~l~~~  207 (812)
T PRK11664        135 ALALLLDVQQG-LRDDLKLLIMSATLDND--R-LQQLLPDAPVIVSEGR---SFPVERRYQPLPAHQRFDEAVARATAEL  207 (812)
T ss_pred             HHHHHHHHHHh-CCccceEEEEecCCCHH--H-HHHhcCCCCEEEecCc---cccceEEeccCchhhhHHHHHHHHHHHH
Confidence            22333344443 34678999999999863  2 3456665544443322   223555554443322211    234444


Q ss_pred             HhccCCCCEEEEecchHHHHHHHHHhhc---CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcE
Q 042003          155 FAESLNPPVLIFVQSKERAKELYGELAF---DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC  231 (248)
Q Consensus       155 ~~~~~~~~~liF~~~~~~~~~l~~~L~~---~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~  231 (248)
                      ++.. .+.+|||+++.++++.+++.|++   .++.+..+||+|+.++|..+++.|++|+.+|+|||+++++|+|+|++++
T Consensus       208 l~~~-~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~  286 (812)
T PRK11664        208 LRQE-SGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRL  286 (812)
T ss_pred             HHhC-CCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceE
Confidence            4443 68999999999999999999987   5788999999999999999999999999999999999999999999999


Q ss_pred             EEeccCCCC
Q 042003          232 VINYDFPDS  240 (248)
Q Consensus       232 Vi~~~~p~~  240 (248)
                      ||++|.|+.
T Consensus       287 VID~Gl~r~  295 (812)
T PRK11664        287 VVDSGLERV  295 (812)
T ss_pred             EEECCCccc
Confidence            999998764

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.96  E-value=1.8e-28  Score=211.55  Aligned_cols=232  Identities=15%  Similarity=0.113  Sum_probs=161.8

Q ss_pred             CcchHHHHHHHhhcC---CCcEEEEcccchhhhc--ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccc
Q 042003            1 LATQTTRECKKLAKG---NKFQIKLMKKELVRST--DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~---~~~~~~~~~~~~~~~~--~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~   75 (248)
                      ||.|+.+.+.+....   .+ ..+...+|+....  .......+++|+|++.       ....+++++++|+||||....
T Consensus       234 La~qi~~~i~~~vg~~~~~g-~~v~v~~Gg~~~~~~~t~~k~~~Ilv~T~~L-------~l~~L~~v~~VVIDEaHEr~~  305 (675)
T PHA02653        234 LVRLHSITLLKSLGFDEIDG-SPISLKYGSIPDELINTNPKPYGLVFSTHKL-------TLNKLFDYGTVIIDEVHEHDQ  305 (675)
T ss_pred             HHHHHHHHHHHHhCccccCC-ceEEEEECCcchHHhhcccCCCCEEEEeCcc-------cccccccCCEEEccccccCcc
Confidence            567888877765433   23 3455556665322  2233367999999752       112478899999999999876


Q ss_pred             cCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCC---------chh
Q 042003           76 VGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS---------EEG  146 (248)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~  146 (248)
                      .+   ..+..+++.......|+++||||++.....+ ..+++++..+.+..  ....++.+.+.....         ...
T Consensus       306 ~~---DllL~llk~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~g--rt~~pV~~~yi~~~~~~~~~~~y~~~~  379 (675)
T PHA02653        306 IG---DIIIAVARKHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPG--GTLFPISEVYVKNKYNPKNKRAYIEEE  379 (675)
T ss_pred             ch---hHHHHHHHHhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCC--CcCCCeEEEEeecCcccccchhhhHHH
Confidence            54   3344444443333458999999998777666 56777887776542  223455555543221         112


Q ss_pred             HHHHHHHHHhc--cCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHh-hcCCceEEEEecccc
Q 042003          147 KLLALRQSFAE--SLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDF-RAGKTWVLIATDVIA  221 (248)
Q Consensus       147 ~~~~l~~~~~~--~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f-~~g~~~ilv~T~~~~  221 (248)
                      +...+..+...  ..++++|||++++++++.+++.|++.  ++.+..+||+|++.  ++.++.| ++|+.+|||||++++
T Consensus       380 k~~~l~~L~~~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAE  457 (675)
T PHA02653        380 KKNIVTALKKYTPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLE  457 (675)
T ss_pred             HHHHHHHHHHhhcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhh
Confidence            22222222221  22568999999999999999999877  68999999999974  5666776 789999999999999


Q ss_pred             cCCCCCCCcEEEecc---CCC---------CcccceecC
Q 042003          222 RGMDFKGVNCVINYD---FPD---------SGAAYIHRI  248 (248)
Q Consensus       222 ~Gidip~~~~Vi~~~---~p~---------~~~~~~qri  248 (248)
                      +|+|+|++++||++|   .|.         |.++|.||.
T Consensus       458 RGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRa  496 (675)
T PHA02653        458 SSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRK  496 (675)
T ss_pred             ccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhc
Confidence            999999999999999   565         777889984

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.96  E-value=2e-28  Score=208.27  Aligned_cols=233  Identities=13%  Similarity=0.109  Sum_probs=159.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+.+.+++++...+ ..+..+.++...    ..+.+|+|+||+++.+...   ..+++++++|+||||++.+..   
T Consensus       170 L~~Q~~~~l~~~~~~~~-~~~~~i~~g~~~----~~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~~~---  238 (501)
T PHA02558        170 LVTQMIDDFVDYRLFPR-EAMHKIYSGTAK----DTDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTGKS---  238 (501)
T ss_pred             HHHHHHHHHHHhccccc-cceeEEecCccc----CCCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccchh---
Confidence            67899999998876543 233333333321    1357999999999865432   246899999999999987543   


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHH--HHhcCCcEEEEEcccc----cccccce-------------------
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELA--RSIMHDAVRVIVGRKN----TASESIK-------------------  135 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~--~~~~~~~~~~~~~~~~----~~~~~~~-------------------  135 (248)
                        +..++.. .++..+++++|||++.......  ..++++.. ......+    .......                   
T Consensus       239 --~~~il~~-~~~~~~~lGLTATp~~~~~~~~~~~~~fG~i~-~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~  314 (501)
T PHA02558        239 --LTSIITK-LDNCKFKFGLTGSLRDGKANILQYVGLFGDIF-KPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGE  314 (501)
T ss_pred             --HHHHHHh-hhccceEEEEeccCCCccccHHHHHHhhCCce-EEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhccc
Confidence              3444444 2345678999999865322211  11223211 1111000    0000000                   


Q ss_pred             ---eEEEEcCCchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC
Q 042003          136 ---QKLVFAGSEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK  210 (248)
Q Consensus       136 ---~~~~~~~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~  210 (248)
                         ..+......+.+...+..+....  .+.+++|||++.++++.+++.|++.+.++..+||+|+.++|..+++.|++|+
T Consensus       315 ~~~~~~~~l~~~~~Rn~~I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~  394 (501)
T PHA02558        315 DYQEEIKYITSHTKRNKWIANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGK  394 (501)
T ss_pred             chHHHHHHHhccHHHHHHHHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCC
Confidence               00001112223444444443322  2578999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEe-cccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          211 TWVLIAT-DVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       211 ~~ilv~T-~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ..+|||| +.+++|+|+|++++||++.+|.|...|+||+
T Consensus       395 ~~vLvaT~~~l~eG~Dip~ld~vIl~~p~~s~~~~~Qri  433 (501)
T PHA02558        395 GIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSI  433 (501)
T ss_pred             CeEEEEEcceeccccccccccEEEEecCCcchhhhhhhh
Confidence            9999998 8999999999999999999999999999986

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.96  E-value=1.9e-28  Score=201.41  Aligned_cols=205  Identities=21%  Similarity=0.298  Sum_probs=141.4

Q ss_pred             CCcEEEeChHHHHHHHhcCC----cccC--ceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHH
Q 042003           37 SCDILISTPLRLRLAIRRKK----IDLS--RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEE  110 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~~~----~~~~--~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~  110 (248)
                      .++|+|+||+++...+....    ..+.  ..+++|+||+|.+.+++ +. .+..+++.+...+.|+++||||+|....+
T Consensus        94 ~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~-~~-~l~~~l~~l~~~~~~~i~~SATlp~~l~~  171 (358)
T TIGR01587        94 LDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYT-LA-LILAVLEVLKDNDVPILLMSATLPKFLKE  171 (358)
T ss_pred             hCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHH-HH-HHHHHHHHHHHcCCCEEEEecCchHHHHH
Confidence            46899999999988877521    1111  23789999999998754 22 25555554445678999999999976665


Q ss_pred             HHHHhcCCcEEEEEcccccccccc-eeEEEE-cCCchhHHHHHHHHHhcc-CCCCEEEEecchHHHHHHHHHhhcCCC--
Q 042003          111 LARSIMHDAVRVIVGRKNTASESI-KQKLVF-AGSEEGKLLALRQSFAES-LNPPVLIFVQSKERAKELYGELAFDGI--  185 (248)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~l~~~~~~~-~~~~~liF~~~~~~~~~l~~~L~~~~~--  185 (248)
                      ........+........  ..... .+.+.. ......+...+..++... .+++++|||+++++++.+++.|++.+.  
T Consensus       172 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~  249 (358)
T TIGR01587       172 YAEKIGYVEFNEPLDLK--EERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEE  249 (358)
T ss_pred             HHhcCCCcccccCCCCc--cccccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCHHHHHHHHHHHHhhcCCC
Confidence            55544322111100100  00011 122211 222223444444444432 368999999999999999999988765  


Q ss_pred             eeEEEecCCCHHHHHH----HHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          186 RAGVIHSDLSQTQREN----AVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       186 ~v~~~~~~~~~~~r~~----~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      .+..+||++++.+|.+    +++.|++|+..+||||+++++|+|+| +++||++..|  +.+|+||+
T Consensus       250 ~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iqr~  313 (358)
T TIGR01587       250 EIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQRL  313 (358)
T ss_pred             eEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEEEEcCCC--HHHHHHHh
Confidence            5999999999999976    48899999999999999999999996 8888888776  67899985

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.95  E-value=2.3e-27  Score=220.12  Aligned_cols=235  Identities=18%  Similarity=0.213  Sum_probs=172.3

Q ss_pred             CcchHHHHHHHhhcCCCc-EEEEcccchhhhc-------ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKF-QIKLMKKELVRST-------DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~-~~~~~~~~~~~~~-------~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~   72 (248)
                      |+.|+.+.++.++...++ ..+..++|+....       .+..+.++|+|+||+.+.+.+...  ...+++++|+||||+
T Consensus       134 La~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l--~~~~i~~iVVDEAD~  211 (1638)
T PRK14701        134 LVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM--KHLKFDFIFVDDVDA  211 (1638)
T ss_pred             HHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH--hhCCCCEEEEECcee
Confidence            688999999999887642 3444555554211       122346999999999988766542  227789999999999


Q ss_pred             ccccC----------cccccchh----Hhh-------------------h--CCCccce-eEEEEeecCchHHHHHHHhc
Q 042003           73 LFEVG----------NLLKHIDP----VVK-------------------A--CSNPSIV-RSLFSATLPDFVEELARSIM  116 (248)
Q Consensus        73 ~~~~~----------~~~~~~~~----~~~-------------------~--~~~~~~~-~i~~SAT~~~~~~~~~~~~~  116 (248)
                      +++|+          .|...+..    +++                   .  ..+...| ++.+|||+++.. .. ..++
T Consensus       212 ml~~~knid~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~-~~-~~l~  289 (1638)
T PRK14701        212 FLKASKNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKG-DR-VKLY  289 (1638)
T ss_pred             ccccccccchhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchh-HH-HHHh
Confidence            98753          14444432    211                   0  0122344 677999998742 22 2345


Q ss_pred             CCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHH---HHHHHHHhhcCCCeeEEEecC
Q 042003          117 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKER---AKELYGELAFDGIRAGVIHSD  193 (248)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~---~~~l~~~L~~~~~~v~~~~~~  193 (248)
                      .++..+.++.......++.+.+...... .+ ..+.++++.. +..+||||++++.   |+.+++.|+..|+++..+||+
T Consensus       290 ~~~l~f~v~~~~~~lr~i~~~yi~~~~~-~k-~~L~~ll~~~-g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~  366 (1638)
T PRK14701        290 RELLGFEVGSGRSALRNIVDVYLNPEKI-IK-EHVRELLKKL-GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK  366 (1638)
T ss_pred             hcCeEEEecCCCCCCCCcEEEEEECCHH-HH-HHHHHHHHhC-CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch
Confidence            6777777777766667777777655433 23 5677777776 5789999999775   589999999999999999995


Q ss_pred             CCHHHHHHHHHHhhcCCceEEEEec----ccccCCCCCC-CcEEEeccCCC---Ccccceec
Q 042003          194 LSQTQRENAVDDFRAGKTWVLIATD----VIARGMDFKG-VNCVINYDFPD---SGAAYIHR  247 (248)
Q Consensus       194 ~~~~~r~~~~~~f~~g~~~ilv~T~----~~~~Gidip~-~~~Vi~~~~p~---~~~~~~qr  247 (248)
                           |...++.|++|+.+|||||+    .+++|||+|+ +++|||||+|.   |...|.|.
T Consensus       367 -----R~~~l~~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~  423 (1638)
T PRK14701        367 -----NKKGFDLFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPT  423 (1638)
T ss_pred             -----HHHHHHHHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccc
Confidence                 88999999999999999994    7899999999 99999999999   87766653

>TIGR01054 rgy reverse gyrase

Probab=99.95  E-value=3.7e-27  Score=214.69  Aligned_cols=225  Identities=18%  Similarity=0.232  Sum_probs=163.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEE--Ecccchhhhc-------ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccc
Q 042003            1 LATQTTRECKKLAKGNKFQIK--LMKKELVRST-------DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEAD   71 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~--~~~~~~~~~~-------~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah   71 (248)
                      ||.|+++.++.+++..++..+  ..++|+....       ....++++|+|+||+++.+.+..  +.. +++++|+||||
T Consensus       133 La~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~--l~~-~~~~iVvDEaD  209 (1171)
T TIGR01054       133 LVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDE--LGP-KFDFIFVDDVD  209 (1171)
T ss_pred             HHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHH--hcC-CCCEEEEeChH
Confidence            689999999999987764333  2344554211       12334699999999999887764  212 89999999999


Q ss_pred             cccccC----------ccccc-chhHh----------------------hhCCCccce--eEEEEeec-CchHHHHHHHh
Q 042003           72 KLFEVG----------NLLKH-IDPVV----------------------KACSNPSIV--RSLFSATL-PDFVEELARSI  115 (248)
Q Consensus        72 ~~~~~~----------~~~~~-~~~~~----------------------~~~~~~~~~--~i~~SAT~-~~~~~~~~~~~  115 (248)
                      .+++++          .|... +..++                      +.. +...|  ++++|||. |....   ..+
T Consensus       210 ~~L~~~k~vd~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~q~~li~~SAT~~p~~~~---~~l  285 (1171)
T TIGR01054       210 ALLKASKNVDKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAI-PGKKRGCLIVSSATGRPRGKR---AKL  285 (1171)
T ss_pred             hhhhccccHHHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhh-hhccCcEEEEEeCCCCccccH---HHH
Confidence            998742          14432 33322                      111 22333  56789994 44332   234


Q ss_pred             cCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecch---HHHHHHHHHhhcCCCeeEEEec
Q 042003          116 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSK---ERAKELYGELAFDGIRAGVIHS  192 (248)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~---~~~~~l~~~L~~~~~~v~~~~~  192 (248)
                      +.+...+.++.......++.+.+.....   +...+.++++.. +.++||||+++   +.|+.+++.|++.|+++..+||
T Consensus       286 ~r~ll~~~v~~~~~~~r~I~~~~~~~~~---~~~~L~~ll~~l-~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg  361 (1171)
T TIGR01054       286 FRELLGFEVGGGSDTLRNVVDVYVEDED---LKETLLEIVKKL-GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHA  361 (1171)
T ss_pred             cccccceEecCccccccceEEEEEeccc---HHHHHHHHHHHc-CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeC
Confidence            4555556666666666777777654433   234566777665 57899999999   9999999999999999999999


Q ss_pred             CCCHHHHHHHHHHhhcCCceEEEEe----cccccCCCCCC-CcEEEeccCCCC
Q 042003          193 DLSQTQRENAVDDFRAGKTWVLIAT----DVIARGMDFKG-VNCVINYDFPDS  240 (248)
Q Consensus       193 ~~~~~~r~~~~~~f~~g~~~ilv~T----~~~~~Gidip~-~~~Vi~~~~p~~  240 (248)
                      +++    +..++.|++|+.+|||||    +++++|+|+|+ +++||+||+|..
T Consensus       362 ~~~----~~~l~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~~  410 (1171)
T TIGR01054       362 TKP----KEDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPKF  410 (1171)
T ss_pred             CCC----HHHHHHHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCCCE
Confidence            997    368999999999999995    89999999999 899999999975

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.

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

Probab=99.95  E-value=1.7e-27  Score=194.58  Aligned_cols=238  Identities=21%  Similarity=0.247  Sum_probs=183.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh----hh---cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV----RS---TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~----~~---~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||+|-++.|+.--..++ .++..-.|..    .+   .-.....+||+|+|.+.+-.+++.+ -.+.+++.+||||+|.+
T Consensus       273 LANQKy~dF~~rYs~Lg-lkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEiHtL  350 (830)
T COG1202         273 LANQKYEDFKERYSKLG-LKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEIHTL  350 (830)
T ss_pred             hhcchHHHHHHHhhccc-ceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeeeeeec
Confidence            78999999998767777 5554444443    11   1223457899999999998888776 56899999999999998


Q ss_pred             cccC--cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHH
Q 042003           74 FEVG--NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLAL  151 (248)
Q Consensus        74 ~~~~--~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  151 (248)
                      -+..  +...-+-..+++ ..+..|+|++|||..+ ..+++..+.-+.+.+     +..+.++..+.+.+.+..+|.+.+
T Consensus       351 ~deERG~RLdGLI~RLr~-l~~~AQ~i~LSATVgN-p~elA~~l~a~lV~y-----~~RPVplErHlvf~~~e~eK~~ii  423 (830)
T COG1202         351 EDEERGPRLDGLIGRLRY-LFPGAQFIYLSATVGN-PEELAKKLGAKLVLY-----DERPVPLERHLVFARNESEKWDII  423 (830)
T ss_pred             cchhcccchhhHHHHHHH-hCCCCeEEEEEeecCC-hHHHHHHhCCeeEee-----cCCCCChhHeeeeecCchHHHHHH
Confidence            7653  333333333444 3357899999999987 677777775555444     233455667888888888899888


Q ss_pred             HHHHhcc--------CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccC
Q 042003          152 RQSFAES--------LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG  223 (248)
Q Consensus       152 ~~~~~~~--------~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G  223 (248)
                      ..+.+..        ..+++|||++|++.|..++..|..+|+++.++|+|++..+|+.+..+|.++++.++|+|-+++.|
T Consensus       424 ~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AG  503 (830)
T COG1202         424 ARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAG  503 (830)
T ss_pred             HHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcC
Confidence            8877532        25699999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEE---eccCCC-Ccccceec
Q 042003          224 MDFKGVNCVI---NYDFPD-SGAAYIHR  247 (248)
Q Consensus       224 idip~~~~Vi---~~~~p~-~~~~~~qr  247 (248)
                      +|+|.-.+|+   -+|.-| |+..|.||
T Consensus       504 VDFPASQVIFEsLaMG~~WLs~~EF~QM  531 (830)
T COG1202         504 VDFPASQVIFESLAMGIEWLSVREFQQM  531 (830)
T ss_pred             CCCchHHHHHHHHHcccccCCHHHHHHH
Confidence            9999544442   344444 77777776

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.95  E-value=3.5e-27  Score=206.24  Aligned_cols=241  Identities=22%  Similarity=0.223  Sum_probs=173.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      ||+|.++.+++ ...+| ++|...+|..+.......+++|+|+|||++-+..++.......++++|+||+|.+.+.. ..
T Consensus        88 La~Ek~~~~~~-~~~~G-irV~~~TgD~~~~~~~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~-RG  164 (766)
T COG1204          88 LAEEKYEEFSR-LEELG-IRVGISTGDYDLDDERLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRT-RG  164 (766)
T ss_pred             HHHHHHHHhhh-HHhcC-CEEEEecCCcccchhhhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcc-cC
Confidence            57788888884 45567 88888888887666667789999999999999999988788999999999999998874 56


Q ss_pred             ccchhHhhhCCC--ccceeEEEEeecCchHHHHHHHhcCCcEEEEEccc--ccccccceeEEEEcCCc--------hhHH
Q 042003           81 KHIDPVVKACSN--PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK--NTASESIKQKLVFAGSE--------EGKL  148 (248)
Q Consensus        81 ~~~~~~~~~~~~--~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~--------~~~~  148 (248)
                      +.+..+......  ...|++++|||+|+ ..++..|+-.++......+.  ....+.....+......        +..+
T Consensus       165 ~~lE~iv~r~~~~~~~~rivgLSATlpN-~~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~  243 (766)
T COG1204         165 PVLESIVARMRRLNELIRIVGLSATLPN-AEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLAL  243 (766)
T ss_pred             ceehhHHHHHHhhCcceEEEEEeeecCC-HHHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHH
Confidence            666666554333  23799999999998 77888887666542111111  11111111222111111        1222


Q ss_pred             HHHHHHHhccCCCCEEEEecchHHHHHHHHHhhc---------------------C----------------CCeeEEEe
Q 042003          149 LALRQSFAESLNPPVLIFVQSKERAKELYGELAF---------------------D----------------GIRAGVIH  191 (248)
Q Consensus       149 ~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~---------------------~----------------~~~v~~~~  191 (248)
                      ..+.+.++.  +++++|||+|++.+...++.|+.                     .                ..+++++|
T Consensus       244 ~~v~~~~~~--~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHh  321 (766)
T COG1204         244 ELVLESLAE--GGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHH  321 (766)
T ss_pred             HHHHHHHhc--CCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccc
Confidence            222222333  68999999999999999988872                     0                13578999


Q ss_pred             cCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEE----ecc-----CCCCcccceec
Q 042003          192 SDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI----NYD-----FPDSGAAYIHR  247 (248)
Q Consensus       192 ~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi----~~~-----~p~~~~~~~qr  247 (248)
                      +|++.++|.-+.+.|+.|+++||+||++++.|+|+|.-++||    -|+     .+.++.+++|+
T Consensus       322 AGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM  386 (766)
T COG1204         322 AGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQM  386 (766)
T ss_pred             cCCCHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhc
Confidence            999999999999999999999999999999999999655554    344     34455566665

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.95  E-value=1.6e-26  Score=208.44  Aligned_cols=228  Identities=18%  Similarity=0.238  Sum_probs=156.0

Q ss_pred             CcchHHHHHHH-hhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc-ccccCc
Q 042003            1 LATQTTRECKK-LAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK-LFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~-~~~~~~   78 (248)
                      ||.|+++.+.. ++...|. .       ..-.+....+++|+|+||+.|++.+..... +++++++||||||. .++.+ 
T Consensus       134 LA~RVA~El~~~lG~~VGY-~-------vrf~~~~s~~t~I~v~TpG~LL~~l~~d~~-Ls~~~~IIIDEAHERsLn~D-  203 (1294)
T PRK11131        134 VANRIAEELETELGGCVGY-K-------VRFNDQVSDNTMVKLMTDGILLAEIQQDRL-LMQYDTIIIDEAHERSLNID-  203 (1294)
T ss_pred             HHHHHHHHHhhhhcceece-e-------ecCccccCCCCCEEEEChHHHHHHHhcCCc-cccCcEEEecCccccccccc-
Confidence            45666666654 4443331 1       111223346799999999999999987654 89999999999994 66655 


Q ss_pred             ccc-cchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCc-----hhHHHHHH
Q 042003           79 LLK-HIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSE-----EGKLLALR  152 (248)
Q Consensus        79 ~~~-~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~l~  152 (248)
                      |.- .+..++..  .++.|+|+||||++.  ..+...+.+.+ .+.+....   ..+...+......     .+....+.
T Consensus       204 fLLg~Lk~lL~~--rpdlKvILmSATid~--e~fs~~F~~ap-vI~V~Gr~---~pVei~y~p~~~~~~~~~~d~l~~ll  275 (1294)
T PRK11131        204 FILGYLKELLPR--RPDLKVIITSATIDP--ERFSRHFNNAP-IIEVSGRT---YPVEVRYRPIVEEADDTERDQLQAIF  275 (1294)
T ss_pred             hHHHHHHHhhhc--CCCceEEEeeCCCCH--HHHHHHcCCCC-EEEEcCcc---ccceEEEeecccccchhhHHHHHHHH
Confidence            432 23333322  246899999999975  34554444444 34333222   2344444443221     12223332


Q ss_pred             HHH---hccCCCCEEEEecchHHHHHHHHHhhcCCCe---eEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCC
Q 042003          153 QSF---AESLNPPVLIFVQSKERAKELYGELAFDGIR---AGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDF  226 (248)
Q Consensus       153 ~~~---~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~---v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidi  226 (248)
                      ..+   .....+++|||+++..+++.+++.|++.+.+   +..+||++++++|..+++.  .|..+|+|||+++++|+|+
T Consensus       276 ~~V~~l~~~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITI  353 (1294)
T PRK11131        276 DAVDELGREGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTV  353 (1294)
T ss_pred             HHHHHHhcCCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhcccc
Confidence            222   1233679999999999999999999987654   7789999999999999886  5778999999999999999


Q ss_pred             CCCcEEEeccC---------------C---CCcccceecC
Q 042003          227 KGVNCVINYDF---------------P---DSGAAYIHRI  248 (248)
Q Consensus       227 p~~~~Vi~~~~---------------p---~~~~~~~qri  248 (248)
                      |++++||++|.               |   .|..+|.||.
T Consensus       354 pgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRa  393 (1294)
T PRK11131        354 PGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRK  393 (1294)
T ss_pred             CcceEEEECCCccccccccccCcccCCeeecCHhhHhhhc
Confidence            99999999973               3   4557899984

>PRK13766 Hef nuclease; Provisional

Probab=99.95  E-value=2.3e-26  Score=205.93  Aligned_cols=245  Identities=22%  Similarity=0.243  Sum_probs=168.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      |+.|+.+.++++....+ ..+..+.|+.  ........+++|+|+||+.+.+.+..+.+.+.+++++|+||||++.+...
T Consensus        70 L~~Q~~~~~~~~~~~~~-~~v~~~~g~~~~~~r~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~  148 (773)
T PRK13766         70 LVEQHAEFFRKFLNIPE-EKIVVFTGEVSPEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYA  148 (773)
T ss_pred             HHHHHHHHHHHHhCCCC-ceEEEEeCCCCHHHHHHHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCcccccccc
Confidence            57888888888765443 3445555544  22333455789999999999998888888899999999999999876542


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHH---HHHHhcCCcEEEE--------------------Eccc--------
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEE---LARSIMHDAVRVI--------------------VGRK--------  127 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~---~~~~~~~~~~~~~--------------------~~~~--------  127 (248)
                      +.... ..... ....+.++++|||+......   ....+......+.                    ....        
T Consensus       149 ~~~i~-~~~~~-~~~~~~il~lTaTP~~~~~~i~~~~~~L~i~~v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~~~i~~  226 (773)
T PRK13766        149 YVYIA-ERYHE-DAKNPLVLGLTASPGSDEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRD  226 (773)
T ss_pred             HHHHH-HHHHh-cCCCCEEEEEEcCCCCCHHHHHHHHHhCCceEEEEcCCCChhHHhhhccceeEEEEeCCcHHHHHHHH
Confidence            33222 22222 23456789999997533221   1222111100000                    0000        


Q ss_pred             ----------------c-c--cc------------ccceeEE--------------------------------------
Q 042003          128 ----------------N-T--AS------------ESIKQKL--------------------------------------  138 (248)
Q Consensus       128 ----------------~-~--~~------------~~~~~~~--------------------------------------  138 (248)
                                      . .  ..            ..+....                                      
T Consensus       227 ~l~~~~~~~l~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~y  306 (773)
T PRK13766        227 LLNEALKDRLKKLKELGVIVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVEALRRY  306 (773)
T ss_pred             HHHHHHHHHHHHHHHCCCcccCCCCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHH
Confidence                            0 0  00            0000000                                      


Q ss_pred             ---------------------------------EEcCCchhHHHHHHHHHhc----cCCCCEEEEecchHHHHHHHHHhh
Q 042003          139 ---------------------------------VFAGSEEGKLLALRQSFAE----SLNPPVLIFVQSKERAKELYGELA  181 (248)
Q Consensus       139 ---------------------------------~~~~~~~~~~~~l~~~~~~----~~~~~~liF~~~~~~~~~l~~~L~  181 (248)
                                                       ..+.....|...+.+++..    ..+.++||||++++.++.+++.|.
T Consensus       307 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~  386 (773)
T PRK13766        307 LERLREEARSSGGSKASKRLVEDPRFRKAVRKAKELDIEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLE  386 (773)
T ss_pred             HHHHHhhccccCCcHHHHHHHhCHHHHHHHHHHHhcccCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHH
Confidence                                             0001112345555555543    457899999999999999999999


Q ss_pred             cCCCeeEEEecC--------CCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          182 FDGIRAGVIHSD--------LSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       182 ~~~~~v~~~~~~--------~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ..++++..+||.        |++.+|.++++.|++|+.++||||+++++|+|+|++++||+||+|+|+.+|+||+
T Consensus       387 ~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~  461 (773)
T PRK13766        387 KEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRK  461 (773)
T ss_pred             hCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHh
Confidence            999999999886        9999999999999999999999999999999999999999999999999999985

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

Probab=99.95  E-value=2.3e-26  Score=192.78  Aligned_cols=223  Identities=18%  Similarity=0.236  Sum_probs=171.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-------hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-------RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.+.++.+.++ +.|.+..|..       ....+..+..+++|+|     +.+..+...+.++.++|+||-|++
T Consensus       323 LA~QH~~~~~~~l~~~~-i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGT-----HALiQd~V~F~~LgLVIiDEQHRF  396 (677)
T COG1200         323 LAEQHYESLRKWLEPLG-IRVALLTGSLKGKARKEILEQLASGEIDIVVGT-----HALIQDKVEFHNLGLVIIDEQHRF  396 (677)
T ss_pred             HHHHHHHHHHHHhhhcC-CeEEEeecccchhHHHHHHHHHhCCCCCEEEEc-----chhhhcceeecceeEEEEeccccc
Confidence            79999999999999999 6677666665       2234455669999999     677778888999999999999994


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  153 (248)
                            .-.-...+.......+.++.||||+-|+.  ++...++|...-.+.........+....+.....++-++.+..
T Consensus       397 ------GV~QR~~L~~KG~~~Ph~LvMTATPIPRT--LAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~  468 (677)
T COG1200         397 ------GVHQRLALREKGEQNPHVLVMTATPIPRT--LALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIRE  468 (677)
T ss_pred             ------cHHHHHHHHHhCCCCCcEEEEeCCCchHH--HHHHHhccccchhhccCCCCCCceEEEEeccccHHHHHHHHHH
Confidence                  33333334432222577899999988744  4445566765555555554555666777666666666677776


Q ss_pred             HHhccCCCCEEEEecchHH--------HHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccC
Q 042003          154 SFAESLNPPVLIFVQSKER--------AKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG  223 (248)
Q Consensus       154 ~~~~~~~~~~liF~~~~~~--------~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G  223 (248)
                      .+.+  +.++.+.|+-+++        |...++.|+..  +++++.+||.|+.+++.+++++|++|+.+|||||.+++.|
T Consensus       469 ei~~--GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVG  546 (677)
T COG1200         469 EIAK--GRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVG  546 (677)
T ss_pred             HHHc--CCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEec
Confidence            6664  7899999987654        45666777643  5679999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEeccCCC
Q 042003          224 MDFKGVNCVINYDFPD  239 (248)
Q Consensus       224 idip~~~~Vi~~~~p~  239 (248)
                      ||+|++++.|+.++-+
T Consensus       547 VdVPnATvMVIe~AER  562 (677)
T COG1200         547 VDVPNATVMVIENAER  562 (677)
T ss_pred             ccCCCCeEEEEechhh
Confidence            9999999999987643

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.95  E-value=7.9e-26  Score=184.66  Aligned_cols=201  Identities=18%  Similarity=0.124  Sum_probs=135.3

Q ss_pred             CCCcEEEeChHHHHHHHhcC----C----cccCceeEEEEeccccccccCc-ccc---cchhHhhhCCCccceeEEEEee
Q 042003           36 FSCDILISTPLRLRLAIRRK----K----IDLSRVEYLVLDEADKLFEVGN-LLK---HIDPVVKACSNPSIVRSLFSAT  103 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~----~----~~~~~~~~lIiDEah~~~~~~~-~~~---~~~~~~~~~~~~~~~~i~~SAT  103 (248)
                      ..++++++||+.+..++...    .    ..+.+++++|+||+|.+..+.. ...   ....+.+. .....++++||||
T Consensus       112 ~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~H~~~~~~~~~~~~~l~~~~~~~~-~~~~~~~i~lSAT  190 (357)
T TIGR03158       112 STPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEFHLYDAKQLVGMLFLLAYMQLIRF-FECRRKFVFLSAT  190 (357)
T ss_pred             CCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecccccCcccchhhhhhhHHHHHHHh-hhcCCcEEEEecC
Confidence            36889999999997665431    1    1257899999999999875430 111   11122222 1234689999999


Q ss_pred             cCchHHHHHHHh--cCCcEEEEEccccc------------------ccccceeEEEEcCCchhHHHHH-------HHHHh
Q 042003          104 LPDFVEELARSI--MHDAVRVIVGRKNT------------------ASESIKQKLVFAGSEEGKLLAL-------RQSFA  156 (248)
Q Consensus       104 ~~~~~~~~~~~~--~~~~~~~~~~~~~~------------------~~~~~~~~~~~~~~~~~~~~~l-------~~~~~  156 (248)
                      +++.........  ++.+.....+..-.                  ..+.+...+..  ....+...+       .+.++
T Consensus       191 ~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~--~~~~~~~~l~~l~~~i~~~~~  268 (357)
T TIGR03158       191 PDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSFRPVLPPVELELIP--APDFKEEELSELAEEVIERFR  268 (357)
T ss_pred             CCHHHHHHHHhccccCceeeeecCcccccCCChhhhccccccccceeccceEEEEEe--CCchhHHHHHHHHHHHHHHHh
Confidence            998777766654  45554333333100                  00234444433  222222222       22222


Q ss_pred             ccCCCCEEEEecchHHHHHHHHHhhcCC--CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe
Q 042003          157 ESLNPPVLIFVQSKERAKELYGELAFDG--IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN  234 (248)
Q Consensus       157 ~~~~~~~liF~~~~~~~~~l~~~L~~~~--~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~  234 (248)
                      ...+++++|||+|++.++.+++.|++.+  ..+..+||.+++.+|++.      ++.+|||||+++++|+|+|.. +|| 
T Consensus       269 ~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-  340 (357)
T TIGR03158       269 QLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-  340 (357)
T ss_pred             ccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-
Confidence            3346799999999999999999999764  578899999999988654      368899999999999999986 555 


Q ss_pred             ccCCCCcccceecC
Q 042003          235 YDFPDSGAAYIHRI  248 (248)
Q Consensus       235 ~~~p~~~~~~~qri  248 (248)
                      ++ |.+...|+||+
T Consensus       341 ~~-p~~~~~yiqR~  353 (357)
T TIGR03158       341 FS-ARDAAAFWQRL  353 (357)
T ss_pred             EC-CCCHHHHhhhc
Confidence            45 89999999996

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.

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

Probab=99.94  E-value=7.3e-27  Score=185.32  Aligned_cols=247  Identities=24%  Similarity=0.318  Sum_probs=184.5

Q ss_pred             CcchHHHHHHHhhcCCCc--EEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccc
Q 042003            1 LATQTTRECKKLAKGNKF--QIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~--~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~   75 (248)
                      ||+|++..+++|-.....  .+..++.|+.   ++...+..+.+|+|+||+++...+..+.+.++.+.++++||++.++.
T Consensus       298 laEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crFlvlDead~lL~  377 (725)
T KOG0349|consen  298 LAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRFLVLDEADLLLG  377 (725)
T ss_pred             HHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEEEEecchhhhhh
Confidence            578999877766554422  2333555554   77788889999999999999999999999999999999999999998


Q ss_pred             cCcccccchhHhhhCCC-----ccceeEEEEeecCc-hHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCC------
Q 042003           76 VGNLLKHIDPVVKACSN-----PSIVRSLFSATLPD-FVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS------  143 (248)
Q Consensus        76 ~~~~~~~~~~~~~~~~~-----~~~~~i~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------  143 (248)
                      .+ +-..+.++......     ...|.+.+|||+.. +...+....+..|..+....++..+..+.+....+..      
T Consensus       378 qg-y~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvHhvv~lv~p~~d~sw  456 (725)
T KOG0349|consen  378 QG-YDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHHVVKLVCPSVDGSW  456 (725)
T ss_pred             cc-cHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhccceeecCCccCccH
Confidence            77 55555555444321     46789999999853 2233444455566666554444333333222211110      


Q ss_pred             -----------------------chhHHHHHH---------HHHhccCCCCEEEEecchHHHHHHHHHhhcCC---CeeE
Q 042003          144 -----------------------EEGKLLALR---------QSFAESLNPPVLIFVQSKERAKELYGELAFDG---IRAG  188 (248)
Q Consensus       144 -----------------------~~~~~~~l~---------~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~---~~v~  188 (248)
                                             +.+..+...         ..++++.-.++||||.++.+|..+.+.++.+|   ++|.
T Consensus       457 ~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scv  536 (725)
T KOG0349|consen  457 CDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCV  536 (725)
T ss_pred             HHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHHHHHHHcCCccceeE
Confidence                                   111111111         12233445689999999999999999998764   6899


Q ss_pred             EEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          189 VIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       189 ~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      .+||+..+.+|++.++.|+.+..+.||||+++++|+||..+-++|+..+|.+...|.|||
T Consensus       537 clhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhri  596 (725)
T KOG0349|consen  537 CLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRI  596 (725)
T ss_pred             EEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhh
Confidence            999999999999999999999999999999999999999999999999999999999997

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.93  E-value=4.6e-25  Score=190.28  Aligned_cols=232  Identities=13%  Similarity=0.054  Sum_probs=151.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcC--------CcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRK--------KIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~--------~~~~~~~~~lIiDEah~   72 (248)
                      |+.||.+.+.++....+ ..+..++|+.  ........+|+|+|++++.+...+.        .+.-..++++|+||||+
T Consensus       310 Lv~QW~~ef~~~~~l~~-~~I~~~tg~~--k~~~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~  386 (732)
T TIGR00603       310 SVEQWKQQFKMWSTIDD-SQICRFTSDA--KERFHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHV  386 (732)
T ss_pred             HHHHHHHHHHHhcCCCC-ceEEEEecCc--ccccccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEcccc
Confidence            46799999998865433 3344444432  1122235789999999876443221        12235788999999999


Q ss_pred             ccccCcccccchhHhhhCCCccceeEEEEeecCchHHH--HHHHhcCCcEEEEEcccc----cccccceeEEEE------
Q 042003           73 LFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEE--LARSIMHDAVRVIVGRKN----TASESIKQKLVF------  140 (248)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~--~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~------  140 (248)
                      +.+.. |..    ++..+.  ....+++|||+......  ....+++. ..+.....+    .....+...-++      
T Consensus       387 lpA~~-fr~----il~~l~--a~~RLGLTATP~ReD~~~~~L~~LiGP-~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~  458 (732)
T TIGR00603       387 VPAAM-FRR----VLTIVQ--AHCKLGLTATLVREDDKITDLNFLIGP-KLYEANWMELQKKGFIANVQCAEVWCPMTPE  458 (732)
T ss_pred             ccHHH-HHH----HHHhcC--cCcEEEEeecCcccCCchhhhhhhcCC-eeeecCHHHHHhCCccccceEEEEEecCCHH
Confidence            86643 333    333321  23468999998642221  12233332 111111100    000011100001      


Q ss_pred             ----------------cCCchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHH
Q 042003          141 ----------------AGSEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENA  202 (248)
Q Consensus       141 ----------------~~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~  202 (248)
                                      ...++.|...+..+++.+  .+.++||||++...+..+++.|.     +..+||+++..+|+.+
T Consensus       459 ~~~~yl~~~~~~k~~l~~~np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~i  533 (732)
T TIGR00603       459 FYREYLRENSRKRMLLYVMNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQI  533 (732)
T ss_pred             HHHHHHHhcchhhhHHhhhChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHH
Confidence                            112235666666666644  47899999999999999998883     5678999999999999


Q ss_pred             HHHhhcC-CceEEEEecccccCCCCCCCcEEEeccCC-CCcccceecC
Q 042003          203 VDDFRAG-KTWVLIATDVIARGMDFKGVNCVINYDFP-DSGAAYIHRI  248 (248)
Q Consensus       203 ~~~f~~g-~~~ilv~T~~~~~Gidip~~~~Vi~~~~p-~~~~~~~qri  248 (248)
                      ++.|++| .+++||+|+++++|+|+|++++||+++.| .|..+|+||+
T Consensus       534 l~~Fr~~~~i~vLv~SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRl  581 (732)
T TIGR00603       534 LQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRL  581 (732)
T ss_pred             HHHHHhCCCccEEEEecccccccCCCCCCEEEEeCCCCCCHHHHHHHh
Confidence            9999875 77999999999999999999999999998 5999999995

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).

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

Probab=99.93  E-value=4.9e-25  Score=194.53  Aligned_cols=211  Identities=20%  Similarity=0.201  Sum_probs=162.7

Q ss_pred             CCcEEEeChHHHHHHHhcC--CcccCc---eeEEEEeccccccccC-cccccchhHhhhCC-CccceeEEEEeecCchHH
Q 042003           37 SCDILISTPLRLRLAIRRK--KIDLSR---VEYLVLDEADKLFEVG-NLLKHIDPVVKACS-NPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~~--~~~~~~---~~~lIiDEah~~~~~~-~~~~~~~~~~~~~~-~~~~~~i~~SAT~~~~~~  109 (248)
                      .++|+..||+++...-.-.  ...+..   +-++||||||++.+|| +|++...++..... .+.+.++++|||.+..++
T Consensus       356 ~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~  435 (941)
T KOG0351|consen  356 IIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRPSYKRLGLLRIRFPGVPFIALTATATERVR  435 (941)
T ss_pred             eEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccccHHHHHHHHHHhhCCCCCeEEeehhccHHHH
Confidence            5799999999886544321  122333   7899999999999997 67777777654432 344789999999998888


Q ss_pred             HHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEE
Q 042003          110 ELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGV  189 (248)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~  189 (248)
                      .-+...++-.... ........+++...+..-...+.....+...-..+..+..||||.++.+|+.+...|++.+.++..
T Consensus       436 ~DIi~~L~l~~~~-~~~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~  514 (941)
T KOG0351|consen  436 EDVIRSLGLRNPE-LFKSSFNRPNLKYEVSPKTDKDALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAF  514 (941)
T ss_pred             HHHHHHhCCCCcc-eecccCCCCCceEEEEeccCccchHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHh
Confidence            7666644322211 222333344555555433333334444444445556789999999999999999999999999999


Q ss_pred             EecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          190 IHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       190 ~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ||+||+..+|+.+-+.|-.++++|+|||=++++|||-||++.||||+.|.|+..|.|.+
T Consensus       515 YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~  573 (941)
T KOG0351|consen  515 YHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEA  573 (941)
T ss_pred             hhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999853

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.92  E-value=4.5e-24  Score=189.89  Aligned_cols=103  Identities=23%  Similarity=0.329  Sum_probs=95.8

Q ss_pred             hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHh-hcCCCeeEEEecCCCHHHHHHHHHHhhcC--CceEEEEeccccc
Q 042003          146 GKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL-AFDGIRAGVIHSDLSQTQRENAVDDFRAG--KTWVLIATDVIAR  222 (248)
Q Consensus       146 ~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L-~~~~~~v~~~~~~~~~~~r~~~~~~f~~g--~~~ilv~T~~~~~  222 (248)
                      .|...+.++++...+.|+||||+++..+..+++.| ...|+++..+||+|+..+|..+++.|+++  ...|||||+++++
T Consensus       479 ~Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgse  558 (956)
T PRK04914        479 PRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSE  558 (956)
T ss_pred             HHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhcc
Confidence            46778888888777889999999999999999999 46699999999999999999999999974  5899999999999


Q ss_pred             CCCCCCCcEEEeccCCCCcccceecC
Q 042003          223 GMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       223 Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+|++.+++||+||+|+|+..|.|||
T Consensus       559 GlNlq~a~~VInfDlP~nP~~~eQRI  584 (956)
T PRK04914        559 GRNFQFASHLVLFDLPFNPDLLEQRI  584 (956)
T ss_pred             CCCcccccEEEEecCCCCHHHHHHHh
Confidence            99999999999999999999999997

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

Probab=99.92  E-value=1.1e-23  Score=185.82  Aligned_cols=219  Identities=18%  Similarity=0.154  Sum_probs=175.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hh----cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RS----TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~----~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||+|++++|+.-.++++ .++.....-.   ++    ..+..+..||+|||     +.+.+..+.+++++++||||-|+ 
T Consensus       655 LA~QHy~tFkeRF~~fP-V~I~~LSRF~s~kE~~~il~~la~G~vDIvIGT-----HrLL~kdv~FkdLGLlIIDEEqR-  727 (1139)
T COG1197         655 LAQQHYETFKERFAGFP-VRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGT-----HRLLSKDVKFKDLGLLIIDEEQR-  727 (1139)
T ss_pred             hHHHHHHHHHHHhcCCC-eeEEEecccCCHHHHHHHHHHHhcCCccEEEec-----hHhhCCCcEEecCCeEEEechhh-
Confidence            79999999999999999 6666555444   22    23455678999999     67778888999999999999999 


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  153 (248)
                           |.-.-++-++. ...+..++.||||+-|++..+.....++...+.+++.++.+  ++.++ .-.+..--..++..
T Consensus       728 -----FGVk~KEkLK~-Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~p--V~T~V-~~~d~~~ireAI~R  798 (1139)
T COG1197         728 -----FGVKHKEKLKE-LRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLP--VKTFV-SEYDDLLIREAILR  798 (1139)
T ss_pred             -----cCccHHHHHHH-HhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcc--eEEEE-ecCChHHHHHHHHH
Confidence                 55556666666 45678899999999999999988887777666666555443  23333 22333334455555


Q ss_pred             HHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcE
Q 042003          154 SFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC  231 (248)
Q Consensus       154 ~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~  231 (248)
                      .+..  ++++....|.++..+++++.|+..  ..++++.||.|+..+-++++..|.+|+.+|||||.+++.|||||++|.
T Consensus       799 El~R--gGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANT  876 (1139)
T COG1197         799 ELLR--GGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANT  876 (1139)
T ss_pred             HHhc--CCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCce
Confidence            5555  689999999999999999999986  568999999999999999999999999999999999999999999999


Q ss_pred             EEeccC
Q 042003          232 VINYDF  237 (248)
Q Consensus       232 Vi~~~~  237 (248)
                      +|.-+.
T Consensus       877 iIIe~A  882 (1139)
T COG1197         877 IIIERA  882 (1139)
T ss_pred             EEEecc
Confidence            986554

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.92  E-value=7.6e-24  Score=180.84  Aligned_cols=149  Identities=22%  Similarity=0.202  Sum_probs=115.3

Q ss_pred             ceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccC--CCCEEEEecchHH
Q 042003           95 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL--NPPVLIFVQSKER  172 (248)
Q Consensus        95 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~liF~~~~~~  172 (248)
                      ..+.+||||.+....++...|..++..+.......  ....+.+++ ....+|...+.+.+....  ++++||||+|++.
T Consensus       409 ~kl~GmTGTa~~~~~El~~~y~l~vv~IPt~kp~~--r~~~~~~v~-~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~  485 (656)
T PRK12898        409 LRLAGMTGTAREVAGELWSVYGLPVVRIPTNRPSQ--RRHLPDEVF-LTAAAKWAAVAARVRELHAQGRPVLVGTRSVAA  485 (656)
T ss_pred             HHHhcccCcChHHHHHHHHHHCCCeEEeCCCCCcc--ceecCCEEE-eCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHH
Confidence            34568999998887788887877765554444332  122233333 345668888888886532  5789999999999


Q ss_pred             HHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCC---CCc-----EEEeccCCCCcccc
Q 042003          173 AKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK---GVN-----CVINYDFPDSGAAY  244 (248)
Q Consensus       173 ~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip---~~~-----~Vi~~~~p~~~~~~  244 (248)
                      ++.+++.|.+.++++..+||.++  +|+..+..+..++..|+|||+.+++|+||+   +++     +||+++.|.|...|
T Consensus       486 se~L~~~L~~~gi~~~~Lhg~~~--~rE~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y  563 (656)
T PRK12898        486 SERLSALLREAGLPHQVLNAKQD--AEEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARID  563 (656)
T ss_pred             HHHHHHHHHHCCCCEEEeeCCcH--HHHHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHH
Confidence            99999999999999999999865  455555556655667999999999999999   666     99999999999999


Q ss_pred             eecC
Q 042003          245 IHRI  248 (248)
Q Consensus       245 ~qri  248 (248)
                      .||+
T Consensus       564 ~hr~  567 (656)
T PRK12898        564 RQLA  567 (656)
T ss_pred             HHhc
Confidence            9985

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.91  E-value=9.9e-24  Score=191.09  Aligned_cols=197  Identities=18%  Similarity=0.236  Sum_probs=138.2

Q ss_pred             cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc-ccccCcccccchhHhhhCCCccceeEEEEeecCchHH
Q 042003           31 TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK-LFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        31 ~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~-~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  109 (248)
                      .+....+..|.++||+.|++.+..... ++++++||+||||. .++.+-....+..++..  .++.++|+||||++.  .
T Consensus       150 ~~~~s~~T~I~~~TdGiLLr~l~~d~~-L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~--rpdLKlIlmSATld~--~  224 (1283)
T TIGR01967       150 HDQVSSNTLVKLMTDGILLAETQQDRF-LSRYDTIIIDEAHERSLNIDFLLGYLKQLLPR--RPDLKIIITSATIDP--E  224 (1283)
T ss_pred             CcccCCCceeeeccccHHHHHhhhCcc-cccCcEEEEcCcchhhccchhHHHHHHHHHhh--CCCCeEEEEeCCcCH--H
Confidence            334456789999999999999877543 79999999999994 66655122335555443  356899999999974  4


Q ss_pred             HHHHHhcCCcEEEEEcccccccccceeEEEEcCCc-----hhHHHH----HHHHHhccCCCCEEEEecchHHHHHHHHHh
Q 042003          110 ELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSE-----EGKLLA----LRQSFAESLNPPVLIFVQSKERAKELYGEL  180 (248)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~----l~~~~~~~~~~~~liF~~~~~~~~~l~~~L  180 (248)
                      .+...+...+ .+.+....   ..+...+......     ..+...    +.++... ..+.+|||+++..+++.+++.|
T Consensus       225 ~fa~~F~~ap-vI~V~Gr~---~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~-~~GdILVFLpg~~EI~~l~~~L  299 (1283)
T TIGR01967       225 RFSRHFNNAP-IIEVSGRT---YPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAE-GPGDILIFLPGEREIRDAAEIL  299 (1283)
T ss_pred             HHHHHhcCCC-EEEECCCc---ccceeEEecccccccchhhhHHHHHHHHHHHHHhh-CCCCEEEeCCCHHHHHHHHHHH
Confidence            4554443334 33333222   2233333322211     122222    3333333 3689999999999999999999


Q ss_pred             hcCC---CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCC
Q 042003          181 AFDG---IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD  239 (248)
Q Consensus       181 ~~~~---~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~  239 (248)
                      ++.+   ..+..+||+|+.++|..+++.+  +..+|++||+++++|+|+|++++||++|.++
T Consensus       300 ~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r  359 (1283)
T TIGR01967       300 RKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTAR  359 (1283)
T ss_pred             HhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCcc
Confidence            8764   4688999999999999987654  3468999999999999999999999999653

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.

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

Probab=99.91  E-value=1e-23  Score=179.32  Aligned_cols=246  Identities=22%  Similarity=0.262  Sum_probs=160.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHHHHHHhcCCcc-cCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRLRLAIRRKKID-LSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~-~~~~~~lIiDEah~~~~~~~   78 (248)
                      |+.|..+.++.++.... .+..+.+... ..........+|+|+||+.+.+.+..+... ++.+.++||||||+-....+
T Consensus       118 Lv~QQ~a~~~~~~~~~~-~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~  196 (746)
T KOG0354|consen  118 LVNQQIACFSIYLIPYS-VTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHP  196 (746)
T ss_pred             HHHHHHHHHhhccCccc-ceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEccccccccccc
Confidence            34455577777776633 2222222111 444456678999999999999999886443 69999999999999887766


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcC-----------------------------------------
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH-----------------------------------------  117 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~-----------------------------------------  117 (248)
                      |...+...+.. +....|++++|||++..+.....-..+                                         
T Consensus       197 Y~~Vmr~~l~~-k~~~~qILgLTASpG~~~~~v~~~I~~L~asldvr~~ssi~~~y~~lr~~~~i~v~~~~~~~~~~~~f  275 (746)
T KOG0354|consen  197 YNNIMREYLDL-KNQGNQILGLTASPGSKLEQVQNVIDNLCASLDVRTESSIKSNYEELREHVQIPVDLSLCERDIEDPF  275 (746)
T ss_pred             HHHHHHHHHHh-hhccccEEEEecCCCccHHHHHHHHHhhheecccchhhhhhhhHHHHhccCcccCcHHHhhhhhhhhH
Confidence            77777676665 334449999999986433222111100                                         


Q ss_pred             --------------------CcE---EE-EEccccccccc--------------------------ce--eEEEE-----
Q 042003          118 --------------------DAV---RV-IVGRKNTASES--------------------------IK--QKLVF-----  140 (248)
Q Consensus       118 --------------------~~~---~~-~~~~~~~~~~~--------------------------~~--~~~~~-----  140 (248)
                                          +..   .. ..........+                          ++  ..+.+     
T Consensus       276 ~~~i~p~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~~~~ll~~~gir~~~~l~~~~~f~  355 (746)
T KOG0354|consen  276 GMIIEPLLQQLQEEGLIEISDKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKYNLALLISDGIRFVDALDYLEDFY  355 (746)
T ss_pred             HHHHHHHHHHHHhcCccccccccccccchhhhhhhhhccCCCccchhhHHHHHHHHHHHHHHhhcchhhHHHHhhhhhhc
Confidence                                000   00 00000000000                          00  00000     


Q ss_pred             ----------------------------------cCCchhHHHHHHHHH----hccCCCCEEEEecchHHHHHHHHHhhc
Q 042003          141 ----------------------------------AGSEEGKLLALRQSF----AESLNPPVLIFVQSKERAKELYGELAF  182 (248)
Q Consensus       141 ----------------------------------~~~~~~~~~~l~~~~----~~~~~~~~liF~~~~~~~~~l~~~L~~  182 (248)
                                                        .+....|+..+.+++    ......++|||+.+++.|..+...|..
T Consensus       356 ~e~~~~k~~~~~~e~~~~~~~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~  435 (746)
T KOG0354|consen  356 EEVALKKYLKLELEARLIRNFTENMNELEHLSLDPPKENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQ  435 (746)
T ss_pred             cccchhHHHHHHhcchhhHHHHHHHHhhhhhhcCCCccChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHh
Confidence                                              000112333333332    333367899999999999999999973


Q ss_pred             ---CCCeeEEEe--------cCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          183 ---DGIRAGVIH--------SDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       183 ---~~~~v~~~~--------~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                         .+++...+-        .+|++.+++++++.|+.|+.++||||+++++|+||+.+++||.||...|+.+++||.
T Consensus       436 ~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrr  512 (746)
T KOG0354|consen  436 LHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRR  512 (746)
T ss_pred             hhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHHh
Confidence               233333333        489999999999999999999999999999999999999999999999999999984

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.91  E-value=1.5e-23  Score=182.58  Aligned_cols=104  Identities=23%  Similarity=0.272  Sum_probs=92.9

Q ss_pred             CchhHHHHHHHHHhc--cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc
Q 042003          143 SEEGKLLALRQSFAE--SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI  220 (248)
Q Consensus       143 ~~~~~~~~l~~~~~~--~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~  220 (248)
                      ....|...+...+..  ..+.++||||+|++.++.+++.|.+.++++..+||.++..++..+..+++.|  .|+|||+.+
T Consensus       409 ~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmA  486 (790)
T PRK09200        409 TLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMA  486 (790)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccch
Confidence            445688888887754  2478999999999999999999999999999999999988888888887766  699999999


Q ss_pred             ccCCCC---CCCc-----EEEeccCCCCcccceecC
Q 042003          221 ARGMDF---KGVN-----CVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       221 ~~Gidi---p~~~-----~Vi~~~~p~~~~~~~qri  248 (248)
                      ++|+|+   |+++     +||++++|.|...|.||+
T Consensus       487 gRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~  522 (790)
T PRK09200        487 GRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLR  522 (790)
T ss_pred             hcCcCCCcccccccccCcEEEeccCCCCHHHHHHhh
Confidence            999999   6998     999999999999999985

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.90  E-value=5.3e-23  Score=176.83  Aligned_cols=242  Identities=20%  Similarity=0.132  Sum_probs=166.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHH-HHHHhcC------CcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRL-RLAIRRK------KIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l-~~~~~~~------~~~~~~~~~lIiDEah~   72 (248)
                      ||.|.++++.++.+.+| +++.++.|+. .+.......++|+++||+.| .+++..+      ...++++.++|+||+|.
T Consensus       109 LA~qdae~~~~l~~~LG-Lsv~~i~g~~~~~~r~~~y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs  187 (745)
T TIGR00963       109 LAQRDAEWMGQVYRFLG-LSVGLILSGMSPEERREAYACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDS  187 (745)
T ss_pred             HHHHHHHHHHHHhccCC-CeEEEEeCCCCHHHHHHhcCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHH
Confidence            79999999999999999 5666666654 44444555799999999999 7777665      34679999999999998


Q ss_pred             ccccC---------c------ccccchhHhhhCCCc-------c------------------------------------
Q 042003           73 LFEVG---------N------LLKHIDPVVKACSNP-------S------------------------------------   94 (248)
Q Consensus        73 ~~~~~---------~------~~~~~~~~~~~~~~~-------~------------------------------------   94 (248)
                      ++-+.         +      .......+.+.+...       .                                    
T Consensus       188 ~LIDeaRtpLiisg~~~~~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~  267 (745)
T TIGR00963       188 ILIDEARTPLIISGPAEKSTELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGVDNLYDLENSPLIHYIN  267 (745)
T ss_pred             HhHHhhhhHHhhcCCCCCchHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCCccccChhhhHHHHHHH
Confidence            86311         0      000000011110000       0                                    


Q ss_pred             -------------------------------------------------------------------------ceeEEEE
Q 042003           95 -------------------------------------------------------------------------IVRSLFS  101 (248)
Q Consensus        95 -------------------------------------------------------------------------~~~i~~S  101 (248)
                                                                                               ..+.+||
T Consensus       268 ~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLhQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmT  347 (745)
T TIGR00963       268 NALKAKELFEKDVDYIVRDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNFFRLYEKLSGMT  347 (745)
T ss_pred             HHHHHHHHHhcCCcEEEECCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeeeeHHHHHhhCchhhccC
Confidence                                                                                     2233555


Q ss_pred             eecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHh--ccCCCCEEEEecchHHHHHHHHH
Q 042003          102 ATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA--ESLNPPVLIFVQSKERAKELYGE  179 (248)
Q Consensus       102 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~liF~~~~~~~~~l~~~  179 (248)
                      +|...+..++...|.-+...+.   ...+...............+|...+.+.+.  ...+.|+||||+|++.++.+.+.
T Consensus       348 GTa~te~~E~~~iY~l~vv~IP---tnkp~~R~d~~d~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~  424 (745)
T TIGR00963       348 GTAKTEEEEFEKIYNLEVVVVP---TNRPVIRKDLSDLVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNL  424 (745)
T ss_pred             CCcHHHHHHHHHHhCCCEEEeC---CCCCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHH
Confidence            5554433333333322211111   111111111111223344567777766552  22378999999999999999999


Q ss_pred             hhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCC-------CcEEEeccCCCCcccceecC
Q 042003          180 LAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKG-------VNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       180 L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~-------~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |.+.++++..+|+.  +.+|+..+..|..+...|+|||+.+++|.||+.       ..+||+++.|.|...|.||+
T Consensus       425 L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~  498 (745)
T TIGR00963       425 LKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLR  498 (745)
T ss_pred             HHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHh
Confidence            99999999999998  889999999999999999999999999999998       55999999999999999984

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.90  E-value=9.7e-23  Score=176.15  Aligned_cols=104  Identities=21%  Similarity=0.268  Sum_probs=90.6

Q ss_pred             CCchhHHHHHHHHHhc--cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          142 GSEEGKLLALRQSFAE--SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~--~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      ....+|...+.+.+..  ..+.++||||+|++.++.+.+.|.+.++++..+||.++..++..+.++++.|  .|+|||+.
T Consensus       404 ~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdm  481 (762)
T TIGR03714       404 ATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSM  481 (762)
T ss_pred             ECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccc
Confidence            3445688888877754  3478999999999999999999999999999999999998888887777777  59999999


Q ss_pred             cccCCCCC---------CCcEEEeccCCCCcccceecC
Q 042003          220 IARGMDFK---------GVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       220 ~~~Gidip---------~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +++|+|+|         ++.+|+++++|..... .||+
T Consensus       482 AgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~  518 (762)
T TIGR03714       482 AGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLR  518 (762)
T ss_pred             cccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhh
Confidence            99999999         9999999999998766 7874

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.

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

Probab=99.90  E-value=3.6e-24  Score=169.68  Aligned_cols=210  Identities=17%  Similarity=0.167  Sum_probs=156.5

Q ss_pred             CCCcEEEeChHHHHHHHhc----CCcccCceeEEEEeccccccccC-cccccchhHhhhC-CCccceeEEEEeecCchHH
Q 042003           36 FSCDILISTPLRLRLAIRR----KKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKAC-SNPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~----~~~~~~~~~~lIiDEah~~~~~~-~~~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~  109 (248)
                      ....++.-||++.......    +...-..+.++++||||++.+|| +|++....+-.+. .-+....+++|||.++...
T Consensus       112 p~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~Vq  191 (641)
T KOG0352|consen  112 PTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQ  191 (641)
T ss_pred             CceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhhccccCcchhhhhhHHhhCCCCceEEeecccChhHH
Confidence            4568999999876544433    22234567899999999999997 6777666553331 1245677899999998887


Q ss_pred             HHHHH--hcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccC-------------CCCEEEEecchHHHH
Q 042003          110 ELARS--IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL-------------NPPVLIFVQSKERAK  174 (248)
Q Consensus       110 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------------~~~~liF~~~~~~~~  174 (248)
                      +-+-.  -+.+|+.+.-  ......++.+...+-....+.+..|.++....-             .+-.||||.|+++|+
T Consensus       192 EDi~~qL~L~~PVAiFk--TP~FR~NLFYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cE  269 (641)
T KOG0352|consen  192 EDIAFQLKLRNPVAIFK--TPTFRDNLFYDNHMKSFITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECE  269 (641)
T ss_pred             HHHHHHHhhcCcHHhcc--CcchhhhhhHHHHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHH
Confidence            75544  2345544322  222223333333233333445555555543221             345899999999999


Q ss_pred             HHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceec
Q 042003          175 ELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHR  247 (248)
Q Consensus       175 ~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qr  247 (248)
                      +++-.|...|++...+|.|+...+|.++-+.|-+++..|+++|..+++|+|-|+++.|||+++|.|+.-|.|.
T Consensus       270 q~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQE  342 (641)
T KOG0352|consen  270 QVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQE  342 (641)
T ss_pred             HHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchhhhHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999874

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

Probab=99.89  E-value=1.1e-22  Score=170.20  Aligned_cols=234  Identities=19%  Similarity=0.161  Sum_probs=153.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+++.+.+.....  .....++|+.....   . ..|.|+|.+++.+.-.......+.+++||+||||++.++. +.
T Consensus        92 L~~Qw~~~~~~~~~~~--~~~g~~~~~~~~~~---~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~-~~  164 (442)
T COG1061          92 LLDQWAEALKKFLLLN--DEIGIYGGGEKELE---P-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPS-YR  164 (442)
T ss_pred             HHHHHHHHHHHhcCCc--cccceecCceeccC---C-CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHH-HH
Confidence            4567765555443332  12333344332221   1 5799999998877532223333579999999999988765 44


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHH---HHhcCCcEEEEEcccc----cccccceeEEEEc------------
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELA---RSIMHDAVRVIVGRKN----TASESIKQKLVFA------------  141 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~---~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~------------  141 (248)
                      .....+.... +    ++++|||++.......   ..+.+ +..+.....+    ....+........            
T Consensus       165 ~~~~~~~~~~-~----~LGLTATp~R~D~~~~~~l~~~~g-~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~  238 (442)
T COG1061         165 RILELLSAAY-P----RLGLTATPEREDGGRIGDLFDLIG-PIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAK  238 (442)
T ss_pred             HHHHhhhccc-c----eeeeccCceeecCCchhHHHHhcC-CeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhh
Confidence            4333333321 1    7999999864331211   12222 2222222110    0111111111111            


Q ss_pred             -------------------------CCchhHHHHHHHHHhcc-CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          142 -------------------------GSEEGKLLALRQSFAES-LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       142 -------------------------~~~~~~~~~l~~~~~~~-~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                                               ...+.+...+...+..+ .+.+++||+.+..++..++..+...+. +..+.|.++
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~  317 (442)
T COG1061         239 ESARFRELLRARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETP  317 (442)
T ss_pred             hhhhhhhhhhhhhhhhHHHHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCC
Confidence                                     11123334444445444 367999999999999999999998887 899999999


Q ss_pred             HHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          196 QTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       196 ~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ..+|+++++.|+.|.+++||++.++.+|+|+|+++++|+..++.|+..|+||+
T Consensus       318 ~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~l  370 (442)
T COG1061         318 KEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRL  370 (442)
T ss_pred             HHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999985

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

Probab=99.87  E-value=1.9e-21  Score=172.57  Aligned_cols=244  Identities=20%  Similarity=0.255  Sum_probs=173.7

Q ss_pred             CcchHHHHHHHhhcCCCc-EEEEcccchhhhc---ccccCCCcEEEeChHHHHHHHhcCC----cccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKF-QIKLMKKELVRST---DLSKFSCDILISTPLRLRLAIRRKK----IDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~i~v~Tp~~l~~~~~~~~----~~~~~~~~lIiDEah~   72 (248)
                      ||+-+.+.++++....+. .+...+.|.....   .+..+.++|++++|.++..++.+..    ..++++++||+||+|.
T Consensus       127 La~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHt  206 (851)
T COG1205         127 LANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHT  206 (851)
T ss_pred             hHhhHHHHHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEeccee
Confidence            677778888888877763 3444455555222   4467889999999999988665532    2478899999999998


Q ss_pred             ccccCcccccc----hhHhhhC--CCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCC---
Q 042003           73 LFEVGNLLKHI----DPVVKAC--SNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS---  143 (248)
Q Consensus        73 ~~~~~~~~~~~----~~~~~~~--~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  143 (248)
                      +-+.  |...+    .+++..+  ...+.|+|++|||+.. ..+....+.+......+..... +...++...+...   
T Consensus       207 YrGv--~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~n-p~e~~~~l~~~~f~~~v~~~g~-~~~~~~~~~~~p~~~~  282 (851)
T COG1205         207 YRGV--QGSEVALLLRRLLRRLRRYGSPLQIICTSATLAN-PGEFAEELFGRDFEVPVDEDGS-PRGLRYFVRREPPIRE  282 (851)
T ss_pred             cccc--chhHHHHHHHHHHHHHhccCCCceEEEEeccccC-hHHHHHHhcCCcceeeccCCCC-CCCceEEEEeCCcchh
Confidence            7542  33333    3332222  2357899999999987 6666777766665553332222 2233333333330   


Q ss_pred             -----chhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHH----HHhhcCC----CeeEEEecCCCHHHHHHHHHHhhc
Q 042003          144 -----EEGKLLALRQSFAES--LNPPVLIFVQSKERAKELY----GELAFDG----IRAGVIHSDLSQTQRENAVDDFRA  208 (248)
Q Consensus       144 -----~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~----~~L~~~~----~~v~~~~~~~~~~~r~~~~~~f~~  208 (248)
                           -.++...+..+....  .+-++++|+.++..++.++    ..+...+    ..+..++++|..++|..+...|++
T Consensus       283 ~~~~~r~s~~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~  362 (851)
T COG1205         283 LAESIRRSALAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKE  362 (851)
T ss_pred             hhhhcccchHHHHHHHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhc
Confidence                 112333333333322  2679999999999999997    4444444    578899999999999999999999


Q ss_pred             CCceEEEEecccccCCCCCCCcEEEeccCCC-CcccceecC
Q 042003          209 GKTWVLIATDVIARGMDFKGVNCVINYDFPD-SGAAYIHRI  248 (248)
Q Consensus       209 g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~-~~~~~~qri  248 (248)
                      |+..++++|++++.|+|+.+++.||..+.|. +..+|.||.
T Consensus       363 g~~~~~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~  403 (851)
T COG1205         363 GELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRA  403 (851)
T ss_pred             CCccEEecchhhhhceeehhhhhHhhcCCCCchHHHHHHhh
Confidence            9999999999999999999999999999999 899999983

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=99.87  E-value=2.2e-21  Score=168.19  Aligned_cols=230  Identities=20%  Similarity=0.209  Sum_probs=158.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcC---CcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRK---KIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~---~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||....+.+.+-....| +.|.-++|...-..-....++|+|+|||++--.-++.   .-.++.++++|+||+|.+.++ 
T Consensus       176 La~Em~~~~~kkl~~~g-i~v~ELTGD~ql~~tei~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~-  253 (1230)
T KOG0952|consen  176 LAAEMVDKFSKKLAPLG-ISVRELTGDTQLTKTEIADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDD-  253 (1230)
T ss_pred             HHHHHHHHHhhhccccc-ceEEEecCcchhhHHHHHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCc-
Confidence            34455555555455556 7788888877433333557999999999884333332   224788999999999998775 


Q ss_pred             cccccchhHhhhC------CCccceeEEEEeecCchHHHHHHHhcCCcEE--EEEcccccccccceeEEEEcCCc-----
Q 042003           78 NLLKHIDPVVKAC------SNPSIVRSLFSATLPDFVEELARSIMHDAVR--VIVGRKNTASESIKQKLVFAGSE-----  144 (248)
Q Consensus        78 ~~~~~~~~~~~~~------~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~-----  144 (248)
                       ..+.++.++...      .....+++++|||+|+ ..+.+.++.-++..  ........ +..+.+.++-.+..     
T Consensus       254 -RGpvlEtiVaRtlr~vessqs~IRivgLSATlPN-~eDvA~fL~vn~~~glfsFd~~yR-PvpL~~~~iG~k~~~~~~~  330 (1230)
T KOG0952|consen  254 -RGPVLETIVARTLRLVESSQSMIRIVGLSATLPN-YEDVARFLRVNPYAGLFSFDQRYR-PVPLTQGFIGIKGKKNRQQ  330 (1230)
T ss_pred             -ccchHHHHHHHHHHHHHhhhhheEEEEeeccCCC-HHHHHHHhcCCCccceeeeccccc-ccceeeeEEeeecccchhh
Confidence             455555554332      2356899999999998 77777777665432  22222222 22233333332222     


Q ss_pred             -----hhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC-----------------------CCeeEEEecCCCH
Q 042003          145 -----EGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD-----------------------GIRAGVIHSDLSQ  196 (248)
Q Consensus       145 -----~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~-----------------------~~~v~~~~~~~~~  196 (248)
                           +.....+.+++..  +.+++|||.+++.+.+.++.|.+.                       ....+++|+||..
T Consensus       331 ~~~~d~~~~~kv~e~~~~--g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r  408 (1230)
T KOG0952|consen  331 KKNIDEVCYDKVVEFLQE--GHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLR  408 (1230)
T ss_pred             hhhHHHHHHHHHHHHHHc--CCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccch
Confidence                 1223344444444  689999999999999999888541                       1467899999999


Q ss_pred             HHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          197 TQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       197 ~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                      .+|.-+.+.|..|.++||+||..++.|+|+| +.+||+-|.+
T Consensus       409 ~DR~l~E~~F~~G~i~vL~cTaTLAwGVNLP-A~aViIKGT~  449 (1230)
T KOG0952|consen  409 SDRQLVEKEFKEGHIKVLCCTATLAWGVNLP-AYAVIIKGTQ  449 (1230)
T ss_pred             hhHHHHHHHHhcCCceEEEecceeeeccCCc-ceEEEecCCc
Confidence            9999999999999999999999999999999 6777766655

>PRK09694 helicase Cas3; Provisional

Probab=99.86  E-value=6.5e-21  Score=168.87  Aligned_cols=206  Identities=18%  Similarity=0.250  Sum_probs=133.8

Q ss_pred             CcEEEeChHHHHHHHhcC-CcccCcee----EEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHH
Q 042003           38 CDILISTPLRLRLAIRRK-KIDLSRVE----YLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA  112 (248)
Q Consensus        38 ~~i~v~Tp~~l~~~~~~~-~~~~~~~~----~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~  112 (248)
                      .+|+|||+.+++..+... ...++.++    +|||||+|.+.. . +...+..+++.+......+|+||||+|...++..
T Consensus       411 api~V~TiDQlL~a~l~~kh~~lR~~~La~svvIiDEVHAyD~-y-m~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L  488 (878)
T PRK09694        411 GQIGVCTIDQVLISVLPVKHRFIRGFGLGRSVLIVDEVHAYDA-Y-MYGLLEAVLKAQAQAGGSVILLSATLPATLKQKL  488 (878)
T ss_pred             CCEEEcCHHHHHHHHHccchHHHHHHhhccCeEEEechhhCCH-H-HHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHH
Confidence            799999998888655442 22233333    899999999743 2 4556677777655566789999999998776543


Q ss_pred             H-HhcCC-c------EEEEE--c--------cccccc-ccceeEE----EEcCCchhHHHHHHHHHhc-cCCCCEEEEec
Q 042003          113 R-SIMHD-A------VRVIV--G--------RKNTAS-ESIKQKL----VFAGSEEGKLLALRQSFAE-SLNPPVLIFVQ  168 (248)
Q Consensus       113 ~-~~~~~-~------~~~~~--~--------~~~~~~-~~~~~~~----~~~~~~~~~~~~l~~~~~~-~~~~~~liF~~  168 (248)
                      . .+.+. +      +....  .        ...... ....+.+    ............+..+.+. ..+++++||||
T Consensus       489 ~~a~~~~~~~~~~~~YPlvt~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~N  568 (878)
T PRK09694        489 LDTYGGHDPVELSSAYPLITWRGVNGAQRFDLSAHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICN  568 (878)
T ss_pred             HHHhccccccccccccccccccccccceeeeccccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEEC
Confidence            3 33211 0      00000  0        000000 0011111    1111111112222333322 23678999999


Q ss_pred             chHHHHHHHHHhhcCC---CeeEEEecCCCHHHHH----HHHHHh-hcCC---ceEEEEecccccCCCCCCCcEEEeccC
Q 042003          169 SKERAKELYGELAFDG---IRAGVIHSDLSQTQRE----NAVDDF-RAGK---TWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       169 ~~~~~~~l~~~L~~~~---~~v~~~~~~~~~~~r~----~~~~~f-~~g~---~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      |++.|+.+++.|++..   .++..+||+++..+|+    ++++.| ++|+   ..|||||+++++|+|+ +.+++|....
T Consensus       569 TV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-d~DvlItdla  647 (878)
T PRK09694        569 LVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-DFDWLITQLC  647 (878)
T ss_pred             CHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-CCCeEEECCC
Confidence            9999999999998764   6899999999999994    567778 5565   4799999999999999 4899999888


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      |  .+.++||+
T Consensus       648 P--idsLiQRa  656 (878)
T PRK09694        648 P--VDLLFQRL  656 (878)
T ss_pred             C--HHHHHHHH
Confidence            8  56888884

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

Probab=99.85  E-value=7.8e-21  Score=149.21  Aligned_cols=209  Identities=19%  Similarity=0.253  Sum_probs=158.2

Q ss_pred             CCCcEEEeChHHHHHHHh---c--CCcccCceeEEEEeccccccccC-cccccchhH--hhhCCCccceeEEEEeecCch
Q 042003           36 FSCDILISTPLRLRLAIR---R--KKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPV--VKACSNPSIVRSLFSATLPDF  107 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~---~--~~~~~~~~~~lIiDEah~~~~~~-~~~~~~~~~--~~~~~~~~~~~i~~SAT~~~~  107 (248)
                      ....++..||+.+...-.   +  ..+....+.++-+||+|+..+|| +|+.....+  ++. .-+...+++++||.+..
T Consensus       185 se~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~dy~~l~ilkr-qf~~~~iigltatatn~  263 (695)
T KOG0353|consen  185 SEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKR-QFKGAPIIGLTATATNH  263 (695)
T ss_pred             ceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCcchHHHHHHHH-hCCCCceeeeehhhhcc
Confidence            357899999998864321   1  34456778899999999999997 566655443  222 23567789999999876


Q ss_pred             HHHHHHHhcCCcEEEEEcccccccccceeEEEEc-CCchhHHHHHHHHHhc-cCCCCEEEEecchHHHHHHHHHhhcCCC
Q 042003          108 VEELARSIMHDAVRVIVGRKNTASESIKQKLVFA-GSEEGKLLALRQSFAE-SLNPPVLIFVQSKERAKELYGELAFDGI  185 (248)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~-~~~~~~liF~~~~~~~~~l~~~L~~~~~  185 (248)
                      ...-+...+.-...+. .+..-..+++++....- .+.++....+..+++. ..++..||||-+.++|++++..|+..|+
T Consensus       264 vl~d~k~il~ie~~~t-f~a~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi  342 (695)
T KOG0353|consen  264 VLDDAKDILCIEAAFT-FRAGFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGI  342 (695)
T ss_pred             hhhHHHHHHhHHhhhe-eecccCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCc
Confidence            6655554433222111 11222334444444333 3445566666666653 4477899999999999999999999999


Q ss_pred             eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCccccee
Q 042003          186 RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIH  246 (248)
Q Consensus       186 ~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~q  246 (248)
                      ....+|.-|.+++|..+-+.|..|++.|+|+|-++++|||-|+++.|||..+|.|+..|.|
T Consensus       343 ~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyq  403 (695)
T KOG0353|consen  343 HAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQ  403 (695)
T ss_pred             cccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999987

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

Probab=99.84  E-value=2.5e-19  Score=138.75  Aligned_cols=197  Identities=21%  Similarity=0.242  Sum_probs=136.8

Q ss_pred             EEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEE
Q 042003           21 KLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLF  100 (248)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~  100 (248)
                      ..+.+|+.++.-    ..+++|+|..++++..       +.+|++||||+|.+.-..  -..+....+.........|.+
T Consensus       173 I~~Lyg~S~~~f----r~plvVaTtHQLlrFk-------~aFD~liIDEVDAFP~~~--d~~L~~Av~~ark~~g~~Iyl  239 (441)
T COG4098         173 IDLLYGDSDSYF----RAPLVVATTHQLLRFK-------QAFDLLIIDEVDAFPFSD--DQSLQYAVKKARKKEGATIYL  239 (441)
T ss_pred             eeeEecCCchhc----cccEEEEehHHHHHHH-------hhccEEEEeccccccccC--CHHHHHHHHHhhcccCceEEE
Confidence            445555443322    3789999999998776       577899999999975322  234445555545566778999


Q ss_pred             EeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHH------HHHHHHHhccC--CCCEEEEecchHH
Q 042003          101 SATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKL------LALRQSFAESL--NPPVLIFVQSKER  172 (248)
Q Consensus       101 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~l~~~~~~~~--~~~~liF~~~~~~  172 (248)
                      |||.+...+..+..  ++...+..+..-...+-..-.+.+..+-..++      ..+..++++..  +.+++||+++++.
T Consensus       240 TATp~k~l~r~~~~--g~~~~~klp~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p~I~~  317 (441)
T COG4098         240 TATPTKKLERKILK--GNLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPEIET  317 (441)
T ss_pred             ecCChHHHHHHhhh--CCeeEeecchhhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEecchHH
Confidence            99998766665543  23333433333222222222233444444333      24556665443  5799999999999


Q ss_pred             HHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe
Q 042003          173 AKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN  234 (248)
Q Consensus       173 ~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~  234 (248)
                      .+++++.|++.  ...++.+|+.  ...|.+..++|++|++++|++|.++++|+.+|++++.+.
T Consensus       318 ~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vl  379 (441)
T COG4098         318 MEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVL  379 (441)
T ss_pred             HHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEe
Confidence            99999999543  3356788886  567999999999999999999999999999999998774

>TIGR00595 priA primosomal protein N'

Probab=99.83  E-value=4.8e-19  Score=150.24  Aligned_cols=220  Identities=20%  Similarity=0.155  Sum_probs=137.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh-------hcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR-------STDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      |+.|+++.+++...    ..+..+.++..       ......+.++|+|+|+..+.       ..+.+++++||||+|..
T Consensus        37 L~~Q~~~~l~~~f~----~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~  105 (505)
T TIGR00595        37 LTPQMIQRFKYRFG----SQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-------LPFKNLGLIIVDEEHDS  105 (505)
T ss_pred             HHHHHHHHHHHHhC----CcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-------CcccCCCEEEEECCCcc
Confidence            56788888876432    22333444331       12234456899999997662       35789999999999987


Q ss_pred             cccCccccc-----chhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccc--ccccccceeEEEEcCCc--
Q 042003           74 FEVGNLLKH-----IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK--NTASESIKQKLVFAGSE--  144 (248)
Q Consensus        74 ~~~~~~~~~-----~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~--  144 (248)
                      .-++.-...     +.....  ...+.+++++|||++.+.....  ..+..........  ....+.+  .++.....  
T Consensus       106 sykq~~~p~y~ar~~a~~ra--~~~~~~vil~SATPsles~~~~--~~g~~~~~~l~~r~~~~~~p~v--~vid~~~~~~  179 (505)
T TIGR00595       106 SYKQEEGPRYHARDVAVYRA--KKFNCPVVLGSATPSLESYHNA--KQKAYRLLVLTRRVSGRKPPEV--KLIDMRKEPR  179 (505)
T ss_pred             ccccccCCCCcHHHHHHHHH--HhcCCCEEEEeCCCCHHHHHHH--hcCCeEEeechhhhcCCCCCeE--EEEecccccc
Confidence            643311111     112222  2357889999999765443333  2222222222111  1111111  11112111  


Q ss_pred             -----hhHHHHHHHHHhccCCCCEEEEecchHH-----------------------------------------------
Q 042003          145 -----EGKLLALRQSFAESLNPPVLIFVQSKER-----------------------------------------------  172 (248)
Q Consensus       145 -----~~~~~~l~~~~~~~~~~~~liF~~~~~~-----------------------------------------------  172 (248)
                           +...+.+.+.+++  +++++||+|++..                                               
T Consensus       180 ~~~ls~~l~~~i~~~l~~--g~qvLvflnrrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp  257 (505)
T TIGR00595       180 QSFLSPELITAIEQTLAA--GEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCP  257 (505)
T ss_pred             cCCccHHHHHHHHHHHHc--CCcEEEEEeCCcCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCC
Confidence                 1223344444444  5799999887654                                               


Q ss_pred             -------------HHHHHHHhhcC--CCeeEEEecCCCHHHH--HHHHHHhhcCCceEEEEecccccCCCCCCCcEEE--
Q 042003          173 -------------AKELYGELAFD--GIRAGVIHSDLSQTQR--ENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI--  233 (248)
Q Consensus       173 -------------~~~l~~~L~~~--~~~v~~~~~~~~~~~r--~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi--  233 (248)
                                   .+++++.|++.  +.++..+|++++...+  +++++.|++|+.+|||+|+.+++|+|+|++++|+  
T Consensus       258 ~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl  337 (505)
T TIGR00595       258 QCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVL  337 (505)
T ss_pred             CCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEE
Confidence                         47788888776  6789999999987665  8899999999999999999999999999999885  


Q ss_pred             eccCCC
Q 042003          234 NYDFPD  239 (248)
Q Consensus       234 ~~~~p~  239 (248)
                      ++|..-
T Consensus       338 ~aD~~l  343 (505)
T TIGR00595       338 DADSGL  343 (505)
T ss_pred             cCcccc
Confidence            555543

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).

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

Probab=99.82  E-value=9.3e-20  Score=160.43  Aligned_cols=227  Identities=18%  Similarity=0.179  Sum_probs=154.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCc---ccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKI---DLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~---~~~~~~~lIiDEah~~~~~~   77 (248)
                      |++.+-..+.+....+| ++|.-.+|..........+.+|+|+||+.. +.+.++..   ...-++++|+||.|.+.+. 
T Consensus       376 LvqE~VgsfSkRla~~G-I~V~ElTgD~~l~~~qieeTqVIV~TPEK~-DiITRk~gdraY~qlvrLlIIDEIHLLhDd-  452 (1674)
T KOG0951|consen  376 LVQEMVGSFSKRLAPLG-ITVLELTGDSQLGKEQIEETQVIVTTPEKW-DIITRKSGDRAYEQLVRLLIIDEIHLLHDD-  452 (1674)
T ss_pred             HHHHHHHHHHhhccccC-cEEEEecccccchhhhhhcceeEEeccchh-hhhhcccCchhHHHHHHHHhhhhhhhcccc-
Confidence            34455555666677778 888888887766666667899999999988 44444322   2345779999999998664 


Q ss_pred             cccccchhHhh----hC--CCccceeEEEEeecCchHHHHHHHhcCCcE-EEEEcccccccccceeEEEEcCC--chhHH
Q 042003           78 NLLKHIDPVVK----AC--SNPSIVRSLFSATLPDFVEELARSIMHDAV-RVIVGRKNTASESIKQKLVFAGS--EEGKL  148 (248)
Q Consensus        78 ~~~~~~~~~~~----~~--~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~--~~~~~  148 (248)
                       ..+.+..+..    ..  ....++.+++|||+|+.. .....+.-++. .+..++..++ .++++.++-+..  ...+.
T Consensus       453 -RGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy~-DV~~Fl~v~~~glf~fd~syRp-vPL~qq~Igi~ek~~~~~~  529 (1674)
T KOG0951|consen  453 -RGPVLESIVARTFRRSESTEEGSRLVGLSATLPNYE-DVASFLRVDPEGLFYFDSSYRP-VPLKQQYIGITEKKPLKRF  529 (1674)
T ss_pred             -cchHHHHHHHHHHHHhhhcccCceeeeecccCCchh-hhHHHhccCcccccccCcccCc-CCccceEeccccCCchHHH
Confidence             3444433322    21  124688999999999843 33332333332 2333333333 334444433322  22222


Q ss_pred             H-----HHHHHHhccCCCCEEEEecchHHHHHHHHHhhc-------------------------------------CCCe
Q 042003          149 L-----ALRQSFAESLNPPVLIFVQSKERAKELYGELAF-------------------------------------DGIR  186 (248)
Q Consensus       149 ~-----~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~-------------------------------------~~~~  186 (248)
                      .     ....+++....++++||+-+++++.+.++.+++                                     ..++
T Consensus       530 qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpyg  609 (1674)
T KOG0951|consen  530 QAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYG  609 (1674)
T ss_pred             HHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhcc
Confidence            2     223344555467999999999999888888863                                     2468


Q ss_pred             eEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEE
Q 042003          187 AGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI  233 (248)
Q Consensus       187 v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi  233 (248)
                      ++++|+||+..+|..+.+.|+.|.+.++|+|..++.|+|+|+-+++|
T Consensus       610 faIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtVii  656 (1674)
T KOG0951|consen  610 FAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVII  656 (1674)
T ss_pred             ceeeccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEe
Confidence            99999999999999999999999999999999999999999666665

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

Probab=99.82  E-value=4.8e-19  Score=161.12  Aligned_cols=238  Identities=14%  Similarity=0.158  Sum_probs=144.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh-hcccccCCCcEEEeChHHHHHHHhcC-----CcccCceeEEEEecccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR-STDLSKFSCDILISTPLRLRLAIRRK-----KIDLSRVEYLVLDEADKLF   74 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i~v~Tp~~l~~~~~~~-----~~~~~~~~~lIiDEah~~~   74 (248)
                      |+.|+.+.+..+....+ .....+++... .........+|+|+|.+++.+.+...     ...+..+++||+||||+..
T Consensus       475 L~~Qa~~~F~~~~~~~~-~~~~~i~~i~~L~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~  553 (1123)
T PRK11448        475 LGEQAEDAFKDTKIEGD-QTFASIYDIKGLEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGY  553 (1123)
T ss_pred             HHHHHHHHHHhcccccc-cchhhhhchhhhhhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCC
Confidence            56788888887643222 11111222111 11122346899999999998776432     2356789999999999963


Q ss_pred             c------cC--------cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEE-------------------
Q 042003           75 E------VG--------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVR-------------------  121 (248)
Q Consensus        75 ~------~~--------~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~-------------------  121 (248)
                      .      .+        .+...+..++.++   +...|++|||+.....    .+++.+..                   
T Consensus       554 ~~d~~~~~~~~~~~~~~~~~~~yr~iL~yF---dA~~IGLTATP~r~t~----~~FG~pv~~Ysl~eAI~DG~Lv~~~~p  626 (1123)
T PRK11448        554 TLDKEMSEGELQFRDQLDYVSKYRRVLDYF---DAVKIGLTATPALHTT----EIFGEPVYTYSYREAVIDGYLIDHEPP  626 (1123)
T ss_pred             ccccccccchhccchhhhHHHHHHHHHhhc---CccEEEEecCCccchh----HHhCCeeEEeeHHHHHhcCCcccCcCC
Confidence            2      00        0123444455543   3457999999864222    22333221                   


Q ss_pred             --EEEcccc--cc---c---cccee---EE--EEcCC----c----------hhHH----HHHHHHHhccCCCCEEEEec
Q 042003          122 --VIVGRKN--TA---S---ESIKQ---KL--VFAGS----E----------EGKL----LALRQSFAESLNPPVLIFVQ  168 (248)
Q Consensus       122 --~~~~~~~--~~---~---~~~~~---~~--~~~~~----~----------~~~~----~~l~~~~~~~~~~~~liF~~  168 (248)
                        +......  ..   .   .....   .+  ...++    .          +...    ..+.+.+....++|+||||.
T Consensus       627 ~~i~t~~~~~gi~~~~~e~~~~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l~~~~~~KtiIF~~  706 (1123)
T PRK11448        627 IRIETRLSQEGIHFEKGEEVEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYLDPTGEGKTLIFAA  706 (1123)
T ss_pred             EEEEEEeccccccccccchhhhcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHhccCCCcEEEEEc
Confidence              1110000  00   0   00000   00  00000    0          0011    11222333333579999999


Q ss_pred             chHHHHHHHHHhhcC------C---CeeEEEecCCCHHHHHHHHHHhhcCCc-eEEEEecccccCCCCCCCcEEEeccCC
Q 042003          169 SKERAKELYGELAFD------G---IRAGVIHSDLSQTQRENAVDDFRAGKT-WVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       169 ~~~~~~~l~~~L~~~------~---~~v~~~~~~~~~~~r~~~~~~f~~g~~-~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                      ++++|+.+++.|++.      +   ..+..++|+++  ++.++++.|+++.. .|+|+++.+.+|+|+|.+++||++.++
T Consensus       707 s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~rpv  784 (1123)
T PRK11448        707 TDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRV  784 (1123)
T ss_pred             CHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEecCC
Confidence            999999999887652      1   24667899875  46789999999876 699999999999999999999999999


Q ss_pred             CCcccceecC
Q 042003          239 DSGAAYIHRI  248 (248)
Q Consensus       239 ~~~~~~~qri  248 (248)
                      .|...|+|||
T Consensus       785 kS~~lf~QmI  794 (1123)
T PRK11448        785 RSRILYEQML  794 (1123)
T ss_pred             CCHHHHHHHH
Confidence            9999999986

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

Probab=99.81  E-value=1.8e-18  Score=149.07  Aligned_cols=221  Identities=24%  Similarity=0.191  Sum_probs=152.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |.+|-+..|+.-....|     +++|..    .+...+.++|+|.+.|.+++.++.--.++++++|+||+|.+.+.. ..
T Consensus       352 LSNQKfRDFk~tF~Dvg-----LlTGDv----qinPeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~e-RG  421 (1248)
T KOG0947|consen  352 LSNQKFRDFKETFGDVG-----LLTGDV----QINPEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVE-RG  421 (1248)
T ss_pred             hccchHHHHHHhccccc-----eeecce----eeCCCcceEeehHHHHHHHHhcccchhhccceEEEeeeeeccccc-cc
Confidence            44566666666555554     344432    334468899999999999999988778999999999999988776 66


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCC-cEEEEEcccccccccceeEEEEcC-----------------
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHD-AVRVIVGRKNTASESIKQKLVFAG-----------------  142 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-----------------  142 (248)
                      -.+++++-. .+...++|++|||.|+ ..+++.|..+- ...+.+......+.++.++++.-.                 
T Consensus       422 vVWEEViIM-lP~HV~~IlLSATVPN-~~EFA~WIGRtK~K~IyViST~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~  499 (1248)
T KOG0947|consen  422 VVWEEVIIM-LPRHVNFILLSATVPN-TLEFADWIGRTKQKTIYVISTSKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGI  499 (1248)
T ss_pred             ccceeeeee-ccccceEEEEeccCCC-hHHHHHHhhhccCceEEEEecCCCccceEEEEEeccceehhhcccchhhhhcc
Confidence            677777777 6788999999999998 66666665431 111111111111111212211100                 


Q ss_pred             -----------------------------------------------CchhH---HHHHHHHHhccCCCCEEEEecchHH
Q 042003          143 -----------------------------------------------SEEGK---LLALRQSFAESLNPPVLIFVQSKER  172 (248)
Q Consensus       143 -----------------------------------------------~~~~~---~~~l~~~~~~~~~~~~liF~~~~~~  172 (248)
                                                                     .+..+   ...+...+.+..--|+||||-+++.
T Consensus       500 ~~a~~~~~~~ak~~~~~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L~k~~lLP~VvFvFSkkr  579 (1248)
T KOG0947|consen  500 KDAKDSLKKEAKFVDVEKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHLRKKNLLPVVVFVFSKKR  579 (1248)
T ss_pred             hhhhhhhcccccccccccccccccccccccCCcCCCCCCCcccccccccccccchHHHHHHHHhhcccCceEEEEEcccc
Confidence                                                           00011   1122222333334589999999999


Q ss_pred             HHHHHHHhhcC---------------------------------------CCeeEEEecCCCHHHHHHHHHHhhcCCceE
Q 042003          173 AKELYGELAFD---------------------------------------GIRAGVIHSDLSQTQRENAVDDFRAGKTWV  213 (248)
Q Consensus       173 ~~~l~~~L~~~---------------------------------------~~~v~~~~~~~~~~~r~~~~~~f~~g~~~i  213 (248)
                      |+..++.|...                                       ..+++++|||+-+--++-+...|..|-.+|
T Consensus       580 Cde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGlVKV  659 (1248)
T KOG0947|consen  580 CDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGLVKV  659 (1248)
T ss_pred             HHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHHHHHHHhcCceEE
Confidence            99999999531                                       136899999999999999999999999999


Q ss_pred             EEEecccccCCCCCCCcEEE
Q 042003          214 LIATDVIARGMDFKGVNCVI  233 (248)
Q Consensus       214 lv~T~~~~~Gidip~~~~Vi  233 (248)
                      |+||.++++|+|+|.-.+|+
T Consensus       660 LFATETFAMGVNMPARtvVF  679 (1248)
T KOG0947|consen  660 LFATETFAMGVNMPARTVVF  679 (1248)
T ss_pred             EeehhhhhhhcCCCceeEEe
Confidence            99999999999999655555

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.80  E-value=2e-18  Score=150.61  Aligned_cols=222  Identities=20%  Similarity=0.165  Sum_probs=150.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHH-HHHHhcCC------cccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRL-RLAIRRKK------IDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l-~~~~~~~~------~~~~~~~~lIiDEah~   72 (248)
                      ||.|.++++..+.+.+| +++.++.|+. .........++|+++||+.| .+.+..+.      ..++.+.++|+||||.
T Consensus       134 LA~rd~e~~~~l~~~LG-lsv~~i~~~~~~~er~~~y~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDs  212 (830)
T PRK12904        134 LAKRDAEWMGPLYEFLG-LSVGVILSGMSPEERREAYAADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDS  212 (830)
T ss_pred             HHHHHHHHHHHHHhhcC-CeEEEEcCCCCHHHHHHhcCCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhh
Confidence            78999999999999999 6666666655 33333335699999999999 77776653      2468899999999997


Q ss_pred             cc-ccC--------------cccccchhHhhhCCCc-------c------------------------------------
Q 042003           73 LF-EVG--------------NLLKHIDPVVKACSNP-------S------------------------------------   94 (248)
Q Consensus        73 ~~-~~~--------------~~~~~~~~~~~~~~~~-------~------------------------------------   94 (248)
                      ++ +..              ..+..+..+...+...       .                                    
T Consensus       213 iLIDeArtpLiiSg~~~~~~~~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~~~ly~~~~~~~~~~i~  292 (830)
T PRK12904        213 ILIDEARTPLIISGPAEDSSELYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHLN  292 (830)
T ss_pred             heeccCCCceeeECCCCcccHHHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCCccccChhhhHHHHHHH
Confidence            76 211              0111111122211100       0                                    


Q ss_pred             -------------------------------------------------------------------------ceeEEEE
Q 042003           95 -------------------------------------------------------------------------IVRSLFS  101 (248)
Q Consensus        95 -------------------------------------------------------------------------~~~i~~S  101 (248)
                                                                                               ..+.+||
T Consensus       293 ~AL~A~~l~~~d~dYiV~dg~V~ivDe~TGR~~~gr~ws~GLHQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmT  372 (830)
T PRK12904        293 QALRAHELFKRDVDYIVKDGEVVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMT  372 (830)
T ss_pred             HHHHHHHHHhcCCcEEEECCEEEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeeeeHHHHHHhcchhcccC
Confidence                                                                                     2233555


Q ss_pred             eecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc--cCCCCEEEEecchHHHHHHHHH
Q 042003          102 ATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE--SLNPPVLIFVQSKERAKELYGE  179 (248)
Q Consensus       102 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~liF~~~~~~~~~l~~~  179 (248)
                      +|...+..++...|.-+...+   +...+...............+|...+.+.+..  ..+.|+||||+|++.++.+++.
T Consensus       373 GTa~te~~E~~~iY~l~vv~I---Ptnkp~~r~d~~d~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~  449 (830)
T PRK12904        373 GTADTEAEEFREIYNLDVVVI---PTNRPMIRIDHPDLIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKL  449 (830)
T ss_pred             CCcHHHHHHHHHHhCCCEEEc---CCCCCeeeeeCCCeEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHH
Confidence            555444333333332221111   11222222221222233555788888888755  4478999999999999999999


Q ss_pred             hhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCC
Q 042003          180 LAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKG  228 (248)
Q Consensus       180 L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~  228 (248)
                      |.+.++++..+|+.  +.+|+..+..|..+...|+|||+.+++|.||+-
T Consensus       450 L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~L  496 (830)
T PRK12904        450 LKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKL  496 (830)
T ss_pred             HHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccC
Confidence            99999999999995  789999999999999999999999999999984

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.80  E-value=4.9e-18  Score=149.01  Aligned_cols=224  Identities=17%  Similarity=0.135  Sum_probs=137.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhh-------cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRS-------TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      |+.|+.+.+++..   + ..+..+.|+...       .....+.++|+|+||+.+.       ..+++++++|+||+|..
T Consensus       202 L~~Q~~~~l~~~f---g-~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~  270 (679)
T PRK05580        202 LTPQMLARFRARF---G-APVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDS  270 (679)
T ss_pred             HHHHHHHHHHHHh---C-CCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCcc
Confidence            5778888887643   2 234444444311       1234456899999997653       45789999999999986


Q ss_pred             cccCcccc--cchhHh-hhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccc--cccccceeEEEEcCC-----
Q 042003           74 FEVGNLLK--HIDPVV-KACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKN--TASESIKQKLVFAGS-----  143 (248)
Q Consensus        74 ~~~~~~~~--~~~~~~-~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~-----  143 (248)
                      .-+..-..  ....+. ......+.+++++|||++.+....+.  .++...+......  ...+.+  .++....     
T Consensus       271 s~~~~~~p~y~~r~va~~ra~~~~~~~il~SATps~~s~~~~~--~g~~~~~~l~~r~~~~~~p~v--~~id~~~~~~~~  346 (679)
T PRK05580        271 SYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQ--QGRYRLLRLTKRAGGARLPEV--EIIDMRELLRGE  346 (679)
T ss_pred             ccccCcCCCCcHHHHHHHHhhccCCCEEEEcCCCCHHHHHHHh--ccceeEEEeccccccCCCCeE--EEEechhhhhhc
Confidence            53321111  111111 11134578999999998765554443  2222222222111  111111  1111111     


Q ss_pred             -----chhHHHHHHHHHhccCCCCEEEEecchH-----------------------------------------------
Q 042003          144 -----EEGKLLALRQSFAESLNPPVLIFVQSKE-----------------------------------------------  171 (248)
Q Consensus       144 -----~~~~~~~l~~~~~~~~~~~~liF~~~~~-----------------------------------------------  171 (248)
                           .....+.+.+.+++  ++++++|+|++.                                               
T Consensus       347 ~~~~ls~~l~~~i~~~l~~--g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~C  424 (679)
T PRK05580        347 NGSFLSPPLLEAIKQRLER--GEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKAC  424 (679)
T ss_pred             ccCCCCHHHHHHHHHHHHc--CCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCC
Confidence                 11122233333332  568999887632                                               


Q ss_pred             -------------HHHHHHHHhhcC--CCeeEEEecCCC--HHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEE-
Q 042003          172 -------------RAKELYGELAFD--GIRAGVIHSDLS--QTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI-  233 (248)
Q Consensus       172 -------------~~~~l~~~L~~~--~~~v~~~~~~~~--~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi-  233 (248)
                                   -++++++.|++.  +.++..+|+++.  .++++.+++.|++|+.+|||+|+.+++|+|+|++++|+ 
T Consensus       425 p~Cg~~~l~~~g~G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~i  504 (679)
T PRK05580        425 PECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGV  504 (679)
T ss_pred             CCCcCCeeEEeeccHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEE
Confidence                         446777777765  778999999986  46789999999999999999999999999999999995 


Q ss_pred             -eccCCCCc
Q 042003          234 -NYDFPDSG  241 (248)
Q Consensus       234 -~~~~p~~~  241 (248)
                       ++|.+-+.
T Consensus       505 l~aD~~l~~  513 (679)
T PRK05580        505 LDADLGLFS  513 (679)
T ss_pred             EcCchhccC
Confidence             44555444

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

Probab=99.79  E-value=2.1e-18  Score=151.27  Aligned_cols=202  Identities=16%  Similarity=0.202  Sum_probs=146.8

Q ss_pred             cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccc-ccCcccccchhHhhhCCCccceeEEEEeecCchHH
Q 042003           31 TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF-EVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        31 ~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  109 (248)
                      .+....+..|-+.|.+.|++.+.+... ++.++++|+||+|.-. +.+-....+..++.. .+...++|.||||+..  +
T Consensus       133 e~~~s~~Trik~mTdGiLlrei~~D~~-Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~-rr~DLKiIimSATld~--~  208 (845)
T COG1643         133 ESKVSPRTRIKVMTDGILLREIQNDPL-LSGYSVVIIDEAHERSLNTDILLGLLKDLLAR-RRDDLKLIIMSATLDA--E  208 (845)
T ss_pred             eccCCCCceeEEeccHHHHHHHhhCcc-cccCCEEEEcchhhhhHHHHHHHHHHHHHHhh-cCCCceEEEEecccCH--H
Confidence            344556789999999999999998766 7999999999999644 322223344444444 4446899999999975  3


Q ss_pred             HHHHHhcCCcEEEEEcccccccccceeEEEEcCCch----hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhc---
Q 042003          110 ELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEE----GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAF---  182 (248)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~---  182 (248)
                      .+ ..++++...+.+....   ..+..++......+    ..+.....+......+.++||.+..++.+..++.|++   
T Consensus       209 rf-s~~f~~apvi~i~GR~---fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~~~~L~~~~l  284 (845)
T COG1643         209 RF-SAYFGNAPVIEIEGRT---YPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERTAEWLEKAEL  284 (845)
T ss_pred             HH-HHHcCCCCEEEecCCc---cceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHHHHHHHhccc
Confidence            33 3455554444433322   22333332222222    2333333344444578999999999999999999998   


Q ss_pred             -CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCC
Q 042003          183 -DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDS  240 (248)
Q Consensus       183 -~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~  240 (248)
                       ....+.++||.++.+++..+++.-..|+.+|+++|++++.++.||++++||+-|..+.
T Consensus       285 ~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~  343 (845)
T COG1643         285 GDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKE  343 (845)
T ss_pred             cCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCcccc
Confidence             3578999999999999999999888888789999999999999999999999888653

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=2.4e-18  Score=150.47  Aligned_cols=84  Identities=25%  Similarity=0.307  Sum_probs=74.0

Q ss_pred             CCchhHHHHHHHHHhc--cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          142 GSEEGKLLALRQSFAE--SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~--~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      .....|..++.+.+..  ..+.|+||||+|++.++.+++.|.+.++++.++|+.+...+++.+.++|+.|.  |+|||+.
T Consensus       424 ~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNm  501 (896)
T PRK13104        424 LTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNM  501 (896)
T ss_pred             cCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCCc--EEEeccC
Confidence            3445677776666532  23789999999999999999999999999999999999999999999999996  9999999


Q ss_pred             cccCCCCC
Q 042003          220 IARGMDFK  227 (248)
Q Consensus       220 ~~~Gidip  227 (248)
                      +++|+||.
T Consensus       502 AGRGtDI~  509 (896)
T PRK13104        502 AGRGTDIV  509 (896)
T ss_pred             ccCCccee
Confidence            99999986

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=99.78  E-value=3.6e-18  Score=144.00  Aligned_cols=217  Identities=19%  Similarity=0.210  Sum_probs=149.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |.+|-|+.+..-.++.|     +.+|..+.    ..++.++|.|.+.|.+++.++..-++.+.++|+||+|.+-+.. ..
T Consensus       184 LSNQKYREl~~EF~DVG-----LMTGDVTI----nP~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkE-RG  253 (1041)
T KOG0948|consen  184 LSNQKYRELLEEFKDVG-----LMTGDVTI----NPDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKE-RG  253 (1041)
T ss_pred             hcchhHHHHHHHhcccc-----eeecceee----CCCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccc-cc
Confidence            34565655555444444     44443322    2367899999999999999999989999999999999998765 44


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhc---CCcEE-EEEcccccccccceeEEEEcCCc------------
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM---HDAVR-VIVGRKNTASESIKQKLVFAGSE------------  144 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~---~~~~~-~~~~~~~~~~~~~~~~~~~~~~~------------  144 (248)
                      -.+++-.-. .+.+.+.+++|||+|+ ..+.+.|.+   +-|-. +.+...   +.+++++++.....            
T Consensus       254 VVWEETIIl-lP~~vr~VFLSATiPN-A~qFAeWI~~ihkQPcHVVYTdyR---PTPLQHyifP~ggdGlylvVDek~~F  328 (1041)
T KOG0948|consen  254 VVWEETIIL-LPDNVRFVFLSATIPN-ARQFAEWICHIHKQPCHVVYTDYR---PTPLQHYIFPAGGDGLYLVVDEKGKF  328 (1041)
T ss_pred             eeeeeeEEe-ccccceEEEEeccCCC-HHHHHHHHHHHhcCCceEEeecCC---CCcceeeeecCCCCeeEEEEeccccc
Confidence            444443333 6778899999999998 555555543   33322 222222   22333443221110            


Q ss_pred             -h---------------------------------------hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC-
Q 042003          145 -E---------------------------------------GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD-  183 (248)
Q Consensus       145 -~---------------------------------------~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~-  183 (248)
                       +                                       +-...+..++.+. ..++|||+-++++|+.++-.+.+. 
T Consensus       329 rednF~~am~~l~~~~~~~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~-~~PVIvFSFSkkeCE~~Alqm~kld  407 (1041)
T KOG0948|consen  329 REDNFQKAMSVLRKAGESDGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERN-YLPVIVFSFSKKECEAYALQMSKLD  407 (1041)
T ss_pred             chHHHHHHHHHhhccCCCccccccccccccCCcCCCCCCcccHHHHHHHHHhhc-CCceEEEEecHhHHHHHHHhhccCc
Confidence             0                                       1112222223332 568999999999999999888541 


Q ss_pred             --------------------------------------CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCC
Q 042003          184 --------------------------------------GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMD  225 (248)
Q Consensus       184 --------------------------------------~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gid  225 (248)
                                                            ..+++++|||+-+--++.+.-.|++|-+++|+||.+++.|+|
T Consensus       408 fN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLN  487 (1041)
T KOG0948|consen  408 FNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLN  487 (1041)
T ss_pred             CCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccC
Confidence                                                  236799999999999999999999999999999999999999


Q ss_pred             CCCCcEEE
Q 042003          226 FKGVNCVI  233 (248)
Q Consensus       226 ip~~~~Vi  233 (248)
                      +|.-++|+
T Consensus       488 MPAkTVvF  495 (1041)
T KOG0948|consen  488 MPAKTVVF  495 (1041)
T ss_pred             CcceeEEE
Confidence            99666554

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

Probab=99.78  E-value=2.5e-18  Score=148.50  Aligned_cols=232  Identities=18%  Similarity=0.178  Sum_probs=150.2

Q ss_pred             HHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhc--CCcccCceeEEEEeccccccccCcccccchh
Q 042003            8 ECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRR--KKIDLSRVEYLVLDEADKLFEVGNLLKHIDP   85 (248)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~--~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~   85 (248)
                      .+..+....| ..+..++|... .....+.-.+.|||.++...++..  +.-.++.+++|||||.|++++.+ ....++.
T Consensus       288 ~l~~~~~~~G-~~ve~y~g~~~-p~~~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~-rg~~lE~  364 (1008)
T KOG0950|consen  288 ALSPFSIDLG-FPVEEYAGRFP-PEKRRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKG-RGAILEL  364 (1008)
T ss_pred             hhhhhccccC-CcchhhcccCC-CCCcccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccc-cchHHHH
Confidence            3445666677 55666664433 333444678999999988776655  33456889999999999999877 5555555


Q ss_pred             Hhh----hCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccccccccc-c-eeEEEEcCCchhHHHHHHHHH----
Q 042003           86 VVK----ACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASES-I-KQKLVFAGSEEGKLLALRQSF----  155 (248)
Q Consensus        86 ~~~----~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~l~~~~----  155 (248)
                      ++.    .+.....|+|+||||+++ ...+..|+ .... +.......+... + .-...+..+   +...+.++-    
T Consensus       365 ~l~k~~y~~~~~~~~iIGMSATi~N-~~lL~~~L-~A~~-y~t~fRPv~L~E~ik~G~~i~~~~---r~~~lr~ia~l~~  438 (1008)
T KOG0950|consen  365 LLAKILYENLETSVQIIGMSATIPN-NSLLQDWL-DAFV-YTTRFRPVPLKEYIKPGSLIYESS---RNKVLREIANLYS  438 (1008)
T ss_pred             HHHHHHHhccccceeEeeeecccCC-hHHHHHHh-hhhh-eecccCcccchhccCCCcccccch---hhHHHHHhhhhhh
Confidence            544    334455789999999987 44444443 2111 111111111000 0 000111111   222222221    


Q ss_pred             ---------------hcc--CCCCEEEEecchHHHHHHHHHhhc------------------------------------
Q 042003          156 ---------------AES--LNPPVLIFVQSKERAKELYGELAF------------------------------------  182 (248)
Q Consensus       156 ---------------~~~--~~~~~liF~~~~~~~~~l~~~L~~------------------------------------  182 (248)
                                     .+.  .+.++||||++++-|+.++..+..                                    
T Consensus       439 ~~~g~~dpD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~  518 (1008)
T KOG0950|consen  439 SNLGDEDPDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLA  518 (1008)
T ss_pred             hhcccCCCcceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHh
Confidence                           111  145699999999999988855521                                    


Q ss_pred             --CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe---ccCC-CCcccceecC
Q 042003          183 --DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN---YDFP-DSGAAYIHRI  248 (248)
Q Consensus       183 --~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~---~~~p-~~~~~~~qri  248 (248)
                        ..++++++|.|++.++|+.+...|++|...|++||++++.|+|+|..+++|-   ++.+ -+.-+|.||+
T Consensus       519 ~ti~~GvAyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~  590 (1008)
T KOG0950|consen  519 KTIPYGVAYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMV  590 (1008)
T ss_pred             eeccccceecccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhh
Confidence              1257899999999999999999999999999999999999999998888873   3333 4667888874

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.77  E-value=7e-18  Score=151.33  Aligned_cols=103  Identities=22%  Similarity=0.284  Sum_probs=88.9

Q ss_pred             hHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcC---CceEEEEeccc
Q 042003          146 GKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAG---KTWVLIATDVI  220 (248)
Q Consensus       146 ~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g---~~~ilv~T~~~  220 (248)
                      .|+..+..++...  .+.++|||+........+.+.|...+++...++|+++..+|..+++.|+..   .+.+|++|.++
T Consensus       471 gKl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAG  550 (1033)
T PLN03142        471 GKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAG  550 (1033)
T ss_pred             hHHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEecccc
Confidence            4555555555432  267999999999999999999999999999999999999999999999753   34678999999


Q ss_pred             ccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          221 ARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       221 ~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +.|+|++.+++||+||+|||+....|++
T Consensus       551 GlGINLt~Ad~VIiyD~dWNP~~d~QAi  578 (1033)
T PLN03142        551 GLGINLATADIVILYDSDWNPQVDLQAQ  578 (1033)
T ss_pred             ccCCchhhCCEEEEeCCCCChHHHHHHH
Confidence            9999999999999999999999988874

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.76  E-value=6.5e-18  Score=146.90  Aligned_cols=105  Identities=26%  Similarity=0.278  Sum_probs=92.5

Q ss_pred             CCchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          142 GSEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      .....|...+.+.+...  .+.|+||||+|+..++.+++.|.+.++++..+|+.+...++..+.++++.|.  |+|||+.
T Consensus       420 ~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnm  497 (796)
T PRK12906        420 PTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNM  497 (796)
T ss_pred             cCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEecc
Confidence            34456888888777433  4789999999999999999999999999999999999888888888888777  9999999


Q ss_pred             cccCCCCC---CCc-----EEEeccCCCCcccceecC
Q 042003          220 IARGMDFK---GVN-----CVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       220 ~~~Gidip---~~~-----~Vi~~~~p~~~~~~~qri  248 (248)
                      +++|.||+   ++.     |||+++.|.|...|.||+
T Consensus       498 AGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~  534 (796)
T PRK12906        498 AGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLR  534 (796)
T ss_pred             ccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHh
Confidence            99999995   889     999999999999999974

>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=99.76  E-value=2.1e-17  Score=116.46  Aligned_cols=103  Identities=48%  Similarity=0.669  Sum_probs=96.4

Q ss_pred             hHHHHHHHHHhccC--CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccC
Q 042003          146 GKLLALRQSFAESL--NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG  223 (248)
Q Consensus       146 ~~~~~l~~~~~~~~--~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G  223 (248)
                      .+...+..++.+..  ++++||||++...++.+++.|.+.+.++..+||+++..+|..+.+.|.+|...++++|+.+++|
T Consensus        12 ~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G   91 (131)
T cd00079          12 EKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARG   91 (131)
T ss_pred             HHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcC
Confidence            67777777777654  6899999999999999999999888899999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEeccCCCCcccceecC
Q 042003          224 MDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       224 idip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +|+|.+++||++++|++...|+|++
T Consensus        92 ~d~~~~~~vi~~~~~~~~~~~~Q~~  116 (131)
T cd00079          92 IDLPNVSVVINYDLPWSPSSYLQRI  116 (131)
T ss_pred             cChhhCCEEEEeCCCCCHHHheecc
Confidence            9999999999999999999999985

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.75  E-value=1.8e-17  Score=144.09  Aligned_cols=89  Identities=29%  Similarity=0.428  Sum_probs=86.1

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc---
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD---  236 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~---  236 (248)
                      +.+++|||++++.++.+++.|.+.|+++..+||+++..+|.++++.|+.|++.|+|||+.+++|+|+|++++||+++   
T Consensus       442 g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP~v~lVvi~Dadi  521 (655)
T TIGR00631       442 NERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADK  521 (655)
T ss_pred             CCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeCCCcEEEEeCccc
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999988   


Q ss_pred             --CCCCcccceecC
Q 042003          237 --FPDSGAAYIHRI  248 (248)
Q Consensus       237 --~p~~~~~~~qri  248 (248)
                        .|.+..+|+||+
T Consensus       522 fG~p~~~~~~iqri  535 (655)
T TIGR00631       522 EGFLRSERSLIQTI  535 (655)
T ss_pred             ccCCCCHHHHHHHh
Confidence              799999999986

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

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

Probab=99.74  E-value=4e-17  Score=136.61  Aligned_cols=196  Identities=18%  Similarity=0.223  Sum_probs=143.1

Q ss_pred             ccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccc-ccCcccccchhHhhhCCCccceeEEEEeecCchHHHHH
Q 042003           34 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF-EVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA  112 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~  112 (248)
                      ......|.+.|.+.|++.+..+.. ++.+++||+||||.-. ..+-....++.+.+.  .+..++|.||||+..   +..
T Consensus       137 ts~~TrikymTDG~LLRE~l~Dp~-LskYsvIIlDEAHERsl~TDiLlGlLKki~~~--R~~LklIimSATlda---~kf  210 (674)
T KOG0922|consen  137 TSKDTRIKYMTDGMLLREILKDPL-LSKYSVIILDEAHERSLHTDILLGLLKKILKK--RPDLKLIIMSATLDA---EKF  210 (674)
T ss_pred             CCCceeEEEecchHHHHHHhcCCc-cccccEEEEechhhhhhHHHHHHHHHHHHHhc--CCCceEEEEeeeecH---HHH
Confidence            344688999999999999987665 6999999999999633 222244455555543  456789999999974   344


Q ss_pred             HHhcCCcEEEEEcccccccccceeEEEEcCCch---hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC----CC
Q 042003          113 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEE---GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD----GI  185 (248)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~----~~  185 (248)
                      ..|+.....+.+.....   ++...+...+..+   ..+....++-...+++-++||.+..++.+.+++.|.+.    +.
T Consensus       211 S~yF~~a~i~~i~GR~f---PVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~  287 (674)
T KOG0922|consen  211 SEYFNNAPILTIPGRTF---PVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACELLRERAKSLPE  287 (674)
T ss_pred             HHHhcCCceEeecCCCC---ceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccc
Confidence            44555544444333322   2333443333332   33444445555556789999999999999999999764    11


Q ss_pred             ----eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          186 ----RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       186 ----~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                          -+.++||+++.+++..+++.-..|..+++++|++++..+.||++.+||+-|.-
T Consensus       288 ~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~v  344 (674)
T KOG0922|consen  288 DCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFV  344 (674)
T ss_pred             cCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCce
Confidence                35789999999999999999999999999999999999999999999988874

>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=99.71  E-value=7.2e-18  Score=107.81  Aligned_cols=71  Identities=41%  Similarity=0.665  Sum_probs=68.1

Q ss_pred             HHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          178 GELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       178 ~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +.|++.++++..+||+++..+|+.+++.|+++...+||||+++++|+|+|++++||++++|+|+..|.||+
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~   71 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRI   71 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHH
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHh
Confidence            36788899999999999999999999999999999999999999999999999999999999999999974

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 ....

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=99.70  E-value=5.7e-16  Score=137.36  Aligned_cols=226  Identities=19%  Similarity=0.181  Sum_probs=150.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |.+|.+..+....... ...+.+.+|..    ...+++.|+|.|.+-|.+++.++...+..+.+||+||+|.+.+.. ..
T Consensus       174 LsNQKyrdl~~~fgdv-~~~vGL~TGDv----~IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~e-RG  247 (1041)
T COG4581         174 LSNQKYRDLLAKFGDV-ADMVGLMTGDV----SINPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRE-RG  247 (1041)
T ss_pred             hhhhHHHHHHHHhhhh-hhhccceecce----eeCCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccc-cc
Confidence            4567776666544433 23345555533    233468899999999999999999999999999999999988765 44


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhc---CCcEEEEEcccccccccceeEEEEc------CCchh-----
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM---HDAVRVIVGRKNTASESIKQKLVFA------GSEEG-----  146 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~-----  146 (248)
                      -..++..-. .+...+++++|||+|+ ..++..|+.   +.+..++ .-...+ .++.++++.-      -+...     
T Consensus       248 ~VWEE~Ii~-lP~~v~~v~LSATv~N-~~EF~~Wi~~~~~~~~~vv-~t~~Rp-vPL~~~~~~~~~l~~lvde~~~~~~~  323 (1041)
T COG4581         248 VVWEEVIIL-LPDHVRFVFLSATVPN-AEEFAEWIQRVHSQPIHVV-STEHRP-VPLEHFVYVGKGLFDLVDEKKKFNAE  323 (1041)
T ss_pred             hhHHHHHHh-cCCCCcEEEEeCCCCC-HHHHHHHHHhccCCCeEEE-eecCCC-CCeEEEEecCCceeeeecccccchhh
Confidence            455555555 6778899999999988 555555553   2222221 111111 1222222111      00000     


Q ss_pred             ----HH--------------------------------------HHHHHHHhccCCCCEEEEecchHHHHHHHHHhhc--
Q 042003          147 ----KL--------------------------------------LALRQSFAESLNPPVLIFVQSKERAKELYGELAF--  182 (248)
Q Consensus       147 ----~~--------------------------------------~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~--  182 (248)
                          ..                                      ..+...+.....-++++|+-++..|+..+..+..  
T Consensus       324 ~~~~a~~~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ld  403 (1041)
T COG4581         324 NFPSANRSLSCFSEKVRETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLD  403 (1041)
T ss_pred             cchhhhhhhhccchhccccCccccccccccccccCCcccccccchHHHhhhhhhcCCceEEEEEchhhHHHHHHHhcccc
Confidence                00                                      0111122222245899999999999988877742  


Q ss_pred             --------------------------CC-------------CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccC
Q 042003          183 --------------------------DG-------------IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG  223 (248)
Q Consensus       183 --------------------------~~-------------~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G  223 (248)
                                                .+             ..++++|+||-+..|+.+.+.|..|-.+++++|.+++.|
T Consensus       404 l~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~G  483 (1041)
T COG4581         404 LVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIG  483 (1041)
T ss_pred             cccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHhccceeEEeehhhhhhh
Confidence                                      11             135789999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEeccC
Q 042003          224 MDFKGVNCVINYDF  237 (248)
Q Consensus       224 idip~~~~Vi~~~~  237 (248)
                      +|+| ++.|+..+.
T Consensus       484 iNmP-artvv~~~l  496 (1041)
T COG4581         484 INMP-ARTVVFTSL  496 (1041)
T ss_pred             cCCc-ccceeeeee
Confidence            9999 555554443

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.69  E-value=3.3e-16  Score=137.03  Aligned_cols=89  Identities=28%  Similarity=0.382  Sum_probs=85.4

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC--
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF--  237 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~--  237 (248)
                      +.+++|||++.+.++.+++.|.+.|+++..+||+++..+|..+++.|+.|+..++|||+.+++|+|+|++++||+++.  
T Consensus       446 g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp~v~lVii~d~ei  525 (652)
T PRK05298        446 GERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADK  525 (652)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccccCCcEEEEeCCcc
Confidence            678999999999999999999999999999999999999999999999999999999999999999999999999875  


Q ss_pred             ---CCCcccceecC
Q 042003          238 ---PDSGAAYIHRI  248 (248)
Q Consensus       238 ---p~~~~~~~qri  248 (248)
                         |.+..+|+||+
T Consensus       526 fG~~~~~~~yiqr~  539 (652)
T PRK05298        526 EGFLRSERSLIQTI  539 (652)
T ss_pred             cccCCCHHHHHHHh
Confidence               78999999985

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.67  E-value=6.7e-16  Score=135.08  Aligned_cols=84  Identities=24%  Similarity=0.296  Sum_probs=73.7

Q ss_pred             CCchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          142 GSEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      .....|..++.+.+...  .+.|+||||+|++.++.++..|...++++.++|+.++..++..+.++|+.|.  |+|||+.
T Consensus       429 ~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnm  506 (908)
T PRK13107        429 LTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNM  506 (908)
T ss_pred             eCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCC
Confidence            33456776666655422  3789999999999999999999999999999999999999999999999999  9999999


Q ss_pred             cccCCCCC
Q 042003          220 IARGMDFK  227 (248)
Q Consensus       220 ~~~Gidip  227 (248)
                      +++|.||.
T Consensus       507 AGRGTDIk  514 (908)
T PRK13107        507 AGRGTDIV  514 (908)
T ss_pred             cCCCccee
Confidence            99999987

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.63  E-value=8.1e-16  Score=136.35  Aligned_cols=204  Identities=22%  Similarity=0.346  Sum_probs=131.5

Q ss_pred             CcEEEeChHHHHHHHhcC-Ccc-c--CceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHH
Q 042003           38 CDILISTPLRLRLAIRRK-KID-L--SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR  113 (248)
Q Consensus        38 ~~i~v~Tp~~l~~~~~~~-~~~-~--~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~  113 (248)
                      ..+.++||-+........ ... +  =....+|+||+|.+.... ....+..+..........+++||||+|+...+...
T Consensus       311 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~-~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~  389 (733)
T COG1203         311 LALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET-MLAALLALLEALAEAGVPVLLMSATLPPFLKEKLK  389 (733)
T ss_pred             ccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc-hHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHH
Confidence            456666665554422211 111 1  123589999999988765 55556666665566678899999999999998888


Q ss_pred             HhcCCcEEEEEccc---cccccccee-EEEEcCCch--hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCee
Q 042003          114 SIMHDAVRVIVGRK---NTASESIKQ-KLVFAGSEE--GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRA  187 (248)
Q Consensus       114 ~~~~~~~~~~~~~~---~~~~~~~~~-~~~~~~~~~--~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v  187 (248)
                      ....+...+.....   ......+.+ .........  ........  ....+++++|.|||+..|..+|+.|+..+.++
T Consensus       390 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v  467 (733)
T COG1203         390 KALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELISE--EVKEGKKVLVIVNTVDRAIELYEKLKEKGPKV  467 (733)
T ss_pred             HHHhcccceeccccccccccccccccccchhhhhhhhHhhhhcchh--hhccCCcEEEEEecHHHHHHHHHHHHhcCCCE
Confidence            77665544433211   000111111 111111110  01111111  12226899999999999999999999988789


Q ss_pred             EEEecCCCHHHHHHHHHHh----hcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceec
Q 042003          188 GVIHSDLSQTQRENAVDDF----RAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHR  247 (248)
Q Consensus       188 ~~~~~~~~~~~r~~~~~~f----~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qr  247 (248)
                      ..+||.+...+|.+.++.+    +.+...|+|||++++.|+|+. .+.+|  .-+..++..+||
T Consensus       468 ~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-fd~mI--Te~aPidSLIQR  528 (733)
T COG1203         468 LLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-FDVLI--TELAPIDSLIQR  528 (733)
T ss_pred             EEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-cCeee--ecCCCHHHHHHH
Confidence            9999999999998887754    456778999999999999986 44443  444455555565

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=99.63  E-value=3.6e-15  Score=130.11  Aligned_cols=221  Identities=24%  Similarity=0.309  Sum_probs=155.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh--------hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV--------RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~   72 (248)
                      |+.|+++.+++++...+...+...|.+.        ....+..++.||+|+|.+-|...+..  +.--+++++++|++|.
T Consensus       137 Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~--L~~~kFdfifVDDVDA  214 (1187)
T COG1110         137 LVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEE--LSKLKFDFIFVDDVDA  214 (1187)
T ss_pred             HHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHH--hcccCCCEEEEccHHH
Confidence            6899999999999777633333324433        12344556899999998766555542  2224688999999998


Q ss_pred             ccccCcccccchhHhhhC-------------------------------------------CCccceeEEEEeecCchH-
Q 042003           73 LFEVGNLLKHIDPVVKAC-------------------------------------------SNPSIVRSLFSATLPDFV-  108 (248)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~-------------------------------------------~~~~~~~i~~SAT~~~~~-  108 (248)
                      ++..+   +.+.+++..+                                           .....+++..|||..+.- 
T Consensus       215 ~Lkas---kNvDriL~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~  291 (1187)
T COG1110         215 ILKAS---KNVDRLLRLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGS  291 (1187)
T ss_pred             HHhcc---ccHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCc
Confidence            87532   1111111110                                           123468899999986633 


Q ss_pred             -HHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecc---hHHHHHHHHHhhcCC
Q 042003          109 -EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQS---KERAKELYGELAFDG  184 (248)
Q Consensus       109 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~---~~~~~~l~~~L~~~~  184 (248)
                       ..+.+.+++    +.++.......++...+...    .......+++++. +.-.|||++.   ++.++.+++.|+..|
T Consensus       292 R~~LfReLlg----FevG~~~~~LRNIvD~y~~~----~~~e~~~elvk~l-G~GgLIfV~~d~G~e~aeel~e~Lr~~G  362 (1187)
T COG1110         292 RLKLFRELLG----FEVGSGGEGLRNIVDIYVES----ESLEKVVELVKKL-GDGGLIFVPIDYGREKAEELAEYLRSHG  362 (1187)
T ss_pred             hHHHHHHHhC----CccCccchhhhheeeeeccC----ccHHHHHHHHHHh-CCCeEEEEEcHHhHHHHHHHHHHHHhcC
Confidence             234444443    33444555555565555433    4555666777777 5689999999   999999999999999


Q ss_pred             CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec----ccccCCCCCC-CcEEEeccCCCC
Q 042003          185 IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD----VIARGMDFKG-VNCVINYDFPDS  240 (248)
Q Consensus       185 ~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~----~~~~Gidip~-~~~Vi~~~~p~~  240 (248)
                      +++..+|++     ++..++.|..|++++||+..    .+-+|+|+|. ++++|.+|.|+-
T Consensus       363 i~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk~  418 (1187)
T COG1110         363 INAELIHAE-----KEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPKF  418 (1187)
T ss_pred             ceEEEeecc-----chhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCCce
Confidence            999999994     47789999999999998774    5789999996 899999999953

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.60  E-value=2.3e-15  Score=96.98  Aligned_cols=74  Identities=49%  Similarity=0.704  Sum_probs=70.3

Q ss_pred             HHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          175 ELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       175 ~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      .+++.|++.++.+..+||+++.++|..+++.|+++...++++|+.+++|+|+|.+++||++++|++...|.||+
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~   75 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRI   75 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhh
Confidence            46778888899999999999999999999999999999999999999999999999999999999999999985

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=99.60  E-value=5.1e-14  Score=119.64  Aligned_cols=86  Identities=24%  Similarity=0.279  Sum_probs=73.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcC---CceEEEEecccccCCCCCCCcEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAG---KTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g---~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      +.+++||..=-....-+.++..-+++....+.|+++.++|.+.++.|...   .+-+|++|-+.+.|||+..++.||.||
T Consensus       487 GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGINL~aADtVIlyD  566 (971)
T KOG0385|consen  487 GHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGINLTAADTVILYD  566 (971)
T ss_pred             CCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccccccccccccccEEEEec
Confidence            78999997665666666666666799999999999999999999999864   456889999999999999999999999


Q ss_pred             CCCCcccce
Q 042003          237 FPDSGAAYI  245 (248)
Q Consensus       237 ~p~~~~~~~  245 (248)
                      .-|||..=+
T Consensus       567 SDWNPQ~DL  575 (971)
T KOG0385|consen  567 SDWNPQVDL  575 (971)
T ss_pred             CCCCchhhh
Confidence            999996433

>cd00268 DEADc DEAD-box helicases

Probab=99.59  E-value=6.4e-15  Score=111.76  Aligned_cols=119  Identities=34%  Similarity=0.463  Sum_probs=95.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh---hcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR---STDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      |+.|+.+.++.+....+ ..+....|+..   ......++++|+|+||+++.+.+.+....+.+++++|+||+|.+.+.+
T Consensus        81 L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~  159 (203)
T cd00268          81 LALQIAEVARKLGKHTN-LKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMG  159 (203)
T ss_pred             HHHHHHHHHHHHhccCC-ceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccC
Confidence            57899999999988777 55555655552   223344589999999999999998888888999999999999988666


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEE
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRV  122 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~  122 (248)
                       +...+..+.+. ....++++++|||+++........++.++..+
T Consensus       160 -~~~~~~~~~~~-l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         160 -FEDQIREILKL-LPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             -hHHHHHHHHHh-CCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence             77777777777 45689999999999999988888888877654

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.

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

Probab=99.58  E-value=8.4e-14  Score=114.26  Aligned_cols=138  Identities=25%  Similarity=0.300  Sum_probs=100.4

Q ss_pred             cceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHH
Q 042003           94 SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERA  173 (248)
Q Consensus        94 ~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~  173 (248)
                      ..|+|+.|||+.+...+...   +......+.+....-+.+. ..-.....++-+..+....++  +.+++|-+-|++.|
T Consensus       386 ~~q~i~VSATPg~~E~e~s~---~~vveQiIRPTGLlDP~ie-vRp~~~QvdDL~~EI~~r~~~--~eRvLVTtLTKkmA  459 (663)
T COG0556         386 IPQTIYVSATPGDYELEQSG---GNVVEQIIRPTGLLDPEIE-VRPTKGQVDDLLSEIRKRVAK--NERVLVTTLTKKMA  459 (663)
T ss_pred             cCCEEEEECCCChHHHHhcc---CceeEEeecCCCCCCCcee-eecCCCcHHHHHHHHHHHHhc--CCeEEEEeehHHHH
Confidence            47999999998864333322   2223333333222222111 110111122233333333333  57999999999999


Q ss_pred             HHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       174 ~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      +.+.++|.+.|+++..+|++...-+|.++++.++.|.++|||+-+.+-+|+|+|.+..|-++|.
T Consensus       460 EdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDA  523 (663)
T COG0556         460 EDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDA  523 (663)
T ss_pred             HHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeec
Confidence            9999999999999999999999999999999999999999999999999999999999998876

>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=99.58  E-value=3.6e-13  Score=110.77  Aligned_cols=207  Identities=22%  Similarity=0.259  Sum_probs=152.3

Q ss_pred             CCCcEEEeChHHHHHHHhc------CCcccCceeEEEEeccccccccCcccccchhHhhh-------------------C
Q 042003           36 FSCDILISTPLRLRLAIRR------KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKA-------------------C   90 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~------~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~-------------------~   90 (248)
                      .++|||||||-.|...+..      ..-.++++.++|+|.||.+...+  +..+..+++.                   +
T Consensus       130 y~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQN--W~Hv~~v~~~lN~~P~~~~~~DfsRVR~w~  207 (442)
T PF06862_consen  130 YSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQN--WEHVLHVFEHLNLQPKKSHDTDFSRVRPWY  207 (442)
T ss_pred             ccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhh--HHHHHHHHHHhccCCCCCCCCCHHHHHHHH
Confidence            3689999999999888874      22358999999999999987543  1112222111                   1


Q ss_pred             C----CccceeEEEEeecCchHHHHHHHhcCCcE---EEEEccc-----ccccccceeEEEEcCCc------hhHHHH--
Q 042003           91 S----NPSIVRSLFSATLPDFVEELARSIMHDAV---RVIVGRK-----NTASESIKQKLVFAGSE------EGKLLA--  150 (248)
Q Consensus        91 ~----~~~~~~i~~SAT~~~~~~~~~~~~~~~~~---~~~~~~~-----~~~~~~~~~~~~~~~~~------~~~~~~--  150 (248)
                      .    ..-.|+|++|+...|+...+....+.+-.   .+.....     .....++.|.+...+..      +.+.+.  
T Consensus       208 Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~  287 (442)
T PF06862_consen  208 LDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSSPADDPDARFKYFT  287 (442)
T ss_pred             HcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCCcchhhhHHHHHHH
Confidence            1    12279999999999999999988665532   1211111     23445566766553332      233322  


Q ss_pred             --HHHHHh-ccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccc--cCCC
Q 042003          151 --LRQSFA-ESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIA--RGMD  225 (248)
Q Consensus       151 --l~~~~~-~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~--~Gid  225 (248)
                        ++.-+. ....+.++||++|.-+--++.+.|++.++....+|..++..+.......|..|+.++|+-|.-+.  +-..
T Consensus       288 ~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~  367 (442)
T PF06862_consen  288 KKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYR  367 (442)
T ss_pred             HHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhce
Confidence              222233 44467999999999999999999999999999999999999999999999999999999998753  6678


Q ss_pred             CCCCcEEEeccCCCCcccc
Q 042003          226 FKGVNCVINYDFPDSGAAY  244 (248)
Q Consensus       226 ip~~~~Vi~~~~p~~~~~~  244 (248)
                      +.++++||.|++|.++.-|
T Consensus       368 irGi~~viFY~~P~~p~fY  386 (442)
T PF06862_consen  368 IRGIRHVIFYGPPENPQFY  386 (442)
T ss_pred             ecCCcEEEEECCCCChhHH
Confidence            8999999999999998755

; GO: 0005634 nucleus

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=99.57  E-value=3.2e-14  Score=115.84  Aligned_cols=230  Identities=16%  Similarity=0.134  Sum_probs=150.7

Q ss_pred             cchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCC--------cccCceeEEEEeccccc
Q 042003            2 ATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKK--------IDLSRVEYLVLDEADKL   73 (248)
Q Consensus         2 ~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~--------~~~~~~~~lIiDEah~~   73 (248)
                      +.||.+.+..|...-+-..+.+...   ..+....++.|+|+|..++...-+++.        +.-+.++++++||+|.+
T Consensus       358 VeQWkqQfk~wsti~d~~i~rFTsd---~Ke~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvv  434 (776)
T KOG1123|consen  358 VEQWKQQFKQWSTIQDDQICRFTSD---AKERFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVV  434 (776)
T ss_pred             HHHHHHHHHhhcccCccceEEeecc---ccccCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccc
Confidence            5799999999887766444444333   334455689999999977755444321        23567999999999999


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHH-------------H--hc--CCcEEE---EEccc------
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR-------------S--IM--HDAVRV---IVGRK------  127 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~-------------~--~~--~~~~~~---~~~~~------  127 (248)
                      .... |++.+..+...|      -+++|||+-.+.+.+..             |  +.  +....+   .+...      
T Consensus       435 PA~M-FRRVlsiv~aHc------KLGLTATLvREDdKI~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy  507 (776)
T KOG1123|consen  435 PAKM-FRRVLSIVQAHC------KLGLTATLVREDDKITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFY  507 (776)
T ss_pred             hHHH-HHHHHHHHHHHh------hccceeEEeeccccccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHH
Confidence            8876 777777766665      37999997443222211             1  00  011111   11110      


Q ss_pred             --ccccccceeEEEEcCCchhHHHHHHHHHhccC--CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHH
Q 042003          128 --NTASESIKQKLVFAGSEEGKLLALRQSFAESL--NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAV  203 (248)
Q Consensus       128 --~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~  203 (248)
                        ......-++..+++-+.. |.....-+++.++  +.|+|||..++......+-.|.+     .++.|.+++.+|..++
T Consensus       508 ~eYL~~~t~kr~lLyvMNP~-KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~K-----pfIYG~Tsq~ERm~IL  581 (776)
T KOG1123|consen  508 REYLRENTRKRMLLYVMNPN-KFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLGK-----PFIYGPTSQNERMKIL  581 (776)
T ss_pred             HHHHhhhhhhhheeeecCcc-hhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHcCC-----ceEECCCchhHHHHHH
Confidence              111111223344444433 4444444444332  78999999999888888877754     3689999999999999


Q ss_pred             HHhhcC-CceEEEEecccccCCCCCCCcEEEeccCC-CCcccceec
Q 042003          204 DDFRAG-KTWVLIATDVIARGMDFKGVNCVINYDFP-DSGAAYIHR  247 (248)
Q Consensus       204 ~~f~~g-~~~ilv~T~~~~~Gidip~~~~Vi~~~~p-~~~~~~~qr  247 (248)
                      +.|+-+ .++-++-+.+....+|+|.++++|+...- -|..+=.||
T Consensus       582 qnFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQR  627 (776)
T KOG1123|consen  582 QNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQR  627 (776)
T ss_pred             HhcccCCccceEEEeeccCccccCCcccEEEEEcccccchHHHHHH
Confidence            999964 67899999999999999999999987654 244443443

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

Probab=99.56  E-value=4.1e-14  Score=124.50  Aligned_cols=199  Identities=17%  Similarity=0.168  Sum_probs=134.5

Q ss_pred             cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHH
Q 042003           35 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS  114 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~  114 (248)
                      .....+++||.+.|++.+.. .-.+.++.++|+||+|.-.-..+|.-.+.+.+-. ..+..++|+||||+..   +....
T Consensus       262 s~~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~-~~p~LkvILMSAT~da---e~fs~  336 (924)
T KOG0920|consen  262 SRETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLP-RNPDLKVILMSATLDA---ELFSD  336 (924)
T ss_pred             CCceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHHHHHhh-hCCCceEEEeeeecch---HHHHH
Confidence            33488999999999999988 3447899999999999865444343333332222 3478899999999873   33333


Q ss_pred             hcCCcEEEEEccccccccc----------------ceeEE-----------EEcCCch---hHHHHHHH-HHhccCCCCE
Q 042003          115 IMHDAVRVIVGRKNTASES----------------IKQKL-----------VFAGSEE---GKLLALRQ-SFAESLNPPV  163 (248)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~----------------~~~~~-----------~~~~~~~---~~~~~l~~-~~~~~~~~~~  163 (248)
                      |++....+.+....-+...                ..+..           ..+-..+   +-+..+.. +......+.+
T Consensus       337 YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~Li~~li~~I~~~~~~GaI  416 (924)
T KOG0920|consen  337 YFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDLIEDLIEYIDEREFEGAI  416 (924)
T ss_pred             HhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHHHHHHHHhcccCCCCceE
Confidence            4444333322211000000                00000           0000111   12222222 2333337899


Q ss_pred             EEEecchHHHHHHHHHhhcC-------CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          164 LIFVQSKERAKELYGELAFD-------GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       164 liF~~~~~~~~~l~~~L~~~-------~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      |||.+...+...+++.|...       ..-+.++|+.|+..+++.+......|..+|+++|++++.+|.|+++-+||+.|
T Consensus       417 LVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNIAETSITIdDVvyVIDsG  496 (924)
T KOG0920|consen  417 LVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETSITIDDVVYVIDSG  496 (924)
T ss_pred             EEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhhhHhhcccccCeEEEEecC
Confidence            99999999999999999642       24678889999999999999999999999999999999999999999999876


Q ss_pred             CC
Q 042003          237 FP  238 (248)
Q Consensus       237 ~p  238 (248)
                      ..
T Consensus       497 ~~  498 (924)
T KOG0920|consen  497 LV  498 (924)
T ss_pred             ee
Confidence            53

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=99.55  E-value=6.3e-14  Score=120.45  Aligned_cols=231  Identities=15%  Similarity=0.155  Sum_probs=143.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcC-----CcccCceeEEEEeccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRK-----KIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~-----~~~~~~~~~lIiDEah~~~~   75 (248)
                      |+.|.++.+.++.+...  ++..+.+..     ....++|.++|.+++.......     .+....+++||+||||+-. 
T Consensus       227 Lv~QA~~af~~~~P~~~--~~n~i~~~~-----~~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi-  298 (875)
T COG4096         227 LVDQAYGAFEDFLPFGT--KMNKIEDKK-----GDTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGI-  298 (875)
T ss_pred             HHHHHHHHHHHhCCCcc--ceeeeeccc-----CCcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhH-
Confidence            45677777777777653  222222211     1125889999999999888764     3445679999999999943 


Q ss_pred             cCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhc-CCcEEEE--------------------E--cccccccc
Q 042003           76 VGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM-HDAVRVI--------------------V--GRKNTASE  132 (248)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~-~~~~~~~--------------------~--~~~~~~~~  132 (248)
                          ......++.++.   .-.+++|||+........-.++ +.|....                    .  ......+.
T Consensus       299 ----~~~~~~I~dYFd---A~~~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~  371 (875)
T COG4096         299 ----YSEWSSILDYFD---AATQGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPD  371 (875)
T ss_pred             ----HhhhHHHHHHHH---HHHHhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcC
Confidence                333335555532   1235679998664443333344 3332211                    0  00000000


Q ss_pred             cc-----------------------eeEEEEcCCchhHHHHHHHHHhc--cC--CCCEEEEecchHHHHHHHHHhhcC--
Q 042003          133 SI-----------------------KQKLVFAGSEEGKLLALRQSFAE--SL--NPPVLIFVQSKERAKELYGELAFD--  183 (248)
Q Consensus       133 ~~-----------------------~~~~~~~~~~~~~~~~l~~~~~~--~~--~~~~liF~~~~~~~~~l~~~L~~~--  183 (248)
                      ..                       ..........+.-...+.+.+..  ..  .+|+||||.+..+|+.+.+.|...  
T Consensus       372 ~~serek~~g~~i~~dd~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~yp  451 (875)
T COG4096         372 AGSEREKLQGEAIDEDDQNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYP  451 (875)
T ss_pred             ccchhhhhhccccCcccccccccccchhccccchHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCc
Confidence            00                       00011111122233455666665  32  469999999999999999999764  


Q ss_pred             ---CCeeEEEecCCCHHHHHHHHHHhhc--CCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          184 ---GIRAGVIHSDLSQTQRENAVDDFRA--GKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       184 ---~~~v~~~~~~~~~~~r~~~~~~f~~--g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                         +--+..+.|+-.  +-+..+..|..  .-..|.++.+.+..|+|+|.+..++.+..-.|...|.||+
T Consensus       452 e~~~~~a~~IT~d~~--~~q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMv  519 (875)
T COG4096         452 EYNGRYAMKITGDAE--QAQALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMV  519 (875)
T ss_pred             cccCceEEEEeccch--hhHHHHHHHHhcCCCCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHh
Confidence               234666666533  33444555544  3457999999999999999999999999999999999985

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

Probab=99.53  E-value=1e-13  Score=116.22  Aligned_cols=199  Identities=16%  Similarity=0.172  Sum_probs=141.0

Q ss_pred             ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc-cccCcccccchhHhhhCCCccceeEEEEeecCchHHH
Q 042003           32 DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEE  110 (248)
Q Consensus        32 ~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~  110 (248)
                      +-..+..-+-+.|.++|++.+..+. .+.++.++||||||.- +..+.....++.+.+.  .+...++++|||+..   +
T Consensus       350 dcTSekTvlKYMTDGmLlREfL~ep-dLasYSViiiDEAHERTL~TDILfgLvKDIar~--RpdLKllIsSAT~DA---e  423 (902)
T KOG0923|consen  350 DCTSEKTVLKYMTDGMLLREFLSEP-DLASYSVIIVDEAHERTLHTDILFGLVKDIARF--RPDLKLLISSATMDA---E  423 (902)
T ss_pred             cccCcceeeeeecchhHHHHHhccc-cccceeEEEeehhhhhhhhhhHHHHHHHHHHhh--CCcceEEeeccccCH---H
Confidence            3344567788999999998887654 4799999999999953 3333355566666664  367889999999874   3


Q ss_pred             HHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHh---ccCCCCEEEEecchHHHHHHHHHhhcC----
Q 042003          111 LARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA---ESLNPPVLIFVQSKERAKELYGELAFD----  183 (248)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~---~~~~~~~liF~~~~~~~~~l~~~L~~~----  183 (248)
                      ....++.+...+.++...   .++..++.....-+---.++..++.   ..+.+-+|||....++.+...+.|.+.    
T Consensus       424 kFS~fFDdapIF~iPGRR---yPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~~~~~L  500 (902)
T KOG0923|consen  424 KFSAFFDDAPIFRIPGRR---YPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKERCRRL  500 (902)
T ss_pred             HHHHhccCCcEEeccCcc---cceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHHHHHHh
Confidence            334566665544443322   2233333322222222223333333   334688999999988888777777542    


Q ss_pred             -----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCC
Q 042003          184 -----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD  239 (248)
Q Consensus       184 -----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~  239 (248)
                           .+-+.++|+.+|.+.+..+++.-..|..+|++||++++..+.|+++.+||+-|...
T Consensus       501 Gski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K  561 (902)
T KOG0923|consen  501 GSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVK  561 (902)
T ss_pred             ccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCcccc
Confidence                 34577889999999999999999999999999999999999999999999887754

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.49  E-value=2e-13  Score=120.51  Aligned_cols=148  Identities=22%  Similarity=0.158  Sum_probs=113.5

Q ss_pred             eeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc--CCCCEEEEecchHHH
Q 042003           96 VRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES--LNPPVLIFVQSKERA  173 (248)
Q Consensus        96 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~  173 (248)
                      .+-+||+|...+..++..-|..+...+   +...+...............+|.+.+.+.+...  .+.|+||||+|++.+
T Consensus       535 kLaGMTGTA~te~~Ef~~iY~L~Vv~I---PTnrP~~R~D~~d~vy~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~s  611 (1025)
T PRK12900        535 KLAGMTGTAETEASEFFEIYKLDVVVI---PTNKPIVRKDMDDLVYKTRREKYNAIVLKVEELQKKGQPVLVGTASVEVS  611 (1025)
T ss_pred             hhcccCCCChhHHHHHHHHhCCcEEEC---CCCCCcceecCCCeEecCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHH
Confidence            456899998776666655553333222   222222222222222355567888888888543  478999999999999


Q ss_pred             HHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCC---CCc-----EEEeccCCCCcccce
Q 042003          174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK---GVN-----CVINYDFPDSGAAYI  245 (248)
Q Consensus       174 ~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip---~~~-----~Vi~~~~p~~~~~~~  245 (248)
                      +.+.+.|...++++.++|+  .+.+|+..+..|..+...|+|||+.+++|.||+   .+.     +||.+..|.|...|.
T Consensus       612 E~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~  689 (1025)
T PRK12900        612 ETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDR  689 (1025)
T ss_pred             HHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHH
Confidence            9999999999999999997  588999999999999999999999999999999   454     449999999999999


Q ss_pred             ecC
Q 042003          246 HRI  248 (248)
Q Consensus       246 qri  248 (248)
                      ||+
T Consensus       690 Ql~  692 (1025)
T PRK12900        690 QLR  692 (1025)
T ss_pred             HHh
Confidence            984

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=99.47  E-value=3.9e-12  Score=108.75  Aligned_cols=101  Identities=24%  Similarity=0.270  Sum_probs=86.4

Q ss_pred             hHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhh-cCCCeeEEEecCCCHHHHHHHHHHhhcCCc--eEEEEeccc
Q 042003          146 GKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELA-FDGIRAGVIHSDLSQTQRENAVDDFRAGKT--WVLIATDVI  220 (248)
Q Consensus       146 ~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~-~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~--~ilv~T~~~  220 (248)
                      .|+..+..++...  .+.++++|..++....-+...|. ..+|++..+.|.++...|...++.|.++..  -+|++|.+.
T Consensus       530 GKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTrvG  609 (923)
T KOG0387|consen  530 GKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTRVG  609 (923)
T ss_pred             chHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEeccc
Confidence            4555555555432  26799999999999999999998 689999999999999999999999997753  478999999


Q ss_pred             ccCCCCCCCcEEEeccCCCCccccee
Q 042003          221 ARGMDFKGVNCVINYDFPDSGAAYIH  246 (248)
Q Consensus       221 ~~Gidip~~~~Vi~~~~p~~~~~~~q  246 (248)
                      +-|+|+..++-||+|||-|||++=.|
T Consensus       610 GLGlNLTgAnRVIIfDPdWNPStD~Q  635 (923)
T KOG0387|consen  610 GLGLNLTGANRVIIFDPDWNPSTDNQ  635 (923)
T ss_pred             ccccccccCceEEEECCCCCCccchH
Confidence            99999999999999999999986444

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=99.46  E-value=7.5e-14  Score=102.72  Aligned_cols=107  Identities=27%  Similarity=0.337  Sum_probs=80.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh----hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV----RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+.+.++.+....+ ..+...+|+.    .......++++|+|+||+++.+.+......+.+++++|+||+|.+..+
T Consensus        56 l~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~  134 (169)
T PF00270_consen   56 LAEQQFERLRKFFSNTN-VRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDE  134 (169)
T ss_dssp             HHHHHHHHHHHHTTTTT-SSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHT
T ss_pred             ccccccccccccccccc-cccccccccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccc
Confidence            57889999999888765 3344444444    222334567999999999999999986557777999999999999887


Q ss_pred             CcccccchhHhhhCCC-ccceeEEEEeecCchHH
Q 042003           77 GNLLKHIDPVVKACSN-PSIVRSLFSATLPDFVE  109 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~-~~~~~i~~SAT~~~~~~  109 (248)
                      + +...+..+...... .+.+++++|||+++..+
T Consensus       135 ~-~~~~~~~i~~~~~~~~~~~~i~~SAT~~~~~~  167 (169)
T PF00270_consen  135 T-FRAMLKSILRRLKRFKNIQIILLSATLPSNVE  167 (169)
T ss_dssp             T-HHHHHHHHHHHSHTTTTSEEEEEESSSTHHHH
T ss_pred             c-HHHHHHHHHHHhcCCCCCcEEEEeeCCChhHh
Confidence            5 77777777776533 36889999999985443

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 ....

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

Probab=99.45  E-value=3.2e-13  Score=113.67  Aligned_cols=198  Identities=16%  Similarity=0.186  Sum_probs=135.2

Q ss_pred             cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccc-ccCcccccchhHhhhCCCccceeEEEEeecCchHH
Q 042003           31 TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF-EVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        31 ~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  109 (248)
                      ++.......|-+.|.+.|++....... ++++..+|+||||.-. +.......++..++.  ..+..+|.+|||+..  +
T Consensus       439 EdvT~~~T~IkymTDGiLLrEsL~d~~-L~kYSviImDEAHERslNtDilfGllk~~lar--RrdlKliVtSATm~a--~  513 (1042)
T KOG0924|consen  439 EDVTSEDTKIKYMTDGILLRESLKDRD-LDKYSVIIMDEAHERSLNTDILFGLLKKVLAR--RRDLKLIVTSATMDA--Q  513 (1042)
T ss_pred             eecCCCceeEEEeccchHHHHHhhhhh-hhheeEEEechhhhcccchHHHHHHHHHHHHh--hccceEEEeeccccH--H
Confidence            344456678999999988877665433 6899999999999643 333344445554443  357889999999974  4


Q ss_pred             HHHHHhcCC-cEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHh---ccCCCCEEEEecchHHHHHHHHHhh----
Q 042003          110 ELARSIMHD-AVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA---ESLNPPVLIFVQSKERAKELYGELA----  181 (248)
Q Consensus       110 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~---~~~~~~~liF~~~~~~~~~l~~~L~----  181 (248)
                      .+.. ++++ |...+.++ .   .++...+......+---.++...+.   ....+.++||....+..+..+..+.    
T Consensus       514 kf~n-fFgn~p~f~IpGR-T---yPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~~~i~~~l~  588 (1042)
T KOG0924|consen  514 KFSN-FFGNCPQFTIPGR-T---YPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLE  588 (1042)
T ss_pred             HHHH-HhCCCceeeecCC-c---cceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHHHHHHHHHH
Confidence            4444 4454 44333322 2   2233334333333322223333332   2235789999988776665554443    


Q ss_pred             c------CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          182 F------DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       182 ~------~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                      .      .+..+..+++.+|..-+..+++.-..|..+++|||++++..+.+|++.+||+.|..
T Consensus       589 ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~  651 (1042)
T KOG0924|consen  589 QLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYC  651 (1042)
T ss_pred             hhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCce
Confidence            2      25689999999999999999999899999999999999999999999999998874

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=99.45  E-value=4.9e-12  Score=111.42  Aligned_cols=87  Identities=15%  Similarity=0.113  Sum_probs=67.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHH---------------------HHHHHHHHhhc-CCce
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQT---------------------QRENAVDDFRA-GKTW  212 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~---------------------~r~~~~~~f~~-g~~~  212 (248)
                      +.|++|||.++..|..+++.|.+.     +....+++++.+.+                     ...++++.|++ +.++
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            479999999999999999998654     23455666654332                     12367888876 6789


Q ss_pred             EEEEecccccCCCCCCCcEEEeccCCCCcccceec
Q 042003          213 VLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHR  247 (248)
Q Consensus       213 ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qr  247 (248)
                      |+|.++.+.+|+|.|.+++++...+..+.. ++|.
T Consensus       594 ilIVvdmllTGFDaP~l~tLyldKplk~h~-LlQa  627 (667)
T TIGR00348       594 LLIVVDMLLTGFDAPILNTLYLDKPLKYHG-LLQA  627 (667)
T ss_pred             EEEEEcccccccCCCccceEEEeccccccH-HHHH
Confidence            999999999999999999999988877654 5664

Members of this family are assumed to differ from each other in DNA site specificity.

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=99.43  E-value=3.1e-12  Score=111.58  Aligned_cols=102  Identities=15%  Similarity=0.158  Sum_probs=67.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHHHHHHhc---CCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRLRLAIRR---KKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l~~~~~~---~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+...+.......-+......-|.. ....+..-+|+|+|+-|+-+.+++..   ...+..+++++|+||+|.+++.
T Consensus       568 LVnQvsa~VyaRF~~~t~~rg~sl~g~ltqEYsinp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~  647 (1330)
T KOG0949|consen  568 LVNQVSANVYARFDTKTFLRGVSLLGDLTQEYSINPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNE  647 (1330)
T ss_pred             HhhhhhHHHHHhhccCccccchhhHhhhhHHhcCCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhcccc
Confidence            4567777777655333223333333333 34444445799999999999999987   4556789999999999998865


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCc
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                      . -.-....++-.   -+|.++++|||+.+
T Consensus       648 e-d~l~~Eqll~l---i~CP~L~LSATigN  673 (1330)
T KOG0949|consen  648 E-DGLLWEQLLLL---IPCPFLVLSATIGN  673 (1330)
T ss_pred             c-cchHHHHHHHh---cCCCeeEEecccCC
Confidence            3 12222222222   46778999999876

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.41  E-value=1.8e-12  Score=110.97  Aligned_cols=200  Identities=16%  Similarity=0.156  Sum_probs=134.5

Q ss_pred             cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccc-ccCcccccchhHhhh--------CCCccceeEEEEeecC
Q 042003           35 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF-EVGNLLKHIDPVVKA--------CSNPSIVRSLFSATLP  105 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~-~~~~~~~~~~~~~~~--------~~~~~~~~i~~SAT~~  105 (248)
                      .....|.++|.+.|++.+.+..+ ++.+..||+||||.-. ..+.....+.++...        +...+...|+||||+-
T Consensus       347 ~e~T~IkFMTDGVLLrEi~~Dfl-L~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~~kpLKLIIMSATLR  425 (1172)
T KOG0926|consen  347 GEDTSIKFMTDGVLLREIENDFL-LTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQIKPLKLIIMSATLR  425 (1172)
T ss_pred             CCCceeEEecchHHHHHHHHhHh-hhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcccCceeEEEEeeeEE
Confidence            34678999999999999987654 7999999999999643 222234444444332        2234678899999985


Q ss_pred             chHHHHHHHhcCCcE-EEEEcccccccccceeEEE---EcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhh
Q 042003          106 DFVEELARSIMHDAV-RVIVGRKNTASESIKQKLV---FAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELA  181 (248)
Q Consensus       106 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~  181 (248)
                      -....--..++..+. .+.+....-+   +.-++.   ......+.+.....+-++.+.+.++||+....++.++++.|+
T Consensus       426 VsDFtenk~LFpi~pPlikVdARQfP---VsIHF~krT~~DYi~eAfrKtc~IH~kLP~G~ILVFvTGQqEV~qL~~kLR  502 (1172)
T KOG0926|consen  426 VSDFTENKRLFPIPPPLIKVDARQFP---VSIHFNKRTPDDYIAEAFRKTCKIHKKLPPGGILVFVTGQQEVDQLCEKLR  502 (1172)
T ss_pred             ecccccCceecCCCCceeeeecccCc---eEEEeccCCCchHHHHHHHHHHHHhhcCCCCcEEEEEeChHHHHHHHHHHH
Confidence            322221122333322 2222221111   111111   112233555666667778888999999999999999999997


Q ss_pred             cC------------------------------------------------------------------------------
Q 042003          182 FD------------------------------------------------------------------------------  183 (248)
Q Consensus       182 ~~------------------------------------------------------------------------------  183 (248)
                      +.                                                                              
T Consensus       503 K~~p~~f~~~k~~k~~k~~~e~k~~~s~~~~~~k~~dfe~Ed~~~~~ed~d~~~~~~~~~~~raa~~~~~De~~~~nge~  582 (1172)
T KOG0926|consen  503 KRFPESFGGVKMKKNVKAFKELKENPSDIGDSNKTDDFEEEDMYESDEDIDQELVDSGFASLRAAFNALADENGSVNGEP  582 (1172)
T ss_pred             hhCccccccchhhhhhhhccccccchhhhccCcccccchhcccccchhhhhhhhhcccchhhhhhhhccccccccccCCc
Confidence            51                                                                              


Q ss_pred             ---------------------CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          184 ---------------------GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       184 ---------------------~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                                           ..-|.++++-++.+.+..+++.-..|..-++|+|++++..+.||++++||+.|..
T Consensus       583 e~d~~e~~~E~~~~~~~~~~~pLyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~  658 (1172)
T KOG0926|consen  583 EKDESEEGQEAEQGKGKFSPGPLYVLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGRV  658 (1172)
T ss_pred             ccchhhhchhhhhccCCCCCCceEEeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccch
Confidence                                 0124556666777778888888888998899999999999999999999987764

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=99.34  E-value=3.9e-11  Score=104.64  Aligned_cols=200  Identities=22%  Similarity=0.210  Sum_probs=117.3

Q ss_pred             hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccc--cc-CcccccchhHhhhCCCccceeEEEEeecC
Q 042003           29 RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF--EV-GNLLKHIDPVVKACSNPSIVRSLFSATLP  105 (248)
Q Consensus        29 ~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~--~~-~~~~~~~~~~~~~~~~~~~~~i~~SAT~~  105 (248)
                      .......+...|+|||--.+       ...++++++||+||-|.-.  +. +.++..-.-........++++|+-|||++
T Consensus       288 ~W~~~~~G~~~vVIGtRSAl-------F~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~Ra~~~~~pvvLgSATPS  360 (730)
T COG1198         288 VWRRARRGEARVVIGTRSAL-------FLPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLRAKKENAPVVLGSATPS  360 (730)
T ss_pred             HHHHHhcCCceEEEEechhh-------cCchhhccEEEEeccccccccCCcCCCcCHHHHHHHHHHHhCCCEEEecCCCC
Confidence            33455667899999994322       3458999999999999754  21 21222111112221346789999999976


Q ss_pred             chHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHH-----HHHHHHHhcc--CCCCEEEEecchHHH-----
Q 042003          106 DFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKL-----LALRQSFAES--LNPPVLIFVQSKERA-----  173 (248)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~l~~~~~~~--~~~~~liF~~~~~~~-----  173 (248)
                        ++...+...+.-..+...............++.+.......     ..+.+.+++.  .+.++|+|.|.+..+     
T Consensus       361 --LES~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C  438 (730)
T COG1198         361 --LESYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLC  438 (730)
T ss_pred             --HHHHHhhhcCceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHHHHHHhcCCeEEEEEccCCccceeec
Confidence              45555443332122222221111111122222333322222     2333333221  167899998877654     


Q ss_pred             -------------------------------------------------------HHHHHHhhcC--CCeeEEEecCCCH
Q 042003          174 -------------------------------------------------------KELYGELAFD--GIRAGVIHSDLSQ  196 (248)
Q Consensus       174 -------------------------------------------------------~~l~~~L~~~--~~~v~~~~~~~~~  196 (248)
                                                                             +++.+.|++.  +.++..+.++.+.
T Consensus       439 ~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~  518 (730)
T COG1198         439 RDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSDTTR  518 (730)
T ss_pred             ccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCeeEEecccHHHHHHHHHHHCCCCcEEEEcccccc
Confidence                                                                   4444444432  4566666666554


Q ss_pred             --HHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          197 --TQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       197 --~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                        ..-+..+..|.+|+.+|||+|+.+..|.|.|+++.|...+.
T Consensus       519 ~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~a  561 (730)
T COG1198         519 RKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDA  561 (730)
T ss_pred             chhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEec
Confidence              23467899999999999999999999999999998865554

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

Probab=99.32  E-value=4.3e-12  Score=103.27  Aligned_cols=182  Identities=18%  Similarity=0.250  Sum_probs=123.6

Q ss_pred             EeChHHHHHHHhcCCcccCceeEEEEeccccc-cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcE
Q 042003           42 ISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV  120 (248)
Q Consensus        42 v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~  120 (248)
                      .+|.++|++....... +..++++|+||||.- +..+.....++..... . +...+|.||||+.   ....+.|++++.
T Consensus       141 y~tDgmLlrEams~p~-l~~y~viiLDeahERtlATDiLmGllk~v~~~-r-pdLk~vvmSatl~---a~Kfq~yf~n~P  214 (699)
T KOG0925|consen  141 YCTDGMLLREAMSDPL-LGRYGVIILDEAHERTLATDILMGLLKEVVRN-R-PDLKLVVMSATLD---AEKFQRYFGNAP  214 (699)
T ss_pred             HhcchHHHHHHhhCcc-cccccEEEechhhhhhHHHHHHHHHHHHHHhh-C-CCceEEEeecccc---hHHHHHHhCCCC
Confidence            4555555555544433 689999999999953 3333456667777665 2 5889999999985   445566777776


Q ss_pred             EEEEcccccccccceeEEEEcCCc-----hhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC---------CCe
Q 042003          121 RVIVGRKNTASESIKQKLVFAGSE-----EGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD---------GIR  186 (248)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~---------~~~  186 (248)
                      .+.+.. .   ..+..+  |....     +..+..+.++-....++-+++|....++.+..++.+...         ..+
T Consensus       215 ll~vpg-~---~PvEi~--Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~  288 (699)
T KOG0925|consen  215 LLAVPG-T---HPVEIF--YTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLK  288 (699)
T ss_pred             eeecCC-C---CceEEE--ecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCce
Confidence            665554 1   122222  22222     233445555555556889999999999999998888642         357


Q ss_pred             eEEEecCCCHHHHHHHHHHhhc---C--CceEEEEecccccCCCCCCCcEEEeccCCC
Q 042003          187 AGVIHSDLSQTQRENAVDDFRA---G--KTWVLIATDVIARGMDFKGVNCVINYDFPD  239 (248)
Q Consensus       187 v~~~~~~~~~~~r~~~~~~f~~---g--~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~  239 (248)
                      |.++|    ++++..+++....   |  ..+|+|+|++++..+.++++.+||+-|+..
T Consensus       289 v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~k  342 (699)
T KOG0925|consen  289 VVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSK  342 (699)
T ss_pred             EEecC----chhhccccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchhh
Confidence            88888    3445555544332   2  347999999999999999999999988764

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.31  E-value=4.4e-11  Score=105.68  Aligned_cols=95  Identities=24%  Similarity=0.197  Sum_probs=68.8

Q ss_pred             hhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccccc
Q 042003          145 EGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR  222 (248)
Q Consensus       145 ~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~  222 (248)
                      ..|..++.+.+...  .+.|+||-|.|++..+.+...|.+.+++..+++..-...+.+-+.++-+.  ..|.|||+.+++
T Consensus       551 ~~k~~ai~~ei~~~~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak~~~~Ea~iia~AG~~--g~VTIATNmAGR  628 (970)
T PRK12899        551 REKYHAIVAEIASIHRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAKNHAQEAEIIAGAGKL--GAVTVATNMAGR  628 (970)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccchhhhHHHHHHhcCCC--CcEEEeeccccC
Confidence            45666655544432  37899999999999999999999999999999987443333333333222  359999999999


Q ss_pred             CCCCCCCc--------EEEeccCCCCc
Q 042003          223 GMDFKGVN--------CVINYDFPDSG  241 (248)
Q Consensus       223 Gidip~~~--------~Vi~~~~p~~~  241 (248)
                      |-||.--.        |||....|+|.
T Consensus       629 GTDIkl~~~v~~~GGLhVIgTer~es~  655 (970)
T PRK12899        629 GTDIKLDEEAVAVGGLYVIGTSRHQSR  655 (970)
T ss_pred             CcccccCchHHhcCCcEEEeeccCchH
Confidence            99987322        77777777665

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

Probab=99.16  E-value=2.7e-10  Score=94.80  Aligned_cols=212  Identities=12%  Similarity=0.061  Sum_probs=146.4

Q ss_pred             ccccCCCcEEEeChHHHHHHHhcCCc----ccCceeEEEEeccccccccC--cccccchhHhhhC----CCccceeEEEE
Q 042003           32 DLSKFSCDILISTPLRLRLAIRRKKI----DLSRVEYLVLDEADKLFEVG--NLLKHIDPVVKAC----SNPSIVRSLFS  101 (248)
Q Consensus        32 ~~~~~~~~i~v~Tp~~l~~~~~~~~~----~~~~~~~lIiDEah~~~~~~--~~~~~~~~~~~~~----~~~~~~~i~~S  101 (248)
                      .....+.+++++.|.+......-+..    .+-...+.++||+|......  .....+.++++.+    .+.+.|++-.|
T Consensus       379 A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~R~L~~L~~~F~~~~~~~~~~~~  458 (1034)
T KOG4150|consen  379 ALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQLRALSDLIKGFEASINMGVYDGD  458 (1034)
T ss_pred             HHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHHHHHHHHHHHHHHhhcCcceEeCC
Confidence            34556899999999888766654433    24456789999999876542  0112333333332    24678999999


Q ss_pred             eecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCch-----h---HH----HHHHHHHhccCCCCEEEEecc
Q 042003          102 ATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEE-----G---KL----LALRQSFAESLNPPVLIFVQS  169 (248)
Q Consensus       102 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~---~~----~~l~~~~~~~~~~~~liF~~~  169 (248)
                      ||+-...+.....+.-+........  ..+..-++..++.+...     +   +.    ..+.+++..  +-++|.||++
T Consensus       459 ~~~K~~~~~~~~~~~~~E~~Li~~D--GSPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~--~~R~IAFC~~  534 (1034)
T KOG4150|consen  459 TPYKDRTRLRSELANLSELELVTID--GSPSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEMVQH--GLRCIAFCPS  534 (1034)
T ss_pred             CCcCCHHHHHHHhcCCcceEEEEec--CCCCccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHHHHc--CCcEEEeccH
Confidence            9998766666554444444443332  22334456666655431     1   11    222233332  5699999999


Q ss_pred             hHHHHHHHHHhhcC----C----CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCc
Q 042003          170 KERAKELYGELAFD----G----IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSG  241 (248)
Q Consensus       170 ~~~~~~l~~~L~~~----~----~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~  241 (248)
                      ++-|+.+....+.-    +    -.+.-+.||...++|..+....-.|+..-+|+|++++.||||.+.+.|++.|+|.|+
T Consensus       535 R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LDAVl~~GFP~S~  614 (1034)
T KOG4150|consen  535 RKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLDAVLHLGFPGSI  614 (1034)
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccceeEEEccCchhH
Confidence            99999776555431    1    145667899999999999999999999999999999999999999999999999999


Q ss_pred             ccceec
Q 042003          242 AAYIHR  247 (248)
Q Consensus       242 ~~~~qr  247 (248)
                      ..+.|.
T Consensus       615 aNl~QQ  620 (1034)
T KOG4150|consen  615 ANLWQQ  620 (1034)
T ss_pred             HHHHHH
Confidence            887764

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=99.15  E-value=1.5e-09  Score=93.26  Aligned_cols=97  Identities=23%  Similarity=0.221  Sum_probs=79.8

Q ss_pred             hHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC--ceEEEEecccc
Q 042003          146 GKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK--TWVLIATDVIA  221 (248)
Q Consensus       146 ~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~--~~ilv~T~~~~  221 (248)
                      .|...|..++.+.  .+.+++||.---....-+...|...+++...+.|++.-.+|+.+++.|...+  +-+|++|.+.+
T Consensus       761 gK~r~L~~LLp~~k~~G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG  840 (941)
T KOG0389|consen  761 GKCRKLKELLPKIKKKGDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGG  840 (941)
T ss_pred             hhHhHHHHHHHHHhhcCCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCc
Confidence            3445555555432  2679999987766667777788888999999999999999999999998765  35789999999


Q ss_pred             cCCCCCCCcEEEeccCCCCcc
Q 042003          222 RGMDFKGVNCVINYDFPDSGA  242 (248)
Q Consensus       222 ~Gidip~~~~Vi~~~~p~~~~  242 (248)
                      .|||+..+++||++|..-||.
T Consensus       841 ~GINLt~An~VIihD~dFNP~  861 (941)
T KOG0389|consen  841 FGINLTCANTVIIHDIDFNPY  861 (941)
T ss_pred             ceecccccceEEEeecCCCCc
Confidence            999999999999999988774

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=99.14  E-value=9.7e-10  Score=98.29  Aligned_cols=101  Identities=22%  Similarity=0.244  Sum_probs=83.3

Q ss_pred             hHHHHHHHHHhccC----------------CCCEEEEecchHHHHHHHHHhhcC-C--CeeEEEecCCCHHHHHHHHHHh
Q 042003          146 GKLLALRQSFAESL----------------NPPVLIFVQSKERAKELYGELAFD-G--IRAGVIHSDLSQTQRENAVDDF  206 (248)
Q Consensus       146 ~~~~~l~~~~~~~~----------------~~~~liF~~~~~~~~~l~~~L~~~-~--~~v~~~~~~~~~~~r~~~~~~f  206 (248)
                      .|+.+|.+++....                +.+++|||.-+....-+.+-|.+. -  +.-..+.|+.++.+|.++.+.|
T Consensus      1310 pKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~F 1389 (1549)
T KOG0392|consen 1310 PKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVERF 1389 (1549)
T ss_pred             hhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHHh
Confidence            56777777775432                458999999999999988888654 2  3344889999999999999999


Q ss_pred             hcC-CceEE-EEecccccCCCCCCCcEEEeccCCCCccccee
Q 042003          207 RAG-KTWVL-IATDVIARGMDFKGVNCVINYDFPDSGAAYIH  246 (248)
Q Consensus       207 ~~g-~~~il-v~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~q  246 (248)
                      +++ .+++| .+|.+.+.|+|+.+++.||.++--|||..=+|
T Consensus      1390 N~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQ 1431 (1549)
T KOG0392|consen 1390 NEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQ 1431 (1549)
T ss_pred             cCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHH
Confidence            998 67766 77899999999999999999999999975444

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=99.13  E-value=1.2e-08  Score=83.83  Aligned_cols=87  Identities=10%  Similarity=0.168  Sum_probs=78.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC-ceE-EEEecccccCCCCCCCcEEEeccC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK-TWV-LIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~-~~i-lv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      +.|.+||+.-..-.+.+...+.++++....+.|..+..+|+...+.|+.++ ..| +++-.+++.|+++..++.|+....
T Consensus       492 ~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaEL  571 (689)
T KOG1000|consen  492 PRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAEL  571 (689)
T ss_pred             CceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEEe
Confidence            679999999999999999999999999999999999999999999998764 343 466688999999999999999999


Q ss_pred             CCCccccee
Q 042003          238 PDSGAAYIH  246 (248)
Q Consensus       238 p~~~~~~~q  246 (248)
                      +||+.-.+|
T Consensus       572 ~wnPgvLlQ  580 (689)
T KOG1000|consen  572 HWNPGVLLQ  580 (689)
T ss_pred             cCCCceEEe
Confidence            999987665

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.12  E-value=1.6e-09  Score=93.72  Aligned_cols=97  Identities=23%  Similarity=0.214  Sum_probs=70.7

Q ss_pred             CchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc
Q 042003          143 SEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI  220 (248)
Q Consensus       143 ~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~  220 (248)
                      ....|..++.+.+...  .+.|+||.+.|++.++.+.+.|.+.+++..++++.-...+-+-+.++=+.|  .|.|||+.+
T Consensus       408 t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa~AG~~g--aVTIATNMA  485 (764)
T PRK12326        408 TAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEEARIIAEAGKYG--AVTVSTQMA  485 (764)
T ss_pred             CHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhHHHHHHhcCCCC--cEEEEecCC
Confidence            3456776666655432  378999999999999999999999999999999874433333333433333  489999999


Q ss_pred             ccCCCCCCC---------------cEEEeccCCCCc
Q 042003          221 ARGMDFKGV---------------NCVINYDFPDSG  241 (248)
Q Consensus       221 ~~Gidip~~---------------~~Vi~~~~p~~~  241 (248)
                      ++|-||.--               =|||-...|+|.
T Consensus       486 GRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSr  521 (764)
T PRK12326        486 GRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSE  521 (764)
T ss_pred             CCccCeecCCCcccchHHHHHcCCcEEEeccCCchH
Confidence            999998722               277777777664

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

Probab=99.10  E-value=5.9e-10  Score=92.36  Aligned_cols=202  Identities=17%  Similarity=0.102  Sum_probs=122.3

Q ss_pred             cchHHHHHHHhhcCCCcEEEEcccchhhhcccc-cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            2 ATQTTRECKKLAKGNKFQIKLMKKELVRSTDLS-KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         2 ~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |..+++.++..+     +.+.+++|.......- ...++.+=||.|+.       .. ...+++.|+||++++.++.+-+
T Consensus       228 A~EV~~r~na~g-----ipCdL~TGeE~~~~~~~~~~a~hvScTVEM~-------sv-~~~yeVAViDEIQmm~Dp~RGw  294 (700)
T KOG0953|consen  228 AHEVYDRLNALG-----IPCDLLTGEERRFVLDNGNPAQHVSCTVEMV-------SV-NTPYEVAVIDEIQMMRDPSRGW  294 (700)
T ss_pred             HHHHHHHhhhcC-----CCccccccceeeecCCCCCcccceEEEEEEe-------ec-CCceEEEEehhHHhhcCcccch
Confidence            444444444433     3355555543221111 12367777776544       11 2668899999999998876445


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHh---cCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI---MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                      .+-..++.. ......+.+     .+..-.+++..   .++...+.....-.+..              -.+.+..-++.
T Consensus       295 AWTrALLGl-~AdEiHLCG-----epsvldlV~~i~k~TGd~vev~~YeRl~pL~--------------v~~~~~~sl~n  354 (700)
T KOG0953|consen  295 AWTRALLGL-AADEIHLCG-----EPSVLDLVRKILKMTGDDVEVREYERLSPLV--------------VEETALGSLSN  354 (700)
T ss_pred             HHHHHHHhh-hhhhhhccC-----CchHHHHHHHHHhhcCCeeEEEeecccCcce--------------ehhhhhhhhcc
Confidence            555555554 222233221     12233344433   34444443222221111              01122233333


Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCe-eEEEecCCCHHHHHHHHHHhhc--CCceEEEEecccccCCCCCCCcEEEe
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIR-AGVIHSDLSQTQRENAVDDFRA--GKTWVLIATDVIARGMDFKGVNCVIN  234 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~r~~~~~~f~~--g~~~ilv~T~~~~~Gidip~~~~Vi~  234 (248)
                      ..++-++|-+ |++..-.+...+++.+.. +++++|++|++.|.+....|.+  ++.+|||||+++++|+|+. ++-||.
T Consensus       355 lk~GDCvV~F-Skk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL~-IrRiiF  432 (700)
T KOG0953|consen  355 LKPGDCVVAF-SKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNLN-IRRIIF  432 (700)
T ss_pred             CCCCCeEEEe-ehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeecccccccccc-eeEEEE
Confidence            3345554432 667888888889887665 9999999999999999999987  8899999999999999996 888888


Q ss_pred             ccCC
Q 042003          235 YDFP  238 (248)
Q Consensus       235 ~~~p  238 (248)
                      ++.-
T Consensus       433 ~sl~  436 (700)
T KOG0953|consen  433 YSLI  436 (700)
T ss_pred             eecc
Confidence            8764

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=99.10  E-value=2.9e-09  Score=92.89  Aligned_cols=66  Identities=20%  Similarity=0.250  Sum_probs=57.2

Q ss_pred             hcCCCeeEEEecCCCHHHHHHHHHHhhcCC---ceEEEEecccccCCCCCCCcEEEeccCCCCccccee
Q 042003          181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGK---TWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIH  246 (248)
Q Consensus       181 ~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~---~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~q  246 (248)
                      +-.|+.+..+||.|+..+|+.+++.|.+..   .-.|.+|.+.+.|||+-+++.||+||+.|||+.=.|
T Consensus       616 ~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~Q  684 (776)
T KOG0390|consen  616 RWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQ  684 (776)
T ss_pred             hhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHH
Confidence            335899999999999999999999998643   346788899999999999999999999999975433

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=99.07  E-value=2.4e-09  Score=95.86  Aligned_cols=84  Identities=23%  Similarity=0.255  Sum_probs=78.9

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhc---CCceEEEEecccccCCCCCCCcEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRA---GKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~---g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      +.++|||..=+....-++++|..++|+.-.+.|+++.+.|++.++.|..   ..+.+|+||-+.+.|||+-.++.||+||
T Consensus       699 GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLatADTVIIFD  778 (1373)
T KOG0384|consen  699 GHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLATADTVIIFD  778 (1373)
T ss_pred             CceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccccceEEEeC
Confidence            6799999999999999999999999999999999999999999999975   4577999999999999999999999999


Q ss_pred             CCCCccc
Q 042003          237 FPDSGAA  243 (248)
Q Consensus       237 ~p~~~~~  243 (248)
                      .-|||..
T Consensus       779 SDWNPQN  785 (1373)
T KOG0384|consen  779 SDWNPQN  785 (1373)
T ss_pred             CCCCcch
Confidence            9999964

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.07  E-value=1e-09  Score=97.07  Aligned_cols=84  Identities=26%  Similarity=0.336  Sum_probs=62.8

Q ss_pred             CCchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          142 GSEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      .....|..++.+.+...  .+.|+||-+.|++..+.+.+.|.+.+++..+++......+-+-+.++-+.|  .|.|||+.
T Consensus       429 ~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk~~~~EA~IIa~AG~~G--aVTIATNM  506 (913)
T PRK13103        429 LTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAKYHEKEAEIIAQAGRPG--ALTIATNM  506 (913)
T ss_pred             cCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccccchhHHHHHHcCCCCC--cEEEeccC
Confidence            34456777776665532  378999999999999999999999999998888875444333333332333  48999999


Q ss_pred             cccCCCCC
Q 042003          220 IARGMDFK  227 (248)
Q Consensus       220 ~~~Gidip  227 (248)
                      +++|-||.
T Consensus       507 AGRGTDIk  514 (913)
T PRK13103        507 AGRGTDIL  514 (913)
T ss_pred             CCCCCCEe
Confidence            99999984

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=98.99  E-value=3.6e-09  Score=79.42  Aligned_cols=122  Identities=28%  Similarity=0.345  Sum_probs=85.3

Q ss_pred             cchHHHHHHHhhcCCCcEEEEcccchh--hhcccccCCC-cEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            2 ATQTTRECKKLAKGNKFQIKLMKKELV--RSTDLSKFSC-DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         2 ~~Q~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~-~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      +.|+.+.+..+.............+..  ........+. +++++|++.+.+.+.........++++|+||+|.+.... 
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~-  145 (201)
T smart00487       67 AEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGG-  145 (201)
T ss_pred             HHHHHHHHHHHhccCCeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCC-
Confidence            456777777766554323333333322  1122223334 999999999999998877777889999999999988643 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVG  125 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  125 (248)
                      +...+..+.... ....+++++|||++.........++.+...+...
T Consensus       146 ~~~~~~~~~~~~-~~~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~~  191 (201)
T smart00487      146 FGDQLEKLLKLL-PKNVQLLLLSATPPEEIENLLELFLNDPVFIDVG  191 (201)
T ss_pred             cHHHHHHHHHhC-CccceEEEEecCCchhHHHHHHHhcCCCEEEeCC
Confidence            666666776663 5678889999999988888888887766555444

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=98.97  E-value=2.7e-09  Score=95.48  Aligned_cols=74  Identities=23%  Similarity=0.095  Sum_probs=51.8

Q ss_pred             CCcEEEeChHHHHHHHhc---CCcccCc----eeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHH
Q 042003           37 SCDILISTPLRLRLAIRR---KKIDLSR----VEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~---~~~~~~~----~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  109 (248)
                      ..+++|||+.+++.....   +...+.-    =+.+|+||+|.+-..  ....+..++.........+++||||+|+...
T Consensus       562 ~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~~--~~~~L~rlL~w~~~lG~~VlLmSATLP~~l~  639 (1110)
T TIGR02562       562 AAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEPE--DLPALLRLVQLAGLLGSRVLLSSATLPPALV  639 (1110)
T ss_pred             cCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCHH--HHHHHHHHHHHHHHcCCCEEEEeCCCCHHHH
Confidence            479999999999877732   1111111    247999999996543  4556777777655667889999999998665


Q ss_pred             HHH
Q 042003          110 ELA  112 (248)
Q Consensus       110 ~~~  112 (248)
                      ...
T Consensus       640 ~~L  642 (1110)
T TIGR02562       640 KTL  642 (1110)
T ss_pred             HHH
Confidence            533

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.

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=98.95  E-value=2e-08  Score=91.43  Aligned_cols=91  Identities=21%  Similarity=0.294  Sum_probs=69.0

Q ss_pred             HHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCC
Q 042003          150 ALRQSFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK  227 (248)
Q Consensus       150 ~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip  227 (248)
                      .+.+++... +++++||++|.+..+.+++.|...  .....++..+.. ..|.++++.|++|+..||+||+.+++|||+|
T Consensus       665 ~i~~l~~~~-~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~  742 (850)
T TIGR01407       665 YIIEITAIT-SPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFP  742 (850)
T ss_pred             HHHHHHHhc-CCCEEEEeCCHHHHHHHHHHHhhhccccCceEEecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccC
Confidence            334444444 679999999999999999999752  112233444433 5788999999999999999999999999999


Q ss_pred             CCc--EEEeccCCC-Ccc
Q 042003          228 GVN--CVINYDFPD-SGA  242 (248)
Q Consensus       228 ~~~--~Vi~~~~p~-~~~  242 (248)
                      +..  .||+.+.|. ++.
T Consensus       743 g~~l~~viI~~LPf~~p~  760 (850)
T TIGR01407       743 GNGLVCLVIPRLPFANPK  760 (850)
T ss_pred             CCceEEEEEeCCCCCCCC
Confidence            865  778899884 443

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.

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.94  E-value=1.7e-08  Score=88.84  Aligned_cols=96  Identities=25%  Similarity=0.294  Sum_probs=71.6

Q ss_pred             CchhHHHHHHHHHhc-c-CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC-ceEEEEecc
Q 042003          143 SEEGKLLALRQSFAE-S-LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK-TWVLIATDV  219 (248)
Q Consensus       143 ~~~~~~~~l~~~~~~-~-~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~-~~ilv~T~~  219 (248)
                      ....|..++.+.+.. + .++|+||.|.|++.++.+.+.|.+.+++..++++.-.  +++.-+-+ +.|+ ..|.|||+.
T Consensus       407 t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~--e~EA~IIa-~AG~~GaVTIATNM  483 (925)
T PRK12903        407 TKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQN--AREAEIIA-KAGQKGAITIATNM  483 (925)
T ss_pred             cHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccch--hhHHHHHH-hCCCCCeEEEeccc
Confidence            344566666655442 2 3789999999999999999999999999999998633  33333222 3443 358999999


Q ss_pred             cccCCCCCCCc--------EEEeccCCCCc
Q 042003          220 IARGMDFKGVN--------CVINYDFPDSG  241 (248)
Q Consensus       220 ~~~Gidip~~~--------~Vi~~~~p~~~  241 (248)
                      +++|-||.--.        |||....|+|.
T Consensus       484 AGRGTDI~Lg~~V~~~GGLhVIgTerheSr  513 (925)
T PRK12903        484 AGRGTDIKLSKEVLELGGLYVLGTDKAESR  513 (925)
T ss_pred             ccCCcCccCchhHHHcCCcEEEecccCchH
Confidence            99999998433        89988888775

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.91  E-value=2.2e-08  Score=88.44  Aligned_cols=84  Identities=31%  Similarity=0.376  Sum_probs=61.4

Q ss_pred             CCchhHHHHHHHHHhc-c-CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHH-HHHHHhhcCCc-eEEEEe
Q 042003          142 GSEEGKLLALRQSFAE-S-LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRE-NAVDDFRAGKT-WVLIAT  217 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~-~-~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~-~~~~~f~~g~~-~ilv~T  217 (248)
                      .....|..++.+.+.. + .+.|+||-+.|++..+.+.+.|.+.+++..+++..-...+++ +++..  .|+. .|-|||
T Consensus       419 ~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIa~--AG~~GaVTIAT  496 (939)
T PRK12902        419 KTEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAKPENVEREAEIVAQ--AGRKGAVTIAT  496 (939)
T ss_pred             cCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCCCcchHhHHHHHHh--cCCCCcEEEec
Confidence            3445677666654442 2 378999999999999999999999999999999973322332 33332  3332 488999


Q ss_pred             cccccCCCCC
Q 042003          218 DVIARGMDFK  227 (248)
Q Consensus       218 ~~~~~Gidip  227 (248)
                      +.+++|-||.
T Consensus       497 NMAGRGTDIk  506 (939)
T PRK12902        497 NMAGRGTDII  506 (939)
T ss_pred             cCCCCCcCEe
Confidence            9999999975

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.87  E-value=2.5e-08  Score=88.07  Aligned_cols=84  Identities=20%  Similarity=0.186  Sum_probs=60.5

Q ss_pred             CCchhHHHHHHHHHh-cc-CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC--HHHHHHHHHHhhcCCceEEEEe
Q 042003          142 GSEEGKLLALRQSFA-ES-LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS--QTQRENAVDDFRAGKTWVLIAT  217 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~-~~-~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~--~~~r~~~~~~f~~g~~~ilv~T  217 (248)
                      .....|..++.+.+. .+ .+.|+||-+.|++..+.+.+.|.+.+++..++++.-.  ..|-+-+.++=+.  ..|.|||
T Consensus       404 ~t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIA~AG~~--G~VTIAT  481 (870)
T CHL00122        404 KDELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPENVRRESEIVAQAGRK--GSITIAT  481 (870)
T ss_pred             eCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCccchhHHHHHHhcCCC--CcEEEec
Confidence            344456665555443 22 2789999999999999999999999999999999732  2333333333222  3489999


Q ss_pred             cccccCCCCC
Q 042003          218 DVIARGMDFK  227 (248)
Q Consensus       218 ~~~~~Gidip  227 (248)
                      +.+++|-||.
T Consensus       482 NMAGRGTDI~  491 (870)
T CHL00122        482 NMAGRGTDII  491 (870)
T ss_pred             cccCCCcCee
Confidence            9999999975

>COG4889 Predicted helicase [General function prediction only]

Probab=98.81  E-value=2.8e-09  Score=92.83  Aligned_cols=85  Identities=14%  Similarity=0.278  Sum_probs=69.1

Q ss_pred             CEEEEecchHHHHHHHHHhhc-------------C--CCeeEEEecCCCHHHHHHHHHH---hhcCCceEEEEecccccC
Q 042003          162 PVLIFVQSKERAKELYGELAF-------------D--GIRAGVIHSDLSQTQRENAVDD---FRAGKTWVLIATDVIARG  223 (248)
Q Consensus       162 ~~liF~~~~~~~~~l~~~L~~-------------~--~~~v~~~~~~~~~~~r~~~~~~---f~~g~~~ilv~T~~~~~G  223 (248)
                      ++|-||.++++.+++++.+..             .  .+++..+.|.|+-.+|.+.+..   |...+++||----.+++|
T Consensus       462 RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSEG  541 (1518)
T COG4889         462 RAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSEG  541 (1518)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhhhcC
Confidence            688999999998888877642             1  2456677899999999666543   566788898888899999


Q ss_pred             CCCCCCcEEEeccCCCCccccee
Q 042003          224 MDFKGVNCVINYDFPDSGAAYIH  246 (248)
Q Consensus       224 idip~~~~Vi~~~~p~~~~~~~q  246 (248)
                      +|+|.++.||.+++-.++.+-+|
T Consensus       542 VDVPaLDsViFf~pr~smVDIVQ  564 (1518)
T COG4889         542 VDVPALDSVIFFDPRSSMVDIVQ  564 (1518)
T ss_pred             CCccccceEEEecCchhHHHHHH
Confidence            99999999999999988877666

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.76  E-value=7.9e-09  Score=85.40  Aligned_cols=206  Identities=19%  Similarity=0.233  Sum_probs=139.1

Q ss_pred             CCCcEEEeChHHHHHHHhcC------CcccCceeEEEEeccccccccCcccccchhHhhhC---C---------------
Q 042003           36 FSCDILISTPLRLRLAIRRK------KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC---S---------------   91 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~------~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~---~---------------   91 (248)
                      ...||+||+|-.|.-++.+.      .-.++++.++|||-||.+...+ +.. +..++..+   +               
T Consensus       384 y~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QN-wEh-l~~ifdHLn~~P~k~h~~DfSRVR~wy  461 (698)
T KOG2340|consen  384 YKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQN-WEH-LLHIFDHLNLQPSKQHDVDFSRVRMWY  461 (698)
T ss_pred             cccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhh-HHH-HHHHHHHhhcCcccccCCChhheehhe
Confidence            36899999999887666632      1247899999999999887544 222 22222211   1               


Q ss_pred             -C----ccceeEEEEeecCchHHHHHHHhcCCcEEEEEc----------ccccccccceeEEEEcCCc----hhHHHHHH
Q 042003           92 -N----PSIVRSLFSATLPDFVEELARSIMHDAVRVIVG----------RKNTASESIKQKLVFAGSE----EGKLLALR  152 (248)
Q Consensus        92 -~----~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~----~~~~~~l~  152 (248)
                       .    .=.|++++|+--.+....+...++.+..-....          ....+..++.+.+ .+.+.    +.+.+...
T Consensus       462 L~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~Gkv~~~~~~~~gsi~~v~~~l~Qvf~ri-~~~si~~~~D~RFkyFv  540 (698)
T KOG2340|consen  462 LDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQSGGSISNVGIPLCQVFQRI-EVKSIIETPDARFKYFV  540 (698)
T ss_pred             eccHHHHHHHHHHHHhhccHHHHHHHHHhhhhhcceeeeccccCCCchhhccchhhhhhhhe-eccCcccCchHHHHHHH
Confidence             0    015778888888887777777776653221111          1112222222332 22222    23333332


Q ss_pred             HHH----hccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc--ccCCCC
Q 042003          153 QSF----AESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI--ARGMDF  226 (248)
Q Consensus       153 ~~~----~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~--~~Gidi  226 (248)
                      .-+    .+....-++||.++..+--++.+++++.+++...+|.-.+...-.+..+.|-.|+..+|+-|.-+  -+-.++
T Consensus       541 ~~ImPq~~k~t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~i  620 (698)
T KOG2340|consen  541 DKIMPQLIKRTESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHI  620 (698)
T ss_pred             HhhchhhcccccCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhhee
Confidence            222    22224568999999999999999999999888888887777777788899999999999999875  477899


Q ss_pred             CCCcEEEeccCCCCcccc
Q 042003          227 KGVNCVINYDFPDSGAAY  244 (248)
Q Consensus       227 p~~~~Vi~~~~p~~~~~~  244 (248)
                      .+++.||+|.+|.+|--|
T Consensus       621 kGVk~vVfYqpP~~P~FY  638 (698)
T KOG2340|consen  621 KGVKNVVFYQPPNNPHFY  638 (698)
T ss_pred             cceeeEEEecCCCCcHHH
Confidence            999999999999998644

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=98.75  E-value=1.4e-08  Score=89.58  Aligned_cols=88  Identities=17%  Similarity=0.173  Sum_probs=79.4

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC---ceEEEEecccccCCCCCCCcEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK---TWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~---~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      +++++.|+.--.-..-+..+|.-.+++-..+.|.+..++|-..++.|....   +.+|.+|.+.+.|+|+..++.||+||
T Consensus       726 gHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadtviifd  805 (1157)
T KOG0386|consen  726 GHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADTVIIFD  805 (1157)
T ss_pred             CcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeecccccccchhhcceEEEec
Confidence            789999998877777888888888999999999999999999999998644   46889999999999999999999999


Q ss_pred             CCCCcccceec
Q 042003          237 FPDSGAAYIHR  247 (248)
Q Consensus       237 ~p~~~~~~~qr  247 (248)
                      .-|++-.+.|+
T Consensus       806 sdwnp~~d~qa  816 (1157)
T KOG0386|consen  806 SDWNPHQDLQA  816 (1157)
T ss_pred             CCCCchhHHHH
Confidence            99999888775

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

Probab=98.73  E-value=1.6e-07  Score=84.96  Aligned_cols=221  Identities=17%  Similarity=0.148  Sum_probs=141.0

Q ss_pred             hHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC-ccccc
Q 042003            4 QTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKH   82 (248)
Q Consensus         4 Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~-~~~~~   82 (248)
                      |...+.+++.+..| ..+...+|.......+....+|+|+||+++..+ +    .....++.|.||+|.+++.. .....
T Consensus      1202 ~~~~w~~~f~~~~G-~~~~~l~ge~s~~lkl~~~~~vii~tpe~~d~l-q----~iQ~v~l~i~d~lh~igg~~g~v~ev 1275 (1674)
T KOG0951|consen 1202 QYRDWEKKFSKLLG-LRIVKLTGETSLDLKLLQKGQVIISTPEQWDLL-Q----SIQQVDLFIVDELHLIGGVYGAVYEV 1275 (1674)
T ss_pred             HHHHHHHhhccccC-ceEEecCCccccchHHhhhcceEEechhHHHHH-h----hhhhcceEeeehhhhhcccCCceEEE
Confidence            45667778888888 677777777777777788899999999998666 2    45788899999999988432 11111


Q ss_pred             ---chhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEE-EEcCCchhHHHH-----HHH
Q 042003           83 ---IDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL-VFAGSEEGKLLA-----LRQ  153 (248)
Q Consensus        83 ---~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~-----l~~  153 (248)
                         +..+..+ ..++.+++++|..+.+ .+.+  ..+.....+...+..++.+...+.- +.....+.....     ...
T Consensus      1276 i~S~r~ia~q-~~k~ir~v~ls~~lan-a~d~--ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~a 1351 (1674)
T KOG0951|consen 1276 ICSMRYIASQ-LEKKIRVVALSSSLAN-ARDL--IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTA 1351 (1674)
T ss_pred             EeeHHHHHHH-HHhheeEEEeehhhcc-chhh--ccccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHH
Confidence               2223333 3457889999999876 3333  2222333333344444433332222 222222222211     111


Q ss_pred             HHh-ccCCCCEEEEecchHHHHHHHHHhhc----------------------CCCeeEEEecCCCHHHHHHHHHHhhcCC
Q 042003          154 SFA-ESLNPPVLIFVQSKERAKELYGELAF----------------------DGIRAGVIHSDLSQTQRENAVDDFRAGK  210 (248)
Q Consensus       154 ~~~-~~~~~~~liF~~~~~~~~~l~~~L~~----------------------~~~~v~~~~~~~~~~~r~~~~~~f~~g~  210 (248)
                      +.+ ...+++++||+++++.|..++..|-.                      ...+.++=|.+++..+..-+-..|+.|.
T Consensus      1352 i~~~a~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~ 1431 (1674)
T KOG0951|consen 1352 IVRHAGNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGA 1431 (1674)
T ss_pred             HHHHhcCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCc
Confidence            121 12367999999999999888766622                      1123333499999999999999999999


Q ss_pred             ceEEEEecccccCCCCCCCcEEEecc
Q 042003          211 TWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       211 ~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      +.++|.+.. ..|+-.. .+.||-+|
T Consensus      1432 i~v~v~s~~-~~~~~~~-~~lVvvmg 1455 (1674)
T KOG0951|consen 1432 IQVCVMSRD-CYGTKLK-AHLVVVMG 1455 (1674)
T ss_pred             EEEEEEEcc-ccccccc-ceEEEEec
Confidence            999999887 7887765 45555433

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.72  E-value=3.6e-08  Score=69.64  Aligned_cols=99  Identities=25%  Similarity=0.165  Sum_probs=64.7

Q ss_pred             cchHHHHHHHhhcCCCcEEEEcccchhhhc---ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            2 ATQTTRECKKLAKGNKFQIKLMKKELVRST---DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         2 ~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      +.|..+.+...... + ..+....+.....   .....+.+++++|++.+...+.........++++|+||+|.+.... 
T Consensus        43 ~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~-  119 (144)
T cd00046          43 ANQVAERLKELFGE-G-IKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQG-  119 (144)
T ss_pred             HHHHHHHHHHHhhC-C-cEEEEEecCcchhHHHHHhcCCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcc-
Confidence            45666666666653 3 3334444433222   2235679999999999998888776667789999999999987654 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeec
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATL  104 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~  104 (248)
                      ..... ...........+++++|||+
T Consensus       120 ~~~~~-~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046         120 FGLLG-LKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             hHHHH-HHHHhhCCccceEEEEeccC
Confidence            22211 11223245677899999995

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=98.72  E-value=2.4e-07  Score=85.06  Aligned_cols=91  Identities=18%  Similarity=0.272  Sum_probs=70.2

Q ss_pred             HHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCC--eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCC
Q 042003          151 LRQSFAESLNPPVLIFVQSKERAKELYGELAFDGI--RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKG  228 (248)
Q Consensus       151 l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~  228 (248)
                      +.+++... +++++||++|.+..+.+++.|.....  ...++.-+++...|..+++.|++++..||++|..+++|||+|+
T Consensus       744 i~~l~~~~-~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg  822 (928)
T PRK08074        744 IAKIAKAT-KGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPG  822 (928)
T ss_pred             HHHHHHhC-CCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCC
Confidence            33443343 67999999999999999999975422  2333444554456888999999988889999999999999997


Q ss_pred             --CcEEEeccCCC-Ccc
Q 042003          229 --VNCVINYDFPD-SGA  242 (248)
Q Consensus       229 --~~~Vi~~~~p~-~~~  242 (248)
                        +++||+.+.|- ++.
T Consensus       823 ~~l~~viI~kLPF~~p~  839 (928)
T PRK08074        823 DELSCLVIVRLPFAPPD  839 (928)
T ss_pred             CceEEEEEecCCCCCCC
Confidence              58999999885 454

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.54  E-value=3e-06  Score=75.55  Aligned_cols=85  Identities=20%  Similarity=0.329  Sum_probs=63.8

Q ss_pred             HHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC-CCeeEEEecCCCHHHHHHHHHHhh----cCCceEEEEecccccC
Q 042003          149 LALRQSFAESLNPPVLIFVQSKERAKELYGELAFD-GIRAGVIHSDLSQTQRENAVDDFR----AGKTWVLIATDVIARG  223 (248)
Q Consensus       149 ~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~-~~~v~~~~~~~~~~~r~~~~~~f~----~g~~~ilv~T~~~~~G  223 (248)
                      ..+.+++. . ++.++||++|.+..+.+++.|... +..+ ..+|..   .+..+++.|+    .|+..||++|..+++|
T Consensus       525 ~~i~~l~~-~-~gg~LVlFtSy~~l~~v~~~l~~~~~~~l-l~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EG  598 (697)
T PRK11747        525 EFLPELLE-K-HKGSLVLFASRRQMQKVADLLPRDLRLML-LVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEG  598 (697)
T ss_pred             HHHHHHHh-c-CCCEEEEeCcHHHHHHHHHHHHHhcCCcE-EEeCCc---hHHHHHHHHHHHhccCCCeEEEEecccccc
Confidence            34444555 3 556999999999999999999743 3333 335542   4566776665    4677899999999999


Q ss_pred             CCCCC--CcEEEeccCCC
Q 042003          224 MDFKG--VNCVINYDFPD  239 (248)
Q Consensus       224 idip~--~~~Vi~~~~p~  239 (248)
                      ||+|+  +++||+.+.|-
T Consensus       599 VD~pGd~l~~vII~kLPF  616 (697)
T PRK11747        599 LDLPGDYLTQVIITKIPF  616 (697)
T ss_pred             ccCCCCceEEEEEEcCCC
Confidence            99996  78999999984

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.53  E-value=2.6e-06  Score=76.38  Aligned_cols=90  Identities=17%  Similarity=0.249  Sum_probs=66.0

Q ss_pred             HHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCC------eeEEEecCCCHHHHHHHHHHhhc----CCceEEEEe--c
Q 042003          151 LRQSFAESLNPPVLIFVQSKERAKELYGELAFDGI------RAGVIHSDLSQTQRENAVDDFRA----GKTWVLIAT--D  218 (248)
Q Consensus       151 l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~------~v~~~~~~~~~~~r~~~~~~f~~----g~~~ilv~T--~  218 (248)
                      +.++.+.. ++.++||++|....+.+++.+.+.+.      .-.++..+-...++.++++.|++    |+..||+|+  .
T Consensus       514 i~~~~~~~-pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~~~~~~~~~l~~f~~~~~~~~gavL~av~gG  592 (705)
T TIGR00604       514 LVEFSKII-PDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETKDAQETSDALERYKQAVSEGRGAVLLSVAGG  592 (705)
T ss_pred             HHHHhhcC-CCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCCCcchHHHHHHHHHHHHhcCCceEEEEecCC
Confidence            33444444 68999999999999999998876432      11233322223577889999964    456799998  7


Q ss_pred             ccccCCCCCC--CcEEEeccCCC-Cc
Q 042003          219 VIARGMDFKG--VNCVINYDFPD-SG  241 (248)
Q Consensus       219 ~~~~Gidip~--~~~Vi~~~~p~-~~  241 (248)
                      .+++|||+++  ++.||..|+|- ++
T Consensus       593 k~sEGIDf~~~~~r~ViivGlPf~~~  618 (705)
T TIGR00604       593 KVSEGIDFCDDLGRAVIMVGIPYEYT  618 (705)
T ss_pred             cccCccccCCCCCcEEEEEccCCCCC
Confidence            8999999997  78999999996 44

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).

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=98.49  E-value=7.7e-07  Score=76.25  Aligned_cols=83  Identities=20%  Similarity=0.238  Sum_probs=67.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhc--CCce-EEEEecccccCCCCCCCcEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRA--GKTW-VLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~--g~~~-ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      ..+++|...=.....-+...|.+.|....-+||....++|+++++.|..  |... .|++-.+.+.|+|+-+.+|+|++|
T Consensus       746 keK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHlilvD  825 (901)
T KOG4439|consen  746 KEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLILVD  825 (901)
T ss_pred             cceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEEEEe
Confidence            4566666544555566677888888899999999999999999999974  4344 456668899999999999999999


Q ss_pred             CCCCcc
Q 042003          237 FPDSGA  242 (248)
Q Consensus       237 ~p~~~~  242 (248)
                      +-||+.
T Consensus       826 lHWNPa  831 (901)
T KOG4439|consen  826 LHWNPA  831 (901)
T ss_pred             cccCHH
Confidence            999984

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=98.48  E-value=9.1e-07  Score=79.21  Aligned_cols=70  Identities=16%  Similarity=0.083  Sum_probs=54.6

Q ss_pred             ccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecC
Q 042003           34 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP  105 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~  105 (248)
                      +.....|+++||..+..-+..+.+.++.+..+||||||++.+.. ....+-++.+. .....-+.++||.+.
T Consensus         4 ly~~ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~-~eaFI~rlyr~-~n~~gfIkafSdsP~   73 (814)
T TIGR00596         4 VYLEGGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESS-QEAFILRLYRQ-KNKTGFIKAFSDNPE   73 (814)
T ss_pred             HhhcCCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccc-cHHHHHHHHHH-hCCCcceEEecCCCc
Confidence            34457899999999999999999999999999999999987654 34444455554 345566788999864

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

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A

Probab=98.46  E-value=5e-07  Score=66.18  Aligned_cols=85  Identities=24%  Similarity=0.385  Sum_probs=63.5

Q ss_pred             HHHHhccCCCCEEEEecchHHHHHHHHHhhcCCC--eeEEEecCCCHHHHHHHHHHhhcCCceEEEEec--ccccCCCCC
Q 042003          152 RQSFAESLNPPVLIFVQSKERAKELYGELAFDGI--RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD--VIARGMDFK  227 (248)
Q Consensus       152 ~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~--~~~~Gidip  227 (248)
                      .++++.. +++++||++|.+..+.+++.++....  ...++..  +..++...++.|++++..||+++.  .+++|+|+|
T Consensus         2 ~~l~~~~-~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~   78 (167)
T PF13307_consen    2 LELISAV-PGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFP   78 (167)
T ss_dssp             HHHHHCC-SSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--E
T ss_pred             hHHHhcC-CCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCC
Confidence            4455555 68999999999999999999987642  2233333  255788999999999999999999  999999999


Q ss_pred             C--CcEEEeccCCC
Q 042003          228 G--VNCVINYDFPD  239 (248)
Q Consensus       228 ~--~~~Vi~~~~p~  239 (248)
                      +  ++.||..+.|.
T Consensus        79 ~~~~r~vii~glPf   92 (167)
T PF13307_consen   79 GDLLRAVIIVGLPF   92 (167)
T ss_dssp             CESEEEEEEES---
T ss_pred             CchhheeeecCCCC
Confidence            6  88999999995

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=98.44  E-value=3e-06  Score=75.59  Aligned_cols=89  Identities=22%  Similarity=0.299  Sum_probs=68.9

Q ss_pred             HHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCe-eEEEecCCCHHHHHHHHHHhhcCCc-eEEEEecccccCC
Q 042003          147 KLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIR-AGVIHSDLSQTQRENAVDDFRAGKT-WVLIATDVIARGM  224 (248)
Q Consensus       147 ~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~r~~~~~~f~~g~~-~ilv~T~~~~~Gi  224 (248)
                      ....+.++++.. +++++||++|.+..+.+++.++..... ....+|..+   +.+.++.|..+.- .++|+|..+++|+
T Consensus       467 ~~~~i~~~~~~~-~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~---~~~~l~~f~~~~~~~~lv~~gsf~EGV  542 (654)
T COG1199         467 LAAYLREILKAS-PGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDE---REELLEKFKASGEGLILVGGGSFWEGV  542 (654)
T ss_pred             HHHHHHHHHhhc-CCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCc---HHHHHHHHHHhcCCeEEEeeccccCcc
Confidence            344555666665 569999999999999999999877653 344455444   4477788876654 8999999999999


Q ss_pred             CCCC--CcEEEeccCCC
Q 042003          225 DFKG--VNCVINYDFPD  239 (248)
Q Consensus       225 dip~--~~~Vi~~~~p~  239 (248)
                      |+|+  .+.||+.+.|.
T Consensus       543 D~~g~~l~~vvI~~lPf  559 (654)
T COG1199         543 DFPGDALRLVVIVGLPF  559 (654)
T ss_pred             cCCCCCeeEEEEEecCC
Confidence            9997  48999999995

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.43  E-value=8.6e-06  Score=71.82  Aligned_cols=103  Identities=5%  Similarity=-0.036  Sum_probs=57.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-------hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-------RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      |+.|+.+.++.......   +..+.++.       .......+..+|+|||...+       ...+.++++||+||-|.-
T Consensus       200 lt~q~~~rl~~~f~~~~---v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAv-------FaP~~~LgLIIvdEEhd~  269 (665)
T PRK14873        200 DVDRLEAALRALLGAGD---VAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAV-------FAPVEDLGLVAIWDDGDD  269 (665)
T ss_pred             hHHHHHHHHHHHcCCCc---EEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeE-------EeccCCCCEEEEEcCCch
Confidence            34567777766543222   22232222       22334556689999995322       245789999999999964


Q ss_pred             c--cc-CcccccchhHhhhCCCccceeEEEEeecCchHHHHHH
Q 042003           74 F--EV-GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR  113 (248)
Q Consensus        74 ~--~~-~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~  113 (248)
                      .  +. +++...-.-........++.+|+.|||++-+......
T Consensus       270 sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSles~~~~~  312 (665)
T PRK14873        270 LLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQALVE  312 (665)
T ss_pred             hhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHh
Confidence            3  11 1121111111122134578899999998865554443

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=98.39  E-value=4.8e-06  Score=75.45  Aligned_cols=82  Identities=18%  Similarity=0.251  Sum_probs=64.4

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCC--CCcEEEecc
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK--GVNCVINYD  236 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip--~~~~Vi~~~  236 (248)
                      .+++++|+++|.+..+.+++.|......+ ...|...  .+..+++.|++++..||++|..+++|+|+|  +...||+.+
T Consensus       646 ~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~k  722 (820)
T PRK07246        646 LQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVITR  722 (820)
T ss_pred             cCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEec
Confidence            36899999999999999999997665444 4444222  246689999998889999999999999997  466788899


Q ss_pred             CC-CCccc
Q 042003          237 FP-DSGAA  243 (248)
Q Consensus       237 ~p-~~~~~  243 (248)
                      .| .++.+
T Consensus       723 LPF~~P~d  730 (820)
T PRK07246        723 LPFDNPED  730 (820)
T ss_pred             CCCCCCCC
Confidence            88 44543

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=98.31  E-value=2.3e-05  Score=68.52  Aligned_cols=91  Identities=20%  Similarity=0.114  Sum_probs=68.2

Q ss_pred             HHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhc----CCceEEEEecccccC
Q 042003          148 LLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRA----GKTWVLIATDVIARG  223 (248)
Q Consensus       148 ~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~----g~~~ilv~T~~~~~G  223 (248)
                      ...+..++... +++++|.+.|....+.+++.|...-.-...+.|..+  .+.+.++.|++    |...||++|+.+.+|
T Consensus       459 ~~~~~~~~~~~-~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweG  535 (636)
T TIGR03117       459 SLSTAAILRKA-QGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTG  535 (636)
T ss_pred             HHHHHHHHHHc-CCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccc
Confidence            35556666655 679999999999999999999764223345556443  34567778876    467899999999999


Q ss_pred             CCC--------C--CCcEEEeccCCCCc
Q 042003          224 MDF--------K--GVNCVINYDFPDSG  241 (248)
Q Consensus       224 idi--------p--~~~~Vi~~~~p~~~  241 (248)
                      ||+        |  .+++||+...|-.+
T Consensus       536 vDv~~~~~~p~~G~~Ls~ViI~kLPF~~  563 (636)
T TIGR03117       536 IDLTHKPVSPDKDNLLTDLIITCAPFGL  563 (636)
T ss_pred             cccCCccCCCCCCCcccEEEEEeCCCCc
Confidence            999        2  48999999988443

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.

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=98.30  E-value=4.8e-06  Score=75.26  Aligned_cols=97  Identities=24%  Similarity=0.292  Sum_probs=83.0

Q ss_pred             hHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC--ceEEEEecccc
Q 042003          146 GKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK--TWVLIATDVIA  221 (248)
Q Consensus       146 ~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~--~~ilv~T~~~~  221 (248)
                      .|+..|.-++.+.  ++.+++||+.-.+...-+...|+..|+--..+.|....++|+..++.|+...  ++.|++|...+
T Consensus      1260 GKLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSgg 1339 (1958)
T KOG0391|consen 1260 GKLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGG 1339 (1958)
T ss_pred             chHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCc
Confidence            4555555444432  2789999998888888888899999999999999999999999999999765  47889999999


Q ss_pred             cCCCCCCCcEEEeccCCCCcc
Q 042003          222 RGMDFKGVNCVINYDFPDSGA  242 (248)
Q Consensus       222 ~Gidip~~~~Vi~~~~p~~~~  242 (248)
                      .|||+-+++.||.||.-||+.
T Consensus      1340 vGiNLtgADTVvFYDsDwNPt 1360 (1958)
T KOG0391|consen 1340 VGINLTGADTVVFYDSDWNPT 1360 (1958)
T ss_pred             cccccccCceEEEecCCCCch
Confidence            999999999999999999984

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=98.19  E-value=1e-05  Score=74.55  Aligned_cols=101  Identities=25%  Similarity=0.263  Sum_probs=87.1

Q ss_pred             hHHHHHHHHH-h--ccCCC--CEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcC--CceEEEEec
Q 042003          146 GKLLALRQSF-A--ESLNP--PVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAG--KTWVLIATD  218 (248)
Q Consensus       146 ~~~~~l~~~~-~--~~~~~--~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g--~~~ilv~T~  218 (248)
                      .|...+.+++ .  ...+.  ++++|+.-.....-+...++..++....++|+++.+.|...++.|.++  ...+++++.
T Consensus       692 ~k~~~l~~ll~~~~~~~~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~k  771 (866)
T COG0553         692 GKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLK  771 (866)
T ss_pred             hHHHHHHHHHHHHHHhhcccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEec
Confidence            4566666666 2  22255  999999999999999999999998999999999999999999999986  456778889


Q ss_pred             ccccCCCCCCCcEEEeccCCCCccccee
Q 042003          219 VIARGMDFKGVNCVINYDFPDSGAAYIH  246 (248)
Q Consensus       219 ~~~~Gidip~~~~Vi~~~~p~~~~~~~q  246 (248)
                      +.+.|+|+..+++||++|+.|++....|
T Consensus       772 agg~glnLt~a~~vi~~d~~wnp~~~~Q  799 (866)
T COG0553         772 AGGLGLNLTGADTVILFDPWWNPAVELQ  799 (866)
T ss_pred             ccccceeecccceEEEeccccChHHHHH
Confidence            9999999999999999999999987665

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=98.17  E-value=2.3e-06  Score=63.44  Aligned_cols=65  Identities=17%  Similarity=0.193  Sum_probs=44.6

Q ss_pred             ccCCCcEEEeChHHHHHHHhcCC-----------cccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEe
Q 042003           34 SKFSCDILISTPLRLRLAIRRKK-----------IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSA  102 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~~~-----------~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SA  102 (248)
                      .....+++++|.+++........           ......+++|+||||+......    ...+..   .....+++|||
T Consensus       108 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH~~~~~~~----~~~i~~---~~~~~~l~lTA  180 (184)
T PF04851_consen  108 DNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAHHYPSDSS----YREIIE---FKAAFILGLTA  180 (184)
T ss_dssp             CBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGGCTHHHHH----HHHHHH---SSCCEEEEEES
T ss_pred             ccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhhhcCCHHH----HHHHHc---CCCCeEEEEEe
Confidence            44578999999999988876421           2345788999999999765432    333333   34566899999


Q ss_pred             ecC
Q 042003          103 TLP  105 (248)
Q Consensus       103 T~~  105 (248)
                      |+.
T Consensus       181 Tp~  183 (184)
T PF04851_consen  181 TPF  183 (184)
T ss_dssp             S-S
T ss_pred             Ccc
Confidence            975

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=98.15  E-value=7e-06  Score=57.41  Aligned_cols=71  Identities=11%  Similarity=-0.013  Sum_probs=43.7

Q ss_pred             cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchH
Q 042003           35 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFV  108 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~  108 (248)
                      .++.-|-++|...+.+.+.+ .....+++++|+||||..-...  ......+..........+|+||||+|...
T Consensus        70 ~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~s--IA~rg~l~~~~~~g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   70 FGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTS--IAARGYLRELAESGEAKVIFMTATPPGSE  140 (148)
T ss_dssp             -SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHH--HHHHHHHHHHHHTTS-EEEEEESS-TT--
T ss_pred             cCCCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHH--HhhheeHHHhhhccCeeEEEEeCCCCCCC
Confidence            34677889999998888876 5557899999999999954332  22222232222234467899999998744

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.00  E-value=5.7e-05  Score=68.42  Aligned_cols=141  Identities=23%  Similarity=0.210  Sum_probs=94.7

Q ss_pred             eeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc--CCCCEEEEecchHHH
Q 042003           96 VRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES--LNPPVLIFVQSKERA  173 (248)
Q Consensus        96 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~  173 (248)
                      .+-+||+|...+..++..-|..+...+   +...+................|.+++.+.+...  .++|+||-+.|++..
T Consensus       565 kLsGMTGTA~tea~Ef~~IY~L~Vv~I---PTnrP~~R~D~~D~vy~t~~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~S  641 (1112)
T PRK12901        565 KLAGMTGTAETEAGEFWDIYKLDVVVI---PTNRPIARKDKEDLVYKTKREKYNAVIEEITELSEAGRPVLVGTTSVEIS  641 (1112)
T ss_pred             hhcccCCCCHHHHHHHHHHhCCCEEEC---CCCCCcceecCCCeEecCHHHHHHHHHHHHHHHHHCCCCEEEEeCcHHHH
Confidence            345899998877676655554343222   222232222222222345556777766655533  378999999999999


Q ss_pred             HHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCC--------CCcEEEeccCCCCc
Q 042003          174 KELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK--------GVNCVINYDFPDSG  241 (248)
Q Consensus       174 ~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip--------~~~~Vi~~~~p~~~  241 (248)
                      +.+.+.|...+++..++++.....+-+-+.++=+.|.  |-|||+.+++|-||.        +==|||-...++|.
T Consensus       642 E~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~Ga--VTIATNMAGRGTDIkLg~~V~e~GGL~VIgTerheSr  715 (1112)
T PRK12901        642 ELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQPGT--VTIATNMAGRGTDIKLSPEVKAAGGLAIIGTERHESR  715 (1112)
T ss_pred             HHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCCCc--EEEeccCcCCCcCcccchhhHHcCCCEEEEccCCCcH
Confidence            9999999999999988888755444444445444444  889999999999997        22377777777664

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=97.95  E-value=0.00022  Score=63.19  Aligned_cols=181  Identities=18%  Similarity=0.107  Sum_probs=112.8

Q ss_pred             CCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC-----cccccchhHhhhCCCccceeEEEEeecCchHHHH
Q 042003           37 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-----NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEEL  111 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~-----~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~  111 (248)
                      ..+-+++..++|.+..   ...+.++|+||+||+--++..-     ........++..+..+...+|+|-|+++...-++
T Consensus       121 ~~~rLivqIdSL~R~~---~~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvdF  197 (824)
T PF02399_consen  121 PYDRLIVQIDSLHRLD---GSLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVDF  197 (824)
T ss_pred             ccCeEEEEehhhhhcc---cccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHHH
Confidence            3577888877775554   2346779999999997665431     1112223334444556778999999999989888


Q ss_pred             HHHhcCCc-EEEEEcccccccc-c------------------------------------ceeEEEEcCCchhHHHHHHH
Q 042003          112 ARSIMHDA-VRVIVGRKNTASE-S------------------------------------IKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus       112 ~~~~~~~~-~~~~~~~~~~~~~-~------------------------------------~~~~~~~~~~~~~~~~~l~~  153 (248)
                      .....++. ..++......+.. +                                    .........   +.......
T Consensus       198 l~~~Rp~~~i~vI~n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~tF~~~  274 (824)
T PF02399_consen  198 LASCRPDENIHVIVNTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISN---DETTFFSE  274 (824)
T ss_pred             HHHhCCCCcEEEEEeeeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCcccccccccc---chhhHHHH
Confidence            88875543 2232221100000 0                                    000000011   12222333


Q ss_pred             HHhccC-CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCC
Q 042003          154 SFAESL-NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGV  229 (248)
Q Consensus       154 ~~~~~~-~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~  229 (248)
                      +..... ++++-||++|...++.+++..+..+.++..++|..+.++   +..   =++.+|++=|+++..|+++...
T Consensus       275 L~~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~d---v~~---W~~~~VviYT~~itvG~Sf~~~  345 (824)
T PF02399_consen  275 LLARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLED---VES---WKKYDVVIYTPVITVGLSFEEK  345 (824)
T ss_pred             HHHHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccc---ccc---ccceeEEEEeceEEEEeccchh
Confidence            333322 567889999999999999999888899999988766653   221   2457899999999999998743

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

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=97.86  E-value=3.8e-05  Score=68.38  Aligned_cols=100  Identities=19%  Similarity=0.204  Sum_probs=80.6

Q ss_pred             hHHHHHHHHHhccC--CCCEEEEecchHHHHHHHHHhhc----------------------CCCeeEEEecCCCHHHHHH
Q 042003          146 GKLLALRQSFAESL--NPPVLIFVQSKERAKELYGELAF----------------------DGIRAGVIHSDLSQTQREN  201 (248)
Q Consensus       146 ~~~~~l~~~~~~~~--~~~~liF~~~~~~~~~l~~~L~~----------------------~~~~v~~~~~~~~~~~r~~  201 (248)
                      .|+-.|++++....  +.|+|||..+......+...|..                      .|..-..+.|+.....|+.
T Consensus      1126 gKmiLLleIL~mceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k 1205 (1567)
T KOG1015|consen 1126 GKMILLLEILRMCEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKK 1205 (1567)
T ss_pred             cceehHHHHHHHHHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHH
Confidence            45556666666443  78999999999888888877752                      1345677889999999999


Q ss_pred             HHHHhhcCC----ceEEEEecccccCCCCCCCcEEEeccCCCCcccce
Q 042003          202 AVDDFRAGK----TWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYI  245 (248)
Q Consensus       202 ~~~~f~~g~----~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~  245 (248)
                      +.+.|.+-.    ...||+|-+.+.|||+-.++-||+||..|||+-=.
T Consensus      1206 ~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDt 1253 (1567)
T KOG1015|consen 1206 WAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDT 1253 (1567)
T ss_pred             HHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccch
Confidence            999998632    24899999999999999999999999999997433

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=97.83  E-value=0.0001  Score=63.87  Aligned_cols=98  Identities=21%  Similarity=0.299  Sum_probs=83.1

Q ss_pred             hHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCc-eEEEEeccccc
Q 042003          146 GKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKT-WVLIATDVIAR  222 (248)
Q Consensus       146 ~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~-~ilv~T~~~~~  222 (248)
                      .|+..|-+++.+.  .+.++++|+.--+....+.++|.-++|....+.|+..-.+|.++++.|+...+ -+|++|-+.+.
T Consensus      1028 gKL~~LDeLL~kLkaegHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGL 1107 (1185)
T KOG0388|consen 1028 GKLVVLDELLPKLKAEGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGL 1107 (1185)
T ss_pred             cceeeHHHHHHHhhcCCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCcc
Confidence            3444444444332  27899999988888999999999999999999999999999999999998654 57899999999


Q ss_pred             CCCCCCCcEEEeccCCCCccc
Q 042003          223 GMDFKGVNCVINYDFPDSGAA  243 (248)
Q Consensus       223 Gidip~~~~Vi~~~~p~~~~~  243 (248)
                      |||+..++.||.||.-|++..
T Consensus      1108 GINLTAADTViFYdSDWNPT~ 1128 (1185)
T KOG0388|consen 1108 GINLTAADTVIFYDSDWNPTA 1128 (1185)
T ss_pred             cccccccceEEEecCCCCcch
Confidence            999999999999999999853

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

Probab=97.71  E-value=6.6e-05  Score=66.56  Aligned_cols=78  Identities=18%  Similarity=0.268  Sum_probs=66.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc-------CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEE
Q 042003          160 NPPVLIFVQSKERAKELYGELAF-------DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV  232 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~-------~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~V  232 (248)
                      .+.+++|.+-=...-.+...|..       ..+.+..+|+.....+..++.+....|..+++++|++++..+.+.++.+|
T Consensus       643 ~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~v  722 (1282)
T KOG0921|consen  643 DGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVYV  722 (1282)
T ss_pred             ccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeEE
Confidence            67889999888888788777753       24688899999999999999999999999999999999999999998888


Q ss_pred             EeccC
Q 042003          233 INYDF  237 (248)
Q Consensus       233 i~~~~  237 (248)
                      |+...
T Consensus       723 id~ck  727 (1282)
T KOG0921|consen  723 IDSCK  727 (1282)
T ss_pred             Eeeee
Confidence            76554

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=97.56  E-value=0.00047  Score=55.27  Aligned_cols=98  Identities=18%  Similarity=0.145  Sum_probs=56.2

Q ss_pred             cchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhc---CCcccCceeEEEEeccccccc
Q 042003            2 ATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRR---KKIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus         2 ~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~---~~~~~~~~~~lIiDEah~~~~   75 (248)
                      ..|+.+.+.++..... ..+....|..   ..........+++|+|.+.+......   +.+..-+++.+|+||+|.+-+
T Consensus        70 ~~~W~~E~~~~~~~~~-~~v~~~~~~~~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~  148 (299)
T PF00176_consen   70 LSQWKEEIEKWFDPDS-LRVIIYDGDSERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKN  148 (299)
T ss_dssp             HHHHHHHHHHHSGT-T-S-EEEESSSCHHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTT
T ss_pred             hhhhhhhhcccccccc-ccccccccccccccccccccccceeeeccccccccccccccccccccccceeEEEeccccccc
Confidence            4688888888886534 2444444443   22233445689999999988711111   112224589999999999854


Q ss_pred             cCcccccchhHhhhCCCccceeEEEEeecC
Q 042003           76 VGNLLKHIDPVVKACSNPSIVRSLFSATLP  105 (248)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~  105 (248)
                      ..   ......+..+.  ....+++|||+-
T Consensus       149 ~~---s~~~~~l~~l~--~~~~~lLSgTP~  173 (299)
T PF00176_consen  149 KD---SKRYKALRKLR--ARYRWLLSGTPI  173 (299)
T ss_dssp             TT---SHHHHHHHCCC--ECEEEEE-SS-S
T ss_pred             cc---ccccccccccc--cceEEeeccccc
Confidence            32   22333333322  455688999974

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=97.46  E-value=0.00042  Score=57.85  Aligned_cols=83  Identities=13%  Similarity=0.117  Sum_probs=73.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC-ce-EEEEecccccCCCCCCCcEEEeccC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK-TW-VLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~-~~-ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      .-|.|||..--.....+.-.|.+.|++|..+-|+|++..|...++.|.+.- +. .|++-.+.+..+|+..+++|+++||
T Consensus       638 t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmDP  717 (791)
T KOG1002|consen  638 TAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMDP  717 (791)
T ss_pred             chhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeecc
Confidence            348999987777777888889999999999999999999999999999864 44 5677799999999999999999999


Q ss_pred             CCCcc
Q 042003          238 PDSGA  242 (248)
Q Consensus       238 p~~~~  242 (248)
                      .||+.
T Consensus       718 WWNpa  722 (791)
T KOG1002|consen  718 WWNPA  722 (791)
T ss_pred             cccHH
Confidence            99985

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=97.37  E-value=0.0036  Score=58.12  Aligned_cols=98  Identities=15%  Similarity=0.105  Sum_probs=59.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhccccc-CCCcEEEeChHHHHHHHhcC-Cc-ccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSK-FSCDILISTPLRLRLAIRRK-KI-DLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~v~Tp~~l~~~~~~~-~~-~~~~~~~lIiDEah~~~~~~   77 (248)
                      |-.|+.+.++.++.... ... -.-........+. ....|+|+|.++|....... .. .-++=-++|+||||+ .   
T Consensus       315 Ld~Q~~~~f~~~~~~~~-~~~-~~~s~~~Lk~~l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHR-S---  388 (962)
T COG0610         315 LDDQTSDEFQSFGKVAF-NDP-KAESTSELKELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHR-S---  388 (962)
T ss_pred             HHHHHHHHHHHHHHhhh-hcc-cccCHHHHHHHHhcCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhh-c---
Confidence            45688899998888765 222 2222222233333 34589999999998888664 11 122333799999999 2   


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                       ..+.+...++... ++...+++|+|+-.
T Consensus       389 -Q~G~~~~~~~~~~-~~a~~~gFTGTPi~  415 (962)
T COG0610         389 -QYGELAKLLKKAL-KKAIFIGFTGTPIF  415 (962)
T ss_pred             -cccHHHHHHHHHh-ccceEEEeeCCccc
Confidence             3333333333322 23678999999743

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=97.33  E-value=0.0012  Score=46.76  Aligned_cols=67  Identities=18%  Similarity=0.268  Sum_probs=48.5

Q ss_pred             HHHHHHHhhcCCC------eeEEEecCCCHHHHHHHHHHhhcCC-ceEEEEecccccCCCCCC--CcEEEeccCCC
Q 042003          173 AKELYGELAFDGI------RAGVIHSDLSQTQRENAVDDFRAGK-TWVLIATDVIARGMDFKG--VNCVINYDFPD  239 (248)
Q Consensus       173 ~~~l~~~L~~~~~------~v~~~~~~~~~~~r~~~~~~f~~g~-~~ilv~T~~~~~Gidip~--~~~Vi~~~~p~  239 (248)
                      .+++++.+...+.      ...++..+.+..+...+++.|++.. ..||+++..+++|+|+|+  ++.||..+.|.
T Consensus         4 m~~v~~~~~~~~~~~~l~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492        4 MESFVQYWKENGILENINKNLLLLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             HHHHHHHHHHcCchhhHhcCCeEEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCC
Confidence            4455555554432      2344555556656788999998754 379999988999999997  57999999985

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=97.24  E-value=0.0012  Score=46.85  Aligned_cols=68  Identities=19%  Similarity=0.262  Sum_probs=46.4

Q ss_pred             HHHHHHHHhhcCCC---eeEEEecCCCHHHHHHHHHHhhcCCc---eEEEEecc--cccCCCCCC--CcEEEeccCCC
Q 042003          172 RAKELYGELAFDGI---RAGVIHSDLSQTQRENAVDDFRAGKT---WVLIATDV--IARGMDFKG--VNCVINYDFPD  239 (248)
Q Consensus       172 ~~~~l~~~L~~~~~---~v~~~~~~~~~~~r~~~~~~f~~g~~---~ilv~T~~--~~~Gidip~--~~~Vi~~~~p~  239 (248)
                      ..+.+++.+++.+.   ...++..+....+..++++.|+++.-   .||+++..  +++|||+|+  ++.||..+.|.
T Consensus         3 ~m~~v~~~~~~~~~~~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPf   80 (142)
T smart00491        3 YLEQVVEYWKENGILEINKPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPF   80 (142)
T ss_pred             HHHHHHHHHHhcCccccCceEEEECCCCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCC
Confidence            34566666665432   22334333333455778888886543   68888887  999999997  68999999995

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=97.24  E-value=0.0015  Score=58.58  Aligned_cols=75  Identities=20%  Similarity=0.354  Sum_probs=65.1

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-cccCCCCCCCcEEEe
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-IARGMDFKGVNCVIN  234 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~~~Gidip~~~~Vi~  234 (248)
                      +.++++.++|+.-|.+.++.+++    .++++..++|+++..+|.++++.+.+|+.+|+|+|.. +...+.++++.+||.
T Consensus       310 g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvVI  389 (681)
T PRK10917        310 GYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVII  389 (681)
T ss_pred             CCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEEE
Confidence            56899999999999988888765    3689999999999999999999999999999999975 455677888888773

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=97.10  E-value=0.0019  Score=58.57  Aligned_cols=73  Identities=22%  Similarity=0.292  Sum_probs=58.9

Q ss_pred             HHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCC-----CeeEE-EecCCCHHHHHHHHHHhhcCCceEEEEeccc
Q 042003          148 LLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDG-----IRAGV-IHSDLSQTQRENAVDDFRAGKTWVLIATDVI  220 (248)
Q Consensus       148 ~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~-----~~v~~-~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~  220 (248)
                      .-.+..+.-...++++++.+||..-+.++++.|++..     ..+.. +||.++..++++.++.|.+|.++|+|+|+.+
T Consensus       113 fg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~F  191 (1187)
T COG1110         113 FGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQF  191 (1187)
T ss_pred             HHHHHHHHHHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHH
Confidence            3344445555557999999999999999999997642     33333 9999999999999999999999999999865

>PRK05580 primosome assembly protein PriA; Validated

Probab=97.07  E-value=0.0076  Score=54.09  Aligned_cols=76  Identities=20%  Similarity=0.301  Sum_probs=64.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      +++++|.+++++.+.++++.|++. +..+..+||+++..+|.+......+|+.+|+|+|...-. ..++++..||.-+
T Consensus       190 g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-~p~~~l~liVvDE  266 (679)
T PRK05580        190 GKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-LPFKNLGLIIVDE  266 (679)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-ccccCCCEEEEEC
Confidence            678999999999999999999764 778999999999999999999999999999999975432 5567788887544

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=97.02  E-value=0.0032  Score=56.10  Aligned_cols=74  Identities=19%  Similarity=0.372  Sum_probs=64.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc-ccCCCCCCCcEEE
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI-ARGMDFKGVNCVI  233 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-~~Gidip~~~~Vi  233 (248)
                      +.++++.++|+.-|.+.++.+++    .+.++..++|+++..+|...++...+|+.+|+|+|... ...+++.++.+||
T Consensus       284 g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvV  362 (630)
T TIGR00643       284 GYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVI  362 (630)
T ss_pred             CCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEE
Confidence            56899999999999998887764    37899999999999999999999999999999999764 4567777888777

>TIGR00595 priA primosomal protein N'

Probab=97.01  E-value=0.0062  Score=52.66  Aligned_cols=76  Identities=22%  Similarity=0.381  Sum_probs=63.9

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      ++++++.++++.-+.++++.|++. +..+.++||+++..+|.+......+|+.+|+|+|...-. .-++++..||.-+
T Consensus        25 g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~lIIVDE  101 (505)
T TIGR00595        25 GKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGLIIVDE  101 (505)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCEEEEEC
Confidence            678999999999999999999764 678999999999999999999999999999999975432 4566788777443

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).

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.84  E-value=0.0057  Score=56.47  Aligned_cols=75  Identities=16%  Similarity=0.255  Sum_probs=64.4

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-cccCCCCCCCcEEEe
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-IARGMDFKGVNCVIN  234 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~~~Gidip~~~~Vi~  234 (248)
                      +.+++|.++|..-|.+.++.+++    .+.++..++|+.+..++.++++.+.+|+.+|+|+|.. +...+.+.++.++|.
T Consensus       500 g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llVI  579 (926)
T TIGR00580       500 GKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLII  579 (926)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEEe
Confidence            56899999999999999988765    3678889999999999999999999999999999974 455677888888774

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.

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.81  E-value=0.01  Score=52.95  Aligned_cols=91  Identities=16%  Similarity=0.123  Sum_probs=72.7

Q ss_pred             hHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcC-C-CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccc
Q 042003          146 GKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFD-G-IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIA  221 (248)
Q Consensus       146 ~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~-~-~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~  221 (248)
                      .|.+....+++..  .++.+||.++.+..+.++.+.|++. + ..+..+|+++++.+|.+......+|+.+|+|+|-.+-
T Consensus       172 GKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAv  251 (665)
T PRK14873        172 DWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAV  251 (665)
T ss_pred             cHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeE
Confidence            4555555555432  2678999999999999999999865 3 5799999999999999999999999999999997663


Q ss_pred             cCCCCCCCcEEEeccC
Q 042003          222 RGMDFKGVNCVINYDF  237 (248)
Q Consensus       222 ~Gidip~~~~Vi~~~~  237 (248)
                      . .=+++...||..+-
T Consensus       252 F-aP~~~LgLIIvdEE  266 (665)
T PRK14873        252 F-APVEDLGLVAIWDD  266 (665)
T ss_pred             E-eccCCCCEEEEEcC
Confidence            3 45667777776554

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=96.71  E-value=0.00062  Score=61.58  Aligned_cols=183  Identities=19%  Similarity=0.138  Sum_probs=96.1

Q ss_pred             EEcccchhhhcccccCCCcEEEeChHHHHHHHhc--CCcccCceeEEEEeccccccccCcccccchhHhhhC------CC
Q 042003           21 KLMKKELVRSTDLSKFSCDILISTPLRLRLAIRR--KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC------SN   92 (248)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~--~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~------~~   92 (248)
                      +.-..|.....-.....++++|+||+++-...+.  ....+.++..+|+||.|++...  +.+.++.+....      ..
T Consensus      1004 ~ie~tgd~~pd~~~v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~--rgPVle~ivsr~n~~s~~t~ 1081 (1230)
T KOG0952|consen 1004 VIELTGDVTPDVKAVREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED--RGPVLEVIVSRMNYISSQTE 1081 (1230)
T ss_pred             eEeccCccCCChhheecCceEEcccccccCccccccchhhhccccceeecccccccCC--CcceEEEEeeccccCccccC
Confidence            3333443322233445789999999998777663  4455789999999999998764  333333332211      12


Q ss_pred             ccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeE------EEEcCCchhHHH-HHHHHHhccCCCCEEE
Q 042003           93 PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQK------LVFAGSEEGKLL-ALRQSFAESLNPPVLI  165 (248)
Q Consensus        93 ~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~-~l~~~~~~~~~~~~li  165 (248)
                      ...+.+++|.-+. ....+..|+.-.+. + ..+....+......      ..++........ .+..+....+.++++|
T Consensus      1082 ~~vr~~glsta~~-na~dla~wl~~~~~-~-nf~~svrpvp~~~~i~gfp~~~~cprm~smnkpa~qaik~~sp~~p~li 1158 (1230)
T KOG0952|consen 1082 EPVRYLGLSTALA-NANDLADWLNIKDM-Y-NFRPSVRPVPLEVHIDGFPGQHYCPRMMSMNKPAFQAIKTHSPIKPVLI 1158 (1230)
T ss_pred             cchhhhhHhhhhh-ccHHHHHHhCCCCc-C-CCCcccccCCceEeecCCCchhcchhhhhcccHHHHHHhcCCCCCceEE
Confidence            3456666654443 36777777655443 1 11111111111111      123333333333 3444444555689999


Q ss_pred             EecchHHHHH----HHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC
Q 042003          166 FVQSKERAKE----LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK  210 (248)
Q Consensus       166 F~~~~~~~~~----l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~  210 (248)
                      |+.++++...    +...+.....+...++.+  ..+-+.++...++..
T Consensus      1159 fv~srrqtrlta~~li~~~~~~~~p~~fl~~d--e~e~e~~~~~~~d~~ 1205 (1230)
T KOG0952|consen 1159 FVSSRRQTRLTALDLIASCATEDNPKQFLNMD--ELELEIIMSKVRDTN 1205 (1230)
T ss_pred             EeecccccccchHhHHhhccCCCCchhccCCC--HHHHHHHHHHhcccc
Confidence            9998775543    333333333344444443  444455555544443

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=96.52  E-value=0.0051  Score=55.14  Aligned_cols=126  Identities=25%  Similarity=0.216  Sum_probs=80.2

Q ss_pred             eEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc-c-CCCCEEEEecchHHHH
Q 042003           97 RSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE-S-LNPPVLIFVQSKERAK  174 (248)
Q Consensus        97 ~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~-~~~~~liF~~~~~~~~  174 (248)
                      +.+||+|...+..++..-|..+...+.+   ..+.......-........|..++.+.+.. + .++|+||-+.+++..+
T Consensus       367 l~gmTGTa~te~~EF~~iY~l~vv~iPT---nrp~~R~D~~D~vy~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE  443 (822)
T COG0653         367 LAGMTGTADTEEEEFDVIYGLDVVVIPT---NRPIIRLDEPDLVYKTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSE  443 (822)
T ss_pred             hcCCCCcchhhhhhhhhccCCceeeccC---CCcccCCCCccccccchHHHHHHHHHHHHHHHhcCCCEEEcCcceecch
Confidence            3467777666555555544333333322   222222323322233445666666555543 2 2789999999999999


Q ss_pred             HHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCC
Q 042003          175 ELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK  227 (248)
Q Consensus       175 ~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip  227 (248)
                      .+.+.|++.+++..++...-...+-+.+.++-+.|  -+-|||+.+++|-||.
T Consensus       444 ~ls~~L~~~~i~h~VLNAk~h~~EA~Iia~AG~~g--aVTiATNMAGRGTDIk  494 (822)
T COG0653         444 LLSKLLRKAGIPHNVLNAKNHAREAEIIAQAGQPG--AVTIATNMAGRGTDIK  494 (822)
T ss_pred             hHHHHHHhcCCCceeeccccHHHHHHHHhhcCCCC--ccccccccccCCcccc
Confidence            99999999999998888875544434444433333  3779999999999986

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=96.49  E-value=0.0037  Score=49.10  Aligned_cols=73  Identities=14%  Similarity=0.188  Sum_probs=48.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh-hcccccCCCcEEEeChHHHHHHHhcCCc-------ccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR-STDLSKFSCDILISTPLRLRLAIRRKKI-------DLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i~v~Tp~~l~~~~~~~~~-------~~~~~~~lIiDEah~   72 (248)
                      ||..=++++..+.+.+| +.+....++.+ ........++|+.+|...+.--+.+..+       ..+.++++||||+|-
T Consensus       130 LA~RD~~~~~~~y~~LG-lsv~~~~~~~~~~~r~~~Y~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs  208 (266)
T PF07517_consen  130 LAKRDAEEMRPFYEFLG-LSVGIITSDMSSEERREAYAADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDS  208 (266)
T ss_dssp             HHHHHHHHHHHHHHHTT---EEEEETTTEHHHHHHHHHSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHH
T ss_pred             HhhccHHHHHHHHHHhh-hccccCccccCHHHHHHHHhCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccce
Confidence            45556778888888889 66666666553 2233344689999999887653332211       257899999999996


Q ss_pred             cc
Q 042003           73 LF   74 (248)
Q Consensus        73 ~~   74 (248)
                      ++
T Consensus       209 ~L  210 (266)
T PF07517_consen  209 IL  210 (266)
T ss_dssp             HT
T ss_pred             EE
Confidence            65

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>PRK10689 transcription-repair coupling factor; Provisional

Probab=96.41  E-value=0.016  Score=54.89  Aligned_cols=75  Identities=17%  Similarity=0.257  Sum_probs=63.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-cccCCCCCCCcEEEe
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-IARGMDFKGVNCVIN  234 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~~~Gidip~~~~Vi~  234 (248)
                      +.+++|.++|..-|.++++.+++.    +.++..++|+.+..++.++++.+.+|..+|+|+|.. +...+++.++.++|.
T Consensus       649 g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLVI  728 (1147)
T PRK10689        649 HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIV  728 (1147)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEEE
Confidence            678999999999999999888753    467888999999999999999999999999999964 445566777887763

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

Probab=96.30  E-value=0.044  Score=48.08  Aligned_cols=75  Identities=17%  Similarity=0.336  Sum_probs=63.7

Q ss_pred             CCCEEEEecchHHHHHHHHHh----hcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc-ccCCCCCCCcEEEe
Q 042003          160 NPPVLIFVQSKERAKELYGEL----AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI-ARGMDFKGVNCVIN  234 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L----~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-~~Gidip~~~~Vi~  234 (248)
                      +.++..-++|.=-|++-++.+    ...|+.+..+.|++....|+++++...+|+++++|+|.++ ...++..+.-+||.
T Consensus       311 G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLVIi  390 (677)
T COG1200         311 GYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLVII  390 (677)
T ss_pred             CCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeEEEE
Confidence            668999999976666555554    5568999999999999999999999999999999999875 67888888888874

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=96.15  E-value=0.0045  Score=57.07  Aligned_cols=90  Identities=20%  Similarity=0.144  Sum_probs=59.5

Q ss_pred             HHHHHHHhhcCCCcEEEEcccchhhhc------ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            5 TTRECKKLAKGNKFQIKLMKKELVRST------DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      |+=.+++|.++++   +..++|...+.      ....+..+|+|++...+..-+.  .+..++++++|+||||.+-++. 
T Consensus       680 WEMElKRwcPglK---ILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~--AFkrkrWqyLvLDEaqnIKnfk-  753 (1958)
T KOG0391|consen  680 WEMELKRWCPGLK---ILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLT--AFKRKRWQYLVLDEAQNIKNFK-  753 (1958)
T ss_pred             hhHHHhhhCCcce---EeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHH--HHHhhccceeehhhhhhhcchh-
Confidence            5556778888765   66778877333      2334457999999876655443  3345788999999999987753 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeec
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATL  104 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~  104 (248)
                       ...+..++..   +..+.++++.|+
T Consensus       754 -sqrWQAllnf---nsqrRLLLtgTP  775 (1958)
T KOG0391|consen  754 -SQRWQALLNF---NSQRRLLLTGTP  775 (1958)
T ss_pred             -HHHHHHHhcc---chhheeeecCCc
Confidence             1233444443   234567888885

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=96.02  E-value=0.018  Score=51.52  Aligned_cols=90  Identities=24%  Similarity=0.315  Sum_probs=69.6

Q ss_pred             hhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcC-CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccc
Q 042003          145 EGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFD-GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIA  221 (248)
Q Consensus       145 ~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~-~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~  221 (248)
                      +.|.+...+.+++.  .++.+|+.++.+....++.+.++.. +.+++++|+++++.+|.+......+|+.+|+|+|-.+-
T Consensus       228 SGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl  307 (730)
T COG1198         228 SGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSAL  307 (730)
T ss_pred             CcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhh
Confidence            35555555555432  2678999999999888888888654 78999999999999999999999999999999996552


Q ss_pred             cCCCCCCCcEEEec
Q 042003          222 RGMDFKGVNCVINY  235 (248)
Q Consensus       222 ~Gidip~~~~Vi~~  235 (248)
                      . .=+++...||.-
T Consensus       308 F-~Pf~~LGLIIvD  320 (730)
T COG1198         308 F-LPFKNLGLIIVD  320 (730)
T ss_pred             c-CchhhccEEEEe
Confidence            2 345567777643

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=95.87  E-value=0.012  Score=45.82  Aligned_cols=37  Identities=27%  Similarity=0.317  Sum_probs=33.4

Q ss_pred             CCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc
Q 042003           36 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK   72 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~   72 (248)
                      ...+|.||||+++..++..+.+.++++.+||+|--|.
T Consensus       176 ~~~~i~vGTP~Rl~kLle~~~L~l~~l~~ivlD~s~~  212 (252)
T PF14617_consen  176 TRVHIAVGTPGRLSKLLENGALSLSNLKRIVLDWSYL  212 (252)
T ss_pred             CCceEEEeChHHHHHHHHcCCCCcccCeEEEEcCCcc
Confidence            4689999999999999999999999999999996543

>PRK14701 reverse gyrase; Provisional

Probab=95.69  E-value=0.057  Score=52.98  Aligned_cols=60  Identities=17%  Similarity=0.232  Sum_probs=53.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC------CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD------GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~------~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      +.+++|.+||+.-+.++++.++..      +..+..+||+++..++.+.++.+.+|+.+|+|+|+-
T Consensus       122 g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        122 GKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             CCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            568999999999999999988762      467789999999999999999999999999999975

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=95.48  E-value=0.54  Score=41.65  Aligned_cols=93  Identities=16%  Similarity=0.282  Sum_probs=61.3

Q ss_pred             hhHHHHHHHHHhc---cCCCCEEEEecchHHHHHHHHHhhcCCC-------eeEEEecCCCHHHHHHHHHHhh----cCC
Q 042003          145 EGKLLALRQSFAE---SLNPPVLIFVQSKERAKELYGELAFDGI-------RAGVIHSDLSQTQRENAVDDFR----AGK  210 (248)
Q Consensus       145 ~~~~~~l~~~~~~---~~~~~~liF~~~~~~~~~l~~~L~~~~~-------~v~~~~~~~~~~~r~~~~~~f~----~g~  210 (248)
                      +.-++.+...+..   ..++-+++|++|.+.-..+.+.++..|+       +-.+.-..-+   -+++++.|.    +|.
T Consensus       611 ~~~l~~l~~~~~nL~~~VPgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~---~~dvl~~Ya~a~~~g~  687 (821)
T KOG1133|consen  611 PEMIKDLGSSISNLSNAVPGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDT---VEDVLEGYAEAAERGR  687 (821)
T ss_pred             hHHHHHHHHHHHHHHhhCCCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCccc---HHHHHHHHHHHhhcCC
Confidence            3344444444432   2268899999999999999999986653       1222222222   344555553    466


Q ss_pred             ceEEEEe--cccccCCCCCC--CcEEEeccCCCC
Q 042003          211 TWVLIAT--DVIARGMDFKG--VNCVINYDFPDS  240 (248)
Q Consensus       211 ~~ilv~T--~~~~~Gidip~--~~~Vi~~~~p~~  240 (248)
                      ..+|++.  --+++|||+.|  .+.|+..|+|..
T Consensus       688 GaiLlaVVGGKlSEGINF~D~LgRaVvvVGlPyP  721 (821)
T KOG1133|consen  688 GAILLAVVGGKLSEGINFSDDLGRAVVVVGLPYP  721 (821)
T ss_pred             CeEEEEEeccccccccccccccccEEEEeecCCC
Confidence            5677555  56899999997  789999999964

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

Probab=95.43  E-value=0.088  Score=49.10  Aligned_cols=75  Identities=19%  Similarity=0.295  Sum_probs=64.8

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-ccccCCCCCCCcEEEe
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-VIARGMDFKGVNCVIN  234 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-~~~~Gidip~~~~Vi~  234 (248)
                      ++++.|.++|-=-|++-++.+++    ..+++..++.-.+.++..++++..++|+++|+|+|. .+..++-+.+.-.+|.
T Consensus       643 GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlII  722 (1139)
T COG1197         643 GKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLII  722 (1139)
T ss_pred             CCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeEEE
Confidence            67899999998777777777765    467889999999999999999999999999999995 5788888888888774

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

Probab=95.33  E-value=0.15  Score=44.34  Aligned_cols=68  Identities=28%  Similarity=0.447  Sum_probs=54.5

Q ss_pred             EEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----cccC-CCCCCCcE
Q 042003          163 VLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----IARG-MDFKGVNC  231 (248)
Q Consensus       163 ~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~~~G-idip~~~~  231 (248)
                      +||.++|++-|.++++.++..     +..+..+.||++...+..   .++.| .+|+|+|+.     +.+| +|+..+++
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~---~l~~~-~~ivVaTPGRllD~i~~~~l~l~~v~~  177 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIE---ALKRG-VDIVVATPGRLLDLIKRGKLDLSGVET  177 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHH---HHhcC-CCEEEECccHHHHHHHcCCcchhhcCE
Confidence            999999999999999888653     467899999998776654   44446 899999973     4555 88888888


Q ss_pred             EEe
Q 042003          232 VIN  234 (248)
Q Consensus       232 Vi~  234 (248)
                      +|.
T Consensus       178 lVl  180 (513)
T COG0513         178 LVL  180 (513)
T ss_pred             EEe
Confidence            874

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=95.12  E-value=0.027  Score=49.81  Aligned_cols=41  Identities=34%  Similarity=0.366  Sum_probs=32.6

Q ss_pred             cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccc
Q 042003           35 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~   75 (248)
                      ...++|+|++...|...+..+.-.+...+.+||||||++.+
T Consensus       180 a~~AdivItNHalL~~~~~~~~~iLP~~~~lIiDEAH~L~d  220 (636)
T TIGR03117       180 ARRCRILFCTHAMLGLAFRDKWGLLPQPDILIVDEAHLFEQ  220 (636)
T ss_pred             cccCCEEEECHHHHHHHhhhhcCCCCCCCEEEEeCCcchHH
Confidence            35789999999988876655433456789999999999874

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.

>TIGR01054 rgy reverse gyrase

Probab=95.11  E-value=0.047  Score=52.04  Aligned_cols=60  Identities=17%  Similarity=0.279  Sum_probs=51.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCe---eEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIR---AGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~---v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      +.+++|.+||+.-+.++++.++..    +..   +..+||+++..+++...+.+.+|..+|+|+|+.
T Consensus       121 g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~  187 (1171)
T TIGR01054       121 GKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTM  187 (1171)
T ss_pred             CCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHH
Confidence            678999999999999999888754    332   346899999999999999999999999999974

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.

>cd00268 DEADc DEAD-box helicases

Probab=95.06  E-value=0.27  Score=36.91  Aligned_cols=71  Identities=17%  Similarity=0.206  Sum_probs=50.5

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----c-ccCCCCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----I-ARGMDFKG  228 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~-~~Gidip~  228 (248)
                      .+.+++|.+++...+.+.++.++..    +..+..++|+.+..+.....+    +...|+|+|..     + ..-.++++
T Consensus        68 ~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~iiv~T~~~l~~~l~~~~~~~~~  143 (203)
T cd00268          68 DGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK----RGPHIVVATPGRLLDLLERGKLDLSK  143 (203)
T ss_pred             CCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhc----CCCCEEEEChHHHHHHHHcCCCChhh
Confidence            3568999999999998887766543    678888999988765543332    56689999952     2 22256777


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      ++++|
T Consensus       144 l~~lI  148 (203)
T cd00268         144 VKYLV  148 (203)
T ss_pred             CCEEE
Confidence            77776

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.

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=94.98  E-value=0.017  Score=45.81  Aligned_cols=73  Identities=18%  Similarity=0.048  Sum_probs=43.5

Q ss_pred             CCcEEEeChHHHHHHHhcC-----Ccc-------cCceeEEEEeccccccccCcc-------cccchhHhhhCCCcccee
Q 042003           37 SCDILISTPLRLRLAIRRK-----KID-------LSRVEYLVLDEADKLFEVGNL-------LKHIDPVVKACSNPSIVR   97 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~~-----~~~-------~~~~~~lIiDEah~~~~~~~~-------~~~~~~~~~~~~~~~~~~   97 (248)
                      .-.|+++|...|...-..+     ++.       -+.=++||+||||..-+...-       ......+.+. . ++.++
T Consensus       136 ~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~-L-P~ARv  213 (303)
T PF13872_consen  136 KEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNR-L-PNARV  213 (303)
T ss_pred             CCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCccCccccHHHHHHHHHHHh-C-CCCcE
Confidence            4579999998887775421     110       012248999999998754310       0122222233 2 45678


Q ss_pred             EEEEeecCchHHHH
Q 042003           98 SLFSATLPDFVEEL  111 (248)
Q Consensus        98 i~~SAT~~~~~~~~  111 (248)
                      +.+|||-..+.+++
T Consensus       214 vY~SATgasep~Nm  227 (303)
T PF13872_consen  214 VYASATGASEPRNM  227 (303)
T ss_pred             EEecccccCCCcee
Confidence            99999976655444

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=94.59  E-value=0.17  Score=43.55  Aligned_cols=60  Identities=23%  Similarity=0.274  Sum_probs=55.1

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      ++.++|.+|+++-+++..+.|...++.+..++++.+..++..++.....|+.+++++|.-
T Consensus        51 ~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe  110 (470)
T TIGR00614        51 DGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPE  110 (470)
T ss_pred             CCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHH
Confidence            568999999999999999999999999999999999999999999999999999999963

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

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=94.41  E-value=0.29  Score=43.79  Aligned_cols=70  Identities=13%  Similarity=0.236  Sum_probs=51.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-----ccc-cCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-----VIA-RGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-----~~~-~Gidip~  228 (248)
                      ..++||.+++++-|.++++.+...     +..+..++|+.+...+...+   + +...|+|+|.     .+. ..+++.+
T Consensus        74 ~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l---~-~~~~IVVgTPgrl~d~l~r~~l~l~~  149 (629)
T PRK11634         74 APQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL---R-QGPQIVVGTPGRLLDHLKRGTLDLSK  149 (629)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHh---c-CCCCEEEECHHHHHHHHHcCCcchhh
Confidence            457999999999999998887642     67888999998876544433   2 3468999995     222 3467778


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      +.+||
T Consensus       150 l~~lV  154 (629)
T PRK11634        150 LSGLV  154 (629)
T ss_pred             ceEEE
Confidence            88776

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=94.28  E-value=0.12  Score=46.14  Aligned_cols=83  Identities=19%  Similarity=0.187  Sum_probs=68.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCC------------------eeEEEecCCCHHHHHHHHHHhhcCC---ceEEEEec
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGI------------------RAGVIHSDLSQTQRENAVDDFRAGK---TWVLIATD  218 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~------------------~v~~~~~~~~~~~r~~~~~~f~~g~---~~ilv~T~  218 (248)
                      +.++|||..+......+.+.|.+..+                  +-.-+.|..+..+|+..+++|.+..   .-++++|.
T Consensus       719 g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllstr  798 (1387)
T KOG1016|consen  719 GEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLSTR  798 (1387)
T ss_pred             CceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehhc
Confidence            55899999999888888888876422                  2346688889999999999998643   24789999


Q ss_pred             ccccCCCCCCCcEEEeccCCCCcc
Q 042003          219 VIARGMDFKGVNCVINYDFPDSGA  242 (248)
Q Consensus       219 ~~~~Gidip~~~~Vi~~~~p~~~~  242 (248)
                      +...|||+=.++-+|.|+..|++.
T Consensus       799 ag~lGinLIsanr~~ifda~wnpc  822 (1387)
T KOG1016|consen  799 AGSLGINLISANRCIIFDACWNPC  822 (1387)
T ss_pred             cccccceeeccceEEEEEeecCcc
Confidence            999999999999999999999875

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=94.20  E-value=0.026  Score=41.59  Aligned_cols=43  Identities=23%  Similarity=0.138  Sum_probs=28.0

Q ss_pred             ccCCCcEEEeChHHHHHHHhcCCcc--cCceeEEEEecccccccc
Q 042003           34 SKFSCDILISTPLRLRLAIRRKKID--LSRVEYLVLDEADKLFEV   76 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~~~~~--~~~~~~lIiDEah~~~~~   76 (248)
                      ....++|+|++..-+.+-...+...  ..+-.++||||||.+.+.
T Consensus       116 ~~~~adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  116 LAKNADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLEDA  160 (174)
T ss_dssp             CGGG-SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGGG
T ss_pred             hcccCCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHHH
Confidence            4456999999987776554332221  233468999999998764

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=94.18  E-value=0.32  Score=41.82  Aligned_cols=70  Identities=11%  Similarity=0.239  Sum_probs=53.0

Q ss_pred             CCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-----ccc-cCCCCCCC
Q 042003          161 PPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-----VIA-RGMDFKGV  229 (248)
Q Consensus       161 ~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-----~~~-~Gidip~~  229 (248)
                      .+++|.++|++-+.++++.++..     +..+..++|+.+...+.+.++    +..+|+|+|.     .+. ..+++.++
T Consensus        73 ~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~----~~~~IvV~Tp~rl~~~l~~~~~~l~~l  148 (460)
T PRK11776         73 VQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE----HGAHIIVGTPGRILDHLRKGTLDLDAL  148 (460)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc----CCCCEEEEChHHHHHHHHcCCccHHHC
Confidence            47999999999999999887642     578899999998866554443    4568999994     222 45778888


Q ss_pred             cEEEe
Q 042003          230 NCVIN  234 (248)
Q Consensus       230 ~~Vi~  234 (248)
                      +++|.
T Consensus       149 ~~lVi  153 (460)
T PRK11776        149 NTLVL  153 (460)
T ss_pred             CEEEE
Confidence            88873

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

Probab=94.00  E-value=0.37  Score=41.16  Aligned_cols=71  Identities=17%  Similarity=0.235  Sum_probs=58.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-------cccCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-------IARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-------~~~Gidip~  228 (248)
                      -.++||.|+|++-+-+++...+..    ++.+...-||++-..++.+++.    ..+|+|||+-       -+.++|+.+
T Consensus       252 ~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs----~PDIVIATPGRlIDHlrNs~sf~lds  327 (691)
T KOG0338|consen  252 ATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRS----RPDIVIATPGRLIDHLRNSPSFNLDS  327 (691)
T ss_pred             ceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhh----CCCEEEecchhHHHHhccCCCccccc
Confidence            458999999999888887666543    6889999999999998888875    6799999974       257888888


Q ss_pred             CcEEEe
Q 042003          229 VNCVIN  234 (248)
Q Consensus       229 ~~~Vi~  234 (248)
                      +.+.|+
T Consensus       328 iEVLvl  333 (691)
T KOG0338|consen  328 IEVLVL  333 (691)
T ss_pred             eeEEEe
Confidence            887764

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=93.76  E-value=0.31  Score=43.31  Aligned_cols=60  Identities=15%  Similarity=0.192  Sum_probs=54.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      ++.++|.+|++.-+++-.+.|+..++.+..+|++++..++..+.+....|..++++.|.-
T Consensus        53 ~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe  112 (591)
T TIGR01389        53 KGLTVVISPLISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPE  112 (591)
T ss_pred             CCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChh
Confidence            467899999999999888999999999999999999999999999999999999988853

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.

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=93.73  E-value=0.18  Score=43.36  Aligned_cols=53  Identities=19%  Similarity=0.304  Sum_probs=47.0

Q ss_pred             EEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          163 VLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       163 ~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      .+||++|++-|-++.+.|..    -++.+..+.|||...-++++++.    ...|+|||+-
T Consensus       266 ~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATPG  322 (731)
T KOG0347|consen  266 ALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATPG  322 (731)
T ss_pred             eEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc----CCCEEEecch
Confidence            89999999999999999965    48899999999999888888876    6789999973

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=93.57  E-value=0.36  Score=41.11  Aligned_cols=70  Identities=16%  Similarity=0.249  Sum_probs=52.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc------cccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV------IARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~------~~~Gidip~~  229 (248)
                      ..+++|.+++++-+.++++.++.    .+.++..++|+.+...+...+.    +..+|+|+|..      ....+++.++
T Consensus        73 ~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~----~~~~IlV~Tp~rl~~~~~~~~~~~~~v  148 (434)
T PRK11192         73 PPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFS----ENQDIVVATPGRLLQYIKEENFDCRAV  148 (434)
T ss_pred             CceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhc----CCCCEEEEChHHHHHHHHcCCcCcccC
Confidence            35799999999999988776654    4678999999998876655443    45689999962      2355677788


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      ++||
T Consensus       149 ~~lV  152 (434)
T PRK11192        149 ETLI  152 (434)
T ss_pred             CEEE
Confidence            8776

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=93.29  E-value=0.33  Score=42.93  Aligned_cols=69  Identities=16%  Similarity=0.265  Sum_probs=51.4

Q ss_pred             CCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-----cccc--CCCCCCC
Q 042003          161 PPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-----VIAR--GMDFKGV  229 (248)
Q Consensus       161 ~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-----~~~~--Gidip~~  229 (248)
                      .++||.+++++-+.++++.+...    ++.+..++|+.+...+...++    +..+|+|+|.     .+..  .+++..+
T Consensus        85 ~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~----~~~dIiV~TP~rL~~~l~~~~~~~l~~v  160 (572)
T PRK04537         85 PRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQ----QGVDVIIATPGRLIDYVKQHKVVSLHAC  160 (572)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHh----CCCCEEEECHHHHHHHHHhccccchhhe
Confidence            58999999999999998877653    678999999998776555443    3568999995     2222  3667777


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      +++|
T Consensus       161 ~~lV  164 (572)
T PRK04537        161 EICV  164 (572)
T ss_pred             eeeE
Confidence            7665

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=92.97  E-value=0.082  Score=42.38  Aligned_cols=40  Identities=20%  Similarity=0.185  Sum_probs=28.9

Q ss_pred             cCCCcEEEeChHHHHHHHhcCC--cccCceeEEEEeccccccc
Q 042003           35 KFSCDILISTPLRLRLAIRRKK--IDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~--~~~~~~~~lIiDEah~~~~   75 (248)
                      ...++|+|++..-|.+-..++.  ..+ .-.++||||||.+.+
T Consensus       209 ~~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00488      209 IEFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hhcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            3579999999988776553322  223 467999999999864

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=92.97  E-value=0.082  Score=42.38  Aligned_cols=40  Identities=20%  Similarity=0.185  Sum_probs=28.9

Q ss_pred             cCCCcEEEeChHHHHHHHhcCC--cccCceeEEEEeccccccc
Q 042003           35 KFSCDILISTPLRLRLAIRRKK--IDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~--~~~~~~~~lIiDEah~~~~   75 (248)
                      ...++|+|++..-|.+-..++.  ..+ .-.++||||||.+.+
T Consensus       209 ~~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00489      209 IEFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hhcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            3579999999988776553322  223 467999999999864

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=92.81  E-value=0.24  Score=42.10  Aligned_cols=72  Identities=15%  Similarity=0.197  Sum_probs=50.6

Q ss_pred             chHHHHHHHhhcCCCcEEEEcccchhhhccc-ccCCCcEEEeChHHHHHHHhcCCcc-------------cCc--eeEEE
Q 042003            3 TQTTRECKKLAKGNKFQIKLMKKELVRSTDL-SKFSCDILISTPLRLRLAIRRKKID-------------LSR--VEYLV   66 (248)
Q Consensus         3 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~i~v~Tp~~l~~~~~~~~~~-------------~~~--~~~lI   66 (248)
                      .|+.+.+.++..  |..++..++|.....+. .-.++|++.+|...+.+.++....-             +-+  +--+|
T Consensus       244 mQW~nEI~~~T~--gslkv~~YhG~~R~~nikel~~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiI  321 (791)
T KOG1002|consen  244 MQWKNEIERHTS--GSLKVYIYHGAKRDKNIKELMNYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRII  321 (791)
T ss_pred             HHHHHHHHHhcc--CceEEEEEecccccCCHHHhhcCcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeee
Confidence            588888888887  44788888887733333 2347999999999888888653211             222  34599


Q ss_pred             Eecccccccc
Q 042003           67 LDEADKLFEV   76 (248)
Q Consensus        67 iDEah~~~~~   76 (248)
                      +||||-+-+.
T Consensus       322 lDEAH~IK~R  331 (791)
T KOG1002|consen  322 LDEAHNIKDR  331 (791)
T ss_pred             hhhhcccccc
Confidence            9999998653

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=92.71  E-value=0.68  Score=39.33  Aligned_cols=71  Identities=15%  Similarity=0.259  Sum_probs=51.4

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----c-ccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----I-ARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~-~~Gidip~~  229 (248)
                      +.+++|.+++++-|.++++.+..    .+.++..++|+.+.......+   . +..+|+|+|..     + ...+++.++
T Consensus        83 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l---~-~~~~IlV~TP~~l~~~l~~~~~~l~~v  158 (423)
T PRK04837         83 QPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVL---E-SGVDILIGTTGRLIDYAKQNHINLGAI  158 (423)
T ss_pred             CceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh---c-CCCCEEEECHHHHHHHHHcCCcccccc
Confidence            35799999999999998776643    378899999998765544433   2 35689999972     1 245677788


Q ss_pred             cEEEe
Q 042003          230 NCVIN  234 (248)
Q Consensus       230 ~~Vi~  234 (248)
                      .++|.
T Consensus       159 ~~lVi  163 (423)
T PRK04837        159 QVVVL  163 (423)
T ss_pred             cEEEE
Confidence            87773

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=92.70  E-value=0.11  Score=48.08  Aligned_cols=42  Identities=21%  Similarity=0.210  Sum_probs=31.9

Q ss_pred             ccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccc
Q 042003           34 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~   75 (248)
                      ....++|+|+.-.-|.+.+......+...+++||||||++.+
T Consensus       413 ~a~~AdivItNHa~L~~~~~~~~~ilp~~~~lIiDEAH~L~d  454 (850)
T TIGR01407       413 NAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPD  454 (850)
T ss_pred             HHhcCCEEEecHHHHHHHhhcccccCCCCCEEEEECcchHHH
Confidence            345799999999888777654433345668999999999974

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.

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=92.66  E-value=0.65  Score=39.89  Aligned_cols=70  Identities=20%  Similarity=0.199  Sum_probs=51.9

Q ss_pred             CCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc------cccCCCCCCCc
Q 042003          161 PPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV------IARGMDFKGVN  230 (248)
Q Consensus       161 ~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~------~~~Gidip~~~  230 (248)
                      .++||.+++++-|.++++.++..    +..+..++|+.+.......+    .+..+|+|||.-      ....+++..++
T Consensus        76 ~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l----~~~~~IiV~TP~rL~~~~~~~~~~l~~v~  151 (456)
T PRK10590         76 VRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKL----RGGVDVLVATPGRLLDLEHQNAVKLDQVE  151 (456)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHH----cCCCcEEEEChHHHHHHHHcCCcccccce
Confidence            36999999999999998887653    56788889998876543322    356789999952      24556788888


Q ss_pred             EEEe
Q 042003          231 CVIN  234 (248)
Q Consensus       231 ~Vi~  234 (248)
                      ++|.
T Consensus       152 ~lVi  155 (456)
T PRK10590        152 ILVL  155 (456)
T ss_pred             EEEe
Confidence            7763

>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=92.45  E-value=0.14  Score=39.80  Aligned_cols=67  Identities=18%  Similarity=0.295  Sum_probs=52.1

Q ss_pred             HHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC----ceEEEEecccccCCCCCCCcEEEeccCCCCcccceec
Q 042003          175 ELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK----TWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHR  247 (248)
Q Consensus       175 ~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~----~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qr  247 (248)
                      .+.+.+.. ++.+.+++++.+...     -.+.++.    ..|+|+=+.+++|+.++++.+......|...++++||
T Consensus       102 ~l~~~~~~-~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~Qm  172 (239)
T PF10593_consen  102 ELPKAISD-GIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQM  172 (239)
T ss_pred             HHHHHHhc-CceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHH
Confidence            44444444 689999997765543     3333333    7899999999999999999999999999999999887

This domain is found associated with a helicase domain of superfamily type II [].

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=92.37  E-value=0.01  Score=52.71  Aligned_cols=83  Identities=17%  Similarity=0.116  Sum_probs=73.7

Q ss_pred             CEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCc-e-EEEEecccccCCCCCCCcEEEeccCCC
Q 042003          162 PVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKT-W-VLIATDVIARGMDFKGVNCVINYDFPD  239 (248)
Q Consensus       162 ~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~-~-ilv~T~~~~~Gidip~~~~Vi~~~~p~  239 (248)
                      +++||+.-..-+.-+.-.|...++....+.|.|+...|...+..|..+.. . .+++..+...|+|+..+++|+..|+-|
T Consensus       541 kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~w  620 (674)
T KOG1001|consen  541 KIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPWW  620 (674)
T ss_pred             ceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchhc
Confidence            99999999999999998898889999999999999999999999996543 3 457789999999999999999999999


Q ss_pred             Ccccc
Q 042003          240 SGAAY  244 (248)
Q Consensus       240 ~~~~~  244 (248)
                      |+..-
T Consensus       621 np~~e  625 (674)
T KOG1001|consen  621 NPAVE  625 (674)
T ss_pred             ChHHH
Confidence            98643

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=92.32  E-value=0.039  Score=53.20  Aligned_cols=85  Identities=22%  Similarity=0.280  Sum_probs=65.4

Q ss_pred             EEEEecchHHHHHHHHHhhcC-CCeeEEEecCCCH-----------HHHHHHHHHhhcCCceEEEEecccccCCCCCCCc
Q 042003          163 VLIFVQSKERAKELYGELAFD-GIRAGVIHSDLSQ-----------TQRENAVDDFRAGKTWVLIATDVIARGMDFKGVN  230 (248)
Q Consensus       163 ~liF~~~~~~~~~l~~~L~~~-~~~v~~~~~~~~~-----------~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~  230 (248)
                      .++|++.+..+....+.++.. ...+..+.|.+.+           ..+.+++..|.....++|++|.++.+|+|+|.++
T Consensus       295 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~~  374 (1606)
T KOG0701|consen  295 GIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKCN  374 (1606)
T ss_pred             heeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhhh
Confidence            677887777777777666543 1233335554321           2257789999999999999999999999999999


Q ss_pred             EEEeccCCCCcccceec
Q 042003          231 CVINYDFPDSGAAYIHR  247 (248)
Q Consensus       231 ~Vi~~~~p~~~~~~~qr  247 (248)
                      .++.++.|.....|+|+
T Consensus       375 ~~~~~~~~~~~~~~vq~  391 (1606)
T KOG0701|consen  375 LVVLFDAPTYYRSYVQK  391 (1606)
T ss_pred             hheeccCcchHHHHHHh
Confidence            99999999999888875

>PRK09401 reverse gyrase; Reviewed

Probab=92.05  E-value=0.59  Score=44.88  Aligned_cols=74  Identities=16%  Similarity=0.280  Sum_probs=54.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEE--ecCCCHHHHHHHHHHhhcCCceEEEEeccc-c---cCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVI--HSDLSQTQRENAVDDFRAGKTWVLIATDVI-A---RGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~--~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-~---~Gidip~~  229 (248)
                      +.+++|.+||+.-+.++++.++..    +..+..+  +++++..++.+..+.+.+|..+|+|+|.-. .   ..+....+
T Consensus       123 g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~~l~~~~~  202 (1176)
T PRK09401        123 GKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDELPKKKF  202 (1176)
T ss_pred             CCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHHhcccccc
Confidence            679999999999999999998765    3344444  455667788888899999999999999521 1   13444446


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      +++|
T Consensus       203 ~~lV  206 (1176)
T PRK09401        203 DFVF  206 (1176)
T ss_pred             CEEE
Confidence            6655

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

Probab=91.92  E-value=1.2  Score=36.92  Aligned_cols=83  Identities=17%  Similarity=0.242  Sum_probs=59.7

Q ss_pred             HHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc--
Q 042003          147 KLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI--  220 (248)
Q Consensus       147 ~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~--  220 (248)
                      .+..+..++.+...-.++|.+++++-|.++++.++..    |..+..+=||++.....  ...+  .+..|||||.-.  
T Consensus       116 aLPIl~~LL~~p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~--~~L~--kkPhilVaTPGrL~  191 (476)
T KOG0330|consen  116 ALPILQRLLQEPKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQA--NQLS--KKPHILVATPGRLW  191 (476)
T ss_pred             HHHHHHHHHcCCCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHH--HHhh--cCCCEEEeCcHHHH
Confidence            4455666666554567999999999999999888765    66888999998865432  3332  356789999742  


Q ss_pred             -----ccCCCCCCCcEEE
Q 042003          221 -----ARGMDFKGVNCVI  233 (248)
Q Consensus       221 -----~~Gidip~~~~Vi  233 (248)
                           ..|+++..+++.|
T Consensus       192 dhl~~Tkgf~le~lk~LV  209 (476)
T KOG0330|consen  192 DHLENTKGFSLEQLKFLV  209 (476)
T ss_pred             HHHHhccCccHHHhHHHh
Confidence                 4677777766654

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=91.47  E-value=0.96  Score=40.43  Aligned_cols=59  Identities=17%  Similarity=0.234  Sum_probs=53.9

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD  218 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~  218 (248)
                      .+.++|.++++.-+.+..+.|+..++.+..++++.+.+++..+.+...+|+.+++++|+
T Consensus        65 ~g~tlVisPl~sL~~dqv~~l~~~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tP  123 (607)
T PRK11057         65 DGLTLVVSPLISLMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAP  123 (607)
T ss_pred             CCCEEEEecHHHHHHHHHHHHHHcCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEECh
Confidence            46899999999999999999999999999999999999999999999999999998884

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=91.01  E-value=1.4  Score=38.08  Aligned_cols=70  Identities=16%  Similarity=0.182  Sum_probs=51.4

Q ss_pred             CCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccCCCCCCCc
Q 042003          161 PPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARGMDFKGVN  230 (248)
Q Consensus       161 ~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip~~~  230 (248)
                      .++||.+++++-+.++++.++..    +..+..++|+.+.....   +.+..+..+|+|+|.-.      ...+.+..++
T Consensus       163 ~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~---~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~  239 (475)
T PRK01297        163 PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQL---KQLEARFCDILVATPGRLLDFNQRGEVHLDMVE  239 (475)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHH---HHHhCCCCCEEEECHHHHHHHHHcCCcccccCc
Confidence            57999999999999988877643    67888999987765433   34556778999999632      2345666777


Q ss_pred             EEE
Q 042003          231 CVI  233 (248)
Q Consensus       231 ~Vi  233 (248)
                      +||
T Consensus       240 ~lV  242 (475)
T PRK01297        240 VMV  242 (475)
T ss_pred             eEE
Confidence            766

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=91.00  E-value=0.26  Score=46.23  Aligned_cols=41  Identities=22%  Similarity=0.244  Sum_probs=32.0

Q ss_pred             cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccc
Q 042003           35 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~   75 (248)
                      ...++|+|+.-.-|...+..+...+...+++||||||++.+
T Consensus       429 a~~AdivItNHalLl~dl~~~~~ilp~~~~lViDEAH~l~d  469 (928)
T PRK08074        429 AKFADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHFEE  469 (928)
T ss_pred             HhcCCEEEECHHHHHHHHhhhcccCCCCCeEEEECCchHHH
Confidence            35789999999888777644433456789999999999874

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=90.82  E-value=1.9  Score=38.99  Aligned_cols=75  Identities=17%  Similarity=0.105  Sum_probs=54.6

Q ss_pred             hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcC--CceEEEEecccc
Q 042003          146 GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAG--KTWVLIATDVIA  221 (248)
Q Consensus       146 ~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g--~~~ilv~T~~~~  221 (248)
                      +.+..+..+.+...+++-+|.|++ .+.+.+-..+++-  ..+|..+||+  +.+|+++...+.++  ..+||++|--+.
T Consensus       434 QvIaFlayLkq~g~~gpHLVVvPs-STleNWlrEf~kwCPsl~Ve~YyGS--q~ER~~lR~~i~~~~~~ydVllTTY~la  510 (941)
T KOG0389|consen  434 QVIAFLAYLKQIGNPGPHLVVVPS-STLENWLREFAKWCPSLKVEPYYGS--QDERRELRERIKKNKDDYDVLLTTYNLA  510 (941)
T ss_pred             HHHHHHHHHHHcCCCCCcEEEecc-hhHHHHHHHHHHhCCceEEEeccCc--HHHHHHHHHHHhccCCCccEEEEEeecc
Confidence            344555555666667899999998 4455555555554  4578899997  68999999999887  678999996655


Q ss_pred             cC
Q 042003          222 RG  223 (248)
Q Consensus       222 ~G  223 (248)
                      .|
T Consensus       511 ~~  512 (941)
T KOG0389|consen  511 AS  512 (941)
T ss_pred             cC
Confidence            43

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

Probab=90.70  E-value=1.3  Score=42.08  Aligned_cols=60  Identities=12%  Similarity=0.095  Sum_probs=52.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhc--CCceEEEEecc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRA--GKTWVLIATDV  219 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~--g~~~ilv~T~~  219 (248)
                      ++.+||.+++++-++.-...|...++++..+.|+++..++.++++.+..  |+.++|++|.-
T Consensus       500 ~GiTLVISPLiSLmqDQV~~L~~~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPE  561 (1195)
T PLN03137        500 PGITLVISPLVSLIQDQIMNLLQANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPE  561 (1195)
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChH
Confidence            4679999999999986666677789999999999999999999998877  88999999973

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=90.49  E-value=1.5  Score=39.83  Aligned_cols=59  Identities=17%  Similarity=0.114  Sum_probs=47.5

Q ss_pred             HhccCCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          155 FAESLNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       155 ~~~~~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      +....+.++.|.++|..-|.+.++.+..    .|.+++.+.|+++.++|...+.      .+|+++|+.
T Consensus        92 l~aL~G~~V~VvTpt~~LA~qdae~~~~l~~~LGLsv~~i~g~~~~~~r~~~y~------~dIvyGT~~  154 (745)
T TIGR00963        92 LNALTGKGVHVVTVNDYLAQRDAEWMGQVYRFLGLSVGLILSGMSPEERREAYA------CDITYGTNN  154 (745)
T ss_pred             HHHHhCCCEEEEcCCHHHHHHHHHHHHHHhccCCCeEEEEeCCCCHHHHHHhcC------CCEEEECCC
Confidence            4444577899999999888888776654    5889999999999888776653      689999987

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.

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=90.28  E-value=0.32  Score=44.91  Aligned_cols=40  Identities=30%  Similarity=0.418  Sum_probs=31.1

Q ss_pred             cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccc
Q 042003           35 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~   75 (248)
                      ...++|+|+.-.-|.+.+..+. .+...+.+||||||++.+
T Consensus       411 a~~AdivItNHall~~~~~~~~-~~p~~~~lIiDEAH~l~~  450 (820)
T PRK07246        411 AKTARLLITNHAYFLTRVQDDK-DFARNKVLVFDEAQKLML  450 (820)
T ss_pred             HHhCCEEEEchHHHHHHHhhcc-CCCCCCEEEEECcchhHH
Confidence            3468999999887777664443 257789999999999874

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=90.21  E-value=0.32  Score=44.12  Aligned_cols=42  Identities=19%  Similarity=0.173  Sum_probs=30.1

Q ss_pred             cCCCcEEEeChHHHHHHHhc-CCcccC--ceeEEEEecccccccc
Q 042003           35 KFSCDILISTPLRLRLAIRR-KKIDLS--RVEYLVLDEADKLFEV   76 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~-~~~~~~--~~~~lIiDEah~~~~~   76 (248)
                      ...++|+|+.-.-|...+.. +...+.  ..+++||||||++.+.
T Consensus       217 a~~AdivVtNH~LLladl~~~~~~iLp~~~~~~lViDEAH~L~d~  261 (697)
T PRK11747        217 IDEADVVVANHDLVLADLELGGGVVLPDPENLLYVLDEGHHLPDV  261 (697)
T ss_pred             HhhCCEEEECcHHHHhhhhccCCcccCCCCCCEEEEECccchHHH
Confidence            35789999998877766643 222233  4778999999999753

>PRK08727 hypothetical protein; Validated

Probab=90.14  E-value=0.23  Score=38.51  Aligned_cols=71  Identities=10%  Similarity=-0.033  Sum_probs=38.4

Q ss_pred             CCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCc
Q 042003           36 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                      .+..+++.+.+.+...+......+.+.+++|+||+|.+..+......+..+.........++|+.|...|.
T Consensus        68 ~~~~~~y~~~~~~~~~~~~~~~~l~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~  138 (233)
T PRK08727         68 AGRSSAYLPLQAAAGRLRDALEALEGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPD  138 (233)
T ss_pred             cCCcEEEEeHHHhhhhHHHHHHHHhcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChh
Confidence            45677777765554433322223567789999999988754322233334443322233445555544443

>PTZ00110 helicase; Provisional

Probab=90.10  E-value=1.2  Score=39.25  Aligned_cols=69  Identities=20%  Similarity=0.290  Sum_probs=49.3

Q ss_pred             CCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-----ccccC-CCCCCCc
Q 042003          161 PPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-----VIARG-MDFKGVN  230 (248)
Q Consensus       161 ~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-----~~~~G-idip~~~  230 (248)
                      ..+||.++|++-|.++++.+++.    +..+..++|+.+.......   +.+ ..+|+|+|.     .+..+ .++..++
T Consensus       204 p~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~---l~~-~~~IlVaTPgrL~d~l~~~~~~l~~v~  279 (545)
T PTZ00110        204 PIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYA---LRR-GVEILIACPGRLIDFLESNVTNLRRVT  279 (545)
T ss_pred             cEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHH---HHc-CCCEEEECHHHHHHHHHcCCCChhhCc
Confidence            46899999999999998888764    4577788888876554333   333 368999996     33333 5677788


Q ss_pred             EEE
Q 042003          231 CVI  233 (248)
Q Consensus       231 ~Vi  233 (248)
                      ++|
T Consensus       280 ~lV  282 (545)
T PTZ00110        280 YLV  282 (545)
T ss_pred             EEE
Confidence            776

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=90.05  E-value=0.48  Score=30.45  Aligned_cols=36  Identities=8%  Similarity=0.173  Sum_probs=31.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      ++++++||++-..+...+..|+..|+.+..+.||+.
T Consensus        51 ~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~   86 (90)
T cd01524          51 DKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYK   86 (90)
T ss_pred             CCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHH
Confidence            578999999877888889999999988999999874

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

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

Probab=90.00  E-value=2  Score=36.92  Aligned_cols=69  Identities=17%  Similarity=0.257  Sum_probs=51.2

Q ss_pred             CEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc--c----ccCCCCCCCcE
Q 042003          162 PVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV--I----ARGMDFKGVNC  231 (248)
Q Consensus       162 ~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~--~----~~Gidip~~~~  231 (248)
                      -.+|.|+|++-|.+++..-++    .|+.+..+|||++..++..-++   . ...|+|||.-  +    -.+.|+..+++
T Consensus       298 i~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk---~-g~EivVaTPgRlid~VkmKatn~~rvS~  373 (731)
T KOG0339|consen  298 IGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK---E-GAEIVVATPGRLIDMVKMKATNLSRVSY  373 (731)
T ss_pred             eEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh---c-CCeEEEechHHHHHHHHhhcccceeeeE
Confidence            466788999999887655443    4788889999999877665555   3 4579999972  2    36888888887


Q ss_pred             EEe
Q 042003          232 VIN  234 (248)
Q Consensus       232 Vi~  234 (248)
                      .++
T Consensus       374 LV~  376 (731)
T KOG0339|consen  374 LVL  376 (731)
T ss_pred             EEE
Confidence            764

>PRK06893 DNA replication initiation factor; Validated

Probab=89.68  E-value=0.24  Score=38.25  Aligned_cols=70  Identities=10%  Similarity=0.006  Sum_probs=37.9

Q ss_pred             CCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCc
Q 042003           37 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                      +..+.+.+..........-...+.+.+++++||+|.+.....+...+..+.........+++++|++.++
T Consensus        67 ~~~~~y~~~~~~~~~~~~~~~~~~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p  136 (229)
T PRK06893         67 QRTAIYIPLSKSQYFSPAVLENLEQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSP  136 (229)
T ss_pred             CCCeEEeeHHHhhhhhHHHHhhcccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCCh
Confidence            4566666654322221111113467889999999987643323334444444433334456677777655

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=89.43  E-value=3  Score=29.97  Aligned_cols=71  Identities=15%  Similarity=0.283  Sum_probs=50.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHH-HHHHHHHHhhcCCceEEEEeccc------ccCCCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQT-QRENAVDDFRAGKTWVLIATDVI------ARGMDFK  227 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~-~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip  227 (248)
                      ...++++.++++..+++.++.+...    +..+..++++.+.. +....+    .++.+|+|+|...      ...+++.
T Consensus        43 ~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilv~T~~~l~~~~~~~~~~~~  118 (169)
T PF00270_consen   43 KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVL----SNQADILVTTPEQLLDLISNGKINIS  118 (169)
T ss_dssp             SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHH----HTTSSEEEEEHHHHHHHHHTTSSTGT
T ss_pred             CCceEEEEeecccccccccccccccccccccccccccccccccccccccc----cccccccccCcchhhccccccccccc
Confidence            3459999999999999888888654    45788889988854 333333    6678899999631      2234666


Q ss_pred             CCcEEE
Q 042003          228 GVNCVI  233 (248)
Q Consensus       228 ~~~~Vi  233 (248)
                      .+++||
T Consensus       119 ~~~~iV  124 (169)
T PF00270_consen  119 RLSLIV  124 (169)
T ss_dssp             TESEEE
T ss_pred             cceeec
Confidence            777666

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 ....

>PF13871 Helicase_C_4: Helicase_C-like

Probab=88.99  E-value=0.34  Score=38.39  Aligned_cols=47  Identities=21%  Similarity=0.290  Sum_probs=39.8

Q ss_pred             HHHHHhhcCCceEEEEecccccCCCCCCC--------cEEEeccCCCCcccceec
Q 042003          201 NAVDDFRAGKTWVLIATDVIARGMDFKGV--------NCVINYDFPDSGAAYIHR  247 (248)
Q Consensus       201 ~~~~~f~~g~~~ilv~T~~~~~Gidip~~--------~~Vi~~~~p~~~~~~~qr  247 (248)
                      ...+.|.+|+.+|+|.|++.+.|+.+.+-        ++-|.+.+|||.+..+|.
T Consensus        52 ~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~  106 (278)
T PF13871_consen   52 AEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQ  106 (278)
T ss_pred             HHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHH
Confidence            45678999999999999999999988742        466889999999988874

>PRK08084 DNA replication initiation factor; Provisional

Probab=88.63  E-value=0.39  Score=37.24  Aligned_cols=69  Identities=6%  Similarity=-0.049  Sum_probs=35.5

Q ss_pred             CCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCc-cceeEEEEeecCc
Q 042003           37 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNP-SIVRSLFSATLPD  106 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~SAT~~~  106 (248)
                      +..+.+.+.+........-.-.+.+.+++++||+|.+.........+..++...... ..++ ++|++.++
T Consensus        73 ~~~v~y~~~~~~~~~~~~~~~~~~~~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~l-i~ts~~~p  142 (235)
T PRK08084         73 GRAVGYVPLDKRAWFVPEVLEGMEQLSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRL-LITGDRPP  142 (235)
T ss_pred             CCeEEEEEHHHHhhhhHHHHHHhhhCCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeE-EEeCCCCh
Confidence            556777666543322211111234568999999999864432334444444443222 2344 44555544

>PRK05642 DNA replication initiation factor; Validated

Probab=88.49  E-value=0.29  Score=37.96  Aligned_cols=70  Identities=11%  Similarity=-0.004  Sum_probs=41.9

Q ss_pred             CCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCc
Q 042003           36 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                      .+..+++.+.+.+......-.-.+.+.+++++|++|.+.....+...+..+...+.....+ ++++++.++
T Consensus        72 ~~~~v~y~~~~~~~~~~~~~~~~~~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~-ilits~~~p  141 (234)
T PRK05642         72 RGEPAVYLPLAELLDRGPELLDNLEQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRR-LLLAASKSP  141 (234)
T ss_pred             CCCcEEEeeHHHHHhhhHHHHHhhhhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCE-EEEeCCCCH
Confidence            3578888888777654321111356678999999998764432444566666554334444 555565444

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

Probab=88.47  E-value=3.8  Score=35.59  Aligned_cols=71  Identities=17%  Similarity=0.223  Sum_probs=52.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----cc-cCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----IA-RGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~~-~Gidip~~  229 (248)
                      +..+||.++|++-|.++.+...+.    +.+...+.|+.+...+..-++   + ..+|+|+|.-     ++ --+|+..+
T Consensus       165 ~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~---~-gvdiviaTPGRl~d~le~g~~~l~~v  240 (519)
T KOG0331|consen  165 GPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLE---R-GVDVVIATPGRLIDLLEEGSLNLSRV  240 (519)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHh---c-CCcEEEeCChHHHHHHHcCCccccce
Confidence            446999999999999999888765    345788899988765544443   3 4689999973     33 34677788


Q ss_pred             cEEEe
Q 042003          230 NCVIN  234 (248)
Q Consensus       230 ~~Vi~  234 (248)
                      ++++.
T Consensus       241 ~ylVL  245 (519)
T KOG0331|consen  241 TYLVL  245 (519)
T ss_pred             eEEEe
Confidence            88873

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=88.45  E-value=0.82  Score=41.10  Aligned_cols=69  Identities=20%  Similarity=0.122  Sum_probs=42.2

Q ss_pred             chHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            3 TQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         3 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      .|+...+.+..+... ..+...+| .....-....++|+++||+.+..    ..+.--.+-.+|+||||.+.+..
T Consensus       202 ~qW~~elek~~~~~~-l~v~v~~g-r~kd~~el~~~dVVltTy~il~~----~~l~~i~w~Riildea~~ikn~~  270 (674)
T KOG1001|consen  202 TQWKTELEKVTEEDK-LSIYVYHG-RTKDKSELNSYDVVLTTYDILKN----SPLVKIKWLRIVLDEAHTIKNKD  270 (674)
T ss_pred             HHHHHHHhccCCccc-eEEEEecc-cccccchhcCCceEEeeHHHhhc----ccccceeEEEEEeccccccCCcc
Confidence            356666644444444 66666666 22222233357899999987764    22222344479999999987754

>smart00450 RHOD Rhodanese Homology Domain

Probab=88.45  E-value=1.1  Score=28.82  Aligned_cols=38  Identities=16%  Similarity=0.251  Sum_probs=32.6

Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCe-eEEEecCCC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIR-AGVIHSDLS  195 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~-v~~~~~~~~  195 (248)
                      ....++++||.+-..+..++..|+..|+. +..+.||+.
T Consensus        54 ~~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~   92 (100)
T smart00450       54 DKDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYK   92 (100)
T ss_pred             CCCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHH
Confidence            33678999999988999999999999886 889999864

An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=88.35  E-value=0.12  Score=39.71  Aligned_cols=73  Identities=11%  Similarity=0.054  Sum_probs=47.4

Q ss_pred             CCCcEEEeChHHHHHHHhc----CCc-----ccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCc
Q 042003           36 FSCDILISTPLRLRLAIRR----KKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~----~~~-----~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                      .+..|+..+.+.+.+.+..    +..     .+.+.+++++|++|.+.+.......+-.+...+.....++|+.|...|.
T Consensus        63 ~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~  142 (219)
T PF00308_consen   63 PGKRVVYLSAEEFIREFADALRDGEIEEFKDRLRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPS  142 (219)
T ss_dssp             TTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TT
T ss_pred             ccccceeecHHHHHHHHHHHHHcccchhhhhhhhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCc
Confidence            4678999998877655432    221     3678999999999998765434455555555544456677777767665


Q ss_pred             hH
Q 042003          107 FV  108 (248)
Q Consensus       107 ~~  108 (248)
                      ..
T Consensus       143 ~l  144 (219)
T PF00308_consen  143 EL  144 (219)
T ss_dssp             TT
T ss_pred             cc
Confidence            44

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

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

Probab=88.31  E-value=1.6  Score=38.41  Aligned_cols=59  Identities=22%  Similarity=0.348  Sum_probs=53.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD  218 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~  218 (248)
                      ++-+||..+-..-.+.=.+.|+..|+.+..+++.++.+++..++..+..|..++|.-++
T Consensus        57 ~G~TLVVSPLiSLM~DQV~~l~~~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisP  115 (590)
T COG0514          57 EGLTLVVSPLISLMKDQVDQLEAAGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISP  115 (590)
T ss_pred             CCCEEEECchHHHHHHHHHHHHHcCceeehhhcccCHHHHHHHHHHHhcCceeEEEECc
Confidence            56899999999998888889999999999999999999999999999999999885543

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=87.69  E-value=4.2  Score=35.90  Aligned_cols=77  Identities=14%  Similarity=0.188  Sum_probs=49.2

Q ss_pred             hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCC
Q 042003          146 GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMD  225 (248)
Q Consensus       146 ~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gid  225 (248)
                      ++...+..-+++...+.+.|.|.+..+|.++.+.|+..+          ++......-+.|..|+.   |--.....|+.
T Consensus       641 qr~~~ii~~mkk~~~etiaVi~kt~~d~~~~~d~lre~~----------~~r~I~k~nq~f~~~~~---vipvy~aKGlE  707 (747)
T COG3973         641 QRNPDIIPRMKKRGSETIAVICKTDHDCKAVMDSLREKD----------SQRTIAKENQRFHHGSD---VIPVYDAKGLE  707 (747)
T ss_pred             HhhHHHHHHHHhcCCCceEEECCcHHHHHHHHHHHhhcc----------hhhHHHhhcccccCCce---EEEeeecccce
Confidence            445555556666656788999999999999999998553          11111222233444442   22234567877


Q ss_pred             CCCCcEEEeccCC
Q 042003          226 FKGVNCVINYDFP  238 (248)
Q Consensus       226 ip~~~~Vi~~~~p  238 (248)
                         .++||.+|+.
T Consensus       708 ---FD~viv~d~s  717 (747)
T COG3973         708 ---FDHVIVVDPS  717 (747)
T ss_pred             ---eeeEEEecch
Confidence               5789998885

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=87.59  E-value=0.27  Score=43.74  Aligned_cols=91  Identities=11%  Similarity=0.053  Sum_probs=50.4

Q ss_pred             HHHHhhcCCCcEEEEcccchhhhccccc------------CCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccc
Q 042003            8 ECKKLAKGNKFQIKLMKKELVRSTDLSK------------FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~   75 (248)
                      +.+.+.+.++-.++.-+-|+...+.++.            .+.+|+|+|.+.+..--..  +.--++.++|+|||+.+-+
T Consensus       632 WaqEisrFlP~~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky--~qkvKWQYMILDEAQAIKS  709 (1185)
T KOG0388|consen  632 WAQEISRFLPSFKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKY--LQKVKWQYMILDEAQAIKS  709 (1185)
T ss_pred             HHHHHHHhCccceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechHHH--HHhhhhhheehhHHHHhhh
Confidence            3334444444344666666664443332            2579999998766432211  1123567999999999765


Q ss_pred             cCcccccchhHhhhCCCccceeEEEEeecC
Q 042003           76 VGNLLKHIDPVVKACSNPSIVRSLFSATLP  105 (248)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~  105 (248)
                      ..  ..-++.++..   ...-.+++|+|+-
T Consensus       710 Ss--S~RWKtLLsF---~cRNRLLLTGTPI  734 (1185)
T KOG0388|consen  710 SS--SSRWKTLLSF---KCRNRLLLTGTPI  734 (1185)
T ss_pred             hh--hhHHHHHhhh---hccceeeecCCcc
Confidence            43  2223333332   1223578999974

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=87.27  E-value=0.69  Score=39.54  Aligned_cols=75  Identities=9%  Similarity=0.061  Sum_probs=42.3

Q ss_pred             CCCcEEEeChHHHHHHHhc----CCc-----ccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCc
Q 042003           36 FSCDILISTPLRLRLAIRR----KKI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~----~~~-----~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                      .+..++..+.+.+.+.+..    +..     ..++.+++++||+|.+.........+..++..+.....++++.|.+.|.
T Consensus       168 ~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~  247 (445)
T PRK12422        168 SGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQ  247 (445)
T ss_pred             cCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHH
Confidence            4688999998776544322    111     2567899999999998654322333333433222233455555545454


Q ss_pred             hHHH
Q 042003          107 FVEE  110 (248)
Q Consensus       107 ~~~~  110 (248)
                      ....
T Consensus       248 ~l~~  251 (445)
T PRK12422        248 DLKA  251 (445)
T ss_pred             HHhh
Confidence            4433

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=87.27  E-value=0.76  Score=30.13  Aligned_cols=36  Identities=11%  Similarity=0.139  Sum_probs=31.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      +++++++|.+-..+...+..|+..|+.+..+.||+.
T Consensus        61 ~~~ivv~C~~G~rs~~aa~~L~~~G~~~~~l~GG~~   96 (100)
T cd01523          61 DQEVTVICAKEGSSQFVAELLAERGYDVDYLAGGMK   96 (100)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHcCceeEEeCCcHH
Confidence            578999999888889999999999999888888874

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=86.98  E-value=0.6  Score=42.10  Aligned_cols=41  Identities=20%  Similarity=0.307  Sum_probs=31.8

Q ss_pred             CCCcEEEeChHHHHHHHhcCCcc--cCceeEEEEecccccccc
Q 042003           36 FSCDILISTPLRLRLAIRRKKID--LSRVEYLVLDEADKLFEV   76 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~~~~--~~~~~~lIiDEah~~~~~   76 (248)
                      ..++++|+++..+......+...  +..-..+|+||||++.++
T Consensus       193 ~~ad~vv~nh~~~~~~~~~~~~~~~~p~~~v~v~DEAH~l~d~  235 (654)
T COG1199         193 ENADLVVTNHALLLADVALEESRILLPENDVVVFDEAHNLPDI  235 (654)
T ss_pred             hhCCEEEEccHHHHhHHHhhhhhccCCcccEEEEeccccchHH
Confidence            46899999999887766554332  346779999999999864

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

Probab=86.86  E-value=3.7  Score=35.27  Aligned_cols=79  Identities=16%  Similarity=0.107  Sum_probs=56.3

Q ss_pred             HHHhccCCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec------cccc
Q 042003          153 QSFAESLNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD------VIAR  222 (248)
Q Consensus       153 ~~~~~~~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~------~~~~  222 (248)
                      ..+... ++++|+.+||+=-+.+-++.+++    ..-.+..+.|..++++|+....     +.+|+|+|+      ..+-
T Consensus        52 ~~l~~~-~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~~w~-----~~kVfvaTPQvveNDl~~G  125 (542)
T COG1111          52 NRLRWF-GGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELWA-----KKKVFVATPQVVENDLKAG  125 (542)
T ss_pred             HHHHhc-CCeEEEecCCchHHHHHHHHHHHHhCCChhheeeecCCCChHHHHHHHh-----hCCEEEeccHHHHhHHhcC
Confidence            344454 44899999997655555555543    3447889999999999988776     367999995      3344


Q ss_pred             CCCCCCCcEEEeccC
Q 042003          223 GMDFKGVNCVINYDF  237 (248)
Q Consensus       223 Gidip~~~~Vi~~~~  237 (248)
                      -+|+.++.++|.=..
T Consensus       126 rid~~dv~~lifDEA  140 (542)
T COG1111         126 RIDLDDVSLLIFDEA  140 (542)
T ss_pred             ccChHHceEEEechh
Confidence            589989998886443

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=86.74  E-value=1.3  Score=28.67  Aligned_cols=37  Identities=14%  Similarity=-0.002  Sum_probs=31.2

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCC-eeEEEecCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGI-RAGVIHSDLS  195 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~-~v~~~~~~~~  195 (248)
                      .++++++||++-..+...+..|+..|+ ++..+.|++.
T Consensus        55 ~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~GG~~   92 (96)
T cd01529          55 RATRYVLTCDGSLLARFAAQELLALGGKPVALLDGGTS   92 (96)
T ss_pred             CCCCEEEEeCChHHHHHHHHHHHHcCCCCEEEeCCCHH
Confidence            367899999998888888889988888 6888899874

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=86.52  E-value=0.94  Score=33.92  Aligned_cols=55  Identities=15%  Similarity=0.239  Sum_probs=30.1

Q ss_pred             ceeEEEEeccccccccCccc----ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhc
Q 042003           61 RVEYLVLDEADKLFEVGNLL----KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM  116 (248)
Q Consensus        61 ~~~~lIiDEah~~~~~~~~~----~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~  116 (248)
                      .=.++|+||||.........    ...-..+.........++++|=.+.. +...++.+.
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~~~-id~~ir~lv  137 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSPSQ-IDKFIRDLV  137 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-GGG-B-HHHHCCE
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCHHH-HhHHHHHHH
Confidence            44699999999987654332    12224555556667788888777654 555555443

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=86.26  E-value=4.4  Score=36.42  Aligned_cols=71  Identities=17%  Similarity=0.118  Sum_probs=52.9

Q ss_pred             hccCCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcE
Q 042003          156 AESLNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC  231 (248)
Q Consensus       156 ~~~~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~  231 (248)
                      ....+..++|.++|..-|.+.++.+..    .|.++..+.|+++.++|+...      ..+|+++|+. +.|+|.=.-++
T Consensus       140 ~al~G~~v~VvTptreLA~qdae~~~~l~~~lGlsv~~i~gg~~~~~r~~~y------~~dIvygT~~-e~~FDyLrd~~  212 (656)
T PRK12898        140 AALAGLPVHVITVNDYLAERDAELMRPLYEALGLTVGCVVEDQSPDERRAAY------GADITYCTNK-ELVFDYLRDRL  212 (656)
T ss_pred             HhhcCCeEEEEcCcHHHHHHHHHHHHHHHhhcCCEEEEEeCCCCHHHHHHHc------CCCEEEECCC-chhhhhccccc
Confidence            334467999999999999888777754    588999999999987666543      3589999975 46777655554


Q ss_pred             EE
Q 042003          232 VI  233 (248)
Q Consensus       232 Vi  233 (248)
                      +.
T Consensus       213 ~~  214 (656)
T PRK12898        213 AL  214 (656)
T ss_pred             cc
Confidence            43

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

Probab=85.75  E-value=3.4  Score=37.98  Aligned_cols=69  Identities=16%  Similarity=0.266  Sum_probs=50.1

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC---CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-ccccCC---------CC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD---GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-VIARGM---------DF  226 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~---~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-~~~~Gi---------di  226 (248)
                      +.++|+.+++++-+.+.++.+++.   ++++..++|+.+.++|..+.    + +.+|+|+|. .+..++         .+
T Consensus        81 ~~~aL~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~~i~----~-~~~IivtTPd~L~~~~L~~~~~~~~~l  155 (742)
T TIGR03817        81 RATALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERRWAR----E-HARYVLTNPDMLHRGILPSHARWARFL  155 (742)
T ss_pred             CcEEEEEcChHHHHHHHHHHHHHhccCCeEEEEEeCCCCHHHHHHHh----c-CCCEEEEChHHHHHhhccchhHHHHHH
Confidence            468999999999999999888765   57888999999987764332    2 368999995 332221         14


Q ss_pred             CCCcEEE
Q 042003          227 KGVNCVI  233 (248)
Q Consensus       227 p~~~~Vi  233 (248)
                      .++++||
T Consensus       156 ~~l~~vV  162 (742)
T TIGR03817       156 RRLRYVV  162 (742)
T ss_pred             hcCCEEE
Confidence            5677776

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.

>KOG3089 consensus Predicted DEAD-box-containing helicase [General function prediction only]

Probab=85.65  E-value=1.2  Score=33.77  Aligned_cols=33  Identities=24%  Similarity=0.478  Sum_probs=30.4

Q ss_pred             CCCcEEEeChHHHHHHHhcCCcccCceeEEEEe
Q 042003           36 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLD   68 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiD   68 (248)
                      +..++-||||+++..+...+.+..+.+.++|+|
T Consensus       195 ~~v~~gIgTp~Ri~~lv~~~~f~~~~lk~iIlD  227 (271)
T KOG3089|consen  195 RVVHLGIGTPGRIKELVKQGGFNLSPLKFIILD  227 (271)
T ss_pred             cceeEeecCcHHHHHHHHhcCCCCCcceeEEee
Confidence            457899999999999999998999999999998

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=85.57  E-value=0.88  Score=37.63  Aligned_cols=38  Identities=13%  Similarity=0.192  Sum_probs=24.0

Q ss_pred             cEEEeChHHHHHHHhcCCcccCceeEEEEecccccccc
Q 042003           39 DILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus        39 ~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      ...+..|..+...+.........++++||||||.+...
T Consensus        61 ~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~   98 (352)
T PF09848_consen   61 KSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTK   98 (352)
T ss_pred             hhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhc
Confidence            34444554444433322334578899999999999873

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK13766 Hef nuclease; Provisional

Probab=85.54  E-value=5.7  Score=36.72  Aligned_cols=73  Identities=21%  Similarity=0.188  Sum_probs=52.6

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcC-C---CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc------cccCCCCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFD-G---IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV------IARGMDFKG  228 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~-~---~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~------~~~Gidip~  228 (248)
                      .++++|+.++++..+.+.++.+++. +   .++..++|+.+..+|.+...     +.+|+|+|.-      +..-+++.+
T Consensus        57 ~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~r~~~~~-----~~~iiv~T~~~l~~~l~~~~~~~~~  131 (773)
T PRK13766         57 KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWE-----KAKVIVATPQVIENDLIAGRISLED  131 (773)
T ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEEeCCCCHHHHHHHHh-----CCCEEEECHHHHHHHHHcCCCChhh
Confidence            3689999999999888887777653 3   37888999999888765553     2468999963      233456667


Q ss_pred             CcEEEecc
Q 042003          229 VNCVINYD  236 (248)
Q Consensus       229 ~~~Vi~~~  236 (248)
                      +++||.=.
T Consensus       132 ~~liVvDE  139 (773)
T PRK13766        132 VSLLIFDE  139 (773)
T ss_pred             CcEEEEEC
Confidence            77777433

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=85.35  E-value=0.34  Score=37.02  Aligned_cols=40  Identities=15%  Similarity=0.194  Sum_probs=22.6

Q ss_pred             ccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccc
Q 042003           34 SKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~   75 (248)
                      ....++|+++|+....+......  ...++++|||||=.+..
T Consensus       167 ~l~~~~vi~~T~~~~~~~~~~~~--~~~~d~vIvDEAsq~~e  206 (236)
T PF13086_consen  167 ILKEADVIFTTLSSAASPFLSNF--KEKFDVVIVDEASQITE  206 (236)
T ss_dssp             HHHT-SEEEEETCGGG-CCGTT-------SEEEETTGGGS-H
T ss_pred             hcccccccccccccchhhHhhhh--cccCCEEEEeCCCCcch
Confidence            34478999999876622222111  12789999999987644

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=85.33  E-value=4.8  Score=37.44  Aligned_cols=58  Identities=22%  Similarity=0.176  Sum_probs=46.6

Q ss_pred             hccCCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          156 AESLNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       156 ~~~~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      ....+..+.|.++|..-|.+.++.+..    .|.++..+.|+++..+|...+      ..+|+++|+.
T Consensus       119 ~al~G~~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~~i~gg~~~~~r~~~y------~~dIvygT~g  180 (896)
T PRK13104        119 NAISGRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGVIYPDMSHKEKQEAY------KADIVYGTNN  180 (896)
T ss_pred             HHhcCCCEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCHHHHHHHh------CCCEEEECCh
Confidence            333467899999999988888877754    488999999999998887665      3689999975

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

Probab=85.24  E-value=3.2  Score=35.66  Aligned_cols=73  Identities=16%  Similarity=0.223  Sum_probs=52.2

Q ss_pred             CEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHH-HHHHHHHhhcCCceEEEEecc-------cccCCCCCCC
Q 042003          162 PVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQ-RENAVDDFRAGKTWVLIATDV-------IARGMDFKGV  229 (248)
Q Consensus       162 ~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~-r~~~~~~f~~g~~~ilv~T~~-------~~~Gidip~~  229 (248)
                      +++|.++++.-+-+++..+...    |..|..+.|.-+-++ ..+....-...+++|||+|+.       ...|+|+.+.
T Consensus       217 RavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~L  296 (620)
T KOG0350|consen  217 RAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHL  296 (620)
T ss_pred             EEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhc
Confidence            7999999999999999999765    445555555544332 233334444567799999974       2689999998


Q ss_pred             cEEEe
Q 042003          230 NCVIN  234 (248)
Q Consensus       230 ~~Vi~  234 (248)
                      ++.|.
T Consensus       297 rfLVI  301 (620)
T KOG0350|consen  297 RFLVI  301 (620)
T ss_pred             eEEEe
Confidence            87764

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=85.11  E-value=9.1  Score=25.91  Aligned_cols=57  Identities=25%  Similarity=0.264  Sum_probs=41.4

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCC---CeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDG---IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~---~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      ..+++++++++...+++..+.+....   ..+..+++........    ....+...++++|..
T Consensus        29 ~~~~~lv~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~i~i~t~~   88 (144)
T cd00046          29 KGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQE----KLLSGKTDIVVGTPG   88 (144)
T ss_pred             cCCCEEEEcCcHHHHHHHHHHHHHHhhCCcEEEEEecCcchhHHH----HHhcCCCCEEEECcH
Confidence            46899999999999988887776543   6788888876555444    222345678888865

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=84.80  E-value=0.64  Score=39.85  Aligned_cols=70  Identities=9%  Similarity=0.002  Sum_probs=41.6

Q ss_pred             CCCcEEEeChHHHHHHHhcC------Cc-----ccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeec
Q 042003           36 FSCDILISTPLRLRLAIRRK------KI-----DLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL  104 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~------~~-----~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~  104 (248)
                      .+..++..|++.+.+.+...      .+     ...+.+++|+||+|.+.........+..++..+.....|+|+.|-..
T Consensus       170 ~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~  249 (450)
T PRK14087        170 SDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKS  249 (450)
T ss_pred             CCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCC
Confidence            45788889988776655321      11     24678999999999886432233444445444333344655554444


Q ss_pred             C
Q 042003          105 P  105 (248)
Q Consensus       105 ~  105 (248)
                      |
T Consensus       250 P  250 (450)
T PRK14087        250 P  250 (450)
T ss_pred             H
Confidence            4

>PF13173 AAA_14: AAA domain

Probab=84.73  E-value=0.96  Score=31.26  Aligned_cols=39  Identities=21%  Similarity=0.255  Sum_probs=25.7

Q ss_pred             ceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeec
Q 042003           61 RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATL  104 (248)
Q Consensus        61 ~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~  104 (248)
                      .-.++++||+|.+.+   +...++.+....  ++.++++++...
T Consensus        61 ~~~~i~iDEiq~~~~---~~~~lk~l~d~~--~~~~ii~tgS~~   99 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPD---WEDALKFLVDNG--PNIKIILTGSSS   99 (128)
T ss_pred             CCcEEEEehhhhhcc---HHHHHHHHHHhc--cCceEEEEccch
Confidence            456899999999865   446666666642  456655555443

>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily

Probab=84.33  E-value=1.7  Score=28.52  Aligned_cols=37  Identities=14%  Similarity=0.181  Sum_probs=30.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCe-eEEEecCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIR-AGVIHSDLS  195 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~-v~~~~~~~~  195 (248)
                      .++++++||.+-..+...+..|...|+. +..+.||+.
T Consensus        60 ~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~   97 (101)
T cd01518          60 KGKKVLMYCTGGIRCEKASAYLKERGFKNVYQLKGGIL   97 (101)
T ss_pred             CCCEEEEECCCchhHHHHHHHHHHhCCcceeeechhHH
Confidence            3678999999877778888899888984 888888864

This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.

>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3

Probab=83.88  E-value=1.4  Score=28.57  Aligned_cols=36  Identities=19%  Similarity=0.125  Sum_probs=30.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      +.++++||.+-..+...+..|...|+.+..+.||+.
T Consensus        56 ~~~iv~~c~~G~rs~~aa~~L~~~G~~v~~l~GG~~   91 (95)
T cd01534          56 GARIVLADDDGVRADMTASWLAQMGWEVYVLEGGLA   91 (95)
T ss_pred             CCeEEEECCCCChHHHHHHHHHHcCCEEEEecCcHH
Confidence            568999999877778888899989999888888864

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=83.82  E-value=5.6  Score=39.35  Aligned_cols=71  Identities=21%  Similarity=0.321  Sum_probs=53.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----------------CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc----
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----------------DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV----  219 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----------------~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~----  219 (248)
                      +.++|+.++++.-+.++++.|+.                .++.+...||+++..+|...++    +..+|||+|.-    
T Consensus        37 ~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V~vrtGDt~~~eR~rll~----~ppdILVTTPEsL~~  112 (1490)
T PRK09751         37 TSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRVGIRTGDTPAQERSKLTR----NPPDILITTPESLYL  112 (1490)
T ss_pred             CCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEEEEEECCCCHHHHHHHhc----CCCCEEEecHHHHHH
Confidence            35799999999999888887752                3678999999999998876543    35689999963    


Q ss_pred             -cc-cC-CCCCCCcEEEe
Q 042003          220 -IA-RG-MDFKGVNCVIN  234 (248)
Q Consensus       220 -~~-~G-idip~~~~Vi~  234 (248)
                       +. .+ -.+.++++||.
T Consensus       113 LLtsk~r~~L~~Vr~VIV  130 (1490)
T PRK09751        113 MLTSRARETLRGVETVII  130 (1490)
T ss_pred             HHhhhhhhhhccCCEEEE
Confidence             12 22 35778888873

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=83.70  E-value=0.63  Score=42.36  Aligned_cols=39  Identities=23%  Similarity=0.202  Sum_probs=26.9

Q ss_pred             CCCcEEEeChHHHHHHHhcCC--cccCceeEEEEeccccccc
Q 042003           36 FSCDILISTPLRLRLAIRRKK--IDLSRVEYLVLDEADKLFE   75 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~~--~~~~~~~~lIiDEah~~~~   75 (248)
                      ..++|||+..+-+.+--.++.  ..+++ .++||||||.+.+
T Consensus       194 ~~advIi~pYnyl~dp~~r~~~~~~l~~-~ivI~DEAHNL~d  234 (705)
T TIGR00604       194 PFANIVLLPYQYLLDPKIRSAVSIELKD-SIVIFDEAHNLDN  234 (705)
T ss_pred             hcCCEEEechHHhcCHHHHHHhhccccc-CEEEEECccchHH
Confidence            468999999876654333322  22333 6899999999875

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).

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=83.69  E-value=7.5  Score=36.24  Aligned_cols=72  Identities=14%  Similarity=0.119  Sum_probs=53.9

Q ss_pred             HHHHHHHHhccCCCCEEEEecchHH----HHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccC
Q 042003          148 LLALRQSFAESLNPPVLIFVQSKER----AKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG  223 (248)
Q Consensus       148 ~~~l~~~~~~~~~~~~liF~~~~~~----~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G  223 (248)
                      ...+..++....+..+-|.+++.--    ++.+...++..|.+|+.+.+++++++|+.++.      .+|+.+|+.. .|
T Consensus       111 vA~l~a~l~al~G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~i~~~~~~~err~~Y~------~dI~YGT~~e-~g  183 (913)
T PRK13103        111 VGTLAVYLNALSGKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIVTPFQPPEEKRAAYA------ADITYGTNNE-FG  183 (913)
T ss_pred             HHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHhcccCCEEEEECCCCCHHHHHHHhc------CCEEEEcccc-cc
Confidence            4455555666668889999988654    44555555667999999999999999998887      7899999765 44


Q ss_pred             CCC
Q 042003          224 MDF  226 (248)
Q Consensus       224 idi  226 (248)
                      +|.
T Consensus       184 FDY  186 (913)
T PRK13103        184 FDY  186 (913)
T ss_pred             cch
Confidence            443

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=83.64  E-value=1.7  Score=29.81  Aligned_cols=36  Identities=28%  Similarity=0.387  Sum_probs=20.9

Q ss_pred             eEEEEeccccccccCcccccchhHhhhCCCccceeEEEEee
Q 042003           63 EYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSAT  103 (248)
Q Consensus        63 ~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  103 (248)
                      .++|+||+|.+.+    ...+..+.........+ +.++++
T Consensus        89 ~~lviDe~~~l~~----~~~l~~l~~l~~~~~~~-vvl~G~  124 (131)
T PF13401_consen   89 VLLVIDEADHLFS----DEFLEFLRSLLNESNIK-VVLVGT  124 (131)
T ss_dssp             EEEEEETTHHHHT----HHHHHHHHHHTCSCBEE-EEEEES
T ss_pred             eEEEEeChHhcCC----HHHHHHHHHHHhCCCCe-EEEEEC
Confidence            6999999999741    23344444433344555 445555

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

Probab=83.60  E-value=2.6  Score=32.93  Aligned_cols=69  Identities=17%  Similarity=0.277  Sum_probs=52.0

Q ss_pred             CEEEEecchHHHHHHHHHhhc---C--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc------cccCCCCCCCc
Q 042003          162 PVLIFVQSKERAKELYGELAF---D--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV------IARGMDFKGVN  230 (248)
Q Consensus       162 ~~liF~~~~~~~~~l~~~L~~---~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~------~~~Gidip~~~  230 (248)
                      .++|.|.+++-|-++.+....   .  +.++.++.||++-+.-++.+..    -..|+|+|+.      =+..+++..+.
T Consensus       112 svlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~----~PhivVgTPGrilALvr~k~l~lk~vk  187 (387)
T KOG0329|consen  112 SVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN----CPHIVVGTPGRILALVRNRSLNLKNVK  187 (387)
T ss_pred             EEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhC----CCeEEEcCcHHHHHHHHhccCchhhcc
Confidence            688999999999888665543   2  6789999999997766666554    5679999973      25677887777


Q ss_pred             EEEe
Q 042003          231 CVIN  234 (248)
Q Consensus       231 ~Vi~  234 (248)
                      +-+.
T Consensus       188 hFvl  191 (387)
T KOG0329|consen  188 HFVL  191 (387)
T ss_pred             eeeh
Confidence            7653

>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]

Probab=83.50  E-value=12  Score=29.26  Aligned_cols=50  Identities=10%  Similarity=0.118  Sum_probs=42.5

Q ss_pred             cceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCC
Q 042003          133 SIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDG  184 (248)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~  184 (248)
                      .++..++-+.+..+.+..+.+.++.  ++.+++|+++.+++++..+.|++.|
T Consensus       163 ~vDav~LDmp~PW~~le~~~~~Lkp--gg~~~~y~P~veQv~kt~~~l~~~g  212 (256)
T COG2519         163 DVDAVFLDLPDPWNVLEHVSDALKP--GGVVVVYSPTVEQVEKTVEALRERG  212 (256)
T ss_pred             ccCEEEEcCCChHHHHHHHHHHhCC--CcEEEEEcCCHHHHHHHHHHHHhcC
Confidence            5667777788888888888888877  5899999999999999999999874

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=83.32  E-value=3.1  Score=36.29  Aligned_cols=69  Identities=16%  Similarity=0.162  Sum_probs=50.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----c--ccCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----I--ARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~--~~Gidip~  228 (248)
                      +=-+||..+|++-|-+.++.|++-    +++++.+-||..-+.     +.-+-.+++|||||+-     +  ..+++.++
T Consensus       141 GlGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~-----E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~  215 (758)
T KOG0343|consen  141 GLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKF-----ELERISQMNILVCTPGRLLQHMDENPNFSTSN  215 (758)
T ss_pred             CceeEEecchHHHHHHHHHHHHHHhhccccccceeecCchhHH-----HHHhhhcCCeEEechHHHHHHhhhcCCCCCCc
Confidence            347999999999999999999864    568899999866433     2233456899999973     1  34555556


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      +.+.|
T Consensus       216 lQmLv  220 (758)
T KOG0343|consen  216 LQMLV  220 (758)
T ss_pred             ceEEE
Confidence            65554

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=83.21  E-value=2.1  Score=36.59  Aligned_cols=75  Identities=12%  Similarity=0.168  Sum_probs=39.7

Q ss_pred             CCcEEEeChHHHHHHHhc----CCc-----cc-CceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCc
Q 042003           37 SCDILISTPLRLRLAIRR----KKI-----DL-SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~----~~~-----~~-~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                      +..+++.|.+.+.+.+..    +..     .. .+.+++++||+|.+.+.......+..++..+.....++++.|...|.
T Consensus       160 ~~~v~yi~~~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~  239 (440)
T PRK14088        160 DLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQ  239 (440)
T ss_pred             CCeEEEEEHHHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHH
Confidence            467888888876554422    211     01 25889999999987653212223333333322334455554444444


Q ss_pred             hHHHH
Q 042003          107 FVEEL  111 (248)
Q Consensus       107 ~~~~~  111 (248)
                      ....+
T Consensus       240 ~l~~l  244 (440)
T PRK14088        240 KLSEF  244 (440)
T ss_pred             HHHHH
Confidence            33333

>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins

Probab=82.00  E-value=15  Score=26.86  Aligned_cols=69  Identities=16%  Similarity=0.174  Sum_probs=47.4

Q ss_pred             HHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeE-EEecCCCHHHHHHHHHHhhcCCceEEEE
Q 042003          147 KLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAG-VIHSDLSQTQRENAVDDFRAGKTWVLIA  216 (248)
Q Consensus       147 ~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~-~~~~~~~~~~r~~~~~~f~~g~~~ilv~  216 (248)
                      -...+.+..+.. +.++.++-.+.+.++.+++.|++.  +..+. .+||.+..++..++++..+....++++.
T Consensus        34 l~~~ll~~~~~~-~~~v~llG~~~~~~~~~~~~l~~~yp~l~i~g~~~g~~~~~~~~~i~~~I~~~~pdiv~v  105 (171)
T cd06533          34 LMPALLELAAQK-GLRVFLLGAKPEVLEKAAERLRARYPGLKIVGYHHGYFGPEEEEEIIERINASGADILFV  105 (171)
T ss_pred             HHHHHHHHHHHc-CCeEEEECCCHHHHHHHHHHHHHHCCCcEEEEecCCCCChhhHHHHHHHHHHcCCCEEEE
Confidence            444455544443 467777778888888888888765  44443 4678888777777888888877776644

E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.

>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily

Probab=81.93  E-value=2.4  Score=27.59  Aligned_cols=36  Identities=19%  Similarity=0.184  Sum_probs=30.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCC-eeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGI-RAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~-~v~~~~~~~~  195 (248)
                      .++++++|++-..+...+..|.+.|+ .+..+.|++.
T Consensus        54 ~~~iv~~c~~g~~s~~~~~~L~~~g~~~v~~l~gG~~   90 (99)
T cd01527          54 ANAIIFHCRSGMRTQQNAERLAAISAGEAYVLEGGLD   90 (99)
T ss_pred             CCcEEEEeCCCchHHHHHHHHHHcCCccEEEeeCCHH
Confidence            57899999998888888999988777 6888899863

This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.

>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain

Probab=81.88  E-value=3.9  Score=27.55  Aligned_cols=36  Identities=22%  Similarity=0.280  Sum_probs=30.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCC-eeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGI-RAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~-~v~~~~~~~~  195 (248)
                      ++++++||++-..+..++..|+..|+ ++..+.|++.
T Consensus        78 ~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~l~GG~~  114 (118)
T cd01449          78 DKPVIVYCGSGVTACVLLLALELLGYKNVRLYDGSWS  114 (118)
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHcCCCCeeeeCChHH
Confidence            67899999998888889999999998 5788888763

TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.

>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family

Probab=81.65  E-value=19  Score=26.64  Aligned_cols=54  Identities=11%  Similarity=0.191  Sum_probs=35.7

Q ss_pred             CCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEE
Q 042003          161 PPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVL  214 (248)
Q Consensus       161 ~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~il  214 (248)
                      .++.++-.+.+.++++++.|++.  +..+.-.||.+++++.+++.+..++...+++
T Consensus        49 ~~vfllG~~~~v~~~~~~~l~~~yP~l~i~g~~g~f~~~~~~~i~~~I~~s~~dil  104 (177)
T TIGR00696        49 LPIFLYGGKPDVLQQLKVKLIKEYPKLKIVGAFGPLEPEERKAALAKIARSGAGIV  104 (177)
T ss_pred             CeEEEECCCHHHHHHHHHHHHHHCCCCEEEEECCCCChHHHHHHHHHHHHcCCCEE
Confidence            45556666667777777777664  4454444777777776777777776666655

The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.

>PRK05728 DNA polymerase III subunit chi; Validated

Probab=81.54  E-value=13  Score=26.39  Aligned_cols=90  Identities=20%  Similarity=0.067  Sum_probs=54.3

Q ss_pred             CchhHHHHHHHHHhccC--CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc
Q 042003          143 SEEGKLLALRQSFAESL--NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI  220 (248)
Q Consensus       143 ~~~~~~~~l~~~~~~~~--~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~  220 (248)
                      ....+...+..++++..  +.+++|.|++.+.++.+=+.|=...-...+=|+.....         ......|+++... 
T Consensus        10 ~~~~~~~~~c~L~~ka~~~g~rv~I~~~d~~~a~~lD~~LW~~~~~sFlPH~~~~~~---------~~~~~PV~l~~~~-   79 (142)
T PRK05728         10 TLSALEALLCELAEKALRAGWRVLVQCEDEEQAEALDEALWTFRDESFLPHGLAGEG---------PAAGQPVLLTWPG-   79 (142)
T ss_pred             CchhHHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHHHHhcCCCCCcCCCCCcCCCC---------CCCCCCEEEEcCC-
Confidence            44456666666666543  78999999999999999888855443444445532211         0123468887311 


Q ss_pred             ccCCCCCCCcEEEeccC--CCCcccc
Q 042003          221 ARGMDFKGVNCVINYDF--PDSGAAY  244 (248)
Q Consensus       221 ~~Gidip~~~~Vi~~~~--p~~~~~~  244 (248)
                        .-+.+..+++||.+.  |...+.|
T Consensus        80 --~~~~~~~~~LinL~~~~p~~~~~F  103 (142)
T PRK05728         80 --KRNANHRDLLINLDGAVPAFAAAF  103 (142)
T ss_pred             --CCCCCCCcEEEECCCCCcchhhcc
Confidence              124455778888765  3344444

>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli

Probab=81.27  E-value=17  Score=26.65  Aligned_cols=69  Identities=13%  Similarity=0.176  Sum_probs=43.4

Q ss_pred             HHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeE-EEecCCCHHHHHHHHHHhhcCCceEEEE
Q 042003          147 KLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAG-VIHSDLSQTQRENAVDDFRAGKTWVLIA  216 (248)
Q Consensus       147 ~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~-~~~~~~~~~~r~~~~~~f~~g~~~ilv~  216 (248)
                      -...+....+.. +.++.++-.+.+.++.+++.|++.  +..+. ..||.++.++..++++..+....++++.
T Consensus        36 l~~~l~~~~~~~-~~~ifllG~~~~~~~~~~~~l~~~yP~l~ivg~~~g~f~~~~~~~i~~~I~~~~pdiv~v  107 (172)
T PF03808_consen   36 LFPDLLRRAEQR-GKRIFLLGGSEEVLEKAAANLRRRYPGLRIVGYHHGYFDEEEEEAIINRINASGPDIVFV  107 (172)
T ss_pred             HHHHHHHHHHHc-CCeEEEEeCCHHHHHHHHHHHHHHCCCeEEEEecCCCCChhhHHHHHHHHHHcCCCEEEE
Confidence            334444444443 456666667777777788888765  44433 4556677777777887777777666543

Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process

>cd01521 RHOD_PspE2 Member of the Rhodanese Homology Domain superfamily

Probab=81.14  E-value=2.4  Score=28.37  Aligned_cols=36  Identities=14%  Similarity=0.126  Sum_probs=30.0

Q ss_pred             CCCEEEEecch--HHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          160 NPPVLIFVQSK--ERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~--~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      +.++++||++-  ..+..++..|+..|+.+..+.|++.
T Consensus        64 ~~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l~GG~~  101 (110)
T cd01521          64 EKLFVVYCDGPGCNGATKAALKLAELGFPVKEMIGGLD  101 (110)
T ss_pred             CCeEEEEECCCCCchHHHHHHHHHHcCCeEEEecCCHH
Confidence            57899999875  3678888899999998889999864

This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins.

>cd01533 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2

Probab=81.00  E-value=3.7  Score=27.33  Aligned_cols=36  Identities=11%  Similarity=0.202  Sum_probs=30.1

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCe--eEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIR--AGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~--v~~~~~~~~  195 (248)
                      +.++++||.+-..+...+..|+..|+.  +..+.||++
T Consensus        66 ~~~ivv~C~~G~rs~~a~~~L~~~G~~~~v~~l~gG~~  103 (109)
T cd01533          66 RTPIVVNCAGRTRSIIGAQSLINAGLPNPVAALRNGTQ  103 (109)
T ss_pred             CCeEEEECCCCchHHHHHHHHHHCCCCcceeEecCCHH
Confidence            568999998877777788999999984  888999974

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue.

>cd01526 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily

Probab=80.95  E-value=1.6  Score=29.88  Aligned_cols=36  Identities=14%  Similarity=0.207  Sum_probs=31.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCC--eeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGI--RAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~--~v~~~~~~~~  195 (248)
                      ++++++||.+-..+...+..|+..|+  ++..+.||+.
T Consensus        72 ~~~ivv~C~~G~rs~~aa~~L~~~G~~~~v~~l~GG~~  109 (122)
T cd01526          72 DSPIYVVCRRGNDSQTAVRKLKELGLERFVRDIIGGLK  109 (122)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHcCCccceeeecchHH
Confidence            67899999988888889999999999  6899999974

This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.72  E-value=13  Score=33.00  Aligned_cols=80  Identities=23%  Similarity=0.206  Sum_probs=46.3

Q ss_pred             cCCCcEEEeChHHHHHHHhcCCc------ccCcee-EEEEeccccccccC--------cccccchhH--hhhCCCcccee
Q 042003           35 KFSCDILISTPLRLRLAIRRKKI------DLSRVE-YLVLDEADKLFEVG--------NLLKHIDPV--VKACSNPSIVR   97 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~~------~~~~~~-~lIiDEah~~~~~~--------~~~~~~~~~--~~~~~~~~~~~   97 (248)
                      ..+..|.++|.+.|...+.+...      ++.+.. +++-||||++-...        +....+...  +.....+.--+
T Consensus        79 nd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nkd~~~  158 (812)
T COG3421          79 NDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNKDNLL  158 (812)
T ss_pred             CCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCCCcee
Confidence            34678999999999888866432      244444 46679999987432        111112221  12212334456


Q ss_pred             EEEEeecCchHHHHHHHh
Q 042003           98 SLFSATLPDFVEELARSI  115 (248)
Q Consensus        98 i~~SAT~~~~~~~~~~~~  115 (248)
                      +.+|||.|. .......|
T Consensus       159 lef~at~~k-~k~v~~ky  175 (812)
T COG3421         159 LEFSATIPK-EKSVEDKY  175 (812)
T ss_pred             ehhhhcCCc-cccHHHHh
Confidence            679999983 44444444

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=80.70  E-value=3.7  Score=30.81  Aligned_cols=40  Identities=15%  Similarity=0.283  Sum_probs=23.6

Q ss_pred             cCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEee
Q 042003           59 LSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSAT  103 (248)
Q Consensus        59 ~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT  103 (248)
                      +.+.+++|||||-++..     ..+..++........++|++.-.
T Consensus        91 ~~~~~vliVDEasmv~~-----~~~~~ll~~~~~~~~klilvGD~  130 (196)
T PF13604_consen   91 LPKKDVLIVDEASMVDS-----RQLARLLRLAKKSGAKLILVGDP  130 (196)
T ss_dssp             -TSTSEEEESSGGG-BH-----HHHHHHHHHS-T-T-EEEEEE-T
T ss_pred             CCcccEEEEecccccCH-----HHHHHHHHHHHhcCCEEEEECCc
Confidence            45568999999998754     34666666655556666666554

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=80.57  E-value=6.8  Score=36.12  Aligned_cols=58  Identities=17%  Similarity=0.237  Sum_probs=45.0

Q ss_pred             HhccCCCCEEEEecchHHHHHHHHHhh----cCCCeeEEEecCCC-HHHHHHHHHHhhcCCceEEEEec
Q 042003          155 FAESLNPPVLIFVQSKERAKELYGELA----FDGIRAGVIHSDLS-QTQRENAVDDFRAGKTWVLIATD  218 (248)
Q Consensus       155 ~~~~~~~~~liF~~~~~~~~~l~~~L~----~~~~~v~~~~~~~~-~~~r~~~~~~f~~g~~~ilv~T~  218 (248)
                      +....+..+.|.++|..-|.+-++.+.    ..|++++.+.|+++ .++|+...      ..+|+++|+
T Consensus       114 l~al~G~~v~VvTpt~~LA~qd~e~~~~l~~~lGl~v~~i~g~~~~~~~r~~~y------~~dIvygT~  176 (790)
T PRK09200        114 LNALEGKGVHLITVNDYLAKRDAEEMGQVYEFLGLTVGLNFSDIDDASEKKAIY------EADIIYTTN  176 (790)
T ss_pred             HHHHcCCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCcHHHHHHhc------CCCEEEECC
Confidence            344457899999999888877766654    46899999999999 77777543      268999995

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

Probab=80.02  E-value=8  Score=33.95  Aligned_cols=70  Identities=9%  Similarity=0.233  Sum_probs=47.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-----cc-ccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-----VI-ARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-----~~-~~Gidip~~  229 (248)
                      +.+++|.+++++-|.++++.++..    +..+..+.|+.+..+..   ..+.. ..+|+|+|.     .+ ..++++.++
T Consensus       196 ~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~---~~l~~-~~~IiV~TPgrL~~~l~~~~~~l~~v  271 (518)
T PLN00206        196 NPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQL---YRIQQ-GVELIVGTPGRLIDLLSKHDIELDNV  271 (518)
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHH---HHhcC-CCCEEEECHHHHHHHHHcCCccchhe
Confidence            457999999999998887776543    45666777776654432   22333 368999994     22 346777778


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      +++|
T Consensus       272 ~~lV  275 (518)
T PLN00206        272 SVLV  275 (518)
T ss_pred             eEEE
Confidence            7776

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	248
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		8e-28
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		9e-25
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-23
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-23
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-23
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-23
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-23
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-23
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-23
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-23
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-23
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		5e-23
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		7e-23
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-21
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		3e-21
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		1e-20
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		1e-18
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		6e-18
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		2e-17
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		3e-17
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		4e-17
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		5e-17
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		5e-17
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		5e-17
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		8e-17
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		8e-17
2jgn_A	185	Ddx3 Helicase Domain Length = 185		2e-16
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		6e-16
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		1e-15
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		2e-15
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		2e-15
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		6e-15
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		6e-15
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		7e-15
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		6e-13
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		8e-13
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		2e-12
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		2e-12
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		4e-12
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		4e-12
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		1e-09
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		2e-09
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		5e-08
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		1e-07
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		1e-07
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		1e-07
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		6e-06
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		2e-04
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		2e-04
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		9e-04
3p4x_A	413	Helicase Domain Of Reverse Gyrase From Thermotoga M		9e-04
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		9e-04

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  120 bits (301), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 76/219 (34%), Positives = 114/219 (52%), Gaps = 3/219 (1%)
Query: 32  DLSKFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACS 91
           DL +  C +L++TP                 +YLVLDEAD++ ++G   +    V +   
Sbjct: 147 DLER-GCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTM 205
Query: 92  NPSIVRS--LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLL 149
            P  VR   +FSAT P  ++ LAR  + + + + VGR  + SE+I QK+V+    + +  
Sbjct: 206 PPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSF 265
Query: 150 ALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAG 209
            L    A   +   L+FV++K+ A  L   L  +G     IH D SQ  RE A+  FR+G
Sbjct: 266 LLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSG 325
Query: 210 KTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           K+ +L+AT V ARG+D   V  VIN+D P     Y+HRI
Sbjct: 326 KSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRI 364

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score =  110 bits (274), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 108/217 (49%), Gaps = 18/217 (8%)
Query: 37  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 96
           + +I++ TP                V+Y +LDEAD+    G  +K ++ ++ AC+    +
Sbjct: 123 NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXG-FIKDVEKILNACNKDKRI 181
Query: 97  RSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEG-----KLLAL 151
             LFSAT P  +  LA+    D   +    K   + +I+Q  V     E      +LL  
Sbjct: 182 -LLFSATXPREILNLAKKYXGDYSFI----KAKINANIEQSYVEVNENERFEALCRLLKN 236
Query: 152 RQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKT 211
           ++ +        L+F ++K   KEL   L   G +AG IH DLSQ+QRE  +  F+  K 
Sbjct: 237 KEFYG-------LVFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI 289
Query: 212 WVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            +LIATDV +RG+D   +NCVINY  P +  +Y HRI
Sbjct: 290 RILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRI 326

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 64/193 (33%), Positives = 98/193 (50%), Gaps = 14/193 (7%)
Query: 62  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 115
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  V E+    
Sbjct: 144 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEVLEMTNKF 195
Query: 116 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKE 175
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 196 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 255
Query: 176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY 235
           L  ++         +H D+ Q +RE+ + +FR+G + VLI+TDV ARG+D   V+ +INY
Sbjct: 256 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 315
Query: 236 DFPDSGAAYIHRI 248
           D P++   YIHRI
Sbjct: 316 DLPNNRELYIHRI 328

>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 =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 63/193 (32%), Positives = 98/193 (50%), Gaps = 14/193 (7%)
Query: 62  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 115
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 181 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 232
Query: 116 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKE 175
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 233 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 292
Query: 176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY 235
           L  ++         +H D+ Q +RE+ + +FR+G + VLI+TDV ARG+D   V+ +INY
Sbjct: 293 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 352
Query: 236 DFPDSGAAYIHRI 248
           D P++   YIHRI
Sbjct: 353 DLPNNRELYIHRI 365

>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 =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 63/193 (32%), Positives = 98/193 (50%), Gaps = 14/193 (7%)
Query: 62  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 115
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 181 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 232
Query: 116 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKE 175
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 233 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 292
Query: 176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY 235
           L  ++         +H D+ Q +RE+ + +FR+G + VLI+TDV ARG+D   V+ +INY
Sbjct: 293 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 352
Query: 236 DFPDSGAAYIHRI 248
           D P++   YIHRI
Sbjct: 353 DLPNNRELYIHRI 365

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 63/193 (32%), Positives = 98/193 (50%), Gaps = 14/193 (7%)
Query: 62  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 115
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 180 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 231
Query: 116 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKE 175
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 232 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 291
Query: 176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY 235
           L  ++         +H D+ Q +RE+ + +FR+G + VLI+TDV ARG+D   V+ +INY
Sbjct: 292 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 351
Query: 236 DFPDSGAAYIHRI 248
           D P++   YIHRI
Sbjct: 352 DLPNNRELYIHRI 364

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  106 bits (264), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 63/193 (32%), Positives = 98/193 (50%), Gaps = 14/193 (7%)
Query: 62  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 115
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 159 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 210
Query: 116 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKE 175
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 211 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 270
Query: 176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY 235
           L  ++         +H D+ Q +RE+ + +FR+G + VLI+TDV ARG+D   V+ +INY
Sbjct: 271 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 330
Query: 236 DFPDSGAAYIHRI 248
           D P++   YIHRI
Sbjct: 331 DLPNNRELYIHRI 343

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 73/254 (28%), Positives = 121/254 (47%), Gaps = 9/254 (3%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPXXXXXXXXXXXXXXS 60
           LA QT    +++ K  K   +L+  +        + +  +++ TP               
Sbjct: 87  LARQTLEVVQEMGKFTKITSQLIVPDSFEKN--KQINAQVIVGTPGTVLDLMRRKLMQLQ 144
Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           +++  VLDEAD + +   L      V +     + +  LFSAT  D V + A+ I+ +A 
Sbjct: 145 KIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQL-VLFSATFADAVRQYAKKIVPNAN 203
Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
            + +       ++IKQ  +   +E  K   L + +        +IFV +K+ A  LYG+L
Sbjct: 204 TLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGVMTIGSSIIFVATKKTANVLYGKL 263
Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD- 239
             +G    ++H DL   +R+  +DDFR G++ VLI T+V+ARG+D   V+ V+NYD P  
Sbjct: 264 KSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTL 323
Query: 240 -----SGAAYIHRI 248
                  A YIHRI
Sbjct: 324 ANGQADPATYIHRI 337

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 73/254 (28%), Positives = 121/254 (47%), Gaps = 9/254 (3%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPXXXXXXXXXXXXXXS 60
           LA QT    +++ K  K   +L+  +        + +  +++ TP               
Sbjct: 87  LARQTLEVVQEMGKFTKITSQLIVPDSFEKN--KQINAQVIVGTPGTVLDLMRRKLMQLQ 144
Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           +++  VLDEAD + +   L      V +     + +  LFSAT  D V + A+ I+ +A 
Sbjct: 145 KIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQL-VLFSATFADAVRQYAKKIVPNAN 203
Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGEL 180
            + +       ++IKQ  +   +E  K   L + +        +IFV +K+ A  LYG+L
Sbjct: 204 TLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKL 263
Query: 181 AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD- 239
             +G    ++H DL   +R+  +DDFR G++ VLI T+V+ARG+D   V+ V+NYD P  
Sbjct: 264 KSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTL 323
Query: 240 -----SGAAYIHRI 248
                  A YIHRI
Sbjct: 324 ANGQADPATYIHRI 337

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 63/193 (32%), Positives = 98/193 (50%), Gaps = 14/193 (7%)
Query: 62  VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI 115
           ++ LVLDEAD++   G      ++ +++ P  +          L SATLP  + E+    
Sbjct: 144 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV--------LISATLPHEILEMTNKF 195
Query: 116 MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKE 175
           M D +R++V R     E IKQ  V    EE K   L   +        +IF  +K +   
Sbjct: 196 MTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW 255
Query: 176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY 235
           L  ++         +H D+ Q +RE+ + +FR+G + VLI+TDV ARG+D   V+ +INY
Sbjct: 256 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 315
Query: 236 DFPDSGAAYIHRI 248
           D P++   YIHRI
Sbjct: 316 DLPNNRELYIHRI 328

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  105 bits (262), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 64/207 (30%), Positives = 103/207 (49%), Gaps = 2/207 (0%)
Query: 40  ILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 99
           I++ TP               +++  +LDEAD++   G   K     +     P+    L
Sbjct: 142 IVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG--FKEQIYQIFTLLPPTTQVVL 199
Query: 100 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 159
            SAT+P+ V E+    M + VR++V +     E IKQ  V    EE K   L   +    
Sbjct: 200 LSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSIS 259
Query: 160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV 219
               +IF  ++ + +EL  +L  D      I+SDL Q +R+  + +FR+G + +LI+TD+
Sbjct: 260 VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL 319
Query: 220 IARGMDFKGVNCVINYDFPDSGAAYIH 246
           +ARG+D + V+ VINYD P +   YIH
Sbjct: 320 LARGIDVQQVSLVINYDLPANKENYIH 346

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  104 bits (259), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 63/207 (30%), Positives = 103/207 (49%), Gaps = 2/207 (0%)
Query: 40  ILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 99
           I++ TP                ++  VLDEAD++   G   +  D   K  SN  +V  L
Sbjct: 136 IIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV--L 193
Query: 100 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 159
            SAT+P  V E+ +  M D +R++V ++    E I+Q  +    EE KL  L   +    
Sbjct: 194 LSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLT 253
Query: 160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV 219
               +IF+ ++ +   L  ++         +H D+ Q +R+  + +FR+G + VLI TD+
Sbjct: 254 ITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDL 313
Query: 220 IARGMDFKGVNCVINYDFPDSGAAYIH 246
           +ARG+D + V+ VINYD P +   YIH
Sbjct: 314 LARGIDVQQVSLVINYDLPTNRENYIH 340

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  103 bits (258), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 63/207 (30%), Positives = 103/207 (49%), Gaps = 2/207 (0%)
Query: 40  ILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 99
           I++ TP                ++  VLDEAD++   G   +  D   K  SN  +V  L
Sbjct: 162 IIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV--L 219
Query: 100 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 159
            SAT+P  V E+ +  M D +R++V ++    E I+Q  +    EE KL  L   +    
Sbjct: 220 LSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLT 279
Query: 160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV 219
               +IF+ ++ +   L  ++         +H D+ Q +R+  + +FR+G + VLI TD+
Sbjct: 280 ITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDL 339
Query: 220 IARGMDFKGVNCVINYDFPDSGAAYIH 246
           +ARG+D + V+ VINYD P +   YIH
Sbjct: 340 LARGIDVQQVSLVINYDLPTNRENYIH 366

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 99.0 bits (245), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 73/258 (28%), Positives = 118/258 (45%), Gaps = 20/258 (7%)
Query: 1   LATQTTRECKKLAKGNKFQIKLM--KKELVRSTDLSKFSCDILISTPXXXXXXXXXXXXX 58
           LA Q   E +K A  +  +I ++          +     C ++I+TP             
Sbjct: 141 LAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFIT 200
Query: 59  XSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA 112
                ++VLDEAD++ ++G       ++ H+         P     +FSAT P+ ++ +A
Sbjct: 201 FEDTRFVVLDEADRMLDMGFSEDMRRIMTHV------TMRPEHQTLMFSATFPEEIQRMA 254
Query: 113 RSIMHDAVRVIVGRKNTASESIKQKL--VFAGSEEGKLLALRQSFAESLNPPVLIFVQSK 170
              + + V V +G    A   +KQ +  V   ++  KL+ +    A+      ++FV++K
Sbjct: 255 GEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADG----TIVFVETK 310
Query: 171 ERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVN 230
             A  L   L+        IH D  Q+QRE A+ DF+ G   VLIAT V +RG+D K + 
Sbjct: 311 RGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIK 370
Query: 231 CVINYDFPDSGAAYIHRI 248
            VINYD P     Y+HRI
Sbjct: 371 HVINYDMPSKIDDYVHRI 388

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 98.6 bits (244), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 63/207 (30%), Positives = 99/207 (47%), Gaps = 2/207 (0%)
Query: 40  ILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL 99
           I++ TP               +++  +LDEAD+    G   K     +     P+    L
Sbjct: 141 IVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSG--FKEQIYQIFTLLPPTTQVVL 198
Query: 100 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL 159
            SAT P+ V E+      + VR++V +     E IKQ  V    EE K   L   +    
Sbjct: 199 LSATXPNDVLEVTTKFXRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSIS 258
Query: 160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV 219
               +IF  ++ + +EL  +L  D      I+SDL Q +R+    +FR+G + +LI+TD+
Sbjct: 259 VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDL 318
Query: 220 IARGMDFKGVNCVINYDFPDSGAAYIH 246
           +ARG+D + V+ VINYD P +   YIH
Sbjct: 319 LARGIDVQQVSLVINYDLPANKENYIH 345

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 110/215 (51%), Gaps = 18/215 (8%)
Query: 37  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 96
           + DI+++TP              S  E +++DEAD +FE+G  +  I  ++   SN  I 
Sbjct: 105 NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMG-FIDDIKIILAQTSNRKIT 163
Query: 97  RSLFSATLPDFVEELARSIM--HDAVRVIVGRKNTASESIKQKLVFAGSE-EGKLLALRQ 153
             LFSAT+P+ + ++ +  +  ++ +   +G  N     ++ K V    +   K+ ALR 
Sbjct: 164 -GLFSATIPEEIRKVVKDFITNYEEIEACIGLAN-----VEHKFVHVKDDWRSKVQALR- 216
Query: 154 SFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWV 213
              E+ +  V++FV+++ R  +L     FD   A  +  DL Q+ R   +D FR G+  +
Sbjct: 217 ---ENKDKGVIVFVRTRNRVAKLV--RLFDN--AIELRGDLPQSVRNRNIDAFREGEYDM 269
Query: 214 LIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           LI TDV +RG+D   V  VIN+D P     YIHRI
Sbjct: 270 LITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRI 304

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 87.4 bits (215), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 61/212 (28%), Positives = 94/212 (44%), Gaps = 4/212 (1%)
Query: 37  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 96
           +  IL+ TP              S     ++DEADK+       K I   + +   P+  
Sbjct: 139 TVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD--FKTIIEQILSFLPPTHQ 196
Query: 97  RSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA 156
             LFSAT P  V+E     +H    + +  + T  + I Q   F   E  KL  L   F+
Sbjct: 197 SLLFSATFPLTVKEFMVKHLHKPYEINLMEELTL-KGITQYYAFV-EERQKLHCLNTLFS 254
Query: 157 ESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIA 216
           +      +IF  S  R + L  ++   G      H+ + Q +R     +FR GK   L+ 
Sbjct: 255 KLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVC 314
Query: 217 TDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           +D++ RG+D + VN VIN+DFP +   Y+HRI
Sbjct: 315 SDLLTRGIDIQAVNVVINFDFPKTAETYLHRI 346

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 85.5 bits (210), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 42/105 (40%), Positives = 61/105 (58%), Gaps = 1/105 (0%)
Query: 144 EEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAV 203
           EE K++ L +   ++  PPVLIF + K     ++  L   G+ A  IH    Q +R  A+
Sbjct: 39  EEAKMVYLLECLQKT-PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAI 97
Query: 204 DDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           + FR GK  VL+ATDV ++G+DF  +  VINYD P+    Y+HRI
Sbjct: 98  EAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRI 142

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 46/123 (37%), Positives = 69/123 (56%), Gaps = 6/123 (4%)
Query: 132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIH 191
           ++IKQ  +   +E  K   L + +        +IFV +K+ A  LYG+L  +G    ++H
Sbjct: 7   DAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILH 66
Query: 192 SDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD------SGAAYI 245
            DL   +R+  +DDFR G++ VLI T+V+ARG+D   V+ V+NYD P         A YI
Sbjct: 67  GDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYI 126
Query: 246 HRI 248
           HRI
Sbjct: 127 HRI 129

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 84.7 bits (208), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 74/262 (28%), Positives = 119/262 (45%), Gaps = 22/262 (8%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDL---SKFSCDILISTPXXXXXXXXXXX- 56
           LA QT +  +++ K   F  +L     VR   L    K S  I+I TP            
Sbjct: 107 LALQTGKVIEQMGK---FYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKF 163
Query: 57  XXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKA----CSNPSIVRSLFSATLPDFVEELA 112
               +++  VLDEAD +        H D  ++       N  ++  LFSAT  D V + A
Sbjct: 164 IDPKKIKVFVLDEADVMIATQG---HQDQSIRIQRMLPRNCQML--LFSATFEDSVWKFA 218
Query: 113 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKER 172
           + ++ D   + + R+    ++IKQ  V   S + K  AL   +        +IF  +++ 
Sbjct: 219 QKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKT 278
Query: 173 AKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV 232
           A  L  EL+ +G +  ++  ++   QR   ++ FR GK  VL+ T+V ARG+D + V+ V
Sbjct: 279 ASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVV 338
Query: 233 INYDFP------DSGAAYIHRI 248
           IN+D P           Y+HRI
Sbjct: 339 INFDLPVDKDGNPDNETYLHRI 360

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 84.7 bits (208), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 74/262 (28%), Positives = 119/262 (45%), Gaps = 22/262 (8%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDL---SKFSCDILISTPXXXXXXXXXXX- 56
           LA QT +  +++ K   F  +L     VR   L    K S  I+I TP            
Sbjct: 123 LALQTGKVIEQMGK---FYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKF 179
Query: 57  XXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKA----CSNPSIVRSLFSATLPDFVEELA 112
               +++  VLDEAD +        H D  ++       N  ++  LFSAT  D V + A
Sbjct: 180 IDPKKIKVFVLDEADVMIATQG---HQDQSIRIQRMLPRNCQML--LFSATFEDSVWKFA 234
Query: 113 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKER 172
           + ++ D   + + R+    ++IKQ  V   S + K  AL   +        +IF  +++ 
Sbjct: 235 QKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKT 294
Query: 173 AKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV 232
           A  L  EL+ +G +  ++  ++   QR   ++ FR GK  VL+ T+V ARG+D + V+ V
Sbjct: 295 ASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVV 354
Query: 233 INYDFP------DSGAAYIHRI 248
           IN+D P           Y+HRI
Sbjct: 355 INFDLPVDKDGNPDNETYLHRI 376

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 84.3 bits (207), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 74/262 (28%), Positives = 119/262 (45%), Gaps = 22/262 (8%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDL---SKFSCDILISTPXXXXXXXXXXX- 56
           LA QT +  +++ K   F  +L     VR   L    K S  I+I TP            
Sbjct: 144 LALQTGKVIEQMGK---FYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKF 200
Query: 57  XXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKA----CSNPSIVRSLFSATLPDFVEELA 112
               +++  VLDEAD +        H D  ++       N  ++  LFSAT  D V + A
Sbjct: 201 IDPKKIKVFVLDEADVMIATQG---HQDQSIRIQRMLPRNCQML--LFSATFEDSVWKFA 255
Query: 113 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKER 172
           + ++ D   + + R+    ++IKQ  V   S + K  AL   +        +IF  +++ 
Sbjct: 256 QKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKT 315
Query: 173 AKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV 232
           A  L  EL+ +G +  ++  ++   QR   ++ FR GK  VL+ T+V ARG+D + V+ V
Sbjct: 316 ASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVV 375
Query: 233 INYDFP------DSGAAYIHRI 248
           IN+D P           Y+HRI
Sbjct: 376 INFDLPVDKDGNPDNETYLHRI 397

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 84.3 bits (207), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 74/262 (28%), Positives = 119/262 (45%), Gaps = 22/262 (8%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDL---SKFSCDILISTPXXXXXXXXXXX- 56
           LA QT +  +++ K   F  +L     VR   L    K S  I+I TP            
Sbjct: 174 LALQTGKVIEQMGK---FYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKF 230
Query: 57  XXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKA----CSNPSIVRSLFSATLPDFVEELA 112
               +++  VLDEAD +        H D  ++       N  ++  LFSAT  D V + A
Sbjct: 231 IDPKKIKVFVLDEADVMIATQG---HQDQSIRIQRMLPRNCQML--LFSATFEDSVWKFA 285
Query: 113 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKER 172
           + ++ D   + + R+    ++IKQ  V   S + K  AL   +        +IF  +++ 
Sbjct: 286 QKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKT 345
Query: 173 AKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV 232
           A  L  EL+ +G +  ++  ++   QR   ++ FR GK  VL+ T+V ARG+D + V+ V
Sbjct: 346 ASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVV 405
Query: 233 INYDFP------DSGAAYIHRI 248
           IN+D P           Y+HRI
Sbjct: 406 INFDLPVDKDGNPDNETYLHRI 427

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 84.0 bits (206), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 47/130 (36%), Positives = 69/130 (53%), Gaps = 6/130 (4%)
Query: 125 GRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDG 184
           G      ++IKQ      +E  K   L + +        +IFV +K+ A  LYG+L  +G
Sbjct: 1   GANEVNVDAIKQLYXDCKNEADKFDVLTELYGVXTIGSSIIFVATKKTANVLYGKLKSEG 60
Query: 185 IRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD----- 239
               ++H DL   +R+  +DDFR G++ VLI T+V+ARG+D   V+ V+NYD P      
Sbjct: 61  HEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQ 120
Query: 240 -SGAAYIHRI 248
              A YIHRI
Sbjct: 121 ADPATYIHRI 130

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 84.0 bits (206), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 46/123 (37%), Positives = 68/123 (55%), Gaps = 6/123 (4%)
Query: 132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIH 191
           ++IKQ      +E  K   L + +        +IFV +K+ A  LYG+L  +G    ++H
Sbjct: 9   DAIKQLYXDCKNEADKFDVLTELYGLXTIGSSIIFVATKKTANVLYGKLKSEGHEVSILH 68
Query: 192 SDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD------SGAAYI 245
            DL   +R+  +DDFR G++ VLI T+V+ARG+D   V+ V+NYD P         A YI
Sbjct: 69  GDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYI 128
Query: 246 HRI 248
           HRI
Sbjct: 129 HRI 131

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 82.4 bits (202), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 46/122 (37%), Positives = 67/122 (54%)
Query: 127 KNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIR 186
           + + SE+I QK+V+    + +   L    A   +   L+FV++K+ A  L   L  +G  
Sbjct: 13  QGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYA 72
Query: 187 AGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIH 246
              IH D SQ  RE A+  FR+GK+ +L+AT V ARG+D   V  VIN+D P     Y+H
Sbjct: 73  CTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVH 132
Query: 247 RI 248
           RI
Sbjct: 133 RI 134

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 80.9 bits (198), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 98/219 (44%), Gaps = 7/219 (3%)
Query: 33  LSKFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN 92
           L K    I++ TP                +++ +LDEADK+ E  ++ + +  + +   +
Sbjct: 123 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRMTPH 182
Query: 93  PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTAS-ESIKQKLVFAGSEEG--KLL 149
              V  +FSATL   +  + R  M D + + V  +   +   ++Q  V     E   KL 
Sbjct: 183 EKQV-MMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLF 241
Query: 150 ALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAG 209
            L      +    V+IFV+S +R   L   L      A  IH  + Q +R +    F+  
Sbjct: 242 DLLDVLEFN---QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF 298
Query: 210 KTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           +  +L+AT++  RGMD + VN   NYD P+    Y+HR+
Sbjct: 299 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 337

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 79.7 bits (195), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 42/115 (36%), Positives = 64/115 (55%)
Query: 132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIH 191
           E IKQ  V    EE K   L   +        +IF  ++ + +EL  +L  D      I+
Sbjct: 2   EGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIY 61
Query: 192 SDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIH 246
           SDL Q +R+  + +FR+G + +LI+TD++ARG+D + V+ VINYD P +   YIH
Sbjct: 62  SDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIH 116

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 97/219 (44%), Gaps = 7/219 (3%)
Query: 33  LSKFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN 92
           L K    I++ TP                +++ +LDE DK+ E  ++ + +  + +   +
Sbjct: 124 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPH 183
Query: 93  PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTAS-ESIKQKLVFAGSEEG--KLL 149
              V  +FSATL   +  + R  M D + + V  +   +   ++Q  V     E   KL 
Sbjct: 184 EKQV-MMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLF 242
Query: 150 ALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAG 209
            L      +    V+IFV+S +R   L   L      A  IH  + Q +R +    F+  
Sbjct: 243 DLLDVLEFN---QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF 299
Query: 210 KTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           +  +L+AT++  RGMD + VN   NYD P+    Y+HR+
Sbjct: 300 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 338

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 97/219 (44%), Gaps = 7/219 (3%)
Query: 33  LSKFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN 92
           L K    I++ TP                +++ +LDE DK+ E  ++ + +  + +   +
Sbjct: 124 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPH 183
Query: 93  PSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTAS-ESIKQKLVFAGSEEG--KLL 149
              V  +FSATL   +  + R  M D + + V  +   +   ++Q  V     E   KL 
Sbjct: 184 EKQV-MMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLF 242
Query: 150 ALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAG 209
            L      +    V+IFV+S +R   L   L      A  IH  + Q +R +    F+  
Sbjct: 243 DLLDVLEFN---QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF 299
Query: 210 KTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           +  +L+AT++  RGMD + VN   NYD P+    Y+HR+
Sbjct: 300 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 338

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 77.8 bits (190), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 127/273 (46%), Gaps = 25/273 (9%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTD-------LSKFSCDILISTPXXXXXXXX 53
           LA Q   E KK+   N    K     LV  TD       ++K   +I+I+TP        
Sbjct: 107 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLE 166
Query: 54  XXXXXXSR-VEYLVLDEADKLFEVG--NLLKHIDPVVKACSNPS---IVRSLFSATLPDF 107
                  R V+Y VLDEAD+L E+G  + L+ I  ++   ++ S   I   LFSATL D 
Sbjct: 167 KYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDK 226
Query: 108 VEELARSIMHDA----VRVIVGRKNTASESIKQKLV----FAGSEEGKLLALRQSFAE-S 158
           V++LA +IM+      +  +   +  A E I Q +V    FA S    +  +++   E  
Sbjct: 227 VQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERD 286
Query: 159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVI---HSDLSQTQRENAVDDFRAGKTWVLI 215
            N   +IF  + +    L   L  +  +   I   H  ++Q +R + V  F+  ++ +L+
Sbjct: 287 SNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV 346
Query: 216 ATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            TDV ARGMDF  V+ V+    P   A YIHRI
Sbjct: 347 CTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 379

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 77.8 bits (190), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 127/273 (46%), Gaps = 25/273 (9%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTD-------LSKFSCDILISTPXXXXXXXX 53
           LA Q   E KK+   N    K     LV  TD       ++K   +I+I+TP        
Sbjct: 158 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLE 217
Query: 54  XXXXXXSR-VEYLVLDEADKLFEVG--NLLKHIDPVVKACSNPS---IVRSLFSATLPDF 107
                  R V+Y VLDEAD+L E+G  + L+ I  ++   ++ S   I   LFSATL D 
Sbjct: 218 KYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDK 277
Query: 108 VEELARSIMHDA----VRVIVGRKNTASESIKQKLV----FAGSEEGKLLALRQSFAE-S 158
           V++LA +IM+      +  +   +  A E I Q +V    FA S    +  +++   E  
Sbjct: 278 VQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERD 337
Query: 159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVI---HSDLSQTQRENAVDDFRAGKTWVLI 215
            N   +IF  + +    L   L  +  +   I   H  ++Q +R + V  F+  ++ +L+
Sbjct: 338 SNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV 397
Query: 216 ATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            TDV ARGMDF  V+ V+    P   A YIHRI
Sbjct: 398 CTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 430

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 77.4 bits (189), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 127/273 (46%), Gaps = 25/273 (9%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTD-------LSKFSCDILISTPXXXXXXXX 53
           LA Q   E KK+   N    K     LV  TD       ++K   +I+I+TP        
Sbjct: 107 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLE 166
Query: 54  XXXXXXSR-VEYLVLDEADKLFEVG--NLLKHIDPVVKACSNPS---IVRSLFSATLPDF 107
                  R V+Y VLDEAD+L E+G  + L+ I  ++   ++ S   I   LFSATL D 
Sbjct: 167 KYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDK 226
Query: 108 VEELARSIMHDA----VRVIVGRKNTASESIKQKLV----FAGSEEGKLLALRQSFAE-S 158
           V++LA +IM+      +  +   +  A E I Q +V    FA S    +  +++   E  
Sbjct: 227 VQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERD 286
Query: 159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVI---HSDLSQTQRENAVDDFRAGKTWVLI 215
            N   +IF  + +    L   L  +  +   I   H  ++Q +R + V  F+  ++ +L+
Sbjct: 287 SNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV 346
Query: 216 ATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            TDV ARGMDF  V+ V+    P   A YIHRI
Sbjct: 347 CTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 379

>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 = 70.9 bits (172), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 34/83 (40%), Positives = 49/83 (59%)
Query: 164 LIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG 223
           ++F ++K   +E+   L   G  A  +H DLSQ +RE  +  FR G+  VL+ATDV ARG
Sbjct: 35  MVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARG 94
Query: 224 MDFKGVNCVINYDFPDSGAAYIH 246
           +D   V+ V++Y  PD   AY H
Sbjct: 95  LDIPQVDLVVHYRLPDRAEAYQH 117

>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 = 70.5 bits (171), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 49/83 (59%)
Query: 164 LIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG 223
           ++F ++K   +E+   L   G  A  +H D+SQ +RE  +  FR G+  VL+ATDV ARG
Sbjct: 32  MVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARG 91
Query: 224 MDFKGVNCVINYDFPDSGAAYIH 246
           +D   V+ V++Y  PD   AY H
Sbjct: 92  LDIPQVDLVVHYRMPDRAEAYQH 114

>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 = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 49/85 (57%)
Query: 164 LIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG 223
           ++FV+ +ER  EL   L   GI    +  ++ Q +R  A+     G+  VL+ATDV ARG
Sbjct: 34  IVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARG 93
Query: 224 MDFKGVNCVINYDFPDSGAAYIHRI 248
           +D   V+ V N+D P SG  Y+HRI
Sbjct: 94  IDIPDVSHVFNFDMPRSGDTYLHRI 118

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 53/106 (50%)
Query: 143 SEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENA 202
           +E  K+  L   F+       +IF  S +R + L  +++  G     IH+ + Q  R   
Sbjct: 27  TERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRV 86
Query: 203 VDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
             DFR G    L+ TD+  RG+D + VN VIN+DFP     Y+HRI
Sbjct: 87  FHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRI 132

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 68.2 bits (165), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 41/122 (33%), Positives = 61/122 (50%), Gaps = 6/122 (4%)
Query: 133 SIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHS 192
           +I+Q  V     + K  AL   +        +IF Q++  AK L  E+  DG +  ++  
Sbjct: 7   NIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSG 66
Query: 193 DLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGA------AYIH 246
           +L+  QR + +  FR GK  VLI T+V ARG+D K V  V+N+D P           Y+H
Sbjct: 67  ELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLH 126
Query: 247 RI 248
           RI
Sbjct: 127 RI 128

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 68.2 bits (165), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 36/104 (34%), Positives = 55/104 (52%)
Query: 144 EEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAV 203
           EE K   L+           +IF ++KE   +L  EL   G     IH  + Q  R + +
Sbjct: 19  EENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVM 78
Query: 204 DDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHR 247
           ++F+ G+   L+ATDV ARG+D + ++ VINYD P    +Y+HR
Sbjct: 79  NEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHR 122

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/136 (30%), Positives = 70/136 (51%), Gaps = 7/136 (5%)
Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSC---DILISTPXXXXXXXXXXXX 57
           LA+Q  RE  K+++G  F+I ++ K  V +      S    DIL++TP            
Sbjct: 110 LASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPP 169
Query: 58  X--XSRVEYLVLDEADKLFEVG--NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR 113
               + VE+LV+DE+DKLFE G       +  +  AC++  + R++FSAT    VE+  +
Sbjct: 170 GIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCK 229
Query: 114 SIMHDAVRVIVGRKNT 129
             + + + V +G +N+
Sbjct: 230 LNLDNVISVSIGARNS 245

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 46/86 (53%)
Query: 163 VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR 222
           V+IFV+S +R   L   L      A  IH  + Q +R +    F+  +  +L+AT++  R
Sbjct: 34  VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR 93
Query: 223 GMDFKGVNCVINYDFPDSGAAYIHRI 248
           GMD + VN   NYD P+    Y+HR+
Sbjct: 94  GMDIERVNIAFNYDMPEDSDTYLHRV 119

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 54.7 bits (130), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 30/107 (28%), Positives = 58/107 (54%), Gaps = 4/107 (3%)
Query: 35  KFSCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 94
           +  C +L++TP                 +Y+VLDEAD++ ++G     I  +++  + PS
Sbjct: 148 QMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMG-FEPQIRKIIEESNMPS 206
Query: 95  IVRS---LFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL 138
            +     +FSAT P  +++LA   +++ + + VGR  + S+SIKQ++
Sbjct: 207 GINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQEI 253

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           H  ++Q +R + V  F+  ++ +L+ TDV ARGMDF  V+ V+    P   A YIHRI
Sbjct: 67  HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 124

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           H  ++Q +R + V  F+  ++ +L+ TDV ARGMDF  V+ V+    P   A YIHRI
Sbjct: 67  HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 124

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           H  ++Q +R + V  F+  ++ +L+ TDV ARGMDF  V+ V+    P   A YIHRI
Sbjct: 67  HGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 124

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 8/105 (7%)
Query: 151 LRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVI------HSDLSQTQRENAV- 203
           +R+      N  +++F   +E AK++  EL  DGI+A          +D   +QRE  + 
Sbjct: 352 IREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLI 411
Query: 204 -DDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHR 247
            D+F  G+  VL+AT V   G+D   V+ V+ Y+   S    I R
Sbjct: 412 LDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQR 456

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 37  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 96
             D +++TP              SRVE  VLDEAD++  +G   + ++ ++ A + PS  
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG-FEEEVEALLSA-TPPSRQ 177
Query: 97  RSLFSATLPDFVEELARSIMHDAVRVIV 124
             LFSATLP + + LA   M + V + V
Sbjct: 178 TLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 37  SCDILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIV 96
             D +++TP              SRVE  VLDEAD++  +G   + ++ ++ A + PS  
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG-FEEEVEALLSA-TPPSRQ 177
Query: 97  RSLFSATLPDFVEELARSIMHDAVRVIV 124
             LFSATLP + + LA   M + V + V
Sbjct: 178 TLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 8/90 (8%)
Query: 39  DILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVG---NLLKHIDPVVKACSNPSI 95
           +I I+TP               R  YLVLDEAD++ ++G    + K +D +      P  
Sbjct: 168 EICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQI-----RPDR 222
Query: 96  VRSLFSATLPDFVEELARSIMHDAVRVIVG 125
              ++SAT P  V +LA   + D + + +G
Sbjct: 223 QTLMWSATWPKEVRQLAEDFLKDYIHINIG 252

>pdb|3P4X|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima Length = 413

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 45/174 (25%), Positives = 71/174 (40%), Gaps = 30/174 (17%)
Query: 78  NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQK 137
           NL   I  V  A + P  +R L               +  D +   VGR  + + +I   
Sbjct: 189 NLKPGILVVSSATAKPRGIRPL---------------LFRDLLNFTVGRLVSVARNITHV 233
Query: 138 LVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQT 197
            + + S+E KL+ L + F +     +LIF Q++E  KELY  L       G   S+    
Sbjct: 234 RISSRSKE-KLVELLEIFRDG----ILIFAQTEEEGKELYEYLKRFKFNVGETWSEF--- 285
Query: 198 QRENAVDDFRAGKTWVLIATDV----IARGMDF-KGVNCVINYDFPDSGAAYIH 246
             E   +DF+ GK  +LI        + RG+D  + +  VI +  P     Y +
Sbjct: 286 --EKNFEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTY 337

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 8/90 (8%)
Query: 39  DILISTPXXXXXXXXXXXXXXSRVEYLVLDEADKLFEVG---NLLKHIDPVVKACSNPSI 95
           +I I+TP               R  YLVLDEAD++ ++G    + K +D +      P  
Sbjct: 154 EICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQI-----RPDR 208
Query: 96  VRSLFSATLPDFVEELARSIMHDAVRVIVG 125
              ++SAT P  V +LA   + D + + +G
Sbjct: 209 QTLMWSATWPKEVRQLAEDFLKDYIHINIG 238

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	248
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	5e-66
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-65
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	7e-64
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	1e-59
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	5e-58
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	7e-58
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	2e-57
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	9e-57
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-56
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-56
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	5e-56
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	9e-56
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-55
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-53
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-52
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	2e-48
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-45
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	1e-39
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	3e-39
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	4e-34
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	2e-33
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	2e-33
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	2e-33
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	4e-33
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	4e-28
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	3e-27
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-26
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	7e-20
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-19
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-17
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	4e-04
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	2e-17
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-16
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	3e-16
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	4e-16
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	4e-16
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-15
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	3e-15
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	7e-15
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	7e-15
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	4e-14
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	8e-13
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	8e-12
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	4e-11
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-11
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	2e-10
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	1e-09
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	2e-09
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	4e-08
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	4e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-06
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	2e-05
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	2e-04
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	2e-04
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	2e-04
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	9e-04

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  209 bits (534), Expect = 5e-66
 Identities = 87/271 (32%), Positives = 135/271 (49%), Gaps = 42/271 (15%)

Query: 1   LATQTTRECKKLAKGNKF-------------QIKLMKKELVRSTDLSKFSCDILISTPLR 47
           LA Q   E +K +  ++              QI+ +++            C +L++TP R
Sbjct: 113 LAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLER-----------GCHLLVATPGR 161

Query: 48  LRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRS--L 99
           L   + R KI L   +YLVLDEAD++ ++G       +++           P  VR   +
Sbjct: 162 LVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDT------MPPKGVRHTMM 215

Query: 100 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEE--GKLLALRQSFAE 157
           FSAT P  ++ LAR  + + + + VGR  + SE+I QK+V+    +    LL L  +  +
Sbjct: 216 FSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGK 275

Query: 158 SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIAT 217
             +   L+FV++K+ A  L   L  +G     IH D SQ  RE A+  FR+GK+ +L+AT
Sbjct: 276 --DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVAT 333

Query: 218 DVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            V ARG+D   V  VIN+D P     Y+HRI
Sbjct: 334 AVAARGLDISNVKHVINFDLPSDIEEYVHRI 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 =  204 bits (521), Expect = 7e-64
 Identities = 74/266 (27%), Positives = 117/266 (43%), Gaps = 36/266 (13%)

Query: 1   LATQTTRECKKLAKGNKF-------------QIKLMKKELVRSTDLSKFSCDILISTPLR 47
           LA Q   E +K A  +               Q + + +            C ++I+TP R
Sbjct: 141 LAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITR-----------GCHVVIATPGR 189

Query: 48  LRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS-----LFSA 102
           L   + R  I      ++VLDEAD++ ++G         ++       +R      +FSA
Sbjct: 190 LLDFVDRTFITFEDTRFVVLDEADRMLDMG-----FSEDMRRIMTHVTMRPEHQTLMFSA 244

Query: 103 TLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP 162
           T P+ ++ +A   + + V V +G    A   +KQ +    ++  K   L +         
Sbjct: 245 TFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEV-NKYAKRSKLIE-ILSEQADG 302

Query: 163 VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR 222
            ++FV++K  A  L   L+        IH D  Q+QRE A+ DF+ G   VLIAT V +R
Sbjct: 303 TIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASR 362

Query: 223 GMDFKGVNCVINYDFPDSGAAYIHRI 248
           G+D K +  VINYD P     Y+HRI
Sbjct: 363 GLDIKNIKHVINYDMPSKIDDYVHRI 388

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  193 bits (491), Expect = 1e-59
 Identities = 61/282 (21%), Positives = 110/282 (39%), Gaps = 49/282 (17%)

Query: 1   LATQTTRECKKLAKGNKFQI----KLMKKELVRS-TDLSKFSCDILISTPLRLRLAIRRK 55
           L  QT    +KLA            + K+E  +      +    IL+ +   +  +  R+
Sbjct: 76  LVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFV--SKNRE 133

Query: 56  KIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNP-SIVRSLFSATLPDFVEELARS 114
           K+   R +++ +D+ D + +     ++ID ++     P  I+R  FS      + E  ++
Sbjct: 134 KLSQKRFDFVFVDDVDAVLKAS---RNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKN 190

Query: 115 I---------------------MHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ 153
           +                       D +   VGR  + + +I    + + S+E KL+ L +
Sbjct: 191 LKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKE-KLVELLE 249

Query: 154 SFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWV 213
            F +     +LIF Q++E  KELY  L       G   S+      E   +DF+ GK  +
Sbjct: 250 IFRDG----ILIFAQTEEEGKELYEYLKRFKFNVGETWSE-----FEKNFEDFKVGKINI 300

Query: 214 LIATDV----IARGMDF-KGVNCVINYDFP--DSGAAYIHRI 248
           LI        + RG+D  + +  VI +  P       YI   
Sbjct: 301 LIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQAS 342

>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 =  188 bits (480), Expect = 5e-58
 Identities = 71/261 (27%), Positives = 125/261 (47%), Gaps = 25/261 (9%)

Query: 1   LATQTTRECKKLAKGNKFQIKL------MKKELVRSTDLSKFSCDILISTPLRLRLAIRR 54
           LA Q  +    L                ++ E+ +   L   +  I++ TP R+   + R
Sbjct: 120 LAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQK---LQMEAPHIIVGTPGRVFDMLNR 176

Query: 55  KKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFV 108
           + +    ++  VLDEAD++   G      ++ + +        N +    L SAT+P  V
Sbjct: 177 RYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKL--------NSNTQVVLLSATMPSDV 228

Query: 109 EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFV 167
            E+ +  M D +R++V ++    E I+Q  +    EE KL  L   + E+L     +IF+
Sbjct: 229 LEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLY-ETLTITQAVIFI 287

Query: 168 QSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK 227
            ++ +   L  ++         +H D+ Q +R+  + +FR+G + VLI TD++ARG+D +
Sbjct: 288 NTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQ 347

Query: 228 GVNCVINYDFPDSGAAYIHRI 248
            V+ VINYD P +   YIHRI
Sbjct: 348 QVSLVINYDLPTNRENYIHRI 368

>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 =  187 bits (478), Expect = 7e-58
 Identities = 74/268 (27%), Positives = 125/268 (46%), Gaps = 41/268 (15%)

Query: 1   LATQTTRECKKLAKGNKF-------------QIKLMKKELVRSTDLSKFSCDILISTPLR 47
           LA Q  +    LA                    + ++               I++ TP R
Sbjct: 101 LALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD------------AQIVVGTPGR 148

Query: 48  LRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFS 101
           +   I+R++    +++  +LDEAD++   G       +   +         P+    L S
Sbjct: 149 VFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLL--------PPTTQVVLLS 200

Query: 102 ATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNP 161
           AT+P+ V E+    M + VR++V +     E IKQ  V    EE K   L   + +S++ 
Sbjct: 201 ATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLY-DSISV 259

Query: 162 P-VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI 220
              +IF  ++ + +EL  +L  D      I+SDL Q +R+  + +FR+G + +LI+TD++
Sbjct: 260 TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLL 319

Query: 221 ARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           ARG+D + V+ VINYD P +   YIHRI
Sbjct: 320 ARGIDVQQVSLVINYDLPANKENYIHRI 347

>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 =  186 bits (475), Expect = 2e-57
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 11/255 (4%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA QT    +++ K  K   +L+  +        + +  +++ TP  +   +RRK + L 
Sbjct: 87  LARQTLEVVQEMGKFTKITSQLIVPD--SFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQ 144

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
           +++  VLDEAD + +   L      V +          LFSAT  D V + A+ I+ +A 
Sbjct: 145 KIKIFVLDEADNMLDQQGLGDQCIRVKRFL-PKDTQLVLFSATFADAVRQYAKKIVPNAN 203

Query: 121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKERAKELYGE 179
            + +       ++IKQ  +   +E  K   L       +     +IFV +K+ A  LYG+
Sbjct: 204 TLELQTNEVNVDAIKQLYMDCKNEADKFDVL-TELYGLMTIGSSIIFVATKKTANVLYGK 262

Query: 180 LAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD 239
           L  +G    ++H DL   +R+  +DDFR G++ VLI T+V+ARG+D   V+ V+NYD P 
Sbjct: 263 LKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPT 322

Query: 240 SGAA------YIHRI 248
                     YIHRI
Sbjct: 323 LANGQADPATYIHRI 337

>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 =  185 bits (472), Expect = 9e-57
 Identities = 75/259 (28%), Positives = 123/259 (47%), Gaps = 16/259 (6%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLS---KFSCDILISTPLR-LRLAIRRKK 56
           LA QT +  +++ K    ++KL     VR   L    K S  I+I TP   L    + K 
Sbjct: 107 LALQTGKVIEQMGKFYP-ELKLA--YAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKF 163

Query: 57  IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM 116
           ID  +++  VLDEAD +            + +     +    LFSAT  D V + A+ ++
Sbjct: 164 IDPKKIKVFVLDEADVMIATQGHQDQSIRIQRML-PRNCQMLLFSATFEDSVWKFAQKVV 222

Query: 117 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKERAKE 175
            D   + + R+    ++IKQ  V   S + K  AL   +  ++     +IF  +++ A  
Sbjct: 223 PDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLY-GAITIAQAMIFCHTRKTASW 281

Query: 176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY 235
           L  EL+ +G +  ++  ++   QR   ++ FR GK  VL+ T+V ARG+D + V+ VIN+
Sbjct: 282 LAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINF 341

Query: 236 DFPDSGAA------YIHRI 248
           D P           Y+HRI
Sbjct: 342 DLPVDKDGNPDNETYLHRI 360

>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 =  185 bits (471), Expect = 1e-56
 Identities = 75/268 (27%), Positives = 120/268 (44%), Gaps = 40/268 (14%)

Query: 1   LATQTTRECKKLAKGNKF-------------QIKLMKKELVRSTDLSKFSCDILISTPLR 47
           LA Q  +    L                    I+ +                ++  TP R
Sbjct: 117 LAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-----------GQHVVAGTPGR 165

Query: 48  LRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFS 101
           +   IRR+ +    ++ LVLDEAD++   G      ++ +++         P+    L S
Sbjct: 166 VFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYL--------PPATQVVLIS 217

Query: 102 ATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNP 161
           ATLP  + E+    M D +R++V R     E IKQ  V    EE K   L   + ++L  
Sbjct: 218 ATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY-DTLTI 276

Query: 162 P-VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI 220
              +IF  +K +   L  ++         +H D+ Q +RE+ + +FR+G + VLI+TDV 
Sbjct: 277 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVW 336

Query: 221 ARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           ARG+D   V+ +INYD P++   YIHRI
Sbjct: 337 ARGLDVPQVSLIINYDLPNNRELYIHRI 364

>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 =  188 bits (479), Expect = 1e-56
 Identities = 74/278 (26%), Positives = 119/278 (42%), Gaps = 35/278 (12%)

Query: 1   LATQTTRECKKLAKGNKFQIKL----------MKKELVRSTDLSKFSCDILISTPLRLRL 50
           LA Q   E KK+   N    K            +  + +   ++K   +I+I+TP RL  
Sbjct: 158 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK---MNKLRPNIVIATPGRLID 214

Query: 51  AIRRKKIDLSR-VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSAT 103
            + +      R V+Y VLDEAD+L E+G       +   +     + S  +I   LFSAT
Sbjct: 215 VLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGIL-NEKNSKSADNIKTLLFSAT 273

Query: 104 LPDFVEELARSIMHDAVRVIVG----RKNTASESIKQKLVFAGSEEGKLLALRQSFAES- 158
           L D V++LA +IM+    + +      +  A E I Q +V +       +       +  
Sbjct: 274 LDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFA-NSIFAAVEHIKKQ 332

Query: 159 ---LNPP--VLIFVQSKERAKELYGEL---AFDGIRAGVIHSDLSQTQRENAVDDFRAGK 210
               +     +IF  + +    L   L       +     H  ++Q +R + V  F+  +
Sbjct: 333 IKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDE 392

Query: 211 TWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           + +L+ TDV ARGMDF  V+ V+    P   A YIHRI
Sbjct: 393 SGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 430

>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 =  183 bits (466), Expect = 5e-56
 Identities = 74/261 (28%), Positives = 117/261 (44%), Gaps = 28/261 (10%)

Query: 1   LATQTTRECKKLAKGNKFQI------KLMKKELVRSTDLSKFSCDILISTPLRLRLAIRR 54
           LA QT++  + L K              ++ +++R   L++ +  IL+ TP R+     R
Sbjct: 101 LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR---LNE-TVHILVGTPGRVLDLASR 156

Query: 55  KKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFV 108
           K  DLS     ++DEADK+           +L  + P  ++         LFSAT P  V
Sbjct: 157 KVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSL--------LFSATFPLTV 208

Query: 109 EELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFV 167
           +E     +H    + +  + T  + I Q   F   E  KL  L   F   L     +IF 
Sbjct: 209 KEFMVKHLHKPYEINLMEELTL-KGITQYYAFV-EERQKLHCLNTLF-SKLQINQAIIFC 265

Query: 168 QSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK 227
            S  R + L  ++   G      H+ + Q +R     +FR GK   L+ +D++ RG+D +
Sbjct: 266 NSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQ 325

Query: 228 GVNCVINYDFPDSGAAYIHRI 248
            VN VIN+DFP +   Y+HRI
Sbjct: 326 AVNVVINFDFPKTAETYLHRI 346

>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 =  184 bits (469), Expect = 9e-56
 Identities = 75/259 (28%), Positives = 123/259 (47%), Gaps = 16/259 (6%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLS---KFSCDILISTPLR-LRLAIRRKK 56
           LA QT +  +++ K    ++KL     VR   L    K S  I+I TP   L    + K 
Sbjct: 174 LALQTGKVIEQMGKFYP-ELKLA--YAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKF 230

Query: 57  IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM 116
           ID  +++  VLDEAD +            + +     +    LFSAT  D V + A+ ++
Sbjct: 231 IDPKKIKVFVLDEADVMIATQGHQDQSIRIQRML-PRNCQMLLFSATFEDSVWKFAQKVV 289

Query: 117 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKERAKE 175
            D   + + R+    ++IKQ  V   S + K  AL   +  ++     +IF  +++ A  
Sbjct: 290 PDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLY-GAITIAQAMIFCHTRKTASW 348

Query: 176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY 235
           L  EL+ +G +  ++  ++   QR   ++ FR GK  VL+ T+V ARG+D + V+ VIN+
Sbjct: 349 LAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINF 408

Query: 236 DFPDSGAA------YIHRI 248
           D P           Y+HRI
Sbjct: 409 DLPVDKDGNPDNETYLHRI 427

>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 =  186 bits (474), Expect = 1e-55
 Identities = 74/278 (26%), Positives = 119/278 (42%), Gaps = 35/278 (12%)

Query: 1   LATQTTRECKKLAKGNKFQIKL----------MKKELVRSTDLSKFSCDILISTPLRLRL 50
           LA Q   E KK+   N    K            +  + +   ++K   +I+I+TP RL  
Sbjct: 107 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNK---MNKLRPNIVIATPGRLID 163

Query: 51  AIRRKKIDLSR-VEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSAT 103
            + +      R V+Y VLDEAD+L E+G       +   +     + S  +I   LFSAT
Sbjct: 164 VLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGIL-NEKNSKSADNIKTLLFSAT 222

Query: 104 LPDFVEELARSIMHDAVRVIVG----RKNTASESIKQKLVFAGSEEGKLLALRQSFAES- 158
           L D V++LA +IM+    + +      +  A E I Q +V +       +       +  
Sbjct: 223 LDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFA-NSIFAAVEHIKKQ 281

Query: 159 ---LNPP--VLIFVQSKERAKELYGEL---AFDGIRAGVIHSDLSQTQRENAVDDFRAGK 210
               +     +IF  + +    L   L       +     H  ++Q +R + V  F+  +
Sbjct: 282 IKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDE 341

Query: 211 TWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           + +L+ TDV ARGMDF  V+ V+    P   A YIHRI
Sbjct: 342 SGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI 379

>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 =  176 bits (448), Expect = 1e-53
 Identities = 85/261 (32%), Positives = 132/261 (50%), Gaps = 33/261 (12%)

Query: 1   LATQTTRECKKLAKGNKF-------------QIKLMKKELVRSTDLSKFSCDILISTPLR 47
           LA Q   E + L                   QIK +K              +I++ TP R
Sbjct: 86  LAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKN------------ANIVVGTPGR 133

Query: 48  LRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDF 107
           +   I R  ++L  V+Y +LDEAD++  +G  +K ++ ++ AC+    +  LFSAT+P  
Sbjct: 134 ILDHINRGTLNLKNVKYFILDEADEMLNMG-FIKDVEKILNACNKDKRI-LLFSATMPRE 191

Query: 108 VEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFV 167
           +  LA+  M D   +    K   + +I+Q  V   +E  +  AL +   ++     L+F 
Sbjct: 192 ILNLAKKYMGDYSFI----KAKINANIEQSYVEV-NENERFEALCR-LLKNKEFYGLVFC 245

Query: 168 QSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK 227
           ++K   KEL   L   G +AG IH DLSQ+QRE  +  F+  K  +LIATDV++RG+D  
Sbjct: 246 KTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVN 305

Query: 228 GVNCVINYDFPDSGAAYIHRI 248
            +NCVINY  P +  +Y+HRI
Sbjct: 306 DLNCVINYHLPQNPESYMHRI 326

>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 =  173 bits (442), Expect = 1e-52
 Identities = 67/258 (25%), Positives = 118/258 (45%), Gaps = 17/258 (6%)

Query: 1   LATQTTRECKKLAKGNKFQIKLM--------KKELVRSTDLSKFSCDILISTPLRLRLAI 52
           LA Q ++E ++ +K     +K+         KK+      L K    I++ TP R+    
Sbjct: 88  LAFQISKEYERFSKYMP-NVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALA 143

Query: 53  RRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELA 112
           R K ++L  +++ +LDE DK+ E  ++ + +  + +          +FSATL   +  + 
Sbjct: 144 RNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMT-PHEKQVMMFSATLSKEIRPVC 202

Query: 113 RSIMHDAVRVIVGRKNTAS-ESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSK 170
           R  M D + + V  +   +   ++Q  V    +  K   L     + L    V+IFV+S 
Sbjct: 203 RKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLL-DVLEFNQVVIFVKSV 260

Query: 171 ERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVN 230
           +R   L   L      A  IH  + Q +R +    F+  +  +L+AT++  RGMD + VN
Sbjct: 261 QRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVN 320

Query: 231 CVINYDFPDSGAAYIHRI 248
              NYD P+    Y+HR+
Sbjct: 321 IAFNYDMPEDSDTYLHRV 338

>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 =  161 bits (410), Expect = 2e-48
 Identities = 66/263 (25%), Positives = 113/263 (42%), Gaps = 41/263 (15%)

Query: 1   LATQTTRECKKLAKGNKF-------------QIKLMKKELVRSTDLSKFSCDILISTPLR 47
           L  Q     + + +                 QI  ++              DI+++TP R
Sbjct: 68  LTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRN------------ADIVVATPGR 115

Query: 48  LRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR--SLFSATLP 105
           L     +  IDLS  E +++DEAD +FE+G     ID +    +  S  +   LFSAT+P
Sbjct: 116 LLDLWSKGVIDLSSFEIVIIDEADLMFEMG----FIDDIKIILAQTSNRKITGLFSATIP 171

Query: 106 DFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLI 165
           + + ++ +  + +   +          +++ K V    +    +   +   +     V++
Sbjct: 172 EEIRKVVKDFITNYEEIEA---CIGLANVEHKFVHVKDDWRSKVQALRENKDKG---VIV 225

Query: 166 FVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMD 225
           FV+++ R  +L          A  +  DL Q+ R   +D FR G+  +LI TDV +RG+D
Sbjct: 226 FVRTRNRVAKLVRLF----DNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLD 281

Query: 226 FKGVNCVINYDFPDSGAAYIHRI 248
              V  VIN+D P     YIHRI
Sbjct: 282 IPLVEKVINFDAPQDLRTYIHRI 304

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score =  151 bits (385), Expect = 1e-45
 Identities = 46/136 (33%), Positives = 78/136 (57%), Gaps = 7/136 (5%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFS---CDILISTPLRLRLAIRRKK- 56
           LA+Q  RE  K+++G  F+I ++ K  V +      S    DIL++TP RL   +++   
Sbjct: 110 LASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPP 169

Query: 57  -IDLSRVEYLVLDEADKLFEVGNL--LKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR 113
            IDL+ VE+LV+DE+DKLFE G       +  +  AC++  + R++FSAT    VE+  +
Sbjct: 170 GIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCK 229

Query: 114 SIMHDAVRVIVGRKNT 129
             + + + V +G +N+
Sbjct: 230 LNLDNVISVSIGARNS 245

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  135 bits (341), Expect = 1e-39
 Identities = 45/129 (34%), Positives = 68/129 (52%), Gaps = 2/129 (1%)

Query: 120 VRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGE 179
             +       AS  + Q++ +   EE K++ L +   +   PPVLIF + K     ++  
Sbjct: 16  ENLYFQSMGAASLDVIQEVEYV-KEEAKMVYLLE-CLQKTPPPVLIFAEKKADVDAIHEY 73

Query: 180 LAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD 239
           L   G+ A  IH    Q +R  A++ FR GK  VL+ATDV ++G+DF  +  VINYD P+
Sbjct: 74  LLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPE 133

Query: 240 SGAAYIHRI 248
               Y+HRI
Sbjct: 134 EIENYVHRI 142

>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 =  133 bits (337), Expect = 3e-39
 Identities = 48/134 (35%), Positives = 68/134 (50%), Gaps = 4/134 (2%)

Query: 117 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP--VLIFVQSKERAK 174
           H      +  + + SE+I QK+V+   E  K   L      +       L+FV++K+ A 
Sbjct: 3   HHHHHENLYFQGSTSENITQKVVWV-EESDKRSFLLD-LLNATGKDSLTLVFVETKKGAD 60

Query: 175 ELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN 234
            L   L  +G     IH D SQ  RE A+  FR+GK+ +L+AT V ARG+D   V  VIN
Sbjct: 61  SLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVIN 120

Query: 235 YDFPDSGAAYIHRI 248
           +D P     Y+HRI
Sbjct: 121 FDLPSDIEEYVHRI 134

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  119 bits (301), Expect = 4e-34
 Identities = 45/118 (38%), Positives = 70/118 (59%), Gaps = 2/118 (1%)

Query: 132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKERAKELYGELAFDGIRAGVI 190
           E IKQ  V    EE K   L   + +S++    +IF  ++ + +EL  +L  D      I
Sbjct: 2   EGIKQFYVNVEEEEYKYECLTDLY-DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60

Query: 191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           +SDL Q +R+  + +FR+G + +LI+TD++ARG+D + V+ VINYD P +   YIHRI
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRI 118

>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 =  118 bits (298), Expect = 2e-33
 Identities = 35/118 (29%), Positives = 55/118 (46%), Gaps = 3/118 (2%)

Query: 132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKERAKELYGELAFDGIRAGVI 190
             ++Q  V    +  K   L     + L    V+IFV+S +R   L   L      A  I
Sbjct: 4   HGLQQYYVKL-KDNEKNRKLFDLL-DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 61

Query: 191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           H  + Q +R +    F+  +  +L+AT++  RGMD + VN   NYD P+    Y+HR+
Sbjct: 62  HRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 119

>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 =  118 bits (298), Expect = 2e-33
 Identities = 42/124 (33%), Positives = 63/124 (50%), Gaps = 8/124 (6%)

Query: 132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKERAKELYGELAFDGIRAGVI 190
            +I+Q  V     + K  AL   +  S+     +IF Q++  AK L  E+  DG +  ++
Sbjct: 6   NNIRQYYVLCEHRKDKYQALCNIY-GSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLL 64

Query: 191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAA------Y 244
             +L+  QR + +  FR GK  VLI T+V ARG+D K V  V+N+D P           Y
Sbjct: 65  SGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETY 124

Query: 245 IHRI 248
           +HRI
Sbjct: 125 LHRI 128

>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 =  118 bits (297), Expect = 2e-33
 Identities = 40/117 (34%), Positives = 57/117 (48%)

Query: 132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIH 191
           + I Q    A   E K   L     +      ++FV+ +ER  EL   L   GI    + 
Sbjct: 2   KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLE 61

Query: 192 SDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            ++ Q +R  A+     G+  VL+ATDV ARG+D   V+ V N+D P SG  Y+HRI
Sbjct: 62  GEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRI 118

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  117 bits (295), Expect = 4e-33
 Identities = 39/123 (31%), Positives = 64/123 (52%), Gaps = 3/123 (2%)

Query: 127 KNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPP-VLIFVQSKERAKELYGELAFDGI 185
               + +I+  ++    EE K   L+     + NP   +IF ++KE   +L  EL   G 
Sbjct: 3   AGLTTRNIEHAVIQV-REENKFSLLKD-VLMTENPDSCIIFCRTKEHVNQLTDELDDLGY 60

Query: 186 RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYI 245
               IH  + Q  R + +++F+ G+   L+ATDV ARG+D + ++ VINYD P    +Y+
Sbjct: 61  PCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYV 120

Query: 246 HRI 248
           HR 
Sbjct: 121 HRT 123

>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 =  105 bits (264), Expect = 4e-28
 Identities = 35/86 (40%), Positives = 50/86 (58%)

Query: 163 VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR 222
            ++F ++K   +E+   L   G  A  +H DLSQ +RE  +  FR G+  VL+ATDV AR
Sbjct: 34  AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAAR 93

Query: 223 GMDFKGVNCVINYDFPDSGAAYIHRI 248
           G+D   V+ V++Y  PD   AY HR 
Sbjct: 94  GLDIPQVDLVVHYRLPDRAEAYQHRS 119

>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 =  105 bits (264), Expect = 3e-27
 Identities = 34/86 (39%), Positives = 50/86 (58%)

Query: 163 VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR 222
            ++F ++K   +E+   L   G  A  +H D+SQ +RE  +  FR G+  VL+ATDV AR
Sbjct: 31  AMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAAR 90

Query: 223 GMDFKGVNCVINYDFPDSGAAYIHRI 248
           G+D   V+ V++Y  PD   AY HR 
Sbjct: 91  GLDIPQVDLVVHYRMPDRAEAYQHRS 116

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score =  103 bits (258), Expect = 1e-26
 Identities = 42/159 (26%), Positives = 74/159 (46%), Gaps = 38/159 (23%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRST-------------DLSKFSCDILISTPLR 47
           LA Q   E +K +              +RS              ++    C +L++TP R
Sbjct: 112 LAIQILSESQKFSLNTP----------LRSCVVYGGADTHSQIREVQM-GCHLLVATPGR 160

Query: 48  LRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVR--SL 99
           L   I + KI L   +Y+VLDEAD++ ++G       +++  +          I R   +
Sbjct: 161 LVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNM------PSGINRQTLM 214

Query: 100 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL 138
           FSAT P  +++LA   +++ + + VGR  + S+SIKQ++
Sbjct: 215 FSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQEI 253

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score = 84.1 bits (209), Expect = 7e-20
 Identities = 35/146 (23%), Positives = 61/146 (41%), Gaps = 42/146 (28%)

Query: 1   LATQTTRECKKLAKGNKF-------------QIKLMKKELVRSTDLSKFSCDILISTPLR 47
           LA Q  +   +  +  +              QI+ +++             +I I+TP R
Sbjct: 114 LAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLER-----------GVEICIATPGR 162

Query: 48  LRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS--------L 99
           L   +   K +L R  YLVLDEAD++ ++G      +P ++      IV          +
Sbjct: 163 LIDFLECGKTNLRRTTYLVLDEADRMLDMG-----FEPQIR-----KIVDQIRPDRQTLM 212

Query: 100 FSATLPDFVEELARSIMHDAVRVIVG 125
           +SAT P  V +LA   + D + + +G
Sbjct: 213 WSATWPKEVRQLAEDFLKDYIHINIG 238

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score = 83.4 bits (207), Expect = 1e-19
 Identities = 38/144 (26%), Positives = 58/144 (40%), Gaps = 41/144 (28%)

Query: 1   LATQTTRECKKLAKGN------------KFQIKLMKKELVRSTDLSKFSCDILISTPLRL 48
           LA     EC K +                 QI+ + K             DI+I+TP RL
Sbjct: 106 LALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDISK-----------GVDIIIATPGRL 154

Query: 49  RLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS--------LF 100
                   ++L  + YLV+DEADK+ ++       +P ++      I+          + 
Sbjct: 155 NDLQMNNSVNLRSITYLVIDEADKMLDME-----FEPQIR-----KILLDVRPDRQTVMT 204

Query: 101 SATLPDFVEELARSIMHDAVRVIV 124
           SAT PD V +LA S + D + V V
Sbjct: 205 SATWPDTVRQLALSYLKDPMIVYV 228

>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 = 80.2 bits (197), Expect = 2e-17
 Identities = 37/161 (22%), Positives = 67/161 (41%), Gaps = 12/161 (7%)

Query: 100 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS----F 155
             A +    EE        +  +   ++   + S+  +    G +  K+  L++      
Sbjct: 297 LRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQL 356

Query: 156 AESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIH--------SDLSQTQRENAVDDFR 207
               N  +++F   +E AK++  EL  DGI+A              LSQ +++  +D+F 
Sbjct: 357 QRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFA 416

Query: 208 AGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            G+  VL+AT V   G+D   V+ V+ Y+   S    I R 
Sbjct: 417 RGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRR 457

>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 = 40.2 bits (93), Expect = 4e-04
 Identities = 21/137 (15%), Positives = 47/137 (34%), Gaps = 3/137 (2%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKF-SCDILISTPLRLRLAIRRKKIDL 59
           L  Q     ++L      +I  +  E         +    ++++TP  +   +   +I L
Sbjct: 64  LVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISL 123

Query: 60  SRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDA 119
             V  +V DEA +       +       +   NP ++    +A+     E++   I +  
Sbjct: 124 EDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVI--GLTASPGSTPEKIMEVINNLG 181

Query: 120 VRVIVGRKNTASESIKQ 136
           +  I  R   + +    
Sbjct: 182 IEHIEYRSENSPDVRPY 198

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score = 77.7 bits (192), Expect = 2e-17
 Identities = 39/135 (28%), Positives = 65/135 (48%), Gaps = 16/135 (11%)

Query: 1   LATQTTRECKKLAKGNKFQIKL------MKKELVRSTDLSKFSCDILISTPLRLRLAIRR 54
           LA QT    +K+ K + F   L      +K E  R   ++    +IL+ TP RL   +  
Sbjct: 109 LAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAER---INN--INILVCTPGRLLQHMDE 163

Query: 55  KK-IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS-LFSATLPDFVEELA 112
                 + ++ LVLDEAD++ ++G     ++ V++    P   ++ LFSAT    V++LA
Sbjct: 164 TVSFHATDLQMLVLDEADRILDMG-FADTMNAVIENL--PKKRQTLLFSATQTKSVKDLA 220

Query: 113 RSIMHDAVRVIVGRK 127
           R  + +   V V  K
Sbjct: 221 RLSLKNPEYVWVHEK 235

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score = 74.1 bits (183), Expect = 2e-16
 Identities = 40/139 (28%), Positives = 59/139 (42%), Gaps = 28/139 (20%)

Query: 1   LATQTTRECKKLAKGNKF-----------QIKLMKKELVRSTDLSKFSCDILISTPLRLR 49
           LA Q   E   +A   K            Q + + +             D +++TP R  
Sbjct: 84  LALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLR-----------GADAVVATPGRAL 132

Query: 50  LAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR--SLFSATLPDF 107
             +R+  +DLSRVE  VLDEAD++  +G      + V    S     R   LFSATLP +
Sbjct: 133 DYLRQGVLDLSRVEVAVLDEADEMLSMG----FEEEVEALLSATPPSRQTLLFSATLPSW 188

Query: 108 VEELARSIMHDAVRVIVGR 126
            + LA   M + V + V +
Sbjct: 189 AKRLAERYMKNPVLINVIK 207

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 74.1 bits (183), Expect = 3e-16
 Identities = 34/134 (25%), Positives = 60/134 (44%), Gaps = 8/134 (5%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLS------KFSCDILISTPLRLRLAIRR 54
           LATQ   E  K+ K       ++ + L+  TD             I+I TP R+   IR 
Sbjct: 84  LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIRE 143

Query: 55  KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS 114
           + +D+     LV+DEAD + ++G  +  +D +        +   +FSAT+P+ ++   + 
Sbjct: 144 QALDVHTAHILVVDEADLMLDMG-FITDVDQIAARM-PKDLQMLVFSATIPEKLKPFLKK 201

Query: 115 IMHDAVRVIVGRKN 128
            M +   V V   +
Sbjct: 202 YMENPTFVHVLEHH 215

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score = 74.3 bits (183), Expect = 4e-16
 Identities = 28/88 (31%), Positives = 50/88 (56%), Gaps = 5/88 (5%)

Query: 39  DILISTPLRLRLAIRRKK-IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 97
            I+I+TP RL   +   K  +L  ++YLV+DEAD++  +      +D ++K    P   +
Sbjct: 163 HIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMD-FETEVDKILKVI--PRDRK 219

Query: 98  S-LFSATLPDFVEELARSIMHDAVRVIV 124
           + LFSAT+   V++L R+ + + V+  V
Sbjct: 220 TFLFSATMTKKVQKLQRAALKNPVKCAV 247

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score = 73.8 bits (182), Expect = 4e-16
 Identities = 28/138 (20%), Positives = 48/138 (34%), Gaps = 27/138 (19%)

Query: 1   LATQTTRECKKLAKGNKF--------------QIKLMKKELVRSTDLSKFSCDILISTPL 46
           +A Q       +    +                   +KK            C I + +P 
Sbjct: 104 IAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK------------CHIAVGSPG 151

Query: 47  RLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD 106
           R++  I    ++   +   +LDEADKL E G+  + I+ +  +    S      SAT P+
Sbjct: 152 RIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSL-PASKQMLAVSATYPE 210

Query: 107 FVEELARSIMHDAVRVIV 124
           F+       M D   V +
Sbjct: 211 FLANALTKYMRDPTFVRL 228

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score = 72.6 bits (179), Expect = 1e-15
 Identities = 32/139 (23%), Positives = 59/139 (42%), Gaps = 23/139 (16%)

Query: 1   LATQTTRECKKLAKGNKFQI------KLMKKELVRSTDLSKFSCDILISTPLRLRLAIRR 54
           LA Q  +    L                ++ E+ +   L   +  I++ TP R+   + R
Sbjct: 110 LAQQIQKVILALGDYMGATCHACIGGTNVRNEMQK---LQAEAPHIVVGTPGRVFDMLNR 166

Query: 55  KKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFSATLPDFV 108
           + +    ++  VLDEAD++   G       + + +        N SI   L SAT+P  V
Sbjct: 167 RYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKL--------NTSIQVVLLSATMPTDV 218

Query: 109 EELARSIMHDAVRVIVGRK 127
            E+ +  M D +R++V ++
Sbjct: 219 LEVTKKFMRDPIRILVKKE 237

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score = 72.8 bits (179), Expect = 3e-15
 Identities = 36/131 (27%), Positives = 58/131 (44%), Gaps = 8/131 (6%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLS---KFSCDILISTPLR-LRLAIRRKK 56
           LA QT +  +++ K    ++KL     VR   L    K S  I+I TP   L    + K 
Sbjct: 174 LALQTGKVIEQMGKFYP-ELKLA--YAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKF 230

Query: 57  IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM 116
           ID  +++  VLDEAD +             ++     +    LFSAT  D V + A+ ++
Sbjct: 231 IDPKKIKVFVLDEADVMIATQGHQDQSI-RIQRMLPRNCQMLLFSATFEDSVWKFAQKVV 289

Query: 117 HDAVRVIVGRK 127
            D   + + R+
Sbjct: 290 PDPNVIKLKRE 300

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score = 70.3 bits (173), Expect = 7e-15
 Identities = 29/146 (19%), Positives = 55/146 (37%), Gaps = 39/146 (26%)

Query: 1   LATQTTRECKKLAKGNKF-------------QIKLMKKELVRSTDLSKFSCDILISTPLR 47
           LA Q  +    LA                    + ++               I++ TP R
Sbjct: 94  LALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD------------AQIVVGTPGR 141

Query: 48  LRLAIRRKKIDLSRVEYLVLDEADKLFEVG------NLLKHIDPVVKACSNPSIVRSLFS 101
           +   I+R++    +++  +LDEAD++   G       +   +         P+    L S
Sbjct: 142 VFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLL--------PPTTQVVLLS 193

Query: 102 ATLPDFVEELARSIMHDAVRVIVGRK 127
           AT+P+ V E+    M + VR++V + 
Sbjct: 194 ATMPNDVLEVTTKFMRNPVRILVKKD 219

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score = 70.3 bits (173), Expect = 7e-15
 Identities = 30/138 (21%), Positives = 60/138 (43%), Gaps = 25/138 (18%)

Query: 1   LATQTTRECKKLAKGNK--------------FQIKLMKKELVRSTDLSKFSCDILISTPL 46
           LA Q ++E ++ +K                    +++KK              I++ TP 
Sbjct: 94  LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN----------CPHIVVGTPG 143

Query: 47  RLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD 106
           R+    R K ++L  +++ +LDE DK+ E  ++ + +  + +   +   V  +FSATL  
Sbjct: 144 RILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQV-MMFSATLSK 202

Query: 107 FVEELARSIMHDAVRVIV 124
            +  + R  M D + + V
Sbjct: 203 EIRPVCRKFMQDPMEIFV 220

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 67.9 bits (167), Expect = 4e-14
 Identities = 27/136 (19%), Positives = 55/136 (40%), Gaps = 27/136 (19%)

Query: 1   LATQTTRECKKLAKGNKF--------------QIKLMKKELVRSTDLSKFSCDILISTPL 46
           LA Q ++ C +++K                   I  +             +  ++I+TP 
Sbjct: 83  LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDD-----------TVHVVIATPG 131

Query: 47  RLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPD 106
           R+   I++    +  V+ +VLDEADKL      ++ ++ ++      +    L+SAT P 
Sbjct: 132 RILDLIKKGVAKVDHVQMIVLDEADKLLSQD-FVQIMEDIILTL-PKNRQILLYSATFPL 189

Query: 107 FVEELARSIMHDAVRV 122
            V++   S +     +
Sbjct: 190 SVQKFMNSHLEKPYEI 205

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score = 65.0 bits (159), Expect = 8e-13
 Identities = 36/131 (27%), Positives = 62/131 (47%), Gaps = 16/131 (12%)

Query: 1   LATQTTRECKKLAKGNKFQIKL------MKKELVRSTDLSKFSCDILISTPLRLRLAIRR 54
           LA QT    K+L   +     L         E  +   L     +I+++TP RL   ++ 
Sbjct: 138 LAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQK---LGN-GINIIVATPGRLLDHMQN 193

Query: 55  KK-IDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRS-LFSATLPDFVEELA 112
                   ++ LV+DEAD++ +VG   + +  ++K    P+  ++ LFSAT    VE+LA
Sbjct: 194 TPGFMYKNLQCLVIDEADRILDVG-FEEELKQIIKLL--PTRRQTMLFSATQTRKVEDLA 250

Query: 113 R-SIMHDAVRV 122
           R S+  + + V
Sbjct: 251 RISLKKEPLYV 261

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 63.5 bits (153), Expect = 8e-12
 Identities = 36/248 (14%), Positives = 83/248 (33%), Gaps = 18/248 (7%)

Query: 19  QIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN 78
             + + K + +  +      +    T    +  +  +K  +        +E+     +  
Sbjct: 252 DTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFL 311

Query: 79  LLKHIDPVVKACSNPSIVR-SLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQK 137
              H+     A       R       L DF   +  +   +  + +  R     + ++  
Sbjct: 312 YTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESV 371

Query: 138 LVFAGSEEGKLLALRQSFAESLNPP----VLIFVQSKERAKELYGEL----AFDGIRAGV 189
                +E  KL  L     E  +       ++FV+++     L   +        ++ G+
Sbjct: 372 SRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGI 431

Query: 190 I--------HSDLSQTQRENAVDDFRA-GKTWVLIATDVIARGMDFKGVNCVINYDFPDS 240
           +        ++ ++   ++  +D F+A G   +LIAT V   G+D    N VI Y++  +
Sbjct: 432 LTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGN 491

Query: 241 GAAYIHRI 248
               I   
Sbjct: 492 VIKMIQTR 499

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 61.4 bits (148), Expect = 4e-11
 Identities = 30/162 (18%), Positives = 63/162 (38%), Gaps = 17/162 (10%)

Query: 104 LPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALR----QSFAESL 159
           L  F  ++  +   +  R +  R     E +++      +E  KL  L     + +    
Sbjct: 329 LKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKP 388

Query: 160 NPPVLIFVQSKERAKELYGEL----AFDGIRAGVI--------HSDLSQTQRENAVDDFR 207
               ++FV+++     L   +    A   ++ G++         + ++   ++  ++ FR
Sbjct: 389 ETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFR 448

Query: 208 A-GKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           A G   +LIAT V   G+D    N VI Y++  +    I   
Sbjct: 449 ASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTR 490

>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 = 61.1 bits (147), Expect = 6e-11
 Identities = 26/162 (16%), Positives = 57/162 (35%), Gaps = 17/162 (10%)

Query: 104 LPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS----FAESL 159
           L +F   +      +  + +  +       +        +E  KL  L       +  + 
Sbjct: 330 LTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNP 389

Query: 160 NPPVLIFVQSKERAKELYGELA----FDGIRAGVI--------HSDLSQTQRENAVDDFR 207
               L+F +++     L   +      + I+ GV+         + ++   ++  +D F+
Sbjct: 390 QTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK 449

Query: 208 AGKT-WVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
             K   +LIAT V   G+D    N V+ Y++  +    I   
Sbjct: 450 TSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVR 491

>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 = 59.6 bits (143), Expect = 2e-10
 Identities = 26/162 (16%), Positives = 57/162 (35%), Gaps = 17/162 (10%)

Query: 104 LPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS----FAESL 159
           L +F   +      +  + +  +       +        +E  KL  L       +  + 
Sbjct: 571 LTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNP 630

Query: 160 NPPVLIFVQSKERAKELYGELA----FDGIRAGVI--------HSDLSQTQRENAVDDFR 207
               L+F +++     L   +      + I+ GV+         + ++   ++  +D F+
Sbjct: 631 QTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK 690

Query: 208 AGKT-WVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
             K   +LIAT V   G+D    N V+ Y++  +    I   
Sbjct: 691 TSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVR 732

>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 = 57.3 bits (137), Expect = 1e-09
 Identities = 26/162 (16%), Positives = 57/162 (35%), Gaps = 17/162 (10%)

Query: 104 LPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS----FAESL 159
           L +F   +      +  + +  +       +        +E  KL  L       +  + 
Sbjct: 571 LTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNP 630

Query: 160 NPPVLIFVQSKERAKELYGEL----AFDGIRAGVIH--------SDLSQTQRENAVDDFR 207
               L+F +++     L   +      + I+ GV+         + ++   ++  +D F+
Sbjct: 631 QTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK 690

Query: 208 AGKT-WVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
             K   +LIAT V   G+D    N V+ Y++  +    I   
Sbjct: 691 TSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVR 732

>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 = 56.6 bits (136), Expect = 2e-09
 Identities = 24/106 (22%), Positives = 44/106 (41%), Gaps = 3/106 (2%)

Query: 146 GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD-GIRAGVIHSDLSQTQRENAVD 204
            ++  L        +  VL+       A +L   L    GIRA V H  +S  +R+ A  
Sbjct: 489 PRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAA 548

Query: 205 DFRAGKTWV--LIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            F    T    L+ +++ + G +F+  + ++ +D P +      RI
Sbjct: 549 WFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRI 594

>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 = 52.1 bits (125), Expect = 4e-08
 Identities = 19/106 (17%), Positives = 42/106 (39%), Gaps = 5/106 (4%)

Query: 128 NTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRA 187
             A  + ++    A + + K+  LR+         ++IF +  E    +           
Sbjct: 317 YEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVF-----LI 371

Query: 188 GVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI 233
             I    S+ +RE  ++ FR G+   ++++ V+  G+D    N  +
Sbjct: 372 PAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGV 417

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 46.4 bits (110), Expect = 4e-06
 Identities = 43/231 (18%), Positives = 82/231 (35%), Gaps = 49/231 (21%)

Query: 37  SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV--GNLLKHIDPVVKACSNPS 94
             DI+I+T  +    +R     +  V+ LV DE   +     G  L+ I  +        
Sbjct: 114 KYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVI--LAHMLGKAQ 171

Query: 95  IVRSLFSATLPDFVEELAR----SIMHDAVR-------VIVGR---------------KN 128
           I+    SAT+ +  EELA      ++    R       V                   + 
Sbjct: 172 II--GLSATIGN-PEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEE 228

Query: 129 TASESIKQK---LVFAGS---EEGKLLALRQSFAESLNPP-------VLIFVQSKERAKE 175
              ++I++K   L+F       E   L L +     L  P       +   ++     ++
Sbjct: 229 LVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEK 288

Query: 176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDF 226
           L   +   G+     H+ L + +R    ++FR G    ++AT  ++ G++ 
Sbjct: 289 LAKAIRG-GV--AFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINT 336

>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 = 45.6 bits (107), Expect = 9e-06
 Identities = 44/252 (17%), Positives = 78/252 (30%), Gaps = 73/252 (28%)

Query: 11  KLAKGNKFQIKLMKKEL-----VRSTDLSK---FSCDILISTPLRLR------LAIRRKK 56
           +       + K  +  L     V++         SC IL++T  R +       A     
Sbjct: 231 QAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTT--RFKQVTDFLSAATTTH 288

Query: 57  IDLSRVEY-LVLDEADKLFEVGNLLKHID------PVVKACS-NPSIVRSLFSATLPDFV 108
           I L      L  DE   L      LK++D      P  +  + NP  + S+ + ++ D +
Sbjct: 289 ISLDHHSMTLTPDEVKSLL-----LKYLDCRPQDLP-REVLTTNPRRL-SIIAESIRDGL 341

Query: 109 E--ELARSIMHDAVRVIVGRK-NTASESIKQKL-----VFAGSEEG-----KLLAL---- 151
              +  + +  D +  I+    N    +  +K+     VF            LL+L    
Sbjct: 342 ATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF---PPSAHIPTILLSLIWFD 398

Query: 152 -----RQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENA---- 202
                       L+   L+  Q KE    +             I+ +L            
Sbjct: 399 VIKSDVMVVVNKLHKYSLVEKQPKESTISIPS-----------IYLELKVKLENEYALHR 447

Query: 203 --VDDFRAGKTW 212
             VD +   KT+
Sbjct: 448 SIVDHYNIPKTF 459

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B* Length = 1054

 Score = 44.7 bits (106), Expect = 2e-05
 Identities = 40/253 (15%), Positives = 87/253 (34%), Gaps = 53/253 (20%)

Query: 1   LATQTTRECKKLAKGNKFQIKL--------MKKELVRSTDLSKFSCDILISTPLRLRLAI 52
           L  Q     +K A+      +         + K    +   +  +  I+I+T   L    
Sbjct: 111 LVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLS--- 167

Query: 53  RRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKAC--SNPSIVRSLF---------- 100
            +   +L   +++ +D+ D + +     K++D ++           +S            
Sbjct: 168 -KHYRELGHFDFIFVDDVDAILKAS---KNVDKLLHLLGFHYDLKTKSWVGEARGCLMVS 223

Query: 101 SATLPDFVEELARSIMHDAVRVI----VGRKNTASESIKQKLVFAGSEEGKLLALRQSFA 156
           +AT         +    +  R +    +G       +++   V   S          S  
Sbjct: 224 TATAK-------KGKKAELFRQLLNFDIGSSRITVRNVEDVAVNDESISTLS-----SIL 271

Query: 157 ESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIA 216
           E L    +I+ ++ E A+E+Y  L  +  R G++ +      ++   + F  G+   LI 
Sbjct: 272 EKLGTGGIIYARTGEEAEEIYESLK-NKFRIGIVTAT-----KKGDYEKFVEGEIDHLIG 325

Query: 217 T----DVIARGMD 225
           T      + RG+D
Sbjct: 326 TAHYYGTLVRGLD 338

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A* Length = 591

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 10/81 (12%)

Query: 165 IFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGM 224
           I+  S++ ++++   L   GI AG  H++L    +      + A +  V++AT  +A GM
Sbjct: 272 IYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT--VAFGM 329

Query: 225 DFKGVN-----CVINYDFPDS 240
              G++      VI++    S
Sbjct: 330 ---GIDKPDVRFVIHHSMSKS 347

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A* Length = 523

 Score = 41.0 bits (97), Expect = 2e-04
 Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 10/85 (11%)

Query: 165 IFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGM 224
           I+  S+ + ++    L   GI A   H+ L    R +  + F+     +++AT  +A GM
Sbjct: 241 IYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVAT--VAFGM 298

Query: 225 DFKGVN-----CVINYDFPDSGAAY 244
              G+N      V+++D P +  +Y
Sbjct: 299 ---GINKPNVRFVVHFDIPRNIESY 320

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Length = 702

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 49/244 (20%), Positives = 84/244 (34%), Gaps = 73/244 (29%)

Query: 37  SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDE----ADKLFEVGNLLKHIDPVVKACSN 92
            CDI+++T  +    IR +   +  V  LV+DE      +  + G  L+ +  V K    
Sbjct: 114 DCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSE--KRGATLEIL--VTKMRRM 169

Query: 93  PSIVRSLF-SATLPDFVEELAR-------------------SIMHDAVRVIVGRKNTASE 132
              +R +  SAT P+ V E+A                     +    + +  G  +T+  
Sbjct: 170 NKALRVIGLSATAPN-VTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRR 228

Query: 133 SIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSK----ERAKELYGELAF------ 182
              ++LV     E                 VL+F  ++    + A +L    A       
Sbjct: 229 VKFEELVEECVAENG--------------GVLVFESTRRGAEKTAVKLSAITAKYVENEG 274

Query: 183 ------------------DGIRAGV--IHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR 222
                             + +R G    H+ L   QR    D FR G   V++AT  +A 
Sbjct: 275 LEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAA 334

Query: 223 GMDF 226
           G++ 
Sbjct: 335 GVNL 338

>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 Length = 780

 Score = 39.1 bits (92), Expect = 9e-04
 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 3/51 (5%)

Query: 173 AKELYGEL---AFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI 220
           A E+Y  L    F   + G++H  LSQ +++  + +F  G+  +L++T VI
Sbjct: 599 AVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVI 649

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	248
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	100.0
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.98
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.98
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.98
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.98
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.98
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.97
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.97
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.97
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.97
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.97
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.96
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.96
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.96
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.96
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.96
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.96
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.96
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.95
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.95
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.94
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.94
3h1t_A	590	Type I site-specific restriction-modification syst	99.94
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.94
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.94
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.94
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.93
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.93
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.93
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.93
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.93
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.93
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.92
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.92
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.92
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.92
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.92
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.91
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.9
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.9
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.89
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.81
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.88
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.88
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.88
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.88
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.86
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.83
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.78
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.77
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.77
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.74
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.74
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.74
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.73
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.73
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.72
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.72
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.71
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.71
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.7
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.69
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.69
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.69
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.56
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.24
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.18
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.18
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.14
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.13
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.62
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.6
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	97.64
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	96.92
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	96.38
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	95.5
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	95.47
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	95.11
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	95.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	94.55
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	94.49
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	94.21
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	93.98
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	93.73
3bor_A	237	Human initiation factor 4A-II; translation initiat	93.41
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	93.03
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	92.95
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	92.85
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	92.76
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	92.63
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	92.48
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	91.52
2l82_A	162	Designed protein OR32; structural genomics, northe	89.35
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	89.25
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	89.03
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	88.9
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	88.78
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	88.65
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	88.65
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	88.65
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	88.34
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	88.09
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	88.04
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	87.69
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	87.42
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	87.21
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	87.1
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	87.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	86.84
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	86.75
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	86.68
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	85.68
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	85.49
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	84.71
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	84.27
2jtq_A	85	Phage shock protein E; solution structure rhodanes	84.16
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	84.15
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	84.05
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	83.5
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	82.98
3nhv_A	144	BH2092 protein; alpha-beta protein, structural gen	82.51
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	82.1
2k0z_A	110	Uncharacterized protein HP1203; A/B domain, struct	81.91
2fsx_A	148	RV0390, COG0607: rhodanese-related sulfurtransfera	81.76
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	81.06
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	80.61
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	80.57
1tq1_A	129	AT5G66040, senescence-associated family protein; C	80.49
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	80.03

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=100.00  E-value=1.2e-42  Score=291.22  Aligned_cols=244  Identities=30%  Similarity=0.437  Sum_probs=214.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.+++++...+ ..+..++|+.   .+......+++|+|+||++|.+++.++...+++++++|+||||++.+++
T Consensus       141 La~Q~~~~~~~~~~~~~-~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~~~~g  219 (434)
T 2db3_A          141 LAIQIFNEARKFAFESY-LKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMG  219 (434)
T ss_dssp             HHHHHHHHHHHHTTTSS-CCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHhccCC-cEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEccHhhhhccC
Confidence            68999999999998877 4555556655   3344456789999999999999999888889999999999999999988


Q ss_pred             cccccchhHhhhCC-CccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHh
Q 042003           78 NLLKHIDPVVKACS-NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFA  156 (248)
Q Consensus        78 ~~~~~~~~~~~~~~-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  156 (248)
                       |...+..++..+. ....|++++|||+++....+...++.++..+...........+.+.+..+.. ..+...+.+++.
T Consensus       220 -f~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~~l~  297 (434)
T 2db3_A          220 -FSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNK-YAKRSKLIEILS  297 (434)
T ss_dssp             -THHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEECCG-GGHHHHHHHHHH
T ss_pred             -cHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEEeCc-HHHHHHHHHHHH
Confidence             8888888888753 5678999999999999999999999998888887776666777777766554 457888888888


Q ss_pred             ccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc
Q 042003          157 ESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD  236 (248)
Q Consensus       157 ~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~  236 (248)
                      ... .++||||++++.++.+++.|++.++++..+||++++.+|+++++.|++|+.+|||||+++++|+|+|++++||+||
T Consensus       298 ~~~-~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d  376 (434)
T 2db3_A          298 EQA-DGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYD  376 (434)
T ss_dssp             HCC-TTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESS
T ss_pred             hCC-CCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEEC
Confidence            764 5699999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccceecC
Q 042003          237 FPDSGAAYIHRI  248 (248)
Q Consensus       237 ~p~~~~~~~qri  248 (248)
                      +|.++.+|+||+
T Consensus       377 ~p~~~~~y~qri  388 (434)
T 2db3_A          377 MPSKIDDYVHRI  388 (434)
T ss_dssp             CCSSHHHHHHHH
T ss_pred             CCCCHHHHHHHh
Confidence            999999999985

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=100.00  E-value=6.7e-41  Score=279.02  Aligned_cols=245  Identities=31%  Similarity=0.425  Sum_probs=215.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      |+.|+++.+++++...+ ..+....|+.   .+......+++|+|+||+++.+.+.++...+.+++++|+||||++.+++
T Consensus       117 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~  195 (410)
T 2j0s_A          117 LAVQIQKGLLALGDYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG  195 (410)
T ss_dssp             HHHHHHHHHHHHTTTTT-CCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHhccCC-eEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhhh
Confidence            67899999999998888 4444445544   2223344678999999999999999888888999999999999998887


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                       +...+..+.+. .+...|++++|||+++...+....++.++..+...........+.+.+......+.+...+.+++..
T Consensus       196 -~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~  273 (410)
T 2j0s_A          196 -FKEQIYDVYRY-LPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDT  273 (410)
T ss_dssp             -THHHHHHHHTT-SCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHHHHHH
T ss_pred             -hHHHHHHHHHh-CccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHHHHHh
Confidence             77888888776 4567899999999999888888888888888877777777778888888888888899999999988


Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      ...+++||||++++.++.+++.|++.++.+..+||++++++|+.+++.|++|+.+|||||+++++|+|+|++++||++|+
T Consensus       274 ~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~  353 (410)
T 2j0s_A          274 LTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDL  353 (410)
T ss_dssp             HTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSC
T ss_pred             cCCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECC
Confidence            77789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      |+|+..|+||+
T Consensus       354 p~s~~~~~Qr~  364 (410)
T 2j0s_A          354 PNNRELYIHRI  364 (410)
T ss_dssp             CSSHHHHHHHH
T ss_pred             CCCHHHHHHhc
Confidence            99999999985

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

Probab=100.00  E-value=4.8e-40  Score=274.37  Aligned_cols=245  Identities=34%  Similarity=0.496  Sum_probs=207.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++++....+ ..+..+.|+.   .+......+++|+|+||+++.+.+..+...+++++++|+||||++.+++
T Consensus       113 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~iViDEah~~~~~~  191 (417)
T 2i4i_A          113 LAVQIYEEARKFSYRSR-VRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMG  191 (417)
T ss_dssp             HHHHHHHHHHHHHTTSS-CCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSBCCTTCCEEEESSHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCcCC-ceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHcCCcChhhCcEEEEEChhHhhccC
Confidence            68899999999998877 4444555554   2233345679999999999999999888888999999999999999888


Q ss_pred             cccccchhHhhhCC---CccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHH
Q 042003           78 NLLKHIDPVVKACS---NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQS  154 (248)
Q Consensus        78 ~~~~~~~~~~~~~~---~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  154 (248)
                       +...+..++....   ....|++++|||+++....+...++.++..+...........+.+.+..+.. ..+...+.++
T Consensus       192 -~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-~~~~~~l~~~  269 (417)
T 2i4i_A          192 -FEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEE-SDKRSFLLDL  269 (417)
T ss_dssp             -CHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC----CCSSEEEEEEECCG-GGHHHHHHHH
T ss_pred             -cHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCCCCccCceEEEEEecc-HhHHHHHHHH
Confidence             8888888877432   2367899999999998888888888888887777666666677777666554 4578888888


Q ss_pred             Hhcc-CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEE
Q 042003          155 FAES-LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI  233 (248)
Q Consensus       155 ~~~~-~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi  233 (248)
                      ++.. .++++||||+++++++.+++.|++.++.+..+||+++.++|.++++.|++|+.+|||||+++++|+|+|++++||
T Consensus       270 l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi  349 (417)
T 2i4i_A          270 LNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVI  349 (417)
T ss_dssp             HHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCCEEEEE
T ss_pred             HHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEE
Confidence            8876 367899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCcccceecC
Q 042003          234 NYDFPDSGAAYIHRI  248 (248)
Q Consensus       234 ~~~~p~~~~~~~qri  248 (248)
                      ++++|+|+..|+||+
T Consensus       350 ~~~~p~s~~~~~Qr~  364 (417)
T 2i4i_A          350 NFDLPSDIEEYVHRI  364 (417)
T ss_dssp             ESSCCSSHHHHHHHH
T ss_pred             EEcCCCCHHHHHHhc
Confidence            999999999999984

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=100.00  E-value=2.8e-40  Score=275.50  Aligned_cols=246  Identities=28%  Similarity=0.421  Sum_probs=209.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      |+.|+++.+++++...+.......+|..   ........+++|+|+||+++.+.+..+...+.+++++|+||||++.+++
T Consensus       120 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~  199 (414)
T 3eiq_A          120 LAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG  199 (414)
T ss_dssp             HHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTT
T ss_pred             HHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccC
Confidence            5789999999999888744444444433   1222333678999999999999999988888999999999999998887


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                       +...+..++.. .....|++++|||+++........++.++..+...........+.+.+......+.+...+..++..
T Consensus       200 -~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  277 (414)
T 3eiq_A          200 -FKDQIYDIFQK-LNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYET  277 (414)
T ss_dssp             -THHHHHHHHTT-SCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHHHHHS
T ss_pred             -cHHHHHHHHHh-CCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHHHHHh
Confidence             77888888777 4568899999999999899999999999988877777777788888888888888899999999998


Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      ...+++||||++++.++.+++.|++.++.+..+||+|+.++|..+++.|++|+.+|||||+++++|+|+|++++||++++
T Consensus       278 ~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~  357 (414)
T 3eiq_A          278 LTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL  357 (414)
T ss_dssp             SCCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSC
T ss_pred             CCCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCC
Confidence            88889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      |+|+..|+||+
T Consensus       358 p~s~~~~~Qr~  368 (414)
T 3eiq_A          358 PTNRENYIHRI  368 (414)
T ss_dssp             CSSTHHHHHHS
T ss_pred             CCCHHHhhhhc
Confidence            99999999996

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=100.00  E-value=1.9e-39  Score=270.22  Aligned_cols=247  Identities=28%  Similarity=0.359  Sum_probs=214.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhc-CCcccCceeEEEEeccccccccCcc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNL   79 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~-~~~~~~~~~~lIiDEah~~~~~~~~   79 (248)
                      ||.|+++.++++....+...+....++.........+++|+|+||+++.+.+.+ +...+.+++++|+||||++.+...+
T Consensus       107 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~~~~  186 (412)
T 3fht_A          107 LALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGH  186 (412)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHSTTTT
T ss_pred             HHHHHHHHHHHHHhhcccceEEEeecCcchhhhhcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhcCCc
Confidence            578999999999887643556656665544444566789999999999999866 5567899999999999998874436


Q ss_pred             cccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccC
Q 042003           80 LKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL  159 (248)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  159 (248)
                      ...+..+... .+...|++++|||+++........++.++..+...........+.+.+........+...+..++....
T Consensus       187 ~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  265 (412)
T 3fht_A          187 QDQSIRIQRM-LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAIT  265 (412)
T ss_dssp             HHHHHHHHHT-SCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHhh-CCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCChHHHHHHHHHHHhhcC
Confidence            6777777766 566789999999999999999999999998888777777778888888888888889999999998877


Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD  239 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~  239 (248)
                      ++++||||++++.++.+++.|++.++.+..+||+|+.++|..+++.|++|+.+|||||+++++|+|+|++++||++|+|+
T Consensus       266 ~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~  345 (412)
T 3fht_A          266 IAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPV  345 (412)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEESSCCB
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEEECCCC
Confidence            88999999999999999999999999999999999999999999999999999999999999999999999999999995


Q ss_pred             ------CcccceecC
Q 042003          240 ------SGAAYIHRI  248 (248)
Q Consensus       240 ------~~~~~~qri  248 (248)
                            +..+|+||+
T Consensus       346 ~~~~~~s~~~~~Qr~  360 (412)
T 3fht_A          346 DKDGNPDNETYLHRI  360 (412)
T ss_dssp             CSSSSBCHHHHHHHH
T ss_pred             CCCCCcchheeeccc
Confidence                  457899984

>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=100.00  E-value=6e-39  Score=265.65  Aligned_cols=245  Identities=31%  Similarity=0.457  Sum_probs=212.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+++.++++++..+ ..+....++... .....+++|+|+||+++.+.+.+....+.+++++|+||||++.+...+.
T Consensus        87 L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~  164 (395)
T 3pey_A           87 LARQTLEVVQEMGKFTK-ITSQLIVPDSFE-KNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLG  164 (395)
T ss_dssp             HHHHHHHHHHHHTTTSC-CCEEEESTTSSC-TTSCBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTHH
T ss_pred             HHHHHHHHHHHHhcccC-eeEEEEecCchh-hhccCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCccccH
Confidence            57899999999988777 344444443322 2233478999999999999998888889999999999999988743366


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCC
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLN  160 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  160 (248)
                      ..+..+... .+...|++++|||+++........++.++..+...........+.+.+........+...+..++....+
T Consensus       165 ~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  243 (395)
T 3pey_A          165 DQCIRVKRF-LPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTI  243 (395)
T ss_dssp             HHHHHHHHT-SCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHHTTTTS
T ss_pred             HHHHHHHHh-CCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHHHhccC
Confidence            777777766 5567899999999999889999999888888877777777777888888888888899999999988878


Q ss_pred             CCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCC-
Q 042003          161 PPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD-  239 (248)
Q Consensus       161 ~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~-  239 (248)
                      +++||||++++.++.+++.|++.++.+..+||+|+.++|.++++.|++|+.+|||||+++++|+|+|++++||++|+|+ 
T Consensus       244 ~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~  323 (395)
T 3pey_A          244 GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTL  323 (395)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESSCCBC
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcCCCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             -----CcccceecC
Q 042003          240 -----SGAAYIHRI  248 (248)
Q Consensus       240 -----~~~~~~qri  248 (248)
                           |+..|+||+
T Consensus       324 ~~~~~s~~~~~Qr~  337 (395)
T 3pey_A          324 ANGQADPATYIHRI  337 (395)
T ss_dssp             TTSSBCHHHHHHHH
T ss_pred             CcCCCCHHHhhHhc
Confidence                 999999984

>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=100.00  E-value=7.3e-39  Score=265.05  Aligned_cols=246  Identities=26%  Similarity=0.359  Sum_probs=205.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhh----cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRS----TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+++.++++....+...+..+.|+...    .......++|+|+||+++.+.+......+.+++++|+||||++.++
T Consensus        88 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~  167 (391)
T 1xti_A           88 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  167 (391)
T ss_dssp             HHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSS
T ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhc
Confidence            578999999999877632556666665421    1222345899999999999999888888899999999999999875


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccccc-ccccceeEEEEcCCchhHHHHHHHHH
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNT-ASESIKQKLVFAGSEEGKLLALRQSF  155 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~  155 (248)
                      ..+...+..++.. .+...|++++|||+++........++.++..+....... ....+.+.+... ....+...+.+++
T Consensus       168 ~~~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~l  245 (391)
T 1xti_A          168 LDMRRDVQEIFRM-TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKL-KDNEKNRKLFDLL  245 (391)
T ss_dssp             HHHHHHHHHHHHT-SCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEEC-CGGGHHHHHHHHH
T ss_pred             cchHHHHHHHHhh-CCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEc-CchhHHHHHHHHH
Confidence            3377777777776 456789999999999999999998988888776655433 334455555444 4556888888888


Q ss_pred             hccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEec
Q 042003          156 AESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY  235 (248)
Q Consensus       156 ~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~  235 (248)
                      ....++++||||+++++++.+++.|++.++.+..+||+++.++|.++++.|++|+.+|||||+++++|+|+|++++||++
T Consensus       246 ~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~  325 (391)
T 1xti_A          246 DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY  325 (391)
T ss_dssp             HHSCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEES
T ss_pred             HhcCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEe
Confidence            88778899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcccceecC
Q 042003          236 DFPDSGAAYIHRI  248 (248)
Q Consensus       236 ~~p~~~~~~~qri  248 (248)
                      ++|+|+..|+||+
T Consensus       326 ~~p~s~~~~~Qr~  338 (391)
T 1xti_A          326 DMPEDSDTYLHRV  338 (391)
T ss_dssp             SCCSSHHHHHHHH
T ss_pred             CCCCCHHHHHHhc
Confidence            9999999999984

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=100.00  E-value=3e-38  Score=262.18  Aligned_cols=243  Identities=29%  Similarity=0.413  Sum_probs=203.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      |+.|+++.++++.+..+ ..+....|+.   ........+++|+|+||+++.+.+.+....+.+++++|+||||++.+.+
T Consensus       101 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~  179 (400)
T 1s2m_A          101 LALQTSQVVRTLGKHCG-ISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD  179 (400)
T ss_dssp             HHHHHHHHHHHHTTTTT-CCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHH
T ss_pred             HHHHHHHHHHHHhcccC-ceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhc
Confidence            57899999999998877 4444555554   2223345678999999999999998887888999999999999988776


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE  157 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  157 (248)
                       +...+..+... .+...+++++|||+++.........+.++..+.... ......+.+.+... ....+...+..++..
T Consensus       180 -~~~~~~~i~~~-~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~-~~~~k~~~l~~~~~~  255 (400)
T 1s2m_A          180 -FKTIIEQILSF-LPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLKGITQYYAFV-EERQKLHCLNTLFSK  255 (400)
T ss_dssp             -HHHHHHHHHTT-SCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCS-SCBCTTEEEEEEEC-CGGGHHHHHHHHHHH
T ss_pred             -hHHHHHHHHHh-CCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEecc-ccccCCceeEEEEe-chhhHHHHHHHHHhh
Confidence             77777777776 456789999999999988888888888776654332 23334455555444 445688888888888


Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      ...+++||||++++.++.+++.|++.++.+..+||+|+.++|..+++.|++|+.+|||||+++++|+|+|++++||++++
T Consensus       256 ~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~  335 (400)
T 1s2m_A          256 LQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDF  335 (400)
T ss_dssp             SCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSC
T ss_pred             cCCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCC
Confidence            77789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccceecC
Q 042003          238 PDSGAAYIHRI  248 (248)
Q Consensus       238 p~~~~~~~qri  248 (248)
                      |+|+..|+||+
T Consensus       336 p~s~~~~~Qr~  346 (400)
T 1s2m_A          336 PKTAETYLHRI  346 (400)
T ss_dssp             CSSHHHHHHHH
T ss_pred             CCCHHHHHHhc
Confidence            99999999984

>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=100.00  E-value=2.9e-39  Score=274.21  Aligned_cols=247  Identities=28%  Similarity=0.359  Sum_probs=98.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhc-CCcccCceeEEEEeccccccccCcc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNL   79 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~-~~~~~~~~~~lIiDEah~~~~~~~~   79 (248)
                      ||.|+++.++++.+..+...+....++.........+++|+|+||+++.+++.+ +.+.+.+++++|+||||++.+...+
T Consensus       174 La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~~  253 (479)
T 3fmp_B          174 LALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGH  253 (479)
T ss_dssp             HHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTTH
T ss_pred             HHHHHHHHHHHHHhhCCCceEEEEeCCccccccccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCCc
Confidence            688999999998876543455555555544444456789999999999999966 4567899999999999998874336


Q ss_pred             cccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccC
Q 042003           80 LKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL  159 (248)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  159 (248)
                      ...+..+.+. .+..+|++++|||++.........++.++..+...........+.+.+..+.....+...+..++....
T Consensus       254 ~~~~~~i~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  332 (479)
T 3fmp_B          254 QDQSIRIQRM-LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAIT  332 (479)
T ss_dssp             HHHHHHHHTT-SCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC----------------------------------
T ss_pred             HHHHHHHHhh-CCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHHHHHhhcc
Confidence            6667777766 556799999999999999999999999998888887777777788888777777788888888888777


Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD  239 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~  239 (248)
                      .++++|||++++.++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||+||+|.
T Consensus       333 ~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~  412 (479)
T 3fmp_B          333 IAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPV  412 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEecCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999995


Q ss_pred             ------CcccceecC
Q 042003          240 ------SGAAYIHRI  248 (248)
Q Consensus       240 ------~~~~~~qri  248 (248)
                            +...|+||+
T Consensus       413 ~~~~~~s~~~~~Qr~  427 (479)
T 3fmp_B          413 DKDGNPDNETYLHRI  427 (479)
T ss_dssp             ---------------
T ss_pred             CCccCCCHHHHHHHh
Confidence                  568999996

>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=100.00  E-value=1.8e-39  Score=268.87  Aligned_cols=245  Identities=30%  Similarity=0.432  Sum_probs=99.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhh--cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRS--TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      |+.|+++.++++....+ ..+....|+...  ......+++|+|+||+++.+.+.++...+.+++++|+||||++.+++ 
T Consensus       101 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~~-  178 (394)
T 1fuu_A          101 LALQIQKVVMALAFHMD-IKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG-  178 (394)
T ss_dssp             HHHHHHHHHHHHTTTSC-CCEEEECSSCCHHHHHHHHHHCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhccCC-eeEEEEeCCCchHHHHhhcCCCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhCCC-
Confidence            57899999999988877 445555554421  11112268999999999999999888888999999999999998887 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES  158 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  158 (248)
                      +...+..+... .+...|++++|||+++...+....++.++..+...........+.+.+......+.+...+..+++..
T Consensus       179 ~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  257 (394)
T 1fuu_A          179 FKEQIYQIFTL-LPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSI  257 (394)
T ss_dssp             CHHHHHHHHHH-SCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC--------------------------------
T ss_pred             cHHHHHHHHHh-CCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHHhcC
Confidence            77888888777 45678999999999998888888888888888777666666667777766666666778888888777


Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                      ..++++|||++++.++.+++.|++.++.+..+||+++.++|.++++.|++|+.+|||||+++++|+|+|++++||++++|
T Consensus       258 ~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p  337 (394)
T 1fuu_A          258 SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLP  337 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCC
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccceecC
Q 042003          239 DSGAAYIHRI  248 (248)
Q Consensus       239 ~~~~~~~qri  248 (248)
                      +|+..|+||+
T Consensus       338 ~s~~~~~Qr~  347 (394)
T 1fuu_A          338 ANKENYIHRI  347 (394)
T ss_dssp             ----------
T ss_pred             CCHHHHHHHc
Confidence            9999999995

>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=100.00  E-value=4.7e-37  Score=251.95  Aligned_cols=239  Identities=33%  Similarity=0.477  Sum_probs=198.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhc--ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRST--DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      |+.|+++.++++....+ ..+....|+....  .....+++|+|+||+++.+.+..+...+.+++++|+||||.+.+++ 
T Consensus        86 L~~q~~~~~~~~~~~~~-~~v~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~-  163 (367)
T 1hv8_A           86 LAIQVADEIESLKGNKN-LKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG-  163 (367)
T ss_dssp             HHHHHHHHHHHHHCSSC-CCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTT-
T ss_pred             HHHHHHHHHHHHhCCCC-ceEEEEECCcchHHHHhhcCCCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhc-
Confidence            57899999999988776 4444455544211  1122378999999999999999888888999999999999998887 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES  158 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  158 (248)
                      +...+..++.. .....+++++|||+++........++++...+.....    ..+.+.+... ....+...+..++...
T Consensus       164 ~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~-~~~~~~~~l~~~l~~~  237 (367)
T 1hv8_A          164 FIKDVEKILNA-CNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKIN----ANIEQSYVEV-NENERFEALCRLLKNK  237 (367)
T ss_dssp             THHHHHHHHHT-SCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCSS----SSSEEEEEEC-CGGGHHHHHHHHHCST
T ss_pred             hHHHHHHHHHh-CCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecCC----CCceEEEEEe-ChHHHHHHHHHHHhcC
Confidence            77777777776 4567899999999999888888888777655543222    2344444443 4556888888888744


Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                       +.+++|||++++.++.+++.|++.++++..+||+++.++|.++++.|++|+.+|||||+++++|+|+|++++||++++|
T Consensus       238 -~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~  316 (367)
T 1hv8_A          238 -EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLP  316 (367)
T ss_dssp             -TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCC
T ss_pred             -CCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecCC
Confidence             6899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccceecC
Q 042003          239 DSGAAYIHRI  248 (248)
Q Consensus       239 ~~~~~~~qri  248 (248)
                      +|+.+|+||+
T Consensus       317 ~s~~~~~Q~~  326 (367)
T 1hv8_A          317 QNPESYMHRI  326 (367)
T ss_dssp             SCHHHHHHHS
T ss_pred             CCHHHhhhcc
Confidence            9999999985

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

Probab=100.00  E-value=5.1e-37  Score=265.80  Aligned_cols=247  Identities=30%  Similarity=0.379  Sum_probs=190.8

Q ss_pred             CcchHHHHHHHhhcC---CCcEEEEcccchhh----hcccccCCCcEEEeChHHHHHHHhcC-CcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKG---NKFQIKLMKKELVR----STDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~---~~~~~~~~~~~~~~----~~~~~~~~~~i~v~Tp~~l~~~~~~~-~~~~~~~~~lIiDEah~   72 (248)
                      ||.|+++.++++...   .....+....|+..    .......+++|+|+||+++.+.+... ...+++++++|+||||+
T Consensus       107 La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~  186 (579)
T 3sqw_A          107 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR  186 (579)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHH
Confidence            688999999987632   11133444444442    12223447999999999999988764 44678899999999999


Q ss_pred             ccccCcccccchhHhhhCC------CccceeEEEEeecCchHHHHHHHhcCCcEEEEEccc----ccccccceeEEEEcC
Q 042003           73 LFEVGNLLKHIDPVVKACS------NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK----NTASESIKQKLVFAG  142 (248)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~------~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~  142 (248)
                      +.+++ |...+..+...+.      ...+|++++|||+++....+..+++.++..+.....    ......+.+......
T Consensus       187 l~~~g-f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~  265 (579)
T 3sqw_A          187 LLEIG-FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISE  265 (579)
T ss_dssp             HTSTT-THHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEES
T ss_pred             hhcCC-CHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEec
Confidence            99998 8887777765532      236799999999999989999888888776654432    222334455555555


Q ss_pred             CchhHH----HHHHHHHhc-cCCCCEEEEecchHHHHHHHHHhhcC---CCeeEEEecCCCHHHHHHHHHHhhcCCceEE
Q 042003          143 SEEGKL----LALRQSFAE-SLNPPVLIFVQSKERAKELYGELAFD---GIRAGVIHSDLSQTQRENAVDDFRAGKTWVL  214 (248)
Q Consensus       143 ~~~~~~----~~l~~~~~~-~~~~~~liF~~~~~~~~~l~~~L~~~---~~~v~~~~~~~~~~~r~~~~~~f~~g~~~il  214 (248)
                      ....+.    ..+...+.. ..+.++||||++++.++.+++.|++.   ++.+..+||+|++++|..+++.|++|+.+||
T Consensus       266 ~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vL  345 (579)
T 3sqw_A          266 KFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGIL  345 (579)
T ss_dssp             STTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEE
T ss_pred             chhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEE
Confidence            433332    333333333 44679999999999999999999876   8999999999999999999999999999999


Q ss_pred             EEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          215 IATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       215 v~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |||+++++|+|+|++++||++++|.++..|+||+
T Consensus       346 VaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~  379 (579)
T 3sqw_A          346 VCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI  379 (579)
T ss_dssp             EECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHH
T ss_pred             EEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhc
Confidence            9999999999999999999999999999999985

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=100.00  E-value=1.1e-36  Score=263.21  Aligned_cols=247  Identities=30%  Similarity=0.386  Sum_probs=189.9

Q ss_pred             CcchHHHHHHHhhcC---CCcEEEEcccchhh----hcccccCCCcEEEeChHHHHHHHhcC-CcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKG---NKFQIKLMKKELVR----STDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~---~~~~~~~~~~~~~~----~~~~~~~~~~i~v~Tp~~l~~~~~~~-~~~~~~~~~lIiDEah~   72 (248)
                      ||.|+++.++++...   .....+....|+..    .......+++|+|+||+++.+.+.+. ...+++++++|+||||+
T Consensus       158 La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~  237 (563)
T 3i5x_A          158 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR  237 (563)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHH
Confidence            688999999987542   11123344444442    12223457999999999999988764 34578899999999999


Q ss_pred             ccccCcccccchhHhhhCC------CccceeEEEEeecCchHHHHHHHhcCCcEEEEEccc----ccccccceeEEEEcC
Q 042003           73 LFEVGNLLKHIDPVVKACS------NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK----NTASESIKQKLVFAG  142 (248)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~------~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~  142 (248)
                      +.+++ |...+..+...+.      ...+|++++|||+++....+..+++.++..+.....    ......+.+.+....
T Consensus       238 l~~~~-f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  316 (563)
T 3i5x_A          238 LLEIG-FRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISE  316 (563)
T ss_dssp             HTSTT-THHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEES
T ss_pred             Hhccc-hHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECc
Confidence            99998 8887777755431      246799999999999889998888888766654322    222334445555554


Q ss_pred             CchhHHH----HHHHHHhc-cCCCCEEEEecchHHHHHHHHHhhcC---CCeeEEEecCCCHHHHHHHHHHhhcCCceEE
Q 042003          143 SEEGKLL----ALRQSFAE-SLNPPVLIFVQSKERAKELYGELAFD---GIRAGVIHSDLSQTQRENAVDDFRAGKTWVL  214 (248)
Q Consensus       143 ~~~~~~~----~l~~~~~~-~~~~~~liF~~~~~~~~~l~~~L~~~---~~~v~~~~~~~~~~~r~~~~~~f~~g~~~il  214 (248)
                      ....+..    .+...+.. ..+.++||||++++.++.+++.|++.   ++.+..+||+|++.+|..+++.|++|+.+||
T Consensus       317 ~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vL  396 (563)
T 3i5x_A          317 KFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGIL  396 (563)
T ss_dssp             STTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEE
T ss_pred             hhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEE
Confidence            4433332    23333332 44679999999999999999999876   8999999999999999999999999999999


Q ss_pred             EEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          215 IATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       215 v~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |||+++++|+|+|++++||++++|.|+..|+||+
T Consensus       397 vaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~  430 (563)
T 3i5x_A          397 VCTDVGARGMDFPNVHEVLQIGVPSELANYIHRI  430 (563)
T ss_dssp             EECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHH
T ss_pred             EEcchhhcCCCcccCCEEEEECCCCchhhhhhhc
Confidence            9999999999999999999999999999999985

>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=100.00  E-value=4.9e-36  Score=243.27  Aligned_cols=235  Identities=27%  Similarity=0.405  Sum_probs=190.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhc--ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRST--DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      |+.|+++.++++++..+ ..+....|+....  .....+++|+|+||+++.+.+..+...+.+++++|+||||++.+++ 
T Consensus        68 L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~-  145 (337)
T 2z0m_A           68 LTRQVASHIRDIGRYMD-TKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMG-  145 (337)
T ss_dssp             HHHHHHHHHHHHTTTSC-CCEEEECTTSCHHHHHHHHTTCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhhhcC-CcEEEEECCcchHHHHhhcCCCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccc-
Confidence            57899999999988877 4455555554211  1122359999999999999998887788999999999999998887 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES  158 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  158 (248)
                      +...+..++.. .+...+++++|||+++........++.++..+...   .....+.+.+.........   ....+...
T Consensus       146 ~~~~~~~~~~~-~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~---~~~~~~~~  218 (337)
T 2z0m_A          146 FIDDIKIILAQ-TSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKDDWRS---KVQALREN  218 (337)
T ss_dssp             CHHHHHHHHHH-CTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS---GGGGGEEEEEEECSSSSHH---HHHHHHTC
T ss_pred             cHHHHHHHHhh-CCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc---cccCCceEEEEEeChHHHH---HHHHHHhC
Confidence            77778877777 45677889999999998888888888777655322   2334455555555544322   22445555


Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                      .+++++|||+++++++.+++.|+    ++..+||+++.++|.++++.|++|+.+|||||+++++|+|+|++++||++++|
T Consensus       219 ~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~  294 (337)
T 2z0m_A          219 KDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAP  294 (337)
T ss_dssp             CCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCC
T ss_pred             CCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCC
Confidence            67899999999999999999997    68899999999999999999999999999999999999999999999999999


Q ss_pred             CCcccceecC
Q 042003          239 DSGAAYIHRI  248 (248)
Q Consensus       239 ~~~~~~~qri  248 (248)
                      +|+..|+||+
T Consensus       295 ~s~~~~~Q~~  304 (337)
T 2z0m_A          295 QDLRTYIHRI  304 (337)
T ss_dssp             SSHHHHHHHH
T ss_pred             CCHHHhhHhc
Confidence            9999999984

>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=100.00  E-value=4.4e-35  Score=252.60  Aligned_cols=241  Identities=17%  Similarity=0.170  Sum_probs=178.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcc-------c--ccCCCcEEEeChHHHHH---HHh--cCCcccCceeEEE
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTD-------L--SKFSCDILISTPLRLRL---AIR--RKKIDLSRVEYLV   66 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~--~~~~~~i~v~Tp~~l~~---~~~--~~~~~~~~~~~lI   66 (248)
                      |+.|+.+.++++    + ..+..+.|+.....       .  ....++|+|+||+++..   ++.  .....+.+++++|
T Consensus        96 L~~q~~~~l~~~----g-i~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iV  170 (591)
T 2v1x_A           96 LMEDQLMVLKQL----G-ISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIA  170 (591)
T ss_dssp             HHHHHHHHHHHH----T-CCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEE
T ss_pred             HHHHHHHHHHhc----C-CcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEE
Confidence            567888888887    3 23444454441111       1  34679999999998742   221  1233467899999


Q ss_pred             EeccccccccC-cccccchhH--hhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCC
Q 042003           67 LDEADKLFEVG-NLLKHIDPV--VKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS  143 (248)
Q Consensus        67 iDEah~~~~~~-~~~~~~~~~--~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  143 (248)
                      +||||++.+|| +|+..+..+  +.. ..+..+++++|||+++........++..+....... ....+++...+.....
T Consensus       171 iDEAH~is~~g~dfr~~~~~l~~l~~-~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~-~~~r~nl~~~v~~~~~  248 (591)
T 2v1x_A          171 VDEVHCCSQWGHDFRPDYKALGILKR-QFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTA-SFNRPNLYYEVRQKPS  248 (591)
T ss_dssp             EETGGGGSTTCTTCCGGGGGGGHHHH-HCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEEC-CCCCTTEEEEEEECCS
T ss_pred             EECcccccccccccHHHHHHHHHHHH-hCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEec-CCCCcccEEEEEeCCC
Confidence            99999999886 366655442  222 224688999999999987777666655443222211 2223334333333222


Q ss_pred             -chhHHHHHHHHHhcc-CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccc
Q 042003          144 -EEGKLLALRQSFAES-LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIA  221 (248)
Q Consensus       144 -~~~~~~~l~~~~~~~-~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~  221 (248)
                       ...+...+.+++... .++++||||++++.++.+++.|+..++.+..+||+|++++|..+++.|.+|+.+|||||++++
T Consensus       249 ~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~  328 (591)
T 2v1x_A          249 NTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFG  328 (591)
T ss_dssp             SHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSC
T ss_pred             cHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhh
Confidence             345667777777643 468999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCcEEEeccCCCCcccceecC
Q 042003          222 RGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       222 ~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +|||+|++++||++++|.|+..|+||+
T Consensus       329 ~GID~p~V~~VI~~~~p~s~~~y~Qr~  355 (591)
T 2v1x_A          329 MGIDKPDVRFVIHHSMSKSMENYYQES  355 (591)
T ss_dssp             TTCCCSCEEEEEESSCCSSHHHHHHHH
T ss_pred             cCCCcccccEEEEeCCCCCHHHHHHHh
Confidence            999999999999999999999999984

>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=100.00  E-value=1.8e-34  Score=246.33  Aligned_cols=235  Identities=17%  Similarity=0.221  Sum_probs=173.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh-------hcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR-------STDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      |+.|+.+.++++    + ..+..+.++..       ......+.++|+++||+++......+.+...+++++|+||||++
T Consensus        77 L~~q~~~~l~~~----g-i~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i  151 (523)
T 1oyw_A           77 LMKDQVDQLQAN----G-VAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCI  151 (523)
T ss_dssp             HHHHHHHHHHHT----T-CCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGG
T ss_pred             HHHHHHHHHHHc----C-CcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCcccc
Confidence            456777777765    2 22333334331       12233456999999999986433333344578999999999999


Q ss_pred             cccC-ccccc---chhHhhhCCCccceeEEEEeecCchHHHH-HHHhc-CCcEEEEEcccccccccceeEEEEcCCchhH
Q 042003           74 FEVG-NLLKH---IDPVVKACSNPSIVRSLFSATLPDFVEEL-ARSIM-HDAVRVIVGRKNTASESIKQKLVFAGSEEGK  147 (248)
Q Consensus        74 ~~~~-~~~~~---~~~~~~~~~~~~~~~i~~SAT~~~~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (248)
                      .+|| .|+..   +..+...+  +..+++++|||+++..... ...+. .++... .....  .+++.....   ....+
T Consensus       152 ~~~g~~fr~~~~~l~~l~~~~--~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~-~~~~~--r~~l~~~v~---~~~~~  223 (523)
T 1oyw_A          152 SQWGHDFRPEYAALGQLRQRF--PTLPFMALTATADDTTRQDIVRLLGLNDPLIQ-ISSFD--RPNIRYMLM---EKFKP  223 (523)
T ss_dssp             CTTSSCCCHHHHGGGGHHHHC--TTSCEEEEESCCCHHHHHHHHHHHTCCSCEEE-ECCCC--CTTEEEEEE---ECSSH
T ss_pred             CcCCCccHHHHHHHHHHHHhC--CCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEE-eCCCC--CCceEEEEE---eCCCH
Confidence            9887 34443   33344442  4578999999999876553 33342 334333 22222  233333222   23456


Q ss_pred             HHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCC
Q 042003          148 LLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK  227 (248)
Q Consensus       148 ~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip  227 (248)
                      ...+.+++....++++||||++++.++.+++.|++.++.+..+||+|+.++|..+++.|++|+.+|||||+++++|+|+|
T Consensus       224 ~~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p  303 (523)
T 1oyw_A          224 LDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKP  303 (523)
T ss_dssp             HHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCT
T ss_pred             HHHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCcc
Confidence            77788888877678999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEeccCCCCcccceecC
Q 042003          228 GVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       228 ~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++++||++++|.|+..|+||+
T Consensus       304 ~v~~VI~~~~p~s~~~y~Qr~  324 (523)
T 1oyw_A          304 NVRFVVHFDIPRNIESYYQET  324 (523)
T ss_dssp             TCCEEEESSCCSSHHHHHHHH
T ss_pred             CccEEEEECCCCCHHHHHHHh
Confidence            999999999999999999984

>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=100.00  E-value=1.5e-34  Score=249.44  Aligned_cols=247  Identities=15%  Similarity=0.102  Sum_probs=135.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh---hcccccCCCcEEEeChHHHHHHHhcCCc-ccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR---STDLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~v~Tp~~l~~~~~~~~~-~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+.+.++++.+..+ ..+..+.|+..   .......+++|+|+||+++.+.+..+.. .+.+++++|+||||++.++
T Consensus        67 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~  145 (556)
T 4a2p_A           67 VYEQQKNVFKHHFERQG-YSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGN  145 (556)
T ss_dssp             HHHHHHHHHHHHHGGGT-CCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTT
T ss_pred             HHHHHHHHHHHHhcccC-ceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCc
Confidence            67899999999988777 44555666552   2223445799999999999999988877 7899999999999999887


Q ss_pred             CcccccchhHhhhC---CCccceeEEEEeecCch-----------HHHHHHHhc------------------CCcEEEEE
Q 042003           77 GNLLKHIDPVVKAC---SNPSIVRSLFSATLPDF-----------VEELARSIM------------------HDAVRVIV  124 (248)
Q Consensus        77 ~~~~~~~~~~~~~~---~~~~~~~i~~SAT~~~~-----------~~~~~~~~~------------------~~~~~~~~  124 (248)
                      +.+...+.......   ..+..+++++|||++..           ...+...+.                  ..+.....
T Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  225 (556)
T 4a2p_A          146 HPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVR  225 (556)
T ss_dssp             SHHHHHHHHHHHHHHCC---CCEEEEEESCCCCTTCSSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHTCCCCEEEE
T ss_pred             chHHHHHHHHHHhhhcccCCCCeEEEEeCCcccCchhhHHHHHHHHHHHHHhcCCeEecchhcchHHHHhcCCCCceEEE
Confidence            74433333333221   13568899999998531           111111111                  11111110


Q ss_pred             cccccccccce---------------e----------------------EE-----------------------------
Q 042003          125 GRKNTASESIK---------------Q----------------------KL-----------------------------  138 (248)
Q Consensus       125 ~~~~~~~~~~~---------------~----------------------~~-----------------------------  138 (248)
                      ...........               .                      +.                             
T Consensus       226 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  305 (556)
T 4a2p_A          226 LVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICT  305 (556)
T ss_dssp             ECCCCSCCHHHHHHHHHHHHHHHHHHHHCC---------CCCSSHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHH
T ss_pred             EcCCCcCChHHHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhhHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHH
Confidence            00000000000               0                      00                             


Q ss_pred             -----------------------------------------------------------EEcCCchhHHHHHHHHHhc--
Q 042003          139 -----------------------------------------------------------VFAGSEEGKLLALRQSFAE--  157 (248)
Q Consensus       139 -----------------------------------------------------------~~~~~~~~~~~~l~~~~~~--  157 (248)
                                                                                 ........|...+.+++..  
T Consensus       306 ~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~~l~~~~  385 (556)
T 4a2p_A          306 EHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAY  385 (556)
T ss_dssp             HHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTHHHHHHHHHCSSSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhHHHHhhhhccCCCCCChHHHHHHHHHHHHh
Confidence                                                                       0000113455556666643  


Q ss_pred             --cCCCCEEEEecchHHHHHHHHHhhcC------------CCeeEEEecCCCHHHHHHHHHHhhc-CCceEEEEeccccc
Q 042003          158 --SLNPPVLIFVQSKERAKELYGELAFD------------GIRAGVIHSDLSQTQRENAVDDFRA-GKTWVLIATDVIAR  222 (248)
Q Consensus       158 --~~~~~~liF~~~~~~~~~l~~~L~~~------------~~~v~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~  222 (248)
                        ..+.++||||+++..++.+++.|++.            |.....+||+|+.++|.++++.|++ |+.+|||||+++++
T Consensus       386 ~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~  465 (556)
T 4a2p_A          386 RYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADE  465 (556)
T ss_dssp             HHCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC----
T ss_pred             cCCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhc
Confidence              34689999999999999999999875            4556667888999999999999999 99999999999999


Q ss_pred             CCCCCCCcEEEeccCCCCcccceecC
Q 042003          223 GMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       223 Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+|+|++++||+||+|+|+.+|+||+
T Consensus       466 GiDip~v~~VI~~d~p~s~~~~~Qr~  491 (556)
T 4a2p_A          466 GIDIVQCNLVVLYEYSGNVTKMIQVR  491 (556)
T ss_dssp             -------CEEEEETCCSCHHHHHHC-
T ss_pred             CCCchhCCEEEEeCCCCCHHHHHHhc
Confidence            99999999999999999999999996

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

Probab=100.00  E-value=4e-33  Score=240.29  Aligned_cols=245  Identities=17%  Similarity=0.141  Sum_probs=151.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhc---ccccCCCcEEEeChHHHHHHHhcCCc-ccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRST---DLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~i~v~Tp~~l~~~~~~~~~-~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+.+.++++.+..+ ..+..+.|+....   .....+++|+|+||+++.+.+..+.. .+.+++++|+||||++.+.
T Consensus        64 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~  142 (555)
T 3tbk_A           64 VYEQQATVFSRYFERLG-YNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKN  142 (555)
T ss_dssp             HHHHHHHHHHHHHHTTT-CCEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTT
T ss_pred             HHHHHHHHHHHHhccCC-cEEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCc
Confidence            67899999999998777 4455566655222   23445699999999999999988777 7899999999999999887


Q ss_pred             CcccccchhHhhhC----CCccceeEEEEeecCch-----------HHHHHHHhcCCcEEEEEcccc-----ccccccee
Q 042003           77 GNLLKHIDPVVKAC----SNPSIVRSLFSATLPDF-----------VEELARSIMHDAVRVIVGRKN-----TASESIKQ  136 (248)
Q Consensus        77 ~~~~~~~~~~~~~~----~~~~~~~i~~SAT~~~~-----------~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~  136 (248)
                      +.+...+...+...    .....+++++|||++..           ...+...+ ... .+......     ........
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~~~~l~~~l-~~~-~~~~~~~~~~~l~~~~~~~~~  220 (555)
T 3tbk_A          143 HPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGVGDAKTAEEAMQHICKLCAAL-DAS-VIATVRDNVAELEQVVYKPQK  220 (555)
T ss_dssp             CHHHHHHHHHHHHHTSSCCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHT-TCS-EEECCCSCHHHHHTTCCCCCE
T ss_pred             chHHHHHHHHHHhhhccccCCCCeEEEEecCcccCccccHHHHHHHHHHHHHhc-CCe-eeeccccCHHHHHhhcCCCce
Confidence            64444444443331    12557999999999542           11111111 111 11110000     00000000


Q ss_pred             EEEEc---------------------------------------------------------------------------
Q 042003          137 KLVFA---------------------------------------------------------------------------  141 (248)
Q Consensus       137 ~~~~~---------------------------------------------------------------------------  141 (248)
                      .....                                                                           
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  300 (555)
T 3tbk_A          221 ISRKVASRTSNTFKCIISQLMKETEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQMADKEEESRVCKAL  300 (555)
T ss_dssp             EEEECCCCSCCHHHHHHHHHHHHHHHHHHTSCHHHHGGGGCCSCCSSSHHHHHHHHHHHHHHHTCCCSSHHHHHHHHHHH
T ss_pred             EEEEecCcccChHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhhhHHHHHHHHHhhhhhccchhhHHHHHHHH
Confidence            00000                                                                           


Q ss_pred             ------------------------------------------------------------------CCchhHHHHHHHHH
Q 042003          142 ------------------------------------------------------------------GSEEGKLLALRQSF  155 (248)
Q Consensus       142 ------------------------------------------------------------------~~~~~~~~~l~~~~  155 (248)
                                                                                        .....|...+.+++
T Consensus       301 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l  380 (555)
T 3tbk_A          301 FLYTSHLRKYNDALIISEDAQMTDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVL  380 (555)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHCC-----HHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhccCCCcCCHHHHHHHHHH
Confidence                                                                              01134555555555


Q ss_pred             hc----cCCCCEEEEecchHHHHHHHHHhhcCC------------CeeEEEecCCCHHHHHHHHHHhhc-CCceEEEEec
Q 042003          156 AE----SLNPPVLIFVQSKERAKELYGELAFDG------------IRAGVIHSDLSQTQRENAVDDFRA-GKTWVLIATD  218 (248)
Q Consensus       156 ~~----~~~~~~liF~~~~~~~~~l~~~L~~~~------------~~v~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~T~  218 (248)
                      ..    ..+.++||||+++..++.+++.|+..+            .+...+||+|++++|.++++.|++ |+.+|||||+
T Consensus       381 ~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~  460 (555)
T 3tbk_A          381 QEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATS  460 (555)
T ss_dssp             HHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECC
T ss_pred             HHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcc
Confidence            43    346899999999999999999998763            344555679999999999999999 9999999999


Q ss_pred             ccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          219 VIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       219 ~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++++|+|+|++++||+||+|+|+.+|+||+
T Consensus       461 ~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~  490 (555)
T 3tbk_A          461 VADEGIDIAECNLVILYEYVGNVIKMIQTR  490 (555)
T ss_dssp             CTTCCEETTSCSEEEEESCCSSCCCEECSS
T ss_pred             hhhcCCccccCCEEEEeCCCCCHHHHHHhc
Confidence            999999999999999999999999999996

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

Probab=100.00  E-value=4.1e-34  Score=252.82  Aligned_cols=247  Identities=18%  Similarity=0.208  Sum_probs=149.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCc-ccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~-~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+.+.++++++..+ ..+..+.|+.   .+......+++|+|+||++|.+.+..+.+ .+.+++++|+||||++.+.
T Consensus        73 L~~Q~~~~~~~~~~~~~-~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~  151 (696)
T 2ykg_A           73 VYEQNKSVFSKYFERHG-YRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQ  151 (696)
T ss_dssp             HHHHHHHHHHHHTTTTT-CCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTT
T ss_pred             HHHHHHHHHHHHhccCC-ceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCc
Confidence            57899999999998777 4455555654   22233345799999999999999998776 7899999999999999876


Q ss_pred             CcccccchhHhhh----CCCccceeEEEEeecCc-------h-HHHHHHH---------------------hcCCcEEEE
Q 042003           77 GNLLKHIDPVVKA----CSNPSIVRSLFSATLPD-------F-VEELARS---------------------IMHDAVRVI  123 (248)
Q Consensus        77 ~~~~~~~~~~~~~----~~~~~~~~i~~SAT~~~-------~-~~~~~~~---------------------~~~~~~~~~  123 (248)
                      ..+...+...+..    ......++++||||+..       . ...+...                     +...|....
T Consensus       152 ~~~~~i~~~~l~~~~~~~~~~~~~il~LTATp~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~l~~~~~~p~~~~  231 (696)
T 2ykg_A          152 HPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFF  231 (696)
T ss_dssp             CHHHHHHHHHHHHHHTTCCSCCCEEEEEESCCCCSSCCSHHHHHHHHHHHHHHTTCCEEECCCTTHHHHHHHSCCCEEEE
T ss_pred             ccHHHHHHHHHHHhhcccCCCCCeEEEEeCccccCccccHHHHHHHHHHHHHhcCCceEeecccchHHHHhhcCCCceeE
Confidence            5444444333322    23466899999999861       1 1111111                     111121111


Q ss_pred             Eccccccc------------------------------------------------------------------------
Q 042003          124 VGRKNTAS------------------------------------------------------------------------  131 (248)
Q Consensus       124 ~~~~~~~~------------------------------------------------------------------------  131 (248)
                      ........                                                                        
T Consensus       232 ~~~~~~~~~~fs~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  311 (696)
T 2ykg_A          232 RKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFL  311 (696)
T ss_dssp             EECCCCSCCHHHHHHHHHHHHHHHHHHHHSTTGGGSSSCCSCCSSSHHHHHHHHHHHHTSCC------CCHHHHHHHHHH
T ss_pred             EecCcccCChHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHHHHHHhhcccchhhhHHHHHHHH
Confidence            00000000                                                                        


Q ss_pred             ---------------------------------------ccceeEEE---------------EcCCchhHHHHHHHHHhc
Q 042003          132 ---------------------------------------ESIKQKLV---------------FAGSEEGKLLALRQSFAE  157 (248)
Q Consensus       132 ---------------------------------------~~~~~~~~---------------~~~~~~~~~~~l~~~~~~  157 (248)
                                                             ..+.+.+.               .......|...+.+++..
T Consensus       312 ~~~~l~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~ll~~  391 (696)
T 2ykg_A          312 YTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQE  391 (696)
T ss_dssp             HHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHHhccchhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence                                                   00000000               000133567777777765


Q ss_pred             c----CCCCEEEEecchHHHHHHHHHhhcCC----CeeEEE--------ecCCCHHHHHHHHHHhhc-CCceEEEEeccc
Q 042003          158 S----LNPPVLIFVQSKERAKELYGELAFDG----IRAGVI--------HSDLSQTQRENAVDDFRA-GKTWVLIATDVI  220 (248)
Q Consensus       158 ~----~~~~~liF~~~~~~~~~l~~~L~~~~----~~v~~~--------~~~~~~~~r~~~~~~f~~-g~~~ilv~T~~~  220 (248)
                      .    .++++||||+++..++.+++.|+..+    +++..+        ||+|+.++|+++++.|++ |+.+|||||+++
T Consensus       392 ~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~  471 (696)
T 2ykg_A          392 EYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVA  471 (696)
T ss_dssp             HHTTCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESS
T ss_pred             HhccCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechh
Confidence            4    46799999999999999999999887    788888        559999999999999998 999999999999


Q ss_pred             ccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          221 ARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       221 ~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++|+|+|++++||+||+|+|+.+|+||+
T Consensus       472 ~~GiDip~v~~VI~~d~p~s~~~~~Qr~  499 (696)
T 2ykg_A          472 DEGIDIAQCNLVILYEYVGNVIKMIQTR  499 (696)
T ss_dssp             CCC---CCCSEEEEESCC--CCCC----
T ss_pred             hcCCcCccCCEEEEeCCCCCHHHHHHhh
Confidence            9999999999999999999999999995

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

Probab=100.00  E-value=6.9e-34  Score=237.06  Aligned_cols=229  Identities=21%  Similarity=0.290  Sum_probs=169.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhh-------cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRS-------TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.++++++ .+ ..+..+.|+...       .....+.++|+|+||+++.+.+..  ..+.+++++|+||||++
T Consensus        76 L~~q~~~~~~~~~~-~~-~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~  151 (414)
T 3oiy_A           76 LVKQTLERLQKLAD-EK-VKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAV  151 (414)
T ss_dssp             HHHHHHHHHHHHCC-SS-CCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHH
T ss_pred             HHHHHHHHHHHHcc-CC-ceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhh
Confidence            68899999999988 66 456666665532       122233499999999999888764  55679999999999987


Q ss_pred             cccC----------ccccc-chhHhhhCC----------CccceeEEEEee-cCchHH-HHHHHhcCCcEEEEEcccccc
Q 042003           74 FEVG----------NLLKH-IDPVVKACS----------NPSIVRSLFSAT-LPDFVE-ELARSIMHDAVRVIVGRKNTA  130 (248)
Q Consensus        74 ~~~~----------~~~~~-~~~~~~~~~----------~~~~~~i~~SAT-~~~~~~-~~~~~~~~~~~~~~~~~~~~~  130 (248)
                      .+++          .|... +..++..+.          ....|++++||| .|.... .+...+..    +........
T Consensus       152 ~~~~~~~d~~l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~~~~  227 (414)
T 3oiy_A          152 LKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSV  227 (414)
T ss_dssp             HHCHHHHHHHHHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCCCCC
T ss_pred             hhccchhhhHHhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCccccc
Confidence            6532          15554 555555421          167899999999 454433 23333322    112223334


Q ss_pred             cccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeE-EEecCCCHHHHHHHHHHhhcC
Q 042003          131 SESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAG-VIHSDLSQTQRENAVDDFRAG  209 (248)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~r~~~~~~f~~g  209 (248)
                      ...+.+.+...    ++...+.++++.. ++++||||++++.++.+++.|+..++++. .+||.    +|+  ++.|++|
T Consensus       228 ~~~i~~~~~~~----~~~~~l~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g  296 (414)
T 3oiy_A          228 ARNITHVRISS----RSKEKLVELLEIF-RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVG  296 (414)
T ss_dssp             CCSEEEEEESS----CCHHHHHHHHHHH-CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTT
T ss_pred             cccchheeecc----CHHHHHHHHHHHc-CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCC
Confidence            44555555433    2445556666664 58999999999999999999999999998 88984    444  9999999


Q ss_pred             CceEEEE----ecccccCCCCCC-CcEEEeccCC--CCcccceecC
Q 042003          210 KTWVLIA----TDVIARGMDFKG-VNCVINYDFP--DSGAAYIHRI  248 (248)
Q Consensus       210 ~~~ilv~----T~~~~~Gidip~-~~~Vi~~~~p--~~~~~~~qri  248 (248)
                      +.+||||    |+++++|+|+|+ +++||+||+|  .|+.+|+||+
T Consensus       297 ~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~  342 (414)
T 3oiy_A          297 KINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQAS  342 (414)
T ss_dssp             SCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHH
T ss_pred             CCeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHh
Confidence            9999999    999999999999 9999999999  9999999984

>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=100.00  E-value=2.4e-32  Score=249.18  Aligned_cols=235  Identities=19%  Similarity=0.187  Sum_probs=173.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      ||.|+++.++++...     +.++.|+..    ...+++|+|+||++|.+++.++...++++++||+||||++.+++ +.
T Consensus       239 La~Q~~~~l~~~~~~-----VglltGd~~----~~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~-rg  308 (1108)
T 3l9o_A          239 LSNQKYRELLAEFGD-----VGLMTGDIT----INPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKE-RG  308 (1108)
T ss_dssp             HHHHHHHHHHHHTSS-----EEEECSSCB----CCCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHH-HH
T ss_pred             HHHHHHHHHHHHhCC-----ccEEeCccc----cCCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccc-hH
Confidence            688999999987763     334555433    33568999999999999999988888999999999999998887 77


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHH--HHHHHhcCCcEEEEEcccccccccceeEEEEcCC---------------
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVE--ELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS---------------  143 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------  143 (248)
                      ..+..++.. .+...|+++||||+++...  .+.......+..+......  +..+.++++....               
T Consensus       309 ~~~e~ii~~-l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~r--p~pl~~~~~~~~~~~~~~~vd~~~~~~~  385 (1108)
T 3l9o_A          309 VVWEETIIL-LPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR--PTPLQHYLFPAHGDGIYLVVDEKSTFRE  385 (1108)
T ss_dssp             HHHHHHHHH-SCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCC--SSCEEEEEEETTSSCCEEEEETTTEECH
T ss_pred             HHHHHHHHh-cCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCC--cccceEEEeecCCcceeeeeccccchhh
Confidence            778888877 4678999999999987422  3444444555444332211  1112222211100               


Q ss_pred             ---------------------------------------chhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCC
Q 042003          144 ---------------------------------------EEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDG  184 (248)
Q Consensus       144 ---------------------------------------~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~  184 (248)
                                                             ...+...+...+.....+++||||++++.|+.++..|...+
T Consensus       386 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~  465 (1108)
T 3l9o_A          386 ENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLD  465 (1108)
T ss_dssp             HHHHHHHTTC-----------------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHH
T ss_pred             hhHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhcc
Confidence                                                   02233344444545556799999999999999999986532


Q ss_pred             C---------------------------------------eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCC
Q 042003          185 I---------------------------------------RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMD  225 (248)
Q Consensus       185 ~---------------------------------------~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gid  225 (248)
                      +                                       +++.+||+|++.+|+.+++.|++|..+|||||+++++|+|
T Consensus       466 ~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GID  545 (1108)
T 3l9o_A          466 FNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLN  545 (1108)
T ss_dssp             HHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCC
T ss_pred             CCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCC
Confidence            2                                       2899999999999999999999999999999999999999


Q ss_pred             CCCCcEEEeccCCCCccc--------ceecC
Q 042003          226 FKGVNCVINYDFPDSGAA--------YIHRI  248 (248)
Q Consensus       226 ip~~~~Vi~~~~p~~~~~--------~~qri  248 (248)
                      +|++++||+++.|.+...        |+||+
T Consensus       546 iP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~  576 (1108)
T 3l9o_A          546 MPAKTVVFTSVRKWDGQQFRWVSGGEYIQMS  576 (1108)
T ss_dssp             C--CEEEESCSEEESSSCEEECCHHHHHHHH
T ss_pred             CCCceEEEecCcccCccccccCCHHHHHHhh
Confidence            999999999888765554        88984

>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=99.98  E-value=1.5e-32  Score=243.21  Aligned_cols=236  Identities=18%  Similarity=0.161  Sum_probs=176.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      ||.|+++.++++.+. + ..+....|+.........+++|+|+||+++.+++.+....+++++++|+||+|.+.+++ +.
T Consensus        80 La~q~~~~~~~l~~~-g-~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~-r~  156 (720)
T 2zj8_A           80 LAEEKFQEFQDWEKI-G-LRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRD-RG  156 (720)
T ss_dssp             GHHHHHHHTGGGGGG-T-CCEEEECSCSSCCCGGGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTT-TH
T ss_pred             HHHHHHHHHHHHHhc-C-CEEEEecCCCCccccccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCc-cc
Confidence            678888888766543 4 45666666554433344579999999999999998877778999999999999998766 66


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEE------EEcCC----chhHHHH
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL------VFAGS----EEGKLLA  150 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~----~~~~~~~  150 (248)
                      ..+..++..+.. +.|+++||||+++ ...+..++...  .+.....   +..+...+      .+...    ...+...
T Consensus       157 ~~~~~ll~~l~~-~~~ii~lSATl~n-~~~~~~~l~~~--~~~~~~r---p~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (720)
T 2zj8_A          157 ATLEVILAHMLG-KAQIIGLSATIGN-PEELAEWLNAE--LIVSDWR---PVKLRRGVFYQGFVTWEDGSIDRFSSWEEL  229 (720)
T ss_dssp             HHHHHHHHHHBT-TBEEEEEECCCSC-HHHHHHHTTEE--EEECCCC---SSEEEEEEEETTEEEETTSCEEECSSTTHH
T ss_pred             HHHHHHHHHhhc-CCeEEEEcCCcCC-HHHHHHHhCCc--ccCCCCC---CCcceEEEEeCCeeeccccchhhhhHHHHH
Confidence            777777766543 7899999999987 46666655321  1111111   11111111      11111    2334555


Q ss_pred             HHHHHhccCCCCEEEEecchHHHHHHHHHhhcC---------------------------------CCeeEEEecCCCHH
Q 042003          151 LRQSFAESLNPPVLIFVQSKERAKELYGELAFD---------------------------------GIRAGVIHSDLSQT  197 (248)
Q Consensus       151 l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~---------------------------------~~~v~~~~~~~~~~  197 (248)
                      +.+.++.  ++++||||+++++++.+++.|.+.                                 ..++..+||+|+.+
T Consensus       230 ~~~~~~~--~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~  307 (720)
T 2zj8_A          230 VYDAIRK--KKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRD  307 (720)
T ss_dssp             HHHHHHT--TCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHH
T ss_pred             HHHHHhC--CCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHH
Confidence            5555554  689999999999999999988653                                 12499999999999


Q ss_pred             HHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe----cc----CCCCcccceecC
Q 042003          198 QRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN----YD----FPDSGAAYIHRI  248 (248)
Q Consensus       198 ~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~----~~----~p~~~~~~~qri  248 (248)
                      +|..+++.|++|..+|||||+++++|+|+|++++||+    ||    .|.|..+|.||+
T Consensus       308 ~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~  366 (720)
T 2zj8_A          308 ERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQML  366 (720)
T ss_dssp             HHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHH
Confidence            9999999999999999999999999999999999999    66    589999999984

>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=99.98  E-value=1.7e-32  Score=245.24  Aligned_cols=247  Identities=15%  Similarity=0.132  Sum_probs=141.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCc-ccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~-~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+.+.++++.+..+ ..+..++|+.   ........+++|+|+||+++.+.+..+.. .+.+++++|+||||++.+.
T Consensus       308 L~~Q~~~~~~~~~~~~~-~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~  386 (797)
T 4a2q_A          308 VYEQQKNVFKHHFERQG-YSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGN  386 (797)
T ss_dssp             HHHHHHHHHHHHHGGGT-CCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTT
T ss_pred             HHHHHHHHHHHhcccCC-ceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCC
Confidence            57899999999988766 4556666665   22233456799999999999999988777 7899999999999999876


Q ss_pred             CcccccchhHhhhC---CCccceeEEEEeecCc-----------hHHHHHHHh------------------cCCcEEEEE
Q 042003           77 GNLLKHIDPVVKAC---SNPSIVRSLFSATLPD-----------FVEELARSI------------------MHDAVRVIV  124 (248)
Q Consensus        77 ~~~~~~~~~~~~~~---~~~~~~~i~~SAT~~~-----------~~~~~~~~~------------------~~~~~~~~~  124 (248)
                      +.+...+..+....   ..+..+++++|||++.           ....+...+                  ...+.....
T Consensus       387 ~~~~~i~~~~~~~~~~~~~~~~~~l~lSATp~~~~~~~~~~~~~~i~~l~~~L~~~~i~~~~~~~~~l~~~~~~~~~~~~  466 (797)
T 4a2q_A          387 HPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVR  466 (797)
T ss_dssp             SHHHHHHHHHHHHHHTTCCCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHSCCCCCEEE
T ss_pred             ccHHHHHHHHHHHhhccCCCCCeEEEEcCCccccccccHHHHHHHHHHHHHhcCCcEEecccccHHHHHHhcCCCceEEE
Confidence            64444433333321   1456889999999853           111111111                  111111110


Q ss_pred             ccccccccc--------------c-ee---------E-------------E-----------------------------
Q 042003          125 GRKNTASES--------------I-KQ---------K-------------L-----------------------------  138 (248)
Q Consensus       125 ~~~~~~~~~--------------~-~~---------~-------------~-----------------------------  138 (248)
                      .........              . ..         .             .                             
T Consensus       467 ~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~l~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  546 (797)
T 4a2q_A          467 LVKRRIHNPFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICT  546 (797)
T ss_dssp             ECCCCSCCHHHHHHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHH
T ss_pred             ecCCCCCcHHHHHHHHHHHHHHHHHHHHHhhHHhhhhccccccchhHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHH
Confidence            000000000              0 00         0             0                             


Q ss_pred             -----------------------------------------------------------EEcCCchhHHHHHHHHHhc--
Q 042003          139 -----------------------------------------------------------VFAGSEEGKLLALRQSFAE--  157 (248)
Q Consensus       139 -----------------------------------------------------------~~~~~~~~~~~~l~~~~~~--  157 (248)
                                                                                 ........|...+.+++..  
T Consensus       547 ~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~  626 (797)
T 4a2q_A          547 EHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAY  626 (797)
T ss_dssp             HHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTHHHHHHHHHCTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhccccHHHHHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHHHh
Confidence                                                                       0000013355556666553  


Q ss_pred             --cCCCCEEEEecchHHHHHHHHHhhcC------------CCeeEEEecCCCHHHHHHHHHHhhc-CCceEEEEeccccc
Q 042003          158 --SLNPPVLIFVQSKERAKELYGELAFD------------GIRAGVIHSDLSQTQRENAVDDFRA-GKTWVLIATDVIAR  222 (248)
Q Consensus       158 --~~~~~~liF~~~~~~~~~l~~~L~~~------------~~~v~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~  222 (248)
                        ..+.++||||++++.++.+++.|+..            |.+...+||+|+..+|.++++.|++ |+.+|||||+++++
T Consensus       627 ~~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~  706 (797)
T 4a2q_A          627 RYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADE  706 (797)
T ss_dssp             HHCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC---
T ss_pred             ccCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhc
Confidence              44689999999999999999999763            4566677899999999999999999 99999999999999


Q ss_pred             CCCCCCCcEEEeccCCCCcccceecC
Q 042003          223 GMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       223 Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+|+|++++||+||+|+|+.+|+||+
T Consensus       707 GIDlp~v~~VI~yd~p~s~~~~iQr~  732 (797)
T 4a2q_A          707 GIDIVQCNLVVLYEYSGNVTKMIQVR  732 (797)
T ss_dssp             ----CCCSEEEEESCCSCHHHHHTC-
T ss_pred             CCCchhCCEEEEeCCCCCHHHHHHhc
Confidence            99999999999999999999999996

>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=99.98  E-value=2.5e-32  Score=231.36  Aligned_cols=245  Identities=20%  Similarity=0.243  Sum_probs=172.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhh--cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRS--TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      |+.|+.+.++++....+ ..+..+.|+...  ......+++|+|+||+.+.+.+..+.+.+.+++++|+||||++.+...
T Consensus        64 L~~q~~~~~~~~~~~~~-~~v~~~~g~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~  142 (494)
T 1wp9_A           64 LVLQHAESFRRLFNLPP-EKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYA  142 (494)
T ss_dssp             HHHHHHHHHHHHBCSCG-GGEEEECSCSCHHHHHHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCH
T ss_pred             HHHHHHHHHHHHhCcch-hheEEeeCCcchhhhhhhccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCCc
Confidence            57899999998874433 235555555422  222334689999999999999988888889999999999999886543


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCch---HHHHHHHhcCCcEEEEEcccccccc---cceeEEE-------------
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDF---VEELARSIMHDAVRVIVGRKNTASE---SIKQKLV-------------  139 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~-------------  139 (248)
                      +......+..  .....+++++|||+...   ...+...+.................   .......             
T Consensus       143 ~~~~~~~~~~--~~~~~~~l~lTaTp~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (494)
T 1wp9_A          143 YVFIAREYKR--QAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRK  220 (494)
T ss_dssp             HHHHHHHHHH--HCSSCCEEEEESCSCSSHHHHHHHHHHTTCCEEEECCTTSTTTGGGCCCCCEEEEEECCCHHHHHHHH
T ss_pred             HHHHHHHHHh--cCCCCeEEEEecCCCCCcHHHHHHHHhcChheeeccCCCcHHHHHhcCCCceeEEecCCcHHHHHHHH
Confidence            3333333333  23567899999999743   3333333322211111000000000   0000000             


Q ss_pred             --------------------------------------------------------------------------------
Q 042003          140 --------------------------------------------------------------------------------  139 (248)
Q Consensus       140 --------------------------------------------------------------------------------  139 (248)
                                                                                                      
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  300 (494)
T 1wp9_A          221 LLREMLRDALKPLAETGLLESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAY  300 (494)
T ss_dssp             HHHHHHHHHHHHHHHHTSSSCCCTTSCHHHHHHHHHHHHHHHTTTCCSTTTHHHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccccccCCCcchhHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHHHhhcHHHHHHH
Confidence                                                                                            


Q ss_pred             ------------------------------------EcCCchhHHHHHHHHHhc----cCCCCEEEEecchHHHHHHHHH
Q 042003          140 ------------------------------------FAGSEEGKLLALRQSFAE----SLNPPVLIFVQSKERAKELYGE  179 (248)
Q Consensus       140 ------------------------------------~~~~~~~~~~~l~~~~~~----~~~~~~liF~~~~~~~~~l~~~  179 (248)
                                                          .......|...+.+++..    ..+.++||||++++.++.+++.
T Consensus       301 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~  380 (494)
T 1wp9_A          301 IKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNE  380 (494)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHTSHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHH
T ss_pred             HHHHHHhhccccchhhhhhhhhHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHH
Confidence                                                000233466667777765    4578999999999999999999


Q ss_pred             hhcCCCeeEEEec--------CCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          180 LAFDGIRAGVIHS--------DLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       180 L~~~~~~v~~~~~--------~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+..++++..+||        +|+.++|+++++.|++|+.+|||||+++++|+|+|++++||++|+|+|+..|.||+
T Consensus       381 L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~  457 (494)
T 1wp9_A          381 LVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRR  457 (494)
T ss_dssp             HHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHH
T ss_pred             HHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHH
Confidence            9999999999999        99999999999999999999999999999999999999999999999999999984

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

Probab=99.98  E-value=8.3e-32  Score=238.49  Aligned_cols=235  Identities=20%  Similarity=0.193  Sum_probs=170.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      ||.|+++.++++.+ .+ ..+....|+.........+++|+|+||+++.+++.++...+++++++|+||+|.+.+++ +.
T Consensus        87 La~q~~~~~~~~~~-~g-~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~-~~  163 (715)
T 2va8_A           87 LTNEKYLTFKDWEL-IG-FKVAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPE-RG  163 (715)
T ss_dssp             HHHHHHHHHGGGGG-GT-CCEEECCSCSSSCCGGGGGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTT-TH
T ss_pred             HHHHHHHHHHHhhc-CC-CEEEEEeCCCCCchhhcCCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcc-cc
Confidence            57788888865544 35 44555666553333233479999999999999998877778999999999999987665 66


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccccccccccee------------EEEEcC------
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQ------------KLVFAG------  142 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~------  142 (248)
                      ..+..++....  +.|+++||||+++ ...+..++.. +. +......   ..+..            ...+..      
T Consensus       164 ~~l~~i~~~~~--~~~ii~lSATl~n-~~~~~~~l~~-~~-~~~~~r~---~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (715)
T 2va8_A          164 PVVESVTIRAK--RRNLLALSATISN-YKQIAKWLGA-EP-VATNWRP---VPLIEGVIYPERKKKEYNVIFKDNTTKKV  235 (715)
T ss_dssp             HHHHHHHHHHH--TSEEEEEESCCTT-HHHHHHHHTC-EE-EECCCCS---SCEEEEEEEECSSTTEEEEEETTSCEEEE
T ss_pred             hHHHHHHHhcc--cCcEEEEcCCCCC-HHHHHHHhCC-Cc-cCCCCCC---CCceEEEEecCCcccceeeecCcchhhhc
Confidence            66777665543  7899999999986 4666665532 11 1111111   01111            111111      


Q ss_pred             -CchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCC------------------------------------C
Q 042003          143 -SEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDG------------------------------------I  185 (248)
Q Consensus       143 -~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~------------------------------------~  185 (248)
                       ..+.+...+.+.+..  ++++||||+++++++.+++.|.+..                                    .
T Consensus       236 ~~~~~~~~~~~~~~~~--~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~  313 (715)
T 2va8_A          236 HGDDAIIAYTLDSLSK--NGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISK  313 (715)
T ss_dssp             ESSSHHHHHHHHHHTT--TCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTT
T ss_pred             ccchHHHHHHHHHHhc--CCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhc
Confidence             124455666666553  6899999999999999999987542                                    2


Q ss_pred             eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe----cc-------CCCCcccceecC
Q 042003          186 RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN----YD-------FPDSGAAYIHRI  248 (248)
Q Consensus       186 ~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~----~~-------~p~~~~~~~qri  248 (248)
                      .+.++||+|+.++|..+++.|++|..+|||||+++++|+|+|++++||+    ||       .|.|..+|.||+
T Consensus       314 ~v~~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~  387 (715)
T 2va8_A          314 GVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMS  387 (715)
T ss_dssp             TEEEECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHH
T ss_pred             CEEEECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHh
Confidence            5899999999999999999999999999999999999999999999999    99       899999999984

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

Probab=99.98  E-value=3.1e-31  Score=240.09  Aligned_cols=234  Identities=20%  Similarity=0.203  Sum_probs=176.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+++.++++...     +..+.|+...    ..+++|+|+||++|.+++.++...+++++++|+||||++.+++ +.
T Consensus       141 La~Q~~~~l~~~~~~-----vglltGd~~~----~~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~-rg  210 (1010)
T 2xgj_A          141 LSNQKYRELLAEFGD-----VGLMTGDITI----NPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKE-RG  210 (1010)
T ss_dssp             HHHHHHHHHHHHHSC-----EEEECSSCEE----CTTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTT-TH
T ss_pred             HHHHHHHHHHHHhCC-----EEEEeCCCcc----CCCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccc-hh
Confidence            678999999987762     4445554432    2368999999999999998888889999999999999998876 66


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHh---cCCcEEEEEcccccccccceeEEEEcC---------Cc----
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSI---MHDAVRVIVGRKNTASESIKQKLVFAG---------SE----  144 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~----  144 (248)
                      ..+..++.. .+...+++++|||+++. .++..++   .+.+..+......  +..+.++++...         ..    
T Consensus       211 ~~~e~il~~-l~~~~~il~LSATi~n~-~e~a~~l~~~~~~~~~vi~~~~r--p~pl~~~~~~~~~~~~~~~~~~~~~~~  286 (1010)
T 2xgj_A          211 VVWEETIIL-LPDKVRYVFLSATIPNA-MEFAEWICKIHSQPCHIVYTNFR--PTPLQHYLFPAHGDGIYLVVDEKSTFR  286 (1010)
T ss_dssp             HHHHHHHHH-SCTTCEEEEEECCCTTH-HHHHHHHHHHHTSCEEEEEECCC--SSCEEEEEEETTSSCCEEEECTTCCBC
T ss_pred             HHHHHHHHh-cCCCCeEEEEcCCCCCH-HHHHHHHHhhcCCCeEEEecCCC--cccceEEEEecCCcceeeeeccccccc
Confidence            667777776 45678999999999873 3344433   3444444332211  122333322211         00    


Q ss_pred             -----------------------------------------hhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC
Q 042003          145 -----------------------------------------EGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD  183 (248)
Q Consensus       145 -----------------------------------------~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~  183 (248)
                                                               ......+...+......++||||++++.|+.+++.|...
T Consensus       287 ~~~~~~~~~~l~~~~~~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~  366 (1010)
T 2xgj_A          287 EENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKL  366 (1010)
T ss_dssp             HHHHHHHHHTCC------------------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTS
T ss_pred             hHHHHHHHHHHhhhhcccccccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhC
Confidence                                                     122333444455544569999999999999999999764


Q ss_pred             CC---------------------------------------eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCC
Q 042003          184 GI---------------------------------------RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGM  224 (248)
Q Consensus       184 ~~---------------------------------------~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gi  224 (248)
                      ++                                       +++.+||+|++.+|+.+++.|++|.++|||||+++++|+
T Consensus       367 ~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GI  446 (1010)
T 2xgj_A          367 DFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGL  446 (1010)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGST
T ss_pred             CCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccC
Confidence            33                                       289999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEe----ccC----CCCcccceecC
Q 042003          225 DFKGVNCVIN----YDF----PDSGAAYIHRI  248 (248)
Q Consensus       225 dip~~~~Vi~----~~~----p~~~~~~~qri  248 (248)
                      |+|++++||+    ||.    |.|+.+|.||+
T Consensus       447 DiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~  478 (1010)
T 2xgj_A          447 NMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMS  478 (1010)
T ss_dssp             TCCBSEEEESCSEEECSSCEEECCHHHHHHHH
T ss_pred             CCCCceEEEeCCcccCCcCCccCCHHHHhHhh
Confidence            9999999999    999    89999999984

>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=99.97  E-value=3e-32  Score=240.70  Aligned_cols=237  Identities=22%  Similarity=0.203  Sum_probs=173.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      ||.|+++.++++.+ .+ ..+....|+.........+++|+|+||+++.+++.++...+++++++|+||+|.+.+++ +.
T Consensus        80 La~q~~~~~~~~~~-~g-~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~-r~  156 (702)
T 2p6r_A           80 LAGEKYESFKKWEK-IG-LRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEK-RG  156 (702)
T ss_dssp             HHHHHHHHHTTTTT-TT-CCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTT-TH
T ss_pred             HHHHHHHHHHHHHh-cC-CEEEEEeCCCCcchhhccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCC-cc
Confidence            57788888865544 35 44555666553333334589999999999999998877778999999999999998766 55


Q ss_pred             ccchhHhhhC--CCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEE------EEcCCc------hh
Q 042003           81 KHIDPVVKAC--SNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKL------VFAGSE------EG  146 (248)
Q Consensus        81 ~~~~~~~~~~--~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~------~~  146 (248)
                      ..+..++..+  ..+..|+++||||+++ ...+..++. .+ .+......   ..+...+      .+....      ..
T Consensus       157 ~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~~l~-~~-~~~~~~r~---~~l~~~~~~~~~~~~~~~~~~~~~~~~  230 (702)
T 2p6r_A          157 ATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEWLD-AD-YYVSDWRP---VPLVEGVLCEGTLELFDGAFSTSRRVK  230 (702)
T ss_dssp             HHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHHHTT-CE-EEECCCCS---SCEEEEEECSSEEEEEETTEEEEEECC
T ss_pred             cHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHHHhC-CC-cccCCCCC---ccceEEEeeCCeeeccCcchhhhhhhh
Confidence            5555554443  2457899999999986 566666553 22 12111111   1111111      111110      01


Q ss_pred             HHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC------------------------------CCeeEEEecCCCH
Q 042003          147 KLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD------------------------------GIRAGVIHSDLSQ  196 (248)
Q Consensus       147 ~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~------------------------------~~~v~~~~~~~~~  196 (248)
                      +...+.+.++.  ++++||||+++++++.+++.|.+.                              +.++..+||+|+.
T Consensus       231 ~~~~~~~~~~~--~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~  308 (702)
T 2p6r_A          231 FEELVEECVAE--NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  308 (702)
T ss_dssp             HHHHHHHHHHT--TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHHhc--CCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCH
Confidence            55566665553  689999999999999999988642                              1368899999999


Q ss_pred             HHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe----cc---CCCCcccceecC
Q 042003          197 TQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN----YD---FPDSGAAYIHRI  248 (248)
Q Consensus       197 ~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~----~~---~p~~~~~~~qri  248 (248)
                      ++|..+++.|++|+.+|||||+++++|+|+|++++||+    ||   .|.|..+|.||+
T Consensus       309 ~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~  367 (702)
T 2p6r_A          309 GQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMA  367 (702)
T ss_dssp             HHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHh
Confidence            99999999999999999999999999999999999999    66   789999999984

>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=99.97  E-value=7.8e-32  Score=243.64  Aligned_cols=247  Identities=15%  Similarity=0.132  Sum_probs=143.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCc-ccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKI-DLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~-~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+++.++++.+..+ ..+..++|+.   .+......+++|+|+||+++.+.+..+.. .+.+++++|+||||++.+.
T Consensus       308 L~~Q~~~~~~~~~~~~~-~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~  386 (936)
T 4a2w_A          308 VYEQQKNVFKHHFERQG-YSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGN  386 (936)
T ss_dssp             HHHHHHHHHHHHHHTTT-CCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTT
T ss_pred             HHHHHHHHHHHHhcccC-ceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCC
Confidence            57899999999988777 4556666655   22233445799999999999999988776 7899999999999999877


Q ss_pred             CcccccchhHhhhC---CCccceeEEEEeecCc-----------hHHHHHH------------------HhcCCcEEEEE
Q 042003           77 GNLLKHIDPVVKAC---SNPSIVRSLFSATLPD-----------FVEELAR------------------SIMHDAVRVIV  124 (248)
Q Consensus        77 ~~~~~~~~~~~~~~---~~~~~~~i~~SAT~~~-----------~~~~~~~------------------~~~~~~~~~~~  124 (248)
                      +.+...+..+....   .....+++++|||++.           ....+..                  .+...+.....
T Consensus       387 ~~~~~i~~~~~~~~~~~~~~~~~~l~LSATp~~~~~~~l~~~~~~i~~L~~~L~~~~i~~~~~~~~~l~~~~~~p~~~~~  466 (936)
T 4a2w_A          387 HPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVR  466 (936)
T ss_dssp             CHHHHHHHHHHHHHHTTCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCSSHHHHHHHSCCCCEEEE
T ss_pred             ccHHHHHHHHHHHhhccCCCcCeEEEecCCcccccchhHHHHHHHHHHHHHhcCCceeecccccHHHHHHhccCCcceEE
Confidence            64444443443321   1456889999999852           1111111                  11122211111


Q ss_pred             ccccccccc--------------c-ee---------E-------------E-----------------------------
Q 042003          125 GRKNTASES--------------I-KQ---------K-------------L-----------------------------  138 (248)
Q Consensus       125 ~~~~~~~~~--------------~-~~---------~-------------~-----------------------------  138 (248)
                      .........              . ..         .             .                             
T Consensus       467 ~~~~~~~~~~~~~l~~l~~~i~~~~~~~l~~~~l~~~~~~~~g~~~y~~~l~~l~k~~~~~~l~~~~~~~~~~~~l~~~~  546 (936)
T 4a2w_A          467 LVKRRIHNPFAAIISNLMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICT  546 (936)
T ss_dssp             ECCCCSCCHHHHHHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSCHHHHHHHHHHHHHHH
T ss_pred             ecccccCcHHHHHHHHHHHHHHHHHHHHHhhhhhhhccccccchHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHH
Confidence            100000000              0 00         0             0                             


Q ss_pred             -----------------------------------------------------------EEcCCchhHHHHHHHHHhc--
Q 042003          139 -----------------------------------------------------------VFAGSEEGKLLALRQSFAE--  157 (248)
Q Consensus       139 -----------------------------------------------------------~~~~~~~~~~~~l~~~~~~--  157 (248)
                                                                                 ........|...+.+++..  
T Consensus       547 ~~l~~~~~al~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~  626 (936)
T 4a2w_A          547 EHLRKYNDALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAY  626 (936)
T ss_dssp             HHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTSTTCCCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhhhcchhHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHhhhccCCCCHHHHHHHHHHHHHh
Confidence                                                                       0000013355555666654  


Q ss_pred             --cCCCCEEEEecchHHHHHHHHHhhcC------------CCeeEEEecCCCHHHHHHHHHHhhc-CCceEEEEeccccc
Q 042003          158 --SLNPPVLIFVQSKERAKELYGELAFD------------GIRAGVIHSDLSQTQRENAVDDFRA-GKTWVLIATDVIAR  222 (248)
Q Consensus       158 --~~~~~~liF~~~~~~~~~l~~~L~~~------------~~~v~~~~~~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~  222 (248)
                        ..+.++||||++++.++.+++.|+..            |.+...+||+|+..+|.++++.|++ |+.+|||||+++++
T Consensus       627 ~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~e  706 (936)
T 4a2w_A          627 RYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADE  706 (936)
T ss_dssp             TSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC---
T ss_pred             ccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhc
Confidence              34689999999999999999999876            5556677899999999999999999 99999999999999


Q ss_pred             CCCCCCCcEEEeccCCCCcccceecC
Q 042003          223 GMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       223 Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+|+|++++||+||+|+|+.+|+||+
T Consensus       707 GIDlp~v~~VI~yD~p~s~~~~iQr~  732 (936)
T 4a2w_A          707 GIDIVQCNLVVLYEYSGNVTKMIQVR  732 (936)
T ss_dssp             ---CCCCSEEEEESCCSCSHHHHCC-
T ss_pred             CCcchhCCEEEEeCCCCCHHHHHHhc
Confidence            99999999999999999999999996

>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=99.97  E-value=4e-32  Score=240.22  Aligned_cols=89  Identities=27%  Similarity=0.452  Sum_probs=80.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC------CCeeEEEecC--------CCHHHHHHHHHHhhcCCceEEEEecccccCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD------GIRAGVIHSD--------LSQTQRENAVDDFRAGKTWVLIATDVIARGMD  225 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~------~~~v~~~~~~--------~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gid  225 (248)
                      ++++||||++++.++.+++.|+..      |+++..+||+        |+.++|.++++.|++|+.+|||||+++++|+|
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GID  479 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLD  479 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSC
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCc
Confidence            689999999999999999999987      8999999999        99999999999999999999999999999999


Q ss_pred             CCCCcEEEeccCCCCcccceecC
Q 042003          226 FKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       226 ip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +|++++||+||+|+|+.+|+||+
T Consensus       480 ip~v~~VI~~d~p~s~~~~~Qr~  502 (699)
T 4gl2_A          480 IKECNIVIRYGLVTNEIAMVQAR  502 (699)
T ss_dssp             CCSCCCCEEESCCCCHHHHHHHH
T ss_pred             cccCCEEEEeCCCCCHHHHHHHc
Confidence            99999999999999999999984

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

Probab=99.97  E-value=4.5e-30  Score=232.42  Aligned_cols=235  Identities=21%  Similarity=0.183  Sum_probs=175.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+++.++++..+   ..+..+.|+..    ....++|+|+||++|.+++......+++++++|+||||++.+++ +.
T Consensus        94 La~Q~~~~l~~~~~~---~~v~~l~G~~~----~~~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~-~g  165 (997)
T 4a4z_A           94 LSNQKFRDFKETFDD---VNIGLITGDVQ----INPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQD-RG  165 (997)
T ss_dssp             GHHHHHHHHHTTC-----CCEEEECSSCE----ECTTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTC-TT
T ss_pred             HHHHHHHHHHHHcCC---CeEEEEeCCCc----cCCCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccc-hH
Confidence            678888888886553   33555666542    23458999999999999998888888999999999999999988 78


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcC---CcEEEEEcccccccccceeEE-------------------
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMH---DAVRVIVGRKNTASESIKQKL-------------------  138 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~-------------------  138 (248)
                      ..+..+... .+...+++++|||+++. .++..|+..   .+..+......  +.++.+++                   
T Consensus       166 ~~~e~ii~~-l~~~v~iIlLSAT~~n~-~ef~~~l~~~~~~~~~vi~~~~r--~~pl~~~v~~~~~~~~~~~~~~~~~~~  241 (997)
T 4a4z_A          166 VVWEEVIIM-LPQHVKFILLSATVPNT-YEFANWIGRTKQKNIYVISTPKR--PVPLEINIWAKKELIPVINQNSEFLEA  241 (997)
T ss_dssp             CCHHHHHHH-SCTTCEEEEEECCCTTH-HHHHHHHHHHHTCCEEEEECSSC--SSCEEEEEEETTEEEEEECTTCCBCHH
T ss_pred             HHHHHHHHh-cccCCCEEEEcCCCCCh-HHHHHHHhcccCCceEEEecCCC--CccceEEEecCCcchhcccchhhhhHH
Confidence            888888877 56789999999999863 355555431   22222111100  01111111                   


Q ss_pred             -------------------------------------------------------------------------EEcCCch
Q 042003          139 -------------------------------------------------------------------------VFAGSEE  145 (248)
Q Consensus       139 -------------------------------------------------------------------------~~~~~~~  145 (248)
                                                                                               .......
T Consensus       242 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  321 (997)
T 4a4z_A          242 NFRKHKEILNGESAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSK  321 (997)
T ss_dssp             HHHHHHHHHC-----------------------------------------------------------------CCCCT
T ss_pred             HHHHHHHHhhccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccch
Confidence                                                                                     0011123


Q ss_pred             hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCC---------------------------------------e
Q 042003          146 GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGI---------------------------------------R  186 (248)
Q Consensus       146 ~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~---------------------------------------~  186 (248)
                      .+...+...+......++||||++++.|+.+++.|...++                                       +
T Consensus       322 ~~~~~li~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~g  401 (997)
T 4a4z_A          322 KTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERG  401 (997)
T ss_dssp             THHHHHHHHHHHTTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTT
T ss_pred             hHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcC
Confidence            4466677777777678999999999999999999977554                                       5


Q ss_pred             eEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCC---------CcccceecC
Q 042003          187 AGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD---------SGAAYIHRI  248 (248)
Q Consensus       187 v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~---------~~~~~~qri  248 (248)
                      +..+||+|++.+|+.+++.|++|..+|||||+++++|+|+|+ ..||+++.|.         |+..|+||+
T Consensus       402 i~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~  471 (997)
T 4a4z_A          402 IAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMA  471 (997)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHH
T ss_pred             eeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHh
Confidence            899999999999999999999999999999999999999999 6666666655         899999984

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

Probab=99.97  E-value=1.5e-31  Score=243.97  Aligned_cols=219  Identities=23%  Similarity=0.298  Sum_probs=163.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhh------cccc-cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRS------TDLS-KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~-~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.+++++ ..+ ..+..+.|+...      ...+ .+.++|+|+||+++.+++..  +.+++++++|+||||++
T Consensus       133 La~Q~~~~l~~l~-~~~-i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l  208 (1104)
T 4ddu_A          133 LVKQTLERLQKLA-DEK-VKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAV  208 (1104)
T ss_dssp             HHHHHHHHHHTTS-CTT-SCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHH
T ss_pred             HHHHHHHHHHHhh-CCC-CeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCcc
Confidence            6889999999987 666 456666665532      1223 33599999999999888774  66789999999999987


Q ss_pred             cc-----------cCccccc-chhHhhhCC----------CccceeEEEEee-cCchHH-HHHHHhcCCcEEEEEccccc
Q 042003           74 FE-----------VGNLLKH-IDPVVKACS----------NPSIVRSLFSAT-LPDFVE-ELARSIMHDAVRVIVGRKNT  129 (248)
Q Consensus        74 ~~-----------~~~~~~~-~~~~~~~~~----------~~~~~~i~~SAT-~~~~~~-~~~~~~~~~~~~~~~~~~~~  129 (248)
                      ..           +| |... +..+++.+.          ....|++++||| .|.... .+......    +.......
T Consensus       209 ~~~~r~~Dr~L~~~g-f~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~  283 (1104)
T 4ddu_A          209 LKASRNIDTLLMMVG-IPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVS  283 (1104)
T ss_dssp             TTSSHHHHHHHHTSS-CCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCC
T ss_pred             ccccccchhhhHhcC-CCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCC
Confidence            65           45 5555 666665422          157899999999 454433 22333322    22333344


Q ss_pred             ccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeE-EEecCCCHHHHHHHHHHhhc
Q 042003          130 ASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAG-VIHSDLSQTQRENAVDDFRA  208 (248)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~r~~~~~~f~~  208 (248)
                      ...++.+.+..+    ++...+.+++... ++++||||++++.++.+++.|+..++++. .+||.     |++ ++.|++
T Consensus       284 ~~~~i~~~~~~~----~k~~~L~~ll~~~-~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~  352 (1104)
T 4ddu_A          284 VARNITHVRISS----RSKEKLVELLEIF-RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKV  352 (1104)
T ss_dssp             CCCCEEEEEESC----CCHHHHHHHHHHH-CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHH
T ss_pred             CcCCceeEEEec----CHHHHHHHHHHhc-CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHC
Confidence            455566666544    2445556666664 58999999999999999999999999998 99992     555 999999


Q ss_pred             CCceEEEE----ecccccCCCCCC-CcEEEeccCCC
Q 042003          209 GKTWVLIA----TDVIARGMDFKG-VNCVINYDFPD  239 (248)
Q Consensus       209 g~~~ilv~----T~~~~~Gidip~-~~~Vi~~~~p~  239 (248)
                      |+.+||||    |+++++|+|+|+ +++||+||+|.
T Consensus       353 G~~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          353 GKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             TSCSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             CCCCEEEEecCCCCeeEecCcCCCCCCEEEEECCCC
Confidence            99999999    999999999999 99999999998

>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=99.96  E-value=2.7e-31  Score=242.13  Aligned_cols=218  Identities=16%  Similarity=0.262  Sum_probs=159.2

Q ss_pred             CcchHHHHHHHhhcCCCcE---EEEcccchhhh------cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccc
Q 042003            1 LATQTTRECKKLAKGNKFQ---IKLMKKELVRS------TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEAD   71 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~---~~~~~~~~~~~------~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah   71 (248)
                      ||.|+++.++++++..++.   .+..++|+...      ...+.+ ++|+|+||++|.+.+.+    +++++++|+||||
T Consensus       111 La~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah  185 (1054)
T 1gku_B          111 LVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVD  185 (1054)
T ss_dssp             HHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHH
T ss_pred             HHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChh
Confidence            6899999999999888741   56666665522      233444 99999999999987765    6799999999999


Q ss_pred             cccccCcccccchhHhhhC----------CCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEc
Q 042003           72 KLFEVGNLLKHIDPVVKAC----------SNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFA  141 (248)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~----------~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  141 (248)
                      ++.+++   ..+..+...+          .+...|++++|||+++. ..+...++.++..+..........++.+.+.  
T Consensus       186 ~~l~~~---~~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~--  259 (1054)
T 1gku_B          186 AILKAS---KNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSSRITVRNVEDVAV--  259 (1054)
T ss_dssp             HHHTST---HHHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCCEECCCCEEEEEE--
T ss_pred             hhhhcc---ccHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCcccCcCCceEEEe--
Confidence            988843   3333333332          13567899999999886 4333333333333333333334445555554  


Q ss_pred             CCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEE----e
Q 042003          142 GSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIA----T  217 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~----T  217 (248)
                        ...+...+..+++.. ++++||||++++.++.+++.|+.. +++..+||++     .++++.|++|+.+||||    |
T Consensus       260 --~~~k~~~L~~ll~~~-~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~-----~~~l~~F~~G~~~VLVaTas~T  330 (1054)
T 1gku_B          260 --NDESISTLSSILEKL-GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATK-----KGDYEKFVEGEIDHLIGTAHYY  330 (1054)
T ss_dssp             --SCCCTTTTHHHHTTS-CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSS-----SHHHHHHHHTSCSEEEEECC--
T ss_pred             --chhHHHHHHHHHhhc-CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccH-----HHHHHHHHcCCCcEEEEecCCC
Confidence              234556677777766 689999999999999999999988 9999999998     37889999999999999    8


Q ss_pred             cccccCCCCCCC-cEEEeccCC
Q 042003          218 DVIARGMDFKGV-NCVINYDFP  238 (248)
Q Consensus       218 ~~~~~Gidip~~-~~Vi~~~~p  238 (248)
                      +++++|+|+|++ ++||++|+|
T Consensus       331 dv~~rGIDip~VI~~VI~~~~P  352 (1054)
T 1gku_B          331 GTLVRGLDLPERIRFAVFVGCP  352 (1054)
T ss_dssp             ----CCSCCTTTCCEEEEESCC
T ss_pred             CeeEeccccCCcccEEEEeCCC
Confidence            999999999995 999999999

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

Probab=99.96  E-value=3.4e-30  Score=220.18  Aligned_cols=237  Identities=13%  Similarity=0.080  Sum_probs=162.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+++.+++++...+ ..+..+.|+.........+++|+|+||+.+.+   .....+++++++|+||||++...    
T Consensus       169 L~~Q~~~~~~~~~~~~~-~~v~~~~~~~~~~~~~~~~~~I~i~T~~~l~~---~~~~~~~~~~liIiDE~H~~~~~----  240 (510)
T 2oca_A          169 LTTQMADDFVDYRLFSH-AMIKKIGGGASKDDKYKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLATGK----  240 (510)
T ss_dssp             HHHHHHHHHHHTTSSCG-GGEEECGGGCCTTGGGCTTCSEEEEEHHHHTT---SCGGGGGGEEEEEEETGGGCCHH----
T ss_pred             HHHHHHHHHHHhhcCCc-cceEEEecCCccccccccCCcEEEEeHHHHhh---chhhhhhcCCEEEEECCcCCCcc----
Confidence            67899999999866655 34555555554433356789999999996543   33456789999999999998652    


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHHHHHH-HhcCCcEEEEEcccc------cccccceeEEEEcC-----------
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVEELAR-SIMHDAVRVIVGRKN------TASESIKQKLVFAG-----------  142 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~-~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~-----------  142 (248)
                       .+..+++. .....+++++|||++........ ..+.++.........      .....+........           
T Consensus       241 -~~~~il~~-~~~~~~~l~lSATp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  318 (510)
T 2oca_A          241 -SISSIISG-LNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKT  318 (510)
T ss_dssp             -HHHHHGGG-CTTCCEEEEEESCGGGCSSCHHHHHHHHCSEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCC
T ss_pred             -cHHHHHHh-cccCcEEEEEEeCCCCCcccHHHhHHhhCCeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccc
Confidence             34445555 34567899999999765322111 111122221111110      00001111111110           


Q ss_pred             ---------CchhHHHHHHHHHhcc---CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC
Q 042003          143 ---------SEEGKLLALRQSFAES---LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK  210 (248)
Q Consensus       143 ---------~~~~~~~~l~~~~~~~---~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~  210 (248)
                               ....+...+.+++...   .+++++||++ .++++.+++.|.+.+.++..+||+|+.++|+++++.|++|+
T Consensus       319 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~  397 (510)
T 2oca_A          319 YQEEIKIITGLSKRNKWIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGK  397 (510)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCC
T ss_pred             hHHHHHHHhccHHHHHHHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCC
Confidence                     1112334444444433   3455666666 89999999999998889999999999999999999999999


Q ss_pred             ceEEEEe-cccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          211 TWVLIAT-DVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       211 ~~ilv~T-~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      .+||||| +++++|+|+|++++||++++|+|+..|.||+
T Consensus       398 ~~vLv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~  436 (510)
T 2oca_A          398 GIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTI  436 (510)
T ss_dssp             SCEEEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHHHHH
T ss_pred             CCEEEEEcChhhcccccccCcEEEEeCCCCCHHHHHHHH
Confidence            9999999 9999999999999999999999999999984

>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=99.96  E-value=5e-29  Score=228.59  Aligned_cols=230  Identities=18%  Similarity=0.120  Sum_probs=166.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hh----cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RS----TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~----~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.++++....+ ..+..+.|..   ..    ..+..+.++|+|+||+.+.     +...+++++++|+||+|++
T Consensus       664 La~Q~~~~~~~~~~~~~-i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-----~~~~~~~l~lvIiDEaH~~  737 (1151)
T 2eyq_A          664 LAQQHYDNFRDRFANWP-VRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRF  737 (1151)
T ss_dssp             HHHHHHHHHHHHSTTTT-CCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGS
T ss_pred             HHHHHHHHHHHHhhcCC-CeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-----CCccccccceEEEechHhc
Confidence            68899999998877776 4444444332   11    1223446999999997553     3466899999999999995


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  153 (248)
                      ..      .....++. ...+.++++||||+++...........+...+...  ......+...... .........+..
T Consensus       738 g~------~~~~~l~~-l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~--~~~r~~i~~~~~~-~~~~~i~~~il~  807 (1151)
T 2eyq_A          738 GV------RHKERIKA-MRANVDILTLTATPIPRTLNMAMSGMRDLSIIATP--PARRLAVKTFVRE-YDSMVVREAILR  807 (1151)
T ss_dssp             CH------HHHHHHHH-HHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCC--CCBCBCEEEEEEE-CCHHHHHHHHHH
T ss_pred             Ch------HHHHHHHH-hcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecC--CCCccccEEEEec-CCHHHHHHHHHH
Confidence            32      22333333 23457899999999887776666554443332211  1122233333322 222223333333


Q ss_pred             HHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcE
Q 042003          154 SFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC  231 (248)
Q Consensus       154 ~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~  231 (248)
                      .+..  +++++|||++++.++.+++.|++.  +.++..+||+|+..+|+++++.|++|+.+|||||+++++|+|+|++++
T Consensus       808 ~l~~--g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~  885 (1151)
T 2eyq_A          808 EILR--GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT  885 (1151)
T ss_dssp             HHTT--TCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEE
T ss_pred             HHhc--CCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcE
Confidence            3332  689999999999999999999887  789999999999999999999999999999999999999999999999


Q ss_pred             EEeccC-CCCcccceecC
Q 042003          232 VINYDF-PDSGAAYIHRI  248 (248)
Q Consensus       232 Vi~~~~-p~~~~~~~qri  248 (248)
                      ||+++. +++..+|.||+
T Consensus       886 VIi~~~~~~~l~~l~Qr~  903 (1151)
T 2eyq_A          886 IIIERADHFGLAQLHQLR  903 (1151)
T ss_dssp             EEETTTTSSCHHHHHHHH
T ss_pred             EEEeCCCCCCHHHHHHHH
Confidence            999998 57888999974

>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=99.96  E-value=7.4e-29  Score=215.86  Aligned_cols=244  Identities=20%  Similarity=0.231  Sum_probs=171.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHH-HHHHhcC------CcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRL-RLAIRRK------KIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l-~~~~~~~------~~~~~~~~~lIiDEah~   72 (248)
                      ||.|+++++..+.+.++ .++.+++|+. .+......+++|+|+||++| .+++..+      .+.++.+.++|+||||.
T Consensus       136 LA~qd~e~~~~l~~~lg-l~v~~i~gg~~~~~r~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~  214 (844)
T 1tf5_A          136 LASRDAEQMGKIFEFLG-LTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDS  214 (844)
T ss_dssp             HHHHHHHHHHHHHHHTT-CCEEECCTTSCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhcC-CeEEEEeCCCCHHHHHHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhh
Confidence            78999999999999999 5566666655 44444456799999999999 5555432      35678999999999999


Q ss_pred             cc-ccC--------------cccccchhHhhhCCC--------ccceeE-----------------EEEeecCchHHHHH
Q 042003           73 LF-EVG--------------NLLKHIDPVVKACSN--------PSIVRS-----------------LFSATLPDFVEELA  112 (248)
Q Consensus        73 ~~-~~~--------------~~~~~~~~~~~~~~~--------~~~~~i-----------------~~SAT~~~~~~~~~  112 (248)
                      ++ +.+              .+...+..+.+.+..        ...|+.                 ++|||.+.....+.
T Consensus       215 mLiDea~tplIisg~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~  294 (844)
T 1tf5_A          215 ILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHIN  294 (844)
T ss_dssp             HHTTTTTCEEEEEEEEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHH
T ss_pred             hhhhccccchhhcCCcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHH
Confidence            87 443              134455666666432        345665                 67888653222221


Q ss_pred             -----HHhcC-CcEEEE-------Ec------------------------------------------------------
Q 042003          113 -----RSIMH-DAVRVI-------VG------------------------------------------------------  125 (248)
Q Consensus       113 -----~~~~~-~~~~~~-------~~------------------------------------------------------  125 (248)
                           ..++. +...+.       +.                                                      
T Consensus       295 ~al~A~~l~~~d~dYiv~dg~v~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmT  374 (844)
T 1tf5_A          295 QALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMT  374 (844)
T ss_dssp             HHHHHHHTCCBTTTEEEETTEEEEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEE
T ss_pred             HHHHHHHHhhcCCceEEecCeeEEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCC
Confidence                 11221 111110       00                                                      


Q ss_pred             ---------------------ccccccccceeE-EEEcCCchhHHHHHHHHHhc--cCCCCEEEEecchHHHHHHHHHhh
Q 042003          126 ---------------------RKNTASESIKQK-LVFAGSEEGKLLALRQSFAE--SLNPPVLIFVQSKERAKELYGELA  181 (248)
Q Consensus       126 ---------------------~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~--~~~~~~liF~~~~~~~~~l~~~L~  181 (248)
                                           +...+.....+. .++ ....+|...+...+..  ..++++||||+|++.++.+++.|.
T Consensus       375 GTa~te~~e~~~iY~l~vv~IPtn~p~~r~d~~d~v~-~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~  453 (844)
T 1tf5_A          375 GTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIY-RTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLK  453 (844)
T ss_dssp             SCCGGGHHHHHHHHCCCEEECCCSSCCCCEECCCEEE-SSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHH
T ss_pred             cccchhHHHHHHHhCCceEEecCCCCcccccCCcEEE-eCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHH
Confidence                                 000011111111 233 3556788888877754  236799999999999999999999


Q ss_pred             cCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCC--------CCcEEEeccCCCCcccceecC
Q 042003          182 FDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK--------GVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       182 ~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip--------~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +.|+++.++||+++..++..+.++|+.|  .|+|||+++++|+|++        ++.+||+++.|.|...|.||+
T Consensus       454 ~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~  526 (844)
T 1tf5_A          454 NKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLR  526 (844)
T ss_dssp             TTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHH
T ss_pred             HCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhc
Confidence            9999999999999888877666666665  5999999999999999        788999999999999999984

>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=99.96  E-value=4.5e-29  Score=235.04  Aligned_cols=243  Identities=16%  Similarity=0.169  Sum_probs=172.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCC--cccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKK--IDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~--~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      ||.|+++.+++.....| .+|...+|+.........+++|+|+|||++..++.+..  ..+++++++|+||+|.+.+ . 
T Consensus       146 La~e~~~~l~~~~~~~g-i~V~~~tGd~~~~~~~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d-~-  222 (1724)
T 4f92_B          146 LVQEMVGSFGKRLATYG-ITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-D-  222 (1724)
T ss_dssp             HHHHHHHHHHHHHTTTT-CCEEECCSSCSSCCTTGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS-T-
T ss_pred             HHHHHHHHHHHHHhhCC-CEEEEEECCCCCCccccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC-c-
Confidence            68899999998888888 66777777765544455679999999999877665543  2478999999999998765 3 


Q ss_pred             ccccchhHhhh------CCCccceeEEEEeecCchHHHHHHHhcCCcE--EEEEcccccccccceeEEEEcCCch--hHH
Q 042003           79 LLKHIDPVVKA------CSNPSIVRSLFSATLPDFVEELARSIMHDAV--RVIVGRKNTASESIKQKLVFAGSEE--GKL  148 (248)
Q Consensus        79 ~~~~~~~~~~~------~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~--~~~  148 (248)
                      ....++.++..      ....+.|+|++|||+|+ .+++..|+..++.  ........ .+..+.+.+.......  ...
T Consensus       223 RG~~lE~~l~rl~~~~~~~~~~~riI~LSATl~N-~~dvA~wL~~~~~~~~~~~~~~~-RPvpL~~~~~~~~~~~~~~~~  300 (1724)
T 4f92_B          223 RGPVLEALVARAIRNIEMTQEDVRLIGLSATLPN-YEDVATFLRVDPAKGLFYFDNSF-RPVPLEQTYVGITEKKAIKRF  300 (1724)
T ss_dssp             THHHHHHHHHHHHHHHHHHTCCCEEEEEECSCTT-HHHHHHHTTCCHHHHEEECCGGG-CSSCEEEECCEECCCCHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHhCCCCCcEEEEecccCC-HHHHHHHhCCCCCCCeEEECCCC-ccCccEEEEeccCCcchhhhh
Confidence            44444433321      13567899999999987 6777777755431  12222222 2233444333222221  122


Q ss_pred             H----HHHHHHhc-cCCCCEEEEecchHHHHHHHHHhhc-------------------------------------CCCe
Q 042003          149 L----ALRQSFAE-SLNPPVLIFVQSKERAKELYGELAF-------------------------------------DGIR  186 (248)
Q Consensus       149 ~----~l~~~~~~-~~~~~~liF~~~~~~~~~l~~~L~~-------------------------------------~~~~  186 (248)
                      .    .+.+.+.. ..++++||||+|++.|+.+++.|.+                                     ...+
T Consensus       301 ~~~~~~~~~~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~G  380 (1724)
T 4f92_B          301 QIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYG  380 (1724)
T ss_dssp             HHHHHHHHHHHTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcC
Confidence            2    22223333 3357999999999999988887742                                     1245


Q ss_pred             eEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe----ccC------CCCcccceecC
Q 042003          187 AGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN----YDF------PDSGAAYIHRI  248 (248)
Q Consensus       187 v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~----~~~------p~~~~~~~qri  248 (248)
                      ++++||||++++|..+++.|++|.++|||||++++.|||+|..++||.    |++      |-++.+|+||+
T Consensus       381 va~HHagL~~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~  452 (1724)
T 4f92_B          381 FAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQML  452 (1724)
T ss_dssp             EEEECSSSCTHHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHH
T ss_pred             EEEEcCCCCHHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhh
Confidence            899999999999999999999999999999999999999999999985    443      45788899984

>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=99.96  E-value=1.2e-29  Score=223.57  Aligned_cols=229  Identities=17%  Similarity=0.187  Sum_probs=155.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhc-------ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRST-------DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.++++.+..+ ..+..+.|+....       ....+.++|+|+||+.+.+     ...+.+++++|+||+|++
T Consensus       429 La~Q~~~~l~~~~~~~g-i~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~  502 (780)
T 1gm5_A          429 LAIQHYRRTVESFSKFN-IHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRF  502 (780)
T ss_dssp             HHHHHHHHHHHHHTCSS-CCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC
T ss_pred             HHHHHHHHHHHHhhhcC-ceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchh
Confidence            68899999999998877 5566666655221       1233469999999987744     456789999999999997


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ  153 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  153 (248)
                      ....  +..+   ..  ....+++++||||+.+......  +.++...............+.....   ... +...+.+
T Consensus       503 g~~q--r~~l---~~--~~~~~~vL~mSATp~p~tl~~~--~~g~~~~s~i~~~p~~r~~i~~~~~---~~~-~~~~l~~  569 (780)
T 1gm5_A          503 GVKQ--REAL---MN--KGKMVDTLVMSATPIPRSMALA--FYGDLDVTVIDEMPPGRKEVQTMLV---PMD-RVNEVYE  569 (780)
T ss_dssp             -------CCC---CS--SSSCCCEEEEESSCCCHHHHHH--HTCCSSCEEECCCCSSCCCCEECCC---CSS-THHHHHH
T ss_pred             hHHH--HHHH---HH--hCCCCCEEEEeCCCCHHHHHHH--HhCCcceeeeeccCCCCcceEEEEe---ccc-hHHHHHH
Confidence            4322  1111   11  2246789999999887554443  3343322222211111122222221   111 2222233


Q ss_pred             HHhc--cCCCCEEEEecchH--------HHHHHHHHhhc---CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc
Q 042003          154 SFAE--SLNPPVLIFVQSKE--------RAKELYGELAF---DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI  220 (248)
Q Consensus       154 ~~~~--~~~~~~liF~~~~~--------~~~~l~~~L~~---~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~  220 (248)
                      .+..  ..+++++|||++.+        .++.+++.|++   .+..+..+||+|++++|+++++.|++|+.+|||||+++
T Consensus       570 ~i~~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vi  649 (780)
T 1gm5_A          570 FVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVI  649 (780)
T ss_dssp             HHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCC
T ss_pred             HHHHHHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCC
Confidence            3322  22679999999654        57888999988   47899999999999999999999999999999999999


Q ss_pred             ccCCCCCCCcEEEeccCCC-CcccceecC
Q 042003          221 ARGMDFKGVNCVINYDFPD-SGAAYIHRI  248 (248)
Q Consensus       221 ~~Gidip~~~~Vi~~~~p~-~~~~~~qri  248 (248)
                      ++|+|+|++++||++++|. +..+|.||+
T Consensus       650 e~GIDiP~v~~VIi~d~~r~~l~~l~Qr~  678 (780)
T 1gm5_A          650 EVGIDVPRANVMVIENPERFGLAQLHQLR  678 (780)
T ss_dssp             CSCSCCTTCCEEEBCSCSSSCTTHHHHHH
T ss_pred             CccccCCCCCEEEEeCCCCCCHHHHHHHh
Confidence            9999999999999999996 677777863

>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=99.96  E-value=1.4e-28  Score=231.67  Aligned_cols=244  Identities=16%  Similarity=0.144  Sum_probs=170.7

Q ss_pred             CcchHHHHHHH-hhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcC--CcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKK-LAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRK--KIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~--~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|.++.+++ +++..+ .+|...+|+.........+++|+|+|||++..++.+.  ...+++++++|+||+|.+.+. 
T Consensus       984 La~q~~~~~~~~f~~~~g-~~V~~ltGd~~~~~~~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~- 1061 (1724)
T 4f92_B          984 LAEQVYMDWYEKFQDRLN-KKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGE- 1061 (1724)
T ss_dssp             HHHHHHHHHHHHHTTTSC-CCEEECCSCHHHHHHHHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGST-
T ss_pred             HHHHHHHHHHHHhchhcC-CEEEEEECCCCcchhhcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCC-
Confidence            57888888765 677777 5666777766444334457899999999998777653  335789999999999998763 


Q ss_pred             cccccchhHhhh------CCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCch--hHH-
Q 042003           78 NLLKHIDPVVKA------CSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEE--GKL-  148 (248)
Q Consensus        78 ~~~~~~~~~~~~------~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~-  148 (248)
                       ....+..++..      ..+.+.|+|++|||+++ ..++..|+..++.....-.....+..+..++.......  .+. 
T Consensus      1062 -rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N-~~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~ 1139 (1724)
T 4f92_B         1062 -NGPVLEVICSRMRYISSQIERPIRIVALSSSLSN-AKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLL 1139 (1724)
T ss_dssp             -THHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTT-HHHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHH
T ss_pred             -CCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCC-HHHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhh
Confidence             33333333221      14567899999999987 67788887554433322223333334444433322221  111 


Q ss_pred             ---HHHHHHH-hccCCCCEEEEecchHHHHHHHHHhhc----------------------------------CCCeeEEE
Q 042003          149 ---LALRQSF-AESLNPPVLIFVQSKERAKELYGELAF----------------------------------DGIRAGVI  190 (248)
Q Consensus       149 ---~~l~~~~-~~~~~~~~liF~~~~~~~~~l~~~L~~----------------------------------~~~~v~~~  190 (248)
                         ..+...+ ....+++++|||+|++.|+.++..|..                                  ...+++++
T Consensus      1140 ~~~~~~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~h 1219 (1724)
T 4f92_B         1140 SMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYL 1219 (1724)
T ss_dssp             TTHHHHHHHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEE
T ss_pred             hhcchHHHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEE
Confidence               1122222 233467999999999999988876632                                  02468999


Q ss_pred             ecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe----------ccCCCCcccceecC
Q 042003          191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN----------YDFPDSGAAYIHRI  248 (248)
Q Consensus       191 ~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~----------~~~p~~~~~~~qri  248 (248)
                      ||+|++++|+.+++.|++|.++|||||+++++|+|+|+.++||.          ...|.++.+|+||+
T Consensus      1220 HagL~~~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~ 1287 (1724)
T 4f92_B         1220 HEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMV 1287 (1724)
T ss_dssp             CTTSCHHHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhh
Confidence            99999999999999999999999999999999999999888883          23466788898874

>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=99.95  E-value=4.9e-29  Score=220.65  Aligned_cols=208  Identities=19%  Similarity=0.234  Sum_probs=155.4

Q ss_pred             ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc-ccccCcccccchhHhhhCCCccceeEEEEeecCchHHH
Q 042003           32 DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK-LFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEE  110 (248)
Q Consensus        32 ~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~-~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~  110 (248)
                      .....+.+|+++||+++.+.+... ..+.+++++|+||+|. .++.......+..+....  +..++++||||++.  ..
T Consensus       180 ~~~~~~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah~R~ld~d~~~~~l~~l~~~~--~~~~iIl~SAT~~~--~~  254 (773)
T 2xau_A          180 NKTSNKTILKYMTDGMLLREAMED-HDLSRYSCIILDEAHERTLATDILMGLLKQVVKRR--PDLKIIIMSATLDA--EK  254 (773)
T ss_dssp             EECCTTCSEEEEEHHHHHHHHHHS-TTCTTEEEEEECSGGGCCHHHHHHHHHHHHHHHHC--TTCEEEEEESCSCC--HH
T ss_pred             cccCCCCCEEEECHHHHHHHHhhC-ccccCCCEEEecCccccccchHHHHHHHHHHHHhC--CCceEEEEeccccH--HH
Confidence            334567899999999999888765 3479999999999996 444332344555555542  46899999999975  34


Q ss_pred             HHHHhcCCcEEEEEcccccccccceeEEEEcCCch---hHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhc-----
Q 042003          111 LARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEE---GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAF-----  182 (248)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~-----  182 (248)
                      +.. ++.+...+......   ..+..++......+   .....+..+.....++++||||+++++++.+++.|++     
T Consensus       255 l~~-~~~~~~vi~v~gr~---~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l  330 (773)
T 2xau_A          255 FQR-YFNDAPLLAVPGRT---YPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQL  330 (773)
T ss_dssp             HHH-HTTSCCEEECCCCC---CCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHH-HhcCCCcccccCcc---cceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhh
Confidence            444 44444334333222   23333332222222   2233444454444578999999999999999999975     


Q ss_pred             ------CCCeeEEEecCCCHHHHHHHHHHhh-----cCCceEEEEecccccCCCCCCCcEEEeccC--------------
Q 042003          183 ------DGIRAGVIHSDLSQTQRENAVDDFR-----AGKTWVLIATDVIARGMDFKGVNCVINYDF--------------  237 (248)
Q Consensus       183 ------~~~~v~~~~~~~~~~~r~~~~~~f~-----~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~--------------  237 (248)
                            .++.+..+||+|++++|..+++.|+     +|+.+|||||+++++|+|+|++++||++|.              
T Consensus       331 ~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~  410 (773)
T 2xau_A          331 VREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVES  410 (773)
T ss_dssp             HHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEE
T ss_pred             cccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccc
Confidence                  5788999999999999999999999     999999999999999999999999999888              


Q ss_pred             ----CCCcccceecC
Q 042003          238 ----PDSGAAYIHRI  248 (248)
Q Consensus       238 ----p~~~~~~~qri  248 (248)
                          |.|..+|.||+
T Consensus       411 L~~~p~S~~s~~QR~  425 (773)
T 2xau_A          411 LLVSPISKASAQQRA  425 (773)
T ss_dssp             EEEEECCHHHHHHHH
T ss_pred             cccccCCHHHHHhhc
Confidence                88999999984

>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=99.95  E-value=1.4e-27  Score=207.46  Aligned_cols=245  Identities=17%  Similarity=0.173  Sum_probs=154.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHH-HHHHhcC------CcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRL-RLAIRRK------KIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l-~~~~~~~------~~~~~~~~~lIiDEah~   72 (248)
                      ||.|+++++..+.+.++ .++.+++|+. .+......+++|+||||++| .+++..+      ...+++++++|+||||.
T Consensus       127 LA~Q~~e~~~~l~~~lg-l~v~~i~GG~~~~~r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~  205 (853)
T 2fsf_A          127 LAQRDAENNRPLFEFLG-LTVGINLPGMPAPAKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDS  205 (853)
T ss_dssp             HHHHHHHHHHHHHHHTT-CCEEECCTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHH
T ss_pred             HHHHHHHHHHHHHHhcC-CeEEEEeCCCCHHHHHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHH
Confidence            78999999999999999 5556666655 33344455799999999999 6777654      25679999999999998


Q ss_pred             cc-ccC--------------cccccchhHhhhCCC-------------------ccceeE--------------------
Q 042003           73 LF-EVG--------------NLLKHIDPVVKACSN-------------------PSIVRS--------------------   98 (248)
Q Consensus        73 ~~-~~~--------------~~~~~~~~~~~~~~~-------------------~~~~~i--------------------   98 (248)
                      ++ +.+              .+...+..+...+..                   ...|+.                    
T Consensus       206 mLiD~a~tpLIiSg~~~~~~~~y~~i~~iv~~L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~  285 (853)
T 2fsf_A          206 ILIDEARTPLIISGPAEDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMD  285 (853)
T ss_dssp             HTTTTTTCEEEEEEC-----------------------------------------------------------------
T ss_pred             HHHhcCcccccccCCCccchhHHHHHHHHHHhchhhhccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCccc
Confidence            87 332              134555566555432                   134433                    


Q ss_pred             ----EEEeecCchHHHHH-----HHhcCCc-------------------------------------EEEEEcccccccc
Q 042003           99 ----LFSATLPDFVEELA-----RSIMHDA-------------------------------------VRVIVGRKNTASE  132 (248)
Q Consensus        99 ----~~SAT~~~~~~~~~-----~~~~~~~-------------------------------------~~~~~~~~~~~~~  132 (248)
                          ++|||.++....+.     ..++...                                     ..+.+........
T Consensus       286 ~~~~Lfsat~~~~~~~i~~al~A~~l~~~d~dYiV~d~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e~~tla  365 (853)
T 2fsf_A          286 EGESLYSPANIMLMHHVTAALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLA  365 (853)
T ss_dssp             -----------------------------------------------------------------------CCCCCEEEE
T ss_pred             ccccccCcccchHHHHHHHHHHHHHHhhcCccceeecCcEEEEecccCcccCCCccchhhhHHHHhcccceecccccccc
Confidence                78888654222111     0111100                                     0111111111111


Q ss_pred             cce----------------------------------------------eEEEEcCCchhHHHHHHHHHhc--cCCCCEE
Q 042003          133 SIK----------------------------------------------QKLVFAGSEEGKLLALRQSFAE--SLNPPVL  164 (248)
Q Consensus       133 ~~~----------------------------------------------~~~~~~~~~~~~~~~l~~~~~~--~~~~~~l  164 (248)
                      .+.                                              +..........|...+.+.+..  ..+.++|
T Consensus       366 ~It~qnyfr~Y~kl~GmTGTa~te~~ef~~iY~l~vv~IPtn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvL  445 (853)
T 2fsf_A          366 SITFQNYFRLYEKLAGMTGTADTEAFEFSSIYKLDTVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVL  445 (853)
T ss_dssp             EEEHHHHHTTSSEEEEEECTTCCCHHHHHHHHCCEEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEE
T ss_pred             eeehHHHHhhhhhhhcCCCCchhHHHHHHHHhCCcEEEcCCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEE
Confidence            111                                              1111223556788888887754  2367999


Q ss_pred             EEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCC---------------
Q 042003          165 IFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGV---------------  229 (248)
Q Consensus       165 iF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~---------------  229 (248)
                      |||+|++.++.+++.|++.|+++.++||.+...++..+.++|+.|  .|+|||+.+++|+||+..               
T Consensus       446 Vft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~  523 (853)
T 2fsf_A          446 VGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTA  523 (853)
T ss_dssp             EEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCS
T ss_pred             EEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhcccchh
Confidence            999999999999999999999999999998888888888889888  599999999999999974               


Q ss_pred             ----------------------cEEEeccCCCCcccceecC
Q 042003          230 ----------------------NCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       230 ----------------------~~Vi~~~~p~~~~~~~qri  248 (248)
                                            .+||+++.|.|...|.||+
T Consensus       524 ~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~  564 (853)
T 2fsf_A          524 EQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLR  564 (853)
T ss_dssp             SHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHH
T ss_pred             HHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhc
Confidence                                  5999999999999999984

>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=99.94  E-value=1e-28  Score=209.16  Aligned_cols=223  Identities=18%  Similarity=0.209  Sum_probs=155.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+.+.++++    +...+..+.|+..      ..++|+|+||+.+......   ...+++++|+||||++.+.+ +.
T Consensus       145 L~~Q~~~~~~~~----~~~~v~~~~g~~~------~~~~Ivv~T~~~l~~~~~~---~~~~~~liIvDEaH~~~~~~-~~  210 (472)
T 2fwr_A          145 LAEQWKERLGIF----GEEYVGEFSGRIK------ELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAES-YV  210 (472)
T ss_dssp             HHHHHHHHGGGG----CGGGEEEBSSSCB------CCCSEEEEEHHHHHHTHHH---HTTTCSEEEEETGGGTTSTT-TH
T ss_pred             HHHHHHHHHHhC----CCcceEEECCCcC------CcCCEEEEEcHHHHHHHHH---hcCCCCEEEEECCcCCCChH-HH
Confidence            467777777774    4231455555432      2478999999998776642   12468999999999988765 43


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCc-------------------hHHHHHHHhcCCcEEE--EEccccc----------
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPD-------------------FVEELARSIMHDAVRV--IVGRKNT----------  129 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~-------------------~~~~~~~~~~~~~~~~--~~~~~~~----------  129 (248)
                          .+.+.+  ...+++++|||+..                   ...++...++..+...  .......          
T Consensus       211 ----~~~~~~--~~~~~l~lSATp~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  284 (472)
T 2fwr_A          211 ----QIAQMS--IAPFRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREK  284 (472)
T ss_dssp             ----HHHHTC--CCSEEEEEESCCCCTTSGGGSHHHHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTH
T ss_pred             ----HHHHhc--CCCeEEEEecCccCCCCHHHHHHHHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHH
Confidence                344442  35678999999873                   1222222222222111  1110000          


Q ss_pred             --------------ccccceeEEE--------------------EcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHH
Q 042003          130 --------------ASESIKQKLV--------------------FAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKE  175 (248)
Q Consensus       130 --------------~~~~~~~~~~--------------------~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~  175 (248)
                                    ....+...+.                    .......|...+.+++....++++||||++.+.++.
T Consensus       285 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~  364 (472)
T 2fwr_A          285 VYKQFLRARGITLRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYR  364 (472)
T ss_dssp             HHHSCSSSCCCTTTCCSSSTTTTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHH
T ss_pred             HHHHHHHhcCccccchhhHHHHHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHhCCCCcEEEEECCHHHHHH
Confidence                          0000000000                    001233577888888888778899999999999999


Q ss_pred             HHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          176 LYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       176 l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +++.|.     +..+||+++..+|+++++.|++|+.+|||||+++++|+|+|++++||++++|+|+..|.||+
T Consensus       365 l~~~l~-----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~  432 (472)
T 2fwr_A          365 ISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRL  432 (472)
T ss_dssp             HHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHH
T ss_pred             HHHHhC-----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHH
Confidence            999984     66789999999999999999999999999999999999999999999999999999999984

>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=99.94  E-value=5.9e-28  Score=202.85  Aligned_cols=187  Identities=12%  Similarity=0.081  Sum_probs=136.4

Q ss_pred             cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHH
Q 042003           35 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS  114 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~  114 (248)
                      ..+..+.++|++.+.+.+.+. ..+.+++++|+||||++ +.. +...+..+......++.|+++||||+++.....   
T Consensus        85 ~~~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~-~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~---  158 (451)
T 2jlq_A           85 TGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPC-SVAARGYISTRVEMGEAAAIFMTATPPGSTDPF---  158 (451)
T ss_dssp             CSSCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC-SHH-HHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSS---
T ss_pred             CCCceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC-Ccc-hHHHHHHHHHhhcCCCceEEEEccCCCccchhh---
Confidence            345689999999998888654 45789999999999987 322 222232333222345789999999998744322   


Q ss_pred             hcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCC
Q 042003          115 IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDL  194 (248)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~  194 (248)
                      +..++..+.... ..+..   .+       ..    +...+... .+++||||+++++++.+++.|++.++.+..+||++
T Consensus       159 ~~~~~~~~~~~~-~~p~~---~~-------~~----~~~~l~~~-~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~  222 (451)
T 2jlq_A          159 PQSNSPIEDIER-EIPER---SW-------NT----GFDWITDY-QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKT  222 (451)
T ss_dssp             CCCSSCEEEEEC-CCCSS---CC-------SS----SCHHHHHC-CSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTT
T ss_pred             hcCCCceEecCc-cCCch---hh-------HH----HHHHHHhC-CCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHH
Confidence            223333332221 11100   00       00    11222333 57999999999999999999999999999999975


Q ss_pred             CHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc--------------------CCCCcccceecC
Q 042003          195 SQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD--------------------FPDSGAAYIHRI  248 (248)
Q Consensus       195 ~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~--------------------~p~~~~~~~qri  248 (248)
                      .    +.+++.|++|+.+|||||+++++|+|+|+ ++||++|                    .|.|..+|+||+
T Consensus       223 ~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~  291 (451)
T 2jlq_A          223 F----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRR  291 (451)
T ss_dssp             H----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHH
T ss_pred             H----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeecccccCCHHHHHHhc
Confidence            4    57899999999999999999999999999 9999999                    999999999984

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

Probab=99.94  E-value=3.9e-27  Score=204.51  Aligned_cols=210  Identities=12%  Similarity=0.096  Sum_probs=132.2

Q ss_pred             ccCCCcEEEeChHHHHHHHhc----CCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHH
Q 042003           34 SKFSCDILISTPLRLRLAIRR----KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        34 ~~~~~~i~v~Tp~~l~~~~~~----~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  109 (248)
                      ...+.+|+|+||+++......    ..+...++++||+||||++...+  ...+..++..+.  ..+++++|||+.....
T Consensus       271 ~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~--~~~~~~il~~~~--~~~~l~lTATP~~~~~  346 (590)
T 3h1t_A          271 VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD--NSNWREILEYFE--PAFQIGMTATPLREDN  346 (590)
T ss_dssp             CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC-----------CHHHHHHST--TSEEEEEESSCSCTTT
T ss_pred             CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc--hHHHHHHHHhCC--cceEEEeccccccccc
Confidence            345789999999999887642    23446779999999999986542  245566666643  3578999999875443


Q ss_pred             HHHHHhcCCcEEEEEccc---ccccccceeEEE----------------------------EcCCch------hH----H
Q 042003          110 ELARSIMHDAVRVIVGRK---NTASESIKQKLV----------------------------FAGSEE------GK----L  148 (248)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~----------------------------~~~~~~------~~----~  148 (248)
                      .....+++.+........   ............                            ......      .+    .
T Consensus       347 ~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~i~  426 (590)
T 3h1t_A          347 RDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGREIPDGEYQTKDFERVIALKARTDAFA  426 (590)
T ss_dssp             HHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC-----------------------CCSHHHHHHHHHTHHHHH
T ss_pred             hhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeeeeccccccccccccccccccccccCCHHHhhhHhcChHHHHHHH
Confidence            333334443222110000   000000000000                            000000      11    1


Q ss_pred             HHHHHHHhcc-CCCCEEEEecchHHHHHHHHHhhcCCC--------eeEEEecCCCHHHHHHHHHHhhcCCce---EEEE
Q 042003          149 LALRQSFAES-LNPPVLIFVQSKERAKELYGELAFDGI--------RAGVIHSDLSQTQRENAVDDFRAGKTW---VLIA  216 (248)
Q Consensus       149 ~~l~~~~~~~-~~~~~liF~~~~~~~~~l~~~L~~~~~--------~v~~~~~~~~~~~r~~~~~~f~~g~~~---ilv~  216 (248)
                      ..+.+.+... ..+++||||+++++|+.+++.|.+.+.        .+..+||+++. +|+++++.|++|+.+   |+||
T Consensus       427 ~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~~~~~~~ilvt  505 (590)
T 3h1t_A          427 KHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQELETSTPVILTT  505 (590)
T ss_dssp             HHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCTTCCCCCEEEE
T ss_pred             HHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCCCCCCCEEEEE
Confidence            2233334432 357999999999999999999976543        37788998764 799999999998766   8899


Q ss_pred             ecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          217 TDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       217 T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+++++|+|+|++++||++++|+|+..|+||+
T Consensus       506 t~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~i  537 (590)
T 3h1t_A          506 SQLLTTGVDAPTCKNVVLARVVNSMSEFKQIV  537 (590)
T ss_dssp             SSTTTTTCCCTTEEEEEEESCCCCHHHHHHHH
T ss_pred             CChhhcCccchheeEEEEEecCCChHHHHHHH
Confidence            99999999999999999999999999999985

>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=99.94  E-value=3.4e-26  Score=199.28  Aligned_cols=244  Identities=19%  Similarity=0.183  Sum_probs=175.1

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHH-HHHHhcC------CcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRL-RLAIRRK------KIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l-~~~~~~~------~~~~~~~~~lIiDEah~   72 (248)
                      ||.|.++++..+.+.++ +++.+++|+. .+......+++|+++||+.| .+++..+      ...++.+.++|+||||.
T Consensus       164 LA~Qdae~m~~l~~~lG-Lsv~~i~gg~~~~~r~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDs  242 (922)
T 1nkt_A          164 LAKRDSEWMGRVHRFLG-LQVGVILATMTPDERRVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDS  242 (922)
T ss_dssp             HHHHHHHHHHHHHHHTT-CCEEECCTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHH
T ss_pred             HHHHHHHHHHHHHhhcC-CeEEEEeCCCCHHHHHHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHH
Confidence            78999999999999999 5666666655 44444455799999999999 6666543      35678999999999998


Q ss_pred             cc-ccC--------------cccccchhHhhhCCC--------ccceeE-----------------EEEeecCchHHHHH
Q 042003           73 LF-EVG--------------NLLKHIDPVVKACSN--------PSIVRS-----------------LFSATLPDFVEELA  112 (248)
Q Consensus        73 ~~-~~~--------------~~~~~~~~~~~~~~~--------~~~~~i-----------------~~SAT~~~~~~~~~  112 (248)
                      ++ +.+              .+...+..+...+..        ...|+.                 ++|||.++....+.
T Consensus       243 mLiDeartPLiiSg~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~  322 (922)
T 1nkt_A          243 ILIDEARTPLIISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLN  322 (922)
T ss_dssp             HHTTGGGSCEEEEEECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHH
T ss_pred             HHHhcCccceeecCCCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHH
Confidence            87 321              255667777777542        566776                 77888765333221


Q ss_pred             H-----HhcC-Cc-------EEEEEc------------------------------------------------------
Q 042003          113 R-----SIMH-DA-------VRVIVG------------------------------------------------------  125 (248)
Q Consensus       113 ~-----~~~~-~~-------~~~~~~------------------------------------------------------  125 (248)
                      .     .++. +.       ..+.+.                                                      
T Consensus       323 ~aL~A~~l~~~d~dYiV~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMT  402 (922)
T 1nkt_A          323 NALKAKELFSRDKDYIVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMT  402 (922)
T ss_dssp             HHHHHHHHCCBTTTEEECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEE
T ss_pred             HHHHHHHHhhcccceeeecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccc
Confidence            1     1222 11       111000                                                      


Q ss_pred             ---------------------cccccccccee-EEEEcCCchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhh
Q 042003          126 ---------------------RKNTASESIKQ-KLVFAGSEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELA  181 (248)
Q Consensus       126 ---------------------~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~  181 (248)
                                           +...+.....+ ..++ .....|...+...+...  .++++||||+|++.++.+++.|+
T Consensus       403 GTa~te~~Ef~~iY~l~vv~IPtn~p~~R~d~~d~v~-~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~  481 (922)
T 1nkt_A          403 GTAQTEAAELHEIYKLGVVSIPTNMPMIREDQSDLIY-KTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFT  481 (922)
T ss_dssp             SCCGGGHHHHHHHHCCEEEECCCSSCCCCEECCCEEE-SCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHH
T ss_pred             cCchhHHHHHHHHhCCCeEEeCCCCCcccccCCcEEE-eCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHH
Confidence                                 00000001111 1233 34567888888777542  36799999999999999999999


Q ss_pred             cCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCC--------------------------------
Q 042003          182 FDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGV--------------------------------  229 (248)
Q Consensus       182 ~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~--------------------------------  229 (248)
                      +.|+++.++||.+...++..+.++|+.|  .|+|||+.+++|+||+..                                
T Consensus       482 ~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  559 (922)
T 1nkt_A          482 KRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSE  559 (922)
T ss_dssp             HTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHH
T ss_pred             HCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHH
Confidence            9999999999998877777777888887  599999999999999975                                


Q ss_pred             --------------------cEEEeccCCCCcccceecC
Q 042003          230 --------------------NCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       230 --------------------~~Vi~~~~p~~~~~~~qri  248 (248)
                                          .+||+++.|.|...|.||+
T Consensus       560 ~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~  598 (922)
T 1nkt_A          560 LPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLR  598 (922)
T ss_dssp             HHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHh
Confidence                                4999999999999999984

>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=99.94  E-value=1.4e-26  Score=209.92  Aligned_cols=104  Identities=23%  Similarity=0.328  Sum_probs=98.2

Q ss_pred             hhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhc-CCCeeEEEecCCCHHHHHHHHHHhhcCC--ceEEEEecccc
Q 042003          145 EGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAF-DGIRAGVIHSDLSQTQRENAVDDFRAGK--TWVLIATDVIA  221 (248)
Q Consensus       145 ~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~-~~~~v~~~~~~~~~~~r~~~~~~f~~g~--~~ilv~T~~~~  221 (248)
                      ..|...+.+++....+++++|||+++..++.+++.|.. .|+++..+||+|+..+|+.+++.|++|+  .+|||||++++
T Consensus       488 ~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~  567 (968)
T 3dmq_A          488 DPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGS  567 (968)
T ss_dssp             SHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTT
T ss_pred             cHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhh
Confidence            46888899999887788999999999999999999995 5999999999999999999999999998  99999999999


Q ss_pred             cCCCCCCCcEEEeccCCCCcccceecC
Q 042003          222 RGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       222 ~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +|+|+|++++||++++|+|+..|.||+
T Consensus       568 ~GlDl~~~~~VI~~d~p~~~~~~~Q~~  594 (968)
T 3dmq_A          568 EGRNFQFASHMVMFDLPFNPDLLEQRI  594 (968)
T ss_dssp             CSSCCTTCCEEECSSCCSSHHHHHHHH
T ss_pred             cCCCcccCcEEEEecCCCCHHHHHHHh
Confidence            999999999999999999999999984

>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=99.94  E-value=4.6e-27  Score=202.45  Aligned_cols=207  Identities=18%  Similarity=0.151  Sum_probs=141.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      ||.|+++.+.+.....    +....|+.    ....+++|+|+||++|   +....+.+++++++|+||||++. .+ +.
T Consensus       269 LA~Qia~~l~~~~g~~----vg~~vG~~----~~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH~l~-~~-~~  335 (666)
T 3o8b_A          269 ATLGFGAYMSKAHGID----PNIRTGVR----TITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECHSTD-ST-TI  335 (666)
T ss_dssp             HHHHHHHHHHHHHSCC----CEEECSSC----EECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTTCCS-HH-HH
T ss_pred             HHHHHHHHHHHHhCCC----eeEEECcE----eccCCCCEEEECcHHH---HhCCCcccCcccEEEEccchhcC-cc-HH
Confidence            5778887666544321    22233332    1456799999999997   45666778899999999998754 33 66


Q ss_pred             ccchhHhhhCCCcc-ceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccC
Q 042003           81 KHIDPVVKACSNPS-IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL  159 (248)
Q Consensus        81 ~~~~~~~~~~~~~~-~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  159 (248)
                      ..+..+++.+.... ..+++||||+++...      ...+...........  .    ........ .       +....
T Consensus       336 ~~l~~Il~~l~~~~~~llil~SAT~~~~i~------~~~p~i~~v~~~~~~--~----i~~~~~~~-~-------l~~~~  395 (666)
T 3o8b_A          336 LGIGTVLDQAETAGARLVVLATATPPGSVT------VPHPNIEEVALSNTG--E----IPFYGKAI-P-------IEAIR  395 (666)
T ss_dssp             HHHHHHHHHTTTTTCSEEEEEESSCTTCCC------CCCTTEEEEECBSCS--S----EEETTEEE-C-------GGGSS
T ss_pred             HHHHHHHHhhhhcCCceEEEECCCCCcccc------cCCcceEEEeecccc--h----hHHHHhhh-h-------hhhcc
Confidence            66777777743322 236788999987321      111111111100000  0    00000000 0       12224


Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEE------
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVI------  233 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi------  233 (248)
                      ++++||||+++++++.+++.|++.++++..+||+|++++       |.+++.+|||||+++++|||+| +++||      
T Consensus       396 ~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~  467 (666)
T 3o8b_A          396 GGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCV  467 (666)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEE
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCccc
Confidence            689999999999999999999999999999999999875       4566679999999999999997 99999      


Q ss_pred             ----ecc-----------CCCCcccceecC
Q 042003          234 ----NYD-----------FPDSGAAYIHRI  248 (248)
Q Consensus       234 ----~~~-----------~p~~~~~~~qri  248 (248)
                          |||           .|.|..+|+||+
T Consensus       468 ~~ViNyDydP~~gl~~~~~P~s~~syiQRi  497 (666)
T 3o8b_A          468 TQTVDFSLDPTFTIETTTVPQDAVSRSQRR  497 (666)
T ss_dssp             EEEEECCCSSSCEEEEEEEECBHHHHHHHH
T ss_pred             ccccccccccccccccccCcCCHHHHHHHh
Confidence                566           899999999995

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

Probab=99.93  E-value=5.5e-27  Score=195.80  Aligned_cols=185  Identities=15%  Similarity=0.101  Sum_probs=132.2

Q ss_pred             CCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhc
Q 042003           37 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM  116 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~  116 (248)
                      +..+.+.|.+.+.+.+.. ...+.+++++|+||+|++ +.+ +......+........+++++||||+++...++...  
T Consensus        70 ~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~~-~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~~~--  144 (431)
T 2v6i_A           70 NEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DPA-SVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPPS--  144 (431)
T ss_dssp             CCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SHH-HHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSCCC--
T ss_pred             CceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-Ccc-HHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhcCC--
Confidence            455777888888777766 556899999999999997 322 233333343332346789999999998743221110  


Q ss_pred             CCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCH
Q 042003          117 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQ  196 (248)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~  196 (248)
                      ..+......                .....+...+.+.+... +++++|||+++++++.+++.|++.++++..+||+   
T Consensus       145 ~~~i~~~~~----------------~~~~~~~~~~~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~---  204 (431)
T 2v6i_A          145 NSPIIDEET----------------RIPDKAWNSGYEWITEF-DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK---  204 (431)
T ss_dssp             SSCCEEEEC----------------CCCSSCCSSCCHHHHSC-SSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT---
T ss_pred             CCceeeccc----------------cCCHHHHHHHHHHHHcC-CCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc---
Confidence            011110000                00001111122334443 5799999999999999999999999999999997   


Q ss_pred             HHHHHHHHHhhcCCceEEEEecccccCCCCCCCcE-----------------EEeccCCCCcccceecC
Q 042003          197 TQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNC-----------------VINYDFPDSGAAYIHRI  248 (248)
Q Consensus       197 ~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~-----------------Vi~~~~p~~~~~~~qri  248 (248)
                       +|+++++.|++|+.+|||||+++++|+|+| +.+                 ||+++.|.+..+|+||+
T Consensus       205 -~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~  271 (431)
T 2v6i_A          205 -TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRR  271 (431)
T ss_dssp             -THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHH
T ss_pred             -cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhh
Confidence             578899999999999999999999999999 544                 67888999999999984

>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=99.93  E-value=3e-25  Score=189.12  Aligned_cols=234  Identities=17%  Similarity=0.193  Sum_probs=154.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+.+.++++.+...   +..+.|+..  ......++|+|+||+++.+...   +....++++|+||||++.+.+   
T Consensus        97 l~~qw~~e~~~~~~~~~---v~~~~g~~~--~~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~~---  165 (500)
T 1z63_A           97 VLKNWEEELSKFAPHLR---FAVFHEDRS--KIKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ---  165 (500)
T ss_dssp             THHHHHHHHHHHCTTSC---EEECSSSTT--SCCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT---
T ss_pred             HHHHHHHHHHHHCCCce---EEEEecCch--hccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCHh---
Confidence            56899999999987654   444445432  2334568999999998865543   334578999999999987654   


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCch-HHH---HHH---------------------------------HhcCCcEEEE
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDF-VEE---LAR---------------------------------SIMHDAVRVI  123 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~-~~~---~~~---------------------------------~~~~~~~~~~  123 (248)
                      ......+..+  .....+++|||+... ..+   +..                                 .++ .+..+.
T Consensus       166 ~~~~~~l~~l--~~~~~l~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~~l-~~~~lr  242 (500)
T 1z63_A          166 TKIFKAVKEL--KSKYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAII-SPFILR  242 (500)
T ss_dssp             SHHHHHHHTS--CEEEEEEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHHHH-TTTEEC
T ss_pred             HHHHHHHHhh--ccCcEEEEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHHHH-hhHeee
Confidence            2223333332  235679999998431 111   111                                 111 111111


Q ss_pred             Ecccc----cccccceeEEEEcCC--------------------------------------------------------
Q 042003          124 VGRKN----TASESIKQKLVFAGS--------------------------------------------------------  143 (248)
Q Consensus       124 ~~~~~----~~~~~~~~~~~~~~~--------------------------------------------------------  143 (248)
                      ....+    ...+.......++.-                                                        
T Consensus       243 r~k~~~~~~~~lp~~~~~~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~  322 (500)
T 1z63_A          243 RTKYDKAIINDLPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLKGGEQSVR  322 (500)
T ss_dssp             CCTTCHHHHTTSCSEEEEEEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHHHCSCCCST
T ss_pred             ecccccchhhcCCCCeEEEEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHhcCccchhh
Confidence            11100    011111111122211                                                        


Q ss_pred             chhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcC-CCeeEEEecCCCHHHHHHHHHHhhcC-Cce-EEEEec
Q 042003          144 EEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFD-GIRAGVIHSDLSQTQRENAVDDFRAG-KTW-VLIATD  218 (248)
Q Consensus       144 ~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~-~~~v~~~~~~~~~~~r~~~~~~f~~g-~~~-ilv~T~  218 (248)
                      ...|...+.+++...  .+.+++|||++...++.+++.|... +.++..+||+++.++|+++++.|++| ..+ +|++|+
T Consensus       323 ~s~K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~  402 (500)
T 1z63_A          323 RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK  402 (500)
T ss_dssp             TCHHHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECC
T ss_pred             cchhHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecc
Confidence            123455555555543  3679999999999999999999885 89999999999999999999999998 454 789999


Q ss_pred             ccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          219 VIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       219 ~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++++|+|+|.+++||++|+|||+..|.||+
T Consensus       403 ~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~  432 (500)
T 1z63_A          403 AGGFGINLTSANRVIHFDRWWNPAVEDQAT  432 (500)
T ss_dssp             CC-CCCCCTTCSEEEESSCCSCC---CHHH
T ss_pred             cccCCCchhhCCEEEEeCCCCCcchHHHHH
Confidence            999999999999999999999999999984

>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=99.93  E-value=6.7e-27  Score=202.41  Aligned_cols=187  Identities=12%  Similarity=0.077  Sum_probs=138.0

Q ss_pred             cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHH
Q 042003           35 KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARS  114 (248)
Q Consensus        35 ~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~  114 (248)
                      ..+..+.++|.+.+.+.+... ..+++++++|+||||++ +.+ +...+..+...+.....|+++||||++.....+.. 
T Consensus       252 tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~-~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~-  327 (618)
T 2whx_A          252 TGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPC-SVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQ-  327 (618)
T ss_dssp             CSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHH-HHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCC-
T ss_pred             CCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-Ccc-HHHHHHHHHHHhcccCccEEEEECCCchhhhhhhc-
Confidence            345567788888887766654 34789999999999997 333 55566666666444678999999999875432221 


Q ss_pred             hcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCC
Q 042003          115 IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDL  194 (248)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~  194 (248)
                        .++..+...... +.              .+...+...+.+. ++++||||++++.++.+++.|++.++++..+||+ 
T Consensus       328 --~~~~~~~v~~~~-~~--------------~~~~~ll~~l~~~-~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~-  388 (618)
T 2whx_A          328 --SNSPIEDIEREI-PE--------------RSWNTGFDWITDY-QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK-  388 (618)
T ss_dssp             --CSSCEEEEECCC-CS--------------SCCSSSCHHHHHC-CSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT-
T ss_pred             --cCCceeeecccC-CH--------------HHHHHHHHHHHhC-CCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH-
Confidence              122222221110 00              0001112222233 6799999999999999999999999999999984 


Q ss_pred             CHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEE--------------------EeccCCCCcccceecC
Q 042003          195 SQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCV--------------------INYDFPDSGAAYIHRI  248 (248)
Q Consensus       195 ~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~V--------------------i~~~~p~~~~~~~qri  248 (248)
                         +|.++++.|++|+.+|||||+++++|+|+| +++|                    |+++.|.|..+|+||+
T Consensus       389 ---~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~  458 (618)
T 2whx_A          389 ---TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRR  458 (618)
T ss_dssp             ---THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHH
T ss_pred             ---HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHHHhc
Confidence               788899999999999999999999999998 9988                    7777799999999985

>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=8.9e-25  Score=159.39  Aligned_cols=117  Identities=38%  Similarity=0.585  Sum_probs=109.3

Q ss_pred             ccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCc
Q 042003          132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKT  211 (248)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~  211 (248)
                      .++.+++..+...+.|...+.++++...++++||||++++.++.+++.|+..++.+..+||+|++.+|..+++.|++|+.
T Consensus         2 ~~i~~~~~~~~~~~~K~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   81 (165)
T 1fuk_A            2 EGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSS   81 (165)
T ss_dssp             --CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCcEEEEEECCcchhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCC
Confidence            35677888777776799999999998878899999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          212 WVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       212 ~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +|||||+++++|+|+|++++||++|+|+|+..|+||+
T Consensus        82 ~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~  118 (165)
T 1fuk_A           82 RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRI  118 (165)
T ss_dssp             SEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSS
T ss_pred             EEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHh
Confidence            9999999999999999999999999999999999996

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

Probab=99.93  E-value=1.3e-25  Score=167.24  Aligned_cols=134  Identities=33%  Similarity=0.562  Sum_probs=108.0

Q ss_pred             HHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEec
Q 042003          113 RSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHS  192 (248)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~  192 (248)
                      ..++.+|..+.++.......++.+.+..+.. +.|...|.+++... ++++||||+++..++.+++.|+..++++..+||
T Consensus         9 ~~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~-~~K~~~L~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg   86 (191)
T 2p6n_A            9 SGVDLGTENLYFQSMGAASLDVIQEVEYVKE-EAKMVYLLECLQKT-PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHG   86 (191)
T ss_dssp             -------------------CCSEEEEEECCG-GGHHHHHHHHHTTS-CSCEEEECSCHHHHHHHHHHHHHHTCCEEEECT
T ss_pred             ccccCCCEEEEECCCCCCCcCceEEEEEcCh-HHHHHHHHHHHHhC-CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeC
Confidence            3467788888877777777888888877664 56999999999876 579999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          193 DLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       193 ~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +|++.+|+++++.|++|+.+|||||+++++|+|+|++++||+||+|+|+..|+||+
T Consensus        87 ~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~  142 (191)
T 2p6n_A           87 GKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRI  142 (191)
T ss_dssp             TSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999985

>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=99.93  E-value=3.6e-28  Score=203.39  Aligned_cols=181  Identities=16%  Similarity=0.148  Sum_probs=118.3

Q ss_pred             EeChHHHHHHHhc--------CCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHH
Q 042003           42 ISTPLRLRLAIRR--------KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR  113 (248)
Q Consensus        42 v~Tp~~l~~~~~~--------~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~  113 (248)
                      ++||+++...+..        ....+++++++|+||||++ +.+ +...+..+.........|+++||||+++....+..
T Consensus        72 v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~-~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~~~~~  149 (440)
T 1yks_A           72 HGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPA-SIAARGWAAHRARANESATILMTATPPGTSDEFPH  149 (440)
T ss_dssp             CCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHH-HHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCC
T ss_pred             ccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-Ccc-hHHHHHHHHHHhccCCceEEEEeCCCCchhhhhhh
Confidence            6777555433322        2234789999999999998 322 33333333333234578999999999875443222


Q ss_pred             HhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecC
Q 042003          114 SIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSD  193 (248)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~  193 (248)
                      .  ..+.......  .+          ........    ..+.+. +++++|||++++.++.+++.|++.++++..+|| 
T Consensus       150 ~--~~~~~~~~~~--~~----------~~~~~~~~----~~l~~~-~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg-  209 (440)
T 1yks_A          150 S--NGEIEDVQTD--IP----------SEPWNTGH----DWILAD-KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR-  209 (440)
T ss_dssp             C--SSCEEEEECC--CC----------SSCCSSSC----HHHHHC-CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS-
T ss_pred             c--CCCeeEeeec--cC----------hHHHHHHH----HHHHhc-CCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc-
Confidence            1  1111111000  00          00111111    222222 689999999999999999999999999999999 


Q ss_pred             CCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe-------------------ccCCCCcccceecC
Q 042003          194 LSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN-------------------YDFPDSGAAYIHRI  248 (248)
Q Consensus       194 ~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~-------------------~~~p~~~~~~~qri  248 (248)
                         ++|.++++.|++|+.+|||||+++++|+|+| +++||+                   ++.|.+..+|+||+
T Consensus       210 ---~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~  279 (440)
T 1yks_A          210 ---KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRR  279 (440)
T ss_dssp             ---SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHH
T ss_pred             ---hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHHHHhc
Confidence               4688999999999999999999999999999 999996                   88999999999984

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

Probab=99.92  E-value=2.6e-25  Score=193.35  Aligned_cols=216  Identities=17%  Similarity=0.123  Sum_probs=155.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccc-cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLS-KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNL   79 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~   79 (248)
                      ||.|+++.+++.    + ..+....|+....... ....+++++|++.+.        ....++++|+||||++.+.+ +
T Consensus       191 LA~Qi~~~l~~~----g-~~v~lltG~~~~iv~TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~-~  256 (677)
T 3rc3_A          191 LAHEIFEKSNAA----G-VPCDLVTGEERVTVQPNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPA-R  256 (677)
T ss_dssp             HHHHHHHHHHHT----T-CCEEEECSSCEECCSTTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTT-T
T ss_pred             HHHHHHHHHHhc----C-CcEEEEECCeeEEecCCCcccceeEecHhHhh--------hcccCCEEEEecceecCCcc-c
Confidence            688999998876    3 3355555654221111 123788888886542        24778999999999998776 7


Q ss_pred             cccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccC
Q 042003           80 LKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL  159 (248)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  159 (248)
                      ...+..++..+.....+++++|||.+. ...+.... +....+.......+..     .  ....      + ..+... 
T Consensus       257 g~~~~~~l~~l~~~~i~il~~SAT~~~-i~~l~~~~-~~~~~v~~~~r~~~l~-----~--~~~~------l-~~l~~~-  319 (677)
T 3rc3_A          257 GWAWTRALLGLCAEEVHLCGEPAAIDL-VMELMYTT-GEEVEVRDYKRLTPIS-----V--LDHA------L-ESLDNL-  319 (677)
T ss_dssp             HHHHHHHHHHCCEEEEEEEECGGGHHH-HHHHHHHH-TCCEEEEECCCSSCEE-----E--CSSC------C-CSGGGC-
T ss_pred             hHHHHHHHHccCccceEEEeccchHHH-HHHHHHhc-CCceEEEEeeecchHH-----H--HHHH------H-HHHHhc-
Confidence            777777777755578899999999543 44444333 3444432221111100     0  0000      0 011122 


Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhc--CCceEEEEecccccCCCCCCCcEEEeccC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRA--GKTWVLIATDVIARGMDFKGVNCVINYDF  237 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~--g~~~ilv~T~~~~~Gidip~~~~Vi~~~~  237 (248)
                      .+..+|||+++++++.+++.|++.++.+..+||+|++++|.++++.|++  |+.+|||||+++++|+|+ ++++||++|.
T Consensus       320 ~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~  398 (677)
T 3rc3_A          320 RPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSL  398 (677)
T ss_dssp             CTTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCS
T ss_pred             CCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCc
Confidence            3566899999999999999999999999999999999999999999999  889999999999999999 8999999999


Q ss_pred             --------------CCCcccceecC
Q 042003          238 --------------PDSGAAYIHRI  248 (248)
Q Consensus       238 --------------p~~~~~~~qri  248 (248)
                                    |.|..+|+||+
T Consensus       399 ~k~~~~~~G~~~~~p~s~~~~~QR~  423 (677)
T 3rc3_A          399 IKPSINEKGERELEPITTSQALQIA  423 (677)
T ss_dssp             BC-----------CBCCHHHHHHHH
T ss_pred             cccccccCCccccccCCHHHHHHHh
Confidence                          77899999984

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

Probab=99.92  E-value=6.5e-25  Score=159.76  Aligned_cols=119  Identities=31%  Similarity=0.525  Sum_probs=109.5

Q ss_pred             cccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhc
Q 042003          129 TASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRA  208 (248)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~  208 (248)
                      ....++.+.+..+. .+.|...|.+++....++++||||++++.++.+++.|...++++..+||+|++.+|..+++.|++
T Consensus         5 ~~~~~i~~~~~~~~-~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~   83 (163)
T 2hjv_A            5 LTTRNIEHAVIQVR-EENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKR   83 (163)
T ss_dssp             -CCCCEEEEEEECC-GGGHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             cCcccceEEEEECC-hHHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHc
Confidence            34456777777665 45699999999988878899999999999999999999999999999999999999999999999


Q ss_pred             CCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          209 GKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       209 g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+.+|||||+++++|+|+|++++||++|+|+|+..|+||+
T Consensus        84 g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~  123 (163)
T 2hjv_A           84 GEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRT  123 (163)
T ss_dssp             TSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHT
T ss_pred             CCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhc
Confidence            9999999999999999999999999999999999999986

>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=99.92  E-value=5.9e-25  Score=161.90  Aligned_cols=119  Identities=34%  Similarity=0.531  Sum_probs=112.6

Q ss_pred             ccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcC
Q 042003          130 ASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAG  209 (248)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g  209 (248)
                      ...++.+.+..+...+.|...+.++++...++++||||++++.++.+++.|...++++..+||+|++.+|..+++.|++|
T Consensus         4 ~~~~i~q~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g   83 (175)
T 2rb4_A            4 TLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDG   83 (175)
T ss_dssp             CBCCEEEEEEECSSHHHHHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTT
T ss_pred             ccCCceEEEEEcCChHhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence            45678899988888888999999999988788999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEecccccCCCCCCCcEEEeccCC------CCcccceecC
Q 042003          210 KTWVLIATDVIARGMDFKGVNCVINYDFP------DSGAAYIHRI  248 (248)
Q Consensus       210 ~~~ilv~T~~~~~Gidip~~~~Vi~~~~p------~~~~~~~qri  248 (248)
                      +.+|||||+++++|+|+|++++||+||+|      .+..+|+||+
T Consensus        84 ~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~  128 (175)
T 2rb4_A           84 KEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRI  128 (175)
T ss_dssp             SCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHH
T ss_pred             CCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHh
Confidence            99999999999999999999999999999      8889999984

>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=99.92  E-value=6.1e-25  Score=161.18  Aligned_cols=117  Identities=29%  Similarity=0.403  Sum_probs=107.9

Q ss_pred             cccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCC
Q 042003          131 SESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGK  210 (248)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~  210 (248)
                      ..++.+++..+.. +.|...+.++++...++++||||++++.++.+++.|...++++..+||+|++.+|..+++.|++|+
T Consensus         3 ~~~i~q~~~~~~~-~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~   81 (172)
T 1t5i_A            3 LHGLQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQ   81 (172)
T ss_dssp             --CCEEEEEECCG-GGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             cCCeEEEEEECCh-HHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCC
Confidence            3457777776654 569999999999887889999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          211 TWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       211 ~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      .+|||||+++++|+|+|++++||+||+|+|+..|+||+
T Consensus        82 ~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~  119 (172)
T 1t5i_A           82 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV  119 (172)
T ss_dssp             CSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHH
T ss_pred             CcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHh
Confidence            99999999999999999999999999999999999984

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

Probab=99.92  E-value=1e-25  Score=196.30  Aligned_cols=181  Identities=14%  Similarity=0.132  Sum_probs=125.0

Q ss_pred             EEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcE
Q 042003           41 LISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV  120 (248)
Q Consensus        41 ~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~  120 (248)
                      -+.+.+.+.+.+... ..+++++++|+||||++.. . +...+..+.........|+++||||+++....+...  ..+.
T Consensus       313 ~~l~~~~l~~~l~~~-~~l~~l~lvViDEaH~~~~-~-~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~--~~~i  387 (673)
T 2wv9_A          313 DVMCHATLTHRLMSP-LRVPNYNLFVMDEAHFTDP-A-SIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT--NSPV  387 (673)
T ss_dssp             EEEEHHHHHHHHHSS-SCCCCCSEEEEESTTCCCH-H-HHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--SSCE
T ss_pred             HHHHhhhhHHHHhcc-cccccceEEEEeCCcccCc-c-HHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc--CCce
Confidence            334444554444443 4679999999999999721 1 122233333332235789999999998753322110  1111


Q ss_pred             EEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHH
Q 042003          121 RVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRE  200 (248)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~  200 (248)
                      ......              ... . ....+...+.+ .++++||||+++++++.+++.|++.++++..+||+    +|+
T Consensus       388 ~~v~~~--------------~~~-~-~~~~~l~~l~~-~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~  446 (673)
T 2wv9_A          388 HDVSSE--------------IPD-R-AWSSGFEWITD-YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYD  446 (673)
T ss_dssp             EEEECC--------------CCS-S-CCSSCCHHHHS-CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHH
T ss_pred             EEEeee--------------cCH-H-HHHHHHHHHHh-CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHH
Confidence            111000              000 0 00111122223 36899999999999999999999999999999994    789


Q ss_pred             HHHHHhhcCCceEEEEecccccCCCCCCCcEEEe--------------------ccCCCCcccceecC
Q 042003          201 NAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN--------------------YDFPDSGAAYIHRI  248 (248)
Q Consensus       201 ~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~--------------------~~~p~~~~~~~qri  248 (248)
                      ++++.|++|+.+|||||+++++|+|+| +++||+                    |++|.|..+|+||+
T Consensus       447 ~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~  513 (673)
T 2wv9_A          447 TEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRR  513 (673)
T ss_dssp             HHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHH
T ss_pred             HHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHHHHh
Confidence            999999999999999999999999999 999998                    56899999999984

>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=99.91  E-value=1.6e-25  Score=188.41  Aligned_cols=185  Identities=15%  Similarity=0.122  Sum_probs=127.2

Q ss_pred             CCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhc
Q 042003           37 SCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM  116 (248)
Q Consensus        37 ~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~  116 (248)
                      +..+.++|.+.+.+.+... ..+++++++|+||||.....  +...+..+.........|+++||||+++....+...  
T Consensus        89 ~~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~--~~~~~~~~~~~~~~~~~~~il~SAT~~~~~~~~~~~--  163 (459)
T 2z83_A           89 NEIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPA--SIAARGYIATKVELGEAAAIFMTATPPGTTDPFPDS--  163 (459)
T ss_dssp             CCSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHH--HHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--
T ss_pred             CcEEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCch--hhHHHHHHHHHhccCCccEEEEEcCCCcchhhhccC--
Confidence            3457788888887777654 45789999999999984211  111111122221235789999999998754322111  


Q ss_pred             CCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCH
Q 042003          117 HDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQ  196 (248)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~  196 (248)
                      ..+......  ..+..          .....    ...+... ++++||||++++.++.+++.|+..++.+..+||.   
T Consensus       164 ~~pi~~~~~--~~~~~----------~~~~~----~~~l~~~-~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~---  223 (459)
T 2z83_A          164 NAPIHDLQD--EIPDR----------AWSSG----YEWITEY-AGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK---  223 (459)
T ss_dssp             SSCEEEEEC--CCCSS----------CCSSC----CHHHHHC-CSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT---
T ss_pred             CCCeEEecc--cCCcc----------hhHHH----HHHHHhc-CCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH---
Confidence            122222111  00000          00111    1223333 6899999999999999999999999999999995   


Q ss_pred             HHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe--------------------ccCCCCcccceecC
Q 042003          197 TQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN--------------------YDFPDSGAAYIHRI  248 (248)
Q Consensus       197 ~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~--------------------~~~p~~~~~~~qri  248 (248)
                       +|+.+++.|++|+.+|||||+++++|+|+|+ ++||+                    |+.|.|..+|+||+
T Consensus       224 -~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~  293 (459)
T 2z83_A          224 -SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRR  293 (459)
T ss_dssp             -CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHH
T ss_pred             -HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhc
Confidence             6788999999999999999999999999999 99999                    66999999999984

>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=99.90  E-value=4e-24  Score=158.59  Aligned_cols=120  Identities=38%  Similarity=0.576  Sum_probs=95.1

Q ss_pred             ccccccceeEEEEcCCchhHHHHHHHHHhcc-CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHh
Q 042003          128 NTASESIKQKLVFAGSEEGKLLALRQSFAES-LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDF  206 (248)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f  206 (248)
                      .....++.+.+..++. +.|...|.++++.. .++++||||++++.++.+++.|+..++++..+||+|++.+|..+++.|
T Consensus        14 ~~~~~~i~q~~~~v~~-~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f   92 (185)
T 2jgn_A           14 GSTSENITQKVVWVEE-SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQF   92 (185)
T ss_dssp             --CCTTEEEEEEECCG-GGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHH
T ss_pred             CCCCCCceEEEEEeCc-HHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHH
Confidence            3445678888877764 56899999998876 467999999999999999999999999999999999999999999999


Q ss_pred             hcCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          207 RAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       207 ~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++|+.+|||||+++++|+|+|++++||++|+|+|+.+|+||+
T Consensus        93 ~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~  134 (185)
T 2jgn_A           93 RSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRI  134 (185)
T ss_dssp             HHTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHH
T ss_pred             HcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHc
Confidence            999999999999999999999999999999999999999984

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

Probab=99.90  E-value=9e-23  Score=182.28  Aligned_cols=103  Identities=22%  Similarity=0.286  Sum_probs=92.0

Q ss_pred             hHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCc---eEEEEeccc
Q 042003          146 GKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKT---WVLIATDVI  220 (248)
Q Consensus       146 ~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~---~ilv~T~~~  220 (248)
                      .|+..+..++...  .+.|+|||+.....+..+.+.|...++++..+||+++..+|+++++.|+++..   .+|++|.++
T Consensus       556 ~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~ag  635 (800)
T 3mwy_W          556 GKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAG  635 (800)
T ss_dssp             HHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHH
T ss_pred             hHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecccc
Confidence            3555666666543  36799999999999999999999999999999999999999999999998654   499999999


Q ss_pred             ccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          221 ARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       221 ~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++|+|+|.+++||+||+|||+..+.||+
T Consensus       636 g~GlNL~~a~~VI~~D~~wnp~~~~Qa~  663 (800)
T 3mwy_W          636 GLGINLMTADTVVIFDSDWNPQADLQAM  663 (800)
T ss_dssp             TTTCCCTTCCEEEESSCCSCSHHHHHHH
T ss_pred             cCCCCccccceEEEecCCCChhhHHHHH
Confidence            9999999999999999999999999974

>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=99.89  E-value=2.3e-23  Score=157.87  Aligned_cols=107  Identities=36%  Similarity=0.553  Sum_probs=101.8

Q ss_pred             CCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccc
Q 042003          142 GSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIA  221 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~  221 (248)
                      ...+.|...+.+++....++++||||++++.++.+++.|...++.+..+||+|++++|+.+++.|++|+.+|||||++++
T Consensus        13 ~~~~~k~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~   92 (212)
T 3eaq_A           13 APVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAA   92 (212)
T ss_dssp             CCTTSHHHHHHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTT
T ss_pred             CCHHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhh
Confidence            34457999999999988789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCcEEEeccCCCCcccceecC
Q 042003          222 RGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       222 ~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +|+|+|++++||++|+|+|+..|+||+
T Consensus        93 ~Gidi~~v~~Vi~~~~p~~~~~~~qr~  119 (212)
T 3eaq_A           93 RGLDIPQVDLVVHYRLPDRAEAYQHRS  119 (212)
T ss_dssp             CSSSCCCBSEEEESSCCSSHHHHHHHH
T ss_pred             cCCCCccCcEEEECCCCcCHHHHHHHh
Confidence            999999999999999999999999984

>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=99.81  E-value=7.4e-25  Score=160.56  Aligned_cols=116  Identities=34%  Similarity=0.514  Sum_probs=107.3

Q ss_pred             cceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCce
Q 042003          133 SIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTW  212 (248)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~  212 (248)
                      ++.+.+..++..+.|...+.++++...++++||||++++.++.+++.|+..++.+..+||+|++.+|..+++.|++|+.+
T Consensus         3 ~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~   82 (170)
T 2yjt_D            3 KIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVN   82 (170)
Confidence            45566666666577899999999887778999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          213 VLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       213 ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |||||+++++|+|+|++++||++|+|+|+..|+||+
T Consensus        83 vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~  118 (170)
T 2yjt_D           83 VLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRI  118 (170)
Confidence            999999999999999999999999999999999996

>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=99.88  E-value=1.4e-22  Score=176.91  Aligned_cols=102  Identities=14%  Similarity=0.144  Sum_probs=89.9

Q ss_pred             HHHHHHHHHhc---cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCc---eEEEEeccc
Q 042003          147 KLLALRQSFAE---SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKT---WVLIATDVI  220 (248)
Q Consensus       147 ~~~~l~~~~~~---~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~---~ilv~T~~~  220 (248)
                      |...+..++..   ..+.|+|||++....++.+.+.|...++.+..+||+++.++|+++++.|++|..   .+|++|+++
T Consensus       400 K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~  479 (644)
T 1z3i_X          400 KMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAG  479 (644)
T ss_dssp             HHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGS
T ss_pred             HHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccc
Confidence            44444444432   346899999999999999999999999999999999999999999999999865   489999999


Q ss_pred             ccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          221 ARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       221 ~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++|+|++++++||+||+|||+..|.||+
T Consensus       480 g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~  507 (644)
T 1z3i_X          480 GCGLNLIGANRLVMFDPDWNPANDEQAM  507 (644)
T ss_dssp             CTTCCCTTEEEEEECSCCSSHHHHHHHH
T ss_pred             cCCcccccCCEEEEECCCCCccHHHHHH
Confidence            9999999999999999999999999974

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

Probab=99.88  E-value=1.1e-22  Score=161.23  Aligned_cols=114  Identities=34%  Similarity=0.521  Sum_probs=105.9

Q ss_pred             ceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceE
Q 042003          134 IKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWV  213 (248)
Q Consensus       134 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~i  213 (248)
                      +.++++.+.. ..|...+..++....++++||||++++.++.+++.|...++.+..+||+|++++|+.+++.|++|+.+|
T Consensus         3 v~~~~i~~~~-~~K~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~v   81 (300)
T 3i32_A            3 YEEEAVPAPV-RGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRV   81 (300)
T ss_dssp             SEEEEEECCS-SSHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCE
T ss_pred             eEEEEEECCH-HHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceE
Confidence            4456665555 569999999998877899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          214 LIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       214 lv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ||||+++++|+|+|++++||+||+|+|...|+||+
T Consensus        82 LVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~  116 (300)
T 3i32_A           82 LVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRS  116 (300)
T ss_dssp             EEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHH
T ss_pred             EEEechhhcCccccceeEEEEcCCCCCHHHHHHHc
Confidence            99999999999999999999999999999999984

>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=99.88  E-value=8.5e-23  Score=178.33  Aligned_cols=190  Identities=22%  Similarity=0.242  Sum_probs=131.1

Q ss_pred             eChHHHHHHHhcCCcccCceeEEEEecccccccc-Ccccc--------------cchhHhh-------hCCCccceeEEE
Q 042003           43 STPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV-GNLLK--------------HIDPVVK-------ACSNPSIVRSLF  100 (248)
Q Consensus        43 ~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~-~~~~~--------------~~~~~~~-------~~~~~~~~~i~~  100 (248)
                      +||++|.+++..+.       ++|+||+|++.+. +.+..              .+...+.       .+.+...|++++
T Consensus       320 ~tpg~LlDyl~~~~-------llVlDEa~~~l~~~~~~~~~~~~~~~~l~~~G~~lp~~l~~~~l~~~e~~~~~~q~i~~  392 (661)
T 2d7d_A          320 STPYTLLDYFPDDF-------MIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYV  392 (661)
T ss_dssp             CCCBCGGGGSCSSC-------EEEEETHHHHHHHHHHHHHHHHHHHHHHHHTTSSCGGGGGSCCCCHHHHHHTCSEEEEE
T ss_pred             CCccHHHHHcccCc-------EEEEecHHHHHHHHHHHHHHHHHHHHHHHHccccchhhhhcccccHHHHhccCCCEEEE
Confidence            89999988875432       8999999986521 10100              0111110       001135788999


Q ss_pred             EeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhc-c-CCCCEEEEecchHHHHHHHH
Q 042003          101 SATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAE-S-LNPPVLIFVQSKERAKELYG  178 (248)
Q Consensus       101 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~-~~~~~liF~~~~~~~~~l~~  178 (248)
                      |||+++.....    ................+.     ........+...+...+.. . .+.++||||+|+..++.+++
T Consensus       393 SAT~~~~~~~~----~~~~~~~~~r~~~l~~p~-----i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~  463 (661)
T 2d7d_A          393 SATPGPYEIEH----TDEMVEQIIRPTGLLDPL-----IDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTD  463 (661)
T ss_dssp             CSSCCHHHHHH----CSSCEEECCCTTCCCCCE-----EEEECSTTHHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHH
T ss_pred             ecCCChhHHHh----hhCeeeeeecccCCCCCe-----EEEecccchHHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHH
Confidence            99987633221    112122111111111111     1122222333444333332 1 36799999999999999999


Q ss_pred             HhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC-----CCCcccceecC
Q 042003          179 ELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF-----PDSGAAYIHRI  248 (248)
Q Consensus       179 ~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~-----p~~~~~~~qri  248 (248)
                      .|++.++++..+||++++.+|.++++.|++|+.+|||||+.+++|+|+|++++||+++.     |.|..+|+||+
T Consensus       464 ~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQr~  538 (661)
T 2d7d_A          464 YLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTI  538 (661)
T ss_dssp             HHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHHHHH
T ss_pred             HHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999998     99999999985

>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=99.88  E-value=1.9e-22  Score=176.25  Aligned_cols=190  Identities=22%  Similarity=0.247  Sum_probs=130.1

Q ss_pred             eChHHHHHHHhcCCcccCceeEEEEecccccccc-Ccccc--------------cchhHhh-------hCCCccceeEEE
Q 042003           43 STPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV-GNLLK--------------HIDPVVK-------ACSNPSIVRSLF  100 (248)
Q Consensus        43 ~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~-~~~~~--------------~~~~~~~-------~~~~~~~~~i~~  100 (248)
                      +||++|.+.+...       .++|+||+|++.+. +.+..              .+...+.       .+.....|++++
T Consensus       314 ~tp~~LlDyl~~~-------~llVlDEah~~~~~~~~~~~~~~~~~~~l~~~G~~lp~~l~~~~l~~~e~~~~~~q~i~~  386 (664)
T 1c4o_A          314 EPPYTLLDYFPED-------FLVFLDESHVTVPQLQGMYRGDYARKKTLVDYGFRLPSALDNRPLRFEEFLERVSQVVFV  386 (664)
T ss_dssp             SCCCCGGGGSCTT-------CEEEEETHHHHHHHHHHHHHHHHHHHHHHHHTTSSCGGGGGSSCCCHHHHHHTCSEEEEE
T ss_pred             CCchHHHHHHhhc-------cEEEEecccccHHHHHHHHHHHHHHHHHHHHccccchhhhhcCcccHHHHHhhcCCEEEE
Confidence            8999888877533       28999999986521 10110              0011110       001135688999


Q ss_pred             EeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHH
Q 042003          101 SATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYG  178 (248)
Q Consensus       101 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~  178 (248)
                      |||+++.....    ................+     .........+...+...+...  .+.++||||+|+..++.+++
T Consensus       387 SAT~~~~~~~~----~~~~~~~~~r~~~l~~p-----~i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~  457 (664)
T 1c4o_A          387 SATPGPFELAH----SGRVVEQIIRPTGLLDP-----LVRVKPTENQILDLMEGIRERAARGERTLVTVLTVRMAEELTS  457 (664)
T ss_dssp             ESSCCHHHHHH----CSEEEEECSCTTCCCCC-----EEEEECSTTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHH
T ss_pred             ecCCCHHHHHh----hhCeeeeeeccCCCCCC-----eEEEecccchHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHH
Confidence            99987633211    11111111111001111     111222223444443333321  36799999999999999999


Q ss_pred             HhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccC-----CCCcccceecC
Q 042003          179 ELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDF-----PDSGAAYIHRI  248 (248)
Q Consensus       179 ~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~-----p~~~~~~~qri  248 (248)
                      .|.+.++++..+||++++.+|.++++.|++|+.+|||||+.+++|+|+|++++||+++.     |.|..+|+||+
T Consensus       458 ~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQr~  532 (664)
T 1c4o_A          458 FLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTI  532 (664)
T ss_dssp             HHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHH
T ss_pred             HHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCcccCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999998     99999999985

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.86  E-value=2.5e-21  Score=165.81  Aligned_cols=149  Identities=19%  Similarity=0.188  Sum_probs=114.2

Q ss_pred             ceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhcc--CCCCEEEEecchHH
Q 042003           95 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAES--LNPPVLIFVQSKER  172 (248)
Q Consensus        95 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~  172 (248)
                      ..+.+||+|+.++..++...|..+  .+.+ +...+.....+.........+|...+.+.+...  .++++||||+|++.
T Consensus       410 ~kL~GMTGTa~te~~Ef~~iY~l~--vv~I-Ptnkp~~R~d~~d~vy~t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~  486 (822)
T 3jux_A          410 EKLAGMTGTAKTEESEFVQVYGME--VVVI-PTHKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEK  486 (822)
T ss_dssp             SEEEEEESSCGGGHHHHHHHSCCC--EEEC-CCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESSHHH
T ss_pred             hHHeEECCCCchHHHHHHHHhCCe--EEEE-CCCCCcceeecCcEEEecHHHHHHHHHHHHHHHhhCCCCEEEEECCHHH
Confidence            467899999998777776666433  2222 333333344443223446667888888877653  37899999999999


Q ss_pred             HHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCC--------CCcEEEeccCCCCcccc
Q 042003          173 AKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFK--------GVNCVINYDFPDSGAAY  244 (248)
Q Consensus       173 ~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip--------~~~~Vi~~~~p~~~~~~  244 (248)
                      ++.+++.|++.|+++.++||+....++..+.++++.|  .|+|||+++++|+|++        +..+||+++.|.|...|
T Consensus       487 sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y  564 (822)
T 3jux_A          487 SELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRID  564 (822)
T ss_dssp             HHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHH
T ss_pred             HHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHH
Confidence            9999999999999999999996555555556666666  5999999999999998        66799999999999999


Q ss_pred             eecC
Q 042003          245 IHRI  248 (248)
Q Consensus       245 ~qri  248 (248)
                      .||+
T Consensus       565 ~qri  568 (822)
T 3jux_A          565 NQLR  568 (822)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            9984

>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=99.83  E-value=1.7e-20  Score=169.73  Aligned_cols=234  Identities=13%  Similarity=0.071  Sum_probs=145.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccc-cCCCcEEEeChHHHHHHHhcCC--cccCceeEEEEecccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLS-KFSCDILISTPLRLRLAIRRKK--IDLSRVEYLVLDEADKLF   74 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~~~i~v~Tp~~l~~~~~~~~--~~~~~~~~lIiDEah~~~   74 (248)
                      |+.|+.+.++.+++..       +.++.   .....+ ..+++|+|+||+++...+....  ..++...++|+||||+..
T Consensus       342 L~~Q~~~~f~~f~~~~-------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~  414 (1038)
T 2w00_A          342 LDYQTMKEYQRFSPDS-------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQ  414 (1038)
T ss_dssp             CCHHHHHHHHTTSTTC-------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTH
T ss_pred             HHHHHHHHHHHhcccc-------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhc
Confidence            7889999999887641       11211   222222 3578999999999998876542  245678999999999965


Q ss_pred             ccCcccccchhHhhhCCCccceeEEEEeecCchHH----HHHHHhcCCcEEEEEccc---ccccccceeEEEE-------
Q 042003           75 EVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE----ELARSIMHDAVRVIVGRK---NTASESIKQKLVF-------  140 (248)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~----~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~-------  140 (248)
                      ..    .....+...+  ++.+++++|||+.....    .....+++++........   .....++...+..       
T Consensus       415 ~~----~~~~~I~~~~--p~a~~lgfTATP~~~~~~~~~~~t~~~FG~~i~~Y~l~~AI~dg~l~p~~v~y~~v~~~~~~  488 (1038)
T 2w00_A          415 FG----EAQKNLKKKF--KRYYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVDYNDVRPQFKS  488 (1038)
T ss_dssp             HH----HHHHHHHHHC--SSEEEEEEESSCCCSTTCTTSCCHHHHHCSEEEEECHHHHHHHTSSCCEEEEECCCCGGGHH
T ss_pred             ch----HHHHHHHHhC--CcccEEEEeCCccccccchhhhHHHHHhCCeeEeecHHHHHhCCCcCCeEEEEEeccchhhh
Confidence            32    2234455553  34789999999875321    122223333221110000   0000000000000       


Q ss_pred             -----------------cCCchhHHHHHHH-HHh---cc--------CCCCEEEEecchHHHHHHHHHhhcCC-------
Q 042003          141 -----------------AGSEEGKLLALRQ-SFA---ES--------LNPPVLIFVQSKERAKELYGELAFDG-------  184 (248)
Q Consensus       141 -----------------~~~~~~~~~~l~~-~~~---~~--------~~~~~liF~~~~~~~~~l~~~L~~~~-------  184 (248)
                                       .-..+.+...+.. +++   ..        .+.+++|||+|+..|..+++.|.+.+       
T Consensus       489 ~~~e~d~~~~~~i~~~~~l~~~~ri~~I~~~Il~~~~~~~~~~~~~~~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~  568 (1038)
T 2w00_A          489 LETETDEKKLSAAENQQAFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKS  568 (1038)
T ss_dssp             HHTCCCHHHHHHTCSTTTTTCHHHHHHHHHHHHHHHHHHTTCSSSSCCCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             ccccccHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhhhcccCCCCcEEEEECCHHHHHHHHHHHHhhhhhhcccc
Confidence                             0012223333322 222   11        23579999999999999999997643       


Q ss_pred             -----CeeE-EEecC----------C----------CHH-----------------------------HHHHHHHHhhcC
Q 042003          185 -----IRAG-VIHSD----------L----------SQT-----------------------------QRENAVDDFRAG  209 (248)
Q Consensus       185 -----~~v~-~~~~~----------~----------~~~-----------------------------~r~~~~~~f~~g  209 (248)
                           .++. ++||+          +          ++.                             .|+++++.|++|
T Consensus       569 ~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g  648 (1038)
T 2w00_A          569 ATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQ  648 (1038)
T ss_dssp             SSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTT
T ss_pred             cccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHHHHHHHHhcccccccchhhhHHHHHHHHHHHcC
Confidence                 4554 45542          2          221                             378899999999


Q ss_pred             CceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          210 KTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       210 ~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +.++||+|+.+.+|+|+|.+ +++.+|.|.+...|+||+
T Consensus       649 ~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaI  686 (1038)
T 2w00_A          649 DIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAF  686 (1038)
T ss_dssp             SSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHH
T ss_pred             CCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehh
Confidence            99999999999999999999 778899999999999985

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

Probab=99.78  E-value=1.4e-18  Score=135.94  Aligned_cols=106  Identities=16%  Similarity=0.241  Sum_probs=93.6

Q ss_pred             CchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcC-CCeeEEEecCCCHHHHHHHHHHhhcC-Cce-EEEEe
Q 042003          143 SEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFD-GIRAGVIHSDLSQTQRENAVDDFRAG-KTW-VLIAT  217 (248)
Q Consensus       143 ~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~-~~~v~~~~~~~~~~~r~~~~~~f~~g-~~~-ilv~T  217 (248)
                      ....|...+.+++...  .+.|+||||++...++.+.+.|... ++.+..+||+++.++|+++++.|++| +.. +|++|
T Consensus        93 ~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st  172 (271)
T 1z5z_A           93 RRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSV  172 (271)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEEC
T ss_pred             ccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEeh
Confidence            3457888888888765  5789999999999999999999885 99999999999999999999999998 666 78999


Q ss_pred             cccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          218 DVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       218 ~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +++++|+|++.+++||+||+|||+..|.||+
T Consensus       173 ~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~  203 (271)
T 1z5z_A          173 KAGGFGINLTSANRVIHFDRWWNPAVEDQAT  203 (271)
T ss_dssp             CTTCCCCCCTTCSEEEECSCCSCTTTC----
T ss_pred             hhhcCCcCcccCCEEEEECCCCChhHHHHHH
Confidence            9999999999999999999999999999985

>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=99.77  E-value=3.3e-19  Score=137.85  Aligned_cols=124  Identities=27%  Similarity=0.351  Sum_probs=104.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++++.+..+ ..+..++|+.   .+......+++|+|+||+++.+.+.++...+++++++|+||||++.+++
T Consensus       114 L~~Q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l~~~~  192 (242)
T 3fe2_A          114 LAQQVQQVAAEYCRACR-LKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMG  192 (242)
T ss_dssp             HHHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEETTHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhhcC-ceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEEeCHHHHhhhC
Confidence            57899999999988887 4455555554   3334455679999999999999999888889999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK  127 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  127 (248)
                       |...+..+++. .+...|++++|||+++....+...++.++..+.++..
T Consensus       193 -~~~~~~~i~~~-~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          193 -FEPQIRKIVDQ-IRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             -CHHHHHHHHTT-SCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC-
T ss_pred             -cHHHHHHHHHh-CCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence             89999999888 4567899999999999999999999999988877654

>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=99.77  E-value=1.2e-18  Score=135.54  Aligned_cols=135  Identities=29%  Similarity=0.449  Sum_probs=101.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.+++++...++ .+..+.|+.   .+......+++|+|+||+++.+.+......+++++++|+||||++.+++
T Consensus       112 L~~q~~~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~  190 (253)
T 1wrb_A          112 LAIQILSESQKFSLNTPL-RSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMG  190 (253)
T ss_dssp             HHHHHHHHHHHHHTTSSC-CEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTT
T ss_pred             HHHHHHHHHHHHhccCCc-eEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEEeCHHHHHhCc
Confidence            678999999999988774 444444444   2333445689999999999999999888888999999999999999887


Q ss_pred             cccccchhHhhhCC-Cc--cceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeE
Q 042003           78 NLLKHIDPVVKACS-NP--SIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQK  137 (248)
Q Consensus        78 ~~~~~~~~~~~~~~-~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  137 (248)
                       |...+..++..+. +.  ..|++++|||+++...++...++.++..+.++.......++++.
T Consensus       191 -~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~q~  252 (253)
T 1wrb_A          191 -FEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQE  252 (253)
T ss_dssp             -CHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC------------
T ss_pred             -hHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCCCCcCCceec
Confidence             8888888887532 22  68999999999999999999999999888887766555555543

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.74  E-value=5.1e-18  Score=135.07  Aligned_cols=125  Identities=24%  Similarity=0.173  Sum_probs=102.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhc-CCcccCceeEEEEeccccccccCcc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEVGNL   79 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~-~~~~~~~~~~lIiDEah~~~~~~~~   79 (248)
                      ||.|+++.++++++..+...+....|+.........+++|+|+||+++.+++.+ +.+.+++++++|+||||++.+...+
T Consensus       174 La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~l~~~~~~  253 (300)
T 3fmo_B          174 LALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGH  253 (300)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHHHHHSTTH
T ss_pred             HHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhhcCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHHHhhccCc
Confidence            688999999999887543556666666544444467899999999999999976 5667899999999999999874338


Q ss_pred             cccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcc
Q 042003           80 LKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGR  126 (248)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  126 (248)
                      ...+..+.+. .+..+|++++|||+++....+...++.+|..+.+..
T Consensus       254 ~~~~~~i~~~-~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~  299 (300)
T 3fmo_B          254 QDQSIRIQRM-LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR  299 (300)
T ss_dssp             HHHHHHHHTT-SCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEECC
T ss_pred             HHHHHHHHHh-CCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEecC
Confidence            8888888877 456899999999999999999999999998876543

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.74  E-value=9.7e-18  Score=127.65  Aligned_cols=123  Identities=25%  Similarity=0.328  Sum_probs=100.1

Q ss_pred             CcchHHHHHHHhhcCC----CcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGN----KFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~----~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      |+.|+++.++++.+..    + ..+....|+.   ........+++|+|+||+++.+.+..+...+++++++|+||||++
T Consensus        84 L~~q~~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~  162 (219)
T 1q0u_A           84 LATQIYHETLKITKFCPKDRM-IVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLM  162 (219)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGC-CCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHH
T ss_pred             HHHHHHHHHHHHhhhcccccc-eEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHH
Confidence            5789999999998766    4 3444555554   223344568999999999999999888888899999999999999


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcc
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGR  126 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  126 (248)
                      .+++ +...+..+...+ +...|++++|||+++...++.+.++.+|..+....
T Consensus       163 ~~~~-~~~~l~~i~~~~-~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          163 LDMG-FITDVDQIAARM-PKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             HHTT-CHHHHHHHHHTS-CTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             hhhC-hHHHHHHHHHhC-CcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence            9887 888888888874 46789999999999999999999999998775443

>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=99.74  E-value=5.5e-18  Score=129.80  Aligned_cols=119  Identities=29%  Similarity=0.363  Sum_probs=96.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++++.. .+ ..+...+|+.   .......++++|+|+||+++.+.+..+...+++++++|+||||++.+++
T Consensus       106 L~~q~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~  183 (228)
T 3iuy_A          106 LALHVEAECSKYSY-KG-LKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDME  183 (228)
T ss_dssp             HHHHHHHHHHHHCC-TT-CCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCEEEECCHHHHHHTT
T ss_pred             HHHHHHHHHHHhcc-cC-ceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceEEEEECHHHHhccc
Confidence            57899999999863 34 3344445544   2233445679999999999999999888889999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEE
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVI  123 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  123 (248)
                       +...+..++.. .+.+.|++++|||+++...++...++.+|..+.
T Consensus       184 -~~~~~~~i~~~-~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~  227 (228)
T 3iuy_A          184 -FEPQIRKILLD-VRPDRQTVMTSATWPDTVRQLALSYLKDPMIVY  227 (228)
T ss_dssp             -CHHHHHHHHHH-SCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEE
T ss_pred             -hHHHHHHHHHh-CCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence             88889998888 456789999999999999999999999887664

>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=99.73  E-value=1.1e-17  Score=129.55  Aligned_cols=126  Identities=33%  Similarity=0.492  Sum_probs=101.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh----hcccccCCCcEEEeChHHHHHHHhcC--CcccCceeEEEEecccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR----STDLSKFSCDILISTPLRLRLAIRRK--KIDLSRVEYLVLDEADKLF   74 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~i~v~Tp~~l~~~~~~~--~~~~~~~~~lIiDEah~~~   74 (248)
                      ||.|+++.++++....+ ..+....|+..    .......+++|+|+||+++.+.+...  ...+++++++|+||||++.
T Consensus       110 L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~  188 (245)
T 3dkp_A          110 LASQIHRELIKISEGTG-FRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLF  188 (245)
T ss_dssp             HHHHHHHHHHHHTTTSC-CCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHH
T ss_pred             HHHHHHHHHHHHhcccC-ceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhc
Confidence            68899999999998888 44455554441    22334567899999999999999876  4678999999999999998


Q ss_pred             ccC--cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEccc
Q 042003           75 EVG--NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRK  127 (248)
Q Consensus        75 ~~~--~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  127 (248)
                      +++  .+...+..++..+.....|+++||||+++...++...++.++..+.++..
T Consensus       189 ~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          189 EDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             HHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             ccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            753  37777778877766778999999999999999999999999998877654

>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=99.73  E-value=1.3e-17  Score=125.75  Aligned_cols=120  Identities=22%  Similarity=0.271  Sum_probs=98.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      |+.|+++.++++.+..+...+....|+.   ........+++|+|+||+++.+.+.++...+++++++|+||||++.+.+
T Consensus        83 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~  162 (206)
T 1vec_A           83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD  162 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhC
Confidence            5789999999998876325555566655   2223345689999999999999999888888999999999999988876


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEE
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRV  122 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~  122 (248)
                       +...+..+...+ +...|++++|||+++...+....++.+|..+
T Consensus       163 -~~~~l~~i~~~~-~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          163 -FVQIMEDIILTL-PKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             -THHHHHHHHHHS-CTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             -cHHHHHHHHHhC-CccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence             888888888874 4578999999999999999999999888654

>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=99.72  E-value=1.2e-17  Score=128.65  Aligned_cols=122  Identities=25%  Similarity=0.283  Sum_probs=95.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh---hcccc-cCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR---STDLS-KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+++.++++++..+.. +....|+..   +.... .+.++|+|+||+++.+.+..+...+++++++|+||||++.++
T Consensus       110 L~~q~~~~~~~~~~~~~~~-~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~  188 (237)
T 3bor_A          110 LAQQIQKVILALGDYMGAT-CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR  188 (237)
T ss_dssp             HHHHHHHHHHHHTTTTTCC-EEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHT
T ss_pred             HHHHHHHHHHHHhhhcCce-EEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchHhhcc
Confidence            5789999999999887733 444444442   22222 334899999999999999888888899999999999999888


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEc
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVG  125 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  125 (248)
                      + +...+..+++. .+...|++++|||+++...++...++.+|..+.+.
T Consensus       189 ~-~~~~l~~i~~~-~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~  235 (237)
T 3bor_A          189 G-FKDQIYEIFQK-LNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVK  235 (237)
T ss_dssp             T-CHHHHHHHHHH-SCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC--
T ss_pred             C-cHHHHHHHHHh-CCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEec
Confidence            7 88888888887 45678999999999999999999999998876543

>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=99.72  E-value=8.5e-18  Score=130.41  Aligned_cols=121  Identities=26%  Similarity=0.333  Sum_probs=99.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhc-CCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRR-KKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~-~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+++.+++++...+ ..+..+.|+.   .+......+++|+|+||+++.+.+.+ ....+++++++|+||||++.++
T Consensus       123 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~~  201 (249)
T 3ber_A          123 LAFQISEQFEALGSSIG-VQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNM  201 (249)
T ss_dssp             HHHHHHHHHHHHHGGGT-CCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHHT
T ss_pred             HHHHHHHHHHHHhccCC-eeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhhcc
Confidence            57899999999988777 4445555554   23334456899999999999999886 4567899999999999999988


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEE
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIV  124 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  124 (248)
                      + +...+..+++. .+...|++++|||+++...++...++.+|..+.+
T Consensus       202 ~-~~~~l~~i~~~-~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v  247 (249)
T 3ber_A          202 D-FETEVDKILKV-IPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV  247 (249)
T ss_dssp             T-CHHHHHHHHHS-SCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             C-hHHHHHHHHHh-CCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEe
Confidence            7 88888888887 4567899999999999999999999999987754

>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=99.71  E-value=1.1e-17  Score=128.31  Aligned_cols=122  Identities=21%  Similarity=0.229  Sum_probs=97.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh--hcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR--STDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      |+.|+++.+++++.......+..+.|+..  .......+++|+|+||+++.+.+..+...+++++++|+||||++.+++.
T Consensus       104 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~  183 (230)
T 2oxc_A          104 IAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGS  183 (230)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTTSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHHSTTS
T ss_pred             HHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhccCCCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHhhcCcc
Confidence            67899999999987652255555666542  2222234799999999999999988888889999999999999988866


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEE
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVI  123 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  123 (248)
                      |...+..+++.+ +...|++++|||+++...+....++++|..+.
T Consensus       184 ~~~~~~~i~~~~-~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~  227 (230)
T 2oxc_A          184 FQEQINWIYSSL-PASKQMLAVSATYPEFLANALTKYMRDPTFVR  227 (230)
T ss_dssp             SHHHHHHHHHHS-CSSCEEEEEESCCCHHHHHHHTTTCSSCEEEC
T ss_pred             hHHHHHHHHHhC-CCCCeEEEEEeccCHHHHHHHHHHcCCCeEEE
Confidence            888888888874 55789999999999998899988988887664

>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=99.71  E-value=1.9e-17  Score=126.38  Aligned_cols=123  Identities=24%  Similarity=0.307  Sum_probs=95.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhc--ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRST--DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      |+.|+++.++++....+ ..+....|+....  .....+++|+|+||+++.+.+.++...+++++++|+||||++.+++ 
T Consensus        94 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~-  171 (224)
T 1qde_A           94 LALQIQKVVMALAFHMD-IKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG-  171 (224)
T ss_dssp             HHHHHHHHHHHHTTTSC-CCEEEECC----------CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhcccC-ceEEEEeCCcchHHHHhcCCCCCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhHHhhhh-
Confidence            57899999999988877 4445555554221  1122349999999999999999888888999999999999998887 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcc
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGR  126 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  126 (248)
                      +...+..+... .+...|++++|||+++...++...++.+|..+.+..
T Consensus       172 ~~~~l~~i~~~-~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~  218 (224)
T 1qde_A          172 FKEQIYQIFTL-LPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKK  218 (224)
T ss_dssp             CHHHHHHHHHH-SCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC---
T ss_pred             hHHHHHHHHHh-CCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecC
Confidence            88888888887 456789999999999999999999999998776544

>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=99.70  E-value=1.2e-17  Score=130.52  Aligned_cols=117  Identities=26%  Similarity=0.276  Sum_probs=95.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcC-CcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~-~~~~~~~~~lIiDEah~~~~~   76 (248)
                      ||.|+++.+++++...+ ..+....|+.   ........+++|+|+||+++.+.+... ...+++++++|+||||++.++
T Consensus       138 La~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah~l~~~  216 (262)
T 3ly5_A          138 LAMQTFGVLKELMTHHV-HTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDV  216 (262)
T ss_dssp             HHHHHHHHHHHHTTTCC-SCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHHHHHHT
T ss_pred             HHHHHHHHHHHHHhhcC-ceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChHHHhhh
Confidence            68899999999998887 4455555554   223334457999999999999988775 467899999999999999998


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcE
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV  120 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~  120 (248)
                      + |...+..+++. .+..+|++++|||+++..+.+.+.+++++.
T Consensus       217 ~-~~~~l~~i~~~-~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          217 G-FEEELKQIIKL-LPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             T-CHHHHHHHHHH-SCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             h-HHHHHHHHHHh-CCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            8 89999999888 456789999999999999999988876554

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.69  E-value=3.5e-17  Score=125.93  Aligned_cols=122  Identities=26%  Similarity=0.290  Sum_probs=97.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh--hcccccCCCcEEEeChHHHHHHHhcC-CcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR--STDLSKFSCDILISTPLRLRLAIRRK-KIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~i~v~Tp~~l~~~~~~~-~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      |+.|+++.++++++..+ ..+..+.|+..  .......+++|+|+||+++.+.+... ...+.+++++|+||||++.+++
T Consensus       109 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~~~~~~  187 (236)
T 2pl3_A          109 LAYQTFEVLRKVGKNHD-FSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMG  187 (236)
T ss_dssp             HHHHHHHHHHHHTTTSS-CCEEEECCC--CHHHHHHHTTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCC-eeEEEEECCCCHHHHHHhCCCCCEEEECHHHHHHHHHhcCCcccccccEEEEeChHHHhcCC
Confidence            57899999999998877 44555555542  11122257999999999999988765 4667899999999999999887


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVG  125 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  125 (248)
                       +...+..++.. .+...|++++|||+++...++.+.++.+|..+.+.
T Consensus       188 -~~~~~~~i~~~-~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~  233 (236)
T 2pl3_A          188 -FADTMNAVIEN-LPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVH  233 (236)
T ss_dssp             -THHHHHHHHHT-SCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECC
T ss_pred             -cHHHHHHHHHh-CCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeC
Confidence             88888888887 45678999999999999999999999999877543

>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=99.69  E-value=3.2e-17  Score=124.81  Aligned_cols=122  Identities=23%  Similarity=0.319  Sum_probs=96.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh---hc-ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR---ST-DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      |+.|+++.++++.+..+...+..+.|+..   .. ......++|+|+||+++.+.+......+++++++|+||||++.++
T Consensus        94 L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~  173 (220)
T 1t6n_A           94 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  173 (220)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSS
T ss_pred             HHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcc
Confidence            57899999999987762255555666542   11 222346799999999999999988888899999999999999875


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEE
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVI  123 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  123 (248)
                      ..+...+..+++. .+...|++++|||+++...++...++.+|..+.
T Consensus       174 ~~~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  219 (220)
T 1t6n_A          174 LDMRRDVQEIFRM-TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  219 (220)
T ss_dssp             HHHHHHHHHHHHT-SCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             cCcHHHHHHHHHh-CCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEe
Confidence            3377778888776 456789999999999999999999999987653

>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=99.69  E-value=4.7e-17  Score=122.65  Aligned_cols=119  Identities=33%  Similarity=0.418  Sum_probs=96.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      |+.|+++.++++.....   +....|+.   ........+++|+|+||+++.+.+..+...+++++++|+||||++.+++
T Consensus        84 L~~q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~  160 (207)
T 2gxq_A           84 LALQVASELTAVAPHLK---VVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG  160 (207)
T ss_dssp             HHHHHHHHHHHHCTTSC---EEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHTT
T ss_pred             HHHHHHHHHHHHhhcce---EEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhccc
Confidence            57899999999887643   33444443   2333344679999999999999999888888999999999999998877


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEE
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIV  124 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  124 (248)
                       +...+..++.. .+...|++++|||+++...++...++++|..+.+
T Consensus       161 -~~~~~~~i~~~-~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~  205 (207)
T 2gxq_A          161 -FEEEVEALLSA-TPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV  205 (207)
T ss_dssp             -CHHHHHHHHHT-SCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             -hHHHHHHHHHh-CCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEc
Confidence             88888888877 4567899999999999999999999999877643

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.56  E-value=9.2e-14  Score=121.71  Aligned_cols=73  Identities=16%  Similarity=0.191  Sum_probs=58.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHH-HHHHhcC------CcccC---ceeEEEEec
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRL-RLAIRRK------KIDLS---RVEYLVLDE   69 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l-~~~~~~~------~~~~~---~~~~lIiDE   69 (248)
                      ||.|.++++..+.+.++ .++.+++|+. .+......+++|+|+||+.+ .+++..+      ...++   ++.++|+||
T Consensus       132 LA~Qdae~m~~l~~~lG-Lsv~~i~Gg~~~~~r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDE  210 (997)
T 2ipc_A          132 LARRDAEWMGPVYRGLG-LSVGVIQHASTPAERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDE  210 (997)
T ss_dssp             HHHHHHHHHHHHHHTTT-CCEEECCTTCCHHHHHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETT
T ss_pred             HHHHHHHHHHHHHHhcC-CeEEEEeCCCCHHHHHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEec
Confidence            78999999999999999 5555555554 44444556799999999999 6777665      24577   899999999


Q ss_pred             ccccc
Q 042003           70 ADKLF   74 (248)
Q Consensus        70 ah~~~   74 (248)
                      +|.++
T Consensus       211 aDsmL  215 (997)
T 2ipc_A          211 VDSIL  215 (997)
T ss_dssp             HHHHT
T ss_pred             hHHHH
Confidence            99876

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.24  E-value=8e-12  Score=107.10  Aligned_cols=84  Identities=18%  Similarity=0.328  Sum_probs=54.4

Q ss_pred             HHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEE--EecccccCCCC
Q 042003          149 LALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLI--ATDVIARGMDF  226 (248)
Q Consensus       149 ~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv--~T~~~~~Gidi  226 (248)
                      ..+.+++... +++++||++|....+.+++.|...  . ...+|..  .++.++++.|+++. .|++  +|..+++|||+
T Consensus       374 ~~l~~~~~~~-~g~~lvff~S~~~~~~v~~~l~~~--~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~  446 (540)
T 2vl7_A          374 ILLKRIYENS-SKSVLVFFPSYEMLESVRIHLSGI--P-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEF  446 (540)
T ss_dssp             HHHHHHHHTC-SSEEEEEESCHHHHHHHHTTCTTS--C-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC----------
T ss_pred             HHHHHHHHhC-CCCEEEEeCCHHHHHHHHHHhccC--c-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceec
Confidence            3444555543 679999999999999999999752  3 3445543  46888999998865 5666  88999999999


Q ss_pred             CC----CcEEEeccCCC
Q 042003          227 KG----VNCVINYDFPD  239 (248)
Q Consensus       227 p~----~~~Vi~~~~p~  239 (248)
                      |+    +++||+++.|.
T Consensus       447 ~~~~~~~~~Vii~~lPf  463 (540)
T 2vl7_A          447 REKENLFESLVLAGLPY  463 (540)
T ss_dssp             -----CEEEEEEESCCC
T ss_pred             CCCcccccEEEEECCCC
Confidence            97    89999999994

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.18  E-value=4.4e-12  Score=95.80  Aligned_cols=101  Identities=18%  Similarity=0.103  Sum_probs=60.2

Q ss_pred             Ccch-HHHHHHHhhcCCCcEEEEcccchhhhc---ccccCCCcEEEeChHHHHHHHhcCC------cccCceeEEEEecc
Q 042003            1 LATQ-TTRECKKLAKGNKFQIKLMKKELVRST---DLSKFSCDILISTPLRLRLAIRRKK------IDLSRVEYLVLDEA   70 (248)
Q Consensus         1 L~~Q-~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~i~v~Tp~~l~~~~~~~~------~~~~~~~~lIiDEa   70 (248)
                      |+.| +.+.++++... + ..+....|+....   .....+++|+|+||+.+.+.+....      ..+.+++++|+|||
T Consensus        94 L~~q~~~~~~~~~~~~-~-~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEa  171 (216)
T 3b6e_A           94 LVEQLFRKEFQPFLKK-W-YRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDEC  171 (216)
T ss_dssp             HHHHHHHHTHHHHHTT-T-SCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC
T ss_pred             HHHHHHHHHHHHHhcc-C-ceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECc
Confidence            4567 77788887765 3 3344455544221   1223469999999999999888743      56789999999999


Q ss_pred             ccccccCcccccchhHhhhC------------CCccceeEEEEee
Q 042003           71 DKLFEVGNLLKHIDPVVKAC------------SNPSIVRSLFSAT  103 (248)
Q Consensus        71 h~~~~~~~~~~~~~~~~~~~------------~~~~~~~i~~SAT  103 (248)
                      |++.+.+.+...+..+....            ..+..+++++|||
T Consensus       172 h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          172 HHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             hhhccCCcHHHHHHHHHHHhcccccccccccCCCCcceEEEeecC
Confidence            99976653343333333221            1256889999998

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=99.18  E-value=1.2e-11  Score=94.88  Aligned_cols=76  Identities=18%  Similarity=0.242  Sum_probs=57.2

Q ss_pred             CCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc-cccCccc-ccchhHhhhCCCccceeEEEEeecCchHHHHHH
Q 042003           36 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL-FEVGNLL-KHIDPVVKACSNPSIVRSLFSATLPDFVEELAR  113 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~-~~~~~~~-~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~  113 (248)
                      .+++|+|+||+++.+.+..   .+++++++|+||||.. .+.+ +. ..+..+....  ++.|++++|||++...  +.+
T Consensus       154 ~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~-~~~~~l~~i~~~~--~~~~~il~SAT~~~~~--~~~  225 (235)
T 3llm_A          154 PHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTD-FLLVVLRDVVQAY--PEVRIVLMSATIDTSM--FCE  225 (235)
T ss_dssp             SSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHH-HHHHHHHHHHHHC--TTSEEEEEECSSCCHH--HHH
T ss_pred             CCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchH-HHHHHHHHHHhhC--CCCeEEEEecCCCHHH--HHH
Confidence            5689999999999999876   3789999999999985 4444 44 4556666653  4689999999999755  555


Q ss_pred             HhcCCc
Q 042003          114 SIMHDA  119 (248)
Q Consensus       114 ~~~~~~  119 (248)
                      ++.+.+
T Consensus       226 ~~~~~p  231 (235)
T 3llm_A          226 YFFNCP  231 (235)
T ss_dssp             HTTSCC
T ss_pred             HcCCCC
Confidence            554443

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=99.14  E-value=3.5e-11  Score=94.80  Aligned_cols=99  Identities=15%  Similarity=0.053  Sum_probs=68.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+.+.+++++...+ ..+..++++.........+++|+|+||+.+.+.   ....+.+++++|+||||++.+.    
T Consensus       169 L~~q~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~---~~~~~~~~~~vIiDEaH~~~~~----  240 (282)
T 1rif_A          169 LTTQMADDFVDYRLFSH-AMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATGK----  240 (282)
T ss_dssp             HHHHHHHHHHHHTSCCG-GGEEECSTTCSSTTCCCTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCCHH----
T ss_pred             HHHHHHHHHHHhccccc-ceEEEEeCCCcchhhhccCCcEEEEchHHHHhh---HHHHHhhCCEEEEECCccCCcc----
Confidence            57899999999877655 334444444433334446789999999876433   2345788999999999998753    


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCchHH
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  109 (248)
                       .+..+++.+ ....+++++|||++....
T Consensus       241 -~~~~il~~~-~~~~~~l~lSATp~~~~~  267 (282)
T 1rif_A          241 -SISSIISGL-NNCMFKFGLSGSLRDGKA  267 (282)
T ss_dssp             -HHHHHTTTC-TTCCEEEEECSSCCTTST
T ss_pred             -cHHHHHHHh-hcCCeEEEEeCCCCCcch
Confidence             344455542 346889999999976543

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.13  E-value=2.9e-09  Score=91.52  Aligned_cols=136  Identities=15%  Similarity=0.150  Sum_probs=81.6

Q ss_pred             ceeEEEEeecCchHHHHHHHhcCC-cEEEE--EcccccccccceeEEEEcCC------c---h----hHHHHHHHHHhcc
Q 042003           95 IVRSLFSATLPDFVEELARSIMHD-AVRVI--VGRKNTASESIKQKLVFAGS------E---E----GKLLALRQSFAES  158 (248)
Q Consensus        95 ~~~i~~SAT~~~~~~~~~~~~~~~-~~~~~--~~~~~~~~~~~~~~~~~~~~------~---~----~~~~~l~~~~~~~  158 (248)
                      ..+|++|||+++ .......+..+ +....  ......+.  -.+..+++..      .   +    .-.+.+.+++...
T Consensus       316 ~svIltSaTL~~-~~~~~~~lGl~~~~~~~~~~~~~~spf--~~~~~l~v~~~~~~~~~~r~~~~~~~l~~~i~~l~~~~  392 (551)
T 3crv_A          316 LSIILMSGTLPP-REYMEKVWGIKRNMLYLDVEREIQKRV--SGSYECYIGVDVTSKYDMRSDNMWKRYADYLLKIYFQA  392 (551)
T ss_dssp             CEEEEEESSCCC-HHHHHHTSCCCSCEEEEEHHHHTTSCC--SCEEEEEEECSCCCCTTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEeeCCCc-HHHHHHHhCCCCccccccceeecCCcC--CCceEEEEeCCCCCccccCCHHHHHHHHHHHHHHHHhC
Confidence            578999999998 55555555443 22210  00111111  1122222111      0   1    1223344444443


Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEe--cccccCCCCC-----CCcE
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIAT--DVIARGMDFK-----GVNC  231 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T--~~~~~Gidip-----~~~~  231 (248)
                       ++.++||++|....+.+++.   .+..+..=..+++   +.+.++.|+.+...||+||  ..+++|||+|     .++.
T Consensus       393 -~g~~lvlF~Sy~~l~~v~~~---~~~~v~~q~~~~~---~~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~  465 (551)
T 3crv_A          393 -KANVLVVFPSYEIMDRVMSR---ISLPKYVESEDSS---VEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISD  465 (551)
T ss_dssp             -SSEEEEEESCHHHHHHHHTT---CCSSEEECCSSCC---HHHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEE
T ss_pred             -CCCEEEEecCHHHHHHHHHh---cCCcEEEcCCCCC---HHHHHHHHHhcCCeEEEEEecceecccccccccCCcceeE
Confidence             67999999999999999973   3334443333445   3557777754444799998  6999999999     4789


Q ss_pred             EEeccCCCC
Q 042003          232 VINYDFPDS  240 (248)
Q Consensus       232 Vi~~~~p~~  240 (248)
                      ||+.+.|..
T Consensus       466 viI~~lPfp  474 (551)
T 3crv_A          466 VVIVGIPYP  474 (551)
T ss_dssp             EEEESCCCC
T ss_pred             EEEEcCCCC
Confidence            999999853

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.62  E-value=3.1e-07  Score=79.83  Aligned_cols=137  Identities=12%  Similarity=0.207  Sum_probs=81.8

Q ss_pred             ceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCC--------chh----HHHHHHHHHhccCCCC
Q 042003           95 IVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGS--------EEG----KLLALRQSFAESLNPP  162 (248)
Q Consensus        95 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~----~~~~l~~~~~~~~~~~  162 (248)
                      ..+|++|||+.+ .......+..+......+.. -+..+  ...+....        .+.    ..+.+.++++.. ++.
T Consensus       376 ~~~il~SaTL~p-~~~~~~~lGl~~~~~~~~sp-f~~~~--~~~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~~-~g~  450 (620)
T 4a15_A          376 SKTIHMSGTLDP-FDFYSDITGFEIPFKKIGEI-FPPEN--RYIAYYDGVSSKYDTLDEKELDRMATVIEDIILKV-KKN  450 (620)
T ss_dssp             SEEEEEESSCCS-HHHHHHHHCCCCCEEECCCC-SCGGG--EEEEEECCC-------CHHHHHHHHHHHHHHHHHH-CSC
T ss_pred             CeEEEEccCCCc-HHHHHHHhCCCceeeecCCC-CCHHH--eEEEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHhC-CCC
Confidence            356899999998 55555555433222222211 11111  11111111        111    123344455544 678


Q ss_pred             EEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec--ccccCCCCCC--CcEEEeccCC
Q 042003          163 VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD--VIARGMDFKG--VNCVINYDFP  238 (248)
Q Consensus       163 ~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~--~~~~Gidip~--~~~Vi~~~~p  238 (248)
                      ++||++|....+.+++.|+..+.+   ...+++..++.++++.|+ ++..||+++.  .+++|||+|+  .+.||+.+.|
T Consensus       451 ~lvlF~Sy~~l~~v~~~l~~~~~~---~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~lP  526 (620)
T 4a15_A          451 TIVYFPSYSLMDRVENRVSFEHMK---EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAGLP  526 (620)
T ss_dssp             EEEEESCHHHHHHHTSSCCSCCEE---CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESSCC
T ss_pred             EEEEeCCHHHHHHHHHHHHhcchh---ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEcCC
Confidence            999999999999999999732222   455566678999999999 8888999985  8999999996  7799999999


Q ss_pred             CC
Q 042003          239 DS  240 (248)
Q Consensus       239 ~~  240 (248)
                      ..
T Consensus       527 fp  528 (620)
T 4a15_A          527 FP  528 (620)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=98.60  E-value=4.6e-08  Score=74.87  Aligned_cols=86  Identities=15%  Similarity=0.009  Sum_probs=55.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+++.++++    +...+..+.|+..      ...+|+|+||+.+......   ...+++++|+||||++.+.. + 
T Consensus       145 L~~q~~~~~~~~----~~~~v~~~~g~~~------~~~~i~v~T~~~l~~~~~~---~~~~~~llIiDEaH~l~~~~-~-  209 (237)
T 2fz4_A          145 LAEQWKERLGIF----GEEYVGEFSGRIK------ELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAES-Y-  209 (237)
T ss_dssp             HHHHHHHHHGGG----CGGGEEEESSSCB------CCCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTTT-H-
T ss_pred             HHHHHHHHHHhC----CCCeEEEEeCCCC------CcCCEEEEeHHHHHhhHHH---hcccCCEEEEECCccCCChH-H-
Confidence            456777776663    3221444444332      3578999999998766542   12468899999999987654 3 


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCc
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                         ..+...+  ...+++++|||++.
T Consensus       210 ---~~i~~~~--~~~~~l~LSATp~r  230 (237)
T 2fz4_A          210 ---VQIAQMS--IAPFRLGLTATFER  230 (237)
T ss_dssp             ---HHHHHTC--CCSEEEEEEESCC-
T ss_pred             ---HHHHHhc--cCCEEEEEecCCCC
Confidence               2344442  25678999999875

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=97.64  E-value=0.00036  Score=55.13  Aligned_cols=95  Identities=12%  Similarity=-0.002  Sum_probs=70.2

Q ss_pred             chhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccc
Q 042003          144 EEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIA  221 (248)
Q Consensus       144 ~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~  221 (248)
                      ...|+..|..++...  .+.+++||+...+...-+.+.+...+++...+.|.....+++ .    .++...+.+.|...+
T Consensus       107 ~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~~k-~----~~~~~~i~Lltsag~  181 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAAA-A----NDFSCTVHLFSSEGI  181 (328)
T ss_dssp             TCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCC
T ss_pred             cCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhhhh-c----ccCCceEEEEECCCC
Confidence            346776666666543  267999999999999999999999999999999985543221 1    244555555577777


Q ss_pred             cCCC-----CCCCcEEEeccCCCCccc
Q 042003          222 RGMD-----FKGVNCVINYDFPDSGAA  243 (248)
Q Consensus       222 ~Gid-----ip~~~~Vi~~~~p~~~~~  243 (248)
                      -|+|     +..++.||.||.-||+..
T Consensus       182 ~gin~~~~nl~~aD~VI~~DsdwNp~~  208 (328)
T 3hgt_A          182 NFTKYPIKSKARFDMLICLDTTVDTSQ  208 (328)
T ss_dssp             CTTTSCCCCCSCCSEEEECSTTCCTTS
T ss_pred             CCcCcccccCCCCCEEEEECCCCCCCC
Confidence            7786     678999999999999876

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=96.92  E-value=0.0026  Score=56.65  Aligned_cols=75  Identities=20%  Similarity=0.248  Sum_probs=64.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-cccCCCCCCCcEEEe
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-IARGMDFKGVNCVIN  234 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~~~Gidip~~~~Vi~  234 (248)
                      +.++++.++++.-+.+.++.+++    .+.++..+||+++..++...++.+.+|+.+|+|+|.. +...+++.++.+||.
T Consensus       417 g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVVI  496 (780)
T 1gm5_A          417 GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVII  496 (780)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEE
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEEe
Confidence            57899999999999888877754    3789999999999999999999999999999999965 455678888888873

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

Probab=96.38  E-value=0.009  Score=49.11  Aligned_cols=75  Identities=11%  Similarity=0.139  Sum_probs=62.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhc---CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccc----cCCCCCCCcE
Q 042003          159 LNPPVLIFVQSKERAKELYGELAF---DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIA----RGMDFKGVNC  231 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~---~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~----~Gidip~~~~  231 (248)
                      .+.+++|.+|++.-+.++++.+++   .+.++..++|+.+..++....+.+.+|..+|+|+|.-.-    .-++...+++
T Consensus        63 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~  142 (414)
T 3oiy_A           63 KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDF  142 (414)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSE
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccE
Confidence            367999999999999999999988   578999999999999999999999999899999996421    1244556777


Q ss_pred             EE
Q 042003          232 VI  233 (248)
Q Consensus       232 Vi  233 (248)
                      ||
T Consensus       143 iV  144 (414)
T 3oiy_A          143 VF  144 (414)
T ss_dssp             EE
T ss_pred             EE
Confidence            66

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

Probab=95.50  E-value=0.032  Score=51.85  Aligned_cols=75  Identities=11%  Similarity=0.139  Sum_probs=62.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc---CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccc----cCCCCCCCcEE
Q 042003          160 NPPVLIFVQSKERAKELYGELAF---DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIA----RGMDFKGVNCV  232 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~---~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~----~Gidip~~~~V  232 (248)
                      +.+++|.++++.-+.++++.+++   .+.++..+||+++..++....+.+.+|..+|+|+|.-.-    .-++..++++|
T Consensus       121 ~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~~l  200 (1104)
T 4ddu_A          121 GKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFV  200 (1104)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCSEE
T ss_pred             CCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcCEE
Confidence            67999999999999999999988   467999999999998999999999999999999996321    11455677777


Q ss_pred             Ee
Q 042003          233 IN  234 (248)
Q Consensus       233 i~  234 (248)
                      |.
T Consensus       201 Vi  202 (1104)
T 4ddu_A          201 FV  202 (1104)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

>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=95.47  E-value=0.032  Score=52.10  Aligned_cols=74  Identities=20%  Similarity=0.296  Sum_probs=63.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-ccccCCCCCCCcEEE
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-VIARGMDFKGVNCVI  233 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-~~~~Gidip~~~~Vi  233 (248)
                      +.+++|.+++..-+++.++.+++    .+.++..+++..+..++...++.+.+|..+|+|+|. .+...+++.++.+||
T Consensus       652 g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lvI  730 (1151)
T 2eyq_A          652 HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLI  730 (1151)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEE
T ss_pred             CCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceEE
Confidence            56899999999999988888764    367899999999999999999999999999999995 455667777887776

>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=95.11  E-value=0.21  Score=37.93  Aligned_cols=71  Identities=18%  Similarity=0.344  Sum_probs=52.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----c--ccCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----I--ARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~--~~Gidip~  228 (248)
                      +.+++|.++++.-+.++++.+++.    +..+..++|+.+...+...+    .+..+|+|+|..     +  ..++++..
T Consensus       111 ~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~I~v~Tp~~l~~~l~~~~~~~l~~  186 (249)
T 3ber_A          111 RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL----AKKPHIIIATPGRLIDHLENTKGFNLRA  186 (249)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH----HTCCSEEEECHHHHHHHHHHSTTCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh----cCCCCEEEECHHHHHHHHHcCCCcCccc
Confidence            467999999999999888877654    78899999998866544333    245789999953     1  24567788


Q ss_pred             CcEEEe
Q 042003          229 VNCVIN  234 (248)
Q Consensus       229 ~~~Vi~  234 (248)
                      ++++|.
T Consensus       187 ~~~lVi  192 (249)
T 3ber_A          187 LKYLVM  192 (249)
T ss_dssp             CCEEEE
T ss_pred             cCEEEE
Confidence            887763

>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=95.00  E-value=0.16  Score=37.50  Aligned_cols=72  Identities=18%  Similarity=0.284  Sum_probs=53.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-c-----ccCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-I-----ARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~-----~~Gidip~  228 (248)
                      ..+++|.++++.-+.++++.+++.     +..+..++|+.+...+.+   .+.++..+|+|+|.- +     ...+++++
T Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~---~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~  158 (220)
T 1t6n_A           82 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE---VLKKNCPHIVVGTPGRILALARNKSLNLKH  158 (220)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHH---HHHHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHH---HHhcCCCCEEEeCHHHHHHHHHhCCCCccc
Confidence            348999999999999988887654     678999999988765543   344566789999953 1     23466777


Q ss_pred             CcEEEe
Q 042003          229 VNCVIN  234 (248)
Q Consensus       229 ~~~Vi~  234 (248)
                      ++++|.
T Consensus       159 ~~~lVi  164 (220)
T 1t6n_A          159 IKHFIL  164 (220)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            887763

>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=94.55  E-value=0.13  Score=38.51  Aligned_cols=69  Identities=13%  Similarity=0.177  Sum_probs=51.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip~  228 (248)
                      +.+++|.+++++-+.++++.+++.     +.++..++|+.+..++...+     ...+|+|+|.-.      ...+++.+
T Consensus        92 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~~l~~~~~~~~~~~~~  166 (230)
T 2oxc_A           92 STQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPGRIKQLIELDYLNPGS  166 (230)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHHHHHHHHHTTSSCGGG
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHHHHHHHHhcCCccccc
Confidence            569999999999999998888753     67889999998876654433     246899999632      23456667


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      ++++|
T Consensus       167 ~~~lV  171 (230)
T 2oxc_A          167 IRLFI  171 (230)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            77766

>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=94.49  E-value=0.083  Score=44.93  Aligned_cols=59  Identities=17%  Similarity=0.249  Sum_probs=55.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD  218 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~  218 (248)
                      .++++|.++++.-+++..+.|+..+..+..++|+.+..++..+...+..|..+++++|.
T Consensus        65 ~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tp  123 (523)
T 1oyw_A           65 NGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAP  123 (523)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECH
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            46899999999999999999999999999999999999999999999999999999995

>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=94.21  E-value=0.085  Score=45.62  Aligned_cols=59  Identities=12%  Similarity=0.093  Sum_probs=54.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHh--hcCCceEEEEec
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDF--RAGKTWVLIATD  218 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f--~~g~~~ilv~T~  218 (248)
                      .+.+||.++++.-+++.++.|++.++.+..++|+++..++..+...+  ..+..+|+++|.
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            56899999999999999999999999999999999999998888888  568889999997

>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=93.98  E-value=0.28  Score=36.86  Aligned_cols=70  Identities=13%  Similarity=0.183  Sum_probs=52.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----cc-cCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----IA-RGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~~-~Gidip~~  229 (248)
                      +.+++|.++++.-+.++++.+++    .+..+..++|+.+.......+..    ..+|+|+|.-     +. ..+++.++
T Consensus       102 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~~~~  177 (242)
T 3fe2_A          102 GPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLECGKTNLRRT  177 (242)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHTSCCCTTC
T ss_pred             CCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCCcccc
Confidence            56799999999999988877765    37889999999987766554432    4689999952     22 34577788


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      +++|
T Consensus       178 ~~lV  181 (242)
T 3fe2_A          178 TYLV  181 (242)
T ss_dssp             CEEE
T ss_pred             cEEE
Confidence            8776

>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=93.73  E-value=0.37  Score=35.01  Aligned_cols=70  Identities=16%  Similarity=0.116  Sum_probs=49.9

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----cc-cCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----IA-RGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~~-~Gidip~  228 (248)
                      +.+++|.++++.-+.++++.+++.     +..+..++|+.+..+....   + .+..+|+|+|.-     +. ...++.+
T Consensus        71 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~i~v~T~~~l~~~~~~~~~~~~~  146 (206)
T 1vec_A           71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR---L-DDTVHVVIATPGRILDLIKKGVAKVDH  146 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH---T-TSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHh---c-CCCCCEEEeCHHHHHHHHHcCCcCccc
Confidence            458999999999999888887643     5788899999886544322   2 345689999962     22 2346667


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      ++++|
T Consensus       147 ~~~lV  151 (206)
T 1vec_A          147 VQMIV  151 (206)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            77776

>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=93.41  E-value=0.24  Score=37.18  Aligned_cols=71  Identities=11%  Similarity=0.200  Sum_probs=44.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-----ccc-cCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-----VIA-RGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-----~~~-~Gidip~~  229 (248)
                      +.+++|.++++.-+.++++.+++.    +..+..++|+.+...   ..+.+..+..+|+|+|.     .+. ..+++..+
T Consensus        98 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~---~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~  174 (237)
T 3bor_A           98 ETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRN---EMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWI  174 (237)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSCSTTC
T ss_pred             CceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHH---HHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccC
Confidence            569999999999999998888654    567778888765433   33445567789999994     222 33566777


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      ++||
T Consensus       175 ~~lV  178 (237)
T 3bor_A          175 KMFV  178 (237)
T ss_dssp             CEEE
T ss_pred             cEEE
Confidence            7776

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=93.03  E-value=0.28  Score=36.66  Aligned_cols=69  Identities=16%  Similarity=0.221  Sum_probs=48.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-c----cc--CCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-I----AR--GMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~----~~--Gidip~  228 (248)
                      +.+++|.++++.-+.++++.+++.    +..+..++|+.+.......+     +..+|+|+|.- +    ..  .++..+
T Consensus        97 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~~~~  171 (236)
T 2pl3_A           97 GLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFHATD  171 (236)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCccccc
Confidence            568999999999999998888754    47888999987755443332     35689999952 1    12  366677


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      ++++|
T Consensus       172 ~~~lV  176 (236)
T 2pl3_A          172 LQMLV  176 (236)
T ss_dssp             CCEEE
T ss_pred             ccEEE
Confidence            77776

>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=92.95  E-value=0.44  Score=34.62  Aligned_cols=71  Identities=15%  Similarity=0.198  Sum_probs=51.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----c-ccCCCCCCCcE
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----I-ARGMDFKGVNC  231 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~-~~Gidip~~~~  231 (248)
                      +.+++|.++++.-+.++++.+++.  +.++..++|+.+.......+.    +..+|+|+|..     + ...+++.++++
T Consensus        72 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~~~  147 (207)
T 2gxq_A           72 KPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL----RGADAVVATPGRALDYLRQGVLDLSRVEV  147 (207)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH----HCCSEEEECHHHHHHHHHHTSSCCTTCSE
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh----CCCCEEEECHHHHHHHHHcCCcchhhceE
Confidence            568999999999999999998765  467888999887654443332    24679999952     1 23456777777


Q ss_pred             EEe
Q 042003          232 VIN  234 (248)
Q Consensus       232 Vi~  234 (248)
                      ||.
T Consensus       148 iVi  150 (207)
T 2gxq_A          148 AVL  150 (207)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            763

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=92.85  E-value=0.34  Score=35.95  Aligned_cols=71  Identities=14%  Similarity=0.255  Sum_probs=47.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC---CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc------cccCCCCCCCc
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD---GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV------IARGMDFKGVN  230 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~---~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~------~~~Gidip~~~  230 (248)
                      +.+++|.++++.-+.++++.+++.   +..+..++|+.+...+...+   .+ ..+|+|+|.-      ....+++.+++
T Consensus        94 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~iiv~Tp~~l~~~~~~~~~~~~~~~  169 (228)
T 3iuy_A           94 GPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDI---SK-GVDIIIATPGRLNDLQMNNSVNLRSIT  169 (228)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHH---HS-CCSEEEECHHHHHHHHHTTCCCCTTCC
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHh---cC-CCCEEEECHHHHHHHHHcCCcCcccce
Confidence            568999999999999999888763   67888889887655443322   23 4689999952      12356777888


Q ss_pred             EEEe
Q 042003          231 CVIN  234 (248)
Q Consensus       231 ~Vi~  234 (248)
                      +||.
T Consensus       170 ~lVi  173 (228)
T 3iuy_A          170 YLVI  173 (228)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7763

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=92.76  E-value=0.22  Score=36.85  Aligned_cols=69  Identities=14%  Similarity=0.192  Sum_probs=44.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip~~  229 (248)
                      +.+++|.++++.-+.++++.+++    .+..+..++|+.+..+....   +.  ..+|+|+|...      ....++..+
T Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~--~~~iiv~Tp~~l~~~~~~~~~~~~~~  156 (224)
T 1qde_A           82 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG---LR--DAQIVVGTPGRVFDNIQRRRFRTDKI  156 (224)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-------------CT--TCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhc---CC--CCCEEEECHHHHHHHHHhCCcchhhC
Confidence            56899999999999988887765    36788899998765544332   22  26899999632      345566777


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      ++||
T Consensus       157 ~~iV  160 (224)
T 1qde_A          157 KMFI  160 (224)
T ss_dssp             CEEE
T ss_pred             cEEE
Confidence            7776

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=92.63  E-value=0.63  Score=35.50  Aligned_cols=71  Identities=21%  Similarity=0.375  Sum_probs=51.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec------cc-ccCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD------VI-ARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~------~~-~~Gidip~  228 (248)
                      +.+++|.++++.-++++++.+++    .+..+..+.|+.+.......+   ..+ .+|+|+|.      .. ..++++..
T Consensus       126 ~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~~~-~~Iiv~Tp~~l~~~~~~~~~~~~~~  201 (262)
T 3ly5_A          126 GTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKL---GNG-INIIVATPGRLLDHMQNTPGFMYKN  201 (262)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHH---HHC-CSEEEECHHHHHHHHHHCTTCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHh---cCC-CCEEEEcHHHHHHHHHccCCccccc
Confidence            57899999999999998888865    356788899988766544333   333 78999994      21 23467788


Q ss_pred             CcEEEe
Q 042003          229 VNCVIN  234 (248)
Q Consensus       229 ~~~Vi~  234 (248)
                      +++||.
T Consensus       202 l~~lVi  207 (262)
T 3ly5_A          202 LQCLVI  207 (262)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            887763

>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=92.48  E-value=0.66  Score=37.29  Aligned_cols=71  Identities=18%  Similarity=0.316  Sum_probs=53.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-c-----ccCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-I-----ARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~-----~~Gidip~  228 (248)
                      +.+++|.++++.-++++++.+++.     +.++..++|+.+.......   +.++..+|+|+|.- +     ...+++..
T Consensus        76 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~iiv~T~~~l~~~~~~~~~~~~~  152 (391)
T 1xti_A           76 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLKH  152 (391)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHH---HhcCCCCEEEECHHHHHHHHHcCCccccc
Confidence            458999999999999988877653     6889999999887665443   44566789999953 2     23456777


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      +++||
T Consensus       153 ~~~vV  157 (391)
T 1xti_A          153 IKHFI  157 (391)
T ss_dssp             CSEEE
T ss_pred             cCEEE
Confidence            77776

>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=91.52  E-value=0.74  Score=34.72  Aligned_cols=70  Identities=17%  Similarity=0.212  Sum_probs=49.8

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-c-----ccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-I-----ARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~-----~~Gidip~~  229 (248)
                      +.+++|.+++++-+.++++.+++.    +..+..++|+.+.......+    .+..+|+|+|.. +     ...+++..+
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~  175 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV----QMGCHLLVATPGRLVDFIEKNKISLEFC  175 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHH----SSCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh----CCCCCEEEECHHHHHHHHHcCCCChhhC
Confidence            358999999999999988887653    56788889988765443322    245689999963 2     223567777


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      +++|
T Consensus       176 ~~lV  179 (253)
T 1wrb_A          176 KYIV  179 (253)
T ss_dssp             CEEE
T ss_pred             CEEE
Confidence            7776

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=89.35  E-value=2.6  Score=27.03  Aligned_cols=43  Identities=26%  Similarity=0.501  Sum_probs=20.7

Q ss_pred             EEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHh
Q 042003          164 LIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDF  206 (248)
Q Consensus       164 liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f  206 (248)
                      ++|.+..+-...+...++..|..+..+.++...+.|.+-++.|
T Consensus         6 vvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleef   48 (162)
T 2l82_A            6 VVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEF   48 (162)
T ss_dssp             EEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHH
T ss_pred             EEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHH
Confidence            3444444444444445555555555555554444444444444

>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=89.25  E-value=2.1  Score=34.31  Aligned_cols=69  Identities=13%  Similarity=0.167  Sum_probs=50.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip~~  229 (248)
                      +.+++|.++++.-+.++++.+++    .+..+..++|+.+..+....+.     ..+|+|+|.-.      ...++...+
T Consensus        89 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~i~v~T~~~l~~~~~~~~~~~~~~  163 (394)
T 1fuu_A           89 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-----DAQIVVGTPGRVFDNIQRRRFRTDKI  163 (394)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-----HCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-----CCCEEEECHHHHHHHHHhCCcchhhC
Confidence            56999999999999988887754    3678999999998766555443     35799999431      223455667


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      ++||
T Consensus       164 ~~vI  167 (394)
T 1fuu_A          164 KMFI  167 (394)
T ss_dssp             CEEE
T ss_pred             cEEE
Confidence            7666

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=89.03  E-value=0.3  Score=31.71  Aligned_cols=36  Identities=8%  Similarity=0.084  Sum_probs=32.4

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      ++++++||.+-..+...+..|+..|+++..+.||+.
T Consensus        55 ~~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~~   90 (108)
T 3gk5_A           55 DKKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGIQ   90 (108)
T ss_dssp             TSCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHHH
T ss_pred             CCeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcHH
Confidence            578999999988899999999999999999999854

>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=88.90  E-value=0.61  Score=43.26  Aligned_cols=72  Identities=11%  Similarity=0.225  Sum_probs=55.9

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CC----eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-cccCCC-CCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GI----RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-IARGMD-FKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~----~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~~~Gid-ip~~  229 (248)
                      +.+++|.++++.-+.++++.++..    +.    .+..++|+.+..++.+..+.+.+  .+|+|+|.. +..-+. +..+
T Consensus        99 ~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~L~~l  176 (1054)
T 1gku_B           99 GKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRELGHF  176 (1054)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTTSCCC
T ss_pred             CCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHHhccC
Confidence            579999999999999988888643    55    78999999999888888888877  889999963 222121 5567


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      ++||
T Consensus       177 ~~lV  180 (1054)
T 1gku_B          177 DFIF  180 (1054)
T ss_dssp             SEEE
T ss_pred             CEEE
Confidence            7766

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

Probab=88.78  E-value=2.3  Score=34.38  Aligned_cols=69  Identities=17%  Similarity=0.251  Sum_probs=50.0

Q ss_pred             CCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----cc-cCCCCCCCc
Q 042003          161 PPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----IA-RGMDFKGVN  230 (248)
Q Consensus       161 ~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~~-~Gidip~~~  230 (248)
                      .+++|.++++.-+.++++.+++    .+..+..++|+.+..+....+   . ...+|+|+|.-     +. ..+++..++
T Consensus       102 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~-~~~~I~v~Tp~~l~~~l~~~~~~~~~~~  177 (417)
T 2i4i_A          102 PISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDL---E-RGCHLLVATPGRLVDMMERGKIGLDFCK  177 (417)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHH---T-TCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHh---h-CCCCEEEEChHHHHHHHHcCCcChhhCc
Confidence            5799999999999999888865    367889999998876544322   2 34689999962     11 235667777


Q ss_pred             EEE
Q 042003          231 CVI  233 (248)
Q Consensus       231 ~Vi  233 (248)
                      +||
T Consensus       178 ~iV  180 (417)
T 2i4i_A          178 YLV  180 (417)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            776

>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=88.65  E-value=2.1  Score=35.21  Aligned_cols=70  Identities=20%  Similarity=0.308  Sum_probs=51.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----cc-cCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----IA-RGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~~-~Gidip~~  229 (248)
                      +.+++|.+++++-+.++++.+++.    +.++..++|+.+...+...+   . ...+|+|+|.-     +. ..+++..+
T Consensus       129 ~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~~Ivv~Tp~~l~~~l~~~~~~l~~~  204 (434)
T 2db3_A          129 RPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECI---T-RGCHVVIATPGRLLDFVDRTFITFEDT  204 (434)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHH---T-TCCSEEEECHHHHHHHHHTTSCCCTTC
T ss_pred             CccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHh---h-cCCCEEEEChHHHHHHHHhCCcccccC
Confidence            458999999999999998888753    56788999998876544333   2 35689999953     22 23567778


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      +++|
T Consensus       205 ~~lV  208 (434)
T 2db3_A          205 RFVV  208 (434)
T ss_dssp             CEEE
T ss_pred             CeEE
Confidence            8776

>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=88.65  E-value=2.9  Score=34.32  Aligned_cols=70  Identities=16%  Similarity=0.214  Sum_probs=52.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcC-CC---eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-cc-----cCCCCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFD-GI---RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-IA-----RGMDFKG  228 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~-~~---~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~~-----~Gidip~  228 (248)
                      .+.+++|.++++.-+.++++.+++. +.   .+..+||+.+..++.....     ..+|+|+|.- +.     ..++...
T Consensus        51 ~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~-----~~~ivv~T~~~l~~~~~~~~~~~~~  125 (494)
T 1wp9_A           51 YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA-----RAKVIVATPQTIENDLLAGRISLED  125 (494)
T ss_dssp             SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHH-----HCSEEEECHHHHHHHHHTTSCCTTS
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhcc-----CCCEEEecHHHHHHHHhcCCcchhh
Confidence            4689999999999999888888765 44   8999999998877655443     3579999953 21     2355667


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      .++||
T Consensus       126 ~~~vI  130 (494)
T 1wp9_A          126 VSLIV  130 (494)
T ss_dssp             CSEEE
T ss_pred             ceEEE
Confidence            77776

>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=88.65  E-value=2  Score=34.58  Aligned_cols=70  Identities=17%  Similarity=0.111  Sum_probs=50.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----c-ccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----I-ARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~-~~Gidip~~  229 (248)
                      +.+++|.++++.-+.++++.++..    +..+..++|+.+.......    ..+..+|+|+|.-     + ....++.++
T Consensus        89 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~  164 (400)
T 1s2m_A           89 KIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR----LNETVHILVGTPGRVLDLASRKVADLSDC  164 (400)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHH----TTSCCSEEEECHHHHHHHHHTTCSCCTTC
T ss_pred             CccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHH----hcCCCCEEEEchHHHHHHHHhCCcccccC
Confidence            568999999999998888877653    6788899998876543222    2356689999952     2 233567777


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      ++||
T Consensus       165 ~~vI  168 (400)
T 1s2m_A          165 SLFI  168 (400)
T ss_dssp             CEEE
T ss_pred             CEEE
Confidence            7776

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=88.34  E-value=0.5  Score=36.95  Aligned_cols=68  Identities=12%  Similarity=0.029  Sum_probs=47.8

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------c-cCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------A-RGMDFK  227 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~-~Gidip  227 (248)
                      +.+++|.+++++-|.++++.++..     +..+....|+.+.....       ....+|+|+|..-      . ..+++.
T Consensus       162 ~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------~~~~~IlV~TP~~l~~~l~~~~~~~l~  234 (300)
T 3fmo_B          162 YPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ-------KISEQIVIGTPGTVLDWCSKLKFIDPK  234 (300)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC-------CCCCSEEEECHHHHHHHHTTTCCCCGG
T ss_pred             CceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh-------cCCCCEEEECHHHHHHHHHhcCCCChh
Confidence            347999999999999988777653     46777888776543211       3456799999642      1 356778


Q ss_pred             CCcEEEe
Q 042003          228 GVNCVIN  234 (248)
Q Consensus       228 ~~~~Vi~  234 (248)
                      .++++|.
T Consensus       235 ~l~~lVl  241 (300)
T 3fmo_B          235 KIKVFVL  241 (300)
T ss_dssp             GCSEEEE
T ss_pred             hceEEEE
Confidence            8888773

>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=88.09  E-value=3.8  Score=32.31  Aligned_cols=71  Identities=14%  Similarity=0.185  Sum_probs=50.6

Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccCCCCC
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARGMDFK  227 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip  227 (248)
                      ..+.+++|.++++.-+.++++.+++    .+..+..++|+.+.......+.     ..+|+|+|...      ...+++.
T Consensus        72 ~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-----~~~iiv~T~~~l~~~~~~~~~~~~  146 (367)
T 1hv8_A           72 NNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLK  146 (367)
T ss_dssp             SSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTT
T ss_pred             cCCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-----CCCEEEecHHHHHHHHHcCCcccc
Confidence            3467999999999999988888865    3678888999887665444333     46799999531      1235566


Q ss_pred             CCcEEE
Q 042003          228 GVNCVI  233 (248)
Q Consensus       228 ~~~~Vi  233 (248)
                      ..++||
T Consensus       147 ~~~~iI  152 (367)
T 1hv8_A          147 NVKYFI  152 (367)
T ss_dssp             SCCEEE
T ss_pred             cCCEEE
Confidence            777766

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=88.04  E-value=0.33  Score=30.97  Aligned_cols=36  Identities=17%  Similarity=0.278  Sum_probs=32.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      ++++++||.+-..+...+..|+..|+++..+.||+.
T Consensus        56 ~~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~   91 (100)
T 3foj_A           56 NETYYIICKAGGRSAQVVQYLEQNGVNAVNVEGGMD   91 (100)
T ss_dssp             TSEEEEECSSSHHHHHHHHHHHTTTCEEEEETTHHH
T ss_pred             CCcEEEEcCCCchHHHHHHHHHHCCCCEEEecccHH
Confidence            578999999999999999999999999999988854

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=87.69  E-value=0.39  Score=30.20  Aligned_cols=35  Identities=17%  Similarity=0.171  Sum_probs=31.0

Q ss_pred             CCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          161 PPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       161 ~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      +++++||.+-..+...+..|+..|+.+..+.||+.
T Consensus        54 ~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~   88 (94)
T 1wv9_A           54 RPLLLVCEKGLLSQVAALYLEAEGYEAMSLEGGLQ   88 (94)
T ss_dssp             SCEEEECSSSHHHHHHHHHHHHHTCCEEEETTGGG
T ss_pred             CCEEEEcCCCChHHHHHHHHHHcCCcEEEEcccHH
Confidence            78999999988899999999999988888888864

>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=87.42  E-value=2.5  Score=34.14  Aligned_cols=70  Identities=14%  Similarity=0.202  Sum_probs=50.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEec-----ccc-cCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATD-----VIA-RGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~-----~~~-~Gidip~~  229 (248)
                      +.+++|.++++.-+.++++.+++.    +..+..++|+.+..+....+.   . ..+|+|+|.     .+. ..++...+
T Consensus       105 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~-~~~ivv~Tp~~l~~~l~~~~~~~~~~  180 (410)
T 2j0s_A          105 ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD---Y-GQHVVAGTPGRVFDMIRRRSLRTRAI  180 (410)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH---H-CCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             CceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhh---c-CCCEEEcCHHHHHHHHHhCCccHhhe
Confidence            579999999999999998888653    567888999988766544333   2 347999995     222 34566677


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      ++||
T Consensus       181 ~~vV  184 (410)
T 2j0s_A          181 KMLV  184 (410)
T ss_dssp             CEEE
T ss_pred             eEEE
Confidence            7776

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

Probab=87.21  E-value=0.94  Score=38.29  Aligned_cols=70  Identities=14%  Similarity=0.135  Sum_probs=49.0

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc-----ccC-C-CCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI-----ARG-M-DFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-----~~G-i-dip~  228 (248)
                      +.+++|.++++.-+.++++.+++.    +..+..++|+.+...+...+.    +..+|+|+|.-.     ..+ + ++.+
T Consensus        52 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~  127 (555)
T 3tbk_A           52 KGKVVFFANQIPVYEQQATVFSRYFERLGYNIASISGATSDSVSVQHII----EDNDIIILTPQILVNNLNNGAIPSLSV  127 (555)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECTTTGGGSCHHHHH----HHCSEEEECHHHHHHHHHTSSSCCGGG
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHHhccCCcEEEEEcCCCcchhhHHHHh----cCCCEEEECHHHHHHHHhcCccccccc
Confidence            678999999999998888888764    889999999987654432221    136799999532     222 2 4556


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      +++||
T Consensus       128 ~~~vV  132 (555)
T 3tbk_A          128 FTLMI  132 (555)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            67666

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=87.00  E-value=1.6  Score=39.15  Aligned_cols=70  Identities=10%  Similarity=0.107  Sum_probs=46.4

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-c----ccC-C-CCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-I----ARG-M-DFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~----~~G-i-dip~  228 (248)
                      ++++||.++++.-+.++++.+++.    +.++..+||+.+...+...+.    +..+|+|+|.- +    ..+ + .+.+
T Consensus       296 ~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~----~~~~Ivv~Tp~~l~~~l~~~~~~~~~~  371 (797)
T 4a2q_A          296 KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI----EDSDIIVVTPQILVNSFEDGTLTSLSI  371 (797)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECCC-----CHHHHH----HTCSEEEECHHHHHHHHHSSSCCCGGG
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHhcccCCceEEEEeCCcchhhhHHHhh----CCCCEEEEchHHHHHHHHhcccccccc
Confidence            679999999999999888887664    889999999987655433222    24679999953 1    222 2 4556


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      +++||
T Consensus       372 ~~~iV  376 (797)
T 4a2q_A          372 FTLMI  376 (797)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            67766

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=86.84  E-value=0.5  Score=34.80  Aligned_cols=70  Identities=16%  Similarity=0.208  Sum_probs=47.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC--------CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----cc-cCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD--------GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----IA-RGMD  225 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~--------~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~~-~Gid  225 (248)
                      +.+++|.++++.-+.++++.+++.        +..+..++|+.+.....   +.+ .+..+|+|+|..     +. ..++
T Consensus        72 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~-~~~~~Iiv~Tp~~l~~~l~~~~~~  147 (219)
T 1q0u_A           72 EVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKAL---EKL-NVQPHIVIGTPGRINDFIREQALD  147 (219)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTT---CCC-SSCCSEEEECHHHHHHHHHTTCCC
T ss_pred             CceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHH---HHc-CCCCCEEEeCHHHHHHHHHcCCCC
Confidence            568999999999999988877543        57788889886543321   112 235689999952     22 2355


Q ss_pred             CCCCcEEE
Q 042003          226 FKGVNCVI  233 (248)
Q Consensus       226 ip~~~~Vi  233 (248)
                      +..++++|
T Consensus       148 ~~~~~~lV  155 (219)
T 1q0u_A          148 VHTAHILV  155 (219)
T ss_dssp             GGGCCEEE
T ss_pred             cCcceEEE
Confidence            66677665

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=86.75  E-value=1.2  Score=37.72  Aligned_cols=71  Identities=11%  Similarity=0.097  Sum_probs=47.1

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc-----ccC-C-CCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI-----ARG-M-DFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-----~~G-i-dip~  228 (248)
                      +.+++|.++++.-+.++++.+++.    +..+..++|+.+...+...+.    +..+|+|+|.-.     ..| + ++..
T Consensus        55 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~  130 (556)
T 4a2p_A           55 KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI----EDSDIIVVTPQILVNSFEDGTLTSLSI  130 (556)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEECCCC-----CHHHHH----HHCSEEEECHHHHHHHHHSSSCCCSTT
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCcchhHHHhh----CCCCEEEECHHHHHHHHHhCccccccc
Confidence            578999999999999888888764    889999999987655433222    136799999532     222 3 5667


Q ss_pred             CcEEEe
Q 042003          229 VNCVIN  234 (248)
Q Consensus       229 ~~~Vi~  234 (248)
                      +++||.
T Consensus       131 ~~~vVi  136 (556)
T 4a2p_A          131 FTLMIF  136 (556)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            777763

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=86.68  E-value=0.6  Score=35.03  Aligned_cols=72  Identities=22%  Similarity=0.286  Sum_probs=48.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----ccc---CCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----IAR---GMDFK  227 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~~~---Gidip  227 (248)
                      +.+++|.++++.-+.++++.+++.    +..+..++|+.....   .......+..+|+|+|.-     +..   ++++.
T Consensus        98 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~  174 (245)
T 3dkp_A           98 GFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAK---KFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLA  174 (245)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHT---TTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHH---HhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccc
Confidence            458999999999999998888764    566777776532211   112223556789999942     112   47788


Q ss_pred             CCcEEEe
Q 042003          228 GVNCVIN  234 (248)
Q Consensus       228 ~~~~Vi~  234 (248)
                      +++++|.
T Consensus       175 ~~~~lVi  181 (245)
T 3dkp_A          175 SVEWLVV  181 (245)
T ss_dssp             TCCEEEE
T ss_pred             cCcEEEE
Confidence            8888763

>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=85.68  E-value=2.5  Score=37.96  Aligned_cols=72  Identities=11%  Similarity=0.109  Sum_probs=53.5

Q ss_pred             hccCCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-c-----c----
Q 042003          156 AESLNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-I-----A----  221 (248)
Q Consensus       156 ~~~~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~-----~----  221 (248)
                      +...+..++|.++|+.-|.+.++.+..    .|.++..+.|+++..+|....      ..+|+++|+. +     .    
T Consensus       120 ~aL~g~~vlVltptreLA~qd~e~~~~l~~~lgl~v~~i~gg~~~~~r~~~~------~~dIv~gTpgrlgfD~L~D~m~  193 (844)
T 1tf5_A          120 NALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAY------AADITYSTNNELGFDYLRDNMV  193 (844)
T ss_dssp             HHTTSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTSCHHHHHHHH------HSSEEEEEHHHHHHHHHHHTTC
T ss_pred             HHHcCCCEEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHhc------CCCEEEECchhhhHHHHHHhhh
Confidence            444467899999999999888777754    588999999999987766543      2689999962 2     1    


Q ss_pred             ---cCCCCCCCcEEE
Q 042003          222 ---RGMDFKGVNCVI  233 (248)
Q Consensus       222 ---~Gidip~~~~Vi  233 (248)
                         ..++...++++|
T Consensus       194 ~~~~~l~lr~~~~lV  208 (844)
T 1tf5_A          194 LYKEQMVQRPLHFAV  208 (844)
T ss_dssp             SSGGGCCCCCCCEEE
T ss_pred             cchhhhcccCCCEEE
Confidence               235667777776

>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=85.49  E-value=2.2  Score=38.22  Aligned_cols=70  Identities=9%  Similarity=0.003  Sum_probs=51.7

Q ss_pred             cCCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccC----
Q 042003          158 SLNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARG----  223 (248)
Q Consensus       158 ~~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~G----  223 (248)
                      ..+..++|.++|+.-|.+.++.+..    .+.++..+.|+++...|....      ..+|+|+|+.-      ..+    
T Consensus       113 l~g~~vlVltPTreLA~Q~~e~~~~l~~~lgl~v~~i~GG~~~~~r~~~~------~~dIvvgTpgrl~fDyLrd~~~~~  186 (853)
T 2fsf_A          113 LTGKGVHVVTVNDYLAQRDAENNRPLFEFLGLTVGINLPGMPAPAKREAY------AADITYGTNNEYGFDYLRDNMAFS  186 (853)
T ss_dssp             TTSSCCEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHHHHHH------HSSEEEEEHHHHHHHHHHHTTCSS
T ss_pred             HcCCcEEEEcCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHhc------CCCEEEECCchhhHHHHHhhhhcc
Confidence            3467899999999999888777654    588999999999987665443      26899999732      122    


Q ss_pred             ---CCCCCCcEEE
Q 042003          224 ---MDFKGVNCVI  233 (248)
Q Consensus       224 ---idip~~~~Vi  233 (248)
                         ++...++++|
T Consensus       187 ~~~~~~~~l~~lV  199 (853)
T 2fsf_A          187 PEERVQRKLHYAL  199 (853)
T ss_dssp             GGGCCCCSCCEEE
T ss_pred             HhHhcccCCcEEE
Confidence               4556677665

>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp, NSR437I, NESG, structural genomics, PSI-2, protein structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A

Probab=84.71  E-value=0.62  Score=30.02  Aligned_cols=36  Identities=11%  Similarity=0.249  Sum_probs=31.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCe-eEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIR-AGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~-v~~~~~~~~  195 (248)
                      .+++++||.+-..+...+..|+..|+. +..+.||+.
T Consensus        52 ~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   88 (106)
T 3hix_A           52 SRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGLA   88 (106)
T ss_dssp             TSCEEEECSSHHHHHHHHHHHHHTTCSCEEECTTHHH
T ss_pred             CCeEEEEECCCChHHHHHHHHHHcCCcCEEEecCCHH
Confidence            578999999988899999999999984 888888854

>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=84.27  E-value=4.6  Score=32.56  Aligned_cols=72  Identities=11%  Similarity=0.152  Sum_probs=50.9

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----c-ccCCCCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----I-ARGMDFKG  228 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~-~~Gidip~  228 (248)
                      .+.+++|.++++.-+.++++.+++.    +..+...+|+.+....   .+.+..+..+|+|+|.-     + ...++...
T Consensus       107 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~  183 (414)
T 3eiq_A          107 KATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAE---VQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKY  183 (414)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHH---HHHHTTTCCSEEEECHHHHHHHHHHTSSCSTT
T ss_pred             CceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHH---HHHHhcCCCCEEEECHHHHHHHHHcCCccccc
Confidence            3578999999999999888888653    5677777887665433   44555677899999952     2 23345666


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      +++||
T Consensus       184 ~~~vV  188 (414)
T 3eiq_A          184 IKMFV  188 (414)
T ss_dssp             CCEEE
T ss_pred             CcEEE
Confidence            77665

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=84.16  E-value=2.9  Score=25.39  Aligned_cols=35  Identities=14%  Similarity=0.145  Sum_probs=29.1

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCe-eEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIR-AGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~-v~~~~~~~~  195 (248)
                      ++++++||.+-..+...+..|++.|+. +..+ |++.
T Consensus        41 ~~~ivv~C~~g~rs~~aa~~L~~~G~~~v~~l-GG~~   76 (85)
T 2jtq_A           41 NDTVKVYCNAGRQSGQAKEILSEMGYTHVENA-GGLK   76 (85)
T ss_dssp             TSEEEEEESSSHHHHHHHHHHHHTTCSSEEEE-EETT
T ss_pred             CCcEEEEcCCCchHHHHHHHHHHcCCCCEEec-cCHH
Confidence            578999999988899999999999884 6666 7754

>3iwh_A Rhodanese-like domain protein; alpha-beta-alpha sandwich, structural genomics, C structural genomics of infectious diseases, csgid; 2.00A {Staphylococcus aureus subsp} PDB: 3mzz_A

Probab=84.15  E-value=0.55  Score=30.24  Aligned_cols=35  Identities=20%  Similarity=0.217  Sum_probs=30.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDL  194 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~  194 (248)
                      ++++++||.+-..+...+..|++.|+.+..+.||+
T Consensus        56 ~~~ivv~C~~G~rS~~aa~~L~~~G~~~~~l~GG~   90 (103)
T 3iwh_A           56 NEIYYIVCAGGVRSAKVVEYLEANGIDAVNVEGGM   90 (103)
T ss_dssp             TSEEEEECSSSSHHHHHHHHHHTTTCEEEEETTHH
T ss_pred             CCeEEEECCCCHHHHHHHHHHHHcCCCEEEecChH
Confidence            56899999998888999999999999888888875

>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=84.05  E-value=3.4  Score=37.38  Aligned_cols=73  Identities=18%  Similarity=0.155  Sum_probs=53.8

Q ss_pred             HhccCCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-c-----c---
Q 042003          155 FAESLNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-I-----A---  221 (248)
Q Consensus       155 ~~~~~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~-----~---  221 (248)
                      ++...+..++|.++|+.-|.+.++.+..    .|.++..+.|+++..+|.....      .+|+++|+. +     .   
T Consensus       147 l~aL~g~~v~VvTpTreLA~Qdae~m~~l~~~lGLsv~~i~gg~~~~~r~~~y~------~DIvygTpgrlgfDyLrD~m  220 (922)
T 1nkt_A          147 LNALAGNGVHIVTVNDYLAKRDSEWMGRVHRFLGLQVGVILATMTPDERRVAYN------ADITYGTNNEFGFDYLRDNM  220 (922)
T ss_dssp             HHHTTTSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHHHHHHH------SSEEEEEHHHHHHHHHHHTT
T ss_pred             HHHHhCCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHhcC------CCEEEECchHhhHHHHHhhh
Confidence            3444467899999999988887777653    5899999999999877765542      689999963 2     1   


Q ss_pred             ----cCCCCCCCcEEE
Q 042003          222 ----RGMDFKGVNCVI  233 (248)
Q Consensus       222 ----~Gidip~~~~Vi  233 (248)
                          ..++...++++|
T Consensus       221 ~~~~~~l~lr~l~~lI  236 (922)
T 1nkt_A          221 AHSLDDLVQRGHHYAI  236 (922)
T ss_dssp             CSSGGGCCCCCCCEEE
T ss_pred             hccHhhhccCCCCEEE
Confidence                135666777766

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=83.50  E-value=2.6  Score=38.21  Aligned_cols=59  Identities=17%  Similarity=0.091  Sum_probs=46.5

Q ss_pred             HhccCCCCEEEEecchHHHHHHHHHhh----cCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          155 FAESLNPPVLIFVQSKERAKELYGELA----FDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       155 ~~~~~~~~~liF~~~~~~~~~l~~~L~----~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      +....+..++|.++|..-|.+.++.+.    ..|.++..+.|+++..+|....      ..+|+++|+.
T Consensus       115 L~aL~G~qv~VvTPTreLA~Qdae~m~~l~~~lGLsv~~i~Gg~~~~~r~~ay------~~DIvyGTpg  177 (997)
T 2ipc_A          115 LNALTGKGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGVIQHASTPAERRKAY------LADVTYVTNS  177 (997)
T ss_dssp             HHHTTCSCCEEEESSHHHHHHHHHHHHHHHHTTTCCEEECCTTCCHHHHHHHH------TSSEEEEEHH
T ss_pred             HHHHhCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHc------CCCEEEECch
Confidence            344446789999999998888777665    4589999999999987776654      3689999964

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

Probab=82.98  E-value=9  Score=29.69  Aligned_cols=69  Identities=14%  Similarity=0.192  Sum_probs=49.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc-----c-cCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI-----A-RGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-----~-~Gidip~~  229 (248)
                      +.+++|.++++.-+.++++.+++    .+..+..++|+.+.......+   .  ..+|+|+|.-.     . ..+++...
T Consensus        56 ~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~--~~~i~v~T~~~l~~~~~~~~~~~~~~  130 (337)
T 2z0m_A           56 GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRV---R--NADIVVATPGRLLDLWSKGVIDLSSF  130 (337)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHHH---T--TCSEEEECHHHHHHHHHTTSCCGGGC
T ss_pred             cCCEEEEeCCHHHHHHHHHHHHHHhhhcCCcEEEEECCcchHHHHhhc---C--CCCEEEECHHHHHHHHHcCCcchhhC
Confidence            67999999999999999888874    357889999998876544332   2  26799999532     1 23455666


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      ++||
T Consensus       131 ~~iV  134 (337)
T 2z0m_A          131 EIVI  134 (337)
T ss_dssp             SEEE
T ss_pred             cEEE
Confidence            6665

>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 2.50A {Bacillus halodurans} PDB: 3o3w_A

Probab=82.51  E-value=0.76  Score=31.55  Aligned_cols=36  Identities=11%  Similarity=0.180  Sum_probs=31.4

Q ss_pred             CCCEEEEecch--HHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          160 NPPVLIFVQSK--ERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~--~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      ++++++||.+-  ..+...+..|+..|+++..+.||+.
T Consensus        72 ~~~ivvyC~~g~~~rs~~aa~~L~~~G~~v~~l~GG~~  109 (144)
T 3nhv_A           72 EKVIITYCWGPACNGATKAAAKFAQLGFRVKELIGGIE  109 (144)
T ss_dssp             TSEEEEECSCTTCCHHHHHHHHHHHTTCEEEEEESHHH
T ss_pred             CCeEEEEECCCCccHHHHHHHHHHHCCCeEEEeCCcHH
Confidence            56899999987  5888999999999999999999854

>3g5j_A Putative ATP/GTP binding protein; N-terminal domain of ATP/GTP binding protein, PSI, MCSG, STR genomics, protein structure initiative; HET: PGE; 1.76A {Clostridium difficile}

Probab=82.10  E-value=1.4  Score=29.31  Aligned_cols=35  Identities=11%  Similarity=0.212  Sum_probs=30.7

Q ss_pred             CCEEEEe-cchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          161 PPVLIFV-QSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       161 ~~~liF~-~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      +++++|| .+-..+...+..|+..|+++..+.||+.
T Consensus        90 ~~ivvyC~~~G~rs~~a~~~L~~~G~~v~~l~GG~~  125 (134)
T 3g5j_A           90 DNIVIYCARGGMRSGSIVNLLSSLGVNVYQLEGGYK  125 (134)
T ss_dssp             SEEEEECSSSSHHHHHHHHHHHHTTCCCEEETTHHH
T ss_pred             CeEEEEECCCChHHHHHHHHHHHcCCceEEEeCcHH
Confidence            7899999 5777888999999999999999999865

>2k0z_A Uncharacterized protein HP1203; A/B domain, structural genomics, unknown function, PSI-2, PR structure initiative; NMR {Helicobacter pylori}

Probab=81.91  E-value=1.6  Score=28.27  Aligned_cols=36  Identities=14%  Similarity=0.160  Sum_probs=31.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      ++++++||.+-..+...+..|+..|+....+.||+.
T Consensus        56 ~~~ivvyC~~G~rs~~aa~~L~~~G~~~~~l~GG~~   91 (110)
T 2k0z_A           56 DKKVLLHCRAGRRALDAAKSMHELGYTPYYLEGNVY   91 (110)
T ss_dssp             SSCEEEECSSSHHHHHHHHHHHHTTCCCEEEESCGG
T ss_pred             CCEEEEEeCCCchHHHHHHHHHHCCCCEEEecCCHH
Confidence            678999999988999999999999985588889865

>2fsx_A RV0390, COG0607: rhodanese-related sulfurtransferase; RV0390 BR SAD DATA with FBAR, structural genomics, PSI; 1.80A {Mycobacterium tuberculosis}

Probab=81.76  E-value=1.2  Score=30.64  Aligned_cols=36  Identities=19%  Similarity=0.207  Sum_probs=31.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCC-eeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGI-RAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~-~v~~~~~~~~  195 (248)
                      ++++++||.+-..+...+..|+..|+ ++..+.||+.
T Consensus        80 ~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~  116 (148)
T 2fsx_A           80 ERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFE  116 (148)
T ss_dssp             -CCEEEECSSSSTHHHHHHHHHHTTCCSEEEETTTTT
T ss_pred             CCEEEEEcCCChhHHHHHHHHHHcCCcceEEEcCChh
Confidence            57899999998888899999999998 5999999974

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=81.06  E-value=1.5  Score=32.05  Aligned_cols=41  Identities=15%  Similarity=0.110  Sum_probs=22.9

Q ss_pred             eeEEEEeccccccccC-cccccchhHhh---hCCCccceeEEEEee
Q 042003           62 VEYLVLDEADKLFEVG-NLLKHIDPVVK---ACSNPSIVRSLFSAT  103 (248)
Q Consensus        62 ~~~lIiDEah~~~~~~-~~~~~~~~~~~---~~~~~~~~~i~~SAT  103 (248)
                      -.++||||||.+.... ...... +++.   .......++++++-.
T Consensus        88 ~~vliIDEAq~l~~~~~~~~e~~-rll~~l~~~r~~~~~iil~tq~  132 (199)
T 2r2a_A           88 GSIVIVDEAQDVWPARSAGSKIP-ENVQWLNTHRHQGIDIFVLTQG  132 (199)
T ss_dssp             TCEEEETTGGGTSBCCCTTCCCC-HHHHGGGGTTTTTCEEEEEESC
T ss_pred             ceEEEEEChhhhccCccccchhH-HHHHHHHhcCcCCeEEEEECCC
Confidence            4589999999985422 112111 2222   223445677777766

>3flh_A Uncharacterized protein LP_1913; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.00A {Lactobacillus plantarum} PDB: 3fnj_A 3i3u_A

Probab=80.61  E-value=0.49  Score=31.51  Aligned_cols=36  Identities=14%  Similarity=0.081  Sum_probs=30.7

Q ss_pred             CCCEEEEecchHH--HHHHHHHhhcCCCeeEEEecCCC
Q 042003          160 NPPVLIFVQSKER--AKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~--~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      ++++++||.+-..  +...+..|+..|+.+..+.||+.
T Consensus        71 ~~~ivvyC~~g~r~~s~~a~~~L~~~G~~v~~l~GG~~  108 (124)
T 3flh_A           71 AKTYVVYDWTGGTTLGKTALLVLLSAGFEAYELAGALE  108 (124)
T ss_dssp             TSEEEEECSSSSCSHHHHHHHHHHHHTCEEEEETTHHH
T ss_pred             CCeEEEEeCCCCchHHHHHHHHHHHcCCeEEEeCCcHH
Confidence            5689999998776  78899999999999888888854

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=80.57  E-value=9.1  Score=28.47  Aligned_cols=64  Identities=19%  Similarity=0.196  Sum_probs=45.8

Q ss_pred             cCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCe-eEEEecCCCHHHHHHHHHHhhcCCceEEEEec
Q 042003          141 AGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIR-AGVIHSDLSQTQRENAVDDFRAGKTWVLIATD  218 (248)
Q Consensus       141 ~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~  218 (248)
                      .+.-..|.......+... +.++++++++..-++++++.+++.+.. +..++|+...             ..+|+|+|.
T Consensus       115 ~~tG~GKT~~a~~~~~~~-~~~~liv~P~~~L~~q~~~~~~~~~~~~v~~~~g~~~~-------------~~~i~v~T~  179 (237)
T 2fz4_A          115 LPTGSGKTHVAMAAINEL-STPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKE-------------LKPLTVSTY  179 (237)
T ss_dssp             ESSSTTHHHHHHHHHHHS-CSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSCBC-------------CCSEEEEEH
T ss_pred             eCCCCCHHHHHHHHHHHc-CCCEEEEeCCHHHHHHHHHHHHhCCCCeEEEEeCCCCC-------------cCCEEEEeH
Confidence            333345555544444444 689999999999999999999887877 8888887542             346777773

>1tq1_A AT5G66040, senescence-associated family protein; CESG, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} SCOP: c.46.1.3

Probab=80.49  E-value=0.93  Score=30.37  Aligned_cols=36  Identities=19%  Similarity=0.188  Sum_probs=31.4

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCe-eEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIR-AGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~-v~~~~~~~~  195 (248)
                      ++++++||.+-..+...+..|+..|+. +..+.||+.
T Consensus        82 ~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~  118 (129)
T 1tq1_A           82 SDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  118 (129)
T ss_dssp             TSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             CCeEEEECCCCcHHHHHHHHHHHcCCCCeEEeCCcHH
Confidence            578999999988889999999998884 888999864

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=80.03  E-value=0.4  Score=41.70  Aligned_cols=40  Identities=23%  Similarity=0.133  Sum_probs=26.2

Q ss_pred             CCCcEEEeChHHHHHHHhcCC----c-ccCceeEEEEeccccccc
Q 042003           36 FSCDILISTPLRLRLAIRRKK----I-DLSRVEYLVLDEADKLFE   75 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~~----~-~~~~~~~lIiDEah~~~~   75 (248)
                      ..+||||+...-+.+...+..    . ....-.++||||||.+.+
T Consensus       174 ~~ADvVV~ny~ylld~~~r~~~~~~~~i~p~~~ivI~DEAHNL~d  218 (620)
T 4a15_A          174 PDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPD  218 (620)
T ss_dssp             GGCSEEEEEHHHHTCHHHHHHHHHHHTCCGGGEEEEETTGGGHHH
T ss_pred             hcCCEEEeCchhhcCHHHHHHHHHhhccCcCCeEEEEECCCchHH
Confidence            468999999876554432211    1 012345899999999975

---

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	248
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	8e-26
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	9e-22
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	4e-17
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	3e-16
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	6e-16
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	1e-15
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-15
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	2e-14
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	3e-14
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	9e-14
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	1e-12
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	2e-12
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	4e-12
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	7e-12
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	9e-12
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	1e-11
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	2e-11
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	4e-10
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	5e-10
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	1e-09
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	4e-09
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	8e-09
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	1e-07
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	3e-06
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	6e-04
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	0.002
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	0.004

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score =  100 bits (250), Expect = 8e-26
 Identities = 23/140 (16%), Positives = 39/140 (27%), Gaps = 20/140 (14%)

Query: 125 GRKNTASESIKQKLVFAGSEE---GKLLALRQSFAESLNPPVLIFVQSKERAKELYGELA 181
           G       +I++  +    E    GK + L            LIF  SK++  EL  +L 
Sbjct: 2   GSVTVPHPNIEEVALSTTGEIPFYGKAIPLEVIKGGR----HLIFCHSKKKCDELAAKLV 57

Query: 182 FDGIRAGVIHSDLSQTQR----------ENAVDDFRAGKTWVLIATDVIARGM---DFKG 228
             GI A   +  L  +             +A+     G    +I  +             
Sbjct: 58  ALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDP 117

Query: 229 VNCVINYDFPDSGAAYIHRI 248
              +     P    +   R 
Sbjct: 118 TFTIETTTLPQDAVSRTQRR 137

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 87.4 bits (216), Expect = 9e-22
 Identities = 32/118 (27%), Positives = 57/118 (48%), Gaps = 3/118 (2%)

Query: 8   ECKKLAKGNKFQIKLMKKELVRSTDLSKF-SCDILISTPLRLRLAIRRKKIDLSRVEYLV 66
           E + L      +I  +         +    + +I++ TP R+   I R  ++L  V+Y +
Sbjct: 91  EIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFI 150

Query: 67  LDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIV 124
           LDEAD++  +G  +K ++ ++ AC N      LFSAT+P  +  LA+  M D   +  
Sbjct: 151 LDEADEMLNMGF-IKDVEKILNAC-NKDKRILLFSATMPREILNLAKKYMGDYSFIKA 206

>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 = 76.5 bits (187), Expect = 4e-17
 Identities = 35/161 (21%), Positives = 64/161 (39%), Gaps = 12/161 (7%)

Query: 100 FSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQ----SF 155
             A +    EE        +  +   ++   + S+  +    G +  K+  L++      
Sbjct: 97  LRAYIKKLYEEAKAGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQL 156

Query: 156 AESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQR--------ENAVDDFR 207
               N  +++F   +E AK++  EL  DGI+A       S+           +  +D+F 
Sbjct: 157 QRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFA 216

Query: 208 AGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            G+  VL+AT V   G+D   V+ V+ Y+   S    I R 
Sbjct: 217 RGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRR 257

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.6 bits (177), Expect = 3e-16
 Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 1/92 (1%)

Query: 33  LSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSN 92
           L K    I++ TP R+    R K ++L  +++ +LDE DK+ E  ++ + +  + +    
Sbjct: 117 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMT-P 175

Query: 93  PSIVRSLFSATLPDFVEELARSIMHDAVRVIV 124
                 +FSATL   +  + R  M D + + V
Sbjct: 176 HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 207

>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 = 71.1 bits (173), Expect = 6e-16
 Identities = 43/115 (37%), Positives = 65/115 (56%)

Query: 134 IKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSD 193
           IKQ  V    EE K   L   +        +IF  ++ + +EL  +L  D      I+SD
Sbjct: 1   IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 60

Query: 194 LSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           L Q +R+  + +FR+G + +LI+TD++ARG+D + V+ VINYD P +   YIHRI
Sbjct: 61  LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRI 115

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 71.4 bits (174), Expect = 1e-15
 Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 2/87 (2%)

Query: 38  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 97
             I++ TP R+   I+R++    +++  +LDEAD++   G   + I  +      P+   
Sbjct: 128 AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFK-EQIYQIFTLLP-PTTQV 185

Query: 98  SLFSATLPDFVEELARSIMHDAVRVIV 124
            L SAT+P+ V E+    M + VR++V
Sbjct: 186 VLLSATMPNDVLEVTTKFMRNPVRILV 212

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.3 bits (171), Expect = 2e-15
 Identities = 25/89 (28%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 38  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 97
             I++ TP R+   + R+ +    ++  VLDEAD++   G     I  + +   N +   
Sbjct: 132 PHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG-FKDQIYDIFQKL-NSNTQV 189

Query: 98  SLFSATLPDFVEELARSIMHDAVRVIVGR 126
            L SAT+P  V E+ +  M D +R++V +
Sbjct: 190 VLLSATMPSDVLEVTKKFMRDPIRILVKK 218

>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 = 68.6 bits (167), Expect = 2e-14
 Identities = 20/110 (18%), Positives = 39/110 (35%), Gaps = 16/110 (14%)

Query: 144 EEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAV 203
            +  +  L  S  E L    +I+ ++ E A+E+Y  L             +    ++   
Sbjct: 10  NDESISTLS-SILEKLGTGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDY 62

Query: 204 DDFRAGKTWVLIAT----DVIARGMDF-KGVNCVINYDFPDSGAAYIHRI 248
           + F  G+   LI T      + RG+D  + +   +    P     +   I
Sbjct: 63  EKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTI 108

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 67.6 bits (164), Expect = 3e-14
 Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 4/91 (4%)

Query: 38  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVR 97
           C +L++TP RL   I + KI L   +Y+VLDEAD+          I  +++  + PS + 
Sbjct: 149 CHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADR-MLDMGFEPQIRKIIEESNMPSGIN 207

Query: 98  S---LFSATLPDFVEELARSIMHDAVRVIVG 125
               +FSAT P  +++LA   +++ + + VG
Sbjct: 208 RQTLMFSATFPKEIQKLAADFLYNYIFMTVG 238

>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 = 65.2 bits (158), Expect = 9e-14
 Identities = 23/85 (27%), Positives = 40/85 (47%)

Query: 163 VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR 222
            L+   +K+ A++L   L   GI+   +HS++   +R   + D R GK  VL+  +++  
Sbjct: 34  TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 93

Query: 223 GMDFKGVNCVINYDFPDSGAAYIHR 247
           G+D   V+ V   D    G     R
Sbjct: 94  GLDIPEVSLVAILDADKEGFLRSER 118

>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 = 61.9 bits (149), Expect = 1e-12
 Identities = 47/118 (39%), Positives = 69/118 (58%), Gaps = 2/118 (1%)

Query: 131 SESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVI 190
           + +I+Q  V     E +  AL +   ++     L+F ++K   KEL   L   G +AG I
Sbjct: 1   NANIEQSYVEVNENE-RFEALCR-LLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAI 58

Query: 191 HSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           H DLSQ+QRE  +  F+  K  +LIATDV++RG+D   +NCVINY  P +  +Y+HRI
Sbjct: 59  HGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRI 116

>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 = 62.2 bits (150), Expect = 2e-12
 Identities = 23/119 (19%), Positives = 47/119 (39%), Gaps = 5/119 (4%)

Query: 130 ASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGV 189
           A  + ++    A + + K+  LR+         ++IF +  E    +             
Sbjct: 63  ALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRIS-----KVFLIPA 117

Query: 190 IHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           I    S+ +RE  ++ FR G+   ++++ V+  G+D    N  +      S   YI R+
Sbjct: 118 ITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRL 176

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.4 bits (148), Expect = 4e-12
 Identities = 33/126 (26%), Positives = 53/126 (42%), Gaps = 4/126 (3%)

Query: 3   TQTTRECKKLAKGNKFQIKLMKKELVRSTDLS--KFSCDILISTPLRLRLAIRRKKIDLS 60
            Q  +    L      Q            D+    +   ++  TP R+   IRR+ +   
Sbjct: 99  VQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTR 158

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAV 120
            ++ LVLDEAD++   G   + I  V +    P+    L SATLP  + E+    M D +
Sbjct: 159 AIKMLVLDEADEMLNKG-FKEQIYDVYRYL-PPATQVVLISATLPHEILEMTNKFMTDPI 216

Query: 121 RVIVGR 126
           R++V R
Sbjct: 217 RILVKR 222

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 60.4 bits (145), Expect = 7e-12
 Identities = 21/105 (20%), Positives = 43/105 (40%)

Query: 144 EEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAV 203
           +   L  L +   E      +I+  S+ + ++    L   GI A   H+ L    R +  
Sbjct: 14  KFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQ 73

Query: 204 DDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
           + F+     +++AT     G++   V  V+++D P +  +Y    
Sbjct: 74  EKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQET 118

>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 = 61.5 bits (148), Expect = 9e-12
 Identities = 29/236 (12%), Positives = 61/236 (25%), Gaps = 50/236 (21%)

Query: 35  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 94
               +I+               I +     +++DEA          +    +        
Sbjct: 74  HTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGY--ISTRVEMGE 131

Query: 95  IVRSLFSATLPDFVEELARS---IMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLAL 151
                 +AT P   +   +S   IM +   +     N+  E +                 
Sbjct: 132 AAGIFMTATPPGSRDPFPQSNAPIMDEEREIPERSWNSGHEWVTDF-------------- 177

Query: 152 RQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKT 211
                       + FV S +   ++   L  +G +   +      ++        R    
Sbjct: 178 --------KGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYIK----TRTNDW 225

Query: 212 WVLIATDVIARGMDFK---------GVNCVINYD----------FPDSGAAYIHRI 248
             ++ TD+   G +FK          +  VI  D           P + ++   R 
Sbjct: 226 DFVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRR 281

>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 = 58.8 bits (141), Expect = 2e-11
 Identities = 42/117 (35%), Positives = 62/117 (52%)

Query: 132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIH 191
           E IKQ  V    EE K   L   +        +IF  +K +   L  ++         +H
Sbjct: 6   EGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMH 65

Query: 192 SDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI 248
            D+ Q +RE+ + +FR+G + VLI+TDV ARG+D   V+ +INYD P++   YIHRI
Sbjct: 66  GDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRI 122

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 55.4 bits (132), Expect = 4e-10
 Identities = 25/91 (27%), Positives = 38/91 (41%), Gaps = 2/91 (2%)

Query: 35  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 94
             +  IL+ TP R+     RK  DLS     ++DEADK+             + +   P+
Sbjct: 117 NETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQ--ILSFLPPT 174

Query: 95  IVRSLFSATLPDFVEELARSIMHDAVRVIVG 125
               LFSAT P  V+E     +H    + + 
Sbjct: 175 HQSLLFSATFPLTVKEFMVKHLHKPYEINLM 205

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

 Score = 55.1 bits (132), Expect = 5e-10
 Identities = 24/85 (28%), Positives = 38/85 (44%)

Query: 163 VLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIAR 222
            L+ V +   A+EL   L   GIRA  +H +L   +R+  + D R G    L+  +++  
Sbjct: 34  TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLRE 93

Query: 223 GMDFKGVNCVINYDFPDSGAAYIHR 247
           G+D   V+ V   D    G     R
Sbjct: 94  GLDIPEVSLVAILDADKEGFLRSER 118

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.2 bits (129), Expect = 1e-09
 Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 2/88 (2%)

Query: 35  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 94
             +  ++I+TP R+   I++    +  V+ +VLDEADKL     + + ++ ++      +
Sbjct: 120 DDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFV-QIMEDIILTL-PKN 177

Query: 95  IVRSLFSATLPDFVEELARSIMHDAVRV 122
               L+SAT P  V++   S +     +
Sbjct: 178 RQILLYSATFPLSVQKFMNSHLEKPYEI 205

>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 = 51.6 bits (123), Expect = 4e-09
 Identities = 27/130 (20%), Positives = 43/130 (33%), Gaps = 17/130 (13%)

Query: 125 GRKNTASESIKQ-KLVFAGS--EEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELA 181
           G       +I++  L   G     GK + L            LIF  SK++  EL  +L 
Sbjct: 1   GSVTVPHPNIEEVALSTTGEIPFYGKAIPLEVIKGGR----HLIFCHSKKKCDELAAKLV 56

Query: 182 FDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKG---VNCVINYDFP 238
             GI A   +  L  +               V++ATD +  G        ++C  +   P
Sbjct: 57  ALGINAVAYYRGLDVSVIPT-------NGDVVVVATDALMTGFTGDFDSVIDCNTSDGKP 109

Query: 239 DSGAAYIHRI 248
               +   R 
Sbjct: 110 QDAVSRTQRR 119

>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 = 52.1 bits (124), Expect = 8e-09
 Identities = 17/61 (27%), Positives = 35/61 (57%)

Query: 188 GVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHR 247
           G++H  LSQ +++  + +F  G+  +L++T VI  G+D    N ++  +    G A +H+
Sbjct: 68  GLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQ 127

Query: 248 I 248
           +
Sbjct: 128 L 128

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 48.5 bits (114), Expect = 1e-07
 Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

Query: 35  KFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPS 94
                I+I TP R+   IR + +D+     LV+DEAD + ++G +   +D +        
Sbjct: 121 NVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFI-TDVDQIAARM-PKD 178

Query: 95  IVRSLFSATLPDFVEELARSIMHDAVRVIV 124
           +   +FSAT+P+ ++   +  M +   V V
Sbjct: 179 LQMLVFSATIPEKLKPFLKKYMENPTFVHV 208

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 211

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

 Score = 44.6 bits (105), Expect = 3e-06
 Identities = 16/67 (23%), Positives = 30/67 (44%)

Query: 182 FDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPDSG 241
               R  + H  + + + E  ++DF   +  VL+ T +I  G+D    N +I       G
Sbjct: 55  VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFG 114

Query: 242 AAYIHRI 248
            A +H++
Sbjct: 115 LAQLHQL 121

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 38.0 bits (87), Expect = 6e-04
 Identities = 14/132 (10%), Positives = 37/132 (28%), Gaps = 21/132 (15%)

Query: 2   ATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSK--------FSCDILISTPLRLRLAIR 53
             Q     +K A+      + +           +         +  I+I+T   L     
Sbjct: 99  VIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLS---- 154

Query: 54  RKKIDLSRVEYLVLDEADKLFEVG-------NLLKHIDPVVK--ACSNPSIVRSLFSATL 104
           +   +L   +++ +D+ D + +         +LL     +              + +AT 
Sbjct: 155 KHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATA 214

Query: 105 PDFVEELARSIM 116
               +      +
Sbjct: 215 KKGKKAELFRQL 226

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 35.7 bits (81), Expect = 0.002
 Identities = 29/116 (25%), Positives = 42/116 (36%), Gaps = 4/116 (3%)

Query: 1   LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLS 60
           LA +     KK  K               S D     CDI+++T  +    IR +   + 
Sbjct: 80  LAGEKYESFKKWEKIGLRIGISTGD--YESRDEHLGDCDIIVTTSEKADSLIRNRASWIK 137

Query: 61  RVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSL-FSATLPDFVEELARSI 115
            V  LV+DE   L            V K       +R +  SAT P+ V E+A  +
Sbjct: 138 AVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEWL 192

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 35.0 bits (79), Expect = 0.004
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 4/87 (4%)

Query: 38  CDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKA--CSNPSI 95
             +L   P RL L    + +       L +DEA  + + G+  +     +       P++
Sbjct: 116 IRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTL 175

Query: 96  VRSLFSATLPDFVEE--LARSIMHDAV 120
                +AT  D   +  +    ++D +
Sbjct: 176 PFMALTATADDTTRQDIVRLLGLNDPL 202

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	248
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.96
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.95
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.94
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.94
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.94
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.94
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.92
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.91
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.9
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.88
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.82
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.81
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.8
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.8
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.8
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.79
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.79
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.77
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.77
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.77
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.76
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.75
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.73
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.67
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.65
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.62
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.62
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.49
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.46
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.37
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.31
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.31
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.09
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.09
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.07
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.03
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	98.8
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	98.74
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.67
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.64
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.25
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.14
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.89
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.7
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.51
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.0
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	95.59
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	95.2
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	95.17
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	95.1
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	95.06
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	91.89
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	90.44
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	89.34
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	88.97
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	88.28
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	87.71
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	87.18
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	87.17
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	86.76
d2b2na1	308	Transcription-repair coupling factor, TRCF {Escher	86.74
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	85.4
d1urha2	120	3-mercaptopyruvate sulfurtransferase {Escherichia	84.58
d1qxna_	137	Polysulfide-sulfur transferase (sulfide dehydrogen	84.19
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	82.25
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	82.25
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	80.85
d1yt8a2	101	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	80.11

>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=1.9e-28  Score=175.63  Aligned_cols=115  Identities=37%  Similarity=0.584  Sum_probs=110.8

Q ss_pred             ceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceE
Q 042003          134 IKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWV  213 (248)
Q Consensus       134 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~i  213 (248)
                      ++++++.++..+.|++.|.++++....+++||||+++..++.+++.|...++++..+||+|+..+|.++++.|++|+.++
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~i   80 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI   80 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSE
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccce
Confidence            46788888888899999999999888899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          214 LIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       214 lv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ||||+++++|+|+|++++||+||+|+|+..|+||+
T Consensus        81 Lv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~  115 (162)
T d1fuka_          81 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRI  115 (162)
T ss_dssp             EEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSS
T ss_pred             eeccccccccccCCCceEEEEeccchhHHHHHhhc
Confidence            99999999999999999999999999999999996

>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=99.95  E-value=1.4e-28  Score=177.35  Aligned_cols=121  Identities=35%  Similarity=0.528  Sum_probs=115.6

Q ss_pred             ccccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhh
Q 042003          128 NTASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFR  207 (248)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~  207 (248)
                      +....+++++++.+.+.+.|.+.|.++++...+.++||||++++.++.+++.|+..++++..+||+++.++|..+++.|+
T Consensus         2 ~~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk   81 (168)
T d2j0sa2           2 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFR   81 (168)
T ss_dssp             GCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCcEEEEEEecChHHHHHHHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHh
Confidence            34567899999999998899999999999888889999999999999999999999999999999999999999999999


Q ss_pred             cCCceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          208 AGKTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       208 ~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +|+.++||||+++++|+|+|++++||+||+|+|+.+|+||+
T Consensus        82 ~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~  122 (168)
T d2j0sa2          82 SGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRI  122 (168)
T ss_dssp             HTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHH
T ss_pred             cCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhh
Confidence            99999999999999999999999999999999999999995

>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=99.94  E-value=3.1e-27  Score=171.15  Aligned_cols=118  Identities=31%  Similarity=0.545  Sum_probs=111.3

Q ss_pred             ccccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcC
Q 042003          130 ASESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAG  209 (248)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g  209 (248)
                      ...++.|++..++. ++|...|.++++...++++||||++++.++.++..|...++.+..+||+++.++|.++++.|++|
T Consensus         3 tl~~i~q~yi~v~~-~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~   81 (171)
T d1s2ma2           3 TLKGITQYYAFVEE-RQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQG   81 (171)
T ss_dssp             BCTTEEEEEEECCG-GGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CccceEEEEEEcCH-HHHHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccC
Confidence            45678888887765 57999999999998889999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          210 KTWVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       210 ~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +.++||||+++++|+|+|++++||+||+|+|+.+|+||+
T Consensus        82 ~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~  120 (171)
T d1s2ma2          82 KVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRI  120 (171)
T ss_dssp             SSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHH
T ss_pred             ccccccchhHhhhccccceeEEEEecCCcchHHHHHHHh
Confidence            999999999999999999999999999999999999995

>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=99.94  E-value=8.4e-27  Score=166.25  Aligned_cols=115  Identities=40%  Similarity=0.626  Sum_probs=108.1

Q ss_pred             ccceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCc
Q 042003          132 ESIKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKT  211 (248)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~  211 (248)
                      .++.+.++.+.. ++|.+.|.++++.. +.++||||+++++++.+++.|+..++.+..+||+++..+|..+++.|++|+.
T Consensus         2 ~nI~~~~i~v~~-~~K~~~L~~ll~~~-~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~   79 (155)
T d1hv8a2           2 ANIEQSYVEVNE-NERFEALCRLLKNK-EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI   79 (155)
T ss_dssp             SSSEEEEEECCG-GGHHHHHHHHHCST-TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSS
T ss_pred             CCeEEEEEEeCh-HHHHHHHHHHHccC-CCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccc
Confidence            467888887755 67999999999875 6799999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          212 WVLIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       212 ~ilv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ++||||+++++|+|+|++++||+||+|+|+.+|+||+
T Consensus        80 ~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~  116 (155)
T d1hv8a2          80 RILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRI  116 (155)
T ss_dssp             SEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHS
T ss_pred             eeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHH
Confidence            9999999999999999999999999999999999985

>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=99.94  E-value=8.6e-27  Score=168.07  Aligned_cols=114  Identities=30%  Similarity=0.418  Sum_probs=108.3

Q ss_pred             ceeEEEEcCCchhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceE
Q 042003          134 IKQKLVFAGSEEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWV  213 (248)
Q Consensus       134 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~i  213 (248)
                      ++++++.+.. ++|.+.|.++++....+++||||++++.++.+++.|++.++++..+||+|+.++|.++++.|++|+.++
T Consensus         2 l~q~~v~~~~-~~K~~~L~~ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~i   80 (168)
T d1t5ia_           2 LQQYYVKLKD-NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI   80 (168)
T ss_dssp             CEEEEEECCG-GGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSE
T ss_pred             cEEEEEEeCh-HHHHHHHHHHHHhCCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhcccccee
Confidence            5678877774 679999999999888889999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          214 LIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       214 lv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ||||+++++|+|+|.+++||+|++|+|+..|+||+
T Consensus        81 Lv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~  115 (168)
T d1t5ia_          81 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV  115 (168)
T ss_dssp             EEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHH
T ss_pred             eeccccccchhhcccchhhhhhhcccchhhHhhhh
Confidence            99999999999999999999999999999999984

>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=99.92  E-value=8.4e-26  Score=166.87  Aligned_cols=105  Identities=20%  Similarity=0.344  Sum_probs=100.5

Q ss_pred             chhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccC
Q 042003          144 EEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARG  223 (248)
Q Consensus       144 ~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G  223 (248)
                      ..+|.+.|..+++...+.++||||+|++.++.+++.|+..++.+..+||+++.++|.++++.|++|+.++||||+++++|
T Consensus        14 ~~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~G   93 (200)
T d1oywa3          14 KFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG   93 (200)
T ss_dssp             CSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTT
T ss_pred             CCcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhc
Confidence            34588899999988878899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcEEEeccCCCCcccceecC
Q 042003          224 MDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       224 idip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +|+|++++|||||+|+|+.+|+||+
T Consensus        94 iD~p~v~~VI~~~~P~~~~~y~qr~  118 (200)
T d1oywa3          94 INKPNVRFVVHFDIPRNIESYYQET  118 (200)
T ss_dssp             TCCTTCCEEEESSCCSSHHHHHHHH
T ss_pred             cCCCCCCEEEECCCccchHHHHHHh
Confidence            9999999999999999999999985

>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=99.91  E-value=1.3e-24  Score=157.44  Aligned_cols=89  Identities=28%  Similarity=0.410  Sum_probs=85.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD  239 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~  239 (248)
                      +.+++|||+++.+++.+++.|+..|+++..+||+|++.+|.++++.|++|+.+|||||+++++|+|+|++++||+||+|.
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p~  110 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADK  110 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEEETTTTS
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEEEecCCc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999995


Q ss_pred             -----CcccceecC
Q 042003          240 -----SGAAYIHRI  248 (248)
Q Consensus       240 -----~~~~~~qri  248 (248)
                           |..+|+||+
T Consensus       111 ~~~~~s~~~yi~R~  124 (181)
T d1t5la2         111 EGFLRSERSLIQTI  124 (181)
T ss_dssp             CSGGGSHHHHHHHH
T ss_pred             ccccccHHHHHHHH
Confidence                 678889984

>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=99.90  E-value=3e-24  Score=153.14  Aligned_cols=89  Identities=28%  Similarity=0.404  Sum_probs=84.8

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFPD  239 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p~  239 (248)
                      ++++||||++++.|+.+++.|++.|+++..+||+|++.+|+++++.|++|+..|||||+++++|+|+|++++||+|++|.
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~~~  110 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADK  110 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTS
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEecccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             Cc-----ccceecC
Q 042003          240 SG-----AAYIHRI  248 (248)
Q Consensus       240 ~~-----~~~~qri  248 (248)
                      +.     .+|+||+
T Consensus       111 ~~~~~~~~~~iq~~  124 (174)
T d1c4oa2         111 EGFLRSERSLIQTI  124 (174)
T ss_dssp             CSGGGSHHHHHHHH
T ss_pred             ccccchhHHHHHHh
Confidence            54     6689874

>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=99.88  E-value=6.9e-24  Score=167.74  Aligned_cols=211  Identities=13%  Similarity=0.094  Sum_probs=132.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC-cc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NL   79 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~-~~   79 (248)
                      ||.|+++.++.+........         ..........++++||+.+...... ...+.+++++|+||||++..++ .+
T Consensus        50 La~q~~~~l~~~~~~~~~~~---------~~~~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~~~~~  119 (305)
T d2bmfa2          50 VAAEMEEALRGLPIRYQTPA---------IRAEHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPASIAA  119 (305)
T ss_dssp             HHHHHHHHTTTSCCBCCC-----------------CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHHHHHH
T ss_pred             HHHHHHHHHhcCCcceeeeE---------EeecccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchhhHHH
Confidence            57777776665443322111         1122334578999999988776654 4457899999999999987654 12


Q ss_pred             cccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEcccccccccceeEEEEcCCchhHHHHHHHHHhccC
Q 042003           80 LKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVGRKNTASESIKQKLVFAGSEEGKLLALRQSFAESL  159 (248)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  159 (248)
                      ...+..+.   .....+++++|||++........  ...+.... . ....            .. .+.. ....+... 
T Consensus       120 ~~~l~~~~---~~~~~~~v~~SAT~~~~~~~~~~--~~~~~~~~-~-~~~~------------~~-~~~~-~~~~~~~~-  177 (305)
T d2bmfa2         120 RGYISTRV---EMGEAAGIFMTATPPGSRDPFPQ--SNAPIMDE-E-REIP------------ER-SWNS-GHEWVTDF-  177 (305)
T ss_dssp             HHHHHHHH---HHTSCEEEEECSSCTTCCCSSCC--CSSCEEEE-E-CCCC------------CS-CCSS-CCHHHHSS-
T ss_pred             HHHHHHhh---ccccceEEEeecCCCcceeeecc--cCCcceEE-E-Eecc------------HH-HHHH-HHHHHHhh-
Confidence            22222222   23567899999998753221100  00011110 0 0000            00 0000 11122222 


Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEec----
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINY----  235 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~----  235 (248)
                      +++++|||+++++++.+++.|++.++++..+||+++...    ...|++|..+++|+|+++++|+|++ +++||.+    
T Consensus       178 ~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~  252 (305)
T d2bmfa2         178 KGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCM  252 (305)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEE
T ss_pred             CCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCce
Confidence            689999999999999999999999999999999986544    4578899999999999999999995 6666533    


Q ss_pred             ------c----------CCCCcccceecC
Q 042003          236 ------D----------FPDSGAAYIHRI  248 (248)
Q Consensus       236 ------~----------~p~~~~~~~qri  248 (248)
                            +          .|.|..+|+||+
T Consensus       253 ~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~  281 (305)
T d2bmfa2         253 KPVILTDGEERVILAGPMPVTHSSAAQRR  281 (305)
T ss_dssp             EEEEECSSSCEEEEEEEEECCHHHHHHHH
T ss_pred             eeeEecCCCCceEEeccccCCHHHHhhhh
Confidence                  3          345677888874

>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=99.82  E-value=4.4e-21  Score=143.79  Aligned_cols=122  Identities=26%  Similarity=0.316  Sum_probs=105.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++++++..+ .++..++|+.   .+...+..+++|+|+||+++.+++..+...+++++++|+||||.+++.+
T Consensus        97 La~Qi~~~~~~l~~~~~-i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~  175 (222)
T d2j0sa1          97 LAVQIQKGLLALGDYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG  175 (222)
T ss_dssp             HHHHHHHHHHHHTTTTT-CCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHhCccc-eeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhhhcC
Confidence            68999999999999988 4444444444   4444556789999999999999999999999999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVG  125 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  125 (248)
                       |...+..+++. .+...|++++|||+++...++.+.++.+|..+.+.
T Consensus       176 -f~~~i~~I~~~-l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         176 -FKEQIYDVYRY-LPPATQVVLISATLPHEILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             -THHHHHHHHTT-SCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             -cHHHHHHHHHh-CCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEEe
Confidence             99999999998 56788999999999999999999999999877543

>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=99.81  E-value=3.3e-20  Score=137.80  Aligned_cols=120  Identities=22%  Similarity=0.270  Sum_probs=103.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++.+.+......+....|+.   .....+..+++|+|+||+++.+++..+...+++++++|+||||.+++.+
T Consensus        83 l~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~  162 (206)
T d1veca_          83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD  162 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT
T ss_pred             hhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEeccccccccc
Confidence            5789999999988766545555555555   4445567889999999999999999999999999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEE
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRV  122 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~  122 (248)
                       |...+..+++. .+.+.|++++|||+++...++.+.++.+|..+
T Consensus       163 -f~~~i~~I~~~-~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         163 -FVQIMEDIILT-LPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             -THHHHHHHHHH-SCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             -hHHHHHHHHHh-CCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence             99999999998 46778999999999999999999999998764

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=9.6e-20  Score=136.29  Aligned_cols=123  Identities=24%  Similarity=0.307  Sum_probs=103.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++++.+..+........+..   .......+.++|+|+||+++.+++.++...+++++++|+||||.+.+.+
T Consensus        92 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~~~  171 (218)
T d2g9na1          92 LAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG  171 (218)
T ss_dssp             HHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTT
T ss_pred             hhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecchhhcCc
Confidence            6889999999999999855555444444   2233344578999999999999999988899999999999999999988


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEEc
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIVG  125 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  125 (248)
                       |...+..+++.+ +.+.|++++|||+++...++.+.++.+|..+.+.
T Consensus       172 -f~~~~~~Il~~~-~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         172 -FKDQIYDIFQKL-NSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             -CHHHHHHHHHHS-CTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             -hHHHHHHHHHhC-CCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence             999999999984 5678999999999999999999999999887654

>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=99.80  E-value=8.8e-21  Score=131.01  Aligned_cols=82  Identities=26%  Similarity=0.329  Sum_probs=75.7

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEecc--
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYD--  236 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~--  236 (248)
                      .++++||||+|++.|+.+++.|+..++++..+|++|+.+       .|++|+.++||||+++++|+| |+++.|||++  
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~  105 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTS  105 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEE
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhh-------hhhhhhcceeehhHHHHhccc-cccceEEEEEec
Confidence            368999999999999999999999999999999999854       478899999999999999999 9999999854  


Q ss_pred             --CCCCcccceecC
Q 042003          237 --FPDSGAAYIHRI  248 (248)
Q Consensus       237 --~p~~~~~~~qri  248 (248)
                        +|.++..|+||+
T Consensus       106 ~~~P~~~~~y~qr~  119 (138)
T d1jr6a_         106 DGKPQDAVSRTQRR  119 (138)
T ss_dssp             TTEECCHHHHHHHH
T ss_pred             CCCCCCHHHHHhHh
Confidence              699999999995

>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=99.80  E-value=2.4e-20  Score=145.80  Aligned_cols=103  Identities=31%  Similarity=0.434  Sum_probs=89.2

Q ss_pred             hHHHHHHHHH----hccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEec--------CCCHHHHHHHHHHhhcCCceE
Q 042003          146 GKLLALRQSF----AESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHS--------DLSQTQRENAVDDFRAGKTWV  213 (248)
Q Consensus       146 ~~~~~l~~~~----~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~--------~~~~~~r~~~~~~f~~g~~~i  213 (248)
                      .|.+.+.+++    ....+.++||||+++..++.+++.|.+.++++..+||        +++..+|..+++.|++|+.+|
T Consensus       143 pK~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~v  222 (286)
T d1wp9a2         143 PKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNV  222 (286)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSE
T ss_pred             cHHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcE
Confidence            3555555554    3455789999999999999999999999999988866        566678999999999999999


Q ss_pred             EEEecccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          214 LIATDVIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       214 lv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      ||||+++++|+|+|++++||+||+|+|+.+|+||+
T Consensus       223 Lv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~  257 (286)
T d1wp9a2         223 LVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRR  257 (286)
T ss_dssp             EEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHH
T ss_pred             EEEccceeccccCCCCCEEEEeCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999984

>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=99.79  E-value=6.8e-20  Score=136.43  Aligned_cols=119  Identities=28%  Similarity=0.377  Sum_probs=100.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++.+....+ ..+....|+.   .+.. ...+++|+|+||+++.+++.++.+.+++++++|+||||.+.+.+
T Consensus        84 l~~q~~~~~~~~~~~~~-~~v~~~~g~~~~~~~~~-~l~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~  161 (208)
T d1hv8a1          84 LAIQVADEIESLKGNKN-LKIAKIYGGKAIYPQIK-ALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG  161 (208)
T ss_dssp             HHHHHHHHHHHHHCSSC-CCEEEECTTSCHHHHHH-HHHTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTT
T ss_pred             cchhhhhhhhhhcccCC-eEEEEeeCCCChHHHHH-hcCCCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCC
Confidence            57899999999998888 4555555554   2222 23479999999999999999998899999999999999999887


Q ss_pred             cccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEE
Q 042003           78 NLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVI  123 (248)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  123 (248)
                       +...+..+++. .+.++|++++|||+++...++++++++++..+.
T Consensus       162 -~~~~i~~I~~~-~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~  205 (208)
T d1hv8a1         162 -FIKDVEKILNA-CNKDKRILLFSATMPREILNLAKKYMGDYSFIK  205 (208)
T ss_dssp             -THHHHHHHHHT-SCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEE
T ss_pred             -ChHHHHHHHHh-CCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEE
Confidence             88889999988 456789999999999999999999999887664

>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=99.79  E-value=6.4e-20  Score=136.35  Aligned_cols=122  Identities=23%  Similarity=0.318  Sum_probs=102.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh----hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV----RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEV   76 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~   76 (248)
                      ||.|+++.++.+....+..++...+|+.    .........++|+|+||+++.+++.++.+.+++++++|+||||.+++.
T Consensus        81 L~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~  160 (207)
T d1t6na_          81 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  160 (207)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSS
T ss_pred             hhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhc
Confidence            5889999999999987756666666665    223334567999999999999999998889999999999999999875


Q ss_pred             CcccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEE
Q 042003           77 GNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVI  123 (248)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  123 (248)
                      ..+...+..+.+. .+...|++++|||+++...++.+.++++|..+.
T Consensus       161 ~~~~~~i~~I~~~-~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~  206 (207)
T d1t6na_         161 LDMRRDVQEIFRM-TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  206 (207)
T ss_dssp             HHHHHHHHHHHHT-SCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             CCcHHHHHHHHHh-CCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEe
Confidence            2388888888888 567889999999999999999999999997764

>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=99.77  E-value=3.8e-20  Score=141.59  Aligned_cols=94  Identities=18%  Similarity=0.354  Sum_probs=81.4

Q ss_pred             chhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEe----cc
Q 042003          144 EEGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIAT----DV  219 (248)
Q Consensus       144 ~~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T----~~  219 (248)
                      ++++...+.++++.. +.++||||++++.++.+++.|+..      +||++++++|.++++.|++|+++|||||    +.
T Consensus        10 ~~~~~~~l~~~l~~~-~~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v   82 (248)
T d1gkub2          10 NDESISTLSSILEKL-GTGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGT   82 (248)
T ss_dssp             SCCCTTTTHHHHTTS-CSCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEEEECC----
T ss_pred             CchHHHHHHHHHHHh-CCCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccch
Confidence            456788889999876 578999999999999999999864      7999999999999999999999999999    67


Q ss_pred             cccCCCCCC-CcEEEeccCCCCcccceecC
Q 042003          220 IARGMDFKG-VNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       220 ~~~Gidip~-~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +++|+|+|+ +++|||||+|+    |.||+
T Consensus        83 ~~rGlDip~~v~~VI~~d~P~----~~~r~  108 (248)
T d1gkub2          83 LVRGLDLPERIRFAVFVGCPS----FRVTI  108 (248)
T ss_dssp             --CCSCCTTTCCEEEEESCCE----EEEEC
T ss_pred             hhhccCccccccEEEEeCCCc----chhhh
Confidence            899999996 99999999995    77764

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.77  E-value=5e-19  Score=131.84  Aligned_cols=121  Identities=24%  Similarity=0.346  Sum_probs=97.9

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNL   79 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~   79 (248)
                      |+.|+++.+..+.............+.. .......++++|+|+||+++.+++..+.+.+++++++|+||||.+++.+ |
T Consensus        90 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~~-f  168 (212)
T d1qdea_          90 LALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG-F  168 (212)
T ss_dssp             HHHHHHHHHHHHTTTSCCCEEEECC----------CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTT-C
T ss_pred             HhhhhhhhhcccccccccceeeEeeccchhHHHHHhcCCcEEEECCCccccccccCceecCcceEEeehhhhhhcccc-h
Confidence            5789999999998888744444433333 2222233478999999999999999999999999999999999999988 9


Q ss_pred             cccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEE
Q 042003           80 LKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVI  123 (248)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  123 (248)
                      ...+..+++. .+..+|++++|||+++...++++.++.+|..+.
T Consensus       169 ~~~v~~I~~~-~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~  211 (212)
T d1qdea_         169 KEQIYQIFTL-LPPTTQVVLLSATMPNDVLEVTTKFMRNPVRIL  211 (212)
T ss_dssp             HHHHHHHHHH-SCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC
T ss_pred             HHHHHHHHHh-CCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            9999999998 567889999999999999999999999997763

>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=99.77  E-value=4e-20  Score=137.04  Aligned_cols=99  Identities=21%  Similarity=0.387  Sum_probs=91.9

Q ss_pred             hhHHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCC
Q 042003          145 EGKLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGM  224 (248)
Q Consensus       145 ~~~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gi  224 (248)
                      ..|...+.++++.+.+.++||||++...++.+++.|.     +..+||+++.++|+++++.|++|+.+|||||+++++|+
T Consensus        78 ~~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gi  152 (200)
T d2fwra1          78 KNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGI  152 (200)
T ss_dssp             SHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSS
T ss_pred             HHHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhccc
Confidence            3588899999998878899999999999999998884     44579999999999999999999999999999999999


Q ss_pred             CCCCCcEEEeccCCCCcccceecC
Q 042003          225 DFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       225 dip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      |+|.+++||++++|+|+.+|+||+
T Consensus       153 dl~~~~~vi~~~~~~s~~~~~Q~i  176 (200)
T d2fwra1         153 DVPDANVGVIMSGSGSAREYIQRL  176 (200)
T ss_dssp             CSCCBSEEEEECCSSCCHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCHHHHHHHH
Confidence            999999999999999999999985

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.76  E-value=3.9e-19  Score=132.14  Aligned_cols=120  Identities=26%  Similarity=0.287  Sum_probs=102.9

Q ss_pred             cchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCc
Q 042003            2 ATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGN   78 (248)
Q Consensus         2 ~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~   78 (248)
                      +.|....+..+....+ .++...+|+.   .....+..+++|+|+||+++.+++..+.+.+++++++|+||||.+.+.+ 
T Consensus        82 ~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~-  159 (206)
T d1s2ma1          82 ALQTSQVVRTLGKHCG-ISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD-  159 (206)
T ss_dssp             HHHHHHHHHHHTTTTT-CCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHH-
T ss_pred             hhhhhhhhhhcccccC-eeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhh-
Confidence            5677888888888888 5555555554   4445567789999999999999999999999999999999999999987 


Q ss_pred             ccccchhHhhhCCCccceeEEEEeecCchHHHHHHHhcCCcEEEEE
Q 042003           79 LLKHIDPVVKACSNPSIVRSLFSATLPDFVEELARSIMHDAVRVIV  124 (248)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  124 (248)
                      |...+..+.+. .+..+|++++|||+|+...++.++++.+|..+.+
T Consensus       160 f~~~v~~I~~~-l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~  204 (206)
T d1s2ma1         160 FKTIIEQILSF-LPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL  204 (206)
T ss_dssp             HHHHHHHHHTT-SCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESC
T ss_pred             hHHHHHHHHHh-CCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999998 4677899999999999999999999999977643

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.75  E-value=1e-18  Score=132.49  Aligned_cols=123  Identities=27%  Similarity=0.414  Sum_probs=103.5

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      ||.|+++.++.+++..+ .++....|+.   .+......+++|+|+||+++.+++..+...+++++++|+||||.+++.+
T Consensus       110 l~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~~lViDEaD~ll~~~  188 (238)
T d1wrba1         110 LAIQILSESQKFSLNTP-LRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMG  188 (238)
T ss_dssp             HHHHHHHHHHHHHTTSS-CCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTT
T ss_pred             hhcchheeeeecccCCC-cEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccccceeeeehhhhhhhhc
Confidence            68899999999999998 4455555544   3344566789999999999999999998999999999999999999887


Q ss_pred             cccccchhHhhhCC---CccceeEEEEeecCchHHHHHHHhcCCcEEEEEc
Q 042003           78 NLLKHIDPVVKACS---NPSIVRSLFSATLPDFVEELARSIMHDAVRVIVG  125 (248)
Q Consensus        78 ~~~~~~~~~~~~~~---~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  125 (248)
                       |...+..+++...   ..++|++++|||+++....+.+.++++|..+.++
T Consensus       189 -f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~vg  238 (238)
T d1wrba1         189 -FEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG  238 (238)
T ss_dssp             -CHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             -cHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEeC
Confidence             9999999887643   2367999999999999999999999999877553

>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=99.73  E-value=1.3e-18  Score=128.34  Aligned_cols=100  Identities=24%  Similarity=0.278  Sum_probs=85.7

Q ss_pred             HHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC------------------------------CCeeEEEecCCCH
Q 042003          147 KLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD------------------------------GIRAGVIHSDLSQ  196 (248)
Q Consensus       147 ~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~------------------------------~~~v~~~~~~~~~  196 (248)
                      ..+.+.+.+++  ++++||||+|++.|+.++..|...                              ..+++++||+|++
T Consensus        29 ~~~l~~~~i~~--~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          29 FEELVEECVAE--NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHHHHT--TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHHHc--CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            34455566665  579999999999999888887531                              1248999999999


Q ss_pred             HHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEe-------ccCCCCcccceecC
Q 042003          197 TQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVIN-------YDFPDSGAAYIHRI  248 (248)
Q Consensus       197 ~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~-------~~~p~~~~~~~qri  248 (248)
                      ++|..+++.|++|.+++||||+++++|+|+|..++||+       ++.|.+..+|+||+
T Consensus       107 ~~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~  165 (201)
T d2p6ra4         107 GQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMA  165 (201)
T ss_dssp             HHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHH
T ss_pred             hhHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHh
Confidence            99999999999999999999999999999999999996       77888999999974

>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=99.67  E-value=1e-16  Score=119.29  Aligned_cols=93  Identities=26%  Similarity=0.435  Sum_probs=83.2

Q ss_pred             hcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecCchHH
Q 042003           30 STDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVE  109 (248)
Q Consensus        30 ~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  109 (248)
                      +......+++|+|+||+++..++.+....+++++++|+||||.+.+++ |...+..+.+. .+++.|++++|||+|+...
T Consensus       116 ~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~~~-f~~~v~~I~~~-~~~~~Q~il~SATl~~~v~  193 (209)
T d1q0ua_         116 ALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMG-FITDVDQIAAR-MPKDLQMLVFSATIPEKLK  193 (209)
T ss_dssp             TTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTT-CHHHHHHHHHT-SCTTCEEEEEESCCCGGGH
T ss_pred             HHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeecccccccc-cHHHHHHHHHH-CCCCCEEEEEEccCCHHHH
Confidence            344566789999999999999999988899999999999999999998 99999999988 4678999999999999999


Q ss_pred             HHHHHhcCCcEEEEE
Q 042003          110 ELARSIMHDAVRVIV  124 (248)
Q Consensus       110 ~~~~~~~~~~~~~~~  124 (248)
                      ++++.++.+|..+.+
T Consensus       194 ~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         194 PFLKKYMENPTFVHV  208 (209)
T ss_dssp             HHHHHHCSSCEEEEC
T ss_pred             HHHHHHCCCCEEEEe
Confidence            999999999887653

>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=99.65  E-value=8.7e-18  Score=127.61  Aligned_cols=89  Identities=19%  Similarity=0.180  Sum_probs=80.1

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHH----------HHHHHHhhcCCceEEEEeccccc---CCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQR----------ENAVDDFRAGKTWVLIATDVIAR---GMDF  226 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r----------~~~~~~f~~g~~~ilv~T~~~~~---Gidi  226 (248)
                      ++++||||+|+++|+.+++.|++.|+++..+|++++++.|          .+.++.|.+|+.+++|+|+++++   |+|+
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giDi  115 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSL  115 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECCC
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCCC
Confidence            6799999999999999999999999999999999999876          46788999999999999999988   7788


Q ss_pred             CCCcEEEeccCCCCcccceecC
Q 042003          227 KGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       227 p~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +.+.+||+++.|.|+.+|+||+
T Consensus       116 d~V~~VI~~d~P~SvesyIQRi  137 (299)
T d1a1va2         116 DPTFTIETTTLPQDAVSRTQRR  137 (299)
T ss_dssp             SSSCEEEEEEEECBHHHHHHHH
T ss_pred             CcceEEEeCCCCCCHHHHHhhc
Confidence            8888999999999999999995

>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=99.62  E-value=1.5e-15  Score=110.23  Aligned_cols=91  Identities=20%  Similarity=0.234  Sum_probs=80.9

Q ss_pred             HHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcC--CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCC
Q 042003          147 KLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFD--GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGM  224 (248)
Q Consensus       147 ~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gi  224 (248)
                      ....+...++.  ++++.+.||.++..+.+++.+.+.  +.++.++||.|+.+++++++..|.+|+++|||||++++.|+
T Consensus        20 i~~~I~~El~r--GgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGi   97 (211)
T d2eyqa5          20 VREAILREILR--GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGI   97 (211)
T ss_dssp             HHHHHHHHHTT--TCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGS
T ss_pred             HHHHHHHHHHc--CCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhcc
Confidence            34445555544  789999999999999999999764  77999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEeccCCC
Q 042003          225 DFKGVNCVINYDFPD  239 (248)
Q Consensus       225 dip~~~~Vi~~~~p~  239 (248)
                      |+|+++++|..+...
T Consensus        98 DvpnA~~iiI~~a~r  112 (211)
T d2eyqa5          98 DIPTANTIIIERADH  112 (211)
T ss_dssp             CCTTEEEEEETTTTS
T ss_pred             CCCCCcEEEEecchh
Confidence            999999999998875

>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=99.62  E-value=3.2e-17  Score=120.13  Aligned_cols=87  Identities=25%  Similarity=0.416  Sum_probs=69.1

Q ss_pred             CCCEEEEecchHHHH--------HHHHHhhcC---CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCC
Q 042003          160 NPPVLIFVQSKERAK--------ELYGELAFD---GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~--------~l~~~L~~~---~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~  228 (248)
                      ++++.+.||.+++.+        ..++.|.+.   ++++..+||.|++++|++++++|++|+++|||||+++++|||+|+
T Consensus        29 g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtViE~GIDip~  108 (206)
T d1gm5a4          29 GGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPR  108 (206)
T ss_dssp             SCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTT
T ss_pred             CCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehhhhccccccC
Confidence            678888898765444        334455432   678899999999999999999999999999999999999999999


Q ss_pred             CcEEEeccCCCCccccee
Q 042003          229 VNCVINYDFPDSGAAYIH  246 (248)
Q Consensus       229 ~~~Vi~~~~p~~~~~~~q  246 (248)
                      ++++|++++|..--+++|
T Consensus       109 a~~iii~~a~~fglsqlh  126 (206)
T d1gm5a4         109 ANVMVIENPERFGLAQLH  126 (206)
T ss_dssp             CCEEEBCSCSSSCTTHHH
T ss_pred             CcEEEEEccCCccHHHHH
Confidence            999999999985444443

>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=99.49  E-value=9.7e-14  Score=105.28  Aligned_cols=104  Identities=16%  Similarity=0.237  Sum_probs=86.4

Q ss_pred             hhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcC-CCeeEEEecCCCHHHHHHHHHHhhcCC-ceEE-EEecc
Q 042003          145 EGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFD-GIRAGVIHSDLSQTQRENAVDDFRAGK-TWVL-IATDV  219 (248)
Q Consensus       145 ~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~-~~~v~~~~~~~~~~~r~~~~~~f~~g~-~~il-v~T~~  219 (248)
                      ..|+..+.+++...  .+.|+||||......+.+...+.+. +.++..+||+++.++|+++++.|.++. ..++ ++|.+
T Consensus        68 S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~  147 (244)
T d1z5za1          68 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKA  147 (244)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCT
T ss_pred             hhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccc
Confidence            35888888887642  4789999999999999998888654 888999999999999999999998764 5565 55578


Q ss_pred             cccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          220 IARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       220 ~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      .+.|+|++.+++||++++|||+..+.|++
T Consensus       148 ~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~  176 (244)
T d1z5za1         148 GGFGINLTSANRVIHFDRWWNPAVEDQAT  176 (244)
T ss_dssp             TCCCCCCTTCSEEEECSCCSCTTTC----
T ss_pred             cccccccchhhhhhhcCchhhhHHHhhhc
Confidence            99999999999999999999999999974

>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=99.46  E-value=7.7e-14  Score=110.59  Aligned_cols=104  Identities=14%  Similarity=0.163  Sum_probs=91.2

Q ss_pred             hhHHHHHHHHHhc---cCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCc---eEEEEec
Q 042003          145 EGKLLALRQSFAE---SLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKT---WVLIATD  218 (248)
Q Consensus       145 ~~~~~~l~~~~~~---~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~---~ilv~T~  218 (248)
                      ..|+..+.+++..   ..+.|+|||++.......+.+.|...++++..++|+++..+|..+++.|+++..   .+|++|.
T Consensus       100 S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~  179 (346)
T d1z3ix1         100 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK  179 (346)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG
T ss_pred             CHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecch
Confidence            3577777666643   346799999999999999999999999999999999999999999999998654   3678889


Q ss_pred             ccccCCCCCCCcEEEeccCCCCcccceecC
Q 042003          219 VIARGMDFKGVNCVINYDFPDSGAAYIHRI  248 (248)
Q Consensus       219 ~~~~Gidip~~~~Vi~~~~p~~~~~~~qri  248 (248)
                      +.+.|+|++.+++||+||++||+..+.|++
T Consensus       180 agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~  209 (346)
T d1z3ix1         180 AGGCGLNLIGANRLVMFDPDWNPANDEQAM  209 (346)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHH
T ss_pred             hhhhccccccceEEEEecCCCccchHhHhh
Confidence            999999999999999999999999888863

>d2p6ra3 c.37.1.19 (A:1-202) 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=99.37  E-value=4.1e-13  Score=98.86  Aligned_cols=112  Identities=25%  Similarity=0.186  Sum_probs=80.8

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+.+.++++.+...  .+....|...........++++++||..+...+.+....+.+++++|+||+|.+.++. +.
T Consensus        80 L~~q~~~~~~~~~~~~~--~v~~~~~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~-r~  156 (202)
T d2p6ra3          80 LAGEKYESFKKWEKIGL--RIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEK-RG  156 (202)
T ss_dssp             HHHHHHHHHTTTTTTTC--CEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTT-TH
T ss_pred             HHHHHHHHHHHHhhccc--cceeeccCcccccccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccc-cc
Confidence            56788888888776553  3444445545555566689999999999999998888888999999999999987765 33


Q ss_pred             ccchhHhhhC--CCccceeEEEEeecCchHHHHHHHhc
Q 042003           81 KHIDPVVKAC--SNPSIVRSLFSATLPDFVEELARSIM  116 (248)
Q Consensus        81 ~~~~~~~~~~--~~~~~~~i~~SAT~~~~~~~~~~~~~  116 (248)
                      ..+..++...  ..++.|+++||||+++ .+++.+++.
T Consensus       157 ~~~~~~l~~i~~~~~~~~~l~lSATl~n-~~~~~~~l~  193 (202)
T d2p6ra3         157 ATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEWLD  193 (202)
T ss_dssp             HHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHHHTT
T ss_pred             hHHHHHHHHHHhcCCCCcEEEEcCCCCc-HHHHHHHcC
Confidence            3232222211  2456899999999976 567766663

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.31  E-value=1.4e-12  Score=95.74  Aligned_cols=109  Identities=15%  Similarity=0.131  Sum_probs=77.2

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNL   79 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~   79 (248)
                      |+.|+++.++++....+........+.. .........++++++||+.+.+.+..+...+++++++|+||||++......
T Consensus        64 L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~  143 (200)
T d1wp9a1          64 LVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAY  143 (200)
T ss_dssp             HHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHH
T ss_pred             HHHHHHHHHHHhhcccccceeeeecccchhHHHHhhhcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcchhH
Confidence            5789999999998877744443333322 333334456799999999999999998888999999999999998765523


Q ss_pred             cccchhHhhhCCCccceeEEEEeecCchHHHH
Q 042003           80 LKHIDPVVKACSNPSIVRSLFSATLPDFVEEL  111 (248)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~  111 (248)
                      ......+...  ..++++++||||++......
T Consensus       144 ~~~~~~~~~~--~~~~~~l~~SATp~~~~~~~  173 (200)
T d1wp9a1         144 VFIAREYKRQ--AKNPLVIGLTASPGSTPEKI  173 (200)
T ss_dssp             HHHHHHHHHH--CSSCCEEEEESCSCSSHHHH
T ss_pred             HHHHHHHHhc--CCCCcEEEEEecCCCcHHHH
Confidence            3333333332  34578999999986544433

>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=99.31  E-value=7.9e-13  Score=101.98  Aligned_cols=74  Identities=19%  Similarity=0.242  Sum_probs=62.9

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCCCCCcEEEeccCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDFKGVNCVINYDFP  238 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidip~~~~Vi~~~~p  238 (248)
                      +++++|||+++.+++.+++.|++.|.+|..+||.+..++++    .|++|+.++||||+++++|+|+ ++++||+.+.+
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~  109 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTA  109 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCce
Confidence            68999999999999999999999999999999999977754    4678999999999999999999 59999998875

>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=99.09  E-value=6e-11  Score=89.63  Aligned_cols=100  Identities=16%  Similarity=0.100  Sum_probs=68.4

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh-------hcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR-------STDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.++++....+ ..+.+..|+..       ...+..+.++|+|||-     .+....+.+++++++||||-|..
T Consensus       144 La~Qh~~~~~~~f~~~~-~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGTh-----sl~~~~~~f~~LglviiDEqH~f  217 (264)
T d1gm5a3         144 LAIQHYRRTVESFSKFN-IHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTH-----ALIQEDVHFKNLGLVIIDEQHRF  217 (264)
T ss_dssp             HHHHHHHHHHHHHTCSS-CCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECT-----THHHHCCCCSCCCEEEEESCCCC
T ss_pred             hhHHHHHHHHHhhhhcc-ccceeeccccchHHHHHHHHHHHCCCCCEEEeeh-----HHhcCCCCccccceeeecccccc
Confidence            68999999999999888 45555555441       2234456799999994     44455666889999999999997


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR  113 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~  113 (248)
                      +-..  +.    .+.. ....+.++.||||+.++...+..
T Consensus       218 gv~Q--r~----~l~~-~~~~~~~l~~SATPiprtl~~~~  250 (264)
T d1gm5a3         218 GVKQ--RE----ALMN-KGKMVDTLVMSATPIPRSMALAF  250 (264)
T ss_dssp             -------C----CCCS-SSSCCCEEEEESSCCCHHHHHHH
T ss_pred             chhh--HH----HHHH-hCcCCCEEEEECCCCHHHHHHHH
Confidence            5332  11    1122 33457889999999886655543

>d1oywa2 c.37.1.19 (A:1-206) 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=99.09  E-value=3.5e-11  Score=88.53  Aligned_cols=117  Identities=15%  Similarity=0.138  Sum_probs=75.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh---hhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV---RSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG   77 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~   77 (248)
                      |+.|..+.++.++.... .......+..   ..........+++++||+.+............+++++|+||||++.+++
T Consensus        77 L~~q~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~  155 (206)
T d1oywa2          77 LMKDQVDQLQANGVAAA-CLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWG  155 (206)
T ss_dssp             HHHHHHHHHHHTTCCEE-EECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTS
T ss_pred             hhhhHHHHHHhhccccc-ccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeeeccc
Confidence            46788888877765432 1111111111   2223344578999999998866555555567889999999999998876


Q ss_pred             cc-cc---cchhHhhhCCCccceeEEEEeecCchHH-HHHHHh-cCCcE
Q 042003           78 NL-LK---HIDPVVKACSNPSIVRSLFSATLPDFVE-ELARSI-MHDAV  120 (248)
Q Consensus        78 ~~-~~---~~~~~~~~~~~~~~~~i~~SAT~~~~~~-~~~~~~-~~~~~  120 (248)
                      .. ..   .+..+...+  +++|++++|||+++... ++..++ +.+|.
T Consensus       156 ~~~~~~~~~~~~l~~~~--~~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         156 HDFRPEYAALGQLRQRF--PTLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             SCCCHHHHGGGGHHHHC--TTSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             cchHHHHHHHHHHHHhC--CCCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            21 11   233344442  46899999999998765 456654 56764

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.07  E-value=9.3e-12  Score=93.77  Aligned_cols=111  Identities=14%  Similarity=0.124  Sum_probs=68.3

Q ss_pred             CcchHHHHHHHhhcCCCcEE---EEcccchh---hhc--ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQI---KLMKKELV---RST--DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~---~~~~~~~~---~~~--~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~   72 (248)
                      |+.|+++.++++.+..+...   .....+..   ...  .....+++|+|+||+++.+.    ...+++++++|+||+|.
T Consensus        98 La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~----~~~~~~~~~vVvDE~d~  173 (237)
T d1gkub1          98 LVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKH----YRELGHFDFIFVDDVDA  173 (237)
T ss_dssp             HHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHC----STTSCCCSEEEESCHHH
T ss_pred             HHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHh----hhhcCCCCEEEEEChhh
Confidence            68899999999988776321   11112211   111  12334689999999977543    23467899999999999


Q ss_pred             ccccCc----------ccccchhHhhhCCCccceeEEEEeecCchHHH-HHHHhc
Q 042003           73 LFEVGN----------LLKHIDPVVKACSNPSIVRSLFSATLPDFVEE-LARSIM  116 (248)
Q Consensus        73 ~~~~~~----------~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~-~~~~~~  116 (248)
                      +++.+.          |...+...... .....|++++|||+++..+. +.+.++
T Consensus       174 ~l~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~~~~i~~SAT~~~~~~~~l~r~ll  227 (237)
T d1gkub1         174 ILKASKNVDKLLHLLGFHYDLKTKSWV-GEARGCLMVSTATAKKGKKAELFRQLL  227 (237)
T ss_dssp             HHTSTHHHHHHHHHTTEEEETTTTEEE-ECCSSEEEECCCCSCCCTTHHHHHHHH
T ss_pred             hhhcccchhHHHHhcCChHHHHHHHhh-CCCCCeEEEEeCCCCcccHHHHHHHHh
Confidence            876431          22222222222 34567899999999865443 334443

>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=99.03  E-value=1.8e-10  Score=85.43  Aligned_cols=100  Identities=18%  Similarity=0.142  Sum_probs=71.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhh-------hcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVR-------STDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKL   73 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~   73 (248)
                      ||.|+++.++++...++ ..+.++.|...       ...+..+..+|+|+|     +.+....+.+++++++|+||-|..
T Consensus       116 La~Q~~~~~~~~~~~~~-~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGt-----hs~l~~~~~f~~LgLiIiDEeH~f  189 (233)
T d2eyqa3         116 LAQQHYDNFRDRFANWP-VRIEMISRFRSAKEQTQILAEVAEGKIDILIGT-----HKLLQSDVKFKDLGLLIVDEEHRF  189 (233)
T ss_dssp             HHHHHHHHHHHHSTTTT-CCEEEESTTSCHHHHHHHHHHHHTTCCSEEEEC-----THHHHSCCCCSSEEEEEEESGGGS
T ss_pred             hHHHHHHHHHHHHhhCC-CEEEeccCcccchhHHHHHHHHhCCCCCEEEee-----hhhhccCCccccccceeeechhhh
Confidence            68999999999999888 55555555441       224455678999999     455556677899999999999985


Q ss_pred             cccCcccccchhHhhhCCCccceeEEEEeecCchHHHHHH
Q 042003           74 FEVGNLLKHIDPVVKACSNPSIVRSLFSATLPDFVEELAR  113 (248)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~  113 (248)
                      .-.     + ...++. ...++.++.+|||+.|+...+..
T Consensus       190 g~k-----Q-~~~l~~-~~~~~~~l~~SATPiprtl~~~~  222 (233)
T d2eyqa3         190 GVR-----H-KERIKA-MRANVDILTLTATPIPRTLNMAM  222 (233)
T ss_dssp             CHH-----H-HHHHHH-HHTTSEEEEEESSCCCHHHHHHH
T ss_pred             hhH-----H-HHHHHh-hCCCCCEEEEecchhHHHHHHHH
Confidence            422     1 122222 23457899999999986655544

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=98.80  E-value=3e-09  Score=81.66  Aligned_cols=96  Identities=16%  Similarity=0.085  Sum_probs=65.7

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+++.+.+++.... ..+...+++...........+++++|++.+.+.   ....+++++++|+||||+..+.    
T Consensus       169 Lv~Q~~~~f~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~i~i~t~qs~~~~---~~~~~~~f~~VIvDEaH~~~a~----  240 (282)
T d1rifa_         169 LTTQMADDFVDYRLFSH-AMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATGK----  240 (282)
T ss_dssp             HHHHHHHHHHHHTSCCG-GGEEECSTTCSSTTCCCTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCCHH----
T ss_pred             hHHHHHHHHHHhhcccc-ccceeecceecccccccccceEEEEeeehhhhh---cccccCCCCEEEEECCCCCCch----
Confidence            57899999999877665 445555555544455556789999998776433   3345688999999999997543    


Q ss_pred             ccchhHhhhCCCccceeEEEEeecCc
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLPD  106 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~~  106 (248)
                       .+..++..+.. ..-.+++|||++.
T Consensus       241 -~~~~il~~~~~-~~~rlGlTaT~~~  264 (282)
T d1rifa_         241 -SISSIISGLNN-CMFKFGLSGSLRD  264 (282)
T ss_dssp             -HHHHHTTTCTT-CCEEEEECSSCCT
T ss_pred             -hHHHHHHhccC-CCeEEEEEeecCC
Confidence             34445554322 2335899999865

>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=98.74  E-value=2.8e-08  Score=69.34  Aligned_cols=99  Identities=23%  Similarity=0.247  Sum_probs=74.5

Q ss_pred             CCchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          142 GSEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      ...++|++++.+.+...  .+.|+||++.|++.++.+++.|++.+++..+++......+-+-+.++-..  ..|.|||+.
T Consensus        14 ~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~Ag~~--g~VtIATNm   91 (175)
T d1tf5a4          14 RTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQK--GAVTIATNM   91 (175)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTST--TCEEEEETT
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhccCC--CceeehhhH
Confidence            45567888777766532  27899999999999999999999999999999987554333333333333  359999999


Q ss_pred             cccCCCCCCCc--------EEEeccCCCCcc
Q 042003          220 IARGMDFKGVN--------CVINYDFPDSGA  242 (248)
Q Consensus       220 ~~~Gidip~~~--------~Vi~~~~p~~~~  242 (248)
                      +++|.|+.--.        |||....|+|..
T Consensus        92 AGRGtDikl~~~v~~~GGLhVI~t~~~~s~R  122 (175)
T d1tf5a4          92 AGRGTDIKLGEGVKELGGLAVVGTERHESRR  122 (175)
T ss_dssp             SSTTCCCCCCTTSGGGTSEEEEESSCCSSHH
T ss_pred             HHcCCCccchHHHHhCCCcEEEEeccCcchh
Confidence            99999986322        778888888764

>d1yksa1 c.37.1.14 (A:185-324) 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=98.67  E-value=2.2e-09  Score=73.32  Aligned_cols=66  Identities=17%  Similarity=0.049  Sum_probs=44.4

Q ss_pred             CCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccC-cccccchhHhhhCCCccceeEEEEeecC
Q 042003           36 FSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVG-NLLKHIDPVVKACSNPSIVRSLFSATLP  105 (248)
Q Consensus        36 ~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~-~~~~~~~~~~~~~~~~~~~~i~~SAT~~  105 (248)
                      ....+.+.|...+.+... ....+.+++++|+||||++...+ ..+..+..+..   ..+.++++||||+|
T Consensus        74 ~~~~~~~~~~~~l~~~~~-~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~---~~~~~~l~lTATPp  140 (140)
T d1yksa1          74 GREVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR---ANESATILMTATPP  140 (140)
T ss_dssp             SSCCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH---TTSCEEEEECSSCT
T ss_pred             cccchhhhhHHHHHHHHh-ccccccceeEEEEccccccChhhHHHHHHHHHHhh---CCCCCEEEEEcCCC
Confidence            346678888887766543 44557899999999999875443 12222332222   34689999999986

>d1a1va1 c.37.1.14 (A:190-325) 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=98.64  E-value=1.6e-08  Score=68.83  Aligned_cols=91  Identities=12%  Similarity=-0.018  Sum_probs=56.6

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |++|+.+.+.+......   .....+     ........+.++|.+.....   ....+++++++|+||+|++....  .
T Consensus        45 l~~q~~~~~~~~~~~~~---~~~~~~-----~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~vIiDE~H~~~~~~--~  111 (136)
T d1a1va1          45 ATLGFGAYMSKAHGVDP---NIRTGV-----RTITTGSPITYSTYGKFLAD---GGCSGGAYDIIICDECHSTDATS--I  111 (136)
T ss_dssp             HHHHHHHHHHHHHSCCC---EEECSS-----CEECCCCSEEEEEHHHHHHT---TGGGGCCCSEEEEETTTCCSHHH--H
T ss_pred             HHHHHHHHHHHHhhccc---cccccc-----cccccccceEEEeeeeeccc---cchhhhcCCEEEEecccccCHHH--H
Confidence            57788888887655443   111111     11223467889998866444   33457899999999999975432  2


Q ss_pred             ccchhHhhhCC-CccceeEEEEeec
Q 042003           81 KHIDPVVKACS-NPSIVRSLFSATL  104 (248)
Q Consensus        81 ~~~~~~~~~~~-~~~~~~i~~SAT~  104 (248)
                      ..+..+++... .....+++||||+
T Consensus       112 ~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1         112 LGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             HHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             HHHHHHHHHHHHCCCCcEEEEeCCC
Confidence            23444555432 3466889999995

>d2fz4a1 c.37.1.19 (A:24-229) 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=98.25  E-value=2.7e-07  Score=67.18  Aligned_cols=85  Identities=16%  Similarity=0.004  Sum_probs=53.3

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLL   80 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~   80 (248)
                      |+.|+.+.++.++...    +....|.      .....+++++|.+.+......   ..+++++||+||||++.+..   
T Consensus       122 L~~q~~~~~~~~~~~~----~~~~~~~------~~~~~~i~i~t~~~~~~~~~~---~~~~~~lvIiDEaH~~~a~~---  185 (206)
T d2fz4a1         122 LAEQWKERLGIFGEEY----VGEFSGR------IKELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAES---  185 (206)
T ss_dssp             HHHHHHHHHGGGCGGG----EEEESSS------CBCCCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTTT---
T ss_pred             hHHHHHHHHHhhcccc----hhhcccc------cccccccccceehhhhhhhHh---hCCcCCEEEEECCeeCCcHH---
Confidence            4567888877765532    2222221      223467999999887665442   23578899999999975432   


Q ss_pred             ccchhHhhhCCCccceeEEEEeecC
Q 042003           81 KHIDPVVKACSNPSIVRSLFSATLP  105 (248)
Q Consensus        81 ~~~~~~~~~~~~~~~~~i~~SAT~~  105 (248)
                        +..+....  .....+++|||+.
T Consensus       186 --~~~i~~~~--~~~~~lgLTATl~  206 (206)
T d2fz4a1         186 --YVQIAQMS--IAPFRLGLTATFE  206 (206)
T ss_dssp             --HHHHHHTC--CCSEEEEEEESCC
T ss_pred             --HHHHHhcc--CCCcEEEEecCCC
Confidence              34444442  2335689999973

>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=98.14  E-value=6.2e-06  Score=58.52  Aligned_cols=84  Identities=29%  Similarity=0.327  Sum_probs=63.5

Q ss_pred             CCchhHHHHHHHHHhcc--CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc
Q 042003          142 GSEEGKLLALRQSFAES--LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV  219 (248)
Q Consensus       142 ~~~~~~~~~l~~~~~~~--~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~  219 (248)
                      .....|++++.+.+...  .++|+||.+.|++..+.+.+.|.+.+++..+++..-...+-+-+.++=+.|  .|-|||+.
T Consensus        14 ~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAeIIAqAG~~G--aVTIATNM   91 (219)
T d1nkta4          14 KTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNM   91 (219)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETT
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHHHHHhcccCC--cEEeeccc
Confidence            45567887777666532  278999999999999999999999999999999974433322233332223  48899999


Q ss_pred             cccCCCCC
Q 042003          220 IARGMDFK  227 (248)
Q Consensus       220 ~~~Gidip  227 (248)
                      +++|-||-
T Consensus        92 AGRGTDI~   99 (219)
T d1nkta4          92 AGRGTDIV   99 (219)
T ss_dssp             CSTTCCCC
T ss_pred             cCCCCcee
Confidence            99999984

>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=97.89  E-value=3.7e-05  Score=57.38  Aligned_cols=75  Identities=19%  Similarity=0.246  Sum_probs=64.1

Q ss_pred             CCCEEEEecchHHHHHHHHHhh----cCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc-ccCCCCCCCcEEEe
Q 042003          160 NPPVLIFVQSKERAKELYGELA----FDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI-ARGMDFKGVNCVIN  234 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~----~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-~~Gidip~~~~Vi~  234 (248)
                      +.++++.+++.--+.+.++.++    ..+..+..+||+++..+|.+++....+|+.+|+|+|.++ ...+.+.++..||.
T Consensus       132 g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~Lglvii  211 (264)
T d1gm5a3         132 GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVII  211 (264)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEE
T ss_pred             ccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceeee
Confidence            6899999999888887776665    457899999999999999999999999999999999765 55677778887774

>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=97.70  E-value=0.00013  Score=53.36  Aligned_cols=75  Identities=20%  Similarity=0.267  Sum_probs=65.9

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc-ccCCCCCCCcEEEe
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI-ARGMDFKGVNCVIN  234 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~-~~Gidip~~~~Vi~  234 (248)
                      ++++++.+|+..-+.+.++.+++    .+..+..+||.++..+|.++.+.+.+|+.+|+|+|.++ ...+.+++...||.
T Consensus       104 g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiIi  183 (233)
T d2eyqa3         104 HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIV  183 (233)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEE
T ss_pred             CCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCccccccceee
Confidence            78999999999999999888875    47789999999999999999999999999999999765 45677778887764

>d1z3ix2 c.37.1.19 (X:92-389) 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=97.51  E-value=6.7e-05  Score=57.34  Aligned_cols=96  Identities=18%  Similarity=0.133  Sum_probs=55.7

Q ss_pred             cchHHHHHHHhhcCCCcEEEEcccchhhhc----------ccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccc
Q 042003            2 ATQTTRECKKLAKGNKFQIKLMKKELVRST----------DLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEAD   71 (248)
Q Consensus         2 ~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah   71 (248)
                      ..|+.+.++++..... ..+...++.....          .......+++++|.+.+.....  .+...+++++|+||+|
T Consensus       126 ~~qW~~Ei~k~~~~~~-~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH  202 (298)
T d1z3ix2         126 VRNWYNEVGKWLGGRV-QPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGH  202 (298)
T ss_dssp             HHHHHHHHHHHHGGGC-CEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGG
T ss_pred             hHHHHHHHHhhcCCce-eEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh--cccccceeeeeccccc
Confidence            4688888888876532 2333333322111          1122346899999887765433  3334568899999999


Q ss_pred             cccccCcccccchhHhhhCCCccceeEEEEeecC
Q 042003           72 KLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP  105 (248)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~  105 (248)
                      .+-+.+   .........+.  ....+++|||+-
T Consensus       203 ~ikn~~---s~~~~a~~~l~--~~~rllLTGTPi  231 (298)
T d1z3ix2         203 RLKNSD---NQTYLALNSMN--AQRRVLISGTPI  231 (298)
T ss_dssp             GCCTTC---HHHHHHHHHHC--CSEEEEECSSCS
T ss_pred             cccccc---chhhhhhhccc--cceeeeecchHH
Confidence            987654   11122222211  234689999984

>d1z63a1 c.37.1.19 (A:432-661) 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=97.00  E-value=0.00055  Score=49.92  Aligned_cols=91  Identities=22%  Similarity=0.154  Sum_probs=53.1

Q ss_pred             cchHHHHHHHhhcCCCcEEEEcccchhhhcccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEeccccccccCcccc
Q 042003            2 ATQTTRECKKLAKGNKFQIKLMKKELVRSTDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLFEVGNLLK   81 (248)
Q Consensus         2 ~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~~~~~~~~   81 (248)
                      ..|+.+.+.++.....   +....+.  .......+.+++++|.+.+.+...   +.--.++++|+||+|.+.+....  
T Consensus        73 ~~~W~~e~~~~~~~~~---~~~~~~~--~~~~~~~~~~vvi~~~~~~~~~~~---l~~~~~~~vI~DEah~~k~~~s~--  142 (230)
T d1z63a1          73 LKNWEEELSKFAPHLR---FAVFHED--RSKIKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQTK--  142 (230)
T ss_dssp             HHHHHHHHHHHCTTSC---EEECSSS--TTSCCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTTSH--
T ss_pred             hhHHHHHHHhhccccc---ceeeccc--cchhhccCcCEEEeeHHHHHhHHH---HhcccceEEEEEhhhcccccchh--
Confidence            4577777777766543   2222211  222233457999999987754332   22346789999999998765411  


Q ss_pred             cchhHhhhCCCccceeEEEEeecC
Q 042003           82 HIDPVVKACSNPSIVRSLFSATLP  105 (248)
Q Consensus        82 ~~~~~~~~~~~~~~~~i~~SAT~~  105 (248)
                       .......+  .....+++|||+-
T Consensus       143 -~~~~~~~l--~a~~r~~LTgTPi  163 (230)
T d1z63a1         143 -IFKAVKEL--KSKYRIALTGTPI  163 (230)
T ss_dssp             -HHHHHHTS--CEEEEEEECSSCS
T ss_pred             -hhhhhhhh--ccceEEEEecchH
Confidence             11222221  1334689999984

>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=95.59  E-value=0.0074  Score=38.70  Aligned_cols=76  Identities=21%  Similarity=0.079  Sum_probs=58.2

Q ss_pred             HHHHHHHHHhccCCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecccccCCCC
Q 042003          147 KLLALRQSFAESLNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVIARGMDF  226 (248)
Q Consensus       147 ~~~~l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~Gidi  226 (248)
                      -++.|..+++.. ..++|+.|.+...++.+.+.|++.++.+..+.+..          .|.++.  +-++...++.|+-+
T Consensus        22 p~~~L~~~i~~~-~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~~~----------~~~~~~--~~i~~~~l~~GF~~   88 (117)
T d2eyqa2          22 PLDALRKFLETF-DGPVVFSVESEGRREALGELLARIKIAPQRIMRLD----------EASDRG--RYLMIGAAEHGFVD   88 (117)
T ss_dssp             TTHHHHHHHTTC-CSCCCEEESSHHHHHHHHHHHGGGTCCCEECSSGG----------GCCTTC--CEEEECCCCSCEEE
T ss_pred             HHHHHHHHHHhC-CCeEEEEECCccHHHHHHHHHHHcCCCceEecChh----------hhcCce--EEEEEecCcccccc
Confidence            356677777765 56899999999999999999999998876654421          233344  55667889999999


Q ss_pred             CCCcEEEec
Q 042003          227 KGVNCVINY  235 (248)
Q Consensus       227 p~~~~Vi~~  235 (248)
                      |+.+.+|.-
T Consensus        89 ~~~~l~vIt   97 (117)
T d2eyqa2          89 TVRNLALIC   97 (117)
T ss_dssp             TTTTEEEEE
T ss_pred             CCCCEEEEE
Confidence            999988853

>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=95.20  E-value=0.053  Score=38.75  Aligned_cols=70  Identities=13%  Similarity=0.149  Sum_probs=53.8

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc------cccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV------IARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~------~~~Gidip~~  229 (248)
                      ..+++|++++++-+.++++.++..    +.++..+.|+.+..+....++   . ..+|+|+|..      -...+++.++
T Consensus        85 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~---~-~~~Ilv~TPgrl~~~~~~~~~~~~~l  160 (222)
T d2j0sa1          85 ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD---Y-GQHVVAGTPGRVFDMIRRRSLRTRAI  160 (222)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH---H-CCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             CceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhc---c-CCeEEeCCCCcHHhcccccccccccc
Confidence            457999999999999998887653    568888999988766555543   2 3589999953      2577788888


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      +++|
T Consensus       161 ~~lV  164 (222)
T d2j0sa1         161 KMLV  164 (222)
T ss_dssp             CEEE
T ss_pred             eeee
Confidence            8887

>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=95.17  E-value=0.067  Score=37.73  Aligned_cols=71  Identities=15%  Similarity=0.196  Sum_probs=53.9

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-----c-ccCCCCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-----I-ARGMDFKG  228 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-----~-~~Gidip~  228 (248)
                      .+.+++|.+++++.|.++++.++.    .+..+..++|+.+..+..+.++     ..+|+|+|+.     + ...+++.+
T Consensus        71 ~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-----~~~IlV~TP~~l~~~l~~~~~~~~~  145 (208)
T d1hv8a1          71 NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLKN  145 (208)
T ss_dssp             SSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTTS
T ss_pred             cCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-----CCCEEEEChHHHHHHHHcCCCCccc
Confidence            356899999999999998877765    3668889999988776555443     3679999952     2 45678888


Q ss_pred             CcEEEe
Q 042003          229 VNCVIN  234 (248)
Q Consensus       229 ~~~Vi~  234 (248)
                      ++++|.
T Consensus       146 l~~lVi  151 (208)
T d1hv8a1         146 VKYFIL  151 (208)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            888873

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) 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=95.06  E-value=0.017  Score=42.40  Aligned_cols=110  Identities=15%  Similarity=0.129  Sum_probs=69.0

Q ss_pred             CcchHHHHHHHhhcCCCcEEEEcccchh-hhcccccCCCcEEEeChHHHHHHHhcC-------CcccCceeEEEEecccc
Q 042003            1 LATQTTRECKKLAKGNKFQIKLMKKELV-RSTDLSKFSCDILISTPLRLRLAIRRK-------KIDLSRVEYLVLDEADK   72 (248)
Q Consensus         1 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~v~Tp~~l~~~~~~~-------~~~~~~~~~lIiDEah~   72 (248)
                      ||.-=++++..+-+.+| ..|.++.... .........+||+.+|...+---+.+.       ....+.+.+.||||+|-
T Consensus       133 LA~RDae~m~~iy~~lG-lsvg~~~~~~~~~~r~~~Y~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDs  211 (273)
T d1tf5a3         133 LASRDAEQMGKIFEFLG-LTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDS  211 (273)
T ss_dssp             HHHHHHHHHHHHHHHTT-CCEEECCTTSCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHH
T ss_pred             ccchhhhHHhHHHHHcC-CCccccccccCHHHHHHHhhCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchh
Confidence            34445677888888888 5555554443 344444457999999998774333322       22367899999999996


Q ss_pred             cc-ccCcccc-------------cchhHhhhCCCccceeEEEEeecCchHHHHHHHhc
Q 042003           73 LF-EVGNLLK-------------HIDPVVKACSNPSIVRSLFSATLPDFVEELARSIM  116 (248)
Q Consensus        73 ~~-~~~~~~~-------------~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~  116 (248)
                      ++ +.. ..+             .++.+.+..    .++-+||+|...+..++..-|.
T Consensus       212 iliDea-rtpliisg~~~~~a~it~q~~f~~y----~~l~gmtgta~~~~~e~~~iy~  264 (273)
T d1tf5a3         212 ILIDEA-RTPLIISGQSMTLATITFQNYFRMY----EKLAGMTGTAKTEEEEFRNIYN  264 (273)
T ss_dssp             HHTTTT-TCEEEEEEEEEEEEEEEHHHHHTTS----SEEEEEESCCGGGHHHHHHHHC
T ss_pred             hhhhcc-CCceEeccCccchhhhhHHHHHHHH----HHHhCCccccHHHHHHHHhccC
Confidence            65 332 111             122333332    3577999998877777766553

>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=91.89  E-value=0.58  Score=32.56  Aligned_cols=72  Identities=17%  Similarity=0.268  Sum_probs=52.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip~  228 (248)
                      ..+++|.+++++-+.++++.++..     ...+..+.|+.+.......   +.++..+|+|+|..-      ...+++.+
T Consensus        69 ~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---l~~~~~~ilI~TP~rl~~~~~~~~~~l~~  145 (207)
T d1t6na_          69 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLKH  145 (207)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHH---HHhcCCCEEEeCcchhhhhccCCceeccc
Confidence            457999999999999998888653     3457788888776554333   334567899999741      34678888


Q ss_pred             CcEEEe
Q 042003          229 VNCVIN  234 (248)
Q Consensus       229 ~~~Vi~  234 (248)
                      +.++|.
T Consensus       146 l~~lVl  151 (207)
T d1t6na_         146 IKHFIL  151 (207)
T ss_dssp             CCEEEE
T ss_pred             cceeeh
Confidence            888873

>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=90.44  E-value=0.56  Score=32.62  Aligned_cols=70  Identities=14%  Similarity=0.086  Sum_probs=50.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC-----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc------cccCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD-----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV------IARGMDFKG  228 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~-----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~------~~~Gidip~  228 (248)
                      +.+++|.+++++.+.++++.+...     +..+....|+.+.......+    ....+++|+|..      -...+++.+
T Consensus        71 ~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l----~~~~~ivv~TPgrl~~~~~~~~~~~~~  146 (206)
T d1veca_          71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL----DDTVHVVIATPGRILDLIKKGVAKVDH  146 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT----TSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHH----HhccCeEEeCCccccccccchhccccc
Confidence            568999999999999998877532     45677778887766554443    346689999953      234567778


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      ++++|
T Consensus       147 l~~lV  151 (206)
T d1veca_         147 VQMIV  151 (206)
T ss_dssp             CCEEE
T ss_pred             cceEE
Confidence            88776

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.34  E-value=0.94  Score=32.03  Aligned_cols=73  Identities=11%  Similarity=0.203  Sum_probs=50.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CC----eeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc-cc-cCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GI----RAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV-IA-RGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~----~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~-~~-~Gidip~~  229 (248)
                      ++++++.++++.-+++.++.+++.    +.    .+..+++..+...+.+.+....  ..+|+|+|.- +. .-.++.+.
T Consensus        86 ~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~Ilv~Tp~~l~~~~~~~~~~  163 (237)
T d1gkub1          86 GKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLR--NFKIVITTTQFLSKHYRELGHF  163 (237)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGG--GCSEEEEEHHHHHHCSTTSCCC
T ss_pred             cCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhcccc--ccceeccChHHHHHhhhhcCCC
Confidence            679999999999999998888642    32    3556677777777766665443  3468999953 32 33456678


Q ss_pred             cEEEe
Q 042003          230 NCVIN  234 (248)
Q Consensus       230 ~~Vi~  234 (248)
                      ++||.
T Consensus       164 ~~vVv  168 (237)
T d1gkub1         164 DFIFV  168 (237)
T ss_dssp             SEEEE
T ss_pred             CEEEE
Confidence            87763

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-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: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=88.97  E-value=1  Score=31.08  Aligned_cols=68  Identities=12%  Similarity=0.136  Sum_probs=41.9

Q ss_pred             cCCCcEEEeChH-------HHHHHHhc--CCcccCceeEEEEeccccccccCcccccchhHhhhCCCccceeEEEEeecC
Q 042003           35 KFSCDILISTPL-------RLRLAIRR--KKIDLSRVEYLVLDEADKLFEVGNLLKHIDPVVKACSNPSIVRSLFSATLP  105 (248)
Q Consensus        35 ~~~~~i~v~Tp~-------~l~~~~~~--~~~~~~~~~~lIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~  105 (248)
                      ..++|++.-.|+       .+.++...  ..-.....+++|+||||.+...+  ...+...+.. .+.+..++++|..+.
T Consensus        44 ~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l~~~a--qNaLLK~LEE-Pp~~t~fiLit~~~~  120 (198)
T d2gnoa2          44 PKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQQA--ANAFLKALEE-PPEYAVIVLNTRRWH  120 (198)
T ss_dssp             CCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCHHH--HHHTHHHHHS-CCTTEEEEEEESCGG
T ss_pred             cCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCCEEEEEeCccccchhh--hhHHHHHHhC-CCCCceeeeccCChh
Confidence            346899998884       33333322  12234678899999999987643  4455555554 455666666665543

>d1yt8a4 c.46.1.2 (A:243-372) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.28  E-value=0.29  Score=31.38  Aligned_cols=37  Identities=16%  Similarity=0.057  Sum_probs=33.1

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCCeeEEEecCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGIRAGVIHSDLS  195 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~~v~~~~~~~~  195 (248)
                      .++++++||.+-..+...+..|++.|+.+..+.||+.
T Consensus        79 ~~~~ivl~C~~G~rS~~aa~~L~~~G~~v~~l~GG~~  115 (130)
T d1yt8a4          79 RGARLVLVDDDGVRANMSASWLAQMGWQVAVLDGLSE  115 (130)
T ss_dssp             BTCEEEEECSSSSHHHHHHHHHHHTTCEEEEECSCCG
T ss_pred             ccceEEeecCCCccHHHHHHHHHHcCCCeEEEcCchH
Confidence            3678999999988899999999999999999999865

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.71  E-value=0.73  Score=32.19  Aligned_cols=70  Identities=13%  Similarity=0.145  Sum_probs=44.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc------cccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV------IARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~------~~~Gidip~~  229 (248)
                      +..++|.+++++.+.++++.+...    ...+...+++.+..++....     ...+|+|+|..      -..++++.++
T Consensus        78 ~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~IvI~TP~~l~~~~~~~~~~l~~l  152 (212)
T d1qdea_          78 APQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-----RDAQIVVGTPGRVFDNIQRRRFRTDKI  152 (212)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C-----TTCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             CcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHh-----cCCcEEEECCCccccccccCceecCcc
Confidence            568999999999999988887543    44566666665544433322     24689999963      2567788888


Q ss_pred             cEEEe
Q 042003          230 NCVIN  234 (248)
Q Consensus       230 ~~Vi~  234 (248)
                      +++|.
T Consensus       153 ~~lVl  157 (212)
T d1qdea_         153 KMFIL  157 (212)
T ss_dssp             CEEEE
T ss_pred             eEEee
Confidence            88873

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.18  E-value=0.35  Score=34.13  Aligned_cols=72  Identities=11%  Similarity=0.124  Sum_probs=46.3

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEecc------cccCCCCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDV------IARGMDFKG  228 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~------~~~Gidip~  228 (248)
                      ...+++|++++++-|.++++.+...    +..+..+.++....+   .......+..+|+|+|+.      -....++..
T Consensus        79 ~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~  155 (218)
T d2g9na1          79 KATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRA---EVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKY  155 (218)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCS---TTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTT
T ss_pred             cCccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhH---HHHHHhcCCCEEEEeCChhHHHHHhcCCccccc
Confidence            3568999999999999998877653    445555555433221   112233456689999963      234567777


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      ++++|
T Consensus       156 l~~lV  160 (218)
T d2g9na1         156 IKMFV  160 (218)
T ss_dssp             CCEEE
T ss_pred             ceEEE
Confidence            88776

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=87.17  E-value=1.2  Score=31.73  Aligned_cols=71  Identities=15%  Similarity=0.166  Sum_probs=51.6

Q ss_pred             CCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip~~  229 (248)
                      +.+++|.+++++.+.++++.+..    .++++..+.|+....++.+.    .....+|+|+|..-      ...+++.++
T Consensus        98 ~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~ivV~TP~~l~~~~~~~~~~l~~v  173 (238)
T d1wrba1          98 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIRE----VQMGCHLLVATPGRLVDFIEKNKISLEFC  173 (238)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHH----HSSCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             CceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhh----cccCCceeecCHHHHHhHHccCceecccc
Confidence            45799999999999999877753    36678888887766554332    33457899999732      356778888


Q ss_pred             cEEEe
Q 042003          230 NCVIN  234 (248)
Q Consensus       230 ~~Vi~  234 (248)
                      .++|.
T Consensus       174 ~~lVi  178 (238)
T d1wrba1         174 KYIVL  178 (238)
T ss_dssp             CEEEE
T ss_pred             ceeee
Confidence            88773

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.76  E-value=2  Score=29.58  Aligned_cols=71  Identities=17%  Similarity=0.110  Sum_probs=52.6

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhc----CCCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccCCCCCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAF----DGIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARGMDFKG  228 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~----~~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip~  228 (248)
                      .....++.+++...+......+..    .+.++...+|+.+.......+    ....+|+|+|...      ...+++.+
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l----~~~~~Ili~TP~~l~~~l~~~~~~l~~  143 (206)
T d1s2ma1          68 NKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRL----NETVHILVGTPGRVLDLASRKVADLSD  143 (206)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHT----TSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             ccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHh----cccceEEEECCcccccccccceeeccc
Confidence            356789999998888777666643    367899999998877655443    3457899999632      45678888


Q ss_pred             CcEEE
Q 042003          229 VNCVI  233 (248)
Q Consensus       229 ~~~Vi  233 (248)
                      ++++|
T Consensus       144 l~~lV  148 (206)
T d1s2ma1         144 CSLFI  148 (206)
T ss_dssp             CCEEE
T ss_pred             ceEEE
Confidence            88887

>d2b2na1 c.37.1.19 (A:26-333) 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=86.74  E-value=2.2  Score=31.55  Aligned_cols=69  Identities=14%  Similarity=0.088  Sum_probs=47.9

Q ss_pred             HHHHHhccCCCCEEEEecchHHHHHHHHHhhcC-CCeeEEEec--CC----------CHHHHHHHHHHhhcCCceEEEEe
Q 042003          151 LRQSFAESLNPPVLIFVQSKERAKELYGELAFD-GIRAGVIHS--DL----------SQTQRENAVDDFRAGKTWVLIAT  217 (248)
Q Consensus       151 l~~~~~~~~~~~~liF~~~~~~~~~l~~~L~~~-~~~v~~~~~--~~----------~~~~r~~~~~~f~~g~~~ilv~T  217 (248)
                      +..+.++. .++++|.|++...|+++++.|+.. +..+..+=+  .+          -..+|..++..+.+++..|+|+|
T Consensus         6 ~a~~~~~~-~~p~lvv~~~~~~A~~l~~~L~~~~~~~v~~fP~~e~lpyd~~s~~~~i~~~R~~~L~~l~~~~~~iiits   84 (308)
T d2b2na1           6 VAEIAERH-AGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVP   84 (308)
T ss_dssp             HHHHHHHC-SSCEEEEESSHHHHHHHHHHHHTTCSSCEEECCCCCSCTTCSSCCCHHHHHHHHHHHHHGGGCCSSEEEEE
T ss_pred             HHHHHHhh-CCCEEEEcCCHHHHHHHHHHHHhcCCCceEEcCCcccCccccCCCChHHHHHHHHHHHHHhhcCCceEEee
Confidence            44455554 689999999999999999999864 333333311  11          12457888888888888888888


Q ss_pred             ccc
Q 042003          218 DVI  220 (248)
Q Consensus       218 ~~~  220 (248)
                      -.+
T Consensus        85 ~~a   87 (308)
T d2b2na1          85 VNT   87 (308)
T ss_dssp             HHH
T ss_pred             chh
Confidence            443

>d1tq1a_ c.46.1.3 (A:) Thiosulfate sulfurtransferase/Senescence-associated protein {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Thiosulfate sulfurtransferase/Senescence-associated protein
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=85.40  E-value=0.21  Score=31.49  Aligned_cols=36  Identities=19%  Similarity=0.181  Sum_probs=31.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCC-eeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGI-RAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~-~v~~~~~~~~  195 (248)
                      ++++++||.+-..+...+..|.+.|+ ++..+.||+.
T Consensus        72 ~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~~  108 (119)
T d1tq1a_          72 SDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  108 (119)
T ss_dssp             TSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             CcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChHH
Confidence            57899999998889999999999988 6999999964

>d1urha2 c.46.1.2 (A:149-268) 3-mercaptopyruvate sulfurtransferase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: 3-mercaptopyruvate sulfurtransferase
species: Escherichia coli [TaxId: 562]

Probab=84.58  E-value=0.77  Score=28.58  Aligned_cols=36  Identities=17%  Similarity=0.157  Sum_probs=31.3

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCC-eeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGI-RAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~-~v~~~~~~~~  195 (248)
                      .+++|+||.+-..+...+..|+..|+ ++..+.|++.
T Consensus        82 ~~~ii~yC~sG~~A~~~~~~L~~lG~~~v~~y~Gs~~  118 (120)
T d1urha2          82 DKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWS  118 (120)
T ss_dssp             SSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCC
T ss_pred             cCceEEEccchhHHHHHHHHHHHcCCCCceEcCCChh
Confidence            67899999998888888889988888 5899999875

>d1qxna_ c.46.1.3 (A:) Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud) {Wolinella succinogenes [TaxId: 844]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud)
species: Wolinella succinogenes [TaxId: 844]

Probab=84.19  E-value=0.42  Score=30.92  Aligned_cols=36  Identities=19%  Similarity=0.187  Sum_probs=31.8

Q ss_pred             CCCCEEEEecchHHHHHHHHHhhcCCC-eeEEEecCC
Q 042003          159 LNPPVLIFVQSKERAKELYGELAFDGI-RAGVIHSDL  194 (248)
Q Consensus       159 ~~~~~liF~~~~~~~~~l~~~L~~~~~-~v~~~~~~~  194 (248)
                      .++++++||.+-..+...+..|++.|+ +|..+.||+
T Consensus        81 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~nV~~l~GG~  117 (137)
T d1qxna_          81 PEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGM  117 (137)
T ss_dssp             TTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCH
T ss_pred             cccceeeeecccchHHHHHHHHHHcCCCcEEEecCHH
Confidence            367899999998899999999999998 688999995

>d1gmxa_ c.46.1.3 (A:) Sulfurtransferase GlpE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Sulfurtransferase GlpE
species: Escherichia coli [TaxId: 562]

Probab=82.25  E-value=0.57  Score=28.77  Aligned_cols=36  Identities=17%  Similarity=0.207  Sum_probs=31.7

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCC-eeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGI-RAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~-~v~~~~~~~~  195 (248)
                      ++++++||.+-..+...+..|.+.|+ ++..+.||+.
T Consensus        58 ~~~ivv~c~~g~rs~~~a~~L~~~G~~~v~~l~GG~~   94 (108)
T d1gmxa_          58 DTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             TSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             cCcccccCCCChHHHHHHHHHHHcCCCCEEEEcChHH
Confidence            67899999998889999999999998 5889999864

>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=82.25  E-value=0.53  Score=32.92  Aligned_cols=61  Identities=16%  Similarity=0.282  Sum_probs=41.1

Q ss_pred             HHHHHHHhhcCCCcEEEEcccchhhh-------cccccCCCcEEEeChHHHHHHHhcCCcccCceeEEEEecccccc
Q 042003            5 TTRECKKLAKGNKFQIKLMKKELVRS-------TDLSKFSCDILISTPLRLRLAIRRKKIDLSRVEYLVLDEADKLF   74 (248)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~i~v~Tp~~l~~~~~~~~~~~~~~~~lIiDEah~~~   74 (248)
                      .++.++++.+.   .++.++.|....       .+...+..+|+|||.      +-...++..+..++||..|+++.
T Consensus        47 ~~~~l~~~~p~---~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt------vIEvGiDvpnA~~iiI~~a~rfG  114 (211)
T d2eyqa5          47 AAERLAELVPE---ARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT------IIETGIDIPTANTIIIERADHFG  114 (211)
T ss_dssp             HHHHHHHHCTT---SCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS------TTGGGSCCTTEEEEEETTTTSSC
T ss_pred             HHHHHHHhCCc---eEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh------hhhhccCCCCCcEEEEecchhcc
Confidence            34444444444   446666666522       234556799999994      55556778999999999999963

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=80.85  E-value=2.9  Score=28.25  Aligned_cols=69  Identities=16%  Similarity=0.156  Sum_probs=49.5

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcC----CCeeEEEecCCCHHHHHHHHHHhhcCCceEEEEeccc------ccCCCCCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFD----GIRAGVIHSDLSQTQRENAVDDFRAGKTWVLIATDVI------ARGMDFKGV  229 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~----~~~v~~~~~~~~~~~r~~~~~~f~~g~~~ilv~T~~~------~~Gidip~~  229 (248)
                      ++++++.++++.-+++.++.+++.    +..+..+|++....++......     ..++++|...      ...+....+
T Consensus        52 ~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~-----~~i~i~t~~~~~~~~~~~~~~~~~~  126 (200)
T d1wp9a1          52 GGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWAR-----AKVIVATPQTIENDLLAGRISLEDV  126 (200)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHHH-----CSEEEECHHHHHHHHHTTSCCTTSC
T ss_pred             CCcEEEEcCchHHHHHHHHHHHHhhcccccceeeeecccchhHHHHhhhc-----ccccccccchhHHHHhhhhhhcccc
Confidence            678999999999888877777653    5678889999998888776543     3577777422      233445566


Q ss_pred             cEEE
Q 042003          230 NCVI  233 (248)
Q Consensus       230 ~~Vi  233 (248)
                      +.||
T Consensus       127 ~~vI  130 (200)
T d1wp9a1         127 SLIV  130 (200)
T ss_dssp             SEEE
T ss_pred             ceEE
Confidence            7666

>d1yt8a2 c.46.1.2 (A:6-106) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=80.11  E-value=0.51  Score=28.50  Aligned_cols=36  Identities=17%  Similarity=0.233  Sum_probs=31.2

Q ss_pred             CCCEEEEecchHHHHHHHHHhhcCCC-eeEEEecCCC
Q 042003          160 NPPVLIFVQSKERAKELYGELAFDGI-RAGVIHSDLS  195 (248)
Q Consensus       160 ~~~~liF~~~~~~~~~l~~~L~~~~~-~v~~~~~~~~  195 (248)
                      ..+++++|++-..+...+..|.+.|+ ++..+.||+.
T Consensus        58 ~~~vv~~~~~g~~s~~~~~~l~~~G~~nV~~l~GG~~   94 (101)
T d1yt8a2          58 DTPITVYDDGEGLAPVAAQRLHDLGYSDVALLDGGLS   94 (101)
T ss_dssp             TSCEEEECSSSSHHHHHHHHHHHTTCSSEEEETTHHH
T ss_pred             CceeeeccchhhhHHHHHHHHHHcCCCcEEEeCChHH
Confidence            57889999999999999999999998 5888899854